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/
2006

  1. O Abul, R Alhajj, F Polat (2006), "A powerful approach for effective finding of significantly differentially expressed genes", IEEE/ACM Transactions on Computational Biology and Bioinformatics, 3(3):220-231

  2. SE Ahnert, K Willbrand, FCS Brown, TMA Fink (2006), "Unbiased pattern detection in microarray data series", Bioinformatics, 22(12):1471-1476.
    [abstract]

  3. Adrian Alexa, Jörg Rahnenführer, Thomas Lengauer (2006), "Improved scoring of functional groups from gene expression data by decorrelating GO graph structure", Bioinformatics, 22(13):1600-1607.
    [abstract]

  4. Michael J Allen, William H Wilson (2006), "The coccolithovirus microarray: an array of uses",

  5. David B Allison, Xiangqin Cui1, Grier P Page1, Mahyar Sabripou (2006), "Microarray data analysis: from disarray to consolidation and consensus", Nature Reviews Genetics, 7:55-65.
    [PDF]

  6. A Almudevar, LB Klebanov, X Qiu, P Salzman, AY Yakovlev (2006), "Utility of correlation measures in analysis of gene expression", NeuroRx, 3(3):384-395.

  7. F Al-Shahrour, P Minguez, J Tárraga, D Montaner, E Alloza, JMM Vaquerizas, L Conde, C Blaschke, J Vera, J Dopazo (2006), "BABELOMICS: a systems biology perspective in the functional annotation of genome-scale experiments", Nucleic Acids Research, 34(web server issue):W472-W476.

  8. Orly Alter (2006), "Discovery of principles of nature from mathematical modeling of DNA microarray data", Proceedings of the National Academy of Sciences, 103(44):16063-16064.

  9. R Amato, A Ciaramella, N Deniskina, C Del Mondo, D di Bernardo, C Donalek, G Longo, G Mangano, G Miele, G Raiconi, A Staiano, R Tagliaferri (2006), "A multi-step approach to time series analysis and gene expression clustering", Bioinformatics, 22(5):589-596.
    [abstract]

  10. Claes R Andersson, Anders Isaksson, Mats G Gustafsson (2006), "Bayesian detection of periodic mRNA time profiles without use of training examples", BMC Bioinformatics, 7:63.
    [abstract]

  11. affymetrix
    Kellie J Archer, Tobias Guennel (2006), "An application for assessing quality of RNA hybridized to Affymetrix GeneChips", Bioinformatics, 22(21):2699-2701.
    [abstract]

  12. Musa H Asyali, Dilek Colak, Omer Demirkaya, Mehmet Inan (2006), "Gene expression profile classification: a review", Current Bioinformatics, 1(1):55-73.
    [abstrat]

  13. Richard P Auburn, Roslin R Russell, Bettina Fischer, Lisa A Meadows, Santiago Sevillano Matilla, Steven Russell (2006), "SimArray: a user-friendly and user-configurable microarray design tool", BMC Bioinformatics, 7:102.
    [abstract]

  14. Catalin C Barbacioru, Yulei Wang, Roger D Canales, Yongming A Sun, David N Keys, Frances Chan, Karen A Poulter, Raymond R Samaha (2006), "Effect of various normalization methods on Applied Biosystems expression array system data", BMC Bioinformatics, 7:533.
    [abstract]

  15. Simon Barkow, Stefan Bleuler, Amela Prelic, Philip Zimmermann, Eckart Zitzler (2006), "BicAT: a biclustering analysis toolbox", Bioinformatics, 22(10):1282-1283.
    [abstract]

  16. Edward D Bearden, Pippa M Simpson, Charlotte A Peterson, Marjorie L Beggs (2006), "Assessing the reliability of amplified RNA used in microarrays: a DUMB table approach", Applied Bioinformatics, 5(2):67-76.

  17. Bradley J Beattie, Peter N Robinson (2006), "Binary state pattern clustering: a digital paradigm for class and biomarker discovery in gene microarray studies of cancer", Journal of Computational Biology, 13(5):1114-1130.
    [abstract]

  18. Alexander Begun (2006), "Robust method for detecting differential gene expression in twin studies", Bioinformatics, 22(23):2905-2909.
    [abstract]

  19. N Belacel, QC Wang, M Cuperlovic-Culf (2006), "Clustering methods for microarray gene expression data", Omics, 10(4):507-531.

  20. lana Belitskaya-Levy (2006), "A generalized clustering problem, with application to DNA microarrays", Statistical Applications in Genetics and Molecular Biology, 5(1):2.
    [abstract]

  21. Anders Bengtsson, Henrik Bengtsson (2006), "Microarray image analysis: background estimation using quantile and morphological filters", BMC Bioinformatics, 7:96.
    [abstract]

  22. Henrik Bengtsson, Ola Hossjer (2006), "Methodological study of affine transformations of gene expression data with proposed robust non-parametric multi-dimensional normalization method", BMC Bioinformatics, 7:100.
    [abstract]

  23. L Ben-Tovim Jones, RW Bean, GJ McLachlan, JX Zhu (2006), "Mixture models for detecting differentially expressed genes in microarrays", International Journal of Neural Systems, 16:353-362.

  24. Daniel Berrar, Ian Bradbury, Werner Dubitzky (2006), "Avoiding model selection bias in small-sample genomic data sets", Bioinformatics, 22(10):1245-1250. (Corrigendum: 22(19):2453 (2006))
    [abstract]

  25. Daniel Berrar, Ian Bradbury, Werner Dubitzky (2006), "Instance-based concept learning from multiclass DNA microarray data", BMC Bioinformatics, 7:73.
    [abstract]

  26. Ghislain Bidaut, Karsten Suhre, Jean-Michel Claverie, Michael F Ochs (2006), "Determination of strongly overlapping signaling activity from microarray data", BMC Bioinformatics, 7:99.
    [abstract]

  27. Jonathon Blake, Christian Schwager, Misha Kapushesky, Alvis Brazma (2006), "ChroCoLoc: an application for calculating the probability of co-localization of microarray gene expression", Bioinformatics, 22:765-767.
    [abstract]

  28. Marta Blangiardo, Simona Toti, Betti Giusti, Rosanna Abbate, Alberto Magi, Filippo Poggi, Luciana Rossi, Francesca Torricelli, Annibale Biggeri (2006) "Using a calibration experiment to assess gene-specific information: full Bayesian and empirical Bayesian models for two-channel microarray data", Bioinformatics, 22:50-57.
    [abstract]

  29. Sankar Bokka, Sunil K Mathur (2006), "A nonparametric likelihood ratio test to identify differentially expressed genes from microarray data", Applied Bioinformatics, 5(4):267-276.

  30. Anne-Laure Boulesteix (2006), "Reader's reaction to "dimension reduction for classification with gene expression microarray Data" by Dai et al (2006)", Statistical Applications in Genetics and Molecular Biology, 5(1):16.
    [abstract]

  31. Anne-Laure Boulesteix, Korbinian Strimmer (2006), "Partial least squares: a versatile tool for the analysis of high-dimensional genomic data", Briefings in Bioinformatics, 8:32-44.
    [PDF]

  32. Alvis Brazma, Helen Parkinson (2006), "ArrayExpress service for reviewers/editors of DNA microarray papers" (correspondence), Nature Biotechnology, 24(11):1321.
    [abstract]

  33. Philippe Broët, Vladimir A. Kuznetsov, Jonas Bergh, Edison T. Liu, Lance D. Miller (2006), "Identifying gene expression changes in breast cancer that distinguish early and late relapse among uncured patients", Bioinformatics, 22(12):1477-1485.
    [abstract]

  34. Ljubomir J. Buturovic (2006), "PCP: a program for supervised classification of gene expression profiles", Bioinformatics, 22:245-247.
    [abstract]

  35. Max Bylesjö, Andreas Sjödin, Daniel Eriksson, Henrik Antti, Thomas Moritz, Stefan Jansson, Johan Trygg (2006), "MASQOT-GUI: spot quality assessment for the two-channel microarray platform", Bioinformatics, 22(20):2554-2555.
    [abstract]

  36. A Callegaro, D Basso, S Bicciato (2006), "A locally adaptive statistical procedure (LAP) to identify differentially expressed chromosomal regions", Bioinformatics, 22(21):2658-2666.
    [abstract]

  37. Roger D Canales, Yuling Luo, James C Willey, Bradley Austermiller, Catalin C Barbacioru, Cecilie Boysen, Kathryn Hunkapiller, Roderick V Jensen, Charles R Knight, Kathleen Y Lee, Yunqing Ma, Botoul Maqsodi, Adam Papallo, Elizabeth Herness Peters, Karen Poulter, Patricia L Ruppel, Raymond R Samaha, Leming Shi, Wen Yang, Lu Zhang, Federico M Goodsaid (2006), "Evaluation of DNA microarray results with quantitative gene expression platforms", Nature Biotechnology, 24:1115-1122.
    [abstract]

  38. E Carlon, T Heim, J Klein Wolterink, GT Barkema (2006), "Comment on: 'Solving the riddle of the bright mismatches: Labeling and effective binding in oligonucleotide arrays' ", Physical Review E, 73:063901.
    [abstract]

  39. Pedro Carmona-Saez, Monica Chagoyen, Andres Rodriguez, Oswaldo Trelles, Jose M Carazo, Alberto Pascual-Montano (2006), "Integrated analysis of gene expression by association rules discovery", BMC Bioinformatics, 7:54.
    [abstract]

  40. Pedro Carmona-Saez, Roberto D Pascual-Marqui, Francisco Tirado, Jose M Carazo, Alberto Pascual-Montano (2006), "Biclustering of gene expression data by non-smooth non-negative matrix factorization", BMC Bioinformatics, 7:78.
    [abstract]

  41. L Carrivick, S Rogers, J Clark, C Campbell, M Girolami, C Cooper (2006), "Identification of prognostic signatures in breast cancer microarray data using Bayesian techniques", Journal of the Royal Society Interface, 3:367-381.
    [abstract]

  42. William H Catherino, Phyllis C Leppert, James H Segars (2006), "The promise and perils of microarray analysis", American Journal of Obstetrics & Gynecology. 195(2):389-393.

  43. Gavin C Cawley, Nicola L C Talbot (2006), "Gene selection in cancer classification using sparse logistic regression with Bayesian regularization", Bioinformatics, 22(19):2348-2355.
    [abstract]

  44. Jeffrey T Chang, Joseph R Nevins (2006), "GATHER: a systems approach to interpreting genomic signatures", Bioinformatics, 22(23):2926-2933.

  45. Chin-Fu Chen, Xin Feng, Jack Szeto (2006), "Identification of critical genes in microarray experiments by a Neuro-Fuzzy", Computational Biology and Chemistry , 30(5):372-381.
    [abstract]

  46. Yian A Chen, Cheng-Chung Chou, Xinghua Lu, Elizabeth H Slate, Konan Peck, Wenying Xu, Eberhard O Voit, Jonas S Almeida (2006), "A multivariate prediction model for microarray cross-hybridization", BMC Bioinformatics, 7:101.
    [abstract]

  47. Chao Cheng, Xiaotu Ma, Xiting Yan, Fengzhu Sun, Lei M Li (2006), "MARD: a new method to detect differential gene expression in treatment-control time courses", Bioinformatics, 22(21):2650-2657.
    [abstract]

  48. H Chipman, R Tibshirani (2006), "Hybrid hierarchical clustering with applications to microarray data", Biostatistics, 7(2):286-301.

  49. HyungJun Cho, Jae K Lee (2006), "Response to comments on 'Bayesian Hierarchical Error Model for Analysis of Gene Expression Data' ", Bioinformatics, 22(19):2452.
    [extract]

  50. A Choudhary, M Brun, J Hua, J Lowey, E Suh, ER Dougherty (2006), "Genetic test bed for feature selection," Bioinformatics, 22(7):837-842.
    [abstract]

  51. Kristin Cobb (2006), "Microarrays: the search for meaning in a vast sea of data", Biomedical Computation Review, 2(6):16-23.
    [PDF]

  52. Ana Conesa, María José Nueda, Alberto Ferrer, Manuel Talón (2006), "maSigPro: a method to identify significantly differential expression profiles in time-course microarray experiments", Bioinformatics, 22(9):1096-1102.
    [abstract]

  53. affymetrix
    L Cope, SM Hartman, HW Gohlmann, JP Tiesman, RA Irizarry (2006), "Analysis of Affymetrix GeneChip data using amplified RNA", Biotechniques, 40(2):165-166, 168, 170.

  54. Alan R. Dabney (2006), "ClaNC: point-and-click software for classifying microarrays to nearest centroids" Bioinformatics, 22:122-123.
    [abstract]

  55. AR Dabney, JD Storey (2006), "A reanalysis of a published Affymetrix GeneChip control dataset" (comment), Genome Biology, 7(3):401.

  56. Jian J. Dai, Linh Lieu, David Rocke (2006), "Dimension reduction for classification with gene expression microarray data", Statistical Applications in Genetics and Molecular Biology, 5(1):6.
    [abstract]

  57. S Datta, S Datta (2006), "Evaluation of clustering algorithms for gene expression data", BMC Bioinformatics, 7(Suppl 4):S17.

  58. Chad A Davis, Fabian Gerick, Volker Hintermair, Caroline C Friedel, Katrin Fundel, Robert Küffner, Ralf Zimmer (2006), "Reliable gene signatures for microarray classification: assessment of stability and performance", Bioinformatics, 22(19):2356-2363.
    [abstract]

  59. Robert P. DeConde, Sarah Hawley, Seth Falcon, Nigel Clegg, Beatrice Knudsen, Ruth Etzioni (2006), "Combining results of microarray experiments: a rank aggregation approach", Statistical Applications in Genetics and Molecular Biology, 5(1):15.
    [abstract]

  61. affymetrix
    Aurelien de Reyniès, Daniela Geromin, Jean-Michel Cayuela, Fabien Petel, Philippe Dessen, François Sigaux, David S Rickman (2006), "Comparison of the latest commercial short and long oligonucleotide microarray technologies", BMC Genomics, 7:51.
    [abstract]

  62. affymetrix
    Dick de Ridder, Frank J T Staal, Jacques J M van Dongen, Marcel J T Reinders (2006), "Maximum significance clustering of oligonucleotide microarrays", Bioinformatics, 22:326-331.
    [abstract]

  63. Ramon Diaz-Uriarte, Sara Alvarez de Andres (2006), "Gene selection and classification of microarray data using random forest", BMC Bioinformatics, 7:3.
    [abstract]

  64. Janko Dietzsch, Nils Gehlenborg, Kay Nieselt (2006), "Mayday - a microarray data analysis workbench", Bioinformatics, 22: 1010-1012.
    [abstract]

  65. Veera D'mello, Ju Y Lee, Clinton C MacDonald, Bin Tian (2006), "Alternative mRNA polyadenylation can potentially affect detection of gene expression by Affymetrix GeneChip(R) arrays", Applied Bioinformatics, 5(4):249-253.

  66. JH Do, DK Choi (2006), "Normalization of microarray data: single-labeled and dual-labeled arrays", Molecules and Cells, 22(3):254-261.
    [PDF]

  67. Sorin Draghici, Purvesh Khatri, Aron C Eklund, Zoltan Szallasi, (2006), "Reliability and reproducibility issues in DNA microarray measurements", Trends in Genetics, 22(2):101-109.
    [abstract]

  68. Timothy MD Ebbels, Bernard F Buxton, David T Jones (2006), "springScape: visualisation of microarray and contextual bioinformatic data using spring embedding and an 'information landscape' ", Bioinformatics, 22(14):e99-e107.
    [abstract]

  69. Elena Edelman, Alessandro Porrello, Justin Guinney, Bala Balakumaran, Andrea Bild, Phillip G Febbo, Sayan Mukherjee (2006), "Analysis of sample set enrichment scores: assaying the enrichment of sets of genes for individual samples in genome-wide expression profiles", Bioinformatics, 22:e108-e116.
    [abstract]

  70. Liat Ein-Dor, Or Zuk, Eytan Domany (2006), "Thousands of samples are needed to generate a robust gene list for predicting outcome in cancer", Proceedings of the National Academy of Sciences, 103(15):5923-5928
    [abstract]

  71. Yedid Elbez, Shlomit Farkash-Amar, Itamar Simoncorresponding (2006), "An analysis of intra array repeats: the good, the bad and the non informative", BMC Genomics, 7:136.
    [abstract]

  72. Kristof Engelen, Bart Naudts, Bart De Moor, Kathleen Marchal (2006), "A calibration method for estimating absolute expression levels from microarray data", Bioinformatics, 22(10):1251-1258.
    [abstract]

  73. Joe Faith, Robert Mintram, Maia Angelova (2006), "Targeted projection pursuit for visualizing gene expression data classifications", Bioinformatics, 22(21):2667-2673.
    [abstract]

  74. Zhuo Fang, Jiong Yang, Yixue Li, Qingming Luo, Lei Liu (2006), "Knowledge guided analysis of microarray data", Journal of Biomedical Informatics, 39(4):401-411.
    [ abstract]

  75. Kurt Fellenberg, Christian H. Busold, Olaf Witt, Andrea Bauer, Boris Beckmann, Nicole Hauser, Marcus Frohme, Stefan Winter, Jurgen Dippon, Jorg D. Hoheisel (2006), "Systematic interpretation of microarray data using experiment annotations", BMC Genomics, 7:319.
    [abstract]

  76. José A. Ferreira, Aeilko Zwinderman (2006), "Approximate sample size calculations with microarray data: an illustration", Statistical Applications in Genetics and Molecular Biology, 5(1):25.
    [abstract]

  78. Richard J Fox, Matthew W Dimmic (2006), "A two-sample Bayesian t-test for microarray data", BMC Bioinformatics, 7:126.
    [abstract]

  79. Felix W Frueh (2006), "Impact of microarray data quality on genomic data submissions to the FDA" (commentary), Nature Biotechnology, 24:1105-1107.
    [abstract]

  80. Andre Fujita, Joao Ricardo Sato, Leonardo de Oliveira Rodrigues, Carlos Eduardo Ferreira, Mari Cleide Sogayar (2006), "Evaluating different methods of microarray data normalization", BMC Bioinformatics, 7:469.
    [abstract]

  81. W Fury, F Batliwalla, PK Gregersen, W Li (2006), "Overlapping probabilities of top ranking gene lists, hypergeometric distribution, and stringency of gene selection criterion", Conference proceedings of Annual International Conference of the IEEE Engineering in Medicine and Biology Society, pp. 5531-5541 (IEEE)
    [abstract]

  82. Mugdha Gadgil, Sarika Mehra, Vivek Kapur, Wei-Shou Hu (2006), "TimeView: for comparative gene expression analysis", Applied Bioinformatics, 5(1):41-44.

  83. Giacomo Gamberoni, Sergio Storari, Stefano Volinia (2006), "Finding biological process modifications in cancer tissues by mining gene expression correlations", BMC Bioinformatics, 7:6.
    [abstract]

  84. Xin Gao (2006), "Construction of null statistics in permutation-based multiple testing for multi-factorial microarray experiments", Bioinformatics, 22(12):1486-1494.
    [abstract]

  85. Olivier Gevaert, Frank De Smet, Dirk Timmerman, Yves Moreau, Bart De Moor (2006), "Predicting the prognosis of breast cancer by integrating clinical and microarray data with Bayesian networks", Bioinformatics, 22:e184-e190.
    [abstract]

  86. E F Glynn, J Chen, A R Mushegian (2006), "Detecting periodic patterns in unevenly spaced gene expression time series using Lomb-Scargle periodograms", Bioinformatics, 22(3):310-316.
    [abstract]

  87. Nicolas Goffard, Georg Weiller (2006), "Extending MapMan: application to legume genome arrays", Bioinformatics, 22(23):2958-2959.
    [abstract]

  88. Darlene R. Goldstein (2006), "Partition resampling and extrapolation averaging: approximation methods for quantifying gene expression in large numbers of short oligonucleotide arrays", Bioinformatics, 22(19):2364-2372.
    [abstract]

  89. Raphael Gottardo, Adrian E. Raftery, Ka Yee Yeung, Roger E. Bumgarner (2006), "Bayesian robust inference for differential gene expression in microarrays with multiple samples", Biometrics, 62(1):10-18.
    [abstract]

  90. Joshua Gould, Gad Getz, Stefano Monti, Michael Reich, Jill P Mesirov (2006), "Comparative gene marker selection suite", Bioinformatics, 22(15):1924-1925.
    [abstract]

  91. Andrew B Goulter, Daniel W Harmer, Kenneth L Clark (2006), "Evaluation of low density array technology for quantitative parallel measurement of multiple genes in human tissue", BMC Genomics, 7:34.
    [abstract]

  92. Kevin A Greer, Matthew R McReynolds, Heddwen L Brooks, James B Hoying (2006), "CARMA: A platform for analyzing microarray datasets that incorporate replicate measures", BMC Bioinformatics, 7:149.
    [abstract]

  93. Gregory A Grothaus, Adeel Mufti, T. M. Murali (2006), "Automatic layout and visualization of biclusters", Algorithms for Molecular Biology, 1:15.
    [abstract]

  94. Thomas Grotkjær, Ole Winther, Birgitte Regenberg, Jens Nielsen, Lars Kai Hansen (2006) "Robust multi-scale clustering of large DNA microarray datasets with the consensus algorithm", Bioinformatics, 22:58-67.
    [abstract]

  95. Lei Guo, Edward K Lobenhofer, Charles Wang, Richard Shippy, Stephen C Harris, Lu Zhang, Nan Mei, Tao Chen, Damir Herman, Federico M Goodsaid, Patrick Hurban, Kenneth L Phillips, Jun Xu, Xutao Deng, Yongming Andrew Sun, Weida Tong, Yvonne P Dragan, Leming Shi (2006), "Rat toxicogenomic study reveals analytical consistency across microarray platforms", Nature Biotechnology, 24:1162-1169.
    [abstract]

  96. Anshuman Gupta, Costas D. Maranas, Réka Albert (2006), "Elucidation of directionality for co-expressed genes: predicting intra-operon termination sites", Bioinformatics, 22:209-214.
    [abstract]

  97. Rashi Gupta, Petri Auvinen, Andrew Thomas, Elja Arjas (2006), "Bayesian hierarchical model for correcting signal saturation in microarrays using pixel intensities", Statistical Applications in Genetics and Molecular Biology, 5(1):20.
    [abstract]

  99. Bettina Harr, Christian Schlötterer (2006), "Comparison of algorithms for the analysis of Affymetrix microarray data as evaluated by co-expression of genes in known operons", Nucleic Acids Research, 34(2):e8.

  100. Feng He, An-Ping Zeng (2006), "In search of functional association from time-series microarray data based on the change trend and level of gene expression", BMC Bioinformatics, 7:69.
    [abstract]

  101. T Heim, J Klein Wolterink, E Carlon, G T Barkema (2006), "Effective affinities in microarray data", Journal of Physics: Condensed Matter, 18:S525-S536.
    [abstract]

  102. affymetrix
    Anne-Mette K Hein, Sylvia Richardson (2006), "A powerful method for detecting differentially expressed genes from GeneChip arrays that does not require replicates", BMC Bioinformatics, 7:353.
    [html]

  103. MJ Hessner, B Xiang, S Jia, R Geoffrey, S Holmes, L Meyer, S Muheisen, X Wang (2006), "Three-color cDNA microarrays with prehybridization quality control yield gene expression data comparable to that of commercial platforms", Physiological Genomics, 25(1):166-178.
    [abstract]

  104. Brandon W Higgs, Jennifer Weller, Jeffrey L Solka (2006), "Spectral embedding finds meaningful (relevant) structure in image and microarray data", BMC Bioinformatics, 7:74.
    [abstract]

  105. Desmond J. Higham, Gabriela Kalna, Milla Kibble (2006), "Spectral clustering and its use in bioinformatics", Journal of Computational and Applied Mathematics, 204(1):25-37.
    [abstract]

  106. affymetrix
    Sepp Hochreiter, Djork-Arne Clevert, Klaus Obermayer (2006), "A new summarization method for affymetrix probe level data", Bioinformatics, 22: 943-949.
    [abstract]

  107. Jörg D. Hoheisel (2006), "Microarray technology: beyond transcript profiling and genotype analysis", Nature Reviews Genetics, 7:200-210.
    [abstract]

  108. Fangxin Hong, Rainer Breitling, Connor W. McEntee, Ben S. Wittner, Jennifer L. Nemhauser, Joanne Chory (2006), "RankProd: a bioconductor package for detecting differentially expressed genes in meta-analysis", Bioinformatics, 22(22):2825-2827.
    [abstract]

  109. Paul Honoré, Samuel Granjeaud, Rebecca Tagett, Stéphane Deraco, Emmanuel Beaudoing, Jacques Rougemont, Stéphane Debono, Pascal Hingamp (2006), "MicroArray Facility: a laboratory information management system with extended support for Nylon based technologies", BMC Genomics, 7:240.
    [abstract]

  110. affymetrix
    Pingzhao Hu, Joseph Beyene, Celia MT Greenwood (2006), "Tests for differential gene expression using weights in oligonucleotide microarray experiments", BMC Genomics, 7:33.
    [abstract]

  111. Z Hu, Fan C, Oh DS, Marron JS, He X, Qaqish BF, Livasy C, Carey LA, Reynolds E, Dressler L, Nobel A, Parker J, Ewend MG, Sawyer LR, Wu J, Liu Y, Nanda R, Tretiakova M, Ruiz Orrico A, Dreher D, Palazzo JP, Perreard L, Nelson E, Mone M, Hansen H, Mullins M, Quackenbush JF, Ellis MJ, Olopade OI, Bernard PS, Perou CM (2006), "The molecular portraits of breast tumors are conserved across microarray platforms", BMC Genomics, 7:96.
    [ abstract]

  112. Xiaohua Hu (2006), "GE-Miner: integration of cluster ensemble and text mining for comprehensive gene expression analysis", International Journal of Bioinformatics Research and Applications, 2(3):325-338.
    [ abstract]

  113. J Hua, Y Balagurunathan, Y Chen, J Lowey, ML Bittner, Z Xiong, E Suh, ER Dougherty (2006), "Normalization benefits microarray-based classification", EURASIP Journal on Bioinformatics and Systems Biology, 2006:43056.
    [abstract]

  114. Desheng Huang, Wei Pan (2006), "Incorporating biological knowledge into distance-based clustering analysis of microarray gene expression data", Bioinformatics, 22(10):1259-1268.
    [abstract]

  115. De-Shuang Huang, Chun-Hou Zheng (2006), "Independent component analysis-based penalized discriminant method for tumor classification using gene expression data", Bioinformatics, 22(15):1855-1862.
    [abstract]

  116. Yifan Huang, Jason C. Hsu, Mario Peruggia, Abigail A. Scott (2006), "Statistical selection of maintenance genes for normalization of gene expressions", Statistical Applications in Genetics and Molecular Biology, 5(1):4.
    [abstract]

  117. Yifan Huang, Haiyan Xu, Violeta Calian, Jason C Hsu (2006), "To permute or not to permute", Bioinformatics, 22(18):2244-2248.
    [abstract]

  118. protein
    Claus Hultschig, Jürgen Kreutzberger, Harald Seitz, Zoltán Konthur, Konrad Büssow, Hans Lehrach (2006), "Recent advances of protein microarrays" Current Opinion in Chemical Biology, 10(1):4-10.
    [abstract]

  119. Curtis Huttenhower, Matt Hibbs, Chad Myers, Olga G Troyanskaya (2006), "A scalable method for integration and functional analysis of multiple microarray datasets", Bioinformatics, 22(23):2890-2897.
    [abstract]

  120. Gordon Hyatt, Rachel Melamed, Richard Park, Reuben Seguritan, Catherine Laplace, Laurent Poirot, Silvia Zucchelli, Reinhard Obst, Michael Matos, Emily Venanzi, Ananda Goldrath, Linh Nguyen, John Luckey, Tetsuya Yamagata, Ann Herman, Jonathan Jacobs, Diane Mathis, Christophe Benoist (2006), "Gene expression microarrays: glimpses of the immunological genome", Nature Immunology, 7:686-691.
    [abstract]

  121. affymetrix
    RA Irizarry, LM Cope, Z Wu (2006), "Feature-level exploration of a published Affymetrix GeneChip control dataset", Genome Biology, 7(8):404.

  122. affymetrix
    Rafael A Irizarry, Zhijin Wu, Harris A Jaffee (2006), "Comparison of Affymetrix GeneChip expression measures", Bioinformatics, 22:789-794.
    [abstract]

  123. Hemant Ishwaran, J Sunil Rao, Udaya B Kogalur (2006), "BAMarrayTM: Java software for Bayesian analysis of variance for microarray data", BMC Bioinformatics, 7:59.
    [abstract]

  124. J Jaeger, R Spang (2006), "Selecting normalization genes for small diagnostic microarrays", BMC Bioinformatics, 7:388.
    [abstract]

  125. Ian B Jeffery, Desmond G Higgins, Aedín C Culhane (2006), "Comparison and evaluation of methods for generating differentially expressed gene lists from microarray data", BMC Bioinformatics, 7:359.
    [abstract]

  126. Hanlee Ji, Ronald W Davis (2006), "Data quality in genomics and microarrays" (commentary), Nature Biotechnology, 24:1112-1113.
    [abstract]

  127. Yuan Ji, Kevin Coombes, Jiexin Zhang, Sijin Wen, James Mitchell, Lajos Pusztai, W Fraser Symmans, Jing Wang (2006), "RefSeq refinements of UniGene-based gene matching improve the correlation of expression measurements between two microarray platforms", Applied Bioinformatics, 5(2):77-88.

  128. Hui Jia, Le Lu, Shiau-Chuen Hng, Jinming Li (2006), "Simulation study of ratio calculation formulae of two-colour cDNA microarray data", Applied Bioinformatics, 5(4):255-266.

  129. Hongmei Jiang, Rebecca W. Doerge (2006), "A two-step multiple comparison procedure for a large number of tests and multiple treatments", Statistical Applications in Genetics and Molecular Biology, 5(1):28.
    [abstract]

  130. Sin-Ho Jung, Woncheol Jang (2006), "How accurately can we control the FDR in analyzing microarray data?", Bioinformatics, 22(14):1730-1736.
    [abstract]

  131. Lars Kaderali, Thomas Zander, Ulrich Faigle, Jürgen Wolf, Joachim L. Schultze, Rainer Schrader (2006), "CASPAR: a hierarchical bayesian approach to predict survival times in cancer from gene expression data", Bioinformatics, 22(12):1495-1502.
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    Suman Sundaresh, Denise L. Doolan, Siddiqua Hirst, Yunxiang Mu, Berkay Unal, D Huw Davies, Philip L Felgner, Pierre Baldi (2006), "Identification of humoral immune responses in protein microarrays using DNA microarray data analysis techniques", Bioinformatics, 22:1760-1766.
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    Xiaowei Zhu, Mark Gerstein, Michael Snyder (2006), "ProCAT: a data analysis approach for protein microarrays", Genome Biology, 7(11):R110.
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2006