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/

More papers from the Critical Assessment of Techniques for Microarray Data Mining Workshop (Dec 18-19, 2000)

2000

  1. Orly Alter, Patrick O Brown, David Botstein (2000), "Singular value decomposition for genome-wide expression data processing and modeling", Proceedings of the National Academy of Sciences, 97(18):10101-10106.
    [PDF ] [ webpage from the authors: genome-www.stanford.edu/SVD/]

  2. S Raychaudhur, JM Stuart, X Liu, PM Small, RB Altman (2000), "Pattern recognition of genomic features with microarrays: site typing of Mycobacterium Tuberculosis strains", Proceedings of the Eighth International Conference on Intelligent Systems for Molecular Biology (AAAI Press), pp.286-295.

  3. A Ben-Dor, L Bruhn, N Friedman, I Nachman, M Schummer, Z Yakhini (2000) "Tissue classification with gene expression profiles", Journal of Computational Biology, 7(3/4):559-583.
    [abstract]

  4. T Beißbarth, K Fellenberg, B Brors, R Arribas-Prat, JM Boer, NC Hauser, M Scheideler, JD Hoheisel, G Schütz, A Poustka, M Vingron (2000), "Processing and quality control of DNA array hybridization data", Bioinformatics, 16:1014-1022.
    [PDF]

  5. M Beibel (2000), "Selection of informative genes in gene expresson based diagnosis: a nonparametric approach", in Lecture Notes in Computer Sciences. Vol 1933. Proceedings of the First International Symposium in Medical Data Analysis (ISMDA2000), eds. R Brause, E Hanisch, pp.300-307 (Springer-Verlag).

  6. B Brors (2000), "Qualitätsstandards für DNA chip-analysen" (in german) Medizinische Genetik, 12:301-303.

  7. Nobert Brandle, Horng-Yang Chen, Horst Bischof (2000), "Robust parametric and semi-parametric spot fitting for spot array images", Proceedings of the Eighth International Conference on Intelligent Systems for Molecular Biology (AAAI Press), pp.46-56.

  8. A Brazma, J Vilo (2000), "Gene expression data analysis", FEBS Letters, 480:17-24.

  9. MPS Brown, WN Grundy, D Lin, C Sugnet, M Ares, Jr. D Haussler (2000), "Knowledge-based analysis of microarray gene expression data by using support vector machines", Proceedings of the National Academy of Sciences, 97:262-267. [ abstract] [PDF ]

  10. AJ Butte, IS Kohane (2000), "Mutual information relevance networks: functional genomics clustering using pairwise entropy measurements", Biocomputing 2000: Proceedings of the Pacific Symposium , 5:415-426.

  11. Andrea Califano, Gustavo Stolovitzky, Yuhai Tu (2000), "Analysis of gene expression microarrays for phenotype classification", Proceedings of the Eighth International Conference on Intelligent Systems for Molecular Biology (AAAI Press), pp.75-85.

  12. A J Carlisle, V V Prabhu, A Elkahloun, J Hudson, J M Trent, W M Linehan, E D Williams, M R Emmert-Buck, L A Liotta, P J Munson, D B Krizman (2000), "Development of a Prostate cDNA Microarray and statistical gene expression analysis package", Molecular Carcinogenesis, 28:12-22.

  13. Yidong Chen, Vishnu G Kamat, Edward R Dougherty, Michael L Bittner, Paul S Meltzer, Jeffrey M Trent (2000), "Expression ratio statistics and its applications to microarray data analysis", Proceedings of SPIE, 3926:142-149,

  14. Y Cheng, GM Church (2000), "Biclustering of expression data", Proceedings of the Eighth International Conference on Intelligent Systems for Molecular Biology (AAAI Press), pp.93-103.

  15. BA Cohen, RD Mitra, JD Hughes, GM Church (2000), "A computational analysis of whole-genome expression data reveals chromosomal domains of gene expression", Nature Genetics, 26(2):183-186.

  16. networks
    P D'haeseleer, S Liang, R Somogyi (2000), "Genetic network inference: from co-expression clustering to reverse engineering", Bioinformatics, 16(8):707-726.

  17. database
    RM Ewing, JM Claverie (2000), "EST database as multi-conditional gene expression datasets", Biocomputing 2000: Proceedings of the Pacific Symposium , 5:427-439.

  18. N Friedman, M Linial, I Nachman, D Pe'er (2000), "Using Bayesian networks to analyze expression data", Journal of Computational Biology, 7(3/4):601-620.
    [abstract]

  19. S Fuhrman, MJ Cunningham, X Wen, G Zweiger, JJ Seihamer, R Somogyi (2000), "The application of Shannon entropy in the identification of putative drug targets", Biosystem, 55:5-14. [ abstract] [PDF ]

  20. TS Furey, N Cristiannini, N Duffy, DW Bednarski, M Schummer, D Haussler (2000), "Support vector machine classification and validation of cancer tissue samples using microarray expression data", Bioinformatics, 16(10):906-914.

  21. Terry Gaasterland, Stefan Bekiranov (2000), "Making the most of microarray data" (news & views), Nature Genetics, 24(3):204-206.

  22. G Getz, E Levine, E Domany (2000), "Coupled two-way clustering analysis of gene microarray data", Proceedings of the National Academy of Sciences, 97(22):12079-12084.

  23. G Getz, E Levine, E Domany, MQ Zhang (2000), "Super-paramagnetic clustering of yeast gene expression profile", Physica A, 279:457-464.

  24. SR Gullans (2000), "Of microarrays and meandering data points", Nature Genetics, 26:4-5.

  25. T Hastie, O Alter, G Sherlock, M Eigen, R Tibshirani, D Bostein, P Brown (2000), "Imputation of missing values in DNA microarrays", Technical Report, Stanford University.

  26. Trevor Hastie, Robert Tibshirani, Michael B Eisen, Ash Alizadeh, Ronald Levy, Louis Staudt, Wing C Chan, David Botstein, Patrick Brown (2000), " 'Gene shaving' as a method for identifying distinct sets of genes with similar expression patterns ", Genome Biology , 1(2): research0003.1-0003.21.
    [PDF ]

  27. P Hegde, R Qi, K Abernathy, C Gay, S Dharap, R Gaspard, JE Hughes, E Snesrud, N Lee N, J Quackenbush (2000), "A concise guide to cDNA microarray analysis", Biotechniques, 29(3):548-550.

  28. Neal S Holter, Madhusmita Mitra, Amos Maritan, Marek Cieplak, Jayanth R Banavar, and Nina V Fedoroff (2000), "Fundamental patterns underlying gene expression profiles: simplicity from complexity", Proceedings of the National Academy of Sciences, 97(15):8409-8414. [PDF]

  29. TR Hughes, MJ Marton, AR Jones, CJ Roberts, R Stoughton, CD Armour, HA Bennett, H Dai, YD He, MJ Kidd, AM King, MR Meyer, D Slade, PY Lum, SB Stepaniants, DD Shoemaker, D Gachotte, K Chakraburtty, J Simon, M Bard, SH Friend (2000), "Functional discovery via a compendium of expression profiles", Cell, 102:109-126.

  30. T Ideker, V Thorsson, AF Siegel, LE Hood (2000), "Testing for differentially-expressed genes by maximum-likelihood analysis of microarray data", Journal of Computational Biology, 7(6):805-818.
    [abstract] [ webpage from the authors: db.systemsbiology.net/software/VERAandSAM/supporting.html]

  31. networks
    Mamoru Kato, Tatsuhiko Tsunoda, Toshihisa Takagi (2000), "Inferring genetic networks from DNA microarray data by multiple regression analysis", Genome Informatics, 11:118-128.

  32. M Kathleen Kerr, Mitchell Martin, Gary A Churchill (2000), "Analysis of variance for gene expression microarray data", Journal of Computational Biology, 7:819-837.
    [abstract]

  33. Hirohisa Kishino, Peter J. Waddell (2000), "Correspondence analysis of genes and tissue types and finding genetic links from microarray data", Genome Informatics, 11:83-95.

  34. Seungchan Kim, Edward R Dougherty, Michael L Bittner, Yidong Chen, Krishnamoorthy Sivakumar, Paul S Meltzer, Jeffery M Trent (2000), "General nonlinear framework for the analysis of gene interaction via multivariate expression arrays", Journal of Biomedical Optics, 5(4):411-424.

  35. S Kim, ER Dougherty, Y Chen, K Sivakumar, P Meltzer, JM Trent, M Bittner (2000), "Multivariate measurement of gene expression relationships.", Genomics, 67(2):201-209.

  36. Mei-Ling Ting Lee, Frank C Kuo, G A Whitmore, Jeffrey Sklar (2000), "Importance of replication in microarray gene expression studies: Statistical methods and evidence from repetitive cDNA hybridizations ", 97(18):9834-9838. Proceedings of the National Academy of Sciences, [PDF]

  37. database
    B Liao, W Hale, CB Epstein, RA Butow, HR Garner (2000), "MAD: a suite of tools for microarray data management and processing", Bioinformatics, 16(10):946-947.

  38. DJ Lockhart, EA Winzeler (2000), "Genomics, gene expression and DNA arrays", Nature, 405(6788):827-836.

  39. E Manduchi, G R Grant, S E McKenzie, G C Overton, S Surrey, C J Stoeckert (2000), "Generation of patterns from gene expression data by assigning confidence to differentially expressed genes", Bioinformatics, 16(8):685-698.
    [PDF]

  40. Kalim U Mir, Edwin M Southern (2000), "Sequence variation in genes and genomic DNA: methods for large-scale analysis", Annual Review of Genome and Human Genetics, 1:329-360.
    [PDF]

  41. EJ Moler, ML Chow, IS Mian (2000), "Analysis of molecular profile data using generative and discriminative methods", Physiological Genomics, 4(2):109-126.

  42. Juan Carlos Oliveros, Christian Blaschke, Javier Herrero, Joaquín Dopazo, Alfonso Valencia (2000), "Expression profiles and biological function", Genome Informatics, 11: 106-117.

  43. Charles M Perou, Patrick O Brown, David Botstein (2000), "Tumor classification using gene expression patterns from DNA microarrays", New Technologies for Life Sciences: A Trends Guide, 67-76.

  44. MR Pocock, TJP Hubbard (2000), "A browser for expression data", Bioinformatics, 16(4):402-403.

  45. S Raychaudhuri, JM Stuart, RB Altman, (2000), "Principal components analysis to summarize microarray experiments: application to sporulation time series", Biocomputing 2000: Proceedings of the Pacific Symposium , 5:452-463.
    [PDF]

  46. Soumya Raychaudhuri, Joshua M Stuart, Xuemin Liu, Peter M Small, Russ B Altman (2000), "Pattern recognition of genomic features with microarrays: site typing of Mycobacterium Tuberculosis Strains", Proceedings of the Eighth International Conference on Intelligent Systems for Molecular Biology (AAAI Press), pp.286-295.

  47. SA Rifkin, K Atteson, J Kim (2000), "Constraint structure analysis of gene expression", Functional & Integrative Genomics, 1(3):174-185.

  48. D T Ross, U Scherf, M B Eisen, C M Perou, C Rees, P Spellman, V Iyer, S S Jeffrey, M Van de Rijn, M Waltham, A Pergamenschikov, J C F Lee, D Lashkari, D Shalon, T G Myers, J N Weinstein, D Botstein, P O Brown (2000), "Systematic variation in gene expression patterns in human cancer cell lines", Nature Genetics, 24(3):227-235. [ abstract] [ webpage from the authors: genome-www.stanford.edu/nci60/ ]

  49. review
    Marta Sanchez-Carbayo, William Bornmann, Carlos Cordon-Cardo (2000), "DNA microchips: technical and practical considerations", Current Organic Chemistry, 4(9):?-?.

  50. DB Searls (2000), "Bioinformatics tools for whole genomes", Annual Review of Genomics and Human Genetics, 1:251-279.
    [PDF ]

  51. EE Schadt, C Li, C Su, WH Wong (2000), "Analyzing high-density oligonucleotide gene expression array data", Journal of Cellular Biochemistry, 80(2):192-202.

  52. database
    U Scherf, D T Ross, M Waltham, L H Smith, J K Lee, L Tanabe, K W Kohn, W C Reinhold, T G Myers, D T Andrews, D A Scudiero, M B Eisen, E A Sausville, Y Pommier, D Botstein, P O Brown & J N Weinstein (2000), "A gene expression database for the molecular pharmacology of cancer", Nature Genetics, 24(3):236-244.

  53. Johannes Schuchhardt, Dieter Beule, Arif Malik, Eryc Wolski, Holger Eickhoff, Hans Lehrach and Hanspeter Herzel (2000), "Normalization strategies for cDNA microarrays" (NAR methods online), Nucleic Acids Research,28(10):E47.

  54. R Sharan, R Shamir (2000), "CLICK: A clustering algorithm with applications to gene expression analysis", Proceedings of the Eighth International Conference on Intelligent Systems for Molecular Biology (AAAI Press), pp.307-316.

  55. Hagit Shatkay, Stephen Edwards, W John Wilbur, Mark Boguski (2000), "Genes, themes, and microarray: using information retrieval for large-scale gene analysis", Proceedings of the Eighth International Conference on Intelligent Systems for Molecular Biology (AAAI Press), pp.317-328.

  56. G Sherlock (2000), "Analysis of large-scale gene expression data", Current Opinion in Immunology, 12:201-205.

  57. D Slonim, P Tamayo, J Mesirov, TR Golub, E Lander (2000) "Class prediction and discovery using gene expression data" Proceedings of the Fourth International Conference on Research in Computational Molecular Biology , pp.263-272.

  58. DJ Stewart (2000), "Making and using DNA microarrays: a short course at Cold Spring Harbor Laboratory" (insight/outlook), Genome Research, 10(1):1-3.

  59. G Stolovitzky, A Califono, Y Tu (2000), "Analysis of gene expression microarrays for phenotype classification", Proceedings of the Eighth International Conference on Intelligent Systems for Molecular Biology (AAAI Press), pp.75-85.

  60. networks
    A Wagner (2000), "Robustness against mutations in genetic networks of yeast", Nature Genetics, 24:355-361.

  61. AHC van Kampen, BDC van Schaik, E Pauws, EMC Michiels, JM Ruijter, HN Caron, R Versteeg, SH Heisterkamp, JAM Leunissen, F Baas, M van der Mee (2000), "USAGE: a web-based approach towards the analysis of SAGE data", Bioinformatics, 16(10):899-905.

  62. networks
    E van Someren, LFA Wessels, MJT Reinders (2000), "Linear modeling of genetic networks from experimental data", Proceedings of the Eighth International Conference on Intelligent Systems for Molecular Biology (AAAI Press), pp.355-366.

  63. J Vilo, B Alvia, I Jonassen, A Robinson, E Ukkonen (2000), "Mining for putative regulatory elements in the yeast genome using gene expression data", Proceedings of the Eighth International Conference on Intelligent Systems for Molecular Biology (AAAI Press), pp.384-394.

  64. Peter J Waddell, Hirohisa Kishino (2000), "Cluster inference methods and graphical models evaluated on NCI60 microarray gene expression data", Genome Informatics, 11:129-140.

  65. E Wang, LD Miller, GA Ohnmacht, ET Liu, FM Marincola (2000), "High-fidelity mRNA amplification for gene profiling", Nature Biotechnology, 18:457-459.

  66. D Wolf, CO Gray, A de Saizieu (2000), "Visualising gene expression in its metabolic context", Briefings in Bioinformatics, 1(3):297-304.

  67. P J Woolf, Y Wang (2000), "A fuzzy logic approach to analyzing gene expression data", Physiological Genomics, 3(1):9-15.

  68. M Xiong, L Jin, W Li, E Boerwinkle (2000), "Computational methods for gene expression-based tumor classification", Biotechniques, 29(6):1264-1268. [abstract]

  69. K Zhang, H Zhao (2000), "Assessing reliability of gene clusters from gene expression data", Functional & Integrative Genomics, 1(3):156-173.

  70. J Zhu, MQ Zhang (2000), "Cluster, function and promoter: analysis of yeast expression array", Biocomputing 2000: Proceedings of the Pacific Symposium , 5:476-487.
    [PDF ]

  71. A Zien, R Kuffner, R Zimmer, T Lengauer (2000), "Analysis of gene expression data with pathway scores", Proceedings of the Eighth International Conference on Intelligent Systems for Molecular Biology (AAAI Press), pp.407-417.
    [PDF ]
2000