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Comparative and Functional Genomics logoLink to Comparative and Functional Genomics
. 2005 Apr;6(3):185–192. doi: 10.1002/cfg.420

Current Awareness on Comparative and Functional Genomics

PMCID: PMC2447519

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Selected References

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  1. Aigner Thomas, Bartnik Eckart, Sohler Florian, Zimmer Ralf. Functional genomics of osteoarthritis: on the way to evaluate disease hypotheses. Clin Orthop Relat Res. 2004 Oct;(427 Suppl):S138–S143. [PubMed] [Google Scholar]
  2. Allen Todd D., Nuss Donald L. Linkage between mitochondrial hypovirulence and viral hypovirulence in the chestnut blight fungus revealed by cDNA microarray analysis. Eukaryot Cell. 2004 Oct;3(5):1227–1232. doi: 10.1128/EC.3.5.1227-1232.2004. [DOI] [PMC free article] [PubMed] [Google Scholar]
  3. Alzate Oscar, Hussain Syed-Rehan A., Goettl Virginia M., Tewari Arun K., Madiai Francesca, Stephens Robert L., Jr, Hackshaw Kevin V. Proteomic identification of brainstem cytosolic proteins in a neuropathic pain model. Brain Res Mol Brain Res. 2004 Sep 28;128(2):193–200. doi: 10.1016/j.molbrainres.2004.06.037. [DOI] [PubMed] [Google Scholar]
  4. Archer David B., Dyer Paul S. From genomics to post-genomics in Aspergillus. Curr Opin Microbiol. 2004 Oct;7(5):499–504. doi: 10.1016/j.mib.2004.08.003. [DOI] [PubMed] [Google Scholar]
  5. Armengaud Patrick, Breitling Rainer, Amtmann Anna. The potassium-dependent transcriptome of Arabidopsis reveals a prominent role of jasmonic acid in nutrient signaling. Plant Physiol. 2004 Sep 3;136(1):2556–2576. doi: 10.1104/pp.104.046482. [DOI] [PMC free article] [PubMed] [Google Scholar]
  6. Babenko Vladimir N., Krylov Dmitri M. Comparative analysis of complete genomes reveals gene loss, acquisition and acceleration of evolutionary rates in Metazoa, suggests a prevalence of evolution via gene acquisition and indicates that the evolutionary rates in animals tend to be conserved. Nucleic Acids Res. 2004 Sep 24;32(17):5029–5035. doi: 10.1093/nar/gkh833. [DOI] [PMC free article] [PubMed] [Google Scholar]
  7. Baross Agnes, Butterfield Yaron S. N., Coughlin Shaun M., Zeng Thomas, Griffith Malachi, Griffith Obi L., Petrescu Anca S., Smailus Duane E., Khattra Jaswinder, McDonald Helen L. Systematic recovery and analysis of full-ORF human cDNA clones. Genome Res. 2004 Oct;14(10B):2083–2092. doi: 10.1101/gr.2473704. [DOI] [PMC free article] [PubMed] [Google Scholar]
  8. Becker Stephen, Cazares Lisa H., Watson Patrice, Lynch Henry, Semmes O. John, Drake Richard R., Laronga Christine. Surfaced-enhanced laser desorption/ionization time-of-flight (SELDI-TOF) differentiation of serum protein profiles of BRCA-1 and sporadic breast cancer. Ann Surg Oncol. 2004 Sep 20;11(10):907–914. doi: 10.1245/ASO.2004.03.557. [DOI] [PubMed] [Google Scholar]
  9. Belosludtsev Yuri Y., Bowerman Dawn, Weil Ryan, Marthandan Nishanth, Balog Robert, Luebke Kevin, Lawson Jonathan, Johnston Stephen A., Lyons C. Rick, Obrien Kevin. Organism identification using a genome sequence-independent universal microarray probe set. Biotechniques. 2004 Oct;37(4):654-8, 660. doi: 10.2144/04374RR02. [DOI] [PubMed] [Google Scholar]
  10. Bernardini Giulia, Renzone Giovanni, Comanducci Maurizio, Mini Roberta, Arena Simona, D'Ambrosio Chiara, Bambini Stefania, Trabalzini Lorenza, Grandi Guido, Martelli Paola. Proteome analysis of Neisseria meningitidis serogroup A. Proteomics. 2004 Oct;4(10):2893–2926. doi: 10.1002/pmic.200400946. [DOI] [PubMed] [Google Scholar]
  11. Bhattacharyya Sudeepa, Siegel Eric R., Petersen Gloria M., Chari Suresh T., Suva Larry J., Haun Randy S. Diagnosis of pancreatic cancer using serum proteomic profiling. Neoplasia. 2004 Sep-Oct;6(5):674–686. doi: 10.1593/neo.04262. [DOI] [PMC free article] [PubMed] [Google Scholar]
  12. Bianchi Fabrizio, Hu Jiangting, Pelosi Giuseppe, Cirincione Rosalia, Ferguson Mary, Ratcliffe Cathy, Di Fiore Pier Paolo, Gatter Kevin, Pezzella Francesco, Pastorino Ugo. Lung cancers detected by screening with spiral computed tomography have a malignant phenotype when analyzed by cDNA microarray. Clin Cancer Res. 2004 Sep 15;10(18 Pt 1):6023–6028. doi: 10.1158/1078-0432.CCR-04-0619. [DOI] [PubMed] [Google Scholar]
  13. Bibikova Marina, Talantov Dimitri, Chudin Eugene, Yeakley Joanne M., Chen Jing, Doucet Dennis, Wickham Eliza, Atkins David, Barker David, Chee Mark. Quantitative gene expression profiling in formalin-fixed, paraffin-embedded tissues using universal bead arrays. Am J Pathol. 2004 Nov;165(5):1799–1807. doi: 10.1016/S0002-9440(10)63435-9. [DOI] [PMC free article] [PubMed] [Google Scholar]
  14. Bino Raoul J., Hall Robert D., Fiehn Oliver, Kopka Joachim, Saito Kazuki, Draper John, Nikolau Basil J., Mendes Pedro, Roessner-Tunali Ute, Beale Michael H. Potential of metabolomics as a functional genomics tool. Trends Plant Sci. 2004 Sep;9(9):418–425. doi: 10.1016/j.tplants.2004.07.004. [DOI] [PubMed] [Google Scholar]
  15. Bièche Ivan, Lerebours Florence, Tozlu Sengül, Espie Marc, Marty Michel, Lidereau Rosette. Molecular profiling of inflammatory breast cancer: identification of a poor-prognosis gene expression signature. Clin Cancer Res. 2004 Oct 15;10(20):6789–6795. doi: 10.1158/1078-0432.CCR-04-0306. [DOI] [PubMed] [Google Scholar]
  16. Blackman Ronald K., Amidon Benjamin S. Microarray approach for cloned library quality assessment and the comprehensive identification of positives from library screens. Biotechniques. 2004 Oct;37(4):536–540. doi: 10.2144/04374BM02. [DOI] [PubMed] [Google Scholar]
  17. Boots Annemieke M., Verhaert Peter D., te Poele Rezie J., Evers Sabine, Coenen-de Roo Christina J., Cleven Jenny, Bos Ebo S. Antigens up the nose: identification of putative biomarkers for nasal tolerance induction functional studies combined with proteomics. J Proteome Res. 2004 Sep-Oct;3(5):1056–1062. doi: 10.1021/pr049907c. [DOI] [PubMed] [Google Scholar]
  18. Borevitz Justin O., Ecker Joseph R. Plant genomics: the third wave. Annu Rev Genomics Hum Genet. 2004;5:443–477. doi: 10.1146/annurev.genom.5.061903.180017. [DOI] [PubMed] [Google Scholar]
  19. Brasaemle Dawn L., Dolios Georgia, Shapiro Lawrence, Wang Rong. Proteomic analysis of proteins associated with lipid droplets of basal and lipolytically stimulated 3T3-L1 adipocytes. J Biol Chem. 2004 Aug 27;279(45):46835–46842. doi: 10.1074/jbc.M409340200. [DOI] [PubMed] [Google Scholar]
  20. Bray James E., Marsden Russell L., Rison Stuart C. G., Savchenko Alexei, Edwards Aled M., Thornton Janet M., Orengo Christine A. A practical and robust sequence search strategy for structural genomics target selection. Bioinformatics. 2004 Jun 16;20(14):2288–2295. doi: 10.1093/bioinformatics/bth240. [DOI] [PubMed] [Google Scholar]
  21. Brazeau Daniel A. Combining genome-wide and targeted gene expression profiling in drug discovery: microarrays and real-time PCR. Drug Discov Today. 2004 Oct 1;9(19):838–845. doi: 10.1016/S1359-6446(04)03231-3. [DOI] [PubMed] [Google Scholar]
  22. Brennan Jonathan P., Wait Robin, Begum Shajna, Bell James R., Dunn Michael J., Eaton Philip. Detection and mapping of widespread intermolecular protein disulfide formation during cardiac oxidative stress using proteomics with diagonal electrophoresis. J Biol Chem. 2004 Aug 2;279(40):41352–41360. doi: 10.1074/jbc.M403827200. [DOI] [PubMed] [Google Scholar]
  23. Breuza Lionel, Halbeisen Regula, Jenö Paul, Otte Stefan, Barlowe Charles, Hong Wanjin, Hauri Hans-Peter. Proteomics of endoplasmic reticulum-Golgi intermediate compartment (ERGIC) membranes from brefeldin A-treated HepG2 cells identifies ERGIC-32, a new cycling protein that interacts with human Erv46. J Biol Chem. 2004 Aug 11;279(45):47242–47253. doi: 10.1074/jbc.M406644200. [DOI] [PubMed] [Google Scholar]
  24. Brunori Lara, Giannoni Federico, Bini Luca, Liberatori Sabrina, Frota Cristiane, Jenner Peter, Thoresen Ove Fredrik, Orefici Graziella, Fattorini Lanfranco. Induction of Mycobacterium avium proteins upon infection of human macrophages. Proteomics. 2004 Oct;4(10):3078–3083. doi: 10.1002/pmic.200300891. [DOI] [PubMed] [Google Scholar]
  25. Bullerwell Charles E., Gray Michael W. Evolution of the mitochondrial genome: protist connections to animals, fungi and plants. Curr Opin Microbiol. 2004 Oct;7(5):528–534. doi: 10.1016/j.mib.2004.08.008. [DOI] [PubMed] [Google Scholar]
  26. Bumann Dirk, Jungblut Peter R., Meyer Thomas F. Helicobacter pylori vaccine development based on combined subproteome analysis. Proteomics. 2004 Oct;4(10):2843–2848. doi: 10.1002/pmic.200400909. [DOI] [PubMed] [Google Scholar]
  27. Caldwell Katherine S., Langridge Peter, Powell Wayne. Comparative sequence analysis of the region harboring the hardness locus in barley and its colinear region in rice. Plant Physiol. 2004 Oct 1;136(2):3177–3190. doi: 10.1104/pp.104.044081. [DOI] [PMC free article] [PubMed] [Google Scholar]
  28. Cao Q. Jackie, Belbin Thomas, Socci Nicholas, Balan Raluca, Prystowsky Michael B., Childs Geoffrey, Jones Joan G. Distinctive gene expression profiles by cDNA microarrays in endometrioid and serous carcinomas of the endometrium. Int J Gynecol Pathol. 2004 Oct;23(4):321–329. doi: 10.1097/01.pgp.0000139646.32997.3a. [DOI] [PubMed] [Google Scholar]
  29. Cargile Benjamin J., Bundy Jonathan L., Stephenson James L., Jr Potential for false positive identifications from large databases through tandem mass spectrometry. J Proteome Res. 2004 Sep-Oct;3(5):1082–1085. doi: 10.1021/pr049946o. [DOI] [PubMed] [Google Scholar]
  30. Carter Scott L., Brechbühler Christian M., Griffin Michael, Bond Andrew T. Gene co-expression network topology provides a framework for molecular characterization of cellular state. Bioinformatics. 2004 May 6;20(14):2242–2250. doi: 10.1093/bioinformatics/bth234. [DOI] [PubMed] [Google Scholar]
  31. Castagna Annalisa, Antonioli Paolo, Astner Hubert, Hamdan Mahmoud, Righetti Sabina Carla, Perego Paola, Zunino Franco, Righetti Pier Giorgio. A proteomic approach to cisplatin resistance in the cervix squamous cell carcinoma cell line A431. Proteomics. 2004 Oct;4(10):3246–3267. doi: 10.1002/pmic.200400835. [DOI] [PubMed] [Google Scholar]
  32. Chain P. S. G., Carniel E., Larimer F. W., Lamerdin J., Stoutland P. O., Regala W. M., Georgescu A. M., Vergez L. M., Land M. L., Motin V. L. Insights into the evolution of Yersinia pestis through whole-genome comparison with Yersinia pseudotuberculosis. Proc Natl Acad Sci U S A. 2004 Sep 9;101(38):13826–13831. doi: 10.1073/pnas.0404012101. [DOI] [PMC free article] [PubMed] [Google Scholar]
  33. Champy Marie-France, Selloum Mohammed, Piard Laetitia, Zeitler Valerie, Caradec Claudia, Chambon Pierre, Auwerx Johan. Mouse functional genomics requires standardization of mouse handling and housing conditions. Mamm Genome. 2004 Oct;15(10):768–783. doi: 10.1007/s00335-004-2393-1. [DOI] [PubMed] [Google Scholar]
  34. Chan Leo Lai, Hodgkiss Ivor John, Wan Jennifer Man-Fan, Lum John Hon-Kei, Mak Abby Sin-Chi, Sit Wai-Hung, Lo Samuel Chun-Lap. Proteomic study of a model causative agent of harmful algal blooms, Prorocentrum triestinum II: the use of differentially expressed protein profiles under different growth phases and growth conditions for bloom prediction. Proteomics. 2004 Oct;4(10):3214–3226. doi: 10.1002/pmic.200300838. [DOI] [PubMed] [Google Scholar]
  35. Chance Mark R., Fiser Andras, Sali Andrej, Pieper Ursula, Eswar Narayanan, Xu Guiping, Fajardo J. Eduardo, Radhakannan Thirumuruhan, Marinkovic Nebojsa. High-throughput computational and experimental techniques in structural genomics. Genome Res. 2004 Oct;14(10B):2145–2154. doi: 10.1101/gr.2537904. [DOI] [PMC free article] [PubMed] [Google Scholar]
  36. Chaurand Pierre, Sanders Melinda E., Jensen Roy A., Caprioli Richard M. Proteomics in diagnostic pathology: profiling and imaging proteins directly in tissue sections. Am J Pathol. 2004 Oct;165(4):1057–1068. doi: 10.1016/S0002-9440(10)63367-6. [DOI] [PMC free article] [PubMed] [Google Scholar]
  37. Chen Jie, Kähne Thilo, Röcken Christoph, Götze Tobias, Yu Jun, Sung Joseph J. Y., Chen Minhu, Hu Pinjin, Malfertheiner Peter, Ebert Matthias P. A. Proteome analysis of gastric cancer metastasis by two-dimensional gel electrophoresis and matrix assisted laser desorption/ionization-mass spectrometry for identification of metastasis-related proteins. J Proteome Res. 2004 Sep-Oct;3(5):1009–1016. doi: 10.1021/pr049916l. [DOI] [PubMed] [Google Scholar]
  38. Chen Nansheng, Lawson Daniel, Bradnam Keith, Harris Todd W., Stein Lincoln D. WormBase as an integrated platform for the C. elegans ORFeome. Genome Res. 2004 Oct;14(10B):2155–2161. doi: 10.1101/gr.2521304. [DOI] [PMC free article] [PubMed] [Google Scholar]
  39. Chen Yann-Jang, Lin Shu-Chun, Kao Tsai, Chang Che-Shoa, Hong Pei-She, Shieh Tzong-Ming, Chang Kuo-Wei. Genome-wide profiling of oral squamous cell carcinoma. J Pathol. 2004 Nov;204(3):326–332. doi: 10.1002/path.1640. [DOI] [PubMed] [Google Scholar]
  40. Chen Yijun, Shi Gongyi, Xia Wei, Kong Christina, Zhao Shuchun, Gaw Allison F., Chen Eunice Y., Yang George P., Giaccia Amato J., Le Quynh-Thu. Identification of hypoxia-regulated proteins in head and neck cancer by proteomic and tissue array profiling. Cancer Res. 2004 Oct 15;64(20):7302–7310. doi: 10.1158/0008-5472.CAN-04-0899. [DOI] [PubMed] [Google Scholar]
  41. Chen Zijun, Peng Bo, Wang Sanying, Peng Xuanxian. Rapid screening of highly efficient vaccine candidates by immunoproteomics. Proteomics. 2004 Oct;4(10):3203–3213. doi: 10.1002/pmic.200300844. [DOI] [PubMed] [Google Scholar]
  42. Chou Kuo-Chen. Insights from modeling the tertiary structure of human BACE2. J Proteome Res. 2004 Sep-Oct;3(5):1069–1072. doi: 10.1021/pr049905s. [DOI] [PubMed] [Google Scholar]
  43. Christopher Kenneth, Liang Yurong, Mueller Thomas F., DeFina Rachel, He Hongzhen, Haley Kathleen J., Exley Mark A., Finn Patricia W., Perkins David L. Analysis of the major histocompatibility complex in graft rejection revisited by gene expression profiles. Transplantation. 2004 Sep 27;78(6):788–798. doi: 10.1097/01.tp.0000128626.13712.88. [DOI] [PubMed] [Google Scholar]
  44. Christopher Mary E., Miranda Manoela, Major Ian T., Constabel C. Peter. Gene expression profiling of systemically wound-induced defenses in hybrid poplar. Planta. 2004 Jun 24;219(6):936–947. doi: 10.1007/s00425-004-1297-3. [DOI] [PubMed] [Google Scholar]
  45. Ciria R., Abreu-Goodger C., Morett E., Merino E. GeConT: gene context analysis. Bioinformatics. 2004 Apr 8;20(14):2307–2308. doi: 10.1093/bioinformatics/bth216. [DOI] [PubMed] [Google Scholar]
  46. Coleman M. A., Lao V. H., Segelke B. W., Beernink P. T. High-throughput, fluorescence-based screening for soluble protein expression. J Proteome Res. 2004 Sep-Oct;3(5):1024–1032. doi: 10.1021/pr049912g. [DOI] [PubMed] [Google Scholar]
  47. Constantin Gabriela D., Krath Britta N., MacFarlane Stuart A., Nicolaisen Mogens, Johansen Ida Elisabeth, Lund Ole S. Virus-induced gene silencing as a tool for functional genomics in a legume species. Plant J. 2004 Nov;40(4):622–631. doi: 10.1111/j.1365-313X.2004.02233.x. [DOI] [PubMed] [Google Scholar]
  48. Coughenour Holly D., Spaulding Reggie S., Thompson Charles M. The synaptic vesicle proteome: a comparative study in membrane protein identification. Proteomics. 2004 Oct;4(10):3141–3155. doi: 10.1002/pmic.200300817. [DOI] [PubMed] [Google Scholar]
  49. Cui Jie-Feng, Liu Yin-Kun, Pan Bo-Shen, Song Hai-Yan, Zhang Yu, Sun Rui-Xia, Chen Jie, Feng Ju-Tao, Tang Zhao-You, Yu Yan-Ling. Differential proteomic analysis of human hepatocellular carcinoma cell line metastasis-associated proteins. J Cancer Res Clin Oncol. 2004 Jul 9;130(10):615–622. doi: 10.1007/s00432-004-0576-5. [DOI] [PMC free article] [PubMed] [Google Scholar]
  50. Cui Jiu-Wei, Wang Jie, He Kun, Jin Bao-Feng, Wang Hong-Xia, Li Wei, Kang Li-Hua, Hu Mei-Ru, Li Hui-Yan, Yu Ming. Proteomic analysis of human acute leukemia cells: insight into their classification. Clin Cancer Res. 2004 Oct 15;10(20):6887–6896. doi: 10.1158/1078-0432.CCR-04-0307. [DOI] [PubMed] [Google Scholar]
  51. Danchin Etienne G. J., Pontarotti Pierre. Statistical evidence for a more than 800-million-year-old evolutionarily conserved genomic region in our genome. J Mol Evol. 2004 Nov;59(5):587–597. doi: 10.1007/s00239-004-2648-1. [DOI] [PubMed] [Google Scholar]
  52. De Cecco Loris, Marchionni Luigi, Gariboldi Manuela, Reid James F., Lagonigro M. Stefania, Caramuta Stefano, Ferrario Cristina, Bussani Erica, Mezzanzanica Delia, Turatti Fabio. Gene expression profiling of advanced ovarian cancer: characterization of a molecular signature involving fibroblast growth factor 2. Oncogene. 2004 Oct 21;23(49):8171–8183. doi: 10.1038/sj.onc.1207979. [DOI] [PubMed] [Google Scholar]
  53. Devauchelle V., Chiocchia G. Quel place pour les puces à ADN dans les maladies inflammatoires? Rev Med Interne. 2004 Oct;25(10):732–739. doi: 10.1016/j.revmed.2004.02.004. [DOI] [PubMed] [Google Scholar]
  54. Dimalanta Eileen T., Lim Alex, Runnheim Rod, Lamers Casey, Churas Chris, Forrest Daniel K., de Pablo Juan J., Graham Michael D., Coppersmith Susan N., Goldstein Steve. A microfluidic system for large DNA molecule arrays. Anal Chem. 2004 Sep 15;76(18):5293–5301. doi: 10.1021/ac0496401. [DOI] [PubMed] [Google Scholar]
  55. Dolinsky T. J., Burgers P. M. J., Karplus K., Baker N. A. SPrCY: comparison of structural predictions in the Saccharomyces cerevisiae genome. Bioinformatics. 2004 Apr 1;20(14):2312–2314. doi: 10.1093/bioinformatics/bth223. [DOI] [PubMed] [Google Scholar]
  56. Donninger Howard, Bonome Tomas, Radonovich Mike, Pise-Masison Cynthia A., Brady John, Shih Joanna H., Barrett J. Carl, Birrer Michael J. Whole genome expression profiling of advance stage papillary serous ovarian cancer reveals activated pathways. Oncogene. 2004 Oct 21;23(49):8065–8077. doi: 10.1038/sj.onc.1207959. [DOI] [PubMed] [Google Scholar]
  57. Downie Andrew, Miyazaki Saori, Bohnert Hans, John Philip, Coleman Julian, Parry Martin, Haslam Richard. Expression profiling of the response of Arabidopsis thaliana to methanol stimulation. Phytochemistry. 2004 Aug;65(16):2305–2316. doi: 10.1016/j.phytochem.2004.07.006. [DOI] [PubMed] [Google Scholar]
  58. Dricot Amélie, Rual Jean-François, Lamesch Philippe, Bertin Nicolas, Dupuy Denis, Hao Tong, Lambert Christophe, Hallez Régis, Delroisse Jean-Marc, Vandenhaute Jean. Generation of the Brucella melitensis ORFeome version 1.1. Genome Res. 2004 Oct;14(10B):2201–2206. doi: 10.1101/gr.2456204. [DOI] [PMC free article] [PubMed] [Google Scholar]
  59. Dumur Catherine I., Nasim Suhail, Best Al M., Archer Kellie J., Ladd Amy C., Mas Valeria R., Wilkinson David S., Garrett Carleton T., Ferreira-Gonzalez Andrea. Evaluation of quality-control criteria for microarray gene expression analysis. Clin Chem. 2004 Sep 13;50(11):1994–2002. doi: 10.1373/clinchem.2004.033225. [DOI] [PubMed] [Google Scholar]
  60. Dvorzhinski Dmitri, Thalasila Anu, Thomas Paul E., Nelson Deirdre, Li Hong, White Eileen, Dipaola Robert S. A novel proteomic coculture model of prostate cancer cell growth. Proteomics. 2004 Oct;4(10):3268–3275. doi: 10.1002/pmic.200400847. [DOI] [PubMed] [Google Scholar]
  61. Eberl Leo, Tümmler Burkhard. Pseudomonas aeruginosa and Burkholderia cepacia in cystic fibrosis: genome evolution, interactions and adaptation. Int J Med Microbiol. 2004 Sep;294(2-3):123–131. doi: 10.1016/j.ijmm.2004.06.022. [DOI] [PubMed] [Google Scholar]
  62. Egelund Jack, Skjøt Michael, Geshi Naomi, Ulvskov Peter, Petersen Bent Larsen. A complementary bioinformatics approach to identify potential plant cell wall glycosyltransferase-encoding genes. Plant Physiol. 2004 Aug 27;136(1):2609–2620. doi: 10.1104/pp.104.042978. [DOI] [PMC free article] [PubMed] [Google Scholar]
  63. Ekstrøm Claus Thorn, Bak Søren, Kristensen Charlotte, Rudemo Mats. Spot shape modelling and data transformations for microarrays. Bioinformatics. 2004 Apr 1;20(14):2270–2278. doi: 10.1093/bioinformatics/bth237. [DOI] [PubMed] [Google Scholar]
  64. Enard Wolfgang, Paabo Svante. Comparative primate genomics. Annu Rev Genomics Hum Genet. 2004;5:351–378. doi: 10.1146/annurev.genom.5.061903.180040. [DOI] [PubMed] [Google Scholar]
  65. Endo Takaho A. Probabilistic nucleotide assembling method for sequencing by hybridization. Bioinformatics. 2004 Apr 8;20(14):2181–2188. doi: 10.1093/bioinformatics/bth202. [DOI] [PubMed] [Google Scholar]
  66. Engellau Jacob, Persson Annette, Bendahl Pär-Ola, Akerman Måns, Domanski Henryk A., Bjerkehagen Bodil, Lilleng Peer, Weide Johan, Rydholm Anders, Alvegård Thor A. Expression profiling using tissue microarray in 211 malignant fibrous histiocytomas confirms the prognostic value of Ki-67. Virchows Arch. 2004 Aug 7;445(3):224–230. doi: 10.1007/s00428-004-1065-6. [DOI] [PubMed] [Google Scholar]
  67. Eriksson Jan, Fenyö David. The statistical significance of protein identification results as a function of the number of protein sequences searched. J Proteome Res. 2004 Sep-Oct;3(5):979–982. doi: 10.1021/pr0499343. [DOI] [PubMed] [Google Scholar]
  68. Espagne Eric, Dupuy Catherine, Huguet Elisabeth, Cattolico Laurence, Provost Bertille, Martins Nathalie, Poirié Marylène, Periquet Georges, Drezen Jean Michel. Genome sequence of a polydnavirus: insights into symbiotic virus evolution. Science. 2004 Oct 8;306(5694):286–289. doi: 10.1126/science.1103066. [DOI] [PubMed] [Google Scholar]
  69. Eymann Christine, Dreisbach Annette, Albrecht Dirk, Bernhardt Jörg, Becher Dörte, Gentner Sandy, Tam Le Thi, Büttner Knut, Buurman Gerrit, Scharf Christian. A comprehensive proteome map of growing Bacillus subtilis cells. Proteomics. 2004 Oct;4(10):2849–2876. doi: 10.1002/pmic.200400907. [DOI] [PubMed] [Google Scholar]
  70. Feng Qian, Yu Huan, Liu Yingying, He Chengqiang, Hu Jingsong, Sang Huachun, Ding Neizheng, Ding Mingxiao, Fung Yin-Wan Wendy, Lau Lok-Ting. Genome comparison of a novel foot-and-mouth disease virus with other FMDV strains. Biochem Biophys Res Commun. 2004 Oct 8;323(1):254–263. doi: 10.1016/j.bbrc.2004.08.086. [DOI] [PubMed] [Google Scholar]
  71. Fernández-Arenas Elena, Molero Gloria, Nombela César, Diez-Orejas Rosalía, Gil Concha. Low virulent strains of Candida albicans: unravelling the antigens for a future vaccine. Proteomics. 2004 Oct;4(10):3007–3020. doi: 10.1002/pmic.200400929. [DOI] [PubMed] [Google Scholar]
  72. Finnskog D., Ressine A., Laurell T., Marko-Varga G. Integrated protein microchip assay with dual fluorescent- and MALDI read-out. J Proteome Res. 2004 Sep-Oct;3(5):988–994. doi: 10.1021/pr0499287. [DOI] [PubMed] [Google Scholar]
  73. Folio Patrice, Chavant Patrick, Chafsey Ingrid, Belkorchia Abdel, Chambon Christophe, Hébraud Michel. Two-dimensional electrophoresis database of Listeria monocytogenes EGDe proteome and proteomic analysis of mid-log and stationary growth phase cells. Proteomics. 2004 Oct;4(10):3187–3201. doi: 10.1002/pmic.200300841. [DOI] [PubMed] [Google Scholar]
  74. Fountoulakis Michael. Application of proteomics technologies in the investigation of the brain. Mass Spectrom Rev. 2004 Jul-Aug;23(4):231–258. doi: 10.1002/mas.10075. [DOI] [PubMed] [Google Scholar]
  75. Franceschetti Marina, Perry Barry, Thompson Benjamin, Hanfrey Colin, Michael Anthony J. Expression proteomics identifies biochemical adaptations and defense responses in transgenic plants with perturbed polyamine metabolism. FEBS Lett. 2004 Oct 22;576(3):477–480. doi: 10.1016/j.febslet.2004.08.085. [DOI] [PubMed] [Google Scholar]
  76. Franscini Nicola, Bachli Esther B., Blau Nenad, Leikauf Maria-Sybille, Schaffner Andreas, Schoedon Gabriele. Gene expression profiling of inflamed human endothelial cells and influence of activated protein C. Circulation. 2004 Oct 25;110(18):2903–2909. doi: 10.1161/01.CIR.0000146344.49689.BB. [DOI] [PubMed] [Google Scholar]
  77. Freiberg Christoph, Brötz-Oesterhelt Heike, Labischinski Harald. The impact of transcriptome and proteome analyses on antibiotic drug discovery. Curr Opin Microbiol. 2004 Oct;7(5):451–459. doi: 10.1016/j.mib.2004.08.010. [DOI] [PubMed] [Google Scholar]
  78. Fujishima Naohito, Hirokawa Makoto, Aiba Namiko, Ichikawa Yoshikazu, Fujishima Masumi, Komatsuda Atsushi, Suzuki Yoshiko, Kawabata Yoshinari, Miura Ikuo, Sawada Ken-ichi. Gene expression profiling of human erythroid progenitors by micro-serial analysis of gene expression. Int J Hematol. 2004 Oct;80(3):239–245. doi: 10.1532/ijh97.04053. [DOI] [PubMed] [Google Scholar]
  79. Fung Kim Y. C., Askovic Srdjan, Basile Franco, Duncan Mark W. A simple and inexpensive approach to interfacing high-performance liquid chromatography and matrix-assisted laser desorption/ionization-time of flight-mass spectrometry. Proteomics. 2004 Oct;4(10):3121–3127. doi: 10.1002/pmic.200300843. [DOI] [PubMed] [Google Scholar]
  80. Fülöp A. K., Falus A. Possibilities and results in the wide-scale genomic analysis of inflammation. Looking for the child among many midwives. Inflamm Res. 2004 Oct;53(10):517–522. doi: 10.1007/s00011-004-1293-x. [DOI] [PubMed] [Google Scholar]
  81. Gao Xue-Qin, Han Jin-Xiang, Huang Hai-Yan, Yan Shi, Song Chang-Zheng, Huang Hai-Nan. Effects of aspirin on metastasis-associated gene expression detected by cDNA microarray. Acta Pharmacol Sin. 2004 Oct;25(10):1327–1333. [PubMed] [Google Scholar]
  82. Gatti L., Chen D., Beretta G. L., Rustici G., Carenini N., Corna E., Colangelo D., Zunino F., Bähler J., Perego P. Global gene expression of fission yeast in response to cisplatin. Cell Mol Life Sci. 2004 Sep;61(17):2253–2263. doi: 10.1007/s00018-004-4218-5. [DOI] [PMC free article] [PubMed] [Google Scholar]
  83. Geer Lewis Y., Markey Sanford P., Kowalak Jeffrey A., Wagner Lukas, Xu Ming, Maynard Dawn M., Yang Xiaoyu, Shi Wenyao, Bryant Stephen H. Open mass spectrometry search algorithm. J Proteome Res. 2004 Sep-Oct;3(5):958–964. doi: 10.1021/pr0499491. [DOI] [PubMed] [Google Scholar]
  84. Gehrmann Marion L., Hathout Yetrib, Fenselau Catherine. Evaluation of metabolic labeling for comparative proteomics in breast cancer cells. J Proteome Res. 2004 Sep-Oct;3(5):1063–1068. doi: 10.1021/pr049906k. [DOI] [PubMed] [Google Scholar]
  85. Gibly Avi, Bonshtien Arale, Balaji Vasudevan, Debbie Paul, Martin Gregory B., Sessa Guido. Identification and expression profiling of tomato genes differentially regulated during a resistance response to Xanthomonas campestris pv. vesicatoria. Mol Plant Microbe Interact. 2004 Nov;17(11):1212–1222. doi: 10.1094/MPMI.2004.17.11.1212. [DOI] [PubMed] [Google Scholar]
  86. Gil Rosario, Latorre Amparo, Moya Andrés. Bacterial endosymbionts of insects: insights from comparative genomics. Environ Microbiol. 2004 Nov;6(11):1109–1122. doi: 10.1111/j.1462-2920.2004.00691.x. [DOI] [PubMed] [Google Scholar]
  87. Gordon Paul M. K., Sensen Christoph W. Osprey: a comprehensive tool employing novel methods for the design of oligonucleotides for DNA sequencing and microarrays. Nucleic Acids Res. 2004 Sep 29;32(17):e133–e133. doi: 10.1093/nar/gnh127. [DOI] [PMC free article] [PubMed] [Google Scholar]
  88. Greenough Carrie, Jenkins Rosalind E., Kitteringham Neil R., Pirmohamed Munir, Park B. Kevin, Pennington Stephen R. A method for the rapid depletion of albumin and immunoglobulin from human plasma. Proteomics. 2004 Oct;4(10):3107–3111. doi: 10.1002/pmic.200300815. [DOI] [PubMed] [Google Scholar]
  89. Grønborg Mads, Bunkenborg Jakob, Kristiansen Troels Zakarias, Jensen Ole Nørregaard, Yeo Charles J., Hruban Ralph H., Maitra Anirban, Goggins Michael G., Pandey Akhilesh. Comprehensive proteomic analysis of human pancreatic juice. J Proteome Res. 2004 Sep-Oct;3(5):1042–1055. doi: 10.1021/pr0499085. [DOI] [PubMed] [Google Scholar]
  90. Grützmann Robert, Pilarsky Christian, Ammerpohl Ole, Lüttges Jutta, Böhme Armin, Sipos Bence, Foerder Melanie, Alldinger Ingo, Jahnke Beatrix, Schackert Hans Konrad. Gene expression profiling of microdissected pancreatic ductal carcinomas using high-density DNA microarrays. Neoplasia. 2004 Sep-Oct;6(5):611–622. doi: 10.1593/neo.04295. [DOI] [PMC free article] [PubMed] [Google Scholar]
  91. Hagopian Jonathan C., Reis Marcelo, Kitajima João P., Bhattacharya Debashish, de Oliveira Mariana C. Comparative analysis of the complete plastid genome sequence of the red alga Gracilaria tenuistipitata var. liui provides insights into the evolution of rhodoplasts and their relationship to other plastids. J Mol Evol. 2004 Oct;59(4):464–477. doi: 10.1007/s00239-004-2638-3. [DOI] [PubMed] [Google Scholar]
  92. Harcus Doreen, Nantel André, Marcil Anne, Rigby Tracey, Whiteway Malcolm. Transcription profiling of cyclic AMP signaling in Candida albicans. Mol Biol Cell. 2004 Jul 21;15(10):4490–4499. doi: 10.1091/mbc.E04-02-0144. [DOI] [PMC free article] [PubMed] [Google Scholar]
  93. Harris Jennifer, Mason Daniel E., Li Jun, Burdick Keith W., Backes Bradley J., Chen Teresa, Shipway Aaron, Van Heeke Gino, Gough Lucy, Ghaemmaghami Amir. Activity profile of dust mite allergen extract using substrate libraries and functional proteomic microarrays. Chem Biol. 2004 Oct;11(10):1361–1372. doi: 10.1016/j.chembiol.2004.08.008. [DOI] [PubMed] [Google Scholar]
  94. Haslinger Christian, Schweifer Norbert, Stilgenbauer Stephan, Döhner Hartmut, Lichter Peter, Kraut Norbert, Stratowa Christian, Abseher Roger. Microarray gene expression profiling of B-cell chronic lymphocytic leukemia subgroups defined by genomic aberrations and VH mutation status. J Clin Oncol. 2004 Oct 1;22(19):3937–3949. doi: 10.1200/JCO.2004.12.133. [DOI] [PubMed] [Google Scholar]
  95. Hata F., Nishimori H., Yasoshima T., Tanaka H., Ohno K., Yanai Y., Ezoe E., Kamiguchi K., Isomura H., Denno R. Profiling analysis of differential gene expression between hematogenous and peritoneal metastatic sublines of human pancreatic cancer using a DNA chip. J Exp Clin Cancer Res. 2004 Sep;23(3):513–520. [PubMed] [Google Scholar]
  96. He Qing-Ye, Cheung Yim Hing, Leung Suet Yi, Yuen Siu Tsan, Chu Kent-Man, Chiu Jen-Fu. Diverse proteomic alterations in gastric adenocarcinoma. Proteomics. 2004 Oct;4(10):3276–3287. doi: 10.1002/pmic.200300916. [DOI] [PubMed] [Google Scholar]
  97. Heredia-Langner Alejandro, Cannon William R., Jarman Kenneth D., Jarman Kristin H. Sequence optimization as an alternative to de novo analysis of tandem mass spectrometry data. Bioinformatics. 2004 Apr 15;20(14):2296–2304. doi: 10.1093/bioinformatics/bth242. [DOI] [PubMed] [Google Scholar]
  98. Hermann Thomas. Using functional genomics to improve productivity in the manufacture of industrial biochemicals. Curr Opin Biotechnol. 2004 Oct;15(5):444–448. doi: 10.1016/j.copbio.2004.07.002. [DOI] [PubMed] [Google Scholar]
  99. Hermansson Monika, Sawaji Yasunobu, Bolton Mark, Alexander Susan, Wallace Andrew, Begum Shajna, Wait Robin, Saklatvala Jeremy. Proteomic analysis of articular cartilage shows increased type II collagen synthesis in osteoarthritis and expression of inhibin betaA (activin A), a regulatory molecule for chondrocytes. J Biol Chem. 2004 Aug 2;279(42):43514–43521. doi: 10.1074/jbc.M407041200. [DOI] [PubMed] [Google Scholar]
  100. Hettick Justin M., Kashon Michael L., Simpson Janet P., Siegel Paul D., Mazurek Gerald H., Weissman David N. Proteomic profiling of intact mycobacteria by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry. Anal Chem. 2004 Oct 1;76(19):5769–5776. doi: 10.1021/ac049410m. [DOI] [PubMed] [Google Scholar]
  101. Hilson Pierre, Allemeersch Joke, Altmann Thomas, Aubourg Sébastien, Avon Alexandra, Beynon Jim, Bhalerao Rishikesh P., Bitton Frédérique, Caboche Michel, Cannoot Bernard. Versatile gene-specific sequence tags for Arabidopsis functional genomics: transcript profiling and reverse genetics applications. Genome Res. 2004 Oct;14(10B):2176–2189. doi: 10.1101/gr.2544504. [DOI] [PMC free article] [PubMed] [Google Scholar]
  102. Hirschberg Daniel, Jägerbrink Theres, Samskog Jenny, Gustafsson Magnus, Ståhlberg Marie, Alvelius Gunvor, Husman Bolette, Carlquist Mats, Jörnvall Hans, Bergman Tomas. Detection of phosphorylated peptides in proteomic analyses using microfluidic compact disk technology. Anal Chem. 2004 Oct 1;76(19):5864–5871. doi: 10.1021/ac040044g. [DOI] [PubMed] [Google Scholar]
  103. Hivnor Chad, Williams Nathan, Singh Fiza, VanVoorhees Abby, Dzubow Leonard, Baldwin Donald, Seykora John. Gene expression profiling of porokeratosis demonstrates similarities with psoriasis. J Cutan Pathol. 2004 Nov;31(10):657–664. doi: 10.1111/j.0303-6987.2004.00247.x. [DOI] [PubMed] [Google Scholar]
  104. Ho Eun-Mi, Chang Hyo-Won, Kim Seung-Il, Kahng Hyung-Yeel, Oh Kye-Heon. Analysis of TNT (2,4,6-trinitrotoluene)-inducible cellular responses and stress shock proteome in Stenotrophomonas sp. OK-5. Curr Microbiol. 2004 Nov;49(5):346–352. doi: 10.1007/s00284-004-4322-7. [DOI] [PubMed] [Google Scholar]
  105. Hong Soon Ho, Kim Jin Sik, Lee Sang Yup, In Yong Ho, Choi Sun Shim, Rih Jeong-Keun, Kim Chang Hoon, Jeong Haeyoung, Hur Cheol Goo, Kim Jae Jong. The genome sequence of the capnophilic rumen bacterium Mannheimia succiniciproducens. Nat Biotechnol. 2004 Sep 19;22(10):1275–1281. doi: 10.1038/nbt1010. [DOI] [PubMed] [Google Scholar]
  106. Hope Ian A., Stevens Jonathan, Garner Anna, Hayes Josie, Cheo David L., Brasch Michael A., Vidal Marc. Feasibility of genome-scale construction of promoter::reporter gene fusions for expression in Caenorhabditis elegans using a multisite gateway recombination system. Genome Res. 2004 Oct;14(10B):2070–2075. doi: 10.1101/gr.2463804. [DOI] [PMC free article] [PubMed] [Google Scholar]
  107. Huang Zhen-Yu, Yang Peng-Yuan, Almofti Mohamad Radwan, Yu Yan-Ling, Rui Yao-Cheng, Yang Peng-Yuan. Comparative analysis of the proteome of left ventricular heart of arteriosclerosis in rat. Life Sci. 2004 Nov 12;75(26):3103–3115. doi: 10.1016/j.lfs.2004.04.054. [DOI] [PubMed] [Google Scholar]
  108. Huber Thomas, Faulkner Geoffrey, Hugenholtz Philip. Bellerophon: a program to detect chimeric sequences in multiple sequence alignments. Bioinformatics. 2004 Apr 8;20(14):2317–2319. doi: 10.1093/bioinformatics/bth226. [DOI] [PubMed] [Google Scholar]
  109. Hubálek Martin, Hernychová Lenka, Brychta Martin, Lenco Juraj, Zechovská Jana, Stulík Jirí. Comparative proteome analysis of cellular proteins extracted from highly virulent Francisella tularensis ssp. tularensis and less virulent F. tularensis ssp. holarctica and F. tularensis ssp. mediaasiatica. Proteomics. 2004 Oct;4(10):3048–3060. doi: 10.1002/pmic.200400939. [DOI] [PubMed] [Google Scholar]
  110. Hughes Timothy R., Robinson Mark D., Mitsakakis Nicholas, Johnston Mark. The promise of functional genomics: completing the encyclopedia of a cell. Curr Opin Microbiol. 2004 Oct;7(5):546–554. doi: 10.1016/j.mib.2004.08.015. [DOI] [PubMed] [Google Scholar]
  111. Hurst A. G. B., Goad D. W., Mohan M., Malayer J. R. Independent downstream gene expression profiles in the presence of estrogen receptor alpha or beta. Biol Reprod. 2004 Jun 16;71(4):1252–1261. doi: 10.1095/biolreprod.104.029421. [DOI] [PubMed] [Google Scholar]
  112. International Human Genome Sequencing Consortium Finishing the euchromatic sequence of the human genome. Nature. 2004 Oct 21;431(7011):931–945. doi: 10.1038/nature03001. [DOI] [PubMed] [Google Scholar]
  113. Iragne Florian, Barré Aurélien, Goffard Nicolas, De Daruvar Antoine. AliasServer: a web server to handle multiple aliases used to refer to proteins. Bioinformatics. 2004 Apr 1;20(14):2331–2332. doi: 10.1093/bioinformatics/bth241. [DOI] [PubMed] [Google Scholar]
  114. Ishikawa Jun, Yamashita Atsushi, Mikami Yuzuru, Hoshino Yasutaka, Kurita Haruyo, Hotta Kunimoto, Shiba Tadayoshi, Hattori Masahira. The complete genomic sequence of Nocardia farcinica IFM 10152. Proc Natl Acad Sci U S A. 2004 Oct 4;101(41):14925–14930. doi: 10.1073/pnas.0406410101. [DOI] [PMC free article] [PubMed] [Google Scholar]
  115. Jacquot Jean-Pierre, Rouhier Nicolas, Navrot Nicolas, Decottignies Jean-Pierre. Generation of polyclonal antibodies against multiple proteins in a single rabbit and subsequent isolation of the specific immunoglobulins as a tool for proteomics research. Biotechnol Appl Biochem. 2004 Oct;40(Pt 2):181–185. doi: 10.1042/BA20030196. [DOI] [PubMed] [Google Scholar]
  116. Jaillon Olivier, Aury Jean-Marc, Brunet Frédéric, Petit Jean-Louis, Stange-Thomann Nicole, Mauceli Evan, Bouneau Laurence, Fischer Cécile, Ozouf-Costaz Catherine, Bernot Alain. Genome duplication in the teleost fish Tetraodon nigroviridis reveals the early vertebrate proto-karyotype. Nature. 2004 Oct 21;431(7011):946–957. doi: 10.1038/nature03025. [DOI] [PubMed] [Google Scholar]
  117. Jansen Ronald, Gerstein Mark. Analyzing protein function on a genomic scale: the importance of gold-standard positives and negatives for network prediction. Curr Opin Microbiol. 2004 Oct;7(5):535–545. doi: 10.1016/j.mib.2004.08.012. [DOI] [PubMed] [Google Scholar]
  118. Jeon Geoung A., Lee Ju-Seog, Patel Vyomesh, Gutkind J. Silvio, Thorgeirsson Snorri S., Kim Eun Cheol, Chu In-Sun, Amornphimoltham Panomwat, Park Myung Hee. Global gene expression profiles of human head and neck squamous carcinoma cell lines. Int J Cancer. 2004 Nov 1;112(2):249–258. doi: 10.1002/ijc.20399. [DOI] [PubMed] [Google Scholar]
  119. Jiang Feng, Yin Zhengnan, Caraway Nancy P., Li Ruiyun, Katz Ruth L. Genomic profiles in stage I primary non small cell lung cancer using comparative genomic hybridization analysis of cDNA microarrays. Neoplasia. 2004 Sep-Oct;6(5):623–635. doi: 10.1593/neo.04142. [DOI] [PMC free article] [PubMed] [Google Scholar]
  120. Ju Xin-Sheng, Zenke Martin. Gene expression profiling of dendritic cells by DNA microarrays. Immunobiology. 2004;209(1-2):155–161. doi: 10.1016/j.imbio.2004.02.005. [DOI] [PubMed] [Google Scholar]
  121. Kainuma Kazuyuki, Katsuno Satoshi, Hashimoto Shigenari, Suzuki Nobuyoshi, Oguchi Tomohiro, Asamura Kenji, Nakajima Kosei, Usami Shin-ichi. Identification of differentially expressed genes in salivary gland tumors with cDNA microarray. Auris Nasus Larynx. 2004 Sep;31(3):261–268. doi: 10.1016/j.anl.2004.03.012. [DOI] [PubMed] [Google Scholar]
  122. Kan Biao, Habibi Hajar, Schmid Monika, Liang Weili, Wang Ruibai, Wang Duochun, Jungblut Peter R. Proteome comparison of Vibrio cholerae cultured in aerobic and anaerobic conditions. Proteomics. 2004 Oct;4(10):3061–3067. doi: 10.1002/pmic.200400944. [DOI] [PubMed] [Google Scholar]
  123. Kaneko Maki, Masui Ryoji, Ake Kojiro, Kousumi Yukihide, Kuramitsu Seiki, Yamaguchi Minoru, Kuyama Hiroki, Ando Eiji, Norioka Shigemi, Nakazawa Takashi. Rapid and sensitive amino-acid sequencing of cloning Thermus thermophilus HB8 ferredoxin by proteomics. J Proteome Res. 2004 Sep-Oct;3(5):983–987. doi: 10.1021/pr049929z. [DOI] [PubMed] [Google Scholar]
  124. Kantardjieff Katherine A., Rupp Bernhard. Protein isoelectric point as a predictor for increased crystallization screening efficiency. Bioinformatics. 2004 Feb 10;20(14):2162–2168. doi: 10.1093/bioinformatics/bth066. [DOI] [PubMed] [Google Scholar]
  125. Kaposi-Novak Pal, Lee Ju-Seog, Mikaelyan Arsen, Patel Vyomesh, Thorgeirsson Snorri S. Oligonucleotide microarray analysis of aminoallyl-labeled cDNA targets from linear RNA amplification. Biotechniques. 2004 Oct;37(4):580, 582-6, 588. doi: 10.2144/04374ST02. [DOI] [PubMed] [Google Scholar]
  126. Katayama Shintaro, Kanamori Mutsumi, Hayashizaki Yoshihide. Integrated analysis of the genome and the transcriptome by FANTOM. Brief Bioinform. 2004 Sep;5(3):249–258. doi: 10.1093/bib/5.3.249. [DOI] [PubMed] [Google Scholar]
  127. Kavsan Vadym, Shostak Katherina, Dmitrenko Vladimir, Chausovskiy Timur, Zozulya Yury, Demotes-Mainard Jacques. Peculiarities of molecular events in human glial tumors revealed by serial analysis of gene expression (SAGE). Exp Oncol. 2004 Sep;26(3):196–204. [PubMed] [Google Scholar]
  128. Kazemi-Pour Nasrin, Condemine Guy, Hugouvieux-Cotte-Pattat Nicole. The secretome of the plant pathogenic bacterium Erwinia chrysanthemi. Proteomics. 2004 Oct;4(10):3177–3186. doi: 10.1002/pmic.200300814. [DOI] [PubMed] [Google Scholar]
  129. Knaust Andreas, Frosch Matthias. Genome-based vaccines. Int J Med Microbiol. 2004 Oct;294(5):295–301. doi: 10.1016/j.ijmm.2004.07.008. [DOI] [PubMed] [Google Scholar]
  130. Komori T., Takemasa I., Higuchi H., Yamasaki M., Ikeda M., Yamamoto H., Ohue M., Nakamori S., Sekimoto M., Matsubara K. Identification of differentially expressed genes involved in colorectal carcinogenesis using a cDNA microarray. J Exp Clin Cancer Res. 2004 Sep;23(3):521–527. [PubMed] [Google Scholar]
  131. Krah Alexander, Wessel Ralf, Pleissner Klaus-Peter. Assessment of protein spot components applying correspondence analysis for peptide mass fingerprint data. Proteomics. 2004 Oct;4(10):2982–2986. doi: 10.1002/pmic.200400926. [DOI] [PubMed] [Google Scholar]
  132. Kunz M., Ibrahim S. M., Koczan D., Scheid S., Thiesen H. J., Gross G. DNA microarray technology and its applications in dermatology. Exp Dermatol. 2004 Oct;13(10):593–606. doi: 10.1111/j.0906-6705.2004.00243.x. [DOI] [PubMed] [Google Scholar]
  133. Kwak Jae-Yong, Ma Tian-Ze, Yoo Min-Jeong, Choi Bok Hee, Kim Han-Gyu, Kim So-Ri, Yim Chang-Yeol, Kwak Yong-Geun. The comparative analysis of serum proteomes for the discovery of biomarkers for acute myeloid leukemia. Exp Hematol. 2004 Sep;32(9):836–842. doi: 10.1016/j.exphem.2004.06.006. [DOI] [PubMed] [Google Scholar]
  134. Lamesch Philippe, Milstein Stuart, Hao Tong, Rosenberg Jennifer, Li Ning, Sequerra Reynaldo, Bosak Stephanie, Doucette-Stamm Lynn, Vandenhaute Jean, Hill David E. C. elegans ORFeome version 3.1: increasing the coverage of ORFeome resources with improved gene predictions. Genome Res. 2004 Oct;14(10B):2064–2069. doi: 10.1101/gr.2496804. [DOI] [PMC free article] [PubMed] [Google Scholar]
  135. Lau Andy T. Y., He Qing-Yu, Chiu Jen-Fu. A proteome analysis of the arsenite response in cultured lung cells: evidence for in vitro oxidative stress-induced apoptosis. Biochem J. 2004 Sep 1;382(Pt 2):641–650. doi: 10.1042/BJ20040224. [DOI] [PMC free article] [PubMed] [Google Scholar]
  136. Le Meur Nolwenn, Lamirault Guillaume, Bihouée Audrey, Steenman Marja, Bédrine-Ferran Hélène, Teusan Raluca, Ramstein Gérard, Léger Jean J. A dynamic, web-accessible resource to process raw microarray scan data into consolidated gene expression values: importance of replication. Nucleic Acids Res. 2004 Oct 8;32(18):5349–5358. doi: 10.1093/nar/gkh870. [DOI] [PMC free article] [PubMed] [Google Scholar]
  137. Lee Heun-Sik, Park Mie-Hee, Yang Suk-Jin, Jung Hai-Young, Byun Sang-Soon, Lee Dong-Seok, Yoo Hyang-Sook, Yeom Young Il, Seo Sang-Beom. Gene expression analysis in human gastric cancer cell line treated with trichostatin A and S-adenosyl-L-homocysteine using cDNA microarray. Biol Pharm Bull. 2004 Oct;27(10):1497–1503. doi: 10.1248/bpb.27.1497. [DOI] [PubMed] [Google Scholar]
  138. Lett H. A NOTE ON TWO CASES OF A FOREIGN BODY IN THE URINARY BLADDER. Br Med J. 1927 Jan 22;1(3446):138–139. doi: 10.1136/bmj.1.3446.138. [DOI] [PMC free article] [PubMed] [Google Scholar]
  139. Li Nan, Shaw Andrew R. E., Zhang Nan, Mak Allan, Li Liang. Lipid raft proteomics: analysis of in-solution digest of sodium dodecyl sulfate-solubilized lipid raft proteins by liquid chromatography-matrix-assisted laser desorption/ionization tandem mass spectrometry. Proteomics. 2004 Oct;4(10):3156–3166. doi: 10.1002/pmic.200400832. [DOI] [PubMed] [Google Scholar]
  140. Liska Adam J., Shevchenko Andrej, Pick Uri, Katz Adriana. Enhanced photosynthesis and redox energy production contribute to salinity tolerance in Dunaliella as revealed by homology-based proteomics. Plant Physiol. 2004 Aug 27;136(1):2806–2817. doi: 10.1104/pp.104.039438. [DOI] [PMC free article] [PubMed] [Google Scholar]
  141. Liu Tao, Qian Wei-Jun, Strittmatter Eric F., Camp David G., 2nd, Anderson Gordon A., Thrall Brian D., Smith Richard D. High-throughput comparative proteome analysis using a quantitative cysteinyl-peptide enrichment technology. Anal Chem. 2004 Sep 15;76(18):5345–5353. doi: 10.1021/ac049485q. [DOI] [PubMed] [Google Scholar]
  142. Liu Xiao-Hua, Qian Ling-Jia, Gong Jing-Bo, Shen Jing, Zhang Xue-Min, Qian Xiao-Hong. Proteomic analysis of mitochondrial proteins in cardiomyocytes from chronic stressed rat. Proteomics. 2004 Oct;4(10):3167–3176. doi: 10.1002/pmic.200300845. [DOI] [PubMed] [Google Scholar]
  143. Lu Henry, Li Weiqun, Noble William Stafford, Payan Donald, Anderson D. C. Riboproteomics of the hepatitis C virus internal ribosomal entry site. J Proteome Res. 2004 Sep-Oct;3(5):949–957. doi: 10.1021/pr0499592. [DOI] [PubMed] [Google Scholar]
  144. Lu Hongchao, Zhu Xiaopeng, Liu Haifeng, Skogerbø Geir, Zhang Jingfen, Zhang Yong, Cai Lun, Zhao Yi, Sun Shiwei, Xu Jingyi. The interactome as a tree--an attempt to visualize the protein-protein interaction network in yeast. Nucleic Acids Res. 2004 Sep 8;32(16):4804–4811. doi: 10.1093/nar/gkh814. [DOI] [PMC free article] [PubMed] [Google Scholar]
  145. Lu Jun, Lal Anita, Merriman Barry, Nelson Stan, Riggins Gregory. A comparison of gene expression profiles produced by SAGE, long SAGE, and oligonucleotide chips. Genomics. 2004 Oct;84(4):631–636. doi: 10.1016/j.ygeno.2004.06.014. [DOI] [PubMed] [Google Scholar]
  146. Maguire Patricia B., Moran Niamh, Cagney Gerard, Fitzgerald Desmond J. Application of proteomics to the study of platelet regulatory mechanisms. Trends Cardiovasc Med. 2004 Aug;14(6):207–220. doi: 10.1016/j.tcm.2004.06.001. [DOI] [PubMed] [Google Scholar]
  147. Mahlamäki Eija H., Kauraniemi Päivikki, Monni Outi, Wolf Maija, Hautaniemi Sampsa, Kallioniemi Anne. High-resolution genomic and expression profiling reveals 105 putative amplification target genes in pancreatic cancer. Neoplasia. 2004 Sep-Oct;6(5):432–439. doi: 10.1593/neo.04130. [DOI] [PMC free article] [PubMed] [Google Scholar]
  148. Marin Kay, Kanesaki Yu, Los Dmitry A., Murata Norio, Suzuki Iwane, Hagemann Martin. Gene expression profiling reflects physiological processes in salt acclimation of Synechocystis sp. strain PCC 6803. Plant Physiol. 2004 Sep 10;136(2):3290–3300. doi: 10.1104/pp.104.045047. [DOI] [PMC free article] [PubMed] [Google Scholar]
  149. Marko-Varga György A., Fehniger Thomas E. Microscale protein expression profiling during disease evolvement. J Chromatogr A. 2004 Oct 22;1053(1-2):279–290. doi: 10.1016/j.chroma.2004.08.115. [DOI] [PubMed] [Google Scholar]
  150. Marques Maria Angela M., Espinosa Benjamin J., Xavier da Silveira Erika K., Pessolani Maria Cristina V., Chapeaurouge Alex, Perales Jonas, Dobos Karen M., Belisle John T., Spencer John S., Brennan Patrick J. Continued proteomic analysis of Mycobacterium leprae subcellular fractions. Proteomics. 2004 Oct;4(10):2942–2953. doi: 10.1002/pmic.200400945. [DOI] [PubMed] [Google Scholar]
  151. Mateos-Cáceres Petra J., García-Méndez Antonio, López Farré Antonio, Macaya Carlos, Núez Antonio, Gómez Juan, Alonso-Orgaz Sergio, Carrasco Carolina, Burgos Marta Escribano, de Andrés Raimundo. Proteomic analysis of plasma from patients during an acute coronary syndrome. J Am Coll Cardiol. 2004 Oct 19;44(8):1578–1583. doi: 10.1016/j.jacc.2004.06.073. [DOI] [PubMed] [Google Scholar]
  152. Mattow Jens, Schmidt Frank, Höhenwarter Wolfgang, Siejak Frank, Schaible Ulrich E., Kaufmann Stefan H. E. Protein identification and tracking in two-dimensional electrophoretic gels by minimal protein identifiers. Proteomics. 2004 Oct;4(10):2927–2941. doi: 10.1002/pmic.200400908. [DOI] [PubMed] [Google Scholar]
  153. Meschia James F. Clinically translated ischemic stroke genomics. Stroke. 2004 Sep 9;35(11 Suppl 1):2735–2739. doi: 10.1161/01.STR.0000143156.32467.fd. [DOI] [PubMed] [Google Scholar]
  154. Metsis Ats, Andersson Ulf, Baurén Göran, Ernfors Patrik, Lönnerberg Peter, Montelius Andreas, Oldin Mats, Pihlak Arno, Linnarsson Sten. Whole-genome expression profiling through fragment display and combinatorial gene identification. Nucleic Acids Res. 2004 Sep 8;32(16):e127–e127. doi: 10.1093/nar/gnh126. [DOI] [PMC free article] [PubMed] [Google Scholar]
  155. Miller Ingrid, Friedlein Arno, Tsangaris George, Maris Antony, Fountoulakis Michael, Gemeiner Manfred. The serum proteome of Equus caballus. Proteomics. 2004 Oct;4(10):3227–3234. doi: 10.1002/pmic.200400846. [DOI] [PubMed] [Google Scholar]
  156. Miller Webb, Makova Kateryna D., Nekrutenko Anton, Hardison Ross C. Comparative genomics. Annu Rev Genomics Hum Genet. 2004;5:15–56. doi: 10.1146/annurev.genom.5.061903.180057. [DOI] [PubMed] [Google Scholar]
  157. Mischel Paul S., Cloughesy Timothy F., Nelson Stanley F. DNA-microarray analysis of brain cancer: molecular classification for therapy. Nat Rev Neurosci. 2004 Oct;5(10):782–792. doi: 10.1038/nrn1518. [DOI] [PubMed] [Google Scholar]
  158. Misteli Tom. Spatial positioning; a new dimension in genome function. Cell. 2004 Oct 15;119(2):153–156. doi: 10.1016/j.cell.2004.09.035. [DOI] [PubMed] [Google Scholar]
  159. Mollenkopf Hans Joachim, Grode Leander, Mattow Jens, Stein Maik, Mann Peggy, Knapp Bernhard, Ulmer Jeffrey, Kaufmann Stefan H. E. Application of mycobacterial proteomics to vaccine design: improved protection by Mycobacterium bovis BCG prime-Rv3407 DNA boost vaccination against tuberculosis. Infect Immun. 2004 Nov;72(11):6471–6479. doi: 10.1128/IAI.72.11.6471-6479.2004. [DOI] [PMC free article] [PubMed] [Google Scholar]
  160. Mueller Rachel Lockridge, Macey J. Robert, Jaekel Martin, Wake David B., Boore Jeffrey L. Morphological homoplasy, life history evolution, and historical biogeography of plethodontid salamanders inferred from complete mitochondrial genomes. Proc Natl Acad Sci U S A. 2004 Sep 13;101(38):13820–13825. doi: 10.1073/pnas.0405785101. [DOI] [PMC free article] [PubMed] [Google Scholar]
  161. Méhul B., Asselineau D., Bernard D., Leclaire J., Régnier M., Schmidt R., Bernerd F. Gene expression profiles of three different models of reconstructed human epidermis and classical cultures of keratinocytes using cDNA arrays. Arch Dermatol Res. 2004 Sep;296(4):145–156. doi: 10.1007/s00403-004-0491-2. [DOI] [PubMed] [Google Scholar]
  162. Newton Kelly A., Pitteri Sharon J., Laskowski Michael, Jr, McLuckey Scott A. Effects of single amino acid substitution on the collision-induced dissociation of intact protein ions: Turkey ovomucoid third domain. J Proteome Res. 2004 Sep-Oct;3(5):1033–1041. doi: 10.1021/pr049910w. [DOI] [PMC free article] [PubMed] [Google Scholar]
  163. Ning Wen, Li Chao-Jun, Kaminski Naftali, Feghali-Bostwick Carol A., Alber Sean M., Di Yuanpu P., Otterbein Sherrie L., Song Ruiping, Hayashi Shizu, Zhou Zhihong. Comprehensive gene expression profiles reveal pathways related to the pathogenesis of chronic obstructive pulmonary disease. Proc Natl Acad Sci U S A. 2004 Oct 5;101(41):14895–14900. doi: 10.1073/pnas.0401168101. [DOI] [PMC free article] [PubMed] [Google Scholar]
  164. Nishidate Toshihiko, Katagiri Toyomasa, Lin Meng-Lay, Mano Yuria, Miki Yoshio, Kasumi Fujio, Yoshimoto Masataka, Tsunoda Tatsuhiko, Hirata Koichi, Nakamura Yusuke. Genome-wide gene-expression profiles of breast-cancer cells purified with laser microbeam microdissection: identification of genes associated with progression and metastasis. Int J Oncol. 2004 Oct;25(4):797–819. [PubMed] [Google Scholar]
  165. Noirot Philippe, Noirot-Gros Marie-Françoise. Protein interaction networks in bacteria. Curr Opin Microbiol. 2004 Oct;7(5):505–512. doi: 10.1016/j.mib.2004.08.005. [DOI] [PubMed] [Google Scholar]
  166. Nosek J., Novotna M., Hlavatovicova Z., Ussery D. W., Fajkus J., Tomaska L. Complete DNA sequence of the linear mitochondrial genome of the pathogenic yeast Candida parapsilosis. Mol Genet Genomics. 2004 Jul 29;272(2):173–180. doi: 10.1007/s00438-004-1046-0. [DOI] [PubMed] [Google Scholar]
  167. Novichkov Pavel S., Omelchenko Marina V., Gelfand Mikhail S., Mironov Andrei A., Wolf Yuri I., Koonin Eugene V. Genome-wide molecular clock and horizontal gene transfer in bacterial evolution. J Bacteriol. 2004 Oct;186(19):6575–6585. doi: 10.1128/JB.186.19.6575-6585.2004. [DOI] [PMC free article] [PubMed] [Google Scholar]
  168. Oh J. E., Krapfenbauer K., Lubec G. Proteomic basis for the possible use of lymphocytes for metabolic screenings. Amino Acids. 2004 Oct 4;27(2):141–147. doi: 10.1007/s00726-004-0127-z. [DOI] [PubMed] [Google Scholar]
  169. Okkels Limei Meng, Müller Eva-Christina, Schmid Monika, Rosenkrands Ida, Kaufmann Stefan H. E., Andersen Peter, Jungblut Peter R. CFP10 discriminates between nonacetylated and acetylated ESAT-6 of Mycobacterium tuberculosis by differential interaction. Proteomics. 2004 Oct;4(10):2954–2960. doi: 10.1002/pmic.200400906. [DOI] [PubMed] [Google Scholar]
  170. Olsen Jesper V., Mann Matthias. Improved peptide identification in proteomics by two consecutive stages of mass spectrometric fragmentation. Proc Natl Acad Sci U S A. 2004 Sep 3;101(37):13417–13422. doi: 10.1073/pnas.0405549101. [DOI] [PMC free article] [PubMed] [Google Scholar]
  171. Ordovas Jose M., Corella Dolores. Nutritional genomics. Annu Rev Genomics Hum Genet. 2004;5:71–118. doi: 10.1146/annurev.genom.5.061903.180008. [DOI] [PubMed] [Google Scholar]
  172. Orsetti Béatrice, Nugoli Mélanie, Cervera Nathalie, Lasorsa Laurence, Chuchana Paul, Ursule Lisa, Nguyen Catherine, Redon Richard, du Manoir Stanislas, Rodriguez Carmen. Genomic and expression profiling of chromosome 17 in breast cancer reveals complex patterns of alterations and novel candidate genes. Cancer Res. 2004 Sep 15;64(18):6453–6460. doi: 10.1158/0008-5472.CAN-04-0756. [DOI] [PubMed] [Google Scholar]
  173. Osiro Denise, Muniz João Renato C., Coleta Filho Helvécio Della, de Sousa Alessandra Alves, Machado Marcos Antonio, Garratt Richard C., Colnago Luiz Alberto. Fatty acid synthesis in Xylella fastidiosa: correlations between genome studies, 13C NMR data, and molecular models. Biochem Biophys Res Commun. 2004 Oct 22;323(3):987–995. doi: 10.1016/j.bbrc.2004.08.183. [DOI] [PubMed] [Google Scholar]
  174. Panse Vikram Govind, Hardeland Ulrike, Werner Thilo, Kuster Bernhard, Hurt Ed. A proteome-wide approach identifies sumoylated substrate proteins in yeast. J Biol Chem. 2004 Jul 30;279(40):41346–41351. doi: 10.1074/jbc.M407950200. [DOI] [PubMed] [Google Scholar]
  175. Pasa-Tolić Ljiljana, Masselon Christophe, Barry Richard C., Shen Yufeng, Smith Richard D. Proteomic analyses using an accurate mass and time tag strategy. Biotechniques. 2004 Oct;37(4):621-4, 626-33, 636 passim. doi: 10.2144/04374RV01. [DOI] [PubMed] [Google Scholar]
  176. Pearson Talima, Busch Joseph D., Ravel Jacques, Read Timothy D., Rhoton Shane D., U'Ren Jana M., Simonson Tatum S., Kachur Sergey M., Leadem Rebecca R., Cardon Michelle L. Phylogenetic discovery bias in Bacillus anthracis using single-nucleotide polymorphisms from whole-genome sequencing. Proc Natl Acad Sci U S A. 2004 Sep 3;101(37):13536–13541. doi: 10.1073/pnas.0403844101. [DOI] [PMC free article] [PubMed] [Google Scholar]
  177. Petros William P., Evans William E. Pharmacogenomics in cancer therapy: is host genome variability important? Trends Pharmacol Sci. 2004 Sep;25(9):457–464. doi: 10.1016/j.tips.2004.07.007. [DOI] [PubMed] [Google Scholar]
  178. Pitarch Aida, Abian Joaquín, Carrascal Montserrat, Sánchez Miguel, Nombela César, Gil Concha. Proteomics-based identification of novel Candida albicans antigens for diagnosis of systemic candidiasis in patients with underlying hematological malignancies. Proteomics. 2004 Oct;4(10):3084–3106. doi: 10.1002/pmic.200400903. [DOI] [PubMed] [Google Scholar]
  179. Pleissner Klaus-Peter, Schmelzer Peter, Wehrl Wolfgang, Jungblut Peter R. Presentation of differentially regulated proteins within a web-accessible proteome database system of microorganisms. Proteomics. 2004 Oct;4(10):2987–2990. doi: 10.1002/pmic.200400927. [DOI] [PubMed] [Google Scholar]
  180. Pogue Robert, Sebald Eiman, King Lily, Kronstadt Erik, Krakow Deborah, Cohn Daniel H. A transcriptional profile of human fetal cartilage. Matrix Biol. 2004 Aug;23(5):299–307. doi: 10.1016/j.matbio.2004.07.003. [DOI] [PubMed] [Google Scholar]
  181. Pop Mihai, Phillippy Adam, Delcher Arthur L., Salzberg Steven L. Comparative genome assembly. Brief Bioinform. 2004 Sep;5(3):237–248. doi: 10.1093/bib/5.3.237. [DOI] [PubMed] [Google Scholar]
  182. Prinz Thorsten, Müller Jörg, Kuhn Karsten, Schäfer Jürgen, Thompson Andrew, Schwarz Josef, Hamon Christian. Characterization of low abundant membrane proteins using the protein sequence tag technology. J Proteome Res. 2004 Sep-Oct;3(5):1073–1081. doi: 10.1021/pr049925u. [DOI] [PubMed] [Google Scholar]
  183. Puente Lawrence G., Carrière Jean-François, Kelly John F., Megeney Lynn A. Comparative analysis of phosphoprotein-enriched myocyte proteomes reveals widespread alterations during differentiation. FEBS Lett. 2004 Sep 10;574(1-3):138–144. doi: 10.1016/j.febslet.2004.08.019. [DOI] [PubMed] [Google Scholar]
  184. Qian Bin, Goldstein Richard A. Performance of an iterated T-HMM for homology detection. Bioinformatics. 2004 Mar 25;20(14):2175–2180. doi: 10.1093/bioinformatics/bth181. [DOI] [PubMed] [Google Scholar]
  185. Qin Li-Xuan, Kerr Kathleen F., Contributing Members of the Toxicogenomics Research Consortium Empirical evaluation of data transformations and ranking statistics for microarray analysis. Nucleic Acids Res. 2004 Oct 12;32(18):5471–5479. doi: 10.1093/nar/gkh866. [DOI] [PMC free article] [PubMed] [Google Scholar]
  186. Qiu Dongru, Fujita Kyoko, Sakuma Yuko, Tanaka Teruo, Ohashi Yoshiaki, Ohshima Hideyuki, Tomita Masaru, Itaya Mitsuhiro. Comparative analysis of physical maps of four Bacillus subtilis (natto) genomes. Appl Environ Microbiol. 2004 Oct;70(10):6247–6256. doi: 10.1128/AEM.70.10.6247-6256.2004. [DOI] [PMC free article] [PubMed] [Google Scholar]
  187. Rhomberg Thomas A., Karlberg Olof, Mini Thierry, Zimny-Arndt Ursula, Wickenberg Ulrika, Röttgen Marlene, Jungblut Peter R., Jenö Paul, Andersson Siv G. E., Dehio Christoph. Proteomic analysis of the sarcosine-insoluble outer membrane fraction of the bacterial pathogen Bartonella henselae. Proteomics. 2004 Oct;4(10):3021–3033. doi: 10.1002/pmic.200400933. [DOI] [PubMed] [Google Scholar]
  188. Riemer Constanze, Neidhold Sabine, Burwinkel Michael, Schwarz Anja, Schultz Julia, Krätzschmar Jörn, Mönning Ursula, Baier Michael. Gene expression profiling of scrapie-infected brain tissue. Biochem Biophys Res Commun. 2004 Oct 15;323(2):556–564. doi: 10.1016/j.bbrc.2004.08.124. [DOI] [PubMed] [Google Scholar]
  189. Ringnér Markus, Veerla Srinivas, Andersson Samuel, Staaf Johan, Häkkinen Jari. ACID: a database for microarray clone information. Bioinformatics. 2004 Feb 12;20(14):2305–2306. doi: 10.1093/bioinformatics/bth089. [DOI] [PubMed] [Google Scholar]
  190. Robinson Stephen J., Cram Dustin J., Lewis Christopher T., Parkin Isobel A. P. Maximizing the efficacy of SAGE analysis identifies novel transcripts in Arabidopsis. Plant Physiol. 2004 Oct;136(2):3223–3233. doi: 10.1104/pp.104.043406. [DOI] [PMC free article] [PubMed] [Google Scholar]
  191. Robson Barry, Mushlin Richard. Genomic messaging system and DNA mark-up language for information-based personalized medicine with clinical and proteome research applications. J Proteome Res. 2004 Sep-Oct;3(5):930–948. doi: 10.1021/pr0341336. [DOI] [PubMed] [Google Scholar]
  192. Rocha Eduardo P. C. Order and disorder in bacterial genomes. Curr Opin Microbiol. 2004 Oct;7(5):519–527. doi: 10.1016/j.mib.2004.08.006. [DOI] [PubMed] [Google Scholar]
  193. Roos Viktoria, Andersson Charlotte I. J., Bülow Leif. Gene expression profiling of Escherichia coli expressing double Vitreoscilla haemoglobin. J Biotechnol. 2004 Oct 19;114(1-2):107–120. doi: 10.1016/j.jbiotec.2004.07.002. [DOI] [PubMed] [Google Scholar]
  194. Rosen Ran, Becher Dörte, Büttner Knut, Biran Dvora, Hecker Michael, Ron Eliora Z. Highly phosphorylated bacterial proteins. Proteomics. 2004 Oct;4(10):3068–3077. doi: 10.1002/pmic.200400890. [DOI] [PubMed] [Google Scholar]
  195. Rozing Gerard, Nägele Edgar, Hörth Patric, Vollmer Martin, Moritz Ralf, Glatz Bernd, Gratzfeld-Hüsgen Angelika. Instrumentation for advanced microseparations in pharmaceutical analysis and proteomics. J Biochem Biophys Methods. 2004 Sep 30;60(3):233–263. doi: 10.1016/j.jbbm.2004.01.005. [DOI] [PubMed] [Google Scholar]
  196. Rual Jean-François, Ceron Julian, Koreth John, Hao Tong, Nicot Anne-Sophie, Hirozane-Kishikawa Tomoko, Vandenhaute Jean, Orkin Stuart H., Hill David E., van den Heuvel Sander. Toward improving Caenorhabditis elegans phenome mapping with an ORFeome-based RNAi library. Genome Res. 2004 Oct;14(10B):2162–2168. doi: 10.1101/gr.2505604. [DOI] [PMC free article] [PubMed] [Google Scholar]
  197. Rual Jean-François, Hirozane-Kishikawa Tomoko, Hao Tong, Bertin Nicolas, Li Siming, Dricot Amélie, Li Ning, Rosenberg Jennifer, Lamesch Philippe, Vidalain Pierre-Olivier. Human ORFeome version 1.1: a platform for reverse proteomics. Genome Res. 2004 Oct;14(10B):2128–2135. doi: 10.1101/gr.2973604. [DOI] [PMC free article] [PubMed] [Google Scholar]
  198. Ruepp Andreas, Zollner Alfred, Maier Dieter, Albermann Kaj, Hani Jean, Mokrejs Martin, Tetko Igor, Güldener Ulrich, Mannhaupt Gertrud, Münsterkötter Martin. The FunCat, a functional annotation scheme for systematic classification of proteins from whole genomes. Nucleic Acids Res. 2004 Oct 14;32(18):5539–5545. doi: 10.1093/nar/gkh894. [DOI] [PMC free article] [PubMed] [Google Scholar]
  199. Ruf Frederique, Sealfon Stuart C. Genomics view of gonadotrope signaling circuits. Trends Endocrinol Metab. 2004 Sep;15(7):331–338. doi: 10.1016/j.tem.2004.07.008. [DOI] [PubMed] [Google Scholar]
  200. Sagoo Gurdeep S., Cork Michael J., Patel Ramila, Tazi-Ahnini Rachid. Genome-wide studies of psoriasis susceptibility loci: a review. J Dermatol Sci. 2004 Sep;35(3):171–179. doi: 10.1016/j.jdermsci.2004.02.009. [DOI] [PubMed] [Google Scholar]
  201. Sam-Yellowe Tobili Y., Florens Laurence, Wang Tongmin, Raine J. Dale, Carucci Daniel J., Sinden Robert, Yates John R., 3rd Proteome analysis of rhoptry-enriched fractions isolated from Plasmodium merozoites. J Proteome Res. 2004 Sep-Oct;3(5):995–1001. doi: 10.1021/pr049926m. [DOI] [PubMed] [Google Scholar]
  202. Schaumburg Jessica, Diekmann Oliver, Hagendorff Petra, Bergmann Simone, Rohde Manfred, Hammerschmidt Sven, Jänsch Lothar, Wehland Jürgen, Kärst Uwe. The cell wall subproteome of Listeria monocytogenes. Proteomics. 2004 Oct;4(10):2991–3006. doi: 10.1002/pmic.200400928. [DOI] [PubMed] [Google Scholar]
  203. Scheible Wolf-Rüdiger, Morcuende Rosa, Czechowski Tomasz, Fritz Christina, Osuna Daniel, Palacios-Rojas Natalia, Schindelasch Dana, Thimm Oliver, Udvardi Michael K., Stitt Mark. Genome-wide reprogramming of primary and secondary metabolism, protein synthesis, cellular growth processes, and the regulatory infrastructure of Arabidopsis in response to nitrogen. Plant Physiol. 2004 Sep;136(1):2483–2499. doi: 10.1104/pp.104.047019. [DOI] [PMC free article] [PubMed] [Google Scholar]
  204. Schrader Jarmo, Moyle Richard, Bhalerao Rupali, Hertzberg Magnus, Lundeberg Joakim, Nilsson Peter, Bhalerao Rishikesh P. Cambial meristem dormancy in trees involves extensive remodelling of the transcriptome. Plant J. 2004 Oct;40(2):173–187. doi: 10.1111/j.1365-313X.2004.02199.x. [DOI] [PubMed] [Google Scholar]
  205. Selbach Matthias, Moese Stefan, Backert Steffen, Jungblut Peter R., Meyer Thomas F. The Helicobacter pylori CagA protein induces tyrosine dephosphorylation of ezrin. Proteomics. 2004 Oct;4(10):2961–2968. doi: 10.1002/pmic.200400915. [DOI] [PubMed] [Google Scholar]
  206. Sharp Robert E., Poroyko Valeriy, Hejlek Lindsey G., Spollen William G., Springer Gordon K., Bohnert Hans J., Nguyen Henry T. Root growth maintenance during water deficits: physiology to functional genomics. J Exp Bot. 2004 Sep 24;55(407):2343–2351. doi: 10.1093/jxb/erh276. [DOI] [PubMed] [Google Scholar]
  207. She Xinwei, Jiang Zhaoshi, Clark Royden A., Liu Ge, Cheng Ze, Tuzun Eray, Church Deanna M., Sutton Granger, Halpern Aaron L., Eichler Evan E. Shotgun sequence assembly and recent segmental duplications within the human genome. Nature. 2004 Oct 21;431(7011):927–930. doi: 10.1038/nature03062. [DOI] [PubMed] [Google Scholar]
  208. Shibata Hiroko, Nakagawa Shinsaku, Mayumi Tadanori, Tsutsumi Yasuo. Development of novel drug delivery system (DDS) technologies for proteomic-based drug development. Biol Pharm Bull. 2004 Oct;27(10):1483–1488. doi: 10.1248/bpb.27.1483. [DOI] [PubMed] [Google Scholar]
  209. Sims Andrew H., Gent Manda E., Robson Geoffrey D., Dunn-Coleman Nigel S., Oliver Stephen G. Combining transcriptome data with genomic and cDNA sequence alignments to make confident functional assignments for Aspergillus nidulans genes. Mycol Res. 2004 Aug;108(Pt 8):853–857. doi: 10.1017/s095375620400067x. [DOI] [PubMed] [Google Scholar]
  210. Sioud Mouldy, Røsok Oystein. Profiling microRNA expression using sensitive cDNA probes and filter arrays. Biotechniques. 2004 Oct;37(4):574-6, 578-80. doi: 10.2144/04374ST01. [DOI] [PubMed] [Google Scholar]
  211. Sironi Luigi, Guerrini Uliano, Tremoli Elena, Miller Ingrid, Gelosa Paolo, Lascialfari Alessandro, Zucca Ileana, Eberini Ivano, Gemeiner Manfred, Paoletti Rodolfo. Analysis of pathological events at the onset of brain damage in stroke-prone rats: a proteomics and magnetic resonance imaging approach. J Neurosci Res. 2004 Oct 1;78(1):115–122. doi: 10.1002/jnr.20219. [DOI] [PubMed] [Google Scholar]
  212. Smith Steven M., Fulton Daniel C., Chia Tansy, Thorneycroft David, Chapple Andrew, Dunstan Hannah, Hylton Christopher, Zeeman Samuel C., Smith Alison M. Diurnal changes in the transcriptome encoding enzymes of starch metabolism provide evidence for both transcriptional and posttranscriptional regulation of starch metabolism in Arabidopsis leaves. Plant Physiol. 2004 Sep 3;136(1):2687–2699. doi: 10.1104/pp.104.044347. [DOI] [PMC free article] [PubMed] [Google Scholar]
  213. Snyder Jennifer A., Haugen Brian J., Buckles Eric L., Lockatell C. Virginia, Johnson David E., Donnenberg Michael S., Welch Rodney A., Mobley Harry L. T. Transcriptome of uropathogenic Escherichia coli during urinary tract infection. Infect Immun. 2004 Nov;72(11):6373–6381. doi: 10.1128/IAI.72.11.6373-6381.2004. [DOI] [PMC free article] [PubMed] [Google Scholar]
  214. Soltis Douglas E., Albert Victor A., Savolainen Vincent, Hilu Khidir, Qiu Yin-Long, Chase Mark W., Farris James S., Stefanović Sasa, Rice Danny W., Palmer Jeffrey D. Genome-scale data, angiosperm relationships, and "ending incongruence": a cautionary tale in phylogenetics. Trends Plant Sci. 2004 Oct;9(10):477–483. doi: 10.1016/j.tplants.2004.08.008. [DOI] [PubMed] [Google Scholar]
  215. Sommer Andrei P. Suffocation of nerve fibers by living nanovesicles: a model simulation--part II. J Proteome Res. 2004 Sep-Oct;3(5):1086–1088. doi: 10.1021/pr049935v. [DOI] [PubMed] [Google Scholar]
  216. Stelling Jörg. Mathematical models in microbial systems biology. Curr Opin Microbiol. 2004 Oct;7(5):513–518. doi: 10.1016/j.mib.2004.08.004. [DOI] [PubMed] [Google Scholar]
  217. Sterky Fredrik, Bhalerao Rupali R., Unneberg Per, Segerman Bo, Nilsson Peter, Brunner Amy M., Charbonnel-Campaa Laurence, Lindvall Jenny Jonsson, Tandre Karolina, Strauss Steven H. A Populus EST resource for plant functional genomics. Proc Natl Acad Sci U S A. 2004 Sep 7;101(38):13951–13956. doi: 10.1073/pnas.0401641101. [DOI] [PMC free article] [PubMed] [Google Scholar]
  218. Stolc Viktor, Gauhar Zareen, Mason Christopher, Halasz Gabor, van Batenburg Marinus F., Rifkin Scott A., Hua Sujun, Herreman Tine, Tongprasit Waraporn, Barbano Paolo Emilio. A gene expression map for the euchromatic genome of Drosophila melanogaster. Science. 2004 Oct 22;306(5696):655–660. doi: 10.1126/science.1101312. [DOI] [PubMed] [Google Scholar]
  219. Strader Michael Brad, Verberkmoes Nathan C., Tabb David L., Connelly Heather M., Barton John W., Bruce Barry D., Pelletier Dale A., Davison Brian H., Hettich Robert L., Larimer Frank W. Characterization of the 70S Ribosome from Rhodopseudomonas palustris using an integrated "top-down" and "bottom-up" mass spectrometric approach. J Proteome Res. 2004 Sep-Oct;3(5):965–978. doi: 10.1021/pr049940z. [DOI] [PubMed] [Google Scholar]
  220. Streit Wolfgang R., Schmitz Ruth A. Metagenomics--the key to the uncultured microbes. Curr Opin Microbiol. 2004 Oct;7(5):492–498. doi: 10.1016/j.mib.2004.08.002. [DOI] [PubMed] [Google Scholar]
  221. Stöver T., Wissel K., Averbeck T., Lenarz T., Altschuler R. A. Charakterisierung der Genexpression im Innenohr und der Hörbahn hörender und ertaubter Ratten mittels Gene-Arrays. Laryngorhinootologie. 2004 Sep;83(9):597–605. doi: 10.1055/s-2004-814503. [DOI] [PubMed] [Google Scholar]
  222. Suganuma Norio, Yamamoto Atsuko, Itou Ai, Hakoyama Tsuneo, Banba Mari, Hata Shingo, Kawaguchi Masayoshi, Kouchi Hiroshi. cDNA macroarray analysis of gene expression in ineffective nodules induced on the Lotus japonicus sen1 mutant. Mol Plant Microbe Interact. 2004 Nov;17(11):1223–1233. doi: 10.1094/MPMI.2004.17.11.1223. [DOI] [PubMed] [Google Scholar]
  223. Supek Fran, Vlahovicek Kristian. INCA: synonymous codon usage analysis and clustering by means of self-organizing map. Bioinformatics. 2004 Apr 1;20(14):2329–2330. doi: 10.1093/bioinformatics/bth238. [DOI] [PubMed] [Google Scholar]
  224. Susko Edward, Roger Andrew J. Estimating and comparing the rates of gene discovery and expressed sequence tag (EST) frequencies in EST surveys. Bioinformatics. 2004 Apr 1;20(14):2279–2287. doi: 10.1093/bioinformatics/bth239. [DOI] [PubMed] [Google Scholar]
  225. Suzuki Yuji, Kawazu Tetsu, Koyama Hiroyuki. RNA isolation from siliques, dry seeds, and other tissues of Arabidopsis thaliana. Biotechniques. 2004 Oct;37(4):542–544. doi: 10.2144/04374BM03. [DOI] [PubMed] [Google Scholar]
  226. Taboada Eduardo N., Acedillo Rey R., Carrillo Catherine D., Findlay Wendy A., Medeiros Diane T., Mykytczuk Oksana L., Roberts Michael J., Valencia C. Alexander, Farber Jeffrey M., Nash John H. E. Large-scale comparative genomics meta-analysis of Campylobacter jejuni isolates reveals low level of genome plasticity. J Clin Microbiol. 2004 Oct;42(10):4566–4576. doi: 10.1128/JCM.42.10.4566-4576.2004. [DOI] [PMC free article] [PubMed] [Google Scholar]
  227. Tian Huan, Cao Liching, Tan Yuping, Williams Stephen, Chen Lili, Matray Tracy, Chenna Ahmed, Moore Sean, Hernandez Vincent, Xiao Vivian. Multiplex mRNA assay using electrophoretic tags for high-throughput gene expression analysis. Nucleic Acids Res. 2004 Sep 8;32(16):e126–e126. doi: 10.1093/nar/gnh119. [DOI] [PMC free article] [PubMed] [Google Scholar]
  228. Tsai Inn-Ho, Chen Yi-Hsuan, Wang Ying-Ming. Comparative proteomics and subtyping of venom phospholipases A2 and disintegrins of Protobothrops pit vipers. Biochim Biophys Acta. 2004 Oct 1;1702(1):111–119. doi: 10.1016/j.bbapap.2004.08.006. [DOI] [PubMed] [Google Scholar]
  229. Tsai Jyh-Ming, Wang Han-Ching, Leu Jiann-Horng, Hsiao He-Hsuan, Wang Andrew H-J, Kou Guang-Hsiung, Lo Chu-Fang. Genomic and proteomic analysis of thirty-nine structural proteins of shrimp white spot syndrome virus. J Virol. 2004 Oct;78(20):11360–11370. doi: 10.1128/JVI.78.20.11360-11370.2004. [DOI] [PMC free article] [PubMed] [Google Scholar]
  230. Tsai Yin Te, Huang Yen Pin, Yu Ching Ta, Lu Chin Lung. MuSiC: a tool for multiple sequence alignment with constraints. Bioinformatics. 2004 Apr 1;20(14):2309–2311. doi: 10.1093/bioinformatics/bth220. [DOI] [PubMed] [Google Scholar]
  231. Tsou Meng-Ting, Ho Jin-Yuan, Lin Chao-Hsiung, Chiu Jen-Hwey. Proteomic analysis finds different myocardial protective mechanisms for median nerve stimulation by electroacupuncture and by local somatothermal stimulation. Int J Mol Med. 2004 Oct;14(4):553–563. [PubMed] [Google Scholar]
  232. Tsutsumi Chizuko, Ueda Masuzu, Miyazaki Yasushi, Yamashita Yoshihiro, Choi Young Lim, Ota Jun, Kaneda Ruri, Koinuma Koji, Fujiwara Shin-ichiro, Kisanuki Hiroyuki. DNA microarray analysis of dysplastic morphology associated with acute myeloid leukemia. Exp Hematol. 2004 Sep;32(9):828–835. doi: 10.1016/j.exphem.2004.06.003. [DOI] [PubMed] [Google Scholar]
  233. Ueda Kenji, Yamashita Atsushi, Ishikawa Jun, Shimada Masafumi, Watsuji Tomo-o, Morimura Kohji, Ikeda Haruo, Hattori Masahira, Beppu Teruhiko. Genome sequence of Symbiobacterium thermophilum, an uncultivable bacterium that depends on microbial commensalism. Nucleic Acids Res. 2004 Sep 21;32(16):4937–4944. doi: 10.1093/nar/gkh830. [DOI] [PMC free article] [PubMed] [Google Scholar]
  234. Uetz Peter, Rajagopala Seesandra V., Dong Yu-An, Haas Jürgen. From ORFeomes to protein interaction maps in viruses. Genome Res. 2004 Oct;14(10B):2029–2033. doi: 10.1101/gr.2583304. [DOI] [PubMed] [Google Scholar]
  235. Vandahl Brian B. S., Birkelund Svend, Christiansen Gunna. Genome and proteome analysis of Chlamydia. Proteomics. 2004 Oct;4(10):2831–2842. doi: 10.1002/pmic.200400940. [DOI] [PubMed] [Google Scholar]
  236. Varnum Susan M., Streblow Daniel N., Monroe Matthew E., Smith Patricia, Auberry Kenneth J., Pasa-Tolic Ljiljana, Wang Dai, Camp David G., 2nd, Rodland Karin, Wiley Steven. Identification of proteins in human cytomegalovirus (HCMV) particles: the HCMV proteome. J Virol. 2004 Oct;78(20):10960–10966. doi: 10.1128/JVI.78.20.10960-10966.2004. [DOI] [PMC free article] [PubMed] [Google Scholar]
  237. Veenstra Timothy D., Prieto Darue A., Conrads Thomas P. Proteomic patterns for early cancer detection. Drug Discov Today. 2004 Oct 15;9(20):889–897. doi: 10.1016/S1359-6446(04)03246-5. [DOI] [PubMed] [Google Scholar]
  238. Vercauteren Freya G. G., Bergeron John J. M., Vandesande Frans, Arckens Lut, Quirion Rémi. Proteomic approaches in brain research and neuropharmacology. Eur J Pharmacol. 2004 Oct 1;500(1-3):385–398. doi: 10.1016/j.ejphar.2004.07.039. [DOI] [PubMed] [Google Scholar]
  239. Verhoeckx Kitty C. M., Bijlsma Sabina, Jespersen Sonja, Ramaker Raymond, Verheij Elwin R., Witkamp Renger F., van der Greef Jan, Rodenburg Richard J. T. Characterization of anti-inflammatory compounds using transcriptomics, proteomics, and metabolomics in combination with multivariate data analysis. Int Immunopharmacol. 2004 Nov;4(12):1499–1514. doi: 10.1016/j.intimp.2004.07.008. [DOI] [PubMed] [Google Scholar]
  240. Vocadlo David J., Bertozzi Carolyn R. A strategy for functional proteomic analysis of glycosidase activity from cell lysates. Angew Chem Int Ed Engl. 2004 Oct 11;43(40):5338–5342. doi: 10.1002/anie.200454235. [DOI] [PubMed] [Google Scholar]
  241. Voisine Pierre, Ruel Marc, Khan Tanveer A., Bianchi Cesario, Xu Shu-Hua, Kohane Isaac, Libermann Towia A., Otu Hasan, Saltiel Alan R., Sellke Frank W. Differences in gene expression profiles of diabetic and nondiabetic patients undergoing cardiopulmonary bypass and cardioplegic arrest. Circulation. 2004 Sep 14;110(11 Suppl 1):II280–II286. doi: 10.1161/01.CIR.0000138974.18839.02. [DOI] [PubMed] [Google Scholar]
  242. Wang Daojing, Park Jennifer S., Chu Julia S. F., Krakowski Ari, Luo Kunxin, Chen David J., Li Song. Proteomic profiling of bone marrow mesenchymal stem cells upon transforming growth factor beta1 stimulation. J Biol Chem. 2004 Aug 9;279(42):43725–43734. doi: 10.1074/jbc.M407368200. [DOI] [PubMed] [Google Scholar]
  243. Wang Ena, Lichtenfels Rudolf, Bükur Jurgen, Ngalame Yvonne, Panelli Monica C., Seliger Barbara, Marincola Francesco M. Ontogeny and oncogenesis balance the transcriptional profile of renal cell cancer. Cancer Res. 2004 Oct 15;64(20):7279–7287. doi: 10.1158/0008-5472.CAN-04-1597. [DOI] [PubMed] [Google Scholar]
  244. Wang Jian, Robinson John F., Khan Hafiz M. R., Carter David E., McKinney James, Miskie Brooke A., Hegele Robert A. Optimizing RNA extraction yield from whole blood for microarray gene expression analysis. Clin Biochem. 2004 Sep;37(9):741–744. doi: 10.1016/j.clinbiochem.2004.03.013. [DOI] [PubMed] [Google Scholar]
  245. Wang Rongchen, Tischner Rudolf, Gutiérrez Rodrigo A., Hoffman Maren, Xing Xiujuan, Chen Mingsheng, Coruzzi Gloria, Crawford Nigel M. Genomic analysis of the nitrate response using a nitrate reductase-null mutant of Arabidopsis. Plant Physiol. 2004 Aug 27;136(1):2512–2522. doi: 10.1104/pp.104.044610. [DOI] [PMC free article] [PubMed] [Google Scholar]
  246. Wang Xiangdong, Zhao Hong, Andersson Roland. Proteomics and leukocytes: an approach to understanding potential molecular mechanisms of inflammatory responses. J Proteome Res. 2004 Sep-Oct;3(5):921–929. doi: 10.1021/pr0499601. [DOI] [PubMed] [Google Scholar]
  247. Wang Yonghui, Hancock William S., Weber Gerhard, Eckerskorn Christoph, Palmer-Toy Darryl. Free flow electrophoresis coupled with liquid chromatography-mass spectrometry for a proteomic study of the human cell line (K562/CR3). J Chromatogr A. 2004 Oct 22;1053(1-2):269–278. [PubMed] [Google Scholar]
  248. Warnock Dale E., Fahy Eoin, Taylor Steven W. Identification of protein associations in organelles, using mass spectrometry-based proteomics. Mass Spectrom Rev. 2004 Jul-Aug;23(4):259–280. doi: 10.1002/mas.10077. [DOI] [PubMed] [Google Scholar]
  249. Warscheid Bettina, Fenselau Catherine. A targeted proteomics approach to the rapid identification of bacterial cell mixtures by matrix-assisted laser desorption/ionization mass spectrometry. Proteomics. 2004 Oct;4(10):2877–2892. doi: 10.1002/pmic.200400911. [DOI] [PubMed] [Google Scholar]
  250. Wehrl Wolfgang, Meyer Thomas F., Jungblut Peter R., Müller Eva-Christina, Szczepek Agnes J. Action and reaction: Chlamydophila pneumoniae proteome alteration in a persistent infection induced by iron deficiency. Proteomics. 2004 Oct;4(10):2969–2981. doi: 10.1002/pmic.200400917. [DOI] [PubMed] [Google Scholar]
  251. Wei Jun S., Greer Braden T., Westermann Frank, Steinberg Seth M., Son Chang-Gue, Chen Qing-Rong, Whiteford Craig C., Bilke Sven, Krasnoselsky Alexei L., Cenacchi Nicola. Prediction of clinical outcome using gene expression profiling and artificial neural networks for patients with neuroblastoma. Cancer Res. 2004 Oct 1;64(19):6883–6891. doi: 10.1158/0008-5472.CAN-04-0695. [DOI] [PMC free article] [PubMed] [Google Scholar]
  252. White Ian R., Pickford Russell, Wood John, Skehel J. Mark, Gangadharan Bevan, Cutler Paul. A statistical comparison of silver and SYPRO Ruby staining for proteomic analysis. Electrophoresis. 2004 Sep;25(17):3048–3054. doi: 10.1002/elps.200405947. [DOI] [PubMed] [Google Scholar]
  253. Whitton Claire, Daub Jennifer, Quail Mike, Hall Neil, Foster Jeremy, Ware Jennifer, Ganatra Mehul, Slatko Barton, Barrell Bart, Blaxter Mark. A genome sequence survey of the filarial nematode Brugia malayi: repeats, gene discovery, and comparative genomics. Mol Biochem Parasitol. 2004 Oct;137(2):215–227. doi: 10.1016/j.molbiopara.2004.05.013. [DOI] [PubMed] [Google Scholar]
  254. Whitworth Kristin, Springer Gordon K., Forrester L. Joe, Spollen William G., Ries Jim, Lamberson William R., Bivens Nathan, Murphy Clifton N., Mathialagan Nagappan, Mathialigan Nagappan. Developmental expression of 2489 gene clusters during pig embryogenesis: an expressed sequence tag project. Biol Reprod. 2004 Jun 2;71(4):1230–1243. doi: 10.1095/biolreprod.104.030239. [DOI] [PubMed] [Google Scholar]
  255. Wiemann Stefan, Arlt Dorit, Huber Wolfgang, Wellenreuther Ruth, Schleeger Simone, Mehrle Alexander, Bechtel Stephanie, Sauermann Mamatha, Korf Ulrike, Pepperkok Rainer. From ORFeome to biology: a functional genomics pipeline. Genome Res. 2004 Oct;14(10B):2136–2144. doi: 10.1101/gr.2576704. [DOI] [PMC free article] [PubMed] [Google Scholar]
  256. Wilmarth Phillip A., Riviere Michael A., Rustvold D. Leif, Lauten Jeffrey D., Madden Theresa E., David Larry L. Two-dimensional liquid chromatography study of the human whole saliva proteome. J Proteome Res. 2004 Sep-Oct;3(5):1017–1023. doi: 10.1021/pr049911o. [DOI] [PubMed] [Google Scholar]
  257. Wu C-C, Nimmakayala P., Santos F. A., Springman R., Scheuring C., Meksem K., Lightfoot D. A., Zhang H-B. Construction and characterization of a soybean bacterial artificial chromosome library and use of multiple complementary libraries for genome physical mapping. Theor Appl Genet. 2004 May 26;109(5):1041–1050. doi: 10.1007/s00122-004-1712-y. [DOI] [PubMed] [Google Scholar]
  258. Xu Ping, Widmer Giovanni, Wang Yingping, Ozaki Luiz S., Alves Joao M., Serrano Myrna G., Puiu Daniela, Manque Patricio, Akiyoshi Donna, Mackey Aaron J. The genome of Cryptosporidium hominis. Nature. 2004 Oct 28;431(7012):1107–1112. doi: 10.1038/nature02977. [DOI] [PubMed] [Google Scholar]
  259. Xu Xiu-Qin, Leow Chon K., Lu Xin, Zhang Xuegong, Liu Jun S., Wong Wing-Hung, Asperger Arndt, Deininger Sören, Eastwood Leung Hon-Chiu. Molecular classification of liver cirrhosis in a rat model by proteomics and bioinformatics. Proteomics. 2004 Oct;4(10):3235–3245. doi: 10.1002/pmic.200400839. [DOI] [PubMed] [Google Scholar]
  260. Yanagisawa Rie, Takano Hirohisa, Inoue Ken-ichiro, Ichinose Takamichi, Yoshida Sei-ichi, Sadakane Kaori, Takeda Ken, Yoshino Shin, Yamaki Kouya, Kumagai Yoshito. Complementary DNA microarray analysis in acute lung injury induced by lipopolysaccharide and diesel exhaust particles. Exp Biol Med (Maywood) 2004 Nov;229(10):1081–1087. doi: 10.1177/153537020422901013. [DOI] [PubMed] [Google Scholar]
  261. Yang Xiaoyu, Dondeti Vijay, Dezube Rebecca, Maynard Dawn M., Geer Lewis Y., Epstein Jonathan, Chen Xiongfong, Markey Sanford P., Kowalak Jeffrey A. DBParser: web-based software for shotgun proteomic data analyses. J Proteome Res. 2004 Sep-Oct;3(5):1002–1008. doi: 10.1021/pr049920x. [DOI] [PubMed] [Google Scholar]
  262. Yokoyama Ryusuke, Nishitani Kazuhiko. Genomic basis for cell-wall diversity in plants. A comparative approach to gene families in rice and Arabidopsis. Plant Cell Physiol. 2004 Sep;45(9):1111–1121. doi: 10.1093/pcp/pch151. [DOI] [PubMed] [Google Scholar]
  263. Yu Jindan, He Shirley, Friedman James S., Akimoto Masayuki, Ghosh Debashis, Mears Alan J., Hicks David, Swaroop Anand. Altered expression of genes of the Bmp/Smad and Wnt/calcium signaling pathways in the cone-only Nrl-/- mouse retina, revealed by gene profiling using custom cDNA microarrays. J Biol Chem. 2004 Jul 28;279(40):42211–42220. doi: 10.1074/jbc.M408223200. [DOI] [PubMed] [Google Scholar]
  264. Yu Yanling, Cui Jiefeng, Wang Xiaoyan, Liu Yinkun, Yang Pengyuan. Studies on peptide acetylation for stable-isotope labeling after 1-D PAGE separation in quantitative proteomics. Proteomics. 2004 Oct;4(10):3112–3120. doi: 10.1002/pmic.200300837. [DOI] [PubMed] [Google Scholar]
  265. Zhang D., Baek S-H, Ho A., Lee H., Jeong Y. S., Kim K. Targeted degradation of proteins by small molecules: a novel tool for functional proteomics. Comb Chem High Throughput Screen. 2004 Nov;7(7):689–697. doi: 10.2174/1386207043328364. [DOI] [PubMed] [Google Scholar]
  266. Zhang Hangning, Sreenivasulu Nese, Weschke Winfriede, Stein Nils, Rudd Stephen, Radchuk Volodymyr, Potokina Elena, Scholz Uwe, Schweizer Patrick, Zierold Uwe. Large-scale analysis of the barley transcriptome based on expressed sequence tags. Plant J. 2004 Oct;40(2):276–290. doi: 10.1111/j.1365-313X.2004.02209.x. [DOI] [PubMed] [Google Scholar]
  267. Zhang Zhaoduo, Shrager Jeff, Jain Monica, Chang Chiung-Wen, Vallon Olivier, Grossman Arthur R. Insights into the survival of Chlamydomonas reinhardtii during sulfur starvation based on microarray analysis of gene expression. Eukaryot Cell. 2004 Oct;3(5):1331–1348. doi: 10.1128/EC.3.5.1331-1348.2004. [DOI] [PMC free article] [PubMed] [Google Scholar]
  268. Zhou Dongsheng, Han Yanping, Song Yajun, Huang Peitang, Yang Ruifu. Comparative and evolutionary genomics of Yersinia pestis. Microbes Infect. 2004 Nov;6(13):1226–1234. doi: 10.1016/j.micinf.2004.08.002. [DOI] [PubMed] [Google Scholar]
  269. Zhou Xiaodong, Dimachkie Mazen M., Xiong Momiao, Tan Filemon K., Arnett Frank C. cDNA microarrays reveal distinct gene expression clusters in idiopathic inflammatory myopathies. Med Sci Monit. 2004 Jun 29;10(7):BR191–BR197. [PubMed] [Google Scholar]
  270. Zhou Xichun, Zhou Jizhong. Improving the signal sensitivity and photostability of DNA hybridizations on microarrays by using dye-doped core-shell silica nanoparticles. Anal Chem. 2004 Sep 15;76(18):5302–5312. doi: 10.1021/ac049472c. [DOI] [PubMed] [Google Scholar]
  271. Zhu J., Lum P. Y., Lamb J., GuhaThakurta D., Edwards S. W., Thieringer R., Berger J. P., Wu M. S., Thompson J., Sachs A. B. An integrative genomics approach to the reconstruction of gene networks in segregating populations. Cytogenet Genome Res. 2004;105(2-4):363–374. doi: 10.1159/000078209. [DOI] [PubMed] [Google Scholar]
  272. Ziebandt Anne-Kathrin, Becher Dörte, Ohlsen Knut, Hacker Jörg, Hecker Michael, Engelmann Susanne. The influence of agr and sigmaB in growth phase dependent regulation of virulence factors in Staphylococcus aureus. Proteomics. 2004 Oct;4(10):3034–3047. doi: 10.1002/pmic.200400937. [DOI] [PubMed] [Google Scholar]
  273. Zimmermann Philip, Hirsch-Hoffmann Matthias, Hennig Lars, Gruissem Wilhelm. GENEVESTIGATOR. Arabidopsis microarray database and analysis toolbox. Plant Physiol. 2004 Sep;136(1):2621–2632. doi: 10.1104/pp.104.046367. [DOI] [PMC free article] [PubMed] [Google Scholar]
  274. de Figueiredo Paul, Roberts Radclyffe L., Nester Eugene W. DARTs: A DNA-based in vitro polypeptide display technology. Proteomics. 2004 Oct;4(10):3128–3140. doi: 10.1002/pmic.200300842. [DOI] [PubMed] [Google Scholar]
  275. de Hoog Carmen L., Mann Matthias. Proteomics. Annu Rev Genomics Hum Genet. 2004;5:267–293. doi: 10.1146/annurev.genom.4.070802.110305. [DOI] [PubMed] [Google Scholar]
  276. van Hemert S., Hoekman A. J., Smits M. A., Rebel J. M. J. Differences in intestinal gene expression profiles in broiler lines varying in susceptibility to malabsorption syndrome. Poult Sci. 2004 Oct;83(10):1675–1682. doi: 10.1093/ps/83.10.1675. [DOI] [PubMed] [Google Scholar]
  277. von Ohsen Niklas, Sommer Ingolf, Zimmer Ralf, Lengauer Thomas. Arby: automatic protein structure prediction using profile-profile alignment and confidence measures. Bioinformatics. 2004 Apr 1;20(14):2228–2235. doi: 10.1093/bioinformatics/bth232. [DOI] [PubMed] [Google Scholar]

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