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- Abee Tjakko, van Schaik Willem, Siezen Roland J. Impact of genomics on microbial food safety. Trends Biotechnol. 2004 Dec;22(12):653–660. doi: 10.1016/j.tibtech.2004.10.007. [DOI] [PubMed] [Google Scholar]
- Accardo M. C., Giordano E., Riccardo S., Digilio F. A., Iazzetti G., Calogero R. A., Furia M. A computational search for box C/D snoRNA genes in the Drosophila melanogaster genome. Bioinformatics. 2004 Jul 9;20(18):3293–3301. doi: 10.1093/bioinformatics/bth394. [DOI] [PubMed] [Google Scholar]
- Adur Javier, Uchide Tsuyoshi, Takizawa Satoshi, Quan Jiexia, Saida Kaname. Real-time polymerase chain reaction quantification of gene expression levels of murine endothelin-A and endothelin-B receptors: gene expression profiles by the standard curve method. J Cardiovasc Pharmacol. 2004 Nov;44 (Suppl 1):S321–S328. doi: 10.1097/01.fjc.0000166270.01926.00. [DOI] [PubMed] [Google Scholar]
- Aggarwal Amit, Leong Siew Hong, Lee Cheryl, Kon Oi Lian, Tan Patrick. Wavelet transformations of tumor expression profiles reveals a pervasive genome-wide imprinting of aneuploidy on the cancer transcriptome. Cancer Res. 2005 Jan 1;65(1):186–194. [PubMed] [Google Scholar]
- Alaoui-Jamali Moulay A., Dupré Isabelle, Qiang He. Prediction of drug sensitivity and drug resistance in cancer by transcriptional and proteomic profiling. Drug Resist Updat. 2004 Aug-Oct;7(4-5):245–255. doi: 10.1016/j.drup.2004.06.004. [DOI] [PubMed] [Google Scholar]
- Aldred Sarah, Grant Melissa M., Griffiths Helen R. The use of proteomics for the assessment of clinical samples in research. Clin Biochem. 2004 Nov;37(11):943–952. doi: 10.1016/j.clinbiochem.2004.09.002. [DOI] [PubMed] [Google Scholar]
- Anderle Markus, Roy Sushmita, Lin Hua, Becker Christopher, Joho Keith. Quantifying reproducibility for differential proteomics: noise analysis for protein liquid chromatography-mass spectrometry of human serum. Bioinformatics. 2004 Jul 29;20(18):3575–3582. doi: 10.1093/bioinformatics/bth446. [DOI] [PubMed] [Google Scholar]
- Anderson Steven P., Howroyd Paul, Liu Jie, Qian Xun, Bahnemann Rainer, Swanson Cynthia, Kwak Mi-Kyoung, Kensler Thomas W., Corton J. Christopher. The transcriptional response to a peroxisome proliferator-activated receptor alpha agonist includes increased expression of proteome maintenance genes. J Biol Chem. 2004 Sep 15;279(50):52390–52398. doi: 10.1074/jbc.M409347200. [DOI] [PubMed] [Google Scholar]
- Antonov Alexey V., Tetko Igor V., Prokopenko Volodymyr V., Kosykh Denis, Mewes Hans W. A web portal for classification of expression data using maximal margin linear programming. Bioinformatics. 2004 Jun 24;20(17):3284–3285. doi: 10.1093/bioinformatics/bth376. [DOI] [PubMed] [Google Scholar]
- Bae Kyounghwa, Mallick Bani K. Gene selection using a two-level hierarchical Bayesian model. Bioinformatics. 2004 Jul 15;20(18):3423–3430. doi: 10.1093/bioinformatics/bth419. [DOI] [PubMed] [Google Scholar]
- Baginsky Sacha, Siddique Asim, Gruissem Wilhelm. Proteome analysis of tobacco bright yellow-2 (BY-2) cell culture plastids as a model for undifferentiated heterotrophic plastids. J Proteome Res. 2004 Nov-Dec;3(6):1128–1137. doi: 10.1021/pr0499186. [DOI] [PubMed] [Google Scholar]
- Bailey Michael J., Beremand Phillip D., Hammer Rick, Reidel Elizabeth, Thomas Terry L., Cassone Vincent M. Transcriptional profiling of circadian patterns of mRNA expression in the chick retina. J Biol Chem. 2004 Sep 23;279(50):52247–52254. doi: 10.1074/jbc.M405679200. [DOI] [PubMed] [Google Scholar]
- Baird David, Johnstone Peter, Wilson Theresa. Normalization of microarray data using a spatial mixed model analysis which includes splines. Bioinformatics. 2004 Jul 1;20(17):3196–3205. doi: 10.1093/bioinformatics/bth384. [DOI] [PubMed] [Google Scholar]
- Balasubramanian Raji, LaFramboise Thomas, Scholtens Denise, Gentleman Robert. A graph-theoretic approach to testing associations between disparate sources of functional genomics data. Bioinformatics. 2004 Jul 15;20(18):3353–3362. doi: 10.1093/bioinformatics/bth405. [DOI] [PubMed] [Google Scholar]
- Baptista Cassio Silva, Vêncio Ricardo Z. N., Abdala Sarah, Valadares Maria Paula, Martins Camila, de Bragança Pereira Carlos Alberto, Zingales Bianca. DNA microarrays for comparative genomics and analysis of gene expression in Trypanosoma cruzi. Mol Biochem Parasitol. 2004 Dec;138(2):183–194. doi: 10.1016/j.molbiopara.2004.06.017. [DOI] [PubMed] [Google Scholar]
- Barad Omer, Meiri Eti, Avniel Amir, Aharonov Ranit, Barzilai Adi, Bentwich Isaac, Einav Uri, Gilad Shlomit, Hurban Patrick, Karov Yael. MicroRNA expression detected by oligonucleotide microarrays: system establishment and expression profiling in human tissues. Genome Res. 2004 Dec;14(12):2486–2494. doi: 10.1101/gr.2845604. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Barber David S., LoPachin Richard M. Proteomic analysis of acrylamide-protein adduct formation in rat brain synaptosomes. Toxicol Appl Pharmacol. 2004 Dec 1;201(2):120–136. doi: 10.1016/j.taap.2004.05.008. [DOI] [PubMed] [Google Scholar]
- Barglow Katherine T., Cravatt Benjamin F. Discovering disease-associated enzymes by proteome reactivity profiling. Chem Biol. 2004 Nov;11(11):1523–1531. doi: 10.1016/j.chembiol.2004.08.023. [DOI] [PubMed] [Google Scholar]
- Barrett Michael T., Scheffer Alicia, Ben-Dor Amir, Sampas Nick, Lipson Doron, Kincaid Robert, Tsang Peter, Curry Bo, Baird Kristin, Meltzer Paul S. Comparative genomic hybridization using oligonucleotide microarrays and total genomic DNA. Proc Natl Acad Sci U S A. 2004 Dec 10;101(51):17765–17770. doi: 10.1073/pnas.0407979101. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Barry Richard, Soloviev Mikhail. Quantitative protein profiling using antibody arrays. Proteomics. 2004 Dec;4(12):3717–3726. doi: 10.1002/pmic.200300877. [DOI] [PubMed] [Google Scholar]
- Basso Manuela, Giraudo Sabrina, Corpillo Davide, Bergamasco Bruno, Lopiano Leonardo, Fasano Mauro. Proteome analysis of human substantia nigra in Parkinson's disease. Proteomics. 2004 Dec;4(12):3943–3952. doi: 10.1002/pmic.200400848. [DOI] [PubMed] [Google Scholar]
- Bertone Paul, Stolc Viktor, Royce Thomas E., Rozowsky Joel S., Urban Alexander E., Zhu Xiaowei, Rinn John L., Tongprasit Waraporn, Samanta Manoj, Weissman Sherman. Global identification of human transcribed sequences with genome tiling arrays. Science. 2004 Nov 11;306(5705):2242–2246. doi: 10.1126/science.1103388. [DOI] [PubMed] [Google Scholar]
- Bettencourt-Dias M., Giet R., Sinka R., Mazumdar A., Lock W. G., Balloux F., Zafiropoulos P. J., Yamaguchi S., Winter S., Carthew R. W. Genome-wide survey of protein kinases required for cell cycle progression. Nature. 2004 Dec 23;432(7020):980–987. doi: 10.1038/nature03160. [DOI] [PubMed] [Google Scholar]
- Bhattacharjee Madhuchhanda, Pritchard Colin C., Nelson Peter S., Arjas Elja. Bayesian integrated functional analysis of microarray data. Bioinformatics. 2004 Jun 4;20(17):2943–2953. doi: 10.1093/bioinformatics/bth338. [DOI] [PubMed] [Google Scholar]
- Bibikova Marina, Yeakley Joanne M., Chudin Eugene, Chen Jing, Wickham Eliza, Wang-Rodriguez Jessica, Fan Jian-Bing. Gene expression profiles in formalin-fixed, paraffin-embedded tissues obtained with a novel assay for microarray analysis. Clin Chem. 2004 Dec;50(12):2384–2386. doi: 10.1373/clinchem.2004.037432. [DOI] [PubMed] [Google Scholar]
- Bilbao-Castro J. R., Sorzano C. O. S., García I., Fernández J. J. Phan3D: design of biological phantoms in 3D electron microscopy. Bioinformatics. 2004 Jun 24;20(17):3286–3288. doi: 10.1093/bioinformatics/bth377. [DOI] [PubMed] [Google Scholar]
- Blanchette Mathieu, Green Eric D., Miller Webb, Haussler David. Reconstructing large regions of an ancestral mammalian genome in silico. Genome Res. 2004 Dec;14(12):2412–2423. doi: 10.1101/gr.2800104. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Blinov Michael L., Faeder James R., Goldstein Byron, Hlavacek William S. BioNetGen: software for rule-based modeling of signal transduction based on the interactions of molecular domains. Bioinformatics. 2004 Jun 24;20(17):3289–3291. doi: 10.1093/bioinformatics/bth378. [DOI] [PubMed] [Google Scholar]
- Bobek Jan, Halada Petr, Angelis Jakub, Vohradský Jiri, Mikulík Karel. Activation and expression of proteins during synchronous germination of aerial spores of Streptomyces granaticolor. Proteomics. 2004 Dec;4(12):3864–3880. doi: 10.1002/pmic.200400818. [DOI] [PubMed] [Google Scholar]
- Boffelli Dario, Weer Claire V., Weng Li, Lewis Keith D., Shoukry Malak I., Pachter Lior, Keys David N., Rubin Edward M. Intraspecies sequence comparisons for annotating genomes. Genome Res. 2004 Nov 15;14(12):2406–2411. doi: 10.1101/gr.3199704. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Bolotin Alexander, Quinquis Benoît, Renault Pierre, Sorokin Alexei, Ehrlich S. Dusko, Kulakauskas Saulius, Lapidus Alla, Goltsman Eugene, Mazur Michael, Pusch Gordon D. Complete sequence and comparative genome analysis of the dairy bacterium Streptococcus thermophilus. Nat Biotechnol. 2004 Nov 14;22(12):1554–1558. doi: 10.1038/nbt1034. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Booth Stephanie, Bowman Christopher, Baumgartner Richard, Dolenko Brion, Sorensen Garrett, Robertson Catherine, Coulthart Michael, Phillipson Clark, Somorjai Rajmund. Molecular classification of scrapie strains in mice using gene expression profiling. Biochem Biophys Res Commun. 2004 Dec 24;325(4):1339–1345. doi: 10.1016/j.bbrc.2004.10.150. [DOI] [PubMed] [Google Scholar]
- Bouwman Freek, Renes Johan, Mariman Edwin. A combination of protein profiling and isotopomer analysis using matrix-assisted laser desorption/ionization-time of flight mass spectrometry reveals an active metabolism of the extracellular matrix of 3T3-L1 adipocytes. Proteomics. 2004 Dec;4(12):3855–3863. doi: 10.1002/pmic.200400861. [DOI] [PubMed] [Google Scholar]
- Boyle Elizabeth I., Weng Shuai, Gollub Jeremy, Jin Heng, Botstein David, Cherry J. Michael, Sherlock Gavin. GO::TermFinder--open source software for accessing Gene Ontology information and finding significantly enriched Gene Ontology terms associated with a list of genes. Bioinformatics. 2004 Aug 5;20(18):3710–3715. doi: 10.1093/bioinformatics/bth456. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Brinkmann Henner, Denk Angelika, Zitzler Jürgen, Joss Jean J., Meyer Axel. Complete mitochondrial genome sequences of the South american and the Australian lungfish: testing of the phylogenetic performance of mitochondrial data sets for phylogenetic problems in tetrapod relationships. J Mol Evol. 2004 Dec;59(6):834–848. doi: 10.1007/s00239-004-0122-8. [DOI] [PubMed] [Google Scholar]
- Bronstein Philip, Marrichi Matthew, DeLisa Matthew P. Dissecting the twin-arginine translocation pathway using genome-wide analysis. Res Microbiol. 2004 Dec;155(10):803–810. doi: 10.1016/j.resmic.2004.06.013. [DOI] [PubMed] [Google Scholar]
- Buehler Eugen C., Sachs Jeffrey R., Shao Kui, Bagchi Ansuman, Ungar Lyle H. The CRASSS plug-in for integrating annotation data with hierarchical clustering results. Bioinformatics. 2004 Jun 16;20(17):3266–3269. doi: 10.1093/bioinformatics/bth362. [DOI] [PubMed] [Google Scholar]
- Buisine Nicolas, Chalmers Ronald. yBlast, a graphical front end for the standalone BLAST suite. Biotechniques. 2004 Dec;37(6):987–989. doi: 10.2144/04376BIN01. [DOI] [PubMed] [Google Scholar]
- Canaves Jaume M., Page Rebecca, Wilson Ian A., Stevens Raymond C. Protein biophysical properties that correlate with crystallization success in Thermotoga maritima: maximum clustering strategy for structural genomics. J Mol Biol. 2004 Dec 3;344(4):977–991. doi: 10.1016/j.jmb.2004.09.076. [DOI] [PubMed] [Google Scholar]
- Carter Clay, Pan Songqin, Zouhar Jan, Avila Emily L., Girke Thomas, Raikhel Natasha V. The vegetative vacuole proteome of Arabidopsis thaliana reveals predicted and unexpected proteins. Plant Cell. 2004 Nov 11;16(12):3285–3303. doi: 10.1105/tpc.104.027078. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Carucci Daniel J. Plasmodium post-genomics: an update. Trends Parasitol. 2004 Dec;20(12):558–561. doi: 10.1016/j.pt.2004.09.007. [DOI] [PubMed] [Google Scholar]
- Chan Steven M., Ermann Joerg, Su Leon, Fathman C. Garrison, Utz Paul J. Protein microarrays for multiplex analysis of signal transduction pathways. Nat Med. 2004 Nov 21;10(12):1390–1396. doi: 10.1038/nm1139. [DOI] [PubMed] [Google Scholar]
- Chandonia John-Marc, Brenner Steven E. Implications of structural genomics target selection strategies: Pfam5000, whole genome, and random approaches. Proteins. 2005 Jan 1;58(1):166–179. doi: 10.1002/prot.20298. [DOI] [PubMed] [Google Scholar]
- Chang Jinsook, Van Remmen Holly, Ward Walter F., Regnier Fred E., Richardson Arlan, Cornell John. Processing of data generated by 2-dimensional gel electrophoresis for statistical analysis: missing data, normalization, and statistics. J Proteome Res. 2004 Nov-Dec;3(6):1210–1218. doi: 10.1021/pr049886m. [DOI] [PubMed] [Google Scholar]
- Chen Jenn-Han, Chang Yu-Wang, Yao Chen-Wen, Chiueh Tzong-Shi, Huang Su-Chin, Chien Ko-Yi, Chen An, Chang Feng-Yee, Wong Chi-Huey, Chen Yu-Ju. Plasma proteome of severe acute respiratory syndrome analyzed by two-dimensional gel electrophoresis and mass spectrometry. Proc Natl Acad Sci U S A. 2004 Nov 30;101(49):17039–17044. doi: 10.1073/pnas.0407992101. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Chen Yu, Xu Dong. Global protein function annotation through mining genome-scale data in yeast Saccharomyces cerevisiae. Nucleic Acids Res. 2004 Dec 7;32(21):6414–6424. doi: 10.1093/nar/gkh978. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Chibani-Chennoufi Sandra, Canchaya Carlos, Bruttin Anne, Brüssow Harald. Comparative genomics of the T4-Like Escherichia coli phage JS98: implications for the evolution of T4 phages. J Bacteriol. 2004 Dec;186(24):8276–8286. doi: 10.1128/JB.186.24.8276-8286.2004. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Chiorino G., Acquadro F., Mello Grand M., Viscomi S., Segir R., Gasparini M., Dotto P. Interpretation of expression-profiling results obtained from different platforms and tissue sources: examples using prostate cancer data. Eur J Cancer. 2004 Nov;40(17):2592–2603. doi: 10.1016/j.ejca.2004.07.029. [DOI] [PubMed] [Google Scholar]
- Chou Kuo-Chen. Molecular therapeutic target for type-2 diabetes. J Proteome Res. 2004 Nov-Dec;3(6):1284–1288. doi: 10.1021/pr049849v. [DOI] [PubMed] [Google Scholar]
- Chromy Brett A., Gonzales Arlene D., Perkins Julie, Choi Megan W., Corzett Michele H., Chang Brian C., Corzett Christopher H., McCutchen-Maloney Sandra L. Proteomic analysis of human serum by two-dimensional differential gel electrophoresis after depletion of high-abundant proteins. J Proteome Res. 2004 Nov-Dec;3(6):1120–1127. doi: 10.1021/pr049921p. [DOI] [PubMed] [Google Scholar]
- Chuang Trees-Juen, Chen Feng-Chi, Chou Meng-Yuan. A comparative method for identification of gene structures and alternatively spliced variants. Bioinformatics. 2004 Jun 24;20(17):3064–3079. doi: 10.1093/bioinformatics/bth368. [DOI] [PubMed] [Google Scholar]
- Clarke Paul A., te Poele Robert, Workman Paul. Gene expression microarray technologies in the development of new therapeutic agents. Eur J Cancer. 2004 Nov;40(17):2560–2591. doi: 10.1016/j.ejca.2004.07.024. [DOI] [PubMed] [Google Scholar]
- Colland Frédéric, Daviet Laurent. Integrating a functional proteomic approach into the target discovery process. Biochimie. 2004 Sep-Oct;86(9-10):625–632. doi: 10.1016/j.biochi.2004.09.014. [DOI] [PubMed] [Google Scholar]
- Cooper Jonathan W., Wang Yueju, Lee Cheng S. Recent advances in capillary separations for proteomics. Electrophoresis. 2004 Dec;25(23-24):3913–3926. doi: 10.1002/elps.200406154. [DOI] [PubMed] [Google Scholar]
- Coppel Ross L., Roos David S., Bozdech Zbynek. The genomics of malaria infection. Trends Parasitol. 2004 Dec;20(12):553–557. doi: 10.1016/j.pt.2004.10.002. [DOI] [PubMed] [Google Scholar]
- Craig Robertson, Cortens John P., Beavis Ronald C. Open source system for analyzing, validating, and storing protein identification data. J Proteome Res. 2004 Nov-Dec;3(6):1234–1242. doi: 10.1021/pr049882h. [DOI] [PubMed] [Google Scholar]
- Craven Rachel A., Stanley Anthea J., Hanrahan Sarah, Totty Nick, Jackson David P., Popescu Razvan, Taylor Allen, Frey Jürgen, Selby Peter J., Patel Poulam M. Identification of proteins regulated by interferon-alpha in resistant and sensitive malignant melanoma cell lines. Proteomics. 2004 Dec;4(12):3998–4009. doi: 10.1002/pmic.200400870. [DOI] [PubMed] [Google Scholar]
- Davezac Noélie, Tondelier Danielle, Lipecka Joanna, Fanen Pascale, Demaugre France, Debski Janusz, Dadlez Michal, Schrattenholz André, Cahill Michael A., Edelman Aleksander. Global proteomic approach unmasks involvement of keratins 8 and 18 in the delivery of cystic fibrosis transmembrane conductance regulator (CFTR)/deltaF508-CFTR to the plasma membrane. Proteomics. 2004 Dec;4(12):3833–3844. doi: 10.1002/pmic.200400850. [DOI] [PubMed] [Google Scholar]
- Deshane Jessy, Chaves Lisa, Sarikonda Kiran Varma, Isbell Scott, Wilson Landon, Kirk Marion, Grubbs Clinton, Barnes Stephen, Meleth Sreelatha, Kim Helen. Proteomics analysis of rat brain protein modulations by grape seed extract. J Agric Food Chem. 2004 Dec 29;52(26):7872–7883. doi: 10.1021/jf040407d. [DOI] [PubMed] [Google Scholar]
- Dettling Marcel. BagBoosting for tumor classification with gene expression data. Bioinformatics. 2004 Oct 5;20(18):3583–3593. doi: 10.1093/bioinformatics/bth447. [DOI] [PubMed] [Google Scholar]
- Diehl Daniela, Lahm Harald, Wolf Eckhard, Bauersachs Stefan. Transcriptome analysis of a human colorectal cancer cell line shows molecular targets of insulin-like growth factor-binding protein-4 overexpression. Int J Cancer. 2005 Feb 10;113(4):588–599. doi: 10.1002/ijc.20580. [DOI] [PubMed] [Google Scholar]
- Ding Li, Sabo Aniko, Berkowicz Nicolas, Meyer Rekha R., Shotland Yoram, Johnson Mark R., Pepin Kymberlie H., Wilson Richard K., Spieth John. EAnnot: a genome annotation tool using experimental evidence. Genome Res. 2004 Dec;14(12):2503–2509. doi: 10.1101/gr.3152604. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Doerks Tobias, von Mering Christian, Bork Peer. Functional clues for hypothetical proteins based on genomic context analysis in prokaryotes. Nucleic Acids Res. 2004 Dec 1;32(21):6321–6326. doi: 10.1093/nar/gkh973. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Dowsey Andrew W., Dunn Michael J., Yang Guang-Zhong. ProteomeGRID: towards a high-throughput proteomics pipeline through opportunistic cluster image computing for two-dimensional gel electrophoresis. Proteomics. 2004 Dec;4(12):3800–3812. doi: 10.1002/pmic.200300894. [DOI] [PubMed] [Google Scholar]
- Dragomir Andrei, Mavroudi Seferina, Bezerianos Anastasios. Som-based class discovery exploring the ICA-reduced features of microarray expression profiles. Comp Funct Genomics. 2004;5(8):596–616. doi: 10.1002/cfg.444. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Durinck Steffen, Allemeersch Joke, Carey Vincent J., Moreau Yves, De Moor Bart. Importing MAGE-ML format microarray data into BioConductor. Bioinformatics. 2004 Jul 15;20(18):3641–3642. doi: 10.1093/bioinformatics/bth396. [DOI] [PubMed] [Google Scholar]
- Ebert Matthias P. A., Meuer Jörn, Wiemer Jan C., Schulz Hans-Ulrich, Reymond Marc A., Traugott Ulrich, Malfertheiner Peter, Röcken Christoph. Identification of gastric cancer patients by serum protein profiling. J Proteome Res. 2004 Nov-Dec;3(6):1261–1266. doi: 10.1021/pr049865s. [DOI] [PubMed] [Google Scholar]
- Egertsdotter U., van Zyl L. M., MacKay J., Peter G., Kirst M., Clark C., Whetten R., Sederoff R. Gene expression during formation of earlywood and latewood in loblolly pine: expression profiles of 350 genes. Plant Biol (Stuttg) 2004 Nov;6(6):654–663. doi: 10.1055/s-2004-830383. [DOI] [PubMed] [Google Scholar]
- Eilbeck Karen, Lewis Suzanna E. Sequence ontology annotation guide. Comp Funct Genomics. 2004;5(8):642–647. doi: 10.1002/cfg.446. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Eisenberger Sabine, Hoppe Godehard, Pyerin Walter, Ackermann Karin. High-quality RNA preparation for transcript profiling of osteocytes from native human bone microdissections. Anal Biochem. 2004 Dec 15;335(2):260–266. doi: 10.1016/j.ab.2004.09.037. [DOI] [PubMed] [Google Scholar]
- Elliott Steven T., Crider David G., Garnham Christopher P., Garham Christopher P., Boheler Kenneth R., Van Eyk Jennifer E. Two-dimensional gel electrophoresis database of murine R1 embryonic stem cells. Proteomics. 2004 Dec;4(12):3813–3832. doi: 10.1002/pmic.200300820. [DOI] [PubMed] [Google Scholar]
- Fahey Marie E., Mills Walter, Higgins Desmond G., Moore Tom. Maternally and paternally silenced imprinted genes differ in their intron content. Comp Funct Genomics. 2004;5(8):572–583. doi: 10.1002/cfg.437. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Feezor Robert J., Baker Henry V., Mindrinos Michael, Hayden Doug, Tannahill Cynthia L., Brownstein Bernard H., Fay Adrian, MacMillan Sandra, Laramie Jason, Xiao Wenzhong. Whole blood and leukocyte RNA isolation for gene expression analyses. Physiol Genomics. 2004 Nov 17;19(3):247–254. doi: 10.1152/physiolgenomics.00020.2004. [DOI] [PubMed] [Google Scholar]
- Feng WangSen, Wang Lusheng, Zhu Daming. CTRD: a fast applet for computing signed translocation distance between genomes. Bioinformatics. 2004 Jun 16;20(17):3256–3257. doi: 10.1093/bioinformatics/bth356. [DOI] [PubMed] [Google Scholar]
- Finley David J., Zhu Baixin, Fahey Thomas J., 3rd Molecular analysis of Hurthle cell neoplasms by gene profiling. Surgery. 2004 Dec;136(6):1160–1168. doi: 10.1016/j.surg.2004.05.061. [DOI] [PubMed] [Google Scholar]
- Finocchiaro Giacomo, Parise Paola, Minardi Simone P., Alcalay Myriam, Müller Heiko. GenePicker: replicate analysis of Affymetrix gene expression microarrays. Bioinformatics. 2004 Jul 15;20(18):3670–3672. doi: 10.1093/bioinformatics/bth416. [DOI] [PubMed] [Google Scholar]
- Fleet James C. Genomic and proteomic approaches for probing the role of vitamin D in health. Am J Clin Nutr. 2004 Dec;80(6 Suppl):1730S–1734S. doi: 10.1093/ajcn/80.6.1730S. [DOI] [PubMed] [Google Scholar]
- Flower Darren R., Attwood Teresa K. Integrative bioinformatics for functional genome annotation: trawling for G protein-coupled receptors. Semin Cell Dev Biol. 2004 Dec;15(6):693–701. doi: 10.1016/j.semcdb.2004.09.008. [DOI] [PubMed] [Google Scholar]
- Fragoso Gilberto, de Coronado Sherri, Haber Margaret, Hartel Frank, Wright Larry. Overview and utilization of the NCI thesaurus. Comp Funct Genomics. 2004;5(8):648–654. doi: 10.1002/cfg.445. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Fukushima Noriyoshi, Sato Norihiro, Prasad Nijaguna, Leach Steven D., Hruban Ralph H., Goggins Michael. Characterization of gene expression in mucinous cystic neoplasms of the pancreas using oligonucleotide microarrays. Oncogene. 2004 Dec 2;23(56):9042–9051. doi: 10.1038/sj.onc.1208117. [DOI] [PubMed] [Google Scholar]
- Fung Kim Y. C., Morris Carol, Sathe Sonal, Sack Robert, Duncan Mark W. Characterization of the in vivo forms of lacrimal-specific proline-rich proteins in human tear fluid. Proteomics. 2004 Dec;4(12):3953–3959. doi: 10.1002/pmic.200300849. [DOI] [PubMed] [Google Scholar]
- Gabaldón Toni, Huynen Martijn A. Shaping the mitochondrial proteome. Biochim Biophys Acta. 2004 Dec 6;1659(2-3):212–220. doi: 10.1016/j.bbabio.2004.07.011. [DOI] [PubMed] [Google Scholar]
- Galvin James E., Ginsberg Stephen D. Expression profiling and pharmacotherapeutic development in the central nervous system. Alzheimer Dis Assoc Disord. 2004 Oct-Dec;18(4):264–269. [PubMed] [Google Scholar]
- Gauthier Daniel J., Gibbs Bernard F., Rabah Nadia, Lazure Claude. Utilization of a new biotinylation reagent in the development of a nondiscriminatory investigative approach for the study of cell surface proteins. Proteomics. 2004 Dec;4(12):3783–3790. doi: 10.1002/pmic.200300860. [DOI] [PubMed] [Google Scholar]
- Giannone S., Strippoli P., Vitale L., Casadei R., Canaider S., Lenzi L., D'Addabbo P., Frabetti F., Facchin F., Farina A. Gene expression profile analysis in human T lymphocytes from patients with Down Syndrome. Ann Hum Genet. 2004 Nov;68(Pt 6):546–554. doi: 10.1046/j.1529-8817.2003.00123.x. [DOI] [PubMed] [Google Scholar]
- Gilbert Don, Ugawa Yoshihiro, Buchhorn Markus, Wee Tan Tin, Mizushima Akira, Kim Hyunchul, Chon Kilnam, Weon Seyeon, Ma Juncai, Ichiyanagi Yoshihiro. Bio-Mirror project for public bio-data distribution. Bioinformatics. 2004 Apr 1;20(17):3238–3240. doi: 10.1093/bioinformatics/bth219. [DOI] [PubMed] [Google Scholar]
- Gilchrist Michael J., Zorn Aaron M., Voigt Jana, Smith James C., Papalopulu Nancy, Amaya Enrique. Defining a large set of full-length clones from a Xenopus tropicalis EST project. Dev Biol. 2004 Jul 15;271(2):498–516. doi: 10.1016/j.ydbio.2004.04.023. [DOI] [PubMed] [Google Scholar]
- Girolami Mark, Breitling Rainer. Biologically valid linear factor models of gene expression. Bioinformatics. 2004 Jun 16;20(17):3021–3033. doi: 10.1093/bioinformatics/bth354. [DOI] [PubMed] [Google Scholar]
- Gisel Andreas, Panetta Maria, Grillo Giorgio, Licciulli Vito Flavio, Liuni Sabino, Saccone Cecilia, Pesole Graziano. DNAfan: a software tool for automated extraction and analysis of user-defined sequence regions. Bioinformatics. 2004 Jul 15;20(18):3676–3679. doi: 10.1093/bioinformatics/bth420. [DOI] [PubMed] [Google Scholar]
- Glas Annuska M., Kersten Marie José, Delahaye Leonie J. M. J., Witteveen Anke T., Kibbelaar Robby E., Velds Arno, Wessels Lodewyk F. A., Joosten Peter, Kerkhoven Ron M., Bernards René. Gene expression profiling in follicular lymphoma to assess clinical aggressiveness and to guide the choice of treatment. Blood. 2004 Sep 2;105(1):301–307. doi: 10.1182/blood-2004-06-2298. [DOI] [PubMed] [Google Scholar]
- Goble Carole, Wroe Chris. The Montagues and the Capulets. Comp Funct Genomics. 2004;5(8):623–632. doi: 10.1002/cfg.442. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Golpon Heiko A., Coldren Christopher D., Zamora Martin R., Cosgrove Gregory P., Moore Mark D., Tuder Rubin M., Geraci Mark W., Voelkel Norbert F. Emphysema lung tissue gene expression profiling. Am J Respir Cell Mol Biol. 2004 Jul 29;31(6):595–600. doi: 10.1165/rcmb.2004-0008OC. [DOI] [PubMed] [Google Scholar]
- Goodchild Amber, Raftery Mark, Saunders Neil F. W., Guilhaus Michael, Cavicchioli Ricardo. Biology of the cold adapted archaeon, Methanococcoides burtonii determined by proteomics using liquid chromatography-tandem mass spectrometry. J Proteome Res. 2004 Nov-Dec;3(6):1164–1176. doi: 10.1021/pr0498988. [DOI] [PubMed] [Google Scholar]
- Gracey Andrew Y., Fraser E. Jane, Li Weizhong, Fang Yongxiang, Taylor Ruth R., Rogers Jane, Brass Andrew, Cossins Andrew R. Coping with cold: An integrative, multitissue analysis of the transcriptome of a poikilothermic vertebrate. Proc Natl Acad Sci U S A. 2004 Nov 18;101(48):16970–16975. doi: 10.1073/pnas.0403627101. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Graham W. Vallen, Tcheng David K., Shirk Andrew L., Attene-Ramos Matias S., Welge Michael E., Gaskins H. Rex. Phylomat: an automated protein motif analysis tool for phylogenomics. J Proteome Res. 2004 Nov-Dec;3(6):1289–1291. doi: 10.1021/pr0499040. [DOI] [PubMed] [Google Scholar]
- Gu Sheng, Du Yuchun, Chen Jin, Liu Zhihe, Bradbury E. Morton, Hu Chien-An A., Chen Xian. Large-scale quantitative proteomic study of PUMA-induced apoptosis using two-dimensional liquid chromatography-mass spectrometry coupled with amino acid-coded mass tagging. J Proteome Res. 2004 Nov-Dec;3(6):1191–1200. doi: 10.1021/pr049893a. [DOI] [PubMed] [Google Scholar]
- Gustafsson John S., Ceasar Robert, Glasbey Chris A., Blomberg Anders, Rudemo Mats. Statistical exploration of variation in quantitative two-dimensional gel electrophoresis data. Proteomics. 2004 Dec;4(12):3791–3799. doi: 10.1002/pmic.200300824. [DOI] [PubMed] [Google Scholar]
- Görg Angelika, Weiss Walter, Dunn Michael J. Current two-dimensional electrophoresis technology for proteomics. Proteomics. 2004 Dec;4(12):3665–3685. doi: 10.1002/pmic.200401031. [DOI] [PubMed] [Google Scholar]
- Haas Brian J., Delcher Arthur L., Wortman Jennifer R., Salzberg Steven L. DAGchainer: a tool for mining segmental genome duplications and synteny. Bioinformatics. 2004 Jul 9;20(18):3643–3646. doi: 10.1093/bioinformatics/bth397. [DOI] [PubMed] [Google Scholar]
- Hallin Peter F., Ussery David W. CBS Genome Atlas Database: a dynamic storage for bioinformatic results and sequence data. Bioinformatics. 2004 Jul 15;20(18):3682–3686. doi: 10.1093/bioinformatics/bth423. [DOI] [PubMed] [Google Scholar]
- Handelsman Jo. Metagenomics: application of genomics to uncultured microorganisms. Microbiol Mol Biol Rev. 2004 Dec;68(4):669–685. doi: 10.1128/MMBR.68.4.669-685.2004. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Haverty Peter M., Hsiao Li-Li, Gullans Steven R., Hansen Ulla, Weng Zhiping. Limited agreement among three global gene expression methods highlights the requirement for non-global validation. Bioinformatics. 2004 Jul 15;20(18):3431–3441. doi: 10.1093/bioinformatics/bth421. [DOI] [PubMed] [Google Scholar]
- Hecker Michael, Völker Uwe. Towards a comprehensive understanding of Bacillus subtilis cell physiology by physiological proteomics. Proteomics. 2004 Dec;4(12):3727–3750. doi: 10.1002/pmic.200401017. [DOI] [PubMed] [Google Scholar]
- Henke R. T., Maitra A., Paik S., Wellstein A. Gene expression analysis in sections and tissue microarrays of archival tissues by mRNA in situ hybridization. Histol Histopathol. 2005 Jan;20(1):225–237. doi: 10.14670/HH-20.225. [DOI] [PubMed] [Google Scholar]
- Hitte Christophe, Derrien Thomas, André Catherine, Ostrander Elaine A., Galibert Francis. CRH_Server: an online comparative and radiation hybrid mapping server for the canine genome. Bioinformatics. 2004 Jul 15;20(18):3665–3667. doi: 10.1093/bioinformatics/bth411. [DOI] [PubMed] [Google Scholar]
- Hochholdinger Frank, Guo Ling, Schnable Patrick S. Lateral roots affect the proteome of the primary root of maize (Zea mays L.). Plant Mol Biol. 2004 Oct;56(3):397–412. doi: 10.1007/s11103-004-3476-9. [DOI] [PubMed] [Google Scholar]
- Hornbaek Tina, Jakobsen Mogens, Dynesen Jens, Nielsen Allan K. Global transcription profiles and intracellular pH regulation measured in Bacillus licheniformis upon external pH upshifts. Arch Microbiol. 2004 Sep 10;182(6):467–474. doi: 10.1007/s00203-004-0729-6. [DOI] [PubMed] [Google Scholar]
- Hsiao A., Worrall D. S., Olefsky J. M., Subramaniam S. Variance-modeled posterior inference of microarray data: detecting gene-expression changes in 3T3-L1 adipocytes. Bioinformatics. 2004 Jun 24;20(17):3108–3127. doi: 10.1093/bioinformatics/bth371. [DOI] [PubMed] [Google Scholar]
- Hsu Jue-Liang, Chou Mong-Kuan, Liang Shih-Shin, Huang Sheng-Yu, Wu Chin-Jen, Shi Fong-Ku, Chen Shu-Hui. Photopolymerized microtips for sample preparation in proteomic analysis. Electrophoresis. 2004 Nov;25(21-22):3840–3847. doi: 10.1002/elps.200406078. [DOI] [PubMed] [Google Scholar]
- Huang Jing, Zhu Heng, Haggarty Stephen J., Spring David R., Hwang Heejun, Jin Fulai, Snyder Michael, Schreiber Stuart L. Finding new components of the target of rapamycin (TOR) signaling network through chemical genetics and proteome chips. Proc Natl Acad Sci U S A. 2004 Nov 11;101(47):16594–16599. doi: 10.1073/pnas.0407117101. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Huang Tao-Wei, Tien An-Chi, Huang Wen-Shien, Lee Yuan-Chii G., Peng Chin-Lin, Tseng Huei-Hun, Kao Cheng-Yan, Huang Chi-Ying F. POINT: a database for the prediction of protein-protein interactions based on the orthologous interactome. Bioinformatics. 2004 Jun 24;20(17):3273–3276. doi: 10.1093/bioinformatics/bth366. [DOI] [PubMed] [Google Scholar]
- Huber Christian G., Walcher Wolfgang, Timperio Anna-Maria, Troiani Sonia, Porceddu Andrea, Zolla Lello. Multidimensional proteomic analysis of photosynthetic membrane proteins by liquid extraction-ultracentrifugation-liquid chromatography-mass spectrometry. Proteomics. 2004 Dec;4(12):3909–3920. doi: 10.1002/pmic.200400823. [DOI] [PubMed] [Google Scholar]
- Hughes Austin L., Friedman Robert. Shedding genomic ballast: extensive parallel loss of ancestral gene families in animals. J Mol Evol. 2004 Dec;59(6):827–833. doi: 10.1007/s00239-004-0115-7. [DOI] [PubMed] [Google Scholar]
- Hupé Philippe, Stransky Nicolas, Thiery Jean-Paul, Radvanyi François, Barillot Emmanuel. Analysis of array CGH data: from signal ratio to gain and loss of DNA regions. Bioinformatics. 2004 Sep 20;20(18):3413–3422. doi: 10.1093/bioinformatics/bth418. [DOI] [PubMed] [Google Scholar]
- Inoue Yasuhiro, Shirane Masatoshi, Miki Chikao, Hiro Junichiro, Tanaka Koji, Kobayashi Minako, Mori Kazushige, Yanagi Hidenori, Kusunoki Masato. Gene expression profiles of colorectal carcinoma in response to neo-adjuvant chemotherapy. Int J Oncol. 2004 Dec;25(6):1641–1649. [PubMed] [Google Scholar]
- Ivshina Anna V., Vodeiko Galina M., Kuznetsov Vladimir A., Volokhov Dmitry, Taffs Rolf, Chizhikov Vladimir I., Levandowski Roland A., Chumakov Konstantin M. Mapping of genomic segments of influenza B virus strains by an oligonucleotide microarray method. J Clin Microbiol. 2004 Dec;42(12):5793–5801. doi: 10.1128/JCM.42.12.5793-5801.2004. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Iwaki Hideaki, Kageyama Susumu, Isono Takahiro, Wakabayashi Yoshihiko, Okada Yusaku, Yoshimura Koji, Terai Akito, Arai Yoichi, Iwamura Hiroshi, Kawakita Mutsushi. Diagnostic potential in bladder cancer of a panel of tumor markers (calreticulin, gamma -synuclein, and catechol-o-methyltransferase) identified by proteomic analysis. Cancer Sci. 2004 Dec;95(12):955–961. doi: 10.1111/j.1349-7006.2004.tb03183.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Jensen Patricia, Magdaleno Susan, Lehman Karen M., Rice Dennis S., Lavallie Edward R., Collins-Racie Lisa, McCoy J. M., Curran Tom. A neurogenomics approach to gene expression analysis in the developing brain. Brain Res Mol Brain Res. 2004 Dec 20;132(2):116–127. doi: 10.1016/j.molbrainres.2004.10.002. [DOI] [PubMed] [Google Scholar]
- Jeyaseelan Samithamby, Chu Hong Wei, Young Scott K., Worthen G. Scott. Transcriptional profiling of lipopolysaccharide-induced acute lung injury. Infect Immun. 2004 Dec;72(12):7247–7256. doi: 10.1128/IAI.72.12.7247-7256.2004. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Jong Kees, Marchiori Elena, Meijer Gerrit, Vaart A. V. D., Ylstra Bauke. Breakpoint identification and smoothing of array comparative genomic hybridization data. Bioinformatics. 2004 Jun 16;20(18):3636–3637. doi: 10.1093/bioinformatics/bth355. [DOI] [PubMed] [Google Scholar]
- Kaluszka Aaron, Gibas Cynthia. Interactive gene-order comparison for multiple small genomes. Bioinformatics. 2004 Jul 15;20(18):3662–3664. doi: 10.1093/bioinformatics/bth406. [DOI] [PubMed] [Google Scholar]
- Kamat Aparna A., Younes Pamela S., Sayeeduddin Mohammad, Wheeler Thomas M., Simpson Joe Leigh, Agoulnik Alexander I. Protein expression profiling of endometriosis: validation of 2-mm tissue microarrays. Fertil Steril. 2004 Dec;82(6):1681–1683. doi: 10.1016/j.fertnstert.2004.06.044. [DOI] [PubMed] [Google Scholar]
- Kanski Jaroslaw, Behring Antje, Pelling Jill, Schöneich Christian. Proteomic identification of 3-nitrotyrosine-containing rat cardiac proteins: effects of biological aging. Am J Physiol Heart Circ Physiol. 2004 Sep 2;288(1):H371–H381. doi: 10.1152/ajpheart.01030.2003. [DOI] [PubMed] [Google Scholar]
- Karlsson Christine, Korayem Ahmed M., Scherfer Christoph, Loseva Olga, Dushay Mitchell S., Theopold Ulrich. Proteomic analysis of the Drosophila larval hemolymph clot. J Biol Chem. 2004 Oct 4;279(50):52033–52041. doi: 10.1074/jbc.M408220200. [DOI] [PubMed] [Google Scholar]
- Kemmer Danielle, Faxén Margareta, Hodges Emily, Lim Jonathan, Herzog Elena, Ljungström Elsebrit, Lundmark Anders, Olsen Mary K., Podowski Raf, Sonnhammer Erik L. L., Nilsson Peter, Reimers Mark, Lenhard Boris, Roberds Steven L., Wahlestedt Claes, Höög Christer, Agarwal Pankaj, Wasserman Wyeth W. Exploring the foundation of genomics: a northern blot reference set for the comparative analysis of transcript profiling technologies. Comp Funct Genomics. 2004;5(8):584–595. doi: 10.1002/cfg.443. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Kezele Phillip R., Ague Jacquelyn M., Nilsson Eric, Skinner Michael K. Alterations in the ovarian transcriptome during primordial follicle assembly and development. Biol Reprod. 2004 Sep 15;72(1):241–255. doi: 10.1095/biolreprod.104.032060. [DOI] [PubMed] [Google Scholar]
- Kim Seong-Jae, Jones Richard C., Cha Chang-Jun, Kweon Ohgew, Edmondson Ricky D., Cerniglia Carl E. Identification of proteins induced by polycyclic aromatic hydrocarbon in Mycobacterium vanbaalenii PYR-1 using two-dimensional polyacrylamide gel electrophoresis and de novo sequencing methods. Proteomics. 2004 Dec;4(12):3899–3908. doi: 10.1002/pmic.200400872. [DOI] [PubMed] [Google Scholar]
- Kitamura Hiroshi, Nakagawa Tomoko, Takayama Michiyo, Kimura Yayoi, Hijikata Atsushi, Hijika Atsushi, Ohara Osamu. Post-transcriptional effects of phorbol 12-myristate 13-acetate on transcriptome of U937 cells. FEBS Lett. 2004 Dec 3;578(1-2):180–184. doi: 10.1016/j.febslet.2004.11.008. [DOI] [PubMed] [Google Scholar]
- Knowlton Nicholas, Dozmorov Igor M., Centola Michael. Microarray Data Analysis Toolbox (MDAT): for normalization, adjustment and analysis of gene expression data. Bioinformatics. 2004 Jul 22;20(18):3687–3690. doi: 10.1093/bioinformatics/bth424. [DOI] [PubMed] [Google Scholar]
- Ko Jae-Heung, Han Kyung-Hwan. Arabidopsis whole-transcriptome profiling defines the features of coordinated regulations that occur during secondary growth. Plant Mol Biol. 2004 May;55(3):433–453. doi: 10.1007/s11103-004-1051-z. [DOI] [PubMed] [Google Scholar]
- Kobi Dominique, Zugmeyer Sandra, Potier Serge, Jaquet-Gutfreund Laurence. Two-dimensional protein map of an "ale"-brewing yeast strain: proteome dynamics during fermentation. FEMS Yeast Res. 2004 Dec;5(3):213–230. doi: 10.1016/j.femsyr.2004.07.004. [DOI] [PubMed] [Google Scholar]
- Koenig-Hoffmann Kerstin, Bonin-Debs Angelika L., Boche Irene, Gawin Beate, Gnirke Andrea, Hergersberg Christoph, Madeo Frank, Kazinski Michael, Klein Matthias, Korherr Christian. High throughput functional genomics: identification of novel genes with tumor suppressor phenotypes. Int J Cancer. 2005 Jan 20;113(3):434–439. doi: 10.1002/ijc.20601. [DOI] [PubMed] [Google Scholar]
- Koike Eiko, Hirano Seishiro, Furuyama Akiko, Kobayashi Takahiro. cDNA microarray analysis of rat alveolar epithelial cells following exposure to organic extract of diesel exhaust particles. Toxicol Appl Pharmacol. 2004 Dec 1;201(2):178–185. doi: 10.1016/j.taap.2004.05.006. [DOI] [PubMed] [Google Scholar]
- Kumar Rashmi N., Radhakrishnan Rangasudhakar, Ha Ji Hee, Dhanasekaran N. Proteome analysis of NIH3T3 cells transformed by activated Galpha12: regulation of leukemia-associated protein SET. J Proteome Res. 2004 Nov-Dec;3(6):1177–1183. doi: 10.1021/pr049896n. [DOI] [PubMed] [Google Scholar]
- Lai Yinglei, Wu Baolin, Chen Liang, Zhao Hongyu. A statistical method for identifying differential gene-gene co-expression patterns. Bioinformatics. 2004 Jul 1;20(17):3146–3155. doi: 10.1093/bioinformatics/bth379. [DOI] [PubMed] [Google Scholar]
- Le Bihan Thierry, Robinson Mark D., Stewart Ian I., Figeys Daniel. Definition and characterization of a "trypsinosome" from specific peptide characteristics by nano-HPLC-MS/MS and in silico analysis of complex protein mixtures. J Proteome Res. 2004 Nov-Dec;3(6):1138–1148. doi: 10.1021/pr049909x. [DOI] [PubMed] [Google Scholar]
- Lee Ju-Seog, Chu In-Sun, Mikaelyan Arsen, Calvisi Diego F., Heo Jeonghoon, Reddy Janardan K., Thorgeirsson Snorri S. Application of comparative functional genomics to identify best-fit mouse models to study human cancer. Nat Genet. 2004 Nov 21;36(12):1306–1311. doi: 10.1038/ng1481. [DOI] [PubMed] [Google Scholar]
- Lee Soojin, Cho Min-Kyu, Jung Jin-Won, Kim Jai-Hoon, Lee Weontae. Exploring protein fold space by secondary structure prediction using data distribution method on Grid platform. Bioinformatics. 2004 Jul 29;20(18):3500–3507. doi: 10.1093/bioinformatics/bth435. [DOI] [PubMed] [Google Scholar]
- Lefler David M., Pafford Roger G., Black Nancy A., Raymond John R., Arthur John M. Identification of proteins in slow continuous ultrafiltrate by reversed-phase chromatography and proteomics. J Proteome Res. 2004 Nov-Dec;3(6):1254–1260. doi: 10.1021/pr0498640. [DOI] [PubMed] [Google Scholar]
- Leinonen Rasko, Diez Federico Garcia, Binns David, Fleischmann Wolfgang, Lopez Rodrigo, Apweiler Rolf. UniProt archive. Bioinformatics. 2004 Mar 25;20(17):3236–3237. doi: 10.1093/bioinformatics/bth191. [DOI] [PubMed] [Google Scholar]
- Li-Pook-Than Jennifer, Carrillo Catherine, Bonen Linda. Variation in mitochondrial transcript profiles of protein-coding genes during early germination and seedling development in wheat. Curr Genet. 2004 Nov 4;46(6):374–380. doi: 10.1007/s00294-004-0544-2. [DOI] [PubMed] [Google Scholar]
- Li Ming D., Kane Justin K., Wang Ju, Ma Jennie Z. Time-dependent changes in transcriptional profiles within five rat brain regions in response to nicotine treatment. Brain Res Mol Brain Res. 2004 Dec 20;132(2):168–180. doi: 10.1016/j.molbrainres.2004.09.009. [DOI] [PubMed] [Google Scholar]
- Li Xia, Rao Shaoqi, Zhang Tianwen, Guo Zheng, Zhang Qingpu, Moser Kathy L., Topol Eric J. An ensemble method for gene discovery based on DNA microarray data. Sci China C Life Sci. 2004 Oct;47(5):396–405. doi: 10.1360/03yc0127. [DOI] [PubMed] [Google Scholar]
- Liao Ben-Yang, Chang Yu-Jung, Ho Jan-Ming, Hwang Ming-Jing. The UniMarker (UM) method for synteny mapping of large genomes. Bioinformatics. 2004 Jun 24;20(17):3156–3165. doi: 10.1093/bioinformatics/bth380. [DOI] [PubMed] [Google Scholar]
- Linder Roland, Dew Dawn, Sudhoff Holger, Theegarten Dirk, Remberger Klaus, Pöppl Siegfried J., Wagner Mathias. The 'subsequent artificial neural network' (SANN) approach might bring more classificatory power to ANN-based DNA microarray analyses. Bioinformatics. 2004 Jul 29;20(18):3544–3552. doi: 10.1093/bioinformatics/bth441. [DOI] [PubMed] [Google Scholar]
- Liu Shaolin, Tinker Nicholas A., Molnar Stephen J., Mather Diane E. EC_oligos: automated and whole-genome primer design for exons within one or between two genomes. Bioinformatics. 2004 Jul 22;20(18):3668–3669. doi: 10.1093/bioinformatics/bth413. [DOI] [PubMed] [Google Scholar]
- Low Teck Yew, Leow Chon Kar, Salto-Tellez Manuel, Chung Maxey C. M. A proteomic analysis of thioacetamide-induced hepatotoxicity and cirrhosis in rat livers. Proteomics. 2004 Dec;4(12):3960–3974. doi: 10.1002/pmic.200400852. [DOI] [PubMed] [Google Scholar]
- Lu ZhaoHui, Hu LiPing, Evers Stefan, Chen Jie, Shen Yan. Differential expression profiling of human pancreatic adenocarcinoma and healthy pancreatic tissue. Proteomics. 2004 Dec;4(12):3975–3988. doi: 10.1002/pmic.200300863. [DOI] [PubMed] [Google Scholar]
- Marathe Rajendra, Guan Zhong, Anandalakshmi Radhamani, Zhao Hongyu, Dinesh-Kumar S. P. Study of Arabidopsis thaliana resistome in response to cucumber mosaic virus infection using whole genome microarray. Plant Mol Biol. 2004 Jul;55(4):501–520. doi: 10.1007/s11103-004-0439-0. [DOI] [PubMed] [Google Scholar]
- Masseroli Marco, Stella Andrea, Meani Natalia, Alcalay Myriam, Pinciroli Francesco. MyWEST: my Web Extraction Software Tool for effective mining of annotations from web-based databanks. Bioinformatics. 2004 Jul 9;20(18):3326–3335. doi: 10.1093/bioinformatics/bth392. [DOI] [PubMed] [Google Scholar]
- Mayr Manuel, Mayr Ursula, Chung Yuen-Li, Yin Xiaoke, Griffiths John R., Xu Qingbo. Vascular proteomics: linking proteomic and metabolomic changes. Proteomics. 2004 Dec;4(12):3751–3761. doi: 10.1002/pmic.200400947. [DOI] [PubMed] [Google Scholar]
- McDonald Daniel M., Chen Hsinchun, Su Hua, Marshall Byron B. Extracting gene pathway relations using a hybrid grammar: the Arizona Relation Parser. Bioinformatics. 2004 Jul 15;20(18):3370–3378. doi: 10.1093/bioinformatics/bth409. [DOI] [PubMed] [Google Scholar]
- McDonald Ryan T., Winters R. Scott, Mandel Mark, Jin Yang, White Peter S., Pereira Fernando. An entity tagger for recognizing acquired genomic variations in cancer literature. Bioinformatics. 2004 Jun 4;20(17):3249–3251. doi: 10.1093/bioinformatics/bth350. [DOI] [PubMed] [Google Scholar]
- McIntyre Alan, Summersgill Brenda, Jafer Osman, Rodriguez Sandrine, Zafarana Gaetano, Oosterhuis J. Wolter, Gillis Ad Jm, Looijenga Leendert, Cooper Colin, Huddart Robert. Defining minimum genomic regions of imbalance involved in testicular germ cell tumors of adolescents and adults through genome wide microarray analysis of cDNA clones. Oncogene. 2004 Dec 2;23(56):9142–9147. doi: 10.1038/sj.onc.1208115. [DOI] [PubMed] [Google Scholar]
- McKinney James L., Murdoch Duncan J., Wang Jian, Robinson John, Biltcliffe Chris, Khan Hafiz M. R., Walker Paul M., Savage Josee, Skerjanc Ilona, Hegele Robert A. Venn analysis as part of a bioinformatic approach to prioritize expressed sequence tags from cardiac libraries. Clin Biochem. 2004 Nov;37(11):953–960. doi: 10.1016/j.clinbiochem.2004.07.010. [DOI] [PubMed] [Google Scholar]
- Mears Rainy, Craven Rachel A., Hanrahan Sarah, Totty Nick, Upton Carol, Young Sarah L., Patel Poulam, Selby Peter J., Banks Rosamonde E. Proteomic analysis of melanoma-derived exosomes by two-dimensional polyacrylamide gel electrophoresis and mass spectrometry. Proteomics. 2004 Dec;4(12):4019–4031. doi: 10.1002/pmic.200400876. [DOI] [PubMed] [Google Scholar]
- Mikkat Stefan, Koy Cornelia, Ulbrich Markus, Ringel Bruno, Glocker Michael O. Mass spectrometric protein structure characterization reveals cause of migration differences of haptoglobin alpha chains in two-dimensional gel electrophoresis. Proteomics. 2004 Dec;4(12):3921–3932. doi: 10.1002/pmic.200400825. [DOI] [PubMed] [Google Scholar]
- Moore Lisa L., Fulton Ashley M., Harrison Marietta L., Geahlen Robert L. Anti-sulfonylbenzoate antibodies as a tool for the detection of nucleotide-binding proteins for functional proteomics. J Proteome Res. 2004 Nov-Dec;3(6):1184–1190. doi: 10.1021/pr0498943. [DOI] [PubMed] [Google Scholar]
- Morris Daniel L., Jr, Sutton Jennifer N., Harper Robert G., Timperman Aaron T. Reversed-phase HPLC separation of human serum employing a novel saw-tooth gradient: toward multidimensional proteome analysis. J Proteome Res. 2004 Nov-Dec;3(6):1149–1154. doi: 10.1021/pr049901n. [DOI] [PubMed] [Google Scholar]
- Murakawa Katsuhiko, Tada Mitsuhiro, Takada Minoru, Tamoto Eiji, Shindoh Gaku, Teramoto Ken-ichi, Matsunaga Akihiro, Komuro Kazuteru, Kanai Motoshi, Kawakami Akiko. Prediction of lymph node metastasis and perineural invasion of biliary tract cancer by selected features from cDNA array data. J Surg Res. 2004 Dec;122(2):184–194. doi: 10.1016/j.jss.2004.06.003. [DOI] [PubMed] [Google Scholar]
- Murray James, Yonally Sky, Aggeler Robert, Marusich Michael F., Capaldi Roderick A. Focused proteomics: towards a high throughput monoclonal antibody-based resolution of proteins for diagnosis of mitochondrial diseases. Biochim Biophys Acta. 2004 Dec 6;1659(2-3):206–211. doi: 10.1016/j.bbabio.2004.07.005. [DOI] [PubMed] [Google Scholar]
- Myers Chad L., Dunham Maitreya J., Kung S. Y., Troyanskaya Olga G. Accurate detection of aneuploidies in array CGH and gene expression microarray data. Bioinformatics. 2004 Jul 29;20(18):3533–3543. doi: 10.1093/bioinformatics/bth440. [DOI] [PubMed] [Google Scholar]
- Neuhäuser Markus, Senske Roswitha. The Baumgartner-Weiss-Schindler test for the detection of differentially expressed genes in replicated microarray experiments. Bioinformatics. 2004 Jul 29;20(18):3553–3564. doi: 10.1093/bioinformatics/bth442. [DOI] [PubMed] [Google Scholar]
- Niu Tianhua, Hu Zhenjun. SNPicker: a graphical tool for primer picking in designing mutagenic endonuclease restriction assays. Bioinformatics. 2004 Jun 16;20(17):3263–3265. doi: 10.1093/bioinformatics/bth360. [DOI] [PubMed] [Google Scholar]
- Noonan James P., Grimwood Jane, Danke Joshua, Schmutz Jeremy, Dickson Mark, Amemiya Chris T., Myers Richard M. Coelacanth genome sequence reveals the evolutionary history of vertebrate genes. Genome Res. 2004 Nov 15;14(12):2397–2405. doi: 10.1101/gr.2972804. [DOI] [PMC free article] [PubMed] [Google Scholar]
- O'Riordan Edmond, Orlova Tatyana N., Mei J Jianfeng, Butt Khalid, Chander Praveen M., Rahman Shafiq, Mya Muong, Hu Rena, Momin Jahangir, Eng Elizabeth W. Bioinformatic analysis of the urine proteome of acute allograft rejection. J Am Soc Nephrol. 2004 Dec;15(12):3240–3248. doi: 10.1097/01.ASN.0000145241.83482.68. [DOI] [PubMed] [Google Scholar]
- Ogihara Yasunari, Mochida Keiichi, Kawaura Kanako, Murai Koji, Seki Motoaki, Kamiya Asako, Shinozaki Kazuo, Carninci Piero, Hayashizaki Yoshihide, Shin-I Tadasu. Construction of a full-length cDNA library from young spikelets of hexaploid wheat and its characterization by large-scale sequencing of expressed sequence tags. Genes Genet Syst. 2004 Aug;79(4):227–232. doi: 10.1266/ggs.79.227. [DOI] [PubMed] [Google Scholar]
- Ohali Anat, Avigad Smadar, Zaizov Rina, Ophir Ron, Horn-Saban Shirley, Cohen Ian J., Meller Isaac, Kollender Yehuda, Issakov Josephine, Yaniv Isaac. Prediction of high risk Ewing's sarcoma by gene expression profiling. Oncogene. 2004 Nov 25;23(55):8997–9006. doi: 10.1038/sj.onc.1208060. [DOI] [PubMed] [Google Scholar]
- Oinn Tom, Addis Matthew, Ferris Justin, Marvin Darren, Senger Martin, Greenwood Mark, Carver Tim, Glover Kevin, Pocock Matthew R., Wipat Anil. Taverna: a tool for the composition and enactment of bioinformatics workflows. Bioinformatics. 2004 Jun 16;20(17):3045–3054. doi: 10.1093/bioinformatics/bth361. [DOI] [PubMed] [Google Scholar]
- Okamura Miwa, Sumida Kayo, Muto Tomoko, Kashida Yoko, Machida Noboru, Watanabe Tomoyuki, Mitsumori Kunitoshi. Analysis of gene expression profiles of forestomach tumors in rasH2 mice initiated with N-ethyl-N-nitrosourea. Arch Toxicol. 2004 Jul 13;78(12):688–696. doi: 10.1007/s00204-004-0589-5. [DOI] [PubMed] [Google Scholar]
- Palmfeldt Johan, Levander Fredrik, Hahn-Hägerdal Bärbel, James Peter. Acidic proteome of growing and resting Lactococcus lactis metabolizing maltose. Proteomics. 2004 Dec;4(12):3881–3898. doi: 10.1002/pmic.200400858. [DOI] [PubMed] [Google Scholar]
- Palotás Miklós, Palotás András, Puskás László G., Kitajka Klára, Pákáski Magdolna, Janka Zoltán, Molnár József, Penke Botond, Kálmán János. Gene expression profile analysis of the rat cortex following treatment with imipramine and citalopram. Int J Neuropsychopharmacol. 2004 Jul 26;7(4):401–413. doi: 10.1017/S1461145704004493. [DOI] [PubMed] [Google Scholar]
- Pan Deng, He Nanhai, Yang Zhiyuan, Liu Haipeng, Xu Xun. Differential gene expression profile in hepatopancreas of WSSV-resistant shrimp (Penaeus japonicus) by suppression subtractive hybridization. Dev Comp Immunol. 2005;29(2):103–112. doi: 10.1016/j.dci.2004.07.001. [DOI] [PubMed] [Google Scholar]
- Pan Qun, Shai Ofer, Misquitta Christine, Zhang Wen, Saltzman Arneet L., Mohammad Naveed, Babak Tomas, Siu Henry, Hughes Timothy R., Morris Quaid D. Revealing global regulatory features of mammalian alternative splicing using a quantitative microarray platform. Mol Cell. 2004 Dec 22;16(6):929–941. doi: 10.1016/j.molcel.2004.12.004. [DOI] [PubMed] [Google Scholar]
- Parkar Mohamed H., Tonetti Maurizio. Gene expression profiles of periodontal ligament cells treated with enamel matrix proteins in vitro: analysis using cDNA arrays. J Periodontol. 2004 Nov;75(11):1539–1546. doi: 10.1902/jop.2004.75.11.1539. [DOI] [PubMed] [Google Scholar]
- Parkinson John, Mitreva Makedonka, Whitton Claire, Thomson Marian, Daub Jennifer, Martin John, Schmid Ralf, Hall Neil, Barrell Bart, Waterston Robert H. A transcriptomic analysis of the phylum Nematoda. Nat Genet. 2004 Nov 14;36(12):1259–1267. doi: 10.1038/ng1472. [DOI] [PubMed] [Google Scholar]
- Patterson Larry T., Potter S. Steven. Profiling gene expression in kidney development. Nephron Exp Nephrol. 2004;98(4):e109–e113. doi: 10.1159/000081554. [DOI] [PubMed] [Google Scholar]
- Pendle Alison F., Clark Gillian P., Boon Reinier, Lewandowska Dominika, Lam Yun Wah, Andersen Jens, Mann Matthias, Lamond Angus I., Brown John W. S., Shaw Peter J. Proteomic analysis of the Arabidopsis nucleolus suggests novel nucleolar functions. Mol Biol Cell. 2004 Oct 20;16(1):260–269. doi: 10.1091/mbc.E04-09-0791. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Peng Xuanxian, Wu Yajun, Chen Jingan, Wang Sanying. Proteomic approach to identify acute phase response-related proteins with low molecular weight in loach skin following injury. Proteomics. 2004 Dec;4(12):3989–3997. doi: 10.1002/pmic.200300864. [DOI] [PubMed] [Google Scholar]
- Pham Tuan D., Zuegg Johannes. A probabilistic measure for alignment-free sequence comparison. Bioinformatics. 2004 Jul 22;20(18):3455–3461. doi: 10.1093/bioinformatics/bth426. [DOI] [PubMed] [Google Scholar]
- Planagumà Jesús, Díaz-Fuertes María, Gil-Moreno Antonio, Abal Miguel, Monge Marta, García Angel, Baró Teresa, Thomson Timothy M., Xercavins Jordi, Alameda Francesc. A differential gene expression profile reveals overexpression of RUNX1/AML1 in invasive endometrioid carcinoma. Cancer Res. 2004 Dec 15;64(24):8846–8853. doi: 10.1158/0008-5472.CAN-04-2066. [DOI] [PubMed] [Google Scholar]
- Pochet Nathalie, De Smet Frank, Suykens Johan A. K., De Moor Bart L. R. Systematic benchmarking of microarray data classification: assessing the role of non-linearity and dimensionality reduction. Bioinformatics. 2004 Jul 1;20(17):3185–3195. doi: 10.1093/bioinformatics/bth383. [DOI] [PubMed] [Google Scholar]
- Pournara Iosifina, Wernisch Lorenz. Reconstruction of gene networks using Bayesian learning and manipulation experiments. Bioinformatics. 2004 Jun 4;20(17):2934–2942. doi: 10.1093/bioinformatics/bth337. [DOI] [PubMed] [Google Scholar]
- Quevillon-Cheruel Sophie, Liger Dominique, Leulliot Nicolas, Graille Marc, Poupon Anne, Li de La Sierra-Gallay Inès, Zhou Cong-Zhao, Collinet Bruno, Janin Joël, Van Tilbeurgh Herman. The Paris-Sud yeast structural genomics pilot-project: from structure to function. Biochimie. 2004 Sep-Oct;86(9-10):617–623. doi: 10.1016/j.biochi.2004.09.013. [DOI] [PubMed] [Google Scholar]
- Rahbar Amir M., Fenselau Catherine. Integration of Jacobson's pellicle method into proteomic strategies for plasma membrane proteins. J Proteome Res. 2004 Nov-Dec;3(6):1267–1277. doi: 10.1021/pr040004t. [DOI] [PubMed] [Google Scholar]
- Rajput Ashish, Singh Bhagirath. Gene expression profiling in type 1 diabetes prone NOD mice immunized with a disease protective autoantigenic peptide. J Autoimmun. 2004 Dec;23(4):311–321. doi: 10.1016/j.jaut.2004.09.002. [DOI] [PubMed] [Google Scholar]
- Ramström Margareta, Ivonin Igor, Johansson Anders, Askmark Håkan, Markides Karin E., Zubarev Roman, Håkansson Per, Aquilonius Sten-Magnus, Bergquist Jonas. Cerebrospinal fluid protein patterns in neurodegenerative disease revealed by liquid chromatography-Fourier transform ion cyclotron resonance mass spectrometry. Proteomics. 2004 Dec;4(12):4010–4018. doi: 10.1002/pmic.200400871. [DOI] [PubMed] [Google Scholar]
- Rapkiewicz Amy V., Espina Virginia, Petricoin Emanuel F., 3rd, Liotta Lance A. Biomarkers of ovarian tumours. Eur J Cancer. 2004 Nov;40(17):2604–2612. doi: 10.1016/j.ejca.2004.05.021. [DOI] [PubMed] [Google Scholar]
- Rebeiz Mark, Posakony James W. GenePalette: a universal software tool for genome sequence visualization and analysis. Dev Biol. 2004 Jul 15;271(2):431–438. doi: 10.1016/j.ydbio.2004.04.011. [DOI] [PubMed] [Google Scholar]
- Reinders Joerg, Lewandrowski Urs, Moebius Jan, Wagner Yvonne, Sickmann Albert. Challenges in mass spectrometry-based proteomics. Proteomics. 2004 Dec;4(12):3686–3703. doi: 10.1002/pmic.200400869. [DOI] [PubMed] [Google Scholar]
- Reyzer Michelle L., Caldwell Robert L., Dugger Teresa C., Forbes James T., Ritter Christoph A., Guix Marta, Arteaga Carlos L., Caprioli Richard M. Early changes in protein expression detected by mass spectrometry predict tumor response to molecular therapeutics. Cancer Res. 2004 Dec 15;64(24):9093–9100. doi: 10.1158/0008-5472.CAN-04-2231. [DOI] [PubMed] [Google Scholar]
- Roberts Michael, Hayes Wayne, Hunt Brian R., Mount Stephen M., Yorke James A. Reducing storage requirements for biological sequence comparison. Bioinformatics. 2004 Jul 15;20(18):3363–3369. doi: 10.1093/bioinformatics/bth408. [DOI] [PubMed] [Google Scholar]
- Robson Barry. The dragon on the gold: myths and realities for data mining in biomedicine and biotechnology using digital and molecular libraries. J Proteome Res. 2004 Nov-Dec;3(6):1113–1119. doi: 10.1021/pr0499242. [DOI] [PubMed] [Google Scholar]
- Robson Paul. The maturing of the human embryonic stem cell transcriptome profile. Trends Biotechnol. 2004 Dec;22(12):609–612. doi: 10.1016/j.tibtech.2004.10.001. [DOI] [PubMed] [Google Scholar]
- Rodionov Dmitry A., Gelfand Mikhail S., Hugouvieux-Cotte-Pattat Nicole. Comparative genomics of the KdgR regulon in Erwinia chrysanthemi 3937 and other gamma-proteobacteria. Microbiology. 2004 Nov;150(Pt 11):3571–3590. doi: 10.1099/mic.0.27041-0. [DOI] [PubMed] [Google Scholar]
- Rong Yongqi, Wang Taiyu, Morgan James I. Identification of candidate Purkinje cell-specific markers by gene expression profiling in wild-type and pcd(3J) mice. Brain Res Mol Brain Res. 2004 Dec 20;132(2):128–145. doi: 10.1016/j.molbrainres.2004.10.015. [DOI] [PubMed] [Google Scholar]
- Rosenfeld Jeffrey A., Sarkar Indra N., Planet Paul J., Figurski David H., DeSalle Rob. ORFcurator: molecular curation of genes and gene clusters in prokaryotic organisms. Bioinformatics. 2004 Jul 22;20(18):3462–3465. doi: 10.1093/bioinformatics/bth427. [DOI] [PubMed] [Google Scholar]
- Saldanha Alok J. Java Treeview--extensible visualization of microarray data. Bioinformatics. 2004 Jun 4;20(17):3246–3248. doi: 10.1093/bioinformatics/bth349. [DOI] [PubMed] [Google Scholar]
- Samuelsson Jim, Dalevi Daniel, Levander Fredrik, Rögnvaldsson Thorsteinn. Modular, scriptable and automated analysis tools for high-throughput peptide mass fingerprinting. Bioinformatics. 2004 Aug 5;20(18):3628–3635. doi: 10.1093/bioinformatics/bth460. [DOI] [PubMed] [Google Scholar]
- Sansone Susanna Assunta, Morrison Norman, Rocca-Serra Philippe, Fostel Jennifer. Standardization Initiatives in the (eco)toxicogenomics domain: a review. Comp Funct Genomics. 2004;5(8):633–641. doi: 10.1002/cfg.447. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Satten Glen A., Datta Somnath, Moura Hercules, Woolfitt Adrian R., Carvalho Maria da G., Carlone George M., De Barun K., Pavlopoulos Antonis, Barr John R. Standardization and denoising algorithms for mass spectra to classify whole-organism bacterial specimens. Bioinformatics. 2004 Jun 24;20(17):3128–3136. doi: 10.1093/bioinformatics/bth372. [DOI] [PubMed] [Google Scholar]
- Sausville Edward A., Holbeck Susan L. Transcription profiling of gene expression in drug discovery and development: the NCI experience. Eur J Cancer. 2004 Nov;40(17):2544–2549. doi: 10.1016/j.ejca.2004.08.006. [DOI] [PubMed] [Google Scholar]
- Sawkins M. C., Farmer A. D., Hoisington D., Sullivan J., Tolopko A., Jiang Z., Ribaut J-M. Comparative map and trait viewer (CMTV): an integrated bioinformatic tool to construct consensus maps and compare QTL and functional genomics data across genomes and experiments. Plant Mol Biol. 2004 Oct;56(3):465–480. doi: 10.1007/s11103-004-4950-0. [DOI] [PubMed] [Google Scholar]
- Semmes O. John, Feng Ziding, Adam Bao-Ling, Banez Lionel L., Bigbee William L., Campos David, Cazares Lisa H., Chan Daniel W., Grizzle William E., Izbicka Elzbieta. Evaluation of serum protein profiling by surface-enhanced laser desorption/ionization time-of-flight mass spectrometry for the detection of prostate cancer: I. Assessment of platform reproducibility. Clin Chem. 2005 Jan;51(1):102–112. doi: 10.1373/clinchem.2004.038950. [DOI] [PubMed] [Google Scholar]
- Sese Jun, Kurokawa Yukinori, Monden Morito, Kato Kikuya, Morishita Shinichi. Constrained clusters of gene expression profiles with pathological features. Bioinformatics. 2004 Jun 24;20(17):3137–3145. doi: 10.1093/bioinformatics/bth373. [DOI] [PubMed] [Google Scholar]
- Seshadri Rekha, Adrian Lorenz, Fouts Derrick E., Eisen Jonathan A., Phillippy Adam M., Methe Barbara A., Ward Naomi L., Nelson William C., Deboy Robert T., Khouri Hoda M. Genome sequence of the PCE-dechlorinating bacterium Dehalococcoides ethenogenes. Science. 2005 Jan 7;307(5706):105–108. doi: 10.1126/science.1102226. [DOI] [PubMed] [Google Scholar]
- Sethuraman Mahadevan, McComb Mark E., Huang Hua, Huang Sequin, Heibeck Tyler, Costello Catherine E., Cohen Richard A. Isotope-coded affinity tag (ICAT) approach to redox proteomics: identification and quantitation of oxidant-sensitive cysteine thiols in complex protein mixtures. J Proteome Res. 2004 Nov-Dec;3(6):1228–1233. doi: 10.1021/pr049887e. [DOI] [PubMed] [Google Scholar]
- Shaw O. J., Harwood C., Steggles L. J., Wipat A. SARGE: a tool for creation of putative genetic networks. Bioinformatics. 2004 Jul 9;20(18):3638–3640. doi: 10.1093/bioinformatics/bth395. [DOI] [PubMed] [Google Scholar]
- Shih Joanna H., Michalowska Aleksandra M., Dobbin Kevin, Ye Yumei, Qiu Ting Hu, Green Jeffrey E. Effects of pooling mRNA in microarray class comparisons. Bioinformatics. 2004 Jul 9;20(18):3318–3325. doi: 10.1093/bioinformatics/bth391. [DOI] [PubMed] [Google Scholar]
- Shishkin S. S., Kovalyov L. I., Kovalyova M. A. Proteomic studies of human and other vertebrate muscle proteins. Biochemistry (Mosc) 2004 Nov;69(11):1283–1298. doi: 10.1007/s10541-005-0074-7. [DOI] [PubMed] [Google Scholar]
- Shoop Elizabeth, Casaes Paulo, Onsongo Getiria, Lesnett Lisa, Petursdottir Erla Osk, Donkor Edward Kofi Yeboah, Tkach Dennis, Cosimini Michael. Data exploration tools for the Gene Ontology database. Bioinformatics. 2004 Jul 22;20(18):3442–3454. doi: 10.1093/bioinformatics/bth425. [DOI] [PubMed] [Google Scholar]
- Simpson Claire L., Hansen Valerie K., Sham Pak C., Collins Andrew, Powell John F., Al-Chalabi Ammar. MaGIC: a program to generate targeted marker sets for genome-wide association studies. Biotechniques. 2004 Dec;37(6):996–999. doi: 10.2144/04376BIN03. [DOI] [PubMed] [Google Scholar]
- Sinden R. E. A proteomic analysis of malaria biology: integration of old literature and new technologies. Int J Parasitol. 2004 Dec;34(13-14):1441–1450. doi: 10.1016/j.ijpara.2004.10.005. [DOI] [PubMed] [Google Scholar]
- Smith Paul M., Ross Günther F., Taylor Robert W., Turnbull Douglass M., Lightowlers Robert N. Strategies for treating disorders of the mitochondrial genome. Biochim Biophys Acta. 2004 Dec 6;1659(2-3):232–239. doi: 10.1016/j.bbabio.2004.09.003. [DOI] [PubMed] [Google Scholar]
- Sommer Andrei P., Miyake Norimune, Wickramasinghe N. Chandra, Narlikar Jayant V., Al-Mufti Shirwan. Functions and possible provenance of primordial proteins. J Proteome Res. 2004 Nov-Dec;3(6):1296–1299. doi: 10.1021/pr049861n. [DOI] [PubMed] [Google Scholar]
- Spijker Sabine, van de Leemput Joyce C. H., Hoekstra Chantal, Boomsma Dorret I., Smit August B. Profiling gene expression in whole blood samples following an in-vitro challenge. Twin Res. 2004 Dec;7(6):564–570. doi: 10.1375/1369052042663878. [DOI] [PubMed] [Google Scholar]
- Spin Joshua M., Nallamshetty Shriram, Tabibiazar Raymond, Ashley Euan A., King Jennifer Y., Chen Mary, Tsao Phillip S., Quertermous Thomas. Transcriptional profiling of in vitro smooth muscle cell differentiation identifies specific patterns of gene and pathway activation. Physiol Genomics. 2004 Aug 31;19(3):292–302. doi: 10.1152/physiolgenomics.00148.2004. [DOI] [PubMed] [Google Scholar]
- Spira Avrum, Beane Jennifer, Pinto-Plata Victor, Kadar Aran, Liu Gang, Shah Vishal, Celli Bartolome, Brody Jerome S. Gene expression profiling of human lung tissue from smokers with severe emphysema. Am J Respir Cell Mol Biol. 2004 Sep 16;31(6):601–610. doi: 10.1165/rcmb.2004-0273OC. [DOI] [PubMed] [Google Scholar]
- Starck Joakim, Källenius Gunilla, Marklund Britt-Inger, Andersson Dan I., Akerlund Thomas. Comparative proteome analysis of Mycobacterium tuberculosis grown under aerobic and anaerobic conditions. Microbiology. 2004 Nov;150(Pt 11):3821–3829. doi: 10.1099/mic.0.27284-0. [DOI] [PubMed] [Google Scholar]
- Stasyk Taras, Huber Lukas A. Zooming in: fractionation strategies in proteomics. Proteomics. 2004 Dec;4(12):3704–3716. doi: 10.1002/pmic.200401048. [DOI] [PubMed] [Google Scholar]
- Steffensen Knut R., Neo Soek Ying, Stulnig Thomas M., Vega Vinsensius B., Rahman Safia S., Schuster Gertrud U., Gustafsson Jan-Ake, Liu Edison T. Genome-wide expression profiling; a panel of mouse tissues discloses novel biological functions of liver X receptors in adrenals. J Mol Endocrinol. 2004 Dec;33(3):609–622. doi: 10.1677/jme.1.01508. [DOI] [PubMed] [Google Scholar]
- Steinhauser Dirk, Usadel Björn, Luedemann Alexander, Thimm Oliver, Kopka Joachim. CSB.DB: a comprehensive systems-biology database. Bioinformatics. 2004 Jul 9;20(18):3647–3651. doi: 10.1093/bioinformatics/bth398. [DOI] [PubMed] [Google Scholar]
- Suzuki Takashi, Ota Tatsuya, Fujiyama Asao, Kasahara Masanori. Construction of a bacterial artificial chromosome library from the inshore hagfish, Eptatretus burgeri: A resource for the analysis of the agnathan genome. Genes Genet Syst. 2004 Aug;79(4):251–253. doi: 10.1266/ggs.79.251. [DOI] [PubMed] [Google Scholar]
- Swanson Willie J., Wong Alex, Wolfner Mariana F., Aquadro Charles F. Evolutionary expressed sequence tag analysis of Drosophila female reproductive tracts identifies genes subjected to positive selection. Genetics. 2004 Nov;168(3):1457–1465. doi: 10.1534/genetics.104.030478. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Tai Siew Leng, Boer Viktor M., Daran-Lapujade Pascale, Walsh Michael C., de Winde Johannes H., Daran Jean-Marc, Pronk Jack T. Two-dimensional transcriptome analysis in chemostat cultures. Combinatorial effects of oxygen availability and macronutrient limitation in Saccharomyces cerevisiae. J Biol Chem. 2004 Oct 20;280(1):437–447. doi: 10.1074/jbc.M410573200. [DOI] [PubMed] [Google Scholar]
- Takahashi Hiro, Masuda Kayoko, Ando Tatsuya, Kobayashi Takeshi, Honda Hiroyuki. Prognostic predictor with multiple fuzzy neural models using expression profiles from DNA microarray for metastases of breast cancer. J Biosci Bioeng. 2004;98(3):193–199. doi: 10.1016/S1389-1723(04)00265-8. [DOI] [PubMed] [Google Scholar]
- Takami Hideto, Takaki Yoshihiro, Chee Gab-Joo, Nishi Shinro, Shimamura Shigeru, Suzuki Hiroko, Matsui Satomi, Uchiyama Ikuo. Thermoadaptation trait revealed by the genome sequence of thermophilic Geobacillus kaustophilus. Nucleic Acids Res. 2004 Dec 1;32(21):6292–6303. doi: 10.1093/nar/gkh970. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Tang Yang, Lu Aigang, Ran Ruiqiong, Aronow Bruce J., Schorry Elizabeth K., Hopkin Robert J., Gilbert Donald L., Glauser Tracy A., Hershey Andrew D., Richtand Neil W. Human blood genomics: distinct profiles for gender, age and neurofibromatosis type 1. Brain Res Mol Brain Res. 2004 Dec 20;132(2):155–167. doi: 10.1016/j.molbrainres.2003.10.014. [DOI] [PubMed] [Google Scholar]
- Taramelli R., Acquati F. The human genome project and the discovery of genetic determinants of cancer susceptibility. Eur J Cancer. 2004 Nov;40(17):2537–2543. doi: 10.1016/j.ejca.2004.07.030. [DOI] [PubMed] [Google Scholar]
- Taulan Magali, Paquet François, Maubert Christophe, Delissen Olivia, Demaille Jacques, Romey Marie-Catherine. Renal toxicogenomic response to chronic uranyl nitrate insult in mice. Environ Health Perspect. 2004 Nov;112(16):1628–1635. doi: 10.1289/txg.7296. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Thomarat Fabienne, Vivarès Christian P., Gouy Manolo. Phylogenetic analysis of the complete genome sequence of Encephalitozoon cuniculi supports the fungal origin of microsporidia and reveals a high frequency of fast-evolving genes. J Mol Evol. 2004 Dec;59(6):780–791. doi: 10.1007/s00239-004-2673-0. [DOI] [PubMed] [Google Scholar]
- Thomas Reuben, Mehrotra Sanjay, Papoutsakis Eleftherios T., Hatzimanikatis Vassily. A model-based optimization framework for the inference on gene regulatory networks from DNA array data. Bioinformatics. 2004 Jul 9;20(17):3221–3235. doi: 10.1093/bioinformatics/bth389. [DOI] [PubMed] [Google Scholar]
- Thompson Michael, Cheran Larisa-Emilia, Zhang Mingquan, Chacko Melissa, Huo Hong, Sadeghi Saman. Label-free detection of nucleic acid and protein microarrays by scanning Kelvin nanoprobe. Biosens Bioelectron. 2005 Feb 15;20(8):1471–1481. doi: 10.1016/j.bios.2004.06.022. [DOI] [PubMed] [Google Scholar]
- Toyoda Mika, Cho Tamaki, Kaminishi Hidenori, Sudoh Masayuki, Chibana Hiroji. Transcriptional profiling of the early stages of germination in Candida albicans by real-time RT-PCR. FEMS Yeast Res. 2004 Dec;5(3):287–296. doi: 10.1016/j.femsyr.2004.08.004. [DOI] [PubMed] [Google Scholar]
- Vaquerizas Juan M., Dopazo Joaquín, Díaz-Uriarte Ramón. DNMAD: web-based diagnosis and normalization for microarray data. Bioinformatics. 2004 Jul 9;20(18):3656–3658. doi: 10.1093/bioinformatics/bth401. [DOI] [PubMed] [Google Scholar]
- Vasilescu Julian, Guo Xuecui, Kast Juergen. Identification of protein-protein interactions using in vivo cross-linking and mass spectrometry. Proteomics. 2004 Dec;4(12):3845–3854. doi: 10.1002/pmic.200400856. [DOI] [PubMed] [Google Scholar]
- Vey Norbert, Mozziconacci Marie-Joëlle, Groulet-Martinec Agnès, Debono Stéphane, Finetti Pascal, Carbuccia Nadine, Beillard Emmanuel, Devilard Elizabeth, Arnoulet Christine, Coso Diane. Identification of new classes among acute myelogenous leukaemias with normal karyotype using gene expression profiling. Oncogene. 2004 Dec 16;23(58):9381–9391. doi: 10.1038/sj.onc.1207910. [DOI] [PubMed] [Google Scholar]
- Wagner Roger A., Tabibiazar Raymond, Powers Jennifer, Bernstein Daniel, Quertermous Thomas. Genome-wide expression profiling of a cardiac pressure overload model identifies major metabolic and signaling pathway responses. J Mol Cell Cardiol. 2004 Dec;37(6):1159–1170. doi: 10.1016/j.yjmcc.2004.09.003. [DOI] [PubMed] [Google Scholar]
- Wan Xiu-Feng, Verberkmoes Nathan C., McCue Lee Ann, Stanek Dawn, Connelly Heather, Hauser Loren J., Wu Liyou, Liu Xueduan, Yan Tingfen, Leaphart Adam. Transcriptomic and proteomic characterization of the Fur modulon in the metal-reducing bacterium Shewanella oneidensis. J Bacteriol. 2004 Dec;186(24):8385–8400. doi: 10.1128/JB.186.24.8385-8400.2004. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Wang J., Coombes K. R., Highsmith W. E., Keating M. J., Abruzzo L. V. Differences in gene expression between B-cell chronic lymphocytic leukemia and normal B cells: a meta-analysis of three microarray studies. Bioinformatics. 2004 Jul 1;20(17):3166–3178. doi: 10.1093/bioinformatics/bth381. [DOI] [PubMed] [Google Scholar]
- Wang Ji-Ping Z., Lindsay Bruce G., Leebens-Mack James, Cui Liying, Wall Kerr, Miller Webb C., dePamphilis Claude W. EST clustering error evaluation and correction. Bioinformatics. 2004 Jun 9;20(17):2973–2984. doi: 10.1093/bioinformatics/bth342. [DOI] [PubMed] [Google Scholar]
- Wang Lingling, Ma Li, Leng Wenchuan, Yang Jian, Zhu Junping, Dong Jie, Xue Ying, Zhe Wan, Li Ruoyu, Jin Qi. Analysis of part of the Trichophyton rubrum ESTs. Sci China C Life Sci. 2004 Oct;47(5):389–395. doi: 10.1360/03yc0107. [DOI] [PubMed] [Google Scholar]
- Wang Yong, Leung Frederick C. C. DNA structure constraint is probably a fundamental factor inducing CpG deficiency in bacteria. Bioinformatics. 2004 Jul 9;20(18):3336–3345. doi: 10.1093/bioinformatics/bth393. [DOI] [PubMed] [Google Scholar]
- Wang Yu, Lu Gang, Wong Winifred P. S., Vliegenthart Johannes F. G., Gerwig Gerrit J., Lam Karen S. L., Cooper Garth J. S., Xu Aimin. Proteomic and functional characterization of endogenous adiponectin purified from fetal bovine serum. Proteomics. 2004 Dec;4(12):3933–3942. doi: 10.1002/pmic.200400826. [DOI] [PubMed] [Google Scholar]
- Wettenhall James M., Smyth Gordon K. limmaGUI: a graphical user interface for linear modeling of microarray data. Bioinformatics. 2004 Aug 5;20(18):3705–3706. doi: 10.1093/bioinformatics/bth449. [DOI] [PubMed] [Google Scholar]
- Wisz Michael S., Suarez Melissa Kimball, Holmes Mark R., Giddings Morgan C. GFSWeb: a web tool for genome-based identification of proteins from mass spectrometric samples. J Proteome Res. 2004 Nov-Dec;3(6):1292–1295. doi: 10.1021/pr049879y. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Wu Chia-Chin, Huang Hsuan-Cheng, Juan Hsueh-Fen, Chen Shui-Tein. GeneNetwork: an interactive tool for reconstruction of genetic networks using microarray data. Bioinformatics. 2004 Jul 22;20(18):3691–3693. doi: 10.1093/bioinformatics/bth428. [DOI] [PubMed] [Google Scholar]
- Wu Huiling, Tian Yuping, Liu Baohong, Lu Haojie, Wang Xiaoyan, Zhai Jianjun, Jin Hong, Yang Pengyuang, Xu Yunmin, Wang Honghai. Titania and alumina sol-gel-derived microfluidics enzymatic-reactors for peptide mapping: design, characterization, and performance. J Proteome Res. 2004 Nov-Dec;3(6):1201–1209. doi: 10.1021/pr049889z. [DOI] [PubMed] [Google Scholar]
- Wulfkuhle Julia, Espina Virginia, Liotta Lance, Petricoin Emanuel. Genomic and proteomic technologies for individualisation and improvement of cancer treatment. Eur J Cancer. 2004 Nov;40(17):2623–2632. doi: 10.1016/j.ejca.2004.05.020. [DOI] [PubMed] [Google Scholar]
- Wyman Stacia K., Jansen Robert K., Boore Jeffrey L. Automatic annotation of organellar genomes with DOGMA. Bioinformatics. 2004 Jun 4;20(17):3252–3255. doi: 10.1093/bioinformatics/bth352. [DOI] [PubMed] [Google Scholar]
- Xiang Rong, Shi Yang, Dillon Deborah A., Negin Brina, Horváth Csaba, Wilkins James A. 2D LC/MS analysis of membrane proteins from breast cancer cell lines MCF7 and BT474. J Proteome Res. 2004 Nov-Dec;3(6):1278–1283. doi: 10.1021/pr049852e. [DOI] [PubMed] [Google Scholar]
- Xu Changxin, Ren Haixia, Wang Sanying, Peng Xuanxian. Proteomic analysis of salt-sensitive outer membrane proteins of Vibrio parahaemolyticus. Res Microbiol. 2004 Dec;155(10):835–842. doi: 10.1016/j.resmic.2004.07.001. [DOI] [PubMed] [Google Scholar]
- Xu Xiaojiang, Wang Lianshui, Ding Dafu. Learning module networks from genome-wide location and expression data. FEBS Lett. 2004 Dec 17;578(3):297–304. doi: 10.1016/j.febslet.2004.11.019. [DOI] [PubMed] [Google Scholar]
- Xu Zhiwei, Escamilla-Treviño Luis, Zeng Lihui, Lalgondar Mallikarjun, Bevan David, Winkel Brenda, Mohamed Ali, Cheng Chi-Lien, Shih Ming-Che, Poulton Jonathan. Functional genomic analysis of Arabidopsis thaliana glycoside hydrolase family 1. Plant Mol Biol. 2004 May;55(3):343–367. doi: 10.1007/s11103-004-0790-1. [DOI] [PubMed] [Google Scholar]
- Yao Yufeng, Sturdevant Daniel E., Otto Michael. Genomewide analysis of gene expression in Staphylococcus epidermidis biofilms: insights into the pathophysiology of S. epidermidis biofilms and the role of phenol-soluble modulins in formation of biofilms. J Infect Dis. 2004 Dec 10;191(2):289–298. doi: 10.1086/426945. [DOI] [PubMed] [Google Scholar]
- Yeom Mijung, Shim Insop, Lee Hye-Jung, Hahm Dae-Hyun. Proteomic analysis of nicotine-associated protein expression in the striatum of repeated nicotine-treated rats. Biochem Biophys Res Commun. 2005 Jan 14;326(2):321–328. doi: 10.1016/j.bbrc.2004.11.034. [DOI] [PubMed] [Google Scholar]
- Yim Eun-Kyoung, Lee Keun-Ho, Bae Jun Sang, Namkoong Sung-Eun, Um Soo-Jong, Park Jong-Sup. Proteomic analysis of antiproliferative effects by treatment of 5-fluorouracil in cervical cancer cells. DNA Cell Biol. 2004 Nov;23(11):769–776. doi: 10.1089/dna.2004.23.769. [DOI] [PubMed] [Google Scholar]
- Yim Eun-Kyoung, Meoyng Jin, Namakoong Sung-Eun, Um Soo-Jong, Park Jong-Sup. Genomic and proteomic expression patterns in HPV-16 E6 gene transfected stable human carcinoma cell lines. DNA Cell Biol. 2004 Dec;23(12):826–835. doi: 10.1089/dna.2004.23.826. [DOI] [PubMed] [Google Scholar]
- Zbilut Joseph P., Giuliani Alessandro, Colosimo Alfredo, Mitchell Julie C., Colafranceschi Mauro, Marwan Norbert, Webber Charles L., Jr, Uversky Vladimir N. Charge and hydrophobicity patterning along the sequence predicts the folding mechanism and aggregation of proteins: a computational approach. J Proteome Res. 2004 Nov-Dec;3(6):1243–1253. doi: 10.1021/pr049883+. [DOI] [PubMed] [Google Scholar]
- Zeng Chunyu, Sanada Hironobu, Watanabe Hidetsuna, Eisner Gilbert M., Felder Robin A., Jose Pedro A. Functional genomics of the dopaminergic system in hypertension. Physiol Genomics. 2004 Nov 17;19(3):233–246. doi: 10.1152/physiolgenomics.00127.2004. [DOI] [PubMed] [Google Scholar]
- Zhang Kangling, Siino Joseph S., Jones Patrick R., Yau Peter M., Bradbury E. Morton. A mass spectrometric "Western blot" to evaluate the correlations between histone methylation and histone acetylation. Proteomics. 2004 Dec;4(12):3765–3775. doi: 10.1002/pmic.200400819. [DOI] [PubMed] [Google Scholar]
- Zheng Jun, Zhao Jinfeng, Tao Yazhong, Wang Jianhua, Liu Yunjun, Fu Junjie, Jin Ying, Gao Peng, Zhang Jinpeng, Bai Yunfeng. Isolation and analysis of water stress induced genes in maize seedlings by subtractive PCR and cDNA macroarray. Plant Mol Biol. 2004 Aug;55(6):807–823. doi: 10.1007/s11103-004-1969-1. [DOI] [PubMed] [Google Scholar]
- Zhu Huai-Qiu, Hu Gang-Qing, Ouyang Zheng-Qing, Wang Jin, She Zhen-Su. Accuracy improvement for identifying translation initiation sites in microbial genomes. Bioinformatics. 2004 Jul 9;20(18):3308–3317. doi: 10.1093/bioinformatics/bth390. [DOI] [PubMed] [Google Scholar]
- Zineh I., Gerhard T., Aquilante C. L., Beitelshees A. L., Beasley B. N., Hartzema A. G. Availability of pharmacogenomics-based prescribing information in drug package inserts for currently approved drugs. Pharmacogenomics J. 2004;4(6):354–358. doi: 10.1038/sj.tpj.6500284. [DOI] [PubMed] [Google Scholar]
- Zischka Hans, Gloeckner Christian Johannes, Klein Christian, Willmann Stefanie, Swiatek-de Lange Magdalena, Ueffing Marius. Improved mass spectrometric identification of gel-separated hydrophobic membrane proteins after sodium dodecyl sulfate removal by ion-pair extraction. Proteomics. 2004 Dec;4(12):3776–3782. doi: 10.1002/pmic.200400851. [DOI] [PubMed] [Google Scholar]
- Zou Minjing, Famulski Konrad S., Parhar Ranjit S., Baitei Essa, Al-Mohanna Futwan A., Farid Nadir R., Shi Yufei. Microarray analysis of metastasis-associated gene expression profiling in a murine model of thyroid carcinoma pulmonary metastasis: identification of S100A4 (Mts1) gene overexpression as a poor prognostic marker for thyroid carcinoma. J Clin Endocrinol Metab. 2004 Dec;89(12):6146–6154. doi: 10.1210/jc.2004-0418. [DOI] [PubMed] [Google Scholar]
- da Silva Rafaela, Lucchinetti Eliana, Pasch Thomas, Schaub Marcus C., Zaugg Michael. Ischemic but not pharmacological preconditioning elicits a gene expression profile similar to unprotected myocardium. Physiol Genomics. 2004 Oct 19;20(1):117–130. doi: 10.1152/physiolgenomics.00166.2004. [DOI] [PubMed] [Google Scholar]
- de la Fuente Alberto, Bing Nan, Hoeschele Ina, Mendes Pedro. Discovery of meaningful associations in genomic data using partial correlation coefficients. Bioinformatics. 2004 Jul 29;20(18):3565–3574. doi: 10.1093/bioinformatics/bth445. [DOI] [PubMed] [Google Scholar]
- dos Santos C. C., Han B., Andrade C. F., Bai X., Uhlig S., Hubmayr R., Tsang M., Lodyga M., Keshavjee S., Slutsky A. S. DNA microarray analysis of gene expression in alveolar epithelial cells in response to TNFalpha, LPS, and cyclic stretch. Physiol Genomics. 2004 Sep 28;19(3):331–342. doi: 10.1152/physiolgenomics.00153.2004. [DOI] [PubMed] [Google Scholar]
