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/
2002

  1. application
    Igor Aizenberg, Ekaterina Myasnikova, Maria Samsonova and John Reinitz (2002), "Temporal classification of Drosophila segmentation gene expression patterns by the multi-valued neural recognition method", Mathematical Biosciences, 176(1):145-159.

  2. DB Allison, CS Coffey (2002), "Two-stage testing in microarray analysis: what is gained?", Journal of Gerontology: Biological Sciences, 57(5):B189-192.

  3. C Ambroise, GJ McLachlan (2002), "Selection bias in gene extraction on the basis of microarray gene-expression data.", Proceedings of the National Academy of Sciences, 99(10):6562-6566.
    [abstract]

  4. R Anbazhagan (2002), "Microarray assistant clone organizer and array simulator", Biotechniques, 32:1398-1402.

  5. Alena A Antipova, Pablo Tamayo, Todd R Golub (2002), "A strategy for oligonucleotide microarray probe reduction", Genome Biology, 3(12):research0073.

  6. I Alexandre, Y Houbion, J Collet, S Hamels, J Demarteau, JL Gala, J Remacle (2002), "Compact disc with both numeric and genomic information as DNA microarray platform", Biotechniques, 33:435-439.

  7. Virginie Aris, Michael Recce (2002), "A method to improve detection of disease using selective expressed genes in microarray data", in Methods of Microarray Data Analysis , eds. SM Lin, KF Johnson (Kluwer Academic), pp. 69-80.

  8. F Azuaje (2002), "A cluster validity framework for genome expression data ", Bioinformatics, 18:319-320.
    [PDF]

  9. Marina Bakay , Yi-Wen Chen , Rehannah Borup , Po Zhao , Kanneboyina Nagaraju, Eric Hoffman (2002), "Sources of variability and effect of experimental approach on expression profiling data interpretation", BMC Bioinformatics, 3:4.
    [ abstract ] [PDF]

  10. Y Balagurunathan, ER Dougherty, Y Chen, ML Bittner, JM Trent (2002), "Simulation of cDNA microarrays via a parameterized random signal model", Journal of Biomedical Optics, 7(3):507-523.
    [ abstract]

  11. CA Ball, G Sherlock, H Parkinson, P Rocca-Sera, C Brooksbank, HC Causton, D Cavalieri, T Gaasterland, P Hingamp, F Holstege, M Ringwald, P Spellman, CJ Stoeckert Jr, JE Stewart, R Taylor, A Brazma, J Quackenbush (2002), "A guide to microarray experiments - an open letter to the scientific journals", Lancet, 360(9338):1019.

  12. CA Ball, G Sherlock, H Parkinson, P Rocca-Sera, C Brooksbank, HC Causton, D Cavalieri, T Gaasterland, P Hingamp, F Holstege, M Ringwald, P Spellman, CJ Stoeckert Jr, JE Stewart, R Taylor, A Brazma, J Quackenbush (2002), "Standards for Microarray data" (Letters), Science, 298(5593):539

  13. Z Bar-Joseph, G Gerber, DK Gifford, TS Jaakkola, I Simon (2002), "A new approach to analyzing gene expression time series data", Proceedings of the Sixth International Conference on Computational Molecular Biology , 39-48.

  14. Y Barash, N Friedman (2002), "Context-specific Bayesian clustering for gene expression data", Journal of Computational Biology, 9(2):169-192.
    [ abstract]

  15. Céline Becquet, Sylvain Blachon, Baptiste Jeudy, Jean-Francois Boulicaut, Olivier Gandrillon (2002), "Strong-association-rule mining for large-scale gene-expression data analysis: a case study on human SAGE data", Genome Biology, 3(12):research0067.

  16. JA Bernstein, AB Khodursky, PH Lin, S Lin-Chao, SN Cohen (2002), "Global analysis of mRNA decay and abundance in Escherichia coli at single-gene resolution using two-color fluorescent DNA microarrays", Proceedings of the National Academy of Sciences, 99(15):9697-9702.
    [abstract]

  17. D Berrar, W Dubitzky, M Granzow, R Eils (2002), "Analysis of gene expression and drug activity data by knowledge-based association mining", in Microarray data analysis II, ed. SM Lin and KF Johnson (Kluwer Academic), pp. ?-?.

  18. Ghislain Bidaut, Jeffrey Grant, Thomas Moloshok, Frank Manion, Michael Ochs (2002), "Application of Bayesian decomposition to gene expression analysis of deletion mutation data", in Microarray data analysis II, ed. SM Lin and KF Johnson (Kluwer Academic), pp. ?-?.

  19. Martin Bilban, Lukas K Buehler, Steven Head, Gernot Desoye, Vito Quaranta (2002), "Normalizing DNA microarray data", Curr. Issurs Mol. Biol. 4:57-64.

  20. Martin Bilban, Lukas K Buehler, Steven Head, Gernot Desoye, Vito Quaranta (2002), "Defining signal thresholds in DNA microarrays: exemplary application for invasive cancer", BMC Genomics, 3:19.
    [ abstract]

  21. networks
    Ashish Bhan, David J Galas, T Gregory Dewey (2002), "A duplication growth model of gene expression networks", Bioinformatics, 18:1486-1493.

  22. Michael A Black, RW Doerge (2002), "Calculation of the minimum number of replicate spots required for detection of significant gene expression fold change in microarray experiments", Bioinformatics, 18:1609-1616.
    [PDF]

  23. T Bo, I Jonassen (2002), "New feature subset selection procedures for classification of expression profiles", Genome Biology, 3(4):research0017.

  24. database
    Michael Bober, Kevin Wiehe, Christina Yung, Tugba Onal Suzek, Matthew Lin, William Baumgartner, Jr, and Raimond Winslow (2002), "CaGE: Cardiac gene expression knowledgebase", Bioinformatics, 18:1013-1014.

  25. Christopher MLS Bouton, Jonathan Pevsner (2002), "DRAGON View: information visualization for annotated microarray data ", Bioinformatics, 18:323-324.

  26. Daniel Bozinov and Jörg Rahnenführer (2002), "Unsupervised technique for robust target separation and analysis of DNA microarray spots through adaptive pixel clustering ", Bioinformatics, 18:747-756.
    [PDF]

  27. Vanessa M Brown, Alex Ossadtchi, Arshad H Khan, Simon R Cherry, Richard M Leahy, Desmond J Smith (2002), "High-throughput imaging of brain gene expression ", Genome Research, 12:244-254.
    [ abstract]

  28. Jenny Bryan, Katherine S Pollard, Mark J van der Laan (2002), "Paired and unpaired comparison and clustering with gene expression data", Statistica Sinica, 12:87-110.

  29. database
    Klaus Bumm, Mingzhong Zheng, Clyde Bailey, Fenghuang Zhan, M Chiriva-Internati, Paul Eddlemon, Julian Terry, Bart Barlogie, John D Shaughnessy, Jr (2002), "CGO: utilizing and integrating gene expression microarray data in clinical research and data management", Bioinformatics, 18:327-328.

  30. Pierre R Bushel, Hisham K Hamadeh, Lee Bennett, James Green, Alan Ableson, Stephen Misener, Cynthia A Afshari, Richard S Paules (2002), "Computational selection of distinct class- and subclass-specific gene expression signatures", Journal of Biomedical Informatics, 35(3):160-170.

  31. Atul Butte (2002), "The use and analysis of microarray data", Nature Reviews Drug Discovery, 1:951-960.
    [PDF]

  32. Jeong-Ho Chang, Kyu-Baek Hwang, Byoung-Tak Zhang (2002), "Analysis of gene expression profiles and drug activity patterns for the molecular pharmacology of cancer (data set 2)", in Microarray data analysis II, ed. SM Lin and KF Johnson (Kluwer Academic), pp. ?-?.

  33. Scott Chapman, Peer Schenk, Kemal Kazan, John Manners (2002), "Using biplots to interpret gene expression patterns in plants ", Bioinformatics, 18:202-204.
    [PDF]

  34. Damien Chaussabel, Alan Sher (2002), "Mining microarray expression data by literature profiling", Genome Biology, 3(10):research0055.

  35. G Chen, N Banerjee, SA Jaradat, TS Tanaka, MSH Ko, Zhang MQ (2002), "Cluster analysis of microarray gene expression data: application to and evaluation with NIA mouse 15K array on ES cell differentiation", Statistica Sinica, 12:241-262.

  36. Y Chen, V Kamat, ER Dougherty, ML Bittner, PS Meltzer, JM Trent (2002), "Ratio statistics of gene expression levels and applications to microarray data analysis", Bioinformatics, 18(9):1207-1215.
    [PDF]

  37. Francesca Chiaromonte, JessicaA Martinelli (2002), "Dimension reduction strategies for analyzing global gene expression data with a response", Mathematical Biosciences, 176(1):123-144.

  38. A Chilingaryan, N Gevorgyan, A Vardanyan, D Jones, A Szabo (2002), "Multivariate approach for selecting sets of differentially expressed genes", Mathematical Biosciences, 176(1):59-69.
    [ abstract]

  39. JD Chismar, T Mondala, H Fox, E Roberts, D Langford, E Masliah, DR Salomon, SR Head (2002), "Analysis of result variability from high-density oligonucleotide arrays comparing same-species and cross-species hybridizations", Biotechniques, 33:516-524.

  40. JH Cho, D Lee, JH Park, K Kim, IB Lee (2002), "Optimal approach for classification of acute leukemia subtypes based on gene expression data", Biotechnology Progress, 18(4):847-854.

  41. Tzu-Ming Chu, Bruce Weir and Russ Wolfinger (2002), "A systematic statistical linear modeling approach to oligonucleotide array experiments", Mathematical Biosciences, 176(1):35-51.

  42. RF Chuaqui, RF Bonner, CJM Best, JW Gillespie, MJ Flaig, SM Hewitt, JL Phillips, DB Krizman, MA Tangrea, M Ahram, WM Linehan, V Knezevic, MR Emmert-Buck (2002), "Post-analysis follow-up and validation of microarray experiments" Nature Genetics, 32(suppl):509-514..

  43. C Colantuoni, G Henry, S Zeger, J Pevsner (2002), "Local mean normalization of microarray element signal intensities across an array surface: quality control and correction of spatially systematic arti", Biotechniques, 32:1316-1320.

  44. C Colantuoni, G Henry, S Zeger, J Pevsner (2002), "SNOMAD (Standardization and NOrmalization of MicroArray Data): web-accessible gene expression data analysis", Bioinformatics, 18(11):1540-1541.
    [PDF]

  45. Charles J Colbourn, Alan C H Ling, Martin Tompa (2002), "Construction of optimal quality control for oligo arrays ", Bioinformatics, 18:529-535.

  46. L Conde, A Mateos, J Herrero, J Dopazo (2002), "Unsupervised reduction of the dimensionality followed by supervised learning with a perceptron improves the classification of conditions in DNA microarray gene expression data", Neural Networks for Signal Processing XII (IEEE Press) eds. Boulard, Adali, Bengio, Larsen, Douglas. pp. 77-86.

  47. GA Churchill (2002), "Fundamentals of experimental design for cDNA microarrays", Nature Genetics, 32(suppl):490-495.

  48. C Colantuoni, G Henry, S Zeger, J Pevsner (2002), "SNOMAD (Standardization and NOrmalization of MicroArray Data): web-accessible gene expression data analysis", Bioinformatics, 18(11):1540-1541.

  49. Charles J Colbourn, Alan C H Ling, Martin Tompa (2002), "Construction of optimal quality control for oligo arrays ", Bioinformatics, 18:529-535.

  50. L Conde, A Mateos, J Herrero, J Dopazo (2002), "Unsupervised reduction of the dimensionality followed by supervised learning with a perceptron improves the classification of conditions in DNA microarray gene expression data", Neural Networks for Signal Processing XII (IEEE Press) eds. Boulard, Adali, Bengio, Larsen, Douglas. pp. 77-86.

  51. T Conway, B Kraus, DL Tucker, DJ Smalley, AF Dorman, L McKibben (2002), "DNA array analysis in a Microsoft Windows environment", Biotechniques, 32(1):110, 112-4, 116, 118-9.

  52. Kevin R Coombes, Keith A. Baggerly, David N. Stivers, Jing Wang, David Gold, His-Guan Sung, Sang-Joon Lee (2002), "Biology-Driven clustering of microarray data: applications to the NCI60 data set", in Microarray data analysis II, ed. SM Lin and KF Johnson (Kluwer Academic), pp. ?-?.

  53. Aedín C Culhane, Guy Perrière, Elizabeth C Considine, Thomas G Cotter, Desmond G Higgins (2002), "Between-group analysis of microarray data", Bioinformatics, 18:1600-1608.
    [PDF]

  54. KD Dahlquist, N Salomonis, K Vranizan, SC Lawlor, BR Conklin (2002), "GenMAPP, a new tool for viewing and analyzing microarray data on biological pathways", Nature Genetics, 31(1):19-20.

  55. Dennise D Dalma-Weiszhausz, Marina E Chicurel, Thomas R Gingeras (2002), "Microarrays and genetic epidemiology: A multipurpose tool for a multifaceted field", Genetic Epidemiology, 23(1):4-20.

  56. Nilanjan Dasgupta, Simon M Lin, Lawrence Carin (2002), "Modeling pharmacogenomics of the NCI-60 anticancer data set: utilizing kernel PLS to correlate the microarray data to therapeutic responses", in Microarray data analysis II, ed. SM Lin and KF Johnson (Kluwer Academic), pp. ?-?.

  57. S Datta, J Arnold (2002), "Some comparisons of clustering and classification techniques applied to transcriptional profiling data", in Advances in Statistics, Combinatorics and Related Areas (World Scientific), pp.63-74.

  58. MJL de Hoon, S Imoto, S Miyano (2002), "Statistical analysis of a small set of time-ordered gene expression data using linear splines", Bioinformatics, 18:1477-1485.
    [PDF]

  59. Frank de Smet, Janick Mathys, Kathleen Marchal, Gert Thijs, Bart De Moor, and Yves Moreau (2002), "Adaptive quality-based clustering of gene expression profiles", Bioinformatics, 18:735-746.
    [PDF]

  60. Marcel Dettling, Peter Bühlmann (2002), "Supervised clustering of genes", Genome Biology, 3(12):research0069.

  61. G Didier, P Brezellec, E Rémy, A Hénaut (2002), "Gene-ANOVA - gene expression analysis of variance", Bioinformatics, 18(3):490-491.
    [PDF]

  62. CHQ Ding (2002), "Analysis of gene expression profiles: class discovery and leaf ordering", Proceedings of the Sixth International Conference on Research in Computational Molecular Biology , pp.127-136.
    [PDF] [ supplement materials from the author: www.nersc.gov/~cding/lymphoma/]

  63. K Dobbin, R Simon (2002), "Comparison of microarray designs for class comparison and class discovery", Bioinformatics, 18(11):1438-1445.
    [PDF]

  64. JM Dodson, PT Charles, DA Stenger, JJ Pancrazio (2002), "Quantitative assessment of filter-based cDNA microarrays: gene expression profiles of human T-lymphoma cell lines", Bioinformatics, 18:953-960.
    [PDF]

  65. J Dopazo (2002) "Microarray data processing and analysis", in Microarray data analysis II, ed. SM Lin and KF Johnson (Kluwer Academic), pp. 43-63.

  66. ER Dougherty, J Barrera, M Brun, S Kim, RM Cesar, Y Chen, M Bittner, JM Trent (2002), "Inference from clustering with application to gene-expression microarrays", Journal of Computational Biology, 9(1):105-126.
    [ abstract]

  67. S Draghici (2002), "Statistical intelligence: effective analysis of high-density microarray data", Drug Discovery Today, 7(11):S55-S63.

  68. S Draghici (2002), "Data analysis and visualization in DNA microarrays", in Introduction to Bioinformatics: A Theoretical and Practical Approach, eds. S Krawetz and D Womble (Humana Press). (to be published in Aug 2002)

  69. RO Dror, JG Murnick, NA Rinaldi (2002), "A Bayesian approach to transcript estimation from gene array data: The BEAM technique", Proceedings of the Sixth International Conference on Research in Computational Molecular Biology , 137-143.

  70. W Dubitzky, M Granzow, D Berrar (2002), "Data mining and machine learning methods for microarray analysis", in Methods of Microarray Data Analysis , eds. SM Lin, KF Johnson (Kluwer Academic), pp. 5-22.

  71. W Dubitzky, D Berrar, M Granzow, R Eils (2002), "Detecting broad-band and selective correlation patters among gene expression and drug activity data", in Microarray data analysis II, ed. SM Lin and KF Johnson (Kluwer Academic), pp. ?-?.

  72. W Dubitzky, M Granzow, D Berrar (2002), "Comparing symbolic and subsymbolic machine learning approaches to classification of cancer and gene indentification", in Methods of Microarray Data Analysis , eds. SM Lin, KF Johnson (Kluwer Academic), pp. 151-166.

  73. Aimee M Dudley, John Aach, Martin A Steffen, George M Church (2002), "Measuring absolute expression with microarrays with a calibrated reference sample and an extended signal intensity range", Proceedings of the National Academy of Sciences, 99(11):7554-7559.
    [abstract]

  74. Sandrine Dudoit, Jane Fridlyand (2002), "A prediction-based resampling method to estimate the number of clusters in a dataset", Genome Biology, 3(7):0036.

  75. Sandrine Dudoit, Jane Fridlyand, Terry Speed (2002), "Comparison of discrimination methods for the classification of tumors using gene expression data", Journal of the American Statistical Association, 97(457):77-87.

  76. Sandrine Dudoit, YH Yang, B Bolstad (2002), "Using R for the analysis of DNA microarray data", R News (online newsletter), 2(1):24-32.

  77. Sandrine Dudoit, Yee Hwa Yang, Terry Speed, Matthew J Callow (2002) "Statistical methods for identifying differentially expressed genes in replicated cDNA microarray experiments", Statistica Sinica, 12(1):111-139.

  78. BP Durbin, JS Hardin, DM Hawkins, David M Rocke (2002), "A variance-stabilizing transformation for gene-expression microarray data", Bioinformatics, 18(suppl 1):S105-S110.
    [PDF]

  79. Mary E Edgerton, Ronald Taylor, John I Powell, Lawrence Hunter, Richard Simon, Edison T Liu (2002), "A bioinformatics tool to select sequences for microarray studies of mouse models of oncogenesis", Bioinformatics, 18:774-775.

  80. Bradley Efron, Robert Tibshirani (2002), "Empirical bayes methods and false discovery rates for microarrays", Genetic Epidemiology, 23(1):70-86.

  81. P Farbrother, S Muller, AA Noegel, L Eichinger (2002), "Comparison of Probe Preparation Methods for DNA Microarrays", Biotechniques, 33:884-888.

  82. HM Fathallah-Shaykh, M Rigen, LJ Zhao, K Bansal, B He, HH Engelhard, L Cerullo, KV Roenn, R Byrne, L Munoz, GL Rosseau, R Glick, T Lichtor, E DiSavino (2002), "Mathematical modeling of noise and discovery of genetic expression classes in gliomas", Oncogene, 21(47):7164-7174.

  83. AL Feldman, NG Costouros, E Wang, M Qian, FM Marincola, HR Alexander, SK Libutti (2002), "Advantages of mRNA amplification for microarray analysis", Biotechniques, 33:906-914.

  84. Kurt Fellenberg, Nicole C. Hauser, Benedikt Brors, Jörg D. Hoheisel, Martin Vingron (2002), "Microarray data warehouse allowing for inclusion of experiment annotations in statistical analysis", Bioinformatics, 18:423-433.

  85. V Filkov, S Skiena, J Zhi (2002), "Analysis techniques for microarray time-series data", Journal of Computational Biology, 9(2):317-330.
    [ abstract]

  86. David B Finkelstein, Rob Ewing, Jeremy Gollub, Fredrik Sterky, Shauna Somerville, J Michael Cherry (2002), "Iterative linear regression by sector", in Methods of Microarray Data Analysis , eds. SM Lin, KF Johnson (Kluwer Academic), pp. 57-68.

  87. GS Firestein, DS Pisetsky (2002), "DNA microarrays: boundless technology or bound by technology? Guidelines for studies using microarray technology" (editorial), Arthritis & Rheumatism, 46(4):859-861. [PDF]

  88. Charless Fowlkes, Qun Shan, Serge Belongie, Jitendra Malik (2002), "Applying classification separability analysis to microarray data", in Microarray data analysis II, ed. SM Lin and KF Johnson (Kluwer Academic), pp. ?-?.

  89. AP Gasch, MB Eisen (2002), "Exploring the conditional coregulation of yeast gene expression through fuzzy k-means clustering", Genome Biology, 3(11):research0059.

  90. D Gershon (2002), "Microarray technology: an array of opportunities", Nature, 416:885-891.
    [PDF]

  91. D Ghosh (2002), "Singular value decomposition regression models for classification of tumors from microarray experiments", Biocomputing 2002: Proceedings of the Pacific Symposium , 7:18-29.

  92. D Ghosh (2002), "Resampling methods for variance estimation of singular value decomposition analyses from microarray experiments", Functional & Integrative Genomics, 2(3):92-97.

  93. Debashis Ghosh, Arul M Chinnaiyan (2002), "Mixture modelling of gene expression data from microarray experiments", Bioinformatics, 18:275-286.
    [PDF]

  94. networks
    Alex Gilman, Adam P Arkin (2002), "Genetic 'CODE': representations and dynamical models of genetic components and networks ", Annual Review of Genomics and Human Genetics, 3:341-369.

  95. DR Goldstein, E Conlon, D Ghosh (2002), "Statistical issues in the clustering of gene expression data", Statistica Sinica, 12(1):219-240.

  96. GJ Gordon, RV Jensen, LL Hsiao, SR Gullans, JE Blumenstock, S Ramaswamy, WG Richards, DJ Sugarbaker , R Bueno (2002), "Translation of microarray data into clinically relevant cancer diagnostic tests using gene expression ratios in lung cancer and mesothelioma", Cancer Research, 62(17):4963-4967.

  97. G Grant, E Manduchi, C Stoeckert Jr. (2002), "Using non-parametric methods in the context of multiple testing to determine differentially expressed genes", in Methods of Microarray Data Analysis , eds. SM Lin, KF Johnson (Kluwer Academic), pp. 37-56. preprint version: [PDF]

  98. networks
    Paul Grosu, Jeffrey P Townsend, Daniel L Hartl, Duccio Cavalieri (2002), "Pathway Processor: a tool for integrating whole-genome expression results into metabolic networks", Genome Research, 12:1121-1126.
    [ abstract]

  99. SK Gruvberger, M Ringner, P Eden, A Borg, M Ferno, C Peterson, P Meltzer (2002), "Expression profiling to predict outcome in breast cancer: the influence of sample selection", Breast Cancer Research, 5:23-26.

  100. Chi C Gu, DC Rao, Gary Stormo, Chindo Hicks, Michael A Province (2002), "Role of gene expression microarray analysis in finding complex disease genes", Genetic Epidemiology, 23(1):37-56.

  101. L Guyon, J Weston, S Banhill, V Vapnik (2002), "Gene selection for cancer classification using support vector machines", Machine Learning, 46:389-422.

  102. Daniel Hanisch, Alexander Zien, Ralf Zimmer, Thomas Lengauer (2002), "Co-clustering of biological networks and gene expression data", Bioinformatics, 18(suppl 1):S145-S154.

  103. K Harshman and M Sanchez-Carbayo (2002), "The application of DNA microarrays to the study of cancer", Current Genomics, 3(4):363-377.

  104. networks
    AJ Hartemink, DK Gifford, TS Jaakkola, RA Young (2002), "Combining location and expression data for principled discovery of genetic regulatory network models ", Biocomputing 2002: Proceedings of the Pacific Symposium , 7:437-449.

  105. IA Hedenfalk, M Ringner, JM Trent, A Borg (2002), "Gene expression in inherited breast cancer", Advances in Cancer Research, 84:1-34.

  106. J Herrero, R Diaz-Uriarte, J Dopazo (2002), "An approach to inferring transcriptional regulation among genes from large-scale expression data", Comparative and Functional Genomics, 4(1):148-154.
    [ abstract]

  107. J Herrero, J Dopazo (2002), "Combining hierarchical clustering and self-organizing maps for exploratory analysis of gene expression patterns", Journal of Proteome Research, 1(5):467-470.

  108. KR Hess (2002), "Coming to grips with microarray data analysis", Trends in Biotechnology, 20(5):226-227.

  109. Reinhard Hoffmann, Thomas Seidl, Martin Dugas (2002), "Profound effect of normalization on detection of differentially expressed genes in oligonucleotide", Genome Biology, 3(7):research0033.

  110. AJ Holloway, RK van Laar, RW Tothill, DDL Bowtell (2002), "Options available - from start to finish - for obtaining data from DNA microarrays", Nature Genetics, 32 (suppl): 481-489.

  111. Christine E. Horak, Michael Snyder (2002), "Global analysis of gene expression in yeast", Functional & Integrative Genomics, 2(4-5):171-180.

  112. DC Hoyle, M Rattray, R Jupp, A Brass (2002), "Making sense of mRNA abundance distributions from microarray data", Bioinformatics, 18:576-584.
    [PDF ]

  113. Limei Hu, Jing Wang, Keith Baggerly, Hua Wang, Gregory N Fuller, Stanley R Hamilton, Kevin R Coombes, Wei Zhang (2002), "Obtaining reliable information from minute amounts of RNA using cDNA microarrays", BMC Genomics, 3:16.
    [ abstract]

  114. Earl Hubbell, Wei-Min Liu, Rui Mei (2002), "Robust estimators for expression analysis", Bioinformatics, 18:1585-1592.
    [PDF]

  115. W Huber, A von Heydebreck, H Sültmann, A Poustka, M Vingron (2002), "Variance stabilization applied to microarray data calibration and to the quantification of differential expression", Bioinformatics, 18(suppl 1):S96-S104.
    [PDF]

  116. LL Hsiao, RV Jensen, T Yoshida, KE Clark, JE Blumenstock, SR Gullans (2002), "Correcting for signal saturation errors in the analysis of microarray data", Biotechniques, 32:330-336.

  117. X Huang, W Pan (2002), "Comparing three methods for variance estimation with duplicated high density oligonucleotide arrays", Functional & Integrative Genomics, 2(3):126-133.

  118. Daehee Hwang, William A Schmitt, George Stephanopoulos, Gregory Stephanopoulos (2002), "Determination of minimum sample size and discriminatory expression patterns in microarray data", Bioinformatics, 18:1184-1193.

  119. Kyu-Baek Hwang, Dong-Yeon Cho, Sang-Wook Park, Sung-Dong Kim, Byoung-Tak Zhang (2002), "Applying machine learning techniques to analysis of gene expression data: cancer diagnosis", in Methods of Microarray Data Analysis , eds. SM Lin, KF Johnson (Kluwer Academic), pp. 167-182.

  120. I Inza, B Sierra, R Blanco, P Larranaga (2002), "Gene selection by sequential search wrapper approaches in microarray cancer class prediction", Journal of Intelligent and Fuzzy Systems, 12(1):25-34.

  121. Christian Iseli, Brian J Stevenson, Sandro J de Souza, Helena B Samaia, Anamaria A Camargo, Kenneth H Buetow, Robert L Strausberg, Andrew JG Simpson, Philipp Bucher, C Victor Jongeneel (2002), "Long-range heterogeneity at the 3' ends of human mRNAs", Genome Research, 12:1068-1074.
    [ abstract]

  122. Ajay N Jain, Taku A Tokuyasu, Antoine M Snijders, Richard Segraves, Donna G Albertson, Daniel Pinkel (2002), "Fully automatic quantification of microarray image data", Genome Research, 12:325-332.
    [ abstract]

  123. Ronald Jansen, Dov Greenbaum, Mark Gerstein (2002), "Relating whole-genome expression data with protein-protein interactions", Genome Research, 12:37-46.
    [ abstract]

  124. Ho-Youl Jung and Hwan-Gue Cho (2002), "An automatic block and spot indexing with k-nearest neighbors graph for microarray image analysis", Bioinformatics, 18: 141-S151.

  125. Lars Kaderali, Alexander Schliep (2002), "Selecting signature oligonucleotides to identify organisms using DNA arrays", Bioinformatics, 18:1340-1349.

  126. Thomas B Kepler, Lynn Crosby, Kevin T Morgan (2002), "Normalization and analysis of DNA microarray data by self-consistency and local regression", Genome Biology, 3(7):research0037.

  127. M Kathleen Kerr, Cindy Afshari, Lee Bennett, Pierre Bushel, Jeanelle Martinez, Nigel Walker, Gary A Churchill (2002), "Statistical analysis of a gene expression microarray experiment with replication", Statistica Sinica, 12(1):203-218.

  128. Purvesh Khatri, Sorin Draghici, G Charles Ostermeier, Stephen A Krawetz (2002), "Profiling gene expression using onto-express", Genomics, 79(2):266-270

  129. JH Kim, DM Shin, YS Lee (2002), "Effect of local background intensities in the normalization of cDNA microarray data with a skewed expression profiles", Experimental and Molecular Medicine, 34(3):224-232.

  130. H Kim, B Zhao, EC Snesrud, BJ Haas, CD Town, J Quackenbush (2002), "Use of RNA and genomic DNA references for inferred comparisons in DNA microarray analyses", Biotechniques, 33:924-930.

  131. S Kim, ER Dougherty, J Barrera, Y Chen, ML Bittner, JM Trent (2002), "Strong feature sets from small samples", Journal of Computational Biology, 9(1):127-146.

  132. Isaac S Kohane, Alvin Kho, Atul J Butte (2002), Microarrays for an Integrative Genomics (MIT Press).

  133. T Konishi (2002) "Parametric treatment of cDNA microarray data", Genome Informatics, 13:280-281.

  134. C Kooperberg, TG Fazzio, JJ Delrow, T Tsukiyama (2002), "Improved background correction for spotted DNA microarrays", Journal of Computational Biology, 9(1):55-66.
    [ abstract]

  135. Charles Kooperberg, Simonetta Sipione, Michael L LeBlanc, Andrew D Strand, Elena Cattaneo, James M Olson (2002), "Evaluating test statistics to select interesting genes in microarray experiments", Human Molecular Genetics, 11:2223-2232.
    [PDF]

  136. EL Korn, LM McShane, JF Troendle, A Rosenwald, R Simon (2002), "Identifying pre-post chemotherapy differences in gene expression in breast tumours: a statistical method appropriate for this aim", British Journal of Cancer, 86(7):1093-1096.

  137. Ravi Kothapalli, Sean J Yoder, Shrikant Mane, Thomas P Loughran Jr (2002), "Microarray results: how accurate are they? ", BMC Bioinformatics, 3:22.
    [ abstract]

  138. P Krajewski, J Bocianowski (2002), "Statistical methods for microarray assays", Journal of Applied Genetics, 43(3):269-278.

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  288. Christopher Workman, Lars Jensen, Hanne Jarmer, Randy Berka, Laurent Gautier, Henrik Nielser, Hans-Henrik Saxild, Claus Nielsen, Søren Brunak, Steen Knudsen (2002), "A new non-linear normalization method for reducing variability in DNA microarray experiments", Genome Biology, 3(9):research0048.

  289. Thomas D Wu (2002), "Large-scale analysis of gene expression profiles", Briefings in Bioinformatics, 3(1):7-17.

  290. Dong Xu, Guangshan Li, Liyou Wu, Jizhong Zhou, Ying Xu (2002), "PRIMEGENS: robust and efficient design of gene-specific probes for microarray analysis", Bioinformatics, 18:1432-1437.

  291. Ying Xu, Victor Olman, and Dong Xu (2002), "Clustering gene expression data using a graph-theoretic approach: an application of minimum spanning trees ", Bioinformatics, 18:536-545.

  292. CH Yang, BR Bakshi, JF Rathman, PE Blower (2002), "Multiscale and Bayesian approaches to data analysis in genomics high-throughput screening", Current Opinion in Drug Discovery & Development, 5(3):428-438.

  293. Ivana V Yang, Emily Chen, Jeremy P Hasseman, Wei Liang, Bryan C Frank, Shuibang Wang, Vasily Sharov, Alexander I Saeed, Joseph White, Jerry Li, et al. (2002), "Within the fold: assessing differential expression measures and reproducibility in microarray assays", Genome Biology, 3(11):research0062.

  294. YH Yang, MJ Buckley, S Dudoit, TP Speed (2002), "Comparison of methods for image analysis on cDNA microarray data", Journal of Computational and Graphic Statistics, 11:108-136.

  295. YH Yang, T Speed (2002), "Design issues for cDNA microarray experiments", Nature Reviews Genetics, 3(8):579-588.
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  296. YH Yang, S Dudoit, P Luu, DM Lin, V Peng, J Ngai, TP Speed, "Normalization for cDNA microarray data: a robust composite method addressing single and multiple slide systematic variation", Nucleic Acids Research, 30(4):e15.
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  297. application
    Eng-Juh Yeoh, Mary E Ross, Sheila A Shurtleff, W Kent William, Divyen Patel, Rami Mahfouz, Fred G Behm, Susana C Raimondi, Mary V Reilling, Anami Patel, Cheng Cheng, Dario Campana, Dawn Wilkins, Xiaodong Zhou, Jinyan Li, Huiqing Liu, Chin-Hon Pui, William E Evans, Clayton Naeve, Limsoon Wong, James R Downing (2002), "Classification, subtype discovery, and prediction of outcome in pediatric acute lymphoblastic leukemia by gene expression profiling", Cancer Cell, 1:133-143.

  298. networks
    MK Yeung, J Tegner, JJ Collins (2002), "Reverse engineering gene networks using singular value decomposition and robust regression", Proceedings of the National Academy of Sciences, 99(9):6163-6168.
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  299. C Yoo, V Thorsson, GF Cooper (2002), "Discovery of causal relationships in a gene-regulation pathway from a mixture of experimental and observational DNA microarray data", Biocomputing 2002: Proceedings of the Pacific Symposium , 7:498-509

  300. Tony Yuen, Elisa Wurmbach, Robert L Pfeffer, Barbara J Ebersole, Stuart C Sealfon (2002), "Accuracy and calibration of commercial oligonucleotide and custom cDNA microarrays", Nucleic Acids Research, 30(10):e48.
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  301. Matthew A Zapala, Daniel J Lockhart, Daniel G Pankratz, Anthony J Garcia, Carrolee Barlow, David J Lockhart (2002), "Software and methods for oligonucleotide and cDNA array data analysis", Genome Biology ,3(6):software0001.

  302. HP Zhang, CY Yu (2002), "Tree-based analysis of microarray data for classifying breast cancer", Frontiers in Bioscince, 7:C63-C67.

  303. MQ Zhang (2002), "Extracting functional information from microarrays: a challenge for functional genomics" (commentary), Proceedings of the National Academy of Sciences, 99:12509-12511.
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  304. Zhen Zhang, Grier Page, Hong Zhang (2002), "Applying classification separability analysis to microarray data", in Methods of Microarray Data Analysis , eds. SM Lin, KF Johnson (Kluwer Academic), pp. 125-136.

  305. Zhen Zhang, Grier Page, Hong Zhang (2002), "Fishing expedition - a supervised approach to extract patterns from a compendium of expression profiles", in Microarray data analysis II, ed. SM Lin and KF Johnson (Kluwer Academic), pp. ?-?.

  306. Xianghong Zhou, Ming-Chih J Kao, Wing Hung Wong (2003), "Transitive functional annotation by shortest-path analysis of gene expression data", Proceedings of the National Academy of Sciences, 99(20):12783-12788.
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  307. Yingyao Zhou, Ruben Abagyan (2002), "Match-only integral distribution (MOID) algorithm for high-density oligonucleotide array analysis", BMC Bioinformatics, 3:3.
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  308. A Zien, J Fluck, R Zimmer, T Lengauer (2002), "Microarrays: How many do you need?", Proceedings of the Sixth International Conference on Research in Computational Molecular Biology , 321-330.
2002