From crittend@itis.com Wed May 19 09:42:21 2004 Date: Sun, 16 May 2004 10:54:59 -0500 From: Lyman/Margaret Crittenden To: Multiple Recipients of Subject: May, 2004 Genomics References Resent-Date: 16 May 2004 16:15:22 -0000 Resent-From: angenmap@genome.ansci.iastate.edu Resent-cc: recipient list not shown: ; [ AnGenMap Discussion Mailing List - Mail distributed to 1054 members ] [ INFO: http://www.genome.iastate.edu/community/discuss.html ] ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ These references can be downloaded in Reference Manager or Procite format at: www.genome.iastate.edu/ftp/ref JOURNAL REFS. (GENOMICS METHODS AND REVIEWS) NLM 5/04 1. Ahmed, A. A.; Vias, M.; Iyer, N. G.; Caldas, C.Brenton, J. D. Microarray segmentation methods significantly influence data precision. Nucleic Acids Res. 32:e50, 2004. ADDRESS: Cancer Genomics Program, Department of Oncology, University of Cambridge, Hutchison/MRC Research Centre, Hills Road, Cambridge CB2 2XZ, UK. Medline UID: 15028803 2. Allocco, D. J.; Kohane, I. S.Butte, A. J. Quantifying the relationship between co-expression, co-regulation and gene function. BMC Bioinformatics. 5:18, 2004. ADDRESS: Informatics Program, Children's Hospital, Boston, MA, USA. allocco@chip.org. Medline UID: 15053845 3. Asyali, M. H.; Shoukri, M. M.; Demirkaya, O.Khabar, K. S. Assessment of reliability of microarray data and estimation of signal thresholds using mixture modeling. Nucleic Acids Res. 32:2323-35, 2004. ADDRESS: Department of Biostatistics, Epidemiology, and Scientific Computing, King Faisal Specialist Hospital and Research Center, PO Box 3354, MBC-03, Riyadh, 11211, Saudi Arabia. asyali@kfshrc.edu.sa. Medline UID: 15113873 4. Bartlett, J. M. Fluorescence in situ hybridization: technical overview. Methods Mol Med. 97:77-87, 2004. ADDRESS: Division of Cancer and Molecular Pathology, University Department of Surgery, Glasgow Royal Infirmary, Scotland, UK. Medline UID: 15064486 5. Bernat, M.; Titos, E.Claria, J. Rapid identification of single nucleotide polymorphisms by fluorescence-based capillary electrophoresis. Genet Mol Res. 1:72-8, 2002. ADDRESS: DNA Unit, Hospital Clinic, Institut d' Investigacions Biomediques August Pi i Sunyer (IDIBAPS), Barcelona 08036, Spain. Medline UID: 14963815 6. Bo, T. H.; Dysvik, B.Jonassen, I. LSimpute: accurate estimation of missing values in microarray data with least squares methods. Nucleic Acids Res. 32:e34, 2004. ADDRESS: Department of Informatics, BCCS, University of Bergen, HIB, N5020 Bergen, Norway. trondb@ii.uib.no. Medline UID: 14978222 7. Brodsky, L.; Leontovich, A.; Shtutman, M.Feinstein, E. Identification and handling of artifactual gene expression profiles emerging in microarray hybridization experiments. Nucleic Acids Res. 32:e46, 2004. ADDRESS: Quark Biotech Inc./QBI Enterprises Ltd, Weizmann Science Park, POB 4071, Ness Ziona 70400 Israel. mbrodsky@actcom.co.il. Medline UID: 14999086 8. Chen, Z. J. and Tew, K. D. Amplified differential gene expression microarray. Methods Mol Biol. 258:95-106, 2004. ADDRESS: Department of Pharmacology, Fox Chase Cancer Center, Philadelphia, PA, USA. Medline UID: 14970459 9. Cherry, S. R. In vivo molecular and genomic imaging: new challenges for imaging physics. Phys Med Biol. 49:R13-48, 2004. ADDRESS: Department of Biomedical Engineering, University of California, Davis, CA, USA. srcherry@ucdavis.edu. Medline UID: 15012005 10. Da, Y. Statistical analysis and experimental design for mapping genes of complex traits in domestic animals. Yi Chuan Xue Bao. 30:1183-92, 2003. ADDRESS: Department of Animal Science, University of Minnesota Saint Paul, Minnesota 55108, USA. yda@umn.edu. Medline UID: 14986439 11. Dan, H. L.; Zhang, Y. L.; Zhang, Y.; Wang, Y. D.; Lai, Z. S.; Yang, Y. J.; Cui, H. H.; Jian, Y. T.; Geng, J.; Ding, Y. Q.; Guo, C. H.Zhou, D. Y. A novel method for preparation of tissue microarray. World J Gastroenterol. 10:579-82, 2004. ADDRESS: Institute of Digestive Medicine, Nanfang Hospital, First Military Medical University, Guangzhou 510515, Guangdong Province, China. henrydan@sina.com. Medline UID: 14966920 12. De Jong, H.; Gouze, J. L.; Hernandez, C.; Page, M.; Sari, T.Geiselmann, J. Qualitative simulation of genetic regulatory networks using piecewise-linear models. Bull Math Biol. 66:301-40, 2004. ADDRESS: Institut National de Recherche en Informatique et en Automatique (INRIA), Unite de recherche Rhone-Alpes, 655 avenue de l'Europe, Montbonnot, 38334 Saint Ismier Cedex, France. hidde.de-jong@inrialpes.fr. Medline UID: 14871568 13. De Preter, K.; Pattyn, F.; Berx, G.; Strumane, K.; Menten, B.; Van Roy, F.; De Paepe, A.; Speleman, F.Vandesompele, J. Combined subtractive cDNA cloning and array CGH: an efficient approach for identification of overexpressed genes in DNA amplicons. BMC Genomics. 5:11, 2004. ADDRESS: Center for Medical Genetics, Ghent University Hospital 1K5, De Pintelaan 185, 9000 Gent, Belgium. katleen.depreter@ugent.be. Medline UID: 15018647 14. Gee, C.; Morrison, J. L.; Thomas, D. C.Gauderman, W. J. Segregation and linkage analysis for longitudinal measurements of a quantitative trait. BMC Genet. 4 Suppl 1:S21, 2003. ADDRESS: Department of Preventive Medicine, University of Southern California, 1540 Alcazar Street, Los Angeles, California, USA. cgee@usc.edu. Medline UID: 14975089 15. Gros, F. >From the messenger RNA saga to the transcriptome era. C R Biol. 326:893-900, 2003. ADDRESS: Academie des sciences, 23, quai de Conti, 75006 Paris, France. zajdman@academie-sciences.fr. Medline UID: 14744095 16. Hashimoto, K. and Ishimori, Y. Preliminary evaluation of electrochemical PNA array for detection of single base mismatch mutations. Lab Chip. 1:61-3, 2001. ADDRESS: Corporate Research and Development Center, Toshiba, 1, Komukai, Toshiba-cho, Saiwai-ku, Kawasaki, 212-8582, Japan. kouji.hashimoto@toshiba.co.jp. Medline UID: 15100891 17. Johnson, M. P.; Haupt, L. M.Griffiths, L. R. Locked nucleic acid (LNA) single nucleotide polymorphism (SNP) genotype analysis and validation using real-time PCR. Nucleic Acids Res. 32:e55, 2004. ADDRESS: Genomics Research Centre, School of Health Science, Griffith University Gold Coast, PMB 50, Gold Coast Mail Centre, QLD 9726, Australia. Medline UID: 15047860 18. Konig, R.; Baldessari, D.; Pollet, N.; Niehrs, C.Eils, R. Reliability of gene expression ratios for cDNA microarrays in multiconditional experiments with a reference design. Nucleic Acids Res. 32:e29, 2004. ADDRESS: Division of Theoretical Bioinformatics, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 580, 69120 Heidelberg, Germany. r.koenig@dkfz.de. Medline UID: 14966261 19. Landry, J. P.; Zhu, X. D.Gregg, J. P. Label-free detection of microarrays of biomolecules by oblique-incidence reflectivity difference microscopy. Opt Lett. 29:581-3, 2004. ADDRESS: Department of Physics, National Science Foundation Center for Biophotonics Science & Technology, University of California at Davis, Davis, California 95616, USA. Medline UID: 15035477 20. Lavine, B. K.; Davidson, C. E.Rayens, W. S. Machine learning based pattern recognition applied to microarray data. Comb Chem High Throughput Screen. 7:115-31, 2004. ADDRESS: Department of Chemistry, Clarkson University, Potsdam, NY 13699-5810, USA. bklab@clarkson.edu. Medline UID: 15032659 21. Leach, M. Gene expression informatics. Methods Mol Biol. 258:153-65, 2004. ADDRESS: Bioinformatics, CuraGen Corporation, New Haven, CT, USA. Medline UID: 14970462 22. Lescallett, J.; Chicurel, M. E.; Lipshutz, R.Dalma-Weiszhausz, D. D. Monitoring eukaryotic gene expression using oligonucleotide microarrays. Methods Mol Biol. 258:71-94, 2004. ADDRESS: Affymetrix Inc., Santa Clara, CA, USA. Medline UID: 14970458 23. Liang, R. Q.; Tan, C. Y.Ruan, K. C. Colorimetric detection of protein microarrays based on nanogold probe coupled with silver enhancement. J Immunol Methods. 285:157-63, 2004. ADDRESS: Key Laboratory of Proteomics, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 320 Yue-Yang Road, Shanghai 200031, China. Medline UID: 14980430 24. Matzke, M.; Aufsatz, W.; Kanno, T.; Daxinger, L.; Papp, I.; Mette, M. F.Matzke, A. J. Genetic analysis of RNA-mediated transcriptional gene silencing. Biochim Biophys Acta. 1677:129-41, 2004. ADDRESS: Institute of Molecular Biology, Austrian Academy of Sciences, Billrothstrasse 11, A-5020, Salzburg, Austria. mmatzke@imb.oeaw.ac.at. Medline UID: 15020054 25. McDermott, J. and Samudrala, R. Enhanced functional information from predicted protein networks. Trends Biotechnol. 22:60-2; discussion 62-3, 2004. ADDRESS: Computational Genomics Group, Department of Microbiology, University of Washington School of Medicine, Seattle, WA 98195, USA. Medline UID: 14757037 26. Nadershahi, A.; Fahrenkrug, S. C.Ellis, L. B. Comparison of computational methods for identifying translation initiation sites in EST data. BMC Bioinformatics. 5:14, 2004. ADDRESS: College of Biological Science, University of Minnesota, St. Paul, MN 55108, USA. nade0043@umn.edu. Medline UID: 15053846 27. Pinhasov, A.; Mei, J.; Amaratunga, D.; Amato, F. A.; Lu, H.; Kauffman, J.; Xin, H.; Brenneman, D. E.; Johnson, D. L.; Andrade-Gordon, P.Ilyin, S. E. Gene expression analysis for high throughput screening applications. Comb Chem High Throughput Screen. 7:133-40, 2004. ADDRESS: Johnson & Johnson Pharmaceutical Research mapsto Development, Spring House, PA 19477, USA. Medline UID: 15032660 28. Schwarz, G.; Baumler, S.; Block, A.; Felsenstein, F. G.Wenzel, G. Determination of detection and quantification limits for SNP allele frequency estimation in DNA pools using real time PCR. Nucleic Acids Res. 32:e24, 2004. ADDRESS: Biotechnology in Plant Protection, EpiGene GmbH, Hohenbachernstrasse 19-21, D-85354 Freising, Germany. gschwarz@wzw.tum.de. Medline UID: 14960708 29. Shimkets, R. A. Gene expression quantitation technology summary. Methods Mol Biol. 258:7-12, 2004. ADDRESS: Drug Discovery, CuraGen Corporation, New Haven, CT, USA. Medline UID: 14970454 30. GeneCalling: transcript profiling coupled to a gene database query. Methods Mol Biol. 258:43-51, 2004. ADDRESS: Drug Discovery, CuraGen Corporation, New Haven, CT, USA. Medline UID: 14970456 31. Technical considerations in quantitating gene expression. Methods Mol Biol. 258:1-6, 2004. ADDRESS: Drug Discovery, CuraGen Corporation, New Haven, CT, USA. Medline UID: 14970453 32. 't Hoen, P. A.; Turk, R.; Boer, J. M.; Sterrenburg, E.; de Menezes, R. X.; van Ommen, G. J.den Dunnen, J. T. Intensity-based analysis of two-colour microarrays enables efficient and flexible hybridization designs. Nucleic Acids Res. 32:e41, 2004. ADDRESS: Center for Human and Clinical Genetics, Leiden University Medical Center, The Netherlands. p.a.c.hoen@lumc.nl. Medline UID: 14982960 33. Takatsu, K.; Yokomaku, T.; Kurata, S.Kanagawa, T. A new approach to SNP genotyping with fluorescently labeled mononucleotides. Nucleic Acids Res. 32:e60, 2004. ADDRESS: Kankyo Engineering Co., Ltd, 2-1-38 Shiohama, Kisarazu, Chiba 292-0838, Japan. Medline UID: 15087492 34. van Eijk, M. J.; Broekhof, J. L.; van der Poel, H. J.; Hogers, R. C.; Schneiders, H.; Kamerbeek, J.; Verstege, E.; van Aart, J. W.; Geerlings, H.; Buntjer, J. B.; van Oeveren, A. J.Vos, P. SNPWave: a flexible multiplexed SNP genotyping technology. Nucleic Acids Res. 32:e47, 2004. ADDRESS: Keygene NV, Agro Business Park 90, PO Box 216, 6700 AE Wageningen, The Netherlands. michiel.van-eijk@keygene.com. Medline UID: 15004220 35. Vilain, C. and Vassart, G. Small amplified RNA-SAGE. Methods Mol Biol. 258:135-52, 2004. ADDRESS: Institute of Interdisciplinary Research (IRIBHM), Univeriste Libre de Bruxelles, Brussels, Belgium. Medline UID: 14970461 36. Wang, J.; Williams, R. W.Manly, K. F. WebQTL: web-based complex trait analysis. Neuroinformatics. 1:299-308, 2003. ADDRESS: Department of Molecular & Cellular Biology, Roswell Park Cancer Institute, Buffalo, NY, USA. Medline UID: 15043217 37. Wu, S.; Liew, A. W.; Yan, H.Yang, M. Cluster analysis of gene expression data based on self-splitting and merging competitive learning. IEEE Trans Inf Technol Biomed. 8:5-15, 2004. ADDRESS: Department of Computer Engineering and Information Technology, City University of Hong Kong, Kowloon, Hong Kong. Medline UID: 15055797 ********************************************************************** 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/