Bibliography on
Microarray Data Analysis

front| books | preprints |
2008 | 2007 | 2006 | 2005 | 2004 | 2003 | 2002 | 2001 | 2000 |
1999 | 1998 | 1997 | 1996 | 1995 | 1994 | 1993 |
core facilities| data| mailing | programs(free) |
analysis groups | labs | companies | short-courses| lists | mirror

© Copyright, 1999-2007 Wentian Li
of North Shore LIJ Research Institute

http://www.nslij-genetics.org/microarray/
2001

  1. John Aach, George M Church (2001), "Aligning gene expression time series with time warping algorithms ", Bioinformatics, 17:495-508. [PDF]

  2. Karl E Adler, Mary C Tyler, Alvydas Mikulskis, Mike O'Malley, Jeff J Broadbent, Eva E Golenko, Andy L Johnson, Steve Lott, Anis H Khimani, Mark N Bobrow (2001) "Signal amplification on microarrays: techniques and advances in tyramide signal amplification (TSA)", Proceedings of SPIE, 4266:96-102.

  3. Orly Alter, Patrick O Brown, David Botstein (2001), "Processing and modeling genome-wide expression data using singular value decomposition", Proceedings of SPIE, 4266:171-186.

  4. KA Baggerly, KR Coombes, KR Hess, DN Stivers, LV Abruzzo, W Zhang (2001), "Identifying differentially expressed genes in cDNA microarray experiments", Journal of Computational Biology, 8(6):639-659.
    [ abstract]

  5. Yoganand Balagurunathan, Edward R Dougherty, Yidong Chen, Michael L Bittner Jeffrey M Trent (2001), "Random signal model for cDNA microarrays", Proceedings of SPIE, 4266:163-170.

  6. P Baldi, AD Long (2001), "A Bayesian framework for the analysis of microarray expression data: regularized t-test and statistical inferences of gene changes", Bioinformatics, 17:509-519. [PDF]

  7. Y Barash, N Friedman (2001), "Context-specific Bayesian clustering for gene expression data", Proceedings of the Fifth International Conference on Research in Computational Molecular Biology , pp.12-20.

  8. KG Becker (2001), "The sharing of cDNA microarray data", Nature Reviews Neuroscience, 2:438-440.

  9. A Ben-Dor, N Friedman, Z Yakhini (2001), "Class discovery in gene expression data", Proceedings of the Fifth International Conference on Research in Computational Molecular Biology , pp.31-38.

  10. Tracy Bergemann, Filemon Quiaoit, Jeffery J Delrow, Lue Ping Zhao (2001), "Statistical issues in signal extraction from microarrays", Proceedings of SPIE, 4266:24-34.

  11. Arindam Bhattacharjee, William G Richards, Jane Staunton, Cheng Li, Stefano Monti, Priya Vasa, Christine Ladd, Javad Beheshti, Raphael Bueno, Michael Gillette, Massimo Loda, Griffin Weber, Eugene J Mark, Eric S Lander, Wing Wong, Bruce E Johnson, Todd R Golub, David J Sugarbaker, Matthew Meyerson (2001), "Classification of human lung carcinomas by mRNA expression profiling reveals distinct adenocarcinoma subclasses", Proceedings of the National Academy of Sciences, 98(24):13790-13795.
    [abstract]

  12. James Borneman, Marek Chrobak, Gianluca Della Vedova, Andres Figueroa, Tao Jiang (2001), "Probe selection algorithms with applications in the analysis of microbial communities ", Bioinformatics, 17:39S-48S.

  13. S Bortoluzzi, F d'Alessi, C Romualdi, G A Danieli (2001), "Differential expression of genes coding for ribosomal proteins in different human tissues", Bioinformatics, 17:1152-1157.

  14. GS Bova, G Parmigiani, JI Epstein, T Wheeler, NR Mucci, MA Rubin (2001), "Web-based tissue microarray image data analysis: initial validation testing through prostate cancer Gleason grading", Hum Pathol. 32(4):417-427.

  15. Norbert Braendle, Horst Bischof, Hilmar Lapp (2001), "Generic and robust approach for the analysis of spot array images", Proceedings of SPIE, 4266:1-12.

  16. Alvis Brazma, Pascal Hingamp, John Quackenbush, Gavin Sherlock, Paul Spellman, Chris Stoeckert, John Aach, Wilhelm Ansorge, Catherine A Ball, Helen C Causton, Terry Gaasterland, Patrick Glenisson, Frank CP Holstege, Irene F Kim, Victor Markowitz, John C. Matese, Helen Parkinson, Alan Robinson, Ugis Sarkans, Steffen Schulze-Kremer, Jason Stewart, Ronald Taylor, Jaak Vilo, Martin Vingron (2001), "Minimum information about a microarray experiment (MIAME)-toward standards for microarray data", Nature Genetics, 29:365-371.

  17. Bobby-Joe Breitkreutz, Paul Jorgensen1, Ashton Breitkreutz, Mike Tyers (2001), "AFM 4.0: a toolbox for DNA microarray analysis", Genome Biology, 2(8):software0001.1-0001.3

  18. CS Brown, PC Goodwin, PK Sorger (2001), "Image metrics in the statistical analysis of DNA microarray data ", Proceedings of the National Academy of Sciences, 98(16):8944-8949.
    [abstract] [PDF]

  19. Pierre R Bushel, Hisham Hamadeh, Lee Bennett, Stella Sieber, Karla Martin, Emile F Nuwaysir, Kate Johnson, Kelli Reynolds, Richard S Paules, Cynthia A Afshari (2001), "MAPS: a microarray project system for gene expression experiment information and data validation", Bioinformatics, 17:564-565.
    [ webpage from the authors: dir.niehs.nih.gov/microarray/software/maps/]

  20. AJ Butte, J Ye, G Niederfellner, K Rett, HU Häring, MF White, and IS Kohane (2001), "Determining significant fold differences in gene expression analysis", Biocomputing 2001: Proceedings of the Pacific Symposium , 6:6-17.
    [PDF]

  21. affymetrix
    Eugene Chudin, Randal Walker, Alan Kosaka, Sue X Wu, Douglas Rabert, Thomas K Chang, Dirk E Kreder (2001), "Assessment of the relationship between signal intensities and transcript concentration for Affymetrix GeneChip arrays", Genome Biology, 3(1): research0005.1-0005.10

  22. Marco Crescenzi, Alessandro Giuliani (2001), "The main biological determinants of tumor line taxonomy elucidated by a principal component analysis of microarray data", FEBS Letters, 507:114-118.

  23. David J Cutler, Michael E Zwick, Minerva M Carrasquillo, Christopher T Yohn, Katherine P Tobin, Carl Kashuk, Debra J Mathews, Nila A Shah, Evan E Eichler, Janet A Warrington, Aravinda Chakravarti (2001), "High-Throughput Variation Detection and Genotyping Using Microarrays ", Genome Research, 11:1913-1925.
    [ abstract]

  24. S Datta (2001), "Exploring relationships in gene expressions: A partial least squares approach", Gene Expression, 9:257-264.

  25. Glena Delenstarr, Herb Cattell, Chao Chen, Andreas N Dorsel, Robert H Kincaid, Khanh Nguyen, Nicholas M Sampas, Shad Schidel, Karen W Shannon, Andrea Tu, Paul K Wolber (2001) "Estimation of the confidence limits of oligonucleotide-array-based measurements of differential expression", Proceedings of SPIE, 4266:120-131.

  26. J Dopazo, E Zanders, I Dragoni, G Amphlett, F Falciani (2001), "Methods and approaches in the analysis of gene expression data", Journal of Immunol Meth. 250:93-112.

  27. Edward R Dougherty, Junior Barrera, Marcel Brun, Seungchan Kim; Roberto M Cesar, Yidong Chen, Michael L Bittner, Jeffery M Trent (2001), "Time series inference from clustering", Proceedings of SPIE, 4266:222-227.

  28. S Draghici (2001), "DNA arrays: the steam engine of the 21st century?", ACM SIGBIO Newsletter, 21(1):2-9.

  29. S Draghici (2001), "Data analysis and visualization in DNA microarrays", in Introduction to Bioinformatics, eds. S Krawetz, D Womble (Humana Press).

  30. S Draghici , A Kuklin, B Hoff, S Shams (2001), "Experimental design, analysis of variance and slide quality assessment in gene expression arrays", Current Opinion in Drug Discovery & Development, 4(3):332-337. [PDF]

  31. B Dysvik, I Jonassen (2001), "J_Express: exploring gene expression data using Java", Bioinformatics, 17:369-370.

  32. B Efron, R Tibshirani, JD Storey, V Tusher (2001), "Empirical Bayes analysis of a microarray experiment", Journal of the American Statistical Association, 96:1151-1160.

  33. Paul H Eilers, Judith M Boer, Gert-Jan van Ommen, Hans C van Houwelingen (2001), "Classification of microarray data with penalized logistic regression", Proceedings of SPIE, 4266:187-198.

  34. Rob M Ewing, J Michael Cherry (2001), "Visualization of expression clusters using Sammon's non-linear mapping", Bioinformatics, 17:658-659.

  35. K Fellenberg, NC Hauser, B Brors, A Neutzner, JD Hoheisel, M Vingron (2001), "Correspondence anaylsis applied to microarray data", Proceedings of the National Academy of Sciences, 98:10781-10786.
    [abstract]

  36. V Filkov, S Skiena, J Zhi (2001), "Analysis techniques for microarray time-series data", Proceedings of the Fifth International Conference on Research in Computational Molecular Biology , pp.124-131.

  37. database
    M Gardiner-Garden, TG Littlejohn (2001), "A comparison of microarray databases", Briefings in Bioinformatics, 2(2):143-158.
    [ abstract ]

  38. DH Geschwind (2001), "Sharing gene expression data: an array of options", Nature Reviews Neuroscience, 2:435-438.

  39. AB Goryachev, PF Macgregor, AM Edwards (2001), "Unfolding of microarray data", Journal of Computational Biology, 8(4):443-461.
    [ abstract]

  40. Alexander J Hartemink, David K Gifford, Tommi S Jaakkola, Richard A Young (2001), "Maximum-likelihood estimation of optimal scaling factors for expression array normalization", Proceedings of SPIE, 4266:132-140.

  41. Trevor Hastie, Robert Tibshirani, David Botstein, Patrick Brown (2001), "Supervised harvesting of expression trees", Genome Biology, 2(1): research0003.1-0003.12.
    [PDF]

  42. Javier Herrero, Alfonso Valencia, and Joaquín Dopazo (2001), "A hierarchical unsupervised growing neural network for clustering gene expression patterns", Bioinformatics, 17:126-136. [PDF]

  43. Hanspeter Herzel, Dieter Beule, Szymon Kielbasa, Jan Korbel, Christine Sers, Arif Malik, Holger Eickhoff, Hans Lehrach, and Johannes Schuchhardt (2001), "Extracting information from cDNA arrays", Chaos, 11(1):98-107.
    [PDF]

  44. Andrew A Hill, Eugene L Brown, Maryann Z Whitley, Greg Tucker-Kellogg, Craig P Hunter, Donna K Slonim (2001), "Evaluation of normalization procedures for oligonucleotide array data based on spiked cRNA controls", Genome Biology, 2(12):research0055.1-0055.13

  45. NS Holter, A Maritan, M Cieplak, NV Fedoroff, JR Banavar (2001), "Dynamic modeling of gene expression data", Proceedings of the National Academy of Sciences, 98(4):1693-1698.
    [abstract] [PDF]

  46. Katsuhisa Horimoto and Hiroyuki Toh (2001), "Statistical estimation of cluster boundaries in gene expression profile data ", Bioinformatics, 17: 1143-1151.

  47. Ying Huang, Manju Prasad, William J Lemon, Heather Hampel, Fred A Wright, Karl Kornacker, Virginia LiVolsi, Wendy Frankel, Richard T Kloos, Charis Eng, Natalia S Pellegata, Albert de la Chapelle (2001), "Gene expression in papillary thyroid carcinoma reveals highly consistent profiles", Proceedings of the National Academy of Sciences, 98(26):15044-15049.
    [abstract]

  48. Lawrence Hunter, Ronald Taylor, Sonia M Leach, Richard Simon (2001), "GEST: A gene expression search tool based on a novel Bayesian similarity metric ", Bioinformatics, 17(suppl 1):S115-S122.

  49. TR Hvidsten, J Komorowski, AK Sandvik, and A Lægreid (2001), "Predicting gene function from gene expressions and ontologies", Biocomputing 2001: Proceedings of the Pacific Symposium , 6:299-310.

  50. RA Irizarry, P Parmigiani, M Guo, T Dracheva, J Jen (2001), "A statistical analysis of radiolabeled gene expression data", Proceedings of Interface 2001, pages ?-?.

  51. TK Jenssen et al. (2001), "A literature network of human genes for high-thtoughput analysis of gene expression Nature Genetics, 28:21-28. (2001).

  52. James R Johnson, Patrick Hurban, Jeff Woessner, Craig M Liddell (2001), "Statistical approaches to analyzing multichip data", Proceedings of SPIE, 4266:199-206.

  53. Kimberly F Johnson, Simon M Lin (2001), "Critical Assessment of Microarray Data Analysis: the 2001 challenge ", Bioinformatics, 17:857-858.

  54. Thomas Kämpke, Markus Kieninger, Michael Mecklenburg (2001), "Efficient primer design algorithms ", Bioinformatics, 17: 214-225.

  55. M Kathleen Kerr, Gary A Churchill (2001), "Statistical design and the analysis of gene expression microarrays, ", Genetical Research, 77(2):123-128. [PDF]

  56. M Kathleen Kerr, Gary A Churchill (2001), "Experimental design for gene expression microarrays,", Biostatistics, 2:183-201.

  57. M Kathleen Kerr, Gary A Churchill (2001), "Bootstrapping cluster analysis: assessing the reliability of conclusions from microarray experiments", Proceedings of the National Academy of Sciences, 98:8961-8965.
    [abstract] [PDF]

  58. M Kathleen Kerr, Edward Leiter, Laurent Picard, Gary A Churchill (2001) "Analysis of a designed microarray experiment", Proceedings of the IEEE-EURASIP Nonlinear Signal and Image Processing Workshop (June 3-6, 2001).

  59. Laura M Kegelmeyer, Lisa Tomascik-Cheeseman, Melina S Burnett, Paul van Hummelen, Andrew J Wyrobek (2001), "Groundtruth approach to accurate quantitation of fluorescence microarrays", Proceedings of SPIE, 4266:35-45.

  60. J Khan, J S Wei, M Ringnér, L H Saal, M Ladanyi, F Westermann, F Berthold, M Schwab, C R Antonescu, C Peterson & P S Meltzer (2001), "Classification and diagnostic prediction of cancers using gene expression profiling and artificial neural networks", Nature Medicine, 7(6):673-679.

  61. JH Kim, L Ohno-Machado, and IS Kohane (2001), "Unsupervised learning from complex data: the matrix incision tree algorithm", Biocomputing 2001: Proceedings of the Pacific Symposium , 6:30-41.
    [PDF]

  62. Seungchan Kim, Edward R Dougherty, Junior Barrera, Yidong Chen, Michael L Bittner, Jeffery M Trent (2001), "Finding robust linear expression-based classifiers", Proceedings of SPIE, 4266:207-212.

  63. application
    U Klein, Y Tu, GA Stolovitzky, M Mattioli, G Cattoretti, H Husson, A Freedman, G Inghirami, L Cro, L Baldini, A Neri, A Califano, R Dalla-Favera (2001), "Gene expression profiling of B cell chronic lymphocytic leukemia reveals a homogeneous phenotype related to memory B cells", Journal of Experimental Medicine, 194(11):1625-1638.

  64. GT Klus, A Song, A Schick, M Wahde, and Z Szallasi (2001), "Mutual information analysis as a tool to assess the role of aneuploidy in the generation of cancer-associated differential gene expression patterns", Biocomputing 2001: Proceedings of the Pacific Symposium , 6:42-51.
    [PDF]

  65. Vladimir A Kuznetsov (2001), "Distribution associated with stochastic processes of gene exxpression in a single eukaryotic cell", EURASIP Journal on Applied Signal Processing, 4:285-296.
    [PDF]

  66. Jae K Lee, Uwe Scherf, Lawrence H Smith, Lorraine Tanabe, John N Weinstein, (2001), "Analysis of gene expression data of the NCl 60 cancer cell lines using Bayesian hierarchical effects model", Proceedings of SPIE, 4266:228-235.

  67. YF Leung, DS Lam, CP Pang (2001), "The miracle of microarray data analysis", Genome Biology, 2:reports4021.

  68. YF Leung, CP Pang CP (2001), "All aboard the chip!", Trends in Biotechnology, 10:430-431.

  69. affymetrix
    Cheng Li, Wing Hung Wong (2001), "Model-based analysis of oligonucleotide arrays: expression index computation and outlier detection", Proceedings of the National Academy of Sciences, 98:31-36.
    [abstract] [PDF]

  70. affymetrix
    Cheng Li, Wing Hung Wong (2001), "Model-based analysis of oligonucleotide arrays: model validation, design issues and standard error application", Genome Biology , 2(8):research0032.1-0032.11. [PDF]

  71. F Li, GD Stormo (2001), "Selection of optimal DNA oligos for gene expression arrays", Bioinformatics, 17:1067-1076.

  72. Hongzhe Li, Fangxin Hong (2001), "Cluster-Rasch models for microarray gene expression data", Genome Biology , 2(8):research0031.1-0031.13. [PDF]

  73. Jinyan Li, Limsoon Wong (2001), "Emerging patterns and gene expression data", Genome Informatics, 12:3-13.

  74. Leping Li, Clarice R Weinberg, Thomas A Darden, Lee G Pedersen (2001), "Gene selection for sample classification based on gene expression data: study of sensitivity to choice of parameters of the GA/KNN method ", Bioinformatics, 17:1131-1142.

  75. Juan Liu, Hitoshi Iba, Mitsuru Ishizuka (2001), "Selecting informative genes with parallel genetic algorithms in tissue classification", Genome Informatics, 12:14-23.

  76. Wei-min Liu, Rui Mei, Daniel M Bartell, Xiaojun Di, Teresa A Webster, Tom Ryder (2001), "Rank-based algorithms for anlaysis of microarrays", Proceedings of SPIE, 4266:56-67.

  77. AD Long, HJ Mangalam, BYP Chan, L Tolleri, GW Hatfield, P Baldi (2001), "Genome expression profiling in Esherichia coli K12: improved statistical inference from DNA microarray data using analysis of variance and a Bayesian statistical framework", Journal of Biological Chemistry, 276:19937-19944.

  78. protein
    Angelika Lueking , Zoltan Konthur, Holger Eickhoff, Konrad Bussow, Hans Lehrach, Dolores J Cahill (2001), "Protein microarrays - a tool for the post-genomic era", Current Genomics, 2(2):151-159.

  79. Stanley D Luck (2001), "Normalization and error estimation for biomedical expression patterns", Proceedings of SPIE, 4266:153-157.

  80. AV Lukashin, R Fuchs (2001), "Analysis of temporal gene expression profiles: clustering by simulated annealing and determining the optimal number of clusters", Bioinformatics, 17:405-414.

  81. database
    H Mangalam, J Stewart, J Zhou, K Schlauch, M Waugh, G Chen, AD Farmer, G Colello, JW Weller (2001), "GeneX: an open source gene expression database and integrated tool set", IBM System Journal, 40(2):552-569.

  82. database
    Elisabetta Manduchi, Angel Pizarro, Christian Stoeckert (2001), "RAD (RNA abundance database): an infrastructure for array data analysis", Proceedings of SPIE, 4266:68-78.

  83. DR Masys, JB Welsh, JL Fink, M Gribskov, I Klacansky, J Corbeil (2001), "Use of keyword hierarchies to interpret gene expression patterns", Bioinformatics, 17:319-326.

  84. Jason C Mills, Jeffrey I Gordon (2001), "A new approach for filtering noise from high-density oligonucleotide microarray datasets", Nucleic Acids Research, 29(15):e72.
    [PDF]

  85. DM Mutch, A Berger, R Mansourian, A Rytz, MA Roberts (2001), "Microarray data analysis: a practical approach for selecting differentially expressed genes", Genome Biology, 2(12):preprint0009

  86. Robert Nadon, Peide Shi, Adonis Skandalis, Erik Woody, Hermann Hubschle, Edward Susko, Nezar Rghei, Peter Ramm (2001), "Statistical inference methods for gene expression arrays", Proceedings of SPIE, 4266:46-55.

  87. MA Newton, CM Kendziorski, CS Richmond, FR Blattner, KW Tsui (2001), "On differential variability of expression ratios: improving statistical inference about gene expression changes from microarray data", Journal of Computational Biology, 8(1):37-52.
    [ abstract] [PDF] [ webpage from the authors: www.stat.wisc.edu/~newton/papers/abstracts/btr139a.html]

  88. PJ Park, M Pagano, and M Bonetti (2001), "A nonparametric scoring algorithm for identifying informative genes from microarray data", Biocomputing 2001: Proceedings of the Pacific Symposium , 6:52-63.
    [PDF]

  89. Paul Pavlidis, William S Noble (2001), "Analysis of strain and regional variation in gene expression in mouse brain", Genome Biology, 2(10): research0042.1-0042.15.

  90. P Pavlidis, J Weston, J Cai, and WN Grundy (2001), "Gene functional classification from heterogeneous data", Proceedings of the Fifth International Conference on Research in Computational Molecular Biology , pp.249-255.
    [PDF]

  91. Dana Pe'er,Aviv Regev, Gal Elidan, Nir Friedman (2001), "Inferring subnetworks from perturbed expression profiles", ISMB'01 , or Bioinformatics, 17(suppl 1):S215-S224.

  92. Paul J Planet, Rob DeSalle, Mark Siddall, Timothy Bael, Indra Neil Sarkar, Scott E. Stanley (2001), "Systematic analysis of DNA microarray data: ordering and interpreting patterns of gene expression", Genome Research, 11:1149-1155.

  93. J Quackenbush (2001), "Computational analysis of microarray analysis", Nature Reviews Genetics, 2:418-427.

  94. Günter Raddatz, Michaela Dehio, Thomas F. Meyer, Christoph Dehio (2001), "PrimeArray: genome-scale primer design for DNA-microarray construction ", Bioinformatics, 17:98-99.

  95. Sridhar Ramaswamy, Pablo Tamayo, Ryan Rifkin, Sayan Mukherjee, Chen-Hsiang Yeang, Michael Angelo, Christine Ladd, Michael Reich, Eva Latulippe, Jill P Mesirov, Tomaso Poggio, William Gerald, Massimo Loda, Eric S Lander, Todd R Golub (2001), "Multiclass cancer diagnosis using tumor gene expression signatures", Proceedings of the National Academy of Sciences, 98:15149-15154.
    [abstract]

  96. Latha Ramdas, Kevin R Coombes, Keith Baggerly, Lynne Abruzzo, W Edward Highsmith, Tammy Krogmann, Stanley R Hamilton, Wei Zhang (2001), "Sources of nonlinearity in cDNA microarray expression measurements", Genome Biology, 2(11): research0047.1-0047.7

  97. S Raychaudhuri, P D Sutphin, J T Chang, R B Altman(2001), "Basic microarray analysis: Grouping and feature reduction", Trends in Biotechnology, 19(5):189-193.

  98. Ben Y Reis, Atul S Butte, Isaac S Kohane (2001), "Extracting knowledge from dynamics in gene expression", Journal of Biomedical Informatics, 34(1):15-27.

  99. David Rocke, Blythe Durbin "A model for measurement error for gene expression arrays", Journal of Computational Biology, 8(6):557-569.
    [ abstract] [PDF]

  100. Frederick P. Roth (2001), "Bringing out the best features of expression data" (insight/outlook), Genome Research, 11:1801-1802.

  101. affymetrix
    Eric E Schadt, Cheng Li, Byron Ellis, Wing H Wong (2001), "Feature extraction and normalization algorithms for high-density oligonucleotide gene expression array data", Journal of Cellular Biochemistry, 84(S37):120-125. [PDF]

  102. affymetrix
    Eric Schadt, Cheng Li, Cheng Su and Wing Hung Wong (2001), "Analyzing high-density oligonucleotide gene expression array data", Journal of Cellular Biochemistry, 80:192-202.

  103. Eran Segal, Ben Taskar, Audrey Gasch, Nir Friedman, Daphne Koller (2001), "Rich probabilistic models for gene expression", ISMB'01

  104. A Sekowska, S Robin , JJ Daudin, A Henaut, A Danchin (2001) "Extracting biological information from DNA arrays: an unexpected link between arginine and methionine metabolism in Bacillus subtilis", Genome Biology, 2:?-?.

  105. G Sherlock (2001), "Analysis of large-scale gene expression data", Briefings in Bioinformatics, 2(4):350-62.

  106. database
    G Sherlock, T Hernandez-Boussard, A Kasarskis, G Binkley, JC Matese, SS Dwight, M Kaloper, S Weng, H Jin, CA Ball, MB Eisen, PT Spellman, PO Brown, D Botstein, JM Cherry (2001), "The Stanford microarray database", Nucleic Acids Research, 29(1):152-155.
    [PDF] [ webpage from the authors: genome-www4.stanford.edu/MicroArray/SMD/]

  107. DD Shoemaker, EE Schadt, et al. (2001), "Experimental annotation of the human genome using microarray technology", Nature, 409:922-927. [PDF]

  108. James N Siedow (2001), "Making sense of microarray" (meeting report), Genome Biology, 2(2): reports4003.1-4003.2
    [ html ] [PDF]

  109. R Sásik, T Hwa, N Iranfar, and WF Loomis (2001) "Percolation clustering: a novel algorithm applied to the clustering of gene expression patterns in dictyostelium development", Biocomputing 2001: Proceedings of the Pacific Symposium , 6:335-347.
    [PDF]

  110. PT Spellman (2001), "The future of publishing microarray data", Briefings in Bioinformatics, 2(4):316-318.

  111. Matthias Steinfath, Wasco Wruck, Henrik Seidel, Hans Lehrach, Uwe Radelof, and John O'Brien (2001), "Automated image analysis for array hybridization experiments ", Bioinformatics, 17:634-641.
    [PDF]

  112. C Stoeckert, A Pizarro, E Manduchi, M Gibson, B Brunk, J Crabtree, J Schug, S Shen-Orr, GC Overton (2001), "A relational schema for both array-based and SAGE gene expression expriments", Bioinformatics, 17:300-308.

  113. Edward B Suh, Edward R Dougherty, Seungchan Kim, Daniel E Russ, Robert L Martino (2001), "Parallel computing methods for analyzing gene expression relationships", Proceedings of SPIE, 4266:213-221.

  114. J Theilhaber, S Bushnell, A Jackson, R Fuchs (2001) "Bayesian estimation of fold-changes in the analysis of gene expression: the PFOLD algorithm", Journal of Computational Biology, 8(6):585-614.
    [ abstract]

  115. Jeffrey G Thomas, James M Olson, Stephen J Tapscott, Lue Ping Zhao (2001), "An efficient and robust statistical modeling approach to discover differentially expressed genes using genomic expression profiles", Genome Research, 11:1227-1236.
    [ abstract]

  116. S Tomiuk, K Hofmann (2001), "Microarray probe selection strategies", Briefings in Bioinformatics, 2(4):329-340.

  117. O Troyanskaya, M Cantor, G Sherlock, P Brown, T Hastie, R Tibshirani, D Botstein, R B Altman (2001), "Missing value estimation methods for DNA microarrays", Bioinformatics, 17(6):520-525. [PDF]

  118. J Tsai, R Sultana, Y Lee, G Pertea, S Karamycheva, V Antonescu, J Cho, B Parvizi, F Cheung, J Quackenbush (2001), "RESOURCERER: a database for annotating and linking microarray resources within and across species", Genome Biology, 2(11):software0002

  119. George C Tseng, Min-Kyu Oh, Lars Rohlin, James C Liao, Wing Hung Wong (2001), "Issues in cDNA microarray analysis: quality filtering, channel normalization, models of variation and assessment of gene effects", Nucleic Acids Research, 29(12):2549-2557.
    [PDF]

  120. V G Tusher, R Tibshirani, G Chu (2001), "Significance analysis of microarrays applied to the ionizing radiation response", Proceedings of the National Academy of Sciences, 98(9):5116-5121.
    [abstract]

  121. Mark J Van Der Laan, Jenny Bryan (2001), "Gene expression analysis with the parametric bootstrap", Biostatistics, 2:445-461.

  122. Kimmo Virtaneva, Fred A Wright, Stephan M Tanner, Bo Yuan, William J Lemon, Michael A Caligiuri, Clara D Bloomfield, Albert de la Chapelle, and Ralf Krahe (2001), "Expression profiling reveals fundamental biological differences in acute myeloid leukemia with isolated trisomy 8 and normal cytogenetics", Proceedings of the National Academy of Sciences, 98(3):1124-1129.
    [abstract]

  123. David Venet, F Pecasse, C Maenhaut, H Bersini (2001), "Separation of samples into their constituents using gene expression data ", ISMB'01

  124. Tuan Vo-Dinh, Minoo Askari (2001), "Micro arrays and biochips: applications and potential in genomics and proteomics", Current Genomics, 2(4):399-415.

  125. J Vohradsky (2001), "Neural network model of gene expression", FASEB Journal, 15:846-854.

  126. Anja von Heydebreck, Wolfgang Huber, Annemarie Poustka, M.Vingron (2001), "Identifying splits with clear separation: a new class discovery method for gene expression data ", ISMB'01 and, Bioinformatics, 17(suppl 1):107-114.

  127. Michael E Wall, Patricia A Dyck, Thomas S Brettin (2001), "SVDMAN - singular value decomposition analysis of microarray data", Bioinformatics, 17:566-568.
    [PDF] [ webpage from the authors: public.lanl.gov/mewall/svdman/]

  128. Xujing Wang, Soumitra Ghosh, and Sun-Wei Guo (2001), "Quantitative quality control in microarray image processing and data acquisition", Nucleic Acids Research, 29(15):e75.

  129. Mike West, Carrie Blanchette, Holly Dressman, Erich Huang, Seiichi Ishida, Rainer Spang, Harry Zuzan, Jeffrey R. Marks, Joseph R. Nevins (2001), "Predicting the clinical status of human breast cancer using gene expression profiles", Proceedings of the National Academy of Sciences, 98:11462-11467.
    [abstract]

  130. J Weston, S Mukherjee, O Chapelle, M Pontil, T Poggio, V Vapnik (2001), "Feature selection for SVMs", Advances in Neural Information Processing Systems (MIT Press), eds. Todd K Leen, Thomas G Dietterich, Volker Tresp, pages 668-674.

  131. Kevin White (2001), "Functional genomics and the study of development, variation and evolution", Nature Reviews Genetics, 2:528-537.

  132. DA Wigle, J Rossant, I Jurisica (2001), "Mining mouse microarray data", Genome Biology, 2(7):review1019.1.1-1019.4

  133. RD Wolfinger, G Gibson, ED Wolfinger, L Bennett, H Hamadeh, P Bushel, C Afshari, RS Paules (2001), "Assessing gene significance from cDNA microarray expression data via mixed models", Journal of Computational Biology, 8(6):625-637.
    [ abstract]

  134. TD Wu (2001), "Analysing gene expression data from DNA microarrays to identify candidate genes", Journal of Pathology, 195:53-65.

  135. Xuhua Xia, Zheng Xie (2001), "AMADA: analysis of microarray data", Bioinformatics, 17(6):569-590.
    [ webpage from the authors: web.hku.hk/~xxia/software/AMADA.htm]

  136. Eric P Xing, Richard M Karp (2001), "CLIFF: clustering of high-dimensional microarray data via iterative feature filtering using normalized cuts", ISMB'01.
    [PDF]

  137. Eric P Xing, Michael I Jordan, Richard M Karp (2001), "Feature selection for high-dimensional genomic microarray data", Proceedings of the Eighteenth International Conference on Machine Learning (Morgan Kauffman), pp.601-608.
    [PDF]

  138. Momiao Xiong, Xiangzhong Fang, and Jinying Zhao (2001), "Biomarker identification by feature wrappers", Genome Research, 11(11):1878-1887.
    [ abstract] [PDF]

  139. Momiao Xiong, Wuju Li, Jinying Zhao, Li Jin, Eric Boerwinkle (2001), "Feature (gene) selection in gene expression-based tumor classification", Molecular Genetics and Metabolism, 73(3):239-247.

  140. Ying Xu, Victor Olman, Dong Xu (2001), "Minimum spanning trees for gene expression data clustering", Genome Informatics, 12:24-33.

  141. MC Yang, QG Ruan, JJ Yang, S Eckenrode, S Wu, RA McIndoe, JX She (2001), "A statistical method for flagging weak spots improves normalization and ratio estimates in microarrays", Physiological Genomics, 7:45-53.
    [abstract] [PDF]

  142. YH Yang, MJ Buckley, TP Speed (2001), "Analysis of cDNA microarray images", Briefings in Bioinformatics, 2(4):341-349.

  143. Yee H Yang, Sandrine Dudoit, Percy Luu, Terence P Speed (2001), "Normalization for cDNA microarry data", Proceedings of SPIE, 4266:141-152.

  144. Chen-Hsiang Yeang, Sridhar Ramaswamy, Pablo Tamayo, S Mukherjee, Ryan M Rifkin, Jill P Mesirov, Todd Golub, Michael Angelo, Michael Reich, Eric Lander, Tomaso Poggio (2001), "Molecular classification of multiple tumor types ", ISMB'01

  145. KY Yeung, WL Ruzzo (2001), "Principal component analysis for clustering gene expression data", Bioinformatics, 17:763-774.

  146. Ka Yee Yeung, Chris Fraley, Alejandro Murua, Adrian E Raftery, Walter L Ruzzo (2001), "Model-based clustering and data transformations for gene expression data", Bioinformatics, 17:977-987
    preprint form: [PDF] [ webpage from the authors: staff.washington.edu/kayee/model/]

  147. KY Yeung, DR Haynor, WL Ruzzo (2001), "Validating clustering for gene expression data", Bioinformatics, 17:309-318.
    [ webpage from the authors: www.cs.washington.edu/homes/ruzzo/cluster/ ]

  148. Heping Zhang, Chang-Yung Yu, Burton Singer, Momiao Xiong (2001), "Recursive partitioning for tumor classification with gene expression microarray data", Proceedings of the National Academy of Sciences, 98(12):6730-6735.
    [abstract]

  149. Zheng Z Zhou, Jaime A Stein, Qien Z Ji (2001), "GLEAMS: a novel approach to high-throughput genetic microarray image capture and analysis", Proceedings of SPIE, 4266:13-23.

  150. Alexander Zien, Thomas Aigner, Ralf Zimmer, Thomas Lengauer (2001), "Centralization: a new method for the normalization of gene expression data", Bioinformatics, 17(Supp. 1):S323-S331.
2001