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/
2007

  1. Miika Ahdesmäki, Harri Lähdesmäki, Andrew Gracey, llya Shmulevich, Olli Yli-Harja (2007), "Robust regression for periodicity detection in non-uniformly sampled time-course gene expression data", BMC Bioinformatics, 8:233.
    [abstract]

  2. Andrew Y Gracey (2007), "Interpreting physiological responses to environmental change through gene expression profiling", Journal of Experimental Biology, 210:1584-1592.
    [abstract]

  3. W Gregory Alvord, Jean A Roayaei, Octavio A Quiñones, Katherine T Schneider (2007), "A microarray analysis for differential gene expression in the soybean genome using Bioconductor and R", Briefings in Bioinformatics, 8:415-431.
    [abstract]

  4. Claudia Angelini, Daniela De Canditiis, Margherita Mutarelli, Marianna Pensky (2007), "A Bayesian approach to estimation and testing in time-course microarray experiments", Statistical Applications in Genetics and Molecular Biology, 6:24.
    [abstract]

  5. Kellie J Archer, Catherine I Dumur, G Scott Taylor, Michael D Chaplin, Anthony Guiseppi-Elie, Geraldine Grant, Andrea Ferreira-Gonzalez, Carleton T. Garrett (2007), "Application of a correlation correction factor in a microarray cross-platform reproducibility study", BMC Bioinformatics, 8:447.
    [abstract]

  6. Magnus Astrand, Petter Mostad, Mats Rudemo (2007), "Improved covariance matrix estimators for weighted analysis of microarray data", Journal of Computational Biology, 14(10):1353-1367.
    [abstract]

  7. C Backes, A Keller, J Kuentzer, B Kneissl, N Comtesse, YA Elnakady, R Müller, E Meese, HP Lenhof (2007), "GeneTrail--advanced gene set enrichment analysis", Nucleic Acids Research, 35(web server issue):W186-W192.

  8. Jangsun Baek, Young Sook Son, Geoffrey J McLachlan (2007), "Segmentation and intensity estimation of microarray images using a gamma-t mixture model", Bioinformatics, 23:458-465.
    [abstract]

  9. Carmiya Bar-Or, Henryk Czosnek, Hinanit Koltai (2007), "Cross-species microarray hybridizations: a developing tool for studying species diversity", Trends in Genetics, 23(4):200-207.

  10. protein
    Sudeepa Bhattacharyya, Stephanie Byrum, Eric R Siegel, Larry J Suva (2007), "Proteomic analysis of bone cancer: a review of current and future developments", Expert Review of Proteomics, 4(3):371-378.
    [ abstract]

  11. Marta Blangiardo, Sylvia Richardson (2007), "Statistical tools for synthesizing lists of differentially expressed features in related experiments", Genome Biology, 8(4):R54,
    [abstract]

  12. Jacob PL Brand, Lang Chen, Xiangqin Cui, Alfred A Bartolucci, Grier P Page, Kyoungmi Kim, Stephen Barnes, Vinodh Srinivasasainagendra, Mark T Beasley, David B Allison (2007), "An adaptive alpha spending algorithm improves the power of statistical inference in microarray data analysis", Bioinformation, 1(10):384-389.
    [abstract]

  13. Grzegorz M Boratyn, Susmita Datta, Somnath Datta (2007), "Incorporation of biological knowledge into distance for clustering genes", Bioinformation, 1(10):396-405.
    [abstract]

  14. Anne-Laure Boulesteix (2007), "WilcoxCV: an R package for fast variable selection in cross-validation", Bioinformatics, 23:1702-1704.
    [abstract]

  15. Anne-Laure Boulesteix, Korbinian Strimmer (2007), "Partial least squares: a versatile tool for the analysis of high-dimensional genomic data", Briefings in Bioinformatics, 8:32-44.
    [abstract]

  16. Mark F Burkart, Jonathan D Wren, Jason I Herschkowitz, Charles M Perou, Harold R Garner (2007), "Clustering microarray-derived gene lists through implicit literature relationships", Bioinformatics, 23:1995-2003.
    [abstract]

  17. Max Bylesjö, Daniel Eriksson, Andreas Sjödin, Stefan Jansson, Thomas Moritz, Johan Trygg (2007), "Orthogonal projections to latent structures as a strategy for microarray data normalization", BMC Bioinformatics, 8:207.
    [abstract]

  18. Zhipeng Cai, Randy Goebel, Mohammad R Salavatipour, Guohui Lin (2007), "Selecting dissimilar genes for multi-class classification, an application in cancer subtyping", BMC Bioinformatics, 8:206.
    [abstract]

  19. Z Cai, R Goebel, MR Salavatipour, Y Shi, L Xu, G Lin (2007), "Selecting genes with dissimilar discrimination strength for sample class prediction", Proceedings of the 5th Asia-Pacific Bioinformatics Conference eds. D Sankoff, L Wang, F Chin, pp. 81-90 (Imperial College Press, London).

  20. R Cangelosi, A Goriely (2007), "Component retention in principal component analysis with application to cDNA microarray data", Biology Direct, 2:2.
    [ abstract]

  21. Kim-Anh Le Cao, Olivier Gonçalves, Philippe Besse, Sébastien Gadat (2007), "Selection of biologically relevant genes with a wrapper stochastic algorithm", Statistical Applications in Genetics and Molecular Biology, 6:29.
    [abstract]

  22. Vincent J Carey, Martin Morgan, Seth Falcon, Ross Lazarus, Robert Gentleman (2007), "GGtools: analysis of genetics of gene expression in bioconductor", Bioinformatics, 23:522-523.
    [abstract]

  23. Tineke Casneuf, Yves Van de Peer, Wolfgang Huber (2007), "In situ analysis of cross-hybridisation on microarrays and the inference of expression correlation", BMC Bioinformatics, 8:461.
    [abstract]

  24. James Chen, Huey-Miin Hsueh, Robert Delongchamp, Chien-Ju Lin, Chen-An Tsai (2007), "Reproducibility of microarray data: a further analysis of microarray quality control (MAQC)data", BMC Bioinformatics, 8:412.
    [abstract]

  25. Jinsong Chen, Mark J. van der Laan, Martyn T. Smith, Alan E. Hubbard (2007), "A comparison of methods to control type I errors in microarray studies", Statistical Applications in Genetics and Molecular Biology, 6:28.
    [abstract]

  26. Junfeng Chen, Vikas Agrawal, Magnus Rattray, Marilyn AL West, Dina A St Clair, Richard W Michelmore, Sean J Coughlan, Blake C Meyers (2007), "A comparison of microarray and MPSS technology platforms for expression analysis of Arabidopsis", BMC Genomics, 8:414.
    [abstract]

  27. affymetrix
    Zhongxue Chen, Monnie McGee, Qingzhong Liu, Richard H Scheuermann (2007), "A distribution free summarization method for Affymetrix GeneChip® arrays", Bioinformatics, 23:321-327.
    [abstract]

  28. Cheng Cheng, Stan Pounds (2007), "False discovery rate paradigms for statistical analyses of microarray gene expression data", Bioinformation, 1(10): 436-446.
    [abstract]

  29. Hyungwon Choi, Ronglai Shen, Arul M Chinnaiyan, Debashis Ghosh (2007), "A latent variable approach for meta-analysis of gene expression data from multiple microarray experiments", BMC Bioinformatics, 8:364.
    [abstract]

  30. V Choi, Y Huang, V Lam, D Potter, R Laubenbacher, K Duca (2007), "Using formal concept analysis for microarray data comparison", Proceedings of the 5th Asia-Pacific Bioinformatics Conference eds. D Sankoff, L Wang, F Chin, pp. 57-66 (Imperial College Press, London).

  31. Jeff W Chou, Tong Zhou, William K Kaufmann, Richard S Paules, Pierre R Bushel (2007), "Extracting gene expression patterns and identifying co-expressed genes from microarray data reveals biologically responsive processes", BMC Bioinformatics, 8:427.
    [abstract]

  32. protein
    MA Coleman, PT Beernink, A Camarero, JS Albala (2007), "Applications of functional protein microarrays: identifying protein-protein interactions in an array format", Methods in Molecular Biology, 385:121-130.

  33. Francesca Cordero, Marco Botta, Raffaele A Calogero (2007), "Microarray data analysis and mining approaches", Briefings in Functional Genomics and Proteomics, 6: 265-281.
    [abstract]

  34. Alan R Dabney, John D Storey (2007), "Normalization of two-channel microarrays accounting for experimental design and intensity-dependent relationships", Genome Biology, 8(3):R44,
    [abstract]

  35. Cyril Dalmasso, Avner Bar-Hen, Philippe Broët (2007), "A constrained polynomial regression procedure for estimating the local False Discovery Rate", BMC Bioinformatics, 8:229.
    [abstract]

  36. affymetrix
    Allen Day, Marc RJ Carlson, Jun Dong, Brian D O'Connor, Stanley F Nelson (2007), "Celsius: a community resource for Affymetrix microarray data", Genome Biology, 8(6):R112,
    [abstract]

  37. J R de Haan, R Wehrens, S Bauerschmidt, E Piek, R C van Schaik, L M C Buydens (2007), "Interpretation of ANOVA models for microarray data using PCA", Bioinformatics, 23:184-190.
    [abstract]

  38. S Dejean, PGP Martin, A Baccini, P Besse (2007), "Clustering time-series gene expression data using smoothing spline derivatives", EURASIP Journal on Bioinformatics and Systems Biology, article ID 70561.

  39. KA Do, GJ McLachlan, RW Bean, S Wen (2007), "Application of gene shaving and mixture models to cluster microarray gene expression data", Cancer Informatics, 2:1-19.

  40. Marta Campo Dell'Orto, Andrea Zangrando, Luca Trentin, Rui Li, Wei-min Liu, Geertruy te Kronnie, Giuseppe Basso, Alexander Kohlmann (2007), "New data on robustness of gene expression signatures in leukemia: comparison of three distinct total RNA preparation procedures", BMC Genomics, 8:188.
    [abstract]

  41. C Desmedt, C Sotiriou (2007), "When should I start using a new biomarker: Focus on expression arrays?", European Journal of Cancer Supplements, 5(5):97-104.
    [ abstract]

  42. Ramón Diaz-Uriarte (2007), "GeneSrF and varSelRF: a web-based tool and R package for gene selection and classification using random forest", BMC Bioinformatics, 8:328.
    [abstract]

  43. Diego Diez, Rebeca Alvarez, Ana Dopazo (2007), "Codelink: an R package for analysis of GE healthcare gene expression bioarrays", Bioinformatics, 23:1168-1169.
    [abstract]

  44. Irina Dinu, John D Potter, Thomas Mueller, Qi Liu, Adeniyi J Adewale, Gian S Jhangri, Gunilla Einecke, Konrad S Famulski, Philip Halloran, Yutaka Yasui (2007), "Improving gene set analysis of microarray data by SAM-GS", BMC Bioinformatics, 8:242.
    [abstract]

  45. Dikla Dotan-Cohen, Avraham A. Melkman, Simon Kasif (2007), "Hierarchical tree snipping: clustering guided by prior knowledge", Bioinformatics, 23:3335-3342.
    [abstract]

  46. Fenghai Duan, Eliot R Spindel, Yu-Hua Li, Robert B Norgren Jr (2007), "Intercenter reliability and validity of the rhesus macaque GeneChip", BMC Genomics, 8:61.
    [abstract]

  47. Mark J Dunning, Mike L Smith, Matthew E Ritchie, Simon Tavare (2007), "beadarray: R classes and methods for Illumina bead-based data", Bioinformatics, 23(16):2183-2184.
    [abstract]

  48. A Dupuy, RM Simon (2007), "Critical review of published microarray studies for cancer outcome and guidelines on statistical analysis and reporting", Journal of National Cancer Institute, 99(2):147-157.

  49. Bradley Efron, Robert Tibshirani (2007), "On testing the significance of sets of genes", Annals of Applied Statistics, 1(1):107-129.
    [abstract]

  50. affymetrix
    Steven A Eschrich, Andrew M Hoerter (2007), "Libaffy: software for processing Affymetrix(R) GeneChip(R) data", Bioinformatics, 23:1562-1564.
    [abstract]

  51. Markus Eszlinger, Knut Krohn, Aleksandra Kukulska, Barbara Jarzab, Ralf Paschke (2007), "Perspectives and limitations of microarray-based gene expression profiling of thyroid tumors", Endocrine Reviews, 28(3):322-338.
    [abstract]

  52. Jianqing Fan, Yue Niu (2007), "Selection and validation of normalization methods for c-DNA microarrays using within-array replications", Bioinformatics, 23(18):2391-2398.
    [abstract]

  53. Rudolf S N Fehrmann, Xiang-yi Li, Ate G J van der Zee, Steven de Jong, Gerard J te Meerman, Elisabeth G E de Vries, Anne P G Crijns (2007), "Profiling studies in ovarian cancer: a review", The Oncologist, 12(8): 960-966.
    [abstract]

  54. affymetrix
    Francesco Ferrari, Stefania Bortoluzzi, Alessandro Coppe, Alexandra Sirota, Marilyn Safran, Michael Shmoish, Sergio Ferrari, Doron Lancet, Gian Antonio Danieli, Silvio Bicciato (2007), "Novel definition files for human GeneChips based on GeneAnnot", BMC Bioinformatics, 8:446.
    [abstract]

  55. Lori A Field, Rick M Jordan, Jennifer A Hadix, Michael A Dunn, Craig D Shriver, Rachel E Ellsworth, Darrell L Ellsworth (2007), "Functional identity of genes detectable in expression profiling assays following globin mRNA reduction of peripheral blood samples", Clinical Biochemistry, 40(7):499-502.
    [ abstract]

  56. EA Fischer, MA Friedman, MK Markey (2007), "Empirical comparison of tests for differential expression on time-series microarray experiments", Genomics, 89(4):460-470.
    [ abstract]

  57. Irit Fishel, Alon Kaufman, Eytan Ruppin (2007), "Meta-analysis of gene expression data: a predictor-based approach", Bioinformatics, 23:1599-1606.
    [abstract]

  58. affymetrix
    Anthony A Fodor, Timothy L Tickle, Christine Richardson (2007), "Towards the uniform distribution of null P values on Affymetrix microarrays", Genome Biology, 8(5):R69.
    [abstract]

  59. Paul Fogel, S Stanley Young, Douglas M Hawkins, Nathalie Ledirac (2007), "Inferential, robust non-negative matrix factorization analysis of microarray data", Bioinformatics, 23(1):44-49
    [abstract]

  60. BJ Frey, D Dueck (2007), "Clustering by passing messages between data points", Science, 315(5814):972-976.
    [abstract]

  61. Tancred Frickey, Georg Weiller (2007), "Analyzing microarray data using CLANS", Bioinformatics, 23:1170-1171.
    [abstract]

  62. L Fu, E Medico (2007), "FLAME, a novel fuzzy clustering method for the analysis of DNA microarray data", BMC Bioinformatics, 8:3.
    [abstract]

  63. Andre Fujita, Joao R Sato, Carlos E Ferreira, Mari C Sogayar (2007), "GEDI: a user-friendly toolbox for analysis of large-scale gene expression data", BMC Bioinformatics, 8:457.
    [abstract]

  64. ES Fung, MK Ng (2007), "On sparse Fisher discriminant method for microarray data analysis", Bioinformation, 2(5):230-234.
    [PDF]

  65. Stan Gaj, Arie van Erk, Rachel IM van Haaften, Chris TA Evelo (2007), "Linking microarray reporters with protein functions", BMC Bioinformatics, 8:360.
    [abstract]

  66. Lars Gidskehaug, Endre Anderssen, Arnar Flatberg, Bjorn K Alsberg (2007), "A framework for significance analysis of gene expression data using dimension reduction methods", BMC Bioinformatics, 8:346.
    [abstract]

  67. Chris A. Glasbey, Thorsten Forster, Peter Ghazal (2007), "Estimation of expression levels in spotted microarrays with saturated pixels", Statistical Applications in Genetics and Molecular Biology, 6:34.
    [abstract]

  68. Jelle J Goeman, Peter Bühlmann (2007), "Analyzing gene expression data in terms of gene sets: methodological issues", Bioinformatics, 23:980-987.
    [abstract]

  69. DR Goldstein, M Delorenzi, R Luthi-Carter, T Sengstag (2007), "Comparison of meta-analysis to combined analysis of a replicated microarray study", in Meta-Analysis and Combining Information in Genetics, eds. R Guerra, DB Allison, D Goldstein (CRC Press), pp.?-?.

  70. Alexander Gordon, Galina Glazko, Xing Qiu, Andrei Yakovlev (2007), "Control of the mean number of false discoveries, Bonferroni and stability of multiple testing", Annals of Applied Statistics, 1(1):179-190.
    [abstract]

  71. Michael Gormley, William Dampier, Adam Ertel, Bilge Karacali, Aydin Tozeren (2007), "Prediction potential of candidate biomarker sets identified and validated on gene expression data from multiple datasets", BMC Bioinformatics, 8:415.
    [abstract]

  72. Mark M Gosink, Howard T Petrie, Nicholas F Tsinoremas (2007), "Electronically subtracting expression patterns from a mixed cell population", Bioinformatics, 23:3328-3334.
    [abstract]

  73. Gerwyn H Green, Peter J Diggle (2007), "On the operational characteristics of the Benjamini and Hochberg false discovery rate procedure", Statistical Applications in Genetics and Molecular Biology, 6:27.
    [abstract]

  74. Jennifer A Greenhall, Matthew A Zapala, Mario Cáceres, Ondrej Libiger, Carrolee Barlow, Nicholas J Schork, David J Lockhart (2007), "Detecting genetic variation in microarray expression data", Genome Research, 17:1228-1235.
    [abstract]

  75. Attila Gyenesei, Ulrich Wagner, Simon Barkow-Oesterreicher, Etzard Stolte, Ralph Schlapbach (2007), "Mining co-regulated gene profiles for the detection of functional associations in gene expression data", Bioinformatics, 23:1927-1935.
    [abstract]

  76. Y Guo, T Hastie, R Tibshirani (2007), "Regularized linear discriminant analysis and its application in microarrays", Biostatistics, 8(1):86-100.

  77. Philippe Haldermans, Ziv Shkedy, Suzy Van Sanden, Tomasz Burzykowski, Marc Aerts (2007), "Using linear mixed models for normalization of cDNA microarrays", Statistical Applications in Genetics and Molecular Biology, 6(1):19.
    [abstract]

  78. Blaise Hanczar, Jianping Hua, Edward R Dougherty (2007), "Decorrelation of the true and estimated classification errors by feature selection in small sample settings", EURASIP Journal on Bioinformatics and Systems Biology, 2007:38473.
    [html]

  79. Johanna Hardin, Aya Mitani, Leanne Hicks, Brian VanKoten (2007), "A robust measure of correlation between two genes on a microarray", BMC Bioinformatics, 8:220.
    [abstract]

  80. B Heidecker, JM Hare (2007), "The use of transcriptomic biomarkers for personalized medicine", Heart Failure Reviews, 12(1):1-11.
    [ abstract]

  81. Glenn Heller, Jing Qin (2007), "Inference on the limiting false discovery rate and the p-value threshold parameter assuming weak dependence between gene expression levels within subject", Statistical Applications in Genetics and Molecular Biology, 6(1):14.
    [abstract]

  82. Michael Hirsch, Stephen Swift, Xiohui Liu (2007), "Optimal search space for clustering gene expression data via consensus", Journal of Computational Biology, 14(10):1327-1341.
    [abstract]

  83. Jason C. Hsu, Jane Chang, Tao Wang, Eiríkur Steingrímsson, Magnús Karl Magnússon, Kristin Bergsteinsdottir(2007), "Statistically designing microarrays and microarray experiments to enhance sensitivity and specificity", Briefings in Bioinformatics, 8:22-31.
    [abstract]

  84. Guangan Hu, Manuel Llinás, Jingguang Li, Peter Rainer Preiser, Zbynek Bozdech (2007), "Selection of long oligonucleotides for gene expression microarrays using weighted rank-sum strategy", BMC Bioinformatics, 8:350.
    [abstract]

  85. Dong Hua, Yinglei Lai (2007), "An ensemble approach to microarray data-based gene prioritization after missing value imputation", Bioinformatics, 23: 747-754
    [abstract]

  86. DW Huang, BT Sherman, Q Tan, JR Collins, WG Alvord, J Roayaei, R Stephens, MW Baseler, HC Lane, RA Lempicki (2007), "The DAVID Gene Functional Classification Tool: a novel biological module-centric algorithm to functionally analyze large gene lists", Genome Biology, 8(9):R183.

  87. DW Huang, BT Sherman, Q Tan, J Kir, D Liu, D Bryant, Y Guo, R Stephens, MW Baseler, HC Lane, RA Lempicki (2007), "DAVID Bioinformatics Resources: expanded annotation database and novel algorithms to better extract biology from large gene lists", Nucleic Acids Research, 35(web server issue):W169-W175.

  88. D Huang, Tommy W S Chow (2007), "Identifying the biologically relevant gene categories based on gene expression and biological data: an example on prostate cancer", Bioinformatics, 23:1503-1510.
    [abstract]

  89. Randall Hulshizer, Eric M Blalock (2007), "Post hoc pattern matching: assigning significance to statistically defined expression patterns in single channel microarray data", BMC Bioinformatics, 8:240.
    [abstract]

  90. Curtis Huttenhower, Avi I Flamholz, Jessica N Landis, Sauhard Sahi, Chad L Myers, Kellen L Olszewski, Matthew A Hibbs, Nathan O Siemers, Olga G Troyanskaya, Hilary A Coller (2007), "Nearest Neighbor Networks: clustering expression data based on gene neighborhoods", BMC Bioinformatics, 8:250.
    [abstract]

  91. John PA Ioannidis, Nikolaos P Polyzos, Thomas A Trikalinos, (2007), "Selective discussion and transparency in microarray research findings for cancer outcomes", European Journal of Cancer, 43(13):1999-2010.
    [ abstract]

  92. Béatrice Jacquelin, Véronique Mayau, Guillaume Brysbaert, Béatrice Regnault, Ousmane M Diop, Fernando Arenzana-Seisdedos, Lars Rogge, Jean-Yves Coppée, Françoise Barré-Sinoussi, Arndt Benecke, Michaela C Müller-Trutwin (2007), "Long oligonucleotide microarrays for African green monkey gene expression profile analysis", FASEB Journal, 21:3262-3271.
    [ abstract]

  93. P Jaluria, K Konstantopoulos, M Betenbaugh, J Shiloach J (2007), "A perspective on microarrays: current applications, pitfalls, and potential uses", Microbial Cell Factories, 6:4.
    [ abstract]

  94. Zhen Jiang, Robert Gentleman (2007), "Extensions to gene set enrichment", Bioinformatics, 23:306-313.
    [abstract]

  95. Yongsung Joo, George Casella, James Booth, Keunbaik Lee, Steven Enkemann (2007), "Normalization of dye bias in microarray data using the mixture of splines model", Statistical Applications in Genetics and Molecular Biology, 6(1):2.
    [abstract]

  96. TS Jorstad, M Langaas, AM Bones (2007), "Understanding sample size: what determines the required number of microarrays for an experiment?", Trends in Plant Science, 12:46-70.
    [ abstract]

  97. AV Kapp, R Tibshirani (2007), "Are clusters found in one dataset present in another dataset?", Biostatistics, 8(1):9-31.

  98. Karen Kapur, Yi Xing1 , Zhengqing Ouyang, Wing Hung Wong (2007), "Exon arrays provide accurate assessments of gene expression", Genome Biology, 8(6):R82.
    [abstract]

  99. Andreas Keller, Christina Backes, Hans-Peter Lenhof (2007), "Computation of significance scores of unweighted Gene Set Enrichment Analyses", BMC Bioinformatics, 8:290.
    [abstract]

  100. Reagan J Kelly, Douglas M Jacobsen, Yan V Sun, Jennifer A Smith, Sharon L R Kardia (2007), "KGraph: a system for visualizing and evaluating complex genetic associations", Bioinformatics, 23:249-251.
    [abstract]

  101. Kathleen F Kerr (2007), "Extended analysis of benchmark datasets for Agilent two-color microarrays", BMC Bioinformatics, 8:371.
    [abstract]

  102. Hyunsoo Kim, Haesun Park (2007), "Sparse non-negative matrix factorizations via alternating non-negativity-constrained least squares for microarray data analysis", Bioinformatics, 23:1495-1502.
    [abstract]

  103. Jihoon Kim, Ju Han Kim (2007), "Difference-based clustering of short time-course microarray data with replicates", BMC Bioinformatics, 8:259.
    [abstract]

  104. Ki-Yeol Kim, Dong Hyuk Ki, Ha Jin Jeong, Hei-Cheul Jeung, Hyun Cheol Chung, Sun Young Rha (2007), "Novel and simple transformation algorithm for combining microarray data sets", BMC Bioinformatics, 8:218.
    [abstract]

  105. Lev Klebanov, Linlin Chen, Andrei Yakovlev (2007), "Revisiting adverse effects of cross-hybridization in Affymetrix gene expression data: do they matter for correlation analysis?", Biology Direct, 2:28.
    [ abstract]

  106. L Klebanov, G Glazko, P Salzman, A Yakovlev, Y Xiao (2007), "A multivariate extension of the gene set enrichment analysis" Journal of Bioinformatics and Computational Biology, 5(5):1139-1153.

  107. Lev Klebanov, Xing Qiu, Stephen Welle, Andrei Yakovlev (2007), "Statistical methods and microarray data" (correspondence), Nature Biotechnology, 25(1):25-26.
    [ abstract]

  108. Lev Klebanov, Andrei Yakovlev (2007), "How high is the level of technical noise in microarray data?", Biology Direct, 2:9.
    [ abstract]

  109. Lev Klebanov, Andrei Yakovlev (2007), "Is there an alternative to increasing the sample size in microarray studies?" Bioinformation, 1(10):429-431.
    [abstract]

  110. Lev Klebanov, Andrei Yakovlev (2007), "Diverse correlation structures in gene expression data and their utility in improving statistical inference", Annals of Applied Statistics, 1(2):538-559.
    [abstract]

  111. L Kumar, ME Futschik (2007), "Mfuzz: A software package for soft clustering of microarray data", Bioinformation, 2(1):5-7.
    [PDF]

  112. affymetrix
    Sunita Kumari, Lalit K Verma, Jennifer W Weller (2007), "AffyMAPSDetector: a software tool to characterize Affymetrix GeneChipTM expression arrays with respect to SNPs", BMC Bioinformatics, 8:276.
    [abstract]

  113. Y Lai (2007), "A moment-based method for estimating the proportion of true null hypotheses and its application to microarray gene expression data", Biostatistics, 8(4):744-755.

  114. Yinglei Lai, Bao-ling Adam, Robert Podolsky, Jin-Xiong She (2007), "A mixture model approach to the tests of concordance and discordance between two large-scale experiments with two-sample groups", Bioinformatics, 23:1243-1250.
    [abstract]

  115. Kevin Le Brigand, Pascal Barbry (2007) "Mediante: a web-based microarray data manager", Bioinformatics, 23:1304-1306.
    [abstract]

  116. Eun-Kyung Lee, Taesung Park (2007), "Exploratory methods for checking quality of microarray data", Bioinformation, 1(10): 423-428.
    [abstract]

  117. Karen Lees, Stephen Roberts, Pari Skamnioti, Sarah Gurr (2007), "Gene microarray analysis using angular distribution decomposition", Journal of Computational Biology, 14(1): 68-83.
    [abstract]

  118. Myoyong Lee, Jeffrey M. Treny, Michael L. Bittner (2007), "Optimization of oligonucleotide microarray fabricated by spotting 65-mer", Analytic Biochemistry, 368(1):61-69.
    [ abstract]

  119. Ryan M Lee, Patrick J Tranel (2007), "Utilization of DNA microarrays in weed science research", Weed Science, 56(2):283-289.
    [ abstract]

  120. Gilad Lerman, Joseph McQuown, Alexandre Blais, Brian D Dynlacht, Guangliang Chen, Bud Mishra (2007), "Functional genomics via multiscale analysis: application to gene expression and ChIP-on-chip data", Bioinformatics, 23:314-320.
    [abstract]

  121. Alex Lewin, Natalia Bochkina, Sylvia Richardson (2007), "Fully Bayesian mixture model for differential gene expression: simulations and model checks", Statistical Applications in Genetics and Molecular Biology, 6:36.
    [abstract]

  122. Peng Liang (2007), "MAQC papers over the cracks" (correspondence), Nature Biotechnology, 25(1):27-28.
    [ abstract]

  123. JG Liao, Khew-Voon Chin (2007), "Logistic regression for disease classification using microarray data: model selection in a large p and small n case", Bioinformatics, 23:1945-1951.
    [abstract]

  124. Wei Keat Lim, Kai Wang, Celine Lefebvre, Andrea Califano (2007), "Comparative analysis of microarray normalization procedures: effects on reverse engineering gene networks", Bioinformatics, 23:i282-i288.
    [abstract]

  125. Dan Lin, Ziv Shkedy, Dani Yekutieli, Tomasz Burzykowski, Hinrich W.H. Göhlmann, An De Bondt, Tim Perera, Tamara Geerts, Luc Bijnens (2007), "Testing for trends in dose-response microarray experiments: a comparison of several testing procedures, multiplicity and resampling-based inference", Statistical Applications in Genetics and Molecular Biology, 6:26.
    [abstract]

  126. Fang Liu, Tor-Kristian Jenssen, Jeff Trimarchi, Claudio Punzo, Connie L Cepko, Lucila Ohno-Machado, Eivind Hovig, Winston Patrick Kuo (2007), "Comparison of hybridization-based and sequencing-based gene expression technologies on biological replicates", BMC Genomics, 8:153.
    [abstract]

  127. affymetrix
    Hongfang Liu, Barry R Zeeberg, Gang Qu, A Gunes Koru, Alessandro Ferrucci, Ari Kahn, Michael C Ryan, Antej Nuhanovic, Peter J Munson, William C Reinhold, David W Kane, John N Weinstein (2007), "AffyProbeMiner: a web resource for computing or retrieving accurately redefined Affymetrix probe sets", Bioinformatics, 23(18):2385-2390.
    [abstract]

  128. Jiajun Liu, Jacqueline M Hughes-Oliver, J Alan Menius, Jr (2007), "Domain-enhanced analysis of microarray data using GO annotations", Bioinformatics, 23:1225-1234.
    [abstract]

  129. Peng Liu, JT Gene Hwang (2007), "Quick calculation for sample size while controlling false discovery rate with application to microarray analysis", Bioinformatics, 23: 739-746.
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  130. Qi Liu, Irina Dinu, Adeniyi J Adewale, John D Potter, Yutaka Yasui (2007), "Comparative evaluation of gene-set analysis methods", BMC Bioinformatics, 8:431.
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  131. Xiaowen Liu, Lusheng Wang (2007), "Computing the maximum similarity bi-clusters of gene expression data", Bioinformatics, 23(1):50-56.
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  133. Shuangge Ma, Jian Huang (2007), "Clustering threshold gradient descent regularization: with applications to microarray studies", Bioinformatics, 23:466-472.
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  134. SC Madeira, AL Oliveira (2007), "An efficient biclustering algorithm for finding genes with similar patterns in time-series expression data", Proceedings of the 5th Asia-Pacific Bioinformatics Conference eds. D Sankoff, L Wang, F Chin, pp. 67-80 (Imperial College Press, London).

  135. Tristan Mary-Huard, Jean-Jacques Daudin, Michela Baccini, Annibale Biggeri, Avner Bar-Hen (2007), "Biases induced by pooling samples in microarray experiments", Bioinformatics, 23:i313-i318.
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  136. Shigeyuki Matsui, Masaaki Ito, Hiroyuki Nishiyama, Hajime Uno, Hirokazu Kotani, Jun Watanabe, Parry Guilford, Anthony Reeve, Masanori Fukushima, Osamu Ogawa (2007), "Genomic characterization of multiple clinical phenotypes of cancer using multivariate linear regression models", Bioinformatics, 23:732-738.
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  137. Ignacio Medina, David Montaner, Joaquín Tárraga, Joaquín Dopazo (2007), "Prophet, a web-based tool for class prediction using microarray data", Bioinformatics, 23:390-391.
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  138. GA Milliken, KA Garrett, SE Travers (2007), "Experimental design for two-color microarrays applied in a pre-existing split-plot experiment", Statistical Applications in Genetics and Molecular Biology, 6:20.
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  139. S Mocellin, CR Rossi (2007), "Principles of gene microarray data analysis", Advances in Experimental Medicine and Biology, 593:19-30.

  140. M Lia Molas, John Z Kiss (2007), "The effect of column purification on cDNA indirect labelling for microarrays", Plant Methods, 3:9.
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  141. Jason Morton, Lior Pachter, Anne Shiu, Bernd Sturmfels (2007), "The cyclohedron test for finding periodic genes in time course expression studies", Statistical Applications in Genetics and Molecular Biology, 6(1):21.
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  142. Nitai D. Mukhopadhyay, Snigdhansu Chatterjee (2007), "Causality and pathway search in microarray time series experiment", Bioinformatics, 23:442-449.
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  143. Radhakrishnan Nagarajan, Meenakshi Upreti (2007), "Qualitative assessment of gene expression in affymetrix genechip arrays", Physica A, 373:486-496.

  144. Radhakrishnan Nagarajan, Meenakshi Upreti, RB Govindan (2007), "Qualitative assessment of cDNA microarray gene expression data using detrended fluctuation analysis", Physica A, 373:503-510.

  145. Joseph R. Nevins, Anil Potti (2007), "Mining gene expression profiles: expression signatures as cancer phenotypes", Nature Reviews Genetics,
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  146. Michael A Newton, Fernando A Quintana, Johan A den Boon, Srikumar Sengupta, Paul Ahlquist (2007), "Random-set methods identify distinct aspects of the enrichment signal in gene-set analysis", Annals of Applied Statistics, 1(1):85-106.
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  147. Björn Nilsson, Petra Håkansson, Mikael Johansson, Sven Nelander, Thoas Fioretos (2007), "Threshold-free high-power methods for the ontological analysis of genome-wide gene-expression studies", Genome Biology, 8(5):R74.
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  148. Eugene Novikov, Emmanuel Barillot (2007), "Software package for automatic microarray image analysis (MAIA)", Bioinformatics, 23: 639-640.
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  149. María José Nueda, Ana Conesa, Johan A. Westerhuis, Huub C. J. Hoefsloot, Age K. Smilde, Manuel Talón, Alberto Ferrer (2007), "Discovering gene expression patterns in time course microarray experiments by ANOVA?SCA", Bioinformatics, 23:1792-1800.
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  150. Rainer Opgen-Rhein, Korbinian Strimmer (2007), "Accurate ranking of differentially expressed genes by a distribution-free shrinkage approach", Statistical Applications in Genetics and Molecular Biology, 6(1):9.
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  151. Yuriy L Orlov, Jiangtao Zhou, Leonard L Lipovich, Atif Shahab, Vladimir A Kuznetsov (2007), "Quality assessment of the Affymetrix U133A&B probesets by target sequence mapping and expression data analysis", In Silico Biology, 7:41.
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  158. Mehdi Pirooznia, Vijayaraj Nagarajan, Youping Deng (2007), "GeneVenn - A web application for comparing gene lists using Venn diagrams", Bioinformation, 1(10):420-422.
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  159. Alex E Pozhitkov, Diethard Tautz, Peter A Noble (2007), "Oligonucleotide microarrays: widely applied -- poorly understood", Briefings in Functional Genomics and Proteomics, 6(2):141-148.
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  162. Thomas E Royce, Joel S Rozowsky, Mark B Gerstein (2007), "Assessing the need for sequence-based normalization in tiling microarray experiments", Bioinformatics, 23:988-997.
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  163. Yvan Saeys, Iñaki Inza, Pedro Larrañaga (2007), "A review of feature selection techniques in bioinformatics", Bioinformatics, 23:2507-2517.
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  165. Remo Sanges, Francesca Cordero, Raffaele A Calogero (2007), "oneChannelGUI: a graphical interface to Bioconductor tools, designed for life scientists who are not familiar with R language", Bioinformatics, 23:3406-3408.
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  175. Yanxin Shi, Michael Klustein, Itamar Simon, Tom Mitchell, Ziv Bar-Joseph (2007), "Continuous hidden process model for time series expression experiments", Bioinformatics, 23:i459-i467.
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  176. Susan J Simmons, Shyamal D Peddada (2007), "Order-restricted inference for ordered gene expression (ORIOGEN) data under heteroscedastic variances", Bioinformation, 1(10): 414-419.
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  179. Jun S Song, Kaveh Maghsoudi, Wei Li, Edward Fox, John Quackenbush, X. Shirley Liu (2007), "Microarray blob-defect removal improves array analysis", Bioinformatics, 23:966-971.
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    Shiping Song, Bin Li, Lihua Wang, Haiping Wu, Jun Hu, Minqian Li and Chunhai Fan (2007), "A cancer protein microarray platform using antibody fragments and its clinical applications", Molecular BioSystems, 3:151-158.
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  181. Frank J Sørensen, Claus L. Andersen, Carsten Wiuf (2007), "SNPTools: a software tool for visualization and analysis of microarray data", Bioinformatics, 23:1550-1552.
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  182. Wolfram Stacklies, Henning Redestig, Matthias Scholz, Dirk Walther, Joachim Selbig (2007), "pcaMethods -- a bioconductor package providing PCA methods for incomplete data", Bioinformatics, 23:1164-1167.
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  184. affymetrix
    MA Stalteri, AP Harrison (2007), "Interpretation of multiple probe sets mapping to the same gene in Affymetrix GeneChips", BMC Bioinformatics, 8(1):13.
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  185. Yijun Sun, Steve Goodison, Jian Li, Li Liu, William Farmerie (2007), "Improved breast cancer prognosis through the combination of clinical and genetic markers", Bioinformatics, 23(1):30-37.
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  189. R Tibshirani, T Hastie (2007), "Outlier sums for differential gene expression analysis", Biostatistics, 8(1):2-8.

  190. Weida Tong, Stephen C Harris, Hong Fang, Leming Shi, Roger Perkins, Federico Goodsaid, Felix W Frueh (2007), "An integrated bioinformatics infrastructure essential for advancing pharmacogenomics and personalized medicine in the context of the FDA's Critical Path Initiative", Drug Discovery Today: Technologies, 4(1):3-8.
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  191. Victor Trevino, Francesco Falciani, Hugo A Barrera-Saldaña (2007), "DNA microarrays: a powerful genomic tool for biomedical and clinical research", Molecular Medicine, 13:527-541.

  192. affymetrix
    Ernest Turro, Natalia Bochkina, Anne-Mette K Hein, Sylvia Richardson (2007), "BGX: a Bioconductor package for the Bayesian integrated analysis of Affymetrix GeneChips", BMC Bioinformatics, 8:440.
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  194. Roy Varshavsky, Assaf Gottlieb, David Horn, Michal Linial (2007), "Unsupervised feature selection under perturbations: meeting the challenges of biological data", Bioinformatics, 23:3343-3349.
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  195. George Vasmatzis, Eric W. Klee, Dagmar M. Kube, Terry M. Therneau, Farhad Kosari (2007), "Quantitating tissue specificity of human genes to facilitate biomarker discovery", Bioinformatics, 23:1348-1355.
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  198. protein
    CC Wang (2007), "Protein array-based multiplexed cytokine assays". Methods in Molecular Biology, 385:177-192.

  199. Lifeng Wang, Guang Chen, Hongzhe Li (2007), "Group SCAD regression analysis for microarray time course gene expression data", Bioinformatics, 23:1486-1494.
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  200. Sijian Wang, Ji Zhu (2007), "Improved centroids estimation for the nearest shrunken centroid classifier", Bioinformatics, 23:972-979.
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  201. Rohan BH Williams, Eva KF Chan, Mark J Cowley, Peter FR Little (2007), "The influence of genetic variation on gene expression", Genome Research, 17:1707-1716.
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  203. Ian A Wood, Peter M Visscher, Kerrie L Mengersen (2007), "Classification based upon gene expression data: bias and precision of error rates", Bioinformatics, 23:1363-1370.
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  204. Zhengpeng Wu, Jiangni Ao, Xuegong Zhang (2007), "Finding distinct biclusters from background in gene expression matrices", Bioinformation, 2(5):207-215.
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  205. Zhijin Wu, Rafael A Irizarry (2007), "A statistical framework for the analysis of microarray probe-level data", Annals of Applied Statistics, 1(2):333-357.
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  207. Y Xiao, J Hua, ER Dougherty (2007), "Quantification of the impact of feature selection on the variance of cross-validation error estimation", EURASIP Journal on Bioinformatics and Systems Biology, article ID 16354.

  208. Lei Xu, Donald Geman, Raimond L Winslow (2007), "Large-scale integration of cancer microarray data identifies a robust common cancer signature", BMC Bioinformatics, 8:275.
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  209. Jianhua Xuan, Yue Wang, Yibin Dong, Yuanjian Feng, Bin Wang, Javed Khan, Maria Bakay, Zuyi Wang, Lauren Pachman, Sara Winokur, Yi-Wen Chen, Robert Clarke, Eric Hoffman (2007), "gene selection for multiclass prediction by weighted Fisher criterion", EURASIP Journal on Bioinformatics and Systems Biology, article ID 64628.

  210. Hyuna Yang, Gary Churchill (2007), "Estimating p-values in small microarray experiments", Bioinformatics, 23(1):38-43.
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  211. Takashi Yoneya, Hiroshi Mamitsuka (2007), "A hidden Markov model-based approach for identifying timing differences in gene expression under different experimental factors", Bioinformatics, 23:842-849.
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  212. Eric Z Yu, Anne E Counterman Burba, Mark Gerstein (2007), "PARE: A tool for comparing protein abundance and mRNA expression data", BMC Bioinformatics, 8:309.
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  213. Shizhu Zang, Ruifang Guo, Liang Zhang, Youyong Lu (2007), "Integration of statistical inference methods and a novel control measure to improve sensitivity and specificity of data analysis in expression profiling studies", Journal of Biomedical Informatics, 40(5):552-560.
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  214. Ji-Gang Zhang, Hong-Wen Deng (2007), "Gene selection for classification of microarray data based on the Bayes error", BMC Bioinformatics, 8:370.
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  215. Shunpu Zhang (2007), "A comprehensive evaluation of SAM, the SAM R-package and a simple modification to improve its performance", BMC Bioinformatics, 8:230.
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  216. Wuyan Zhang, Alicia Carriquiry, Dan Nettleton, Jack CM Dekkers (2007), "Pooling mRNA in microarray experiments and its effect on power", Bioinformatics, 23:1217-1224.
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  217. Xiuwen Zheng, Hung-Chung Huang, Wenyuan Li, Peng Liu, Quan-Zhen Li, Ying Liu (2007), "Modeling nonlinearity in dilution design microarray data", Bioinformatics, 23:1339-1347.
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  218. H Zhao, AWC Liew, H Yan (2007), "A new strategy of geometrical biclustering for microarray data analysis", Proceedings of the 5th Asia-Pacific Bioinformatics Conference eds. D Sankoff, L Wang, F Chin, pp. 47-56 (Imperial College Press, London).

  219. Hongya Zhao, Hong Yan (2007), "HoughFeature, a novel method for assessing drug effects in three-color cDNA microarray experiments", BMC Bioinformatics, 8:256.
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  220. Qiang Zhao, Jianguo Sun (2007), "Cox survival analysis of microarray gene expression data using correlation principal component regression", Statistical Applications in Genetics and Molecular Biology, 6(1):16.
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  221. Xin Zhou, David P Tuck (2007), "MSVM-RFE: extensions of SVM-RFE for multiclass gene selection on DNA microarray data", Bioinformatics, 23:1106-1114.
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  222. Scott D Zuyderduyn (2007), "Statistical analysis and significance testing of serial analysis of gene expression data using a Poisson mixture model", BMC Bioinformatics, 8:282.
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2007