Microarray


&
Data


Analysis
This is a collection of papers with emphasis on analysis of microarray (a.k.a. DNA chip) data. General reviews on microarray may be included. Analysis of gene network is only occasionally included. However, papers on microarray technology itself are not usually in. Papers on results of microarray expriments are also not emphasized here.


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Last update on November 27, 2002.


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2003

  1. Sorin Draghici, Purvesh Khatri, Rui P Martins, G Charles Ostermeier, Stephen A Krawetz (2003),
    "Global functional profiling of gene expression",
    Genomics, to appear.
    [PDF]
2002

  1. 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. DB Allison, GL Gadbury, M Heo, JR Fernández, CK Lee, TA Prolla, R Weindruch (2002),
    "A mixture model approach for the analysis of microarray gene expression data",
    Computational Statistics & Data Analysis, to appear.

  4. 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.

  5. 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.

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

  7. 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]

  8. Z Bar-Joseph, G Gerber, DK Gifford, TS Jaakkola, I Simon (2002),
    "A new approach to analyzing gene expression time series data",
    in RECOMB 2002: Proceedings of the Sixth Annual International Conference on Computational Biology , ?-? (ACM Press).

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

  10. 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.

  11. 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. ?-?.

  12. 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. ?-?.

  13. M Bilban, LK Buehler, S Head, G Desoye, V Quaranta (2002),
    "Defining signal thresholds in DNA microarrays: exemplary application for invasive cancer",
    BMC Genomics, 3:19.
    [ abstract]

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

  15. 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.

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

  17. 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.

  18. 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.

  19. 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.

  20. 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.

  21. 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. ?-?.

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

  23. Damien Chaussabel, Alan Sher (2002),
    "Mining microarray expression data by literature profiling",
    Genome Biology, 3(10):research0055.1-0055.16.

  24. 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.

  25. 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.

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

  27. 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.

  28. 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.

  29. 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.

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

  31. 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.

  32. 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.

  33. 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. ?-?.

  34. 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.

  35. 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.

  36. 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. ??.

  37. 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), to appear.

  38. 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.

  39. G Didier, P Brezellec, E Rémy, A Hénaut (2002),
    "Gene-ANOVA - gene expression analysis of variance",
    Bioinformatics, in press.

  40. CHQ Ding (2002),
    "Analysis of gene expression profiles: class discovery and leaf ordering",
    in RECOMB 2002: Proceedings of the Sixth Annual International Conference on Computational Biology , 127-136 (ACM Press).
    [ webpage from the author] [PDF]

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

  42. 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.

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

  44. 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.

  45. S Draghici (2002),
    "Statistical intelligence: effective analysis of high-density microarray data",
    Drug Discovery Today, in press.

  46. 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)

  47. RO Dror, JG Murnick, NA Rinaldi (2002),
    "A Bayesian approach to transcript estimation from gene array data: The BEAM technique",
    in RECOMB 2002: Proceedings of the Sixth Annual International Conference on Computational Biology , ?-? (ACM Press).

  48. 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.

  49. 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. ?-?.

  50. 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.

  51. 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.

  52. Sandrine Dudoit, Jane Fridlyand (2002),
    "A prediction-based resampling method to estimate the number of clusters in a dataset",
    Genome Biology, 3(7):0036.1-0036.21.

  53. 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.

  54. Sandrine Dudoit, YH Yang (2002), "Bioconductor R packages for exploratory analysis and normalization of cDNA microarray data",
    in The Analysis of Gene Expression Data: Methods and Software, eds. G Parmigiani, ES Garrett, RA Irizarry and SL Zeger (Springer), to appear.

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

  56. 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.

  57. BP Durbin, JS Hardin, DM Hawkins, DM Rocke (2002),
    "A variance-stabilizing transformation for gene-expression microarray data",
    Bioinformatics, 18:105S-110S.

  58. 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.

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

  60. 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.

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

  62. 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.

  63. 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]

  64. 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. ??.

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

  66. D Ghosh (2002),
    "Singular value decomposition regression models for classification of tumors from microarray experiments",
    PSB02

  67. D Ghosh (2002),
    "Resampling methods for variance estimation of singular value decomposition analyses from microarray experiments",
    Functional and Integrative Genomics, to appear.

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

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

  70. 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.

  71. 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]

  72. 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.

  73. 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.

  74. AJ Hartemink, DK Gifford, TS Jaakkola, RA Young (2002),
    "Combining location and expression data for principled discovery of genetic regulatory network models ",
    PSB02

  75. 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, in press.

  76. 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.

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

  78. Reinhard Hoffmann, Thomas Seidl, Martin Dugas (2002),
    "Profound effect of normalization on detection of differentially expressed genes in oligonucleotide",
    Genome Biology , 3(7):research0033.1 - 0033.11

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

  80. 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, to appear.

  81. 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.

  82. X Huang, W Pan (2002),
    "Comparing three methods for variance estimation with duplicated high density oligonucleotide arrays",
    Functional & Integrative Genomics, to appear.

  83. 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.

  84. Rafael A Irizarry, Bridget Hobbs, Francois Collin, Yasmin D Beazer-Barclay, Kristen J Antonellis, Uwe Scherf, Terence P Speed (2002),
    "Exploration, normalization, adn summaries of high density oligonucleotide array probe level data",
    Biostatistics, to appear.

  85. 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.

  86. 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.

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

  88. 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):research0037.1 - 0037.12

  89. 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.

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

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

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

  93. Charles Kooperberg, Simonetta Sipione, Michael L LeBlanc, Andrew D Strand, Elena Cattaneo, James M Olson (2002),
    "Human evaluating test-statistics to select interesting genes in microarray experiments",
    Molecular Genetics, to appear.

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

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

  96. TC Kroll, S Wölfl (2002),
    "Ranking: a closer look on globalisation methods for normalisation of gene expression arrays",
    Nucleic Acids Research, 30(11):e50.
    [ PDF ]

  97. VA Kuznetsov, GD Knott, RF Bonner (2002),
    "General statistics of stochastic process of gene expression in eukaryotic cells",
    Genetics, 161(3):1321-1332.

  98. Winston Patrick Kuo, Tor-Kristian Jenssen, Atul J Butte, Lucila Ohno-Machado, Isaac S. Kohane (2002),
    "Analysis of matched mRNA measurements from two different microarray technologies ",
    Bioinformatics, 18:405-412.

  99. MP Kurhekar, S Adak, S Jhunjhunwala, K Raghupathy (2002),
    "Genome-wide pathway analysis and visualization using gene expression data ",
    PSB02

  100. J Landgrebe, W Wurst, G Welzl (2002),
    "Permutation-validated principal components analysis of microarray data",
    Genome Biology, 3(4):research0019.

  101. CJ Langmead, AK Yan, CR McClung, BR Donald (2002),
    "Phase-independent rhythmic analysis of genome-wide expression patterns",
    in RECOMB 2002: Proceedings of the Sixth Annual International Conference on Computational Biology , ?-? (ACM Press).

  102. Emmanuel N Lazaridis, Dominic Sinibaldi, Gregory Bloom, Shrikant Mane, Richard Jove (2002),
    "A simple method to improve probe set estimates from oligonucleotide arrays",
    Mathematical Biosciences, 176(1):53-58.

  103. Laura Lazzeroni, Art Owen (2002),
    "Plaid models for gene expression data",
    Statistica Sinica, 12(1):61-86.

  104. ML Lee, W Lu, GA Whitmore, D Beier (2002),
    "Models for microarray gene expression data",
    Journal of Biopharm Stat., 12(1):1-19.

  105. Peter D Lee, Robert Sladek, Celia MT Greenwood, Thomas J Hudson (2002),
    "Control genes and variability: absence of ubiquitous reference transcripts in diverse mammalian expression studies",
    Genome Research, 12:292-297.

  106. YF Leung (2002),
    "Microarray data analysis for dummies... and experts too?",
    Trends in Biochemical Sciences, 27:433-434.

  107. YF Leung (2002),
    "Unravel the mystery of microarray data analysis",
    Trends in Biotechnology, 20(9):366.

  108. Ker-Chau Li, Ming Yan, Shinsheng Yuan (2002),
    "A simple statistical model for depicting the CDC15-synchronized yeast cell-cycle regulated gene expression data",
    Statistica Sinica, 12(1):141-158.

  109. Jinyan Li, Limsoon Wong (2002),
    "Identifying good diagnostic gene groups from gene expression profiles using the concept of emerging patterns",
    Bioinformatics, 18:725-734.

  110. Leping Li, Lee G Pedersen, Thomas A Darden, Clarice Weinberg (2002),
    "Computational analysis of leukemia microarray expression data using the GA/KNN method",
    in Methods of Microarray Data Analysis , eds. SM Lin, KF Johnson (Kluwer Academic), pp. 81-96.

  111. Yi-Ju Li, Ling Zhang, Marcy Speer, Eden Martin (2002),
    "Evaluation of current methods of testing differential gene expression and beyond",
    in Microarray data analysis II, ed. SM Lin and KF Johnson (Kluwer Academic), pp. ?-?.

  112. Wentian Li, Yaning Yang (2002)
    "Zipf's law in importance of genes for cancer classification using microarray Data",
    Journal of Theoretical Biology, 219(4):539-551.
    [PDF].

  113. Wentian Li, Yaning Yang (2002),
    "How many genes are needed for a discriminant microarray data analysis?",
    in Methods of Microarray Data Analysis , eds. SM Lin, KF Johnson (Kluwer Academic), pp. 137-150.
    preprint version: [ MS-WORD]

  114. Wuju Li, Momiao Xiong (2002),
    "Tclass: tumor classification system based on gene expression profile",
    Bioinformatics, 18:325-326.

  115. X Li, W Gu, S Mohan, DJ Baylink (2002),
    "DNA microarrays: their use and misuse",
    Microcirculation, 9(1):13-22.

  116. Wolfram Liebermeister (2002),
    "Linear modes of gene expression determined by independent component analysis",
    Bioinformatics, 18:51-60.

  117. Simon M Lin, Kimberly F Johnson (2002),
    Methods of Microarray Data Analysis: Papers from CAMDA'00 (Kluwer Academic).
    [ link to amazon ]

  118. Simon M Lin, Xuejun Liao, Patrick McConnell, Korkut Vata, Lawrence Carin, Pascal Goldschmidt (2002),
    "Using functional genomic units to corroborate user experiments with the Rosetta compendium",
    in Microarray data analysis II, ed. SM Lin and KF Johnson (Kluwer Academic), pp. 91-103.

  119. I Lonnstedt, T Speed (2001),
    "Replicated microarray data",
    Statistica Sinica, 12(1):31-46.

  120. Brad Love, David R Rank, Sharron G Penn, David A Jenkins, Russell S Thomas (2002),
    "A conditional density error model for the statistical analysis of microarray data",
    Bioinformatics, 18:1064-1072.

  121. J Lu, S Hardy, W Tao, S Muse, B Weir, S Spruill (2002),
    "Classical statistical approaches to molecular classification of cancer from gene expression profiling",
    in Methods of Microarray Data Analysis , eds. SM Lin, KF Johnson (Kluwer Academic), pp. 97-108.

  122. Philippe Marc and Claude Jacq (2002),
    "Arrayplot for visualization and normalization of cDNA microarray data ",
    Bioinformatics, 18:888-889.

  123. DR Masys (2002),
    "Database designs for microarray data",
    Pharmacogenomics, 1(4):232-233.

  124. A Mateos, J Herrero, J Dopazo (2002),
    "Using perceptrons for supervised classification of DNA microarray samples: obtaining the optimal level of information and finding differentially expressed genes",
    Artifitial Neural Networks - ICANN 2002 (Springer), pp. 577-582.

  125. A Mateos, J Herrero, J Tamames, J Dopazo (2002)
    "Supervised neural networks for clustering conditions in DNA array data after reducing noise by clustering gene expression profiles",
    in Microarray data analysis II, ed. SM Lin and KF Johnson (Kluwer Academic), pp. 91-103.

  126. GJ McLachlan, RW Bean, D Peel (2002),
    "A mixture model-based approach to the clustering of microarray expression data",
    Bioinformatics, 18:413-422.

  127. MA Mendez, C Hodar, C Vulpe, M Gonzalez, V Cambiazo (2002),
    "Discriminant analysis to evaluate clustering of gene expression data",
    FEBS Letts, 522(1-3):24-28.

  128. Jatin Misra, William Schmitt, Daehee Hwang, Li-Li Hsiao, Steve Gullans, George Stephanopoulos, Gregory Stephanopoulos (2002)
    "Interactive exploration of microarray gene expression patterns in a reduced dimensional space",
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