Bibliography on
Microarray Data Analysis

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© Copyright, 1999-2010 Wentian Li
of North Shore LIJ Research Institute

http://www.nslij-genetics.org/microarray/
1999

  1. U Alon, N Barkai, DA Notterman, K Gish, S Ybarra, D Mack, AJ Levine (1999), "Broad patterns of gene expression revealed by clustering analysis of tumor and normal colon tissues probed by oligonucleotide arrays", Proceedings of the National Academy of Sciences, 96(12):6745-6750.
    [abstract(Medline)] [PDF] [ webpage from the authors: microarray.princeton.edu/oncology/]

  2. networks
    T Akutsu, S Miyano, S Kuhara (1999) "Identification of genetic networks from a small number of gene expression patterns under the Boolean network model", Biocomputing'99: Proceedings of the Pacific Symposium, 4:17-28.
    [PDF]

  3. database
    Richard Baldock, Duncan Davidson (1999), "Gene expression databases", in Genetic Databases , ed Martin J Bishop pp.247-68 (Academic Press). [ from the publisher ]

  4. Joel Lloyd Bellenson (1999) "Expression data and the bioinformatics challenges", in DNA Microarray (practical approach series, 205), ed. Mark Schena (Oxford Univ Press) [ from oxford ]

  5. Amir Ben-Dor, Zohar Yakhini (1999), "Clustering gene expression patterns", Journal of Computational Biology, 6(3/4):281-298.
    [ abstract] [PDF] [ webpage from the authors: www.cs.washington.edu/homes/amirbd/BioClust/Webpn/ ]

  6. M Bittner, Meltzer P, J Trent (1999), "Data analysis and integration: of steps and arrows", Nature Genetics, 22(3):213-215.

  7. R Brent (1999), "Functional genomics: Learning to think about gene expression data", Current Biology, 9(9):R338-R341.

  8. review
    P Brown, D Bostein (1999), "Exploring the new world of the genome with DNA microarrays", Nature Genetics, 21(1 suppl):33-37.
    [ abstract(Medline)] [chipping forecast]

  9. P Bucher (1999), "Regulatory elements and expression profiles", Current Opinion in Structural Biology, 9(3):400-407.
    [abstract(Medline)]

  10. networks
    Ting Chen, Vladimir Filkov, Steven S. Skiena (1999), "Identifying gene regulatory networks from experimental data", Proceedings of the Third International Conference on Research in Computational Molecular Biology , pp.94-103.

  11. Yidong Chen, Olga Ermolaeva, Michael L Bittner, Paul Meltzer, Jeffery Trent, Edward R Dougherty, Sinan Batman (1999), "Clustering analysis for gene expression data", Proceedings of SPIE, 3602:422-428.

  12. JM Claverie (1999), "Computational methods for the identification of differential and coordinated gene expression", Human Molecular Genetics, 8(10):1821-1832.
    [abstract(Medline)] [PDF]

  13. C Debouck, PN Goodfellow (1999), "DNA microarrays in drug discovery and development", Nature Genetics, 21(1 suppl):48-50.
    [abstract(Medline)] [chipping forecast]

  14. JL DeRisi, VR Iyer (1999), "Genomics and array technology", Current Opinion in Oncology, 11(1):76-79.
    [ abstract(Medline)]

  15. application
    P D'haeseleer, X Wen, S Fuhrman, R Somogyi (1999), "Linear modeling of mRNA expression levels during CNS developement and injury", Biocomputing'99: Proceedings of the Pacific Symposium, 4:41-52.
    [ html ]

  16. DJ Duggan, M Bittner, Y Chen, P Meltzer, JM Trent (1999), "Expression profiling using cDNA microarrays", Nature Genetics, 21(1 suppl):10-14.
    [chipping forecast]

  17. review
    MB Eisen, PO Brown (1999), "DNA arrays for analysis of gene expression", Methods of Enzymology, 303:179-205.

  18. R Ekins, FW Chu (1999), "Microarrays: their origins and applications", Trends in Biotechnology, 17:217-218.
    [PDF]

  19. RM Ewing, AB Kahla, O Poirot, F Lopez, S Audic, JM Claverie (1999), "Large-scale statistical analyses of rice ESTs reveal correlated patterns of gene expression", Genome Research, 9:950-959.

  20. D Gerhold, T Rushmore, CT Caskey (1999), "DNA chips: promising toys have become powerful tools", Trends in Biochemical Sciences, 24(5): 168-173.
    [abstract(Medline)]

  21. TR Golub, DK Slonim, P Tamayo, C Huard, M Caasenbeek, JP Mesirov, H Coller, ML Loh, JR Downing, MA Caligiuri, CD Bloomfield, ES Lander (1999), "Molecular classification of cancer: class discovery and class prediction by gene expression monitoring", Science, 286:531-537.
    [PDF] [ webpage from the authors: www.genome.wi.mit.edu/MPR/cancer_class.html]

  22. Samuel Granjeaud, François Bertucci, Bertrand R Jordan (1999), "Expression profiling: DNA arrays in many guises", BioEssays, 21(9):781-790.
    [ abstract]

  23. JG Hacia (1999), "Resequencing and mutational analysis using oligonucleotide microarrays", Nature Genetics, 21(1 suppl):42-47.
    [abstract(Medline)] [chipping forecast]

  24. Erez Hartuv, Armin Schmitt, jorg Lange, Sebastian Meirer-Ewert, Hans Lehrach, Ron Shamir (1999), "An algorithm for clustinering cDNAs for gene expression analysis", Proceedings of the Third International Conference on Research in Computational Molecular Biology , pp.

  25. R Herwig, AJ Poustka, C Muller, C Bull, H Lehrach, J O'Brien (1999), "Large-scale clustering of cDNA-fingerprinting data", Genome Research, 9:1093-1105.

  26. LJ Heyer, S Kruglyak, S Yooseph (1999), "Exploring expression data: identification and analysis of coexpressed genes", Genome Research, 9:1106-1115.

  27. review
    S Huang (1999), "Gene expression profiling, genetic networks, and cellular states: an integrating concept for tumorigenesis and drug discovery", Journal of Molecular Medicine, 77(6):469-480.
    [abstract(Medline)]

  28. A Isaksson, U Landegren (1999), "Accessing genomic information: alternatives to PCR", Current Opinion in Biotechnology, 10(1):11-15.
    [PDF]

  29. EG Jennings, RA Young (1999), "Genome expression on the world wide web", Trends in Genetics, 15(5):202-204.

  30. CM Kao (1999), "Functional genomic technologies: Creating new paradigms for fundamental and applied biology", Biotechnology Progress,15(3):304-311.

  31. Richard M Karp, KaYee Yeung (1999), "Algorithms for choosing differential gene expression experiments", Proceedings of the Third International Conference on Research in Computational Molecular Biology , pp.208-217.

  32. L Khan, ML Bittner, Y Chen, PS Meltzer, JM Trent (1999) "DNA microarray technology: the anticipated impact on the study of human disease", Biochim Biophys Acta, 1423(2):M17-M28. [abstract(Medline)]

  33. DH Kozian, BJ Kirschbaum (1999), "Comparative gene-expression analysis", Trends in Biotechnology, 17(2):73-78.
    [abstract(Medline)]

  34. Mitsuteru Nakao, Hidemasa Bono, Shuichi Kawashima, Tomomi Kamiya, Kazushige Sato, Susumu Goto, Minoru Kanehisa (1999), "Genome-scale gene expression analysis and pathway reconstruction in KEGG", Genome Informatics, 10:94-103.

  35. P Ross-Macdonald, PSR Coelho, T Roemer, S Agarwal, A Kumar, R Jansen, KH Cheung, A Sheehan, D Symoniatis, L Umansky, M Heidtman, FK Nelsen, H Iwasaki, K Hager, M Gerstein, P Miller, GS Roeder, M Snyder (1999), "Large-scale analysis of the yeast genome by transposon tagging and gene disruption", Nature, 402:413-418.

  36. networks
    MG Samsonova, VN Serov (1999) "NetWork: An interactive interface to the tools for analysis of genetic network structure and dynamics", Biocomputing'99: Proceedings of the Pacific Symposium, 4:102-111.
    [PDF]

  37. RJ Sapolsky, L Hsie , A Berno , G Ghandour , M Mittmann , JB Fan (1999), "High-throughput polymorphism screening and genotyping with high-density oligonucleotide arrays", Genetic Analysis, 14(5-6):187-192. [abstract(Medline)]

  38. RA Shimkets, Lowe DG, Tai JT, Sehl P, Jin H, Yang R, Predki PF, Rothberg BE, Murtha MT, Roth ME, Shenoy SG, Windemuth A, Simpson JW, Simons JF, Daley MP, Gold SA, McKenna MP, Hillan K, Went GT, Rothberg JM. (1999), "Gene expression analysis by transcript profiling coupled to a gene database query", Nature Biotechnology, 17(8):798-803.

  39. Roland Somogyi (1999), "Making sense of gene-expression data", Pharmainformatics (a Trends Guide), 17-24.

  40. E Southern, K Mir, M Shchepinov (1999), "Molecular interactions on microarrays", Nature Genetics, 21(1 suppl):5-9.
    [abstract(Medline)] [chipping forecast]

  41. networks
    Z Szallasi (1999), "Genetic network analysis in light of massively parallel biological data acquisition", Biocomputing'99: Proceedings of the Pacific Symposium, 4:5-16.
    [abstract(Medline)] [PDF]

  42. P Tamayo, D Slonim, J Mesirov, Q Zhu, S Kitareewan, E Dmitrovsky, ES Lander, TR Golub (1999), "Interpreting patterns of gene expression with self-organizing maps: Methods and application to hematopoietic differentiation", Proceedings of the National Academy of Sciences, 96(6):2907-2912.
    [PDF] [abstract(Medline)] [ GENECLUSTER program]

  43. L Tanabe, LH Smith, JK Lee, U Scherf, L Hunter, JN Weinstein (1999), "MedMiner: An internet tool for filtering and organizing biomedical information, with application to gene expression profiling", BioTechniques, 27:1210-1217.

  44. networks
    S Tavazoie, JD Hughes, MJ Campbell, RJ Cho, GM Church (1999), "Systematic determination of genetic network architecture", Nature Genetics, 22(3):281-285.

  45. R Tibshirani, T Hastie, M Eisen, D Ross, D Botstein, P Brown (1999), "Clustering methods for the analysis of DNA microarray data", Technical Report, Stanford University.

  46. P Toronen, M Kolehmainen, G Wong, E Castren (1999), "Analysis of gene expression data using self-organizing maps", FEBS Letters, 451(2):142-146.
    [abstract(Medline)]

  47. D Warburton (1999), "Comparative genomic hybridization: FISH and chips in our future? ", Teratology, 59(5):321-322.

  48. SJ Watson, H Akil (1999), "Gene chips and arrays revealed: a primer on their power and their uses", Biol Psychiatry, 45(5):533-543.

  49. networks
    DC Weaver, CT Workman, GD Stormo (1999), "Modeling regulatory networks with weight matrices", Biocomputing'99: Proceedings of the Pacific Symposium, 4:112-123.
    [PDF]

  50. J Wittes, HP Friedman (1999), "Searching for evidence of altered gene expression: a comment on statistical analysis of microarray data", Journal of National Cancer Institute, 91(5):400-401.
    [abstract(Medline)]

  51. MQ Zhang (1999), "Large-scale gene expression data analysis: A new challenge to computational biologists", Genome Research, 9(8):681-688.
    [abstract(Medline)]
1999