From crittend@itis.com Wed Oct 15 12:12:54 2003 Date: Tue, 14 Oct 2003 20:33:08 -0700 From: Lyman/Margaret Crittenden To: Multiple Recipients of Subject: September and October Genomics References Resent-Date: 15 Oct 2003 01:37:25 -0000 Resent-From: angenmap@genome.ansci.iastate.edu Resent-cc: recipient list not shown: ; [ AnGenMap Discussion Mailing List - Mail distributed to 988 members ] [ INFO: http://www.genome.iastate.edu/community/discuss.html ] ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Below are both the September and October, 2003 references. You probably did not get the September references due virus problems at Iowa State. JOURNAL REFS. (GENOMICS METHODS AND REVIEWS) NLM 9/03 1. Albini, G.; Falque, M.Joets, J. ActionMap: A web-based software that automates loci assignments to framework maps. Nucleic Acids Res. 31:3815-8, 2003. ADDRESS: UMR de Genetique Vegetale du Moulon, Ferme du Moulon, 91190 Gif-sur-Yvette, France. Medline UID: 22709027 2. Coessens, B.; Thijs, G.; Aerts, S.; Marchal, K.; De Smet, F.; Engelen, K.; Glenisson, P.; Moreau, Y.; Mathys, J.De Moor, B. INCLUSive: A web portal and service registry for microarray and regulatory sequence analysis. Nucleic Acids Res. 31:3468-70, 2003. ADDRESS: ESAT-SCD, Katholieke Universiteit Leuven, Kasteelpark Arenberg 10, 3001 Leuven, Belgium. bcoessen@esat.kuleuven.ac.be. Medline UID: 22708947 3. Draghici, S.; Khatri, P.; Bhavsar, P.; Shah, A.; Krawetz, S. A.Tainsky, M. A. Onto-Tools, the toolkit of the modern biologist: Onto-Express, Onto-Compare, Onto-Design and Onto-Translate. Nucleic Acids Res. 31:3775-81, 2003. ADDRESS: Department of Computer Science, Wayne State University, 431 State Hall, Detroit, MI 48202, USA. sod@cs.wayne.edu. Medline UID: 22709017 4. el-Meanawy, M. A.; Barathan, S.; Hayden, P. S.; Iyengar, S. K.; Schelling, J. R.Sedor, J. R. Serial analysis of gene expression. Methods Mol Med. 86:257-74, 2003. ADDRESS: Department of Medicine, O'Brien Renal Research Center, Case Western Reserve University, Cleveland, OH, USA. Medline UID: 22769251 5. Emrich, S. J.; Lowe, M.Delcher, A. L. PROBEmer: A web-based software tool for selecting optimal DNA oligos. Nucleic Acids Res. 31:3746-50, 2003. ADDRESS: Interdepartmental Bioinformatics and Computational Biology, Iowa State University, Rockville, MD, USA. semrich@iastate.edu. Medline UID: 22709010 6. Gershon, D. Proteomics technologies: probing the proteome. Nature. 424:581-7, 2003. Medline UID: 22773407 7. When the chips are down. Nature. 424:585, 2003. Medline UID: 22773410 8. Halees, A. S.; Leyfer, D.Weng, Z. PromoSer: A large-scale mammalian promoter and transcription start site identification service. Nucleic Acids Res. 31:3554-9, 2003. ADDRESS: Bioinformatics Program, Boston University, 44 Cummington Street, Boston, MA 02215, USA. Medline UID: 22708965 9. Herrero, J.; Al-Shahrour, F.; Diaz-Uriarte, R.; Mateos, A.; Vaquerizas, J. M.; Santoyo, J.Dopazo, J. GEPAS: A web-based resource for microarray gene expression data analysis. Nucleic Acids Res. 31:3461-7, 2003. ADDRESS: Bioinformatics Unit, Centro Nacional de Investigaciones Oncologicas, c/Melchor Fernandez Almagro 3, 28029, Madrid, Spain. Medline UID: 22708946 10. Horng, J. T.; Lin, F. M.; Lin, J. H.; Huang, H. D.Liu, B. J. Database of repetitive elements in complete genomes and data mining using transcription factor binding sites. IEEE Trans Inf Technol Biomed. 7:93-100, 2003. ADDRESS: Department of Computer Science and Information Engineering, National Central University, Jung-li City 320, Taiwan, ROC. horng@db.csie.ncu.edu.tw. Medline UID: 22717802 11. Hotz-Wagenblatt, A.; Hankeln, T.; Ernst, P.; Glatting, K. H.; Schmidt, E. R.Suhai, S. ESTAnnotator: A tool for high throughput EST annotation. Nucleic Acids Res. 31:3716-9, 2003. ADDRESS: Department of Molecular Biophysics, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 580, D-69120 Heidelberg, Germany. hotz-wagenblatt@dkfz.de. Medline UID: 22709002 12. Howbrook, D. N.; van der Valk, A. M.; O'Shaughnessy, M. C.; Sarker, D. K.; Baker, S. C.Lloyd, A. W. Developments in microarray technologies. Drug Discov Today. 8:642-51, 2003. ADDRESS: School of Pharmacy and Biomolecular Sciences, University of Brighton, Moulsecoomb, Brighton BN2 4GJ, UK. Medline UID: 22749652 13. Kakazu, N.; Bar-Am, I.; Hada, S.; Ago, H.Abe, T. A new chromosome banding technique, spectral color banding (SCAN), for full characterization of chromosomal abnormalities. Genes Chromosomes Cancer. 37:412-6, 2003. ADDRESS: Department of Hygiene, Kyoto Prefectural University of Medicine, Kyoto, Japan. kakazu@basic.kpu-m.ac.jp. Medline UID: 22683266 14. Knudsen, S.; Workman, C.; Sicheritz-Ponten, T.Friis, C. GenePublisher: Automated analysis of DNA microarray data. Nucleic Acids Res. 31:3471-6, 2003. ADDRESS: Center for Biological Sequence Analysis, BioCentrum-DTU, 2800 Lyngby, Denmark. steen@cbs.dtu.dk. Medline UID: 22708948 15. Kohara, Y.; Noda, H.; Okano, K.Kambara, H. DNA hybridization using "bead-array": probe-attached beads arrayed in a capillary in a predetermined order. Nucleic Acids Res Suppl. 83-4, 2001. ADDRESS: Central Research Laboratory, Hitachi Ltd., 1-280 Higashi-koigakubo, Kokubunji, Tokyo 185-8601, Japan. Medline UID: 22720789 16. Kwok, P. Y. and Chen, X. Detection of single nucleotide polymorphisms. Curr Issues Mol Biol. 5:43-60, 2003. ADDRESS: Cardiovascular Research Institute, University of California, 505 Parnassus Avenue, Long 1332A, Box 0130, San Francisco, CA 94143-0130, USA. kwok@cvrimail.ucsf.edu. Medline UID: 22677679 17. Lapidot, M. and Pilpel, Y. Comprehensive quantitative analyses of the effects of promoter sequence elements on mRNA transcription. Nucleic Acids Res. 31:3824-8, 2003. ADDRESS: Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, 76100, Israel. Medline UID: 22709030 18. Luc, N.; Risler, J. L.; Bergeron, A.Raffinot, M. Gene teams: a new formalization of gene clusters for comparative genomics. Comput Biol Chem. 27:59-67, 2003. ADDRESS: CNRS - Laboratoire Genome et Informatique, Tour Evry 2, 523, Place des Terrasses de 1'Agora, 91034 Evry, France. Medline UID: 22682946 19. Nielsen, H. B.; Wernersson, R.Knudsen, S. Design of oligonucleotides for microarrays and perspectives for design of multi-transcriptome arrays. Nucleic Acids Res. 31:3491-6, 2003. ADDRESS: Center for Biological Sequence Analysis, BioCentrum-DTU, Technical University of Denmark, Building 208, 2800 Lyngby, Denmark. hbjorn@cbs.dtu.dk. Medline UID: 22708952 20. Okano, K.; Uematsu, C.; Shen, M.Kambara, H. Classified fingerprinting: A method of comprehensive analysis for comparing megabase genomes. Nucleic Acids Res Suppl. 93-4, 2001. ADDRESS: Biosystems Research Department, Central Research Laboratory, Hitachi Ltd. Medline UID: 22720794 21. Rao, J. S. and Li, J. Statistical methods for chip calibration and saturation effects in antibody-spiked gene expression data. Respir Physiol Neurobiol. 135:109-19, 2003. ADDRESS: Case Western Reserve University, 10900 Euclid Avenue, 160 Peter B. Lewis Building, Cleveland, OH 44106, USA. sunil@hal.cwru.edu. Medline UID: 22695774 22. Raychaudhuri, S.; Chang, J. T.; Imam, F.Altman, R. B. The computational analysis of scientific literature to define and recognize gene expression clusters. Nucleic Acids Res. 31:4553-60, 2003. ADDRESS: Department of Genetics and. Department of Biochemistry, Stanford University, Stanford, CA 94305, USA. Medline UID: 22770820 23. Roven, C. and Bussemaker, H. J. REDUCE: An online tool for inferring cis-regulatory elements and transcriptional module activities from microarray data. Nucleic Acids Res. 31:3487-90, 2003. ADDRESS: Department of Biological Sciences, Columbia University, New York, NY, USA. Medline UID: 22708951 24. Satoh, N.; Satou, Y.; Davidson, B.Levine, M. Ciona intestinalis: an emerging model for whole-genome analyses. Trends Genet. 19:376-81, 2003. ADDRESS: Department of Zoology, Graduate School of Science, Kyoto University, Sakyo-ku, Kyoto 606-8502, Japan. satoh@ascidian.zool.kyoto-u.ac.jp. Medline UID: 22736110 25. Sauer, S. and Gut, I. G. Extension of the GOOD assay for genotyping single nucleotide polymorphisms by matrix-assisted laser desorption/ionization mass spectrometry. Rapid Commun Mass Spectrom. 17:1265-72, 2003. ADDRESS: Max-Planck-Institute for Molecular Genetics, Abteilung Lehrach, Ihnestrasse 73, 14195 Berlin-Dahlem, Germany. Medline UID: 22695759 26. Tang, Z.; Mori, T.; Takarada, T.Maeda, M. Single nucleotide polymorphisms (SNPs) assay using reversible association and dispersion of DNA-linked colloidal nanoparticles. Nucleic Acids Res Suppl. 165-6, 2001. ADDRESS: Department of Applied Chemistry, Graduate School of Engineering, Kyushu University, 6-10-1 Hakozaki, Higashi-ku, Fukuoka 812-8581, Japan. Medline UID: 22720830 27. Tilstone, C. DNA microarrays: vital statistics. Nature. 424:610-2, 2003. Medline UID: 22787135 28. Tolstrup, N.; Nielsen, P. S.; Kolberg, J. G.; Frankel, A. M.; Vissing, H.Kauppinen, S. OligoDesign: Optimal design of LNA (locked nucleic acid) oligonucleotide capture probes for gene expression profiling. Nucleic Acids Res. 31:3758-62, 2003. ADDRESS: Department of Functional Genomics, Exiqon, Bygstubben 9, DK-2950 Vedbaek, Denmark. tolstrup@exiqon.com. Medline UID: 22709013 29. Uematsu, C.; Makino, I.Okano, K. Real-time detection of PCR products for comparative analysis of expressed genes using module-shuffling TaqMan probes (MTPs). Nucleic Acids Res Suppl. 211-2, 2002. ADDRESS: Biosystems Research Department, Central Research Laboratory, Hitachi, Ltd., 1-280, Higashi-koigakubo Kokubunji-shi, Tokyo, 185-8601, Japan. Medline UID: 22785317 30. Yeramian, E. and Jones, L. GeneFizz: A web tool to compare genetic (coding/non-coding) and physical (helix/coil) segmentations of DNA sequences. Gene discovery and evolutionary perspectives. Nucleic Acids Res. 31:3843-9, 2003. ADDRESS: Unite de Bio-Informatique Structurale, URA CNRS 2185, Institut Pasteur, 75724 Paris Cedex 15, France. yeramian@pasteur.fr. Medline UID: 22709035 31. Zhong, S.; Li, C.Wong, W. H. ChipInfo: Software for extracting gene annotation and gene ontology information for microarray analysis. Nucleic Acids Res. 31:3483-6, 2003. ADDRESS: Department of Biostatistics, Harvard School of Public Health, 655 Huntington Avenue, Boston, MA 02115, USA. Medline UID: 22708950 32. Zhou, Y. and Abagyan, R. Algorithms for high-density oligonucleotide array. Curr Opin Drug Discov Devel. 6:339-45, 2003. ADDRESS: Genomics Institute, Novartis Research Foundation, 10675 John Jay Hopkins Drive, San Diego, CA 92121, USA. Medline UID: 22718015 JOURNAL REFS.(GENOMICS METHODS AND REVIEWS) NLM 10/03 1. Akilesh, S.; Shaffer, D. J.Roopenian, D. Customized molecular phenotyping by quantitative gene expression and pattern recognition analysis. Genome Res. 13:1719-27, 2003. ADDRESS: The Jackson Laboratory, Bar Harbor, Maine 04609, USA. Medline UID: 22723763 2. Cahill, D. J. and Nordhoff, E. Protein arrays and their role in proteomics. Adv Biochem Eng Biotechnol. 83:177-87, 2003. ADDRESS: Max-Planck-Institute for Molecular Genetics, Ihnestrasse 73, 14195 Berlin, Germany. cahill@molgen.mpg.de. Medline UID: 22815612 3. Dobbin, K.; Shih, J. H.Simon, R. Questions and answers on design of dual-label microarrays for identifying differentially expressed genes. J Natl Cancer Inst. 95:1362-9, 2003. ADDRESS: Biometric Research Branch, Division of Cancer Treatment and Diagnosis, National Cancer Institute, Bethesda, MD 20892-7434, USA. dobbinke@mail.nih.gov. Medline UID: 22857751 4. Forster, T.; Roy, D.Ghazal, P. Experiments using microarray technology: limitations and standard operating procedures. J Endocrinol. 178:195-204, 2003. ADDRESS: Scottish Centre for Genomic Technology and Informatics (GTI), The University of Edinburgh, Medical School, Little France Crescent, Edinburgh EH16 4SB, UK. marilyn.horne@ed.ac.uk. Medline UID: 22786530 5. Furlanello, C.; Serafini, M.; Merler, S.Jurman, G. An accelerated procedure for recursive feature ranking on microarray data. Neural Netw. 16:641-8, 2003. ADDRESS: ITC-irst, v. Sommarive 18, Povo, I-38050 Trento, Italy. furlan@itc.it. Medline UID: 22735529 6. Habeck, M. New approach to gene expression analysis. Drug Discov Today. 8:427-8, 2003. Medline UID: 22686374 7. Hariharan, R. The analysis of microarray data. Pharmacogenomics. 4:477-97, 2003. ADDRESS: Strand Genomics Private Limited, and Indian Institute of Science, Bangalore, India, 560080. ramesh@strandgenomics.com. Medline UID: 22717012 8. Johansson, A.; Karlsson, P.Gyllensten, U. A novel method for automatic genotyping of microsatellite markers based on parametric pattern recognition. Hum Genet. 113:316-24, 2003. ADDRESS: Department of Genetics and Pathology, Rudbeck Laboratory, Uppsala University, 571 85, Uppsala, Sweden. Medline UID: 22808984 9. Kim, P. M. and Tidor, B. Subsystem identification through dimensionality reduction of large-scale gene expression data. Genome Res. 13:1706-18, 2003. ADDRESS: Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA. Medline UID: 22723762 10. Stich, N.; Gandhum, A.; Matushin, V.; Mayer, C.; Bauer, G.Schalkhammer, T. Nanofilms and nanoclusters: energy sources driving fluorophores of biochip bound labels. J Nanosci Nanotechnol. 1:397-405, 2001. ADDRESS: Kluyver Laboratorium for Biotechnology, TU Delft, Julianalaan 67, 2628 BC Delft, The Netherlands. Medline UID: 22795517 11. Storey, J. D. and Tibshirani, R. Statistical significance for genomewide studies. Proc Natl Acad Sci U S A. 100:9440-5, 2003. ADDRESS: Department of Biostatistics, University of Washington, Seattle, WA 98195, USA. jstorey@u.washington.edu. Medline UID: 22784726 12. Tilquin, P.; Van Keilegom, I.; Coppieters, W.; Le Boulenge, E.Baret, P. V. Non-parametric interval mapping in half-sib designs: use of midranks to account for ties. Genet Res. 81:221-8, 2003. ADDRESS: Unite de Genetique, Faculte d'ingenierie biologique, agronomique et environnementale, Universite catholique de Louvain, Croix du Sud 2 hte 14, B-1348 Louvain-la-Neuve, Belgium. Medline UID: 22810558 13. Vainrub, A. and Pettitt, B. M. Sensitive quantitative nucleic acid detection using oligonucleotide microarrays. J Am Chem Soc. 125:7798-9, 2003. ADDRESS: Department of Chemistry, University of Houston, Houston, TX 77204-5003, USA. Medline UID: 22708294 14. Wu, R.; Ma, C. X.; Zhao, W.Casella, G. Functional mapping for quantitative trait loci governing growth rates: a parametric model. Physiol Genomics. 14:241-9, 2003. ADDRESS: Department of Statistics, University of Florida, Gainesville, Florida 32611, USA. rwu@stat.ufl.edu. Medline UID: 22804547 15. Xin, W.; Ma, J.Huang, D. W. Construction of linear functional expression elements with DNA and RNA hybrid primers: a flexible and fast method for proteomics. Biotechnol Lett. 25:273-7, 2003. ADDRESS: Institute of Zoology, Chinese Academy of Sciences, Beijing 100080, PR China. Medline UID: 22764364 ********************************************************************** Margaret and Lyman Crittenden e-mail: crittend@itis.com 8550 Highway 19 Phone: 608-798-0791 Cross Plains, WI 53528 *********************************************************************** ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -o U.S. PIG GENOME COORDINATION PROJECT - sponsored by USDA/CSREES -o WEB: http://www.genome.iastate.edu/