Skip to main content
NCBI home page
Comparative and Functional Genomics logoLink to Comparative and Functional Genomics
. 2002 Oct;3(5):461–468. doi: 10.1002/cfg.120

Current Awareness on Comparative and Functional Genomics

PMCID: PMC2447335

Full Text

The Full Text of this article is available as a PDF (117.6 KB).

Selected References

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

  1. Aigaki T., Ohsako T., Toba G., Seong K., Matsuo T. The gene search system: its application to functional genomics in Drosophila melanogaster. J Neurogenet. 2001;15(3-4):169–178. doi: 10.3109/01677060109167374. [DOI] [PubMed] [Google Scholar]
  2. Aizenberg Igor, Myasnikova Ekaterina, Samsonova Maria, Reinitz John. Temporal classification of Drosophila segmentation gene expression patterns by the multi-valued neural recognition method. Math Biosci. 2002 Mar;176(1):145–159. doi: 10.1016/s0025-5564(01)00104-3. [DOI] [PubMed] [Google Scholar]
  3. Akhtar Ruth A., Reddy Akhilesh B., Maywood Elizabeth S., Clayton Jonathan D., King Verdun M., Smith Andrew G., Gant Timothy W., Hastings Michael H., Kyriacou Charalambos P. Circadian cycling of the mouse liver transcriptome, as revealed by cDNA microarray, is driven by the suprachiasmatic nucleus. Curr Biol. 2002 Apr 2;12(7):540–550. doi: 10.1016/s0960-9822(02)00759-5. [DOI] [PubMed] [Google Scholar]
  4. Al Moustafa Ala-Eddin, Alaoui-Jamali Moulay A., Batist Gerald, Hernandez-Perez Maite, Serruya Corinne, Alpert Lesley, Black Martin J., Sladek Robert, Foulkes William D. Identification of genes associated with head and neck carcinogenesis by cDNA microarray comparison between matched primary normal epithelial and squamous carcinoma cells. Oncogene. 2002 Apr 18;21(17):2634–2640. doi: 10.1038/sj.onc.1205351. [DOI] [PubMed] [Google Scholar]
  5. Albers Sonja-Verena, Driessen Arnold M. Signal peptides of secreted proteins of the archaeon Sulfolobus solfataricus: a genomic survey. Arch Microbiol. 2002 Jan 11;177(3):209–216. doi: 10.1007/s00203-001-0386-y. [DOI] [PubMed] [Google Scholar]
  6. Aloy Patrick, Oliva Baldomero, Querol Enrique, Aviles Francesc X., Russell Robert B. Structural similarity to link sequence space: new potential superfamilies and implications for structural genomics. Protein Sci. 2002 May;11(5):1101–1116. doi: 10.1110/ps.3950102. [DOI] [PMC free article] [PubMed] [Google Scholar]
  7. Anantharaman Vivek, Koonin Eugene V., Aravind L. Comparative genomics and evolution of proteins involved in RNA metabolism. Nucleic Acids Res. 2002 Apr 1;30(7):1427–1464. doi: 10.1093/nar/30.7.1427. [DOI] [PMC free article] [PubMed] [Google Scholar]
  8. Ball G., Mian S., Holding F., Allibone R. O., Lowe J., Ali S., Li G., McCardle S., Ellis I. O., Creaser C. An integrated approach utilizing artificial neural networks and SELDI mass spectrometry for the classification of human tumours and rapid identification of potential biomarkers. Bioinformatics. 2002 Mar;18(3):395–404. doi: 10.1093/bioinformatics/18.3.395. [DOI] [PubMed] [Google Scholar]
  9. Ball Kristen D., Trevors J. T. Bacterial genomics: the use of DNA microarrays and bacterial artificial chromosomes. J Microbiol Methods. 2002 May;49(3):275–284. doi: 10.1016/s0167-7012(01)00375-x. [DOI] [PubMed] [Google Scholar]
  10. Bandara Lasantha R., Kennedy Sandy. Toxicoproteomics -- a new preclinical tool. Drug Discov Today. 2002 Apr 1;7(7):411–418. doi: 10.1016/s1359-6446(02)02211-0. [DOI] [PubMed] [Google Scholar]
  11. Bannantine John P., Baechler Emily, Zhang Qing, Li LingLing, Kapur Vivek. Genome scale comparison of Mycobacterium avium subsp. paratuberculosis with Mycobacterium avium subsp. avium reveals potential diagnostic sequences. J Clin Microbiol. 2002 Apr;40(4):1303–1310. doi: 10.1128/JCM.40.4.1303-1310.2002. [DOI] [PMC free article] [PubMed] [Google Scholar]
  12. Bansal Arvind K., Meyer Terrance E. Evolutionary analysis by whole-genome comparisons. J Bacteriol. 2002 Apr;184(8):2260–2272. doi: 10.1128/JB.184.8.2260-2272.2002. [DOI] [PMC free article] [PubMed] [Google Scholar]
  13. Bao Paul, Frutos Anthony G., Greef Charles, Lahiri Joydeep, Muller Uwe, Peterson Todd C., Warden Laurence, Xie Xinying. High-sensitivity detection of DNA hybridization on microarrays using resonance light scattering. Anal Chem. 2002 Apr 15;74(8):1792–1797. doi: 10.1021/ac0111964. [DOI] [PubMed] [Google Scholar]
  14. Bashyam Murali D. Understanding cancer metastasis: an urgent need for using differential gene expression analysis. Cancer. 2002 Mar 15;94(6):1821–1829. doi: 10.1002/cncr.10362. [DOI] [PubMed] [Google Scholar]
  15. Beck Stefan, Sakurai Takashi, Eustace Brenda K., Beste Gerald, Schier Robert, Rudert Fritz, Jay Daniel G. Fluorophore-assisted light inactivation: a high-throughput tool for direct target validation of proteins. Proteomics. 2002 Mar;2(3):247–255. doi: 10.1002/1615-9861(200203)2:3<247::aid-prot247>3.0.co;2-k. [DOI] [PubMed] [Google Scholar]
  16. Benson M., Svensson P. A., Carlsson B., Jernås M., Reinholdt J., Cardell L. O., Carlsson L. DNA microarrays to study gene expression in allergic airways. Clin Exp Allergy. 2002 Feb;32(2):301–308. doi: 10.1046/j.1365-2222.2002.01300.x. [DOI] [PubMed] [Google Scholar]
  17. Bentley S. D., Chater K. F., Cerdeño-Tárraga A-M, Challis G. L., Thomson N. R., James K. D., Harris D. E., Quail M. A., Kieser H., Harper D. Complete genome sequence of the model actinomycete Streptomyces coelicolor A3(2). Nature. 2002 May 9;417(6885):141–147. doi: 10.1038/417141a. [DOI] [PubMed] [Google Scholar]
  18. Berggren W. Travis, Takova Tsetska, Olson Marilyn C., Eis Peggy S., Kwiatkowski Robert W., Smith Lloyd M. Multiplexed gene expression analysis using the invader RNA assay with MALDI-TOF mass spectrometry detection. Anal Chem. 2002 Apr 15;74(8):1745–1750. doi: 10.1021/ac011167t. [DOI] [PubMed] [Google Scholar]
  19. Blythe Martin J., Doytchinova Irini A., Flower Darren R. JenPep: a database of quantitative functional peptide data for immunology. Bioinformatics. 2002 Mar;18(3):434–439. doi: 10.1093/bioinformatics/18.3.434. [DOI] [PubMed] [Google Scholar]
  20. Bossio Robert E., Marshall Alan G. Baseline resolution of isobaric phosphorylated and sulfated peptides and nucleotides by electrospray ionization FTICR ms: another step toward mass spectrometry-based proteomics. Anal Chem. 2002 Apr 1;74(7):1674–1679. doi: 10.1021/ac0108461. [DOI] [PubMed] [Google Scholar]
  21. Braun Pascal, Hu Yanhui, Shen Binghua, Halleck Allison, Koundinya Malvika, Harlow Ed, LaBaer Joshua. Proteome-scale purification of human proteins from bacteria. Proc Natl Acad Sci U S A. 2002 Mar 5;99(5):2654–2659. doi: 10.1073/pnas.042684199. [DOI] [PMC free article] [PubMed] [Google Scholar]
  22. Buchan Daniel W. A., Shepherd Adrian J., Lee David, Pearl Frances M. G., Rison Stuart C. G., Thornton Janet M., Orengo Christine A. Gene3D: structural assignment for whole genes and genomes using the CATH domain structure database. Genome Res. 2002 Mar;12(3):503–514. doi: 10.1101/gr.213802. [DOI] [PMC free article] [PubMed] [Google Scholar]
  23. Buraczynska Monika, Mears Alan J., Zareparsi Sepideh, Farjo Rafal, Filippova Elena, Yuan Yukun, MacNee Sean P., Hughes Bret, Swaroop Anand. Gene expression profile of native human retinal pigment epithelium. Invest Ophthalmol Vis Sci. 2002 Mar;43(3):603–607. [PubMed] [Google Scholar]
  24. Cao Min, Kobel Phil A., Morshedi Maud M., Wu Ming Fang Winston, Paddon Chris, Helmann John D. Defining the Bacillus subtilis sigma(W) regulon: a comparative analysis of promoter consensus search, run-off transcription/macroarray analysis (ROMA), and transcriptional profiling approaches. J Mol Biol. 2002 Feb 22;316(3):443–457. doi: 10.1006/jmbi.2001.5372. [DOI] [PubMed] [Google Scholar]
  25. Chakraborty Asish, Regnier Fred E. Global internal standard technology for comparative proteomics. J Chromatogr A. 2002 Mar 8;949(1-2):173–184. doi: 10.1016/s0021-9673(02)00047-x. [DOI] [PubMed] [Google Scholar]
  26. Chambergo Felipe S., Bonaccorsi Eric D., Ferreira Ari J. S., Ramos Augusto S. P., Ferreira Júnior José Ribamar, Abrahão-Neto José, Farah João P. Simon, El-Dorry Hamza. Elucidation of the metabolic fate of glucose in the filamentous fungus Trichoderma reesei using expressed sequence tag (EST) analysis and cDNA microarrays. J Biol Chem. 2002 Feb 1;277(16):13983–13988. doi: 10.1074/jbc.M107651200. [DOI] [PubMed] [Google Scholar]
  27. Chan J. Y., Chen L. K., Chang J. F., Ting H. M., Goy C., Chen J. L., Hwang J. J., Chen F. D., Chen D. J., Ngo F. Q. Differential gene expression in a DNA double-strand-break repair mutant XRS-5 defective in Ku80: analysis by cDNA microarray. J Radiat Res. 2001 Dec;42(4):371–385. doi: 10.1269/jrr.42.371. [DOI] [PubMed] [Google Scholar]
  28. Chance Mark R., Bresnick Anne R., Burley Stephen K., Jiang Jian-Sheng, Lima Christopher D., Sali Andrej, Almo Steven C., Bonanno Jeffrey B., Buglino John A., Boulton Simon. Structural genomics: a pipeline for providing structures for the biologist. Protein Sci. 2002 Apr;11(4):723–738. doi: 10.1110/ps.4570102. [DOI] [PMC free article] [PubMed] [Google Scholar]
  29. Chauhan Bharesh K., Reed Nathan A., Zhang Weijia, Duncan Melinda K., Kilimann Manfred W., Cvekl Ales. Identification of genes downstream of Pax6 in the mouse lens using cDNA microarrays. J Biol Chem. 2002 Jan 14;277(13):11539–11548. doi: 10.1074/jbc.M110531200. [DOI] [PubMed] [Google Scholar]
  30. Chen Mingsheng, Presting Gernot, Barbazuk W. Brad, Goicoechea Jose Luis, Blackmon Barbara, Fang Guangchen, Kim Hyeran, Frisch David, Yu Yeisoo, Sun Shouhong. An integrated physical and genetic map of the rice genome. Plant Cell. 2002 Mar;14(3):537–545. doi: 10.1105/tpc.010485. [DOI] [PMC free article] [PubMed] [Google Scholar]
  31. Chen Wenqiong, Provart Nicholas J., Glazebrook Jane, Katagiri Fumiaki, Chang Hur-Song, Eulgem Thomas, Mauch Felix, Luan Sheng, Zou Guangzhou, Whitham Steve A. Expression profile matrix of Arabidopsis transcription factor genes suggests their putative functions in response to environmental stresses. Plant Cell. 2002 Mar;14(3):559–574. doi: 10.1105/tpc.010410. [DOI] [PMC free article] [PubMed] [Google Scholar]
  32. Chiaromonte Francesca, Martinelli Jessica. Dimension reduction strategies for analyzing global gene expression data with a response. Math Biosci. 2002 Mar;176(1):123–144. doi: 10.1016/s0025-5564(01)00106-7. [DOI] [PubMed] [Google Scholar]
  33. Cho Jae-Chang, Tiedje James M. Quantitative detection of microbial genes by using DNA microarrays. Appl Environ Microbiol. 2002 Mar;68(3):1425–1430. doi: 10.1128/AEM.68.3.1425-1430.2002. [DOI] [PMC free article] [PubMed] [Google Scholar]
  34. Clark Jeremy, Edwards Sandra, John Megan, Flohr Penny, Gordon Tony, Maillard Karine, Giddings Ian, Brown Carolanne, Bagherzadeh Azadeh, Campbell Colin. Identification of amplified and expressed genes in breast cancer by comparative hybridization onto microarrays of randomly selected cDNA clones. Genes Chromosomes Cancer. 2002 May;34(1):104–114. doi: 10.1002/gcc.10039. [DOI] [PubMed] [Google Scholar]
  35. Clarke G. D. Paul, Beiko Robert G., Ragan Mark A., Charlebois Robert L. Inferring genome trees by using a filter to eliminate phylogenetically discordant sequences and a distance matrix based on mean normalized BLASTP scores. J Bacteriol. 2002 Apr;184(8):2072–2080. doi: 10.1128/JB.184.8.2072-2080.2002. [DOI] [PMC free article] [PubMed] [Google Scholar]
  36. Clarkson Michael R., Murphy Madeline, Gupta Sunil, Lambe Teresa, Mackenzie Harald S., Godson Catherine, Martin Finian, Brady Hugh R. High glucose-altered gene expression in mesangial cells. Actin-regulatory protein gene expression is triggered by oxidative stress and cytoskeletal disassembly. J Biol Chem. 2002 Jan 9;277(12):9707–9712. doi: 10.1074/jbc.M109172200. [DOI] [PubMed] [Google Scholar]
  37. Cobon Gary S., Verrills Nicole, Papakostopoulos Penny, Eastwood Hayden, Linnane Anthony W. The proteomics of ageing. Biogerontology. 2002;3(1-2):133–136. doi: 10.1023/a:1015240304287. [DOI] [PubMed] [Google Scholar]
  38. Consoli L., Lefèvre A., Zivy M., de Vienne D., Damerval C. QTL analysis of proteome and transcriptome variations for dissecting the genetic architecture of complex traits in maize. Plant Mol Biol. 2002 Mar-Apr;48(5-6):575–581. doi: 10.1023/a:1014840810203. [DOI] [PubMed] [Google Scholar]
  39. Cui L., Rzomp K. A., Fan Q., Martin S. K., Williams J. Plasmodium falciparum: differential display analysis of gene expression during gametocytogenesis. Exp Parasitol. 2001 Dec;99(4):244–254. doi: 10.1006/expr.2001.4669. [DOI] [PubMed] [Google Scholar]
  40. Curto Ernest V., Lambert Glenna W., Davis Richard L., Wilborn Teresa W., Dooley Thomas P. Biomarkers of human skin cells identified using DermArray DNA arrays and new bioinformatics methods. Biochem Biophys Res Commun. 2002 Mar 8;291(4):1052–1064. doi: 10.1006/bbrc.2002.6542. [DOI] [PubMed] [Google Scholar]
  41. Dahse Regine, Berndt Alexander, Kosmehl Hartwig. Total RNA-based target design for microarray analysis of defined tumor areas. Biotechniques. 2002 Apr;32(4):744–748. doi: 10.2144/02324bm05. [DOI] [PubMed] [Google Scholar]
  42. Davidsson Pia, Westman-Brinkmalm Ann, Nilsson Carol L., Lindbjer Maria, Paulson Linda, Andreasen Niels, Sjögren Magnus, Blennow Kaj. Proteome analysis of cerebrospinal fluid proteins in Alzheimer patients. Neuroreport. 2002 Apr 16;13(5):611–615. doi: 10.1097/00001756-200204160-00015. [DOI] [PubMed] [Google Scholar]
  43. De Las Rivas Javier, Lozano Juan Jose, Ortiz Angel R. Comparative analysis of chloroplast genomes: functional annotation, genome-based phylogeny, and deduced evolutionary patterns. Genome Res. 2002 Apr;12(4):567–583. doi: 10.1101/gr.209402. [DOI] [PMC free article] [PubMed] [Google Scholar]
  44. Delpuech Oona, Trabut Jean-Baptiste, Carnot Françoise, Feuillard Jean, Brechot Christian, Kremsdorf Dina. Identification, using cDNA macroarray analysis, of distinct gene expression profiles associated with pathological and virological features of hepatocellular carcinoma. Oncogene. 2002 Apr 25;21(18):2926–2937. doi: 10.1038/sj.onc.1205392. [DOI] [PubMed] [Google Scholar]
  45. Didier G., Brézellec P., Remy E., Hénaut A. GeneANOVA--gene expression analysis of variance. Bioinformatics. 2002 Mar;18(3):490–491. doi: 10.1093/bioinformatics/18.3.490. [DOI] [PubMed] [Google Scholar]
  46. Dierick Jean-François, Dieu Marc, Remacle José, Raes Martine, Roepstorff Peter, Toussaint Olivier. Proteomics in experimental gerontology. Exp Gerontol. 2002 May;37(5):721–734. doi: 10.1016/s0531-5565(02)00004-9. [DOI] [PubMed] [Google Scholar]
  47. Dougherty Edward R., Barrera Junior, Brun Marcel, Kim Seungchan, Cesar Roberto M., Chen Yidong, Bittner Michael, Trent Jeffrey M. Inference from clustering with application to gene-expression microarrays. J Comput Biol. 2002;9(1):105–126. doi: 10.1089/10665270252833217. [DOI] [PubMed] [Google Scholar]
  48. Dougherty Joseph D., Geschwind Daniel H. Subtraction-coupled custom microarray analysis for gene discovery and gene expression studies in the CNS. Chem Senses. 2002 Mar;27(3):293–298. doi: 10.1093/chemse/27.3.293. [DOI] [PubMed] [Google Scholar]
  49. Duffield Giles E., Best Jonathan D., Meurers Bernhard H., Bittner Anton, Loros Jennifer J., Dunlap Jay C. Circadian programs of transcriptional activation, signaling, and protein turnover revealed by microarray analysis of mammalian cells. Curr Biol. 2002 Apr 2;12(7):551–557. doi: 10.1016/s0960-9822(02)00765-0. [DOI] [PubMed] [Google Scholar]
  50. Egelhofer Volker, Gobom Johan, Seitz Harald, Giavalisco Patrick, Lehrach Hans, Nordhoff Eckhard. Protein identification by MALDI-TOF-MS peptide mapping: a new strategy. Anal Chem. 2002 Apr 15;74(8):1760–1771. doi: 10.1021/ac011204g. [DOI] [PubMed] [Google Scholar]
  51. Endo Makoto, Matsubara Hitoshi, Kokubun Takao, Masuko Hiromi, Takahata Yoshihito, Tsuchiya Tohru, Fukuda Hiroo, Demura Taku, Watanabe Masao. The advantages of cDNA microarray as an effective tool for identification of reproductive organ-specific genes in a model legume, Lotus japonicus. FEBS Lett. 2002 Mar 13;514(2-3):229–237. doi: 10.1016/s0014-5793(02)02371-2. [DOI] [PubMed] [Google Scholar]
  52. Eriksson Jan, Fenyö David. A model of random mass-matching and its use for automated significance testing in mass spectrometric proteome analysis. Proteomics. 2002 Mar;2(3):262–270. doi: 10.1002/1615-9861(200203)2:3<262::aid-prot262>3.0.co;2-w. [DOI] [PubMed] [Google Scholar]
  53. Ettinger Anna, Ostroff Rachel, Brien Jeanne, Polisky Barry. In-process monitoring of protein purification with thin film silicon sensor technology. Biotechniques. 2002 Apr;32(4):934–938. doi: 10.2144/02324pt05. [DOI] [PubMed] [Google Scholar]
  54. Eymann Christine, Homuth Georg, Scharf Christian, Hecker Michael. Bacillus subtilis functional genomics: global characterization of the stringent response by proteome and transcriptome analysis. J Bacteriol. 2002 May;184(9):2500–2520. doi: 10.1128/JB.184.9.2500-2520.2002. [DOI] [PMC free article] [PubMed] [Google Scholar]
  55. Farjo Rafal, Yu Jindan, Othman Mohammad I., Yoshida Shigeo, Sheth Sujata, Glaser Tom, Baehr Wolfgang, Swaroop Anand. Mouse eye gene microarrays for investigating ocular development and disease. Vision Res. 2002 Feb;42(4):463–470. doi: 10.1016/s0042-6989(01)00219-x. [DOI] [PubMed] [Google Scholar]
  56. Fellenberg Kurt, Hauser Nicole C., Brors Benedikt, Hoheisel Jörg D., Vingron Martin. Microarray data warehouse allowing for inclusion of experiment annotations in statistical analysis. Bioinformatics. 2002 Mar;18(3):423–433. doi: 10.1093/bioinformatics/18.3.423. [DOI] [PubMed] [Google Scholar]
  57. Fernandes John, Brendel Volker, Gai Xiaowu, Lal Shailesh, Chandler Vicki L., Elumalai Rangasamy P., Galbraith David W., Pierson Elizabeth A., Walbot Virginia. Comparison of RNA expression profiles based on maize expressed sequence tag frequency analysis and micro-array hybridization. Plant Physiol. 2002 Mar;128(3):896–910. doi: 10.1104/pp.010681. [DOI] [PMC free article] [PubMed] [Google Scholar]
  58. Forsyth R. Allyn, Haselbeck Robert J., Ohlsen Kari L., Yamamoto Robert T., Xu Howard, Trawick John D., Wall Daniel, Wang Liangsu, Brown-Driver Vickie, Froelich Jamie M. A genome-wide strategy for the identification of essential genes in Staphylococcus aureus. Mol Microbiol. 2002 Mar;43(6):1387–1400. doi: 10.1046/j.1365-2958.2002.02832.x. [DOI] [PubMed] [Google Scholar]
  59. Fratelli Maddalena, Demol Hans, Puype Magda, Casagrande Simona, Eberini Ivano, Salmona Mario, Bonetto Valentina, Mengozzi Manuela, Duffieux Francis, Miclet Emeric. Identification by redox proteomics of glutathionylated proteins in oxidatively stressed human T lymphocytes. Proc Natl Acad Sci U S A. 2002 Mar 19;99(6):3505–3510. doi: 10.1073/pnas.052592699. [DOI] [PMC free article] [PubMed] [Google Scholar]
  60. Gaiser Timo, Thorns Christoph, Merz Hartmut, Noack Frank, Feller Alfred C., Lange Karin. Gene profiling in anaplastic large-cell lymphoma-derived cell lines with cDNA expression arrays. J Hematother Stem Cell Res. 2002 Apr;11(2):423–428. doi: 10.1089/152581602753658619. [DOI] [PubMed] [Google Scholar]
  61. Galagan James E., Nusbaum Chad, Roy Alice, Endrizzi Matthew G., Macdonald Pendexter, FitzHugh Will, Calvo Sarah, Engels Reinhard, Smirnov Serge, Atnoor Deven. The genome of M. acetivorans reveals extensive metabolic and physiological diversity. Genome Res. 2002 Apr;12(4):532–542. doi: 10.1101/gr.223902. [DOI] [PMC free article] [PubMed] [Google Scholar]
  62. Golemis Erica A., Tew Kenneth D., Dadke Disha. Protein interaction-targeted drug discovery: evaluating critical issues. Biotechniques. 2002 Mar;32(3):636-8, 640, 642 passim. doi: 10.2144/02323dd01. [DOI] [PubMed] [Google Scholar]
  63. Grant Ethan P., Pickard Michael D., Briskin Michael J., Gutierrez-Ramos Jose-Carlos. Gene expression profiles: creating new perspectives in arthritis research. Arthritis Rheum. 2002 Apr;46(4):874–884. doi: 10.1002/art.10014. [DOI] [PubMed] [Google Scholar]
  64. Gu Xun, Vander Velden Kent. DIVERGE: phylogeny-based analysis for functional-structural divergence of a protein family. Bioinformatics. 2002 Mar;18(3):500–501. doi: 10.1093/bioinformatics/18.3.500. [DOI] [PubMed] [Google Scholar]
  65. Guckenberger Matthias, Kurz Sebastian, Aepinus Christian, Theiss Stephanie, Haller Sabine, Leimbach Thomas, Panzner Ursula, Weber Jacqueline, Paul Hubert, Unkmeir Alexandra. Analysis of the heat shock response of Neisseria meningitidis with cDNA- and oligonucleotide-based DNA microarrays. J Bacteriol. 2002 May;184(9):2546–2551. doi: 10.1128/JB.184.9.2546-2551.2002. [DOI] [PMC free article] [PubMed] [Google Scholar]
  66. Gutmann David H., Hedrick Nicolé M., Li Jun, Nagarajan Rakesh, Perry Arie, Watson Mark A. Comparative gene expression profile analysis of neurofibromatosis 1-associated and sporadic pilocytic astrocytomas. Cancer Res. 2002 Apr 1;62(7):2085–2091. [PubMed] [Google Scholar]
  67. Gutmann David H., Huang Zhi-yong, Hedrick Nicolé M., Ding Hao, Guha Abhijit, Watson Mark A. Mouse glioma gene expression profiling identifies novel human glioma-associated genes. Ann Neurol. 2002 Mar;51(3):393–405. doi: 10.1002/ana.10145. [DOI] [PubMed] [Google Scholar]
  68. Gómez-Fabre Pedro M., Helou Khalil, Ståhl Fredrik. Predictions based on the rat-mouse comparative map provide mapping information on over 6000 new rat genes. Mamm Genome. 2002 Apr;13(4):189–193. doi: 10.1007/s00335-001-2131-x. [DOI] [PubMed] [Google Scholar]
  69. Haas Gaby, Karaali Galip, Ebermayer Karl, Metzger Wolfram G., Lamer Stephanie, Zimny-Arndt Ursula, Diescher Susanne, Goebel Ulf B., Vogt Konstanze, Roznowski Artur B. Immunoproteomics of Helicobacter pylori infection and relation to gastric disease. Proteomics. 2002 Mar;2(3):313–324. doi: 10.1002/1615-9861(200203)2:3<313::aid-prot313>3.0.co;2-7. [DOI] [PubMed] [Google Scholar]
  70. Hanash S. M., Madoz-Gurpide J., Misek D. E. Identification of novel targets for cancer therapy using expression proteomics. Leukemia. 2002 Apr;16(4):478–485. doi: 10.1038/sj.leu.2402412. [DOI] [PubMed] [Google Scholar]
  71. Harrison Paul, Kumar Anuj, Lan Ning, Echols Nathaniel, Snyder Michael, Gerstein Mark. A small reservoir of disabled ORFs in the yeast genome and its implications for the dynamics of proteome evolution. J Mol Biol. 2002 Feb 22;316(3):409–419. doi: 10.1006/jmbi.2001.5343. [DOI] [PubMed] [Google Scholar]
  72. Hernández-Macedo Maria L., Ferraz André, Rodríguez Jaime, Ottoboni Laura M. M., De Mello Maricilda Palandi. Iron-regulated proteins in Phanerochaete chrysosporium and Lentinula edodes: differential analysis by sodium dodecyl sulfate polyacrylamide gel electrophoresis and two-dimensional polyacrylamide gel electrophoresis profiles. Electrophoresis. 2002 Feb;23(4):655–661. doi: 10.1002/1522-2683(200202)23:4<655::AID-ELPS655>3.0.CO;2-S. [DOI] [PubMed] [Google Scholar]
  73. Hu L., Cogdell D. E., Jia Y. J., Hamilton S. R., Zhang W. Monitoring of cDNA microarray with common primer target and hybridization specificity with selected targets. Biotechniques. 2002 Mar;32(3):528, 530-2, 534. [PubMed] [Google Scholar]
  74. Hu Y., Wang Z., Wang Y., Bao F., Li N., Peng Z., Li J. Identification of brassinosteroid responsive genes in Arabidopsis by cDNA array. Sci China C Life Sci. 2001 Dec;44(6):637–643. doi: 10.1007/BF02879358. [DOI] [PubMed] [Google Scholar]
  75. Huang Wei, Sher Yuh-Pyng, Peck Konan, Fung Yuan Cheng B. Matching gene activity with physiological functions. Proc Natl Acad Sci U S A. 2002 Mar 5;99(5):2603–2608. doi: 10.1073/pnas.042684399. [DOI] [PMC free article] [PubMed] [Google Scholar]
  76. Isfort Robert J., Wang Feng, Greis Kenneth D., Sun Yiping, Keough Thomas W., Bodine Sue C., Anderson N. Leigh. Proteomic analysis of rat soleus and tibialis anterior muscle following immobilization. J Chromatogr B Analyt Technol Biomed Life Sci. 2002 Apr 5;769(2):323–332. doi: 10.1016/s1570-0232(02)00021-1. [DOI] [PubMed] [Google Scholar]
  77. Issaq Haleem J., Veenstra Timothy D., Conrads Thomas P., Felschow Donna. The SELDI-TOF MS approach to proteomics: protein profiling and biomarker identification. Biochem Biophys Res Commun. 2002 Apr 5;292(3):587–592. doi: 10.1006/bbrc.2002.6678. [DOI] [PubMed] [Google Scholar]
  78. Jiang Yuqiu, Harlocker Susan L., Molesh David A., Dillon David C., Stolk John A., Houghton Raymond L., Repasky Elizabeth A., Badaro Roberto, Reed Steven G., Xu Jiangchun. Discovery of differentially expressed genes in human breast cancer using subtracted cDNA libraries and cDNA microarrays. Oncogene. 2002 Mar 28;21(14):2270–2282. doi: 10.1038/sj.onc.1205278. [DOI] [PubMed] [Google Scholar]
  79. Jones J., Field J. K., Risk J. M. A comparative guide to gene prediction tools for the bioinformatics amateur. Int J Oncol. 2002 Apr;20(4):697–705. doi: 10.3892/ijo.20.4.697. [DOI] [PubMed] [Google Scholar]
  80. Jun Ji Hyung, Kim Cheol Soo, Cho Dae Shik, Kwak June Myoung, Ha Chan Man, Park Yu Shin, Cho Baik Ho, Patton David A., Nam Hong Gil. Random antisense cDNA mutagenesis as an efficient functional genomic approach in higher plants. Planta. 2001 Dec 12;214(5):668–674. doi: 10.1007/s004250100668. [DOI] [PubMed] [Google Scholar]
  81. Kahsay Robel Y., Wang Guoli, Dongre Nataraj, Gao Guang, Dunbrack Roland L., Jr CASA: a server for the critical assessment of protein sequence alignment accuracy. Bioinformatics. 2002 Mar;18(3):496–497. doi: 10.1093/bioinformatics/18.3.496. [DOI] [PubMed] [Google Scholar]
  82. Kanamoto Takashi, Hellman Ulf, Heldin Carl-Henrik, Souchelnytskyi Serhiy. Functional proteomics of transforming growth factor-beta1-stimulated Mv1Lu epithelial cells: Rad51 as a target of TGFbeta1-dependent regulation of DNA repair. EMBO J. 2002 Mar 1;21(5):1219–1230. doi: 10.1093/emboj/21.5.1219. [DOI] [PMC free article] [PubMed] [Google Scholar]
  83. Kantety Ramesh V., La Rota Mauricio, Matthews David E., Sorrells Mark E. Data mining for simple sequence repeats in expressed sequence tags from barley, maize, rice, sorghum and wheat. Plant Mol Biol. 2002 Mar-Apr;48(5-6):501–510. doi: 10.1023/a:1014875206165. [DOI] [PubMed] [Google Scholar]
  84. Kapatral Vinayak, Anderson Iain, Ivanova Natalia, Reznik Gary, Los Tamara, Lykidis Athanasios, Bhattacharyya Anamitra, Bartman Allen, Gardner Warren, Grechkin Galina. Genome sequence and analysis of the oral bacterium Fusobacterium nucleatum strain ATCC 25586. J Bacteriol. 2002 Apr;184(7):2005–2018. doi: 10.1128/JB.184.7.2005-2018.2002. [DOI] [PMC free article] [PubMed] [Google Scholar]
  85. Karsi Attila, Cao Dongfeng, Li Ping, Patterson Andrea, Kocabas Arif, Feng Jinian, Ju Zhenlin, Mickett Kathryn D., Liu Zhanjiang. Transcriptome analysis of channel catfish (Ictalurus punctatus): initial analysis of gene expression and microsatellite-containing cDNAs in the skin. Gene. 2002 Feb 20;285(1-2):157–168. doi: 10.1016/s0378-1119(02)00414-6. [DOI] [PubMed] [Google Scholar]
  86. Kaur Harpreet, Raghava G. P. S. BetaTPred: prediction of beta-TURNS in a protein using statistical algorithms. Bioinformatics. 2002 Mar;18(3):498–499. doi: 10.1093/bioinformatics/18.3.498. [DOI] [PubMed] [Google Scholar]
  87. Kierzek Andrzej M. STOCKS: STOChastic Kinetic Simulations of biochemical systems with Gillespie algorithm. Bioinformatics. 2002 Mar;18(3):470–481. doi: 10.1093/bioinformatics/18.3.470. [DOI] [PubMed] [Google Scholar]
  88. Klein Christoph A., Seidl Stefan, Petat-Dutter Karina, Offner Sonja, Geigl Jochen B., Schmidt-Kittler Oleg, Wendler Nicole, Passlick Bernward, Huber Rudolf M., Schlimok Günter. Combined transcriptome and genome analysis of single micrometastatic cells. Nat Biotechnol. 2002 Apr;20(4):387–392. doi: 10.1038/nbt0402-387. [DOI] [PubMed] [Google Scholar]
  89. Klose Joachim, Nock Christina, Herrmann Marion, Stühler Kai, Marcus Katrin, Blüggel Martin, Krause Eberhard, Schalkwyk Leonard C., Rastan Sohaila, Brown Steve D. M. Genetic analysis of the mouse brain proteome. Nat Genet. 2002 Mar 25;30(4):385–393. doi: 10.1038/ng861. [DOI] [PubMed] [Google Scholar]
  90. Kraggerud Sigrid Marie, Skotheim Rolf I., Szymanska Jadwiga, Eknaes Mette, Fosså Sophie D., Stenwig Anna E., Peltomäki Päivi, Lothe Ragnhild A. Genome profiles of familial/bilateral and sporadic testicular germ cell tumors. Genes Chromosomes Cancer. 2002 Jun;34(2):168–174. doi: 10.1002/gcc.10058. [DOI] [PubMed] [Google Scholar]
  91. Kroll T., Odyvanova L., Clement J. H., Platzer C., Naumann A., Marr N., Höffken K., Wölfl S. Molecular characterization of breast cancer cell lines by expression profiling. J Cancer Res Clin Oncol. 2002 Jan 9;128(3):125–134. doi: 10.1007/s00432-001-0308-z. [DOI] [PMC free article] [PubMed] [Google Scholar]
  92. Kuo Winston Patrick, Jenssen Tor-Kristian, Butte Atul J., Ohno-Machado Lucila, Kohane Isaac S. Analysis of matched mRNA measurements from two different microarray technologies. Bioinformatics. 2002 Mar;18(3):405–412. doi: 10.1093/bioinformatics/18.3.405. [DOI] [PubMed] [Google Scholar]
  93. König Simone, Grote Jens. Hydrophobic targets for MALDI mass spectrometry. Biotechniques. 2002 Apr;32(4):912, 914-5. [PubMed] [Google Scholar]
  94. Lagerström-Fermér Maria, Larhammar Dan, Johnsen Elsy, Landegren Ulf. Comparative genomics by capture PCR. Genomics. 2002 Mar;79(3):432–436. [PubMed] [Google Scholar]
  95. Lee Christopher, Grasso Catherine, Sharlow Mark F. Multiple sequence alignment using partial order graphs. Bioinformatics. 2002 Mar;18(3):452–464. doi: 10.1093/bioinformatics/18.3.452. [DOI] [PubMed] [Google Scholar]
  96. Lee Sanggyu, Clark Terry, Chen Jianjun, Zhou Guolin, Scott L. Ridgway, Rowley Janet D., Wang San Ming. Correct identification of genes from serial analysis of gene expression tag sequences. Genomics. 2002 Apr;79(4):598–602. doi: 10.1006/geno.2002.6730. [DOI] [PubMed] [Google Scholar]
  97. Lehr Stefan, Kotzka Jorg, Knebel Birgit, Schiller Martina, Krone Wilhelm, Muller-Wieland Dirk. Primary skin fibroblasts as human model system for proteome analysis. Proteomics. 2002 Mar;2(3):280–287. doi: 10.1002/1615-9861(200203)2:3<280::aid-prot280>3.0.co;2-w. [DOI] [PubMed] [Google Scholar]
  98. Leplae Raphael, Hubbard Tim J. P. MaxBench: evaluation of sequence and structure comparison methods. Bioinformatics. 2002 Mar;18(3):494–495. doi: 10.1093/bioinformatics/18.3.494. [DOI] [PubMed] [Google Scholar]
  99. Li Biaoru, Perabekam Supriya, Liu Ge, Yin Mei, Song Shiwen, Larson Alan. Experimental and bioinformatics comparison of gene expression between T cells from TIL of liver cancer and T cells from UniGene. J Gastroenterol. 2002;37(4):275–282. doi: 10.1007/s005350200035. [DOI] [PubMed] [Google Scholar]
  100. Li Ching, Chen Chin-Chuan, Yang Te-Hsun, Tzai Tzong-Shin, Huang Chia-Hui, Liou Ji-Tzung, Su Ih-Jen, Tzeng Ching-Cherng, Chiu Allen W., Shieh Biehuoy. Establishment of a mini-gene expression database for bladder tumor. J Formos Med Assoc. 2002 Feb;101(2):104–109. [PubMed] [Google Scholar]
  101. Li S., Xia X., Zhang X., Suen J. Regression of tumors by IFN-alpha electroporation gene therapy and analysis of the responsible genes by cDNA array. Gene Ther. 2002 Mar;9(6):390–397. doi: 10.1038/sj.gt.3301645. [DOI] [PubMed] [Google Scholar]
  102. Lim Seung Oe, Park Sung-Jun, Kim Won, Park Sung Gyoo, Kim Hie-Joon, Kim Yong-Il, Sohn Tae-Sung, Noh Jae-Hyung, Jung Guhung. Proteome analysis of hepatocellular carcinoma. Biochem Biophys Res Commun. 2002 Mar 8;291(4):1031–1037. doi: 10.1006/bbrc.2002.6547. [DOI] [PubMed] [Google Scholar]
  103. Liu Hongbin, Lin Dayin, Yates John R., 3rd Multidimensional separations for protein/peptide analysis in the post-genomic era. Biotechniques. 2002 Apr;32(4):898–passim. doi: 10.2144/02324pt01. [DOI] [PubMed] [Google Scholar]
  104. Lopez Mary F., Melov Simon. Applied proteomics: mitochondrial proteins and effect on function. Circ Res. 2002 Mar 8;90(4):380–389. doi: 10.1161/hh0402.105757. [DOI] [PubMed] [Google Scholar]
  105. Lorenz W. Walter, Dean Jeffrey F. D. SAGE profiling and demonstration of differential gene expression along the axial developmental gradient of lignifying xylem in loblolly pine (Pinus taeda). Tree Physiol. 2002 Apr;22(5):301–310. doi: 10.1093/treephys/22.5.301. [DOI] [PubMed] [Google Scholar]
  106. Lukacsovich T., Yamamoto D. Trap a gene and find out its function: toward functional genomics in Drosophila. J Neurogenet. 2001;15(3-4):147–168. doi: 10.3109/01677060109167373. [DOI] [PubMed] [Google Scholar]
  107. Ma Bin, Tromp John, Li Ming. PatternHunter: faster and more sensitive homology search. Bioinformatics. 2002 Mar;18(3):440–445. doi: 10.1093/bioinformatics/18.3.440. [DOI] [PubMed] [Google Scholar]
  108. Marvin K. W., Keelan J. A., Eykholt R. L., Sato T. A., Mitchell M. D. Use of cDNA arrays to generate differential expression profiles for inflammatory genes in human gestational membranes delivered at term and preterm. Mol Hum Reprod. 2002 Apr;8(4):399–408. doi: 10.1093/molehr/8.4.399. [DOI] [PubMed] [Google Scholar]
  109. McLachlan G. J., Bean R. W., Peel D. A mixture model-based approach to the clustering of microarray expression data. Bioinformatics. 2002 Mar;18(3):413–422. doi: 10.1093/bioinformatics/18.3.413. [DOI] [PubMed] [Google Scholar]
  110. Middleton Frank A., Mirnics Karoly, Pierri Joseph N., Lewis David A., Levitt Pat. Gene expression profiling reveals alterations of specific metabolic pathways in schizophrenia. J Neurosci. 2002 Apr 1;22(7):2718–2729. doi: 10.1523/JNEUROSCI.22-07-02718.2002. [DOI] [PMC free article] [PubMed] [Google Scholar]
  111. Mills Allen P., Jr Gene expression profiling diagnosis through DNA molecular computation. Trends Biotechnol. 2002 Apr;20(4):137–140. doi: 10.1016/s0167-7799(01)01915-1. [DOI] [PubMed] [Google Scholar]
  112. Monribot-Espagne Christelle, Boucherie Hélian. Differential gel exposure, a new methodology for the two-dimensional comparison of protein samples. Proteomics. 2002 Mar;2(3):229–240. doi: 10.1002/1615-9861(200203)2:3<229::aid-prot229>3.0.co;2-k. [DOI] [PubMed] [Google Scholar]
  113. Moran Nancy A. Microbial minimalism: genome reduction in bacterial pathogens. Cell. 2002 Mar 8;108(5):583–586. doi: 10.1016/s0092-8674(02)00665-7. [DOI] [PubMed] [Google Scholar]
  114. Mousses Spyro, Bubendorf Lukas, Wagner Urs, Hostetter Galen, Kononen Juha, Cornelison Robert, Goldberger Natalie, Elkahloun Abdel G., Willi Niels, Koivisto Pasi. Clinical validation of candidate genes associated with prostate cancer progression in the CWR22 model system using tissue microarrays. Cancer Res. 2002 Mar 1;62(5):1256–1260. [PubMed] [Google Scholar]
  115. Naiki Takafumi, Nagaki Masahito, Shidoji Yoshihiro, Kojima Hisanori, Imose Motoaki, Kato Tomohiro, Ohishi Nobuko, Yagi Kunio, Moriwaki Hisataka. Analysis of gene expression profile induced by hepatocyte nuclear factor 4alpha in hepatoma cells using an oligonucleotide microarray. J Biol Chem. 2002 Feb 7;277(16):14011–14019. doi: 10.1074/jbc.M105403200. [DOI] [PubMed] [Google Scholar]
  116. Nakajima Hideaki, Takenaka Masaru, Kaimori Jun-Ya, Nagasawa Yasuyuki, Kosugi Atsushi, Kawamoto Shouko, Imai Enyu, Hori Masatsugu, Okubo Kousaku. Gene expression profile of renal proximal tubules regulated by proteinuria. Kidney Int. 2002 May;61(5):1577–1587. doi: 10.1046/j.1523-1755.2002.00300.x. [DOI] [PubMed] [Google Scholar]
  117. Napoli Claudio, de Nigris Filomena, Welch John S., Calara Federico B., Stuart Robert O., Glass Christopher K., Palinski Wulf. Maternal hypercholesterolemia during pregnancy promotes early atherogenesis in LDL receptor-deficient mice and alters aortic gene expression determined by microarray. Circulation. 2002 Mar 19;105(11):1360–1367. doi: 10.1161/hc1102.106792. [DOI] [PubMed] [Google Scholar]
  118. Nassif Xavier. Genomics of Neisseria meningitidis. Int J Med Microbiol. 2002 Feb;291(6-7):419–423. doi: 10.1078/1438-4221-00148. [DOI] [PubMed] [Google Scholar]
  119. Ness S. R., Terpstra W., Krzywinski M., Marra M. A., Jones S. J. M. Assembly of fingerprint contigs: parallelized FPC. Bioinformatics. 2002 Mar;18(3):484–485. doi: 10.1093/bioinformatics/18.3.484. [DOI] [PubMed] [Google Scholar]
  120. Ning Xue-Han, Chen Shi-Han, Xu Cheng-Su, Li Linheng, Yao Lena Y., Qian Kun, Krueger Julia J., Hyyti Outi M., Portman Michael A. Hypothermic protection of the ischemic heart via alterations in apoptotic pathways as assessed by gene array analysis. J Appl Physiol (1985) 2002 May;92(5):2200–2207. doi: 10.1152/japplphysiol.01035.2001. [DOI] [PubMed] [Google Scholar]
  121. O'Neill Eric E., Brock Chris J., von Kriegsheim Alexander F., Pearce Andrew C., Dwek Raymond A., Watson Steve P., Hebestreit Holger F. Towards complete analysis of the platelet proteome. Proteomics. 2002 Mar;2(3):288–305. doi: 10.1002/1615-9861(200203)2:3<288::aid-prot288>3.0.co;2-0. [DOI] [PubMed] [Google Scholar]
  122. Oh Min-Kyu, Rohlin Lars, Kao Katy C., Liao James C. Global expression profiling of acetate-grown Escherichia coli. J Biol Chem. 2002 Jan 28;277(15):13175–13183. doi: 10.1074/jbc.M110809200. [DOI] [PubMed] [Google Scholar]
  123. Ohi Melanie D., Link Andrew J., Ren Liping, Jennings Jennifer L., McDonald W. Hayes, Gould Kathleen L. Proteomics analysis reveals stable multiprotein complexes in both fission and budding yeasts containing Myb-related Cdc5p/Cef1p, novel pre-mRNA splicing factors, and snRNAs. Mol Cell Biol. 2002 Apr;22(7):2011–2024. doi: 10.1128/MCB.22.7.2011-2024.2002. [DOI] [PMC free article] [PubMed] [Google Scholar]
  124. Ohki Ruri, Yamamoto Keiji, Mano Hiroyuki, Lee Richard T., Ikeda Uichi, Shimada Kazuyuki. Identification of mechanically induced genes in human monocytic cells by DNA microarrays. J Hypertens. 2002 Apr;20(4):685–691. doi: 10.1097/00004872-200204000-00026. [DOI] [PubMed] [Google Scholar]
  125. Oztur Z. Neslihan, Talamé Valentina, Deyholos Michael, Michalowski Christine B., Galbraith David W., Gozukirmizi Nermin, Tuberosa Roberto, Bohnert Hans J. Monitoring large-scale changes in transcript abundance in drought- and salt-stressed barley. Plant Mol Biol. 2002 Mar-Apr;48(5-6):551–573. doi: 10.1023/a:1014875215580. [DOI] [PubMed] [Google Scholar]
  126. Qi Zhen-Yu, Li Yao, Ying Kang, Wu Chao-Qun, Tang Rong, Zhou Zong-Xiang, Chen Zhong-Ping, Hui Guo-Zhen, Xie Yi. Isolation of novel differentially expressed genes related to human glioma using cDNA microarray and characterizations of two novel full-length genes. J Neurooncol. 2002 Feb;56(3):197–208. doi: 10.1023/a:1015079705841. [DOI] [PubMed] [Google Scholar]
  127. Ramaswamy Sridhar, Golub Todd R. DNA microarrays in clinical oncology. J Clin Oncol. 2002 Apr 1;20(7):1932–1941. doi: 10.1200/JCO.2002.20.7.1932. [DOI] [PubMed] [Google Scholar]
  128. Rao JianYu, Seligson David, Hemstreet George P. Protein expression analysis using quantitative fluorescence image analysis on tissue microarray slides. Biotechniques. 2002 Apr;32(4):924-6, 928-30, 932. doi: 10.2144/02324pt04. [DOI] [PubMed] [Google Scholar]
  129. Raouf A., Seth A. Discovery of osteoblast-associated genes using cDNA microarrays. Bone. 2002 Mar;30(3):463–471. doi: 10.1016/s8756-3282(01)00699-8. [DOI] [PubMed] [Google Scholar]
  130. Reddy Vaka S., Ali Gul S., Reddy Anireddy S. N. Genes encoding calmodulin-binding proteins in the Arabidopsis genome. J Biol Chem. 2002 Jan 8;277(12):9840–9852. doi: 10.1074/jbc.M111626200. [DOI] [PubMed] [Google Scholar]
  131. Reynolds Mark A. Microarray technology GEM microarrays and drug discovery. J Ind Microbiol Biotechnol. 2002 Mar;28(3):180–185. doi: 10.1038/sj/jim/7000136. [DOI] [PubMed] [Google Scholar]
  132. Richards Paul, Lees John. Functional proteomics using microchannel plate detectors. Proteomics. 2002 Mar;2(3):256–261. doi: 10.1002/1615-9861(200203)2:3<256::aid-prot256>3.0.co;2-k. [DOI] [PubMed] [Google Scholar]
  133. Rickert Andreas M., Premstaller Andreas, Gebhardt Christiane, Oefner Peter J. Genotyping of Snps in a polyploid genome by pyrosequencing. Biotechniques. 2002 Mar;32(3):592-3, 596-8, 600 passim. doi: 10.2144/02323rr01. [DOI] [PubMed] [Google Scholar]
  134. Robinson William H., Steinman Lawrence, Utz Paul J. Proteomics technologies for the study of autoimmune disease. Arthritis Rheum. 2002 Apr;46(4):885–893. doi: 10.1002/art.10129. [DOI] [PubMed] [Google Scholar]
  135. Rouillard Jean-Marie, Herbert Christopher J., Zuker Michael. OligoArray: genome-scale oligonucleotide design for microarrays. Bioinformatics. 2002 Mar;18(3):486–487. doi: 10.1093/bioinformatics/18.3.486. [DOI] [PubMed] [Google Scholar]
  136. Rubenwolf Susanne, Niewöhner Jens, Meyer Elisabeth, Petit-Frère Corinne, Rudert Fritz, Hoffmann Philipp R., Ilag Leodevico L. Functional proteomics using chromophore-assisted laser inactivation. Proteomics. 2002 Mar;2(3):241–246. doi: 10.1002/1615-9861(200203)2:3<241::aid-prot241>3.0.co;2-7. [DOI] [PubMed] [Google Scholar]
  137. Rupp Heinz, Maisch Bernhard. Funktionelle Genomik des druckbelasteten Kardiozyten: Etomoxir bei Herzinsuffizienz? Herz. 2002 Mar;27(2):166–173. doi: 10.1007/s00059-002-2357-8. [DOI] [PubMed] [Google Scholar]
  138. Rämet Mika, Manfruelli Pascal, Pearson Alan, Mathey-Prevot Bernard, Ezekowitz R. Alan B. Functional genomic analysis of phagocytosis and identification of a Drosophila receptor for E. coli. Nature. 2002 Mar 24;416(6881):644–648. doi: 10.1038/nature735. [DOI] [PubMed] [Google Scholar]
  139. Saalbach Gerhard, Erik Pinar, Wienkoop Stefanie. Characterisation by proteomics of peribacteroid space and peribacteroid membrane preparations from pea (Pisum sativum) symbiosomes. Proteomics. 2002 Mar;2(3):325–337. doi: 10.1002/1615-9861(200203)2:3<325::aid-prot325>3.0.co;2-w. [DOI] [PubMed] [Google Scholar]
  140. Sardi Iacopo, Tintori Veronica, Marchi Cinzia, Veltroni Marinella, Lippi Alma, Tucci Fabio, Tamburini Angela, Bernini Gabriella, Faulkner Lawrence. Molecular profiling of high-risk neuroblastoma by cDNA array. Int J Mol Med. 2002 May;9(5):541–545. [PubMed] [Google Scholar]
  141. Scanlan Matthew J., Gordon Claudia M., Williamson Barbara, Lee Sang-Yull, Chen Yao-Tseng, Stockert Elisabeth, Jungbluth Achim, Ritter Gerd, Jäger Dirk, Jäger Elke. Identification of cancer/testis genes by database mining and mRNA expression analysis. Int J Cancer. 2002 Apr 1;98(4):485–492. doi: 10.1002/ijc.10276. [DOI] [PubMed] [Google Scholar]
  142. Scheideler Marcel, Schlaich Nikolaus L., Fellenberg Kurt, Beissbarth Tim, Hauser Nicole C., Vingron Martin, Slusarenko Alan J., Hoheisel Jorg D. Monitoring the switch from housekeeping to pathogen defense metabolism in Arabidopsis thaliana using cDNA arrays. J Biol Chem. 2001 Dec 17;277(12):10555–10561. doi: 10.1074/jbc.M104863200. [DOI] [PubMed] [Google Scholar]
  143. Schmidt Heiko A., Strimmer Korbinian, Vingron Martin, von Haeseler Arndt. TREE-PUZZLE: maximum likelihood phylogenetic analysis using quartets and parallel computing. Bioinformatics. 2002 Mar;18(3):502–504. doi: 10.1093/bioinformatics/18.3.502. [DOI] [PubMed] [Google Scholar]
  144. Schubert Maria, Petersson Ulrika A., Haas Brian J., Funk Christiane, Schröder Wolfgang P., Kieselbach Thomas. Proteome map of the chloroplast lumen of Arabidopsis thaliana. J Biol Chem. 2001 Nov 21;277(10):8354–8365. doi: 10.1074/jbc.M108575200. [DOI] [PubMed] [Google Scholar]
  145. Schweitzer Barry, Roberts Scott, Grimwade Brian, Shao Weiping, Wang Minjuan, Fu Qin, Shu Quiping, Laroche Isabelle, Zhou Zhimin, Tchernev Velizar T. Multiplexed protein profiling on microarrays by rolling-circle amplification. Nat Biotechnol. 2002 Apr;20(4):359–365. doi: 10.1038/nbt0402-359. [DOI] [PMC free article] [PubMed] [Google Scholar]
  146. Seki Motoaki, Narusaka Mari, Kamiya Asako, Ishida Junko, Satou Masakazu, Sakurai Tetsuya, Nakajima Maiko, Enju Akiko, Akiyama Kenji, Oono Youko. Functional annotation of a full-length Arabidopsis cDNA collection. Science. 2002 Mar 21;296(5565):141–145. doi: 10.1126/science.1071006. [DOI] [PubMed] [Google Scholar]
  147. Shedden Kerby, Cooper Stephen. Analysis of cell-cycle-specific gene expression in human cells as determined by microarrays and double-thymidine block synchronization. Proc Natl Acad Sci U S A. 2002 Mar 19;99(7):4379–4384. doi: 10.1073/pnas.062569899. [DOI] [PMC free article] [PubMed] [Google Scholar]
  148. Shoemaker Randy, Keim Paul, Vodkin Lila, Retzel Ernest, Clifton Sandra W., Waterston Robert, Smoller David, Coryell Virginia, Khanna Anupama, Erpelding John. A compilation of soybean ESTs: generation and analysis. Genome. 2002 Apr;45(2):329–338. doi: 10.1139/g01-150. [DOI] [PubMed] [Google Scholar]
  149. Shusta Eric V., Boado Ruben J., Mathern Gary W., Pardridge William M. Vascular genomics of the human brain. J Cereb Blood Flow Metab. 2002 Mar;22(3):245–252. doi: 10.1097/00004647-200203000-00001. [DOI] [PubMed] [Google Scholar]
  150. Slesarev Alexei I., Mezhevaya Katja V., Makarova Kira S., Polushin Nikolai N., Shcherbinina Olga V., Shakhova Vera V., Belova Galina I., Aravind L., Natale Darren A., Rogozin Igor B. The complete genome of hyperthermophile Methanopyrus kandleri AV19 and monophyly of archaeal methanogens. Proc Natl Acad Sci U S A. 2002 Apr 2;99(7):4644–4649. doi: 10.1073/pnas.032671499. [DOI] [PMC free article] [PubMed] [Google Scholar]
  151. Smith E. J., Shi L., Smith G. Expressed sequence tags for the chicken genome from a normalized 10-day-old white leghorn whole-embryo cDNA library. 3. DNA sequence analysis of genetic variation in commercial chicken populations. Genome. 2002 Apr;45(2):261–267. doi: 10.1139/g01-155. [DOI] [PubMed] [Google Scholar]
  152. Staudt Louis M. Gene expression profiling of lymphoid malignancies. Annu Rev Med. 2002;53:303–318. doi: 10.1146/annurev.med.53.082901.103941. [DOI] [PubMed] [Google Scholar]
  153. Stone Roger T., Grosse W. Michael, Casas Eduardo, Smith Timothy P. L., Keele John W., Bennett Gary L. Use of bovine EST data and human genomic sequences to map 100 gene-specific bovine markers. Mamm Genome. 2002 Apr;13(4):211–215. doi: 10.1007/s00335-001-2124-9. [DOI] [PubMed] [Google Scholar]
  154. Stuart Gary W., Moffett Karen, Leader Jeffery J. A comprehensive vertebrate phylogeny using vector representations of protein sequences from whole genomes. Mol Biol Evol. 2002 Apr;19(4):554–562. doi: 10.1093/oxfordjournals.molbev.a004111. [DOI] [PubMed] [Google Scholar]
  155. Su Andrew I., Cooke Michael P., Ching Keith A., Hakak Yaron, Walker John R., Wiltshire Tim, Orth Anthony P., Vega Raquel G., Sapinoso Lisa M., Moqrich Aziz. Large-scale analysis of the human and mouse transcriptomes. Proc Natl Acad Sci U S A. 2002 Mar 19;99(7):4465–4470. doi: 10.1073/pnas.012025199. [DOI] [PMC free article] [PubMed] [Google Scholar]
  156. Takeuchi Hideaki, Fujiyuki Tomoko, Shirai Kenichi, Matsuo Yuko, Kamikouchi Azusa, Fujinawa Yumi, Kato Azusa, Tsujimoto Atsumi, Kubo Takeo. Identification of genes expressed preferentially in the honeybee mushroom bodies by combination of differential display and cDNA microarray. FEBS Lett. 2002 Feb 27;513(2-3):230–234. doi: 10.1016/s0014-5793(02)02319-0. [DOI] [PubMed] [Google Scholar]
  157. Tammi Martti T., Arner Erik, Britton Tom, Andersson Björn. Separation of nearly identical repeats in shotgun assemblies using defined nucleotide positions, DNPs. Bioinformatics. 2002 Mar;18(3):379–388. doi: 10.1093/bioinformatics/18.3.379. [DOI] [PubMed] [Google Scholar]
  158. Tan Chen, Li Jiang, Wang Jieru, Xiang Qiu, Zhang Xiaomei, Dong Li, Shen Shourong, Liang Songping, Li Guiyuan. Proteomic analysis of differential protein expression in human nasopharyngeal carcinoma cells induced by NAG7 transfection. Proteomics. 2002 Mar;2(3):306–312. doi: 10.1002/1615-9861(200203)2:3<306::aid-prot306>3.0.co;2-#. [DOI] [PubMed] [Google Scholar]
  159. Tan Sandra, Seow Teck Keong, Liang Rosa Cynthia M. Y., Koh Shiuan, Lee Christine P. C., Chung Maxey C. M., Hooi Shing Chuan. Proteome analysis of butyrate-treated human colon cancer cells (HT-29). Int J Cancer. 2002 Apr 1;98(4):523–531. doi: 10.1002/ijc.10236. [DOI] [PubMed] [Google Scholar]
  160. Templin Markus F., Stoll Dieter, Schrenk Monika, Traub Petra C., Vöhringer Christian F., Joos Thomas O. Protein microarray technology. Trends Biotechnol. 2002 Apr;20(4):160–166. doi: 10.1016/s0167-7799(01)01910-2. [DOI] [PubMed] [Google Scholar]
  161. Terashima Hiromichi, Fukuchi Satoshi, Nakai Kenta, Arisawa Mikio, Hamada Kenji, Yabuki Nami, Kitada Kunio. Sequence-based approach for identification of cell wall proteins in Saccharomyces cerevisiae. Curr Genet. 2002 Jan 25;40(5):311–316. doi: 10.1007/s00294-001-0264-9. [DOI] [PubMed] [Google Scholar]
  162. Ueda Hiroki R., Matsumoto Akira, Kawamura Miho, Iino Masamitsu, Tanimura Teiichi, Hashimoto Seiichi. Genome-wide transcriptional orchestration of circadian rhythms in Drosophila. J Biol Chem. 2002 Feb 19;277(16):14048–14052. doi: 10.1074/jbc.C100765200. [DOI] [PubMed] [Google Scholar]
  163. Van Driessche Nancy, Shaw Chad, Katoh Mariko, Morio Takahiro, Sucgang Richard, Ibarra Miroslava, Kuwayama Hidekazu, Saito Tamao, Urushihara Hideko, Maeda Mineko. A transcriptional profile of multicellular development in Dictyostelium discoideum. Development. 2002 Apr;129(7):1543–1552. doi: 10.1242/dev.129.7.1543. [DOI] [PubMed] [Google Scholar]
  164. Vincens Pierre, Badel-Chagnon Anne, André Cécile, Hazout Serge. D-ASSIRC: distributed program for finding sequence similarities in genomes. Bioinformatics. 2002 Mar;18(3):446–451. doi: 10.1093/bioinformatics/18.3.446. [DOI] [PubMed] [Google Scholar]
  165. Vuilleumier S., Pagni M. The elusive roles of bacterial glutathione S-transferases: new lessons from genomes. Appl Microbiol Biotechnol. 2002 Feb;58(2):138–146. doi: 10.1007/s00253-001-0836-0. [DOI] [PubMed] [Google Scholar]
  166. Wahde Mattias, Klus Gregory T., Bittner Michael L., Chen Yidong, Szallasi Zoltan. Assessing the significance of consistently mis-regulated genes in cancer associated gene expression matrices. Bioinformatics. 2002 Mar;18(3):389–394. doi: 10.1093/bioinformatics/18.3.389. [DOI] [PubMed] [Google Scholar]
  167. Wallace Caroline A., Ali Saira, Glazier Anne M., Norsworthy Penny J., Carlos Danilo C., Scott James, Freeman Tom C., Stanton Lawrence W., Kwitek Anne E., Aitman Timothy J. Radiation hybrid mapping of 70 rat genes from a data set of differentially expressed genes. Mamm Genome. 2002 Apr;13(4):194–197. doi: 10.1007/s00335-001-2140-9. [DOI] [PubMed] [Google Scholar]
  168. Wang Pinglang, Ding Fei, Chiang Hsienyuan, Thompson Robert C., Watson Stanley J., Meng Fan. ProbeMatchDB--a web database for finding equivalent probes across microarray platforms and species. Bioinformatics. 2002 Mar;18(3):488–489. doi: 10.1093/bioinformatics/18.3.488. [DOI] [PubMed] [Google Scholar]
  169. Wang Shihong, Zhang Xiang, Regnier Fred E. Quantitative proteomics strategy involving the selection of peptides containing both cysteine and histidine from tryptic digests of cell lysates. J Chromatogr A. 2002 Mar 8;949(1-2):153–162. doi: 10.1016/s0021-9673(01)01509-6. [DOI] [PubMed] [Google Scholar]
  170. Warrington Janet A., Shah Nila A., Chen Xiyin, Janis Michael, Liu Chunmei, Kondapalli Sangeetha, Reyes Vivian, Savage Michael P., Zhang Zhaomei, Watts Richard. New developments in high-throughput resequencing and variation detection using high density microarrays. Hum Mutat. 2002 Apr;19(4):402–409. doi: 10.1002/humu.10075. [DOI] [PubMed] [Google Scholar]
  171. Washburn Michael P., Ulaszek Ryan, Deciu Cosmin, Schieltz David M., Yates John R., 3rd Analysis of quantitative proteomic data generated via multidimensional protein identification technology. Anal Chem. 2002 Apr 1;74(7):1650–1657. doi: 10.1021/ac015704l. [DOI] [PubMed] [Google Scholar]
  172. Weckwerth Wolfram, Fiehn Oliver. Can we discover novel pathways using metabolomic analysis? Curr Opin Biotechnol. 2002 Apr;13(2):156–160. doi: 10.1016/s0958-1669(02)00299-9. [DOI] [PubMed] [Google Scholar]
  173. Wellmann Axel, Wollscheid Volker, Lu Hong, Ma Zhan Lu, Albers Peter, Schütze Karin, Rohde Volker, Behrens Peter, Dreschers Stefan, Ko Yon. Analysis of microdissected prostate tissue with ProteinChip arrays--a way to new insights into carcinogenesis and to diagnostic tools. Int J Mol Med. 2002 Apr;9(4):341–347. [PubMed] [Google Scholar]
  174. Wen Zezhang T., Burne Robert A. Functional genomics approach to identifying genes required for biofilm development by Streptococcus mutans. Appl Environ Microbiol. 2002 Mar;68(3):1196–1203. doi: 10.1128/AEM.68.3.1196-1203.2002. [DOI] [PMC free article] [PubMed] [Google Scholar]
  175. West Lisandra, Yang Desiree, Stephens Craig. Use of the Caulobacter crescentus genome sequence to develop a method for systematic genetic mapping. J Bacteriol. 2002 Apr;184(8):2155–2166. doi: 10.1128/JB.184.8.2155-2166.2002. [DOI] [PMC free article] [PubMed] [Google Scholar]
  176. Whitfield Charles W., Band Mark R., Bonaldo Maria F., Kumar Charu G., Liu Lei, Pardinas Jose R., Robertson Hugh M., Soares M. Bento, Robinson Gene E. Annotated expressed sequence tags and cDNA microarrays for studies of brain and behavior in the honey bee. Genome Res. 2002 Apr;12(4):555–566. doi: 10.1101/gr.5302. [DOI] [PMC free article] [PubMed] [Google Scholar]
  177. Williams R. M. The yeast lifecycle and DNA array technology. J Ind Microbiol Biotechnol. 2002 Mar;28(3):186–191. doi: 10.1038/sj.jim.7000200. [DOI] [PubMed] [Google Scholar]
  178. Zhao Qing, Kho Alvin, Kenney Anna Marie, Yuk Di Dong-in, Kohane Isaac, Rowitch David H. Identification of genes expressed with temporal-spatial restriction to developing cerebellar neuron precursors by a functional genomic approach. Proc Natl Acad Sci U S A. 2002 Apr 16;99(8):5704–5709. doi: 10.1073/pnas.082092399. [DOI] [PMC free article] [PubMed] [Google Scholar]
  179. van Buuren Marianne L., Salvi Silvio, Morgante Michele, Serhani Bahia, Tuberosa Roberto. Comparative genomic mapping between a 754 kb region flanking DREB1A in Arabidopsis thaliana and maize. Plant Mol Biol. 2002 Mar-Apr;48(5-6):741–750. doi: 10.1023/a:1014890008579. [DOI] [PubMed] [Google Scholar]

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

RESOURCES