Bibliography on
Microarray Data Analysis

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

http://www.nslij-genetics.org/microarray/
2005

  1. LV Abruzzo, KY Lee, A Fuller, A Silverman, MJ Keating, LJ Medeiros, KR Coombes (2005), "Validation of oligonucleotide microarray data using microfluidic low-density arrays: a new statistical method to normalize real-time RT-PCR data", Biotechniques, 38(5):785-792.

  2. affymetrix
    LV Abruzzo, J Wang, M Kapoor, L Jeffrey Medeiros, MJ Keating, W Edward Highsmith, LL Barron, CC Cromwell, KR Coombes (2005), "Biological validation of differentially expressed genes in chronic lymphocytic leukemia identified by applying multiple statistical methods to oligonucleotide microarrays", Journal of Molecular Diagnostics, 7(3):337-345.
    [abstract]

  3. Osman Abul, Reda Alhajj, Faruk Polat, Ken Barker (2005), "Finding differentially expressed genes for pattern generation", Bioinformatics, 21(4):445-450.
    [abstract]

  4. Jesus S Aguilar-Ruiz (2005), "Shifting and scaling patterns from gene expression data", Bioinformatics, 21(20):3840-3845.
    [abstract]

  5. R Alberts, P Terpstra, L V Bystrykh, G de Haan, R C Jansen (2005), "A statistical multiprobe model for analyzing cis and trans genes in genetical genomics experiments with short-oligonucleotide arrays", Genetics, 171(3):1437-1439.
    [abstract]

  6. Naomi Altman (2005), "Replication, variation and normalisation in microarray experiments", Applied Bioinformatics, 4(1):33-44.

  7. F Al-Shahrour, R Diaz-Uriarte, J Dopazo (2005), "Discovering molecular functions significantly related to phenotypes by combining gene expression data and biological information", Bioinformatics, 21(13):2988-2993.
    [abstract]

  8. Alexey V Antonov, Igor V. Tetko, Denis Kosykh, Dmitrij Surmeli, Hans-Werner Mewes (2005), "Exploiting scale-free information from expression data for cancer classification", Computational Biology and Chemistry , 29(4):288-293.
    [ abstract]

  9. Gary L Argraves, Saurin Jani, Jeremy L Barth, W Scott Argraves (2005), "ArrayQuest: a web resource for the analysis of DNA microarray data", BMC Bioinformatics, 6:287.
    [abstract]

  10. Musa H Asyali, Musa Alci (2005), "Reliability analysis of microarray data using fuzzy c-means and normal mixture modeling based classification methods", Bioinformatics, 21(5):644-649.
    [abstract]

  11. L Badea, D Tilivea (2005), "Sparse factorizations of gene expression guided by binding data", Pacific Symposium on Biocomputing, 10:447-458.

  12. David J Bakewell, Ernst Wit (2005), "Weighted analysis of microarray gene expression using maximum-likelihood", Bioinformatics, 21(6):723-729.
    [abstract]

  13. R Balasubramaniyan, E Hullermeier, N Weskamp, J Kamper (2005), "Clustering of gene expression data using a local shape-based similarity measure", Bioinformatics, 21(7):1069-1077.
    [abstract]

  14. Michael T. Barrett (2005), "Stacking the chips for biological discovery", Nature Genetics, 37:S1.
    [abstract]

  15. WT Barry, AB Nobel, FA Wright (2005), "Significance analysis of functional categories in gene expression studies: a structured permutation approach", Bioinformatics, 21(9):1943-1949.
    [abstract]

  16. Florent Baty, Michel P Bihl, Guy Perrière, Aedín C Culhane, Martin H Brutsche (2005), "Optimized between-group classification: a new jackknife-based gene selection procedure for genome-wide expression data", BMC Bioinformatics, 6:239.
    [abstract]

  17. Yoram Ben-Shaul, Hagai Bergman, Hermona Soreq (2005), "Identifying subtle interrelated changes in functional gene categories using continuous measures of gene expression", Bioinformatics, 21(7):1129-1137.
    [abstract]

  18. L Ben-Tovim Jones, RW Bean, GJ McLachlan, J Zhu (2005), "Application of mixture models to detect differentially expressed genes", Lecture Notes in Computer Science, Vol.3578, pp.422-431.

  19. affymetrix
    Soumyaroop Bhattacharya, Thomas J Mariani (2005), "Transformation of expression intensities across generations of Affymetrix microarrays using sequence matching and regression modeling", Nucleic Acids Research, 33(18):e157.
    [abstract]

  20. networks
    DR Bickel (2005), "Probabilities of spurious connections in gene networks: application to expression time series", Bioinformatics, 21(7):1121-1118.
    [abstract]

  21. Nadia Bolshakova, Francisco Azuaje, Pádraig Cunningham (2005), "An integrated tool for microarray data clustering and cluster validity assessment", Bioinformatics, 21(4):451-455.
    [abstract]

  22. Nadia Bolshakova, Padraig Cunningham (2005), "cluML: a markup language for clustering and cluster validity assessment of microarray data", Applied Bioinformatics, 4(3):211-213.

  23. PC Boutros, AB Okey (2005), "Unsupervised pattern recognition: an introduction to the whys and wherefores of clustering microarray data", Briefings in Bioinformatics, 6(4):331-343.
    [abstract]

  24. J Boyle (2005), "Gene-Expression Omnibus integration and clustering tools in SeqExpress", Bioinformatics, 21(10):2550-2551.
    [abstract]

  25. Rainer Breitling, Pawel Herzyk (2005), "Rank-based methods as a non-parametric alternative of the t-statistic for the analysis of biological microarray data", Journal of Bioinformatics and Computational Biology, 3(5):1171-1189.
    [abstract]

  26. DJ Brennan, SL O'Brien, A Fagan, AC Culhane, DG Higgins, MJ Duffy, WM Gallagher (2005), "Application of DNA microarray technology in determining breast cancer prognosis and therapeutic response", Expert Opin Biol Ther., 5(8):1069-1083.

  27. Per Broberg (2005), "A comparative review of estimates of the proportion unchanged genes and the false discovery rate", BMC Bioinformatics, 6:199.
    [abstract]

  28. Andreas Buness, Wolfgang Huber, Klaus Steiner, Holger Sultmann, Annemarie Poustka (2005), "arrayMagic: two-colour cDNA microarray quality control and preprocessing", Bioinformatics, 21(4):554-556.
    [abstract]

  29. CH Busold, S Winter, N Hauser, A Bauer, J Dippon, JD Hoheisel, K Fellenberg (2005), "Integration of GO annotations in Correspondence Analysis: facilitating the interpretation of microarray data", Bioinformatics, 21(10):2424-2429.
    [abstract]

  30. Max Bylesjö, Daniel Eriksson, Andreas Sjödin, Michael Sjöström, Stefan Jansson, Henrik Antti, Johan Trygg (2005), "MASQOT: a method for cDNA microarray spot quality control", BMC Bioinformatics, 6:250.
    [abstract]

  31. P Cahan, AM Ahmad, H Burke, S Fu, Y Lai, L Florea, N Dharker, T Kobrinski, P Kale, TA McCaffrey (2005), "List of lists-annotated (LOLA): A database for annotation and comparison of published microarray gene lists", Gene, 360(1):78-82.
    [ abstract]

  32. Gilles Caraux, Sylvie Pinloche (2005), "PermutMatrix: a graphical environment to arrange gene expression profiles in optimal linear order", Bioinformatics, 21(7):1280-1281.
    [abstract]

  33. affymetrix
    Scott L Carter, Aron C Eklund, Brigham H Mecham, Isaac S Kohane, Zoltan Szallasi (2005), "Redefinition of Affymetrix probe sets by sequence overlap with cDNA microarray probes reduces cross-platform inconsistencies in cancer-associated gene expression measurements", BMC Bioinformatics, 6:107.
    [abstract]

  34. Shin-Huang Chan, Li-Ju Chen, Nan-Hwa CHow, Hsiao-Sheng Liu (2005), "An ancova approach to normalize microarray data, and its performance to existing methods", Journal of Bioinformatics and Computational Biology, 3(2):257-268.
    [abstract]

  35. Zeke SH Chan, N Kasabov, Lesley Collins (2005), "A hybrid genetic algorithm and expectation maximization method for global gene trajectory clustering", Journal of Bioinformatics and Computational Biology, 3(5):1227-1242.
    [abstract]

  36. HY Chang, DS Nuyten, JB Sneddon, T Hastie, R Tibshirani, T Sorlie, H Dai, YD He, LJ van't Veer, H Bartelink, M van de Rijn, PO Brown, MJ van de Vijver (2005), "Robustness, scalability, and integration of a wound-response gene expression signature in predicting breast cancer survival", Proceedings of the National Academy of Sciences, 102(10):3738-3743.
    [abstract]

  37. DT Chen, JJ Chen, SJ Soong (2005), "Probe rank approaches for gene selection in oligonucleotide arrays with a small number of replicates", Bioinformatics, 21(12):2861-2866.
    [abstract]

  38. Jie Chen (2005), "Identification of significant periodic genes in microarray gene expression data", BMC Bioinformatics, 6:286.
    [abstract]

  39. Jung Kyoon Choi, Ungsik Yu, Ook Joon Yoo, Sangsoo Kim (2005), "Differential coexpression analysis using microarray data and its application to human cancer", Bioinformatics, 21(24):4348-4355.
    [abstract]

  40. Jeff W. Chou, Richard S. Paules, Pierre R. Bushel (2005), "Systematic variation normalization in microarray data to get gene expression comparison unbiased", Journal of Bioinformatics and Computational Biology, 3(2):225-241.
    [abstract]

  41. Wei Chu, Zoubin Ghahramani, Francesco Falciani, David L Wild (2005), "Biomarker discovery in microarray gene expression data with Gaussian processes", Bioinformatics, 21(16):3385-3393.
    [abstract]

  42. IG Costa, A Schonhuth, A Schliep (2005), "The Graphical Query Language: a tool for analysis of gene expression time-courses", Bioinformatics, 21(10):2544-2545.
    [abstract]

  43. Q Cui, B Liu, T Jiang, S Ma (2005), "Characterizing the dynamic connectivity between genes by variable parameter regression and Kalman filtering based on temporal gene expression data", Bioinformatics, 21(8):1538-1541.
    [abstract]

  44. X Cui, JT Hwang, J Qiu, NJ Blades, GA Churchill (2005), "Improved statistical tests for differential gene expression by shrinking variance components estimates", Biostatistics, 6(1):59-75.

  45. AC Culhane, J Thioulouse, G Perriere, DG Higgins (2005), "MADE4: an R package for multivariate analysis of gene expression data", Bioinformatics, 21(11):2789-2790.
    [abstract]

  46. Tomaz Curk, Janez Demsar, Qikai Xu, Gregor Leban, Uros Petrovic, Ivan Bratko, Gad Shaulsky, Blaz Zupan (2005), "Microarray data mining with visual programming", Bioinformatics, 21(3):396-398.
    [abstract]

  47. Alan R Dabney (2005), "Classification of microarrays to nearest centroids", Bioinformatics, 21(22):4148-4154.
    [abstract]

  48. affymetrix
    M Dai, P Wang, AD Boyd, G Kostov, B Athey, EG Jones, WE Bunney, RM Myers, TP Speed, H Akil, SJ Watson, F Meng (2005), "Evolving gene/transcript definitions significantly alter the interpretation of GeneChip data", Nucleic Acids Research, 33(20):e175.

  49. Davide D'Alimonte, David Lowe, Ian T Nabney, Vassilis Mersinias, Colin P Smith (2005), "MILVA: An interactive tool for the exploration of multidimensional microarray data", Bioinformatics, 21(22):4192-4193.
    [abstract]

  50. Cyril Dalmasso, Philippe Broët, Thierry Moreau (2005), "A simple procedure for estimating the false discovery rate", Bioinformatics, 21(5):660-668.
    [abstract]

  51. S Datta, S Datta (2005), "Empirical Bayes screening of many p-values with applications to microarray studies", Bioinformatics, 21(9):1987-1994.
    [abstract]

  52. Kevin Dawson, Raymond L Rodriguez, Wasyl Malyj (2005), "Sample phenotype clusters in high-density oligonucleotide microarray data sets are revealed using Isomap, a nonlinear algorithm", BMC Bioinformatics, 6:195.
    [abstract]

  53. Nema Dean, Adrian E Raftery (2005), "Normal uniform mixture differential gene expression detection for cDNA microarrays", BMC Bioinformatics, 6:173.
    [abstract]

  54. Paul Delmar, Stephane Robin, Jean Jacques Daudin (2005), "VarMixt: efficient variance modelling for the differential analysis of replicated gene expression data", Bioinformatics, 21(4):502-508.
    [abstract]

  55. O Demirkaya, MH Asyali, MM Shoukri (2005), "Segmentation of cDNA microarray spots using markov random field modeling", Bioinformatics, 21(13):2994-3000.
    [abstract]

  56. M Dettling, E Gabrielson, G Parmigiani (2005), "Searching for differentially expressed gene combinations", Genome Biology, 6(10):R88

  57. R Diaz-Uriarte (2005), "Supervised methods with genomic data: a review and cautionary view", in Data Analysis and Visualization in Genomics and Protepmics eds. F Azuaje, J Dopazo, pp.193-214 (Wiley).

  58. Vito Di Gesú, Raffaele Giancarlo, Giosué Lo Bosco, Alessandra Raimondi, Davide Scaturro (2005), "GenClust: A genetic algorithm for clustering gene expression data", BMC Bioinformatics, 6:289.
    [abstract]

  59. Chris Ding, Hanchuan Peng (2005), "Minimum redundancy feature selection from microarray gene expression data", Journal of Bioinformatics and Computational Biology, 3(2):185-205.
    [abstract]

  60. KA DiVito, RL Camp (2005), "Tissue microarrays - automated analysis and future directions", Breast Cancer Online, 8:e38.
    [abstract]

  61. Amira Djebbari, Svetlana Karamycheva, Eleanor Howe, John Quackenbush (2005), "MeSHer: identifying biological concepts in microarray assays based on PubMed references and MeSH terms", Bioinformatics, 21(15):3324-3326.
    [abstract]

  62. affymetrix
    KK Dobbin, DG Beer, M Meyerson, TJ Yeatman, WL Gerald, JW Jacobson, B Conley, KH Buetow, M Heiskanen, RM Simon, JD Minna, L Girard, DE Misek, JM Taylor, S Hanash, K Naoki, DN Hayes, C Ladd-Acosta, SA Enkemann, A Viale, TJ Giordano (2005), "Interlaboratory comparability study of cancer gene expression analysis using oligonucleotide microarrays", Clin Cancer Res., 11:565-572.

  63. KK Dobbin, ES Kawasaki, DW Petersen, RM Simon (2005), "Characterizing dye bias in microarray experiments", Bioinformatics, 21(10):2430-2437.
    [abstract]

  64. Kevin Dobbin, Richard Simon (2005), "Sample size determination in microarray experiments for class comparison and prognostic classification", Biostatistics, 6:27-38.

  65. ER Dougherty (2005), "Feature-selection overfitting with small-sample classifier design", IEEE Intelligent Systems, 20(6):64-66.
    [abstract] [PDF]

  66. S Draghici, M Chatterjee, MA Tainsky (2005), "Epitomics: serum screening for the early detection of cancer on microarrays using complex panels of tumor antigens", Expert Review of Molecular Diagnostics, 5(5):735-743.
    [abstract]

  67. R D Drummond, A Pinheiro, C S Rocha, M Menossi (2005), "ISER: selection of differentially expressed genes from DNA array data by non-linear data transformations and local fitting", Bioinformatics, 21(24):4427-4429.
    [abstract]

  68. D Dueck, QD Morris, BJ Frey (2005), "Multi-way clustering of microarray data using probabilistic sparse matrix factorization", Bioinformatics, 21(Suppl 1):i144-i151.
    [abstract]

  69. Steffen Durinck, Yves Moreau, Arek Kasprzyk, Sean Davis, Bart De Moor, Alvis Brazma, Wolfgang Huber (2005), "BioMart and Bioconductor: a powerful link between biological databases and microarray data analysis", Bioinformatics, 21(16):3439-3440.
    [abstract]

  70. JE Eckel, C Gennings, TM Therneau, LD Burgoon, DR Boverhof, TR Zacharewski (2005), "Normalization of two-channel microarray experiments: a semiparametric approach", Bioinformatics, 21(7):1078-1083.
    [abstract]

  71. JW Edwards, GP Page, G Gadbury, M Heo, T Kayo, R Weindruch, DB Allison (2005), "Empirical Bayes estimation of gene-specific effects in micro-array research", Funct Integr Genomics. 5(1):32-39.

  72. Liat Ein-Dor, Itai Kela, Gad Getz, David Givol, Eytan Domany (2005), "Outcome signature genes in breast cancer: is there a unique set?", Bioinformatics, 21(2):171-178.
    [abstract]

  73. Claus T Ekstrom, Soren Bak, Mats Rudemo (2005), "Pixel-level signal modelling with spatial correlation for two-colour microarrays", Statistical Applications in Genetics and Molecular Biology, 4(1):6.
    [abstract]

  74. affymetrix
    Laura L. Elo, Leo Lahti, Heli Skottman, Minna Kyläniemi, Riitta Lahesmaa, Tero Aittokallio (2005), "Integrating probe-level expression changes across generations of Affymetrix arrays", Nucleic Acids Research, 33(22):e193.
    [abstract]

  75. Stephen Erickson, Chiara Sabatti (2005), "Empirical Bayes estimation of a sparse vector of gene expression changes", Statistical Applications in Genetics and Molecular Biology, 4(1):22.
    [abstract]

  76. J Ernst, GJ Nau, Z Bar-Joseph (2005), "Clustering short time series gene expression data", Bioinformatics, 21(Suppl 1):i159-i168.
    [abstract]

  77. review
    Hassan M. Fathallah-Shaykh (2005), "Microarrays: applications and pitfalls", Archives of Neurology, 62(11):1669-1672.
    [abstract]

  78. Hassan M. Fathallah-Shaykh (2005), "Noise and rank-dependent geometrical filter improves sensitivity of highly specific discovery by microarrays", Bioinformatics, 21(23):4255-4262.
    [abstract]

  79. Fulvia Ferrazzi, Paolo Magni, Riccardo Bellazzi (2005), "Random walk models for Bayesian clustering of gene expression profiles", Applied Bioinformatics, 4(4):263-276.

  80. Guri Feten, Trygve Almøy, Are H Aastveit (2005), "Prediction of missing values in microarray and use of mixed models to evaluate the predictors", Statistical Applications in Genetics and Molecular Biology, 4(1):10.
    [abstract]

  81. Gersende Fort, Sophie Lambert-Lacroix (2005), "Classification using partial least squares with penalized logistic regression", Bioinformatics, 21(7):1104-1111.
    [abstract]

  82. Li M Fu, Casey S Fu-Liu (2005), "Evaluation of gene importance in microarray data based upon probability of selection", BMC Bioinformatics, 6:67.
    [abstract]

  83. WJ Fu, ER Dougherty, B Mallick, RJ Carroll (2005), "How many samples are needed to build a classifier: a general sequential approach", Bioinformatics, 21(1):63-70.
    [abstract]

  84. WJ Fu, RJ Carroll, S Wang (2005), "Estimating misclassification error with small samples via bootstrap cross-validation", Bioinformatics, 21(9):1979-1986.
    [abstract]

  85. Matthias E Futschik, Bronwyn Carlisle (2005), "Noise-robust soft clustering of gene expression time-course data", Journal of Bioinformatics and Computational Biology, 3(4):965-988.
    [abstract]

  86. ME Futschik, T Crompton (2005), "OLIN: optimized normalization, visualization and quality testing of two-channel microarray data", Bioinformatics, 21(8):1724-1726.
    [abstract]

  87. Xin Gao, Peter XK Song (2005), "Nonparametric tests for differential gene expression and interaction effects in multi-factorial microarray experiments", BMC Bioinformatics, 6:186.
    [abstract]

  88. Yuan Gao, George Church (2005), "Improving molecular cancer class discovery through sparse non-negative matrix factorization", Bioinformatics, 21(21):3970-3975.
    [abstract]

  89. Nikhil Garge, Grier Page, Alan Sprague, Bernard Gorman, David Allison (2005), "Reproducible clusters from microarray research: Whither?", BMC Bioinformatics, 6(supp 2):S10.
    [abstract]

  90. JJ Goeman, J Oosting, AM Cleton-Jansen, JK Anninga, HC van Houwelingen (2005), "Testing association of a pathway with survival using gene expression data", Bioinformatics, 21(9):1950-1957.
    [abstract]

  91. Liang Goh, Nikola Kasabov (2005), "An integrated feature selection and classification method to select minimum number of variables on the case study of gene expression data", Journal of Bioinformatics and Computational Biology, 3(5):1107-1136.
    [abstract]

  92. affymetrix
    DL Gold, J Wang, KR Coombes (2005), "Inter-gene correlation on oligonucleotide arrays: how much does normalization matter?", American Journal of Pharmacogenomics, 5(4):271-279.

  93. GR Grant, J Liu, CJ Stoeckert Jr. (2005), "A practical false discovery rate approach to identifying patterns of differential expression in microarray data", Bioinformatics, 21(11):2684-2690.
    [abstract]

  94. Obi L Griffith, Erin D Pleasance, Debra L Fulton, Mehrdad Oveisi, Martin Ester, Asim S Siddiqui, Steven JM Jones (2005), "Assessment and integration of publicly available SAGE, cDNA microarray, and oligonucleotide microarray expression data for global coexpression analyses", Genomics, 86(4):476-488.
    [abstract]

  95. Zhong Guan, Hongyu Zhao (2005), "A semiparametric approach for marker gene selection based on gene expression data ", Bioinformatics, 21(4):529-536.
    [abstract] [PDF]

  96. J Gui, H Li (2005), "Penalized Cox regression analysis in the high-dimensional and low-sample size settings, with applications to microarray gene expression data", Bioinformatics, 21(13):3001-3008.
    [abstract]

  97. Xu Guo, Wei Pan (2005), "Using weighted permutation scores to detect differntial gene expression with microarray data", Journal of Bioinformatics and Computational Biology, 3(4):989-1006.
    [abstract]

  98. Arief Gusnanto, Alexander Ploner, Yudi Pawitan (2005), "Fold-change estimation of differentially expressed genes using mixture mixed-model", Statistical Applications in Genetics and Molecular Biology, 4(1):26.
    [abstract]

  99. David Hancock, Michael Wilson, Giles Velarde, Norman Morrison, Andrew Hayes, Helen Hulme, A Joseph Wood, Karim Nashar, Douglas B Kell, Andy Brass (2005), "maxdLoad2 and maxdBrowse: standards-compliant tools for microarray experimental annotation, data management and dissemination", BMC Bioinformatics, 6:264.
    [abstract]

  100. Julia Handl, Joshua Knowles, Douglas B Kell (2005), "Computational cluster validation in post-genomic data analysis", Bioinformatics, 21(15):3201-3212.
    [abstract]

  101. affymetrix
    Anne-Mette K Hein, Sylvia Richardson, Helen C Causton, Graeme K Ambler, Peter J Green (2005), "BGX: a fully Bayesian integrated approach to the analysis of Affymetrix GeneChip data", Biostatistics, 6(3):349-373.
    [ abstract]

  102. Christelle Hennequet-Antier, Helene Chiapello, Karine Piot, Severine Degrelle, Isabelle Hue, Jean-Paul Renard, Francois Rodolphe, Stephane Robin (2005), "AnovArray: a set of SAS macros for the analysis of variance of gene expression data", BMC Bioinformatics, 6:150.
    [abstract]

  103. LJ Heyer, DZ Moskowitz, JA Abele, P Karnik, D Choi, AM Campbell, EE Oldham, BK Akin (2005), "MAGIC Tool: integrated microarray data analysis", Bioinformatics, 21(9):2114-2115.
    [abstract]

  104. Matthew A Hibbs, Nathaniel C Dirksen, Kai Li, Olga G Troyanskaya (2005), "Visualization methods for statistical analysis of microarray clusters", BMC Bioinformatics, 6:115.
    [abstract]

  105. Ina Hoeschele, Hua Li (2005), "A note on joint versus gene-specific mixed model analysis of microarray gene expression data", Biostatistics, 6:183-186.

  106. T Hsing, LY Liu, M Brun, ER Dougherty (2005), "The coefficient of intrinsic dependence (feature selection using el CID)", Pattern Recognition, 38(5):623-636.
    [PDF]

  107. J Hu, M Kapoor, W Zhang, SR Hamilton, KR Coombes (2005), "Analysis of dose-response effects on gene expression data with comparison of two microarray platforms", Bioinformatics, 21(17):3524-3529.
    [abstract]

  108. J Hu, F Zou, FA Wright (2005), "Practical FDR-based sample size calculations in microarray experiments", Bioinformatics, 21(15):3264-3272.
    [abstract]

  109. Pingzhao Hu, Celia M.T. Greenwood, Joseph Beyene (2005), "Integrative analysis of multiple gene expression profiles with quality-adjusted effect size models", BMC Bioinformatics, 6:128
    [abstract]

  110. J Hua, Z Xiong, J Lowey, E Suh, ER Dougherty (2005), "Optimal number of features as a function of sample size for various classification rules", Bioinformatics , 21(8):1509-1515.
    [abstract]

  111. TM Huang, V Kecman (2005), "Gene extraction for cancer diagnosis by support vector machines - an improvement", Artificial Intelligence in Medicine, 35(1):185-194.
    [ abstract]

  112. JC Huang, QD Morris, TR Hughes, BJ Frey (2005), "GenXHC: a probabilistic generative model for cross-hybridization compensation in high-density genome-wide microarray data", Bioinformatics, 21(Suppl 1):i222-i231.
    [abstract]

  113. Xiaohong Huang, Wei Pan, Xinqiang Han, Yingjie Chen, Leslie W Miller, Jennifer Hall (2005), "Borrowing information from relevant microarray studies for sample classification using weighted partial least squares", Computational Biology and Chemistry , 29(3):204-211.
    [abstract]

  114. Rafael A Irizarry, Daniel Warren, Forrest Spencer, Irene F Kim, Shyam Biswal, Bryan C Frank, Edward Gabrielson, Joe G N Garcia, Joel Geoghegan, Gregory Germino, Constance Griffin0, Sara C Hilmer, Eric Hoffman, Anne E Jedlicka, Ernest Kawasaki, Francisco Martínez-Murillo, Laura Morsberger, Hannah Lee, David Petersen, John Quackenbush, Alan Scott, Michael Wilson, Yanqin Yang, Shui Qing Ye , Wayne Yu (2005), "Multiple-laboratory comparison of microarray platforms", Nature Methods, 2:337-344.
    [abstract]

  115. Jochen Jaeger, Dieter Weichenhan, Boris Ivandic, Rainer Spang (2005), "Early diagnostic marker panel determination for microarray based clinical studies", Statistical Applications in Genetics and Molecular Biology, 4(1):9.
    [abstract]

  116. Nitin Jain, HyungJun Cho, Michael O'Connell, Jae K Lee (2005), "Rank-invariant resampling based estimation of false discovery rate for analysis of small sample microarray data", BMC Bioinformatics, 6:187.
    [abstract]

  117. Liping Ji, Kian-Lee Tan (2005), "Identifying time-lagged gene clusters using gene expression data", Bioinformatics , 21(4):509-516.
    [abstract]

  118. Yuan Ji, Kam-Wah Tsui, KyungMann Kim (2005), "A novel means of using gene clusters in a two-step empirical Bayes method for predicting classes of samples", Bioinformatics, 21(7):1055-1061.
    [abstract]

  119. Y Ji, C Wu, P Liu, J Wang, KR Coombes (2005), "Applications of beta-mixture models in bioinformatics", Bioinformatics, 21(9):2118-2122.
    [abstract]

  120. Thanyaluk Jirapech-Umpai, Stuart Aitken (2005), "Feature selection and classification for microarray data analysis: evolutionary methods for identifying predictive genes", BMC Bioinformatics, 6:148
    [abstract]

  121. Rebecka Jörnsten, Hui-Yu Wang, William J. Welsh, Ming Ouyang (2005), "DNA microarray data imputation and significance analysis of differential expression", Bioinformatics, 21(22):4155-4161.
    [abstract]

  122. Laurent Jourdren, Stéphane Le Crom (2005), "Doelan: a solution for quality control monitoring of microarray production", Bioinformatics, 21(22):4194-4195.
    [abstract]

  123. Sin-Ho Jung (2005), "Sample size for FDR-control in microarray data analysis", Bioinformatics, 21(14):3097-3104.
    [abstract]

  124. Sin-Ho Jung, Heejung Bang, Stanley Young (2005), "Sample size calculation for multiple testing in microarray data analysis", Biostatistics, 6:157-169.

  125. Mads Kærn, Timothy C. Elston, William J. Blake & James J. Collins (2005), "Stochasticity in gene expression: from theories to phenotypes", Nature Reviews Genetics, 6:451-464.
    [abstract]

  126. K Kato, R Yamashita, R Matoba, M Monden, S Noguchi, T Takagi, K Nakai (2005), "Cancer gene expression database (CGED): a database for gene expression profiling with accompanying clinical information of human cancer tissues", Nucleic Acids Research, 33:D533-D536.

  127. Raya Khanin, Ernst Wit (2005), "Design of large time-course microarray experiments with two channels", Applied Bioinformatics, 4(4):253-261.

  128. P Khatri, S Draghici(2005), "Ontological analysis of gene expression data: current tools, limitations, and open problems", Bioinformatics, 21(18):3587-3595.
    [abstract]

  129. Byung Soo Kim, Inyoung Kim, Sunho Lee, Sangcheol Kim, Sun Young Rha, Hyun Cheol Chung (2005), "Statistical methods of translating microarray data into clinically relevant diagnostic information in colorectal cancer", Bioinformatics, 21(4):517-528.
    [abstract]

  130. DW Kim, KH Lee, D Lee (2005), "Detecting clusters of different geometrical shapes in microarray gene expression data", Bioinformatics, 21(9):1927-1934.
    [abstract]

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  267. affymetrix
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  301. networks
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2005