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- Agrawal Deepak, Chen Tingan, Irby Rosalyn, Quackenbush John, Chambers Ann F., Szabo Marianna, Cantor Alan, Coppola Domenico, Yeatman Timothy J. Osteopontin identified as colon cancer tumor progression marker. C R Biol. 2003 Oct-Nov;326(10-11):1041–1043. doi: 10.1016/j.crvi.2003.09.007. [DOI] [PubMed] [Google Scholar]
- Ahn Woong Shick, Kim Ko-Woon, Bae Su Mi, Yoon Joo Hee, Lee Joon Mo, Namkoong Sung Eun, Kim Jin Hong, Kim Chong Kook, Lee Young Joo, Kim Yong-Wan. Targeted cellular process profiling approach for uterine leiomyoma using cDNA microarray, proteomics and gene ontology analysis. Int J Exp Pathol. 2003 Dec;84(6):267–279. doi: 10.1111/j.0959-9673.2003.00362.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Auffray Charles, Imbeaud Sandrine, Roux-Rouquié Magali, Hood Leroy. From functional genomics to systems biology: concepts and practices. C R Biol. 2003 Oct-Nov;326(10-11):879–892. doi: 10.1016/j.crvi.2003.09.033. [DOI] [PubMed] [Google Scholar]
- Baggerman G., Clynen E., Huybrechts J., Verleyen P., Clerens S., De Loof A., Schoofs L. Peptide profiling of a single Locusta migratoria corpus cardiacum by nano-LC tandem mass spectrometry. Peptides. 2003 Oct;24(10):1475–1485. doi: 10.1016/j.peptides.2003.08.014. [DOI] [PubMed] [Google Scholar]
- Barker D. LVB: parsimony and simulated annealing in the search for phylogenetic trees. Bioinformatics. 2004 Jan 22;20(2):274–275. doi: 10.1093/bioinformatics/btg402. [DOI] [PubMed] [Google Scholar]
- Baud Sébastien, Vaultier Marie-Noëlle, Rochat Christine. Structure and expression profile of the sucrose synthase multigene family in Arabidopsis. J Exp Bot. 2004 Feb;55(396):397–409. doi: 10.1093/jxb/erh047. [DOI] [PubMed] [Google Scholar]
- Baudouin-Cornu Peggy, Schuerer Katja, Marlière Philippe, Thomas Dominique. Intimate evolution of proteins. Proteome atomic content correlates with genome base composition. J Biol Chem. 2003 Nov 29;279(7):5421–5428. doi: 10.1074/jbc.M306415200. [DOI] [PubMed] [Google Scholar]
- Belbin Thomas J., Gaspar John, Haigentz Missak, Perez-Soler Roman, Keller Steven M., Prystowsky Michael B., Childs Geoffrey, Socci Nicholas D. Indirect measurements of differential gene expression with cDNA microarrays. Biotechniques. 2004 Feb;36(2):310–314. doi: 10.2144/04362MT02. [DOI] [PubMed] [Google Scholar]
- Belland Robert J., Nelson David E., Virok Dezso, Crane Deborah D., Hogan Daniel, Sturdevant Daniel, Beatty Wandy L., Caldwell Harlan D. Transcriptome analysis of chlamydial growth during IFN-gamma-mediated persistence and reactivation. Proc Natl Acad Sci U S A. 2003 Dec 12;100(26):15971–15976. doi: 10.1073/pnas.2535394100. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Bellgard Matthew, Hunter Adam, Kenworthy William. Microarray analysis using bioinformatics analysis audit trails (BAATs). C R Biol. 2003 Oct-Nov;326(10-11):1083–1087. doi: 10.1016/j.crvi.2003.09.005. [DOI] [PubMed] [Google Scholar]
- Benito Monica, Parker Joel, Du Quan, Wu Junyuan, Xiang Dong, Perou Charles M., Marron J. S. Adjustment of systematic microarray data biases. Bioinformatics. 2004 Jan 1;20(1):105–114. doi: 10.1093/bioinformatics/btg385. [DOI] [PubMed] [Google Scholar]
- Bertucci François, Loriod Béatrice, Nasser Valéry, Granjeaud Samuel, Tagett Rebecca, Braud Anne-Chantal, Patrice Viens, Houlgatte Rémi, Daniel Birnbaum, Nguyen Catherine. Gene expression profiling of breast carcinomas using nylon DNA arrays. C R Biol. 2003 Oct-Nov;326(10-11):1031–1039. doi: 10.1016/j.crvi.2003.09.010. [DOI] [PubMed] [Google Scholar]
- Biden Trevor J., Robinson Darren, Cordery Damien, Hughes William E., Busch Anna K. Chronic effects of fatty acids on pancreatic beta-cell function: new insights from functional genomics. Diabetes. 2004 Feb;53 (Suppl 1):S159–S165. doi: 10.2337/diabetes.53.2007.s159. [DOI] [PubMed] [Google Scholar]
- Blüthgen Nils, Kiełbasa Szymon M., Cajavec Branka, Herzel Hanspeter. HOMGL-comparing genelists across species and with different accession numbers. Bioinformatics. 2004 Jan 1;20(1):125–126. doi: 10.1093/bioinformatics/btg379. [DOI] [PubMed] [Google Scholar]
- Bortoli Sylvie, Renault Valérie, Eveno Eric, Auffray Charles, Butler-Browne Gill, Piétu Geneviève. Gene expression profiling of human satellite cells during muscular aging using cDNA arrays. Gene. 2003 Dec 4;321:145–154. doi: 10.1016/j.gene.2003.08.025. [DOI] [PubMed] [Google Scholar]
- Boutros Michael, Kiger Amy A., Armknecht Susan, Kerr Kim, Hild Marc, Koch Britta, Haas Stefan A., Paro Renato, Perrimon Norbert, Heidelberg Fly Array Consortium Genome-wide RNAi analysis of growth and viability in Drosophila cells. Science. 2004 Feb 6;303(5659):832–835. doi: 10.1126/science.1091266. [DOI] [PubMed] [Google Scholar]
- Braga-Neto Ulisses, Hashimoto Ronaldo, Dougherty Edward R., Nguyen Danh V., Carroll Raymond J. Is cross-validation better than resubstitution for ranking genes? Bioinformatics. 2004 Jan 22;20(2):253–258. doi: 10.1093/bioinformatics/btg399. [DOI] [PubMed] [Google Scholar]
- Bro Christoffer, Regenberg Birgitte, Nielsen Jens. Genome-wide transcriptional response of a Saccharomyces cerevisiae strain with an altered redox metabolism. Biotechnol Bioeng. 2004 Feb 5;85(3):269–276. doi: 10.1002/bit.10899. [DOI] [PubMed] [Google Scholar]
- Brodie Ryan, Roper Rachel L., Upton Chris. JDotter: a Java interface to multiple dotplots generated by dotter. Bioinformatics. 2004 Jan 22;20(2):279–281. doi: 10.1093/bioinformatics/btg406. [DOI] [PubMed] [Google Scholar]
- Brown J. Steven, Kuhn David, Wisser Randall, Power Emilio, Schnell Raymond. Quantification of sources of variation and accuracy of sequence discrimination in a replicated microarray experiment. Biotechniques. 2004 Feb;36(2):324–332. doi: 10.2144/04362MT04. [DOI] [PubMed] [Google Scholar]
- Bueno Raphael, Loughlin Kevin R., Powell Martha H., Gordon Gavin J. A diagnostic test for prostate cancer from gene expression profiling data. J Urol. 2004 Feb;171(2 Pt 1):903–906. doi: 10.1097/01.ju.0000095446.10443.52. [DOI] [PubMed] [Google Scholar]
- Bunai Keigo, Ariga Masanori, Inoue Taro, Nozaki Manabu, Ogane Shinya, Kakeshita Hiroshi, Nemoto Tadashi, Nakanishi Hiroshi, Yamane Kunio. Profiling and comprehensive expression analysis of ABC transporter solute-binding proteins of Bacillus subtilis membrane based on a proteomic approach. Electrophoresis. 2004 Jan;25(1):141–155. doi: 10.1002/elps.200305676. [DOI] [PubMed] [Google Scholar]
- Burger Albert, Davidson Duncan, Baldock Richard. Formalization of mouse embryo anatomy. Bioinformatics. 2004 Jan 22;20(2):259–267. doi: 10.1093/bioinformatics/btg400. [DOI] [PubMed] [Google Scholar]
- Butterfield D. Allan, Boyd-Kimball Debra, Castegna Alessandra. Proteomics in Alzheimer's disease: insights into potential mechanisms of neurodegeneration. J Neurochem. 2003 Sep;86(6):1313–1327. doi: 10.1046/j.1471-4159.2003.01948.x. [DOI] [PubMed] [Google Scholar]
- Carter Mark G., Piao Yulan, Dudekula Dawood B., Qian Yong, VanBuren Vincent, Sharov Alexei A., Tanaka Tetsuya S., Martin Patrick R., Bassey Uwem C., Stagg Carole A. The NIA cDNA project in mouse stem cells and early embryos. C R Biol. 2003 Oct-Nov;326(10-11):931–940. doi: 10.1016/j.crvi.2003.09.008. [DOI] [PubMed] [Google Scholar]
- Cecconi Daniela, Astner Hubert, Donadelli Massimo, Palmieri Marta, Missiaglia Edoardo, Hamdan Mahmoud, Scarpa Aldo, Righetti Pier Giorgio. Proteomic analysis of pancreatic ductal carcinoma cells treated with 5-aza-2'-deoxycytidine. Electrophoresis. 2003 Dec;24(24):4291–4303. doi: 10.1002/elps.200305724. [DOI] [PubMed] [Google Scholar]
- Chan Leo Lai, Hodgkiss Ivor John, Lu Songhui, Lo Samuel Chun-Lap. Use of two-dimensional gel electrophoresis proteome reference maps of dinoflagellates for species recognition of causative agents of harmful algal blooms. Proteomics. 2004 Jan;4(1):180–192. doi: 10.1002/pmic.200300548. [DOI] [PubMed] [Google Scholar]
- Chapman Brad A., Bowers John E., Schulze Stefan R., Paterson Andrew H. A comparative phylogenetic approach for dating whole genome duplication events. Bioinformatics. 2004 Jan 22;20(2):180–185. doi: 10.1093/bioinformatics/bth022. [DOI] [PubMed] [Google Scholar]
- Chiang Jung-Hsien, Yu Hsu-Chun, Hsu Huai-Jen. GIS: a biomedical text-mining system for gene information discovery. Bioinformatics. 2004 Jan 1;20(1):120–121. doi: 10.1093/bioinformatics/btg369. [DOI] [PubMed] [Google Scholar]
- Cho Chang-Won, Lee So-Hee, Choi Jiyeon, Park Soo-Jin, Ha Dong-Jin, Kim Hyo-Jeong, Kim Chan-Wha. Improvement of the two-dimensional gel electrophoresis analysis for the proteome study of Halobacterium salinarum. Proteomics. 2003 Dec;3(12):2325–2329. doi: 10.1002/pmic.200300525. [DOI] [PubMed] [Google Scholar]
- Chung Yeun-Jun, Jonkers Jos, Kitson Hannah, Fiegler Heike, Humphray Sean, Scott Carol, Hunt Sarah, Yu Yuejin, Nishijima Ichiko, Velds Arno. A whole-genome mouse BAC microarray with 1-Mb resolution for analysis of DNA copy number changes by array comparative genomic hybridization. Genome Res. 2004 Jan;14(1):188–196. doi: 10.1101/gr.1878804. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Clarkson Richard W. E., Watson Christine J. Microarray analysis of the involution switch. J Mammary Gland Biol Neoplasia. 2003 Jul;8(3):309–319. doi: 10.1023/b:jomg.0000010031.53310.92. [DOI] [PubMed] [Google Scholar]
- Connor E. E., Sonstegard T. S., Keele J. W., Bennett G. L., Williams J. L., Papworth R., Van Tassell C. P., Ashwell M. S. Physical and linkage mapping of mammary-derived expressed sequence tags in cattle. Genomics. 2004 Jan;83(1):148–152. doi: 10.1016/s0888-7543(03)00218-0. [DOI] [PubMed] [Google Scholar]
- Conrads Thomas P., Zhou Ming, Petricoin Emmanuel F., 3rd, Liotta Lance, Veenstra Timothy D. Cancer diagnosis using proteomic patterns. Expert Rev Mol Diagn. 2003 Jul;3(4):411–420. doi: 10.1586/14737159.3.4.411. [DOI] [PubMed] [Google Scholar]
- Corpillo Davide, Gardini Giulia, Vaira Anna Maria, Basso Manuela, Aime Silvio, Accotto Gian Paolo, Fasano Mauro. Proteomics as a tool to improve investigation of substantial equivalence in genetically modified organisms: the case of a virus-resistant tomato. Proteomics. 2004 Jan;4(1):193–200. doi: 10.1002/pmic.200300540. [DOI] [PubMed] [Google Scholar]
- Crass T., Antes I., Basekow R., Bork P., Buning C., Christensen M., Claussen H., Ebeling C., Ernst P., Gailus-Durner V. The Helmholtz Network for Bioinformatics: an integrative web portal for bioinformatics resources. Bioinformatics. 2004 Jan 22;20(2):268–270. doi: 10.1093/bioinformatics/btg398. [DOI] [PubMed] [Google Scholar]
- Daibata Masanori, Matsuo Yoshinobu, Machida Hisanori, Taguchi Takahiro, Ohtsuki Yuji, Taguchi Hirokuni. Differential gene-expression profiling in the leukemia cell lines derived from indolent and aggressive phases of CD56+ T-cell large granular lymphocyte leukemia. Int J Cancer. 2004 Mar 1;108(6):845–851. doi: 10.1002/ijc.11647. [DOI] [PubMed] [Google Scholar]
- Dalla Emiliano, Verardo Roberto, Lazarević Dejan, Marchionni Luigi, Reid James F., Bahar Nabil, Klarić Enio, Marcuzzi Giacomo, Marzio Riccardo, Belgrano Anna. LNCIB human full-length cDNAs collection: towards a better comprehension of the human transcriptome. C R Biol. 2003 Oct-Nov;326(10-11):967–970. doi: 10.1016/j.crvi.2003.09.029. [DOI] [PubMed] [Google Scholar]
- Darling Aaron E., Mau Bob, Blattner Frederick R., Perna Nicole T. GRIL: genome rearrangement and inversion locator. Bioinformatics. 2004 Jan 1;20(1):122–124. doi: 10.1093/bioinformatics/btg378. [DOI] [PubMed] [Google Scholar]
- Datta Susmita, Satten Glen A., Benos Dale J., Xia Jiazeng, Heslin Martin J., Datta Somnath. An empirical bayes adjustment to increase the sensitivity of detecting differentially expressed genes in microarray experiments. Bioinformatics. 2004 Jan 22;20(2):235–242. doi: 10.1093/bioinformatics/btg396. [DOI] [PubMed] [Google Scholar]
- De Angelis Maria, Gobbetti Marco. Environmental stress responses in Lactobacillus: a review. Proteomics. 2004 Jan;4(1):106–122. doi: 10.1002/pmic.200300497. [DOI] [PubMed] [Google Scholar]
- Deng Minghua, Zhang Kui, Mehta Shipra, Chen Ting, Sun Fengzhu. Prediction of protein function using protein-protein interaction data. J Comput Biol. 2003;10(6):947–960. doi: 10.1089/106652703322756168. [DOI] [PubMed] [Google Scholar]
- Devlin Paul Francis, Yanovsky Marcelo Javier, Kay Steve A. A genomic analysis of the shade avoidance response in Arabidopsis. Plant Physiol. 2003 Nov 26;133(4):1617–1629. doi: 10.1104/pp.103.034397. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Dickinson Danielle N., La Duc Myron T., Haskins William E., Gornushkin Igor, Winefordner James D., Powell David H., Venkateswaran Kasthuri. Species differentiation of a diverse suite of Bacillus spores by mass spectrometry-based protein profiling. Appl Environ Microbiol. 2004 Jan;70(1):475–482. doi: 10.1128/AEM.70.1.475-482.2004. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Doolan D. L., Aguiar J. C., Weiss W. R., Sette A., Felgner P. L., Regis D. P., Quinones-Casas P., Yates J. R., 3rd, Blair P. L., Richie T. L. Utilization of genomic sequence information to develop malaria vaccines. J Exp Biol. 2003 Nov;206(Pt 21):3789–3802. doi: 10.1242/jeb.00615. [DOI] [PubMed] [Google Scholar]
- Doumith Michel, Cazalet Christel, Simoes Natalie, Frangeul Lionel, Jacquet Christine, Kunst Frank, Martin Paul, Cossart Pascale, Glaser Philippe, Buchrieser Carmen. New aspects regarding evolution and virulence of Listeria monocytogenes revealed by comparative genomics and DNA arrays. Infect Immun. 2004 Feb;72(2):1072–1083. doi: 10.1128/IAI.72.2.1072-1083.2004. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Dyrskjøt Lars. Classification of bladder cancer by microarray expression profiling: towards a general clinical use of microarrays in cancer diagnostics. Expert Rev Mol Diagn. 2003 Sep;3(5):635–647. doi: 10.1586/14737159.3.5.635. [DOI] [PubMed] [Google Scholar]
- Eisenhaber Birgit, Wildpaner Michael, Schultz Carolyn J., Borner Georg H. H., Dupree Paul, Eisenhaber Frank. Glycosylphosphatidylinositol lipid anchoring of plant proteins. Sensitive prediction from sequence- and genome-wide studies for Arabidopsis and rice. Plant Physiol. 2003 Dec;133(4):1691–1701. doi: 10.1104/pp.103.023580. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Emrich Scott J., Aluru Srinivas, Fu Yan, Wen Tsui-Jung, Narayanan Mahesh, Guo Ling, Ashlock Daniel A., Schnable Patrick S. A strategy for assembling the maize (Zea mays L.) genome. Bioinformatics. 2004 Jan 22;20(2):140–147. doi: 10.1093/bioinformatics/bth017. [DOI] [PubMed] [Google Scholar]
- Fargiano Antonio A., Desai Kartiki V., Green Jeffrey E. Interrogating mouse mammary cancer models: insights from gene expression profiling. J Mammary Gland Biol Neoplasia. 2003 Jul;8(3):321–334. doi: 10.1023/b:jomg.0000010032.05234.6f. [DOI] [PubMed] [Google Scholar]
- Gan Li, Ye Shiming, Chu Alan, Anton Kristin, Yi Saili, Vincent Valerie A., von Schack David, Chin Daniel, Murray Joseph, Lohr Scott. Identification of cathepsin B as a mediator of neuronal death induced by Abeta-activated microglial cells using a functional genomics approach. J Biol Chem. 2003 Nov 10;279(7):5565–5572. doi: 10.1074/jbc.M306183200. [DOI] [PubMed] [Google Scholar]
- Gass Sandra, Harris Jessica, Ormandy Chris, Brisken Cathrin. Using gene expression arrays to elucidate transcriptional profiles underlying prolactin function. J Mammary Gland Biol Neoplasia. 2003 Jul;8(3):269–285. doi: 10.1023/b:jomg.0000010029.85796.63. [DOI] [PubMed] [Google Scholar]
- Ge Hong, Chuang Yao-Yu Eric, Zhao Shuping, Tong Min, Tsai Mong-Hsun, Temenak Joseph J., Richards Allen L., Ching Wei-Mei. Comparative genomics of Rickettsia prowazekii Madrid E and Breinl strains. J Bacteriol. 2004 Jan;186(2):556–565. doi: 10.1128/JB.186.2.556-565.2004. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Giaever Guri, Flaherty Patrick, Kumm Jochen, Proctor Michael, Nislow Corey, Jaramillo Daniel F., Chu Angela M., Jordan Michael I., Arkin Adam P., Davis Ronald W. Chemogenomic profiling: identifying the functional interactions of small molecules in yeast. Proc Natl Acad Sci U S A. 2004 Jan 12;101(3):793–798. doi: 10.1073/pnas.0307490100. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Gibbings J. George, Cook Brian P., Dufault Michael R., Madden Stephen L., Khuri Sawsan, Turnbull Chris J., Dunwell Jim M. Global transcript analysis of rice leaf and seed using SAGE technology. Plant Biotechnol J. 2003 Jul;1(4):271–285. doi: 10.1046/j.1467-7652.2003.00026.x. [DOI] [PubMed] [Google Scholar]
- Godl Klaus, Wissing Josef, Kurtenbach Alexander, Habenberger Peter, Blencke Stephanie, Gutbrod Heidrun, Salassidis Kostadinos, Stein-Gerlach Matthias, Missio Andrea, Cotten Matt. An efficient proteomics method to identify the cellular targets of protein kinase inhibitors. Proc Natl Acad Sci U S A. 2003 Dec 10;100(26):15434–15439. doi: 10.1073/pnas.2535024100. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Goh Chern-Sing, Lan Ning, Douglas Shawn M., Wu Baolin, Echols Nathaniel, Smith Andrew, Milburn Duncan, Montelione Gaetano T., Zhao Hongyu, Gerstein Mark. Mining the structural genomics pipeline: identification of protein properties that affect high-throughput experimental analysis. J Mol Biol. 2004 Feb 6;336(1):115–130. doi: 10.1016/j.jmb.2003.11.053. [DOI] [PubMed] [Google Scholar]
- Goldstein Adrian M. Changing paradigms in dermatology: proteomics: a new approach to skin disease. Clin Dermatol. 2003 Sep-Oct;21(5):370–374. doi: 10.1016/j.clindermatol.2003.08.014. [DOI] [PubMed] [Google Scholar]
- Gott Jonatha M. Expanding genome capacity via RNA editing. C R Biol. 2003 Oct-Nov;326(10-11):901–908. doi: 10.1016/j.crvi.2003.09.004. [DOI] [PubMed] [Google Scholar]
- Grant Jeffrey D., Somers Luke A., Zhang Yue, Manion Frank J., Bidaut Ghislain, Ochs Michael F. FGDP: functional genomics data pipeline for automated, multiple microarray data analyses. Bioinformatics. 2004 Jan 22;20(2):282–283. doi: 10.1093/bioinformatics/btg407. [DOI] [PubMed] [Google Scholar]
- Green Jeffrey E., Desai Kartiki, Ye Yumei, Kavanaugh Claudine, Calvo Alfonso, Huh Jung-Im. Genomic approaches to understanding mammary tumor progression in transgenic mice and responses to therapy. Clin Cancer Res. 2004 Jan 1;10(1 Pt 2):385S–390S. doi: 10.1158/1078-0432.ccr-031201. [DOI] [PubMed] [Google Scholar]
- Greshock Joel, Naylor Tara L., Margolin Adam, Diskin Sharon, Cleaver Stephen H., Futreal P. Andrew, deJong Pieter J., Zhao Shaying, Liebman Michael, Weber Barbara L. 1-Mb resolution array-based comparative genomic hybridization using a BAC clone set optimized for cancer gene analysis. Genome Res. 2003 Dec 12;14(1):179–187. doi: 10.1101/gr.1847304. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Gros François. From the messenger RNA saga to the transcriptome era. C R Biol. 2003 Oct-Nov;326(10-11):893–900. doi: 10.1016/j.crvi.2003.09.009. [DOI] [PubMed] [Google Scholar]
- Gunaratne Preethi H., Wu Jia Qian, Garcia Angela M., Hulyk Steven, Worley Kim C., Margolin Judith F., Gibbs Richard A. Concatenation cDNA sequencing for transcriptome analysis. C R Biol. 2003 Oct-Nov;326(10-11):971–977. doi: 10.1016/j.crvi.2003.09.032. [DOI] [PubMed] [Google Scholar]
- Han Ze-Guang, Zhao Guo-Ping, Chen Zhu. Transcriptome study in China. C R Biol. 2003 Oct-Nov;326(10-11):949–957. doi: 10.1016/j.crvi.2003.09.021. [DOI] [PubMed] [Google Scholar]
- Hanke Guy Thomas, Kimata-Ariga Yoko, Taniguchi Isao, Hase Toshiharu. A post genomic characterization of Arabidopsis ferredoxins. Plant Physiol. 2003 Dec 18;134(1):255–264. doi: 10.1104/pp.103.032755. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Hayashizaki Yoshihide. The Riken mouse genome encyclopedia project. C R Biol. 2003 Oct-Nov;326(10-11):923–929. doi: 10.1016/j.crvi.2003.09.018. [DOI] [PubMed] [Google Scholar]
- Hayes Finbarr. Transposon-based strategies for microbial functional genomics and proteomics. Annu Rev Genet. 2003;37:3–29. doi: 10.1146/annurev.genet.37.110801.142807. [DOI] [PubMed] [Google Scholar]
- He Qing-Yu, Chen Jia, Kung Hsiang-Fu, Yuen Anthony Po-Wing, Chiu Jen-Fu. Identification of tumor-associated proteins in oral tongue squamous cell carcinoma by proteomics. Proteomics. 2004 Jan;4(1):271–278. doi: 10.1002/pmic.200300550. [DOI] [PubMed] [Google Scholar]
- Heazlewood Joshua L., Tonti-Filippini Julian S., Gout Alexander M., Day David A., Whelan James, Millar A. Harvey. Experimental analysis of the Arabidopsis mitochondrial proteome highlights signaling and regulatory components, provides assessment of targeting prediction programs, and indicates plant-specific mitochondrial proteins. Plant Cell. 2003 Dec 11;16(1):241–256. doi: 10.1105/tpc.016055. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Hegde Priti S., White Ian R., Debouck Christine. Interplay of transcriptomics and proteomics. Curr Opin Biotechnol. 2003 Dec;14(6):647–651. doi: 10.1016/j.copbio.2003.10.006. [DOI] [PubMed] [Google Scholar]
- Henshall Susan. Tissue microarrays. J Mammary Gland Biol Neoplasia. 2003 Jul;8(3):347–358. doi: 10.1023/b:jomg.0000010034.43145.86. [DOI] [PubMed] [Google Scholar]
- Herath Chandana B., Shiojima Satoshi, Ishiwata Hiroko, Katsuma Susumu, Kadowaki Tadashi, Ushizawa Koichi, Imai Kei, Takahashi Toru, Hirasawa Akira, Tsujimoto Gozoh. Pregnancy-associated changes in genome-wide gene expression profiles in the liver of cow throughout pregnancy. Biochem Biophys Res Commun. 2004 Jan 16;313(3):666–680. doi: 10.1016/j.bbrc.2003.11.151. [DOI] [PubMed] [Google Scholar]
- Herranen Mirkka, Battchikova Natalia, Zhang Pengpeng, Graf Alexander, Sirpiö Sari, Paakkarinen Virpi, Aro Eva-Mari. Towards functional proteomics of membrane protein complexes in Synechocystis sp. PCC 6803. Plant Physiol. 2004 Jan;134(1):470–481. doi: 10.1104/pp.103.032326. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Hide Winston, Smedley Damian, McCarthy Mark, Kelso Janet. Application of eVOC: controlled vocabularies for unifying gene expression data. C R Biol. 2003 Oct-Nov;326(10-11):1089–1096. doi: 10.1016/j.crvi.2003.09.030. [DOI] [PubMed] [Google Scholar]
- Higgins Vincent J., Rogers Peter J., Dawes Ian W. Application of genome-wide expression analysis to identify molecular markers useful in monitoring industrial fermentations. Appl Environ Microbiol. 2003 Dec;69(12):7535–7540. doi: 10.1128/AEM.69.12.7535-7540.2003. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Hofacker I. L., Priwitzer B., Stadler P. F. Prediction of locally stable RNA secondary structures for genome-wide surveys. Bioinformatics. 2004 Jan 22;20(2):186–190. doi: 10.1093/bioinformatics/btg388. [DOI] [PubMed] [Google Scholar]
- Huang Lingyun, Li Bingxia, Luo Chen, Xie Jinyun, Chen Ping, Liang Songping. Proteome comparative analysis of gynogenetic haploid and diploid embryos of goldfish (Carassius auratus). Proteomics. 2004 Jan;4(1):235–243. doi: 10.1002/pmic.200300553. [DOI] [PubMed] [Google Scholar]
- Huang Shir-Ly, Wu Li-Cheng, Liang Han-Kuen, Pan Kuan-Ting, Horng Jorng-Tzong, Ko Ming-Tat. PGTdb: a database providing growth temperatures of prokaryotes. Bioinformatics. 2004 Jan 22;20(2):276–278. doi: 10.1093/bioinformatics/btg403. [DOI] [PubMed] [Google Scholar]
- Hudson Matthew E., Quail Peter H. Identification of promoter motifs involved in the network of phytochrome A-regulated gene expression by combined analysis of genomic sequence and microarray data. Plant Physiol. 2003 Dec;133(4):1605–1616. doi: 10.1104/pp.103.030437. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Ikeo Kazuho, Ishi-i Jun, Tamura Takurou, Gojobori Takashi, Tateno Yoshio. CIBEX: center for information biology gene expression database. C R Biol. 2003 Oct-Nov;326(10-11):1079–1082. doi: 10.1016/j.crvi.2003.09.034. [DOI] [PubMed] [Google Scholar]
- Ippel Johannes H., Pouvreau Laurice, Kroef Toos, Gruppen Harry, Versteeg Geurt, van den Putten Peter, Struik Paul C., van Mierlo Carlo P. M. In vivo uniform (15)N-isotope labelling of plants: using the greenhouse for structural proteomics. Proteomics. 2004 Jan;4(1):226–234. doi: 10.1002/pmic.200300506. [DOI] [PubMed] [Google Scholar]
- Islas Sara, Becerra Arturo, Luisi P. Luigi, Lazcano Antonio. Comparative genomics and the gene complement of a minimal cell. Orig Life Evol Biosph. 2004 Feb;34(1-2):243–256. doi: 10.1023/b:orig.0000009844.90540.52. [DOI] [PubMed] [Google Scholar]
- Iwata Shin-ichi, Nomoto Masahiro, Morioka Hirofumi, Miyata Atsuro. Gene expression profiling in the midbrain of striatal 6-hydroxydopamine-injected mice. Synapse. 2004 Mar 15;51(4):279–286. doi: 10.1002/syn.10307. [DOI] [PubMed] [Google Scholar]
- Jenson S. D., Robetorye R. S., Bohling S. D., Schumacher J. A., Morgan J. W., Lim M. S., Elenitoba-Johnson K. S. J. Validation of cDNA microarray gene expression data obtained from linearly amplified RNA. Mol Pathol. 2003 Dec;56(6):307–312. doi: 10.1136/mp.56.6.307. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Jiang Lei, He Lin, Fountoulakis Michael. Comparison of protein precipitation methods for sample preparation prior to proteomic analysis. J Chromatogr A. 2004 Jan 16;1023(2):317–320. doi: 10.1016/j.chroma.2003.10.029. [DOI] [PubMed] [Google Scholar]
- Jiao Yuling, Yang Hongjuan, Ma Ligeng, Sun Ning, Yu Haiyuan, Liu Tie, Gao Ying, Gu Hongya, Chen Zhangliang, Wada Masamitsu. A genome-wide analysis of blue-light regulation of Arabidopsis transcription factor gene expression during seedling development. Plant Physiol. 2003 Nov 6;133(4):1480–1493. doi: 10.1104/pp.103.029439. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Jim Kam, Parmar Kush, Singh Mona, Tavazoie Saeed. A cross-genomic approach for systematic mapping of phenotypic traits to genes. Genome Res. 2004 Jan;14(1):109–115. doi: 10.1101/gr.1586704. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Jin Sun Hee, Cho Eun Hye, Ko Jung Eun, Jung Eun Hee, Ahn Byungchan, Hahm Jong Ryeal, Kim Jae Won, Kim Choong Won, Kim Deok Ryong. Comparative analysis of nuclear proteins of B cells in different developmental stages. Proteomics. 2003 Dec;3(12):2428–2436. doi: 10.1002/pmic.200300576. [DOI] [PubMed] [Google Scholar]
- Joo Won-A, Kang Mee-Jeong, Son Won-kyu, Lee Hyun-Ju, Lee Do-Youn, Lee Eunil, Kim Chan-Wha. Monitoring protein expression by proteomics: human plasma exposed to benzene. Proteomics. 2003 Dec;3(12):2402–2411. doi: 10.1002/pmic.200300616. [DOI] [PubMed] [Google Scholar]
- Juretic Nikoleta, Bureau Thomas E., Bruskiewich Richard M. Transposable element annotation of the rice genome. Bioinformatics. 2004 Jan 22;20(2):155–160. doi: 10.1093/bioinformatics/bth019. [DOI] [PubMed] [Google Scholar]
- Kamada Tomoe, Nito Kazumasa, Hayashi Hiroshi, Mano Shoji, Hayashi Makoto, Nishimura Mikio. Functional differentiation of peroxisomes revealed by expression profiles of peroxisomal genes in Arabidopsis thaliana. Plant Cell Physiol. 2003 Dec;44(12):1275–1289. doi: 10.1093/pcp/pcg173. [DOI] [PubMed] [Google Scholar]
- Kang Hio Chung, Kim Il-Jin, Park Jae-Hyun, Shin Yong, Ku Ja-Lok, Jung Mi Sun, Yoo Byong Chul, Kim Hark Kyun, Park Jae-Gahb. Identification of genes with differential expression in acquired drug-resistant gastric cancer cells using high-density oligonucleotide microarrays. Clin Cancer Res. 2004 Jan 1;10(1 Pt 1):272–284. doi: 10.1158/1078-0432.ccr-1025-3. [DOI] [PubMed] [Google Scholar]
- Kao Katy C., Yang Young-Lyeol, Boscolo Riccardo, Sabatti Chiara, Roychowdhury Vwani, Liao James C. Transcriptome-based determination of multiple transcription regulator activities in Escherichia coli by using network component analysis. Proc Natl Acad Sci U S A. 2003 Dec 23;101(2):641–646. doi: 10.1073/pnas.0305287101. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Kato Kikuya. Adaptor-tagged competitive PCR: study of the mammalian nervous system. C R Biol. 2003 Oct-Nov;326(10-11):941–947. doi: 10.1016/j.crvi.2003.09.013. [DOI] [PubMed] [Google Scholar]
- Kawaji Hideya, Takenaka Yoichi, Matsuda Hideo. Graph-based clustering for finding distant relationships in a large set of protein sequences. Bioinformatics. 2004 Jan 22;20(2):243–252. doi: 10.1093/bioinformatics/btg397. [DOI] [PubMed] [Google Scholar]
- Kerr M. Kathleen. Linear models for microarray data analysis: hidden similarities and differences. J Comput Biol. 2003;10(6):891–901. doi: 10.1089/106652703322756131. [DOI] [PubMed] [Google Scholar]
- Khawaja Xavier, Xu Jun, Liang Jin-Jun, Barrett James E. Proteomic analysis of protein changes developing in rat hippocampus after chronic antidepressant treatment: Implications for depressive disorders and future therapies. J Neurosci Res. 2004 Feb 15;75(4):451–460. doi: 10.1002/jnr.10869. [DOI] [PubMed] [Google Scholar]
- Kikuchi Miki, Hatano Naoya, Yokota Sadaki, Shimozawa Nobuyuki, Imanaka Tsuneo, Taniguchi Hisaaki. Proteomic analysis of rat liver peroxisome: presence of peroxisome-specific isozyme of Lon protease. J Biol Chem. 2003 Oct 15;279(1):421–428. doi: 10.1074/jbc.M305623200. [DOI] [PubMed] [Google Scholar]
- Kim Chang-Hoon, Kim Do Kyun, Choi Seung Jin, Choi Kun Ho, Song Kyoung Seob, Chi Janghoon, Koo Ja Seok, Hwang Seung Yong, Yoon Joo-Heon, Seong Je Kyung. Proteomic and transcriptomic analysis of interleukin-1beta treated lung carcinoma cell line. Proteomics. 2003 Dec;3(12):2454–2471. doi: 10.1002/pmic.200300643. [DOI] [PubMed] [Google Scholar]
- Kim Hyun J., Ishidou E., Kitagawa E., Momose Y., Iwahashi H. A yeast DNA microarray for the evaluation of toxicity in environmental water containing burned ash. Environ Monit Assess. 2004 Mar;92(1-3):253–272. doi: 10.1023/b:emas.0000014504.03500.41. [DOI] [PubMed] [Google Scholar]
- Kim Okhee, Park Misun, Kang Hoil, Lim Sinae, Lee Choon-Taek. Differential protein expressions induced by adenovirus-mediated p16 gene transfer into Balb/c nude mouse. Proteomics. 2003 Dec;3(12):2412–2419. doi: 10.1002/pmic.200300542. [DOI] [PubMed] [Google Scholar]
- Kim Seung Il, Kim Jin Young, Kim Eun A., Kwon Kyung-Hoon, Kim Kyung-Wook, Cho Kun, Lee Jeong Hwa, Nam Myung Hee, Yang Deok-Chun, Yoo Jong Shin. Proteome analysis of hairy root from Panax ginseng C.A. Meyer using peptide fingerprinting, internal sequencing and expressed sequence tag data. Proteomics. 2003 Dec;3(12):2379–2392. doi: 10.1002/pmic.200300619. [DOI] [PubMed] [Google Scholar]
- Kim Seung Il, Song Seung Youl, Kim Kyung Wook, Ho Eun Mi, Oh Kye Heon. Proteomic analysis of the benzoate degradation pathway in Acinetobacter sp. KS-1. Res Microbiol. 2003 Dec;154(10):697–703. doi: 10.1016/j.resmic.2003.09.003. [DOI] [PubMed] [Google Scholar]
- Kim Seung-Ki, Wang Kyu-Chang, Hong Soo Jin, Chung Chun-Kee, Lim Su-Young, Kim Young-Yim, Chi Je G., Kim Chong Jai, Chung You-Nam, Kim Hyun Jib. Gene expression profile analyses of cortical dysplasia by cDNA arrays. Epilepsy Res. 2003 Oct;56(2-3):175–183. doi: 10.1016/j.eplepsyres.2003.09.003. [DOI] [PubMed] [Google Scholar]
- Kim Sun Tae, Cho Kyu Seong, Yu Seok, Kim Sang Gon, Hong Jong Chan, Han Chang-deok, Bae Dong Won, Nam Myung Hee, Kang Kyu Young. Proteomic analysis of differentially expressed proteins induced by rice blast fungus and elicitor in suspension-cultured rice cells. Proteomics. 2003 Dec;3(12):2368–2378. doi: 10.1002/pmic.200300577. [DOI] [PubMed] [Google Scholar]
- Kim Sun Tae, Kim Hyun Soo, Kim Han Ju, Kim Sang Gon, Kang Sun Young, Lim Dong Bin, Kang Kyu Young. Prefractionation of protein samples for proteome analysis by sodium dodecyl sulfate-polyacrylamide gel electrophoresis. Mol Cells. 2003 Dec 31;16(3):316–322. [PubMed] [Google Scholar]
- Kim Yong-Ou, Park Sang-Joon, Balaban Robert S., Nirenberg Marshall, Kim Yongsok. A functional genomic screen for cardiogenic genes using RNA interference in developing Drosophila embryos. Proc Natl Acad Sci U S A. 2003 Dec 18;101(1):159–164. doi: 10.1073/pnas.0307205101. [DOI] [PMC free article] [PubMed] [Google Scholar]
- King Ross D., Whelan Kenneth E., Jones Ffion M., Reiser Philip G. K., Bryant Christopher H., Muggleton Stephen H., Kell Douglas B., Oliver Stephen G. Functional genomic hypothesis generation and experimentation by a robot scientist. Nature. 2004 Jan 15;427(6971):247–252. doi: 10.1038/nature02236. [DOI] [PubMed] [Google Scholar]
- Kofuji Rumiko, Sumikawa Naomi, Yamasaki Misuzu, Kondo Kimihiko, Ueda Kunihiko, Ito Motomi, Hasebe Mitsuyasu. Evolution and divergence of the MADS-box gene family based on genome-wide expression analyses. Mol Biol Evol. 2003 Aug 29;20(12):1963–1977. doi: 10.1093/molbev/msg216. [DOI] [PubMed] [Google Scholar]
- Kreps Joel, Budworth Paul, Goff Steve, Wang Ronglin. Identification of putative plant cold responsive regulatory elements by gene expression profiling and a pattern enumeration algorithm. Plant Biotechnol J. 2003 Sep;1(5):345–352. doi: 10.1046/j.1467-7652.2003.00032.x. [DOI] [PubMed] [Google Scholar]
- Kuhl Joseph C., Cheung Foo, Yuan Qiaoping, Martin William, Zewdie Yayeh, McCallum John, Catanach Andrew, Rutherford Paul, Sink Kenneth C., Jenderek Maria. A unique set of 11,008 onion expressed sequence tags reveals expressed sequence and genomic differences between the monocot orders Asparagales and Poales. Plant Cell. 2003 Dec 11;16(1):114–125. doi: 10.1105/tpc.017202. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Kwon Kyung-Hoon, Kim Mioak, Kim Jin Young, Kim Kyung Wook, Kim Seung Il, Park Young Mok, Yoo Jong Shin. Efficiency improvement of peptide identification for an organism without complete genome sequence, using expressed sequence tag database and tandem mass spectral data. Proteomics. 2003 Dec;3(12):2305–2309. doi: 10.1002/pmic.200300620. [DOI] [PubMed] [Google Scholar]
- Lapointe Jacques, Li Chunde, Higgins John P., van de Rijn Matt, Bair Eric, Montgomery Kelli, Ferrari Michelle, Egevad Lars, Rayford Walter, Bergerheim Ulf. Gene expression profiling identifies clinically relevant subtypes of prostate cancer. Proc Natl Acad Sci U S A. 2004 Jan 7;101(3):811–816. doi: 10.1073/pnas.0304146101. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Leader David P. BugView: a browser for comparing genomes. Bioinformatics. 2004 Jan 1;20(1):129–130. doi: 10.1093/bioinformatics/btg383. [DOI] [PubMed] [Google Scholar]
- Lee Chih-Lei, Hsiao He-Hsuan, Lin Chia-Wei, Wu Szu-Pei, Huang Shiuan-Yi, Wu Chi-Yue, Wang Andrew H-J, Khoo Kay-Hooi. Strategic shotgun proteomics approach for efficient construction of an expression map of targeted protein families in hepatoma cell lines. Proteomics. 2003 Dec;3(12):2472–2486. doi: 10.1002/pmic.200300586. [DOI] [PubMed] [Google Scholar]
- Lee Do-Yup, Park Yong-Cheol, Kim Hyo-Jin, Ryu Yeon-Woo, Seo Jin-Ho. Proteomic analysis of Candida magnoliae strains by two-dimensional gel electrophoresis and mass spectrometry. Proteomics. 2003 Dec;3(12):2330–2338. doi: 10.1002/pmic.200300568. [DOI] [PubMed] [Google Scholar]
- Lee Eung Goo, Kim Jae Hoon, Shin Yong Seung, Shin Gee Wook, Suh Myung Deuk, Kim Dae Yong, Kim Yong Hwan, Kim Gon Sup, Jung Tae Sung. Establishment of a two-dimensional electrophoresis map for Neospora caninum tachyzoites by proteomics. Proteomics. 2003 Dec;3(12):2339–2350. doi: 10.1002/pmic.200300617. [DOI] [PubMed] [Google Scholar]
- Lee Shinyoung, Kim Joonyul, Son Jun-Seock, Nam Jongmin, Jeong Dong-Hoon, Lee Keunsub, Jang Seonghoe, Yoo Jihye, Lee Jinwon, Lee Dong-Yeon. Systematic reverse genetic screening of T-DNA tagged genes in rice for functional genomic analyses: MADS-box genes as a test case. Plant Cell Physiol. 2003 Dec;44(12):1403–1411. doi: 10.1093/pcp/pcg156. [DOI] [PubMed] [Google Scholar]
- Lee Yoonsuk, Lee Eun Kyoung, Cho Yong Wan, Matsui Takuya, Kang In-Cheol, Kim Tai-Sun, Han Moon Hi. ProteoChip: a highly sensitive protein microarray prepared by a novel method of protein immobilization for application of protein-protein interaction studies. Proteomics. 2003 Dec;3(12):2289–2304. doi: 10.1002/pmic.200300541. [DOI] [PubMed] [Google Scholar]
- Lemke Ney, Herédia Fabiana, Barcellos Cláudia K., Dos Reis Adriana N., Mombach José C. M. Essentiality and damage in metabolic networks. Bioinformatics. 2004 Jan 1;20(1):115–119. doi: 10.1093/bioinformatics/btg386. [DOI] [PubMed] [Google Scholar]
- Leonard P., Sharp T., Henderson S., Hewitt D., Pringle J., Sandison A., Goodship A., Whelan J., Boshoff C. Gene expression array profile of human osteosarcoma. Br J Cancer. 2003 Dec 15;89(12):2284–2288. doi: 10.1038/sj.bjc.6601389. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Li Ailing, Li Hongwei, Jin Gang, Xiu Ruijuan. A proteomic study on cell cycle progression of endothelium exposed to tumor conditioned medium and the possible role of cyclin D1/E. Clin Hemorheol Microcirc. 2003;29(3-4):383–390. [PubMed] [Google Scholar]
- Li Jiangning, Adams Larry, Schwartz S. M., Bumgarner Roger E. RNA amplification, fidelity and reproducibility of expression profiling. C R Biol. 2003 Oct-Nov;326(10-11):1021–1030. doi: 10.1016/j.crvi.2003.09.015. [DOI] [PubMed] [Google Scholar]
- Li Ka Wan, Hornshaw Martin P., Van Der Schors Roel C., Watson Rod, Tate Stephen, Casetta Bruno, Jimenez Connie R., Gouwenberg Yvonne, Gundelfinger Eckart D., Smalla Karl-Heinz. Proteomics analysis of rat brain postsynaptic density. Implications of the diverse protein functional groups for the integration of synaptic physiology. J Biol Chem. 2003 Oct 7;279(2):987–1002. doi: 10.1074/jbc.M303116200. [DOI] [PubMed] [Google Scholar]
- Li Meihua, Lin Yu-Min, Hasegawa Suguru, Shimokawa Takashi, Murata Kohei, Kameyama Masao, Ishikawa Osamu, Katagiri Toyomasa, Tsunoda Tatsuhiko, Nakamura Yusuke. Genes associated with liver metastasis of colon cancer, identified by genome-wide cDNA microarray. Int J Oncol. 2004 Feb;24(2):305–312. [PubMed] [Google Scholar]
- Li Qingsheng, Schacker Timothy, Carlis John, Beilman Gregory, Nguyen Phuong, Haase Ashley T. Functional genomic analysis of the response of HIV-1-infected lymphatic tissue to antiretroviral therapy. J Infect Dis. 2004 Feb 5;189(4):572–582. doi: 10.1086/381396. [DOI] [PubMed] [Google Scholar]
- Liao Li, Noble William Stafford. Combining pairwise sequence similarity and support vector machines for detecting remote protein evolutionary and structural relationships. J Comput Biol. 2003;10(6):857–868. doi: 10.1089/106652703322756113. [DOI] [PubMed] [Google Scholar]
- Lilien Ryan H., Farid Hany, Donald Bruce R. Probabilistic disease classification of expression-dependent proteomic data from mass spectrometry of human serum. J Comput Biol. 2003;10(6):925–946. doi: 10.1089/106652703322756159. [DOI] [PubMed] [Google Scholar]
- Liu Jing, Dehbi Mohammed, Moeck Greg, Arhin Francis, Bauda Pascale, Bergeron Dominique, Callejo Mario, Ferretti Vincent, Ha Nhuan, Kwan Tony. Antimicrobial drug discovery through bacteriophage genomics. Nat Biotechnol. 2004 Jan 11;22(2):185–191. doi: 10.1038/nbt932. [DOI] [PubMed] [Google Scholar]
- Liu Lei, Gong George, Liu Yong, Natarajan Shreedhar, Larkin Denis M., Everts-van der Wind Annelie, Rebeiz Mark, Beever Jonathan E. Multi-species comparative mapping in silico using the COMPASS strategy. Bioinformatics. 2004 Jan 22;20(2):148–154. doi: 10.1093/bioinformatics/bth018. [DOI] [PubMed] [Google Scholar]
- Liu Ying, Sturley Stephen L. Nutritional genomics in yeast models. Nutrition. 2004 Jan;20(1):166–172. doi: 10.1016/j.nut.2003.09.026. [DOI] [PubMed] [Google Scholar]
- Lock Christopher B., Heller Renu A. Gene microarray analysis of multiple sclerosis lesions. Trends Mol Med. 2003 Dec;9(12):535–541. doi: 10.1016/j.molmed.2003.10.008. [DOI] [PubMed] [Google Scholar]
- Loni Lucia, De Braud Filippo, Zinzani Pier Luigi, Danesi Romano. Pharmacogenetics and proteomics of anticancer drugs in non-Hodgkin's lymphoma. Leuk Lymphoma. 2003;44 (Suppl 3):S115–S122. doi: 10.1080/10428190310001623676. [DOI] [PubMed] [Google Scholar]
- Lue Rina Y. P., Chen Grace Y. J., Hu Yi, Zhu Qing, Yao Shao Q. Versatile protein biotinylation strategies for potential high-throughput proteomics. J Am Chem Soc. 2004 Feb 4;126(4):1055–1062. doi: 10.1021/ja037914g. [DOI] [PubMed] [Google Scholar]
- Lum Pek Yee, Armour Christopher D., Stepaniants Sergey B., Cavet Guy, Wolf Maria K., Butler J. Scott, Hinshaw Jerald C., Garnier Philippe, Prestwich Glenn D., Leonardson Amy. Discovering modes of action for therapeutic compounds using a genome-wide screen of yeast heterozygotes. Cell. 2004 Jan 9;116(1):121–137. doi: 10.1016/s0092-8674(03)01035-3. [DOI] [PubMed] [Google Scholar]
- Mackintosh James A., Choi Hung-Yoon, Bae Soo-Han, Veal Duncan A., Bell Philip J., Ferrari Belinda C., Van Dyk Derek D., Verrills Nicole M., Paik Young-Ki, Karuso Peter. A fluorescent natural product for ultra sensitive detection of proteins in one-dimensional and two-dimensional gel electrophoresis. Proteomics. 2003 Dec;3(12):2273–2288. doi: 10.1002/pmic.200300578. [DOI] [PubMed] [Google Scholar]
- Mahadevan R., Schilling C. H. The effects of alternate optimal solutions in constraint-based genome-scale metabolic models. Metab Eng. 2003 Oct;5(4):264–276. doi: 10.1016/j.ymben.2003.09.002. [DOI] [PubMed] [Google Scholar]
- Maitra Anirban, Hansel Donna E., Argani Pedram, Ashfaq Raheela, Rahman Ayman, Naji Ali, Deng Shaoping, Geradts Joseph, Hawthorne LesleyAnn, House Michael G. Global expression analysis of well-differentiated pancreatic endocrine neoplasms using oligonucleotide microarrays. Clin Cancer Res. 2003 Dec 1;9(16 Pt 1):5988–5995. [PubMed] [Google Scholar]
- Martin Daniel B., Gifford David R., Wright Michael E., Keller Andrew, Yi Eugene, Goodlett David R., Aebersold Reudi, Nelson Peter S. Quantitative proteomic analysis of proteins released by neoplastic prostate epithelium. Cancer Res. 2004 Jan 1;64(1):347–355. doi: 10.1158/0008-5472.can-03-2062. [DOI] [PubMed] [Google Scholar]
- Marzolf Bruz, Johnson Michael H. Validation of microarray image analysis accuracy. Biotechniques. 2004 Feb;36(2):304–308. doi: 10.2144/04362MT01. [DOI] [PubMed] [Google Scholar]
- Matukumalli Lakshmi K., Grefenstette John J., Sonstegard Tad S., Van Tassell Curtis P. EST-PAGE--managing and analyzing EST data. Bioinformatics. 2004 Jan 22;20(2):286–288. doi: 10.1093/bioinformatics/btg411. [DOI] [PubMed] [Google Scholar]
- McCarroll Steven A., Murphy Coleen T., Zou Sige, Pletcher Scott D., Chin Chen-Shan, Jan Yuh Nung, Kenyon Cynthia, Bargmann Cornelia I., Li Hao. Comparing genomic expression patterns across species identifies shared transcriptional profile in aging. Nat Genet. 2004 Jan 18;36(2):197–204. doi: 10.1038/ng1291. [DOI] [PubMed] [Google Scholar]
- McGuffin Liam J., Street Stefano, Sørensen Søren-Aksel, Jones David T. The genomic threading database. Bioinformatics. 2004 Jan 1;20(1):131–132. doi: 10.1093/bioinformatics/btg387. [DOI] [PubMed] [Google Scholar]
- McMullen Colleen A., Andrade Francisco H., Stahl John S. Functional and genomic changes in the mouse ocular motor system in response to light deprivation from birth. J Neurosci. 2004 Jan 7;24(1):161–169. doi: 10.1523/JNEUROSCI.3234-03.2004. [DOI] [PMC free article] [PubMed] [Google Scholar]
- McShane Lisa M., Shih Joanna H., Michalowska Aleksandra M. Statistical issues in the design and analysis of gene expression microarray studies of animal models. J Mammary Gland Biol Neoplasia. 2003 Jul;8(3):359–374. doi: 10.1023/b:jomg.0000010035.57912.5a. [DOI] [PubMed] [Google Scholar]
- Mihoub Fatma, Mistou Michel-Yves, Guillot Alain, Leveau Jean-Yves, Boubetra Abdelkader, Billaux François. Cold adaptation of Escherichia coli: microbiological and proteomic approaches. Int J Food Microbiol. 2003 Dec 31;89(2-3):171–184. doi: 10.1016/s0168-1605(03)00119-3. [DOI] [PubMed] [Google Scholar]
- Miller Ingrid, Teinfalt Monika, Leschnik Michael, Wait Robin, Gemeiner Manfred. Nonreducing two-dimensional gel electrophoresis for the detection of Bence Jones proteins in serum and urine. Proteomics. 2004 Jan;4(1):257–260. doi: 10.1002/pmic.200300546. [DOI] [PubMed] [Google Scholar]
- Minamikawa-Tachino Reiko, Kabuyama Noriko, Gotoh Toshiyuki, Kagei Seiichiro, Naruse Masatoshi, Kisu Yasutomo, Togashi Takushi, Sugano Sumio, Usami Hitohide, Nomura Nobuo. High-throughput classification of images of cells transfected with cDNA clones. C R Biol. 2003 Oct-Nov;326(10-11):993–1001. doi: 10.1016/j.crvi.2003.09.014. [DOI] [PubMed] [Google Scholar]
- Mobasheri A., Airley R., Foster C. S., Schulze-Tanzil G., Shakibaei M. Post-genomic applications of tissue microarrays: basic research, prognostic oncology, clinical genomics and drug discovery. Histol Histopathol. 2004 Jan;19(1):325–335. doi: 10.14670/HH-19.325. [DOI] [PubMed] [Google Scholar]
- Nagase Takahiro, Kikuno Reiko, Ohara Osamu. The Kazusa cDNA project for identification of unknown human transcripts. C R Biol. 2003 Oct-Nov;326(10-11):959–966. doi: 10.1016/j.crvi.2003.09.020. [DOI] [PubMed] [Google Scholar]
- Nam Myung Hee, Heo Eun Joo, Kim Jin Young, Kim Seung Il, Kwon Kyung-Hoon, Seo Jong Bok, Kwon Ohoak, Yoo Jong Shin, Park Young Mok. Proteome analysis of the responses of Panax ginseng C. A. Meyer leaves to high light: use of electrospray ionization quadrupole-time of flight mass spectrometry and expressed sequence tag data. Proteomics. 2003 Dec;3(12):2351–2367. doi: 10.1002/pmic.200300509. [DOI] [PubMed] [Google Scholar]
- Nanjo Yohei, Asatsuma Satoru, Itoh Kimiko, Hori Hidetaka, Mitsui Toshiaki. Proteomic identification of alpha-amylase isoforms encoded by RAmy3B/3C from germinating rice seeds. Biosci Biotechnol Biochem. 2004 Jan;68(1):112–118. doi: 10.1271/bbb.68.112. [DOI] [PubMed] [Google Scholar]
- Narasimhan Sukanya, Caimano Melissa J., Liang Fang Ting, Santiago Felix, Laskowski Michelle, Philipp Mario T., Pachner Andrew R., Radolf Justin D., Fikrig Erol, Camaino Melissa J. Borrelia burgdorferi transcriptome in the central nervous system of non-human primates. Proc Natl Acad Sci U S A. 2003 Dec 11;100(26):15953–15958. doi: 10.1073/pnas.2432412100. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Ng Yuk Yin, van Kessel Berris, Lokhorst Henk M., Baert Miranda R. M., van den Burg Caroline M. M., Bloem Andries C., Staal Frank J. T. Gene-expression profiling of CD34+ cells from various hematopoietic stem-cell sources reveals functional differences in stem-cell activity. J Leukoc Biol. 2003 Nov 21;75(2):314–323. doi: 10.1189/jlb.0603287. [DOI] [PubMed] [Google Scholar]
- Nobis William, Ren Xiaoning, Suchyta Steven P., Suchyta Thomas R., Zanella Adroaldo J., Coussens Paul M. Development of a porcine brain cDNA library, EST database, and microarray resource. Physiol Genomics. 2003 Dec 16;16(1):153–159. doi: 10.1152/physiolgenomics.00099.2003. [DOI] [PubMed] [Google Scholar]
- Noël-Georis Isabelle, Vallaeys Tatiana, Chauvaux Renaud, Monchy Sébastien, Falmagne Paul, Mergeay Max, Wattiez Ruddy. Global analysis of the Ralstonia metallidurans proteome: prelude for the large-scale study of heavy metal response. Proteomics. 2004 Jan;4(1):151–179. doi: 10.1002/pmic.200300551. [DOI] [PubMed] [Google Scholar]
- O'Rourke Sean M., Herskowitz Ira. Unique and redundant roles for HOG MAPK pathway components as revealed by whole-genome expression analysis. Mol Biol Cell. 2003 Oct 31;15(2):532–542. doi: 10.1091/mbc.E03-07-0521. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Ogasawara Osamu, Kawamoto Shoko, Okubo Kousaku. Zipf's law and human transcriptomes: an explanation with an evolutionary model. C R Biol. 2003 Oct-Nov;326(10-11):1097–1101. doi: 10.1016/j.crvi.2003.09.031. [DOI] [PubMed] [Google Scholar]
- Ohlmeier Steffen, Kastaniotis Alexander J., Hiltunen J. Kalervo, Bergmann Ulrich. The yeast mitochondrial proteome, a study of fermentative and respiratory growth. J Biol Chem. 2003 Nov 3;279(6):3956–3979. doi: 10.1074/jbc.M310160200. [DOI] [PubMed] [Google Scholar]
- Orton R. J., Sellers W. I., Gerloff D. L. YETI: Yeast Exploration Tool Integrator. Bioinformatics. 2004 Jan 22;20(2):284–285. doi: 10.1093/bioinformatics/btg408. [DOI] [PubMed] [Google Scholar]
- Palma Marco, DeLuca Darrow, Worgall Stefan, Quadri Luis E. N. Transcriptome analysis of the response of Pseudomonas aeruginosa to hydrogen peroxide. J Bacteriol. 2004 Jan;186(1):248–252. doi: 10.1128/JB.186.1.248-252.2004. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Perelman Susana, Mazzella María Agustina, Muschietti Jorge, Zhu Tong, Casal Jorge J. Finding unexpected patterns in microarray data. Plant Physiol. 2003 Dec;133(4):1717–1725. doi: 10.1104/pp.103.028753. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Poland Julia, Urbani Andrea, Lage Hermann, Schnölzer Martina, Sinha Pranav. Study of the development of thermoresistance in human pancreatic carcinoma cell lines using proteome analysis. Electrophoresis. 2004 Jan;25(1):173–183. doi: 10.1002/elps.200305698. [DOI] [PubMed] [Google Scholar]
- Pollet Nicolas, Delius Hajo, Niehrs Christof. In situ analysis of gene expression in Xenopus embryos. C R Biol. 2003 Oct-Nov;326(10-11):1011–1017. doi: 10.1016/j.crvi.2003.09.019. [DOI] [PubMed] [Google Scholar]
- Prlić Andreas, Domingues Francisco S., Lackner Peter, Sippl Manfred J. WILMA-automated annotation of protein sequences. Bioinformatics. 2004 Jan 1;20(1):127–128. doi: 10.1093/bioinformatics/btg380. [DOI] [PubMed] [Google Scholar]
- Pyo Jaehoon, Hwang Sun-Il, Oh Jisun, Lee So-Jin, Kang Sun-Cheol, Kim Jong-Sang, Lim Jinkyu. Characterization of a bovine pregnancy-associated protein using two-dimensional gel electrophoresis, N-terminal sequencing and mass spectrometry. Proteomics. 2003 Dec;3(12):2420–2427. doi: 10.1002/pmic.200300618. [DOI] [PubMed] [Google Scholar]
- Pérez A. J., Thode G., Trelles O. AnaGram: protein function assignment. Bioinformatics. 2004 Jan 22;20(2):291–292. doi: 10.1093/bioinformatics/btg414. [DOI] [PubMed] [Google Scholar]
- Raza Shaan M., Fuller Gregory N., Rhee Chang Hun, Huang Suyun, Hess Kenneth, Zhang Wei, Sawaya Raymond. Identification of necrosis-associated genes in glioblastoma by cDNA microarray analysis. Clin Cancer Res. 2004 Jan 1;10(1 Pt 1):212–221. doi: 10.1158/1078-0432.ccr-0155-3. [DOI] [PubMed] [Google Scholar]
- Reinke Valerie, Gil Inigo San, Ward Samuel, Kazmer Keith. Genome-wide germline-enriched and sex-biased expression profiles in Caenorhabditis elegans. Development. 2003 Dec 10;131(2):311–323. doi: 10.1242/dev.00914. [DOI] [PubMed] [Google Scholar]
- Reymond Nancie, Charles Hubert, Duret Laurent, Calevro Federica, Beslon Guillaume, Fayard Jean-Michel. ROSO: optimizing oligonucleotide probes for microarrays. Bioinformatics. 2004 Jan 22;20(2):271–273. doi: 10.1093/bioinformatics/btg401. [DOI] [PubMed] [Google Scholar]
- Rocca-Serra Philippe, Brazma Alvis, Parkinson Helen, Sarkans Ugis, Shojatalab Mohammadreza, Contrino Sergio, Vilo Jaak, Abeygunawardena Niran, Mukherjee Gaurab, Holloway Ele. ArrayExpress: a public database of gene expression data at EBI. C R Biol. 2003 Oct-Nov;326(10-11):1075–1078. doi: 10.1016/j.crvi.2003.09.026. [DOI] [PubMed] [Google Scholar]
- Rosati Barbara, Grau Frederic, Kuehler Anneke, Rodriguez Samantha, McKinnon David. Comparison of different probe-level analysis techniques for oligonucleotide microarrays. Biotechniques. 2004 Feb;36(2):316–322. doi: 10.2144/04362MT03. [DOI] [PubMed] [Google Scholar]
- Rudolph Michael C., McManaman James L., Hunter Larry, Phang Tzulip, Neville Margaret C. Functional development of the mammary gland: use of expression profiling and trajectory clustering to reveal changes in gene expression during pregnancy, lactation, and involution. J Mammary Gland Biol Neoplasia. 2003 Jul;8(3):287–307. doi: 10.1023/b:jomg.0000010030.73983.57. [DOI] [PubMed] [Google Scholar]
- Sakabe Noboru Jo, de Souza Jorge E. S., Galante Pedro A. F., de Oliveira Paulo S. L., Passetti Fábio, Brentani Helena, Osório Elisson C., Zaiats André C., Leerkes Maarten R., Kitajima João Paulo. ORESTES are enriched in rare exon usage variants affecting the encoded proteins. C R Biol. 2003 Oct-Nov;326(10-11):979–985. doi: 10.1016/j.crvi.2003.09.027. [DOI] [PubMed] [Google Scholar]
- Sarry Jean-Emmanuel, Sommerer Nicolas, Sauvage François-Xavier, Bergoin Alexis, Rossignol Michel, Albagnac Guy, Romieu Charles. Grape berry biochemistry revisited upon proteomic analysis of the mesocarp. Proteomics. 2004 Jan;4(1):201–215. doi: 10.1002/pmic.200300499. [DOI] [PubMed] [Google Scholar]
- Schaub Stefan, Rush David, Wilkins John, Gibson Ian W., Weiler Tracey, Sangster Kevin, Nicolle Lindsay, Karpinski Martin, Jeffery John, Nickerson Peter. Proteomic-based detection of urine proteins associated with acute renal allograft rejection. J Am Soc Nephrol. 2004 Jan;15(1):219–227. doi: 10.1097/01.asn.0000101031.52826.be. [DOI] [PubMed] [Google Scholar]
- Schmitt William A., Jr, Stephanopoulos Gregory. Prediction of transcriptional profiles of Synechocystis PCC6803 by dynamic autoregressive modeling of DNA microarray data. Biotechnol Bioeng. 2003 Dec 30;84(7):855–863. doi: 10.1002/bit.10843. [DOI] [PubMed] [Google Scholar]
- Schramm A., Apostolov O., Sitek B., Pfeiffer K., Stühler K., Meyer H. E., Havers W., Eggert A. Proteomics: techniques and applications in cancer research. Klin Padiatr. 2003 Nov-Dec;215(6):293–297. doi: 10.1055/s-2003-45502. [DOI] [PubMed] [Google Scholar]
- Schwaenen Carsten, Nessling Michelle, Wessendorf Swen, Salvi Tatjana, Wrobel Gunnar, Radlwimmer Bernhard, Kestler Hans A., Haslinger Christian, Stilgenbauer Stephan, Döhner Hartmut. Automated array-based genomic profiling in chronic lymphocytic leukemia: development of a clinical tool and discovery of recurrent genomic alterations. Proc Natl Acad Sci U S A. 2004 Jan 16;101(4):1039–1044. doi: 10.1073/pnas.0304717101. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Schüller Christoph, Mamnun Yasmine M., Mollapour Mehdi, Krapf Gerd, Schuster Michael, Bauer Bettina E., Piper Peter W., Kuchler Karl. Global phenotypic analysis and transcriptional profiling defines the weak acid stress response regulon in Saccharomyces cerevisiae. Mol Biol Cell. 2003 Nov 14;15(2):706–720. doi: 10.1091/mbc.E03-05-0322. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Segal Mark R., Dahlquist Kam D., Conklin Bruce R. Regression approaches for microarray data analysis. J Comput Biol. 2003;10(6):961–980. doi: 10.1089/106652703322756177. [DOI] [PubMed] [Google Scholar]
- Sesterhenn Thomas M., Slaven Bradley E., Smulian A. George, Cushion Melanie T. Generation of sequencing libraries for the Pneumocystis Genome project. J Eukaryot Microbiol. 2003;50 (Suppl):663–665. doi: 10.1111/j.1550-7408.2003.tb00676.x. [DOI] [PubMed] [Google Scholar]
- Seta Karen A., Millhorn David E. Functional genomics approach to hypoxia signaling. J Appl Physiol (1985) 2004 Feb;96(2):765–773. doi: 10.1152/japplphysiol.00836.2003. [DOI] [PubMed] [Google Scholar]
- Shatkay Hagit, Feldman Ronen. Mining the biomedical literature in the genomic era: an overview. J Comput Biol. 2003;10(6):821–855. doi: 10.1089/106652703322756104. [DOI] [PubMed] [Google Scholar]
- Shen Yufeng, Tolić Nikola, Masselon Christophe, Pasa-Tolić Ljiljana, Camp David G., 2nd, Hixson Kim K., Zhao Rui, Anderson Gordon A., Smith Richard D. Ultrasensitive proteomics using high-efficiency on-line micro-SPE-nanoLC-nanoESI MS and MS/MS. Anal Chem. 2004 Jan 1;76(1):144–154. doi: 10.1021/ac030096q. [DOI] [PubMed] [Google Scholar]
- Shmueli Orit, Horn-Saban Shirley, Chalifa-Caspi Vered, Shmoish Michael, Ophir Ron, Benjamin-Rodrig Hila, Safran Marilyn, Domany Eytan, Lancet Doron. GeneNote: whole genome expression profiles in normal human tissues. C R Biol. 2003 Oct-Nov;326(10-11):1067–1072. doi: 10.1016/j.crvi.2003.09.012. [DOI] [PubMed] [Google Scholar]
- Simon Richard. Using DNA microarrays for diagnostic and prognostic prediction. Expert Rev Mol Diagn. 2003 Sep;3(5):587–595. doi: 10.1586/14737159.3.5.587. [DOI] [PubMed] [Google Scholar]
- Sims Andrew H., Robson Geoffrey D., Hoyle David C., Oliver Stephen G., Turner Geoffrey, Prade Rolf A., Russell Hugh H., Dunn-Coleman Nigel S., Gent Manda E. Use of expressed sequence tag analysis and cDNA microarrays of the filamentous fungus Aspergillus nidulans. Fungal Genet Biol. 2004 Feb;41(2):199–212. doi: 10.1016/j.fgb.2003.11.005. [DOI] [PubMed] [Google Scholar]
- Sjölander Kimmen. Phylogenomic inference of protein molecular function: advances and challenges. Bioinformatics. 2004 Jan 22;20(2):170–179. doi: 10.1093/bioinformatics/bth021. [DOI] [PubMed] [Google Scholar]
- Smith Clare V., Sacchettini James C. Mycobacterium tuberculosis: a model system for structural genomics. Curr Opin Struct Biol. 2003 Dec;13(6):658–664. doi: 10.1016/j.sbi.2003.10.004. [DOI] [PubMed] [Google Scholar]
- Son Won-Kyu, Lee Do-Youn, Lee Sung-Han, Joo Won-A, Kim Chan-Wha. Analysis of proteins expressed in rat plasma exposed to dioxin using 2-dimensional gel electrophoresis. Proteomics. 2003 Dec;3(12):2393–2401. doi: 10.1002/pmic.200300605. [DOI] [PubMed] [Google Scholar]
- Sparre Thomas, Bergholdt Regine, Nerup Jørn, Pociot Flemming. Application of genomics and proteomics in Type 1 diabetes pathogenesis research. Expert Rev Mol Diagn. 2003 Nov;3(6):743–757. doi: 10.1586/14737159.3.6.743. [DOI] [PubMed] [Google Scholar]
- Sprenger Richard R., Speijer Dave, Back Jaap Willem, De Koster Chris G., Pannekoek Hans, Horrevoets Anton J. G. Comparative proteomics of human endothelial cell caveolae and rafts using two-dimensional gel electrophoresis and mass spectrometry. Electrophoresis. 2004 Jan;25(1):156–172. doi: 10.1002/elps.200305675. [DOI] [PubMed] [Google Scholar]
- Srinivasan Prakash, Abraham Eappen G., Ghosh Anil K., Valenzuela Jesus, Ribeiro Jose M. C., Dimopoulos George, Kafatos Fotis C., Adams John H., Fujioka Hisashi, Jacobs-Lorena Marcelo. Analysis of the Plasmodium and Anopheles transcriptomes during oocyst differentiation. J Biol Chem. 2003 Nov 19;279(7):5581–5587. doi: 10.1074/jbc.M307587200. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Stanssens Patrick, Zabeau Marc, Meersseman Geert, Remes Gwen, Gansemans Yannick, Storm Niels, Hartmer Ralf, Honisch Christiane, Rodi Charles P., Böcker Sebastian. High-throughput MALDI-TOF discovery of genomic sequence polymorphisms. Genome Res. 2004 Jan;14(1):126–133. doi: 10.1101/gr.1692304. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Stevens E. V., Liotta L. A., Kohn E. C. Proteomic analysis for early detection of ovarian cancer: a realistic approach? Int J Gynecol Cancer. 2003 Nov-Dec;13 (Suppl 2):133–139. doi: 10.1111/j.1525-1438.2003.13358.x. [DOI] [PubMed] [Google Scholar]
- Strauss Arnold W. Tandem mass spectrometry in discovery of disorders of the metabolome. J Clin Invest. 2004 Feb;113(3):354–356. doi: 10.1172/JCI20924. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Strominger Jack L., Byrne Michael C., Wilson S. Brian. Regulation of dendritic cell subsets by NKT cells. C R Biol. 2003 Oct-Nov;326(10-11):1045–1048. doi: 10.1016/j.crvi.2003.09.023. [DOI] [PubMed] [Google Scholar]
- Strothmann Kai, Simoni Manuela, Mathur Premendu, Siakhamary Susan, Nieschlag Eberhard, Gromoll Jörg. Gene expression profiling of mouse Sertoli cell lines. Cell Tissue Res. 2003 Dec 2;315(2):249–257. doi: 10.1007/s00441-003-0834-x. [DOI] [PubMed] [Google Scholar]
- Stuitje Antoine R., Verbree Elizabeth C., van der Linden Karin H., Mietkiewska Elzbieta M., Nap Jan-Peter, Kneppers Tarcies J. A. Seed-expressed fluorescent proteins as versatile tools for easy (co)transformation and high-throughput functional genomics in Arabidopsis. Plant Biotechnol J. 2003 Jul;1(4):301–309. doi: 10.1046/j.1467-7652.2003.00028.x. [DOI] [PubMed] [Google Scholar]
- Swamy S. M. K., Tan P., Zhu Y. Z., Lu J., Achuth H. N., Moochhala S. Role of phenytoin in wound healing: microarray analysis of early transcriptional responses in human dermal fibroblasts. Biochem Biophys Res Commun. 2004 Feb 13;314(3):661–666. doi: 10.1016/j.bbrc.2003.12.146. [DOI] [PubMed] [Google Scholar]
- Takashima Motonari, Kuramitsu Yasuhiro, Yokoyama Yuuichiro, Iizuka Norio, Toda Toshifusa, Sakaida Isao, Okita Kiwamu, Oka Masaaki, Nakamura Kazuyuki. Proteomic profiling of heat shock protein 70 family members as biomarkers for hepatitis C virus-related hepatocellular carcinoma. Proteomics. 2003 Dec;3(12):2487–2493. doi: 10.1002/pmic.200300621. [DOI] [PubMed] [Google Scholar]
- Tanaka N., Konishi H., Khan M. M. K., Komatsu S. Proteome analysis of rice tissues by two-dimensional electrophoresis: an approach to the investigation of gibberellin regulated proteins. Mol Genet Genomics. 2003 Nov 21;270(6):485–496. doi: 10.1007/s00438-003-0929-9. [DOI] [PubMed] [Google Scholar]
- Tong Amy Hin Yan, Lesage Guillaume, Bader Gary D., Ding Huiming, Xu Hong, Xin Xiaofeng, Young James, Berriz Gabriel F., Brost Renee L., Chang Michael. Global mapping of the yeast genetic interaction network. Science. 2004 Feb 6;303(5659):808–813. doi: 10.1126/science.1091317. [DOI] [PubMed] [Google Scholar]
- Towbin Harry, Bair Kenneth W., DeCaprio James A., Eck Michael J., Kim Sunkyu, Kinder Frederick R., Morollo Anthony, Mueller Dieter R., Schindler Patrick, Song Hyun Kyu. Proteomics-based target identification: bengamides as a new class of methionine aminopeptidase inhibitors. J Biol Chem. 2003 Oct 8;278(52):52964–52971. doi: 10.1074/jbc.M309039200. [DOI] [PubMed] [Google Scholar]
- Tsai Chen-An, Hsueh Huey-miin, Chen James J. Estimation of false discovery rates in multiple testing: application to gene microarray data. Biometrics. 2003 Dec;59(4):1071–1081. doi: 10.1111/j.0006-341x.2003.00123.x. [DOI] [PubMed] [Google Scholar]
- Tsoi Stephen C. M., Cale Jacqueline M., Bird Ian M., Ewart Vanya, Brown Laura L., Douglas Susan. Use of human cDNA microarrays for identification of differentially expressed genes in Atlantic salmon liver during Aeromonas salmonicida infection. Mar Biotechnol (NY) 2003 Sep 29;5(6):545–554. doi: 10.1007/s10126-002-0112-z. [DOI] [PubMed] [Google Scholar]
- Tsoka Sophia, Ouzounis Christos A. Metabolic database systems for the analysis of genome-wide function. Biotechnol Bioeng. 2003 Dec 30;84(7):750–755. doi: 10.1002/bit.10881. [DOI] [PubMed] [Google Scholar]
- Tsubakihara Masako, Williams Neal K., Keogh Anne, dos Remedios Cristobal G. Comparison of gene expression between left atria and left ventricles from non-diseased humans. Proteomics. 2004 Jan;4(1):261–270. doi: 10.1002/pmic.200300539. [DOI] [PubMed] [Google Scholar]
- Unami Akira, Shinohara Yasuo, Kajimoto Kazuaki, Baba Yoshinobu. Comparison of gene expression profiles between white and brown adipose tissues of rat by microarray analysis. Biochem Pharmacol. 2004 Feb 1;67(3):555–564. doi: 10.1016/j.bcp.2003.09.010. [DOI] [PubMed] [Google Scholar]
- Ventelon-Debout Marjolaine, Delalande François, Brizard Jean-Paul, Diemer Hélène, Van Dorsselaer Alain, Brugidou Christophe. Proteome analysis of cultivar-specific deregulations of Oryza sativa indica and O. sativa japonica cellular suspensions undergoing rice yellow mottle virus infection. Proteomics. 2004 Jan;4(1):216–225. doi: 10.1002/pmic.200300502. [DOI] [PubMed] [Google Scholar]
- Vierstraete Evy, Verleyen Peter, Baggerman Geert, D'Hertog Wannes, Van den Bergh Gert, Arckens Lutgarde, De Loof Arnold, Schoofs Liliane. A proteomic approach for the analysis of instantly released wound and immune proteins in Drosophila melanogaster hemolymph. Proc Natl Acad Sci U S A. 2004 Jan 5;101(2):470–475. doi: 10.1073/pnas.0304567101. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Wang Jingqiang, Xue Yanfen, Feng Xiaoli, Li Xiaolei, Wang Hao, Li Wei, Zhao Caifeng, Cheng Xiaojie, Ma Yanhe, Zhou Peijin. An analysis of the proteomic profile for Thermoanaerobacter tengcongensis under optimal culture conditions. Proteomics. 2004 Jan;4(1):136–150. doi: 10.1002/pmic.200300504. [DOI] [PubMed] [Google Scholar]
- Wang Juhui, Caron Christophe, Mistou Michel-Yves, Gitton Christophe, Trubuil Alain. PARIS: a proteomic analysis and resources indexation system. Bioinformatics. 2004 Jan 1;20(1):133–135. doi: 10.1093/bioinformatics/btg389. [DOI] [PubMed] [Google Scholar]
- Wang Pauline W., Chu Linda, Guttman David S. Complete sequence and evolutionary genomic analysis of the Pseudomonas aeruginosa transposable bacteriophage D3112. J Bacteriol. 2004 Jan;186(2):400–410. doi: 10.1128/JB.186.2.400-410.2004. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Wang Song, Ethier Stewart. A generalized likelihood ratio test to identify differentially expressed genes from microarray data. Bioinformatics. 2004 Jan 1;20(1):100–104. doi: 10.1093/bioinformatics/btg384. [DOI] [PubMed] [Google Scholar]
- Watson Adam, Mata Juan, Bähler Jürg, Carr Anthony, Humphrey Tim. Global gene expression responses of fission yeast to ionizing radiation. Mol Biol Cell. 2003 Dec 10;15(2):851–860. doi: 10.1091/mbc.E03-08-0569. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Weeks Mark E., James David C., Robinson Gary K., Smales C. Mark. Global changes in gene expression observed at the transition from growth to stationary phase in Listeria monocytogenes ScottA batch culture. Proteomics. 2004 Jan;4(1):123–135. doi: 10.1002/pmic.200300527. [DOI] [PubMed] [Google Scholar]
- Wei Ho-Chun, Shu Huidy, Price James V. Functional genomic analysis of the 61D-61F region of the third chromosome of Drosophila melanogaster. Genome. 2003 Dec;46(6):1049–1058. doi: 10.1139/g03-081. [DOI] [PubMed] [Google Scholar]
- Weigelt Britta, Glas Annuska M., Wessels Lodewyk F. A., Witteveen Anke T., Peterse Johannes L., van't Veer Laura J. Gene expression profiles of primary breast tumors maintained in distant metastases. Proc Natl Acad Sci U S A. 2003 Dec 9;100(26):15901–15905. doi: 10.1073/pnas.2634067100. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Weinstein John N., Pommier Yves. Transcriptomic analysis of the NCI-60 cancer cell lines. C R Biol. 2003 Oct-Nov;326(10-11):909–920. doi: 10.1016/j.crvi.2003.08.005. [DOI] [PubMed] [Google Scholar]
- Wheelock Asa M., Zhang Lu, Tran Mai-Uyen, Morin Dexter, Penn Sharron, Buckpitt Alan R., Plopper Charles G. Isolation of rodent airway epithelial cell proteins facilitates in vivo proteomics studies of lung toxicity. Am J Physiol Lung Cell Mol Physiol. 2003 Oct 31;286(2):L399–L410. doi: 10.1152/ajplung.00072.2003. [DOI] [PubMed] [Google Scholar]
- Whiteside Martin A., Chen Dung-Tsa, Desmond Renee A., Abdulkadir Sarki A., Johanning Gary L. A novel time-course cDNA microarray analysis method identifies genes associated with the development of cisplatin resistance. Oncogene. 2004 Jan 22;23(3):744–752. doi: 10.1038/sj.onc.1207164. [DOI] [PubMed] [Google Scholar]
- Wichert Sofia, Fokianos Konstantinos, Strimmer Korbinian. Identifying periodically expressed transcripts in microarray time series data. Bioinformatics. 2004 Jan 1;20(1):5–20. doi: 10.1093/bioinformatics/btg364. [DOI] [PubMed] [Google Scholar]
- Wiedenheft Blake, Stedman Kenneth, Roberto Francisco, Willits Deborah, Gleske Anne-Kathrin, Zoeller Luisa, Snyder Jamie, Douglas Trevor, Young Mark. Comparative genomic analysis of hyperthermophilic archaeal Fuselloviridae viruses. J Virol. 2004 Feb;78(4):1954–1961. doi: 10.1128/JVI.78.4.1954-1961.2004. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Wiemann Stefan, Mehrle Alexander, Bechtel Stephanie, Wellenreuther Ruth, Pepperkok Rainer, Poustka Annemarie, German cDNA Consortium CDNAs for functional genomics and proteomics: the German Consortium. C R Biol. 2003 Oct-Nov;326(10-11):1003–1009. doi: 10.1016/j.crvi.2003.09.036. [DOI] [PubMed] [Google Scholar]
- Won Yonggwan, Song Ho-Jun, Kang Taek Won, Kim Jung-Ja, Han Byoung-Don, Lee Seung-Won. Pattern analysis of serum proteome distinguishes renal cell carcinoma from other urologic diseases and healthy persons. Proteomics. 2003 Dec;3(12):2310–2316. doi: 10.1002/pmic.200300590. [DOI] [PubMed] [Google Scholar]
- Wren Jonathan D., Garner Harold R. Shared relationship analysis: ranking set cohesion and commonalities within a literature-derived relationship network. Bioinformatics. 2004 Jan 22;20(2):191–198. doi: 10.1093/bioinformatics/btg390. [DOI] [PubMed] [Google Scholar]
- Xiao Zhen, Conrads Thomas P., Lucas David A., Janini George M., Schaefer Carl F., Buetow Kenneth H., Issaq Haleem J., Veenstra Timothy D. Direct ampholyte-free liquid-phase isoelectric peptide focusing: application to the human serum proteome. Electrophoresis. 2004 Jan;25(1):128–133. doi: 10.1002/elps.200305700. [DOI] [PubMed] [Google Scholar]
- Yamashita Riu, Suzuki Yutaka, Nakai Kenta, Sugano Sumio. Small open reading frames in 5' untranslated regions of mRnas. C R Biol. 2003 Oct-Nov;326(10-11):987–991. doi: 10.1016/j.crvi.2003.09.028. [DOI] [PubMed] [Google Scholar]
- Yoshimura Yoshiyuki, Yamauchi Yoshio, Shinkawa Takashi, Taoka Masato, Donai Hitomi, Takahashi Nobuhiro, Isobe Toshiaki, Yamauchi Takashi. Molecular constituents of the postsynaptic density fraction revealed by proteomic analysis using multidimensional liquid chromatography-tandem mass spectrometry. J Neurochem. 2004 Feb;88(3):759–768. doi: 10.1046/j.1471-4159.2003.02136.x. [DOI] [PubMed] [Google Scholar]
- Yu Ji Hoon, Yun Shin Young, Lim Joo Weon, Kim Hyeyoung, Kim Kyung Hwan. Mass spectrometry and tandem mass spectrometry analysis of rat mitochondrial ATP synthase: up-regulation in pancreatic acinar cells treated with cerulein. Proteomics. 2003 Dec;3(12):2437–2445. doi: 10.1002/pmic.200300585. [DOI] [PubMed] [Google Scholar]
- Yu Ji Hoon, Yun Shin Young, Lim Joo Weon, Kim Hyeyoung, Kim Kyung Hwan. Proteome analysis of rat pancreatic acinar cells: implication for cerulein-induced acute pancreatitis. Proteomics. 2003 Dec;3(12):2446–2453. doi: 10.1002/pmic.200300545. [DOI] [PubMed] [Google Scholar]
- Zhang Bo, Su Yong-Ping, Ai Guo-Ping, Liu Xiao-Hong, Wang Feng-Chao, Cheng Tian-Min. Differentially expressed proteins of gamma-ray irradiated mouse intestinal epithelial cells by two-dimensional electrophoresis and MALDI-TOF mass spectrometry. World J Gastroenterol. 2003 Dec;9(12):2726–2731. doi: 10.3748/wjg.v9.i12.2726. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Zhang Hong-Gang, Xiu Rui-Juan. Micro-vascular medicine and proteomics. Clin Hemorheol Microcirc. 2003;29(3-4):189–192. [PubMed] [Google Scholar]
- Zhang Rulin, Barker Lisa, Pinchev Deborah, Marshall John, Rasamoelisolo Michèle, Smith Chris, Kupchak Peter, Kireeva Inga, Ingratta Leslee, Jackowski George. Mining biomarkers in human sera using proteomic tools. Proteomics. 2004 Jan;4(1):244–256. doi: 10.1002/pmic.200300495. [DOI] [PubMed] [Google Scholar]
- Zhang Yu, Waterman Michael S. An Eulerian path approach to global multiple alignment for DNA sequences. J Comput Biol. 2003;10(6):803–819. doi: 10.1089/106652703322756096. [DOI] [PubMed] [Google Scholar]
- Zhao Po, Seo Jinwook, Wang Zuyi, Wang Yue, Shneiderman Ben, Hoffman Eric P. In vivo filtering of in vitro expression data reveals MyoD targets. C R Biol. 2003 Oct-Nov;326(10-11):1049–1065. doi: 10.1016/j.crvi.2003.09.035. [DOI] [PubMed] [Google Scholar]
- Zheng Lianxing, Liu Jun, Batalov Sergei, Zhou Demin, Orth Anthony, Ding Sheng, Schultz Peter G. An approach to genomewide screens of expressed small interfering RNAs in mammalian cells. Proc Natl Acad Sci U S A. 2003 Dec 19;101(1):135–140. doi: 10.1073/pnas.2136685100. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Zhu Qingsong, Deng Youping, Vanka Phaneendra, Brown Susan J., Muthukrishnan Subbaratnam, Kramer Karl J. Computational identification of novel chitinase-like proteins in the Drosophila melanogaster genome. Bioinformatics. 2004 Jan 22;20(2):161–169. doi: 10.1093/bioinformatics/bth020. [DOI] [PubMed] [Google Scholar]
- Zimdahl Heike, Nyakatura Gerald, Brandt Petra, Schulz Herbert, Hummel Oliver, Fartmann Berthold, Brett David, Droege Marcus, Monti Jan, Lee Young-Ae. A SNP map of the rat genome generated from cDNA sequences. Science. 2004 Feb 6;303(5659):807–807. doi: 10.1126/science.1092427. [DOI] [PubMed] [Google Scholar]
- von Mering Christian, Zdobnov Evgeny M., Tsoka Sophia, Ciccarelli Francesca D., Pereira-Leal Jose B., Ouzounis Christos A., Bork Peer. Genome evolution reveals biochemical networks and functional modules. Proc Natl Acad Sci U S A. 2003 Dec 12;100(26):15428–15433. doi: 10.1073/pnas.2136809100. [DOI] [PMC free article] [PubMed] [Google Scholar]
