Skip to main content
NCBI home page
Comparative and Functional Genomics logoLink to Comparative and Functional Genomics
. 2004 Apr;5(3):295–302. doi: 10.1002/cfg.352

Current Awareness on Comparative and Functional Genomics

PMCID: PMC2447439

Full Text

The Full Text of this article is available as a PDF (132.9 KB).

Selected References

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

  1. Absi Tarek S., Sundt Thoralf M., 3rd, Tung William S., Moon Marc, Lee Jason K., Damiano Ralph R., Jr, Thompson Robert W. Altered patterns of gene expression distinguishing ascending aortic aneurysms from abdominal aortic aneurysms: complementary DNA expression profiling in the molecular characterization of aortic disease. J Thorac Cardiovasc Surg. 2003 Aug;126(2):344–357. doi: 10.1016/s0022-5223(02)73576-9. [DOI] [PubMed] [Google Scholar]
  2. Achaz Guillaume, Coissac Eric, Netter Pierre, Rocha Eduardo P. C. Associations between inverted repeats and the structural evolution of bacterial genomes. Genetics. 2003 Aug;164(4):1279–1289. doi: 10.1093/genetics/164.4.1279. [DOI] [PMC free article] [PubMed] [Google Scholar]
  3. Agarwal Ameeta K., Rogers P. David, Baerson Scott R., Jacob Melissa R., Barker Katherine S., Cleary John D., Walker Larry A., Nagle Dale G., Clark Alice M. Genome-wide expression profiling of the response to polyene, pyrimidine, azole, and echinocandin antifungal agents in Saccharomyces cerevisiae. J Biol Chem. 2003 Jun 24;278(37):34998–35015. doi: 10.1074/jbc.M306291200. [DOI] [PubMed] [Google Scholar]
  4. Aldridge Beau A., Lim So Dug, Baumann Amanda K., Hosseini Seyed, Buck Whitney, Almekinder Tara L., Sun Carrie Q., Petros John A. Automated sequencing of complete mitochondrial genomes from laser-capture microdissected samples. Biotechniques. 2003 Sep;35(3):606-7, 609-10, 612. doi: 10.2144/03353dd04. [DOI] [PubMed] [Google Scholar]
  5. Allen Timothy E., Herrgård Markus J., Liu Mingzhu, Qiu Yu, Glasner Jeremy D., Blattner Frederick R., Palsson Bernhard Ø. Genome-scale analysis of the uses of the Escherichia coli genome: model-driven analysis of heterogeneous data sets. J Bacteriol. 2003 Nov;185(21):6392–6399. doi: 10.1128/JB.185.21.6392-6399.2003. [DOI] [PMC free article] [PubMed] [Google Scholar]
  6. Aloy Patrick, Russell Robert B. Understanding and predicting protein assemblies with 3D structures. Comp Funct Genomics. 2003;4(4):410–415. doi: 10.1002/cfg.310. [DOI] [PMC free article] [PubMed] [Google Scholar]
  7. Amundson Sally A., Bittner Michael, Fornace Albert J., Jr Functional genomics as a window on radiation stress signaling. Oncogene. 2003 Sep 1;22(37):5828–5833. doi: 10.1038/sj.onc.1206681. [DOI] [PubMed] [Google Scholar]
  8. Anholt Robert R. H., Dilda Christy L., Chang Sherman, Fanara Juan-José, Kulkarni Nalini H., Ganguly Indrani, Rollmann Stephanie M., Kamdar Kim P., Mackay Trudy F. C. The genetic architecture of odor-guided behavior in Drosophila: epistasis and the transcriptome. Nat Genet. 2003 Sep 7;35(2):180–184. doi: 10.1038/ng1240. [DOI] [PubMed] [Google Scholar]
  9. Armstrong Scott A., Golub Todd R., Korsmeyer Stanley J. MLL-rearranged leukemias: insights from gene expression profiling. Semin Hematol. 2003 Oct;40(4):268–273. doi: 10.1016/s0037-1963(03)00196-3. [DOI] [PubMed] [Google Scholar]
  10. Astorga-Wells Juan, Jörnvall Hans, Bergman Tomas. A microfluidic electrocapture device in sample preparation for protein analysis by MALDI mass spectrometry. Anal Chem. 2003 Oct 1;75(19):5213–5219. doi: 10.1021/ac0300901. [DOI] [PubMed] [Google Scholar]
  11. Autio Reija, Hautaniemi Sampsa, Kauraniemi Päivikki, Yli-Harja Olli, Astola Jaakko, Wolf Maija, Kallioniemi Anne. CGH-Plotter: MATLAB toolbox for CGH-data analysis. Bioinformatics. 2003 Sep 1;19(13):1714–1715. doi: 10.1093/bioinformatics/btg230. [DOI] [PubMed] [Google Scholar]
  12. Baar Claudia, Eppinger Mark, Raddatz Guenter, Simon Jörg, Lanz Christa, Klimmek Oliver, Nandakumar Ramkumar, Gross Roland, Rosinus Andrea, Keller Heike. Complete genome sequence and analysis of Wolinella succinogenes. Proc Natl Acad Sci U S A. 2003 Sep 19;100(20):11690–11695. doi: 10.1073/pnas.1932838100. [DOI] [PMC free article] [PubMed] [Google Scholar]
  13. Baggerly Keith A., Morris Jeffrey S., Wang Jing, Gold David, Xiao Lian-Chun, Coombes Kevin R. A comprehensive approach to the analysis of matrix-assisted laser desorption/ionization-time of flight proteomics spectra from serum samples. Proteomics. 2003 Sep;3(9):1667–1672. doi: 10.1002/pmic.200300522. [DOI] [PubMed] [Google Scholar]
  14. Bagirov A. M., Ferguson B., Ivkovic S., Saunders G., Yearwood J. New algorithms for multi-class cancer diagnosis using tumor gene expression signatures. Bioinformatics. 2003 Sep 22;19(14):1800–1807. doi: 10.1093/bioinformatics/btg238. [DOI] [PubMed] [Google Scholar]
  15. Bailey Michael J., Beremand Phillip D., Hammer Rick, Bell-Pedersen Deborah, Thomas Terry L., Cassone Vincent M. Transcriptional profiling of the chick pineal gland, a photoreceptive circadian oscillator and pacemaker. Mol Endocrinol. 2003 Jul 24;17(10):2084–2095. doi: 10.1210/me.2003-0121. [DOI] [PubMed] [Google Scholar]
  16. Bar-Joseph Ziv, Gerber Georg, Simon Itamar, Gifford David K., Jaakkola Tommi S. Comparing the continuous representation of time-series expression profiles to identify differentially expressed genes. Proc Natl Acad Sci U S A. 2003 Aug 21;100(18):10146–10151. doi: 10.1073/pnas.1732547100. [DOI] [PMC free article] [PubMed] [Google Scholar]
  17. Barker Jonathan A., Thornton Janet M. An algorithm for constraint-based structural template matching: application to 3D templates with statistical analysis. Bioinformatics. 2003 Sep 1;19(13):1644–1649. doi: 10.1093/bioinformatics/btg226. [DOI] [PubMed] [Google Scholar]
  18. Basik Mark, Mousses Spyro, Trent Jeffrey. Integration of genomic technologies for accelerated cancer drug development. Biotechniques. 2003 Sep;35(3):580-2, 584, 586 passim. doi: 10.2144/03353dd01. [DOI] [PubMed] [Google Scholar]
  19. Bauer Andrea, Beckmann Boris, Busold Christian, Brandt Ole, Kusnezow Wlad, Pullat Janne, Aign Verena, Fellenberg Kurt, Fleischer Robert, Jacob Anette, Frohme Marcus, Hoheisel Jörg D. Use of complex DNA and antibody microarrays as tools in functional analyses. Comp Funct Genomics. 2003;4(5):520–524. doi: 10.1002/cfg.320. [DOI] [PMC free article] [PubMed] [Google Scholar]
  20. Becerra M., Lombardía L. J., González-Siso M. I., Rodríguez-Belmonte E., Hauser N. C., Cerdán M. E. Genome-wide analysis of the yeast transcriptome upon heat and cold shock. Comp Funct Genomics. 2003;4(4):366–375. doi: 10.1002/cfg.301. [DOI] [PMC free article] [PubMed] [Google Scholar]
  21. Beisson Frédéric, Koo Abraham J. K., Ruuska Sari, Schwender Jörg, Pollard Mike, Thelen Jay J., Paddock Troy, Salas Joaquín J., Savage Linda, Milcamps Anne. Arabidopsis genes involved in acyl lipid metabolism. A 2003 census of the candidates, a study of the distribution of expressed sequence tags in organs, and a web-based database. Plant Physiol. 2003 Jun;132(2):681–697. doi: 10.1104/pp.103.022988. [DOI] [PMC free article] [PubMed] [Google Scholar]
  22. Bell Rachel E., Ben-Tal Nir. In silico identification of functional protein interfaces. Comp Funct Genomics. 2003;4(4):420–423. doi: 10.1002/cfg.309. [DOI] [PMC free article] [PubMed] [Google Scholar]
  23. Bendt Anne K., Burkovski Andreas, Schaffer Steffen, Bott Michael, Farwick Mike, Hermann Thomas. Towards a phosphoproteome map of Corynebacterium glutamicum. Proteomics. 2003 Aug;3(8):1637–1646. doi: 10.1002/pmic.200300494. [DOI] [PubMed] [Google Scholar]
  24. Bente Meike, Harder Simone, Wiesgigl Martina, Heukeshoven Jochen, Gelhaus Christoph, Krause Eberhard, Clos Joachim, Bruchhaus Iris. Developmentally induced changes of the proteome in the protozoan parasite Leishmania donovani. Proteomics. 2003 Sep;3(9):1811–1829. doi: 10.1002/pmic.200300462. [DOI] [PubMed] [Google Scholar]
  25. Bertsch Martina, Kassner Richard J. Selective staining of proteins with hydrophobic surface sites on a native electrophoretic gel. J Proteome Res. 2003 Sep-Oct;2(5):469–475. doi: 10.1021/pr025579+. [DOI] [PubMed] [Google Scholar]
  26. Binz Pierre-Alain, Abdi Fadi, Affolter Michael, Allard Laure, Barblan Jachen, Bhardwaj Sanjeev, Bienvenut Willy V., Bulet Philippe, Burgess Jennifer, Carrette Odile. Proteomics application exercise of the Swiss Proteomics Society: report of the SPS'02 session. Proteomics. 2003 Aug;3(8):1562–1566. doi: 10.1002/pmic.200300458. [DOI] [PubMed] [Google Scholar]
  27. Blick Robert J., Revel Andrew T., Hansen Eric J. FindGDPs: identification of primers for labeling microbial transcriptomes for DNA microarray analysis. Bioinformatics. 2003 Sep 1;19(13):1718–1719. doi: 10.1093/bioinformatics/btg218. [DOI] [PMC free article] [PubMed] [Google Scholar]
  28. Borner Georg H. H., Lilley Kathryn S., Stevens Timothy J., Dupree Paul. Identification of glycosylphosphatidylinositol-anchored proteins in Arabidopsis. A proteomic and genomic analysis. Plant Physiol. 2003 May 1;132(2):568–577. doi: 10.1104/pp.103.021170. [DOI] [PMC free article] [PubMed] [Google Scholar]
  29. Braun Pascal, LaBaer Josh. High throughput protein production for functional proteomics. Trends Biotechnol. 2003 Sep;21(9):383–388. doi: 10.1016/S0167-7799(03)00189-6. [DOI] [PubMed] [Google Scholar]
  30. Brazilian National Genome Project Consortium The complete genome sequence of Chromobacterium violaceum reveals remarkable and exploitable bacterial adaptability. Proc Natl Acad Sci U S A. 2003 Sep 18;100(20):11660–11665. doi: 10.1073/pnas.1832124100. [DOI] [PMC free article] [PubMed] [Google Scholar]
  31. Brock Jonathan W. C., Hinton Davinia J. S., Cotham William E., Metz Thomas O., Thorpe Suzanne R., Baynes John W., Ames Jennifer M. Proteomic analysis of the site specificity of glycation and carboxymethylation of ribonuclease. J Proteome Res. 2003 Sep-Oct;2(5):506–513. doi: 10.1021/pr0340173. [DOI] [PubMed] [Google Scholar]
  32. Bromley Elizabeth, Leeds Nicola, Clark Julie, McGregor Emma, Ward Malcolm, Dunn Michael J., Tomley Fiona. Defining the protein repertoire of microneme secretory organelles in the apicomplexan parasite Eimeria tenella. Proteomics. 2003 Aug;3(8):1553–1561. doi: 10.1002/pmic.200300479. [DOI] [PubMed] [Google Scholar]
  33. Bucca Giselda, Brassington Anna M. E., Hotchkiss Graham, Mersinias Vassilios, Smith Colin P. Negative feedback regulation of dnaK, clpB and lon expression by the DnaK chaperone machine in Streptomyces coelicolor, identified by transcriptome and in vivo DnaK-depletion analysis. Mol Microbiol. 2003 Oct;50(1):153–166. doi: 10.1046/j.1365-2958.2003.03696.x. [DOI] [PubMed] [Google Scholar]
  34. Buell C. Robin, Joardar Vinita, Lindeberg Magdalen, Selengut Jeremy, Paulsen Ian T., Gwinn Michelle L., Dodson Robert J., Deboy Robert T., Durkin A. Scott, Kolonay James F. The complete genome sequence of the Arabidopsis and tomato pathogen Pseudomonas syringae pv. tomato DC3000. Proc Natl Acad Sci U S A. 2003 Aug 19;100(18):10181–10186. doi: 10.1073/pnas.1731982100. [DOI] [PMC free article] [PubMed] [Google Scholar]
  35. Bunai Keigo, Nozaki Manabu, Hamano Miyuki, Ogane Shinya, Inoue Taro, Nemoto Tadashi, Nakanishi Hiroshi, Yamane Kunio. Proteomic analysis of acrylamide gel separated proteins immobilized on polyvinylidene difluoride membranes following proteolytic digestion in the presence of 80% acetonitrile. Proteomics. 2003 Sep;3(9):1738–1749. doi: 10.1002/pmic.200300529. [DOI] [PubMed] [Google Scholar]
  36. Butterfield D. A., Castegna A. Proteomic analysis of oxidatively modified proteins in Alzheimer's disease brain: insights into neurodegeneration. Cell Mol Biol (Noisy-le-grand) 2003 Jul;49(5):747–751. [PubMed] [Google Scholar]
  37. Carrette Odile, Demalte Isabelle, Scherl Alexander, Yalkinoglu Oezkarn, Corthals Garry, Burkhard Pierre, Hochstrasser Denis F., Sanchez Jean-Charles. A panel of cerebrospinal fluid potential biomarkers for the diagnosis of Alzheimer's disease. Proteomics. 2003 Aug;3(8):1486–1494. doi: 10.1002/pmic.200300470. [DOI] [PubMed] [Google Scholar]
  38. Carver Tim, Bleasby Alan. The design of Jemboss: a graphical user interface to EMBOSS. Bioinformatics. 2003 Sep 22;19(14):1837–1843. doi: 10.1093/bioinformatics/btg251. [DOI] [PubMed] [Google Scholar]
  39. Chanda Sumit K., White Suhaila, Orth Anthony P., Reisdorph Richard, Miraglia Loren, Thomas Russell S., DeJesus Paul, Mason Daniel E., Huang Qihong, Vega Raquel. Genome-scale functional profiling of the mammalian AP-1 signaling pathway. Proc Natl Acad Sci U S A. 2003 Sep 26;100(21):12153–12158. doi: 10.1073/pnas.1934839100. [DOI] [PMC free article] [PubMed] [Google Scholar]
  40. Che F. Y., Eipper B. A., Mains R. E., Fricker L. D. Quantitative peptidomics of pituitary glands from mice deficient in copper transport. Cell Mol Biol (Noisy-le-grand) 2003 Jul;49(5):713–722. [PubMed] [Google Scholar]
  41. Chemale Gustavo, van Rossum Arjan J., Jefferies James R., Barrett John, Brophy Peter M., Ferreira Henrique B., Zaha Arnaldo. Proteomic analysis of the larval stage of the parasite Echinococcus granulosus: causative agent of cystic hydatid disease. Proteomics. 2003 Aug;3(8):1633–1636. doi: 10.1002/pmic.200300487. [DOI] [PubMed] [Google Scholar]
  42. Chen I-Peng, Haehnel Urs, Altschmied Lothar, Schubert Ingo, Puchta Holger. The transcriptional response of Arabidopsis to genotoxic stress - a high-density colony array study (HDCA). Plant J. 2003 Sep;35(6):771–786. doi: 10.1046/j.1365-313x.2003.01847.x. [DOI] [PubMed] [Google Scholar]
  43. Chen Limin, Goryachev Andrew, Sun Jin, Kim Peter, Zhang Hui, Phillips M. James, Macgregor Pascale, Lebel Sylvie, Edwards Aled M., Cao Qiongfang. Altered expression of genes involved in hepatic morphogenesis and fibrogenesis are identified by cDNA microarray analysis in biliary atresia. Hepatology. 2003 Sep;38(3):567–576. doi: 10.1053/jhep.2003.50363. [DOI] [PubMed] [Google Scholar]
  44. Chen Shuangyan, Jin Weizheng, Wang Mingyi, Zhang Fan, Zhou Jie, Jia Qiaojun, Wu Yunrong, Liu Feiyan, Wu Ping. Distribution and characterization of over 1000 T-DNA tags in rice genome. Plant J. 2003 Oct;36(1):105–113. doi: 10.1046/j.1365-313x.2003.01860.x. [DOI] [PubMed] [Google Scholar]
  45. Chen Wan-Nan U., Yu Li-Rong, Strittmatter Eric F., Thrall Brian D., Camp David G., 2nd, Smith Richard D. Detection of in situ labeled cell surface proteins by mass spectrometry: application to the membrane subproteome of human mammary epithelial cells. Proteomics. 2003 Aug;3(8):1647–1651. doi: 10.1002/pmic.200300468. [DOI] [PubMed] [Google Scholar]
  46. Chen Wei, Fu Xiaobing, Sun Xiaoqing, Sun Tongzhu, Zhao Zhili, Sheng Zhiyong. Analysis of differentially expressed genes in keloids and normal skin with cDNA microarray. J Surg Res. 2003 Aug;113(2):208–216. doi: 10.1016/s0022-4804(03)00188-4. [DOI] [PubMed] [Google Scholar]
  47. Chi Jen-Tsan, Chang Howard Y., Haraldsen Guttorm, Jahnsen Frode L., Troyanskaya Olga G., Chang Dustin S., Wang Zhen, Rockson Stanley G., van de Rijn Matt, Botstein David. Endothelial cell diversity revealed by global expression profiling. Proc Natl Acad Sci U S A. 2003 Sep 8;100(19):10623–10628. doi: 10.1073/pnas.1434429100. [DOI] [PMC free article] [PubMed] [Google Scholar]
  48. Chowers Itay, Gunatilaka Tushara L., Farkas Ronald H., Qian Jiang, Hackam Abigail S., Duh Elia, Kageyama Masaaki, Wang Chenwei, Vora Amit, Campochiaro Peter A. Identification of novel genes preferentially expressed in the retina using a custom human retina cDNA microarray. Invest Ophthalmol Vis Sci. 2003 Sep;44(9):3732–3741. doi: 10.1167/iovs.02-1080. [DOI] [PubMed] [Google Scholar]
  49. Clarke William, Silverman Benjamin C., Zhang Zhen, Chan Daniel W., Klein Andrew S., Molmenti Ernesto P. Characterization of renal allograft rejection by urinary proteomic analysis. Ann Surg. 2003 May;237(5):660–665. doi: 10.1097/01.SLA.0000064293.57770.42. [DOI] [PMC free article] [PubMed] [Google Scholar]
  50. Cole Steve W., Galic Zoran, Zack Jerome A. Controlling false-negative errors in microarray differential expression analysis: a PRIM approach. Bioinformatics. 2003 Sep 22;19(14):1808–1816. doi: 10.1093/bioinformatics/btg242. [DOI] [PubMed] [Google Scholar]
  51. Colinge Jacques, Magnin Jérôme, Dessingy Thierry, Giron Marc, Masselot Alexandre. Improved peptide charge state assignment. Proteomics. 2003 Aug;3(8):1434–1440. doi: 10.1002/pmic.200300489. [DOI] [PubMed] [Google Scholar]
  52. Colinge Jacques, Masselot Alexandre, Giron Marc, Dessingy Thierry, Magnin Jérôme. OLAV: towards high-throughput tandem mass spectrometry data identification. Proteomics. 2003 Aug;3(8):1454–1463. doi: 10.1002/pmic.200300485. [DOI] [PubMed] [Google Scholar]
  53. Coombes Kevin R., Fritsche Herbert A., Jr, Clarke Charlotte, Chen Jeng-Neng, Baggerly Keith A., Morris Jeffrey S., Xiao Lian-Chun, Hung Mien-Chie, Kuerer Henry M. Quality control and peak finding for proteomics data collected from nipple aspirate fluid by surface-enhanced laser desorption and ionization. Clin Chem. 2003 Oct;49(10):1615–1623. doi: 10.1373/49.10.1615. [DOI] [PubMed] [Google Scholar]
  54. Creevey C. J., McInerney J. O. CRANN: detecting adaptive evolution in protein-coding DNA sequences. Bioinformatics. 2003 Sep 1;19(13):1726–1726. doi: 10.1093/bioinformatics/btg225. [DOI] [PubMed] [Google Scholar]
  55. Cuppen Edwin, van der Linden Alexander M., Jansen Gert, Plasterk Ronald H. A. Proteins interacting with Caenorhabditis elegans Galpha subunits. Comp Funct Genomics. 2003;4(5):479–491. doi: 10.1002/cfg.318. [DOI] [PMC free article] [PubMed] [Google Scholar]
  56. Damoc Eugen, Youhnovski Nikolay, Crettaz David, Tissot Jean-Daniel, Przybylski Michael. High resolution proteome analysis of cryoglobulins using Fourier transform-ion cyclotron resonance mass spectrometry. Proteomics. 2003 Aug;3(8):1425–1433. doi: 10.1002/pmic.200300482. [DOI] [PubMed] [Google Scholar]
  57. Date Shailesh V., Marcotte Edward M. Discovery of uncharacterized cellular systems by genome-wide analysis of functional linkages. Nat Biotechnol. 2003 Aug 17;21(9):1055–1062. doi: 10.1038/nbt861. [DOI] [PubMed] [Google Scholar]
  58. Davids Wagied, Fuxelius Hans-Henrik, Andersson Siv G. E. The Journey to smORFland. Comp Funct Genomics. 2003;4(5):537–541. doi: 10.1002/cfg.325. [DOI] [PMC free article] [PubMed] [Google Scholar]
  59. Davidsson P., Brinkmalm A., Karlsson G., Persson R., Lindbjer M., Puchades M., Folkesson S., Paulson L., Dahl A., Rymo L. Clinical mass spectrometry in neuroscience. Proteomics and peptidomics. Cell Mol Biol (Noisy-le-grand) 2003 Jul;49(5):681–688. [PubMed] [Google Scholar]
  60. DeFilippis Victor, Raggo Camilo, Moses Ashlee, Früh Klaus. Functional genomics in virology and antiviral drug discovery. Trends Biotechnol. 2003 Oct;21(10):452–457. doi: 10.1016/S0167-7799(03)00207-5. [DOI] [PMC free article] [PubMed] [Google Scholar]
  61. Denef Vincent J., Park Joonhong, Rodrigues Jorge L. M., Tsoi Tamara V., Hashsham Syed A., Tiedje James M. Validation of a more sensitive method for using spotted oligonucleotide DNA microarrays for functional genomics studies on bacterial communities. Environ Microbiol. 2003 Oct;5(10):933–943. doi: 10.1046/j.1462-2920.2003.00490.x. [DOI] [PubMed] [Google Scholar]
  62. Desai Apurva A., Innocenti Federico, Ratain Mark J. Pharmacogenomics: road to anticancer therapeutics nirvana? Oncogene. 2003 Sep 29;22(42):6621–6628. doi: 10.1038/sj.onc.1206958. [DOI] [PubMed] [Google Scholar]
  63. Deshusses Jacques M. P., Burgess Jennifer A., Scherl Alexander, Wenger Yvan, Walter Nadia, Converset Véronique, Paesano Salvo, Corthals Garry L., Hochstrasser Denis F., Sanchez Jean-Charles. Exploitation of specific properties of trifluoroethanol for extraction and separation of membrane proteins. Proteomics. 2003 Aug;3(8):1418–1424. doi: 10.1002/pmic.200300492. [DOI] [PubMed] [Google Scholar]
  64. Desiderio D. M., Zhan X. The human pituitary proteome: the characterization of differentially expressed proteins in an adenoma compared to a control. Cell Mol Biol (Noisy-le-grand) 2003 Jul;49(5):689–712. [PubMed] [Google Scholar]
  65. Dhillon Inderjit S., Marcotte Edward M., Roshan Usman. Diametrical clustering for identifying anti-correlated gene clusters. Bioinformatics. 2003 Sep 1;19(13):1612–1619. doi: 10.1093/bioinformatics/btg209. [DOI] [PubMed] [Google Scholar]
  66. Dorn Gabriele, Hall Jonathan, Hüsken Dieter, Lange Jörg, Martin Pierre, Natt Francois, Wishart William L., Weiler Jan. A role for oligonucleotide-based RNA-knock down technologies in functional genomics. Nucleosides Nucleotides Nucleic Acids. 2003 May-Aug;22(5-8):641–644. doi: 10.1081/NCN-120021970. [DOI] [PubMed] [Google Scholar]
  67. Dowsey Andrew W., Dunn Michael J., Yang Guang-Zhong. The role of bioinformatics in two-dimensional gel electrophoresis. Proteomics. 2003 Aug;3(8):1567–1596. doi: 10.1002/pmic.200300459. [DOI] [PubMed] [Google Scholar]
  68. Du Jian-Jun, Dou Ke-Feng, Peng Shu-You, Xiao Hua-Sheng, Wang Wei-Zhong, Guan Wen-Xian, Wang Zhong-Hua, Gao Zhi-Qing, Liu Ying-Bin. cDNA suppression subtraction library for screening down-regulated genes in gastric carcinoma. World J Gastroenterol. 2003 Jul;9(7):1439–1443. doi: 10.3748/wjg.v9.i7.1439. [DOI] [PMC free article] [PubMed] [Google Scholar]
  69. Duzhak T., Emerson M. R., Chakrabarty A., Alterman M. A., LeVine S. M. Analysis of protein induction in the CNS of SJL mice with experimental allergic encephalomyelitis by proteomic screening and immunohistochemistry. Cell Mol Biol (Noisy-le-grand) 2003 Jul;49(5):723–732. [PubMed] [Google Scholar]
  70. Espanhol Aline R., Macedo Cláudia, Junta Cristina M., Cardoso Renato Sousa, Victorero Geneviève, Loriod Beatrice, Nguyen Catherine, Jordan Bertrand, Passos Geraldo A. S. Gene expression profiling during thymus ontogeny and its association with TCRVbeta8.1-Dbeta2.1 rearrangements of inbred mouse strains. Mol Cell Biochem. 2003 Oct;252(1-2):223–228. doi: 10.1023/a:1025556510001. [DOI] [PubMed] [Google Scholar]
  71. Evans Edward C., Horn Troy, Wagner Mary Ann, Eschenbrenner Michel, Mujer Cesar V., DelVecchio Vito G. Isolation protocol for two-dimensional-polyacrylamide gel electrophoresis analysis of Haloferax volcanii proteome. Biotechniques. 2003 Sep;35(3):478-80, 482. doi: 10.2144/03353bm07. [DOI] [PubMed] [Google Scholar]
  72. Fachado Alberto, Rodriguez Alexandro, Molina Judith, Silvério Jaline C., Marino Ana P. M. P., Pinto Luzia M. O., Angel Sergio O., Infante Juan F., Traub-Cseko Yara, Amendoeira Regina R. Long-term protective immune response elicited by vaccination with an expression genomic library of Toxoplasma gondii. Infect Immun. 2003 Sep;71(9):5407–5411. doi: 10.1128/IAI.71.9.5407-5411.2003. [DOI] [PMC free article] [PubMed] [Google Scholar]
  73. Feldker Dorine E. M., de Kloet E. Ronald, Kruk Menno R., Datson Nicole A. Large-scale gene expression profiling of discrete brain regions: potential, limitations, and application in genetics of aggressive behavior. Behav Genet. 2003 Sep;33(5):537–548. doi: 10.1023/a:1025726801047. [DOI] [PubMed] [Google Scholar]
  74. Ferguson P. Lee, Smith Richard D. Proteome analysis by mass spectrometry. Annu Rev Biophys Biomol Struct. 2003 Jan 28;32:399–424. doi: 10.1146/annurev.biophys.32.110601.141854. [DOI] [PubMed] [Google Scholar]
  75. Ferrando Adolfo A., Look A. Thomas. Gene expression profiling in T-cell acute lymphoblastic leukemia. Semin Hematol. 2003 Oct;40(4):274–280. doi: 10.1016/s0037-1963(03)00195-1. [DOI] [PubMed] [Google Scholar]
  76. Ferrè Fabrizio, Via Allegra, Ausiello Gabriele, Brannetti Barbara, Zanzoni Andreas, Helmer-Citterich Manuela. Development of computational tools for the inference of protein interaction specificity rules and functional annotation using structural information. Comp Funct Genomics. 2003;4(4):416–419. doi: 10.1002/cfg.304. [DOI] [PMC free article] [PubMed] [Google Scholar]
  77. Firneisz Gábor, Zehavi Idit, Vermes Csaba, Hanyecz Anita, Frieman Joshua A., Glant Tibor T. Identification and quantification of disease-related gene clusters. Bioinformatics. 2003 Sep 22;19(14):1781–1786. doi: 10.1093/bioinformatics/btg252. [DOI] [PubMed] [Google Scholar]
  78. Gabdoulline Razif R., Hoffmann René, Leitner Florian, Wade Rebecca C. ProSAT: functional annotation of protein 3D structures. Bioinformatics. 2003 Sep 1;19(13):1723–1725. doi: 10.1093/bioinformatics/btg220. [DOI] [PubMed] [Google Scholar]
  79. Gadal Franck, Bozic Christophe, Pillot-Brochet Céline, Malinge Sophie, Wagner Sarah, Le Cam Aurélie, Buffat Laurent, Crepin Michel, Iris François. Integrated transcriptome analysis of the cellular mechanisms associated with Ha-ras-dependent malignant transformation of the human breast epithelial MCF7 cell line. Nucleic Acids Res. 2003 Oct 1;31(19):5789–5804. doi: 10.1093/nar/gkg762. [DOI] [PMC free article] [PubMed] [Google Scholar]
  80. Gadgil Himanshu S., Pabst Karen M., Giorgianni Francesco, Umstot Edward S., Desiderio Dominic M., Beranova-Giorgianni Sarka, Gerling Ivan C., Pabst Michael J. Proteome of monocytes primed with lipopolysaccharide: analysis of the abundant proteins. Proteomics. 2003 Sep;3(9):1767–1780. doi: 10.1002/pmic.200300532. [DOI] [PubMed] [Google Scholar]
  81. Galindo Cristi L., Sha Jian, Ribardo Deborah A., Fadl Amin A., Pillai Lakshmi, Chopra Ashok K. Identification of Aeromonas hydrophila cytotoxic enterotoxin-induced genes in macrophages using microarrays. J Biol Chem. 2003 Jun 24;278(41):40198–40212. doi: 10.1074/jbc.M305788200. [DOI] [PubMed] [Google Scholar]
  82. Galinsky Vitaly L. Automatic registration of microarray images. I. Rectangular grid. Bioinformatics. 2003 Sep 22;19(14):1824–1831. doi: 10.1093/bioinformatics/btg259. [DOI] [PubMed] [Google Scholar]
  83. Galinsky Vitaly L. Automatic registration of microarray images. II. Hexagonal grid. Bioinformatics. 2003 Sep 22;19(14):1832–1836. doi: 10.1093/bioinformatics/btg260. [DOI] [PubMed] [Google Scholar]
  84. Gammill Laura S., Bronner-Fraser Marianne. Neural crest specification: migrating into genomics. Nat Rev Neurosci. 2003 Oct;4(10):795–805. doi: 10.1038/nrn1219. [DOI] [PubMed] [Google Scholar]
  85. Geller Sue C., Gregg Jeff P., Hagerman Paul, Rocke David M. Transformation and normalization of oligonucleotide microarray data. Bioinformatics. 2003 Sep 22;19(14):1817–1823. doi: 10.1093/bioinformatics/btg245. [DOI] [PubMed] [Google Scholar]
  86. Gentzel Marc, Köcher Thomas, Ponnusamy Saravanan, Wilm Matthias. Preprocessing of tandem mass spectrometric data to support automatic protein identification. Proteomics. 2003 Aug;3(8):1597–1610. doi: 10.1002/pmic.200300486. [DOI] [PubMed] [Google Scholar]
  87. Gissi Carmela, Pesole Graziano. Transcript mapping and genome annotation of ascidian mtDNA using EST data. Genome Res. 2003 Aug 12;13(9):2203–2212. doi: 10.1101/gr.1227803. [DOI] [PMC free article] [PubMed] [Google Scholar]
  88. Goldsmith-Fischman Sharon, Honig Barry. Structural genomics: computational methods for structure analysis. Protein Sci. 2003 Sep;12(9):1813–1821. doi: 10.1110/ps.0242903. [DOI] [PMC free article] [PubMed] [Google Scholar]
  89. Golubov Andrey, Heesemann Jürgen, Rakin Alexander. Uncovering genomic differences in human pathogenic Yersinia enterocolitica. FEMS Immunol Med Microbiol. 2003 Sep 22;38(2):107–111. doi: 10.1016/S0928-8244(03)00182-2. [DOI] [PubMed] [Google Scholar]
  90. Gong Shiaoching, Zheng Chen, Doughty Martin L., Losos Kasia, Didkovsky Nicholas, Schambra Uta B., Nowak Norma J., Joyner Alexandra, Leblanc Gabrielle, Hatten Mary E. A gene expression atlas of the central nervous system based on bacterial artificial chromosomes. Nature. 2003 Oct 30;425(6961):917–925. doi: 10.1038/nature02033. [DOI] [PubMed] [Google Scholar]
  91. González-Maeso Javier, Yuen Tony, Ebersole Barbara J., Wurmbach Elisa, Lira Alena, Zhou Mingming, Weisstaub Noelia, Hen Rene, Gingrich Jay A., Sealfon Stuart C. Transcriptome fingerprints distinguish hallucinogenic and nonhallucinogenic 5-hydroxytryptamine 2A receptor agonist effects in mouse somatosensory cortex. J Neurosci. 2003 Oct 1;23(26):8836–8843. doi: 10.1523/JNEUROSCI.23-26-08836.2003. [DOI] [PMC free article] [PubMed] [Google Scholar]
  92. Grzeskowiak Rafal, Witt Henning, Drungowski Mario, Thermann Rolf, Hennig Steffen, Perrot Andreas, Osterziel Karl J., Klingbiel Dirk, Scheid Stefanie, Spang Rainer. Expression profiling of human idiopathic dilated cardiomyopathy. Cardiovasc Res. 2003 Aug 1;59(2):400–411. doi: 10.1016/s0008-6363(03)00426-7. [DOI] [PubMed] [Google Scholar]
  93. Guillaume Elisabeth, Zimmermann Catherine, Burkhard Pierre R., Hochstrasser Denis F., Sanchez Jean-Charles. A potential cerebrospinal fluid and plasmatic marker for the diagnosis of Creutzfeldt-Jakob disease. Proteomics. 2003 Aug;3(8):1495–1499. doi: 10.1002/pmic.200300478. [DOI] [PubMed] [Google Scholar]
  94. Guo Xu, Qi Huilin, Verfaillie Catherine M., Pan Wei. Statistical significance analysis of longitudinal gene expression data. Bioinformatics. 2003 Sep 1;19(13):1628–1635. doi: 10.1093/bioinformatics/btg206. [DOI] [PubMed] [Google Scholar]
  95. Güimil R., Beier M., Scheffler M., Rebscher H., Funk J., Wixmerten A., Baum M., Hermann C., Tahedl H., Moschel E. Geniom technology--the benchtop array facility. Nucleosides Nucleotides Nucleic Acids. 2003 May-Aug;22(5-8):1721–1723. doi: 10.1081/NCN-120023122. [DOI] [PubMed] [Google Scholar]
  96. Haas Brian J., Delcher Arthur L., Mount Stephen M., Wortman Jennifer R., Smith Roger K., Jr, Hannick Linda I., Maiti Rama, Ronning Catherine M., Rusch Douglas B., Town Christopher D. Improving the Arabidopsis genome annotation using maximal transcript alignment assemblies. Nucleic Acids Res. 2003 Oct 1;31(19):5654–5666. doi: 10.1093/nar/gkg770. [DOI] [PMC free article] [PubMed] [Google Scholar]
  97. Haferlach Torsten, Kohlmann Alexander, Kern Wolfgang, Hiddemann Wolfgang, Schnittger Susanne, Schoch Claudia. Gene expression profiling as a tool for the diagnosis of acute leukemias. Semin Hematol. 2003 Oct;40(4):281–295. doi: 10.1016/s0037-1963(03)00193-8. [DOI] [PubMed] [Google Scholar]
  98. Halitschke Rayko, Gase Klaus, Hui Dequan, Schmidt Dominik D., Baldwin Ian T. Molecular interactions between the specialist herbivore Manduca sexta (lepidoptera, sphingidae) and its natural host Nicotiana attenuata. VI. Microarray analysis reveals that most herbivore-specific transcriptional changes are mediated by fatty acid-amino acid conjugates. Plant Physiol. 2003 Apr;131(4):1894–1902. doi: 10.1104/pp.102.018184. [DOI] [PMC free article] [PubMed] [Google Scholar]
  99. Harrison Andrew, Pearl Frances, Sillitoe Ian, Slidel Tim, Mott Richard, Thornton Janet, Orengo Christine. Recognizing the fold of a protein structure. Bioinformatics. 2003 Sep 22;19(14):1748–1759. doi: 10.1093/bioinformatics/btg240. [DOI] [PubMed] [Google Scholar]
  100. Hashimoto Shin-Ichi, Morohoshi Kei, Suzuki Takuji, Matsushima Kouji. Lipopolysaccharide-inducible gene expression profile in human monocytes. Scand J Infect Dis. 2003;35(9):619–627. [PubMed] [Google Scholar]
  101. Hattori Masahiro, Okuno Yasushi, Goto Susumu, Kanehisa Minoru. Development of a chemical structure comparison method for integrated analysis of chemical and genomic information in the metabolic pathways. J Am Chem Soc. 2003 Oct 1;125(39):11853–11865. doi: 10.1021/ja036030u. [DOI] [PubMed] [Google Scholar]
  102. Hayano Toshiya, Yanagida Mitsuaki, Yamauchi Yoshio, Shinkawa Takashi, Isobe Toshiaki, Takahashi Nobuhiro. Proteomic analysis of human Nop56p-associated pre-ribosomal ribonucleoprotein complexes. Possible link between Nop56p and the nucleolar protein treacle responsible for Treacher Collins syndrome. J Biol Chem. 2003 May 30;278(36):34309–34319. doi: 10.1074/jbc.M304304200. [DOI] [PubMed] [Google Scholar]
  103. He Xiu-Yun, Zhuang Yu-Hui, Zhang Xiao-Gang, Li Guo-Li. Comparative proteome analysis of culture supernatant proteins of Mycobacterium tuberculosis H37Rv and H37Ra. Microbes Infect. 2003 Aug;5(10):851–856. doi: 10.1016/s1286-4579(03)00179-5. [DOI] [PubMed] [Google Scholar]
  104. Heazlewood Joshua L., Howell Katharine A., Whelan James, Millar A. Harvey. Towards an analysis of the rice mitochondrial proteome. Plant Physiol. 2003 May;132(1):230–242. doi: 10.1104/pp.102.018986. [DOI] [PMC free article] [PubMed] [Google Scholar]
  105. Hedvat Cyrus V., Comenzo Raymond L., Teruya-Feldstein Julie, Olshen Adam B., Ely Scott A., Osman Keren, Zhang Yana, Kalakonda Nagesh, Nimer Stephen D. Insights into extramedullary tumour cell growth revealed by expression profiling of human plasmacytomas and multiple myeloma. Br J Haematol. 2003 Sep;122(5):728–744. doi: 10.1046/j.1365-2141.2003.04481.x. [DOI] [PubMed] [Google Scholar]
  106. Hellerstein Marc K. In vivo measurement of fluxes through metabolic pathways: the missing link in functional genomics and pharmaceutical research. Annu Rev Nutr. 2003 Apr 16;23:379–402. doi: 10.1146/annurev.nutr.23.011702.073045. [DOI] [PubMed] [Google Scholar]
  107. Henikoff Steven, Comai Luca. Single-nucleotide mutations for plant functional genomics. Annu Rev Plant Biol. 2003;54:375–401. doi: 10.1146/annurev.arplant.54.031902.135009. [DOI] [PubMed] [Google Scholar]
  108. Hering Joachim A., Innocent Peter R., Haris Parvez I. Neuro-fuzzy structural classification of proteins for improved protein secondary structure prediction. Proteomics. 2003 Aug;3(8):1464–1475. doi: 10.1002/pmic.200300457. [DOI] [PubMed] [Google Scholar]
  109. Herrmann Paul C., Gillespie John W., Charboneau Lu, Bichsel Verena E., Paweletz Cloud P., Calvert Valerie S., Kohn Elise C., Emmert-Buck Michael R., Liotta Lance A., Petricoin Emanuel F., 3rd Mitochondrial proteome: altered cytochrome c oxidase subunit levels in prostate cancer. Proteomics. 2003 Sep;3(9):1801–1810. doi: 10.1002/pmic.200300461. [DOI] [PubMed] [Google Scholar]
  110. Herron-Olson Lisa, Freeman John, Zhang Qing, Retzel Ernest F., Kapur Vivek. MGView: an alignment and visualization tool to enhance gap closure of microbial genomes. Nucleic Acids Res. 2003 Sep 1;31(17):e106–e106. doi: 10.1093/nar/gng107. [DOI] [PMC free article] [PubMed] [Google Scholar]
  111. Hestvik Anne Lise K., Hmama Zakaria, Av-Gay Yossef. Kinome analysis of host response to mycobacterial infection: a novel technique in proteomics. Infect Immun. 2003 Oct;71(10):5514–5522. doi: 10.1128/IAI.71.10.5514-5522.2003. [DOI] [PMC free article] [PubMed] [Google Scholar]
  112. Hilario Melanie, Kalousis Alexandros, Müller Markus, Pellegrini Christian. Machine learning approaches to lung cancer prediction from mass spectra. Proteomics. 2003 Sep;3(9):1716–1719. doi: 10.1002/pmic.200300523. [DOI] [PubMed] [Google Scholar]
  113. Hilson Pierre, Small Ian, Kuiper Martin T. R. European consortia building integrated resources for Arabidopsis functional genomics. Curr Opin Plant Biol. 2003 Oct;6(5):426–429. doi: 10.1016/s1369-5266(03)00086-4. [DOI] [PubMed] [Google Scholar]
  114. Hinchliffe Stewart J., Isherwood Karen E., Stabler Richard A., Prentice Michael B., Rakin Alexander, Nichols Richard A., Oyston Petra C. F., Hinds Jason, Titball Richard W., Wren Brendan W. Application of DNA microarrays to study the evolutionary genomics of Yersinia pestis and Yersinia pseudotuberculosis. Genome Res. 2003 Sep;13(9):2018–2029. doi: 10.1101/gr.1507303. [DOI] [PMC free article] [PubMed] [Google Scholar]
  115. Hiratsuka Masaharu, Inoue Toshiaki, Toda Tosifusa, Kimura Narimichi, Shirayoshi Yasuaki, Kamitani Hideki, Watanabe Takashi, Ohama Eisaku, Tahimic Candice G. T., Kurimasa Akihiro. Proteomics-based identification of differentially expressed genes in human gliomas: down-regulation of SIRT2 gene. Biochem Biophys Res Commun. 2003 Sep 26;309(3):558–566. doi: 10.1016/j.bbrc.2003.08.029. [DOI] [PubMed] [Google Scholar]
  116. Honys David, Twell David. Comparative analysis of the Arabidopsis pollen transcriptome. Plant Physiol. 2003 Jun;132(2):640–652. doi: 10.1104/pp.103.020925. [DOI] [PMC free article] [PubMed] [Google Scholar]
  117. Howard Brandon A., Wang Michael Z., Campa Michael J., Corro Christina, Fitzgerald Michael C., Patz Edward F., Jr Identification and validation of a potential lung cancer serum biomarker detected by matrix-assisted laser desorption/ionization-time of flight spectra analysis. Proteomics. 2003 Sep;3(9):1720–1724. doi: 10.1002/pmic.200300514. [DOI] [PubMed] [Google Scholar]
  118. Huang Meng-Er, Rio Anne-Gaelle, Nicolas Alain, Kolodner Richard D. A genomewide screen in Saccharomyces cerevisiae for genes that suppress the accumulation of mutations. Proc Natl Acad Sci U S A. 2003 Sep 12;100(20):11529–11534. doi: 10.1073/pnas.2035018100. [DOI] [PMC free article] [PubMed] [Google Scholar]
  119. Huang Xiaoqiu, Wang Jianmin, Aluru Srinivas, Yang Shiaw-Pyng, Hillier LaDeana. PCAP: a whole-genome assembly program. Genome Res. 2003 Sep;13(9):2164–2170. doi: 10.1101/gr.1390403. [DOI] [PMC free article] [PubMed] [Google Scholar]
  120. Hui Dequan, Iqbal Javeed, Lehmann Katja, Gase Klaus, Saluz Hans Peter, Baldwin Ian T. Molecular interactions between the specialist herbivore Manduca sexta (lepidoptera, sphingidae) and its natural host Nicotiana attenuata: V. microarray analysis and further characterization of large-scale changes in herbivore-induced mRNAs. Plant Physiol. 2003 Apr;131(4):1877–1893. doi: 10.1104/pp.102.018176. [DOI] [PMC free article] [PubMed] [Google Scholar]
  121. Huntley Derek, Hummerich Holger, Smedley Damian, Kittivoravitkul Sasivimol, McCarthy Mark, Little Peter, Sergot Marek. GANESH: software for customized annotation of genome regions. Genome Res. 2003 Sep;13(9):2195–2202. doi: 10.1101/gr.698103. [DOI] [PMC free article] [PubMed] [Google Scholar]
  122. Iourgenko Vadim, Zhang Wenjun, Mickanin Craig, Daly Ira, Jiang Can, Hexham Jonathan M., Orth Anthony P., Miraglia Loren, Meltzer Jodi, Garza Dan. Identification of a family of cAMP response element-binding protein coactivators by genome-scale functional analysis in mammalian cells. Proc Natl Acad Sci U S A. 2003 Sep 23;100(21):12147–12152. doi: 10.1073/pnas.1932773100. [DOI] [PMC free article] [PubMed] [Google Scholar]
  123. Itoh T., Takasuga A., Watanabe T., Sugimoto Y. Mapping of 1400 expressed sequence tags in the bovine genome using a somatic cell hybrid panel. Anim Genet. 2003 Oct;34(5):362–370. doi: 10.1046/j.1365-2052.2003.01014.x. [DOI] [PubMed] [Google Scholar]
  124. Jansen Ronald, Yu Haiyuan, Greenbaum Dov, Kluger Yuval, Krogan Nevan J., Chung Sambath, Emili Andrew, Snyder Michael, Greenblatt Jack F., Gerstein Mark. A Bayesian networks approach for predicting protein-protein interactions from genomic data. Science. 2003 Oct 17;302(5644):449–453. doi: 10.1126/science.1087361. [DOI] [PubMed] [Google Scholar]
  125. Jenner Richard G., Maillard Karine, Cattini Nicola, Weiss Robin A., Boshoff Chris, Wooster Richard, Kellam Paul. Kaposi's sarcoma-associated herpesvirus-infected primary effusion lymphoma has a plasma cell gene expression profile. Proc Natl Acad Sci U S A. 2003 Aug 18;100(18):10399–10404. doi: 10.1073/pnas.1630810100. [DOI] [PMC free article] [PubMed] [Google Scholar]
  126. Johnsson Nils, Johnsson Kai. A fusion of disciplines: chemical approaches to exploit fusion proteins for functional genomics. Chembiochem. 2003 Sep 5;4(9):803–810. doi: 10.1002/cbic.200200603. [DOI] [PubMed] [Google Scholar]
  127. Jones Andrew, Wastling Jonathan, Hunt Ela. Proposal for a standard representation of two-dimensional gel electrophoresis data. Comp Funct Genomics. 2003;4(5):492–501. doi: 10.1002/cfg.323. [DOI] [PMC free article] [PubMed] [Google Scholar]
  128. Jones Susan, Thornton Janet M. Protein-DNA interactions: the story so far and a new method for prediction. Comp Funct Genomics. 2003;4(4):428–431. doi: 10.1002/cfg.303. [DOI] [PMC free article] [PubMed] [Google Scholar]
  129. Joshi Rajani R., Jyothi S. Ab-initio prediction and reliability of protein structural genomics by PROPAINOR algorithm. Comput Biol Chem. 2003 Jul;27(3):241–252. doi: 10.1016/s0097-8485(02)00074-8. [DOI] [PubMed] [Google Scholar]
  130. Kaderbhai Naheed N., Broadhurst David I., Ellis David I., Goodacre Royston, Kell Douglas B. Functional genomics via metabolic footprinting: monitoring metabolite secretion by Escherichia coli tryptophan metabolism mutants using FT-IR and direct injection electrospray mass spectrometry. Comp Funct Genomics. 2003;4(4):376–391. doi: 10.1002/cfg.302. [DOI] [PMC free article] [PubMed] [Google Scholar]
  131. Kerk David, Bulgrien Joshua, Smith Douglas W., Gribskov Michael. Arabidopsis proteins containing similarity to the universal stress protein domain of bacteria. Plant Physiol. 2003 Mar;131(3):1209–1219. doi: 10.1104/pp.102.016006. [DOI] [PMC free article] [PubMed] [Google Scholar]
  132. Kiechle Frederick L., Holland-Staley Carol A. Genomics, transcriptomics, proteomics, and numbers. Arch Pathol Lab Med. 2003 Sep;127(9):1089–1097. doi: 10.5858/2003-127-1089-GTPAN. [DOI] [PubMed] [Google Scholar]
  133. Kirkness Ewen F., Bafna Vineet, Halpern Aaron L., Levy Samuel, Remington Karin, Rusch Douglas B., Delcher Arthur L., Pop Mihai, Wang Wei, Fraser Claire M. The dog genome: survey sequencing and comparative analysis. Science. 2003 Sep 26;301(5641):1898–1903. doi: 10.1126/science.1086432. [DOI] [PubMed] [Google Scholar]
  134. Koj Aleksander, Jura Jolanta. Complex analysis of genes involved in the inflammatory response: interleukin-1-induced differential transcriptome of cultured human hepatoma HepG2 cells. Acta Biochim Pol. 2003;50(3):573–582. [PubMed] [Google Scholar]
  135. Kondo Tadashi, Seike Masahiro, Mori Yasuharu, Fujii Kazuyasu, Yamada Tesshi, Hirohashi Setsuo. Application of sensitive fluorescent dyes in linkage of laser microdissection and two-dimensional gel electrophoresis as a cancer proteomic study tool. Proteomics. 2003 Sep;3(9):1758–1766. doi: 10.1002/pmic.200300531. [DOI] [PubMed] [Google Scholar]
  136. Krayl Martin, Benndorf Dirk, Loffhagen Norbert, Babel Wolfgang. Use of proteomics and physiological characteristics to elucidate ecotoxic effects of methyl tert-butyl ether in Pseudomonas putida KT2440. Proteomics. 2003 Aug;3(8):1544–1552. doi: 10.1002/pmic.200300477. [DOI] [PubMed] [Google Scholar]
  137. Kreil David P., Ouzounis Christos A. Comparison of sequence masking algorithms and the detection of biased protein sequence regions. Bioinformatics. 2003 Sep 1;19(13):1672–1681. doi: 10.1093/bioinformatics/btg212. [DOI] [PubMed] [Google Scholar]
  138. Kyng Kasper J., May Alfred, Kølvraa Steen, Bohr Vilhelm A. Gene expression profiling in Werner syndrome closely resembles that of normal aging. Proc Natl Acad Sci U S A. 2003 Oct 3;100(21):12259–12264. doi: 10.1073/pnas.2130723100. [DOI] [PMC free article] [PubMed] [Google Scholar]
  139. Landegren Ulf, Dahl Fredrik, Nilsson Mats, Fredriksson Simon, Banér Johan, Gullberg Mats, Jarvius Jonas, Gustafsdottir Sigrun, Söderberg Ola, Ericsson Olle, Stenberg Johan, Schallmeiner Edith. Padlock and proximity probes for in situ and array-based analyses: tools for the post-genomic era. Comp Funct Genomics. 2003;4(5):525–530. doi: 10.1002/cfg.326. [DOI] [PMC free article] [PubMed] [Google Scholar]
  140. Laws R. J., Bergemann T. L., Quiaoit F., Zhao L. P. SignalViewer: analyzing microarray images. Bioinformatics. 2003 Sep 1;19(13):1716–1717. doi: 10.1093/bioinformatics/btg208. [DOI] [PubMed] [Google Scholar]
  141. Le Roch Karine G., Zhou Yingyao, Blair Peter L., Grainger Muni, Moch J. Kathleen, Haynes J. David, De La Vega Patricia, Holder Anthony A., Batalov Serge, Carucci Daniel J. Discovery of gene function by expression profiling of the malaria parasite life cycle. Science. 2003 Jul 31;301(5639):1503–1508. doi: 10.1126/science.1087025. [DOI] [PubMed] [Google Scholar]
  142. Lee Kwan R., Lin Xiwu, Park Daniel C., Eslava Sergio. Megavariate data analysis of mass spectrometric proteomics data using latent variable projection method. Proteomics. 2003 Sep;3(9):1680–1686. doi: 10.1002/pmic.200300515. [DOI] [PubMed] [Google Scholar]
  143. Lefkovits Ivan. Quantitative proteomics of lymphocytes. Comp Funct Genomics. 2003;4(5):531–536. doi: 10.1002/cfg.322. [DOI] [PMC free article] [PubMed] [Google Scholar]
  144. Leinonen Rasko, Nardone Francesco, Oyewole Olalekan, Redaschi Nicole, Stoehr Peter. The EMBL sequence version archive. Bioinformatics. 2003 Sep 22;19(14):1861–1862. doi: 10.1093/bioinformatics/btg248. [DOI] [PubMed] [Google Scholar]
  145. Li Cui, Chen Zhuchu, Xiao Zhiqiang, Wu Xiaoying, Zhan Xianquan, Zhang Xiaopeng, Li Maoyu, Li JianLing, Feng Xueping, Liang Songping. Comparative proteomics analysis of human lung squamous carcinoma. Biochem Biophys Res Commun. 2003 Sep 12;309(1):253–260. doi: 10.1016/j.bbrc.2003.08.001. [DOI] [PubMed] [Google Scholar]
  146. Li Li, Stoeckert Christian J., Jr, Roos David S. OrthoMCL: identification of ortholog groups for eukaryotic genomes. Genome Res. 2003 Sep;13(9):2178–2189. doi: 10.1101/gr.1224503. [DOI] [PMC free article] [PubMed] [Google Scholar]
  147. Li Shuyu, Cutler Gene, Liu Jane Jijun, Hoey Timothy, Chen Liangbiao, Schultz Peter G., Liao Jiayu, Ling Xuefeng Bruce. A comparative analysis of HGSC and Celera human genome assemblies and gene sets. Bioinformatics. 2003 Sep 1;19(13):1597–1605. doi: 10.1093/bioinformatics/btg219. [DOI] [PubMed] [Google Scholar]
  148. Liao Xiang, Ying Tianyi, Wang Hengliang, Wang Jie, Shi Zhaoxing, Feng Erling, Wei Kaihua, Wang Yuelan, Zhang Xuemin, Huang Liuyu. A two-dimensional proteome map of Shigella flexneri. Electrophoresis. 2003 Aug;24(16):2864–2882. doi: 10.1002/elps.200305519. [DOI] [PubMed] [Google Scholar]
  149. Lin Ying, Huang Ruochun, Chen Li-Pai, Lisoukov Henry, Lu Zhen-Hai, Li Shiyong, Wang Cheng C., Huang Ruo-Pan. Profiling of cytokine expression by biotin-labeled-based protein arrays. Proteomics. 2003 Sep;3(9):1750–1757. doi: 10.1002/pmic.200300530. [DOI] [PubMed] [Google Scholar]
  150. Linial Michal. Fishing with (Proto)Net-a principled approach to protein target selection. Comp Funct Genomics. 2003;4(5):542–548. doi: 10.1002/cfg.328. [DOI] [PMC free article] [PubMed] [Google Scholar]
  151. Liu Jinyuan, Blaylock Laura A., Endre Gabriella, Cho Jennifer, Town Christopher D., VandenBosch Kathryn A., Harrison Maria J. Transcript profiling coupled with spatial expression analyses reveals genes involved in distinct developmental stages of an arbuscular mycorrhizal symbiosis. Plant Cell. 2003 Sep;15(9):2106–2123. doi: 10.1105/tpc.014183. [DOI] [PMC free article] [PubMed] [Google Scholar]
  152. Liu Lian-Xin, Jiang Hong-Chi, Liu Zhi-Hua, Zhu An-Long, Zhou Jing, Zhang Wei-Hui, Wang Xiu-Qin, Wu Min. Gene expression profiles of hepatoma cell line BEL-7402. Hepatogastroenterology. 2003 Sep-Oct;50(53):1496–1501. [PubMed] [Google Scholar]
  153. Maathuis Frans J. M., Filatov Victor, Herzyk Pawel, Krijger Gerard C., Axelsen Kristian B., Chen Sixue, Green Brian J., Li Yi, Madagan Kathryn L., Sánchez-Fernández Rocío. Transcriptome analysis of root transporters reveals participation of multiple gene families in the response to cation stress. Plant J. 2003 Sep;35(6):675–692. doi: 10.1046/j.1365-313x.2003.01839.x. [DOI] [PubMed] [Google Scholar]
  154. Mamone Gianfranco, Caira Simonetta, Garro Giuseppina, Nicolai Adalgisa, Ferranti Pasquale, Picariello Gianluca, Malorni Antonio, Chianese Lina, Addeo Francesco. Casein phosphoproteome: identification of phosphoproteins by combined mass spectrometry and two-dimensional gel electrophoresis. Electrophoresis. 2003 Aug;24(16):2824–2837. doi: 10.1002/elps.200305545. [DOI] [PubMed] [Google Scholar]
  155. Mao Chunhong, Cushman John C., May Gregory D., Weller Jennifer W. ESTAP--an automated system for the analysis of EST data. Bioinformatics. 2003 Sep 1;19(13):1720–1722. doi: 10.1093/bioinformatics/btg205. [DOI] [PubMed] [Google Scholar]
  156. Markey Mia K., Tourassi Georgia D., Floyd Carey E., Jr Decision tree classification of proteins identified by mass spectrometry of blood serum samples from people with and without lung cancer. Proteomics. 2003 Sep;3(9):1678–1679. doi: 10.1002/pmic.200300521. [DOI] [PubMed] [Google Scholar]
  157. Marongiu Alessandro, Palazzari Paolo, Rosato Vittorio. Designing hardware for protein sequence analysis. Bioinformatics. 2003 Sep 22;19(14):1739–1740. doi: 10.1093/bioinformatics/btg228. [DOI] [PubMed] [Google Scholar]
  158. Martelli Pier Luigi, Fariselli Piero, Tasco Gianluca, Casadio Rita. The prediction of membrane protein structure and genome structural annotation. Comp Funct Genomics. 2003;4(4):406–409. doi: 10.1002/cfg.308. [DOI] [PMC free article] [PubMed] [Google Scholar]
  159. Maruyama-Nakashita Akiko, Inoue Eri, Watanabe-Takahashi Akiko, Yamaya Tomoyuki, Takahashi Hideki. Transcriptome profiling of sulfur-responsive genes in Arabidopsis reveals global effects of sulfur nutrition on multiple metabolic pathways. Plant Physiol. 2003 May 8;132(2):597–605. doi: 10.1104/pp.102.019802. [DOI] [PMC free article] [PubMed] [Google Scholar]
  160. Maruyama Nobuyuki, Fukuda Takako, Saka Shiori, Inui Nauko, Kotoh Junko, Miyagawa Mayumi, Hayashi Misa, Sawada Machiko, Moriyama Tatsuya, Utsumi Shigeru. Molecular and structural analysis of electrophoretic variants of soybean seed storage proteins. Phytochemistry. 2003 Oct;64(3):701–708. doi: 10.1016/s0031-9422(03)00385-6. [DOI] [PubMed] [Google Scholar]
  161. Mayers Carl, Duffield Melanie, Rowe Sonya, Miller Julie, Lingard Bryan, Hayward Sarah, Titball Richard W. Analysis of known bacterial protein vaccine antigens reveals biased physical properties and amino acid composition. Comp Funct Genomics. 2003;4(5):468–478. doi: 10.1002/cfg.319. [DOI] [PMC free article] [PubMed] [Google Scholar]
  162. McClure John, Wit Ernst. Post-normalization quality assessment visualization of microarray data. Comp Funct Genomics. 2003;4(5):460–467. doi: 10.1002/cfg.317. [DOI] [PMC free article] [PubMed] [Google Scholar]
  163. McHardy Alice C., Tauch Andreas, Rückert Christian, Pühler Alfred, Kalinowski Jörn. Genome-based analysis of biosynthetic aminotransferase genes of Corynebacterium glutamicum. J Biotechnol. 2003 Sep 4;104(1-3):229–240. doi: 10.1016/s0168-1656(03)00161-5. [DOI] [PubMed] [Google Scholar]
  164. McShan D. C., Rao S., Shah I. PathMiner: predicting metabolic pathways by heuristic search. Bioinformatics. 2003 Sep 1;19(13):1692–1698. doi: 10.1093/bioinformatics/btg217. [DOI] [PMC free article] [PubMed] [Google Scholar]
  165. Medjahed Djamel, Luke Brian T., Tontesh Tawady S., Smythers Gary W., Munroe David J., Lemkin Peter F. Tissue Molecular Anatomy Project (TMAP): an expression database for comparative cancer proteomics. Proteomics. 2003 Aug;3(8):1445–1453. doi: 10.1002/pmic.200300488. [DOI] [PubMed] [Google Scholar]
  166. Merino Emilio F., Fernandez-Becerra Carmen, Madeira Alda M. B. N., Machado Ariane L., Durham Alan, Gruber Arthur, Hall Neil, del Portillo Hernando A. Pilot survey of expressed sequence tags (ESTs) from the asexual blood stages of Plasmodium vivax in human patients. Malar J. 2003 Jul 21;2:21–21. doi: 10.1186/1475-2875-2-21. [DOI] [PMC free article] [PubMed] [Google Scholar]
  167. Mi Huaiyu, Vandergriff Jody, Campbell Michael, Narechania Apurva, Majoros William, Lewis Suzanna, Thomas Paul D., Ashburner Michael. Assessment of genome-wide protein function classification for Drosophila melanogaster. Genome Res. 2003 Sep;13(9):2118–2128. doi: 10.1101/gr.771603. [DOI] [PMC free article] [PubMed] [Google Scholar]
  168. Mian Shahid, Ball Graham, Hornbuckle Jo, Holding Finn, Carmichael James, Ellis Ian, Ali Selman, Li Geng, McArdle Stephanie, Creaser Colin. A prototype methodology combining surface-enhanced laser desorption/ionization protein chip technology and artificial neural network algorithms to predict the chemoresponsiveness of breast cancer cell lines exposed to Paclitaxel and Doxorubicin under in vitro conditions. Proteomics. 2003 Sep;3(9):1725–1737. doi: 10.1002/pmic.200300526. [DOI] [PubMed] [Google Scholar]
  169. Mitchell A. L., Reich J. R., Attwood T. K. PRECIS: protein reports engineered from concise information in SWISS-PROT. Bioinformatics. 2003 Sep 1;19(13):1664–1671. doi: 10.1093/bioinformatics/btg204. [DOI] [PubMed] [Google Scholar]
  170. Mohan Deepa, Pasa-Tolić Ljiljana, Masselon Christophe D., Tolić Nikola, Bogdanov Bogdan, Hixson Kim K., Smith Richard D., Lee Cheng S. Integration of electrokinetic-based multidimensional separation/concentration platform with electrospray ionization-Fourier transform ion cyclotron resonance-mass spectrometry for proteome analysis of Shewanella oneidensis. Anal Chem. 2003 Sep 1;75(17):4432–4440. doi: 10.1021/ac0342572. [DOI] [PubMed] [Google Scholar]
  171. Mooney Sean D., Altman Russ B. MutDB: annotating human variation with functionally relevant data. Bioinformatics. 2003 Sep 22;19(14):1858–1860. doi: 10.1093/bioinformatics/btg241. [DOI] [PubMed] [Google Scholar]
  172. Mostaguir Khaled, Hoogland Christine, Binz Pierre-Alain, Appel Ron D. The Make 2D-DB II package: conversion of federated two-dimensional gel electrophoresis databases into a relational format and interconnection of distributed databases. Proteomics. 2003 Aug;3(8):1441–1444. doi: 10.1002/pmic.200300483. [DOI] [PubMed] [Google Scholar]
  173. Mádi András, Mikkat Stefan, Ringel Bruno, Ulbrich Markus, Thiesen Hans-Jürgen, Glocker Michael O. Mass spectrometric proteome analysis for profiling temperature-dependent changes of protein expression in wild-type Caenorhabditis elegans. Proteomics. 2003 Aug;3(8):1526–1534. doi: 10.1002/pmic.200300490. [DOI] [PubMed] [Google Scholar]
  174. Nagata Toshihito, Takahashi Yasuo, Ishii Yukimoto, Asai Satoshi, Nishida Yayoi, Murata Akiko, Koshinaga Tsugumichi, Fukuzawa Masahiro, Hamazaki Minoru, Asami Keiko. Transcriptional profiling in hepatoblastomas using high-density oligonucleotide DNA array. Cancer Genet Cytogenet. 2003 Sep;145(2):152–160. doi: 10.1016/s0165-4608(03)00065-7. [DOI] [PubMed] [Google Scholar]
  175. Nakazono Mikio, Qiu Fang, Borsuk Lisa A., Schnable Patrick S. Laser-capture microdissection, a tool for the global analysis of gene expression in specific plant cell types: identification of genes expressed differentially in epidermal cells or vascular tissues of maize. Plant Cell. 2003 Mar;15(3):583–596. doi: 10.1105/tpc.008102. [DOI] [PMC free article] [PubMed] [Google Scholar]
  176. Nawarak Jiraporn, Sinchaikul Supachok, Wu Chi-Yue, Liau Ming-Yi, Phutrakul Suree, Chen Shui-Tein. Proteomics of snake venoms from Elapidae and Viperidae families by multidimensional chromatographic methods. Electrophoresis. 2003 Aug;24(16):2838–2854. doi: 10.1002/elps.200305552. [DOI] [PubMed] [Google Scholar]
  177. Nelson Karen E., Fleischmann Robert D., DeBoy Robert T., Paulsen Ian T., Fouts Derrick E., Eisen Jonathan A., Daugherty Sean C., Dodson Robert J., Durkin A. Scott, Gwinn Michelle. Complete genome sequence of the oral pathogenic Bacterium porphyromonas gingivalis strain W83. J Bacteriol. 2003 Sep;185(18):5591–5601. doi: 10.1128/JB.185.18.5591-5601.2003. [DOI] [PMC free article] [PubMed] [Google Scholar]
  178. Nemeth-Cawley Jennifer F., Tangarone Bruce S., Rouse Jason C. "Top Down" characterization is a complementary technique to peptide sequencing for identifying protein species in complex mixtures. J Proteome Res. 2003 Sep-Oct;2(5):495–505. doi: 10.1021/pr034008u. [DOI] [PubMed] [Google Scholar]
  179. Neville Padraic, Tan Pei-Yi, Mann Geoffrey, Wolfinger Russ. Generalizable mass spectrometry mining used to identify disease state biomarkers from blood serum. Proteomics. 2003 Sep;3(9):1710–1715. doi: 10.1002/pmic.200300516. [DOI] [PubMed] [Google Scholar]
  180. Nishizuka Satoshi, Chen Sing-Tsung, Gwadry Fuad G., Alexander Jes, Major Sylvia M., Scherf Uwe, Reinhold William C., Waltham Mark, Charboneau Lu, Young Lynn. Diagnostic markers that distinguish colon and ovarian adenocarcinomas: identification by genomic, proteomic, and tissue array profiling. Cancer Res. 2003 Sep 1;63(17):5243–5250. [PubMed] [Google Scholar]
  181. Pallen Mark J., Chaudhuri Roy R., Henderson Ian R. Genomic analysis of secretion systems. Curr Opin Microbiol. 2003 Oct;6(5):519–527. doi: 10.1016/j.mib.2003.09.005. [DOI] [PubMed] [Google Scholar]
  182. Papazisi Leka, Gorton Timothy S., Kutish Gerald, Markham Philip F., Browning Glenn F., Nguyen Di Kim, Swartzell Steven, Madan Anup, Mahairas Greg, Geary Steven J. The complete genome sequence of the avian pathogen Mycoplasma gallisepticum strain R(low). Microbiology. 2003 Sep;149(Pt 9):2307–2316. doi: 10.1099/mic.0.26427-0. [DOI] [PubMed] [Google Scholar]
  183. Parisi Valerio, De Fonzo Valeria, Aluffi-Pentini Filippo. STRING: finding tandem repeats in DNA sequences. Bioinformatics. 2003 Sep 22;19(14):1733–1738. doi: 10.1093/bioinformatics/btg268. [DOI] [PubMed] [Google Scholar]
  184. Park Keun-Joon, Kanehisa Minoru. Prediction of protein subcellular locations by support vector machines using compositions of amino acids and amino acid pairs. Bioinformatics. 2003 Sep 1;19(13):1656–1663. doi: 10.1093/bioinformatics/btg222. [DOI] [PubMed] [Google Scholar]
  185. Park Paul C., Taylor Michael D., Mainprize Todd G., Becker Laurence E., Ho Michael, Dura Wieslaw T., Squire Jeremy, Rutka James T. Transcriptional profiling of medulloblastoma in children. J Neurosurg. 2003 Sep;99(3):534–541. doi: 10.3171/jns.2003.99.3.0534. [DOI] [PubMed] [Google Scholar]
  186. Pavlidis Paul, Li Qinghong, Noble William Stafford. The effect of replication on gene expression microarray experiments. Bioinformatics. 2003 Sep 1;19(13):1620–1627. doi: 10.1093/bioinformatics/btg227. [DOI] [PubMed] [Google Scholar]
  187. Pawliczak R., Shelhamer J. H. Application of functional genomics in allergy and clinical immunology. Allergy. 2003 Oct;58(10):973–980. doi: 10.1034/j.1398-9995.2003.00283.x. [DOI] [PubMed] [Google Scholar]
  188. Peyrl Andreas, Krapfenbauer Kurt, Slavc Irene, Yang Jae-Won, Strobel Thomas, Lubec Gert. Protein profiles of medulloblastoma cell lines DAOY and D283: identification of tumor-related proteins and principles. Proteomics. 2003 Sep;3(9):1781–1800. doi: 10.1002/pmic.200300460. [DOI] [PubMed] [Google Scholar]
  189. Pichon Christophe, Felden Brice. Intergenic sequence inspector: searching and identifying bacterial RNAs. Bioinformatics. 2003 Sep 1;19(13):1707–1709. doi: 10.1093/bioinformatics/btg235. [DOI] [PubMed] [Google Scholar]
  190. Ping Peipei. Identification of novel signaling complexes by functional proteomics. Circ Res. 2003 Oct 3;93(7):595–603. doi: 10.1161/01.RES.0000093221.98213.E0. [DOI] [PubMed] [Google Scholar]
  191. Porchet Raymonde, Probst Alphonse, Bouras Constantin, Dráberová Eduarda, Dráber Pavel, Riederer Beat M. Analysis of glial acidic fibrillary protein in the human entorhinal cortex during aging and in Alzheimer's disease. Proteomics. 2003 Aug;3(8):1476–1485. doi: 10.1002/pmic.200300456. [DOI] [PubMed] [Google Scholar]
  192. Prasad J. C., Comeau S. R., Vajda S., Camacho C. J. Consensus alignment for reliable framework prediction in homology modeling. Bioinformatics. 2003 Sep 1;19(13):1682–1691. doi: 10.1093/bioinformatics/btg211. [DOI] [PubMed] [Google Scholar]
  193. Purohit Parul V., Rocke David M. Discriminant models for high-throughput proteomics mass spectrometer data. Proteomics. 2003 Sep;3(9):1699–1703. doi: 10.1002/pmic.200300518. [DOI] [PubMed] [Google Scholar]
  194. Pédron Thierry, Thibault Christelle, Sansonetti Philippe J. The invasive phenotype of Shigella flexneri directs a distinct gene expression pattern in the human intestinal epithelial cell line Caco-2. J Biol Chem. 2003 Jun 17;278(36):33878–33886. doi: 10.1074/jbc.M303749200. [DOI] [PubMed] [Google Scholar]
  195. Quach Thuy Tien T., Li Nan, Richards Dawn P., Zheng Jing, Keller Bernd O., Li Liang. Development and applications of in-gel CNBr/tryptic digestion combined with mass spectrometry for the analysis of membrane proteins. J Proteome Res. 2003 Sep-Oct;2(5):543–552. doi: 10.1021/pr0340126. [DOI] [PubMed] [Google Scholar]
  196. Rehman Khurram S., Yin Su, Mayhew Bobbie A., Word R. Ann, Rainey William E. Human myometrial adaptation to pregnancy: cDNA microarray gene expression profiling of myometrium from non-pregnant and pregnant women. Mol Hum Reprod. 2003 Nov;9(11):681–700. doi: 10.1093/molehr/gag078. [DOI] [PubMed] [Google Scholar]
  197. Rexroth Sascha, Meyer zu Tittingdorf Jürgen M. W., Krause Frank, Dencher Norbert A., Seelert Holger. Thylakoid membrane at altered metabolic state: challenging the forgotten realms of the proteome. Electrophoresis. 2003 Aug;24(16):2814–2823. doi: 10.1002/elps.200305543. [DOI] [PubMed] [Google Scholar]
  198. Reymond Marc A., Steinert Ralf, Eder Frank, Lippert Hans. Ethical and regulatory issues arising from proteomic research and technology. Proteomics. 2003 Aug;3(8):1387–1396. doi: 10.1002/pmic.200300481. [DOI] [PubMed] [Google Scholar]
  199. Righetti Pier Giorgio, Castagna Annalisa, Herbert Ben, Reymond Frederic, Rossier Joël S. Prefractionation techniques in proteome analysis. Proteomics. 2003 Aug;3(8):1397–1407. doi: 10.1002/pmic.200300472. [DOI] [PubMed] [Google Scholar]
  200. Robinson William H., Fontoura Paulo, Lee Byung J., de Vegvar Henry E. Neuman, Tom Jennifer, Pedotti Rosetta, DiGennaro Carla D., Mitchell Dennis J., Fong Derek, Ho Peggy P-K. Protein microarrays guide tolerizing DNA vaccine treatment of autoimmune encephalomyelitis. Nat Biotechnol. 2003 Aug 10;21(9):1033–1039. doi: 10.1038/nbt859. [DOI] [PubMed] [Google Scholar]
  201. Rodríguez-Ortega Manuel J., Grøsvik Bjørn Einar, Rodríguez-Ariza Antonio, Goksøyr Anders, López-Barea Juan. Changes in protein expression profiles in bivalve molluscs (Chamaelea gallina) exposed to four model environmental pollutants. Proteomics. 2003 Aug;3(8):1535–1543. doi: 10.1002/pmic.200300491. [DOI] [PubMed] [Google Scholar]
  202. Russo Giuseppe, Zegar Charles, Giordano Antonio. Advantages and limitations of microarray technology in human cancer. Oncogene. 2003 Sep 29;22(42):6497–6507. doi: 10.1038/sj.onc.1206865. [DOI] [PubMed] [Google Scholar]
  203. Ryu Jin-Woo, Kim Hyung-Jee, Lee Young-Sun, Myong Na-Hye, Hwang Cheol-Hoh, Lee Gae-Sung, Yom Heng-Cherl. The proteomics approach to find biomarkers in gastric cancer. J Korean Med Sci. 2003 Aug;18(4):505–509. doi: 10.3346/jkms.2003.18.4.505. [DOI] [PMC free article] [PubMed] [Google Scholar]
  204. Rückert C., Pühler A., Kalinowski J. Genome-wide analysis of the L-methionine biosynthetic pathway in Corynebacterium glutamicum by targeted gene deletion and homologous complementation. J Biotechnol. 2003 Sep 4;104(1-3):213–228. doi: 10.1016/s0168-1656(03)00158-5. [DOI] [PubMed] [Google Scholar]
  205. Sanchez Jean-Charles, Converset Véronique, Nolan Anna, Schmid Gerhard, Wang Steven, Heller Manfred, Sennitt Matthew V., Hochstrasser Denis F., Cawthorne Michael A. Effect of rosiglitazone on the differential expression of obesity and insulin resistance associated proteins in lep/lep mice. Proteomics. 2003 Aug;3(8):1500–1520. doi: 10.1002/pmic.200300484. [DOI] [PubMed] [Google Scholar]
  206. Savaldi-Goldstein Sigal, Aviv Dvora, Davydov Olga, Fluhr Robert. Alternative splicing modulation by a LAMMER kinase impinges on developmental and transcriptome expression. Plant Cell. 2003 Apr;15(4):926–938. doi: 10.1105/tpc.011056. [DOI] [PMC free article] [PubMed] [Google Scholar]
  207. Saviozzi Silvia, Calogero Raffaele A. Microarray probe expression measures, data normalization and statistical validation. Comp Funct Genomics. 2003;4(4):442–446. doi: 10.1002/cfg.312. [DOI] [PMC free article] [PubMed] [Google Scholar]
  208. Scheffler N. Karoline, Falick Arnold M., Hall Steven C., Ray William C., Post Deborah M., Munson Robert S., Jr, Gibson Bradford W. Proteome of Haemophilus ducreyi by 2-D SDS-PAGE and mass spectrometry: strain variation, virulence, and carbohydrate expression. J Proteome Res. 2003 Sep-Oct;2(5):523–533. doi: 10.1021/pr0340025. [DOI] [PubMed] [Google Scholar]
  209. Schuler Mary A., Werck-Reichhart Daniele. Functional genomics of P450s. Annu Rev Plant Biol. 2003;54:629–667. doi: 10.1146/annurev.arplant.54.031902.134840. [DOI] [PubMed] [Google Scholar]
  210. Sebastiano Roberto, Citterio Attilio, Lapadula Marta, Righetti Pier Giorgio. A new deuterated alkylating agent for quantitative proteomics. Rapid Commun Mass Spectrom. 2003;17(21):2380–2386. doi: 10.1002/rcm.1206. [DOI] [PubMed] [Google Scholar]
  211. Shah N. H., King D. C., Shah P. N., Fedoroff N. V. A tool-kit for cDNA microarray and promoter analysis. Bioinformatics. 2003 Sep 22;19(14):1846–1848. doi: 10.1093/bioinformatics/btg253. [DOI] [PubMed] [Google Scholar]
  212. Sharan Roded, Maron-Katz Adi, Shamir Ron. CLICK and EXPANDER: a system for clustering and visualizing gene expression data. Bioinformatics. 2003 Sep 22;19(14):1787–1799. doi: 10.1093/bioinformatics/btg232. [DOI] [PubMed] [Google Scholar]
  213. Shaw Margaret M., Riederer Beat M. Sample preparation for two-dimensional gel electrophoresis. Proteomics. 2003 Aug;3(8):1408–1417. doi: 10.1002/pmic.200300471. [DOI] [PubMed] [Google Scholar]
  214. Siew Naomi, Fischer Daniel. Unravelling the ORFan Puzzle. Comp Funct Genomics. 2003;4(4):432–441. doi: 10.1002/cfg.311. [DOI] [PMC free article] [PubMed] [Google Scholar]
  215. Slotta Douglas J., Heath Lenwood S., Ramakrishnan Naren, Helm Rich, Potts Malcolm. Clustering mass spectrometry data using order statistics. Proteomics. 2003 Sep;3(9):1687–1691. doi: 10.1002/pmic.200300517. [DOI] [PubMed] [Google Scholar]
  216. Soga Tomoyoshi, Ohashi Yoshiaki, Ueno Yuki, Naraoka Hisako, Tomita Masaru, Nishioka Takaaki. Quantitative metabolome analysis using capillary electrophoresis mass spectrometry. J Proteome Res. 2003 Sep-Oct;2(5):488–494. doi: 10.1021/pr034020m. [DOI] [PubMed] [Google Scholar]
  217. Sotiriou Christos, Neo Soek-Ying, McShane Lisa M., Korn Edward L., Long Philip M., Jazaeri Amir, Martiat Philippe, Fox Steve B., Harris Adrian L., Liu Edison T. Breast cancer classification and prognosis based on gene expression profiles from a population-based study. Proc Natl Acad Sci U S A. 2003 Aug 13;100(18):10393–10398. doi: 10.1073/pnas.1732912100. [DOI] [PMC free article] [PubMed] [Google Scholar]
  218. Starita-Geribaldi Mireille, Roux Françoise, Garin Jérôme, Chevallier Daniel, Fénichel Patrick, Pointis Georges. Development of narrow immobilized pH gradients covering one pH unit for human seminal plasma proteomic analysis. Proteomics. 2003 Aug;3(8):1611–1619. doi: 10.1002/pmic.200300493. [DOI] [PubMed] [Google Scholar]
  219. Steil Leif, Hoffmann Tamara, Budde Ina, Völker Uwe, Bremer Erhard. Genome-wide transcriptional profiling analysis of adaptation of Bacillus subtilis to high salinity. J Bacteriol. 2003 Nov;185(21):6358–6370. doi: 10.1128/JB.185.21.6358-6370.2003. [DOI] [PMC free article] [PubMed] [Google Scholar]
  220. Stone Laura S., Vulchanova Lucy. The pain of antisense: in vivo application of antisense oligonucleotides for functional genomics in pain and analgesia. Adv Drug Deliv Rev. 2003 Aug 28;55(8):1081–1112. doi: 10.1016/s0169-409x(03)00105-4. [DOI] [PubMed] [Google Scholar]
  221. Takagaki Kazuchika, Katsuma Susumu, Horio Tatsuya, Kaminishi Yoshinori, Hada Yuko, Tanaka Teruo, Ohgi Tadaaki, Yano Junichi. cDNA microarray analysis of altered gene expression in Ara-C-treated leukemia cells. Biochem Biophys Res Commun. 2003 Sep 19;309(2):351–358. doi: 10.1016/j.bbrc.2003.08.009. [DOI] [PubMed] [Google Scholar]
  222. Takahashi K., Ishikawa N., Sadamoto Y., Sasamoto H., Ohta S., Shiozawa A., Miyoshi F., Naito Y., Nakayama Y., Tomita M. E-Cell 2: multi-platform E-Cell simulation system. Bioinformatics. 2003 Sep 1;19(13):1727–1729. doi: 10.1093/bioinformatics/btg221. [DOI] [PubMed] [Google Scholar]
  223. Tan Paul K., Downey Thomas J., Spitznagel Edward L., Jr, Xu Pin, Fu Dadin, Dimitrov Dimiter S., Lempicki Richard A., Raaka Bruce M., Cam Margaret C. Evaluation of gene expression measurements from commercial microarray platforms. Nucleic Acids Res. 2003 Oct 1;31(19):5676–5684. doi: 10.1093/nar/gkg763. [DOI] [PMC free article] [PubMed] [Google Scholar]
  224. Tatay Jacob W., Feng Xin, Sobczak Nancy, Jiang Hao, Chen Chin-Fu, Kirova Roumyana, Struble Craig, Wang Nan Jiang, Tonellato Peter J. Multiple approaches to data-mining of proteomic data based on statistical and pattern classification methods. Proteomics. 2003 Sep;3(9):1704–1709. doi: 10.1002/pmic.200300512. [DOI] [PubMed] [Google Scholar]
  225. Thibaud-Nissen Françoise, Shealy Robin T., Khanna Anupama, Vodkin Lila O. Clustering of microarray data reveals transcript patterns associated with somatic embryogenesis in soybean. Plant Physiol. 2003 May;132(1):118–136. doi: 10.1104/pp.103.019968. [DOI] [PMC free article] [PubMed] [Google Scholar]
  226. Thomas Paul D., Campbell Michael J., Kejariwal Anish, Mi Huaiyu, Karlak Brian, Daverman Robin, Diemer Karen, Muruganujan Anushya, Narechania Apurva. PANTHER: a library of protein families and subfamilies indexed by function. Genome Res. 2003 Sep;13(9):2129–2141. doi: 10.1101/gr.772403. [DOI] [PMC free article] [PubMed] [Google Scholar]
  227. Tjandra Donny, Wong Stephen, Shen Weimin, Pulliam Brian, Yu Elaine, Esserman Laura. An XML message broker framework for exchange and integration of microarray data. Bioinformatics. 2003 Sep 22;19(14):1844–1845. doi: 10.1093/bioinformatics/btg246. [DOI] [PubMed] [Google Scholar]
  228. Tramontano Anna. Comparative modelling techniques: where are we? Comp Funct Genomics. 2003;4(4):402–405. doi: 10.1002/cfg.306. [DOI] [PMC free article] [PubMed] [Google Scholar]
  229. Umar Arzu, Ooms Marja P., Luider Theo M., Grootegoed J. Anton, Brinkmann Albert O. Proteomic profiling of epididymis and vas deferens: identification of proteins regulated during rat genital tract development. Endocrinology. 2003 Jun 19;144(10):4637–4647. doi: 10.1210/en.2003-0404. [DOI] [PubMed] [Google Scholar]
  230. Unwin Richard D., Craven Rachel A., Harnden Patricia, Hanrahan Sarah, Totty Nick, Knowles Margaret, Eardley Ian, Selby Peter J., Banks Rosamonde E. Proteomic changes in renal cancer and co-ordinate demonstration of both the glycolytic and mitochondrial aspects of the Warburg effect. Proteomics. 2003 Aug;3(8):1620–1632. doi: 10.1002/pmic.200300464. [DOI] [PubMed] [Google Scholar]
  231. Urbanczyk-Wochniak Ewa, Luedemann Alexander, Kopka Joachim, Selbig Joachim, Roessner-Tunali Ute, Willmitzer Lothar, Fernie Alisdair R. Parallel analysis of transcript and metabolic profiles: a new approach in systems biology. EMBO Rep. 2003 Sep 12;4(10):989–993. doi: 10.1038/sj.embor.embor944. [DOI] [PMC free article] [PubMed] [Google Scholar]
  232. Utaida S., Dunman P. M., Macapagal D., Murphy E., Projan S. J., Singh V. K., Jayaswal R. K., Wilkinson B. J. Genome-wide transcriptional profiling of the response of Staphylococcus aureus to cell-wall-active antibiotics reveals a cell-wall-stress stimulon. Microbiology. 2003 Oct;149(Pt 10):2719–2732. doi: 10.1099/mic.0.26426-0. [DOI] [PubMed] [Google Scholar]
  233. Valencia Alfonso. Multiple sequence alignments as tools for protein structure and function prediction. Comp Funct Genomics. 2003;4(4):424–427. doi: 10.1002/cfg.313. [DOI] [PMC free article] [PubMed] [Google Scholar]
  234. Verjovski-Almeida Sergio, DeMarco Ricardo, Martins Elizabeth A. L., Guimarães Pedro E. M., Ojopi Elida P. B., Paquola Apuã C. M., Piazza João P., Nishiyama Milton Y., Jr, Kitajima João P., Adamson Rachel E. Transcriptome analysis of the acoelomate human parasite Schistosoma mansoni. Nat Genet. 2003 Sep 14;35(2):148–157. doi: 10.1038/ng1237. [DOI] [PubMed] [Google Scholar]
  235. Vinayagam A., Shi J., Pugalenthi G., Meenakshi B., Blundell T. L., Sowdhamini R. DDBASE2.0: updated domain database with improved identification of structural domains. Bioinformatics. 2003 Sep 22;19(14):1760–1764. doi: 10.1093/bioinformatics/btg233. [DOI] [PubMed] [Google Scholar]
  236. Vuadens Françoise, Benay Corinne, Crettaz David, Gallot Denis, Sapin Vincent, Schneider Philippe, Bienvenut Willy-Vincent, Lémery Didier, Quadroni Manfredo, Dastugue Bernard. Identification of biologic markers of the premature rupture of fetal membranes: proteomic approach. Proteomics. 2003 Aug;3(8):1521–1525. doi: 10.1002/pmic.200300455. [DOI] [PubMed] [Google Scholar]
  237. Wagner Michael, Naik Dayanand, Pothen Alex. Protocols for disease classification from mass spectrometry data. Proteomics. 2003 Sep;3(9):1692–1698. doi: 10.1002/pmic.200300519. [DOI] [PubMed] [Google Scholar]
  238. Walcher Wolfgang, Franze Thomas, Weller Michael G., Pöschl Ulrich, Huber Christian G. Liquid- and gas-phase nitration of bovine serum albumin studied by LC-MS and LC-MS/MS using monolithic columns. J Proteome Res. 2003 Sep-Oct;2(5):534–542. doi: 10.1021/pr034034s. [DOI] [PubMed] [Google Scholar]
  239. Wall D. P., Fraser H. B., Hirsh A. E. Detecting putative orthologs. Bioinformatics. 2003 Sep 1;19(13):1710–1711. doi: 10.1093/bioinformatics/btg213. [DOI] [PubMed] [Google Scholar]
  240. Wang Jian, Kraemer Eileen. GFPE: gene-finding program evaluation. Bioinformatics. 2003 Sep 1;19(13):1712–1713. doi: 10.1093/bioinformatics/btg216. [DOI] [PubMed] [Google Scholar]
  241. Wang Michael Z., Howard Brandon, Campa Michael J., Patz Edward F., Jr, Fitzgerald Michael C. Analysis of human serum proteins by liquid phase isoelectric focusing and matrix-assisted laser desorption/ionization-mass spectrometry. Proteomics. 2003 Sep;3(9):1661–1666. doi: 10.1002/pmic.200300513. [DOI] [PubMed] [Google Scholar]
  242. Wang Rongchen, Okamoto Mamoru, Xing Xiujuan, Crawford Nigel M. Microarray analysis of the nitrate response in Arabidopsis roots and shoots reveals over 1,000 rapidly responding genes and new linkages to glucose, trehalose-6-phosphate, iron, and sulfate metabolism. Plant Physiol. 2003 Jun;132(2):556–567. doi: 10.1104/pp.103.021253. [DOI] [PMC free article] [PubMed] [Google Scholar]
  243. Ward J. J., McGuffin L. J., Buxton B. F., Jones D. T. Secondary structure prediction with support vector machines. Bioinformatics. 2003 Sep 1;19(13):1650–1655. doi: 10.1093/bioinformatics/btg223. [DOI] [PubMed] [Google Scholar]
  244. Washburn Michael P., Ulaszek Ryan R., Yates John R., 3rd Reproducibility of quantitative proteomic analyses of complex biological mixtures by multidimensional protein identification technology. Anal Chem. 2003 Oct 1;75(19):5054–5061. doi: 10.1021/ac034120b. [DOI] [PubMed] [Google Scholar]
  245. Watson Bonnie S., Asirvatham Victor S., Wang Liangjiang, Sumner Lloyd W. Mapping the proteome of barrel medic (Medicago truncatula). Plant Physiol. 2003 Mar;131(3):1104–1123. doi: 10.1104/pp.102.019034. [DOI] [PMC free article] [PubMed] [Google Scholar]
  246. Weckwerth Wolfram. Metabolomics in systems biology. Annu Rev Plant Biol. 2003;54:669–689. doi: 10.1146/annurev.arplant.54.031902.135014. [DOI] [PubMed] [Google Scholar]
  247. Weiler Tracey, Sauder Patricia, Cheng Keding, Ens Werner, Standing Kenneth, Wilkins John A. A proteomics-based approach for monoclonal antibody characterization. Anal Biochem. 2003 Oct 15;321(2):217–225. doi: 10.1016/s0003-2697(03)00469-x. [DOI] [PubMed] [Google Scholar]
  248. Wendisch Volker F. Genome-wide expression analysis in Corynebacterium glutamicum using DNA microarrays. J Biotechnol. 2003 Sep 4;104(1-3):273–285. doi: 10.1016/s0168-1656(03)00147-0. [DOI] [PubMed] [Google Scholar]
  249. Wienkoop Stefanie, Saalbach Gerhard. Proteome analysis. Novel proteins identified at the peribacteroid membrane from Lotus japonicus root nodules. Plant Physiol. 2003 Mar;131(3):1080–1090. doi: 10.1104/pp.102.015362. [DOI] [PMC free article] [PubMed] [Google Scholar]
  250. Wortman Jennifer R., Haas Brian J., Hannick Linda I., Smith Roger K., Jr, Maiti Rama, Ronning Catherine M., Chan Agnes P., Yu Chunhui, Ayele Mulu, Whitelaw Catherine A. Annotation of the Arabidopsis genome. Plant Physiol. 2003 Jun;132(2):461–468. doi: 10.1104/pp.103.022251. [DOI] [PMC free article] [PubMed] [Google Scholar]
  251. Wride Michael A., Mansergh Fiona C., Adams Steffan, Everitt Rebecca, Minnema Stephanie E., Rancourt Derrick E., Evans Martin J. Expression profiling and gene discovery in the mouse lens. Mol Vis. 2003 Aug 22;9:360–396. [PubMed] [Google Scholar]
  252. Wu Baolin, Abbott Tom, Fishman David, McMurray Walter, Mor Gil, Stone Kathryn, Ward David, Williams Kenneth, Zhao Hongyu. Comparison of statistical methods for classification of ovarian cancer using mass spectrometry data. Bioinformatics. 2003 Sep 1;19(13):1636–1643. doi: 10.1093/bioinformatics/btg210. [DOI] [PubMed] [Google Scholar]
  253. Wu Ping, Ma Ligeng, Hou Xingliang, Wang Mingyi, Wu Yungrong, Liu Feiyan, Deng Xing Wang. Phosphate starvation triggers distinct alterations of genome expression in Arabidopsis roots and leaves. Plant Physiol. 2003 Jul;132(3):1260–1271. doi: 10.1104/pp.103.021022. [DOI] [PMC free article] [PubMed] [Google Scholar]
  254. Xu Dong, Olman Victor, Wang Li, Xu Ying. EXCAVATOR: a computer program for efficiently mining gene expression data. Nucleic Acids Res. 2003 Oct 1;31(19):5582–5589. doi: 10.1093/nar/gkg783. [DOI] [PMC free article] [PubMed] [Google Scholar]
  255. Yamada Kayoko, Lim Jun, Dale Joseph M., Chen Huaming, Shinn Paul, Palm Curtis J., Southwick Audrey M., Wu Hank C., Kim Christopher, Nguyen Michelle. Empirical analysis of transcriptional activity in the Arabidopsis genome. Science. 2003 Oct 31;302(5646):842–846. doi: 10.1126/science.1088305. [DOI] [PubMed] [Google Scholar]
  256. Yang Jaemo, Park Sunchung, Kamdem D. Pascal, Keathley Daniel E., Retzel Ernest, Paule Charlie, Kapur Vivek, Han Kyung-Hwan. Novel gene expression profiles define the metabolic and physiological processes characteristic of wood and its extractive formation in a hardwood tree species, Robinia pseudoacacia. Plant Mol Biol. 2003 Jul;52(5):935–956. doi: 10.1023/a:1025445427284. [DOI] [PubMed] [Google Scholar]
  257. Ying Hao, Suzuki Hideyo, Furumoto Hiroko, Walker Robert, Meltzer Paul, Willingham Mark C., Cheng Sheue-Yann. Alterations in genomic profiles during tumor progression in a mouse model of follicular thyroid carcinoma. Carcinogenesis. 2003 Jul 17;24(9):1467–1479. doi: 10.1093/carcin/bgg111. [DOI] [PubMed] [Google Scholar]
  258. Yoon Byung-Il, Li Guang-Xun, Kitada Kunio, Kawasaki Yasushi, Igarashi Katsuhide, Kodama Yukio, Inoue Tomoaki, Kobayashi Kazuko, Kanno Jun, Kim Dae-Yong. Mechanisms of benzene-induced hematotoxicity and leukemogenicity: cDNA microarray analyses using mouse bone marrow tissue. Environ Health Perspect. 2003 Aug;111(11):1411–1420. doi: 10.1289/ehp.6164. [DOI] [PMC free article] [PubMed] [Google Scholar]
  259. Yuan Xianglin, Desiderio Dominic M. Proteomics analysis of phosphotyrosyl-proteins in human lumbar cerebrospinal fluid. J Proteome Res. 2003 Sep-Oct;2(5):476–487. doi: 10.1021/pr025589a. [DOI] [PubMed] [Google Scholar]
  260. Yuan Xin, Shao Yu, Bystroff Christopher. Ab initio protein structure prediction using pathway models. Comp Funct Genomics. 2003;4(4):397–401. doi: 10.1002/cfg.305. [DOI] [PMC free article] [PubMed] [Google Scholar]
  261. Yuza Yuki, Agawa Miyuki, Matsuzaki Masaharu, Yamada Hisashi, Urashima Mitsuyoshi. Gene and protein expression profiling during differentiation of neuroblastoma cells triggered by 13-cis retinoic acid. J Pediatr Hematol Oncol. 2003 Sep;25(9):715–720. doi: 10.1097/00043426-200309000-00008. [DOI] [PubMed] [Google Scholar]
  262. Zhan Fenghuang, Barlogie Bart, Shaughnessy John., Jr Toward the identification of distinct molecular and clinical entities of multiple myeloma using global gene expression profiling. Semin Hematol. 2003 Oct;40(4):308–320. doi: 10.1016/s0037-1963(03)00197-5. [DOI] [PubMed] [Google Scholar]
  263. Zhang Wei, Zhou Ge, Zhao Yingxin, White Michael A., Zhao Yingming. Affinity enrichment of plasma membrane for proteomics analysis. Electrophoresis. 2003 Aug;24(16):2855–2863. doi: 10.1002/elps.200305569. [DOI] [PubMed] [Google Scholar]
  264. Zhang Yue-Qing, Ren Shuang-Xi, Li Hua-Lin, Wang Yong-Xiang, Fu Gang, Yang Jian, Qin Zhi-Qiang, Miao You-Gang, Wang Wen-Yi, Chen Run-Sheng. Genome-based analysis of virulence genes in a non-biofilm-forming Staphylococcus epidermidis strain (ATCC 12228). Mol Microbiol. 2003 Sep;49(6):1577–1593. doi: 10.1046/j.1365-2958.2003.03671.x. [DOI] [PubMed] [Google Scholar]
  265. Zheng Ping-Pin, Luider Theo M., Pieters Rob, Avezaat Cees J. J., van den Bent Martin J., Sillevis Smitt Peter A. E., Kros Johan M. Identification of tumor-related proteins by proteomic analysis of cerebrospinal fluid from patients with primary brain tumors. J Neuropathol Exp Neurol. 2003 Aug;62(8):855–862. doi: 10.1093/jnen/62.8.855. [DOI] [PubMed] [Google Scholar]
  266. Zhong Jingping, Haynes Paul A., Zhang Shiping, Yang Xinping, Andon Nancy L., Eckert Donna, Yates John R., 3rd, Wang Xun, Budworth Paul. Development of a system for the study of protein-protein interactions in planta: characterization of a TATA-box binding protein complex in Oryza sativa. J Proteome Res. 2003 Sep-Oct;2(5):514–522. doi: 10.1021/pr034023z. [DOI] [PubMed] [Google Scholar]
  267. Zhong Wenwan, Yeung Edward S. High-throughput analysis of total RNA expression profiles by capillary gel electrophoresis. Anal Chem. 2003 Sep 1;75(17):4415–4422. doi: 10.1021/ac034395r. [DOI] [PubMed] [Google Scholar]
  268. Zhou Yan, Luoh Shiuh-Ming, Zhang Yan, Watanabe Colin, Wu Thomas D., Ostland Michael, Wood William I., Zhang Zemin. Genome-wide identification of chromosomal regions of increased tumor expression by transcriptome analysis. Cancer Res. 2003 Sep 15;63(18):5781–5784. [PubMed] [Google Scholar]
  269. Zhu Heng, Bilgin Metin, Snyder Michael. Proteomics. Annu Rev Biochem. 2003;72:783–812. doi: 10.1146/annurev.biochem.72.121801.161511. [DOI] [PubMed] [Google Scholar]
  270. Zhu Hongtu, Yu Chang-Yung, Zhang Heping. Tree-based disease classification using protein data. Proteomics. 2003 Sep;3(9):1673–1677. doi: 10.1002/pmic.200300520. [DOI] [PubMed] [Google Scholar]
  271. Zhu Tong. Global analysis of gene expression using GeneChip microarrays. Curr Opin Plant Biol. 2003 Oct;6(5):418–425. doi: 10.1016/s1369-5266(03)00083-9. [DOI] [PubMed] [Google Scholar]
  272. Zhu Wei, Schlueter Shannon D., Brendel Volker. Refined annotation of the Arabidopsis genome by complete expressed sequence tag mapping. Plant Physiol. 2003 Jun;132(2):469–484. doi: 10.1104/pp.102.018101. [DOI] [PMC free article] [PubMed] [Google Scholar]
  273. Zierhut M., Mizuki N., Ohno S., Inoko H., Gül A., Onoé K., Isogai E. Immunology and functional genomics of Behçet's disease. Cell Mol Life Sci. 2003 Sep;60(9):1903–1922. doi: 10.1007/s00018-003-2333-3. [DOI] [PMC free article] [PubMed] [Google Scholar]
  274. de Bono Bernard, Trowsdale John. Exploring the immunogenome with bioinformatics. Semin Immunol. 2003 Aug;15(4):233–238. doi: 10.1016/s1044-5323(03)00049-6. [DOI] [PubMed] [Google Scholar]
  275. de Longueville Francoise, Atienzar Franck A., Marcq Laurence, Dufrane Simon, Evrard Stéphanie, Wouters Lydia, Leroux Florence, Bertholet Vincent, Gerin Brigitte, Whomsley Rhys. Use of a low-density microarray for studying gene expression patterns induced by hepatotoxicants on primary cultures of rat hepatocytes. Toxicol Sci. 2003 Jul 25;75(2):378–392. doi: 10.1093/toxsci/kfg196. [DOI] [PubMed] [Google Scholar]
  276. de Parseval Nathalie, Lazar Vladimir, Casella Jean-François, Benit Laurence, Heidmann Thierry. Survey of human genes of retroviral origin: identification and transcriptome of the genes with coding capacity for complete envelope proteins. J Virol. 2003 Oct;77(19):10414–10422. doi: 10.1128/JVI.77.19.10414-10422.2003. [DOI] [PMC free article] [PubMed] [Google Scholar]
  277. de los Reyes B. G., Morsy M., Gibbons J., Varma T. S. N., Antoine W., McGrath J. M., Halgren R., Redus M. A snapshot of the low temperature stress transcriptome of developing rice seedlings (Oryza sativa L.) via ESTs from subtracted cDNA library. Theor Appl Genet. 2003 Jun 25;107(6):1071–1082. doi: 10.1007/s00122-003-1344-7. [DOI] [PubMed] [Google Scholar]
  278. di Bernardo Diego, Down Thomas, Hubbard Tim. ddbRNA: detection of conserved secondary structures in multiple alignments. Bioinformatics. 2003 Sep 1;19(13):1606–1611. doi: 10.1093/bioinformatics/btg229. [DOI] [PubMed] [Google Scholar]
  279. van Lis Robert, Atteia Ariane, Mendoza-Hernández Guillermo, González-Halphen Diego. Identification of novel mitochondrial protein components of Chlamydomonas reinhardtii. A proteomic approach. Plant Physiol. 2003 May;132(1):318–330. doi: 10.1104/pp.102.018325. [DOI] [PMC free article] [PubMed] [Google Scholar]
  280. van Nimwegen Erik. Scaling laws in the functional content of genomes. Trends Genet. 2003 Sep;19(9):479–484. doi: 10.1016/S0168-9525(03)00203-8. [DOI] [PubMed] [Google Scholar]
  281. van Wees Saskia C. M., Chang Hur-Song, Zhu Tong, Glazebrook Jane. Characterization of the early response of Arabidopsis to Alternaria brassicicola infection using expression profiling. Plant Physiol. 2003 May 15;132(2):606–617. doi: 10.1104/pp.103.022186. [DOI] [PMC free article] [PubMed] [Google Scholar]

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

RESOURCES