Bibliography on
Microarray Data Analysis

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© Copyright, 1999-2008 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. 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]

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

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

  6. 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]

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

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

  9. 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]

  10. 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.

  11. 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]

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

  13. 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.

  14. 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]

  15. 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]

  16. 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.

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

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

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

  20. 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]

  21. 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.

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

  23. 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.

  24. 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]

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

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

  27. 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]

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

  29. 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.

  30. 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]

  31. 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]

  32. 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]

  33. 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]

  34. 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]

  35. 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]

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

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

  38. 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]

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

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

  41. 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.

  42. 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]

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

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

  45. 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.

  46. 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]

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

  48. 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]

  49. 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.

  50. 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.

  51. 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]

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

  53. 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]

  54. 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]

  55. 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]

  56. 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.

  57. 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.

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

  59. 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]

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

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

  62. 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]

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

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

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

  66. 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.

  67. 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]

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

  69. 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]

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

  71. 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]

  72. 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.

  73. M Zucknick, S Richardson, EA Stronach (2008), "Comparing the characteristics of gene expression profiles derived by univariate and multivariate classification methods", Statistical Applications in Genetics and Molecular Biology, 7:7.
2008