Bibliography on
Microarray Data Analysis

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© Copyright, 1999-2007 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. Roland Somogyi (1999), "Making sense of gene-expression data", Pharmainformatics (a Trends Guide), 17-24.

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

  40. 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]

  41. 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]

  42. 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.

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

  44. 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.

  45. 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)]

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

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

  48. 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]

  49. 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)]

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