From crittend@itis.com Mon Jun 21 10:22:13 2004 Date: Sat, 12 Jun 2004 11:24:07 -0500 From: Lyman/Margaret Crittenden To: Multiple Recipients of Subject: June 2004, Genomics References Resent-Date: 13 Jun 2004 04:12:24 -0000 Resent-From: angenmap@genome.ansci.iastate.edu Resent-cc: recipient list not shown: ; [ AnGenMap Discussion Mailing List - Mail distributed to 1061 members ] [ INFO: http://www.genome.iastate.edu/community/discuss.html ] ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ These references can be downloaded in Reference Manager or Procite format at: http://www.genome.iastate.edu/ftp/ref/ JOURNAL REFS. (GENOMICS METHODS AND REVIEWS) NLM 6/04 1. Abdallah, J. M.; Mangin, B.; Goffinet, B.; Cierco-Ayrolles, C.Perez-Enciso, M. A comparison between methods for linkage disequilibrium fine mapping of quantitative trait loci. Genet Res. 83:41-7, 2004. ADDRESS: Station d'amelioration genetique des animaux, Institut national de la recherche agronomique, Castanet-Tolosan, France. abdallah@germinal.toulouse.inra.fr. Medline UID: 15125065 2. Aimone, J. B. and Gage, F. H. Unbiased characterization of high-density oligonucleotide microarrays using probe-level statistics. J Neurosci Methods. 135:27-33, 2004. ADDRESS: Laboratory of Genetics, The Salk Institute of Biological Studies, 10010 North Torrey Pines Road, La Jolla, CA 92037, USA. Medline UID: 15020086 3. Beer, M. A. and Tavazoie, S. Predicting gene expression from sequence. Cell. 117:185-98, 2004. ADDRESS: Lewis-Sigler Institute for Integrative Genomics and Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA. Medline UID: 15084257 4. Bhattacharya, S.; Long, D.Lyons-Weiler, J. Overcoming confounded controls in the analysis of gene expression data from microarray experiments. Appl Bioinformatics. 2:197-208, 2003. ADDRESS: Center for Biomedical Informatics, University of Pittsburgh, Pittsburgh, PA 15232, USA. Medline UID: 15130791 5. Breitling, R.; Amtmann, A.Herzyk, P. Iterative Group Analysis (iGA): a simple tool to enhance sensitivity and facilitate interpretation of microarray experiments. BMC Bioinformatics. 5:34, 2004. ADDRESS: Plant Science Group, Institute of Biomedical and Life Sciences, University of Glasgow, Glasgow G12 8QQ, United Kingdom. r.breitling@bio.gla.ac.uk. Medline UID: 15050037 6. Brereton, R. G. and Devonshire, M. Genotyping using single nucleotide polymorphism, fluorescence spectroscopy and pattern recognition. Analyst. 129:249-53, 2004. ADDRESS: School of Chemistry, University of Bristol, Cantock's Close, Bristol BS8 1TS, UK. Medline UID: 14978528 7. Cheadle, C.; Cho-Chung, Y. S.; Becker, K. G.Vawter, M. P. Application of z-score transformation to Affymetrix data. Appl Bioinformatics. 2:209-17, 2003. ADDRESS: Cellular Biochemistry Section, Basic Research Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA. cheadle@mail.nih.gov. Medline UID: 15130792 8. Chen, G.; Hata, N.Zhang, M. Q. Transcription factor binding element detection using functional clustering of mutant expression data. Nucleic Acids Res. 32:2362-71, 2004. ADDRESS: Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, NY 11724, USA. Medline UID: 15115798 9. Chen, X. N. and Korenberg, J. R. BAC mapping using fluorescence in situ hybridization. Methods Mol Biol. 255:131-41, 2004. ADDRESS: Department of Human Genetics and Pediatrics, Cedars-Sinai Medical Center, University of California, Los Angeles, USA. Medline UID: 15020820 10. Cockett, N. E. Current status of the ovine genome map. Cytogenet Genome Res. 102:76-8, 2003. ADDRESS: Utah State University, Logan, UT 84322-4800, USA. Noelle.Cockett@usu.edu. Medline UID: 14970682 11. Dodgson, J. B. Chicken genome sequence: a centennial gift to poultry genetics. Cytogenet Genome Res. 102:291-6, 2003. ADDRESS: Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, Michigan 488242-4320, USA. dodgson@msu.edu. Medline UID: 14970719 12. Elliott, D. Pathways of post-transcriptional gene regulation in mammalian germ cell development. Cytogenet Genome Res. 103:210-6, 2003. ADDRESS: Institute of Human Genetics, Centre for Life Central Parkway, University of Newcastle upon Tyne, Newcastle, England. David.Elliott@ncl.ac.uk. Medline UID: 15051941 13. Fixe, F.; Chu, V.; Prazeres, D. M.Conde, J. P. An on-chip thin film photodetector for the quantification of DNA probes and targets in microarrays. Nucleic Acids Res. 32:e70, 2004. ADDRESS: INESC Microsistemas e Nanotecnologias (INESC-MN), Rua Alves Redol, 9, 1000-029 Lisboa, Portugal. ffixe@inesc-mn.pt. Medline UID: 15148343 14. Gao, X.; Gulari, E.Zhou, X. In situ synthesis of oligonucleotide microarrays. Biopolymers. 73:579-96, 2004. ADDRESS: Department of Chemistry, University of Houston, Houston, TX 77004-5003, USA. xgao@uh.edu. Medline UID: 15048782 15. Gentile, A.; D'Alessandro, L.Medico, E. Gene trapping: a multi-purpose tool for functional genomics. Biotechnol Genet Eng Rev. 20:77-100, 2003. ADDRESS: Institute for Cancer Research and Treatment, University of Torino Medical School, S.P. 142, km. 3.95, 10060 Candiolo, TO, Italy. Medline UID: 14997847 16. Goldsmith, Z. G. and Dhanasekaran, N. The microrevolution: applications and impacts of microarray technology on molecular biology and medicine (review). Int J Mol Med. 13:483-95, 2004. ADDRESS: Fels Institute for Cancer Research and Molecular Biology, Temple University School of Medicine, Philadelphia, PA 19140, USA. Medline UID: 15010847 17. Gowda, M.; Jantasuriyarat, C.; Dean, R. A.Wang, G. L. Robust-LongSAGE (RL-SAGE): a substantially improved LongSAGE method for gene discovery and transcriptome analysis. Plant Physiol. 134:890-7, 2004. ADDRESS: Department of Plant Pathology, Ohio State University, Columbus, Ohio 43210, USA. Medline UID: 15020752 18. Guffanti, A.; Finocchiaro, G.; Reid, J. F.; Luzi, L.; Alcalay, M.; Confalonieri, S.; Lassandro, L.Muller, H. Automated DNA chip annotation tables at IFOM: the importance of synchronisation and cross-referencing of sequence databases. Appl Bioinformatics. 2:245-9, 2003. ADDRESS: FIRC Institute of Molecular Oncology, Milan, Italy. guffanti@ifom-firc.it. Medline UID: 15130796 19. Han, E. S.; Wu, Y.; McCarter, R.; Nelson, J. F.; Richardson, A.Hilsenbeck, S. G. Reproducibility, sources of variability, pooling, and sample size: important considerations for the design of high-density oligonucleotide array experiments. J Gerontol A Biol Sci Med Sci. 59:306-15, 2004. ADDRESS: Department of Biological Science, The University of Tulsa, Oklahoma 74104, USA. eun-han@utulsa.edu. Medline UID: 15071073 20. Jansen, R. C. and Nap, J. P. Regulating gene expression: surprises still in store. Trends Genet. 20:223-5, 2004. ADDRESS: Groningen Bioinformatics Centre (GBIC), University of Groningen (RUG), PO Box 800, NL-9700 AV Groningen, The Netherlands. r.c.jansen@cs.rug.nl. Medline UID: 15109773 21. Ji, M.; Hou, P.; Li, S.; He, N.Lu, Z. Microarray-based method for genotyping of functional single nucleotide polymorphisms using dual-color fluorescence hybridization. Mutat Res. 548:97-105, 2004. ADDRESS: Chien-Shiung Wu Laboratory, Department of Biological Science and Medical Engineering, Southeast University, Nanjing 210096, China. Medline UID: 15063140 22. Lavorgna, G.; Dahary, D.; Lehner, B.; Sorek, R.; Sanderson, C. M.Casari, G. In search of antisense. Trends Biochem Sci. 29:88-94, 2004. ADDRESS: Human Molecular Genetics Unit, Dibit-San Raffaele Scientific Institute, Via Olgettina 58, 20132 Milan, Italy. giovanni.lavorgna@hsr.it. Medline UID: 15102435 23. Leung, Y. F. and Pang, C. P. EYE on bioinformatics: dissecting complex disease traits in silico. Appl Bioinformatics. 1:69-80, 2002. ADDRESS: Department of Ophthalmology and Visual Sciences, The Chinese University of Hong Kong, Kowloon, Hong Kong. Medline UID: 15130846 24. Lindlof, A. Gene identification through large-scale EST sequence processing. Appl Bioinformatics. 2:123-9, 2003. ADDRESS: Department of Computer Science, University of Skovde, Skovde, Sweden. angelica@ida.his.se. Medline UID: 15130797 25. Luo, Z. W. and Ma, L. An improved formulation of marker heterozygosity in recurrent selection and backcross schemes. Genet Res. 83:49-53, 2004. ADDRESS: School of Biosciences, The University of Birmingham Edgbaston, UK. z.luo@bham.ac.uk. Medline UID: 15125066 26. Lyons-Weiler, J. Profound normalisation challenges remain in the analysis of data from microarray experiments. Appl Bioinformatics. 2:193-5, 2003. Medline UID: 15130790 27. Mahony, S.; McInerney, J. O.; Smith, T. J.Golden, A. Gene prediction using the Self-Organizing Map: automatic generation of multiple gene models. BMC Bioinformatics. 5:23, 2004. ADDRESS: National Centre for Biomedical Engineering Science, NUI, Galway, Galway, Ireland. shaun.mahony@nuigalway.ie. Medline UID: 15070404 28. Mattick, J. S. RNA regulation: a new genetics? Nat Rev Genet. 5:316-23, 2004. ADDRESS: ARC Special Research Centre for Functional and Applied Genomics, Institute for Molecular Bioscience, University of Queensland, Brisbane, Queensland 4072, Australia. j.mattick@imb.uq.edu.au. Medline UID: 15131654 29. Melton, L. Protein arrays: proteomics in multiplex. Nature. 429:101-7, 2004. ADDRESS: Novartis Foundation, London, UK. Medline UID: 15129287 30. Nunez-Garcia, J.; Mersinias, V.; Cho, K. H.; Smith, C. P.Wolkenhauer, O. The statistical distribution of the intensity of pixels within spots of DNA microarrays: what is the appropriate single-value representative? Appl Bioinformatics. 2:229-39, 2003. ADDRESS: Veterinary Laboratories Agency, Addlestone, Surrey, UK. Medline UID: 15130794 31. Olivier, M.; Brady, S.Cox, D. R. Radiation hybrid mapping with BAC ends. Methods Mol Biol. 255:163-9, 2004. ADDRESS: Human and Molecular Genetics Center, Medical College of Wisconsin, Milwaukee, USA. Medline UID: 15020823 32. Ray, A.; Macwana, S.; Ayoubi, P.; Hall, L. T.; Prade, R.Mort, A. J. Negative subtraction hybridization: an efficient method to isolate large numbers of condition-specific cDNAs. BMC Genomics. 5:22, 2004. ADDRESS: Department of Biochemistry and Molecular Biology, Oklahoma State University, Stillwater, OK 74078, USA. aray@biochem.okstate.edu. Medline UID: 15050035 33. Romanov, M. N.; Price, J. A.Dodgson, J. B. Integration of animal linkage and BAC contig maps using overgo hybridization. Cytogenet Genome Res. 102:277-81, 2003. ADDRESS: Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, Mich, USA. Medline UID: 14970717 34. Roth, V. and Lange, T. Bayesian class discovery in microarray datasets. IEEE Trans Biomed Eng. 51:707-18, 2004. ADDRESS: Institute for Computational Science, ETH Zurich, Hirschengraben 84, CH-8092 Zurich, Switzerland. vroth@inf.ethz.ch. Medline UID: 15132496 35. Rothschild, M. F. Porcine genomics delivers new tools and results: this little piggy did more than just go to market. Genet Res. 83:1-6, 2004. ADDRESS: Department of Animal Science, Center for Integrated Animal Genomics, Iowa State University, Ames 50011, USA. mfrothsc@iastate.edu. Medline UID: 15125061 36. Schneider, T. D. Consensus sequence Zen. Appl Bioinformatics. 1:111-9, 2002. ADDRESS: Laboratory of Experimental and Computational Biology, National Cancer Institute at Frederick, National Institutes of Health, Frederick, MD 21702-1201, USA. toms@ncifcrf.gov. Medline UID: 15130839 37. Smajs, D.; Norris, S. J.Weinstock, G. M. Construction of small genome BAC library for functional and genomic applications. Methods Mol Biol. 255:47-56, 2004. ADDRESS: Department of Microbiology and Molecular Genetics, University of Texas-Houston Medical School, USA. Medline UID: 15020814 38. Smirnov, D. A.; Burdick, J. T.; Morley, M.Cheung, V. G. Method for manufacturing whole-genome microarrays by rolling circle amplification. Genes Chromosomes Cancer. 40:72-7, 2004. ADDRESS: Department of Genetics, University of Pennsylvania, Philadelphia 19104-4318, USA. Medline UID: 15034872 39. Snijders, A. M.; Segraves, R.; Blackwood, S.; Pinkel, D.Albertson, D. G. BAC microarray-based comparative genomic hybridization. Methods Mol Biol. 256:39-56, 2004. ADDRESS: Comprehensive Cancer Center, University of California, San Francisco, USA. Medline UID: 15024158 40. Taib, Z. Statistical analysis of oligonucleotide microarray data. C R Biol. 327:175-80, 2004. ADDRESS: Department of Biostatistics, AstraZeneca R&D, Molndal, 431 83 Molndal, Sweden. ziad.taib@astrazeneca.com. Medline UID: 15127888 41. Tang, F.; Flood, E. M.; Pertsemlidis, A.Garner, H. R. SNPCEQer II: the integrated detection and analysis of SNPs in DNA sequences. Appl Bioinformatics. 2:151-4, 2003. ADDRESS: Eugene McDermott Center for Human Growth and Development, The University of Texas Southwestern Medical Center, Dallas, TX 75390, USA. Medline UID: 15130800 42. Vainrub, A. and Pettitt, B. M. Theoretical aspects of genomic variation screening using DNA microarrays. Biopolymers. 73:614-20, 2004. ADDRESS: Department of Chemistry, University of Houston, Houston, TX 77204-5003, USA. Medline UID: 15048785 43. van Driel, R. and Fransz, P. Nuclear architecture and genome functioning in plants and animals: what can we learn from both? Exp Cell Res. 296:86-90, 2004. ADDRESS: Swammerdam Institute for Life Sciences, BioCentrum Amsterdam, University of Amsterdam, 1098 SM Amsterdam, The Netherlands. van.driel@science.uva.nl. Medline UID: 15120998 44. van Hijum, S. A.; Garcia de la Nava, J.; Trelles, O.; Kok, J.Kuipers, O. P. MicroPreP: a cDNA microarray data pre-processing framework. Appl Bioinformatics. 2:241-4, 2003. ADDRESS: Molecular Genetics, University of Groningen, Groningen Biomolecular Sciences and Biotechnology Institute, Haren, The Netherlands. s.a.f.t.van.hijum@biol.rug.nl. Medline UID: 15130795 45. Wang, Y. and Guo, S. W. Statistical methods for detecting genomic alterations through array-based comparative genomic hybridization (CGH). Front Biosci. 9:540-9, 2004. ADDRESS: Department of Statistics and Applied Probability, University of California, Santa Barbara, California 93106, USA. yuedong@pstat.ucsb.edu. Medline UID: 14766389 46. Weise, A.; Heller, A.; Starke, H.; Mrasek, K.; Kuechler, A.; Pool-Zobel, B. L.; Claussen, U.Liehr, T. Multitude multicolor chromosome banding (mMCB) - a comprehensive one-step multicolor FISH banding method. Cytogenet Genome Res. 103:34-9, 2003. ADDRESS: Institute of Human Genetics and Anthropology, University of Jena, Jena, Germany. Medline UID: 15004461 47. Wenderfer, S. E. and Monaco, J. J. Exon trapping for positional cloning and fingerprinting. Methods Mol Biol. 256:7-20, 2004. ADDRESS: Department of Pediatrics, University of Texas Houston, Texas, USA. Medline UID: 15024156 48. Yuen, P. K.; Li, G.; Bao, Y.Muller, U. R. Microfluidic devices for fluidic circulation and mixing improve hybridization signal intensity on DNA arrays. Lab Chip. 3:46-50, 2003. ADDRESS: Biochemical Technologies, Corning Incorporated, Corning, NY 14831-0001, USA. yuenp@corning.com. Medline UID: 15100805 ********************************************************************** Margaret and Lyman Crittenden e-mail: crittend@itis.com 8550 Highway 19 Phone: 608-798-0791 Cross Plains, WI 53528 *********************************************************************** ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -o NAGRP BIOINFORMATICS COODINATION PROJECT - Sponsored by USDA/CSREES -o WEB: http://www.genome.iastate.edu/