Skip to main content
Comparative and Functional Genomics logoLink to Comparative and Functional Genomics
. 2003 Oct;4(5):560–567. doi: 10.1002/cfg.230

Current Awareness on Comparative and Functional Genomics

PMCID: PMC2447285

Full Text

The Full Text of this article is available as a PDF (121.0 KB).

Selected References

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

  1. Abe Takashi, Kanaya Shigehiko, Kinouchi Makoto, Ichiba Yuta, Kozuki Tokio, Ikemura Toshimichi. Informatics for unveiling hidden genome signatures. Genome Res. 2003 Apr;13(4):693–702. doi: 10.1101/gr.634603. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2. Adams Michael W. W., Dailey Harry A., DeLucas Lawrence J., Luo Ming, Prestegard James H., Rose John P., Wang Bi-Cheng. The Southeast Collaboratory for Structural Genomics: a high-throughput gene to structure factory. Acc Chem Res. 2003 Mar;36(3):191–198. doi: 10.1021/ar0101382. [DOI] [PubMed] [Google Scholar]
  3. Ahmed Nuzhat, Oliva Karen, Wang Yao, Quinn Michael, Rice Greg. Proteomic profiling of proteins associated with urokinase plasminogen activator receptor in a colon cancer cell line using an antisense approach. Proteomics. 2003 Mar;3(3):288–298. doi: 10.1002/pmic.200390042. [DOI] [PubMed] [Google Scholar]
  4. Ahram Mamoun, Flaig Michael J., Gillespie John W., Duray Paul H., Linehan W. Marston, Ornstein David K., Niu Shulan, Zhao Yingming, Petricoin Emanuel F., 3rd, Emmert-Buck Michael R. Evaluation of ethanol-fixed, paraffin-embedded tissues for proteomic applications. Proteomics. 2003 Apr;3(4):413–421. doi: 10.1002/pmic.200390056. [DOI] [PubMed] [Google Scholar]
  5. Alaiya Ayodele A., Roblick Uwe J., Franzén Bo, Bruch Hans-Peter, Auer Gert. Protein expression profiling in human lung, breast, bladder, renal, colorectal and ovarian cancers. J Chromatogr B Analyt Technol Biomed Life Sci. 2003 Apr 5;787(1):207–222. doi: 10.1016/s1570-0232(02)00559-7. [DOI] [PubMed] [Google Scholar]
  6. Alter Orly, Brown Patrick O., Botstein David. Generalized singular value decomposition for comparative analysis of genome-scale expression data sets of two different organisms. Proc Natl Acad Sci U S A. 2003 Mar 11;100(6):3351–3356. doi: 10.1073/pnas.0530258100. [DOI] [PMC free article] [PubMed] [Google Scholar]
  7. Amon Peter, Ivanov Igor. Genomic DNA labeling for hybridization with DNA arrays. Biotechniques. 2003 Apr;34(4):700-2, 704. doi: 10.2144/03344bm03. [DOI] [PubMed] [Google Scholar]
  8. Anderson D. C., Li Weiqun, Payan Donald G., Noble William Stafford. A new algorithm for the evaluation of shotgun peptide sequencing in proteomics: support vector machine classification of peptide MS/MS spectra and SEQUEST scores. J Proteome Res. 2003 Mar-Apr;2(2):137–146. doi: 10.1021/pr0255654. [DOI] [PubMed] [Google Scholar]
  9. Antoniadis A., Lambert-Lacroix S., Leblanc F. Effective dimension reduction methods for tumor classification using gene expression data. Bioinformatics. 2003 Mar 22;19(5):563–570. doi: 10.1093/bioinformatics/btg062. [DOI] [PubMed] [Google Scholar]
  10. Arava Yoav, Wang Yulei, Storey John D., Liu Chih Long, Brown Patrick O., Herschlag Daniel. Genome-wide analysis of mRNA translation profiles in Saccharomyces cerevisiae. Proc Natl Acad Sci U S A. 2003 Mar 26;100(7):3889–3894. doi: 10.1073/pnas.0635171100. [DOI] [PMC free article] [PubMed] [Google Scholar]
  11. Archakov Alexander I., Govorun Vadim M., Dubanov Alexander V., Ivanov Yuri D., Veselovsky Alexander V., Lewi Paul, Janssen Paul. Protein-protein interactions as a target for drugs in proteomics. Proteomics. 2003 Apr;3(4):380–391. doi: 10.1002/pmic.200390053. [DOI] [PubMed] [Google Scholar]
  12. Ballot Eric, Bruneel Arnaud, Labas Valérie, Johanet Catherine. Identification of rat targets of anti-soluble liver antigen autoantibodies by serologic proteome analysis. Clin Chem. 2003 Apr;49(4):634–643. doi: 10.1373/49.4.634. [DOI] [PubMed] [Google Scholar]
  13. Banci Lucia, Rosato Antonio. Structural genomics of proteins involved in copper homeostasis. Acc Chem Res. 2003 Mar;36(3):215–221. doi: 10.1021/ar010120r. [DOI] [PubMed] [Google Scholar]
  14. Bandow Julia Elisabeth, Becher Dörte, Büttner Knut, Hochgräfe Falko, Freiberg Christoph, Brötz Heike, Hecker Michael. The role of peptide deformylase in protein biosynthesis: a proteomic study. Proteomics. 2003 Mar;3(3):299–306. doi: 10.1002/pmic.200390043. [DOI] [PubMed] [Google Scholar]
  15. Banks Rosamonde E., Craven Rachel A., Harnden Patricia A., Selby Peter J. Use of a sensitive EnVision +-based detection system for Western blotting: avoidance of streptavidin binding to endogenous biotin and biotin-containing proteins in kidney and other tissues. Proteomics. 2003 Apr;3(4):558–561. doi: 10.1002/pmic.200390069. [DOI] [PubMed] [Google Scholar]
  16. Barrier Marianne, Bustamante Carlos D., Yu Jiaye, Purugganan Michael D. Selection on rapidly evolving proteins in the Arabidopsis genome. Genetics. 2003 Feb;163(2):723–733. doi: 10.1093/genetics/163.2.723. [DOI] [PMC free article] [PubMed] [Google Scholar]
  17. Bauersachs Stefan, Blum Helmut, Mallok Sylvia, Wenigerkind Hendrik, Rief Stephanie, Prelle Katja, Wolf Eckhard. Regulation of ipsilateral and contralateral bovine oviduct epithelial cell function in the postovulation period: a transcriptomics approach. Biol Reprod. 2002 Oct 30;68(4):1170–1177. doi: 10.1095/biolreprod.102.010660. [DOI] [PubMed] [Google Scholar]
  18. Baugh L. Ryan, Hill Andrew A., Slonim Donna K., Brown Eugene L., Hunter Craig P. Composition and dynamics of the Caenorhabditis elegans early embryonic transcriptome. Development. 2003 Mar;130(5):889–900. doi: 10.1242/dev.00302. [DOI] [PubMed] [Google Scholar]
  19. Begley Thomas J., Rosenbach Ari S., Ideker Trey, Samson Leona D. Damage recovery pathways in Saccharomyces cerevisiae revealed by genomic phenotyping and interactome mapping. Mol Cancer Res. 2002 Dec;1(2):103–112. [PubMed] [Google Scholar]
  20. Bennett Michael D., Leitch Ilia J., Price H. James, Johnston J. Spencer. Comparisons with Caenorhabditis (approximately 100 Mb) and Drosophila (approximately 175 Mb) using flow cytometry show genome size in Arabidopsis to be approximately 157 Mb and thus approximately 25% larger than the Arabidopsis genome initiative estimate of approximately 125 Mb. Ann Bot. 2003 Apr;91(5):547–557. doi: 10.1093/aob/mcg057. [DOI] [PMC free article] [PubMed] [Google Scholar]
  21. Bennett Steven P., Nevill-Manning Craig G., Brutlag Douglas L. 3MOTIF: visualizing conserved protein sequence motifs in the protein structure database. Bioinformatics. 2003 Mar 1;19(4):541–542. doi: 10.1093/bioinformatics/btf862. [DOI] [PubMed] [Google Scholar]
  22. Bennetzen Jeffrey L., Ma Jianxin. The genetic colinearity of rice and other cereals on the basis of genomic sequence analysis. Curr Opin Plant Biol. 2003 Apr;6(2):128–133. doi: 10.1016/s1369-5266(03)00015-3. [DOI] [PubMed] [Google Scholar]
  23. Berka Jan, Ruiz-Martinez Marie C., Hammond Richard, Minarik Marek, Foret Frantisek, Sosic Zoran, Kleparnik Karel, Karger Barry L. Application of high-resolution capillary array electrophoresis with automated fraction collection for GeneCalling trade mark analysis of the yeast genomic DNA. Electrophoresis. 2003 Feb;24(4):639–647. doi: 10.1002/elps.200390075. [DOI] [PubMed] [Google Scholar]
  24. Berriz Gabriel F., White James V., King Oliver D., Roth Frederick P. GoFish finds genes with combinations of Gene Ontology attributes. Bioinformatics. 2003 Apr 12;19(6):788–789. doi: 10.1093/bioinformatics/btg088. [DOI] [PubMed] [Google Scholar]
  25. Bertani G. R., Johnson R. K., Robic A., Pomp D. Mapping of porcine ESTs obtained from the anterior pituitary. Anim Genet. 2003 Apr;34(2):132–134. doi: 10.1046/j.1365-2052.2003.00962.x. [DOI] [PubMed] [Google Scholar]
  26. Bertucci François, Viens Patrice, Tagett Rebecca, Nguyen Catherine, Houlgatte Rémi, Birnbaum Daniel. DNA arrays in clinical oncology: promises and challenges. Lab Invest. 2003 Mar;83(3):305–316. doi: 10.1097/01.lab.0000059936.28369.19. [DOI] [PubMed] [Google Scholar]
  27. Bicciato S., Luchini A., Di Bello C. PCA disjoint models for multiclass cancer analysis using gene expression data. Bioinformatics. 2003 Mar 22;19(5):571–578. doi: 10.1093/bioinformatics/btg051. [DOI] [PubMed] [Google Scholar]
  28. Blaxall Burns C., Tschannen-Moran Bryn M., Milano Carmelo A., Koch Walter J. Differential gene expression and genomic patient stratification following left ventricular assist device support. J Am Coll Cardiol. 2003 Apr 2;41(7):1096–1106. doi: 10.1016/s0735-1097(03)00043-3. [DOI] [PubMed] [Google Scholar]
  29. Blekas Konstantinos, Fotiadis Dimitrios I., Likas Aristidis. Greedy mixture learning for multiple motif discovery in biological sequences. Bioinformatics. 2003 Mar 22;19(5):607–617. doi: 10.1093/bioinformatics/btg037. [DOI] [PubMed] [Google Scholar]
  30. Boneca Ivo G., de Reuse Hilde, Epinat Jean-Charles, Pupin Maude, Labigne Agnès, Moszer Ivan. A revised annotation and comparative analysis of Helicobacter pylori genomes. Nucleic Acids Res. 2003 Mar 15;31(6):1704–1714. doi: 10.1093/nar/gkg250. [DOI] [PMC free article] [PubMed] [Google Scholar]
  31. Brudno Michael, Do Chuong B., Cooper Gregory M., Kim Michael F., Davydov Eugene, NISC Comparative Sequencing Program. Green Eric D., Sidow Arend, Batzoglou Serafim. LAGAN and Multi-LAGAN: efficient tools for large-scale multiple alignment of genomic DNA. Genome Res. 2003 Mar 12;13(4):721–731. doi: 10.1101/gr.926603. [DOI] [PMC free article] [PubMed] [Google Scholar]
  32. Bruneau Jean-Michel, Maillet Isabelle, Tagat Eric, Legrand Raymond, Supatto Françoise, Fudali Claude, Caer Jean-Pierre Le, Labas Valérie, Lecaque Dominique, Hodgson John. Drug induced proteome changes in Candida albicans: comparison of the effect of beta(1,3) glucan synthase inhibitors and two triazoles, fluconazole and itraconazole. Proteomics. 2003 Mar;3(3):325–336. doi: 10.1002/pmic.200390046. [DOI] [PubMed] [Google Scholar]
  33. Buchrieser Carmen, Rusniok Christophe, Kunst Frank, Cossart Pascale, Glaser Philippe, Listeria Consortium Comparison of the genome sequences of Listeria monocytogenes and Listeria innocua: clues for evolution and pathogenicity. FEMS Immunol Med Microbiol. 2003 Apr 1;35(3):207–213. doi: 10.1016/S0928-8244(02)00448-0. [DOI] [PubMed] [Google Scholar]
  34. Bunney William E., Bunney Blynn G., Vawter Marquis P., Tomita Hiroaki, Li Jun, Evans Simon J., Choudary Prabhakara V., Myers Richard M., Jones Edward G., Watson Stanley J. Microarray technology: a review of new strategies to discover candidate vulnerability genes in psychiatric disorders. Am J Psychiatry. 2003 Apr;160(4):657–666. doi: 10.1176/appi.ajp.160.4.657. [DOI] [PubMed] [Google Scholar]
  35. Butt Yoki Kwok-Chu, Lum John Hon-Kei, Lo Samuel Chun-Lap. Proteomic identification of plant proteins probed by mammalian nitric oxide synthase antibodies. Planta. 2002 Nov 16;216(5):762–771. doi: 10.1007/s00425-002-0926-y. [DOI] [PubMed] [Google Scholar]
  36. Camon Evelyn, Magrane Michele, Barrell Daniel, Binns David, Fleischmann Wolfgang, Kersey Paul, Mulder Nicola, Oinn Tom, Maslen John, Cox Anthony. The Gene Ontology Annotation (GOA) project: implementation of GO in SWISS-PROT, TrEMBL, and InterPro. Genome Res. 2003 Mar 12;13(4):662–672. doi: 10.1101/gr.461403. [DOI] [PMC free article] [PubMed] [Google Scholar]
  37. Castrillo Juan I., Hayes Andrew, Mohammed Shabaz, Gaskell Simon J., Oliver Stephen G. An optimized protocol for metabolome analysis in yeast using direct infusion electrospray mass spectrometry. Phytochemistry. 2003 Mar;62(6):929–937. doi: 10.1016/s0031-9422(02)00713-6. [DOI] [PubMed] [Google Scholar]
  38. Chen Guoan, Gharib Tarek G., Thomas Dafydd G., Huang Chiang-Ching, Misek David E., Kuick Rork D., Giordano Thomas J., Iannettoni Mark D., Orringer Mark B., Hanash Samir M. Proteomic analysis of eIF-5A in lung adenocarcinomas. Proteomics. 2003 Apr;3(4):496–504. doi: 10.1002/pmic.200390063. [DOI] [PubMed] [Google Scholar]
  39. Chen Tianbao, Farragher Susan, Bjourson Anthony J., Orr David F., Rao Pingfan, Shaw Chris. Granular gland transcriptomes in stimulated amphibian skin secretions. Biochem J. 2003 Apr 1;371(Pt 1):125–130. doi: 10.1042/BJ20021343. [DOI] [PMC free article] [PubMed] [Google Scholar]
  40. Chinnusamy Viswanathan, Ohta Masaru, Kanrar Siddhartha, Lee Byeong-Ha, Hong Xuhui, Agarwal Manu, Zhu Jian-Kang. ICE1: a regulator of cold-induced transcriptome and freezing tolerance in Arabidopsis. Genes Dev. 2003 Apr 2;17(8):1043–1054. doi: 10.1101/gad.1077503. [DOI] [PMC free article] [PubMed] [Google Scholar]
  41. Chou Kuo-Chen, Elrod David W. Prediction of enzyme family classes. J Proteome Res. 2003 Mar-Apr;2(2):183–190. doi: 10.1021/pr0255710. [DOI] [PubMed] [Google Scholar]
  42. Chowdhary Bhanu P., Raudsepp Terje, Kata Srinivas R., Goh Glenda, Millon Lee V., Allan Veronica, Piumi François, Guérin Gérard, Swinburne June, Binns Matthew. The first-generation whole-genome radiation hybrid map in the horse identifies conserved segments in human and mouse genomes. Genome Res. 2003 Apr;13(4):742–751. doi: 10.1101/gr.917503. [DOI] [PMC free article] [PubMed] [Google Scholar]
  43. Claverie Jean-Michel, Monchois Vincent, Audic Stéphane, Poirot Olivier, Abergel Chantal. In Ssarch of new anti-bacterial target genes: a comparative/structural genomics approach. Comb Chem High Throughput Screen. 2002 Nov;5(7):511–522. doi: 10.2174/1386207023330002. [DOI] [PubMed] [Google Scholar]
  44. Cohen Georges N., Barbe Valérie, Flament Didier, Galperin Michael, Heilig Roland, Lecompte Odile, Poch Olivier, Prieur Daniel, Quérellou Joël, Ripp Raymond. An integrated analysis of the genome of the hyperthermophilic archaeon Pyrococcus abyssi. Mol Microbiol. 2003 Mar;47(6):1495–1512. doi: 10.1046/j.1365-2958.2003.03381.x. [DOI] [PubMed] [Google Scholar]
  45. Collins Francis S., Green Eric D., Guttmacher Alan E., Guyer Mark S., US National Human Genome Research Institute A vision for the future of genomics research. Nature. 2003 Apr 14;422(6934):835–847. doi: 10.1038/nature01626. [DOI] [PubMed] [Google Scholar]
  46. Conlon Erin M., Liu X. Shirley, Lieb Jason D., Liu Jun S. Integrating regulatory motif discovery and genome-wide expression analysis. Proc Natl Acad Sci U S A. 2003 Mar 7;100(6):3339–3344. doi: 10.1073/pnas.0630591100. [DOI] [PMC free article] [PubMed] [Google Scholar]
  47. Cutler Paul, Heald Geoffrey, White Ian R., Ruan Jason. A novel approach to spot detection for two-dimensional gel electrophoresis images using pixel value collection. Proteomics. 2003 Apr;3(4):392–401. doi: 10.1002/pmic.200390054. [DOI] [PubMed] [Google Scholar]
  48. Datta Susmita, Datta Somnath. Comparisons and validation of statistical clustering techniques for microarray gene expression data. Bioinformatics. 2003 Mar 1;19(4):459–466. doi: 10.1093/bioinformatics/btg025. [DOI] [PubMed] [Google Scholar]
  49. Delseny Michel. Towards an accurate sequence of the rice genome. Curr Opin Plant Biol. 2003 Apr;6(2):101–105. doi: 10.1016/s1369-5266(03)00010-4. [DOI] [PubMed] [Google Scholar]
  50. Deng Wen, Liou Shian-Ren, Plunkett Guy, 3rd, Mayhew George F., Rose Debra J., Burland Valerie, Kodoyianni Voula, Schwartz David C., Blattner Frederick R. Comparative genomics of Salmonella enterica serovar Typhi strains Ty2 and CT18. J Bacteriol. 2003 Apr;185(7):2330–2337. doi: 10.1128/JB.185.7.2330-2337.2003. [DOI] [PMC free article] [PubMed] [Google Scholar]
  51. Di Giovanni Simone, Knoblach Susan M., Brandoli Cinzia, Aden Sadia A., Hoffman Eric P., Faden Alan I. Gene profiling in spinal cord injury shows role of cell cycle in neuronal death. Ann Neurol. 2003 Apr;53(4):454–468. doi: 10.1002/ana.10472. [DOI] [PubMed] [Google Scholar]
  52. Ding Chunming, Cantor Charles R. A high-throughput gene expression analysis technique using competitive PCR and matrix-assisted laser desorption ionization time-of-flight MS. Proc Natl Acad Sci U S A. 2003 Mar 6;100(6):3059–3064. doi: 10.1073/pnas.0630494100. [DOI] [PMC free article] [PubMed] [Google Scholar]
  53. Dobrindt Ulrich, Agerer Franziska, Michaelis Kai, Janka Andreas, Buchrieser Carmen, Samuelson Martin, Svanborg Catharina, Gottschalk Gerhard, Karch Helge, Hacker Jörg. Analysis of genome plasticity in pathogenic and commensal Escherichia coli isolates by use of DNA arrays. J Bacteriol. 2003 Mar;185(6):1831–1840. doi: 10.1128/JB.185.6.1831-1840.2003. [DOI] [PMC free article] [PubMed] [Google Scholar]
  54. Dores Robert M., Lecaudé Stéphanie, Bauer David, Danielson Phillip B. Analyzing the evolution of the opioid/orphanin gene family. Mass Spectrom Rev. 2002 Jul-Aug;21(4):220–243. doi: 10.1002/mas.10029. [DOI] [PubMed] [Google Scholar]
  55. Dumke Roger, Catrein Ina, Pirkil Elsbeth, Herrmann Richard, Jacobs Enno. Subtyping of Mycoplasma pneumoniae isolates based on extended genome sequencing and on expression profiles. Int J Med Microbiol. 2003 Feb;292(7-8):513–525. doi: 10.1078/1438-4221-00231. [DOI] [PubMed] [Google Scholar]
  56. Dumur Catherine I., Dechsukhum Chavaboon, Ware Joy L., Cofield Stacey S., Best Al M., Wilkinson David S., Garrett Carleton T., Ferreira-Gonzalez Andrea. Genome-wide detection of LOH in prostate cancer using human SNP microarray technology. Genomics. 2003 Mar;81(3):260–269. doi: 10.1016/s0888-7543(03)00020-x. [DOI] [PubMed] [Google Scholar]
  57. Dwyer Donard S., Ardizzone Timothy D. Mimicry of dimerization by synthetic peptides designed to target homologous regions of proteins. Proteomics. 2003 Mar;3(3):317–324. doi: 10.1002/pmic.200390045. [DOI] [PubMed] [Google Scholar]
  58. Edvardsson Ulrika, von Löwenhielm Helena Brockenhuus, Panfilov Oleg, Nyström Ann-Christin, Nilsson Fredrik, Dahllöf Björn. Hepatic protein expression of lean mice and obese diabetic mice treated with peroxisome proliferator-activated receptor activators. Proteomics. 2003 Apr;3(4):468–478. doi: 10.1002/pmic.200390061. [DOI] [PubMed] [Google Scholar]
  59. Emes Richard D., Goodstadt Leo, Winter Eitan E., Ponting Chris P. Comparison of the genomes of human and mouse lays the foundation of genome zoology. Hum Mol Genet. 2003 Apr 1;12(7):701–709. doi: 10.1093/hmg/ddg078. [DOI] [PubMed] [Google Scholar]
  60. Ermolaeva Maria D., Wu Martin, Eisen Jonathan A., Salzberg Steven L. The age of the Arabidopsis thaliana genome duplication. Plant Mol Biol. 2003 Apr;51(6):859–866. doi: 10.1023/a:1023001130337. [DOI] [PubMed] [Google Scholar]
  61. Frank Ronald. High-density synthetic peptide microarrays: emerging tools for functional genomics and proteomics. Comb Chem High Throughput Screen. 2002 Sep;5(6):429–440. doi: 10.2174/1386207023330165. [DOI] [PubMed] [Google Scholar]
  62. Fu Glenn K., Stuve Laura L. Construction of cDNA libraries for highly efficient DNA sequencing from the 3' end of expressed genes. Biotechniques. 2003 Apr;34(4):758-62, 764, 766. doi: 10.2144/03344st05. [DOI] [PubMed] [Google Scholar]
  63. Galagan James E., Calvo Sarah E., Borkovich Katherine A., Selker Eric U., Read Nick D., Jaffe David, FitzHugh William, Ma Li-Jun, Smirnov Serge, Purcell Seth. The genome sequence of the filamentous fungus Neurospora crassa. Nature. 2003 Apr 24;422(6934):859–868. doi: 10.1038/nature01554. [DOI] [PubMed] [Google Scholar]
  64. Galeva Nadezhda, Yakovlev Dmitry, Koen Yakov, Duzhak Tatyana, Alterman Michail. Direct identification of cytochrome P450 isozymes by matrix-assisted laser desorption/ionization time of flight-based proteomic approach. Drug Metab Dispos. 2003 Apr;31(4):351–355. doi: 10.1124/dmd.31.4.351. [DOI] [PubMed] [Google Scholar]
  65. Galibert Francis, André Catherine. Le génome du chien: un modèle alternatif pour l'analyse fonctionnelle des gènes de mammifères. Bull Acad Natl Med. 2002;186(8):1489–1502. [PubMed] [Google Scholar]
  66. García de la Nava Jorge, Santaella Daniel Franco, Cuenca Alba Jesús, María Carazo José, Trelles Oswaldo, Pascual-Montano Alberto. Engene: the processing and exploratory analysis of gene expression data. Bioinformatics. 2003 Mar 22;19(5):657–658. doi: 10.1093/bioinformatics/btg028. [DOI] [PubMed] [Google Scholar]
  67. Garry Robert F., Dash Srikanta. Proteomics computational analyses suggest that hepatitis C virus E1 and pestivirus E2 envelope glycoproteins are truncated class II fusion proteins. Virology. 2003 Mar 15;307(2):255–265. doi: 10.1016/s0042-6822(02)00065-x. [DOI] [PubMed] [Google Scholar]
  68. Geoffroy Marie-Claude, Floquet Stéphanie, Métais Arnaud, Nassif Xavier, Pelicic Vladimir. Large-scale analysis of the meningococcus genome by gene disruption: resistance to complement-mediated lysis. Genome Res. 2003 Mar;13(3):391–398. doi: 10.1101/gr.664303. [DOI] [PMC free article] [PubMed] [Google Scholar]
  69. Georgi Laura L., Wang Ying, Reighard Gregory L., Mao Long, Wing Rod A., Abbott Albert G. Comparison of peach and Arabidopsis genomic sequences: fragmentary conservation of gene neighborhoods. Genome. 2003 Apr;46(2):268–276. doi: 10.1139/g03-004. [DOI] [PubMed] [Google Scholar]
  70. Geschwind Daniel H. DNA microarrays: translation of the genome from laboratory to clinic. Lancet Neurol. 2003 May;2(5):275–282. doi: 10.1016/s1474-4422(03)00379-x. [DOI] [PubMed] [Google Scholar]
  71. Giardine Belinda, Elnitski Laura, Riemer Cathy, Makalowska Izabela, Schwartz Scott, Miller Webb, Hardison Ross C. GALA, a database for genomic sequence alignments and annotations. Genome Res. 2003 Apr;13(4):732–741. doi: 10.1101/gr.603103. [DOI] [PMC free article] [PubMed] [Google Scholar]
  72. Gnatenko Dmitri V., Dunn John J., McCorkle Sean R., Weissmann David, Perrotta Peter L., Bahou Wadie F. Transcript profiling of human platelets using microarray and serial analysis of gene expression. Blood. 2002 Nov 14;101(6):2285–2293. doi: 10.1182/blood-2002-09-2797. [DOI] [PubMed] [Google Scholar]
  73. Gonzalez Ramon, Tao Han, Purvis J. E., York S. W., Shanmugam K. T., Ingram L. O. Gene array-based identification of changes that contribute to ethanol tolerance in ethanologenic Escherichia coli: comparison of KO11 (parent) to LY01 (resistant mutant). Biotechnol Prog. 2003 Mar-Apr;19(2):612–623. doi: 10.1021/bp025658q. [DOI] [PubMed] [Google Scholar]
  74. Goshe Michael B., Blonder Josip, Smith Richard D. Affinity labeling of highly hydrophobic integral membrane proteins for proteome-wide analysis. J Proteome Res. 2003 Mar-Apr;2(2):153–161. doi: 10.1021/pr0255607. [DOI] [PubMed] [Google Scholar]
  75. Gotoh Koshichi, Oishi Michio. Screening of gene-associated polymorphisms by use of in-gel competitive reassociation and EST (cDNA) array hybridization. Genome Res. 2003 Mar;13(3):492–495. doi: 10.1101/gr.434103. [DOI] [PMC free article] [PubMed] [Google Scholar]
  76. Grant Barth D., Wilkinson Hilary A. Functional genomic maps in Caenorhabditis elegans. Curr Opin Cell Biol. 2003 Apr;15(2):206–212. doi: 10.1016/s0955-0674(03)00014-0. [DOI] [PubMed] [Google Scholar]
  77. Grate L. R., Bhattacharyya C., Jordan M. I., Mian I. S. Integrated analysis of transcript profiling and protein sequence data. Mech Ageing Dev. 2003 Jan;124(1):109–114. doi: 10.1016/s0047-6374(02)00174-4. [DOI] [PubMed] [Google Scholar]
  78. Guillot Alain, Gitton Christophe, Anglade Patricia, Mistou Michel-Yves. Proteomic analysis of Lactococcus lactis, a lactic acid bacterium. Proteomics. 2003 Mar;3(3):337–354. doi: 10.1002/pmic.200390047. [DOI] [PubMed] [Google Scholar]
  79. Guo Feng-Biao, Ou Hong-Yu, Zhang Chun-Ting. ZCURVE: a new system for recognizing protein-coding genes in bacterial and archaeal genomes. Nucleic Acids Res. 2003 Mar 15;31(6):1780–1789. doi: 10.1093/nar/gkg254. [DOI] [PMC free article] [PubMed] [Google Scholar]
  80. Gururaja T. L., Li W., Payan D. G., Anderson D. C. Utility of peptide-protein affinity complexes in proteomics: identification of interaction partners of a tumor suppressor peptide. J Pept Res. 2003 Apr;61(4):163–176. doi: 10.1034/j.1399-3011.2003.00044.x. [DOI] [PubMed] [Google Scholar]
  81. Hamdan Mahmoud, Righetti Pier Giorgio. Modern strategies for protein quantification in proteome analysis: advantages and limitations. Mass Spectrom Rev. 2002 Jul-Aug;21(4):287–302. doi: 10.1002/mas.10032. [DOI] [PubMed] [Google Scholar]
  82. Han Bin, Xue Yongbiao. Genome-wide intraspecific DNA-sequence variations in rice. Curr Opin Plant Biol. 2003 Apr;6(2):134–138. doi: 10.1016/s1369-5266(03)00004-9. [DOI] [PubMed] [Google Scholar]
  83. Havlis Jan, Thomas Henrik, Sebela Marek, Shevchenko Andrej. Fast-response proteomics by accelerated in-gel digestion of proteins. Anal Chem. 2003 Mar 15;75(6):1300–1306. doi: 10.1021/ac026136s. [DOI] [PubMed] [Google Scholar]
  84. Hecker Michael, Engelmann Susanne, Cordwell Stuart J. Proteomics of Staphylococcus aureus--current state and future challenges. J Chromatogr B Analyt Technol Biomed Life Sci. 2003 Apr 5;787(1):179–195. doi: 10.1016/s1570-0232(02)00907-8. [DOI] [PubMed] [Google Scholar]
  85. Heijne Wilbert H. M., Stierum Rob H., Slijper Monique, van Bladeren Peter J., van Ommen Ben. Toxicogenomics of bromobenzene hepatotoxicity: a combined transcriptomics and proteomics approach. Biochem Pharmacol. 2003 Mar 1;65(5):857–875. doi: 10.1016/s0006-2952(02)01613-1. [DOI] [PubMed] [Google Scholar]
  86. Heinemann Udo, Büssow Konrad, Mueller Uwe, Umbach Patrick. Facilities and methods for the high-throughput crystal structural analysis of human proteins. Acc Chem Res. 2003 Mar;36(3):157–163. doi: 10.1021/ar010129t. [DOI] [PubMed] [Google Scholar]
  87. Herrero J., Díaz-Uriarte R., Dopazo J. Gene expression data preprocessing. Bioinformatics. 2003 Mar 22;19(5):655–656. doi: 10.1093/bioinformatics/btg040. [DOI] [PubMed] [Google Scholar]
  88. Hikkel Imrich, Lucau-Danila Ancuta, Delaveau Thierry, Marc Philippe, Devaux Frédéric, Jacq Claude. A general strategy to uncover transcription factor properties identifies a new regulator of drug resistance in yeast. J Biol Chem. 2003 Jan 14;278(13):11427–11432. doi: 10.1074/jbc.M208549200. [DOI] [PubMed] [Google Scholar]
  89. Holme Petter, Huss Mikael, Jeong Hawoong. Subnetwork hierarchies of biochemical pathways. Bioinformatics. 2003 Mar 1;19(4):532–538. doi: 10.1093/bioinformatics/btg033. [DOI] [PubMed] [Google Scholar]
  90. Horn Carsten, Offen Nils, Nystedt Sverker, Häcker Udo, Wimmer Ernst A. piggyBac-based insertional mutagenesis and enhancer detection as a tool for functional insect genomics. Genetics. 2003 Feb;163(2):647–661. doi: 10.1093/genetics/163.2.647. [DOI] [PMC free article] [PubMed] [Google Scholar]
  91. Horner D. S., Pesole G. The estimation of relative site variability among aligned homologous protein sequences. Bioinformatics. 2003 Mar 22;19(5):600–606. doi: 10.1093/bioinformatics/btg063. [DOI] [PubMed] [Google Scholar]
  92. Huang Guewha Steven, Hong Meng-Yen, Liu Yung-Chuan. Incorporation of DNA chip technology to the simulation and validation of flux analysis in yeast diauxic growth. Life Sci. 2003 Apr 18;72(22):2525–2531. doi: 10.1016/s0024-3205(03)00138-3. [DOI] [PubMed] [Google Scholar]
  93. Huang Ruo-Pan. Protein arrays, an excellent tool in biomedical research. Front Biosci. 2003 May 1;8:d559–d576. doi: 10.2741/1017. [DOI] [PubMed] [Google Scholar]
  94. Hubálek Martin, Hernychová Lenka, Havlasová Jana, Kasalová Irena, Neubauerová Vera, Stulík Jirí, Macela Ales, Lundqvist Margaretha, Larsson Pär. Towards proteome database of Francisella tularensis. J Chromatogr B Analyt Technol Biomed Life Sci. 2003 Apr 5;787(1):149–177. doi: 10.1016/s1570-0232(02)00730-4. [DOI] [PubMed] [Google Scholar]
  95. Hwang Daehee, Alevizos Ilias, Schmitt William A., Misra Jatin, Ohyama Hiroe, Todd Randy, Mahadevappa Mamatha, Warrington Janet A., Stephanopoulos George, Wong David T. Genomic dissection for characterization of cancerous oral epithelium tissues using transcription profiling. Oral Oncol. 2003 Apr;39(3):259–268. doi: 10.1016/s1368-8375(02)00108-2. [DOI] [PubMed] [Google Scholar]
  96. Hynes Sean O., McGuire Jim, Falt Tobias, Wadström Torkel. The rapid detection of low molecular mass proteins differentially expressed under biological stress for four Helicobacter spp. using ProteinChip technology. Proteomics. 2003 Mar;3(3):273–278. doi: 10.1002/pmic.200390040. [DOI] [PubMed] [Google Scholar]
  97. Iacobuzio-Donahue Christine A., Maitra Anirban, Olsen Mari, Lowe Anson W., van Heek N. Tjarda, Rosty Christophe, Walter Kim, Sato Norihiro, Parker Antony, Ashfaq Raheela. Exploration of global gene expression patterns in pancreatic adenocarcinoma using cDNA microarrays. Am J Pathol. 2003 Apr;162(4):1151–1162. doi: 10.1016/S0002-9440(10)63911-9. [DOI] [PMC free article] [PubMed] [Google Scholar]
  98. Iliopoulos Ioannis, Tsoka Sophia, Andrade Miguel A., Enright Anton J., Carroll Mark, Poullet Patrick, Promponas Vassilis, Liakopoulos Theodore, Palaios Giorgos, Pasquier Claude. Evaluation of annotation strategies using an entire genome sequence. Bioinformatics. 2003 Apr 12;19(6):717–726. doi: 10.1093/bioinformatics/btg077. [DOI] [PubMed] [Google Scholar]
  99. Islam Nazrul, Tsujimoto Hisashi, Hirano Hisashi. Proteome analysis of diploid, tetraploid and hexaploid wheat: towards understanding genome interaction in protein expression. Proteomics. 2003 Apr;3(4):549–557. doi: 10.1002/pmic.200390068. [DOI] [PubMed] [Google Scholar]
  100. Islam Nazrul, Tsujimoto Hisashi, Hirano Hisashi. Wheat proteomics: relationship between fine chromosome deletion and protein expression. Proteomics. 2003 Mar;3(3):307–316. doi: 10.1002/pmic.200390044. [DOI] [PubMed] [Google Scholar]
  101. Izawa Takeshi, Takahashi Yuji, Yano Masahiro. Comparative biology comes into bloom: genomic and genetic comparison of flowering pathways in rice and Arabidopsis. Curr Opin Plant Biol. 2003 Apr;6(2):113–120. doi: 10.1016/s1369-5266(03)00014-1. [DOI] [PubMed] [Google Scholar]
  102. Jensen L. J., Gupta R., Staerfeldt H-H, Brunak S. Prediction of human protein function according to Gene Ontology categories. Bioinformatics. 2003 Mar 22;19(5):635–642. doi: 10.1093/bioinformatics/btg036. [DOI] [PubMed] [Google Scholar]
  103. Jewett Andrew I., Huang Conrad C., Ferrin Thomas E. MINRMS: an efficient algorithm for determining protein structure similarity using root-mean-squared-distance. Bioinformatics. 2003 Mar 22;19(5):625–634. doi: 10.1093/bioinformatics/btg035. [DOI] [PubMed] [Google Scholar]
  104. Jiang Yide, Zhang Wen, Kondo Keichii, Klco Jeffery M., St Martin Thia B., Dufault Michael R., Madden Stephen L., Kaelin William G., Jr, Nacht Mariana. Gene expression profiling in a renal cell carcinoma cell line: dissecting VHL and hypoxia-dependent pathways. Mol Cancer Res. 2003 Apr;1(6):453–462. [PubMed] [Google Scholar]
  105. Johansson Daniel, Lindgren Petter, Berglund Anders. A multivariate approach applied to microarray data for identification of genes with cell cycle-coupled transcription. Bioinformatics. 2003 Mar 1;19(4):467–473. doi: 10.1093/bioinformatics/btg017. [DOI] [PubMed] [Google Scholar]
  106. Jones Laurie J., Haugland Richard P., Singer Victoria L. Development and characterization of the NanoOrange protein quantitation assay: a fluorescence-based assay of proteins in solution. Biotechniques. 2003 Apr;34(4):850-4, 856, 858 passim. doi: 10.2144/03344pt03. [DOI] [PubMed] [Google Scholar]
  107. Kamme Fredrik, Erlander Mark G. Global gene expression analysis of single cells. Curr Opin Drug Discov Devel. 2003 Mar;6(2):231–236. [PubMed] [Google Scholar]
  108. Kanehisa Minoru, Bork Peer. Bioinformatics in the post-sequence era. Nat Genet. 2003 Mar;33 (Suppl):305–310. doi: 10.1038/ng1109. [DOI] [PubMed] [Google Scholar]
  109. Kasturi Jyotsna, Acharya Raj, Ramanathan Murali. An information theoretic approach for analyzing temporal patterns of gene expression. Bioinformatics. 2003 Mar 1;19(4):449–458. doi: 10.1093/bioinformatics/btg020. [DOI] [PubMed] [Google Scholar]
  110. Kawakami Takao, Nagata Takuya, Muraguchi Atsushi, Nishimura Toshihide. Proteomic approach to apoptotic thymus maturation. J Chromatogr B Analyt Technol Biomed Life Sci. 2003 Apr 5;787(1):223–229. doi: 10.1016/s1570-0232(02)00174-5. [DOI] [PubMed] [Google Scholar]
  111. Khan Arshad H., Ossadtchi Alex, Leahy Richard M., Smith Desmond J. Error-correcting microarray design. Genomics. 2003 Feb;81(2):157–165. doi: 10.1016/s0888-7543(02)00032-0. [DOI] [PubMed] [Google Scholar]
  112. Khodarev Nikolai N., Park James, Kataoka Yasushi, Nodzenski Edwardine, Hellman Samuel, Roizman Bernard, Weichselbaum Ralph R., Pelizzari Charles A. Receiver operating characteristic analysis: a general tool for DNA array data filtration and performance estimation. Genomics. 2003 Feb;81(2):202–209. doi: 10.1016/s0888-7543(02)00042-3. [DOI] [PubMed] [Google Scholar]
  113. Kiernan Urban A., Tubbs Kemmons A., Nedelkov Dobrin, Niederkofler Eric E., McConnell Elizabeth, Nelson Randall W. Comparative urine protein phenotyping using mass spectrometric immunoassay. J Proteome Res. 2003 Mar-Apr;2(2):191–197. doi: 10.1021/pr025574c. [DOI] [PubMed] [Google Scholar]
  114. Kikuchi Shinichi, Tominaga Daisuke, Arita Masanori, Takahashi Katsutoshi, Tomita Masaru. Dynamic modeling of genetic networks using genetic algorithm and S-system. Bioinformatics. 2003 Mar 22;19(5):643–650. doi: 10.1093/bioinformatics/btg027. [DOI] [PubMed] [Google Scholar]
  115. Kikuchi Takefumi, Daigo Yataro, Katagiri Toyomasa, Tsunoda Tatsuhiko, Okada Koichi, Kakiuchi Soji, Zembutsu Hitoshi, Furukawa Yoichi, Kawamura Masafumi, Kobayashi Koichi. Expression profiles of non-small cell lung cancers on cDNA microarrays: identification of genes for prediction of lymph-node metastasis and sensitivity to anti-cancer drugs. Oncogene. 2003 Apr 10;22(14):2192–2205. doi: 10.1038/sj.onc.1206288. [DOI] [PubMed] [Google Scholar]
  116. Kim Heenam, Snesrud Erik C., Haas Brian, Cheung Foo, Town Christopher D., Quackenbush John. Gene expression analyses of Arabidopsis chromosome 2 using a genomic DNA amplicon microarray. Genome Res. 2003 Mar;13(3):327–340. doi: 10.1101/gr.552003. [DOI] [PMC free article] [PubMed] [Google Scholar]
  117. Klapa Maria I., Aon Juan-Carlos, Stephanopoulos Gregory. Ion-trap mass spectrometry used in combination with gas chromatography for high-resolution metabolic flux determination. Biotechniques. 2003 Apr;34(4):832-6, 838, 840 passim. doi: 10.2144/03344pt02. [DOI] [PubMed] [Google Scholar]
  118. Kluger Yuval, Basri Ronen, Chang Joseph T., Gerstein Mark. Spectral biclustering of microarray data: coclustering genes and conditions. Genome Res. 2003 Apr;13(4):703–716. doi: 10.1101/gr.648603. [DOI] [PMC free article] [PubMed] [Google Scholar]
  119. Konishi Hirosato, Komatsu Setsuko. A proteomics approach to investigating promotive effects of brassinolide on lamina inclination and root growth in rice seedlings. Biol Pharm Bull. 2003 Apr;26(4):401–408. doi: 10.1248/bpb.26.401. [DOI] [PubMed] [Google Scholar]
  120. Kumar Yadunanda, Tatu Utpal. Stress protein flux during recovery from simulated ischemia: induced heat shock protein 70 confers cytoprotection by suppressing JNK activation and inhibiting apoptotic cell death. Proteomics. 2003 Apr;3(4):513–526. doi: 10.1002/pmic.200390065. [DOI] [PubMed] [Google Scholar]
  121. Kusnezow Wlad, Jacob Anette, Walijew Alexandra, Diehl Frank, Hoheisel Jörg D. Antibody microarrays: an evaluation of production parameters. Proteomics. 2003 Mar;3(3):254–264. doi: 10.1002/pmic.200390038. [DOI] [PubMed] [Google Scholar]
  122. Kyogoku Yoshimasa, Fujiyoshi Yoshinori, Shimada Ichio, Nakamura Haruki, Tsukihara Tomitake, Akutsu Hideo, Odahara Takayuki, Okada Tetsuji, Nomura Nobuo. Structural genomics of membrane proteins. Acc Chem Res. 2003 Mar;36(3):199–206. doi: 10.1021/ar0101279. [DOI] [PubMed] [Google Scholar]
  123. König Simone, Schmidt Oliver, Rose Karin, Thanos Solon, Besselmann Michael, Zeller Martin. Sodium dodecyl sulfate versus acid-labile surfactant gel electrophoresis: comparative proteomic studies on rat retina and mouse brain. Electrophoresis. 2003 Feb;24(4):751–756. doi: 10.1002/elps.200390090. [DOI] [PubMed] [Google Scholar]
  124. Lamé Michael W., Jones A. Daniel, Wilson Dennis W., Segall Hank J. Protein targets of 1,4-benzoquinone and 1,4-naphthoquinone in human bronchial epithelial cells. Proteomics. 2003 Apr;3(4):479–495. doi: 10.1002/pmic.200390062. [DOI] [PubMed] [Google Scholar]
  125. Lange B. Markus, Ghassemian Majid. Genome organization in Arabidopsis thaliana: a survey for genes involved in isoprenoid and chlorophyll metabolism. Plant Mol Biol. 2003 Apr;51(6):925–948. doi: 10.1023/a:1023005504702. [DOI] [PubMed] [Google Scholar]
  126. LeBlanc Michael, Kooperberg Charles, Grogan Thomas M., Miller Thomas P. Directed indices for exploring gene expression data. Bioinformatics. 2003 Apr 12;19(6):686–693. doi: 10.1093/bioinformatics/btg079. [DOI] [PubMed] [Google Scholar]
  127. Lee Jong-Min, Calkins Marcus J., Chan Kaimin, Kan Yuet Wai, Johnson Jeffrey A. Identification of the NF-E2-related factor-2-dependent genes conferring protection against oxidative stress in primary cortical astrocytes using oligonucleotide microarray analysis. J Biol Chem. 2003 Jan 28;278(14):12029–12038. doi: 10.1074/jbc.M211558200. [DOI] [PubMed] [Google Scholar]
  128. Lee Kyungjoon, Kohane Isaac S., Butte Atul J. PGAGENE: integrating quantitative gene-specific results from the NHLBI programs for genomic applications. Bioinformatics. 2003 Apr 12;19(6):778–779. doi: 10.1093/bioinformatics/btg066. [DOI] [PubMed] [Google Scholar]
  129. Lee M-K, Ren C. W., Yan B., Cox B., Zhang H-B, Romanov M. N., Sizemore F. G., Suchyta S. P., Peters E., Dodgson J. B. Construction and characterization of three BAC libraries for analysis of the chicken genome. Anim Genet. 2003 Apr;34(2):151–152. doi: 10.1046/j.1365-2052.2003.00965_5.x. [DOI] [PubMed] [Google Scholar]
  130. Lee Samuel A., Wormsley Steven, Kamoun Sophien, Lee Austin F. S., Joiner Keith, Wong Brian. An analysis of the Candida albicans genome database for soluble secreted proteins using computer-based prediction algorithms. Yeast. 2003 May;20(7):595–610. doi: 10.1002/yea.988. [DOI] [PubMed] [Google Scholar]
  131. Levit-Binnun Nava, Lindner Ariel B., Zik Ory, Eshhar Zelig, Moses Elisha. Quantitative detection of protein arrays. Anal Chem. 2003 Mar 15;75(6):1436–1441. doi: 10.1021/ac0261350. [DOI] [PubMed] [Google Scholar]
  132. Li Li, Brunk Brian P., Kissinger Jessica C., Pape Deana, Tang Keliang, Cole Robert H., Martin John, Wylie Todd, Dante Mike, Fogarty Steven J. Gene discovery in the apicomplexa as revealed by EST sequencing and assembly of a comparative gene database. Genome Res. 2003 Mar;13(3):443–454. doi: 10.1101/gr.693203. [DOI] [PMC free article] [PubMed] [Google Scholar]
  133. Li Nan, Mak Allan, Richards Dawn P., Naber Claudia, Keller Bernd O., Li Liang, Shaw Andrew R. E. Monocyte lipid rafts contain proteins implicated in vesicular trafficking and phagosome formation. Proteomics. 2003 Apr;3(4):536–548. doi: 10.1002/pmic.200390067. [DOI] [PubMed] [Google Scholar]
  134. Lifanov Alexander P., Makeev Vsevolod J., Nazina Anna G., Papatsenko Dmitri A. Homotypic regulatory clusters in Drosophila. Genome Res. 2003 Apr;13(4):579–588. doi: 10.1101/gr.668403. [DOI] [PMC free article] [PubMed] [Google Scholar]
  135. Liu Gui-Rong, Edwards Kelly, Eisenstark Abraham, Fu Ying-Mei, Liu Wei-Qiao, Sanderson Kenneth E., Johnston Randal N., Liu Shu-Lin. Genomic diversification among archival strains of Salmonella enterica serovar typhimurium LT7. J Bacteriol. 2003 Apr;185(7):2131–2142. doi: 10.1128/JB.185.7.2131-2142.2003. [DOI] [PMC free article] [PubMed] [Google Scholar]
  136. Liu Lian-Xin, Liu Zhi-Hua, Jiang Hong-Chi, Zhang Wei-Hui, Qi Shu-Yi, Hu Jie, Wang Xiu-Qin, Wu Min. Gene expression profiles of hepatoma cell line HLE. World J Gastroenterol. 2003 Apr;9(4):683–687. doi: 10.3748/wjg.v9.i4.683. [DOI] [PMC free article] [PubMed] [Google Scholar]
  137. Liu Yongqing, Zhou Jizhong, Omelchenko Marina V., Beliaev Alex S., Venkateswaran Amudhan, Stair Julia, Wu Liyou, Thompson Dorothea K., Xu Dong, Rogozin Igor B. Transcriptome dynamics of Deinococcus radiodurans recovering from ionizing radiation. Proc Natl Acad Sci U S A. 2003 Mar 21;100(7):4191–4196. doi: 10.1073/pnas.0630387100. [DOI] [PMC free article] [PubMed] [Google Scholar]
  138. Lo Jane, Lee Sorcheng, Xu Min, Liu Feng, Ruan Hua, Eun Alvin, He Yawen, Ma Weiping, Wang Weefuen, Wen Zilong. 15000 unique zebrafish EST clusters and their future use in microarray for profiling gene expression patterns during embryogenesis. Genome Res. 2003 Mar;13(3):455–466. doi: 10.1101/gr.885403. [DOI] [PMC free article] [PubMed] [Google Scholar]
  139. Lopez Frédéric, Pichereaux Carole, Burlet-Schiltz Odile, Pradayrol Lucien, Monsarrat Bernard, Estève Jean-Pierre. Improved sensitivity of biomolecular interaction analysis mass spectrometry for the identification of interacting molecules. Proteomics. 2003 Apr;3(4):402–412. doi: 10.1002/pmic.200390055. [DOI] [PubMed] [Google Scholar]
  140. Luan Yihui, Li Hongzhe. Clustering of time-course gene expression data using a mixed-effects model with B-splines. Bioinformatics. 2003 Mar 1;19(4):474–482. doi: 10.1093/bioinformatics/btg014. [DOI] [PubMed] [Google Scholar]
  141. Luche Sylvie, Santoni Véronique, Rabilloud Thierry. Evaluation of nonionic and zwitterionic detergents as membrane protein solubilizers in two-dimensional electrophoresis. Proteomics. 2003 Mar;3(3):249–253. doi: 10.1002/pmic.200390037. [DOI] [PubMed] [Google Scholar]
  142. Lupi Alessandro, Messana Irene, Denotti Gloria, Schininà Maria Eugenia, Gambarini Gianluca, Fadda Maria Benedetta, Vitali Alberto, Cabras Tiziana, Piras Vincenzo, Patamia Maria. Identification of the human salivary cystatin complex by the coupling of high-performance liquid chromatography and ion-trap mass spectrometry. Proteomics. 2003 Apr;3(4):461–467. doi: 10.1002/pmic.200390060. [DOI] [PubMed] [Google Scholar]
  143. Lyons-Weiler James, Patel Satish, Bhattacharya Soumyaroop. A classification-based machine learning approach for the analysis of genome-wide expression data. Genome Res. 2003 Mar;13(3):503–512. doi: 10.1101/gr.104003. [DOI] [PMC free article] [PubMed] [Google Scholar]
  144. Mannhaupt Gertrud, Montrone Corinna, Haase Dirk, Mewes H. Werner, Aign Verena, Hoheisel Jörg D., Fartmann Berthold, Nyakatura Gerald, Kempken Frank, Maier Josef. What's in the genome of a filamentous fungus? Analysis of the Neurospora genome sequence. Nucleic Acids Res. 2003 Apr 1;31(7):1944–1954. doi: 10.1093/nar/gkg293. [DOI] [PMC free article] [PubMed] [Google Scholar]
  145. Marín Ignacio. Evolution of chromatin-remodeling complexes: comparative genomics reveals the ancient origin of "novel" compensasome genes. J Mol Evol. 2003 May;56(5):527–539. doi: 10.1007/s00239-002-2422-1. [DOI] [PubMed] [Google Scholar]
  146. Masseroli M., Cerveri P., Pelicci P. G., Alcalay M. GAAS: gene array analyzer software for management, analysis and visualization of gene expression data. Bioinformatics. 2003 Apr 12;19(6):774–775. doi: 10.1093/bioinformatics/btg071. [DOI] [PubMed] [Google Scholar]
  147. Massey Steven E., Moura Gabriela, Beltrão Pedro, Almeida Ricardo, Garey James R., Tuite Mick F., Santos Manuel A. S. Comparative evolutionary genomics unveils the molecular mechanism of reassignment of the CTG codon in Candida spp. Genome Res. 2003 Apr;13(4):544–557. doi: 10.1101/gr.811003. [DOI] [PMC free article] [PubMed] [Google Scholar]
  148. Matsui Hiroshi, Suzuki Kazuhiro, Hasumi Masaru, Koike Hidekazu, Okugi Hironobu, Nakazato Haruki, Yamanaka Hidetoshi. Gene expression profiles of human BPH (II): Optimization of laser-capture microdissection and utilization of cDNA microarray. Anticancer Res. 2003 Jan-Feb;23(1A):195–200. [PubMed] [Google Scholar]
  149. Matthiesen R., Lundsgaard M., Welinder K. G., Bauw G. Interpreting peptide mass spectra by VEMS. Bioinformatics. 2003 Apr 12;19(6):792–793. doi: 10.1093/bioinformatics/btg059. [DOI] [PubMed] [Google Scholar]
  150. Meyer Folker, Goesmann Alexander, McHardy Alice C., Bartels Daniela, Bekel Thomas, Clausen Jörn, Kalinowski Jörn, Linke Burkhard, Rupp Oliver, Giegerich Robert. GenDB--an open source genome annotation system for prokaryote genomes. Nucleic Acids Res. 2003 Apr 15;31(8):2187–2195. doi: 10.1093/nar/gkg312. [DOI] [PMC free article] [PubMed] [Google Scholar]
  151. Michaut Lydia, Flister Susanne, Neeb Martin, White Kevin P., Certa Ulrich, Gehring Walter J. Analysis of the eye developmental pathway in Drosophila using DNA microarrays. Proc Natl Acad Sci U S A. 2003 Mar 24;100(7):4024–4029. doi: 10.1073/pnas.0630561100. [DOI] [PMC free article] [PubMed] [Google Scholar]
  152. Migliaccio S., Marino M. Estrogens and estrogen receptors: new actors in the plot of transcriptional regulation of genomic responses. Calcif Tissue Int. 2003 Jan 15;72(3):181–182. doi: 10.1007/s00223-002-1042-5. [DOI] [PubMed] [Google Scholar]
  153. Miller Raymond D., Duan Shenghui, Lovins Elizabeth G., Kloss Ellen F., Kwok Pui-Yan. Efficient high-throughput resequencing of genomic DNA. Genome Res. 2003 Mar 12;13(4):717–720. doi: 10.1101/gr.886203. [DOI] [PMC free article] [PubMed] [Google Scholar]
  154. Milohanic Eliane, Glaser Philippe, Coppée Jean-Yves, Frangeul Lionel, Vega Yolanda, Vázquez-Boland José A., Kunst Frank, Cossart Pascale, Buchrieser Carmen. Transcriptome analysis of Listeria monocytogenes identifies three groups of genes differently regulated by PrfA. Mol Microbiol. 2003 Mar;47(6):1613–1625. doi: 10.1046/j.1365-2958.2003.03413.x. [DOI] [PubMed] [Google Scholar]
  155. Mischel Paul S., Shai Ruty, Shi Tao, Horvath Steve, Lu Kan V., Choe Gheeyoung, Seligson David, Kremen Thomas J., Palotie Aarno, Liau Linda M. Identification of molecular subtypes of glioblastoma by gene expression profiling. Oncogene. 2003 Apr 17;22(15):2361–2373. doi: 10.1038/sj.onc.1206344. [DOI] [PubMed] [Google Scholar]
  156. Molle Virginie, Nakaura Yoshiko, Shivers Robert P., Yamaguchi Hirotake, Losick Richard, Fujita Yasutaro, Sonenshein Abraham L. Additional targets of the Bacillus subtilis global regulator CodY identified by chromatin immunoprecipitation and genome-wide transcript analysis. J Bacteriol. 2003 Mar;185(6):1911–1922. doi: 10.1128/JB.185.6.1911-1922.2003. [DOI] [PMC free article] [PubMed] [Google Scholar]
  157. Morelle Sandrine, Carbonnelle Etienne, Nassif Xavier. The REP2 repeats of the genome of Neisseria meningitidis are associated with genes coordinately regulated during bacterial cell interaction. J Bacteriol. 2003 Apr;185(8):2618–2627. doi: 10.1128/JB.185.8.2618-2627.2003. [DOI] [PMC free article] [PubMed] [Google Scholar]
  158. Musgrave David, Zhang Xiaoying, Dinger Marcel. Archaeal genome organization and stress responses: implications for the origin and evolution of cellular life. Astrobiology. 2002 Fall;2(3):241–253. doi: 10.1089/153110702762027835. [DOI] [PubMed] [Google Scholar]
  159. Mîinea Cristinel P., Lienhard Gustav E. Stoichiometry of site-specific protein phosphorylation estimated with phosphopeptide-specific antibodies. Biotechniques. 2003 Apr;34(4):828–831. doi: 10.2144/03344pt01. [DOI] [PubMed] [Google Scholar]
  160. Nakajima Futoshi, Nishimori Hidefumi, Hata Fumitake, Yasoshima Takahiro, Nomura Hiroki, Tanaka Hiroshi, Ohno Keisuke, Yanai Yoshiyuki, Kamiguchi Kenjiro, Sato Noriyuki. Gene expression screening using a cDNA macroarray to clarify the mechanisms of peritoneal dissemination of pancreatic cancer. Surg Today. 2003;33(3):190–195. doi: 10.1007/s005950300042. [DOI] [PubMed] [Google Scholar]
  161. Nandi Tannistha, Dash Debasis, Ghai Rohit, B-Rao Chandrika, Kannan K., Brahmachari Samir K., Ramakrishnan C., Ramachandran Srinivasan. A novel complexity measure for comparative analysis of protein sequences from complete genomes. J Biomol Struct Dyn. 2003 Apr;20(5):657–668. doi: 10.1080/07391102.2003.10506882. [DOI] [PubMed] [Google Scholar]
  162. Nicolls Mark R., D'Antonio Jason M., Hutton John C., Gill Ronald G., Czwornog Jennifer L., Duncan Mark W. Proteomics as a tool for discovery: proteins implicated in Alzheimer's disease are highly expressed in normal pancreatic islets. J Proteome Res. 2003 Mar-Apr;2(2):199–205. doi: 10.1021/pr025576x. [DOI] [PubMed] [Google Scholar]
  163. Nishiyama Nobuhiro, Koizumi Fumiaki, Okazaki Soichiro, Matsumura Yasuhiro, Nishio Kazuto, Kataoka Kazunori. Differential gene expression profile between PC-14 cells treated with free cisplatin and cisplatin-incorporated polymeric micelles. Bioconjug Chem. 2003 Mar-Apr;14(2):449–457. doi: 10.1021/bc025555t. [DOI] [PubMed] [Google Scholar]
  164. Nunes Luiz R., Rosato Yoko B., Muto Nair H., Yanai Giane M., da Silva Vivian S., Leite Daniela B., Gonçalves Edmilson R., de Souza Alessandra A., Coletta-Filho Helvécio D., Machado Marcos A. Microarray analyses of Xylella fastidiosa provide evidence of coordinated transcription control of laterally transferred elements. Genome Res. 2003 Apr;13(4):570–578. doi: 10.1101/gr.930803. [DOI] [PMC free article] [PubMed] [Google Scholar]
  165. O'Connell Brenda C., Cheung Ann F., Simkevich Carl P., Tam Wanny, Ren Xiaojia, Mateyak Maria K., Sedivy John M. A large scale genetic analysis of c-Myc-regulated gene expression patterns. J Biol Chem. 2003 Jan 14;278(14):12563–12573. doi: 10.1074/jbc.M210462200. [DOI] [PubMed] [Google Scholar]
  166. Ogihara Yasunari, Mochida Keiichi, Nemoto Yasue, Murai Koji, Yamazaki Yukiko, Shin-I Tadasu, Kohara Yuji. Correlated clustering and virtual display of gene expression patterns in the wheat life cycle by large-scale statistical analyses of expressed sequence tags. Plant J. 2003 Mar;33(6):1001–1011. doi: 10.1046/j.1365-313x.2003.01687.x. [DOI] [PubMed] [Google Scholar]
  167. Ojaimi Caroline, Brooks Chad, Casjens Sherwood, Rosa Patricia, Elias Abdallah, Barbour Alan, Jasinskas Algis, Benach Jorge, Katona Laura, Radolf Justin. Profiling of temperature-induced changes in Borrelia burgdorferi gene expression by using whole genome arrays. Infect Immun. 2003 Apr;71(4):1689–1705. doi: 10.1128/IAI.71.4.1689-1705.2003. [DOI] [PMC free article] [PubMed] [Google Scholar]
  168. Ong Shao-En, Foster Leonard J., Mann Matthias. Mass spectrometric-based approaches in quantitative proteomics. Methods. 2003 Feb;29(2):124–130. doi: 10.1016/s1046-2023(02)00303-1. [DOI] [PubMed] [Google Scholar]
  169. Pagé Nicolas, Gérard-Vincent Manon, Ménard Patrice, Beaulieu Maude, Azuma Masayuki, Dijkgraaf Gerrit J. P., Li Huijuan, Marcoux José, Nguyen Thuy, Dowse Tim. A Saccharomyces cerevisiae genome-wide mutant screen for altered sensitivity to K1 killer toxin. Genetics. 2003 Mar;163(3):875–894. doi: 10.1093/genetics/163.3.875. [DOI] [PMC free article] [PubMed] [Google Scholar]
  170. Pan Songqin, Gu Sheng, Bradbury E. Morton, Chen Xian. Single peptide-based protein identification in human proteome through MALDI-TOF MS coupled with amino acids coded mass tagging. Anal Chem. 2003 Mar 15;75(6):1316–1324. doi: 10.1021/ac020482s. [DOI] [PubMed] [Google Scholar]
  171. Park Taesung, Yi Sung-Gon, Lee Seungmook, Lee Seung Yeoun, Yoo Dong-Hyun, Ahn Jun-Ik, Lee Yong-Sung. Statistical tests for identifying differentially expressed genes in time-course microarray experiments. Bioinformatics. 2003 Apr 12;19(6):694–703. doi: 10.1093/bioinformatics/btg068. [DOI] [PubMed] [Google Scholar]
  172. Patterson Scott D., Aebersold Ruedi H. Proteomics: the first decade and beyond. Nat Genet. 2003 Mar;33 (Suppl):311–323. doi: 10.1038/ng1106. [DOI] [PubMed] [Google Scholar]
  173. Pepe Margaret Sullivan, Longton Gary, Anderson Garnet L., Schummer Michel. Selecting differentially expressed genes from microarray experiments. Biometrics. 2003 Mar;59(1):133–142. doi: 10.1111/1541-0420.00016. [DOI] [PubMed] [Google Scholar]
  174. Peregrin-Alvarez José Manuel, Tsoka Sophia, Ouzounis Christos A. The phylogenetic extent of metabolic enzymes and pathways. Genome Res. 2003 Mar;13(3):422–427. doi: 10.1101/gr.246903. [DOI] [PMC free article] [PubMed] [Google Scholar]
  175. Pertea Geo, Huang Xiaoqiu, Liang Feng, Antonescu Valentin, Sultana Razvan, Karamycheva Svetlana, Lee Yuandan, White Joseph, Cheung Foo, Parvizi Babak. TIGR Gene Indices clustering tools (TGICL): a software system for fast clustering of large EST datasets. Bioinformatics. 2003 Mar 22;19(5):651–652. doi: 10.1093/bioinformatics/btg034. [DOI] [PubMed] [Google Scholar]
  176. Peters Joseph E., Thate Timothy E., Craig Nancy L. Definition of the Escherichia coli MC4100 genome by use of a DNA array. J Bacteriol. 2003 Mar;185(6):2017–2021. doi: 10.1128/JB.185.6.2017-2021.2003. [DOI] [PMC free article] [PubMed] [Google Scholar]
  177. Philip-Couderc Pierre, Smih Fatima, Pelat Michel, Vidal Cyril, Verwaerde Patrick, Pathak Atul, Buys Sophie, Galinier Michel, Senard Jean-Michel, Rouet Philippe. Cardiac transcriptome analysis in obesity-related hypertension. Hypertension. 2003 Feb 24;41(3):414–421. doi: 10.1161/01.HYP.0000057573.32425.95. [DOI] [PubMed] [Google Scholar]
  178. Pieper Rembert, Su Qin, Gatlin Christine L., Huang Shih-Ting, Anderson N. Leigh, Steiner Sandra. Multi-component immunoaffinity subtraction chromatography: an innovative step towards a comprehensive survey of the human plasma proteome. Proteomics. 2003 Apr;3(4):422–432. doi: 10.1002/pmic.200390057. [DOI] [PubMed] [Google Scholar]
  179. Pitarch Aida, Sánchez Miguel, Nombela César, Gil Concha. Analysis of the Candida albicans proteome. I. Strategies and applications. J Chromatogr B Analyt Technol Biomed Life Sci. 2003 Apr 5;787(1):101–128. doi: 10.1016/s1570-0232(02)00761-4. [DOI] [PubMed] [Google Scholar]
  180. Pitarch Aida, Sánchez Miguel, Nombela César, Gil Concha. Analysis of the Candida albicans proteome. II. Protein information technology on the Net (update 2002). J Chromatogr B Analyt Technol Biomed Life Sci. 2003 Apr 5;787(1):129–148. doi: 10.1016/s1570-0232(02)00762-6. [DOI] [PubMed] [Google Scholar]
  181. Piñeiro C., Barros-Velázquez J., Vázquez J., Figueras A., Gallardo J. M. Proteomics as a tool for the investigation of seafood and other marine products. J Proteome Res. 2003 Mar-Apr;2(2):127–135. doi: 10.1021/pr0200083. [DOI] [PubMed] [Google Scholar]
  182. Plant J. C., Percy I., Bates T., Gastard J., de Nercy Y. H. Incidence of gallbladder disease in Canada, England, and France. Lancet. 1973 Aug 4;2(7823):249–251. doi: 10.1016/s0140-6736(73)93148-6. [DOI] [PubMed] [Google Scholar]
  183. Polen T., Rittmann D., Wendisch V. F., Sahm H. DNA microarray analyses of the long-term adaptive response of Escherichia coli to acetate and propionate. Appl Environ Microbiol. 2003 Mar;69(3):1759–1774. doi: 10.1128/AEM.69.3.1759-1774.2003. [DOI] [PMC free article] [PubMed] [Google Scholar]
  184. Porwollik Steffen, Frye Jonathan, Florea Liliana D., Blackmer Felisa, McClelland Michael. A non-redundant microarray of genes for two related bacteria. Nucleic Acids Res. 2003 Apr 1;31(7):1869–1876. doi: 10.1093/nar/gkg298. [DOI] [PMC free article] [PubMed] [Google Scholar]
  185. Presting Gernot G. Mapping multiple co-sequenced T-DNA integration sites within the Arabidopsis genome. Bioinformatics. 2003 Mar 22;19(5):579–586. doi: 10.1093/bioinformatics/btg049. [DOI] [PubMed] [Google Scholar]
  186. Read T. D., Myers G. S. A., Brunham R. C., Nelson W. C., Paulsen I. T., Heidelberg J., Holtzapple E., Khouri H., Federova N. B., Carty H. A. Genome sequence of Chlamydophila caviae (Chlamydia psittaci GPIC): examining the role of niche-specific genes in the evolution of the Chlamydiaceae. Nucleic Acids Res. 2003 Apr 15;31(8):2134–2147. doi: 10.1093/nar/gkg321. [DOI] [PMC free article] [PubMed] [Google Scholar]
  187. Regelmann Jochen, Schüle Thomas, Josupeit Frank S., Horak Jaroslav, Rose Matthias, Entian Karl-Dieter, Thumm Michael, Wolf Dieter H. Catabolite degradation of fructose-1,6-bisphosphatase in the yeast Saccharomyces cerevisiae: a genome-wide screen identifies eight novel GID genes and indicates the existence of two degradation pathways. Mol Biol Cell. 2003 Apr;14(4):1652–1663. doi: 10.1091/mbc.E02-08-0456. [DOI] [PMC free article] [PubMed] [Google Scholar]
  188. Rehm Till, Huber Robert, Holak Tad A. Application of NMR in structural proteomics: screening for proteins amenable to structural analysis. Structure. 2002 Dec;10(12):1613–1618. doi: 10.1016/s0969-2126(02)00894-8. [DOI] [PubMed] [Google Scholar]
  189. Ren Shuang-Xi, Fu Gang, Jiang Xiu-Gao, Zeng Rong, Miao You-Gang, Xu Hai, Zhang Yi-Xuan, Xiong Hui, Lu Gang, Lu Ling-Feng. Unique physiological and pathogenic features of Leptospira interrogans revealed by whole-genome sequencing. Nature. 2003 Apr 24;422(6934):888–893. doi: 10.1038/nature01597. [DOI] [PubMed] [Google Scholar]
  190. Rhoades Kristina, Wong-Staal Flossie. Inverse Genomics as a powerful tool to identify novel targets for the treatment of neurodegenerative diseases. Mech Ageing Dev. 2003 Jan;124(1):125–132. doi: 10.1016/s0047-6374(02)00175-6. [DOI] [PubMed] [Google Scholar]
  191. Riedel Kathrin, Arevalo-Ferro Catalina, Reil Gerold, Görg Angelika, Lottspeich Friedrich, Eberl Leo. Analysis of the quorum-sensing regulon of the opportunistic pathogen Burkholderia cepacia H111 by proteomics. Electrophoresis. 2003 Feb;24(4):740–750. doi: 10.1002/elps.200390089. [DOI] [PubMed] [Google Scholar]
  192. Rodriguez S., Jafer O., Goker H., Summersgill B. M., Zafarana G., Gillis A. J. M., van Gurp R. J. H. L. M., Oosterhuis J. W., Lu Y-J, Huddart R. Expression profile of genes from 12p in testicular germ cell tumors of adolescents and adults associated with i(12p) and amplification at 12p11.2-p12.1. Oncogene. 2003 Mar 27;22(12):1880–1891. doi: 10.1038/sj.onc.1206302. [DOI] [PubMed] [Google Scholar]
  193. Rogers P. David, Barker Katherine S. Genome-wide expression profile analysis reveals coordinately regulated genes associated with stepwise acquisition of azole resistance in Candida albicans clinical isolates. Antimicrob Agents Chemother. 2003 Apr;47(4):1220–1227. doi: 10.1128/AAC.47.4.1220-1227.2003. [DOI] [PMC free article] [PubMed] [Google Scholar]
  194. Rogers P. David, Thornton Justin, Barker Katherine S., McDaniel D. Olga, Sacks Gordon S., Swiatlo Edwin, McDaniel Larry S. Pneumolysin-dependent and -independent gene expression identified by cDNA microarray analysis of THP-1 human mononuclear cells stimulated by Streptococcus pneumoniae. Infect Immun. 2003 Apr;71(4):2087–2094. doi: 10.1128/IAI.71.4.2087-2094.2003. [DOI] [PMC free article] [PubMed] [Google Scholar]
  195. Rombauts Stephane, Van De Peer Yves, Rouzé Pierre. AFLPinSilico, simulating AFLP fingerprints. Bioinformatics. 2003 Apr 12;19(6):776–777. doi: 10.1093/bioinformatics/btg090. [DOI] [PubMed] [Google Scholar]
  196. Rosen Ran, Ron Eliora Z. Proteome analysis in the study of the bacterial heat-shock response. Mass Spectrom Rev. 2002 Jul-Aug;21(4):244–265. doi: 10.1002/mas.10031. [DOI] [PubMed] [Google Scholar]
  197. Rothemund Deborah L., Locke Vicki L., Liew Audrey, Thomas Theresa M., Wasinger Valerie, Rylatt Dennis B. Depletion of the highly abundant protein albumin from human plasma using the Gradiflow. Proteomics. 2003 Mar;3(3):279–287. doi: 10.1002/pmic.200390041. [DOI] [PubMed] [Google Scholar]
  198. Sabounchi-Schütt F., Aström J., Hellman U., Eklund A., Grunewald J. Changes in bronchoalveolar lavage fluid proteins in sarcoidosis: a proteomics approach. Eur Respir J. 2003 Mar;21(3):414–420. doi: 10.1183/09031936.03.00060902. [DOI] [PubMed] [Google Scholar]
  199. Sadowski Michael I., Parish John Howard. Automated generation and refinement of protein signatures: case study with G-protein coupled receptors. Bioinformatics. 2003 Apr 12;19(6):727–734. doi: 10.1093/bioinformatics/btg075. [DOI] [PubMed] [Google Scholar]
  200. Saito Rintaro, Suzuki Harukazu, Hayashizaki Yoshihide. Construction of reliable protein-protein interaction networks with a new interaction generality measure. Bioinformatics. 2003 Apr 12;19(6):756–763. doi: 10.1093/bioinformatics/btg070. [DOI] [PubMed] [Google Scholar]
  201. Santamaria Enrique, Avila Matías A., Latasa M. Ujue, Rubio Angel, Martin-Duce Antonio, Lu Shelly C., Mato José M., Corrales Fernando J. Functional proteomics of nonalcoholic steatohepatitis: mitochondrial proteins as targets of S-adenosylmethionine. Proc Natl Acad Sci U S A. 2003 Mar 11;100(6):3065–3070. doi: 10.1073/pnas.0536625100. [DOI] [PMC free article] [PubMed] [Google Scholar]
  202. Satoh Nori. The ascidian tadpole larva: comparative molecular development and genomics. Nat Rev Genet. 2003 Apr;4(4):285–295. doi: 10.1038/nrg1042. [DOI] [PubMed] [Google Scholar]
  203. Sawyer T. K., Chorev M. Peptide revolution: genomics, proteomics and therapeutics. Biotechniques. 2003 Mar;34(3):594-6, 598-9. doi: 10.2144/03343dd01. [DOI] [PubMed] [Google Scholar]
  204. Scherer A., Krause A., Walker J. R., Sutton S. E., Serón D., Raulf F., Cooke M. P. Optimized protocol for linear RNA amplification and application to gene expression profiling of human renal biopsies. Biotechniques. 2003 Mar;34(3):546-50, 552-4, 556. doi: 10.2144/03343rr01. [DOI] [PubMed] [Google Scholar]
  205. Schlingemann Joerg, Hess Jochen, Wrobel Gunnar, Breitenbach Ute, Gebhardt Christoffer, Steinlein Peter, Kramer Heidi, Fürstenberger Gerhard, Hahn Meinhard, Angel Peter. Profile of gene expression induced by the tumour promotor TPA in murine epithelial cells. Int J Cancer. 2003 May 10;104(6):699–708. doi: 10.1002/ijc.11008. [DOI] [PubMed] [Google Scholar]
  206. Schoof Heiko, Karlowski Wojciech M. Comparison of rice and Arabidopsis annotation. Curr Opin Plant Biol. 2003 Apr;6(2):106–112. doi: 10.1016/s1369-5266(03)00003-7. [DOI] [PubMed] [Google Scholar]
  207. Schuster Martin, Lostroh C. Phoebe, Ogi Tomoo, Greenberg E. P. Identification, timing, and signal specificity of Pseudomonas aeruginosa quorum-controlled genes: a transcriptome analysis. J Bacteriol. 2003 Apr;185(7):2066–2079. doi: 10.1128/JB.185.7.2066-2079.2003. [DOI] [PMC free article] [PubMed] [Google Scholar]
  208. Schwab Wilfried. Metabolome diversity: too few genes, too many metabolites? Phytochemistry. 2003 Mar;62(6):837–849. doi: 10.1016/s0031-9422(02)00723-9. [DOI] [PubMed] [Google Scholar]
  209. Shabaan Amr M., Mohamed Magdy M., Abdallah Mohga S., Ibrahim Hayat M., Karim Amr M. Analysis of Schistosoma mansoni genes using the expressed sequence tag approach. Acta Biochim Pol. 2003;50(1):259–268. [PubMed] [Google Scholar]
  210. Shaughnessy John D., Jr Global gene expression profiling in the study of multiple myeloma. Int J Hematol. 2003 Apr;77(3):213–225. doi: 10.1007/BF02983777. [DOI] [PubMed] [Google Scholar]
  211. Shen Shihua, Jing Yuxiang, Kuang Tingyun. Proteomics approach to identify wound-response related proteins from rice leaf sheath. Proteomics. 2003 Apr;3(4):527–535. doi: 10.1002/pmic.200390066. [DOI] [PubMed] [Google Scholar]
  212. Shih Edward S. C., Hwang Ming-Jing. Protein structure comparison by probability-based matching of secondary structure elements. Bioinformatics. 2003 Apr 12;19(6):735–741. doi: 10.1093/bioinformatics/btg058. [DOI] [PubMed] [Google Scholar]
  213. Simpson P. J., Stanton C., Fitzgerald G. F., Ross R. P. Genomic diversity and relatedness of bifidobacteria isolated from a porcine cecum. J Bacteriol. 2003 Apr;185(8):2571–2581. doi: 10.1128/JB.185.8.2571-2581.2003. [DOI] [PMC free article] [PubMed] [Google Scholar]
  214. Stanley Nicola R., Britton Robert A., Grossman Alan D., Lazazzera Beth A. Identification of catabolite repression as a physiological regulator of biofilm formation by Bacillus subtilis by use of DNA microarrays. J Bacteriol. 2003 Mar;185(6):1951–1957. doi: 10.1128/JB.185.6.1951-1957.2003. [DOI] [PMC free article] [PubMed] [Google Scholar]
  215. Staunton David, Owen Jo, Campbell Iain D. NMR and structural genomics. Acc Chem Res. 2003 Mar;36(3):207–214. doi: 10.1021/ar010119s. [DOI] [PubMed] [Google Scholar]
  216. Stern Michael D., Anisimov Sergey V., Boheler Kenneth R. Can transcriptome size be estimated from SAGE catalogs? Bioinformatics. 2003 Mar 1;19(4):443–448. doi: 10.1093/bioinformatics/btg018. [DOI] [PubMed] [Google Scholar]
  217. Stintzi Alain. Gene expression profile of Campylobacter jejuni in response to growth temperature variation. J Bacteriol. 2003 Mar;185(6):2009–2016. doi: 10.1128/JB.185.6.2009-2016.2003. [DOI] [PMC free article] [PubMed] [Google Scholar]
  218. Sturn Alexander, Mlecnik Bernhard, Pieler Roland, Rainer Johannes, Truskaller Thomas, Trajanoski Zlatko. Client-server environment for high-performance gene expression data analysis. Bioinformatics. 2003 Apr 12;19(6):772–773. doi: 10.1093/bioinformatics/btg074. [DOI] [PubMed] [Google Scholar]
  219. Subramanian Subbaya, Madgula Vamsi M., George Ranjan, Mishra Rakesh K., Pandit Madhusudhan W., Kumar Chanderashekar S., Singh Lalji. Triplet repeats in human genome: distribution and their association with genes and other genomic regions. Bioinformatics. 2003 Mar 22;19(5):549–552. doi: 10.1093/bioinformatics/btg029. [DOI] [PubMed] [Google Scholar]
  220. Subramanian Subbaya, Mishra Rakesh K., Singh Lalji. Genome-wide analysis of Bkm sequences (GATA repeats): predominant association with sex chromosomes and potential role in higher order chromatin organization and function. Bioinformatics. 2003 Apr 12;19(6):681–685. doi: 10.1093/bioinformatics/btg067. [DOI] [PubMed] [Google Scholar]
  221. Sumner Lloyd W., Mendes Pedro, Dixon Richard A. Plant metabolomics: large-scale phytochemistry in the functional genomics era. Phytochemistry. 2003 Mar;62(6):817–836. doi: 10.1016/s0031-9422(02)00708-2. [DOI] [PubMed] [Google Scholar]
  222. Sun Jibin, van den Heuvel Joop, Soucaille Philippe, Qu Yinbo, Zeng An-Ping. Comparative genomic analysis of dha regulon and related genes for anaerobic glycerol metabolism in bacteria. Biotechnol Prog. 2003 Mar-Apr;19(2):263–272. doi: 10.1021/bp025739m. [DOI] [PubMed] [Google Scholar]
  223. Sunyaev Shamil, Liska Adam J., Golod Alexander, Shevchenko Anna, Shevchenko Andrej. MultiTag: multiple error-tolerant sequence tag search for the sequence-similarity identification of proteins by mass spectrometry. Anal Chem. 2003 Mar 15;75(6):1307–1315. doi: 10.1021/ac026199a. [DOI] [PubMed] [Google Scholar]
  224. Svensson Marcus, Sköld Karl, Svenningsson Per, Andren Per E. Peptidomics-based discovery of novel neuropeptides. J Proteome Res. 2003 Mar-Apr;2(2):213–219. doi: 10.1021/pr020010u. [DOI] [PubMed] [Google Scholar]
  225. Talamo Fabio, D'Ambrosio Chiara, Arena Simona, Del Vecchio Prisco, Ledda Luigi, Zehender Goffredo, Ferrara Lino, Scaloni Andrea. Proteins from bovine tissues and biological fluids: defining a reference electrophoresis map for liver, kidney, muscle, plasma and red blood cells. Proteomics. 2003 Apr;3(4):440–460. doi: 10.1002/pmic.200390059. [DOI] [PubMed] [Google Scholar]
  226. Tan Zhi-Jun, Hu Xian-Gui, Cao Gui-Song, Tang Yan. Analysis of gene expression profile of pancreatic carcinoma using cDNA microarray. World J Gastroenterol. 2003 Apr;9(4):818–823. doi: 10.3748/wjg.v9.i4.818. [DOI] [PMC free article] [PubMed] [Google Scholar]
  227. Tang Yang, Nee Alex C., Lu Aigang, Ran Ruiqiong, Sharp Frank R. Blood genomic expression profile for neuronal injury. J Cereb Blood Flow Metab. 2003 Mar;23(3):310–319. doi: 10.1097/01.WCB.0000048518.34839.DE. [DOI] [PubMed] [Google Scholar]
  228. Tao Wen, Hangoc Giao, Hawes John W., Si Yue, Cooper Scott, Broxmeyer Hal E. Profiling of differentially expressed apoptosis-related genes by cDNA arrays in human cord blood CD34+ cells treated with etoposide. Exp Hematol. 2003 Mar;31(3):251–260. doi: 10.1016/s0301-472x(02)01083-4. [DOI] [PubMed] [Google Scholar]
  229. Thevis Mario, Ogorzalek Loo Rachel R., Loo Joseph A. In-gel derivatization of proteins for cysteine-specific cleavages and their analysis by mass spectrometry. J Proteome Res. 2003 Mar-Apr;2(2):163–172. doi: 10.1021/pr025568g. [DOI] [PubMed] [Google Scholar]
  230. Tillier Elisabeth R. M., Lui Thomas W. H. Using multiple interdependency to separate functional from phylogenetic correlations in protein alignments. Bioinformatics. 2003 Apr 12;19(6):750–755. doi: 10.1093/bioinformatics/btg072. [DOI] [PubMed] [Google Scholar]
  231. Tocchetti Arianna, Confalonieri Stefano, Scita Giorgio, Di Fiore Pier Paolo, Betsholtz Christer. In silico analysis of the EPS8 gene family: genomic organization, expression profile, and protein structure. Genomics. 2003 Feb;81(2):234–244. doi: 10.1016/s0888-7543(03)00002-8. [DOI] [PubMed] [Google Scholar]
  232. Toda Tosifusa, Sugimoto Masanobu. Proteome analysis of Epstein-Barr virus-transformed B-lymphoblasts and the proteome database. J Chromatogr B Analyt Technol Biomed Life Sci. 2003 Apr 5;787(1):197–206. doi: 10.1016/s1570-0232(02)00495-6. [DOI] [PubMed] [Google Scholar]
  233. Toppo Stefano, Cannata Nicola, Fontana Paolo, Romualdi Chiara, Laveder Paolo, Bertocco Emanuela, Lanfranchi Gerolamo, Valle Giorgio. TRAIT (TRAnscript Integrated Table): a knowledgebase of human skeletal muscle transcripts. Bioinformatics. 2003 Mar 22;19(5):661–662. doi: 10.1093/bioinformatics/btg045. [DOI] [PubMed] [Google Scholar]
  234. Trail Frances, Xu Jin Rong, San Miguel Phillip, Halgren Robert G., Kistler H. Corby. Analysis of expressed sequence tags from Gibberella zeae (anamorph Fusarium graminearum). Fungal Genet Biol. 2003 Mar;38(2):187–197. doi: 10.1016/s1087-1845(02)00529-7. [DOI] [PubMed] [Google Scholar]
  235. Trost Elmar, Hackl Hubert, Maurer Michael, Trajanoski Zlatko. Java editor for biological pathways. Bioinformatics. 2003 Apr 12;19(6):786–787. doi: 10.1093/bioinformatics/btg052. [DOI] [PubMed] [Google Scholar]
  236. Umar Arzu, Luider Theo M., Berrevoets Cor A., Grootegoed J. Anton, Brinkmann Albert O. Proteomic analysis of androgen-regulated protein expression in a mouse fetal vas deferens cell line. Endocrinology. 2003 Apr;144(4):1147–1154. doi: 10.1210/en.2002-220974. [DOI] [PubMed] [Google Scholar]
  237. Unneberg Per, Wennborg Anders, Larsson Magnus. Transcript identification by analysis of short sequence tags--influence of tag length, restriction site and transcript database. Nucleic Acids Res. 2003 Apr 15;31(8):2217–2226. doi: 10.1093/nar/gkg313. [DOI] [PMC free article] [PubMed] [Google Scholar]
  238. Upreti Raj K., Kumar Manoj, Shankar V. Bacterial glycoproteins: functions, biosynthesis and applications. Proteomics. 2003 Apr;3(4):363–379. doi: 10.1002/pmic.200390052. [DOI] [PubMed] [Google Scholar]
  239. Ureta-Vidal Abel, Ettwiller Laurence, Birney Ewan. Comparative genomics: genome-wide analysis in metazoan eukaryotes. Nat Rev Genet. 2003 Apr;4(4):251–262. doi: 10.1038/nrg1043. [DOI] [PubMed] [Google Scholar]
  240. Vaughan Duncan A., Morishima H., Kadowaki K. Diversity in the Oryza genus. Curr Opin Plant Biol. 2003 Apr;6(2):139–146. doi: 10.1016/s1369-5266(03)00009-8. [DOI] [PubMed] [Google Scholar]
  241. Venet David. MatArray: a Matlab toolbox for microarray data. Bioinformatics. 2003 Mar 22;19(5):659–660. doi: 10.1093/bioinformatics/btg046. [DOI] [PubMed] [Google Scholar]
  242. Vincentelli Renaud, Bignon Christophe, Gruez Arnaud, Canaan Stephane, Sulzenbacher Gerlind, Tegoni Mariella, Campanacci Valérie, Cambillau Christian. Medium-scale structural genomics: strategies for protein expression and crystallization. Acc Chem Res. 2003 Mar;36(3):165–172. doi: 10.1021/ar010130s. [DOI] [PubMed] [Google Scholar]
  243. Vinga Susana, Almeida Jonas. Alignment-free sequence comparison-a review. Bioinformatics. 2003 Mar 1;19(4):513–523. doi: 10.1093/bioinformatics/btg005. [DOI] [PubMed] [Google Scholar]
  244. Virolle Thierry, Krones-Herzig Anja, Baron Veronique, De Gregorio Giorgia, Adamson Eileen D., Mercola Dan. Egr1 promotes growth and survival of prostate cancer cells. Identification of novel Egr1 target genes. J Biol Chem. 2003 Jan 29;278(14):11802–11810. doi: 10.1074/jbc.M210279200. [DOI] [PubMed] [Google Scholar]
  245. Vivanco Fernando, López-Bescós Lorenzo, Tuñn José, Egido Jesús. Proteómica y enfermedad cardiovascular. Rev Esp Cardiol. 2003 Mar;56(3):289–302. doi: 10.1016/s0300-8932(03)76865-1. [DOI] [PubMed] [Google Scholar]
  246. Voss S. R., Prudic K. L., Oliver J. C., Shaffer H. B. Candidate gene analysis of metamorphic timing in ambystomatid salamanders. Mol Ecol. 2003 May;12(5):1217–1223. doi: 10.1046/j.1365-294x.2003.01806.x. [DOI] [PubMed] [Google Scholar]
  247. Wagner Victoria E., Bushnell Daniel, Passador Luciano, Brooks Andrew I., Iglewski Barbara H. Microarray analysis of Pseudomonas aeruginosa quorum-sensing regulons: effects of growth phase and environment. J Bacteriol. 2003 Apr;185(7):2080–2095. doi: 10.1128/JB.185.7.2080-2095.2003. [DOI] [PMC free article] [PubMed] [Google Scholar]
  248. Wakefield Matthew J., Graves Jennifer A. Marshall. The kangaroo genome. Leaps and bounds in comparative genomics. EMBO Rep. 2003 Feb;4(2):143–147. doi: 10.1038/sj.embor.embor739. [DOI] [PMC free article] [PubMed] [Google Scholar]
  249. Wang Guoqing, Zhang Yan, Chen Biao, Cheng Jing. Preliminary studies on Alzheimer's disease using cDNA microarrays. Mech Ageing Dev. 2003 Jan;124(1):115–124. doi: 10.1016/s0047-6374(02)00188-4. [DOI] [PubMed] [Google Scholar]
  250. Wang Hai-Tao, Kong Jian-Ping, Ding Fang, Wang Xiu-Qin, Wang Ming-Rong, Liu Lian-Xin, Wu Min, Liu Zhi-Hua. Analysis of gene expression profile induced by EMP-1 in esophageal cancer cells using cDNA Microarray. World J Gastroenterol. 2003 Mar;9(3):392–398. doi: 10.3748/wjg.v9.i3.392. [DOI] [PMC free article] [PubMed] [Google Scholar]
  251. Wang Jianxin, Liang Ping. DigiNorthern, digital expression analysis of query genes based on ESTs. Bioinformatics. 2003 Mar 22;19(5):653–654. doi: 10.1093/bioinformatics/btg044. [DOI] [PubMed] [Google Scholar]
  252. Wang Young Y., Cheng Paul, Chan Daniel W. A simple affinity spin tube filter method for removing high-abundant common proteins or enriching low-abundant biomarkers for serum proteomic analysis. Proteomics. 2003 Mar;3(3):243–248. doi: 10.1002/pmic.200390036. [DOI] [PubMed] [Google Scholar]
  253. Ware Doreen, Stein Lincoln. Comparison of genes among cereals. Curr Opin Plant Biol. 2003 Apr;6(2):121–127. doi: 10.1016/s1369-5266(03)00012-8. [DOI] [PubMed] [Google Scholar]
  254. Weekes John, Watson Ronald R., Dunn Michael J. Murine retrovirus infection and the effect of chronic alcohol consumption: proteomic analysis of cardiac protein expression. Alcohol Alcohol. 2003 Mar-Apr;38(2):103–108. doi: 10.1093/alcalc/agg037. [DOI] [PubMed] [Google Scholar]
  255. Weiss Marjan M., Kuipers Ernst J., Postma Cindy, Snijders Antoine M., Siccama Ivar, Pinkel Daniel, Westerga Johan, Meuwissen Stefan G. M., Albertson Donna G., Meijer Gerrit A. Genomic profiling of gastric cancer predicts lymph node status and survival. Oncogene. 2003 Mar 27;22(12):1872–1879. doi: 10.1038/sj.onc.1206350. [DOI] [PubMed] [Google Scholar]
  256. White Ian R., Man Wai J., Bryant Duncan, Bugelski Peter, Camilleri Patrick, Cutler Paul, Hayes William, Holbrook Joanna D., Kramer Kerstin, Lord Peter G. Protein expression changes in the Sprague Dawley rat liver proteome following administration of peroxisome proliferator activated receptor alpha and gamma ligands. Proteomics. 2003 Apr;3(4):505–512. doi: 10.1002/pmic.200390064. [DOI] [PubMed] [Google Scholar]
  257. Williams Noelle Sevilir, Gaynor Richard B., Scoggin Shane, Verma Udit, Gokaslan Tunc, Simmang Clifford, Fleming Jason, Tavana Denise, Frenkel Eugene, Becerra Carlos. Identification and validation of genes involved in the pathogenesis of colorectal cancer using cDNA microarrays and RNA interference. Clin Cancer Res. 2003 Mar;9(3):931–946. [PubMed] [Google Scholar]
  258. Wilson David S., Nock Steffen. Recent developments in protein microarray technology. Angew Chem Int Ed Engl. 2003 Feb 3;42(5):494–500. doi: 10.1002/anie.200390150. [DOI] [PubMed] [Google Scholar]
  259. Wipf Daniel, Benjdia Marlam, Rikirsch Enno, Zimmermann Sabine, Tegeder Mechthild, Frommer Wolf B. An expression cDNA library for suppression cloning in yeast mutants, complementation of a yeast his4 mutant, and EST analysis from the symbiotic basidiomycete Hebeloma cylindrosporum. Genome. 2003 Apr;46(2):177–181. doi: 10.1139/g02-121. [DOI] [PubMed] [Google Scholar]
  260. Wong Lily Y., Hafeman Andrea, Boyd Victoria L., Bodeau John, Lazaruk Katherine D., Liew Sueh-Ning, Casey Peter, Belonogoff Victor, Bit Somaya, Sumner Craig. Assessing gene expression variation in normal human tissues using GeneTag, a novel, global, sensitive profiling method. J Biotechnol. 2003 Mar 20;101(3):199–217. doi: 10.1016/s0168-1656(02)00301-2. [DOI] [PubMed] [Google Scholar]
  261. Wong Philip, Kolesov Grigory, Frishman Dmitrij, Houry Walid A. Phylogenetic web profiler. Bioinformatics. 2003 Apr 12;19(6):782–783. doi: 10.1093/bioinformatics/btg064. [DOI] [PubMed] [Google Scholar]
  262. Woods Amina S., Moyer Susanne C., Wang Hay-Yan J., Wise Roy A. Interaction of chlorisondamine with the neuronal nicotinic acetylcholine receptor. J Proteome Res. 2003 Mar-Apr;2(2):207–212. doi: 10.1021/pr025578h. [DOI] [PubMed] [Google Scholar]
  263. Wu Yimin, Wang Xiangyun, Liu Xia, Wang Yufeng. Data-mining approaches reveal hidden families of proteases in the genome of malaria parasite. Genome Res. 2003 Apr;13(4):601–616. doi: 10.1101/gr.913403. [DOI] [PMC free article] [PubMed] [Google Scholar]
  264. Wubbolts Richard, Leckie Rachel S., Veenhuizen Peter T. M., Schwarzmann Guenter, Möbius Wiebke, Hoernschemeyer Joerg, Slot Jan-Willem, Geuze Hans J., Stoorvogel Willem. Proteomic and biochemical analyses of human B cell-derived exosomes. Potential implications for their function and multivesicular body formation. J Biol Chem. 2003 Jan 7;278(13):10963–10972. doi: 10.1074/jbc.M207550200. [DOI] [PubMed] [Google Scholar]
  265. Wulfkuhle Julia D., Liotta Lance A., Petricoin Emanuel F. Proteomic applications for the early detection of cancer. Nat Rev Cancer. 2003 Apr;3(4):267–275. doi: 10.1038/nrc1043. [DOI] [PubMed] [Google Scholar]
  266. Xiong Shaoxiang, Ding Qinxue, Zhao Zhengwen, Chen Wenzhang, Wang Guanghui, Liu Shaojun. A new method to improve sensitivity and resolution in matrix-assisted laser desorption/ionization time of flight mass spectrometry. Proteomics. 2003 Mar;3(3):265–272. doi: 10.1002/pmic.200390039. [DOI] [PubMed] [Google Scholar]
  267. Yamagishi J., Isobe R., Takebuchi T., Bando H. DNA microarrays of baculovirus genomes: differential expression of viral genes in two susceptible insect cell lines. Arch Virol. 2003 Mar;148(3):587–597. doi: 10.1007/s00705-002-0922-3. [DOI] [PubMed] [Google Scholar]
  268. Yamazaki Mami, Nakajima Jun-ichiro, Yamanashi Mutsuki, Sugiyama Mitsuyo, Makita Yukiko, Springob Karin, Awazuhara Motoko, Saito Kazuki. Metabolomics and differential gene expression in anthocyanin chemo-varietal forms of Perilla frutescens. Phytochemistry. 2003 Mar;62(6):987–995. doi: 10.1016/s0031-9422(02)00721-5. [DOI] [PubMed] [Google Scholar]
  269. Yang Sang Hwa, Kim Jong Sik, Oh Tae Jeong, Kim Myung Soon, Lee Sun Woo, Woo Suk Kyung, Cho Hyun Sill, Choi Yung Hyun, Kim Young Ho, Rha Sun Young. Genome-scale analysis of resveratrol-induced gene expression profile in human ovarian cancer cells using a cDNA microarray. Int J Oncol. 2003 Apr;22(4):741–750. [PubMed] [Google Scholar]
  270. Ye Qing-Hai, Qin Lun-Xiu, Forgues Marshonna, He Ping, Kim Jin Woo, Peng Amy C., Simon Richard, Li Yan, Robles Ana I., Chen Yidong. Predicting hepatitis B virus-positive metastatic hepatocellular carcinomas using gene expression profiling and supervised machine learning. Nat Med. 2003 Mar 17;9(4):416–423. doi: 10.1038/nm843. [DOI] [PubMed] [Google Scholar]
  271. Ye Yuzhen, Jaroszewski Lukasz, Li Weizhong, Godzik Adam. A segment alignment approach to protein comparison. Bioinformatics. 2003 Apr 12;19(6):742–749. doi: 10.1093/bioinformatics/btg073. [DOI] [PubMed] [Google Scholar]
  272. Yee Adelinda, Pardee Keith, Christendat Dinesh, Savchenko Alexei, Edwards Aled M., Arrowsmith Cheryl H. Structural proteomics: toward high-throughput structural biology as a tool in functional genomics. Acc Chem Res. 2003 Mar;36(3):183–189. doi: 10.1021/ar010126g. [DOI] [PubMed] [Google Scholar]
  273. Yelick Pamela C., Schilling Thomas F. Molecular dissection of craniofacial development using zebrafish. Crit Rev Oral Biol Med. 2002;13(4):308–322. doi: 10.1177/154411130201300402. [DOI] [PubMed] [Google Scholar]
  274. Yoda Hiroki, Momoi Akihiro, Esguerra Camila V., Meyer Dirk, Driever Wolfgang, Kondoh Hisato, Furutani-Seiki Makoto. An expression pattern screen for genes involved in the induction of the posterior nervous system of zebrafish. Differentiation. 2003 Mar;71(2):152–162. doi: 10.1046/j.1432-0436.2003.710206.x. [DOI] [PubMed] [Google Scholar]
  275. Yuan Yinan, SanMiguel Phillip J., Bennetzen Jeffrey L. High-Cot sequence analysis of the maize genome. Plant J. 2003 Apr;34(2):249–255. doi: 10.1046/j.1365-313x.2003.01716.x. [DOI] [PubMed] [Google Scholar]
  276. Zewail Amani, Xie Michael W., Xing Yi, Lin Lan, Zhang P. Fred, Zou Wei, Saxe Jonathan P., Huang Jing. Novel functions of the phosphatidylinositol metabolic pathway discovered by a chemical genomics screen with wortmannin. Proc Natl Acad Sci U S A. 2003 Mar 3;100(6):3345–3350. doi: 10.1073/pnas.0530118100. [DOI] [PMC free article] [PubMed] [Google Scholar]
  277. Zhang Chun-Ting, Zhang Ren, Ou Hong-Yu. The Z curve database: a graphic representation of genome sequences. Bioinformatics. 2003 Mar 22;19(5):593–599. doi: 10.1093/bioinformatics/btg041. [DOI] [PubMed] [Google Scholar]
  278. Zhang Li-Yong, Ying Wan-Tao, Mao You-Sheng, He Hong-Zhi, Liu Yu, Wang Hui-Xin, Liu Fang, Wang Kun, Zhang De-Chao, Wang Ying. Loss of clusterin both in serum and tissue correlates with the tumorigenesis of esophageal squamous cell carcinoma via proteomics approaches. World J Gastroenterol. 2003 Apr;9(4):650–654. doi: 10.3748/wjg.v9.i4.650. [DOI] [PMC free article] [PubMed] [Google Scholar]
  279. de Vos Sven, Hofmann Wolf-Karsten, Grogan Thomas M., Krug Utz, Schrage Mathew, Miller Thomas P., Braun Jonathan G., Wachsman William, Koeffler H. Phillip, Said Jonathan W. Gene expression profile of serial samples of transformed B-cell lymphomas. Lab Invest. 2003 Feb;83(2):271–285. doi: 10.1097/01.lab.0000053913.85892.e9. [DOI] [PubMed] [Google Scholar]
  280. tom Dieck Heike, Döring Frank, Roth Hans-Peter, Daniel Hannelore. Changes in rat hepatic gene expression in response to zinc deficiency as assessed by DNA arrays. J Nutr. 2003 Apr;133(4):1004–1010. doi: 10.1093/jn/133.4.1004. [DOI] [PubMed] [Google Scholar]
  281. van Duin M., Woolson H., Mallinson D., Black D. Genomics in target and drug discovery. Biochem Soc Trans. 2003 Apr;31(2):429–432. doi: 10.1042/bst0310429. [DOI] [PubMed] [Google Scholar]

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

RESOURCES