Skip to main content
NCBI home page
Comparative and Functional Genomics logoLink to Comparative and Functional Genomics
. 2005 Feb-Mar;6(1-2):97–112. doi: 10.1002/cfg.419

Current Awareness on Comparative and Functional Genomics

PMCID: PMC2448604

Full Text

The Full Text of this article is available as a PDF (245.7 KB).

Selected References

These references are in PubMed. This may not be the complete list of references from this article.

  1. Abba Martin C., Drake Jeffrey A., Hawkins Kathleen A., Hu Yuhui, Sun Hongxia, Notcovich Cintia, Gaddis Sally, Sahin Aysegul, Baggerly Keith, Aldaz C. Marcelo. Transcriptomic changes in human breast cancer progression as determined by serial analysis of gene expression. Breast Cancer Res. 2004 Jul 6;6(5):R499–R513. doi: 10.1186/bcr899. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2. Alba Rob, Fei Zhangjun, Payton Paxton, Liu Yang, Moore Shanna L., Debbie Paul, Cohn Jonathan, D'Ascenzo Mark, Gordon Jeffrey S., Rose Jocelyn K. C. ESTs, cDNA microarrays, and gene expression profiling: tools for dissecting plant physiology and development. Plant J. 2004 Sep;39(5):697–714. doi: 10.1111/j.1365-313X.2004.02178.x. [DOI] [PubMed] [Google Scholar]
  3. Aldred Micheala A., Huang Ying, Liyanarachchi Sandya, Pellegata Natalia S., Gimm Oliver, Jhiang Sissy, Davuluri Ramana V., de la Chapelle Albert, Eng Charis. Papillary and follicular thyroid carcinomas show distinctly different microarray expression profiles and can be distinguished by a minimum of five genes. J Clin Oncol. 2004 Sep 1;22(17):3531–3539. doi: 10.1200/JCO.2004.08.127. [DOI] [PubMed] [Google Scholar]
  4. Alfonso Patricia, Rivera José, Hernáez Bruno, Alonso Covadonga, Escribano José M. Identification of cellular proteins modified in response to African swine fever virus infection by proteomics. Proteomics. 2004 Jul;4(7):2037–2046. doi: 10.1002/pmic.200300742. [DOI] [PubMed] [Google Scholar]
  5. Allal Abdelkarim S., Kähne Thilo, Reverdin Alexandra K., Lippert Hans, Schlegel Werner, Reymond Marc-André. Radioresistance-related proteins in rectal cancer. Proteomics. 2004 Aug;4(8):2261–2269. doi: 10.1002/pmic.200300854. [DOI] [PubMed] [Google Scholar]
  6. Allard Laure, Lescuyer Pierre, Burgess Jennifer, Leung Kit-Yi, Ward Malcolm, Walter Nadia, Burkhard Pierre R., Corthals Garry, Hochstrasser Denis F., Sanchez Jean-Charles. ApoC-I and ApoC-III as potential plasmatic markers to distinguish between ischemic and hemorrhagic stroke. Proteomics. 2004 Aug;4(8):2242–2251. doi: 10.1002/pmic.200300809. [DOI] [PubMed] [Google Scholar]
  7. Allet Nadia, Barrillat Nicolas, Baussant Thierry, Boiteau Celia, Botti Paolo, Bougueleret Lydie, Budin Nicolas, Canet Denis, Carraud Stéphanie, Chiappe Diego. In vitro and in silico processes to identify differentially expressed proteins. Proteomics. 2004 Aug;4(8):2333–2351. doi: 10.1002/pmic.200300840. [DOI] [PubMed] [Google Scholar]
  8. Almeras Lionel, Lefranc Didier, Drobecq Hervé, de Seze Jérome, Dubucquoi Sylvain, Vermersch Patrick, Prin Lionel. New antigenic candidates in multiple sclerosis: identification by serological proteome analysis. Proteomics. 2004 Jul;4(7):2184–2194. doi: 10.1002/pmic.200300732. [DOI] [PubMed] [Google Scholar]
  9. Almstrup Kristian, Hoei-Hansen Christina E., Wirkner Ute, Blake Jonathon, Schwager Christian, Ansorge Wilhelm, Nielsen John E., Skakkebaek Niels E., Rajpert-De Meyts Ewa, Leffers Henrik. Embryonic stem cell-like features of testicular carcinoma in situ revealed by genome-wide gene expression profiling. Cancer Res. 2004 Jul 15;64(14):4736–4743. doi: 10.1158/0008-5472.CAN-04-0679. [DOI] [PubMed] [Google Scholar]
  10. Amsterdam Adam, Nissen Robert M., Sun Zhaoxia, Swindell Eric C., Farrington Sarah, Hopkins Nancy. Identification of 315 genes essential for early zebrafish development. Proc Natl Acad Sci U S A. 2004 Jul 15;101(35):12792–12797. doi: 10.1073/pnas.0403929101. [DOI] [PMC free article] [PubMed] [Google Scholar]
  11. Anderssen R. S., Wu Y., Dolferus R., Saunders I. An a posteriori strategy for enhancing gene discovery in anonymous cDNA microarray experiments. Bioinformatics. 2004 Feb 26;20(11):1721–1727. doi: 10.1093/bioinformatics/bth152. [DOI] [PubMed] [Google Scholar]
  12. Andreini Claudia, Bertini Ivano, Rosato Antonio. A hint to search for metalloproteins in gene banks. Bioinformatics. 2004 Feb 12;20(9):1373–1380. doi: 10.1093/bioinformatics/bth095. [DOI] [PubMed] [Google Scholar]
  13. Angeles Castillejo M., Amiour Nardjis, Dumas-Gaudot Eliane, Rubiales Diego, Jorrín Jesús V. A proteomic approach to studying plant response to crenate broomrape (Orobanche crenata) in pea (Pisum sativum). Phytochemistry. 2004 Jun;65(12):1817–1828. doi: 10.1016/j.phytochem.2004.03.029. [DOI] [PubMed] [Google Scholar]
  14. Antelmann Haike, Sapolsky Ron, Miller Brian, Ferrari Eugenio, Chotani Gopal, Weyler Walter, Gaertner Alfred, Hecker Michael. Quantitative proteome profiling during the fermentation process of pleiotropic Bacillus subtilis mutants. Proteomics. 2004 Aug;4(8):2408–2424. doi: 10.1002/pmic.200300752. [DOI] [PubMed] [Google Scholar]
  15. Arai Masafumi, Okumura Kosuke, Satake Masanobu, Shimizu Toshio. Proteome-wide functional classification and identification of prokaryotic transmembrane proteins by transmembrane topology similarity comparison. Protein Sci. 2004 Aug;13(8):2170–2183. doi: 10.1110/ps.04814404. [DOI] [PMC free article] [PubMed] [Google Scholar]
  16. Arnaud Marie-Claire, Gazarian Tatyana, Palacios Rodriguez Yadira, Gazarian Karlen, Sakanyan Vehary. Array assessment of phage-displayed peptide mimics of Human Immunodeficiency Virus type 1 gp41 immunodominant epitope: binding to antibodies of infected individuals. Proteomics. 2004 Jul;4(7):1959–1964. doi: 10.1002/pmic.200300725. [DOI] [PubMed] [Google Scholar]
  17. Arndt Peter F., Hwa Terence. Regional and time-resolved mutation patterns of the human genome. Bioinformatics. 2004 Jul 10;20(10):1482–1485. doi: 10.1093/bioinformatics/bth105. [DOI] [PubMed] [Google Scholar]
  18. Asamizu Erika, Nakamura Yasukazu, Sato Shusei, Tabata Satoshi. Characteristics of the Lotus japonicus gene repertoire deduced from large-scale expressed sequence tag (EST) analysis. Plant Mol Biol. 2004 Feb;54(3):405–414. doi: 10.1023/B:PLAN.0000036372.46942.b8. [DOI] [PubMed] [Google Scholar]
  19. Ashida Shingo, Nakagawa Hidewaki, Katagiri Toyomasa, Furihata Mutsuo, Iiizumi Megumi, Anazawa Yoshio, Tsunoda Tatsuhiko, Takata Ryo, Kasahara Kotaro, Miki Tsuneharu. Molecular features of the transition from prostatic intraepithelial neoplasia (PIN) to prostate cancer: genome-wide gene-expression profiles of prostate cancers and PINs. Cancer Res. 2004 Sep 1;64(17):5963–5972. doi: 10.1158/0008-5472.CAN-04-0020. [DOI] [PubMed] [Google Scholar]
  20. Aston Christopher, Jiang Lixin, Sokolov Boris P. Microarray analysis of postmortem temporal cortex from patients with schizophrenia. J Neurosci Res. 2004 Sep 15;77(6):858–866. doi: 10.1002/jnr.20208. [DOI] [PubMed] [Google Scholar]
  21. Avram Diana, Romijn Edwin P., Pap Everard H. W., Heck Albert J. R., Wirtz Karel W. A. Identification of proteins in activated human neutrophils susceptible to tyrosyl radical attack. A proteomic study using a tyrosylating fluorophore. Proteomics. 2004 Aug;4(8):2397–2407. doi: 10.1002/pmic.200300755. [DOI] [PubMed] [Google Scholar]
  22. Azad Rajeev K., Borodovsky Mark. Probabilistic methods of identifying genes in prokaryotic genomes: connections to the HMM theory. Brief Bioinform. 2004 Jun;5(2):118–130. doi: 10.1093/bib/5.2.118. [DOI] [PubMed] [Google Scholar]
  23. Azumi Kaoru, Fujie Manabu, Usami Takeshi, Miki Yasufumi, Satoh Nori. A cDNA microarray technique applied for analysis of global gene expression profiles in tributyltin-exposed ascidians. Mar Environ Res. 2004 Aug-Dec;58(2-5):543–546. doi: 10.1016/j.marenvres.2004.03.042. [DOI] [PubMed] [Google Scholar]
  24. Baczek Tomasz. Fractionation of peptides and identification of proteins from Saccharomyces cerevisiae in proteomics with the use of reversed-phase capillary liquid chromatography and pI-based approach. J Pharm Biomed Anal. 2004 Jun 29;35(4):895–904. doi: 10.1016/j.jpba.2004.02.032. [DOI] [PubMed] [Google Scholar]
  25. Bahou Wadie F., Gnatenko Dmitri V. Platelet transcriptome: the application of microarray analysis to platelets. Semin Thromb Hemost. 2004 Aug;30(4):473–484. doi: 10.1055/s-2004-833482. [DOI] [PubMed] [Google Scholar]
  26. Bahrman Nasser, Negroni Luc, Jaminon Odile, Le Gouis Jacques. Wheat leaf proteome analysis using sequence data of proteins separated by two-dimensional electrophoresis. Proteomics. 2004 Sep;4(9):2672–2684. doi: 10.1002/pmic.200300798. [DOI] [PubMed] [Google Scholar]
  27. Bai Yu, Galetskiy Dmitry, Damoc Eugen, Paschen Christian, Liu Zhiqiang, Griese Mathias, Liu Shuying, Przybylski Michael. High resolution mass spectrometric alveolar proteomics: identification of surfactant protein SP-A and SP-D modifications in proteinosis and cystic fibrosis patients. Proteomics. 2004 Aug;4(8):2300–2309. doi: 10.1002/pmic.200400855. [DOI] [PubMed] [Google Scholar]
  28. Banks David J., Porcella Stephen F., Barbian Kent D., Beres Stephen B., Philips Lauren E., Voyich Jovanka M., DeLeo Frank R., Martin Judith M., Somerville Greg A., Musser James M. Progress toward characterization of the group A Streptococcus metagenome: complete genome sequence of a macrolide-resistant serotype M6 strain. J Infect Dis. 2004 Jul 20;190(4):727–738. doi: 10.1086/422697. [DOI] [PubMed] [Google Scholar]
  29. Bantscheff Marcus, Ringel Bruno, Madi András, Schnabel Ralf, Glocker Michael O., Thiesen Hans-Jürgen. Differential proteome analysis and mass spectrometric characterization of germ line development-related proteins of Caenorhabditis elegans. Proteomics. 2004 Aug;4(8):2283–2295. doi: 10.1002/pmic.200400807. [DOI] [PubMed] [Google Scholar]
  30. Bard Martin P., Hegmans Joost P., Hemmes Annabrita, Luider Theo M., Willemsen Rob, Severijnen Lies-Anne A., van Meerbeeck Jan P., Burgers Sjaak A., Hoogsteden Henk C., Lambrecht Bart N. Proteomic analysis of exosomes isolated from human malignant pleural effusions. Am J Respir Cell Mol Biol. 2004 Feb 19;31(1):114–121. doi: 10.1165/rcmb.2003-0238OC. [DOI] [PubMed] [Google Scholar]
  31. Barker Katherine S., Crisp Sarah, Wiederhold Nathan, Lewis Russell E., Bareither Bart, Eckstein James, Barbuch Robert, Bard Martin, Rogers P. David. Genome-wide expression profiling reveals genes associated with amphotericin B and fluconazole resistance in experimentally induced antifungal resistant isolates of Candida albicans. J Antimicrob Chemother. 2004 Jun 16;54(2):376–385. doi: 10.1093/jac/dkh336. [DOI] [PubMed] [Google Scholar]
  32. Bartholomay Lyric C., Cho Wen-Long, Rocheleau Thomas A., Boyle Jon P., Beck Eric T., Fuchs Jeremy F., Liss Paul, Rusch Michael, Butler Katherine M., Wu Roy Chen-Chih. Description of the transcriptomes of immune response-activated hemocytes from the mosquito vectors Aedes aegypti and Armigeres subalbatus. Infect Immun. 2004 Jul;72(7):4114–4126. doi: 10.1128/IAI.72.7.4114-4126.2004. [DOI] [PMC free article] [PubMed] [Google Scholar]
  33. Barzaghi Dagania, Isbister Jenefir D., Lauer Kimberly P., Born Timothy L. Use of surface-enhanced laser desorption/ionization -time of flight to explore bacterial proteomes. Proteomics. 2004 Sep;4(9):2624–2628. doi: 10.1002/pmic.200300782. [DOI] [PubMed] [Google Scholar]
  34. Basso D., Millino C., Greco E., Romualdi C., Fogar P., Valerio A., Bellin M., Zambon C-F, Navaglia F., Dussini N. Altered glucose metabolism and proteolysis in pancreatic cancer cell conditioned myoblasts: searching for a gene expression pattern with a microarray analysis of 5000 skeletal muscle genes. Gut. 2004 Aug;53(8):1159–1166. doi: 10.1136/gut.2003.024471. [DOI] [PMC free article] [PubMed] [Google Scholar]
  35. Bastien Olivier, Lespinats Sylvain, Roy Sylvaine, Métayer Karine, Fertil Bernard, Codani Jean-Jacques, Maréchal Eric. Analysis of the compositional biases in Plasmodium falciparum genome and proteome using Arabidopsis thaliana as a reference. Gene. 2004 Jul 21;336(2):163–173. doi: 10.1016/j.gene.2004.04.029. [DOI] [PubMed] [Google Scholar]
  36. Basu Chhandak, Halfhill Matthew D., Mueller Thomas C., Stewart C. Neal., Jr Weed genomics: new tools to understand weed biology. Trends Plant Sci. 2004 Aug;9(8):391–398. doi: 10.1016/j.tplants.2004.06.003. [DOI] [PubMed] [Google Scholar]
  37. Baxevanis Andreas D. Using genomic databases for sequence-based biological discovery. Mol Med. 2003 Sep-Dec;9(9-12):185–192. [PMC free article] [PubMed] [Google Scholar]
  38. Beissbarth Tim, Speed Terence P. GOstat: find statistically overrepresented Gene Ontologies within a group of genes. Bioinformatics. 2004 Feb 12;20(9):1464–1465. doi: 10.1093/bioinformatics/bth088. [DOI] [PubMed] [Google Scholar]
  39. Belacel Nabil, Cuperlović-Culf Miroslava, Laflamme Mark, Ouellette Rodney. Fuzzy J-Means and VNS methods for clustering genes from microarray data. Bioinformatics. 2004 Feb 26;20(11):1690–1701. doi: 10.1093/bioinformatics/bth142. [DOI] [PubMed] [Google Scholar]
  40. Bell K. S., Sebaihia M., Pritchard L., Holden M. T. G., Hyman L. J., Holeva M. C., Thomson N. R., Bentley S. D., Churcher L. J. C., Mungall K. Genome sequence of the enterobacterial phytopathogen Erwinia carotovora subsp. atroseptica and characterization of virulence factors. Proc Natl Acad Sci U S A. 2004 Jul 19;101(30):11105–11110. doi: 10.1073/pnas.0402424101. [DOI] [PMC free article] [PubMed] [Google Scholar]
  41. Bergemann T. L., Laws R. J., Quiaoit F., Zhao L. P. A statistically driven approach for image segmentation and signal extraction in cDNA microarrays. J Comput Biol. 2004;11(4):695–713. doi: 10.1089/cmb.2004.11.695. [DOI] [PubMed] [Google Scholar]
  42. Berman Piotr, Bertone Paul, Dasgupta Bhaskar, Gerstein Mark, Kao Ming-Yang, Snyder Michael. Fast optimal genome tiling with applications to microarray design and homology search. J Comput Biol. 2004;11(4):766–785. doi: 10.1089/cmb.2004.11.766. [DOI] [PubMed] [Google Scholar]
  43. Bestel-Corre Gwénaëlle, Gianinazzi Silvio, Dumas-Gaudot Eliane. Impact of sewage sludges on Medicago truncatula symbiotic proteome. Phytochemistry. 2004 Jun;65(11):1651–1659. doi: 10.1016/j.phytochem.2004.04.037. [DOI] [PubMed] [Google Scholar]
  44. Blagoev Blagoy, Ong Shao-En, Kratchmarova Irina, Mann Matthias. Temporal analysis of phosphotyrosine-dependent signaling networks by quantitative proteomics. Nat Biotechnol. 2004 Aug 15;22(9):1139–1145. doi: 10.1038/nbt1005. [DOI] [PubMed] [Google Scholar]
  45. Blonder Josip, Rodriguez-Galan Maria C., Chan King C., Lucas David A., Yu Li-Rong, Conrads Thomas P., Issaq Haleem J., Young Howard A., Veenstra Timothy D. Analysis of murine natural killer cell microsomal proteins using two-dimensional liquid chromatography coupled to tandem electrospray ionization mass spectrometry. J Proteome Res. 2004 Jul-Aug;3(4):862–870. doi: 10.1021/pr049927e. [DOI] [PubMed] [Google Scholar]
  46. Blonder Josip, Terunuma Atsushi, Conrads Thomas P., Chan King C., Yee Carole, Lucas David A., Schaefer Carl F., Yu Li-Rong, Issaq Haleem J., Veenstra Timothy D. A proteomic characterization of the plasma membrane of human epidermis by high-throughput mass spectrometry. J Invest Dermatol. 2004 Oct;123(4):691–699. doi: 10.1111/j.0022-202X.2004.23421.x. [DOI] [PubMed] [Google Scholar]
  47. Blum Jason L., Knoebl Iris, Larkin Patrick, Kroll Kevin J., Denslow Nancy D. Use of suppressive subtractive hybridization and cDNA arrays to discover patterns of altered gene expression in the liver of dihydrotestosterone and 11-ketotestosterone exposed adult male largemouth bass (Micropterus salmoides). Mar Environ Res. 2004 Aug-Dec;58(2-5):565–569. doi: 10.1016/j.marenvres.2004.03.046. [DOI] [PubMed] [Google Scholar]
  48. Blüggel Martin, Bailey Sonja, Körting Gerhard, Stephan Christian, Reidegeld Kai A., Thiele Herbert, Apweiler Rolf, Hamacher Michael, Meyer Helmut E. Towards data management of the HUPO Human Brain Proteome Project pilot phase. Proteomics. 2004 Aug;4(8):2361–2362. doi: 10.1002/pmic.200400867. [DOI] [PubMed] [Google Scholar]
  49. Boja Emily S., Sokoloski Edward A., Fales Henry M. Divinyl sulfone as a postdigestion modifier for enhancing the a(1) Ion in MS/MS and postsource decay: potential applications in proteomics. Anal Chem. 2004 Jul 15;76(14):3958–3970. doi: 10.1021/ac049774e. [DOI] [PubMed] [Google Scholar]
  50. Boonjakuakul Jenni K., Syvanen Michael, Suryaprasad Arun, Bowlus Christopher L., Solnick Jay V. Transcription profile of Helicobacter pylori in the human stomach reflects its physiology in vivo. J Infect Dis. 2004 Jul 30;190(5):946–956. doi: 10.1086/423142. [DOI] [PubMed] [Google Scholar]
  51. Boore Jeffrey L., Medina Monica, Rosenberg Lewis A. Complete sequences of the highly rearranged molluscan mitochondrial genomes of the Scaphopod Graptacme eborea and the bivalve Mytilus edulis. Mol Biol Evol. 2004 Mar 10;21(8):1492–1503. doi: 10.1093/molbev/msh090. [DOI] [PubMed] [Google Scholar]
  52. Boshoff Helena I. M., Myers Timothy G., Copp Brent R., McNeil Michael R., Wilson Michael A., Barry Clifton E., 3rd The transcriptional responses of Mycobacterium tuberculosis to inhibitors of metabolism: novel insights into drug mechanisms of action. J Biol Chem. 2004 Jul 9;279(38):40174–40184. doi: 10.1074/jbc.M406796200. [DOI] [PubMed] [Google Scholar]
  53. Bouchal Pavel, Precechtelová Petra, Zdráhal Zbynek, Kucera Igor. Protein composition of Paracoccus denitrificans cells grown on various electron acceptors and in the presence of azide. Proteomics. 2004 Sep;4(9):2662–2671. doi: 10.1002/pmic.200400833. [DOI] [PubMed] [Google Scholar]
  54. Bourne S., Polak J. M., Hughes S. P. F., Buttery L. D. K. Osteogenic differentiation of mouse embryonic stem cells: differential gene expression analysis by cDNA microarray and purification of osteoblasts by cadherin-11 magnetically activated cell sorting. Tissue Eng. 2004 May-Jun;10(5-6):796–806. doi: 10.1089/1076327041348293. [DOI] [PubMed] [Google Scholar]
  55. Boussau Bastien, Karlberg E. Olof, Frank A. Carolin, Legault Boris-Antoine, Andersson Siv G. E. Computational inference of scenarios for alpha-proteobacterial genome evolution. Proc Natl Acad Sci U S A. 2004 Jun 21;101(26):9722–9727. doi: 10.1073/pnas.0400975101. [DOI] [PMC free article] [PubMed] [Google Scholar]
  56. Boutell Jonathan M., Hart Darren J., Godber Benjamin L. J., Kozlowski Roland Z., Blackburn Jonathan M. Functional protein microarrays for parallel characterisation of p53 mutants. Proteomics. 2004 Jul;4(7):1950–1958. doi: 10.1002/pmic.200300722. [DOI] [PubMed] [Google Scholar]
  57. Boyle John. SeqExpress: desktop analysis and visualization tool for gene expression experiments. Bioinformatics. 2004 Feb 26;20(10):1649–1650. doi: 10.1093/bioinformatics/bth123. [DOI] [PubMed] [Google Scholar]
  58. Bredemeyer Andrew J., Lewis Renate M., Malone James P., Davis Alan E., Gross Julia, Townsend R. Reid, Ley Timothy J. A proteomic approach for the discovery of protease substrates. Proc Natl Acad Sci U S A. 2004 Jul 27;101(32):11785–11790. doi: 10.1073/pnas.0402353101. [DOI] [PMC free article] [PubMed] [Google Scholar]
  59. Brennan Cameron, Zhang Yunyu, Leo Christopher, Feng Bin, Cauwels Craig, Aguirre Andrew J., Kim Minjung, Protopopov Alexei, Chin Lynda. High-resolution global profiling of genomic alterations with long oligonucleotide microarray. Cancer Res. 2004 Jul 15;64(14):4744–4748. doi: 10.1158/0008-5472.CAN-04-1241. [DOI] [PubMed] [Google Scholar]
  60. Bro Christoffer, Nielsen Jens. Impact of 'ome' analyses on inverse metabolic engineering. Metab Eng. 2004 Jul;6(3):204–211. doi: 10.1016/j.ymben.2003.11.005. [DOI] [PubMed] [Google Scholar]
  61. Brouzés Eric, Farge Emmanuel. Interplay of mechanical deformation and patterned gene expression in developing embryos. Curr Opin Genet Dev. 2004 Aug;14(4):367–374. doi: 10.1016/j.gde.2004.06.005. [DOI] [PubMed] [Google Scholar]
  62. Brown Margaret, Davies Ian M., Moffat Colin F., Robinson Craig, Redshaw John, Craft John A. Identification of transcriptional effects of ethynyl oestradiol in male plaice (Pleuronectes platessa) by suppression subtractive hybridisation and a nylon macroarray. Mar Environ Res. 2004 Aug-Dec;58(2-5):559–563. doi: 10.1016/j.marenvres.2004.03.045. [DOI] [PubMed] [Google Scholar]
  63. Brugière Sabine, Kowalski Solène, Ferro Myriam, Seigneurin-Berny Daphné, Miras Stéphane, Salvi Daniel, Ravanel Stéphane, d'Hérin Pierre, Garin Jérôme, Bourguignon Jacques. The hydrophobic proteome of mitochondrial membranes from Arabidopsis cell suspensions. Phytochemistry. 2004 Jun;65(12):1693–1707. doi: 10.1016/j.phytochem.2004.03.028. [DOI] [PubMed] [Google Scholar]
  64. Brunner Han G., van Driel Marc A. From syndrome families to functional genomics. Nat Rev Genet. 2004 Jul;5(7):545–551. doi: 10.1038/nrg1383. [DOI] [PubMed] [Google Scholar]
  65. Brüggemann Holger, Henne Anke, Hoster Frank, Liesegang Heiko, Wiezer Arnim, Strittmatter Axel, Hujer Sandra, Dürre Peter, Gottschalk Gerhard. The complete genome sequence of Propionibacterium acnes, a commensal of human skin. Science. 2004 Jul 30;305(5684):671–673. doi: 10.1126/science.1100330. [DOI] [PubMed] [Google Scholar]
  66. Bustin Stephen A., Dorudi Sina. Gene expression profiling for molecular staging and prognosis prediction in colorectal cancer. Expert Rev Mol Diagn. 2004 Sep;4(5):599–607. doi: 10.1586/14737159.4.5.599. [DOI] [PubMed] [Google Scholar]
  67. Cacabelos Ramón, Fernández-Novoa Lucía, Corzo Lola, Amado Luís, Pichel Victor, Lombardi Valter, Kubota Yasuhiko. Phenotypic profiles and functional genomics in Alzheimer's disease and in dementia with a vascular component. Neurol Res. 2004 Jul;26(5):459–480. doi: 10.1179/016164104225017677. [DOI] [PubMed] [Google Scholar]
  68. Campostrini Natascia, Pascali Jennifer, Hamdan Mahmoud, Astner Hubert, Marimpietri Danilo, Pastorino Fabio, Ponzoni Mirco, Righetti Pier Giorgio. Proteomic analysis of an orthotopic neuroblastoma xenograft animal model. J Chromatogr B Analyt Technol Biomed Life Sci. 2004 Sep 5;808(2):279–286. doi: 10.1016/j.jchromb.2004.05.013. [DOI] [PubMed] [Google Scholar]
  69. Casu Rosanne E., Dimmock Christine M., Chapman Scott C., Grof Christopher P. L., McIntyre C. Lynne, Bonnett Graham D., Manners John M. Identification of differentially expressed transcripts from maturing stem of sugarcane by in silico analysis of stem expressed sequence tags and gene expression profiling. Plant Mol Biol. 2004 Mar;54(4):503–517. doi: 10.1023/B:PLAN.0000038255.96128.41. [DOI] [PubMed] [Google Scholar]
  70. Cavallaro Sebastiano, D'Agata Velia, Alessi Enrico, Coffa Salvatore, Alkon Daniel L., Manickam Pachiappan, Ciotti Maria Teresa, Possenti Roberta, Bonini Paolo, Marlier Lionel. Gene expression profiles of apoptotic neurons. Genomics. 2004 Sep;84(3):485–496. doi: 10.1016/j.ygeno.2004.04.006. [DOI] [PubMed] [Google Scholar]
  71. Cekaite Lina, Haug Ola, Myklebost Ola, Aldrin Magne, Østenstad Bjørn, Holden Marit, Frigessi Arnoldo, Hovig Eivind, Sioud Mouldy. Analysis of the humoral immune response to immunoselected phage-displayed peptides by a microarray-based method. Proteomics. 2004 Sep;4(9):2572–2582. doi: 10.1002/pmic.200300768. [DOI] [PubMed] [Google Scholar]
  72. Cha Taewoon, Guo Athena, Jun Yongseok, Pei Duanqing, Pei Duanquing, Zhu Xiao-Yang. Immobilization of oriented protein molecules on poly(ethylene glycol)-coated Si(111). Proteomics. 2004 Jul;4(7):1965–1976. doi: 10.1002/pmic.200300747. [DOI] [PubMed] [Google Scholar]
  73. Chaisson Mark, Pevzner Pavel, Tang Haixu. Fragment assembly with short reads. Bioinformatics. 2004 Apr 1;20(13):2067–2074. doi: 10.1093/bioinformatics/bth205. [DOI] [PubMed] [Google Scholar]
  74. Chalifa-Caspi Vered, Yanai Itai, Ophir Ron, Rosen Naomi, Shmoish Michael, Benjamin-Rodrig Hila, Shklar Maxim, Stein Tsippi Iny, Shmueli Orit, Safran Marilyn. GeneAnnot: comprehensive two-way linking between oligonucleotide array probesets and GeneCards genes. Bioinformatics. 2004 Feb 12;20(9):1457–1458. doi: 10.1093/bioinformatics/bth081. [DOI] [PubMed] [Google Scholar]
  75. Chen H-W, Yu S-L, Chen W-J, Yang P-C, Chien C-T, Chou H-Y, Li H-N, Peck K., Huang C-H, Lin F-Y. Dynamic changes of gene expression profiles during postnatal development of the heart in mice. Heart. 2004 Aug;90(8):927–934. doi: 10.1136/hrt.2002.006734. [DOI] [PMC free article] [PubMed] [Google Scholar]
  76. Chen James J., Delongchamp Robert R., Tsai Chen-An, Hsueh Huey-miin, Sistare Frank, Thompson Karol L., Desai Varsha G., Fuscoe James C. Analysis of variance components in gene expression data. Bioinformatics. 2004 Feb 12;20(9):1436–1446. doi: 10.1093/bioinformatics/bth118. [DOI] [PubMed] [Google Scholar]
  77. Chen Jia, He Qing-Yu, Yuen Anthony Po-Wing, Chiu Jeng-Fu. Proteomics of buccal squamous cell carcinoma: the involvement of multiple pathways in tumorigenesis. Proteomics. 2004 Aug;4(8):2465–2475. doi: 10.1002/pmic.200300762. [DOI] [PubMed] [Google Scholar]
  78. Chen Tsute, Hosogi Yumiko, Nishikawa Kiyoshi, Abbey Kevin, Fleischmann Robert D., Walling Jennifer, Duncan Margaret J. Comparative whole-genome analysis of virulent and avirulent strains of Porphyromonas gingivalis. J Bacteriol. 2004 Aug;186(16):5473–5479. doi: 10.1128/JB.186.16.5473-5479.2004. [DOI] [PMC free article] [PubMed] [Google Scholar]
  79. Cheng Jill, Sun Shaw, Tracy Adam, Hubbell Earl, Morris Joseph, Valmeekam Venu, Kimbrough Andrew, Cline Melissa S., Liu Guoying, Shigeta Ron. NetAffx Gene Ontology Mining Tool: a visual approach for microarray data analysis. Bioinformatics. 2004 Feb 12;20(9):1462–1463. doi: 10.1093/bioinformatics/bth087. [DOI] [PubMed] [Google Scholar]
  80. Chernokalskaya Elena, Gutierrez Sara, Pitt Aldo M., Leonard Jack T. Ultrafiltration for proteomic sample preparation. Electrophoresis. 2004 Aug;25(15):2461–2468. doi: 10.1002/elps.200405998. [DOI] [PubMed] [Google Scholar]
  81. Chevalier François, Rofidal Valérie, Vanova Pavlina, Bergoin Alexis, Rossignol Michel. Proteomic capacity of recent fluorescent dyes for protein staining. Phytochemistry. 2004 Jun;65(11):1499–1506. doi: 10.1016/j.phytochem.2004.04.019. [DOI] [PubMed] [Google Scholar]
  82. Chien Minchen, Morozova Irina, Shi Shundi, Sheng Huitao, Chen Jing, Gomez Shawn M., Asamani Gifty, Hill Kendra, Nuara John, Feder Marc. The genomic sequence of the accidental pathogen Legionella pneumophila. Science. 2004 Sep 24;305(5692):1966–1968. doi: 10.1126/science.1099776. [DOI] [PubMed] [Google Scholar]
  83. Cho HyungJun, Lee Jae K. Bayesian hierarchical error model for analysis of gene expression data. Bioinformatics. 2004 Mar 25;20(13):2016–2025. doi: 10.1093/bioinformatics/bth192. [DOI] [PubMed] [Google Scholar]
  84. Chou Kuo-Chen. Insights from modeling three-dimensional structures of the human potassium and sodium channels. J Proteome Res. 2004 Jul-Aug;3(4):856–861. doi: 10.1021/pr049931q. [DOI] [PubMed] [Google Scholar]
  85. Chromy Brett A., Perkins Julie, Heidbrink Jenny L., Gonzales Arlene D., Murphy Gloria A., Fitch J. Patrick, McCutchen-Maloney Sandra L. Proteomic characterization of host response to Yersinia pestis and near neighbors. Biochem Biophys Res Commun. 2004 Jul 23;320(2):474–479. doi: 10.1016/j.bbrc.2004.05.199. [DOI] [PubMed] [Google Scholar]
  86. Church S. Advances in two-dimensional gel matching technology. Biochem Soc Trans. 2004 Jun;32(PT3):511–516. doi: 10.1042/BST0320511. [DOI] [PubMed] [Google Scholar]
  87. Churchill Gary A. Using ANOVA to analyze microarray data. Biotechniques. 2004 Aug;37(2):173-5, 177. doi: 10.2144/04372TE01. [DOI] [PubMed] [Google Scholar]
  88. Cicatiello Luigi, Scafoglio Claudio, Altucci Lucia, Cancemi Massimo, Natoli Guido, Facchiano Angelo, Iazzetti Giovanni, Calogero Raffaele, Biglia Nicoletta, De Bortoli Michele. A genomic view of estrogen actions in human breast cancer cells by expression profiling of the hormone-responsive transcriptome. J Mol Endocrinol. 2004 Jun;32(3):719–775. doi: 10.1677/jme.0.0320719. [DOI] [PubMed] [Google Scholar]
  89. Clegg Nigel, Abbott Denise, Ferguson Camari, Coleman Roger, Nelson Peter S. Characterization and comparative analyses of transcriptomes from the normal and neoplastic human prostate. Prostate. 2004 Aug 1;60(3):227–239. doi: 10.1002/pros.20055. [DOI] [PubMed] [Google Scholar]
  90. Coaker Gitta L., Willard Belinda, Kinter Michael, Stockinger Eric J., Francis David M. Proteomic analysis of resistance mediated by Rcm 2.0 and Rcm 5.1, two loci controlling resistance to bacterial canker of tomato. Mol Plant Microbe Interact. 2004 Sep;17(9):1019–1028. doi: 10.1094/MPMI.2004.17.9.1019. [DOI] [PubMed] [Google Scholar]
  91. Cochrane Fiona C., Davin Laurence B., Lewis Norman G. The Arabidopsis phenylalanine ammonia lyase gene family: kinetic characterization of the four PAL isoforms. Phytochemistry. 2004 Jun;65(11):1557–1564. doi: 10.1016/j.phytochem.2004.05.006. [DOI] [PubMed] [Google Scholar]
  92. Coker Jeffrey Scott, Davies Eric. Identifying adaptor contamination when mining DNA sequence data. Biotechniques. 2004 Aug;37(2):194–198. doi: 10.2144/04372BM03. [DOI] [PubMed] [Google Scholar]
  93. Colinge Jacques, Masselot Alexandre, Cusin Isabelle, Mahé Eve, Niknejad Anne, Argoud-Puy Ghislaine, Reffas Samia, Bederr Nassima, Gleizes Anne, Rey Pierre-Antoine. High-performance peptide identification by tandem mass spectrometry allows reliable automatic data processing in proteomics. Proteomics. 2004 Jul;4(7):1977–1984. doi: 10.1002/pmic.200300708. [DOI] [PubMed] [Google Scholar]
  94. Colland Frédéric, Jacq Xavier, Trouplin Virginie, Mougin Christelle, Groizeleau Caroline, Hamburger Alexandre, Meil Alain, Wojcik Jérôme, Legrain Pierre, Gauthier Jean-Michel. Functional proteomics mapping of a human signaling pathway. Genome Res. 2004 Jul;14(7):1324–1332. doi: 10.1101/gr.2334104. [DOI] [PMC free article] [PubMed] [Google Scholar]
  95. Conrads T. P., Fusaro V. A., Ross S., Johann D., Rajapakse V., Hitt B. A., Steinberg S. M., Kohn E. C., Fishman D. A., Whitely G. High-resolution serum proteomic features for ovarian cancer detection. Endocr Relat Cancer. 2004 Jun;11(2):163–178. doi: 10.1677/erc.0.0110163. [DOI] [PubMed] [Google Scholar]
  96. Cornell Michael, Paton Norman W., Oliver Stephen G. A critical and integrated view of the yeast interactome. Comp Funct Genomics. 2004;5(5):382–402. doi: 10.1002/cfg.412. [DOI] [PMC free article] [PubMed] [Google Scholar]
  97. Cornilescu Gabriel, Cornilescu Claudia C., Zhao Qin, Frederick Ronnie O., Peterson Francis C., Thao Sandy, Markley John L. Solution structure of a homodimeric hypothetical protein, At5g22580, a structural genomics target from Arabidopsis thaliana. J Biomol NMR. 2004 Jul;29(3):387–390. doi: 10.1023/B:JNMR.0000032525.70677.16. [DOI] [PubMed] [Google Scholar]
  98. Costa L. da F., Barbosa M. S., Manoel E. T. M., Streicher J., Müller G. B. Mathematical characterization of three-dimensional gene expression patterns. Bioinformatics. 2004 Feb 26;20(11):1653–1662. doi: 10.1093/bioinformatics/bth135. [DOI] [PubMed] [Google Scholar]
  99. Coulson Richard M. R., Hall Neil, Ouzounis Christos A. Comparative genomics of transcriptional control in the human malaria parasite Plasmodium falciparum. Genome Res. 2004 Jul 15;14(8):1548–1554. doi: 10.1101/gr.2218604. [DOI] [PMC free article] [PubMed] [Google Scholar]
  100. Coyne Kathryn J., Burkholder JoAnn M., Feldman Robert A., Hutchins David A., Cary S. Craig. Modified serial analysis of gene expression method for construction of gene expression profiles of microbial eukaryotic species. Appl Environ Microbiol. 2004 Sep;70(9):5298–5304. doi: 10.1128/AEM.70.9.5298-5304.2004. [DOI] [PMC free article] [PubMed] [Google Scholar]
  101. Craig Robertson, Beavis Ronald C. TANDEM: matching proteins with tandem mass spectra. Bioinformatics. 2004 Feb 19;20(9):1466–1467. doi: 10.1093/bioinformatics/bth092. [DOI] [PubMed] [Google Scholar]
  102. Cutillas Pedro R., Chalkley Robert J., Hansen Kirk C., Cramer Rainer, Norden Anthony G. W., Waterfield Mike D., Burlingame Alma L., Unwin Robert J. The urinary proteome in Fanconi syndrome implies specificity in the reabsorption of proteins by renal proximal tubule cells. Am J Physiol Renal Physiol. 2004 May 12;287(3):F353–F364. doi: 10.1152/ajprenal.00018.2004. [DOI] [PubMed] [Google Scholar]
  103. D'Ascenzo Mark D., Collmer Alan, Martin Gregory B. PeerGAD: a peer-review-based and community-centric web application for viewing and annotating prokaryotic genome sequences. Nucleic Acids Res. 2004 Jun 7;32(10):3124–3135. doi: 10.1093/nar/gkh615. [DOI] [PMC free article] [PubMed] [Google Scholar]
  104. Dahan Sivan, Knutton Stuart, Shaw Robert K., Crepin Valerie F., Dougan Gordon, Frankel Gad. Transcriptome of enterohemorrhagic Escherichia coli O157 adhering to eukaryotic plasma membranes. Infect Immun. 2004 Sep;72(9):5452–5459. doi: 10.1128/IAI.72.9.5452-5459.2004. [DOI] [PMC free article] [PubMed] [Google Scholar]
  105. Darling Aaron C. E., Mau Bob, Blattner Frederick R., Perna Nicole T. Mauve: multiple alignment of conserved genomic sequence with rearrangements. Genome Res. 2004 Jul;14(7):1394–1403. doi: 10.1101/gr.2289704. [DOI] [PMC free article] [PubMed] [Google Scholar]
  106. Dasu M. R. K., Barrow R. E., Hawkins H. K., McCauley R. L. Gene expression profiles of giant hairy naevi. J Clin Pathol. 2004 Aug;57(8):849–855. doi: 10.1136/jcp.2003.014274. [DOI] [PMC free article] [PubMed] [Google Scholar]
  107. Dautry François, Ribet Carole. L'interférence par l'ARN: vers une génomique fonctionnelle chez les mammifères ? Med Sci (Paris) 2004 Aug-Sep;20(8-9):815–819. doi: 10.1051/medsci/2004208-9815. [DOI] [PubMed] [Google Scholar]
  108. De Paepe Annelies, Vuylsteke Marnik, Van Hummelen Paul, Zabeau Marc, Van Der Straeten Dominique. Transcriptional profiling by cDNA-AFLP and microarray analysis reveals novel insights into the early response to ethylene in Arabidopsis. Plant J. 2004 Aug;39(4):537–559. doi: 10.1111/j.1365-313X.2004.02156.x. [DOI] [PubMed] [Google Scholar]
  109. Degauque Nicolas, Schadendorf Dirk, Brouard Sophie, Guillet Marina, Sébille Fabien, Höhn Hanni, Pallier Annaïck, Ruiz Catherine, Dupont Alexandre, Chapin Stéphane. Blood T-cell Vbeta transcriptome in melanoma patients. Int J Cancer. 2004 Jul 10;110(5):721–729. doi: 10.1002/ijc.20149. [DOI] [PubMed] [Google Scholar]
  110. Delongchamp Robert R., Bowyer John F., Chen James J., Kodell Ralph L. Multiple-testing strategy for analyzing cDNA array data on gene expression. Biometrics. 2004 Sep;60(3):774–782. doi: 10.1111/j.0006-341X.2004.00228.x. [DOI] [PubMed] [Google Scholar]
  111. Demir Ayşe Y., Demol Hans, Puype Magda, de Goeij Anton F. P. M., Dunselman Gerard A. J., Herrler Andreas, Evers Johannes L. H., Vandekerckhove Joël, Groothuis Patrick G. Proteome analysis of human mesothelial cells during epithelial to mesenchymal transitions induced by shed menstrual effluent. Proteomics. 2004 Sep;4(9):2608–2623. doi: 10.1002/pmic.200300827. [DOI] [PubMed] [Google Scholar]
  112. Denef V. J., Park J., Tsoi T. V., Rouillard J-M, Zhang H., Wibbenmeyer J. A., Verstraete W., Gulari E., Hashsham S. A., Tiedje J. M. Biphenyl and benzoate metabolism in a genomic context: outlining genome-wide metabolic networks in Burkholderia xenovorans LB400. Appl Environ Microbiol. 2004 Aug;70(8):4961–4970. doi: 10.1128/AEM.70.8.4961-4970.2004. [DOI] [PMC free article] [PubMed] [Google Scholar]
  113. Djordjevic Michael A. Sinorhizobium meliloti metabolism in the root nodule: a proteomic perspective. Proteomics. 2004 Jul;4(7):1859–1872. doi: 10.1002/pmic.200300802. [DOI] [PubMed] [Google Scholar]
  114. Dobson Anthony T., Raja Rajiv, Abeyta Michael J., Taylor Theresa, Shen Shehua, Haqq Christopher, Pera Renee A. Reijo. The unique transcriptome through day 3 of human preimplantation development. Hum Mol Genet. 2004 May 18;13(14):1461–1470. doi: 10.1093/hmg/ddh157. [DOI] [PubMed] [Google Scholar]
  115. Doherty Mary K., McLean Lynn, Hayter Julia R., Pratt Julie M., Robertson Duncan H. L., El-Shafei Abdel, Gaskell Simon J., Beynon Robert J. The proteome of chicken skeletal muscle: changes in soluble protein expression during growth in a layer strain. Proteomics. 2004 Jul;4(7):2082–2093. doi: 10.1002/pmic.200300716. [DOI] [PubMed] [Google Scholar]
  116. Du Yi, Meng Fanyu, Patrie Steven M., Miller Leah M., Kelleher Neil L. Improved molecular weight-based processing of intact proteins for interrogation by quadrupole-enhanced FT MS/MS. J Proteome Res. 2004 Jul-Aug;3(4):801–806. doi: 10.1021/pr0499489. [DOI] [PMC free article] [PubMed] [Google Scholar]
  117. Duarte Natalie C., Herrgård Markus J., Palsson Bernhard Ø. Reconstruction and validation of Saccharomyces cerevisiae iND750, a fully compartmentalized genome-scale metabolic model. Genome Res. 2004 Jun 14;14(7):1298–1309. doi: 10.1101/gr.2250904. [DOI] [PMC free article] [PubMed] [Google Scholar]
  118. Dumont Debora, Noben Jean-Paul, Raus Jef, Stinissen Piet, Robben Johan. Proteomic analysis of cerebrospinal fluid from multiple sclerosis patients. Proteomics. 2004 Jul;4(7):2117–2124. doi: 10.1002/pmic.200300715. [DOI] [PubMed] [Google Scholar]
  119. Dumur Catherine I., Garrett Carleton T., Archer Kellie J., Nasim Suhail, Wilkinson David S., Ferreira-Gonzalez Andrea. Evaluation of a linear amplification method for small samples used on high-density oligonucleotide microarray analysis. Anal Biochem. 2004 Aug 15;331(2):314–321. doi: 10.1016/j.ab.2004.03.040. [DOI] [PubMed] [Google Scholar]
  120. Dumur Jérôme, Jahier Joseph, Bancel Emmanuelle, Laurière Michel, Bernard Michel, Branlard Gérard. Proteomic analysis of aneuploid lines in the homeologous group 1 of the hexaploid wheat cultivar Courtot. Proteomics. 2004 Sep;4(9):2685–2695. doi: 10.1002/pmic.200300800. [DOI] [PubMed] [Google Scholar]
  121. Duncan Robert C., Salotra Poonam, Goyal Neena, Akopyants Natalia S., Beverley Stephen M., Nakhasi Hira L. The application of gene expression microarray technology to kinetoplastid research. Curr Mol Med. 2004 Sep;4(6):611–621. doi: 10.2174/1566524043360221. [DOI] [PubMed] [Google Scholar]
  122. Dunkley T. P. J., Dupree P., Watson R. B., Lilley K. S. The use of isotope-coded affinity tags (ICAT) to study organelle proteomes in Arabidopsis thaliana. Biochem Soc Trans. 2004 Jun;32(PT3):520–523. doi: 10.1042/BST0320520. [DOI] [PubMed] [Google Scholar]
  123. Durr Eberhard, Yu Jingyi, Krasinska Karolina M., Carver Lucy A., Yates John R., Testa Jacqueline E., Oh Phil, Schnitzer Jan E. Direct proteomic mapping of the lung microvascular endothelial cell surface in vivo and in cell culture. Nat Biotechnol. 2004 Jul 18;22(8):985–992. doi: 10.1038/nbt993. [DOI] [PubMed] [Google Scholar]
  124. Emes Richard D., Riley Matthew C., Laukaitis Christina M., Goodstadt Leo, Karn Robert C., Ponting Chris P. Comparative evolutionary genomics of androgen-binding protein genes. Genome Res. 2004 Jul 15;14(8):1516–1529. doi: 10.1101/gr.2540304. [DOI] [PMC free article] [PubMed] [Google Scholar]
  125. Famili A. Fazel, Liu Ganming, Liu Ziying. Evaluation and optimization of clustering in gene expression data analysis. Bioinformatics. 2004 Feb 12;20(10):1535–1545. doi: 10.1093/bioinformatics/bth124. [DOI] [PubMed] [Google Scholar]
  126. Fan Xiaolian, She Yi-Min, Bagshaw Rick D., Callahan John W., Schachter Harry, Mahuran Don J. A method for proteomic identification of membrane-bound proteins containing Asn-linked oligosaccharides. Anal Biochem. 2004 Sep 1;332(1):178–186. doi: 10.1016/j.ab.2004.05.038. [DOI] [PubMed] [Google Scholar]
  127. Finehout Erin J., Franck Zsofia, Lee Kelvin H. Towards two-dimensional electrophoresis mapping of the cerebrospinal fluid proteome from a single individual. Electrophoresis. 2004 Aug;25(15):2564–2575. doi: 10.1002/elps.200406012. [DOI] [PubMed] [Google Scholar]
  128. Finnie Christine, Steenholdt Torben, Roda Noguera Oriol, Knudsen Søren, Larsen Jørgen, Brinch-Pedersen Henrik, Bach Holm Preben, Olsen Ole, Svensson Birte. Environmental and transgene expression effects on the barley seed proteome. Phytochemistry. 2004 Jun;65(11):1619–1627. doi: 10.1016/j.phytochem.2004.04.018. [DOI] [PubMed] [Google Scholar]
  129. Fiévet Julie, Dillmann Christine, Lagniel Gilles, Davanture Marlène, Negroni Luc, Labarre Jean, de Vienne Dominique. Assessing factors for reliable quantitative proteomics based on two-dimensional gel electrophoresis. Proteomics. 2004 Jul;4(7):1939–1949. doi: 10.1002/pmic.200300731. [DOI] [PubMed] [Google Scholar]
  130. Flechner Stuart M., Kurian Sunil M., Head Steven R., Sharp Starlette M., Whisenant Thomas C., Zhang Jie, Chismar Jeffrey D., Horvath Steve, Mondala Tony, Gilmartin Timothy. Kidney transplant rejection and tissue injury by gene profiling of biopsies and peripheral blood lymphocytes. Am J Transplant. 2004 Sep;4(9):1475–1489. doi: 10.1111/j.1600-6143.2004.00526.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  131. Fowler Larry J., Lovell Michael O., Izbicka Elzbieta. Fine-needle aspiration in PreservCyt: a novel and reproducible method for possible ancillary proteomic pattern expression of breast neoplasms by SELDI-TOF. Mod Pathol. 2004 Aug;17(8):1012–1020. doi: 10.1038/modpathol.3800116. [DOI] [PubMed] [Google Scholar]
  132. Francki Michael G., Mullan Daniel J. Application of comparative genomics to narrow-leafed lupin (Lupinus angustifolius L.) using sequence information from soybean and Arabidopsis. Genome. 2004 Aug;47(4):623–632. doi: 10.1139/g04-010. [DOI] [PubMed] [Google Scholar]
  133. Fraser Andrew G., Marcotte Edward M. Development through the eyes of functional genomics. Curr Opin Genet Dev. 2004 Aug;14(4):336–342. doi: 10.1016/j.gde.2004.06.015. [DOI] [PubMed] [Google Scholar]
  134. Frazier Monica C., Jackson Kimberly M., Jankowska-Stephens Ewa, Anderson Mark G., Harris Wayne B. Proteomic analysis of proteins altered by dibenzoylmethane in human prostatic cancer LNCaP cells. Proteomics. 2004 Sep;4(9):2814–2821. doi: 10.1002/pmic.200400834. [DOI] [PubMed] [Google Scholar]
  135. Friedberg Iddo, Jaroszewski Lukasz, Ye Yuzhen, Godzik Adam. The interplay of fold recognition and experimental structure determination in structural genomics. Curr Opin Struct Biol. 2004 Jun;14(3):307–312. doi: 10.1016/j.sbi.2004.04.005. [DOI] [PubMed] [Google Scholar]
  136. Frisk Anders, Schurr Jill R., Wang Guoshun, Bertucci Donna C., Marrero Luis, Hwang Sung Hei, Hassett Daniel J., Schurr Michael J. Transcriptome analysis of Pseudomonas aeruginosa after interaction with human airway epithelial cells. Infect Immun. 2004 Sep;72(9):5433–5438. doi: 10.1128/IAI.72.9.5433-5438.2004. [DOI] [PMC free article] [PubMed] [Google Scholar]
  137. Frith Martin C., Halees Anason S., Hansen Ulla, Weng Zhiping. Site2genome: locating short DNA sequences in whole genomes. Bioinformatics. 2004 Feb 12;20(9):1468–1469. doi: 10.1093/bioinformatics/bth094. [DOI] [PubMed] [Google Scholar]
  138. Fuentes Manuel, Segura Rosa L., Abian Olga, Betancor Lorena, Hidalgo Aurelio, Mateo Cesar, Fernandez-Lafuente Roberto, Guisan Jose M. Determination of protein-protein interactions through aldehyde-dextran intermolecular cross-linking. Proteomics. 2004 Sep;4(9):2602–2607. doi: 10.1002/pmic.200300766. [DOI] [PubMed] [Google Scholar]
  139. Fujii Kiyonaga, Nakano Tomoyo, Kawamura Takeshi, Usui Fumihiko, Bando Yasuhiko, Wang Rong, Nishimura Toshihide. Multidimensional protein profiling technology and its application to human plasma proteome. J Proteome Res. 2004 Jul-Aug;3(4):712–718. doi: 10.1021/pr030007q. [DOI] [PubMed] [Google Scholar]
  140. Fujimoto Nariaki, Igarashi Katsuhide, Kanno Junn, Honda Hiroaki, Inoue Tohru. Identification of estrogen-responsive genes in the GH3 cell line by cDNA microarray analysis. J Steroid Biochem Mol Biol. 2004 Jul;91(3):121–129. doi: 10.1016/j.jsbmb.2004.02.006. [DOI] [PubMed] [Google Scholar]
  141. Fujiwara Kyoko, Ochiai Masako, Ohta Tsutomu, Ohki Misao, Aburatani Hiroyuki, Nagao Minako, Sugimura Takashi, Nakagama Hitoshi. Global gene expression analysis of rat colon cancers induced by a food-borne carcinogen, 2-amino-1-methyl-6-phenylimidazo[4,5-b]pyridine. Carcinogenesis. 2004 Apr 1;25(8):1495–1505. doi: 10.1093/carcin/bgh155. [DOI] [PubMed] [Google Scholar]
  142. Fujiwara Satsuki, Tanaka Noriko, Kaneda Takashi, Takayama Seiji, Isogai Akira, Che Fang-Sik. Rice cDNA microarray-based gene expression profiling of the response to flagellin perception in cultured rice cells. Mol Plant Microbe Interact. 2004 Sep;17(9):986–998. doi: 10.1094/MPMI.2004.17.9.986. [DOI] [PubMed] [Google Scholar]
  143. Furutani-Seiki Makoto, Sasado Takao, Morinaga Chikako, Suwa Hiroshi, Niwa Katsutoshi, Yoda Hiroki, Deguchi Tomonori, Hirose Yukihiro, Yasuoka Akihito, Henrich Thorsten. A systematic genome-wide screen for mutations affecting organogenesis in Medaka, Oryzias latipes. Mech Dev. 2004 Jul;121(7-8):647–658. doi: 10.1016/j.mod.2004.04.016. [DOI] [PubMed] [Google Scholar]
  144. García Angel, Zitzmann Nicole, Watson Steve P. Analyzing the platelet proteome. Semin Thromb Hemost. 2004 Aug;30(4):485–489. doi: 10.1055/s-2004-833483. [DOI] [PubMed] [Google Scholar]
  145. Ge Yue, Molloy Mark P., Chamberlain Jeffrey S., Andrews Philip C. Differential expression of the skeletal muscle proteome in mdx mice at different ages. Electrophoresis. 2004 Aug;25(15):2576–2585. doi: 10.1002/elps.200406013. [DOI] [PubMed] [Google Scholar]
  146. Gelfi Cecilia, Viganò Agnese, Ripamonti Marilena, Wait Robin, Begum Shajna, Biguzzi Eugenia, Castaman Giancarlo, Faioni Elena Maria. A proteomic analysis of changes in prothrombin and plasma proteins associated with the G20210A mutation. Proteomics. 2004 Jul;4(7):2151–2159. doi: 10.1002/pmic.200300724. [DOI] [PubMed] [Google Scholar]
  147. Genschel Ulrich. Coenzyme A biosynthesis: reconstruction of the pathway in archaea and an evolutionary scenario based on comparative genomics. Mol Biol Evol. 2004 Mar 10;21(7):1242–1251. doi: 10.1093/molbev/msh119. [DOI] [PubMed] [Google Scholar]
  148. Getchell Thomas V., Peng Xuejun, Green C. Paul, Stromberg Arnold J., Chen Kuey-Chu, Mattson Mark P., Getchell Marilyn L. In silico analysis of gene expression profiles in the olfactory mucosae of aging senescence-accelerated mice. J Neurosci Res. 2004 Aug 1;77(3):430–452. doi: 10.1002/jnr.20157. [DOI] [PubMed] [Google Scholar]
  149. Ghosh Debashis. Mixture models for assessing differential expression in complex tissues using microarray data. Bioinformatics. 2004 Feb 26;20(11):1663–1669. doi: 10.1093/bioinformatics/bth139. [DOI] [PubMed] [Google Scholar]
  150. Ghosh Dhiman, Krokhin Oleg, Antonovici Mihaela, Ens Werner, Standing Kenneth G., Beavis Ronald C., Wilkins John A. Lectin affinity as an approach to the proteomic analysis of membrane glycoproteins. J Proteome Res. 2004 Jul-Aug;3(4):841–850. doi: 10.1021/pr049937f. [DOI] [PubMed] [Google Scholar]
  151. Gohil Kishorchandra. Functional genomics identifies novel and diverse molecular targets of nutrients in vivo. Biol Chem. 2004 Aug;385(8):691–696. doi: 10.1515/BC.2004.085. [DOI] [PubMed] [Google Scholar]
  152. Golfier G., Dang M. Tran, Dauphinot L., Graison E., Rossier J., Potier M-C. VARAN: a web server for variability analysis of DNA microarray experiments. Bioinformatics. 2004 Feb 12;20(10):1641–1643. doi: 10.1093/bioinformatics/bth117. [DOI] [PubMed] [Google Scholar]
  153. Goodchild Amber, Saunders Neil F. W., Ertan Haluk, Raftery Mark, Guilhaus Michael, Curmi Paul M. G., Cavicchioli Ricardo. A proteomic determination of cold adaptation in the Antarctic archaeon, Methanococcoides burtonii. Mol Microbiol. 2004 Jul;53(1):309–321. doi: 10.1111/j.1365-2958.2004.04130.x. [DOI] [PubMed] [Google Scholar]
  154. Goodman Teresa, Schulenberg Birte, Steinberg Thomas H., Patton Wayne F. Detection of phosphoproteins on electroblot membranes using a small-molecule organic fluorophore. Electrophoresis. 2004 Aug;25(15):2533–2538. doi: 10.1002/elps.200406008. [DOI] [PubMed] [Google Scholar]
  155. Gottlieb David M., Schultz Jakob, Bruun Susanne W., Jacobsen Susanne, Søndergaard Ib. Multivariate approaches in plant science. Phytochemistry. 2004 Jun;65(11):1531–1548. doi: 10.1016/j.phytochem.2004.04.008. [DOI] [PubMed] [Google Scholar]
  156. Granger Laure, Martin Edwige, Ségalat Laurent. Mos as a tool for genome-wide insertional mutagenesis in Caenorhabditis elegans: results of a pilot study. Nucleic Acids Res. 2004 Aug 13;32(14):e117–e117. doi: 10.1093/nar/gnh111. [DOI] [PMC free article] [PubMed] [Google Scholar]
  157. Grasso Catherine, Lee Christopher. Combining partial order alignment and progressive multiple sequence alignment increases alignment speed and scalability to very large alignment problems. Bioinformatics. 2004 Feb 12;20(10):1546–1556. doi: 10.1093/bioinformatics/bth126. [DOI] [PubMed] [Google Scholar]
  158. Gravett Michael G., Novy Miles J., Rosenfeld Ron G., Reddy Ashok P., Jacob Thomas, Turner Mark, McCormack Ashley, Lapidus Jodi A., Hitti Jane, Eschenbach David A. Diagnosis of intra-amniotic infection by proteomic profiling and identification of novel biomarkers. JAMA. 2004 Jul 28;292(4):462–469. doi: 10.1001/jama.292.4.462. [DOI] [PubMed] [Google Scholar]
  159. Greetham Darren, Morgan Charly, Campbell Alison M., van Rossum Arjan J., Barrett John, Brophy Peter M. Evidence of glutathione transferase complexing and signaling in the model nematode Caenorhabditis elegans using a pull-down proteomic assay. Proteomics. 2004 Jul;4(7):1989–1995. doi: 10.1002/pmic.200300719. [DOI] [PubMed] [Google Scholar]
  160. Griffin Julian L., Bonney Stephanie A., Mann Chris, Hebbachi Abdul M., Gibbons Geoff F., Nicholson Jeremy K., Shoulders Carol C., Scott James. An integrated reverse functional genomic and metabolic approach to understanding orotic acid-induced fatty liver. Physiol Genomics. 2004 Apr 13;17(2):140–149. doi: 10.1152/physiolgenomics.00158.2003. [DOI] [PubMed] [Google Scholar]
  161. Griffin Julian L. Metabolic profiles to define the genome: can we hear the phenotypes? Philos Trans R Soc Lond B Biol Sci. 2004 Jun 29;359(1446):857–871. doi: 10.1098/rstb.2003.1411. [DOI] [PMC free article] [PubMed] [Google Scholar]
  162. Griffin Matthew D., Xing Nianzeng, Kumar Rajiv. Gene expression profiles in dendritic cells conditioned by 1alpha,25-dihydroxyvitamin D3 analog. J Steroid Biochem Mol Biol. 2004 May;89-90(1-5):443–448. doi: 10.1016/j.jsbmb.2004.03.039. [DOI] [PubMed] [Google Scholar]
  163. Grill Constance, Gheyas Ferdous, Dayananth Priya, Jin Weihong, Ding Wei, Qiu Ping, Wang Luquan, Doll Ronald J., English Jessie M. Analysis of the ERK1,2 transcriptome in mammary epithelial cells. Biochem J. 2004 Aug 1;381(Pt 3):635–644. doi: 10.1042/BJ20031688. [DOI] [PMC free article] [PubMed] [Google Scholar]
  164. Grimm M-O, Hartmann F. H., Schulz W. A. MicroarraysTechnik und Potenzial beim Prostatakarzinom. Urologe A. 2004 Jun;43(6):653–658. doi: 10.1007/s00120-004-0578-6. [DOI] [PubMed] [Google Scholar]
  165. Grover Corrinne E., Kim HyeRan, Wing Rod A., Paterson Andrew H., Wendel Jonathan F. Incongruent patterns of local and global genome size evolution in cotton. Genome Res. 2004 Jul 15;14(8):1474–1482. doi: 10.1101/gr.2673204. [DOI] [PMC free article] [PubMed] [Google Scholar]
  166. Grozdanov Lubomir, Raasch Carsten, Schulze Jürgen, Sonnenborn Ulrich, Gottschalk Gerhard, Hacker Jörg, Dobrindt Ulrich. Analysis of the genome structure of the nonpathogenic probiotic Escherichia coli strain Nissle 1917. J Bacteriol. 2004 Aug;186(16):5432–5441. doi: 10.1128/JB.186.16.5432-5441.2004. [DOI] [PMC free article] [PubMed] [Google Scholar]
  167. Grützmann Robert, Saeger Hans Detlev, Lüttges Jutta, Schackert Hans Konrad, Kalthoff Holger, Klöppel Günter, Pilarsky Christian. Microarray-based gene expression profiling in pancreatic ductal carcinoma: status quo and perspectives. Int J Colorectal Dis. 2004 Jan 24;19(5):401–413. doi: 10.1007/s00384-003-0563-3. [DOI] [PubMed] [Google Scholar]
  168. Guda Chittibabu, Fahy Eoin, Subramaniam Shankar. MITOPRED: a genome-scale method for prediction of nucleus-encoded mitochondrial proteins. Bioinformatics. 2004 Mar 22;20(11):1785–1794. doi: 10.1093/bioinformatics/bth171. [DOI] [PubMed] [Google Scholar]
  169. Gullberg Jonas, Jonsson Pär, Nordström Anders, Sjöström Michael, Moritz Thomas. Design of experiments: an efficient strategy to identify factors influencing extraction and derivatization of Arabidopsis thaliana samples in metabolomic studies with gas chromatography/mass spectrometry. Anal Biochem. 2004 Aug 15;331(2):283–295. doi: 10.1016/j.ab.2004.04.037. [DOI] [PubMed] [Google Scholar]
  170. Haagerup Annette, Bjerke Torbjørn, Schiøtz Peter Oluf, Dahl Ronald, Binderup Helle Glud, Tan Qihua, Kruse Torben Arvid. Atopic dermatitis -- a total genome-scan for susceptibility genes. Acta Derm Venereol. 2004;84(5):346–352. doi: 10.1080/00015550410034426. [DOI] [PubMed] [Google Scholar]
  171. Hall Jennifer L., Grindle Suzanne, Han Xinqiang, Fermin David, Park Soon, Chen Yingjie, Bache Robert J., Mariash Ami, Guan Zhanjun, Ormaza Sofia. Genomic profiling of the human heart before and after mechanical support with a ventricular assist device reveals alterations in vascular signaling networks. Physiol Genomics. 2004 May 19;17(3):283–291. doi: 10.1152/physiolgenomics.00004.2004. [DOI] [PubMed] [Google Scholar]
  172. Halligan Brian D., Dratz Edward A., Feng Xin, Twigger Simon N., Tonellato Peter J., Greene Andrew S. Peptide identification using peptide amino acid attribute vectors. J Proteome Res. 2004 Jul-Aug;3(4):813–820. doi: 10.1021/pr0499444. [DOI] [PubMed] [Google Scholar]
  173. Hamatani Toshio, Carter Mark G., Sharov Alexei A., Ko Minoru S. H. Dynamics of global gene expression changes during mouse preimplantation development. Dev Cell. 2004 Jan;6(1):117–131. doi: 10.1016/s1534-5807(03)00373-3. [DOI] [PubMed] [Google Scholar]
  174. Han Jun, Schey Kevin L. Proteolysis and mass spectrometric analysis of an integral membrane: aquaporin 0. J Proteome Res. 2004 Jul-Aug;3(4):807–812. doi: 10.1021/pr049945w. [DOI] [PubMed] [Google Scholar]
  175. Hanisch Daniel, Sohler Florian, Zimmer Ralf. ToPNet--an application for interactive analysis of expression data and biological networks. Bioinformatics. 2004 Feb 12;20(9):1470–1471. doi: 10.1093/bioinformatics/bth096. [DOI] [PubMed] [Google Scholar]
  176. Harris Michael N., Ozpolat Bulent, Abdi Fadi, Gu Sheng, Legler Allison, Mawuenyega Kwasi G., Tirado-Gomez Maribel, Lopez-Berestein Gabriel, Chen Xian. Comparative proteomic analysis of all-trans-retinoic acid treatment reveals systematic posttranscriptional control mechanisms in acute promyelocytic leukemia. Blood. 2004 May 13;104(5):1314–1323. doi: 10.1182/blood-2004-01-0046. [DOI] [PubMed] [Google Scholar]
  177. Hart Courtenay, Schulenberg Birte, Patton Wayne F. Selective proteome-wide detection of hydrophobic integral membrane proteins using a novel fluorescence-based staining technology. Electrophoresis. 2004 Aug;25(15):2486–2493. doi: 10.1002/elps.200406001. [DOI] [PubMed] [Google Scholar]
  178. Hart G. T., Shaffer D. J., Akilesh S., Brown A. C., Moran L., Roopenian D. C., Baker P. J. Quantitative gene expression profiling implicates genes for susceptibility and resistance to alveolar bone loss. Infect Immun. 2004 Aug;72(8):4471–4479. doi: 10.1128/IAI.72.8.4471-4479.2004. [DOI] [PMC free article] [PubMed] [Google Scholar]
  179. Hathout Yetrib, Gehrmann Marion L., Chertov Andrei, Fenselau Catherine. Proteomic phenotyping: metastatic and invasive breast cancer. Cancer Lett. 2004 Jul 16;210(2):245–253. doi: 10.1016/j.canlet.2004.01.019. [DOI] [PubMed] [Google Scholar]
  180. Hauser Peter, Schwarz Christoph, Mitterbauer Christa, Regele Heinz M., Mühlbacher Ferdinand, Mayer Gert, Perco Paul, Mayer Bernd, Meyer Timothy W., Oberbauer Rainer. Genome-wide gene-expression patterns of donor kidney biopsies distinguish primary allograft function. Lab Invest. 2004 Mar;84(3):353–361. doi: 10.1038/labinvest.3700037. [DOI] [PubMed] [Google Scholar]
  181. Haverty Peter M., Weng Zhiping. CisML: an XML-based format for sequence motif detection software. Bioinformatics. 2004 Mar 4;20(11):1815–1817. doi: 10.1093/bioinformatics/bth162. [DOI] [PubMed] [Google Scholar]
  182. Hayduk Eric J., Choe Leila H., Lee Kelvin H. A two-dimensional electrophoresis map of Chinese hamster ovary cell proteins based on fluorescence staining. Electrophoresis. 2004 Aug;25(15):2545–2556. doi: 10.1002/elps.200406010. [DOI] [PubMed] [Google Scholar]
  183. Hedegaard Jakob, Horn Per, Lametsch René, Søndergaard Møller Hanne, Roepstorff Peter, Bendixen Christian, Bendixen Emøke. UDP-glucose pyrophosphorylase is upregulated in carriers of the porcine RN- mutation in the AMP-activated protein kinase. Proteomics. 2004 Aug;4(8):2448–2454. doi: 10.1002/pmic.200300761. [DOI] [PubMed] [Google Scholar]
  184. Heinemeyer Jesco, Eubel Holger, Wehmhöner Dirk, Jänsch Lothar, Braun Hans-Peter. Proteomic approach to characterize the supramolecular organization of photosystems in higher plants. Phytochemistry. 2004 Jun;65(12):1683–1692. doi: 10.1016/j.phytochem.2004.04.022. [DOI] [PubMed] [Google Scholar]
  185. Heinloth Alexandra N., Irwin Richard D., Boorman Gary A., Nettesheim Paul, Fannin Rickie D., Sieber Stella O., Snell Michael L., Tucker Charles J., Li Leping, Travlos Gregory S. Gene expression profiling of rat livers reveals indicators of potential adverse effects. Toxicol Sci. 2004 Apr 14;80(1):193–202. doi: 10.1093/toxsci/kfh145. [DOI] [PubMed] [Google Scholar]
  186. Hellman K., Alaiya A. A., Schedvins K., Steinberg W., Hellström A-C, Auer G. Protein expression patterns in primary carcinoma of the vagina. Br J Cancer. 2004 Jul 19;91(2):319–326. doi: 10.1038/sj.bjc.6601944. [DOI] [PMC free article] [PubMed] [Google Scholar]
  187. Helman Paul, Veroff Robert, Atlas Susan R., Willman Cheryl. A Bayesian network classification methodology for gene expression data. J Comput Biol. 2004;11(4):581–615. doi: 10.1089/cmb.2004.11.581. [DOI] [PubMed] [Google Scholar]
  188. Henrich Thorsten, Ramialison Mirana, Segerdell Erik, Westerfield Monte, Furutani-Seiki Makoto, Wittbrodt Joachim, Kondoh Hisato. GSD: a genetic screen database. Mech Dev. 2004 Jul;121(7-8):959–963. doi: 10.1016/j.mod.2004.02.006. [DOI] [PubMed] [Google Scholar]
  189. Hering Joachim A., Innocent Peter R., Haris Parvez I. Towards developing a protein infrared spectra databank (PISD) for proteomics research. Proteomics. 2004 Aug;4(8):2310–2319. doi: 10.1002/pmic.200300808. [DOI] [PubMed] [Google Scholar]
  190. Herzog Angelika, Kindermann Birgit, Döring Frank, Daniel Hannelore, Wenzel Uwe. Pleiotropic molecular effects of the pro-apoptotic dietary constituent flavone in human colon cancer cells identified by protein and mRNA expression profiling. Proteomics. 2004 Aug;4(8):2455–2464. doi: 10.1002/pmic.200300754. [DOI] [PubMed] [Google Scholar]
  191. Hildebrandt Michelle A. T., Salavaggione Oreste E., Martin Yvette N., Flynn Heather C., Jalal Syed, Wieben Eric D., Weinshilboum Richard M. Human SULT1A3 pharmacogenetics: gene duplication and functional genomic studies. Biochem Biophys Res Commun. 2004 Sep 3;321(4):870–878. doi: 10.1016/j.bbrc.2004.07.038. [DOI] [PubMed] [Google Scholar]
  192. Hinton Jay C. D., Hautefort Isabelle, Eriksson Sofia, Thompson Arthur, Rhen Mikael. Benefits and pitfalls of using microarrays to monitor bacterial gene expression during infection. Curr Opin Microbiol. 2004 Jun;7(3):277–282. doi: 10.1016/j.mib.2004.04.009. [DOI] [PubMed] [Google Scholar]
  193. Hirai Masami Yokota, Yano Mitsuru, Goodenowe Dayan B., Kanaya Shigehiko, Kimura Tomoko, Awazuhara Motoko, Arita Masanori, Fujiwara Toru, Saito Kazuki. Integration of transcriptomics and metabolomics for understanding of global responses to nutritional stresses in Arabidopsis thaliana. Proc Natl Acad Sci U S A. 2004 Jun 15;101(27):10205–10210. doi: 10.1073/pnas.0403218101. [DOI] [PMC free article] [PubMed] [Google Scholar]
  194. Hirano Hisashi, Islam Nazrul, Kawasaki Hiroshi. Technical aspects of functional proteomics in plants. Phytochemistry. 2004 Jun;65(11):1487–1498. doi: 10.1016/j.phytochem.2004.05.019. [DOI] [PubMed] [Google Scholar]
  195. Hofacker I. L., Stadler P. F., Stocsits R. R. Conserved RNA secondary structures in viral genomes: a survey. Bioinformatics. 2004 Jul 10;20(10):1495–1499. doi: 10.1093/bioinformatics/bth108. [DOI] [PubMed] [Google Scholar]
  196. Hoffmann Geoffrey W. Proteomic analyser with applications to diagnostics and vaccines. J Theor Biol. 2004 Jun 21;228(4):459–465. doi: 10.1016/j.jtbi.2004.02.011. [DOI] [PMC free article] [PubMed] [Google Scholar]
  197. Hogarth Caroline J., Fitzpatrick Julie L., Nolan Andrea M., Young Fiona J., Pitt Andrew, Eckersall P. David. Differential protein composition of bovine whey: a comparison of whey from healthy animals and from those with clinical mastitis. Proteomics. 2004 Jul;4(7):2094–2100. doi: 10.1002/pmic.200300723. [DOI] [PubMed] [Google Scholar]
  198. Holden Matthew T. G., Feil Edward J., Lindsay Jodi A., Peacock Sharon J., Day Nicholas P. J., Enright Mark C., Foster Tim J., Moore Catrin E., Hurst Laurence, Atkin Rebecca. Complete genomes of two clinical Staphylococcus aureus strains: evidence for the rapid evolution of virulence and drug resistance. Proc Natl Acad Sci U S A. 2004 Jun 22;101(26):9786–9791. doi: 10.1073/pnas.0402521101. [DOI] [PMC free article] [PubMed] [Google Scholar]
  199. Holland Cathrine M., Saidi Samir A., Evans Amanda L., Sharkey Andrew M., Latimer John A., Crawford Robin A. F., Charnock-Jones D. Stephen, Print Cristin G., Smith Stephen K. Transcriptome analysis of endometrial cancer identifies peroxisome proliferator-activated receptors as potential therapeutic targets. Mol Cancer Ther. 2004 Aug;3(8):993–1001. [PubMed] [Google Scholar]
  200. Holleman Amy, Cheok Meyling H., den Boer Monique L., Yang Wenjian, Veerman Anjo J. P., Kazemier Karin M., Pei Deqing, Cheng Cheng, Pui Ching-Hon, Relling Mary V. Gene-expression patterns in drug-resistant acute lymphoblastic leukemia cells and response to treatment. N Engl J Med. 2004 Aug 5;351(6):533–542. doi: 10.1056/NEJMoa033513. [DOI] [PubMed] [Google Scholar]
  201. Hollich Volker, Johnson Eric, Furlong Eileen E., Beckmann Boris, Carlson Joseph, Celniker Susan E., Hoheisel Jörg D. Creation of a minimal tiling path of genomic clones for Drosophila: provision of a common resource. Biotechniques. 2004 Aug;37(2):282–284. doi: 10.2144/04372MT01. [DOI] [PubMed] [Google Scholar]
  202. Holtkamp Nikola, Reuss David E., Atallah Isis, Kuban Ralf-Jürgen, Hartmann Christian, Mautner Victor-F, Frahm Silke, Friedrich Reinhard E., Algermissen Bernd, Pham Van-Anh. Subclassification of nerve sheath tumors by gene expression profiling. Brain Pathol. 2004 Jul;14(3):258–264. doi: 10.1111/j.1750-3639.2004.tb00062.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  203. Hong S. H., Kim T. Y., Lee S. Y. Phylogenetic analysis based on genome-scale metabolic pathway reaction content. Appl Microbiol Biotechnol. 2004 Jun 9;65(2):203–210. doi: 10.1007/s00253-004-1641-3. [DOI] [PubMed] [Google Scholar]
  204. Honoré Bent, Østergaard Morten, Vorum Henrik. Functional genomics studied by proteomics. Bioessays. 2004 Aug;26(8):901–915. doi: 10.1002/bies.20075. [DOI] [PubMed] [Google Scholar]
  205. Hoogland Christine, Mostaguir Khaled, Sanchez Jean-Charles, Hochstrasser Denis F., Appel Ron D. SWISS-2DPAGE, ten years later. Proteomics. 2004 Aug;4(8):2352–2356. doi: 10.1002/pmic.200300830. [DOI] [PubMed] [Google Scholar]
  206. Hooshdaran Massoumeh Z., Barker Katherine S., Hilliard George M., Kusch Harald, Morschhäuser Joachim, Rogers P. David. Proteomic analysis of azole resistance in Candida albicans clinical isolates. Antimicrob Agents Chemother. 2004 Jul;48(7):2733–2735. doi: 10.1128/AAC.48.7.2733-2735.2004. [DOI] [PMC free article] [PubMed] [Google Scholar]
  207. Horne A. B., Hodgman T. C., Spence H. D., Dalby A. R. Constructing an enzyme-centric view of metabolism. Bioinformatics. 2004 Apr 8;20(13):2050–2055. doi: 10.1093/bioinformatics/bth199. [DOI] [PubMed] [Google Scholar]
  208. Hoyt Peter R., Doktycz Mitchel J. Optimized beadmilling of tissues for high-throughput RNA production and microarray-based analyses. Anal Biochem. 2004 Sep 1;332(1):100–108. doi: 10.1016/j.ab.2004.04.025. [DOI] [PubMed] [Google Scholar]
  209. Hozumi Akiko, Satouh Yuhkoh, Ishibe Daisuke, Kaizu Maiko, Konno Aru, Ushimaru Yuji, Toda Tosifusa, Inaba Kazuo. Local database and the search program for proteomic analysis of sperm proteins in the ascidian Ciona intestinalis. Biochem Biophys Res Commun. 2004 Jul 9;319(4):1241–1246. doi: 10.1016/j.bbrc.2004.05.118. [DOI] [PubMed] [Google Scholar]
  210. Huang Chun-Ming, Foster K. Wade, DeSilva Tivanka S., Van Kampen Kent R., Elmets Craig A., Tang De-Chu C. Identification of Bacillus anthracis proteins associated with germination and early outgrowth by proteomic profiling of anthrax spores. Proteomics. 2004 Sep;4(9):2653–2661. doi: 10.1002/pmic.200400831. [DOI] [PubMed] [Google Scholar]
  211. Huber Wolfgang, Gentleman Robert. matchprobes: a Bioconductor package for the sequence-matching of microarray probe elements. Bioinformatics. 2004 Feb 26;20(10):1651–1652. doi: 10.1093/bioinformatics/bth133. [DOI] [PubMed] [Google Scholar]
  212. Huff Jennifer L., Hansen Lori M., Solnick Jay V. Gastric transcription profile of Helicobacter pylori infection in the rhesus macaque. Infect Immun. 2004 Sep;72(9):5216–5226. doi: 10.1128/IAI.72.9.5216-5226.2004. [DOI] [PMC free article] [PubMed] [Google Scholar]
  213. Huson Daniel H., Steel Mike. Phylogenetic trees based on gene content. Bioinformatics. 2004 Mar 25;20(13):2044–2049. doi: 10.1093/bioinformatics/bth198. [DOI] [PubMed] [Google Scholar]
  214. Husson Hervé, Manavalan Partha, Akmaev Viatcheslav R., Russo Ryan J., Cook Brian, Richards Brenda, Barberio Dana, Liu Dongyu, Cao Xiaohong, Landes Gregory M. New insights into ADPKD molecular pathways using combination of SAGE and microarray technologies. Genomics. 2004 Sep;84(3):497–510. doi: 10.1016/j.ygeno.2004.03.009. [DOI] [PubMed] [Google Scholar]
  215. Hutter Bernd, Schaab Christoph, Albrecht Sebastian, Borgmann Matthias, Brunner Nina A., Freiberg Christoph, Ziegelbauer Karl, Rock Charles O., Ivanov Igor, Loferer Hannes. Prediction of mechanisms of action of antibacterial compounds by gene expression profiling. Antimicrob Agents Chemother. 2004 Aug;48(8):2838–2844. doi: 10.1128/AAC.48.8.2838-2844.2004. [DOI] [PMC free article] [PubMed] [Google Scholar]
  216. Huynen Martijn A., Snel Berend, van Noort Vera. Comparative genomics for reliable protein-function prediction from genomic data. Trends Genet. 2004 Aug;20(8):340–344. doi: 10.1016/j.tig.2004.06.003. [DOI] [PubMed] [Google Scholar]
  217. Ida Hisashi, Boylan Sharon A., Weigel Andrea L., Smit-McBride Zeljka, Chao Anne, Gao James, Buchoff Patee, Wistow Graeme, Hjelmeland Leonard M. EST analysis of mouse retina and RPE/choroid cDNA libraries. Mol Vis. 2004 Jul 6;10:439–444. [PubMed] [Google Scholar]
  218. Ihmels Jan, Bergmann Sven, Barkai Naama. Defining transcription modules using large-scale gene expression data. Bioinformatics. 2004 Mar 25;20(13):1993–2003. doi: 10.1093/bioinformatics/bth166. [DOI] [PubMed] [Google Scholar]
  219. Imin Nijat, De Jong Femke, Mathesius Ulrike, van Noorden Giel, Saeed Nasir A., Wang Xin-Ding, Rose Ray J., Rolfe Barry G. Proteome reference maps of Medicago truncatula embryogenic cell cultures generated from single protoplasts. Proteomics. 2004 Jul;4(7):1883–1896. doi: 10.1002/pmic.200300803. [DOI] [PubMed] [Google Scholar]
  220. Imin Nijat, Kerim Tursun, Rolfe Barry G., Weinman Jeremy J. Effect of early cold stress on the maturation of rice anthers. Proteomics. 2004 Jul;4(7):1873–1882. doi: 10.1002/pmic.200300738. [DOI] [PubMed] [Google Scholar]
  221. Islam Nazrul, Lonsdale M., Upadhyaya N. M., Higgins T. J., Hirano H., Akhurst R. Protein extraction from mature rice leaves for two-dimensional gel electrophoresis and its application in proteome analysis. Proteomics. 2004 Jul;4(7):1903–1908. doi: 10.1002/pmic.200300816. [DOI] [PubMed] [Google Scholar]
  222. Ito Y., Eiguchi M., Kurata N. Establishment of an enhancer trap system with Ds and GUS for functional genomics in rice. Mol Genet Genomics. 2004 Jun 18;271(6):639–650. doi: 10.1007/s00438-004-1023-7. [DOI] [PubMed] [Google Scholar]
  223. Iwafuchi Hideto, Mori Naoyoshi, Takahashi Takashi, Yatabe Yasushi. Phenotypic composition of salivary gland tumors: an application of principal [corrected] component analysis to tissue microarray data. Mod Pathol. 2004 Jul;17(7):803–810. doi: 10.1038/modpathol.3800122. [DOI] [PubMed] [Google Scholar]
  224. Jaffe Jacob D., Stange-Thomann Nicole, Smith Cherylyn, DeCaprio David, Fisher Sheila, Butler Jonathan, Calvo Sarah, Elkins Tim, FitzGerald Michael G., Hafez Nabil. The complete genome and proteome of Mycoplasma mobile. Genome Res. 2004 Aug;14(8):1447–1461. doi: 10.1101/gr.2674004. [DOI] [PMC free article] [PubMed] [Google Scholar]
  225. Jarman Simon N. Amplicon: software for designing PCR primers on aligned DNA sequences. Bioinformatics. 2004 Feb 12;20(10):1644–1645. doi: 10.1093/bioinformatics/bth121. [DOI] [PubMed] [Google Scholar]
  226. Ji Wan, Zhou Wenli, Gregg Keqin, Lindpaintner Klaus, Davis Sara, Davis Scott. A method for gene expression analysis by oligonucleotide arrays from minute biological materials. Anal Biochem. 2004 Aug 15;331(2):329–339. doi: 10.1016/j.ab.2004.03.039. [DOI] [PubMed] [Google Scholar]
  227. Ji Xinglai, Yuan Yuan, Li-Ling Jesse, Li Yanda, Sun Zhirong. HMMGEP: clustering gene expression data using hidden Markov models. Bioinformatics. 2004 Feb 26;20(11):1799–1800. doi: 10.1093/bioinformatics/bth145. [DOI] [PubMed] [Google Scholar]
  228. Jin Ming, Opalek Judy M., Marsh Clay B., Wu Haifeng M. Proteome comparison of alveolar macrophages with monocytes reveals distinct protein characteristics. Am J Respir Cell Mol Biol. 2004 May 6;31(3):322–329. doi: 10.1165/rcmb.2004-0080OC. [DOI] [PubMed] [Google Scholar]
  229. Jinawath Natini, Furukawa Yoichi, Hasegawa Suguru, Li Meihua, Tsunoda Tatsuhiko, Satoh Seiji, Yamaguchi Toshiharu, Imamura Hiroshi, Inoue Masatomo, Shiozaki Hitoshi. Comparison of gene-expression profiles between diffuse- and intestinal-type gastric cancers using a genome-wide cDNA microarray. Oncogene. 2004 Sep 2;23(40):6830–6844. doi: 10.1038/sj.onc.1207886. [DOI] [PubMed] [Google Scholar]
  230. Jones Alexandra M. E., Thomas Vincent, Truman Bill, Lilley Kathryn, Mansfield John, Grant Murray. Specific changes in the Arabidopsis proteome in response to bacterial challenge: differentiating basal and R-gene mediated resistance. Phytochemistry. 2004 Jun;65(12):1805–1816. doi: 10.1016/j.phytochem.2004.04.005. [DOI] [PubMed] [Google Scholar]
  231. Jones Dawn L., Petty June, Hoyle David C., Hayes Andrew, Oliver Stephen G., Riba-Garcia Isabel, Gaskell Simon J., Stateva Lubomira. Genome-wide analysis of the effects of heat shock on a Saccharomyces cerevisiae mutant with a constitutively activated cAMP-dependent pathway. Comp Funct Genomics. 2004;5(5):419–431. doi: 10.1002/cfg.415. [DOI] [PMC free article] [PubMed] [Google Scholar]
  232. Jorge Erika C., Monteiro-Vitorello Claudia B., Alves Helena J., Silva Clarissa S., Balan Rachel G., Patricio Mateus, Coutinho Luiz L. EST analysis of mRNAs expressed during embryogenesis in Gallus gallus. Int J Dev Biol. 2004 Jun;48(4):333–337. doi: 10.1387/ijdb.031775ej. [DOI] [PubMed] [Google Scholar]
  233. Juan Hsueh-Fen, Chen Jenn-Han, Hsu Wei-Tse, Huang Su-Ching, Chen Shui-Tein, Yi-Chung Lin John, Chang Yu-Wang, Chiang Chih-Yin, Wen Li-Li, Chan De-Chuan. Identification of tumor-associated plasma biomarkers using proteomic techniques: from mouse to human. Proteomics. 2004 Sep;4(9):2766–2775. doi: 10.1002/pmic.200400785. [DOI] [PubMed] [Google Scholar]
  234. Jugdutt Bodh I., Sawicki Grzegorz. AT1 receptor blockade alters metabolic, functional and structural proteins after reperfused myocardial infarction: detection using proteomics. Mol Cell Biochem. 2004 Aug;263(1-2):179–188. [PubMed] [Google Scholar]
  235. Jura Jolanta, Wegrzyn Paulina, Zarebski Adrian, Władyka Benedykt, Koj Aleksander. Identification of changes in the transcriptome profile of human hepatoma HepG2 cells stimulated with interleukin-1 beta. Biochim Biophys Acta. 2004 Jun 28;1689(2):120–133. doi: 10.1016/j.bbadis.2004.03.002. [DOI] [PubMed] [Google Scholar]
  236. Kaczmarek Krzysztof, Walczak Beata, de Jong Sijmen, Vandeginste Bernard G. M. Preprocessing of two-dimensional gel electrophoresis images. Proteomics. 2004 Aug;4(8):2377–2389. doi: 10.1002/pmic.200300758. [DOI] [PubMed] [Google Scholar]
  237. Kahveci Tamer, Ljosa Vebjorn, Singh Ambuj K. Speeding up whole-genome alignment by indexing frequency vectors. Bioinformatics. 2004 Apr 8;20(13):2122–2134. doi: 10.1093/bioinformatics/bth212. [DOI] [PubMed] [Google Scholar]
  238. Kaiser Thorsten, Kamal Haytham, Rank Andreas, Kolb Hans-Jochem, Holler Ernst, Ganser Arnold, Hertenstein Bernd, Mischak Harald, Weissinger Eva Maria. Proteomics applied to the clinical follow-up of patients after allogeneic hematopoietic stem cell transplantation. Blood. 2004 Mar 30;104(2):340–349. doi: 10.1182/blood-2004-02-0518. [DOI] [PubMed] [Google Scholar]
  239. Kang Yisheng, Durfee Tim, Glasner Jeremy D., Qiu Yu, Frisch David, Winterberg Kelly M., Blattner Frederick R. Systematic mutagenesis of the Escherichia coli genome. J Bacteriol. 2004 Aug;186(15):4921–4930. doi: 10.1128/JB.186.15.4921-4930.2004. [DOI] [PMC free article] [PubMed] [Google Scholar]
  240. Karababa Mahir, Coste Alix T., Rognon Bénédicte, Bille Jacques, Sanglard Dominique. Comparison of gene expression profiles of Candida albicans azole-resistant clinical isolates and laboratory strains exposed to drugs inducing multidrug transporters. Antimicrob Agents Chemother. 2004 Aug;48(8):3064–3079. doi: 10.1128/AAC.48.8.3064-3079.2004. [DOI] [PMC free article] [PubMed] [Google Scholar]
  241. Katogi Rei, Nakatani Yuki, Shin-i Tadasu, Kohara Yuji, Inohaya Keiji, Kudo Akira. Large-scale analysis of the genes involved in fin regeneration and blastema formation in the medaka, Oryzias latipes. Mech Dev. 2004 Jul;121(7-8):861–872. doi: 10.1016/j.mod.2004.03.015. [DOI] [PubMed] [Google Scholar]
  242. Kauer Gerhard, Blöcker Helmut. Analysis of disturbed images. Bioinformatics. 2004 Feb 12;20(9):1381–1387. doi: 10.1093/bioinformatics/bth099. [DOI] [PubMed] [Google Scholar]
  243. Keil Adam, Shepson Paul B. Development of a chemical ionization ion trap mass spectrometric method for trace level determination of molecular halogens. Anal Chem. 2004 Jul 15;76(14):3951–3957. doi: 10.1021/ac049934m. [DOI] [PubMed] [Google Scholar]
  244. Kell Douglas B. Metabolomics and systems biology: making sense of the soup. Curr Opin Microbiol. 2004 Jun;7(3):296–307. doi: 10.1016/j.mib.2004.04.012. [DOI] [PubMed] [Google Scholar]
  245. Kellis Manolis, Patterson Nick, Birren Bruce, Berger Bonnie, Lander Eric S. Methods in comparative genomics: genome correspondence, gene identification and regulatory motif discovery. J Comput Biol. 2004;11(2-3):319–355. doi: 10.1089/1066527041410319. [DOI] [PubMed] [Google Scholar]
  246. Kerkhoven Robert, van Enckevort Frank H. J., Boekhorst Jos, Molenaar Douwe, Siezen Roland J. Visualization for genomics: the Microbial Genome Viewer. Bioinformatics. 2004 Feb 26;20(11):1812–1814. doi: 10.1093/bioinformatics/bth159. [DOI] [PubMed] [Google Scholar]
  247. Kersey Paul J., Duarte Jorge, Williams Allyson, Karavidopoulou Youla, Birney Ewan, Apweiler Rolf. The International Protein Index: an integrated database for proteomics experiments. Proteomics. 2004 Jul;4(7):1985–1988. doi: 10.1002/pmic.200300721. [DOI] [PubMed] [Google Scholar]
  248. Kestler H. A., Küfer R. Wertigkeit und Notwendigkeit bioinformatischer Methoden zur Mikroarray-Datenanalyse. Urologe A. 2004 Jun;43(6):669–674. doi: 10.1007/s00120-004-0577-7. [DOI] [PubMed] [Google Scholar]
  249. Khaitovich Philipp, Muetzel Bjoern, She Xinwei, Lachmann Michael, Hellmann Ines, Dietzsch Janko, Steigele Stephan, Do Hong-Hai, Weiss Gunter, Enard Wolfgang. Regional patterns of gene expression in human and chimpanzee brains. Genome Res. 2004 Aug;14(8):1462–1473. doi: 10.1101/gr.2538704. [DOI] [PMC free article] [PubMed] [Google Scholar]
  250. Khan Md Monowar Karim, Komatsu Setsuko. Rice proteomics: recent developments and analysis of nuclear proteins. Phytochemistry. 2004 Jun;65(12):1671–1681. doi: 10.1016/j.phytochem.2004.04.012. [DOI] [PubMed] [Google Scholar]
  251. Kho Yoonjung, Kim Sung Chan, Jiang Chen, Barma Deb, Kwon Sung Won, Cheng Jinke, Jaunbergs Janis, Weinbaum Carolyn, Tamanoi Fuyuhiko, Falck John. A tagging-via-substrate technology for detection and proteomics of farnesylated proteins. Proc Natl Acad Sci U S A. 2004 Aug 12;101(34):12479–12484. doi: 10.1073/pnas.0403413101. [DOI] [PMC free article] [PubMed] [Google Scholar]
  252. Khorasani Maryam Zadeh, Hennig Steffen, Imre Gabriele, Asakawa Shuichi, Palczewski Stefanie, Berger Anja, Hori Hiroshi, Naruse Kiyoshi, Mitani Hiroshi, Shima Akihiro. A first generation physical map of the medaka genome in BACs essential for positional cloning and clone-by-clone based genomic sequencing. Mech Dev. 2004 Jul;121(7-8):903–913. doi: 10.1016/j.mod.2004.03.024. [DOI] [PubMed] [Google Scholar]
  253. Kim Byung Soo, Rha Sun Young, Cho Ga Bee, Chung Hyun Cheol. Spearman's footrule as a measure of cDNA microarray reproducibility. Genomics. 2004 Aug;84(2):441–448. doi: 10.1016/j.ygeno.2004.02.015. [DOI] [PubMed] [Google Scholar]
  254. Kim Il-Chan, Kweon Hee-Seok, Kim Young Ja, Kim Chang-Bae, Gye Myung Chan, Lee Wan-Ok, Lee Yong-Sung, Lee Jae-Seong. The complete mitochondrial genome of the javeline goby Acanthogobius hasta (Perciformes, Gobiidae) and phylogenetic considerations. Gene. 2004 Jul 21;336(2):147–153. doi: 10.1016/j.gene.2004.04.009. [DOI] [PubMed] [Google Scholar]
  255. Kim Jeong Lim, Jung Hak Hyun. Proteomic analysis of cholesteatoma. Acta Otolaryngol. 2004 Sep;124(7):783–788. doi: 10.1080/00016480410017882. [DOI] [PubMed] [Google Scholar]
  256. Kim Seong-Youl, Chudapongse Nuannoi, Lee Sang-Min, Levin Michael C., Oh Jae-Taek, Park Hae-Joon, Ho Ing K. Proteomic analysis of phosphotyrosyl proteins in the rat brain: effect of butorphanol dependence. J Neurosci Res. 2004 Sep 15;77(6):867–877. doi: 10.1002/jnr.20214. [DOI] [PubMed] [Google Scholar]
  257. Kim Yang-Hoon, Han Kyung Yeon, Lee Kibeom, Heo Joo-Hyung, Kang Hyun Ah, Lee Jeewon. Comparative proteome analysis of Hansenula polymorpha DL1 and A16. Proteomics. 2004 Jul;4(7):2005–2013. doi: 10.1002/pmic.200300739. [DOI] [PubMed] [Google Scholar]
  258. Kim Yang-Hoon, Park Jin-Seung, Cho Jae-Yong, Cho Kwang Myung, Park Young-Hoon, Lee Jeewon. Proteomic response analysis of a threonine-overproducing mutant of Escherichia coli. Biochem J. 2004 Aug 1;381(Pt 3):823–829. doi: 10.1042/BJ20031763. [DOI] [PMC free article] [PubMed] [Google Scholar]
  259. Kimura Shuhei, Kawasaki Takuji, Hatakeyama Mariko, Naka Takashi, Konishi Fumikazu, Konagaya Akihiko. OBIYagns: a grid-based biochemical simulator with a parameter estimator. Bioinformatics. 2004 Feb 12;20(10):1646–1648. doi: 10.1093/bioinformatics/bth122. [DOI] [PubMed] [Google Scholar]
  260. Kimura T., Jindo T., Narita T., Naruse K., Kobayashi D., Shin-I T., Kitagawa T., Sakaguchi T., Mitani H., Shima A. Large-scale isolation of ESTs from medaka embryos and its application to medaka developmental genetics. Mech Dev. 2004 Jul;121(7-8):915–932. doi: 10.1016/j.mod.2004.03.033. [DOI] [PubMed] [Google Scholar]
  261. Kinser Shawn, Jia Qunshan, Li Maioxing, Laughter Ashley, Cornwell Paul, Corton J. Christopher, Pestka James. Gene expression profiling in spleens of deoxynivalenol-exposed mice: immediate early genes as primary targets. J Toxicol Environ Health A. 2004 Sep 24;67(18):1423–1441. doi: 10.1080/15287390490483827. [DOI] [PubMed] [Google Scholar]
  262. Kluger Harriet M., Kluger Yuval, Gilmore-Hebert Maureen, DiVito Kyle, Chang Joseph T., Rodov Sofya, Mironenko Olga, Kacinski Barry M., Perkins Archibald S., Sapi Eva. cDNA microarray analysis of invasive and tumorigenic phenotypes in a breast cancer model. Lab Invest. 2004 Mar;84(3):320–331. doi: 10.1038/labinvest.3700044. [DOI] [PubMed] [Google Scholar]
  263. Koide Tie, Zaini Paulo A., Moreira Leandro M., Vêncio Ricardo Z. N., Matsukuma Adriana Y., Durham Alan M., Teixeira Diva C., El-Dorry Hamza, Monteiro Patrícia B., da Silva Ana Claudia R. DNA microarray-based genome comparison of a pathogenic and a nonpathogenic strain of Xylella fastidiosa delineates genes important for bacterial virulence. J Bacteriol. 2004 Aug;186(16):5442–5449. doi: 10.1128/JB.186.16.5442-5449.2004. [DOI] [PMC free article] [PubMed] [Google Scholar]
  264. Korbel Jan O., Jensen Lars J., von Mering Christian, Bork Peer. Analysis of genomic context: prediction of functional associations from conserved bidirectionally transcribed gene pairs. Nat Biotechnol. 2004 Jul;22(7):911–917. doi: 10.1038/nbt988. [DOI] [PubMed] [Google Scholar]
  265. Koskinen Heikki, Pehkonen Petri, Vehniäinen Eeva, Krasnov Aleksei, Rexroad Caird, Afanasyev Sergey, Mölsa Hannu, Oikari Aimo. Response of rainbow trout transcriptome to model chemical contaminants. Biochem Biophys Res Commun. 2004 Jul 30;320(3):745–753. doi: 10.1016/j.bbrc.2004.06.024. [DOI] [PubMed] [Google Scholar]
  266. Kouvelis Vassili N., Ghikas Dimitri V., Typas Milton A. The analysis of the complete mitochondrial genome of Lecanicillium muscarium (synonym Verticillium lecanii) suggests a minimum common gene organization in mtDNAs of Sordariomycetes: phylogenetic implications. Fungal Genet Biol. 2004 Oct;41(10):930–940. doi: 10.1016/j.fgb.2004.07.003. [DOI] [PubMed] [Google Scholar]
  267. Kramer Armin, Feilner Tanja, Possling Alexandra, Radchuk Volodymyr, Weschke Winfriede, Bürkle Lukas, Kersten Birgit. Identification of barley CK2alpha targets by using the protein microarray technology. Phytochemistry. 2004 Jun;65(12):1777–1784. doi: 10.1016/j.phytochem.2004.04.009. [DOI] [PubMed] [Google Scholar]
  268. Kreil David P., Karp Natasha A., Lilley Kathryn S. DNA microarray normalization methods can remove bias from differential protein expression analysis of 2D difference gel electrophoresis results. Bioinformatics. 2004 Mar 25;20(13):2026–2034. doi: 10.1093/bioinformatics/bth193. [DOI] [PubMed] [Google Scholar]
  269. Kreunin Paweena, Urquidi Virginia, Lubman David M., Goodison Steve. Identification of metastasis-associated proteins in a human tumor metastasis model using the mass-mapping technique. Proteomics. 2004 Sep;4(9):2754–2765. doi: 10.1002/pmic.200300767. [DOI] [PMC free article] [PubMed] [Google Scholar]
  270. Krieg René C., Knuechel Ruth, Schiffmann Elliot, Liotta Lance A., Petricoin Emanuel F., 3rd, Herrmann Paul C. Mitochondrial proteome: cancer-altered metabolism associated with cytochrome c oxidase subunit level variation. Proteomics. 2004 Sep;4(9):2789–2795. doi: 10.1002/pmic.200300796. [DOI] [PubMed] [Google Scholar]
  271. Krzywinski Martin, Bosdet Ian, Smailus Duane, Chiu Readman, Mathewson Carrie, Wye Natasja, Barber Sarah, Brown-John Mabel, Chan Susanna, Chand Steve. A set of BAC clones spanning the human genome. Nucleic Acids Res. 2004 Jul 9;32(12):3651–3660. doi: 10.1093/nar/gkh700. [DOI] [PMC free article] [PubMed] [Google Scholar]
  272. Kumar Sudhir, Tamura Koichiro, Nei Masatoshi. MEGA3: Integrated software for Molecular Evolutionary Genetics Analysis and sequence alignment. Brief Bioinform. 2004 Jun;5(2):150–163. doi: 10.1093/bib/5.2.150. [DOI] [PubMed] [Google Scholar]
  273. Kusch H., Biswas K., Schwanfelder S., Engelmann S., Rogers P. D., Hecker M., Morschhäuser J. A proteomic approach to understanding the development of multidrug-resistant Candida albicans strains. Mol Genet Genomics. 2004 Apr 28;271(5):554–565. doi: 10.1007/s00438-004-0984-x. [DOI] [PubMed] [Google Scholar]
  274. Kuznetsov Vadim Yu, Ivanov Yuri D., Archakov Alexander I. Atomic force microscopy revelation of molecular complexes in the multiprotein cytochrome P450 2B4-containing system. Proteomics. 2004 Aug;4(8):2390–2396. doi: 10.1002/pmic.200300751. [DOI] [PubMed] [Google Scholar]
  275. König Rainer, Eils Roland. Gene expression analysis on biochemical networks using the Potts spin model. Bioinformatics. 2004 Jul 10;20(10):1500–1505. doi: 10.1093/bioinformatics/bth109. [DOI] [PubMed] [Google Scholar]
  276. Lal Sean, Lui Rodney, Nguyen Lisa, Macdonald Peter, Denyer Gareth, dos Remedios Cristobal. Increases in leukocyte cluster of differentiation antigen expression during cardiopulmonary bypass in patients undergoing heart transplantation. Proteomics. 2004 Jul;4(7):1918–1926. doi: 10.1002/pmic.200300756. [DOI] [PubMed] [Google Scholar]
  277. Lan Lefu, Chen Wei, Lai Ying, Suo Jinfeng, Kong Zhaosheng, Li Can, Lu Ying, Zhang Yujun, Zhao Xiangyu, Zhang Xiansheng. Monitoring of gene expression profiles and isolation of candidate genes involved in pollination and fertilization in rice ( Oryza sativa L.) with a 10K cDNA microarray. Plant Mol Biol. 2004 Mar;54(4):471–487. doi: 10.1023/B:PLAN.0000038254.58491.c7. [DOI] [PubMed] [Google Scholar]
  278. Le Bihan Marie-Catherine, Tarelli Edward, Coulton Gary R. Evaluation of an integrated strategy for proteomic profiling of skeletal muscle. Proteomics. 2004 Sep;4(9):2739–2753. doi: 10.1002/pmic.200300759. [DOI] [PubMed] [Google Scholar]
  279. Leclerc Nathalie, Luppen Cynthia A., Ho Vincent V., Nagpal Shailender, Hacia Joseph G., Smith Elisheva, Frenkel Baruch. Gene expression profiling of glucocorticoid-inhibited osteoblasts. J Mol Endocrinol. 2004 Aug;33(1):175–193. doi: 10.1677/jme.0.0330175. [DOI] [PubMed] [Google Scholar]
  280. Lee Hyang Woo, Choe Yon Ho, Kim Dae Kyong, Jung Sung Yun, Lee Na Gyong. Proteomic analysis of a ferric uptake regulator mutant of Helicobacter pylori: regulation of Helicobacter pylori gene expression by ferric uptake regulator and iron. Proteomics. 2004 Jul;4(7):2014–2027. doi: 10.1002/pmic.200300740. [DOI] [PubMed] [Google Scholar]
  281. Lee Ju-Seog, Chu In-Sun, Heo Jeonghoon, Calvisi Diego F., Sun Zongtang, Roskams Tania, Durnez Anne, Demetris Anthony J., Thorgeirsson Snorri S. Classification and prediction of survival in hepatocellular carcinoma by gene expression profiling. Hepatology. 2004 Sep;40(3):667–676. doi: 10.1002/hep.20375. [DOI] [PubMed] [Google Scholar]
  282. Lee Myeong Sup, Hanspers Kristina, Barker Christopher S., Korn Abner P., McCune Joseph M. Gene expression profiles during human CD4+ T cell differentiation. Int Immunol. 2004 Jun 21;16(8):1109–1124. doi: 10.1093/intimm/dxh112. [DOI] [PubMed] [Google Scholar]
  283. Lefebvre Christophe, Cocquerelle Claude, Vandenbulcke Franck, Hot David, Huot Ludovic, Lemoine Yves, Salzet Michel. Transcriptomic analysis in the leech Theromyzon tessulatum: involvement of cystatin B in innate immunity. Biochem J. 2004 Jun 15;380(Pt 3):617–625. doi: 10.1042/BJ20040478. [DOI] [PMC free article] [PubMed] [Google Scholar]
  284. Leigh James A., Ward Philip N., Field Terrence R. The exploitation of the genome in the search for determinants of virulence in Streptococcus uberis. Vet Immunol Immunopathol. 2004 Aug;100(3-4):145–149. doi: 10.1016/j.vetimm.2004.04.004. [DOI] [PubMed] [Google Scholar]
  285. Lescuyer Pierre, Allard Laure, Zimmermann-Ivol Catherine G., Burgess Jennifer A., Hughes-Frutiger Séverine, Burkhard Pierre R., Sanchez Jean-Charles, Hochstrasser Denis F. Identification of post-mortem cerebrospinal fluid proteins as potential biomarkers of ischemia and neurodegeneration. Proteomics. 2004 Aug;4(8):2234–2241. doi: 10.1002/pmic.200300822. [DOI] [PubMed] [Google Scholar]
  286. Levander Fredrik, Rögnvaldsson Thorsteinn, Samuelsson Jim, James Peter. Automated methods for improved protein identification by peptide mass fingerprinting. Proteomics. 2004 Sep;4(9):2594–2601. doi: 10.1002/pmic.200300804. [DOI] [PubMed] [Google Scholar]
  287. Levanon Erez Y., Eisenberg Eli, Yelin Rodrigo, Nemzer Sergey, Hallegger Martina, Shemesh Ronen, Fligelman Zipora Y., Shoshan Avi, Pollock Sarah R., Sztybel Dan. Systematic identification of abundant A-to-I editing sites in the human transcriptome. Nat Biotechnol. 2004 Jul 18;22(8):1001–1005. doi: 10.1038/nbt996. [DOI] [PubMed] [Google Scholar]
  288. Li Junyu, Liu Sheng, Osterman Travis, Zhang Yinong, Coppage Heather, Pedrick Nathan, Witzmann Frank A. A software utility for creating interactive maps for 2D gel-based proteomics. Anal Biochem. 2004 Sep 1;332(1):187–190. doi: 10.1016/j.ab.2004.03.058. [DOI] [PubMed] [Google Scholar]
  289. Li Leping, Umbach David M., Terry Paul, Taylor Jack A. Application of the GA/KNN method to SELDI proteomics data. Bioinformatics. 2004 Feb 12;20(10):1638–1640. doi: 10.1093/bioinformatics/bth098. [DOI] [PubMed] [Google Scholar]
  290. Li M., Rosenshine I., Tung S. L., Wang X. H., Friedberg D., Hew C. L., Leung K. Y. Comparative proteomic analysis of extracellular proteins of enterohemorrhagic and enteropathogenic Escherichia coli strains and their ihf and ler mutants. Appl Environ Microbiol. 2004 Sep;70(9):5274–5282. doi: 10.1128/AEM.70.9.5274-5282.2004. [DOI] [PMC free article] [PubMed] [Google Scholar]
  291. Li Rugang, Rimmer Roger, Buchwaldt Lone, Sharpe Andrew G., Séguin-Swartz Ginette, Coutu Cathy, Hegedus Dwayne D. Interaction of Sclerotinia sclerotiorum with a resistant Brassica napus cultivar: expressed sequence tag analysis identifies genes associated with fungal pathogenesis. Fungal Genet Biol. 2004 Aug;41(8):735–753. doi: 10.1016/j.fgb.2004.03.001. [DOI] [PubMed] [Google Scholar]
  292. Li Xin-Ming, Patel Bhavinkumar B., Blagoi Elena L., Patterson Maketa D., Seeholzer Steven H., Seehozer Steven H., Zhang Tao, Damle Shirish, Gao Zhenqiang, Boman Bruce. Analyzing alkaline proteins in human colon crypt proteome. J Proteome Res. 2004 Jul-Aug;3(4):821–833. doi: 10.1021/pr049942j. [DOI] [PubMed] [Google Scholar]
  293. Li Y., Wasser S., Lim S. G., Tan T. M. C. Genome-wide expression profiling of RNA interference of hepatitis B virus gene expression and replication. Cell Mol Life Sci. 2004 Aug;61(16):2113–2124. doi: 10.1007/s00018-004-4111-2. [DOI] [PMC free article] [PubMed] [Google Scholar]
  294. Li Yang, Chia Jer Ming, Bartfai Richard, Christoffels Alan, Yue Gen Hua, Ding Ke, Ho Mei Yin, Hill James A., Stupka Elia, Orban Laszlo. Comparative analysis of the testis and ovary transcriptomes in zebrafish by combining experimental and computational tools. Comp Funct Genomics. 2004;5(5):403–418. doi: 10.1002/cfg.418. [DOI] [PMC free article] [PubMed] [Google Scholar]
  295. Li Zheng, Chan Christina. Integrating gene expression and metabolic profiles. J Biol Chem. 2004 Apr 23;279(26):27124–27137. doi: 10.1074/jbc.M403494200. [DOI] [PubMed] [Google Scholar]
  296. Lim Megan S., Elenitoba-Johnson Kojo S. J. Proteomics in pathology research. Lab Invest. 2004 Oct;84(10):1227–1244. doi: 10.1038/labinvest.3700167. [DOI] [PubMed] [Google Scholar]
  297. Liska Adam J., Popov Andrei V., Sunyaev Shamil, Coughlin Peg, Habermann Bianca, Shevchenko Anna, Bork Peer, Karsenti Eric, Shevchenko Andrej. Homology-based functional proteomics by mass spectrometry: application to the Xenopus microtubule-associated proteome. Proteomics. 2004 Sep;4(9):2707–2721. doi: 10.1002/pmic.200300813. [DOI] [PubMed] [Google Scholar]
  298. Liska Adam J. The morality of problem selection in proteomics. Proteomics. 2004 Jul;4(7):1929–1931. doi: 10.1002/pmic.200300714. [DOI] [PubMed] [Google Scholar]
  299. Liu Chang-Gong, Calin George Adrian, Meloon Brian, Gamliel Nir, Sevignani Cinzia, Ferracin Manuela, Dumitru Calin Dan, Shimizu Masayoshi, Zupo Simona, Dono Mariella. An oligonucleotide microchip for genome-wide microRNA profiling in human and mouse tissues. Proc Natl Acad Sci U S A. 2004 Jun 21;101(26):9740–9744. doi: 10.1073/pnas.0403293101. [DOI] [PMC free article] [PubMed] [Google Scholar]
  300. Liu Hongbin, Sadygov Rovshan G., Yates John R., 3rd A model for random sampling and estimation of relative protein abundance in shotgun proteomics. Anal Chem. 2004 Jul 15;76(14):4193–4201. doi: 10.1021/ac0498563. [DOI] [PubMed] [Google Scholar]
  301. Liu Jinfeng, Hegyi Hedi, Acton Thomas B., Montelione Gaetano T., Rost Burkhard. Automatic target selection for structural genomics on eukaryotes. Proteins. 2004 Aug 1;56(2):188–200. doi: 10.1002/prot.20012. [DOI] [PubMed] [Google Scholar]
  302. Liu Xin, Ma Li, Zhang Jian-Feng, Lu Ying-Tang. Determination of single-cell gene expression in Arabidopsis by capillary electrophoresis with laser induced fluorescence detection. J Chromatogr B Analyt Technol Biomed Life Sci. 2004 Sep 5;808(2):241–247. doi: 10.1016/j.jchromb.2004.05.011. [DOI] [PubMed] [Google Scholar]
  303. Loschelder Heike, Homann Anke, Ogrzewalla Karsten, Link Gerhard. Proteomics-based sequence analysis of plant gene expression--the chloroplast transcription apparatus. Phytochemistry. 2004 Jun;65(12):1785–1793. doi: 10.1016/j.phytochem.2004.04.034. [DOI] [PubMed] [Google Scholar]
  304. Lu X-C May, Williams Anthony J., Yao Changping, Berti Rossana, Hartings Jed A., Whipple Rebecca, Vahey Maryanne T., Polavarapu Ratna G., Woller Kimberly L., Tortella Frank C. Microarray analysis of acute and delayed gene expression profile in rats after focal ischemic brain injury and reperfusion. J Neurosci Res. 2004 Sep 15;77(6):843–857. doi: 10.1002/jnr.20218. [DOI] [PubMed] [Google Scholar]
  305. Lum Amy M., Huang Jianqiang, Hutchinson C. Richard, Kao Camilla M. Reverse engineering of industrial pharmaceutical-producing actinomycete strains using DNA microarrays. Metab Eng. 2004 Jul;6(3):186–196. doi: 10.1016/j.ymben.2003.12.001. [DOI] [PubMed] [Google Scholar]
  306. Lurin Claire, Andrés Charles, Aubourg Sébastien, Bellaoui Mohammed, Bitton Frédérique, Bruyère Clémence, Caboche Michel, Debast Cédrig, Gualberto José, Hoffmann Beate. Genome-wide analysis of Arabidopsis pentatricopeptide repeat proteins reveals their essential role in organelle biogenesis. Plant Cell. 2004 Jul 21;16(8):2089–2103. doi: 10.1105/tpc.104.022236. [DOI] [PMC free article] [PubMed] [Google Scholar]
  307. Luyendyk James P., Mattes William B., Burgoon Lyle D., Zacharewski Timothy R., Maddox Jane F., Cosma Gregory N., Ganey Patricia E., Roth Robert A. Gene expression analysis points to hemostasis in livers of rats cotreated with lipopolysaccharide and ranitidine. Toxicol Sci. 2004 Apr 14;80(1):203–213. doi: 10.1093/toxsci/kfh146. [DOI] [PubMed] [Google Scholar]
  308. Lynch Michael D., Gill Ryan T., Stephanopoulos Gregory. Mapping phenotypic landscapes using DNA micro-arrays. Metab Eng. 2004 Jul;6(3):177–185. doi: 10.1016/j.ymben.2004.01.002. [DOI] [PubMed] [Google Scholar]
  309. López-Bigas Núria, Ouzounis Christos A. Genome-wide identification of genes likely to be involved in human genetic disease. Nucleic Acids Res. 2004 Jun 4;32(10):3108–3114. doi: 10.1093/nar/gkh605. [DOI] [PMC free article] [PubMed] [Google Scholar]
  310. Lü Jining, Qian Jun, Izvolsky Konstantin I., Cardoso Wellington V. Global analysis of genes differentially expressed in branching and non-branching regions of the mouse embryonic lung. Dev Biol. 2004 Sep 15;273(2):418–435. doi: 10.1016/j.ydbio.2004.05.035. [DOI] [PubMed] [Google Scholar]
  311. Ma Hong, Kafri Tal. A single-LTR HIV-1 vector optimized for functional genomics applications. Mol Ther. 2004 Jul;10(1):139–149. doi: 10.1016/j.ymthe.2004.04.012. [DOI] [PubMed] [Google Scholar]
  312. Maccarrone Giuseppina, Milfay Dale, Birg Isabel, Rosenhagen Marcus, Holsboer Florian, Grimm Rudolf, Bailey Jerome, Zolotarjova Nina, Turck Christoph W. Mining the human cerebrospinal fluid proteome by immunodepletion and shotgun mass spectrometry. Electrophoresis. 2004 Jul;25(14):2402–2412. doi: 10.1002/elps.200305909. [DOI] [PubMed] [Google Scholar]
  313. Macht Marcus, Marquardt Andreas, Deininger Sören-Oliver, Damoc Eugen, Kohlmann Markus, Przybylski Michael. "Affinity-proteomics": direct protein identification from biological material using mass spectrometric epitope mapping. Anal Bioanal Chem. 2003 Aug 30;378(4):1102–1111. doi: 10.1007/s00216-003-2159-8. [DOI] [PubMed] [Google Scholar]
  314. Magnani Agnese, Barbucci Rolando, Lamponi Stefania, Chiumento Antonio, Paffetti Alessandro, Trabalzini Lorenza, Martelli Paola, Santucci Annalisa. Two-step elution of human serum proteins from different glass-modified bioactive surfaces: a comparative proteomic analysis of adsorption patterns. Electrophoresis. 2004 Jul;25(14):2413–2424. doi: 10.1002/elps.200305826. [DOI] [PubMed] [Google Scholar]
  315. Magrini Vincent, Warren Wesley C., Wallis John, Goldman William E., Xu Jian, Mardis Elaine R., McPherson John D. Fosmid-based physical mapping of the Histoplasma capsulatum genome. Genome Res. 2004 Aug;14(8):1603–1609. doi: 10.1101/gr.2361404. [DOI] [PMC free article] [PubMed] [Google Scholar]
  316. Manthey Katja, Krajinski Franziska, Hohnjec Natalija, Firnhaber Christian, Pühler Alfred, Perlick Andreas M., Küster Helge. Transcriptome profiling in root nodules and arbuscular mycorrhiza identifies a collection of novel genes induced during Medicago truncatula root endosymbioses. Mol Plant Microbe Interact. 2004 Oct;17(10):1063–1077. doi: 10.1094/MPMI.2004.17.10.1063. [DOI] [PubMed] [Google Scholar]
  317. Marchand Christophe, Le Maréchal Pierre, Meyer Yves, Miginiac-Maslow Myroslawa, Issakidis-Bourguet Emmanuelle, Decottignies Paulette. New targets of Arabidopsis thioredoxins revealed by proteomic analysis. Proteomics. 2004 Sep;4(9):2696–2706. doi: 10.1002/pmic.200400805. [DOI] [PubMed] [Google Scholar]
  318. Mariadason John M., Arango Diego, Augenlicht Leonard H. Customizing chemotherapy for colon cancer: the potential of gene expression profiling. Drug Resist Updat. 2004 Jun;7(3):209–218. doi: 10.1016/j.drup.2004.05.001. [DOI] [PubMed] [Google Scholar]
  319. Matsuzaki S., Canis M., Vaurs-Barrière C., Pouly J. L., Boespflug-Tanguy O., Penault-Llorca F., Dechelotte P., Dastugue B., Okamura K., Mage G. DNA microarray analysis of gene expression profiles in deep endometriosis using laser capture microdissection. Mol Hum Reprod. 2004 Aug 6;10(10):719–728. doi: 10.1093/molehr/gah097. [DOI] [PubMed] [Google Scholar]
  320. Matthiesen Rune, Bunkenborg Jakob, Stensballe Allan, Jensen Ole N., Welinder Karen G., Bauw Guy. Database-independent, database-dependent, and extended interpretation of peptide mass spectra in VEMS V2.0. Proteomics. 2004 Sep;4(9):2583–2593. doi: 10.1002/pmic.200300792. [DOI] [PubMed] [Google Scholar]
  321. Matyash Alexey, Chung Ho-Ryun, Jäckle Herbert. Genome-wide mapping of in vivo targets of the Drosophila transcription factor Kruppel. J Biol Chem. 2004 May 6;279(29):30689–30696. doi: 10.1074/jbc.M403345200. [DOI] [PubMed] [Google Scholar]
  322. Mayer Michael, Yang Jerry, Gitlin Irina, Gracias David H., Whitesides George M. Micropatterned agarose gels for stamping arrays of proteins and gradients of proteins. Proteomics. 2004 Aug;4(8):2366–2376. doi: 10.1002/pmic.200300748. [DOI] [PubMed] [Google Scholar]
  323. McHardy Alice C., Goesmann Alexander, Pühler Alfred, Meyer Folker. Development of joint application strategies for two microbial gene finders. Bioinformatics. 2004 Feb 26;20(10):1622–1631. doi: 10.1093/bioinformatics/bth137. [DOI] [PubMed] [Google Scholar]
  324. McManus Donald P., Hu Wei, Brindley Paul J., Feng Zheng, Han Ze-Guang. Schistosome transcriptome analysis at the cutting edge. Trends Parasitol. 2004 Jul;20(7):301–304. doi: 10.1016/j.pt.2004.04.011. [DOI] [PubMed] [Google Scholar]
  325. Meek Sarah E. M., Lane William S., Piwnica-Worms Helen. Comprehensive proteomic analysis of interphase and mitotic 14-3-3-binding proteins. J Biol Chem. 2004 May 25;279(31):32046–32054. doi: 10.1074/jbc.M403044200. [DOI] [PubMed] [Google Scholar]
  326. Meinke Andreas, Henics Tamas, Nagy Eszter. Bacterial genomes pave the way to novel vaccines. Curr Opin Microbiol. 2004 Jun;7(3):314–320. doi: 10.1016/j.mib.2004.04.008. [DOI] [PubMed] [Google Scholar]
  327. Merritt Joshua, Edwards Jeremy S. Assaying gene function by growth competition experiment. Metab Eng. 2004 Jul;6(3):212–219. doi: 10.1016/j.ymben.2003.10.009. [DOI] [PubMed] [Google Scholar]
  328. Meskauskas Audrius, Lehmann-Horn Frank, Jurkat-Rott Karin. Sight: automating genomic data-mining without programming skills. Bioinformatics. 2004 Feb 26;20(11):1718–1720. doi: 10.1093/bioinformatics/bth151. [DOI] [PubMed] [Google Scholar]
  329. Messana Irene, Cabras Tiziana, Inzitari Rosanna, Lupi Alessandro, Zuppi Cecilia, Olmi Chiara, Fadda Maria Benedetta, Cordaro Massimo, Giardina Bruno, Castagnola Massimo. Characterization of the human salivary basic proline-rich protein complex by a proteomic approach. J Proteome Res. 2004 Jul-Aug;3(4):792–800. doi: 10.1021/pr049953c. [DOI] [PubMed] [Google Scholar]
  330. Meyers Blake C., Scalabrin Simone, Morgante Michele. Mapping and sequencing complex genomes: let's get physical! Nat Rev Genet. 2004 Aug;5(8):578–588. doi: 10.1038/nrg1404. [DOI] [PubMed] [Google Scholar]
  331. Meyers Blake C., Tej Shivakundan Singh, Vu Tam H., Haudenschild Christian D., Agrawal Vikas, Edberg Steve B., Ghazal Hassan, Decola Shannon. The use of MPSS for whole-genome transcriptional analysis in Arabidopsis. Genome Res. 2004 Aug;14(8):1641–1653. doi: 10.1101/gr.2275604. [DOI] [PMC free article] [PubMed] [Google Scholar]
  332. Meyers Blake C., Vu Tam H., Tej Shivakundan Singh, Ghazal Hassan, Matvienko Marta, Agrawal Vikas, Ning Jianchang, Haudenschild Christian D. Analysis of the transcriptional complexity of Arabidopsis thaliana by massively parallel signature sequencing. Nat Biotechnol. 2004 Jul 11;22(8):1006–1011. doi: 10.1038/nbt992. [DOI] [PubMed] [Google Scholar]
  333. Millar A. Harvey, Trend Alice E., Heazlewood Joshua L. Changes in the mitochondrial proteome during the anoxia to air transition in rice focus around cytochrome-containing respiratory complexes. J Biol Chem. 2004 Jul 16;279(38):39471–39478. doi: 10.1074/jbc.M406015200. [DOI] [PubMed] [Google Scholar]
  334. Miller Dylan V., Leontovich Alexey A., Lingle Wilma L., Suman Vera J., Mertens Maureen L., Lillie James, Ingalls Kimberly A., Perez Edith A., Ingle James N., Couch Fergus J. Utilizing Nottingham Prognostic Index in microarray gene expression profiling of breast carcinomas. Mod Pathol. 2004 Jul;17(7):756–764. doi: 10.1038/modpathol.3800114. [DOI] [PubMed] [Google Scholar]
  335. Miranda Guy, Mahé Marie-Françoise, Leroux Christine, Martin Patrice. Proteomic tools to characterize the protein fraction of Equidae milk. Proteomics. 2004 Aug;4(8):2496–2509. doi: 10.1002/pmic.200300765. [DOI] [PubMed] [Google Scholar]
  336. Mitulović Goran, Stingl Christoph, Smoluch Marek, Swart Remco, Chervet Jean-Pierre, Steinmacher Ines, Gerner Christopher, Mechtler Karl. Automated, on-line two-dimensional nano liquid chromatography tandem mass spectrometry for rapid analysis of complex protein digests. Proteomics. 2004 Sep;4(9):2545–2557. doi: 10.1002/pmic.200300806. [DOI] [PubMed] [Google Scholar]
  337. Mocellin Simone, Wang Ena, Panelli Monica, Pilati Pierluigi, Marincola Francesco M. DNA array-based gene profiling in tumor immunology. Clin Cancer Res. 2004 Jul 15;10(14):4597–4606. doi: 10.1158/1078-0432.CCR-04-0327. [DOI] [PubMed] [Google Scholar]
  338. Moini Mehdi, Huang Hsiaoling. Application of capillary electrophoresis/ electrospray ionization-mass spectrometry to subcellular proteomics of Escherichia coli ribosomal proteins. Electrophoresis. 2004 Jul;25(13):1981–1987. doi: 10.1002/elps.200305906. [DOI] [PubMed] [Google Scholar]
  339. Monticone Massimiliano, Liu Yi, Tonachini Laura, Mastrogiacomo Maddalena, Parodi Stefano, Quarto Rodolfo, Cancedda Ranieri, Castagnola Patrizio. Gene expression profile of human bone marrow stromal cells determined by restriction fragment differential display analysis. J Cell Biochem. 2004 Jul 1;92(4):733–744. doi: 10.1002/jcb.20120. [DOI] [PubMed] [Google Scholar]
  340. Mooney Brian P., Krishnan H. B., Thelen Jay J. High-throughput peptide mass fingerprinting of soybean seed proteins: automated workflow and utility of UniGene expressed sequence tag databases for protein identification. Phytochemistry. 2004 Jun;65(12):1733–1744. doi: 10.1016/j.phytochem.2004.04.011. [DOI] [PubMed] [Google Scholar]
  341. Moore Jamie M. R., Galicia Sarah J., McReynolds Andrea C., Nguyen Ngoc-Ha, Scanlan Thomas S., Guy R. Kiplin. Quantitative proteomics of the thyroid hormone receptor-coregulator interactions. J Biol Chem. 2004 Apr 19;279(26):27584–27590. doi: 10.1074/jbc.M403453200. [DOI] [PubMed] [Google Scholar]
  342. Moreira Andrés, Maass Alejandro. TIP: protein backtranslation aided by genetic algorithms. Bioinformatics. 2004 Apr 1;20(13):2148–2149. doi: 10.1093/bioinformatics/bth204. [DOI] [PubMed] [Google Scholar]
  343. Moritz Robert L., Ji Hong, Schütz Frédéric, Connolly Lisa M., Kapp Eugene A., Speed Terence P., Simpson Richard J. A proteome strategy for fractionating proteins and peptides using continuous free-flow electrophoresis coupled off-line to reversed-phase high-performance liquid chromatography. Anal Chem. 2004 Aug 15;76(16):4811–4824. doi: 10.1021/ac049717l. [DOI] [PubMed] [Google Scholar]
  344. Morley Michael, Molony Cliona M., Weber Teresa M., Devlin James L., Ewens Kathryn G., Spielman Richard S., Cheung Vivian G. Genetic analysis of genome-wide variation in human gene expression. Nature. 2004 Jul 21;430(7001):743–747. doi: 10.1038/nature02797. [DOI] [PMC free article] [PubMed] [Google Scholar]
  345. Mukhopadhyay Sanghamitra, Miller Richard D., Summersgill James T. Analysis of altered protein expression patterns of Chlamydia pneumoniae by an integrated proteome-works system. J Proteome Res. 2004 Jul-Aug;3(4):878–883. doi: 10.1021/pr0400031. [DOI] [PubMed] [Google Scholar]
  346. Murray James, Marusich Michael F., Capaldi Roderick A., Aggeler Robert. Focused proteomics: monoclonal antibody-based isolation of the oxidative phosphorylation machinery and detection of phosphoproteins using a fluorescent phosphoprotein gel stain. Electrophoresis. 2004 Aug;25(15):2520–2525. doi: 10.1002/elps.200406006. [DOI] [PubMed] [Google Scholar]
  347. Mycko Marcin P., Papoian Ruben, Boschert Ursula, Raine Cedric S., Selmaj Krzysztof W. Microarray gene expression profiling of chronic active and inactive lesions in multiple sclerosis. Clin Neurol Neurosurg. 2004 Jun;106(3):223–229. doi: 10.1016/j.clineuro.2004.02.019. [DOI] [PubMed] [Google Scholar]
  348. Méchin Valérie, Balliau Thierry, Château-Joubert Sophie, Davanture Marlène, Langella Olivier, Négroni Luc, Prioul Jean-Louis, Thévenot Claudine, Zivy Michel, Damerval Catherine. A two-dimensional proteome map of maize endosperm. Phytochemistry. 2004 Jun;65(11):1609–1618. doi: 10.1016/j.phytochem.2004.04.035. [DOI] [PubMed] [Google Scholar]
  349. Müller-Tidow Carsten, Diederichs Sven, Thomas Michael, Serve Hubert. Genome-wide screening for prognosis-predicting genes in early-stage non-small-cell lung cancer. Lung Cancer. 2004 Aug;45 (Suppl 2):S145–S150. doi: 10.1016/j.lungcan.2004.07.979. [DOI] [PubMed] [Google Scholar]
  350. Nagarajan Niranjan, Yona Golan. Automatic prediction of protein domains from sequence information using a hybrid learning system. Bioinformatics. 2004 Feb 12;20(9):1335–1360. doi: 10.1093/bioinformatics/bth086. [DOI] [PubMed] [Google Scholar]
  351. Nakagawa Ichiro, Nakata Masanobu, Kawabata Shigetada, Hamada Shigeyuki. Transcriptome analysis and gene expression profiles of early apoptosis-related genes in Streptococcus pyogenes-infected epithelial cells. Cell Microbiol. 2004 Oct;6(10):939–952. doi: 10.1111/j.1462-5822.2004.00412.x. [DOI] [PubMed] [Google Scholar]
  352. Nakagawa Takao, Schwartz Joan P. Gene expression profiles of reactive astrocytes in dopamine-depleted striatum. Brain Pathol. 2004 Jul;14(3):275–280. doi: 10.1111/j.1750-3639.2004.tb00064.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  353. Nakamura Takemichi, Dohmae Naoshi, Takio Koji. Characterization of a digested protein complex with quantitative aspects: an approach based on accurate mass chromatographic analysis with Fourier transform-ion cyclotron resonance mass spectrometry. Proteomics. 2004 Sep;4(9):2558–2566. doi: 10.1002/pmic.200300812. [DOI] [PubMed] [Google Scholar]
  354. Naruse Kiyoshi, Hori Hiroshi, Shimizu Nobuyoshi, Kohara Yuji, Takeda Hiroyuki. Medaka genomics: a bridge between mutant phenotype and gene function. Mech Dev. 2004 Jul;121(7-8):619–628. doi: 10.1016/j.mod.2004.04.014. [DOI] [PubMed] [Google Scholar]
  355. National Comprehensive Cancer Network (NCCN) NCCN makes changes to its guidelines for treating fever and neutropenia. J Support Oncol. 2004 Jul-Aug;2(4):319–355. [PubMed] [Google Scholar]
  356. Nelson Randall W., Nedelkov Dobrin, Tubbs Kemmons A., Kiernan Urban A. Quantitative mass spectrometric immunoassay of insulin like growth factor 1. J Proteome Res. 2004 Jul-Aug;3(4):851–855. doi: 10.1021/pr0499388. [DOI] [PubMed] [Google Scholar]
  357. Newton Russell P., Brenton A. Gareth, Smith Chris J., Dudley Edward. Plant proteome analysis by mass spectrometry: principles, problems, pitfalls and recent developments. Phytochemistry. 2004 Jun;65(11):1449–1485. doi: 10.1016/j.phytochem.2004.04.015. [DOI] [PubMed] [Google Scholar]
  358. Ng Kar-wai, Lawson Jonathan, Garner Harold R. PathoGene: a pathogen coding sequence discovery and analysis resource. Biotechniques. 2004 Aug;37(2):218, 220-2. doi: 10.2144/04372ST01. [DOI] [PubMed] [Google Scholar]
  359. Ng Ray Kit, Lau Carol Yee Lam, Lee Simon Ming Yuen, Tsui Stephen Kwok Wing, Fung Kwok Pui, Waye Mary Miu Yee. cDNA microarray analysis of early gene expression profiles associated with hepatitis B virus X protein-mediated hepatocarcinogenesis. Biochem Biophys Res Commun. 2004 Sep 24;322(3):827–835. doi: 10.1016/j.bbrc.2004.07.188. [DOI] [PubMed] [Google Scholar]
  360. Nguyen Tu N., Ejaz Arvin D., Brancieri Mark A., Mikula Amy M., Nelson Karen E., Gill Steven R., Noll Kenneth M. Whole-genome expression profiling of Thermotoga maritima in response to growth on sugars in a chemostat. J Bacteriol. 2004 Jul;186(14):4824–4828. doi: 10.1128/JB.186.14.4824-4828.2004. [DOI] [PMC free article] [PubMed] [Google Scholar]
  361. Nilsson R. Henrik, Larsson Karl-Henrik, Ursing Björn M. galaxie--CGI scripts for sequence identification through automated phylogenetic analysis. Bioinformatics. 2004 Feb 19;20(9):1447–1452. doi: 10.1093/bioinformatics/bth119. [DOI] [PubMed] [Google Scholar]
  362. Nilsson Stefan, Ramström Margareta, Palmblad Magnus, Axelsson Ove, Bergquist Jonas. Explorative study of the protein composition of amniotic fluid by liquid chromatography electrospray ionization Fourier transform ion cyclotron resonance mass spectrometry. J Proteome Res. 2004 Jul-Aug;3(4):884–889. doi: 10.1021/pr0499545. [DOI] [PubMed] [Google Scholar]
  363. Nühse Thomas S., Stensballe Allan, Jensen Ole N., Peck Scott C. Phosphoproteomics of the Arabidopsis plasma membrane and a new phosphorylation site database. Plant Cell. 2004 Aug 12;16(9):2394–2405. doi: 10.1105/tpc.104.023150. [DOI] [PMC free article] [PubMed] [Google Scholar]
  364. O'Toole Nicholas, Grabowski Marek, Otwinowski Zbyszek, Minor Wladek, Cygler Miroslaw. The structural genomics experimental pipeline: insights from global target lists. Proteins. 2004 Aug 1;56(2):201–210. doi: 10.1002/prot.20060. [DOI] [PubMed] [Google Scholar]
  365. Ohki-Kaneda Ruri, Ohashi Jun, Yamamoto Keiji, Ueno Shuichi, Ota Jun, Choi Young Lim, Koinuma Koji, Yamashita Yoshihiro, Misawa Yoshio, Fuse Katsuo. Cardiac function-related gene expression profiles in human atrial myocytes. Biochem Biophys Res Commun. 2004 Aug 6;320(4):1328–1336. doi: 10.1016/j.bbrc.2004.06.090. [DOI] [PubMed] [Google Scholar]
  366. Ohki Ruri, Yamamoto Keiji, Ueno Shuichi, Mano Hiroyuki, Misawa Yoshio, Fuse Katsuo, Ikeda Uichi, Shimada Kazuyuki. Transcriptional profile of genes induced in human atrial myocardium with pressure overload. Int J Cardiol. 2004 Sep;96(3):381–387. doi: 10.1016/j.ijcard.2003.07.025. [DOI] [PubMed] [Google Scholar]
  367. Oliveri Paola, Davidson Eric H. Gene regulatory network controlling embryonic specification in the sea urchin. Curr Opin Genet Dev. 2004 Aug;14(4):351–360. doi: 10.1016/j.gde.2004.06.004. [DOI] [PubMed] [Google Scholar]
  368. Ong Eng Shi, Len Shea Mei, Lee Audrey Chee Huay, Chui Paul, Chooi Kum Fai. Proteomic analysis of mouse liver for the evaluation of effects of Scutellariae radix by liquid chromatography with tandem mass spectrometry. Rapid Commun Mass Spectrom. 2004;18(21):2522–2530. doi: 10.1002/rcm.1654. [DOI] [PubMed] [Google Scholar]
  369. Ornstein David K., Rayford Walter, Fusaro Vincent A., Conrads Thomas P., Ross Sally J., Hitt Ben A., Wiggins Wesley W., Veenstra Timothy D., Liotta Lance A., Petricoin Emanuel F., 3rd Serum proteomic profiling can discriminate prostate cancer from benign prostates in men with total prostate specific antigen levels between 2.5 and 15.0 ng/ml. J Urol. 2004 Oct;172(4 Pt 1):1302–1305. doi: 10.1097/01.ju.0000139572.88463.39. [DOI] [PubMed] [Google Scholar]
  370. Osta Mike A., Christophides George K., Vlachou Dina, Kafatos Fotis C. Innate immunity in the malaria vector Anopheles gambiae: comparative and functional genomics. J Exp Biol. 2004 Jul;207(Pt 15):2551–2563. doi: 10.1242/jeb.01066. [DOI] [PubMed] [Google Scholar]
  371. Ote Manabu, Mita Kazuei, Kawasaki Hideki, Seki Motoaki, Nohata Junko, Kobayashi Masahiko, Shimada Toru. Microarray analysis of gene expression profiles in wing discs of Bombyx mori during pupal ecdysis. Insect Biochem Mol Biol. 2004 Aug;34(8):775–784. doi: 10.1016/j.ibmb.2004.04.002. [DOI] [PubMed] [Google Scholar]
  372. Palotás András, Puskás László G., Kitajka Klára, Palotás Miklós, Molnár József, Pákáski Magdolna, Janka Zoltán, Penke Botond, Kálmán János. Altered response to mirtazapine on gene expression profile of lymphocytes from Alzheimer's patients. Eur J Pharmacol. 2004 Aug 30;497(3):247–254. doi: 10.1016/j.ejphar.2004.06.059. [DOI] [PubMed] [Google Scholar]
  373. Pan Jonathan Z., Jörnsten Rebecka, Hart Ronald P. Screening anti-inflammatory compounds in injured spinal cord with microarrays: a comparison of bioinformatics analysis approaches. Physiol Genomics. 2004 Apr 13;17(2):201–214. doi: 10.1152/physiolgenomics.00177.2003. [DOI] [PubMed] [Google Scholar]
  374. Pandey Ritu, Guru Raghavendra K., Mount David W. Pathway Miner: extracting gene association networks from molecular pathways for predicting the biological significance of gene expression microarray data. Bioinformatics. 2004 May 14;20(13):2156–2158. doi: 10.1093/bioinformatics/bth215. [DOI] [PubMed] [Google Scholar]
  375. Pandit S. B., Balaji S., Srinivasan N. Structural and functional characterization of gene products encoded in the human genome by homology detection. IUBMB Life. 2004 Jun;56(6):317–331. doi: 10.1080/15216540400006105. [DOI] [PMC free article] [PubMed] [Google Scholar]
  376. Panicker Resmi C., Huang Xuan, Yao Shao Q. Recent advances in peptide-based microarray technologies. Comb Chem High Throughput Screen. 2004 Sep;7(6):547–556. doi: 10.2174/1386207043328517. [DOI] [PubMed] [Google Scholar]
  377. Pappas Christopher T., Sram Jakub, Moskvin Oleg V., Ivanov Pavel S., Mackenzie R. Christopher, Choudhary Madhusudan, Land Miriam L., Larimer Frank W., Kaplan Samuel, Gomelsky Mark. Construction and validation of the Rhodobacter sphaeroides 2.4.1 DNA microarray: transcriptome flexibility at diverse growth modes. J Bacteriol. 2004 Jul;186(14):4748–4758. doi: 10.1128/JB.186.14.4748-4758.2004. [DOI] [PMC free article] [PubMed] [Google Scholar]
  378. Parani Madasamy, Rudrabhatla Sairam, Myers Rachel, Weirich Heatherbea, Smith Bruce, Leaman Douglas W., Goldman Stephen L. Microarray analysis of nitric oxide responsive transcripts in Arabidopsis. Plant Biotechnol J. 2004 Jul;2(4):359–366. doi: 10.1111/j.1467-7652.2004.00085.x. [DOI] [PubMed] [Google Scholar]
  379. Park Yong-Jin, Dixit Anupam, Yoo Jae-Woong, Bennetzen Jeff. Further evidence of microcolinearity between barley and rice genomes at two orthologous regions. Mol Cells. 2004 Jun 30;17(3):492–502. [PubMed] [Google Scholar]
  380. Parkinson John, Anthony Alasdair, Wasmuth James, Schmid Ralf, Hedley Ann, Blaxter Mark. PartiGene--constructing partial genomes. Bioinformatics. 2004 Feb 26;20(9):1398–1404. doi: 10.1093/bioinformatics/bth101. [DOI] [PubMed] [Google Scholar]
  381. Parodi-Talice Adriana, Durán Rosario, Arrambide Nicolás, Prieto Victoria, Piñeyro María Dolores, Pritsch Otto, Cayota Alfonso, Cerveñansky Carlos, Robello Carlos. Proteome analysis of the causative agent of Chagas disease: Trypanosoma cruzi. Int J Parasitol. 2004 Jul;34(8):881–886. doi: 10.1016/j.ijpara.2004.05.002. [DOI] [PubMed] [Google Scholar]
  382. Paterson A. H., Bowers J. E., Chapman B. A. Ancient polyploidization predating divergence of the cereals, and its consequences for comparative genomics. Proc Natl Acad Sci U S A. 2004 May 25;101(26):9903–9908. doi: 10.1073/pnas.0307901101. [DOI] [PMC free article] [PubMed] [Google Scholar]
  383. Pavesi G., Mauri G., Iannelli F., Gissi C., Pesole G. GeneSyn: a tool for detecting conserved gene order across genomes. Bioinformatics. 2004 Feb 19;20(9):1472–1474. doi: 10.1093/bioinformatics/bth102. [DOI] [PubMed] [Google Scholar]
  384. Peng Xuanxian, Ye Xintai, Wang Sanying. Identification of novel immunogenic proteins of Shigella flexneri 2a by proteomic methodologies. Vaccine. 2004 Jul 29;22(21-22):2750–2756. doi: 10.1016/j.vaccine.2004.01.038. [DOI] [PubMed] [Google Scholar]
  385. Petricoin Emanuel F., Ornstein David K., Liotta Lance A. Clinical proteomics: Applications for prostate cancer biomarker discovery and detection. Urol Oncol. 2004 Jul-Aug;22(4):322–328. doi: 10.1016/j.urolonc.2004.04.011. [DOI] [PubMed] [Google Scholar]
  386. Pickart Michael A., Sivasubbu Sridhar, Nielsen Aubrey L., Shriram Sabitha, King Richard A., Ekker Stephen C. Functional genomics tools for the analysis of zebrafish pigment. Pigment Cell Res. 2004 Oct;17(5):461–470. doi: 10.1111/j.1600-0749.2004.00189.x. [DOI] [PubMed] [Google Scholar]
  387. Pisitkun Trairak, Shen Rong-Fong, Knepper Mark A. Identification and proteomic profiling of exosomes in human urine. Proc Natl Acad Sci U S A. 2004 Aug 23;101(36):13368–13373. doi: 10.1073/pnas.0403453101. [DOI] [PMC free article] [PubMed] [Google Scholar]
  388. Polen Tino, Wendisch Volker F. Genomewide expression analysis in amino acid-producing bacteria using DNA microarrays. Appl Biochem Biotechnol. 2004 Jul-Sep;118(1-3):215–232. doi: 10.1385/abab:118:1-3:215. [DOI] [PubMed] [Google Scholar]
  389. Poliness Anne E., Healey Martin G., Brennecke Shaun P., Moses Eric K. Proteomic approaches in endometriosis research. Proteomics. 2004 Jul;4(7):1897–1902. doi: 10.1002/pmic.200300791. [DOI] [PubMed] [Google Scholar]
  390. Poon H. F., Castegna A., Farr S. A., Thongboonkerd V., Lynn B. C., Banks W. A., Morley J. E., Klein J. B., Butterfield D. A. Quantitative proteomics analysis of specific protein expression and oxidative modification in aged senescence-accelerated-prone 8 mice brain. Neuroscience. 2004;126(4):915–926. doi: 10.1016/j.neuroscience.2004.04.046. [DOI] [PubMed] [Google Scholar]
  391. Poon Terence C. W., Chan K. C. Allen, Ng Pak-Cheung, Chiu Rossa W. K., Ang Irene L., Tong Yu-Kwan, Ng Enders K. O., Cheng Frankie W. T., Li Albert M., Hon Ellis K. L. Serial analysis of plasma proteomic signatures in pediatric patients with severe acute respiratory syndrome and correlation with viral load. Clin Chem. 2004 Jun 3;50(8):1452–1455. doi: 10.1373/clinchem.2004.035352. [DOI] [PMC free article] [PubMed] [Google Scholar]
  392. Poroyko Valeriy, Calugaru Vladimir, Fredricksen Mark, Bohnert Hans J. Virtual-SAGE: a new approach to EST data analysis. DNA Res. 2004 Apr 30;11(2):145–152. doi: 10.1093/dnares/11.2.145. [DOI] [PubMed] [Google Scholar]
  393. Posadas Edwin M., Davidson Ben, Kohn Elise C. Proteomics and ovarian cancer: implications for diagnosis and treatment: a critical review of the recent literature. Curr Opin Oncol. 2004 Sep;16(5):478–484. doi: 10.1097/00001622-200409000-00012. [DOI] [PubMed] [Google Scholar]
  394. Pounds Stan, Cheng Cheng. Improving false discovery rate estimation. Bioinformatics. 2004 Feb 26;20(11):1737–1745. doi: 10.1093/bioinformatics/bth160. [DOI] [PubMed] [Google Scholar]
  395. Power Peter M., Jones Robert A., Beacham Ifor R., Bucholtz Carolyn, Jennings Michael P. Whole genome analysis reveals a high incidence of non-optimal codons in secretory signal sequences of Escherichia coli. Biochem Biophys Res Commun. 2004 Sep 24;322(3):1038–1044. doi: 10.1016/j.bbrc.2004.08.022. [DOI] [PubMed] [Google Scholar]
  396. Prados Julien, Kalousis Alexandros, Sanchez Jean-Charles, Allard Laure, Carrette Odile, Hilario Melanie. Mining mass spectra for diagnosis and biomarker discovery of cerebral accidents. Proteomics. 2004 Aug;4(8):2320–2332. doi: 10.1002/pmic.200400857. [DOI] [PubMed] [Google Scholar]
  397. Price John, Laxmi Ashverya, St Martin Steven K., Jang Jyan-Chyun. Global transcription profiling reveals multiple sugar signal transduction mechanisms in Arabidopsis. Plant Cell. 2004 Jul 23;16(8):2128–2150. doi: 10.1105/tpc.104.022616. [DOI] [PMC free article] [PubMed] [Google Scholar]
  398. Price Ray M., Tulsyan Nirman, Dermody James J., Schwalb Marvin, Soteropoulos Patricia, Castronuovo John J., Jr Gene expression after crush injury of human saphenous vein: using microarrays to define the transcriptional profile. J Am Coll Surg. 2004 Sep;199(3):411–418. doi: 10.1016/j.jamcollsurg.2004.04.023. [DOI] [PubMed] [Google Scholar]
  399. Print Cristin, Valtola Reija, Evans Amanda, Lessan Khashayar, Malik Shazia, Smith Stephen. Soluble factors from human endometrium promote angiogenesis and regulate the endothelial cell transcriptome. Hum Reprod. 2004 Jul 8;19(10):2356–2366. doi: 10.1093/humrep/deh411. [DOI] [PubMed] [Google Scholar]
  400. Pérez Antonio J., Perez-Iratxeta Carolina, Bork Peer, Thode Guillermo, Andrade Miguel A. Gene annotation from scientific literature using mappings between keyword systems. Bioinformatics. 2004 Apr 1;20(13):2084–2091. doi: 10.1093/bioinformatics/bth207. [DOI] [PubMed] [Google Scholar]
  401. Qiu Ting Hu, Chandramouli Gadisetti V. R., Hunter Kent W., Alkharouf Nawal W., Green Jeffrey E., Liu Edison T. Global expression profiling identifies signatures of tumor virulence in MMTV-PyMT-transgenic mice: correlation to human disease. Cancer Res. 2004 Sep 1;64(17):5973–5981. doi: 10.1158/0008-5472.CAN-04-0242. [DOI] [PubMed] [Google Scholar]
  402. Quiring Rebecca, Wittbrodt Beate, Henrich Thorsten, Ramialison Mirana, Burgtorf Carola, Lehrach Hans, Wittbrodt Joachim. Large-scale expression screening by automated whole-mount in situ hybridization. Mech Dev. 2004 Jul;121(7-8):971–976. doi: 10.1016/j.mod.2004.03.031. [DOI] [PubMed] [Google Scholar]
  403. Rais Isam, Karas Michael, Schägger Hermann. Two-dimensional electrophoresis for the isolation of integral membrane proteins and mass spectrometric identification. Proteomics. 2004 Sep;4(9):2567–2571. doi: 10.1002/pmic.200400829. [DOI] [PubMed] [Google Scholar]
  404. Rajashekara Gireesh, Glasner Jeremy D., Glover David A., Splitter Gary A. Comparative whole-genome hybridization reveals genomic islands in Brucella species. J Bacteriol. 2004 Aug;186(15):5040–5051. doi: 10.1128/JB.186.15.5040-5051.2004. [DOI] [PMC free article] [PubMed] [Google Scholar]
  405. Randić Milan, Lers Nella, Plavić Dejan, Basak Subhash C. On invariants of a 2-D proteome map derived from neighborhood graphs. J Proteome Res. 2004 Jul-Aug;3(4):778–785. doi: 10.1021/pr049957h. [DOI] [PubMed] [Google Scholar]
  406. Rangel Claudia, Angus John, Ghahramani Zoubin, Lioumi Maria, Sotheran Elizabeth, Gaiba Alessia, Wild David L., Falciani Francesco. Modeling T-cell activation using gene expression profiling and state-space models. Bioinformatics. 2004 Feb 12;20(9):1361–1372. doi: 10.1093/bioinformatics/bth093. [DOI] [PubMed] [Google Scholar]
  407. Ranjan Priya, Kao Yu-Ying, Jiang Hongying, Joshi Chandrashekhar P., Harding Scott A., Tsai Chung-Jui. Suppression subtractive hybridization-mediated transcriptome analysis from multiple tissues of aspen (Populus tremuloides) altered in phenylpropanoid metabolism. Planta. 2004 May 14;219(4):694–704. doi: 10.1007/s00425-004-1291-9. [DOI] [PubMed] [Google Scholar]
  408. Rao P. S. Srinivasa, Yamada Yoshiyuki, Tan Yuen Peng, Leung Ka Yin. Use of proteomics to identify novel virulence determinants that are required for Edwardsiella tarda pathogenesis. Mol Microbiol. 2004 Jul;53(2):573–586. doi: 10.1111/j.1365-2958.2004.04123.x. [DOI] [PubMed] [Google Scholar]
  409. Rao Rupa S., Visuri Steven R., McBride Mary T., Albala Joanna S., Matthews Dennis L., Coleman Matthew A. Comparison of multiplexed techniques for detection of bacterial and viral proteins. J Proteome Res. 2004 Jul-Aug;3(4):736–742. doi: 10.1021/pr034130t. [DOI] [PubMed] [Google Scholar]
  410. Reddy Vaka S., Reddy Anireddy S. N. Proteomics of calcium-signaling components in plants. Phytochemistry. 2004 Jun;65(12):1745–1776. doi: 10.1016/j.phytochem.2004.04.033. [DOI] [PubMed] [Google Scholar]
  411. Reich M., Ohm K., Angelo M., Tamayo P., Mesirov J. P. GeneCluster 2.0: an advanced toolset for bioarray analysis. Bioinformatics. 2004 Feb 26;20(11):1797–1798. doi: 10.1093/bioinformatics/bth138. [DOI] [PubMed] [Google Scholar]
  412. Reid Gavin E., Roberts Kade D., Kapp Eugene A., Simpson Richard I. Statistical and mechanistic approaches to understanding the gas-phase fragmentation behavior of methionine sulfoxide containing peptides. J Proteome Res. 2004 Jul-Aug;3(4):751–759. doi: 10.1021/pr0499646. [DOI] [PubMed] [Google Scholar]
  413. Resing Katheryn A., Meyer-Arendt Karen, Mendoza Alex M., Aveline-Wolf Lauren D., Jonscher Karen R., Pierce Kevin G., Old William M., Cheung Hiu T., Russell Steven, Wattawa Joy L. Improving reproducibility and sensitivity in identifying human proteins by shotgun proteomics. Anal Chem. 2004 Jul 1;76(13):3556–3568. doi: 10.1021/ac035229m. [DOI] [PubMed] [Google Scholar]
  414. Rhodes Daniel R., Yu Jianjun, Shanker K., Deshpande Nandan, Varambally Radhika, Ghosh Debashis, Barrette Terrence, Pandey Akhilesh, Chinnaiyan Arul M. Large-scale meta-analysis of cancer microarray data identifies common transcriptional profiles of neoplastic transformation and progression. Proc Natl Acad Sci U S A. 2004 Jun 7;101(25):9309–9314. doi: 10.1073/pnas.0401994101. [DOI] [PMC free article] [PubMed] [Google Scholar]
  415. Ricciarelli Roberta, d'Abramo Cristina, Massone Sara, Marinari Umberto, Pronzato Maria, Tabaton Massimo. Microarray analysis in Alzheimer's disease and normal aging. IUBMB Life. 2004 Jun;56(6):349–354. doi: 10.1080/15216540412331286002. [DOI] [PubMed] [Google Scholar]
  416. Roberts Michael, Hunt Brian R., Yorke James A., Bolanos Randall A., Delcher Arthur L. A preprocessor for shotgun assembly of large genomes. J Comput Biol. 2004;11(4):734–752. doi: 10.1089/cmb.2004.11.734. [DOI] [PubMed] [Google Scholar]
  417. Robinson Andrew J., Love Christopher G., Batley Jacqueline, Barker Gary, Edwards David. Simple sequence repeat marker loci discovery using SSR primer. Bioinformatics. 2004 Feb 12;20(9):1475–1476. doi: 10.1093/bioinformatics/bth104. [DOI] [PubMed] [Google Scholar]
  418. Robson Barry, Mushlin Richard. Clinical and pharmacogenomic data mining: 2. A simple method for the combination of information from associations and multivariances to facilitate analysis, decision, and design in clinical research and practice. J Proteome Res. 2004 Jul-Aug;3(4):697–711. doi: 10.1021/pr0340680. [DOI] [PubMed] [Google Scholar]
  419. Rodionov Dmitry A., Vitreschak Alexey G., Mironov Andrey A., Gelfand Mikhail S. Comparative genomics of the methionine metabolism in Gram-positive bacteria: a variety of regulatory systems. Nucleic Acids Res. 2004 Jun 23;32(11):3340–3353. doi: 10.1093/nar/gkh659. [DOI] [PMC free article] [PubMed] [Google Scholar]
  420. Rodland Karin D. Proteomics and cancer diagnosis: the potential of mass spectrometry. Clin Biochem. 2004 Jul;37(7):579–583. doi: 10.1016/j.clinbiochem.2004.05.011. [DOI] [PubMed] [Google Scholar]
  421. Rogozin Igor B., Makarova Kira S., Wolf Yuri I., Koonin Eugene V. Computational approaches for the analysis of gene neighbourhoods in prokaryotic genomes. Brief Bioinform. 2004 Jun;5(2):131–149. doi: 10.1093/bib/5.2.131. [DOI] [PubMed] [Google Scholar]
  422. Roncada P., Carta F., Zannotti M., Malagutti L., Sciaraffia F., Greppi G. F. Swine ochratoxicosis: proteomic investigation of epatic bioindicators. Vet Res Commun. 2004 Aug;28 (Suppl 1):371–375. doi: 10.1023/b:verc.0000045449.93697.c8. [DOI] [PubMed] [Google Scholar]
  423. Rose Jocelyn K. C., Bashir Sajid, Giovannoni James J., Jahn Molly M., Saravanan Ramu Subramanian. Tackling the plant proteome: practical approaches, hurdles and experimental tools. Plant J. 2004 Sep;39(5):715–733. doi: 10.1111/j.1365-313X.2004.02182.x. [DOI] [PubMed] [Google Scholar]
  424. Rose Keith, Bougueleret Lydie, Baussant Thierry, Böhm Günter, Botti Paolo, Colinge Jacques, Cusin Isabelle, Gaertner Hubert, Gleizes Anne, Heller Manfred. Industrial-scale proteomics: from liters of plasma to chemically synthesized proteins. Proteomics. 2004 Jul;4(7):2125–2150. doi: 10.1002/pmic.200300718. [DOI] [PubMed] [Google Scholar]
  425. Ross Jeffrey S., Schenkein David P., Kashala Oscar, Linette Gerald P., Stec James, Symmans W. Fraser, Pusztai Lajos, Hortobagyi Gabriel N. Pharmacogenomics. Adv Anat Pathol. 2004 Jul;11(4):211–220. doi: 10.1097/01.pap.0000131825.77317.ee. [DOI] [PubMed] [Google Scholar]
  426. Rybak Jascha-N, Scheurer Simone B., Neri Dario, Elia Giuliano. Purification of biotinylated proteins on streptavidin resin: a protocol for quantitative elution. Proteomics. 2004 Aug;4(8):2296–2299. doi: 10.1002/pmic.200300780. [DOI] [PubMed] [Google Scholar]
  427. Sadlier Denise M., Connolly Susan B., Kieran Niamh E., Roxburgh Sarah, Brazil Derek P., Kairaitis Lukas, Wang Y., Harris David C. H., Doran Peter, Brady Hugh R. Sequential extracellular matrix-focused and baited-global cluster analysis of serial transcriptomic profiles identifies candidate modulators of renal tubulointerstitial fibrosis in murine adriamycin-induced nephropathy. J Biol Chem. 2004 Mar 18;279(28):29670–29680. doi: 10.1074/jbc.M313408200. [DOI] [PubMed] [Google Scholar]
  428. Saghatelian Alan, Jessani Nadim, Joseph Arul, Humphrey Mark, Cravatt Benjamin F. Activity-based probes for the proteomic profiling of metalloproteases. Proc Natl Acad Sci U S A. 2004 Jun 25;101(27):10000–10005. doi: 10.1073/pnas.0402784101. [DOI] [PMC free article] [PubMed] [Google Scholar]
  429. Saigo Hiroto, Vert Jean-Philippe, Ueda Nobuhisa, Akutsu Tatsuya. Protein homology detection using string alignment kernels. Bioinformatics. 2004 Feb 26;20(11):1682–1689. doi: 10.1093/bioinformatics/bth141. [DOI] [PubMed] [Google Scholar]
  430. Saito Mariko, Szakall Istvan, Toth Reka, Kovacs Krisztina M., Oros Melinda, Prasad Vidudala V. T. S., Blumenberg Miroslav, Vadasz Csaba. Mouse striatal transcriptome analysis: effects of oral self-administration of alcohol. Alcohol. 2004 Apr;32(3):223–241. doi: 10.1016/j.alcohol.2004.02.005. [DOI] [PubMed] [Google Scholar]
  431. Saitoh Noriko, Spahr Chris S., Patterson Scott D., Bubulya Paula, Neuwald Andrew F., Spector David L. Proteomic analysis of interchromatin granule clusters. Mol Biol Cell. 2004 May 28;15(8):3876–3890. doi: 10.1091/mbc.E04-03-0253. [DOI] [PMC free article] [PubMed] [Google Scholar]
  432. Sanchez Jean-Charles, Guillaume Elisabeth, Lescuyer Pierre, Allard Laure, Carrette Odile, Scherl Alex, Burgess Jennifer, Corthals Garry L., Burkhard Pierre R., Hochstrasser Denis F. Cystatin C as a potential cerebrospinal fluid marker for the diagnosis of Creutzfeldt-Jakob disease. Proteomics. 2004 Aug;4(8):2229–2233. doi: 10.1002/pmic.200300799. [DOI] [PubMed] [Google Scholar]
  433. Santos Pedro M., Benndorf Dirk, Sá-Correia Isabel. Insights into Pseudomonas putida KT2440 response to phenol-induced stress by quantitative proteomics. Proteomics. 2004 Sep;4(9):2640–2652. doi: 10.1002/pmic.200300793. [DOI] [PubMed] [Google Scholar]
  434. Sappl Pia G., Heazlewood Joshua L., Millar A. Harvey. Untangling multi-gene families in plants by integrating proteomics into functional genomics. Phytochemistry. 2004 Jun;65(11):1517–1530. doi: 10.1016/j.phytochem.2004.04.021. [DOI] [PubMed] [Google Scholar]
  435. Saravanan Ramu S., Rose Jocelyn K. C. A critical evaluation of sample extraction techniques for enhanced proteomic analysis of recalcitrant plant tissues. Proteomics. 2004 Sep;4(9):2522–2532. doi: 10.1002/pmic.200300789. [DOI] [PubMed] [Google Scholar]
  436. Sarnighausen Eric, Wurtz Virginie, Heintz Dimitri, Van Dorsselaer Alain, Reski Ralf. Mapping of the Physcomitrella patens proteome. Phytochemistry. 2004 Jun;65(11):1589–1607. doi: 10.1016/j.phytochem.2004.04.028. [DOI] [PubMed] [Google Scholar]
  437. Sarto Cecilia, Valsecchi Cristina, Magni Fulvio, Tremolada Lucia, Arizzi Carmelo, Cordani Nicoletta, Casellato Stefano, Doro Giancarlo, Favini Paolo, Perego Roberto A. Expression of heat shock protein 27 in human renal cell carcinoma. Proteomics. 2004 Aug;4(8):2252–2260. doi: 10.1002/pmic.200300797. [DOI] [PubMed] [Google Scholar]
  438. Sato Trey K., Panda Satchidananda, Miraglia Loren J., Reyes Teresa M., Rudic Radu D., McNamara Peter, Naik Kinnery A., FitzGerald Garret A., Kay Steve A., Hogenesch John B. A functional genomics strategy reveals Rora as a component of the mammalian circadian clock. Neuron. 2004 Aug 19;43(4):527–537. doi: 10.1016/j.neuron.2004.07.018. [DOI] [PubMed] [Google Scholar]
  439. Sawasaki Tatsuya, Hasegawa Yoshinori, Morishita Ryo, Seki Motoaki, Shinozaki Kazuo, Endo Yaeta. Genome-scale, biochemical annotation method based on the wheat germ cell-free protein synthesis system. Phytochemistry. 2004 Jun;65(11):1549–1555. doi: 10.1016/j.phytochem.2004.04.023. [DOI] [PubMed] [Google Scholar]
  440. Sawicki Grzegorz, Jugdutt Bodh I. Detection of regional changes in protein levels in the in vivo canine model of acute heart failure following ischemia-reperfusion injury: functional proteomics studies. Proteomics. 2004 Jul;4(7):2195–2202. doi: 10.1002/pmic.200300746. [DOI] [PubMed] [Google Scholar]
  441. Sazuka Takashi, Keta Sumie, Shiratake Katsuhiro, Yamaki Shohei, Shibata Daisuke. A proteomic approach to identification of transmembrane proteins and membrane-anchored proteins of Arabidopsis thaliana by peptide sequencing. DNA Res. 2004 Apr 30;11(2):101–113. doi: 10.1093/dnares/11.2.101. [DOI] [PubMed] [Google Scholar]
  442. Schaefer Heike, Chervet Jean-Pierre, Bunse Christian, Joppich Cornelia, Meyer Helmut E., Marcus Katrin. A peptide preconcentration approach for nano-high-performance liquid chromatography to diminish memory effects. Proteomics. 2004 Sep;4(9):2541–2544. doi: 10.1002/pmic.200300801. [DOI] [PubMed] [Google Scholar]
  443. Schattner Peter, Decatur Wayne A., Davis Carrie A., Ares Manuel, Jr, Fournier Maurille J., Lowe Todd M. Genome-wide searching for pseudouridylation guide snoRNAs: analysis of the Saccharomyces cerevisiae genome. Nucleic Acids Res. 2004 Aug 11;32(14):4281–4296. doi: 10.1093/nar/gkh768. [DOI] [PMC free article] [PubMed] [Google Scholar]
  444. Schlesier Bernhard, Berna Anne, Bernier François, Mock Hans-Peter. Proteome analysis differentiates between two highly homologues germin-like proteins in Arabidopsis thaliana ecotypes Col-0 and Ws-2. Phytochemistry. 2004 Jun;65(11):1565–1574. doi: 10.1016/j.phytochem.2004.04.027. [DOI] [PubMed] [Google Scholar]
  445. Schmid Gerhard M., Converset Véronique, Walter Nadia, Sennitt Matthew V., Leung Kit-Yi, Byers Helen, Ward Malcolm, Hochstrasser Denis F., Cawthorne Michael A., Sanchez Jean-Charles. Effect of high-fat diet on the expression of proteins in muscle, adipose tissues, and liver of C57BL/6 mice. Proteomics. 2004 Aug;4(8):2270–2282. doi: 10.1002/pmic.200300810. [DOI] [PubMed] [Google Scholar]
  446. Schmid Molly B. Seeing is believing: the impact of structural genomics on antimicrobial drug discovery. Nat Rev Microbiol. 2004 Sep;2(9):739–746. doi: 10.1038/nrmicro978. [DOI] [PubMed] [Google Scholar]
  447. Schrader Jarmo, Nilsson Jeanette, Mellerowicz Ewa, Berglund Anders, Nilsson Peter, Hertzberg Magnus, Sandberg Göran. A high-resolution transcript profile across the wood-forming meristem of poplar identifies potential regulators of cambial stem cell identity. Plant Cell. 2004 Aug 17;16(9):2278–2292. doi: 10.1105/tpc.104.024190. [DOI] [PMC free article] [PubMed] [Google Scholar]
  448. Schulenberg Birte, Goodman Terrie N., Aggeler Robert, Capaldi Roderick A., Patton Wayne F. Characterization of dynamic and steady-state protein phosphorylation using a fluorescent phosphoprotein gel stain and mass spectrometry. Electrophoresis. 2004 Aug;25(15):2526–2532. doi: 10.1002/elps.200406007. [DOI] [PubMed] [Google Scholar]
  449. Schulenberg Birte, Patton Wayne F. Combining microscale solution-phase isoelectric focusing with Multiplexed Proteomics dye staining to analyze protein post-translational modifications. Electrophoresis. 2004 Aug;25(15):2539–2544. doi: 10.1002/elps.200406009. [DOI] [PubMed] [Google Scholar]
  450. Schönbach Christian. From masking repeats to identifying functional repeats in the mouse transcriptome. Brief Bioinform. 2004 Jun;5(2):107–117. doi: 10.1093/bib/5.2.107. [DOI] [PubMed] [Google Scholar]
  451. Sebat Jonathan, Lakshmi B., Troge Jennifer, Alexander Joan, Young Janet, Lundin Pär, Månér Susanne, Massa Hillary, Walker Megan, Chi Maoyen. Large-scale copy number polymorphism in the human genome. Science. 2004 Jul 23;305(5683):525–528. doi: 10.1126/science.1098918. [DOI] [PubMed] [Google Scholar]
  452. Secko David M., Insall Robert H., Spiegelman George B., Weeks Gerry. The identification of Dictyostelium phosphoproteins altered in response to the activation of RasG. Proteomics. 2004 Sep;4(9):2629–2639. doi: 10.1002/pmic.200300788. [DOI] [PubMed] [Google Scholar]
  453. Semizarov Dimitri, Kroeger Paul, Fesik Stephen. siRNA-mediated gene silencing: a global genome view. Nucleic Acids Res. 2004 Jul 22;32(13):3836–3845. doi: 10.1093/nar/gkh714. [DOI] [PMC free article] [PubMed] [Google Scholar]
  454. Shankar Renu, Cullinane Fiona, Brennecke Shaun Patrick, Moses Eric Keith. Applications of proteomic methodologies to human pregnancy research: a growing gestation approaching delivery? Proteomics. 2004 Jul;4(7):1909–1917. doi: 10.1002/pmic.200300790. [DOI] [PubMed] [Google Scholar]
  455. Sharma Deepak, Issac Biju, Raghava G. P. S., Ramaswamy R. Spectral Repeat Finder (SRF): identification of repetitive sequences using Fourier transformation. Bioinformatics. 2004 Feb 19;20(9):1405–1412. doi: 10.1093/bioinformatics/bth103. [DOI] [PubMed] [Google Scholar]
  456. Shen Y., Tolić N., Masselon C., Pasa-Tolić L., Camp D. G., 2nd, Lipton M. S., Anderson G. A., Smith R. D. Nanoscale proteomics. Anal Bioanal Chem. 2003 Nov 29;378(4):1037–1045. doi: 10.1007/s00216-003-2329-8. [DOI] [PubMed] [Google Scholar]
  457. Shima James E., McLean Derek J., McCarrey John R., Griswold Michael D. The murine testicular transcriptome: characterizing gene expression in the testis during the progression of spermatogenesis. Biol Reprod. 2004 Mar 17;71(1):319–330. doi: 10.1095/biolreprod.103.026880. [DOI] [PubMed] [Google Scholar]
  458. Shimaoka Taise, Ohnishi Miwa, Sazuka Takashi, Mitsuhashi Naoto, Hara-Nishimura Ikuko, Shimazaki Ken-Ichiro, Maeshima Masayoshi, Yokota Akiho, Tomizawa Ken-Ichi, Mimura Tetsuro. Isolation of intact vacuoles and proteomic analysis of tonoplast from suspension-cultured cells of Arabidopsis thaliana. Plant Cell Physiol. 2004 Jun;45(6):672–683. doi: 10.1093/pcp/pch099. [DOI] [PubMed] [Google Scholar]
  459. Shipkova Maria, Beck Hermann, Voland Antje, Armstrong Victor W., Gröne Hermann-Josef, Oellerich Michael, Wieland Eberhard. Identification of protein targets for mycophenolic acid acyl glucuronide in rat liver and colon tissue. Proteomics. 2004 Sep;4(9):2728–2738. doi: 10.1002/pmic.200300836. [DOI] [PubMed] [Google Scholar]
  460. Signor Luca, Tigani Bruno, Beckmann Nicolau, Falchetto Rocco, Stoeckli Markus. Two-dimensional electrophoresis protein profiling and identification in rat bronchoalveolar lavage fluid following allergen and endotoxin challenge. Proteomics. 2004 Jul;4(7):2101–2110. doi: 10.1002/pmic.200300727. [DOI] [PubMed] [Google Scholar]
  461. Slabas A. R., Ndimba B., Simon W. J., Chivasa S. Proteomic analysis of the Arabidopsis cell wall reveals unexpected proteins with new cellular locations. Biochem Soc Trans. 2004 Jun;32(PT3):524–528. doi: 10.1042/BST0320524. [DOI] [PubMed] [Google Scholar]
  462. Smith Scott D., She Yi-Min, Roberts Eve A., Sarkar Bibudhendra. Using immobilized metal affinity chromatography, two-dimensional electrophoresis and mass spectrometry to identify hepatocellular proteins with copper-binding ability. J Proteome Res. 2004 Jul-Aug;3(4):834–840. doi: 10.1021/pr049941r. [DOI] [PubMed] [Google Scholar]
  463. Sogayar Mari Cleide, Camargo Anamaria A., Bettoni Fabiana, Carraro Dirce Maria, Pires Lilian C., Parmigiani Raphael B., Ferreira Elisa N., de Sá Moreira Eloísa, do Rosário D de O Latorre Maria, Simpson Andrew J. G. A transcript finishing initiative for closing gaps in the human transcriptome. Genome Res. 2004 Jun 14;14(7):1413–1423. doi: 10.1101/gr.2111304. [DOI] [PMC free article] [PubMed] [Google Scholar]
  464. Sohler Florian, Hanisch Daniel, Zimmer Ralf. New methods for joint analysis of biological networks and expression data. Bioinformatics. 2004 Jul 10;20(10):1517–1521. doi: 10.1093/bioinformatics/bth112. [DOI] [PubMed] [Google Scholar]
  465. Soltys Scott G., Le Quynh-Thu, Shi Gongyi, Tibshirani Robert, Giaccia A. J., Koong Albert C. The use of plasma surface-enhanced laser desorption/ionization time-of-flight mass spectrometry proteomic patterns for detection of head and neck squamous cell cancers. Clin Cancer Res. 2004 Jul 15;10(14):4806–4812. doi: 10.1158/1078-0432.CCR-03-0469. [DOI] [PubMed] [Google Scholar]
  466. Song Yajun, Tong Zongzhong, Wang Jin, Wang Li, Guo Zhaobiao, Han Yanpin, Zhang Jianguo, Pei Decui, Zhou Dongsheng, Qin Haiou. Complete genome sequence of Yersinia pestis strain 91001, an isolate avirulent to humans. DNA Res. 2004 Jun 30;11(3):179–197. doi: 10.1093/dnares/11.3.179. [DOI] [PubMed] [Google Scholar]
  467. Spira Avrum, Beane Jennifer, Shah Vishal, Liu Gang, Schembri Frank, Yang Xuemei, Palma John, Brody Jerome S. Effects of cigarette smoke on the human airway epithelial cell transcriptome. Proc Natl Acad Sci U S A. 2004 Jun 21;101(27):10143–10148. doi: 10.1073/pnas.0401422101. [DOI] [PMC free article] [PubMed] [Google Scholar]
  468. Sriuranpong Virote, Mutirangura Apiwat, Gillespie John W., Patel Vyomesh, Amornphimoltham Panomwat, Molinolo Alfredo A., Kerekhanjanarong Veerachai, Supanakorn Siripornchai, Supiyaphun Pakpoom, Rangdaeng Samreung. Global gene expression profile of nasopharyngeal carcinoma by laser capture microdissection and complementary DNA microarrays. Clin Cancer Res. 2004 Aug 1;10(15):4944–4958. doi: 10.1158/1078-0432.CCR-03-0757. [DOI] [PubMed] [Google Scholar]
  469. Staes An, Demol Hans, Van Damme Jozef, Martens Lennart, Vandekerckhove Joël, Gevaert Kris. Global differential non-gel proteomics by quantitative and stable labeling of tryptic peptides with oxygen-18. J Proteome Res. 2004 Jul-Aug;3(4):786–791. doi: 10.1021/pr049956p. [DOI] [PubMed] [Google Scholar]
  470. Stark Alexander, Shkumatov Alexander, Russell Robert B. Finding functional sites in structural genomics proteins. Structure. 2004 Aug;12(8):1405–1412. doi: 10.1016/j.str.2004.05.012. [DOI] [PubMed] [Google Scholar]
  471. Steiner Guido, Suter Laura, Boess Franziska, Gasser Rodolfo, de Vera Maria Cristina, Albertini Silvio, Ruepp Stefan. Discriminating different classes of toxicants by transcript profiling. Environ Health Perspect. 2004 Aug;112(12):1236–1248. doi: 10.1289/txg.7036. [DOI] [PMC free article] [PubMed] [Google Scholar]
  472. Stern David B., Hanson Maureen R., Barkan Alice. Genetics and genomics of chloroplast biogenesis: maize as a model system. Trends Plant Sci. 2004 Jun;9(6):293–301. doi: 10.1016/j.tplants.2004.04.001. [DOI] [PubMed] [Google Scholar]
  473. Stojanovic Nikola, Dewar Ken. Identifying multiple alignment regions satisfying simple formulas and patterns. Bioinformatics. 2004 Mar 25;20(13):2140–2142. doi: 10.1093/bioinformatics/bth196. [DOI] [PubMed] [Google Scholar]
  474. Stoyanova Radka, Querec Troy D., Brown Truman R., Patriotis Christos. Normalization of single-channel DNA array data by principal component analysis. Bioinformatics. 2004 Mar 22;20(11):1772–1784. doi: 10.1093/bioinformatics/bth170. [DOI] [PubMed] [Google Scholar]
  475. Strittmatter Eric F., Kangas Lars J., Petritis Konstantinos, Mottaz Heather M., Anderson Gordon A., Shen Yufeng, Jacobs Jon M., Camp David G., 2nd, Smith Richard D. Application of peptide LC retention time information in a discriminant function for peptide identification by tandem mass spectrometry. J Proteome Res. 2004 Jul-Aug;3(4):760–769. doi: 10.1021/pr049965y. [DOI] [PubMed] [Google Scholar]
  476. Sung Ho Joong, Kim Yoon Suk, Kim In Sik, Jang Sung-Wuk, Kim Yoon Rim, Na Doe Sun, Han Ki Hoon, Hwang Byung Gil, Park Dong Suk, Ko Jesang. Proteomic analysis of differential protein expression in neuropathic pain and electroacupuncture treatment models. Proteomics. 2004 Sep;4(9):2805–2813. doi: 10.1002/pmic.200300821. [DOI] [PubMed] [Google Scholar]
  477. Suzuki Masanori, Hayashizaki Yoshihide. Mouse-centric comparative transcriptomics of protein coding and non-coding RNAs. Bioessays. 2004 Aug;26(8):833–843. doi: 10.1002/bies.20084. [DOI] [PubMed] [Google Scholar]
  478. Suzuki Takashi, Shin-I Tadasu, Kohara Yuji, Kasahara Masanori. Transcriptome analysis of hagfish leukocytes: a framework for understanding the immune system of jawless fishes. Dev Comp Immunol. 2004 Aug;28(10):993–1003. doi: 10.1016/j.dci.2004.04.005. [DOI] [PubMed] [Google Scholar]
  479. Swertz Morris A., De Brock E. O., Van Hijum Sacha A. F. T., De Jong Anne, Buist Girbe, Baerends Richard J. S., Kok Jan, Kuipers Oscar P., Jansen Ritsert C. Molecular Genetics Information System (MOLGENIS): alternatives in developing local experimental genomics databases. Bioinformatics. 2004 Apr 1;20(13):2075–2083. doi: 10.1093/bioinformatics/bth206. [DOI] [PubMed] [Google Scholar]
  480. Swidzinski Jodi A., Leaver Christopher J., Sweetlove Lee J. A proteomic analysis of plant programmed cell death. Phytochemistry. 2004 Jun;65(12):1829–1838. doi: 10.1016/j.phytochem.2004.04.020. [DOI] [PubMed] [Google Scholar]
  481. Süle A., Vanrobaeys F., Hajós Gy, Van Beeumen J., Devreese B. Proteomic analysis of small heat shock protein isoforms in barley shoots. Phytochemistry. 2004 Jun;65(12):1853–1863. doi: 10.1016/j.phytochem.2004.03.030. [DOI] [PubMed] [Google Scholar]
  482. Tabuchi Mari, Baba Yoshinobu. Self-contained on-chip cell culture and pretreatment system. J Proteome Res. 2004 Jul-Aug;3(4):871–877. doi: 10.1021/pr0499500. [DOI] [PubMed] [Google Scholar]
  483. Tagawa Hiroyuki, Tsuzuki Shinobu, Suzuki Ritsuro, Karnan Sivasundaram, Ota Akinobu, Kameoka Yoshihiro, Suguro Miyuki, Matsuo Keitaro, Yamaguchi Motoko, Okamoto Masataka. Genome-wide array-based comparative genomic hybridization of diffuse large B-cell lymphoma: comparison between CD5-positive and CD5-negative cases. Cancer Res. 2004 Sep 1;64(17):5948–5955. doi: 10.1158/0008-5472.CAN-03-4056. [DOI] [PubMed] [Google Scholar]
  484. Tagu D., Prunier-Leterme N., Legeai F., Gauthier J-P, Duclert A., Sabater-Muñoz B., Bonhomme J., Simon J-C. Annotated expressed sequence tags for studies of the regulation of reproductive modes in aphids. Insect Biochem Mol Biol. 2004 Aug;34(8):809–822. doi: 10.1016/j.ibmb.2004.05.001. [DOI] [PubMed] [Google Scholar]
  485. Tamaoki Masanori, Matsuyama Takashi, Nakajima Nobuyoshi, Aono Mitsuko, Kubo Akihiro, Saji Hikaru. A method for diagnosis of plant environmental stresses by gene expression profiling using a cDNA macroarray. Environ Pollut. 2004 Sep;131(1):137–145. doi: 10.1016/j.envpol.2004.01.008. [DOI] [PubMed] [Google Scholar]
  486. Tan Yongxi, Shi Leming, Tong Weida, Hwang G. T. Gene, Wang Charles. Multi-class tumor classification by discriminant partial least squares using microarray gene expression data and assessment of classification models. Comput Biol Chem. 2004 Jul;28(3):235–244. doi: 10.1016/j.compbiolchem.2004.05.002. [DOI] [PubMed] [Google Scholar]
  487. Tanaka N., Fujita M., Handa H., Murayama S., Uemura M., Kawamura Y., Mitsui T., Mikami S., Tozawa Y., Yoshinaga T. Proteomics of the rice cell: systematic identification of the protein populations in subcellular compartments. Mol Genet Genomics. 2004 Apr 7;271(5):566–576. doi: 10.1007/s00438-004-1002-z. [DOI] [PubMed] [Google Scholar]
  488. Tautz Diethard, Lässig Michael. Of statistics and genomes. Trends Genet. 2004 Aug;20(8):344–346. doi: 10.1016/j.tig.2004.06.002. [DOI] [PubMed] [Google Scholar]
  489. Telleria Jenny, Barnabé Christian, Hide Mallorie, Bañuls Anne-Laure, Tibayrenc Michel. Predominant clonal evolution leads to a close parity between gene expression profiles and subspecific phylogeny in Trypanosoma cruzi. Mol Biochem Parasitol. 2004 Sep;137(1):133–141. doi: 10.1016/j.molbiopara.2004.05.006. [DOI] [PubMed] [Google Scholar]
  490. Tenzer Angela, Hofstetter Barbara, Sauser Christelle, Bodis Stephan, Schubiger August P., Bonny Christophe, Pruschy Martin. Profiling treatment-specific post-translational modifications in a complex proteome with subtractive substrate phage display. Proteomics. 2004 Sep;4(9):2796–2804. doi: 10.1002/pmic.200400811. [DOI] [PubMed] [Google Scholar]
  491. Teuffel Oliver, Dettling Marcel, Cario Gunnar, Stanulla Martin, Schrappe Martin, Bühlmann Peter, Niggli Felix K., Schäfer Beat W. Gene expression profiles and risk stratification in childhood acute lymphoblastic leukemia. Haematologica. 2004 Jul;89(7):801–808. [PubMed] [Google Scholar]
  492. Thompson Deanna M., King Kevin R., Wieder Kenneth J., Toner Mehmet, Yarmush Martin L., Jayaraman Arul. Dynamic gene expression profiling using a microfabricated living cell array. Anal Chem. 2004 Jul 15;76(14):4098–4103. doi: 10.1021/ac0354241. [DOI] [PubMed] [Google Scholar]
  493. Thongboonkerd Visith. Proteomics in nephrology: current status and future directions. Am J Nephrol. 2004 Jun 16;24(3):360–378. doi: 10.1159/000079148. [DOI] [PubMed] [Google Scholar]
  494. Tian Chaoguang, Wan Ping, Sun Shouhong, Li Jiayang, Chen Mingsheng. Genome-wide analysis of the GRAS gene family in rice and Arabidopsis. Plant Mol Biol. 2004 Mar;54(4):519–532. doi: 10.1023/B:PLAN.0000038256.89809.57. [DOI] [PubMed] [Google Scholar]
  495. Tomasinsig Linda, Scocchi Marco, Mettulio Romina, Zanetti Margherita. Genome-wide transcriptional profiling of the Escherichia coli response to a proline-rich antimicrobial peptide. Antimicrob Agents Chemother. 2004 Sep;48(9):3260–3267. doi: 10.1128/AAC.48.9.3260-3267.2004. [DOI] [PMC free article] [PubMed] [Google Scholar]
  496. Tong Xin, Campbell John W., Balázsi Gábor, Kay Krin A., Wanner Barry L., Gerdes Svetlana Y., Oltvai Zoltán N. Genome-scale identification of conditionally essential genes in E. coli by DNA microarrays. Biochem Biophys Res Commun. 2004 Sep 10;322(1):347–354. doi: 10.1016/j.bbrc.2004.07.110. [DOI] [PubMed] [Google Scholar]
  497. Torres-Muñoz Jorge E., Van Waveren Corina, Keegan Martha G., Bookman Richard J., Petito Carol K. Gene expression profiles in microdissected neurons from human hippocampal subregions. Brain Res Mol Brain Res. 2004 Aug 23;127(1-2):105–114. doi: 10.1016/j.molbrainres.2004.05.017. [DOI] [PubMed] [Google Scholar]
  498. Toyoda Tetsuro, Wada Akiyoshi. Omic space: coordinate-based integration and analysis of genomic phenomic interactions. Bioinformatics. 2004 Mar 22;20(11):1759–1765. doi: 10.1093/bioinformatics/bth165. [DOI] [PubMed] [Google Scholar]
  499. Trisiriroj Arunee, Jeyachok Narumon, Chen Shui-Tein. Proteomics characterization of different bran proteins between aromatic and nonaromatic rice (Oryza sativa L. ssp. indica). Proteomics. 2004 Jul;4(7):2047–2057. doi: 10.1002/pmic.200300729. [DOI] [PubMed] [Google Scholar]
  500. Tseng Chi Feng, Lin Chia Ching, Huang Hsing Yi, Liu Huei Chun, Mao Simon J. T. Antioxidant role of human haptoglobin. Proteomics. 2004 Aug;4(8):2221–2228. doi: 10.1002/pmic.200300787. [DOI] [PubMed] [Google Scholar]
  501. Tzafrir Iris, Pena-Muralla Rosanna, Dickerman Allan, Berg Michael, Rogers Rebecca, Hutchens Steven, Sweeney T. Colleen, McElver John, Aux George, Patton David. Identification of genes required for embryo development in Arabidopsis. Plant Physiol. 2004 Jul;135(3):1206–1220. doi: 10.1104/pp.104.045179. [DOI] [PMC free article] [PubMed] [Google Scholar]
  502. Ueda Hiroki R., Chen Wenbin, Minami Yoichi, Honma Sato, Honma Kenichi, Iino Masamitsu, Hashimoto Seiichi. Molecular-timetable methods for detection of body time and rhythm disorders from single-time-point genome-wide expression profiles. Proc Natl Acad Sci U S A. 2004 Jul 23;101(31):11227–11232. doi: 10.1073/pnas.0401882101. [DOI] [PMC free article] [PubMed] [Google Scholar]
  503. Ullmann Reinhard, Morbini Patrizia, Halbwedl Iris, Bongiovanni Massimo, Gogg-Kammerer Margit, Papotti Mauro, Gabor Sabine, Renner Heiko, Popper Helmut Hans. Protein expression profiles in adenocarcinomas and squamous cell carcinomas of the lung generated using tissue microarrays. J Pathol. 2004 Jul;203(3):798–807. doi: 10.1002/path.1584. [DOI] [PubMed] [Google Scholar]
  504. Ussery David W., Hallin Peter F., Lagesen Karin, Wassenaar Trudy M. Genome update: tRNAs in sequenced microbial genomes. Microbiology. 2004 Jun;150(Pt 6):1603–1606. doi: 10.1099/mic.0.27260-0. [DOI] [PubMed] [Google Scholar]
  505. Vaidyanathan Seetharaman, Kell Douglas B., Goodacre Royston. Selective detection of proteins in mixtures using electrospray ionization mass spectrometry: influence of instrumental settings and implications for proteomics. Anal Chem. 2004 Sep 1;76(17):5024–5032. doi: 10.1021/ac049684+. [DOI] [PubMed] [Google Scholar]
  506. Valot Benoît, Gianinazzi Silvio, Eliane Dumas-Gaudot. Sub-cellular proteomic analysis of a Medicago truncatula root microsomal fraction. Phytochemistry. 2004 Jun;65(12):1721–1732. doi: 10.1016/j.phytochem.2004.04.010. [DOI] [PubMed] [Google Scholar]
  507. Van Walle Ivo, Lasters Ignace, Wyns Lode. Align-m--a new algorithm for multiple alignment of highly divergent sequences. Bioinformatics. 2004 Feb 12;20(9):1428–1435. doi: 10.1093/bioinformatics/bth116. [DOI] [PubMed] [Google Scholar]
  508. Vanhentenrijk Vera, De Wolf-Peeters Chris, Wlodarska Iwona, Belgian Programme of Interuniversity Poles of Attraction Comparative expressed sequence hybridization studies of hairy cell leukemia show uniform expression profile and imprint of spleen signature. Blood. 2004 Mar 11;104(1):250–255. doi: 10.1182/blood-2004-01-0181. [DOI] [PubMed] [Google Scholar]
  509. Ventura Marco, Brüssow Harald. Temporal transcription map of the virulent Streptococcus thermophilus bacteriophage Sfi19. Appl Environ Microbiol. 2004 Aug;70(8):5041–5046. doi: 10.1128/AEM.70.8.5041-5046.2004. [DOI] [PMC free article] [PubMed] [Google Scholar]
  510. Verhagen Bas W. M., Glazebrook Jane, Zhu Tong, Chang Hur-Song, van Loon L. C., Pieterse Corné M. J. The transcriptome of rhizobacteria-induced systemic resistance in arabidopsis. Mol Plant Microbe Interact. 2004 Aug;17(8):895–908. doi: 10.1094/MPMI.2004.17.8.895. [DOI] [PubMed] [Google Scholar]
  511. Verjovski-Almeida Sergio, Leite Luciana C. C., Dias-Neto Emmanuel, Menck Carlos F. M., Wilson R. Alan. Schistosome transcriptome: insights and perspectives for functional genomics. Trends Parasitol. 2004 Jul;20(7):304–308. doi: 10.1016/j.pt.2004.04.012. [DOI] [PubMed] [Google Scholar]
  512. Vertegaal Alfred C. O., Ogg Stephen C., Jaffray Ellis, Rodriguez Manuel S., Hay Ronald T., Andersen Jens S., Mann Matthias, Lamond Angus I. A proteomic study of SUMO-2 target proteins. J Biol Chem. 2004 Jun 2;279(32):33791–33798. doi: 10.1074/jbc.M404201200. [DOI] [PubMed] [Google Scholar]
  513. Vilain Sébastien, Cosette Pascal, Hubert Marie, Lange Catherine, Junter Guy-Alain, Jouenne Thierry. Proteomic analysis of agar gel-entrapped Pseudomonas aeruginosa. Proteomics. 2004 Jul;4(7):1996–2004. doi: 10.1002/pmic.200300707. [DOI] [PubMed] [Google Scholar]
  514. Vlahou Antonia, Giannopoulos Aris, Gregory Betsy W., Manousakas Theodoros, Kondylis Filippos I., Wilson Lori L., Schellhammer Paul F., Wright George L., Jr, Semmes O. John. Protein profiling in urine for the diagnosis of bladder cancer. Clin Chem. 2004 Aug;50(8):1438–1441. doi: 10.1373/clinchem.2003.028035. [DOI] [PubMed] [Google Scholar]
  515. Vo Thuy D., Greenberg Harvey J., Palsson Bernhard O. Reconstruction and functional characterization of the human mitochondrial metabolic network based on proteomic and biochemical data. J Biol Chem. 2004 Jun 17;279(38):39532–39540. doi: 10.1074/jbc.M403782200. [DOI] [PubMed] [Google Scholar]
  516. Voit Eberhard O., Almeida Jonas. Decoupling dynamical systems for pathway identification from metabolic profiles. Bioinformatics. 2004 Feb 26;20(11):1670–1681. doi: 10.1093/bioinformatics/bth140. [DOI] [PubMed] [Google Scholar]
  517. Walz Christina, Giavalisco Patrick, Schad Martina, Juenger Melanie, Klose Joachim, Kehr Julia. Proteomics of curcurbit phloem exudate reveals a network of defence proteins. Phytochemistry. 2004 Jun;65(12):1795–1804. doi: 10.1016/j.phytochem.2004.04.006. [DOI] [PubMed] [Google Scholar]
  518. Wang Daojing, Jensen Ronald H., Williams Katherine E., Pallavicini Maria G. Differential protein expression in MCF7 breast cancer cells transfected with ErbB2, neomycin resistance and luciferase plus yellow fluorescent protein. Proteomics. 2004 Jul;4(7):2175–2183. doi: 10.1002/pmic.200300728. [DOI] [PubMed] [Google Scholar]
  519. Wang Haixing, Kachman Maureen T., Schwartz Donald R., Cho Kathleen R., Lubman David M. Comprehensive proteome analysis of ovarian cancers using liquid phase separation, mass mapping and tandem mass spectrometry: a strategy for identification of candidate cancer biomarkers. Proteomics. 2004 Aug;4(8):2476–2495. doi: 10.1002/pmic.200300763. [DOI] [PubMed] [Google Scholar]
  520. Wang Liangsu, Trawick John D., Yamamoto Robert, Zamudio Carlos. Genome-wide operon prediction in Staphylococcus aureus. Nucleic Acids Res. 2004 Jul 13;32(12):3689–3702. doi: 10.1093/nar/gkh694. [DOI] [PMC free article] [PubMed] [Google Scholar]
  521. Wang Q. Tian, Piotrowska Karolina, Ciemerych Maria Anna, Milenkovic Ljiljana, Scott Matthew P., Davis Ronald W., Zernicka-Goetz Magdalena. A genome-wide study of gene activity reveals developmental signaling pathways in the preimplantation mouse embryo. Dev Cell. 2004 Jan;6(1):133–144. doi: 10.1016/s1534-5807(03)00404-0. [DOI] [PubMed] [Google Scholar]
  522. Wang Qian, Brown Stuart, Roos David S., Nussenzweig Victor, Bhanot Purnima. Transcriptome of axenic liver stages of Plasmodium yoelii. Mol Biochem Parasitol. 2004 Sep;137(1):161–168. doi: 10.1016/j.molbiopara.2004.06.001. [DOI] [PubMed] [Google Scholar]
  523. Wang Sue-Jane, Chen James J. Sample size for identifying differentially expressed genes in microarray experiments. J Comput Biol. 2004;11(4):714–726. doi: 10.1089/cmb.2004.11.714. [DOI] [PubMed] [Google Scholar]
  524. Wang X-C, Xu S-Y, Wu X-Y, Song H-D, Mao Y-F, Fan H-Y, Yu F., Mou B., Gu Y-Y, Xu L-Q. Gene expression profiling in human insulinoma tissue: genes involved in the insulin secretion pathway and cloning of novel full-length cDNAs. Endocr Relat Cancer. 2004 Jun;11(2):295–303. doi: 10.1677/erc.0.0110295. [DOI] [PubMed] [Google Scholar]
  525. Wang Yongqiang, Zhang Pingbo, Fujii Hiroshi, Banno Yutaka, Yamamoto Kohji, Aso Yoichi. Proteomic studies of lipopolysaccharide-induced polypeptides in the silkworm, Bombyx mori. Biosci Biotechnol Biochem. 2004 Aug;68(8):1821–1823. doi: 10.1271/bbb.68.1821. [DOI] [PubMed] [Google Scholar]
  526. Wang Yuh-Tai, Huang Zhu-Jun, Chang Hung-Min. Proteomic analysis of human leukemic U937 cells incubated with conditioned medium of mononuclear cells stimulated by proteins from dietary mushroom of Agrocybe aegerita. J Proteome Res. 2004 Jul-Aug;3(4):890–896. doi: 10.1021/pr049922h. [DOI] [PubMed] [Google Scholar]
  527. Wassenaar Trudy M. Risk assessment prediction from genome sequences: promises and dreams. J Food Prot. 2004 Sep;67(9):2053–2057. doi: 10.4315/0362-028x-67.9.2053. [DOI] [PubMed] [Google Scholar]
  528. Watson Bonnie S., Lei Zhentian, Dixon Richard A., Sumner Lloyd W. Proteomics of Medicago sativa cell walls. Phytochemistry. 2004 Jun;65(12):1709–1720. doi: 10.1016/j.phytochem.2004.04.026. [DOI] [PubMed] [Google Scholar]
  529. Wei Chia-Lin, Ng Patrick, Chiu Kuo Ping, Wong Chee Hong, Ang Chin Chin, Lipovich Leonard, Liu Edison T., Ruan Yijun. 5' Long serial analysis of gene expression (LongSAGE) and 3' LongSAGE for transcriptome characterization and genome annotation. Proc Natl Acad Sci U S A. 2004 Jul 22;101(32):11701–11706. doi: 10.1073/pnas.0403514101. [DOI] [PMC free article] [PubMed] [Google Scholar]
  530. Wendl Michael C., Yang Shiaw-Pyng. Gap statistics for whole genome shotgun DNA sequencing projects. Bioinformatics. 2004 Feb 12;20(10):1527–1534. doi: 10.1093/bioinformatics/bth120. [DOI] [PubMed] [Google Scholar]
  531. Wenzel Uwe, Herzog Angelika, Kuntz Sabine, Daniel Hannelore. Protein expression profiling identifies molecular targets of quercetin as a major dietary flavonoid in human colon cancer cells. Proteomics. 2004 Jul;4(7):2160–2174. doi: 10.1002/pmic.200300726. [DOI] [PubMed] [Google Scholar]
  532. Wenzl Peter, Carling Jason, Kudrna David, Jaccoud Damian, Huttner Eric, Kleinhofs Andris, Kilian Andrzej. Diversity Arrays Technology (DArT) for whole-genome profiling of barley. Proc Natl Acad Sci U S A. 2004 Jun 10;101(26):9915–9920. doi: 10.1073/pnas.0401076101. [DOI] [PMC free article] [PubMed] [Google Scholar]
  533. White C. Nicole, Chan Daniel W., Zhang Zhen. Bioinformatics strategies for proteomic profiling. Clin Biochem. 2004 Jul;37(7):636–641. doi: 10.1016/j.clinbiochem.2004.05.004. [DOI] [PubMed] [Google Scholar]
  534. White John H. Profiling 1,25-dihydroxyvitamin D3-regulated gene expression by microarray analysis. J Steroid Biochem Mol Biol. 2004 May;89-90(1-5):239–244. doi: 10.1016/j.jsbmb.2004.03.074. [DOI] [PubMed] [Google Scholar]
  535. Whitelegge Julian P., Katz Jonathan E., Pihakari Katianna A., Hale Rebecca, Aguilera Rodrigo, Gómez Stephen M., Faull Kym F., Vavilin Dmitrii, Vermaas Willem. Subtle modification of isotope ratio proteomics; an integrated strategy for expression proteomics. Phytochemistry. 2004 Jun;65(11):1507–1515. doi: 10.1016/j.phytochem.2004.05.018. [DOI] [PubMed] [Google Scholar]
  536. Wienkoop Stefanie, Zoeller Daniela, Ebert Berit, Simon-Rosin Ulrike, Fisahn Joachim, Glinski Mirko, Weckwerth Wolfram. Cell-specific protein profiling in Arabidopsis thaliana trichomes: identification of trichome-located proteins involved in sulfur metabolism and detoxification. Phytochemistry. 2004 Jun;65(11):1641–1649. doi: 10.1016/j.phytochem.2004.03.026. [DOI] [PubMed] [Google Scholar]
  537. Wijnands M. V. W., van Erk M. J., Doornbos R. P., Krul C. A. M., Woutersen R. A. Do aberrant crypt foci have predictive value for the occurrence of colorectal tumours? Potential of gene expression profiling in tumours. Food Chem Toxicol. 2004 Oct;42(10):1629–1639. doi: 10.1016/j.fct.2004.05.008. [DOI] [PubMed] [Google Scholar]
  538. Wilmarth Phillip A., Taube Jennifer R., Riviere Michael A., Duncan Melinda K., David Larry L. Proteomic and sequence analysis of chicken lens crystallins reveals alternate splicing and translational forms of beta B2 and beta A2 crystallins. Invest Ophthalmol Vis Sci. 2004 Aug;45(8):2705–2715. doi: 10.1167/iovs.04-0131. [DOI] [PubMed] [Google Scholar]
  539. Wong Joshua H., Cai Nick, Balmer Yves, Tanaka Charlene K., Vensel William H., Hurkman William J., Buchanan Bob B. Thioredoxin targets of developing wheat seeds identified by complementary proteomic approaches. Phytochemistry. 2004 Jun;65(11):1629–1640. doi: 10.1016/j.phytochem.2004.05.010. [DOI] [PubMed] [Google Scholar]
  540. Wong Y. F., Cheung T. H., Lo K. W. K., Wang V. W., Chan C. S., Ng T. B., Chung T. K. H., Mok S. C. Protein profiling of cervical cancer by protein-biochips: proteomic scoring to discriminate cervical cancer from normal cervix. Cancer Lett. 2004 Aug 10;211(2):227–234. doi: 10.1016/j.canlet.2004.02.014. [DOI] [PubMed] [Google Scholar]
  541. Wu Christine C., MacCoss Michael J., Howell Kathryn E., Matthews Dwight E., Yates John R., 3rd Metabolic labeling of mammalian organisms with stable isotopes for quantitative proteomic analysis. Anal Chem. 2004 Sep 1;76(17):4951–4959. doi: 10.1021/ac049208j. [DOI] [PubMed] [Google Scholar]
  542. Wu Wei, Huang Wei, Qi Jianfeng, Chou Yi-Te, Torng Eric, Watson J. Throck. 'Signature sets', minimal fragment sets for identifying protein disulfide structures with cyanylation-based mass mapping methodology. J Proteome Res. 2004 Jul-Aug;3(4):770–777. doi: 10.1021/pr049961t. [DOI] [PubMed] [Google Scholar]
  543. Wu Wei, Noble William S. Genomic data visualization on the Web. Bioinformatics. 2004 Feb 26;20(11):1804–1805. doi: 10.1093/bioinformatics/bth154. [DOI] [PubMed] [Google Scholar]
  544. Xiao Xueyuan, Zhao Xiaodong, Liu Jiankai, Guo Fuzheng, Liu Danhui, He Dacheng. Discovery of laryngeal carcinoma by serum proteomic pattern analysis. Sci China C Life Sci. 2004 Jun;47(3):219–223. doi: 10.1007/BF03182766. [DOI] [PubMed] [Google Scholar]
  545. Xie Yang, Jeong Kyeong S., Pan Wei, Khodursky Arkady, Carlin Bradley P. A case study on choosing normalization methods and test statistics for two-channel microarray data. Comp Funct Genomics. 2004;5(5):432–444. doi: 10.1002/cfg.416. [DOI] [PMC free article] [PubMed] [Google Scholar]
  546. Xiong Momiao, Zhao Jinying, Xiong Hao. Network-based regulatory pathways analysis. Bioinformatics. 2004 Apr 8;20(13):2056–2066. doi: 10.1093/bioinformatics/bth201. [DOI] [PubMed] [Google Scholar]
  547. Xu Yuan, Ramos Eduardo J. b., Middleton Frank, Romanova Irina, Quinn Robert, Chen Chung, Das Undurti, Inui Akio, Meguid Michael M. Gene expression profiles post Roux-en-Y gastric bypass. Surgery. 2004 Aug;136(2):246–252. doi: 10.1016/j.surg.2004.04.027. [DOI] [PubMed] [Google Scholar]
  548. Yajima William, Hall J. Christopher, Kav Nat N. V. Proteome-level differences between auxinic-herbicide-susceptible and -resistant wild mustard (Sinapis arvensis L.). J Agric Food Chem. 2004 Aug 11;52(16):5063–5070. doi: 10.1021/jf0495284. [DOI] [PubMed] [Google Scholar]
  549. Yamaguchi Tomoya, Nakayama Katsuhiro, Hayashi Takami, Yazaki Junshi, Kishimoto Naoki, Kikuchi Shoshi, Koike Setsuo. cDNA microarray analysis of rice anther genes under chilling stress at the microsporogenesis stage revealed two genes with DNA transposon Castaway in the 5'-flanking region. Biosci Biotechnol Biochem. 2004 Jun;68(6):1315–1323. doi: 10.1271/bbb.68.1315. [DOI] [PubMed] [Google Scholar]
  550. Yang Howard H., Hu Ying, Buetow Kenneth H., Lee Maxwell P. A computational approach to measuring coherence of gene expression in pathways. Genomics. 2004 Jul;84(1):211–217. doi: 10.1016/j.ygeno.2004.01.007. [DOI] [PubMed] [Google Scholar]
  551. Yang Shihui, Perna Nicole T., Cooksey Donald A., Okinaka Yasushi, Lindow Steven E., Ibekwe A. Mark, Keen Noel T., Yang Ching-Hong. Genome-wide identification of plant-upregulated genes of Erwinia chrysanthemi 3937 using a GFP-based IVET leaf array. Mol Plant Microbe Interact. 2004 Sep;17(9):999–1008. doi: 10.1094/MPMI.2004.17.9.999. [DOI] [PubMed] [Google Scholar]
  552. Yates John R., 3rd Mass spectral analysis in proteomics. Annu Rev Biophys Biomol Struct. 2004;33:297–316. doi: 10.1146/annurev.biophys.33.111502.082538. [DOI] [PubMed] [Google Scholar]
  553. Yauk Carole L., Berndt M. Lynn, Williams Andrew, Douglas George R. Comprehensive comparison of six microarray technologies. Nucleic Acids Res. 2004 Aug 27;32(15):e124–e124. doi: 10.1093/nar/gnh123. [DOI] [PMC free article] [PubMed] [Google Scholar]
  554. Yin Zhikang, Stead David, Selway Laura, Walker Janet, Riba-Garcia Isabel, McLnerney Tracey, Gaskell Simon, Oliver Stephen G., Cash Philip, Brown Alistair J. P. Proteomic response to amino acid starvation in Candida albicans and Saccharomyces cerevisiae. Proteomics. 2004 Aug;4(8):2425–2436. doi: 10.1002/pmic.200300760. [DOI] [PubMed] [Google Scholar]
  555. Yokoo Hideki, Kondo Tadashi, Fujii Kazuyasu, Yamada Tesshi, Todo Satoru, Hirohashi Setsuo. Proteomic signature corresponding to alpha fetoprotein expression in liver cancer cells. Hepatology. 2004 Sep;40(3):609–617. doi: 10.1002/hep.20372. [DOI] [PubMed] [Google Scholar]
  556. Yokoyama Yuichiro, Kuramitsu Yasuhiro, Takashima Motonari, Iizuka Norio, Toda Toshifusa, Terai Shuji, Sakaida Isao, Oka Masaaki, Nakamura Kazuyuki, Okita Kiwamu. Proteomic profiling of proteins decreased in hepatocellular carcinoma from patients infected with hepatitis C virus. Proteomics. 2004 Jul;4(7):2111–2116. doi: 10.1002/pmic.200300712. [DOI] [PubMed] [Google Scholar]
  557. Young Travis W., Mei Fang C., Yang Gong, Thompson-Lanza Jennifer A., Liu Jinsong, Cheng Xiaodong. Activation of antioxidant pathways in ras-mediated oncogenic transformation of human surface ovarian epithelial cells revealed by functional proteomics and mass spectrometry. Cancer Res. 2004 Jul 1;64(13):4577–4584. doi: 10.1158/0008-5472.CAN-04-0222. [DOI] [PubMed] [Google Scholar]
  558. Yu Min, Chen Dong-Mei, Hu Gang, Wang Hai. Proteomic response analysis of endothelial cells of human coronary artery to stimulation with carbachol. Acta Pharmacol Sin. 2004 Sep;25(9):1124–1130. [PubMed] [Google Scholar]
  559. Yuan Jeffrey, Bush Bruce, Elbrecht Alex, Liu Yuan, Zhang Theresa, Zhao Wenqing, Blevins Richard. Enhanced homology searching through genome reading frame predetermination. Bioinformatics. 2004 Feb 19;20(9):1416–1427. doi: 10.1093/bioinformatics/bth115. [DOI] [PubMed] [Google Scholar]
  560. Yuan Quan, Fontenele-Neto Jose D., Fricker Lloyd D. Effect of voluntary exercise on genetically obese Cpefat/fat mice: quantitative proteomics of serum. Obes Res. 2004 Jul;12(7):1179–1188. doi: 10.1038/oby.2004.147. [DOI] [PubMed] [Google Scholar]
  561. Yun Hae-Sun, Jeong Won-Il, Do Sun-Hee, Jeong Da-Hee, Jung Yi-Rang, Park Jin-Kyu, Cho Eun-Mi, Jeong Kyu-Shik. Proteome analysis by bio-active ceramic water in rat liver: contribution to antioxidant enzyme expression, SOD I. Biochem Biophys Res Commun. 2004 Jul 30;320(3):852–859. doi: 10.1016/j.bbrc.2004.06.033. [DOI] [PubMed] [Google Scholar]
  562. Zareparsi Sepideh, Hero Alfred, Zack Donald J., Williams Robert W., Swaroop Anand. Seeing the unseen: Microarray-based gene expression profiling in vision. Invest Ophthalmol Vis Sci. 2004 Aug;45(8):2457–2462. doi: 10.1167/iovs.04-0183. [DOI] [PubMed] [Google Scholar]
  563. Zehender Hartmut, Le Goff Francois, Lehmann Natalie, Filipuzzi Ireos, Mayr Lorenz M. SpeedScreen: The "missing link" between genomics and lead discovery. J Biomol Screen. 2004 Sep;9(6):498–505. doi: 10.1177/1087057104267605. [DOI] [PubMed] [Google Scholar]
  564. Zelter Alex, Bencina Mojca, Bowman Barry J., Yarden Oded, Read Nick D. A comparative genomic analysis of the calcium signaling machinery in Neurospora crassa, Magnaporthe grisea, and Saccharomyces cerevisiae. Fungal Genet Biol. 2004 Sep;41(9):827–841. doi: 10.1016/j.fgb.2004.05.001. [DOI] [PubMed] [Google Scholar]
  565. Zeng Fanyi, Baldwin Don A., Schultz Richard M. Transcript profiling during preimplantation mouse development. Dev Biol. 2004 Aug 15;272(2):483–496. doi: 10.1016/j.ydbio.2004.05.018. [DOI] [PubMed] [Google Scholar]
  566. Zhang Cunjie, Doherty-Kirby Amanda, Huystee Rv Robert van, Lajoie Gilles. Investigation of cationic peanut peroxidase glycans by electrospray ionization mass spectrometry. Phytochemistry. 2004 Jun;65(11):1575–1588. doi: 10.1016/j.phytochem.2004.03.031. [DOI] [PubMed] [Google Scholar]
  567. Zhang Jianbing, Li Qinggang, Nguyen Thanh-Dung, Tremblay Tammy-Lynn, Stone Emily, To Rebecca, Kelly John, Roger MacKenzie C. A pentavalent single-domain antibody approach to tumor antigen discovery and the development of novel proteomics reagents. J Mol Biol. 2004 Jul 30;341(1):161–169. doi: 10.1016/j.jmb.2004.05.069. [DOI] [PubMed] [Google Scholar]
  568. Zhang Jie, Hu Hualing, Gao Mingxia, Yang Pengyuan, Zhang Xiangmin. Comprehensive two-dimensional chromatography and capillary electrophoresis coupled with tandem time-of-flight mass spectrometry for high-speed proteome analysis. Electrophoresis. 2004 Jul;25(14):2374–2383. doi: 10.1002/elps.200405956. [DOI] [PubMed] [Google Scholar]
  569. Zhang Nan, Li Nan, Li Liang. Liquid chromatography MALDI MS/MS for membrane proteome analysis. J Proteome Res. 2004 Jul-Aug;3(4):719–727. doi: 10.1021/pr034116g. [DOI] [PubMed] [Google Scholar]
  570. Zhang Qin, Riechers Dean E. Proteomic characterization of herbicide safener-induced proteins in the coleoptile of Triticum tauschii seedlings. Proteomics. 2004 Jul;4(7):2058–2071. doi: 10.1002/pmic.200300733. [DOI] [PubMed] [Google Scholar]
  571. Zhang ZhaoLei, Gerstein Mark. Large-scale analysis of pseudogenes in the human genome. Curr Opin Genet Dev. 2004 Aug;14(4):328–335. doi: 10.1016/j.gde.2004.06.003. [DOI] [PubMed] [Google Scholar]
  572. Zhang Zhen, Bast Robert C., Jr, Yu Yinhua, Li Jinong, Sokoll Lori J., Rai Alex J., Rosenzweig Jason M., Cameron Bonnie, Wang Young Y., Meng Xiao-Ying. Three biomarkers identified from serum proteomic analysis for the detection of early stage ovarian cancer. Cancer Res. 2004 Aug 15;64(16):5882–5890. doi: 10.1158/0008-5472.CAN-04-0746. [DOI] [PubMed] [Google Scholar]
  573. Zhao Bing, Yeo Chew Chieng, Lee Chee Chow, Geng Anli, Chew Fook Tim, Poh Chit Laa. Proteome analysis of gentisate-induced response in Pseudomonas alcaligenes NCIB 9867. Proteomics. 2004 Jul;4(7):2028–2036. doi: 10.1002/pmic.200300730. [DOI] [PubMed] [Google Scholar]
  574. Zheng Jie, Close Timothy J., Jiang Tao, Lonardi Stefano. Efficient selection of unique and popular oligos for large EST databases. Bioinformatics. 2004 Apr 1;20(13):2101–2112. doi: 10.1093/bioinformatics/bth210. [DOI] [PubMed] [Google Scholar]
  575. Zheng Junfang, Liu Guirong, Zhu Wanfu, Zhou Yuguang, Liu Shulin. Phylogenetic clusters of rhizobia revealed by genome structures. Sci China C Life Sci. 2004 Jun;47(3):268–278. doi: 10.1007/BF03182772. [DOI] [PubMed] [Google Scholar]
  576. Zhong Shaobin, Khodursky Arkady, Dykhuizen Daniel E., Dean Antony M. Evolutionary genomics of ecological specialization. Proc Natl Acad Sci U S A. 2004 Aug 2;101(32):11719–11724. doi: 10.1073/pnas.0404397101. [DOI] [PMC free article] [PubMed] [Google Scholar]
  577. Zhou Dongsheng, Han Yanping, Dai Erhei, Song Yajun, Pei Decui, Zhai Junhui, Du Zongmin, Wang Jin, Guo Zhaobiao, Yang Ruifu. Defining the genome content of live plague vaccines by use of whole-genome DNA microarray. Vaccine. 2004 Sep 3;22(25-26):3367–3374. doi: 10.1016/j.vaccine.2004.02.035. [DOI] [PubMed] [Google Scholar]
  578. Zhou Dongsheng, Han Yanping, Song Yajun, Tong Zongzhong, Wang Jin, Guo Zhaobiao, Pei Decui, Pang Xin, Zhai Junhui, Li Min. DNA microarray analysis of genome dynamics in Yersinia pestis: insights into bacterial genome microevolution and niche adaptation. J Bacteriol. 2004 Aug;186(15):5138–5146. doi: 10.1128/JB.186.15.5138-5146.2004. [DOI] [PMC free article] [PubMed] [Google Scholar]
  579. Zhou Fang X., Bonin Jaclyn, Predki Paul F. Development of functional protein microarrays for drug discovery: progress and challenges. Comb Chem High Throughput Screen. 2004 Sep;7(6):539–546. doi: 10.2174/1386207043328490. [DOI] [PubMed] [Google Scholar]
  580. Zhou Yong, Gu Guangyu, Goodlett David R., Zhang Terry, Pan Catherine, Montine Thomas J., Montine Kathleen S., Aebersold Ruedi H., Zhang Jing. Analysis of alpha-synuclein-associated proteins by quantitative proteomics. J Biol Chem. 2004 Jul 1;279(37):39155–39164. doi: 10.1074/jbc.M405456200. [DOI] [PubMed] [Google Scholar]
  581. Zhuang Z., Lee Y-S, Zeng W., Furuta M., Valyi-Nagy T., Johnson M. D., Vnencak-Jones C. L., Woltjer R. L., Weil R. J. Molecular genetic and proteomic analysis of synchronous malignant gliomas. Neurology. 2004 Jun 22;62(12):2316–2319. doi: 10.1212/wnl.62.12.2316. [DOI] [PubMed] [Google Scholar]
  582. Zilberstein Gleb, Korol Leonid, Bukshpan Shmuel, Baskin Emanuil. Parallel isoelectric focusing chip. Proteomics. 2004 Sep;4(9):2533–2540. doi: 10.1002/pmic.200300794. [DOI] [PubMed] [Google Scholar]
  583. Zolodz Melissa D., Wood Karl V., Regnier Fred E., Geahlen Robert L. New approach for analysis of the phosphotyrosine proteome and its application to the chicken B cell line, DT40. J Proteome Res. 2004 Jul-Aug;3(4):743–750. doi: 10.1021/pr049967i. [DOI] [PubMed] [Google Scholar]
  584. de Hoon M. J. L., Imoto S., Nolan J., Miyano S. Open source clustering software. Bioinformatics. 2004 Feb 10;20(9):1453–1454. doi: 10.1093/bioinformatics/bth078. [DOI] [PubMed] [Google Scholar]
  585. de Magalhães João Pedro, Toussaint Olivier. GenAge: a genomic and proteomic network map of human ageing. FEBS Lett. 2004 Jul 30;571(1-3):243–247. doi: 10.1016/j.febslet.2004.07.006. [DOI] [PubMed] [Google Scholar]
  586. de Souza Alessandra A., Takita Marco A., Coletta-Filho Helvécio D., Caldana Camila, Yanai Giane M., Muto Nair H., de Oliveira Regina C., Nunes Luiz R., Machado Marcos A. Gene expression profile of the plant pathogen Xylella fastidiosa during biofilm formation in vitro. FEMS Microbiol Lett. 2004 Aug 15;237(2):341–353. doi: 10.1016/j.femsle.2004.06.055. [DOI] [PubMed] [Google Scholar]
  587. van Delft J. H. M., van Agen E., van Breda S. G. J., Herwijnen M. H., Staal Y. C. M., Kleinjans J. C. S. Discrimination of genotoxic from non-genotoxic carcinogens by gene expression profiling. Carcinogenesis. 2004 Feb 12;25(7):1265–1276. doi: 10.1093/carcin/bgh108. [DOI] [PubMed] [Google Scholar]

Articles from Comparative and Functional Genomics are provided here courtesy of Wiley

RESOURCES