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- Aburatani Sachiyo, Goto Kousuke, Saito Shigeru, Fumoto Masaki, Imaizumi Akira, Sugaya Nobuyoshi, Murakami Hiroo, Sato Makihiko, Toh Hiroyuki, Horimoto Katsuhisa. ASIAN: a website for network inference. Bioinformatics. 2004 May 6;20(16):2853–2856. doi: 10.1093/bioinformatics/bth296. [DOI] [PubMed] [Google Scholar]
- Adryan Boris, Schuh Reinhard. Gene-Ontology-based clustering of gene expression data. Bioinformatics. 2004 Apr 29;20(16):2851–2852. doi: 10.1093/bioinformatics/bth289. [DOI] [PubMed] [Google Scholar]
- Ahmed Farid, Torrado Mario, Zinovieva Rina D., Senatorov Vladimir V., Wistow Graeme, Tomarev Stanislav I. Gene expression profile of the rat eye iridocorneal angle: NEIBank expressed sequence tag analysis. Invest Ophthalmol Vis Sci. 2004 Sep;45(9):3081–3090. doi: 10.1167/iovs.04-0302. [DOI] [PubMed] [Google Scholar]
- Aivaliotis Michalis, Corvey Carsten, Tsirogianni Irene, Karas Michael, Tsiotis Georgios. Membrane proteome analysis of the green-sulfur bacterium Chlorobium tepidum. Electrophoresis. 2004 Oct;25(20):3468–3474. doi: 10.1002/elps.200406079. [DOI] [PubMed] [Google Scholar]
- Akesson Mats, Förster Jochen, Nielsen Jens. Integration of gene expression data into genome-scale metabolic models. Metab Eng. 2004 Oct;6(4):285–293. doi: 10.1016/j.ymben.2003.12.002. [DOI] [PubMed] [Google Scholar]
- Alexander Hannah, Stegner Andrew L., Wagner-Mann Colette, Du Bois Garrett C., Alexander Stephen, Sauter Edward R. Proteomic analysis to identify breast cancer biomarkers in nipple aspirate fluid. Clin Cancer Res. 2004 Nov 15;10(22):7500–7510. doi: 10.1158/1078-0432.CCR-04-1002. [DOI] [PubMed] [Google Scholar]
- Alexandersson Erik, Saalbach Gerhard, Larsson Christer, Kjellbom Per. Arabidopsis plasma membrane proteomics identifies components of transport, signal transduction and membrane trafficking. Plant Cell Physiol. 2004 Nov;45(11):1543–1556. doi: 10.1093/pcp/pch209. [DOI] [PubMed] [Google Scholar]
- Alexandridis Roxana, Lin Shili, Irwin Mark. Class discovery and classification of tumor samples using mixture modeling of gene expression data--a unified approach. Bioinformatics. 2004 Apr 29;20(16):2545–2552. doi: 10.1093/bioinformatics/bth281. [DOI] [PubMed] [Google Scholar]
- Almeida Luiz G. P., Paixão Roger, Souza Rangel C., Costa Gisele C. da, Barrientos Frank J. A., Santos M. Trindade dos, Almeida Darcy F. de, Vasconcelos Ana Tereza R. A System for Automated Bacterial (genome) Integrated Annotation--SABIA. Bioinformatics. 2004 Apr 15;20(16):2832–2833. doi: 10.1093/bioinformatics/bth273. [DOI] [PubMed] [Google Scholar]
- Attoor Sanju, Dougherty Edward R., Chen Yidong, Bittner Michael L., Trent Jeffrey M. Which is better for cDNA-microarray-based classification: ratios or direct intensities. Bioinformatics. 2004 Sep 28;20(16):2513–2520. doi: 10.1093/bioinformatics/bth272. [DOI] [PubMed] [Google Scholar]
- Bae Tae-Jung, Kim Min-Sik, Kim Jun-Woo, Kim Bong-Woo, Choo Hyo-Jung, Lee Joong-Won, Kim Ki-Bum, Lee Chang Seok, Kim Ji-Hyun, Chang Sun Young. Lipid raft proteome reveals ATP synthase complex in the cell surface. Proteomics. 2004 Nov;4(11):3536–3548. doi: 10.1002/pmic.200400952. [DOI] [PubMed] [Google Scholar]
- Bahk Young Yil, Kim Suk Am, Kim Ji-Soo, Euh Hyung-Jin, Bai Gil-Han, Cho Sang-Nae, Kim Yu Sam. Antigens secreted from Mycobacterium tuberculosis: identification by proteomics approach and test for diagnostic marker. Proteomics. 2004 Nov;4(11):3299–3307. doi: 10.1002/pmic.200400980. [DOI] [PubMed] [Google Scholar]
- Bajic Vladimir B., Tan Sin Lam, Suzuki Yutaka, Sugano Sumio. Promoter prediction analysis on the whole human genome. Nat Biotechnol. 2004 Nov;22(11):1467–1473. doi: 10.1038/nbt1032. [DOI] [PubMed] [Google Scholar]
- Baliga Nitin S., Bonneau Richard, Facciotti Marc T., Pan Min, Glusman Gustavo, Deutsch Eric W., Shannon Paul, Chiu Yulun, Weng Rueyhung Sting, Gan Rueichi Richie. Genome sequence of Haloarcula marismortui: a halophilic archaeon from the Dead Sea. Genome Res. 2004 Nov;14(11):2221–2234. doi: 10.1101/gr.2700304. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Bar-Joseph Ziv. Analyzing time series gene expression data. Bioinformatics. 2004 May 6;20(16):2493–2503. doi: 10.1093/bioinformatics/bth283. [DOI] [PubMed] [Google Scholar]
- Bengtsson Bengt O. Modelling the evolution of genomes with integrated external and internal functions. J Theor Biol. 2004 Nov 21;231(2):271–278. doi: 10.1016/j.jtbi.2004.06.021. [DOI] [PubMed] [Google Scholar]
- Bennetzen Jeffrey L., Coleman Craig, Liu Renyi, Ma Jianxin, Ramakrishna Wusirika. Consistent over-estimation of gene number in complex plant genomes. Curr Opin Plant Biol. 2004 Dec;7(6):732–736. doi: 10.1016/j.pbi.2004.09.003. [DOI] [PubMed] [Google Scholar]
- Bergen H. Robert, 3rd, Zeldenrust Steven R., Butz Malinda L., Snow Denise S., Dyck Peter J., Dyck P. James B., Klein Christopher J., O'Brien John F., Thibodeau Stephen N., Muddiman David C. Identification of transthyretin variants by sequential proteomic and genomic analysis. Clin Chem. 2004 Jun 24;50(9):1544–1552. doi: 10.1373/clinchem.2004.033266. [DOI] [PubMed] [Google Scholar]
- Bidaut Ghislain, Ochs Michael F. ClutrFree: cluster tree visualization and interpretation. Bioinformatics. 2004 May 14;20(16):2869–2871. doi: 10.1093/bioinformatics/bth307. [DOI] [PubMed] [Google Scholar]
- Blakesley Robert W., Hansen Nancy F., Mullikin James C., Thomas Pamela J., McDowell Jennifer C., Maskeri Baishali, Young Alice C., Benjamin Beatrice, Brooks Shelise Y., Coleman Bradley I. An intermediate grade of finished genomic sequence suitable for comparative analyses. Genome Res. 2004 Oct 12;14(11):2235–2244. doi: 10.1101/gr.2648404. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Boehm Andreas M., Grosse-Coosmann Florian, Sickmann Albert. Command line tool for calculating theoretical MS spectra for given sequences. Bioinformatics. 2004 May 27;20(16):2889–2891. doi: 10.1093/bioinformatics/bth328. [DOI] [PubMed] [Google Scholar]
- Bonchev Danail. Complexity analysis of yeast proteome network. Chem Biodivers. 2004 Feb;1(2):312–326. doi: 10.1002/cbdv.200490028. [DOI] [PubMed] [Google Scholar]
- Bosinger Steven E., Hosiawa Karoline A., Cameron Mark J., Persad Desmond, Ran Longsi, Xu Luoling, Boulassel Mohamed R., Parenteau Monique, Fournier Jocelyn, Rud Erling W. Gene expression profiling of host response in models of acute HIV infection. J Immunol. 2004 Dec 1;173(11):6858–6863. doi: 10.4049/jimmunol.173.11.6858. [DOI] [PubMed] [Google Scholar]
- Boutros Paul C., Okey Allan B. PUNS: transcriptomic- and genomic-in silico PCR for enhanced primer design. Bioinformatics. 2004 Apr 8;20(15):2399–2400. doi: 10.1093/bioinformatics/bth257. [DOI] [PubMed] [Google Scholar]
- Braatsch Stephan, Moskvin Oleg V., Klug Gabriele, Gomelsky Mark. Responses of the Rhodobacter sphaeroides transcriptome to blue light under semiaerobic conditions. J Bacteriol. 2004 Nov;186(22):7726–7735. doi: 10.1128/JB.186.22.7726-7735.2004. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Broët Philippe, Lewin Alex, Richardson Sylvia, Dalmasso Cyril, Magdelenat Henri. A mixture model-based strategy for selecting sets of genes in multiclass response microarray experiments. Bioinformatics. 2004 Apr 29;20(16):2562–2571. doi: 10.1093/bioinformatics/bth285. [DOI] [PubMed] [Google Scholar]
- Bull Todd M., Coldren Christopher D., Moore Mark, Sotto-Santiago Sylk M., Pham David V., Nana-Sinkam S. Patrick, Voelkel Norbert F., Geraci Mark W. Gene microarray analysis of peripheral blood cells in pulmonary arterial hypertension. Am J Respir Crit Care Med. 2004 Jun 23;170(8):911–919. doi: 10.1164/rccm.200312-1686OC. [DOI] [PubMed] [Google Scholar]
- Burt David W. The chicken genome and the developmental biologist. Mech Dev. 2004 Sep;121(9):1129–1135. doi: 10.1016/j.mod.2004.04.020. [DOI] [PubMed] [Google Scholar]
- Casstevens Terry M., Buckler Edward S. GDPC: connecting researchers with multiple integrated data sources. Bioinformatics. 2004 Apr 22;20(16):2839–2840. doi: 10.1093/bioinformatics/bth277. [DOI] [PubMed] [Google Scholar]
- Chalk Alistair M., Wennerberg Martin, Sonnhammer Erik L. L. Sfixem--graphical sequence feature display in Java. Bioinformatics. 2004 Apr 15;20(15):2488–2490. doi: 10.1093/bioinformatics/bth265. [DOI] [PubMed] [Google Scholar]
- Chan Elaine W. S., Chattopadhaya Souvik, Panicker Resmi C., Huang Xuan, Yao Shao Q. Developing photoactive affinity probes for proteomic profiling: hydroxamate-based probes for metalloproteases. J Am Chem Soc. 2004 Nov 10;126(44):14435–14446. doi: 10.1021/ja047044i. [DOI] [PubMed] [Google Scholar]
- Che Fa-Yun, Fricker Lloyd D. Quantitative peptidomics of mouse pituitary: comparison of different stable isotopic tags. J Mass Spectrom. 2005 Feb;40(2):238–249. doi: 10.1002/jms.743. [DOI] [PubMed] [Google Scholar]
- Chen Hong-Chu, Lee Hsiao-Ching, Lin Tsai-Yun, Li Wen-Hsiung, Chen Bor-Sen. Quantitative characterization of the transcriptional regulatory network in the yeast cell cycle. Bioinformatics. 2004 Mar 25;20(12):1914–1927. doi: 10.1093/bioinformatics/bth178. [DOI] [PubMed] [Google Scholar]
- Chen Li, Oughtred Rose, Berman Helen M., Westbrook John. TargetDB: a target registration database for structural genomics projects. Bioinformatics. 2004 May 6;20(16):2860–2862. doi: 10.1093/bioinformatics/bth300. [DOI] [PubMed] [Google Scholar]
- Chignard Nicolas, Beretta Laura. Proteomics for hepatocellular carcinoma marker discovery. Gastroenterology. 2004 Nov;127(5 Suppl 1):S120–S125. doi: 10.1053/j.gastro.2004.09.025. [DOI] [PubMed] [Google Scholar]
- Chikayama Eisuke, Kurotani Atsushi, Kuroda Yutaka, Yokoyama Shigeyuki. ProteoMix: an integrated and flexible system for interactively analyzing large numbers of protein sequences. Bioinformatics. 2004 Apr 22;20(16):2836–2838. doi: 10.1093/bioinformatics/bth276. [DOI] [PubMed] [Google Scholar]
- Cho Jae-We, Kim Jeong Jung, Park Sung Goo, Lee Do Hee, Lee Sang Chul, Kim Hyeoung-Joon, Park Byoung Chul, Cho Sayeon. Identification of B-cell translocation gene 1 as a biomarker for monitoring the remission of acute myeloid leukemia. Proteomics. 2004 Nov;4(11):3456–3463. doi: 10.1002/pmic.200400968. [DOI] [PubMed] [Google Scholar]
- Choudhuri Jomuna V., Schleiermacher Chris, Kurtz Stefan, Giegerich Robert. GenAlyzer: interactive visualization of sequence similarities between entire genomes. Bioinformatics. 2004 Feb 26;20(12):1964–1965. doi: 10.1093/bioinformatics/bth161. [DOI] [PubMed] [Google Scholar]
- Chung Youn Wook, Oh Hae Yeun, Kim Ji Yeong, Kim Jae-Hong, Kim Ick Young. Allergen-induced proteolytic cleavage of annexin-1 and activation of cytosolic phospholipase A2 in the lungs of a mouse model of asthma. Proteomics. 2004 Nov;4(11):3328–3334. doi: 10.1002/pmic.200400895. [DOI] [PubMed] [Google Scholar]
- Clifton Sandra W., Minx Patrick, Fauron Christiane M-R, Gibson Michael, Allen James O., Sun Hui, Thompson Melissa, Barbazuk W. Brad, Kanuganti Suman, Tayloe Catherine. Sequence and comparative analysis of the maize NB mitochondrial genome. Plant Physiol. 2004 Nov;136(3):3486–3503. doi: 10.1104/pp.104.044602. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Colditz Frank, Nyamsuren Oyunbileg, Niehaus Karsten, Eubel Holger, Braun Hans-Peter, Krajinski Franziska. Proteomic approach: identification of Medicago truncatula proteins induced in roots after infection with the pathogenic oomycete Aphanomyces euteiches. Plant Mol Biol. 2004 May;55(1):109–120. doi: 10.1007/s11103-004-0499-1. [DOI] [PubMed] [Google Scholar]
- Conley E. J., Nduati V., Gonzalez-Hernandez J. L., Mesfin A., Trudeau-Spanjers M., Chao S., Lazo G. R., Hummel D. D., Anderson O. D., Qi L. L. A 2600-locus chromosome bin map of wheat homoeologous group 2 reveals interstitial gene-rich islands and colinearity with rice. Genetics. 2004 Oct;168(2):625–637. doi: 10.1534/genetics.104.034801. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Contento Anthony L., Kim Sang-Jin, Bassham Diane C. Transcriptome profiling of the response of Arabidopsis suspension culture cells to Suc starvation. Plant Physiol. 2004 Aug 13;135(4):2330–2347. doi: 10.1104/pp.104.044362. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Costantini Maria. An analysis of sponge genomes. Gene. 2004 Nov 24;342(2):321–325. doi: 10.1016/j.gene.2004.08.025. [DOI] [PubMed] [Google Scholar]
- Csurös Miklós, Milosavljevic Aleksandar. Pooled Genomic Indexing (PGI): analysis and design of experiments. J Comput Biol. 2004;11(5):1001–1021. doi: 10.1089/cmb.2004.11.1001. [DOI] [PubMed] [Google Scholar]
- Da Lee Rhee, Rhee Gyu Seek, An Sang Mi, Kim Soon Sun, Kwack Seung Jun, Seok Ji Hyun, Chae Soo Yeong, Park Chul Hoon, Yoon Hyo Jung, Cho Dae Hyun. Differential gene profiles in developing embryo and fetus after in utero exposure to ethanol. J Toxicol Environ Health A. 2004 Dec;67(23-24):2073–2084. doi: 10.1080/15287390490515001. [DOI] [PubMed] [Google Scholar]
- Dafforn Alan, Chen Pengchin, Deng Glenn, Herrler Michael, Iglehart Dawn, Koritala Sriveda, Lato Susan, Pillarisetty Susheela, Purohit Reshma, Wang Martin. Linear mRNA amplification from as little as 5 ng total RNA for global gene expression analysis. Biotechniques. 2004 Nov;37(5):854–857. doi: 10.2144/04375PF01. [DOI] [PubMed] [Google Scholar]
- Darvas F., Dormán G., Krajcsi P., Puskás L. G., Kovári Z., Lörincz Z., Urge L. Recent advances in chemical genomics. Curr Med Chem. 2004 Dec;11(23):3119–3145. doi: 10.2174/0929867043363848. [DOI] [PubMed] [Google Scholar]
- Desai Kartiki V., Michalowska Aleksandra M., Kondaiah Paturu, Ward Jerrold M., Shih Joanna H., Green Jeffrey E. Gene expression profiling identifies a unique androgen-mediated inflammatory/immune signature and a PTEN (phosphatase and tensin homolog deleted on chromosome 10)-mediated apoptotic response specific to the rat ventral prostate. Mol Endocrinol. 2004 Sep 9;18(12):2895–2907. doi: 10.1210/me.2004-0033. [DOI] [PubMed] [Google Scholar]
- Dharmadi Yandi, Gonzalez Ramon. DNA microarrays: experimental issues, data analysis, and application to bacterial systems. Biotechnol Prog. 2004 Sep-Oct;20(5):1309–1324. doi: 10.1021/bp0400240. [DOI] [PubMed] [Google Scholar]
- Dodd Lori E., Korn Edward L., McShane Lisa M., Chandramouli G. V. R., Chuang Eric Y. Correcting log ratios for signal saturation in cDNA microarrays. Bioinformatics. 2004 May 14;20(16):2685–2693. doi: 10.1093/bioinformatics/bth309. [DOI] [PubMed] [Google Scholar]
- Drnevich Jenny M., Reedy Melissa M., Ruedi Elizabeth A., Rodriguez-Zas Sandra, Hughes Kimberly A. Quantitative evolutionary genomics: differential gene expression and male reproductive success in Drosophila melanogaster. Proc Biol Sci. 2004 Nov 7;271(1554):2267–2273. doi: 10.1098/rspb.2004.2880. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Ebbole Daniel J., Jin Yuan, Thon Michael, Pan Huaqin, Bhattarai Eric, Thomas Terry, Dean Ralph. Gene discovery and gene expression in the rice blast fungus, Magnaporthe grisea: analysis of expressed sequence tags. Mol Plant Microbe Interact. 2004 Dec;17(12):1337–1347. doi: 10.1094/MPMI.2004.17.12.1337. [DOI] [PubMed] [Google Scholar]
- Engström Ylva, Loseva Olga, Theopold Ulrich. Proteomics of the Drosophila immune response. Trends Biotechnol. 2004 Nov;22(11):600–605. doi: 10.1016/j.tibtech.2004.09.002. [DOI] [PubMed] [Google Scholar]
- Eriksson Lennart, Antti Henrik, Gottfries Johan, Holmes Elaine, Johansson Erik, Lindgren Fredrik, Long Ingrid, Lundstedt Torbjörn, Trygg Johan, Wold Svante. Using chemometrics for navigating in the large data sets of genomics, proteomics, and metabonomics (gpm). Anal Bioanal Chem. 2004 Sep 22;380(3):419–429. doi: 10.1007/s00216-004-2783-y. [DOI] [PubMed] [Google Scholar]
- Espinosa-Soto Carlos, Padilla-Longoria Pablo, Alvarez-Buylla Elena R. A gene regulatory network model for cell-fate determination during Arabidopsis thaliana flower development that is robust and recovers experimental gene expression profiles. Plant Cell. 2004 Oct 14;16(11):2923–2939. doi: 10.1105/tpc.104.021725. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Eyers L., George I., Schuler L., Stenuit B., Agathos S. N., El Fantroussi Said. Environmental genomics: exploring the unmined richness of microbes to degrade xenobiotics. Appl Microbiol Biotechnol. 2004 Aug 13;66(2):123–130. doi: 10.1007/s00253-004-1703-6. [DOI] [PubMed] [Google Scholar]
- Fey M. F. Genomics and proteomics: expression arrays in clinical oncology. Ann Oncol. 2004;15 (Suppl 4):iv163–iv165. doi: 10.1093/annonc/mdh921. [DOI] [PubMed] [Google Scholar]
- Flanagan Keith, Stevens Robert, Pocock Matthew, Lee Pete, Wipat Anil. Ontology for genome comparison and genomic rearrangements. Comp Funct Genomics. 2004;5(6-7):537–544. doi: 10.1002/cfg.436. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Fofanov Yuriy, Luo Yi, Katili Charles, Wang Jim, Belosludtsev Yuri, Powdrill Thomas, Belapurkar Chetan, Fofanov Viacheslav, Li Tong-Bin, Chumakov Sergey. How independent are the appearances of n-mers in different genomes? Bioinformatics. 2004 Apr 15;20(15):2421–2428. doi: 10.1093/bioinformatics/bth266. [DOI] [PubMed] [Google Scholar]
- Friedman Adam, Perrimon Norbert. Genome-wide high-throughput screens in functional genomics. Curr Opin Genet Dev. 2004 Oct;14(5):470–476. doi: 10.1016/j.gde.2004.07.010. [DOI] [PubMed] [Google Scholar]
- Friedman Robert, Ekollu Vikram, Rose John R., Hughes Austin L. Dblox: a genome-wide test for ancient segmental duplication. Bioinformatics. 2004 May 14;20(16):2834–2835. doi: 10.1093/bioinformatics/bth275. [DOI] [PubMed] [Google Scholar]
- Fu Yan, Hsia An-Ping, Guo Ling, Schnable Patrick S. Types and frequencies of sequencing errors in methyl-filtered and high c0t maize genome survey sequences. Plant Physiol. 2004 Aug 6;135(4):2040–2045. doi: 10.1104/pp.104.041640. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Fu Yan, Yang Qiang, Sun Ruixiang, Li Dequan, Zeng Rong, Ling Charles X., Gao Wen. Exploiting the kernel trick to correlate fragment ions for peptide identification via tandem mass spectrometry. Bioinformatics. 2004 Mar 25;20(12):1948–1954. doi: 10.1093/bioinformatics/bth186. [DOI] [PubMed] [Google Scholar]
- Fukuchi Satoshi, Nishikawa Ken. Estimation of the number of authentic orphan genes in bacterial genomes. DNA Res. 2004 Aug 31;11(4):219-31, 311-313. [PubMed] [Google Scholar]
- Gao Haichun, Wang Yue, Liu Xueduan, Yan Tingfen, Wu Liyou, Alm Eric, Arkin Adam, Thompson Dorothea K., Zhou Jizhong. Global transcriptome analysis of the heat shock response of Shewanella oneidensis. J Bacteriol. 2004 Nov;186(22):7796–7803. doi: 10.1128/JB.186.22.7796-7803.2004. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Gao Li-Zhi, Innan Hideki. Very low gene duplication rate in the yeast genome. Science. 2004 Nov 19;306(5700):1367–1370. doi: 10.1126/science.1102033. [DOI] [PubMed] [Google Scholar]
- Ge Yue, Rajkumar Lakshmanswamy, Guzman Raphael C., Nandi Satyabrata, Patton Wayne F., Agnew Brian J. Multiplexed fluorescence detection of phosphorylation, glycosylation, and total protein in the proteomic analysis of breast cancer refractoriness. Proteomics. 2004 Nov;4(11):3464–3467. doi: 10.1002/pmic.200400957. [DOI] [PubMed] [Google Scholar]
- Gillanders Elizabeth M., Xu Jianfeng, Chang Bao-li, Lange Ethan M., Wiklund Fredrik, Bailey-Wilson Joan E., Baffoe-Bonnie Agnes, Jones MaryPat, Gildea Derek, Riedesel Erica. Combined genome-wide scan for prostate cancer susceptibility genes. J Natl Cancer Inst. 2004 Aug 18;96(16):1240–1247. doi: 10.1093/jnci/djh228. [DOI] [PubMed] [Google Scholar]
- Gkoutos G. V., Green E. C. J., Mallon A-M, Blake A., Greenaway S., Hancock J. M., Davidson D. Ontologies for the description of mouse phenotypes. Comp Funct Genomics. 2004;5(6-7):545–551. doi: 10.1002/cfg.430. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Glöckner G., Lehmann R., Romualdi A., Pradella S., Schulte-Spechtel U., Schilhabel M., Wilske B., Sühnel J., Platzer M. Comparative analysis of the Borrelia garinii genome. Nucleic Acids Res. 2004 Nov 16;32(20):6038–6046. doi: 10.1093/nar/gkh953. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Grad Yonatan H., Roth Frederick P., Halfon Marc S., Church George M. Prediction of similarly acting cis-regulatory modules by subsequence profiling and comparative genomics in Drosophila melanogaster and D.pseudoobscura. Bioinformatics. 2004 May 14;20(16):2738–2750. doi: 10.1093/bioinformatics/bth320. [DOI] [PubMed] [Google Scholar]
- Grünblatt E., Mandel S., Jacob-Hirsch J., Zeligson S., Amariglo N., Rechavi G., Li J., Ravid R., Roggendorf W., Riederer P. Gene expression profiling of parkinsonian substantia nigra pars compacta; alterations in ubiquitin-proteasome, heat shock protein, iron and oxidative stress regulated proteins, cell adhesion/cellular matrix and vesicle trafficking genes. J Neural Transm (Vienna) 2004 Sep 30;111(12):1543–1573. doi: 10.1007/s00702-004-0212-1. [DOI] [PubMed] [Google Scholar]
- Gu Weisong, Bertone Alicia L. Generation and performance of an equine-specific large-scale gene expression microarray. Am J Vet Res. 2004 Dec;65(12):1664–1673. doi: 10.2460/ajvr.2004.65.1664. [DOI] [PubMed] [Google Scholar]
- Gupta S., Zink D., Korn B., Vingron M., Haas S. A. Genome wide identification and classification of alternative splicing based on EST data. Bioinformatics. 2004 Apr 29;20(16):2579–2585. doi: 10.1093/bioinformatics/bth288. [DOI] [PubMed] [Google Scholar]
- Gutiérrez Rodrigo A., Larson Matthew D., Wilkerson Curtis. The plant-specific database. Classification of Arabidopsis proteins based on their phylogenetic profile. Plant Physiol. 2004 Aug;135(4):1888–1892. doi: 10.1104/pp.104.043687. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Han Yanping, Zhou Dongsheng, Pang Xin, Song Yajun, Zhang Ling, Bao Jingyue, Tong Zongzhong, Wang Jin, Guo Zhaobiao, Zhai Junhui. Microarray analysis of temperature-induced transcriptome of Yersinia pestis. Microbiol Immunol. 2004;48(11):791–805. doi: 10.1111/j.1348-0421.2004.tb03605.x. [DOI] [PubMed] [Google Scholar]
- Haubold Bernhard, Wiehe Thomas. Comparative genomics: methods and applications. Naturwissenschaften. 2004 Jun 25;91(9):405–421. doi: 10.1007/s00114-004-0542-8. [DOI] [PubMed] [Google Scholar]
- Hendrickson E. L., Kaul R., Zhou Y., Bovee D., Chapman P., Chung J., Conway de Macario E., Dodsworth J. A., Gillett W., Graham D. E. Complete genome sequence of the genetically tractable hydrogenotrophic methanogen Methanococcus maripaludis. J Bacteriol. 2004 Oct;186(20):6956–6969. doi: 10.1128/JB.186.20.6956-6969.2004. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Higa R. H., Montagner A. J., Togawa R. C., Kuser P. R., Yamagishi M. E. B., Mancini A. L., Pappas G., Jr, Miura R. T., Horita L. G., Neshich G. ConSSeq: a web-based application for analysis of amino acid conservation based on HSSP database and within context of structure. Bioinformatics. 2004 Mar 25;20(12):1983–1985. doi: 10.1093/bioinformatics/bth185. [DOI] [PubMed] [Google Scholar]
- Huang Chun-Ming. Comparative proteomic analysis of human whole saliva. Arch Oral Biol. 2004 Dec;49(12):951–962. doi: 10.1016/j.archoralbio.2004.06.003. [DOI] [PubMed] [Google Scholar]
- Huang Xiaoqiu, Ye Liang, Chou Hui-Hsien, Yang I-Hsuan, Chao Kun-Mao. Efficient combination of multiple word models for improved sequence comparison. Bioinformatics. 2004 Apr 29;20(16):2529–2533. doi: 10.1093/bioinformatics/bth279. [DOI] [PubMed] [Google Scholar]
- Huminiecki Lukasz, Wolfe Kenneth H. Divergence of spatial gene expression profiles following species-specific gene duplications in human and mouse. Genome Res. 2004 Oct;14(10A):1870–1879. doi: 10.1101/gr.2705204. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Hung Shih-Chieh, Chang Ching-Fang, Ma Hsiao-Li, Chen Tain-Hsiung, Low-Tone Ho Larry. Gene expression profiles of early adipogenesis in human mesenchymal stem cells. Gene. 2004 Sep 29;340(1):141–150. doi: 10.1016/j.gene.2004.06.028. [DOI] [PubMed] [Google Scholar]
- Ihara Naoya, Takasuga Akiko, Mizoshita Kazunori, Takeda Haruko, Sugimoto Mayumi, Mizoguchi Yasushi, Hirano Takashi, Itoh Tomohito, Watanabe Toshio, Reed Kent M. A comprehensive genetic map of the cattle genome based on 3802 microsatellites. Genome Res. 2004 Oct;14(10A):1987–1998. doi: 10.1101/gr.2741704. [DOI] [PMC free article] [PubMed] [Google Scholar]
- International Chicken Genome Sequencing Consortium Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolution. Nature. 2004 Dec 9;432(7018):695–716. doi: 10.1038/nature03154. [DOI] [PubMed] [Google Scholar]
- Jang Joung S., Cho Hee Y., Lee Young J., Ha Woo S., Kim Hwal W. The differential proteome profile of stomach cancer: identification of the biomarker candidates. Oncol Res. 2004;14(10):491–499. doi: 10.3727/0965040042380441. [DOI] [PubMed] [Google Scholar]
- Jang Won Gu, Kim Hye Soon, Park Keun-Gyu, Park Yong Bok, Yoon Kun-Ho, Han Seong-Wook, Hur Seung-Ho, Park Kyong Soo, Lee In-Kyu. Analysis of proteome and transcriptome of tumor necrosis factor alpha stimulated vascular smooth muscle cells with or without alpha lipoic acid. Proteomics. 2004 Nov;4(11):3383–3393. doi: 10.1002/pmic.200400972. [DOI] [PubMed] [Google Scholar]
- Jansen Erik, Laven Joop S. E., Dommerholt Henri B. R., Polman Jan, van Rijt Cindy, van den Hurk Caroline, Westland Jolanda, Mosselman Sietse, Fauser Bart C. J. M. Abnormal gene expression profiles in human ovaries from polycystic ovary syndrome patients. Mol Endocrinol. 2004 Aug 12;18(12):3050–3063. doi: 10.1210/me.2004-0074. [DOI] [PubMed] [Google Scholar]
- Ji Liping, Tan Kian-Lee. Mining gene expression data for positive and negative co-regulated gene clusters. Bioinformatics. 2004 May 14;20(16):2711–2718. doi: 10.1093/bioinformatics/bth312. [DOI] [PubMed] [Google Scholar]
- Jiang Honglin, Whitworth Kristin M., Bivens Nathan J., Ries James E., Woods Rami J., Forrester Lawrence J., Springer Gordon K., Mathialagan Nagappan, Agca Cansu, Prather Randall S. Large-scale generation and analysis of expressed sequence tags from porcine ovary. Biol Reprod. 2004 Aug 11;71(6):1991–2002. doi: 10.1095/biolreprod.104.031831. [DOI] [PubMed] [Google Scholar]
- Kabuyama Yukihito, Resing Katheryn A., Ahn Natalie G. Applying proteomics to signaling networks. Curr Opin Genet Dev. 2004 Oct;14(5):492–498. doi: 10.1016/j.gde.2004.07.001. [DOI] [PubMed] [Google Scholar]
- Kang Jeong Gu, Pyo Young Jae, Cho Jin Won, Cho Myeon Haeng. Comparative proteome analysis of differentially expressed proteins induced by K+ deficiency in Arabidopsis thaliana. Proteomics. 2004 Nov;4(11):3549–3559. doi: 10.1002/pmic.200400898. [DOI] [PubMed] [Google Scholar]
- Kao Wei-Chun, Chen Yet-Ran, Yi Eugene C., Lee Hookeun, Tian Qiang, Wu Keh-Ming, Tsai Shih-Feng, Yu Steve S-F, Chen Yu-Ju, Aebersold Ruedi. Quantitative proteomic analysis of metabolic regulation by copper ions in Methylococcus capsulatus (Bath). J Biol Chem. 2004 Sep 22;279(49):51554–51560. doi: 10.1074/jbc.M408013200. [DOI] [PubMed] [Google Scholar]
- Kap-Soon Noh, Do-Youn Lee, Hak Cha Jung, Joo Won-A, Lee Eunil, Chan-Wha Kim. Protein biomarkers in the plasma of workers occupationally exposed to polycyclic aromatic hydrocarbons. Proteomics. 2004 Nov;4(11):3505–3513. doi: 10.1002/pmic.200400964. [DOI] [PubMed] [Google Scholar]
- Kasukawa Takeya, Katayama Shintaro, Kawaji Hideya, Suzuki Harukazu, Hume David A., Hayashizaki Yoshihide. Construction of representative transcript and protein sets of human, mouse, and rat as a platform for their transcriptome and proteome analysis. Genomics. 2004 Dec;84(6):913–921. doi: 10.1016/j.ygeno.2004.08.011. [DOI] [PubMed] [Google Scholar]
- Kearney Joseph B., Wheeler Scott R., Estes Patricia, Parente Beth, Crews Stephen T. Gene expression profiling of the developing Drosophila CNS midline cells. Dev Biol. 2004 Nov 15;275(2):473–492. doi: 10.1016/j.ydbio.2004.08.047. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Khanna Sangeeta, Cheng Georgiana, Gong Bendi, Mustari Michael J., Porter John D. Genome-wide transcriptional profiles are consistent with functional specialization of the extraocular muscle layers. Invest Ophthalmol Vis Sci. 2004 Sep;45(9):3055–3066. doi: 10.1167/iovs.03-1385. [DOI] [PubMed] [Google Scholar]
- Kim Hyo-Jin, Lee Do-Yup, Lee Dae-Hee, Park Yong-Cheol, Kweon Dae-Hyuk, Ryu Yeon-Woo, Seo Jin-Ho. Strategic proteome analysis of Candida magnoliae with an unsequenced genome. Proteomics. 2004 Nov;4(11):3588–3599. doi: 10.1002/pmic.200400966. [DOI] [PubMed] [Google Scholar]
- Kim Ki-Bum, Kim Sang-Il, Choo Hyo-Jung, Kim Ji-Hyun, Ko Young-Gyu. Two-dimensional electrophoretic analysis reveals that lipid rafts are intact at physiological temperature. Proteomics. 2004 Nov;4(11):3527–3535. doi: 10.1002/pmic.200401001. [DOI] [PubMed] [Google Scholar]
- Kim Nam-Kuk, Joh Joong-Ho, Park Hye-Ran, Kim Oun-Hyun, Park Beom-Young, Lee Chang-Soo. Differential expression profiling of the proteomes and their mRNAs in porcine white and red skeletal muscles. Proteomics. 2004 Nov;4(11):3422–3428. doi: 10.1002/pmic.200400976. [DOI] [PubMed] [Google Scholar]
- Kim Seung Il, Kim Jin Young, Yun Sung-Ho, Kim Jung-Hyun, Leem Sun-Hee, Lee Chulhyun. Proteome analysis of Pseudomonas sp. K82 biodegradation pathways. Proteomics. 2004 Nov;4(11):3610–3621. doi: 10.1002/pmic.200400977. [DOI] [PubMed] [Google Scholar]
- Kim Sun Tae, Yu Seok, Kim Sang Gon, Kim Han Ju, Kang Sun Young, Hwang Du Hyeon, Jang Yu Sin, Kang Kyu Young. Proteome analysis of rice blast fungus (Magnaporthe grisea) proteome during appressorium formation. Proteomics. 2004 Nov;4(11):3579–3587. doi: 10.1002/pmic.200400969. [DOI] [PubMed] [Google Scholar]
- Kim Yong-Sam, Hwang Soo Young, Oh Sejeong, Sohn Hosung, Kang Hye-Yeon, Lee Jeong-Hwa, Cho Eun-Wie, Kim Jin-Young, Yoo Jong Shin, Kim Nam-Soon. Identification of target proteins of N-acetylglucosaminyl-transferase V and fucosyltransferase 8 in human gastric tissues by glycomic approach. Proteomics. 2004 Nov;4(11):3353–3358. doi: 10.1002/pmic.200401026. [DOI] [PubMed] [Google Scholar]
- Kirst Matias, Myburg Alexander A., De León José P. G., Kirst Mariana E., Scott Jay, Sederoff Ronald. Coordinated genetic regulation of growth and lignin revealed by quantitative trait locus analysis of cDNA microarray data in an interspecific backcross of eucalyptus. Plant Physiol. 2004 Aug 6;135(4):2368–2378. doi: 10.1104/pp.103.037960. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Konradi Christine, Westin Jenny E., Carta Manolo, Eaton Molly E., Kuter Katarzyna, Dekundy Andrzej, Lundblad Martin, Cenci M. Angela. Transcriptome analysis in a rat model of L-DOPA-induced dyskinesia. Neurobiol Dis. 2004 Nov;17(2):219–236. doi: 10.1016/j.nbd.2004.07.005. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Korotkiy Maksym, Middelburg Rutger, Dekker Henk, van Harmelen Frank, Lankelma Jan. A tool for gene expression based PubMed search through combining data sources. Bioinformatics. 2004 Mar 25;20(12):1980–1982. doi: 10.1093/bioinformatics/bth183. [DOI] [PubMed] [Google Scholar]
- Korpelainen Helena. The evolutionary processes of mitochondrial and chloroplast genomes differ from those of nuclear genomes. Naturwissenschaften. 2004 Sep 28;91(11):505–518. doi: 10.1007/s00114-004-0571-3. [DOI] [PubMed] [Google Scholar]
- Kouchi Hiroshi, Shimomura Kenshiro, Hata Shingo, Hirota Atsuko, Wu Guo-Jiang, Kumagai Hirotaka, Tajima Shigeyuki, Suganuma Norio, Suzuki Akihiro, Aoki Toshio. Large-scale analysis of gene expression profiles during early stages of root nodule formation in a model legume, Lotus japonicus. DNA Res. 2004 Aug 31;11(4):263–274. doi: 10.1093/dnares/11.4.263. [DOI] [PubMed] [Google Scholar]
- Kovács Gábor M., Davison Andrew J., Zakhartchouk Alexender N., Harrach Balázs. Analysis of the first complete genome sequence of an Old World monkey adenovirus reveals a lineage distinct from the six human adenovirus species. J Gen Virol. 2004 Oct;85(Pt 10):2799–2807. doi: 10.1099/vir.0.80225-0. [DOI] [PubMed] [Google Scholar]
- Kramer Richard, Cohen Dalia. Functional genomics to new drug targets. Nat Rev Drug Discov. 2004 Nov;3(11):965–972. doi: 10.1038/nrd1552. [DOI] [PubMed] [Google Scholar]
- Krishnan Arun, Tang Francis. Exhaustive whole-genome tandem repeats search. Bioinformatics. 2004 May 14;20(16):2702–2710. doi: 10.1093/bioinformatics/bth311. [DOI] [PubMed] [Google Scholar]
- Kuerer Henry M., Coombes Kevin R., Chen Jeng-Neng, Xiao Lianchun, Clarke Charlotte, Fritsche Herbert, Krishnamurthy Savitri, Marcy Sylvie, Hung Mien-Chie, Hunt Kelly K. Association between ductal fluid proteomic expression profiles and the presence of lymph node metastases in women with breast cancer. Surgery. 2004 Nov;136(5):1061–1069. doi: 10.1016/j.surg.2004.04.011. [DOI] [PubMed] [Google Scholar]
- Kuhn Kenneth, Baker Shawn C., Chudin Eugene, Lieu Minh-Ha, Oeser Steffen, Bennett Holly, Rigault Philippe, Barker David, McDaniel Timothy K., Chee Mark S. A novel, high-performance random array platform for quantitative gene expression profiling. Genome Res. 2004 Nov;14(11):2347–2356. doi: 10.1101/gr.2739104. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Kumar Anand, Smith Barry, Novotny Daniel D. Biomedical informatics and granularity. Comp Funct Genomics. 2004;5(6-7):501–508. doi: 10.1002/cfg.429. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Kumar Anuj, Seringhaus Michael, Biery Matthew C., Sarnovsky Robert J., Umansky Lara, Piccirillo Stacy, Heidtman Matthew, Cheung Kei-Hoi, Dobry Craig J., Gerstein Mark B. Large-scale mutagenesis of the yeast genome using a Tn7-derived multipurpose transposon. Genome Res. 2004 Oct;14(10A):1975–1986. doi: 10.1101/gr.2875304. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Kurogochi Masaki, Nishimura Shin-Ichiro, Lee Yuan Chuan. Mechanism-based fluorescent labeling of beta-galactosidases. An efficient method in proteomics for glycoside hydrolases. J Biol Chem. 2004 Aug 12;279(43):44704–44712. doi: 10.1074/jbc.M401718200. [DOI] [PubMed] [Google Scholar]
- Kutuzova Galina D., Deluca Hector F. Gene expression profiles in rat intestine identify pathways for 1,25-dihydroxyvitamin D(3) stimulated calcium absorption and clarify its immunomodulatory properties. Arch Biochem Biophys. 2004 Dec 15;432(2):152–166. doi: 10.1016/j.abb.2004.09.004. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Kyoda Koji, Baba Kotaro, Onami Shuichi, Kitano Hiroaki. DBRF-MEGN method: an algorithm for deducing minimum equivalent gene networks from large-scale gene expression profiles of gene deletion mutants. Bioinformatics. 2004 May 27;20(16):2662–2675. doi: 10.1093/bioinformatics/bth306. [DOI] [PubMed] [Google Scholar]
- Lacayo Norman J., Meshinchi Soheil, Kinnunen Paivi, Yu Ron, Wang Yan, Stuber Christianna M., Douglas Lorrie, Wahab Romina, Becton David L., Weinstein Howard. Gene expression profiles at diagnosis in de novo childhood AML patients identify FLT3 mutations with good clinical outcomes. Blood. 2004 Jul 13;104(9):2646–2654. doi: 10.1182/blood-2003-12-4449. [DOI] [PubMed] [Google Scholar]
- Lai Jinsheng, Dey Nrisingha, Kim Cheol-Soo, Bharti Arvind K., Rudd Stephen, Mayer Klaus F. X., Larkins Brian A., Becraft Philip, Messing Joachim. Characterization of the maize endosperm transcriptome and its comparison to the rice genome. Genome Res. 2004 Oct;14(10A):1932–1937. doi: 10.1101/gr.2780504. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Lanckriet Gert R. G., De Bie Tijl, Cristianini Nello, Jordan Michael I., Noble William Stafford. A statistical framework for genomic data fusion. Bioinformatics. 2004 May 6;20(16):2626–2635. doi: 10.1093/bioinformatics/bth294. [DOI] [PubMed] [Google Scholar]
- Lane C. S., Nisar S., Griffiths W. J., Fuller B. J., Davidson B. R., Hewes J., Welham K. J., Patterson L. H. Identification of cytochrome P450 enzymes in human colorectal metastases and the surrounding liver: a proteomic approach. Eur J Cancer. 2004 Sep;40(14):2127–2134. doi: 10.1016/j.ejca.2004.04.029. [DOI] [PubMed] [Google Scholar]
- Laval Guillaume, Excoffier Laurent. SIMCOAL 2.0: a program to simulate genomic diversity over large recombining regions in a subdivided population with a complex history. Bioinformatics. 2004 Apr 29;20(15):2485–2487. doi: 10.1093/bioinformatics/bth264. [DOI] [PubMed] [Google Scholar]
- Lawrence Carolyn J., Zmasek Christian M., Dawe R. Kelly, Malmberg Russell L. LumberJack: a heuristic tool for sequence alignment exploration and phylogenetic inference. Bioinformatics. 2004 Mar 25;20(12):1977–1979. doi: 10.1093/bioinformatics/bth180. [DOI] [PubMed] [Google Scholar]
- Lazo G. R., Chao S., Hummel D. D., Edwards H., Crossman C. C., Lui N., Matthews D. E., Carollo V. L., Hane D. L., You F. M. Development of an expressed sequence tag (EST) resource for wheat (Triticum aestivum L.): EST generation, unigene analysis, probe selection and bioinformatics for a 16,000-locus bin-delineated map. Genetics. 2004 Oct;168(2):585–593. doi: 10.1534/genetics.104.034777. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Lazzarato F., Franceschinis G., Botta M., Cordero F., Calogero R. A. RRE: a tool for the extraction of non-coding regions surrounding annotated genes from genomic datasets. Bioinformatics. 2004 Apr 29;20(16):2848–2850. doi: 10.1093/bioinformatics/bth287. [DOI] [PubMed] [Google Scholar]
- Le Roch Karine G., Johnson Jeffrey R., Florens Laurence, Zhou Yingyao, Santrosyan Andrey, Grainger Munira, Yan S. Frank, Williamson Kim C., Holder Anthony A., Carucci Daniel J. Global analysis of transcript and protein levels across the Plasmodium falciparum life cycle. Genome Res. 2004 Nov;14(11):2308–2318. doi: 10.1101/gr.2523904. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Lee Ah Young, Goo Park Sung, Kho Chang Won, Young Park Sun, Cho Sayeon, Lee Sang Chul, Lee Do Hee, Myung Pyung Keun, Park Byoung Chul. Identification of the degradome of Isp-1, a major intracellular serine protease of Bacillus subtilis, by two-dimensional gel electrophoresis and matrix- assisted laser desorption/ionization-time of flight analysis. Proteomics. 2004 Nov;4(11):3437–3445. doi: 10.1002/pmic.200400997. [DOI] [PubMed] [Google Scholar]
- Lee Ah Young, Park Byoung Chul, Jang Mi, Cho Sayeon, Lee Do Hee, Lee Sang Chul, Myung Pyung Keun, Park Sung Goo. Identification of caspase-3 degradome by two-dimensional gel electrophoresis and matrix-assisted laser desorption/ionization-time of flight analysis. Proteomics. 2004 Nov;4(11):3429–3436. doi: 10.1002/pmic.200400979. [DOI] [PubMed] [Google Scholar]
- Lee Hyun-Ju, Lee Do-Youn, Joo Won-A, Sul Donggeun, Lee Eunil, Kim Chan-Wha. Differential expression of proteins in rat plasma exposed to benzene. Proteomics. 2004 Nov;4(11):3498–3504. doi: 10.1002/pmic.200400996. [DOI] [PubMed] [Google Scholar]
- Lee Jong-Sik, Hong Un-Sook, Lee Tae H., Yoon Sungjoo Kim, Yoon Jong-Bok. Mass spectrometric analysis of tumor necrosis factor receptor-associated factor 1 ubiquitination mediated by cellular inhibitor of apoptosis 2. Proteomics. 2004 Nov;4(11):3376–3382. doi: 10.1002/pmic.200401000. [DOI] [PubMed] [Google Scholar]
- Lee Kyunghee, Kye Minsu, Jang Joung Soon, Lee Ok Jae, Kim Taehyo, Lim Dongbin. Proteomic analysis revealed a strong association of a high level of alpha1-antitrypsin in gastric juice with gastric cancer. Proteomics. 2004 Nov;4(11):3343–3352. doi: 10.1002/pmic.200400960. [DOI] [PubMed] [Google Scholar]
- Lee Moon-Sup, Joo Won-A, Kim Chan-Wha. Identification of a novel protein D3UPCA from Halobacterium salinarum and prediction of its function. Proteomics. 2004 Nov;4(11):3622–3631. doi: 10.1002/pmic.200400978. [DOI] [PubMed] [Google Scholar]
- Lenz H-J. Pharmacogenomics and colorectal cancer. Ann Oncol. 2004;15 (Suppl 4):iv173–iv177. doi: 10.1093/annonc/mdh923. [DOI] [PubMed] [Google Scholar]
- Li Ker-Chau, Liu Ching-Ti, Sun Wei, Yuan Shinsheng, Yu Tianwei. A system for enhancing genome-wide coexpression dynamics study. Proc Natl Acad Sci U S A. 2004 Oct 18;101(44):15561–15566. doi: 10.1073/pnas.0402962101. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Li Long Shan, Kim Hyunki, Rhee Hwanseok, Kim Se Hoon, Shin Dong Hwan, Chung Kyung Young, Park Kang-Sik, Paik Young-Ki, Chang Joon, Kim Hoguen. Proteomic analysis distinguishes basaloid carcinoma as a distinct subtype of nonsmall cell lung carcinoma. Proteomics. 2004 Nov;4(11):3394–3400. doi: 10.1002/pmic.200400901. [DOI] [PubMed] [Google Scholar]
- Li Song, Chou Hui-Hsien. LUCY2: an interactive DNA sequence quality trimming and vector removal tool. Bioinformatics. 2004 May 6;20(16):2865–2866. doi: 10.1093/bioinformatics/bth302. [DOI] [PubMed] [Google Scholar]
- Li Tao, Zhang Chengliang, Ogihara Mitsunori. A comparative study of feature selection and multiclass classification methods for tissue classification based on gene expression. Bioinformatics. 2004 Apr 15;20(15):2429–2437. doi: 10.1093/bioinformatics/bth267. [DOI] [PubMed] [Google Scholar]
- Liao J. G., Lin Yong, Selvanayagam Zachariah E., Shih Weichung Joe. A mixture model for estimating the local false discovery rate in DNA microarray analysis. Bioinformatics. 2004 May 14;20(16):2694–2701. doi: 10.1093/bioinformatics/bth310. [DOI] [PubMed] [Google Scholar]
- Liao Lujian, Cheng Dongmei, Wang Jian, Duong Duc M., Losik Tatyana G., Gearing Marla, Rees Howard D., Lah James J., Levey Allan I., Peng Junmin. Proteomic characterization of postmortem amyloid plaques isolated by laser capture microdissection. J Biol Chem. 2004 Jun 25;279(35):37061–37068. doi: 10.1074/jbc.M403672200. [DOI] [PubMed] [Google Scholar]
- Liebel Urban, Kindler Bjoern, Pepperkok Rainer. 'Harvester': a fast meta search engine of human protein resources. Bioinformatics. 2004 Feb 26;20(12):1962–1963. doi: 10.1093/bioinformatics/bth146. [DOI] [PubMed] [Google Scholar]
- Liew Choong-Chin, Dzau Victor J. Molecular genetics and genomics of heart failure. Nat Rev Genet. 2004 Nov;5(11):811–825. doi: 10.1038/nrg1470. [DOI] [PubMed] [Google Scholar]
- Linkiewicz A. M., Qi L. L., Gill B. S., Ratnasiri A., Echalier B., Chao S., Lazo G. R., Hummel D. D., Anderson O. D., Akhunov E. D. A 2500-locus bin map of wheat homoeologous group 5 provides insights on gene distribution and colinearity with rice. Genetics. 2004 Oct;168(2):665–676. doi: 10.1534/genetics.104.034835. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Linney Elwood, Dobbs-McAuliffe Betsy, Sajadi Hedieh, Malek Renae L. Microarray gene expression profiling during the segmentation phase of zebrafish development. Comp Biochem Physiol C Toxicol Pharmacol. 2004 Jul;138(3):351–362. doi: 10.1016/j.cca.2004.08.008. [DOI] [PubMed] [Google Scholar]
- Litvinov L., Gene A., Napolitano A. La bilateralidad en el cáncer de mama. Prensa Med Argent. 1971 Jan 1;57(44):2004–2008. [PubMed] [Google Scholar]
- Llinás Manuel, DeRisi Joseph L. Pernicious plans revealed: Plasmodium falciparum genome wide expression analysis. Curr Opin Microbiol. 2004 Aug;7(4):382–387. doi: 10.1016/j.mib.2004.06.014. [DOI] [PubMed] [Google Scholar]
- Lundstrom K. Structural genomics on membrane proteins: mini review. Comb Chem High Throughput Screen. 2004 Aug;7(5):431–439. doi: 10.2174/1386207043328634. [DOI] [PubMed] [Google Scholar]
- Luo Feng, Khan Latifur, Bastani Farokh, Yen I-Ling, Zhou Jizhong. A dynamically growing self-organizing tree (DGSOT) for hierarchical clustering gene expression profiles. Bioinformatics. 2004 May 6;20(16):2605–2617. doi: 10.1093/bioinformatics/bth292. [DOI] [PubMed] [Google Scholar]
- Luscombe Nicholas M., Babu M. Madan. GenCompass: a universal system for analysing gene expression for any genome. Trends Biotechnol. 2004 Nov;22(11):552–555. doi: 10.1016/j.tibtech.2004.08.013. [DOI] [PubMed] [Google Scholar]
- Luscombe Nicholas M., Babu M. Madan, Yu Haiyuan, Snyder Michael, Teichmann Sarah A., Gerstein Mark. Genomic analysis of regulatory network dynamics reveals large topological changes. Nature. 2004 Sep 16;431(7006):308–312. doi: 10.1038/nature02782. [DOI] [PubMed] [Google Scholar]
- Ma Hong-Wu, Zhao Xue-Ming, Yuan Ying-Jin, Zeng An-Ping. Decomposition of metabolic network into functional modules based on the global connectivity structure of reaction graph. Bioinformatics. 2004 Mar 22;20(12):1870–1876. doi: 10.1093/bioinformatics/bth167. [DOI] [PubMed] [Google Scholar]
- Mansourian Robert, Mutch David M., Antille Nicolas, Aubert Jerome, Fogel Paul, Le Goff Jean-Marc, Moulin Julie, Petrov Anton, Rytz Andreas, Voegel Johannes J. The Global Error Assessment (GEA) model for the selection of differentially expressed genes in microarray data. Bioinformatics. 2004 May 14;20(16):2726–2737. doi: 10.1093/bioinformatics/bth319. [DOI] [PubMed] [Google Scholar]
- Marsden Brian, Abagyan Ruben. SAD--a normalized structural alignment database: improving sequence-structure alignments. Bioinformatics. 2004 Apr 15;20(15):2333–2344. doi: 10.1093/bioinformatics/bth244. [DOI] [PubMed] [Google Scholar]
- Marshall Owen J. PerlPrimer: cross-platform, graphical primer design for standard, bisulphite and real-time PCR. Bioinformatics. 2004 Apr 8;20(15):2471–2472. doi: 10.1093/bioinformatics/bth254. [DOI] [PubMed] [Google Scholar]
- Matsumoto Fuminori, Obayashi Takeshi, Sasaki-Sekimoto Yuko, Ohta Hiroyuki, Takamiya Ken-ichiro, Masuda Tatsuru. Gene expression profiling of the tetrapyrrole metabolic pathway in Arabidopsis with a mini-array system. Plant Physiol. 2004 Aug;135(4):2379–2391. doi: 10.1104/pp.104.042408. [DOI] [PMC free article] [PubMed] [Google Scholar]
- McAuliffe Jon D., Pachter Lior, Jordan Michael I. Multiple-sequence functional annotation and the generalized hidden Markov phylogeny. Bioinformatics. 2004 Feb 26;20(12):1850–1860. doi: 10.1093/bioinformatics/bth153. [DOI] [PubMed] [Google Scholar]
- McLeod Michael P., Qin Xiang, Karpathy Sandor E., Gioia Jason, Highlander Sarah K., Fox George E., McNeill Thomas Z., Jiang Huaiyang, Muzny Donna, Jacob Leni S. Complete genome sequence of Rickettsia typhi and comparison with sequences of other rickettsiae. J Bacteriol. 2004 Sep;186(17):5842–5855. doi: 10.1128/JB.186.17.5842-5855.2004. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Messing Joachim, Bharti Arvind K., Karlowski Wojciech M., Gundlach Heidrun, Kim Hye Ran, Yu Yeisoo, Wei Fusheng, Fuks Galina, Soderlund Carol A., Mayer Klaus F. X. Sequence composition and genome organization of maize. Proc Natl Acad Sci U S A. 2004 Sep 23;101(40):14349–14354. doi: 10.1073/pnas.0406163101. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Mestres Jordi. Computational chemogenomics approaches to systematic knowledge-based drug discovery. Curr Opin Drug Discov Devel. 2004 May;7(3):304–313. [PubMed] [Google Scholar]
- Miftahudin, Ross K., Ma X-F, Mahmoud A. A., Layton J., Milla M. A. Rodriguez, Chikmawati T., Ramalingam J., Feril O., Pathan M. S. Analysis of expressed sequence tag loci on wheat chromosome group 4. Genetics. 2004 Oct;168(2):651–663. doi: 10.1534/genetics.104.034827. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Miguel Ricardo Núez. Sequence patterns derived from the automated prediction of functional residues in structurally-aligned homologous protein families. Bioinformatics. 2004 Apr 8;20(15):2380–2389. doi: 10.1093/bioinformatics/bth255. [DOI] [PubMed] [Google Scholar]
- Mirkin Sebastian, Nikas George, Hsiu Jeng-Gwang, Díaz José, Oehninger Sergio. Gene expression profiles and structural/functional features of the peri-implantation endometrium in natural and gonadotropin-stimulated cycles. J Clin Endocrinol Metab. 2004 Nov;89(11):5742–5752. doi: 10.1210/jc.2004-0605. [DOI] [PubMed] [Google Scholar]
- Miyake Tsutomu, Amemiya Chris T. BAC libraries and comparative genomics of aquatic chordate species. Comp Biochem Physiol C Toxicol Pharmacol. 2004 Jul;138(3):233–244. doi: 10.1016/j.cca.2004.07.001. [DOI] [PubMed] [Google Scholar]
- Mogass Michael, York Timothy P., Li Lin, Rujirabanjerd Sinitdhorn, Shiang Rita. Genomewide analysis of gene expression associated with Tcof1 in mouse neuroblastoma. Biochem Biophys Res Commun. 2004 Dec 3;325(1):124–132. doi: 10.1016/j.bbrc.2004.10.004. [DOI] [PubMed] [Google Scholar]
- Monastyrskaya Galina, Fushan Alexey, Abaev Igor, Filyukova Olga, Kostina Maria, Pecherskih Emily, Sverdlov Eugene. Genome-wide comparison reveals great inter- and intraspecies variability in B. pseudomallei and B. mallei pathogens. Res Microbiol. 2004 Nov;155(9):781–793. doi: 10.1016/j.resmic.2004.05.014. [DOI] [PubMed] [Google Scholar]
- Monosi B., Wisser R. J., Pennill L., Hulbert S. H. Full-genome analysis of resistance gene homologues in rice. Theor Appl Genet. 2004 Aug 10;109(7):1434–1447. doi: 10.1007/s00122-004-1758-x. [DOI] [PubMed] [Google Scholar]
- Monteiro-Vitorello Claudia B., Camargo Luis E. A., Van Sluys Marie A., Kitajima João P., Truffi Daniela, do Amaral Alexandre M., Harakava Ricardo, de Oliveira Julio C. F., Wood Derek, de Oliveira Mariana C. The genome sequence of the gram-positive sugarcane pathogen Leifsonia xyli subsp. xyli. Mol Plant Microbe Interact. 2004 Aug;17(8):827–836. doi: 10.1094/MPMI.2004.17.8.827. [DOI] [PubMed] [Google Scholar]
- Moran Mary Ann, Buchan Alison, González José M., Heidelberg John F., Whitman William B., Kiene Ronald P., Henriksen James R., King Gary M., Belas Robert, Fuqua Clay. Genome sequence of Silicibacter pomeroyi reveals adaptations to the marine environment. Nature. 2004 Dec 16;432(7019):910–913. doi: 10.1038/nature03170. [DOI] [PubMed] [Google Scholar]
- Motyka Shawn A., Englund Paul T. RNA interference for analysis of gene function in trypanosomatids. Curr Opin Microbiol. 2004 Aug;7(4):362–368. doi: 10.1016/j.mib.2004.06.004. [DOI] [PubMed] [Google Scholar]
- Mungall Christopher J. Obol: integrating language and meaning in bio-ontologies. Comp Funct Genomics. 2004;5(6-7):509–520. doi: 10.1002/cfg.435. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Munkvold J. D., Greene R. A., Bermudez-Kandianis C. E., La Rota C. M., Edwards H., Sorrells S. F., Dake T., Benscher D., Kantety R., Linkiewicz A. M. Group 3 chromosome bin maps of wheat and their relationship to rice chromosome 1. Genetics. 2004 Oct;168(2):639–650. doi: 10.1534/genetics.104.034819. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Möhring Thomas, Kellmann Markus, Jürgens Michael, Schrader Michael. Top-down identification of endogenous peptides up to 9 kDa in cerebrospinal fluid and brain tissue by nanoelectrospray quadrupole time-of-flight tandem mass spectrometry. J Mass Spectrom. 2005 Feb;40(2):214–226. doi: 10.1002/jms.741. [DOI] [PubMed] [Google Scholar]
- Müller-Hagen Gerit, Beinert Thomas, Sommer Anette. Aspects of lung cancer gene expression profiling. Curr Opin Drug Discov Devel. 2004 May;7(3):290–303. [PubMed] [Google Scholar]
- Norden Anthony G. W., Sharratt Peter, Cutillas Pedro R., Cramer Rainer, Gardner Sharon C., Unwin Robert J. Quantitative amino acid and proteomic analysis: very low excretion of polypeptides >750 Da in normal urine. Kidney Int. 2004 Nov;66(5):1994–2003. doi: 10.1111/j.1523-1755.2004.00970.x. [DOI] [PubMed] [Google Scholar]
- O'Donoghue Seán I., Meyer Joachim E. W., Schafferhans Andrea, Fries Karsten. The SRS 3D module: integrating structures, sequences and features. Bioinformatics. 2004 Apr 15;20(15):2476–2478. doi: 10.1093/bioinformatics/bth260. [DOI] [PubMed] [Google Scholar]
- Oh Jisun, Pyo Jae-Hoon, Jo Eun-Hyun, Hwang Sun-Il, Kang Sun-Chul, Jung Jae-Hwan, Park Eui-Kyun, Kim Shin-Yoon, Choi Je-Yong, Lim Jinkyu. Establishment of a near-standard two-dimensional human urine proteomic map. Proteomics. 2004 Nov;4(11):3485–3497. doi: 10.1002/pmic.200401018. [DOI] [PubMed] [Google Scholar]
- Oh Sangnam, Im Hosub, Oh Eunha, Lee Joohyun, Khim Jin-Young, Mun Joohee, Kim Yanghee, Lee Eunil, Kim Joon, Sul Donggeun. Effects of benzo(a)pyrene on protein expression in Jurkat T-cells. Proteomics. 2004 Nov;4(11):3514–3526. doi: 10.1002/pmic.200400981. [DOI] [PubMed] [Google Scholar]
- Omoto Charlotte K., Toso Marc, Tang Keliang, Sibley L. David. Expressed sequence tag (EST) analysis of Gregarine gametocyst development. Int J Parasitol. 2004 Oct;34(11):1265–1271. doi: 10.1016/j.ijpara.2004.08.004. [DOI] [PubMed] [Google Scholar]
- Ong Catherine, Ooi Chia Huey, Wang Dongling, Chong Hweeling, Ng Kim Chong, Rodrigues Fiona, Lee May Ann, Tan Patrick. Patterns of large-scale genomic variation in virulent and avirulent Burkholderia species. Genome Res. 2004 Nov;14(11):2295–2307. doi: 10.1101/gr.1608904. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Ovcharenko Ivan, Stubbs Lisa, Loots Gabriela G. Interpreting mammalian evolution using Fugu genome comparisons. Genomics. 2004 Nov;84(5):890–895. doi: 10.1016/j.ygeno.2004.07.011. [DOI] [PubMed] [Google Scholar]
- Page Rebecca, Stevens Raymond C. Crystallization data mining in structural genomics: using positive and negative results to optimize protein crystallization screens. Methods. 2004 Nov;34(3):373–389. doi: 10.1016/j.ymeth.2004.03.026. [DOI] [PubMed] [Google Scholar]
- Pan Xuewen, Yuan Daniel S., Xiang Dong, Wang Xiaoling, Sookhai-Mahadeo Sharon, Bader Joel S., Hieter Philip, Spencer Forrest, Boeke Jef D. A robust toolkit for functional profiling of the yeast genome. Mol Cell. 2004 Nov 5;16(3):487–496. doi: 10.1016/j.molcel.2004.09.035. [DOI] [PubMed] [Google Scholar]
- Park Bokyung, Jeong Seul-Ki, Lee Won-Suk, Seong Je Kyung, Paik Young-Ki. A simple pattern classification method for alcohol-responsive proteins that are differentially expressed in mouse brain. Proteomics. 2004 Nov;4(11):3369–3375. doi: 10.1002/pmic.200400958. [DOI] [PubMed] [Google Scholar]
- Park Bokyung, Oh Seung-Hyun, Seong Je-Kyung, Paik Young-Ki. A strain-specific alteration of proteomic expression in mouse liver fructose 1,6-bisphosphatase isoforms by alcohol. Proteomics. 2004 Nov;4(11):3413–3421. doi: 10.1002/pmic.200400975. [DOI] [PubMed] [Google Scholar]
- Park Hee Jin, Lee Do Hee, Park Sung Goo, Lee Sang Chul, Cho Sayeon, Kim Ha Kun, Kim Jae Jong, Bae Hyunsu, Park Byoung Chul. Proteome analysis of red deer antlers. Proteomics. 2004 Nov;4(11):3642–3653. doi: 10.1002/pmic.200401027. [DOI] [PubMed] [Google Scholar]
- Park Soo-Jin, Joo Won-A, Choi Jiyeon, Lee So-Hee, Kim Chan-Wha. Identification and characterization of inosine monophosphate dehydrogenase from Halobacterium salinarum. Proteomics. 2004 Nov;4(11):3632–3641. doi: 10.1002/pmic.200400921. [DOI] [PubMed] [Google Scholar]
- Park Yong-Doo, Kim So-Yeon, Jang Hee-Sun, Seo Eun-Young, Namkung Jung-Hyun, Park Hyung-Seok, Cho Sang Yun, Paik Young-Ki, Yang Jun-Mo. Towards a proteomic analysis of atopic dermatitis: a two-dimensional-polyacrylamide gel electrophoresis/mass spectrometric analysis of cultured patient-derived fibroblasts. Proteomics. 2004 Nov;4(11):3446–3455. doi: 10.1002/pmic.200400998. [DOI] [PubMed] [Google Scholar]
- Parkinson Helen, Aitken Stuart, Baldock Richard A., Bard Jonathan B. L., Burger Albert, Hayamizu Terry F., Rector Alan, Ringwald Martin, Rogers Jeremy, Rosse Cornelius. The SOFG Anatomy Entry List (SAEL): an annotation tool for functional genomics data. Comp Funct Genomics. 2004;5(6-7):521–527. doi: 10.1002/cfg.434. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Parton Laura E., Diraison Frédérique, Neill Suzanne E., Ghosh Sujoy K., Rubino Mark A., Bisi John E., Briscoe Celia P., Rutter Guy A. Impact of PPARgamma overexpression and activation on pancreatic islet gene expression profile analyzed with oligonucleotide microarrays. Am J Physiol Endocrinol Metab. 2004 May 4;287(3):E390–E404. doi: 10.1152/ajpendo.00016.2004. [DOI] [PubMed] [Google Scholar]
- Pasquier C., Girardot F., Jevardat de Fombelle K., Christen R. THEA: ontology-driven analysis of microarray data. Bioinformatics. 2004 May 6;20(16):2636–2643. doi: 10.1093/bioinformatics/bth295. [DOI] [PubMed] [Google Scholar]
- Paulson Linda, Persson Rita, Karlsson Gösta, Silberring Jerzy, Bierczynska-Krzysik Anna, Ekman Rolf, Westman-Brinkmalm Ann. Proteomics and peptidomics in neuroscience. Experience of capabilities and limitations in a neurochemical laboratory. J Mass Spectrom. 2005 Feb;40(2):202–213. doi: 10.1002/jms.740. [DOI] [PubMed] [Google Scholar]
- Pedrioli Patrick G. A., Eng Jimmy K., Hubley Robert, Vogelzang Mathijs, Deutsch Eric W., Raught Brian, Pratt Brian, Nilsson Erik, Angeletti Ruth H., Apweiler Rolf. A common open representation of mass spectrometry data and its application to proteomics research. Nat Biotechnol. 2004 Nov;22(11):1459–1466. doi: 10.1038/nbt1031. [DOI] [PubMed] [Google Scholar]
- Peltier Jean-Benoit, Ytterberg A. Jimmy, Sun Qi, van Wijk Klaas J. New functions of the thylakoid membrane proteome of Arabidopsis thaliana revealed by a simple, fast, and versatile fractionation strategy. J Biol Chem. 2004 Aug 20;279(47):49367–49383. doi: 10.1074/jbc.M406763200. [DOI] [PubMed] [Google Scholar]
- Peng J. H., Zadeh H., Lazo G. R., Gustafson J. P., Chao S., Anderson O. D., Qi L. L., Echalier B., Gill B. S., Dilbirligi M. Chromosome bin map of expressed sequence tags in homoeologous group 1 of hexaploid wheat and homoeology with rice and Arabidopsis. Genetics. 2004 Oct;168(2):609–623. doi: 10.1534/genetics.104.034793. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Penkett Christopher J., Bähler Jürg. Navigating public microarray databases. Comp Funct Genomics. 2004;5(6-7):471–479. doi: 10.1002/cfg.427. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Phadtare Sangita, Inouye Masayori. Genome-wide transcriptional analysis of the cold shock response in wild-type and cold-sensitive, quadruple-csp-deletion strains of Escherichia coli. J Bacteriol. 2004 Oct;186(20):7007–7014. doi: 10.1128/JB.186.20.7007-7014.2004. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Phee Bong-Kwan, Cho Jin-Hwan, Park Sebyul, Jung Jin Hee, Lee Youn-Hyung, Jeon Jong-Seong, Bhoo Seong Hee, Hahn Tae-Ryong. Proteomic analysis of the response of Arabidopsis chloroplast proteins to high light stress. Proteomics. 2004 Nov;4(11):3560–3568. doi: 10.1002/pmic.200400982. [DOI] [PubMed] [Google Scholar]
- Pieler R., Sanchez-Cabo F., Hackl H., Thallinger G. G., Trajanoski Z. ArrayNorm: comprehensive normalization and analysis of microarray data. Bioinformatics. 2004 Apr 8;20(12):1971–1973. doi: 10.1093/bioinformatics/bth174. [DOI] [PubMed] [Google Scholar]
- Pinto Luciana Rossini, Oliveira Karine Miranda, Ulian Eugênio César, Garcia Antonio Augusto Franco, de Souza Anete Pereira. Survey in the sugarcane expressed sequence tag database (SUCEST) for simple sequence repeats. Genome. 2004 Oct;47(5):795–804. doi: 10.1139/g04-055. [DOI] [PubMed] [Google Scholar]
- Pisarchik Alexander, Wortsman Jacobo, Slominski Andrzej. A novel microarray to evaluate stress-related genes in skin: effect of ultraviolet light radiation. Gene. 2004 Oct 27;341:199–207. doi: 10.1016/j.gene.2004.06.046. [DOI] [PubMed] [Google Scholar]
- Porollo Aleksey A., Adamczak Rafal, Meller Jaroslaw. POLYVIEW: a flexible visualization tool for structural and functional annotations of proteins. Bioinformatics. 2004 Apr 8;20(15):2460–2462. doi: 10.1093/bioinformatics/bth248. [DOI] [PubMed] [Google Scholar]
- Prentice Howard, Webster Keith A. Genomic and proteomic profiles of heart disease. Trends Cardiovasc Med. 2004 Oct;14(7):282–288. doi: 10.1016/j.tcm.2004.08.001. [DOI] [PubMed] [Google Scholar]
- Price Alkes L., Eskin Eleazar, Pevzner Pavel A. Whole-genome analysis of Alu repeat elements reveals complex evolutionary history. Genome Res. 2004 Nov;14(11):2245–2252. doi: 10.1101/gr.2693004. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Pérez-Enciso M., Misztal I. Qxpak: a versatile mixed model application for genetical genomics and QTL analyses. Bioinformatics. 2004 May 27;20(16):2792–2798. doi: 10.1093/bioinformatics/bth331. [DOI] [PubMed] [Google Scholar]
- Qi L. L., Echalier B., Chao S., Lazo G. R., Butler G. E., Anderson O. D., Akhunov E. D., Dvorák J., Linkiewicz A. M., Ratnasiri A. A chromosome bin map of 16,000 expressed sequence tag loci and distribution of genes among the three genomes of polyploid wheat. Genetics. 2004 Oct;168(2):701–712. doi: 10.1534/genetics.104.034868. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Qian A., Meals R. A., Rajfer J., Gonzalez-Cadavid N. F. Comparison of gene expression profiles between Peyronie's disease and Dupuytren's contracture. Urology. 2004 Aug;64(2):399–404. doi: 10.1016/j.urology.2004.04.006. [DOI] [PubMed] [Google Scholar]
- Qu Yi, Xu Shizhong. Supervised cluster analysis for microarray data based on multivariate Gaussian mixture. Bioinformatics. 2004 Mar 25;20(12):1905–1913. doi: 10.1093/bioinformatics/bth177. [DOI] [PubMed] [Google Scholar]
- Querec Troy D., Stoyanova Radka, Ross Eric, Patriotis Christos. A novel approach for increasing sensitivity and correcting saturation artifacts of radioactively labeled cDNA arrays. Bioinformatics. 2004 Mar 25;20(12):1955–1961. doi: 10.1093/bioinformatics/bth188. [DOI] [PubMed] [Google Scholar]
- Quintana Francisco J., Hagedorn Peter H., Elizur Gad, Merbl Yifat, Domany Eytan, Cohen Irun R. Functional immunomics: microarray analysis of IgG autoantibody repertoires predicts the future response of mice to induced diabetes. Proc Natl Acad Sci U S A. 2004 Aug 12;101 (Suppl 2):14615–14621. doi: 10.1073/pnas.0404848101. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Randall Arlo Z., Baldi Pierre, Villarreal Luis P. Structural proteomics of the poxvirus family. Artif Intell Med. 2004 Jun;31(2):105–115. doi: 10.1016/j.artmed.2004.01.006. [DOI] [PubMed] [Google Scholar]
- Randhawa H. S., Dilbirligi M., Sidhu D., Erayman M., Sandhu D., Bondareva S., Chao S., Lazo G. R., Anderson O. D., Miftahudin Deletion mapping of homoeologous group 6-specific wheat expressed sequence tags. Genetics. 2004 Oct;168(2):677–686. doi: 10.1534/genetics.104.034843. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Rao Raj R., Calhoun John D., Qin Xiaoting, Rekaya Romdhane, Clark Jason K., Stice Steven L. Comparative transcriptional profiling of two human embryonic stem cell lines. Biotechnol Bioeng. 2004 Nov 5;88(3):273–286. doi: 10.1002/bit.20245. [DOI] [PubMed] [Google Scholar]
- Raphael Benjamin, Zhi Degui, Tang Haixu, Pevzner Pavel. A novel method for multiple alignment of sequences with repeated and shuffled elements. Genome Res. 2004 Nov;14(11):2336–2346. doi: 10.1101/gr.2657504. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Ren Yi, He Qing-Yu, Fan Jianqing, Jones Brian, Zhou Yuan, Xie Yi, Cheung Chung-Yan, Wu Adrian, Chiu Jen-Fu, Peiris J. S. Malik. The use of proteomics in the discovery of serum biomarkers from patients with severe acute respiratory syndrome. Proteomics. 2004 Nov;4(11):3477–3484. doi: 10.1002/pmic.200400897. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Rishi A. S., Munir Shirin, Kapur Vivek, Nelson Neil D., Goyal Arun. Identification and analysis of safener-inducible expressed sequence tags in Populus using a cDNA microarray. Planta. 2004 Sep 18;220(2):296–306. doi: 10.1007/s00425-004-1356-9. [DOI] [PubMed] [Google Scholar]
- Ritter B., Blondeau F., Denisov A. Yu, Gehring K., McPherson P. S. Molecular mechanisms in clathrin-mediated membrane budding revealed through subcellular proteomics. Biochem Soc Trans. 2004 Nov;32(Pt 5):769–773. doi: 10.1042/BST0320769. [DOI] [PubMed] [Google Scholar]
- Robles Víctor, Larrañaga Pedro, Peña José M., Menasalvas Ernestina, Pérez María S., Herves Vanessa, Wasilewska Anita. Bayesian network multi-classifiers for protein secondary structure prediction. Artif Intell Med. 2004 Jun;31(2):117–136. doi: 10.1016/j.artmed.2004.01.009. [DOI] [PubMed] [Google Scholar]
- Roelofsen Han, Balgobind Reshma, Vonk Roel J. Proteomic analyzes of copper metabolism in an in vitro model of Wilson disease using surface enhanced laser desorption/ionization-time of flight-mass spectrometry. J Cell Biochem. 2004 Nov 1;93(4):732–740. doi: 10.1002/jcb.20226. [DOI] [PubMed] [Google Scholar]
- Roh Gu Seob, Shin Younghyun, Seo Seong-Won, Yoon Bo Ra, Yeo Sinkoo, Park Sung Jin, Cho Jin Won, Kwack KyuBum. Proteome analysis of differential protein expression in allergen-induced asthmatic mice lung after dexamethasone treatment. Proteomics. 2004 Nov;4(11):3318–3327. doi: 10.1002/pmic.200400930. [DOI] [PubMed] [Google Scholar]
- Ross Mary E., Mahfouz Rami, Onciu Mihaela, Liu Hsi-Che, Zhou Xiaodong, Song Guangchun, Shurtleff Sheila A., Pounds Stanley, Cheng Cheng, Ma Jing. Gene expression profiling of pediatric acute myelogenous leukemia. Blood. 2004 Jun 29;104(12):3679–3687. doi: 10.1182/blood-2004-03-1154. [DOI] [PubMed] [Google Scholar]
- Ruotolo Brandon T., Gillig Kent J., Woods Amina S., Egan Thomas F., Ugarov Michael V., Schultz J. Albert, Russell David H. Analysis of phosphorylated peptides by ion mobility-mass spectrometry. Anal Chem. 2004 Nov 15;76(22):6727–6733. doi: 10.1021/ac0498009. [DOI] [PubMed] [Google Scholar]
- Rupp Steffen. Proteomics on its way to study host-pathogen interaction in Candida albicans. Curr Opin Microbiol. 2004 Aug;7(4):330–335. doi: 10.1016/j.mib.2004.06.006. [DOI] [PubMed] [Google Scholar]
- Sabounchi-Schütt Fariba, Mikko Mikael, Eklund Anders, Grunewald Johan, AStröm Jonas. Serum protein pattern in sarcoidosis analysed by a proteomics approach. Sarcoidosis Vasc Diffuse Lung Dis. 2004 Oct;21(3):182–190. [PubMed] [Google Scholar]
- Saunders Neil F. W., Curmi Paul M. G., Cavicchioli Ricardo. An online database for the detection of novel archaeal sequences in human ESTs. Bioinformatics. 2004 Apr 15;20(15):2361–2362. doi: 10.1093/bioinformatics/bth249. [DOI] [PubMed] [Google Scholar]
- Schiltz Séverine, Gallardo Karine, Huart Myriam, Negroni Luc, Sommerer Nicolas, Burstin Judith. Proteome reference maps of vegetative tissues in pea. An investigation of nitrogen mobilization from leaves during seed filling. Plant Physiol. 2004 Aug 6;135(4):2241–2260. doi: 10.1104/pp.104.041947. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Schlueter Jessica A., Dixon Phillip, Granger Cheryl, Grant David, Clark Lynn, Doyle Jeff J., Shoemaker Randy C. Mining EST databases to resolve evolutionary events in major crop species. Genome. 2004 Oct;47(5):868–876. doi: 10.1139/g04-047. [DOI] [PubMed] [Google Scholar]
- Scobioala Sergiu, Klocke Rainer, Michel Günter, Kuhlmann Michael, Nikol Sigrid. Proteomics: state of the art and its application in cardiovascular research. Curr Med Chem. 2004 Dec;11(24):3203–3218. doi: 10.2174/0929867043363767. [DOI] [PubMed] [Google Scholar]
- Sellheyer Klaus, Belbin Thomas J. DNA microarrays: from structural genomics to functional genomics. The applications of gene chips in dermatology and dermatopathology. J Am Acad Dermatol. 2004 Nov;51(5):681–696. doi: 10.1016/j.jaad.2004.03.038. [DOI] [PubMed] [Google Scholar]
- Seo Jinwook, Bakay Marina, Chen Yi-Wen, Hilmer Sara, Shneiderman Ben, Hoffman Eric P. Interactively optimizing signal-to-noise ratios in expression profiling: project-specific algorithm selection and detection p-value weighting in Affymetrix microarrays. Bioinformatics. 2004 Apr 29;20(16):2534–2544. doi: 10.1093/bioinformatics/bth280. [DOI] [PubMed] [Google Scholar]
- Seo Jong Bok, Kim Hye Sook, Jung Gyoo Yeol, Nam Myung Hee, Chung Joo Hee, Kim Jin Young, Yoo Jong Shin, Kim Chan Wha, Kwon Ohoak. Psychrophilicity of Bacillus psychrosaccharolyticus: a proteomic study. Proteomics. 2004 Nov;4(11):3654–3659. doi: 10.1002/pmic.200401025. [DOI] [PubMed] [Google Scholar]
- Shahid Masood M., Nishikawa Tomotaro, Fukuoka Shu-Ichi, Njenga Peter K., Tsudzuki Takahiko, Kadowaki Koh-Ichi. The complete nucleotide sequence of wild rice (Oryza nivara) chloroplast genome: first genome wide comparative sequence analysis of wild and cultivated rice. Gene. 2004 Sep 29;340(1):133–139. doi: 10.1016/j.gene.2004.06.008. [DOI] [PubMed] [Google Scholar]
- Shin Su Jeon, Lee Sung-Eun, Boo Jung Hyun, Kim Mihyang, Yoon Young-Dae, Kim Su-il, Mook-Jung Inhee. Profiling proteins related to amyloid deposited brain of Tg2576 mice. Proteomics. 2004 Nov;4(11):3359–3368. doi: 10.1002/pmic.200400961. [DOI] [PubMed] [Google Scholar]
- Shin Yong-seung, Lee Eung-goo, Shin Gee-wook, Kim Young-rim, Lee Eun-young, Kim Jae-hoon, Jang Hwan, Gershwin Laurel J., Kim Dae-yong, Kim Yong-hwan. Identification of antigenic proteins from Neospora caninum recognized by bovine immunoglobulins M, E, A and G using immunoproteomics. Proteomics. 2004 Nov;4(11):3600–3609. doi: 10.1002/pmic.200400963. [DOI] [PubMed] [Google Scholar]
- Shipkova Maria, Spielbauer Bettina, Voland Antje, Gröne Hermann-Josef, Armstrong Victor W., Oellerich Michael, Wieland Eberhard. cDNA microarray analysis reveals new candidate genes possibly linked to side effects under mycophenolate mofetil therapy. Transplantation. 2004 Oct 27;78(8):1145–1152. doi: 10.1097/01.tp.0000137262.06252.05. [DOI] [PubMed] [Google Scholar]
- Sieber Stephan A., Mondala Tony S., Head Steven R., Cravatt Benjamin F. Microarray platform for profiling enzyme activities in complex proteomes. J Am Chem Soc. 2004 Dec 8;126(48):15640–15641. doi: 10.1021/ja044286+. [DOI] [PubMed] [Google Scholar]
- Simillion Cedric, Vandepoele Klaas, Van de Peer Yves. Recent developments in computational approaches for uncovering genomic homology. Bioessays. 2004 Nov;26(11):1225–1235. doi: 10.1002/bies.20127. [DOI] [PubMed] [Google Scholar]
- Smales C. M., Dinnis D. M., Stansfield S. H., Alete D., Sage E. A., Birch J. R., Racher A. J., Marshall C. T., James D. C. Comparative proteomic analysis of GS-NS0 murine myeloma cell lines with varying recombinant monoclonal antibody production rate. Biotechnol Bioeng. 2004 Nov 20;88(4):474–488. doi: 10.1002/bit.20272. [DOI] [PubMed] [Google Scholar]
- Smid Marcel, Dorssers Lambert C. J. GO-Mapper: functional analysis of gene expression data using the expression level as a score to evaluate Gene Ontology terms. Bioinformatics. 2004 May 6;20(16):2618–2625. doi: 10.1093/bioinformatics/bth293. [DOI] [PubMed] [Google Scholar]
- Smith Kaleigh, Hallett Mike. Towards quality control for DNA microarrays. J Comput Biol. 2004;11(5):945–970. doi: 10.1089/cmb.2004.11.945. [DOI] [PubMed] [Google Scholar]
- Song Wen Jun, Qin Qi Wei, Qiu Jin, Huang Can Hua, Wang Fan, Hew Choy Leong. Functional genomics analysis of Singapore grouper iridovirus: complete sequence determination and proteomic analysis. J Virol. 2004 Nov;78(22):12576–12590. doi: 10.1128/JVI.78.22.12576-12590.2004. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Sontag Eduardo, Kiyatkin Anatoly, Kholodenko Boris N. Inferring dynamic architecture of cellular networks using time series of gene expression, protein and metabolite data. Bioinformatics. 2004 Mar 22;20(12):1877–1886. doi: 10.1093/bioinformatics/bth173. [DOI] [PubMed] [Google Scholar]
- Stankiewicz Pawełl, Shaw Christine J., Withers Marjorie, Inoue Ken, Lupski James R. Serial segmental duplications during primate evolution result in complex human genome architecture. Genome Res. 2004 Nov;14(11):2209–2220. doi: 10.1101/gr.2746604. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Stathopoulos Angelike, Levine Michael. Whole-genome analysis of Drosophila gastrulation. Curr Opin Genet Dev. 2004 Oct;14(5):477–484. doi: 10.1016/j.gde.2004.07.004. [DOI] [PubMed] [Google Scholar]
- Steinhauser Dirk, Junker Björn H., Luedemann Alexander, Selbig Joachim, Kopka Joachim. Hypothesis-driven approach to predict transcriptional units from gene expression data. Bioinformatics. 2004 Mar 25;20(12):1928–1939. doi: 10.1093/bioinformatics/bth182. [DOI] [PubMed] [Google Scholar]
- Stentz Frankie B., Kitabchi Abbas E. Transcriptome and proteome expression in activated human CD4 and CD8 T-lymphocytes. Biochem Biophys Res Commun. 2004 Nov 12;324(2):692–696. doi: 10.1016/j.bbrc.2004.09.113. [DOI] [PubMed] [Google Scholar]
- Stevens E. V., Posadas E. M., Davidson B., Kohn E. C. Proteomics in cancer. Ann Oncol. 2004;15 (Suppl 4):iv167–iv171. doi: 10.1093/annonc/mdh922. [DOI] [PubMed] [Google Scholar]
- Storms Henricus F., van der Heijden Robert, Tjaden Ubbo R., van der Greef Jan. Capillary isoelectric focusing-mass spectrometry for shotgun approach in proteomics. Electrophoresis. 2004 Oct;25(20):3461–3467. doi: 10.1002/elps.200406087. [DOI] [PubMed] [Google Scholar]
- Stoyanova Radka, Upson John J., Patriotis Christos, Ross Eric A., Henske Elizabeth P., Datta Ketaki, Boman Bruce, Clapper Margie L., Knudson Alfred G., Bellacosa Alfonso. Use of RNA amplification in the optimal characterization of global gene expression using cDNA microarrays. J Cell Physiol. 2004 Dec;201(3):359–365. doi: 10.1002/jcp.20074. [DOI] [PubMed] [Google Scholar]
- Strøm Claes C., Kruhøffer Mogens, Knudsen Steen, Stensgaard-Hansen Frank, Jonassen Thomas E. N., Orntoft Torben F., Haunsø Stig, Sheikh Søren P. Identification of a core set of genes that signifies pathways underlying cardiac hypertrophy. Comp Funct Genomics. 2004;5(6-7):459–470. doi: 10.1002/cfg.428. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Suh Soo-Kyung, Hood Brian L., Kim Bong-Jo, Conrads Thomas P., Veenstra Timothy D., Song Byoung J. Identification of oxidized mitochondrial proteins in alcohol-exposed human hepatoma cells and mouse liver. Proteomics. 2004 Nov;4(11):3401–3412. doi: 10.1002/pmic.200400971. [DOI] [PubMed] [Google Scholar]
- Suyama Mikita, Torrents David, Bork Peer. BLAST2GENE: a comprehensive conversion of BLAST output into independent genes and gene fragments. Bioinformatics. 2004 Mar 22;20(12):1968–1970. doi: 10.1093/bioinformatics/bth172. [DOI] [PubMed] [Google Scholar]
- Swigonová Zuzana, Lai Jinsheng, Ma Jianxin, Ramakrishna Wusirika, Llaca Victor, Bennetzen Jeffrey L., Messing Joachim. Close split of sorghum and maize genome progenitors. Genome Res. 2004 Oct;14(10A):1916–1923. doi: 10.1101/gr.2332504. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Symersky J., Zhang Y., Schormann N., Li S., Bunzel R., Pruett P., Luan C. H., Luo M. Structural genomics of Caenorhabditis elegans: structure of the BAG domain. Acta Crystallogr D Biol Crystallogr. 2004 Aug 26;60(Pt 9):1606–1610. doi: 10.1107/S0907444904017603. [DOI] [PubMed] [Google Scholar]
- Tao Lidan, Yu Xinlei, Snyder A. Peter, Li Liang. Bacterial identification by protein mass mapping combined with an experimentally derived protein mass database. Anal Chem. 2004 Nov 15;76(22):6609–6617. doi: 10.1021/ac049391g. [DOI] [PubMed] [Google Scholar]
- Tempel Wolfram, Liu Zhi-Jie, Schubot Florian D., Shah Ashit, Weinberg Michael V., Jenney Francis E., Jr, Arendall W. Bryan, 3rd, Adams Michael W. W., Richardson Jane S., Richardson David C. Structural genomics of Pyrococcus furiosus: X-ray crystallography reveals 3D domain swapping in rubrerythrin. Proteins. 2004 Dec 1;57(4):878–882. doi: 10.1002/prot.20280. [DOI] [PubMed] [Google Scholar]
- Tenedini Elena, Fagioli Maria Elena, Vianelli Nicola, Tazzari Pier Luigi, Ricci Francesca, Tagliafico Enrico, Ricci Paolo, Gugliotta Luigi, Martinelli Giovanni, Tura Sante. Gene expression profiling of normal and malignant CD34-derived megakaryocytic cells. Blood. 2004 Jul 22;104(10):3126–3135. doi: 10.1182/blood-2003-07-2597. [DOI] [PubMed] [Google Scholar]
- Tenney Aaron E., Brown Randall H., Vaske Charles, Lodge Jennifer K., Doering Tamara L., Brent Michael R. Gene prediction and verification in a compact genome with numerous small introns. Genome Res. 2004 Oct 12;14(11):2330–2335. doi: 10.1101/gr.2816704. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Thiede Bernd, Rudel Thomas. Proteome analysis of apoptotic cells. Mass Spectrom Rev. 2004 Sep-Oct;23(5):333–349. doi: 10.1002/mas.10079. [DOI] [PubMed] [Google Scholar]
- Trempat Pascal, Villalva Claire, Xerri Luc, Armstrong Florence, Duplantier Marie-Michele, Delsol Georges, Brousset Pierre. Gene expression profiling in anaplastic large cell lymphoma and Hodgkin's disease. Leuk Lymphoma. 2004 Oct;45(10):2001–2006. doi: 10.1080/10428190410001713189. [DOI] [PubMed] [Google Scholar]
- Tromp Gerard, Kuivaniemi Helena, Romero Roberto, Chaiworapongsa Tinnakorn, Kim Yeon Mee, Kim Mi Ran, Maymon Eli, Edwin Samuel. Genome-wide expression profiling of fetal membranes reveals a deficient expression of proteinase inhibitor 3 in premature rupture of membranes. Am J Obstet Gynecol. 2004 Oct;191(4):1331–1338. doi: 10.1016/j.ajog.2004.07.010. [DOI] [PubMed] [Google Scholar]
- Usui Tomohiko, Yamagami Satoru, Yokoo Seiichi, Mimura Tatsuya, Ono Kyoko, Amano Shiro. Gene expression profile in corneal neovascularization identified by immunology related macroarray. Mol Vis. 2004 Nov 8;10:832–836. [PubMed] [Google Scholar]
- Utsubo Ryoko, Sonoda Yoshiko, Takahashi Reiko, Iijima Shiro, Aizu-Yokota Eriko, Kasahara Tadashi. Proteome analysis of focal adhesion kinase (FAK)-overexpressing cells. Biol Pharm Bull. 2004 Nov;27(11):1735–1741. doi: 10.1248/bpb.27.1735. [DOI] [PubMed] [Google Scholar]
- Verhagen Bas W. M., Glazebrook Jane, Zhu Tong, Chang Hur-Song, van Loon L. C., Pieterse Corné M. J. The transcriptome of rhizobacteria-induced systemic resistance in arabidopsis. Mol Plant Microbe Interact. 2004 Aug;17(8):895–908. doi: 10.1094/MPMI.2004.17.8.895. [DOI] [PubMed] [Google Scholar]
- Walker P. Roy, Smith Brandon, Liu Qing Yan, Famili A. Fazel, Valdés Julio J., Liu Ziying, Lach Boleslaw. Data mining of gene expression changes in Alzheimer brain. Artif Intell Med. 2004 Jun;31(2):137–154. doi: 10.1016/j.artmed.2004.01.008. [DOI] [PubMed] [Google Scholar]
- Wallis John W., Aerts Jan, Groenen Martien A. M., Crooijmans Richard P. M. A., Layman Dan, Graves Tina A., Scheer Debra E., Kremitzki Colin, Fedele Mary J., Mudd Nancy K. A physical map of the chicken genome. Nature. 2004 Dec 9;432(7018):761–764. doi: 10.1038/nature03030. [DOI] [PubMed] [Google Scholar]
- Wang Jiren, Li Kuo-Bin, Sung Wing-Kin. G-PRIMER: greedy algorithm for selecting minimal primer set. Bioinformatics. 2004 Apr 8;20(15):2473–2475. doi: 10.1093/bioinformatics/bth259. [DOI] [PubMed] [Google Scholar]
- Wang Ju, Ma Jennie Z., Li Ming D. Normalization of cDNA microarray data using wavelet regressions. Comb Chem High Throughput Screen. 2004 Dec;7(8):783–791. doi: 10.2174/1386207043328274. [DOI] [PubMed] [Google Scholar]
- Wang Min-Long, Hsu Chia-Mei, Chang Liang-Chi, Wang Co-Shine, Su Ting-Ho, Huang Yih-Jong John, Jiang Liwen, Jauh Guang-Yuh. Gene expression profiles of cold-stored and fresh pollen to investigate pollen germination and growth. Plant Cell Physiol. 2004 Oct;45(10):1519–1528. doi: 10.1093/pcp/pch174. [DOI] [PubMed] [Google Scholar]
- Weber Griffin, Vinterbo Staal, Ohno-Machado Lucila. Multivariate selection of genetic markers in diagnostic classification. Artif Intell Med. 2004 Jun;31(2):155–167. doi: 10.1016/j.artmed.2004.01.011. [DOI] [PubMed] [Google Scholar]
- Williams Alexander G., Williams Robert W. GenomeMixer: a complex genetic cross simulator. Bioinformatics. 2004 Oct 12;20(15):2491–2492. doi: 10.1093/bioinformatics/bth269. [DOI] [PubMed] [Google Scholar]
- Williams Kenneth, Wu Terence, Colangelo Christopher, Nairn Angus C. Recent advances in neuroproteomics and potential application to studies of drug addiction. Neuropharmacology. 2004;47 (Suppl 1):148–166. doi: 10.1016/j.neuropharm.2004.07.009. [DOI] [PubMed] [Google Scholar]
- Wilson Ian D., Barker Gary L. A., Beswick Richard W., Shepherd Sophie K., Lu Chungui, Coghill Jane A., Edwards David, Owen Philippa, Lyons Rebecca, Parker Jill S. A transcriptomics resource for wheat functional genomics. Plant Biotechnol J. 2004 Nov;2(6):495–506. doi: 10.1111/j.1467-7652.2004.00096.x. [DOI] [PubMed] [Google Scholar]
- Wong Prudence W. H., Lam T. W., Lu N., Ting H. F., Yiu S. M. An efficient algorithm for optimizing whole genome alignment with noise. Bioinformatics. 2004 May 14;20(16):2676–2684. doi: 10.1093/bioinformatics/bth308. [DOI] [PubMed] [Google Scholar]
- Xia Qingyou, Zhou Zeyang, Lu Cheng, Cheng Daojun, Dai Fangyin, Li Bin, Zhao Ping, Zha Xingfu, Cheng Tingcai, Chai Chunli. A draft sequence for the genome of the domesticated silkworm (Bombyx mori). Science. 2004 Dec 10;306(5703):1937–1940. doi: 10.1126/science.1102210. [DOI] [PubMed] [Google Scholar]
- Yamakawa Seiyei, Ando Kohei, Chisaka Aya, Yoshida Kazuya, Shinmyo Atsuhiko, Kohchi Takayuki. Systematic transient assays of promoter activities for leaf-specific genes identified by gene-expression profiling with cDNA microarrays in Arabidopsis thaliana. J Biosci Bioeng. 2004;98(2):140–143. doi: 10.1016/S1389-1723(04)70257-1. [DOI] [PubMed] [Google Scholar]
- Yamamoto Satoko, Asanuma Takao, Takagi Toshihisa, Fukuda Ken Ichiro. The molecule role ontology: an ontology for annotation of signal transduction pathway molecules in the scientific literature. Comp Funct Genomics. 2004;5(6-7):528–536. doi: 10.1002/cfg.432. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Yamashita Taro, Honda Masao, Takatori Hajime, Nishino Ryuhei, Hoshino Nobuaki, Kaneko Shuichi. Genome-wide transcriptome mapping analysis identifies organ-specific gene expression patterns along human chromosomes. Genomics. 2004 Nov;84(5):867–875. doi: 10.1016/j.ygeno.2004.08.008. [DOI] [PubMed] [Google Scholar]
- Yan L., Ge H., Li H., Lieber S. C., Natividad F., Resuello R. R. G., Kim S-J, Akeju S., Sun A., Loo K. Gender-specific proteomic alterations in glycolytic and mitochondrial pathways in aging monkey hearts. J Mol Cell Cardiol. 2004 Nov;37(5):921–929. doi: 10.1016/j.yjmcc.2004.06.012. [DOI] [PubMed] [Google Scholar]
- Yang Zheng Rong. Mining gene expression data based on template theory. Bioinformatics. 2004 May 27;20(16):2759–2766. doi: 10.1093/bioinformatics/bth323. [DOI] [PubMed] [Google Scholar]
- Yeo Marie, Park Hyun-kyung, Kim Dong-Kyu, Cho Sung Won, Kim Young Suk, Cho Sang Yun, Paik Young-ki, Hahm Ki-Baik. Restoration of heat shock protein70 suppresses gastric mucosal inducible nitric oxide synthase expression induced by Helicobacter pylori. Proteomics. 2004 Nov;4(11):3335–3342. doi: 10.1002/pmic.200400951. [DOI] [PubMed] [Google Scholar]
- Yeo Sinkoo, Roh Gu Seob, Kim Dong-Hoon, Lee Jung Min, Seo Seong-Won, Cho Jin Won, Kim Chan-Wha, Kwack KyuBum. Quantitative profiling of plasma peptides in asthmatic mice using liquid chromatography and mass spectrometry. Proteomics. 2004 Nov;4(11):3308–3317. doi: 10.1002/pmic.200400918. [DOI] [PubMed] [Google Scholar]
- Yoo Changwon, Cooper Gregory F. An evaluation of a system that recommends microarray experiments to perform to discover gene-regulation pathways. Artif Intell Med. 2004 Jun;31(2):169–182. doi: 10.1016/j.artmed.2004.01.018. [DOI] [PubMed] [Google Scholar]
- Yu Ju-Kyung, Dake Trevor M., Singh Sukhwinder, Benscher David, Li Wanlong, Gill Bikram, Sorrells Mark E. Development and mapping of EST-derived simple sequence repeat markers for hexaploid wheat. Genome. 2004 Oct;47(5):805–818. doi: 10.1139/g04-057. [DOI] [PubMed] [Google Scholar]
- Yuan Jian-Ping, Li Tao, Chen Hua-Biao, Li Zhen-Hong, Yang Gui-Zhen, Hu Bao-Yu, Shi Xiao-Dong, Tong Shan-Qing, Li Yi-Xue, Guo Xiao-Kui. Analysis of gene expression profile in gastric cancer cells stimulated with Helicobacter pylori isogenic strains. J Med Microbiol. 2004 Oct;53(Pt 10):965–974. doi: 10.1099/jmm.0.45634-0. [DOI] [PubMed] [Google Scholar]
- Yuan Xianglin, Desiderio Dominic M. Human cerebrospinal fluid peptidomics. J Mass Spectrom. 2005 Feb;40(2):176–181. doi: 10.1002/jms.737. [DOI] [PubMed] [Google Scholar]
- Yuk Jong Seol, Jung Se-Hui, Jung Jae-Wan, Hong Duk-Geun, Han Jeong-A, Kim Young-Myeong, Ha Kwon-Soo. Analysis of protein interactions on protein arrays by a wavelength interrogation-based surface plasmon resonance biosensor. Proteomics. 2004 Nov;4(11):3468–3476. doi: 10.1002/pmic.200400879. [DOI] [PubMed] [Google Scholar]
- Zappacosta Francesca, Annan Roland S. N-terminal isotope tagging strategy for quantitative proteomics: results-driven analysis of protein abundance changes. Anal Chem. 2004 Nov 15;76(22):6618–6627. doi: 10.1021/ac049169b. [DOI] [PubMed] [Google Scholar]
- Zhang D., Choi D. W., Wanamaker S., Fenton R. D., Chin A., Malatrasi M., Turuspekov Y., Walia H., Akhunov E. D., Kianian P. Construction and evaluation of cDNA libraries for large-scale expressed sequence tag sequencing in wheat (Triticum aestivum L.). Genetics. 2004 Oct;168(2):595–608. doi: 10.1534/genetics.104.034785. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Zhang Shu-Dong, Gant Timothy W. A statistical framework for the design of microarray experiments and effective detection of differential gene expression. Bioinformatics. 2004 Jun 4;20(16):2821–2828. doi: 10.1093/bioinformatics/bth336. [DOI] [PubMed] [Google Scholar]
- Zhang Yan, Eberhard David A., Frantz Gretchen D., Dowd Patrick, Wu Thomas D., Zhou Yan, Watanabe Colin, Luoh Shiuh-Ming, Polakis Paul, Hillan Kenneth J. GEPIS--quantitative gene expression profiling in normal and cancer tissues. Bioinformatics. 2004 Apr 8;20(15):2390–2398. doi: 10.1093/bioinformatics/bth256. [DOI] [PubMed] [Google Scholar]
- Zhao Shaying, Shetty Jyoti, Hou Lihua, Delcher Arthur, Zhu Baoli, Osoegawa Kazutoyo, de Jong Pieter, Nierman William C., Strausberg Robert L., Fraser Claire M. Human, mouse, and rat genome large-scale rearrangements: stability versus speciation. Genome Res. 2004 Sep 13;14(10A):1851–1860. doi: 10.1101/gr.2663304. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Zhou Shiguo, Kile Andrew, Bechner Michael, Place Michael, Kvikstad Erika, Deng Wen, Wei Jun, Severin Jessica, Runnheim Rodney, Churas Christopher. Single-molecule approach to bacterial genomic comparisons via optical mapping. J Bacteriol. 2004 Nov;186(22):7773–7782. doi: 10.1128/JB.186.22.7773-7782.2004. [DOI] [PMC free article] [PubMed] [Google Scholar]
- de Fourmestraux Valérie, Neubauer Heike, Poussin Carine, Farmer Pierre, Falquet Laurent, Burcelin Rémy, Delorenzi Mauro, Thorens Bernard. Transcript profiling suggests that differential metabolic adaptation of mice to a high fat diet is associated with changes in liver to muscle lipid fluxes. J Biol Chem. 2004 Sep 17;279(49):50743–50753. doi: 10.1074/jbc.M408014200. [DOI] [PubMed] [Google Scholar]
- van den Berg Noëlani, Crampton Bridget G., Hein Ingo, Birch Paul R. J., Berger Dave K. High-throughput screening of suppression subtractive hybridization cDNA libraries using DNA microarray analysis. Biotechniques. 2004 Nov;37(5):818–824. doi: 10.2144/04375RR02. [DOI] [PubMed] [Google Scholar]
