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/
2008

  1. Priit Adler, Jüri Reimand, Jürgen Jänes, Raivo Kolde, Hedi Peterson, Jaak Vilo (2008), "KEGGanim: pathway animations for high-throughput data", Bioinformatics, 24(4): 588-590.
    [abstract]

  2. affymetrix
    R Alberts, G Vera, R C Jansen (2008), "affyGG: computational protocols for genetical genomics with Affymetrix arrays", Bioinformatics, 24(3):433-434.
    [abstract]

  3. D Amaratunga, J Cabrera, V Kovtun (2008), "Microarray learning with ABC", Biostatistics, 9(1):128-136.

  4. affymetrix
    Jose M Arteaga-Salas, Harry Zuzan, William B Langdon, Graham J G Upton, Andrew P Harrison (2008), "An overview of image-processing methods for Affymetrix GeneChips", Briefings in Bioinformatics, 9:25-33.
    [abstract]

  5. M Astrand, P Mostad, M Rudemo (2008), "Empirical Bayes models for multiple probe type microarrays at the probe level", BMC Bioinformatics, 9:156.
    [abstract]

  6. Keith A. Baggerly, Kevin R. Coombes (2008), "Run batch effects potentially compromise the usefulness of genomic signatures for ovarian cancer", Journal of Clinical Oncology, 26(7):1186-1187.
    [ abstract]

  7. Tathagata Banerjee, Rahul Mukerjee (2008), "Optimal factorial designs for cDNA microarray experiments", Annals of Applied Statistics, 2(1):366-385.
    [abstract]

  8. William T Barry, Andrew B Nobel, Fred A Wright (2008), "A statistical framework for testing functional categories in microarray data", Annals of Applied Statistics, 2(1):286-315.
    [abstract]

  9. SM Bentzen (2008), "From cellular to high-throughput predictive assays in radiation oncology: challenges and opportunities", Seminars in Radiation Oncology, 18(2):75-88.

  10. Marta Blangiardo, Sylvia Richardson (2008), "A Bayesian calibration model for combining different pre-processing methods in Affymetrix chips",
    BMC Bioinformatics, 9:512
    [abstract]

  11. AL Boulesteix, C Strobl, T Augustin, M Daumer (2008), "Evaluating microarray-based classifiers: an overview", Cancer Informatics, 6:77-97.
    [html]

  12. Rosemary Braun, Leslie Cope, Giovanni Parmigiani (2008), "Identifying differential correlation in gene/pathway combinations", BMC Bioinformatics, 9:488
    [abstract]

  13. Laurent Bréhélin, Olivier Gascuel, and Olivier Martin (2008), "Using repeated measurements to validate hierarchical gene clusters", Bioinformatics, 24(5):682-688
    [abstract]

  14. CJ Burden (2008), "Understanding the physics of oligonucleotide microarrays: The Affymetrix spike-in data reanalyzed", Physical Biology, 5:016004.
    [abstract]

  15. S Calza, D Valentini, Y Pawitan (2008), "Normalization of oligonucleotide arrays based on the least-variant set of genes", BMC Bioinformatics, 9(1):140.
    [abstract]

  16. Lin S Chen, John D Storey (2008), "Eigen-R2 for dissecting variation in high-dimensional studies", Bioinformatics, 24(19):2260-2262.
    [abstract]

  17. Rong Chen, Rohan Mallelwar, Ajit Thosar, Shivkumar Venkatasubrahmanyam, Atul J Butte (2008), "GeneChaser: Identifying all biological and clinical conditions in which genes of interest are differentially expressed", BMC Bioinformatics, 9:548
    [abstract]

  18. Xi Chen, Lily Wang, Jonathan D. Smith, Bing Zhang (2008), "Supervised principal component analysis for gene set enrichment of microarray data with continuous or survival outcomes", Bioinformatics, 24:2474-2481.
    [abstract]

  19. V Choi, Y Huang, V Lam, D Potter, R Laubenbacher, K Duca (2008), "Using formal concept analysis for microarray data comparison", Journal of Bioinformatics and Computational Biology, 6(1):65-75.

  20. Li-Yeh Chuang, Hsueh-Wei Chang, Chung-Jui Tu, Cheng-Hong Yang (2008), "Improved binary PSO for feature selection using gene expression data", Computational Biology and Chemistry, 32(1):29-38.
    [ abstract]

  21. Robert Clarke, Habtom W Ressom, Antai Wang, Jianhua Xuan, Minetta C Liu, Edmund A Gehan, Yue Wang (2008), "The properties of high-dimensional data spaces: implications for exploring gene and protein expression data", Nature Reviews Cancer, 8:37-49.
    [abstract]

  22. Luca Corradi, Marco Fato, Ivan Porro, Silvia Scaglione, Livia Torterolo (2008), "A Web-based and Grid-enabled dChip version for the analysis of large sets of gene expression data", BMC Bioinformatics, 9:480
    [abstract]

  23. Elissa J Cosgrove, Yingchun Zhou, Timothy S Gardner, Eric D Kolaczyk (2008), "Predicting gene targets of perturbations via network-based filtering of mRNA expression compendia", Bioinformatics, 24:2482-2490.
    [abstract]

  24. M Demissie, B Mascialino, S Calza, Y Pawitan (2008), "Unequal group variances in microarray data analyses", Bioinformatics, to appear.

  25. Xutao Deng, Huimin Geng, Hesham H. Ali (2008), "A Hidden Markov Model approach to predicting yeast gene function from sequential gene expression data", International Journal of Bioinformatics Research and Applications, 4(3):263-273.
    [ abstract]

  26. AA Desai, P Hysi, JG Garcia (2008), "Integrating genomic and clinical medicine: searching for susceptibility genes in complex lung diseases", Translational Research, 151(4):181-193.

  27. Marcilio CP De Souto, Ivan G Costa, Daniel SA de Araujo, Teresa B Ludermir, Alexander Schliep (2008), "Clustering cancer gene expression data: a comparative study", BMC Bioinformatics, 9:497
    [abstract]

  28. Karthik Devarajan (2008), "Nonnegative matrix factorization: an analytical and interpretive tool in computational biology", PLoS Computational Biology, 4(7):e1000029.
    [ abstract]

  29. Mikhail F Dozmorov, Kimberly D Kyker, Paul J Hauser, Ricardo Saban, David D Buethe, Igor Dozmorov, Michael B Centola, Daniel J Culkin, Robert E Hurst (2008), "From microarray to biology: an integrated experimental, statistical and in silico analysis of how the extracellular matrix modulates the phenotype of cancer cells", BMC Bioinformatics, 9(suppl 9):S4.

  30. Sorin Draghici, Adi L. Tarca, Longfei Yu, Stephen Ethier, and Roberto Romero (2008), "KUTE-BASE: storing, downloading and exporting MIAME-compliant microarray experiments in minutes rather than hours", Bioinformatics, 24(5):738-740.
    [abstract]

  31. Michal Draminski, Alvaro Rada-Iglesias, Stefan Enroth, Claes Wadelius, Jacek Koronacki, Jan Komorowski (2008), "Monte Carlo feature selection for supervised classification", Bioinformatics, 24:110-117.
    [abstract]

  32. Liping Du, Shuanhu Wu, Alan Wee-Chung Liew, David K Smith, Hong Yan (2008), "Spectral analysis of microarray gene expression time series data of Plasmodium falciparum", International Journal of Bioinformatics Research and Applications, 4(3):337-349.
    [ abstract]

  33. Pan Du, Warren A. Kibbe, Simon M. Lin (2008), "lumi: a pipeline for processing Illumina microarray", Bioinformatics, 24(13):1547-1548.
    [abstract]

  34. Zhihua Du, Yiwei Wang, Zhen Ji (2008), "PK-means: A new algorithm for gene clustering", Computational Biology and Chemistry, 32(4):243-247.
    [ abstract]

  35. Dorothea Emig, Melissa S Cline, Thomas Lengauer, Mario Albrecht (2008), "Integrating expression data with domain interaction networks", Bioinformatics, 24(21):2546-2548.
    [abstract]

  36. O Ericsson, Jarvius J, Schallmeiner E, Howell M, Nong RY, Reuter H, Hahn M, Stenberg J, Nilsson M, Landegren U. (2008), "A dual-tag microarray platform for high-performance nucleic acid and protein analyses", Nucleic Acids Research, to appear.

  37. CR Farber, AJ Lusis (2008), "Integrating global gene expression analysis and genetics", Advances in Genetics, 60:571-601.

  38. E Ferkingstad, A Frigessi, H Lyng (2008), "Indirect genomic effects on survival from gene expression data", Genome Biology, 9(3):R58.

  39. JA Ferreiraa, SO Nyangoma (2008), "A multivariate version of the Benjamini?Hochberg method", Journal of Multivariate Analysis, to appear.
    [ abstract]

  40. Holger Fröhlich, Tim Beißbarth, Achim Tresch, Dennis Kostka, Juby Jacob, Rainer Spang, F Markowetz (2008), "Analyzing gene perturbation screens with nested effects models in R and bioconductor", Bioinformatics, 24(21):2549-2550.
    [abstract]

  41. K Fundel, J Haag, PM Gebhard, R Zimmer, T Aigner (2008), "Normalization strategies for mRNA expression data in cartilage research", Osteoarthritis and Cartilage, to appear.
    [abstract]

  42. R García-Escudero, JM Paramio (2008), "Gene expression profiling as a tool for basic analysis and clinical application of human cancer", Molecular carcinogenesis, to appear.

  43. Raffaele Giancarlo, Davide Scaturro, Filippo Utro (2008), "Computational cluster validation for microarray data analysis: experimental assessment of clest, consensus clustering, figure of merit, gap statistics and model explorer", BMC Bioinformatics, 9:462
    [abstract]

  44. VS Gomase, S Tagore, KV Kale (2008), "Microarray: an approach for current drug targets", Current Drug Metabolism, 9(3):221-231.

  45. Michael Gormley, Aydin Tozeren (2008), "Expression profiles of switch-like genes accurately classify tissue and infectious disease phenotypes in model-based classification", BMC Bioinformatics, 9:486
    [abstract]

  46. B Haibe-Kains, C Desmedt, C Sotiriou, G Bontempi (2008), "A comparative study of survival models for breast cancer prognostication based on microarray data: does a single gene beat them all?", Bioinformatics, 24(19):2200-2208.
    [abstract]

  47. Morihiro Hayashida, Fuyan Sun, Sachiyo Aburatani, Katsuhisa Horimoto, Tatsuya Akutsu (2008), "Integer programming-based approach to allocation of reporter genes for cell array analysis", International Journal of Bioinformatics Research and Applications, 4(4):385-399.
    [ abstract]

  48. Z He, J Zhou (2008), "Empirical evaluation of a new method for calculating signal to noise ratio (SNR) for microarray data analysis", Applied and Environmental Microbiology, to appear.

  49. A D Hershey, D Burdine, C Liu, T G Nick, D L Gilbert, T A Glauser (2008), "Assessing quality and normalization of microarrays: case studies using neurological genomic data", Acta Neurologica Scandinavica, to appear.
    [abstract]

  50. Rattikorn Hewett, Phongphun Kijsanayothin (2008), "Tumor classification ranking from microarray data", BMC Genomics, 9(suppl 2):S21.
    [abstract]

  51. Fangxin Hong, Rainer Breitling (2008), "A comparison of meta-analysis methods for detecting differentially expressed genes in microarray experiments", Bioinformatics, 24:374-382.
    [abstract]

  52. Jianhua Hu (2008), "Cancer outlier detection based on likelihood ratio test", Bioinformatics, 24(19):2193-2199.
    [abstract]

  53. Manuela Hummel, Reinhard Meister, Ulrich Mansmann (2008), "GlobalANCOVA: exploration and assessment of gene group effects", Bioinformatics, 24:78-85.
    [abstract]

  54. Susan McLean Hunter, Fiona C Mansergh, Martin J Evans (2008), "Optimization of minuscule samples for use with cDNA microarrays", Journal of Biochemical and Biophysical Methods, to appear.
    [ abstract]

  55. BH Hwang, HJ Cha (2008), "Quantitative oligonucleotide microarray data analysis with an artificial standard probe strategy. Biosensors & Bioelectronics, to appear.

  56. W Jiang, S Varma, R Simon (2008), "Calculating confidence intervals for prediction error in microarray classification using resampling", Statistical Applications in Genetics and Molecular Biology, 7:8.

  57. A Joshi, Y Van de Peer, T Michoel (2008), "Analysis of a Gibbs sampler method for model based clustering of gene expression data", Bioinformatics, 24:176-183.
    [abstract]

  58. Tommy S Jørstad, Herman Midelfart, Atle M Bones (2008), "A mixture model approach to sample size estimation in two-sample comparative microarray experiments", BMC Bioinformatics, 9:117.
    [abstract]

  59. Giuseppe Jurman, Stefano Merler, Annalisa Barla, Silvano Paoli, Antonio Galea, Cesare Furlanello (2008), "Algebraic stability indicators for ranked lists in molecular profiling", Bioinformatics, 24:258-264.
    [abstract]

  60. Koji Kadota, Yuji Nakai, Kentaro Shimizu (2008), "A weighted average difference method for detecting differentially expressed genes from microarray data", Algorithms for Molecular Biology, 3:8.
    [abstract]

  61. Rei Kakuhata, Masahiro Watanabe, Takenori Yamamoto, Eriko Obana, Naoshi Yamazaki, Masatoshi Kataoka, Toshihiko Ooie, Yoshinobu Baba, Tomoshige Hori, Yasuo Shinohara (2008), "Importance of probe location for quantitative comparison of signal intensities among genes in microarray analysis", Journal of Biochemical and Biophysical Methods, to appear.
    [abstract]

  62. Andreas Keller, Christina Backes, Maher Al-Awadhi, Andreas Gerasch, Jan Küntzer, Oliver Kohlbacher, Michael Kaufmann, Hans-Peter Lenhof (2008), "GeneTrailExpress: a web-based pipeline for the statistical evaluation of microarray experiments", BMC Bioinformatics, 9:552
    [abstract]

  63. Ryan Kelley, Hoda Feizi, Trey Ideker (2008), "Correcting for gene-specific dye bias in DNA microarrays using the method of maximum likelihood", Bioinformatics, 24:71-77.
    [abstract]

  64. Chang Sik Kim (2008), "Self-organizing maps with statistical phase synchronization (SOMPS) for analyzing cell cycle-specific gene expression data", Statistical Applications in Genetics and Molecular Biology, 7:1.
    [abstract]

  65. Jaehee Kim, Haseong Kim (2008), "Clustering of change patterns using Fourier coefficients", Bioinformatics, 24:184-191.
    [abstract]

  66. TA Knijnenburg, LFA Wessels, MJT Reinders (2008), "Creating gene set activity profiles with time-series expression data", International Journal of Bioinformatics Research and Applications, 4(3):306-323.
    [ abstract]

  67. H Koltai, C Weingarten-Baror (2008), "Specificity of DNA microarray hybridization: characterization, effectors and approaches for data correction", Nucleic Acids Research, to appear.

  68. X Kong, V Mas, KJ Archer (2008), "A non-parametric meta-analysis approach for combining independent microarray datasets: application using two microarray datasets pertaining to chronic allograft nephropathy", BMC Genomics, 9:98.
    [abstract]

  69. Tomokazu Konishi (2008), "Data distribution of short oligonucleotide expression arrays and its application to the construction of a generalized intellectual framework", Statistical Applications in Genetics and Molecular Biology, 7:25.
    [abstract]

  70. Tomokazu Konishi, Fumikazu Konishi, Shigeru Takasaki, Kohei Inoue, Koji Nakayama, Akihiko Konagaya (2008), "Coincidence between transcriptome analyses on different microarray platforms using a parametric framework", PLoS ONE, 3(10):e3555.
    [ abstract]

  71. Sun-Yuan Kung, Man-Wai Mak (2008), "Feature selection for self-supervised classification with applications to microarray and sequence data", IEEE Journal of Selected Topics in Signal Processing, 2(3):297-309
    [ abstract]

  72. Yinglei Lai (2008), "Genome-wide co-expression based prediction of differential expressions", Bioinformatics, 24(5):666-673.
    [abstract]

  73. Chang-Tsun Li, Yinyin Yuan, Roland Wilson (2008) "An unsupervised conditional random fields approach for clustering gene expression time series", Bioinformatics, 24:2467-2473.
    [abstract]

  74. Guo-Zheng Li, Hua-Long Bu, Mary Qu Yang, Xue-Qiang Zeng, Jack Y Yang (2008), "Selecting subsets of newly extracted features from PCA and PLS in microarray data analysis", BMC Genomics, 9(suppl 2):S24.
    [abstract]

  75. J Li, JP Fine (2008), "ROC analysis with multiple classes and multiple tests: methodology and its application in microarray studies", Biostatistics, to appear.

  76. Illumina
    SM Lin, P Du, W Huber, WA Kibbe (2008), "Model-based variance-stabilizing transformation for Illumina microarray data", Nucleic Acids Research, 36(2):e11.

  77. Rongheng Lin, Shuangshuang Dai, Richard D Irwin, Alexandra N Heinloth, Gary A Boorman, Leping Li (2008), "Gene set enrichment analysis for non-monotone association and multiple experimental categories", BMC Bioinformatics, 9:481
    [abstract]

  78. BH Liu, CH Goh, LL Ooi, KM Hui (2008), "Identification of unique and common low abundance tumour-specific transcripts by suppression subtractive hybridization and oligonucleotide probe array analysis", Oncogene, to appear.

  79. affymetrix
    Hsi-Che Liu Chien-Yu Chen, Yu-Ting Liu, Cheng-Bang Chu, Der-Cherng Liang, Lee-Yung Shih, Chih-Jen Lin (2008), "Cross-generation and cross-laboratory predictions of Affymetrix microarrays by rank-based methods", Journal of Biomedical Informatics, to appear
    [abstract]

  80. James Long, Mitchell Roth (2008), "Synthetic microarray data generation with RANGE and NEMO", Bioinformatics, 24:132-134.
    [abstract]

  81. Fabrício Martins Lopes, David Corrêa Martins Jr, Roberto M Cesar Jr (2008), "Feature selection environment for genomic applications", BMC Bioinformatics, 9:451
    [abstract]
    Correction: 10:285 (2009)
    [abstract]

  82. Shuangge Ma and Jian Huang (2009), "Penalized feature selection and classification in bioinformatics", Briefings in Bioinformatics, 9:392-403.
    [abstract]

  83. Paolo Magni, Fulvia Ferrazzi, Lucia Sacchi, Riccardo Bellazzi (2008), "TimeClust: a clustering tool for gene expression time series", Bioinformatics, 24(3):430-432
    [abstract]

  84. protein
    N Marthandan, S Klyza, S Li, YU Kwon, T Kodadek, HR Garner (2008) "Construction and evaluation of an automated light directed protein-detecting microarray synthesizer", IEEE Transactions on Nanobioscience, 7(1):20-27.

  85. Daniele Masotti, Christine Nardini, Simona Rossi, Elena Bonora, Giovanni Romeo, Stefano Volinia, Luca Benini (2008), "TOM: enhancement and extension of a tool suite for in silico approaches to multigenic hereditary disorders", Bioinformatics, 24(3):428-429.
    [abstract]

  86. PE Meyer, C Schretter, G Bontempi (2008), "Information-iheoretic feature selection in microarray data using variable complementarity", IEEE Journal of Selected Topics in Signal Processing, 2(3):261-274
    [ abstract]

  87. JA Morris, SA Gayther, IJ Jacobs, C Jones (2008), "A suite of Perl modules for handling Microarray data", Bioinformatics, to appear.

  88. Dougu Nam and Seon-Young Kim (2008), "Gene-set approach for expression pattern analysis", Briefings in Bioinformatics, 9:189-197.
    [abstract]

  89. Dan Nettleton, Justin Recknor, James M. Reecy (2008), "Identification of differentially expressed gene categories in microarray studies using nonparametric multivariate analysis", Bioinformatics, 24:192-201.
    [abstract]

  90. Terri T Ni, William J Lemon, Yu Shyr, Tao P Zhong (2008), "Use of normalization methods for analysis of microarrays containing a high degree of gene effects", BMC Bioinformatics, 9:505.
    [abstract]

  91. F Ojeda, JA Suykens, B De Moor (2008), "Low rank updated LS-SVM classifiers for fast variable selection", Neural Networks, 21(2-3):437-449.

  92. K Owzar, W T Barry, S-H Jung, I Sohn, S L George (2008), "Statistical challenges in preprocessing in microarray experiments in cancer", Clinical Cancer Research, 14(19):5959-5966.
    [ abstract]

  93. Z Pan, Y Li, D Zhou, J Tang, M Zhang, P Xiao, Z Lu (2008), "Ultrasonic approach to enhance signal-to-noise in three dimensional microarray", Analytical Biochemistry, to appear.

  94. F Parvaresh, H Vikalo, S Misra, B Hassibi (2008), "Recovering sparse signals using sparse measurement matrices in compressed DNA microarrays", IEEE Journal of Selected Topics in Signal Processing, 2(3):275-285
    [ abstract]

  95. Richard D Pearson (2008), "A comprehensive re-analysis of the Golden Spike data: Towards a benchmark for differential expression methods", BMC Bioinformatics, 9:164.
    [abstract]

  96. P Pedotti, PA 't Hoen, E Vreugdenhil, GJ Schenk, RH Vossen, Y Ariyurek, M de Hollander, R Kuiper, GJ van Ommen, JT den Dunnen, JM Boer, RX de Menezes (2008), "Can subtle changes in gene expression be consistently detected with different microarray platforms?", BMC Genomics, 9:124.
    [abstract]

  97. Carl R Pelz, Molly Kulesz-Martin, Grover Bagby, Rosalie C Sears (2008), "Global rank-invariant set normalization (GRSN) to reduce systematic distortions in microarray data", BMC Bioinformatics, 9:520
    [abstract]

  98. A Ptitsyn (2008), "Stochastic resonance reveals "pilot light" expression in mammalian genes", PLoS ONE, 3(3):e1842.

  99. M Qureshi, A Ivens (2008), "A software framework for microarray and gene expression object model (MAGE-OM) array design annotation", BMC Genomics, 9:133.
    [abstract]

  100. J Rausenberger, M Kollmann (2008), "Quantifying origins of cell-to-cell variations in gene expression", Biophysical Journal, to appear.

  101. Wolfgang Raffelsberger, Yannick Krause, Luc Moulinier, David Kieffer, Anne-Laure Morand, Laurent Brino, Olivier Poch (2008), "RReportGenerator: automatic reports from routine statistical analysis using R", Bioinformatics, 24:276-278.
    [abstract]

  102. E A Rakha, M E El-Sayed, J S Reis-Filho I O Ellis (2008), "Expression profiling technology: its contribution to our understanding of breast cancer", Histopathology, 52(1):67-81.
    [ abstract]

  103. Robert W Reid, Anthony A Fodor (2008), "Determining gene expression on a single pair of microarrays", BMC Bioinformatics, 9:489
    [abstract]

  104. Antonio Reverter, Eva K F Chan (2008), "Combining partial correlation and an information theory approach to the reversed engineering of gene co-expression networks", Bioinformatics, 24:2491-2497.
    [abstract]

  105. Alexander L Richards, Peter Holmans, Michael C O'Donovan, Michael J Owen, Lesley Jones (2008), "A comparison of four clustering methods for brain expression microarray data", BMC Bioinformatics, 9:490
    [abstract]

  106. Peter C Roberts (2008), "Gene expression microarray data analysis demystified", Biotechnology Annual Review, 14:29-61.

  107. N Rosenfeld, Aharonov R, Meiri E, Rosenwald S, Spector Y, Zepeniuk M, Benjamin H, Shabes N, Tabak S, Levy A, Lebanony D, Goren Y, Silberschein E, Targan N, Ben-Ari A, Gilad S, Sion-Vardy N, Tobar A, Feinmesser M, Kharenko O, Nativ O, Nass D, Perelman M, Yosepovich A, Shalmon B, Polak-Charcon S, Fridman E, Avniel A, Bentwich I, Bentwich Z, Cohen D, Chajut A, Barshack I (2008), "MicroRNAs accurately identify cancer tissue origin", Nature Biotechnology, to appear.

  108. SA Salem, LB Jack, AK Nandi (2008), "Investigation of self-organizing oscillator networks for use in clustering microarray data", IEEE Transactions on Nanobioscience, 7(1):65-79.

  109. Audrey Sassolas, Béatrice D Leca-Bouvier, Loïc J Blum (2008), "DNA Biosensors and microarrays", Chemical Reviews, 108(1):109-139.
    [ abstract]

  110. A A Shabalin, H Tjelmeland, C Fan, C M Perou, A B Nobel (2008), "Merging two gene-expression studies via cross-platform normalization", Bioinformatics, 24(9):1154-1160.
    [ abstract]

  111. Leming Shi, Roger G Perkins, Hong Fang, Weida Tong (2008), "Reproducible and reliable microarray results through quality control: good laboratory proficiency and appropriate data analysis practices are essential", Current Opinion in Biotechnology, 19(1):10-18.
    [ abstract]

  112. Sarah Song, Michael A Black (2008), "Microarray-based gene set analysis: a comparison of current methods", BMC Bioinformatics, 9:502
    [abstract]

  113. Satish Tadepalli, Naren Ramakrishnan, Layne T Watson, Bhubaneshwar Mishra, Richard F Helm (2008), "Simultaneous segmenting multiple gene expression time courses by analysing cluster dynamics", Proceedings of the 6th Asia-Pacific Bioinformatics Conference eds. A Brazma, S Miyano, T Akutsu, pp.297-306 (Imperial College Press).

  114. YD Tan, M Fornage, H Xu (2008), "Ranking analysis of F-atatistics for microarray data", BMC Bioinformatics, 9:142.
    [abstract]

  115. Nathan L Tintle, Aaron A Best, Matthew DeJongh, Dirk Van Bruggen, Fred Heffron, Steffen Porwollik, Ronald C Taylor (2008), "Gene set analyses for interpreting microarray experiments on prokaryotic organisms", BMC Bioinformatics, 9:469
    [abstract]

  116. H Vikalo, B Hassibi, A Hassibi (2008), "Modeling and estimation for real-time microarrays", IEEE Journal of Selected Topics in Signal Processing, 2(3):286-296.
    [ abstract]

  117. D Voduc, C Kenney, TO Nielsen (2008), "Tissue microarrays in clinical oncology", Seminars in Radiation Oncology, 18(2):89-97.

  118. Brandie D Wagner, Gary O Zerbe, Sharon Mexal, Sherry S Leonard (2008), "Permutation-based adjustments for the significance of partial regression coefficients in microarray data analysis", Genetic Epidemiology, 32(1):1-8.
    [ abstract]

  119. H Wang, X He (2008), "An enhanced quantile approach for assessing differential gene expressions", Biometrics, to appear.

  120. L Wang, M Montano, M Rarick, P Sebastiani (2008), "Conditional clustering of temporal expression profiles", BMC Bioinformatics, 9(1):147.
    [abstract]

  121. Li Wang, Ji Zhu, Hui Zou (2008), "Hybrid huberized support vector machines for microarray classification and gene selection", Bioinformatics, 24(3):412-419.
    [abstract]

  122. Z Wang, F Yang, DW Ho, S Swift, A Tucker, X Liu (2008), "Stochastic dynamic modeling of short gene expression time-series data", IEEE Transactions on Nanobioscience, 7(1):44-55.

  123. Zhi Wei, Hongzhe Li (2008), "A hidden spatial-temporal Markov random field model for network-based analysis of time course gene expression data", Annals of Applied Statistics, 2(1):408-429.
    [abstract]

  124. CL Willman (2008), "Has gene expression profiling improved diagnosis, classification, and outcome prediction in AML?", Best Practice & Research. Clinical Haematology, 21(1):21-28.

  125. affymetrix
    Illumina
    Wing-Cheong Wong, Marie Loh, Frank Eisenhaber (2008), "On the necessity of different statistical treatment for Illumina BeadChip and Affymetrix GeneChip data and its significance for biological interpretation", Biology Direct, 3:23.
    [ abstract]

  126. Huiling Xiong, Dapeng Zhang, Christopher J Martyniuk, Vance L Trudeau, Xuhua Xia (2008), "Using Generalized Procrustes Analysis (GPA) for normalization of cDNA microarray data", BMC Bioinformatics, 9:25.
    [abstract]

  127. L Xu, AC Tan, RL Winslow, D Geman (2008), "Merging microarray data from separate breast cancer studies provides a robust prognostic test", BMC Bioinformatics, 9:125.
    [abstract]

  128. Tao Xu, LinFang Du, Yan Zhou (2008), "Evaluation of GO-based functional similarity measures using S. cerevisiae protein interaction and expression profile data", BMC Bioinformatics, 9:472
    [abstract]

  129. Xiaojiang Xu, Yingdong Zhao, Richard Simon (2008), "Gene set expression comparison kit for BRB-ArrayTools", Bioinformatics, 24:137-139.
    [abstract]

  130. Da Yang, Yanhui Li, Hui Xiao, Qing Liu, Min Zhang, Jing Zhu, Wencai Ma, Chen Yao, Jing Wang, Dong Wang, Zheng Guo, Baofeng Yang (2008), "Gaining confidence in biological interpretation of the microarray data: the functional consistence of the significant GO categories", Bioinformatics, 24:265-271
    [abstract]

  131. Jigang Zhang, Jian Li, Hongwen Deng (2008), "Class-specific correlations of gene expressions: identification and their effects on clustering analyses", American Journal of Human Genetics, 83:269-277.
    [ abstract]

  132. Wei Zhang, Shiwei Duan, Emily O Kistner, Wasim K Bleibel, R Stephanie Huang, Tyson A Clark, Tina X Chen, Anthony C Schweitzer, John E Blume, Nancy J Cox, M Eileen Dolan (2008), "Evaluation of genetic variation contributing to differences in gene expression between populations", American Journal of Human Genetics, 82(3):631-640.
    [ abstract]

  133. Yi Zhang, Chris Ding, Tao Li (2008), "Gene selection algorithm by combining reliefF and mRMR", BMC Genomics, 9(suppl 2):S27.
    [abstract]

  134. JX Zhu, GJ McLachlan, L Ben-Tovim, I Wood (2008), "On selection biases with prediction rules formed from gene expression data", Journal of Statistical Planning and Inference, 38:374-386.

  135. Elias Zintzaras, John P.A. Ioannidis (2008), "Meta-analysis for ranked discovery datasets: Theoretical framework and empirical demonstration for microarrays", Computational Biology and Chemistry, 32(1):39-47.
    [ abstract]

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2008