From crittend@itis.com Mon Nov 29 12:10:58 2004 Date: Thu, 18 Nov 2004 15:57:29 -0600 From: Lyman/Margaret Crittenden To: Multiple Recipients of Subject: November, 2004 Genomics References Resent-Date: Thu, 18 Nov 2004 22:10:33 +0000 Resent-From: angenmap@genome.ansci.iastate.edu Resent-cc: recipient list not shown: ; [ AnGenMap Discussion Mailing List - Mail distributed to 1102 members ] [ INFO: http://www.genome.iastate.edu/community/discuss.html ] ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ These may be downloaded in to Procite or Reference Manager at http://www.genome.iastate.edu/ftp/ref/ JOURNAL REFS. (GENOMICS METHODS AND REVIEWS) NLM 11/04 1. Breitling, R.; Amtmann, A.Herzyk, P. Graph-based iterative Group Analysis enhances microarray interpretation. BMC Bioinformatics. 5:100, 2004. ADDRESS: Institute of Biomedical and Life Sciences, University of Glasgow, Glasgow G12 8QQ, United Kingdom. r.breitling@bio.gla.ac.uk. Medline UID: 15272936 2. Chittur, S. V. DNA microarrays: tools for the 21st Century. Comb Chem High Throughput Screen. 7:531-7, 2004. ADDRESS: Center for Functional Genomics, University at Albany, East Campus, DB 227, One University Place, Rensselaer, NY 12144, USA. schittur@albany.edu. Medline UID: 15379624 3. Coombes, B. K.; Hardwidge, P. R.Finlay, B. B. Interpreting the host-pathogen dialogue through microarrays. Adv Appl Microbiol. 54:291-331, 2004. ADDRESS: Biotechnology Laboratory, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada. Medline UID: 15251285 4. Cowell, J. K. High throughput determination of gains and losses of genetic material using high resolution BAC arrays and comparative genomic hybridization. Comb Chem High Throughput Screen. 7:587-96, 2004. ADDRESS: Department of Cancer Genetics, Roswell Park Cancer Institute, Buffalo, NY 14263, USA. john.cowell@roswellpark.org. Medline UID: 15379630 5. Daub, C. O.; Steuer, R.; Selbig, J.Kloska, S. Estimating mutual information using B-spline functions--an improved similarity measure for analysing gene expression data. BMC Bioinformatics. 5:118, 2004. ADDRESS: Max Planck Institute of Molecular Plant Physiology, Potsdam, 14424, Germany. carsten.daub@cgb.ki.se. Medline UID: 15339346 6. de Brevern, A. G.; Hazout, S.Malpertuy, A. Influence of microarrays experiments missing values on the stability of gene groups by hierarchical clustering. BMC Bioinformatics. 5:114, 2004. ADDRESS: Equipe de Bioinformatique Genomique et Moleculaire (EBGM), INSERM E0346, Universite Denis DIDEROT-Paris 7, case 7113, 2, place Jussieu, 75251 Paris, France. alexandre.debrevern@ebgm.jussieu.fr. Medline UID: 15324460 7. Deplancke, B.; Dupuy, D.; Vidal, M.Walhout, A. J. A gateway-compatible yeast one-hybrid system. Genome Res. 14:2093-101, 2004. ADDRESS: Program in Gene Function and Expression, University of Massachusetts Medical School, Worcester, Massachusetts 01605, USA. Medline UID: 15489331 8. Flikka, K.; Yadetie, F.; Laegreid, A.Jonassen, I. XHM: a system for detection of potential cross hybridizations in DNA microarrays. BMC Bioinformatics. 5:117, 2004. ADDRESS: Computational Biology Unit, Bergen Center for Computational Science, UNIFOB/UiB, Thormoehlensgt,55, N-5008 Bergen, Norway. flikka@ii.uib.no. Medline UID: 15333145 9. Freimer, N. and Sabatti, C. The use of pedigree, sib-pair and association studies of common diseases for genetic mapping and epidemiology. Nat Genet. 36:1045-51, 2004. ADDRESS: Center for Neurobehavioral Genetics, Neuropsychiatric Institute, Los Angeles, CA 90095, USA. nfreimer@mednet.ucla.edu . Medline UID: 15454942 10. Gautier, L.; Moller, M.; Friis-Hansen, L.Knudsen, S. Alternative mapping of probes to genes for Affymetrix chips. BMC Bioinformatics. 5:111, 2004. ADDRESS: Center for Biological Sequence Analysis, Technical University of Denmark, 2800 Lyngby, Denmark. laurent@cbs.dtu.dk. Medline UID: 15310390 11. Gebauer, F. and Hentze, M. W. Molecular mechanisms of translational control. Nat Rev Mol Cell Biol. 5:827-35, 2004. ADDRESS: Centre de Regulacio Genomica, Passeig Maritim 37-49, 08003-Barcelona, Spain. fatima.gebauer@crg.es. Medline UID: 15459663 12. Hackl, H.; Cabo, F. S.; Sturn, A.; Wolkenhauer, O.Trajanoski, Z. Analysis of DNA microarray data. Curr Top Med Chem. 4:1357-70, 2004. ADDRESS: Institute for Genomics and Bioinformatics and Christian Doppler Laboratory for Genomics and Bioinformatics, Graz University of Technology, Petersgasse 14, A-8010 Graz, Austria. Medline UID: 15379650 13. Hou, P.; Ji, M.; Li, S.Lu, Z. Microarray-based approach for high-throughput genotyping of single-nucleotide polymorphisms with layer-by-layer dual-color fluorescence hybridization. Clin Chem. 50:1955-7, 2004. ADDRESS: Chien-Shiung Wu Laboratory, Department of Biological Science and Medical Engineering, Southeast University, Nanjing 210096, China. Medline UID: 15484337 14. Huber, M.; Wei, T. F.; Muller, U. R.; Lefebvre, P. A.; Marla, S. S.Bao, Y. P. Gold nanoparticle probe-based gene expression analysis with unamplified total human RNA. Nucleic Acids Res. 32:e137, 2004. ADDRESS: Nanosphere Inc., 4088 Commercial Ave., Northbrook, IL 60062, USA. Medline UID: 15475384 15. Karopka, T.; Scheel, T.; Bansemer, S.Glass, A. Automatic construction of gene relation networks using text mining and gene expression data. Med Inform Internet Med. 29:169-83, 2004. ADDRESS: Institute of Medical Informatics and Biometry, University of Rostock, Rembrandt-Strasse 16/17, 18055 Rostock, Germany. thomas.karopka@medizin.uni-rostock.de. Medline UID: 15370996 16. Koehne, J. E.; Chen, H.; Cassell, A. M.; Ye, Q.; Han, J.; Meyyappan, M.Li, J. Miniaturized multiplex label-free electronic chip for rapid nucleic acid analysis based on carbon nanotube nanoelectrode arrays. Clin Chem. 50:1886-93, 2004. ADDRESS: Center for Nanotechnology, NASA Ames Research Center, Moffett Field, CA 94035, USA. Medline UID: 15319319 17. Laubenbacher, R. and Stigler, B. A computational algebra approach to the reverse engineering of gene regulatory networks. J Theor Biol. 229:523-37, 2004. ADDRESS: Virginia Bioinformatics Institute at Virginia Tech, 1880 Pratt Drive, Building XV, Blacksburg, VA 24061, USA. reinhard@vbi.vt.edu. Medline UID: 15246788 18. Le Meur, N.; Lamirault, G.; Bihouee, A.; Steenman, M.; Bedrine-Ferran, H.; Teusan, R.; Ramstein, G.Leger, J. J. A dynamic, web-accessible resource to process raw microarray scan data into consolidated gene expression values: importance of replication. Nucleic Acids Res. 32:5349-58, 2004. ADDRESS: Ouest genopole, Institut du Thorax, Institut National de la Sante et de la Recherche Medicale (UMR 533), Faculte de Medecine, 44035 Nantes, France. nolwenn.lemeur@nantes.inserm.fr. Medline UID: 15475389 19. Liu, B.; Cui, Q.; Jiang, T.Ma, S. A combinational feature selection and ensemble neural network method for classification of gene expression data. BMC Bioinformatics. 5:136, 2004. ADDRESS: National Laboratory of Pattern Recognition, Institute of Automation, Chinese Academy of Sciences, Beijing 100080, P. R. China. bliu@nlpr.ia.ac.cn. Medline UID: 15450124 20. Milanesi, L. and Rogozin, I. B. ESTMAP: a system for expressed sequence tags mapping on genomic sequences. IEEE Trans Nanobioscience. 2:75-8, 2003. ADDRESS: CNR-ITB, Via Frotelli Corni, 93, Segrate, MI 20090, Italy. Medline UID: 15382662 21. Miyaki, K.; Omae, K.; Murata, M.; Tanahashi, N.; Saito, I.Watanabe, K. High throughput multiple combination extraction from large scale polymorphism data by exact tree method. J Hum Genet. 49:455-62, 2004. ADDRESS: Department of Preventive Medicine and Public Health, School of Medicine, Keio University, 35 Shinanomachi, Shinjuku-ku, Tokyo 160-8582, Japan. miyaki@sc.itc.keio.ac.jp. Medline UID: 15309679 22. Panicker, R. C.; Huang, X.Yao, S. Q. Recent advances in peptide-based microarray technologies. Comb Chem High Throughput Screen. 7:547-56, 2004. ADDRESS: Department of Chemistry, National University of Singapore, 3 Science Drive 3, 117543, Republic of Singapore. Medline UID: 15379626 23. Pask, R.; Rance, H. E.; Barratt, B. J.; Nutland, S.; Smyth, D. J.; Sebastian, M.; Twells, R. C.; Smith, A.; Lam, A. C.; Smink, L. J.; Walker, N. M.Todd, J. A. Investigating the utility of combining phi29 whole genome amplification and highly multiplexed single nucleotide polymorphism BeadArray genotyping. BMC Biotechnol. 4:15, 2004. ADDRESS: Juvenile Diabetes Research Foundation/Wellcome Trust Diabetes, Inflammation Laboratory, Cambridge Institute for Medical Research, University of Cambridge, Wellcome Trust/MRC Building, Cambridge, CB2 2XY, UK. rebecca.pask@cimr.cam.ac.uk. Medline UID: 15279678 24. Qin, L. X. and Kerr, K. F. Empirical evaluation of data transformations and ranking statistics for microarray analysis. Nucleic Acids Res. 32:5471-9, 2004. ADDRESS: Department of Biostatistics, University of Washington, F-600 Health Sciences Building 1705 NE Pacific Street, Box 357232, Seattle, WA 98195, USA. CORPORATE NAME: Contributing Members of the Toxicogenomics Research Consortium. Medline UID: 15479783 25. Reed, G. H. and Wittwer, C. T. Sensitivity and specificity of single-nucleotide polymorphism scanning by high-resolution melting analysis. Clin Chem. 50:1748-54, 2004. ADDRESS: Department of Pathology, University of Utah Medical Center, 5B418, 50 N Medical Dr, Salt Lake City 84132, USA. Medline UID: 15308590 26. Rong, S.; Wen-li, M.; Cui-hua, L.; Yan-bin, S.; Xiang-ming, M.Wen-ling, Z. An oligonucleotide microarray bait for isolation of target gene fragments. J Biochem Mol Biol. 37:148-52, 2004. ADDRESS: Institute of Molecular Biology, First Military Medical University, Guangzhou 510515, P.R. China. Medline UID: 15469689 27. Wakai, J.; Takagi, A.; Nakayama, M.; Miya, T.; Miyahara, T.; Iwanaga, T.; Takenaka, S.; Ikeda, Y.Amano, M. A novel method of identifying genetic mutations using an electrochemical DNA array. Nucleic Acids Res. 32:e141, 2004. ADDRESS: TUM Gene, Inc., 3-1 Kazusa-Koito Kimitsu, Chiba 292-1149 Japan. Medline UID: 15498924 28. Wang, H. M.; Ma, W. L.; Huang, H.; Xiao, W. W.; Wang, Y.Zheng, W. L. DNA microarray probe preparation by gel isolation nested PCR. J Biochem Mol Biol. 37:356-61, 2004. ADDRESS: Institute of Molecular Biology, First Uniform Medical University, Guangzhou 510515, P.R. China. Medline UID: 15469719 29. Wei, Q.; Liu, S.; Huang, J.; Mao, X.; Chu, X.; Wang, Y.; Qiu, M.; Mao, Y.; Xie, Y.Li, Y. Comparison of hybridization behavior between double and single strands of targets and the application of asymmetric PCR targets in cDNA microarray. J Biochem Mol Biol. 37:439-44, 2004. ADDRESS: State Key Laboratory of Genetic Engineering, Institute of Genetics, School of Life Science, Fudan University, Shanghai 200433, P.R. China. Medline UID: 15469731 30. Yan, P. S.; Wei, S. H.Huang, T. H. Methylation-specific oligonucleotide microarray. Methods Mol Biol. 287:251-60, 2004. ADDRESS: Division of Human Cancer Genetics, Department of Molecular Virology, Immunology and Molecular Genetics, The Ohio State University, Columbus, USA. Medline UID: 15273417 31. Yoon, D.; Yi, S. G.; Kim, J. H.Park, T. Two-stage normalization using background intensities in cDNA microarray data. BMC Bioinformatics. 5:97, 2004. ADDRESS: Seoul National University, San56-l, Shin Lim-Dong, Kwan Ak-Ku, Seoul 151-747, Republic of Korea. avanti@chollian.net. Medline UID: 15268767 32. Zhou, G. H.; Shirakura, H.; Kamahori, M.; Okano, K.; Nagai, K.Kambara, H. A gel-free SNP genotyping method: bioluminometric assay coupled with modified primer extension reactions (BAMPER) directly from double-stranded PCR products. Hum Mutat. 24:155-63, 2004. ADDRESS: Hitachi, Ltd., Central Research Laboratory, Tokyo, Japan. Medline UID: 15241797 ********************************************************************** Margaret and Lyman Crittenden e-mail: crittend@itis.com 8550 Highway 19 Phone: 608-798-0791 Cross Plains, WI 53528 *********************************************************************** ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -o NAGRP BIOINFORMATICS COORDINATION PROJECT - Sponsored by USDA/CSREES -o WEB: http://www.genome.iastate.edu/