From crittend@itis.com Wed Aug 13 14:41:55 2003 Date: Thu, 19 Jun 2003 12:41:06 -0700 From: Lyman/Margaret Crittenden To: Multiple Recipients of Subject: June, 2003 Genomics References Resent-Date: 19 Jun 2003 17:45:08 -0000 Resent-From: angenmap@genome.ansci.iastate.edu Resent-cc: recipient list not shown: ; [ AnGenMap Discussion Mailing List - Mail distributed to 931 members ] [ INFO: http://www.genome.iastate.edu/community/discuss.html ] ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ JOURNAL REFS. (GENOMICS METHODS AND REVIEWS) NLM 6/03 1. Aebersold, R. and Cravatt, B. F. Proteomics--advances, applications and the challenges that remain. Trends Biotechnol. 20:S1-2, 2002. Medline UID: 22457571 2. Antipova, A. A.; Tamayo, P.Golub, T. R. A strategy for oligonucleotide microarray probe reduction. Genome Biol. 3:RESEARCH0073, 2002. ADDRESS: Center for Genome Research, Whitehead Institute/Massachusetts Institute of Technology, Cambridge, MA 02139, USA. Medline UID: 22426059 3. Atwood, L. D. and Heard-Costa, N. L. Limits of fine-mapping a quantitative trait. Genet Epidemiol. 24:99-106, 2003. ADDRESS: Department of Neurology, Boston University School of Medicine, 715 Albany Street B-609, Boston, MA 02118, USA. lda@bu.edu. Medline UID: 22435495 4. Barker, G.; Batley, J.; O' Sullivan, H.; Edwards, K. J.Edwards, D. Redundancy based detection of sequence polymorphisms in expressed sequence tag data using autoSNP. Bioinformatics. 19:421-2, 2003. ADDRESS: Institute of Arable Crop Research, Long Ashton, Bristol, BS41 9AF, UK. Medline UID: 22471709 5. Becker, N.; Nieters, A.Rittgen, W. Single nucleotide polymorphism--disease relationships: statistical issues for the performance of association studies. Mutat Res. 525:11-8, 2003. ADDRESS: Deutsches Krebsforschungszentrum, Division of Clinical Epidemiology, Im Neuenheimer Feld 280, Heidelberg 69120, Germany. n.becker@dkfz.de. Medline UID: 22538894 6. Becquet, C.; Blachon, S.; Jeudy, B.; Boulicaut, J. F.Gandrillon, O. Strong-association-rule mining for large-scale gene-expression data analysis: a case study on human SAGE data. Genome Biol. 3:RESEARCH0067, 2002. ADDRESS: Equipe Signalisations et identites cellulaires, Centre de Genetique Moleculaire et Cellulaire CNRS UMR 5534, Universite Claude Bernard Lyon 1, 16 rue Dubois, F-69622 Villeurbanne cedex, France. Medline UID: 22426053 7. Bjorheim, J.; Abrahamsen, T. W.; Kristensen, A. T.; Gaudernack, G.Ekstrom, P. O. Approach to analysis of single nucleotide polymorphisms by automated constant denaturant capillary electrophoresis. Mutat Res. 526:75-83, 2003. ADDRESS: Department of Immunology, Section for Immunotherapy, Institute for Cancer Research, The Norwegian Radium Hospital, Oslo 0310, Norway. Medline UID: 22600661 8. Boengler, K.; Pipp, F.; Schaper, W.Deindl, E. Rapid identification of differentially expressed genes by combination of SSH and MOS. Lab Invest. 83:759-61, 2003. ADDRESS: Max-Planck-Institute for Physiological and Clinical Research, Department of Experimental Cardiology, Bad Nauheim, Germany. Medline UID: 22631256 9. Bugni, J. M. and Drinkwater, N. R. Representational difference analysis of gene expression. Methods Mol Biol. 222:385-97, 2003. ADDRESS: McArdle Laboratory for Cancer Research, University of Wisconsin Medical School, Madison, USA. Medline UID: 22596317 10. Cardon, L. R. and Abecasis, G. R. Using haplotype blocks to map human complex trait loci. Trends Genet. 19:135-40, 2003. ADDRESS: Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK. lon.cardon@well.ox.ac.uk. Medline UID: 22503857 11. Chen, G. Y.; Uttamchandani, M.; Lue, R. Y.; Lesaicherrea, M. L.Yao, S. Q. Array-based technologies and their applications in proteomics. Curr Top Med Chem. 3:705-24, 2003. ADDRESS: Department of Chemistry, National University of Singapore, Republic of Singapore, 117543. Medline UID: 22458672 12. Chen, J. J.; Lee, S.; Zhou, G.; Rowley, J. D.Wang, S. M. Generation of longer cDNA fragments from SAGE tags for gene. Methods Mol Biol. 221:207-22, 2003. ADDRESS: Section of Hematology and Oncology, University of Chicago Medical Center, IL, USA. Medline UID: 22589251 13. de Jong, H.; Geiselmann, J.; Hernandez, C.Page, M. Genetic Network Analyzer: qualitative simulation of genetic regulatory networks. Bioinformatics. 19:336-44, 2003. ADDRESS: INRIA Rhone-Alpes, 655 avenue de l'Europe, Montbonnot, 38334 Saint Ismier CEDEX, France. Hidde.de-Jong@inrialpes.fr. Medline UID: 22471696 14. Elia, G.; Silacci, M.; Scheurer, S.; Scheuermann, J.Neri, D. Affinity-capture reagents for protein arrays. Trends Biotechnol. 20:S19-22, 2002. ADDRESS: Institute of Pharmaceutical Sciences, Swiss Federal Institute of Technology Zurich, Winterthurerstrasse 190, CH-8057 Zurich, Switzerland. giueli@pharma.anbi.ethz.ch. Medline UID: 22457575 15. Gaunt, T. R.; Hinks, L. J.; Rassoulian, H.Day, I. N. Manual 768 or 384 well microplate gel 'dry' electrophoresis for PCR checking and SNP genotyping. Nucleic Acids Res. 31:e48, 2003. ADDRESS: Human Genetics Division, Duthie Building (Mp808), School of Medicine, Southampton University Hospital, Tremona Road, Southampton SO16 6YD, UK. Medline UID: 22598223 16. Glidden, D. V.; Liang, K. Y.; Chiu, Y. F.Pulver, A. E. Multipoint affected sibpair linkage methods for localizing susceptibility genes of complex diseases. Genet Epidemiol. 24:107-17, 2003. ADDRESS: Department of Epidemiology and Biostatistics, Box 560, University of California, San Francisco, CA 94143-0560, USA. dave@biostat.ucsf.edu. Medline UID: 22435496 17. Goncalves, J. and Marks, W. L. Roles and requirements for a research microarray database. IEEE Eng Med Biol Mag. 21:154-7, 2002. Medline UID: 22501230 18. Hahn, L. W.; Ritchie, M. D.Moore, J. H. Multifactor dimensionality reduction software for detecting gene-gene and gene-environment interactions. Bioinformatics. 19:376-82, 2003. ADDRESS: Program in Human Genetics and Department of Molecular Physiology and Biophysics, Vanderbilt University Medical School, Nashville, TN 37232-0700, USA. Medline UID: 22471701 19. King, O. D.; Foulger, R. E.; Dwight, S. S.; White, J. V.Roth, F. P. Predicting gene function from patterns of annotation. Genome Res. 13:896-904, 2003. ADDRESS: Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02115, USA. Medline UID: 22612963 20. Lee, Y. S. and Mrksich, M. Protein chips: from concept to practice. Trends Biotechnol. 20:S14-8, 2002. ADDRESS: Dept Chemistry and Institute for Biophysical Dynamics, The University of Chicago, 5735 South Ellis Ave, Chicago, IL 60637, USA. Medline UID: 22457574 21. Lin, S. L. Peptide library construction from RNA-PCR-derived RNAs. Methods Mol Biol. 221:289-93, 2003. ADDRESS: Epiclone Inc., San Diego, CA, USA. Medline UID: 22589257 22. Lin, S. L. and Ji, H. cDNA library construction using in vitro transcriptional amplification. Methods Mol Biol. 221:93-101, 2003. ADDRESS: Epiclone Inc., San Diego, CA, USA. Medline UID: 22589241 23. Lin, S. L. and Ying, S. Y. mRNA/cDNA library construction using RNA-polymerase cycling reaction. Methods Mol Biol. 221:129-43, 2003. ADDRESS: Epiclone Inc., San Diego, CA, USA. Medline UID: 22589244 24. Reiner, A.; Yekutieli, D.Benjamini, Y. Identifying differentially expressed genes using false discovery rate controlling procedures. Bioinformatics. 19:368-75, 2003. ADDRESS: Department of Statistics and Operations Research, The Sackler Faculty of Exact Sciences, Tel-Aviv University, Tel-Aviv 69978, Israel. anatr@post.tau.ac.il. Medline UID: 22471700 25. Satagopan, J. M. and Panageas, K. S. A statistical perspective on gene expression data analysis. Stat Med. 22:481-99, 2003. ADDRESS: Department of Epidemiology and Biostatistics, Memorial Sloan-Kettering Cancer Center, 1275 York Avenue, New York, NY 10021, USA. satago@biosta.mskcc.org. Medline UID: 22417746 26. Sellers, T. A. and Yates, J. R. Review of proteomics with applications to genetic epidemiology. Genet Epidemiol. 24:83-98, 2003. ADDRESS: Division of Epidemiology, Department of Health Sciences Research, Mayo Clinic, 200 First Street SW, Rochester, MN 55905, USA. sellers@mayo.edu. Medline UID: 22435494 27. Tost, J. and Gut, I. G. Genotyping single nucleotide polymorphisms by mass spectrometry. Mass Spectrom Rev. 21:388-418, 2002. ADDRESS: Centre National de Genotypage, Batiment G2, 2 Rue Gaston Cremieux, 91057 Evry Cedex, France. Medline UID: 22552594 28. Townsend, J. P. and Hartl, D. L. Bayesian analysis of gene expression levels: statistical quantification of relative mRNA level across multiple strains or treatments. Genome Biol. 3:RESEARCH0071, 2002. ADDRESS: Department of Organismic and Evolutionary Biology, Harvard University, 26 Oxford Street, Cambridge, MA 02138, USA. townsend@nature.berkeley.edu. Medline UID: 22426057 29. Toyoda, T. and Konagaya, A. KnowledgeEditor: a new tool for interactive modeling and analyzing biological pathways based on microarray data. Bioinformatics. 19:433-4, 2003. ADDRESS: Bioinformatics Group, Genomic Sciences Center, RIKEN, 1-7-22 Suehiro, Tsurumi, Yokohama, Kanagawa, 230-0045, Japan. bioinfo@gsc.riken.go.jp. Medline UID: 22471715 30. Tsai, C. A.; Chen, Y. J.Chen, J. J. Testing for differentially expressed genes with microarray data. Nucleic Acids Res. 31:e52, 2003. ADDRESS: Division of Biometry and Risk Assessment, National Center for Toxicological Research, Food and Drug Administration, Jefferson, AR 72079, USA. Medline UID: 22598227 31. Winslow, R. L. and Boguski, M. S. Genome informatics: current status and future prospects. Circ Res. 92:953-61, 2003. ADDRESS: The Whitaker Biomedical Engineering Institute and Center for Cardiovascular Bioinformatics and Modeling, The Johns Hopkins University School of Medicine, Baltimore, Md 21218, USA. rwinslow@bme.jhu.edu. Medline UID: 22635312 32. Ying, S. Y. and Lin, S. L. Subtractive cloning of differential genes using RNA-PCR. Methods Mol Biol. 221:253-9, 2003. ADDRESS: Department of Cell and Neurobiology, Keck School of Medicine, University of Southern California, Los Angeles, USA. Medline UID: 22589254 33. Zhumabayeva, B.; Chang, C.; McKinley, J.; Diatchenko, L.Siebert, P. D. Generation of full-length cDNA libraries enriched for differentially expressed genes. Methods Mol Biol. 221:223-37, 2003. ADDRESS: BD Biosciences Clontech, Palo Alto, CA, USA. Medline UID: 22589252 ********************************************************************** 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/