From crittend@itis.com Wed Aug 13 15:32:47 2003 Date: Tue, 12 Aug 2003 16:52:45 -0700 From: Lyman/Margaret Crittenden To: Multiple Recipients of Subject: August, 2003 Mapping References Resent-Date: 12 Aug 2003 21:49:26 -0000 Resent-From: angenmap@genome.ansci.iastate.edu Resent-cc: recipient list not shown: ; [ AnGenMap Discussion Mailing List - Mail distributed to 952 members ] [ INFO: http://www.genome.iastate.edu/community/discuss.html ] ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ JOURNAL REFS. (GENOMICS METHODS AND REVIEWS) NLM 8/03 1. Aebersold, R. Quantitative proteome analysis: methods and applications. J Infect Dis. 187 Suppl 2:S315-20, 2003. ADDRESS: Institute for Systems Biology, Seattle, Washington 98103, USA. raebersold@systemsbiology.org. Medline UID: 22676532 2. Breyne, P.; Dreesen, R.; Cannoot, B.; Rombaut, D.; Vandepoele, K.; Rombauts, S.; Vanderhaeghen, R.; Inze, D.Zabeau, M. Quantitative cDNA-AFLP analysis for genome-wide expression studies. Mol Genet Genomics. 269:173-9, 2003. ADDRESS: Department of Plant Systems Biology, Flanders Interuniversity Institute for Biotechnology, Ghent University, K.L. Ledeganckstraat 35, Belgium. Medline UID: 22641396 3. de Boer, E.; Rodriguez, P.; Bonte, E.; Krijgsveld, J.; Katsantoni, E.; Heck, A.; Grosveld, F.Strouboulis, J. Efficient biotinylation and single-step purification of tagged transcription factors in mammalian cells and transgenic mice. Proc Natl Acad Sci U S A. 100:7480-5, 2003. ADDRESS: Department of Cell Biology, Erasmus Medical Center, P.O. Box 1738, 3000 DR Rotterdam, The Netherlands. Medline UID: 22709145 4. Detours, V.; Dumont, J. E.; Bersini, H.Maenhaut, C. Integration and cross-validation of high-throughput gene expression data: comparing heterogeneous data sets. FEBS Lett. 546:98-102, 2003. ADDRESS: IRIBHM, Free University of Brussels, Bldg C, Campus Erasme, 808 route de Lennik, B-1070 Brussels, Belgium. vdetours@ulb.ac.be. Medline UID: 22713225 5. Ding, C. and Cantor, C. R. Direct molecular haplotyping of long-range genomic DNA with M1-PCR. Proc Natl Acad Sci U S A. 100:7449-53, 2003. ADDRESS: Bioinformatics Program and Center for Advanced Biotechnology, Boston University, 36 Cummington Street, Boston, MA 02215, USA. Medline UID: 22709149 6. Fjell, C. D.; Bosdet, I.; Schein, J. E.; Jones, S. J.Marra, M. A. Internet Contig Explorer (iCE)--a tool for visualizing clone fingerprint maps. Genome Res. 13:1244-9, 2003. ADDRESS: Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, BC V5Z 4E6, Canada. Medline UID: 22683289 7. Held, G. A.; Grinstein, G.Tu, Y. Modeling of DNA microarray data by using physical properties of hybridization. Proc Natl Acad Sci U S A. 100:7575-80, 2003. ADDRESS: IBM Thomas J. Watson Research Center, Yorktown Heights, NY 10598, USA. gaheld@us.ibm.com. Medline UID: 22709187 8. Kasukawa, T.; Furuno, M.; Nikaido, I.; Bono, H.; Hume, D. A.; Bult, C.; Hill, D. P.; Baldarelli, R.; Gough, J.; Kanapin, A.; Matsuda, H.; Schriml, L. M.; Hayashizaki, Y.; Okazaki, Y.Quackenbush, J. Development and evaluation of an automated annotation pipeline and cDNA annotation system. Genome Res. 13:1542-51, 2003. ADDRESS: Laboratory for Genome Exploration Research Group, RIKEN Genomic Sciences Center (GSC), RIKEN Yokohama Institute, Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan. Medline UID: 22703381 9. Kelso, J.; Visagie, J.; Theiler, G.; Christoffels, A.; Bardien, S.; Smedley, D.; Otgaar, D.; Greyling, G.; Jongeneel, C. V.; McCarthy, M. I.; Hide, T.Hide, W. eVOC: a controlled vocabulary for unifying gene expression data. Genome Res. 13:1222-30, 2003. ADDRESS: South African National Bioinformatics Institute, University of the Western Cape, Bellville, South Africa. Medline UID: 22683287 10. Lai, Y.; Shinde, D.; Arnheim, N.Sun, F. The mutation process of microsatellites during the polymerase chain reaction. J Comput Biol. 10:143-55, 2003. ADDRESS: Department of Mathematics, University of Southern California, Los Angeles, CA 90089-1113, USA. Medline UID: 22689372 11. Latorra, D.; Campbell, K.; Wolter, A.Hurley, J. M. Enhanced allele-specific PCR discrimination in SNP genotyping using 3' locked nucleic acid (LNA) primers. Hum Mutat. 22:79-85, 2003. ADDRESS: Proligo LLC, Boulder, Colorado, USA. dlatorra@qwest.net. Medline UID: 22699250 12. Levine, M. and Tjian, R. Transcription regulation and animal diversity. Nature. 424:147-51, 2003. ADDRESS: Department of Molecular and Cell Biology, Division of Genetics and Development, Center for Integrative Genomics, University of California, Berkeley, 401 Barker Hall, Berkeley, California 94720, USA. mlevine@uclink4.berkeley.edu. Medline UID: 22737997 13. Mariani, S. M. Functional genomics: a holistic approach. MedGenMed. 5:19, 2003. ADDRESS: Medscape General Medicine. Medline UID: 22711220 14. Min, T. FISH techniques. Methods Mol Biol. 220:193-212, 2003. ADDRESS: Academic Haematology and Cytogenetics, The Royal Marsden NHS Trust, Sutton, Surrey, England. Medline UID: 22616788 15. Mukherjee, S.; Tamayo, P.; Rogers, S.; Rifkin, R.; Engle, A.; Campbell, C.; Golub, T. R.Mesirov, J. P. Estimating dataset size requirements for classifying DNA microarray data. J Comput Biol. 10:119-42, 2003. ADDRESS: Whitehead Institute/Massachusetts Institute of Technology Center for Genome Research, Cambridge, MA 02139, USA. sayan@genome.wi.mit.edu. Medline UID: 22689371 16. Nilsson, K. P. and Inganas, O. Chip and solution detection of DNA hybridization using a luminescent zwitterionic polythiophene derivative. Nat Mater. 2:419-24, 2003. ADDRESS: Biomolecular and Organic Electronics, IFM, Linkoping University, SE-581 83 Linkoping, Sweden. petni@ifm.liu.se. Medline UID: 22660562 17. Pleasance, E. D.; Marra, M. A.Jones, S. J. Assessment of SAGE in transcript identification. Genome Res. 13:1203-15, 2003. ADDRESS: Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver V5Z 4E6, Canada. Medline UID: 22683272 18. Rhodius, V. A. and LaRossa, R. A. Uses and pitfalls of microarrays for studying transcriptional regulation. Curr Opin Microbiol. 6:114-9, 2003. ADDRESS: Department of Microbiology and Immunology, University of California, Genentech Hall, 600 16th Street, San Francisco, CA 94143-2200, USA. rhodius@itsa.ucsf.edu. Medline UID: 22617909 19. Seeman, N. C. Biochemistry and structural DNA nanotechnology: an evolving symbiotic relationship. Biochemistry. 42:7259-69, 2003. ADDRESS: Department of Chemistry, New York University, New York 10003, USA. ned.seeman@nyu.edu. Medline UID: 22694198 20. Svensson, B. A.; Kreeft, A. J.; van Ommen, G. J.; den Dunnen, J. T.Boer, J. M. GeneHopper: a web-based search engine to link gene-expression platforms through GenBank accession numbers. Genome Biol. 4:R35, 2003. ADDRESS: Center for Human and Clinical Genetics/Leiden Genome Technology Center, Leiden University Medical Center, The Netherlands. Medline UID: 22619655 21. Svrakic, N. M.; Nesic, O.; Dasu, M. R.; Herndon, D.Perez-Polo, J. R. Statistical approach to DNA chip analysis. Recent Prog Horm Res. 58:75-93, 2003. ADDRESS: Department of Psychiatry, Washington University School of Medicine, St. Louis, Missouri 63110, USA. nenad@tci.wustl.edu. Medline UID: 22679826 22. Urakawa, H.; El Fantroussi, S.; Smidt, H.; Smoot, J. C.; Tribou, E. H.; Kelly, J. J.; Noble, P. A.Stahl, D. A. Optimization of single-base-pair mismatch discrimination in oligonucleotide microarrays. Appl Environ Microbiol. 69:2848-56, 2003. ADDRESS: Department of Civil and Environmental Engineering, University of Washington, Seattle, WA 98195, USA. Medline UID: 22617478 23. Werner, T.; Fessele, S.; Maier, H.Nelson, P. J. Computer modeling of promoter organization as a tool to study transcriptional coregulation. FASEB J. 17:1228-37, 2003. ADDRESS: GSF-National Research Center for Environment and Health, Institute of Experimental Genetics, Neuherberg, Germany. Medline UID: 22715886 24. Williams, R. R. Transcription and the territory: the ins and outs of gene positioning. Trends Genet. 19:298-302, 2003. ADDRESS: Lymphocyte Development Group, MRC Clinical Sciences Centre, Imperial College School of Medicine, Hammersmith Campus, Du Cane Road, London W12 0NN, UK. ruth.williams@csc.mrc.ac.uk. Medline UID: 22687310 25. Yang, Y.; Hoh, J.; Broger, C.; Neeb, M.; Edington, J.; Lindpaintner, K.Ott, J. Statistical methods for analyzing microarray feature data with replications. J Comput Biol. 10:157-69, 2003. ADDRESS: Laboratory of Statistical Genetics, Rockefeller University, New York, NY 10021, USA. yyang@linkage.rockefeller.edu. Medline UID: 22689373 26. Yeung, K. Y.; Medvedovic, M.Bumgarner, R. E. Clustering gene-expression data with repeated measurements. Genome Biol. 4:R34, 2003. ADDRESS: Department of Microbiology, University of Washington, Seattle, WA 98195, USA. kayee@u.washington.edu. Medline UID: 22619654 ********************************************************************** 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/