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/
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. affymetrix
    Rudi Alberts, Peter Terpstra, Menno Hardonk, Leonid V Bystrykh, Gerald de Haan, Rainer Breitling, Jan-Peter Nap, Ritsert C Jansen (2007), "A verification protocol for the probe sequences of Affymetrix genome arrays reveals high probe accuracy for studies in mouse, human and rat", BMC Bioinformatics, 8:132
    [abstract]

  3. O Alter (2007), "Genomic signal processing: from matrix algebra to genetic networks", Methods in Molecular Biology, 377:17-60.

  4. 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]

  5. 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]

  6. 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]

  7. 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]

  8. 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.

  9. 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]

  10. Sanghamitra Bandyopadhyay, Anirban Mukhopadhyay, and Ujjwal Maulik (2007), "An improved algorithm for clustering gene expression data", Bioinformatics, 23(21):2859-2865
    [abstract]

  11. 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.

  12. 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]

  13. affymetrix
    Kathe E Bjork, Karen Kafadar (2007), "Systematic order-dependent effect in expression values, variance, detection calls and differential expression in Affymetrix GeneChips®", Bioinformatics, 23(21):2873-2880
    [abstract]

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

  15. HM Bøvelstad, S Nygård, HL Størvold, M Aldrin, Ø Borgan, A Frigessi, OC Lingjærde (2007), "Predicting survival from microarray data?a comparative study", Bioinformatics, 23(16):2080-2087.
    [abstract]

  16. 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]

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

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

  19. 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]

  20. Andreas Buness, Ruprecht Kuner, Markus Ruschhaupt, Annemarie Poustka, Holger Sültmann, Achim Tresch (2007), "Identification of aberrant chromosomal regions from gene expression microarray studies applied to human breast cancer", Bioinformatics, 23(17):2273-2280.
    [abstract]

  21. 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]

  22. 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]

  23. 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]

  24. 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).

  25. affymetrix
    Alexander C Cambon, Abdelnaby Khalyfa, Nigel GF Cooper, Caryn M Thompson (2007), "Analysis of probe level patterns in Affymetrix microarray data", BMC Bioinformatics, 8:146
    [abstract]

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

  27. 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]

  28. 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]

  29. 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]

  30. Duccio Cavalieri, Cinzia Castagnini, Simona Toti, Karolina Maciag, Thomas Kelder, Luca Gambineri, Samuele Angioli, Piero Dolara (2007), "Eu.Gene Analyzer a tool for integrating gene expression data with pathway databases", Bioinformatics, 23(19):2631-2632.
    [abstract]

  31. JJ Chen (2007), "Key aspects of analyzing microarray gene-expression data", Pharmacogenomics, 8(5):473-482.

  32. 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]

  33. James J Chen, Taewon Lee, Robert R Delongchamp, Tao Chen, Chen-An Tsai (2007), "Significance analysis of groups of genes in expression profiling studies Bioinformatics, 23(16): 2104-2112.
    [abstract]

  34. James J Chen, Chen-An Tsai, ShengLi Tzeng, Chun-Houh Chen (2007), "Gene selection with multiple ordering criteria", BMC Bioinformatics, 8:74
    [abstract]

  35. 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]

  36. 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]

  37. Linlin Chen, Lev Klebanov, Andrei Yakovlev (2007), "Normality of gene expression revisited", Journal of Biological Systems, 15(1):39-48.
    [ abstract]

  38. 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]

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

  40. KO Cheng, NF Law, WC Siu, TH Lau (2008), "BiVisu: software tool for bicluster detection and visualization", Bioinformatics, 23(17):2342-2344.
    [abstract]

  41. Lin Cheung, David W Cheung, Ben Kao, Kevin Y Yip, Michael K Ng (2007), "On mining micro-array data by Order-Preserving Submatrix", International Journal of Bioinformatics Research and Applications, 3(1):42-64.
    [ abstract]

  42. 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]

  43. 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).

  44. 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]

  45. 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.

  46. Erin M Conlon, Joon J Song, Anna Liu (2007), "Bayesian meta-analysis models for microarray data: a comparative study", BMC Bioinformatics, 8:80.
    [abstract]

  47. Kevin R Coombes, Jing Wang, Keith A Baggerly (2007), "Microarrays: retracing steps" (correspondence), Nature Medicine, 13:1276-1277.
    [ abstract]

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

  49. 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]

  50. Manhong Dai, Pinglang Wang, Elvis Jakupovic, Stanley J. Watson, and Fan Meng (2007), "Web-based GeneChip analysis system for large-scale collaborative projects", Bioinformatics, 23(16):2185-2187
    [abstract]

  51. 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]

  52. Antonis Daskalakis, Dionisis Cavouras, Panagiotis Bougioukos, Spiros Kostopoulos, Dimitris Glotsos, Ioannis Kalatzis, George C. Kagadis, Christos Argyropoulos, George Nikiforidis (2007), "Improving gene quantification by adjustable spot-image restoration", Bioinformatics, 23(17):2265-2272.
    [abstract]

  53. 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]

  54. 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]

  55. 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.

  56. 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.

  57. 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]

  58. 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]

  59. Thomas Dhollander, Qizheng Sheng, Karen Lemmens, Bart De Moor, Kathleen Marchal, Yves Moreau (2009), "Query-driven module discovery in microarray data", Bioinformatics, 23(19):2573-2580.
    [abstract]

  60. 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]

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

  62. 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]

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

  64. 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]

  65. 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]

  66. 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.

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

  68. Laura L Elo, Henna Järvenpää, Matej Oresic, Riitta Lahesmaa, Tero Aittokallio (2007), "Systematic construction of gene coexpression networks with applications to human T helper cell differentiation process", Bioinformatics, 23(16): 2096-2103.
    [abstract]

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

  70. 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]

  71. 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]

  72. 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]

  73. 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]

  74. 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]

  75. 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]

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

  77. 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]

  78. 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]

  79. Gabriela V Cohen Freue, Zsuzsanna Hollander, Enqing Shen, Ruben H Zamar, Robert Balshaw, Andreas Scherer, Bruce McManus, Paul Keown, W Robert McMaster, Raymond T Ng (2007), "MDQC: a new quality assessment method for microarrays based on quality control reports", Bioinformatics, 23(23):3162-3169
    [abstract]

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

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

  82. Holger Fröhlich, Nora Speer, Annemarie Poustka, Tim Beißbarth (2007), "GOSim -- an R-package for computation of information theoretic GO similarities between terms and gene products", BMC Bioinformatics, 8:166
    [abstract]

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

  84. Wataru Fujibuchi, Larisa Kiseleva, Takeaki Taniguchi, Hajime Harada, and Paul Horton (2007). "CellMontage: similar expression profile search server", Bioinformatics, 23(22):3103-3104.
    [abstract]

  85. 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]

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

  87. Daniel P Gaile, Jeffrey C Miecznikowski (2007), "Putative null distributions corresponding to tests of differential expression in the Golden Spike dataset are intensity dependent", BMC Genomics, 8:105.
    [abstract]

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

  89. Giacomo Gamberoni, Evelina Lamma, Gianluca Lodo, Jlenia Marchesini, Nicoletta Mascellani, Simona Rossi, Sergio Storari, Luca Tagliavini, Stefano Volinia (2007), "Fun&Co: identification of key functional differences in transcriptomes", Bioinformatics, 23(20):2725-2732.
    [abstract]

  90. Raad Z. Gharaibeh, Anthony A. Fodor, Cynthia J. Gibas (2007), "Software Note: Using probe secondary structure information to enhance Affymetrix GeneChip background estimates", Computational Biology and Chemistry, 31(2):92-98.
    [ abstract]

  91. 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]

  92. 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]

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

  94. Nicolas Goffard, Georg Weiller (2007), "GeneBins: a database for classifying gene expression data, with application to plant genome arrays", BMC Bioinformatics, 8:87
    [abstract]

  95. 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.?-?.

  96. 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]

  97. 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]

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

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

  100. Steffen Grossmann, Sebastian Bauer, Peter N. Robinson, and Martin Vingron (2007), "Improved detection of overrepresentation of Gene-Ontology annotations with parent?child analysis", Bioinformatics, 23(22):3024-3031.
    [abstract]

  101. Arief Gusnanto, Brian Tom, Philippa Burns, Iain Macaulay, Daphne C. Thijssen-Timmer, Marloes R. Tijssen, Cordelia Langford, Nicholas Watkins, Willem Ouwehand, Carlo Berzuini, Frank Dudbridge (2007), "Improving the power to detect differentially expressed genes in comparative microarray experiments by including information from self?self hybridizations", Computational Biology and Chemistry, 31(3):178-185.
    [ abstract]

  102. 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]

  103. 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]

  104. 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]

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

  106. 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]

  107. DA Hanauer, DR Rhodes, C Sinha-Kumar, AM Chinnaiyan (2007), "Bioinformatics approaches in the study of cancer", Current Molecular Medicine, 7(1):133-141.

  108. 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]

  109. Blaise Hanczar, Jean-Daniel Zucker, Corneliu Henegar, Lorenza Saitta (2007), "Feature construction from synergic pairs to improve microarray-based classification", Bioinformatics, 23(21):2866-2872.
    [abstract]

  110. Chris Harbron, Kai-Ming Chang, and Marie C. South (2007), "RefPlus: an R package extending the RMA Algorithm", Bioinformatics, 23(18):2493-2494.
    [abstract]

  111. 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]

  112. affymetrix
    Andrew P Harrison, Caroline E Johnston, Christine A Orengo (2007), "Establishing a major cause of discrepancy in the calibration of Affymetrix GeneChips", BMC Bioinformatics, 8:195.
    [abstract]

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

  114. 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]

  115. Matthew A Hibbs, David C Hess, Chad L Myers, Curtis Huttenhower, Kai Li, Olga G Troyanskaya (2007), "Exploring the functional landscape of gene expression: directed search of large microarray compendia", Bioinformatics, 23(20):2692-2699
    [abstract]

  116. 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]

  117. 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]

  118. 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]

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

  120. 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.

  121. 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.

  122. 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]

  123. protein
    Michael E. Hudson, Irina Pozdnyakova, Kenneth Haines, Gil Mor, Michael Snyder (2007), "Identification of differentially expressed proteins in ovarian cancer using high-density protein microarrays", Proceedings of National Academy of Sciences, 104:17494-17499.
    [abstract]

  124. 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]

  125. 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.
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  126. 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.
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  127. 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.
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  130. W Evan Johnson, Cheng Li, Ariel Rabinovic (2007), "Adjusting batch effects in microarray expression data using empirical Bayes methods", Biostatistics, 8(1):118-127.
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  131. 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.
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  132. Rebecka Jörnsten, Ming Ouyang, Hui-Yu Wang (2007), "A meta-data based method for DNA microarray imputation", BMC Bioinformatics, 8:109
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  134. AV Kapp, R Tibshirani (2007), "Are clusters found in one dataset present in another dataset?", Biostatistics, 8(1):9-31.

  135. Karen Kapur, Yi Xing1 , Zhengqing Ouyang, Wing Hung Wong (2007), "Exon arrays provide accurate assessments of gene expression", Genome Biology, 8(6):R82.
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  136. Andreas Keller, Christina Backes, Hans-Peter Lenhof (2007), "Computation of significance scores of unweighted Gene Set Enrichment Analyses", BMC Bioinformatics, 8:290.
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  137. 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.
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  138. Kathleen F Kerr (2007), "Extended analysis of benchmark datasets for Agilent two-color microarrays", BMC Bioinformatics, 8:371.
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  139. Hye Young Kim, Seo Eun Lee, Min Jung Kim, Jin Il Han, Bo Kyung Kim, Yong Sung Lee, Young Seek Lee, Jin Hyuk Kim (2007), "Characterization and simulation of cDNA microarray spots using a novel mathematical model", BMC Bioinformatics, 8:485
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  140. 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.
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  141. Jihoon Kim, Ju Han Kim (2007), "Difference-based clustering of short time-course microarray data with replicates", BMC Bioinformatics, 8:259.
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  142. 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.
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  143. Kyungpil Kim, Shibo Zhang, Keni Jiang, Li Cai, In-Beum Lee, Lewis J Feldman, Haiyan Huang (2007), "Measuring similarities between gene expression profiles through new data transformations", BMC Bioinformatics, 8:29
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  146. Lev Klebanov, Xing Qiu, Stephen Welle, Andrei Yakovlev (2007), "Statistical methods and microarray data" (correspondence), Nature Biotechnology, 25(1):25-26.
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  147. Lev Klebanov, Andrei Yakovlev (2007), "How high is the level of technical noise in microarray data?", Biology Direct, 2:9.
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  148. Lev Klebanov, Andrei Yakovlev (2007), "Is there an alternative to increasing the sample size in microarray studies?" Bioinformation, 1(10):429-431.
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  152. 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.
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  154. 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.
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  156. Eun-Kyung Lee, Taesung Park (2007), "Exploratory methods for checking quality of microarray data", Bioinformation, 1(10): 423-428.
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  158. NH Lee, AI Saeed (2007), "Microarrays: an overview", Methods in Molecular Biology, 353:265-300.

  159. Ryan M Lee, Patrick J Tranel (2007), "Utilization of DNA microarrays in weed science research", Weed Science, 56(2):283-289.
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  160. Karen Lees, Stephen Roberts, Pari Skamnioti, Sarah Gurr (2007), "Gene microarray analysis using angular distribution decomposition", Journal of Computational Biology, 14(1): 68-83.
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  162. 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.
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  165. 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.
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  166. Alan Wee-Chung Liew, Jun Xian, Shuanhu Wu, David Smith, Hong Yan (2007), "Spectral estimation in unevenly sampled space of periodically expressed microarray time series data", BMC Bioinformatics, 8:137
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  168. 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.
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  170. 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.
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  171. 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.
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  172. Jiajun Liu, Jacqueline M Hughes-Oliver, J Alan Menius, Jr (2007), "Domain-enhanced analysis of microarray data using GO annotations", Bioinformatics, 23:1225-1234.
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  173. 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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  174. 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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  175. Xiaowen Liu, Lusheng Wang (2007), "Computing the maximum similarity bi-clusters of gene expression data", Bioinformatics, 23(1):50-56.
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  176. Xuejun Liu, Kevin K Lin, Bogi Andersen, Magnus Rattray (2007), "Including probe-level uncertainty in model-based gene expression clustering", BMC Bioinformatics, 8:98
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  178. Claudio Lottaz, Joern Toedling, Rainer Spang (2007), "Annotation-based distance measures for patient subgroup discovery in clinical microarray studies", Bioinformatics, 23(17):2256-2264.
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  181. protein
    M Lubomirski, MR D'Andrea, SM Belkowski, J Cabrera, JM Dixon, D Amaratunga (2007), "A consolidated approach to analyzing data from high-throughput protein microarrays with an application to immune response profiling in humansw", Journal of Computational Biology, 14(3):350-359.

  182. Andy G Lynch, David E Neal, John D Kelly, Glyn J Burtt, Natalie P Thorne (2007), "Missing channels in two-colour microarray experiments: Combining single-channel and two-channel data", BMC Bioinformatics, 8:26
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  183. Shuangge Ma, Jian Huang (2007), "Clustering threshold gradient descent regularization: with applications to microarray studies", Bioinformatics, 23:466-472.
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  184. Shuangge Ma, Jian Huang (2007), "Additive risk survival model with microarray data" BMC Bioinformatics, 8:192
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  187. R Maglietta, A Piepoli, D Catalano, F Licciulli, M Carella, S Liuni, G Pesole, F Perri, N Ancona (2007), "Statistical assessment of functional categories of genes deregulated in pathological conditions by using microarray data", Bioinformatics, 23(16):2063-2072.
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  188. Samuel OM Manda, Rebecca E Walls, Mark S Gilthorpe (2007), "A full Bayesian hierarchical mixture model for the variance of gene differential expression", BMC Bioinformatics, 8:124
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  189. Laetitia Marisa, Jean-Laurent Ichanté, Nancie Reymond, Lawrence Aggerbeck, Hervé Delacroix, Marie-Hélène Mucchielli-Giorgi (2007), "MAnGO: an interactive R-based tool for two-colour microarray analysis", Bioinformatics, 23(17):2339-2341.
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  190. 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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  191. 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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  192. 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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  193. Cécile Militon, Sébastien Rimour, Mohieddine Missaoui, Corinne Biderre, Vincent Barra, David Hill, Anne Moné, Geneviève Gagne, Harald Meier, Eric Peyretaillade, Pierre Peyret (2007), "PhylArray: phylogenetic probe design algorithm for microarray", Bioinformatics, 23(19):2550-2557.
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  194. 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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  195. Pablo Minguez, Fátima Al-Shahrour, David Montaner, and Joaquín Dopazo (2007), "Functional profiling of microarray experiments using text-mining derived bioentities", Bioinformatics, 23(22):3098-3099
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  196. S Mocellin, CR Rossi (2007), "Principles of gene microarray data analysis", Advances in Experimental Medicine and Biology, 593:19-30.

  197. 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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  198. Carla S. Möller-Levet, Catharine M. West, and Crispin J. Miller (2007), "Exploiting sample variability to enhance multivariate analysis of microarray data", Bioinformatics, 23(20):2733-2740
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  199. 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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  200. Minca Mramor, Gregor Leban, Janez Demsar, Blaz Zupan (2007), "Visualization-based cancer microarray data classification analysis", Bioinformatics, 23(16):2147-2154.
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  201. Nitai D. Mukhopadhyay, Snigdhansu Chatterjee (2007), "Causality and pathway search in microarray time series experiment", Bioinformatics, 23:442-449.
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  202. Radhakrishnan Nagarajan, Meenakshi Upreti (2007), "Qualitative assessment of gene expression in affymetrix genechip arrays", Physica A, 373:486-496.

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

  204. Joseph R. Nevins, Anil Potti (2007), "Mining gene expression profiles: expression signatures as cancer phenotypes", Nature Reviews Genetics,
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  205. 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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  206. 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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  207. Roland Nilsson, José M Peña, Johan Björkegren, Jesper Tegnér (2007), "Detecting multivariate differentially expressed genes", BMC Bioinformatics, 8:150
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  208. Eugene Novikov, Emmanuel Barillot (2007), "Software package for automatic microarray image analysis (MAIA)", Bioinformatics, 23: 639-640.
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  209. 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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  210. L Omberg, G H Golub, O Alter (2007), "A tensor higher-order singular value decomposition for integrative analysis of DNA microarray data from different studies," Proceedings of the National Academy of Sciences, 104(47):18371-18376
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  211. 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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  212. 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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  213. Alicia Oshlack, Adrien E Chabot, Gordon K Smyth, Yoav Gilad (2007), "Using DNA microarrays to study gene expression in closely related species", Bioinformatics, 23:1235-1242
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  214. A Oshlack, D Emslie, L Corcoran, GK Smyth (2007), "Normalization of boutique two-color microarrays with a high proportion of differentially expressed probes", Genome Biology, 8(1):R2,
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  215. Nikhil R Pal, Kripamoy Aguan, Animesh Sharma, Shun-ichi Amari (2007), "Discovering biomarkers from gene expression data for predicting cancer subgroups using neural networks and relational fuzzy clustering", BMC Bioinformatics, 8:5
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  216. MY Park, T Hastie, R Tibshirani (2007), "Averaged gene expressions for regression", Biostatistics, 8(2):212-227.

  217. Brian J Parker, Simon Gunter, Justin Bedo (2007), "Stratification bias in low signal microarray studies", BMC Bioinformatics, 8:326.
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  218. Elena Perelman, Alexander Ploner, Stefano Calza, Yudi Pawitan (2007), "Detecting differential expression in microarray data: comparison of optimal procedures", BMC Bioinformatics, 8(1):28.
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  219. Vasyl Pihur, Susmita Datta, Somnath Datta (2007), "Weighted rank aggregation of cluster validation measures: a Monte Carlo cross-entropy approach", Bioinformatics, 23:1607-1615.
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  220. Francisco R Pinto, João A Carriço, Mário Ramirez, Jonas S Almeida (2007), "Ranked Adjusted Rand: integrating distance and partition information in a measure of clustering agreement", BMC Bioinformatics, 8:44
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  221. 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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  222. Yvonne E Pittelkow, Susan R Wilson (2007), "h-Profile plots for the discovery and exploration of patterns in gene expression data with an application to time course data", BMC Bioinformatics, 8:486
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  223. 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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  224. Ido Priness, Oded Maimon, Irad Ben-Gal (2007), "Evaluation of gene-expression clustering via mutual information distance measure", BMC Bioinformatics, 8:111
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  225. Kay Prüfer, Bjoern Muetzel, Hong-Hai Do, Gunter Weiss, Philipp Khaitovich, Erhard Rahm, Svante Pääbo, Michael Lachmann, Wolfgang Enard (2007), "FUNC: a package for detecting significant associations between gene sets and ontological annotations", BMC Bioinformatics, 8:41
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  226. J Quackenbush (2007), "Extracting biology from high-dimensional biological data", Journal of Experimental Biology, 210(9):1507-1517.

  227. Nandini Raghavan, An M. I. M. De Bondt, Willem Talloen, Dieder Moechars, Hinrich W. H. Göhlmann, Dhammika Amaratunga (2007), "The high-level similarity of some disparate gene expression measures", Bioinformatics, 23(22):3032-3038.
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  228. Anat Reiner-Benaim, Daniel Yekutieli, Noah E Letwin, Gregory I Elmer, Norman H Lee, Neri Kafkafi, Yoav Benjamini (2007), "Associating quantitative behavioral traits with gene expression in the brain: searching for diamonds in the hay", Bioinformatics, 23(17):2239-2246.
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  229. DR Rhodes, S Kalyana-Sundaram, V Mahavisno, R Varambally, J Yu, BB Briggs, TR Barrette, MJ Anstet, C Kincead-Beal, P Kulkarni, S Varambally, D Ghosh, AM Chinnaiyan (2007), "Oncomine 3.0: genes, pathways, and networks in a collection of 18,000 cancer gene expression profiles", Neoplasia, 9(2):166-180.

  230. ME Ritchie, J Silver, A Oshlack, M Holmes, D Diyagama, A Holloway, GK Smyth (2007), "A comparison of background correction methods for two-colour microarrays", Bioinformatics, 23(20):2700-2707.
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  231. Mark D. Robinson, Gordon K. Smyth (2007), "Moderated statistical tests for assessing differences in tag abundance", Bioinformatics, 23(21):2881-2887
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  232. affymetrix
    Mark D Robinson, Terence P Speed (2007), "A comparison of Affymetrix gene expression arrays", BMC Bioinformatics, 8:449.
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  233. 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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  234. Yvan Saeys, Iñaki Inza, Pedro Larrañaga (2007), "A review of feature selection techniques in bioinformatics", Bioinformatics, 23:2507-2517.
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  235. D Sahoo, DL Dill, R Tibshirani, SK Plevritis (2007), "Extracting binary signals from microarray time-course data", Nucleic Acids Research, 35(11):3705-3712.

  236. Rickard Sandberg, Ola Larsson (2007), "Improved precision and accuracy for microarrays using updated probe set definitions", BMC Bioinformatics, 8:48
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  237. 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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  238. Stefanie Scheid, Rainer Spang (2007), "Compensating for unknown confounders in microarray data analysis using filtered permutations", Journal of Computational Biology, 14(5):669-681.
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  239. Andreas W Schreiber, Ute Baumann (2007), "A framework for gene expression analysis", Bioinformatics, 23:191-197
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  240. Joachim L Schultze, Daniela Eggle (2007), "IlluminaGUI: Graphical User Interface for analyzing gene expression data generated on the Illumina platform", Bioinformatics, 23:1431-1433.
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  241. Martin Schumacher, Harald Binder, Thomas Gerds (2007), "Assessment of survival prediction models based on microarray data", Bioinformatics, 23:1768-1774.
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  242. Eugene F Schuster, Eric Blanc, Linda Partridge, Janet M Thornton (2007), "Correcting for sequence biases in present/absent calls", Genome Biology, 8(6):R125.
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  243. Davis Sean, Paul S Meltzer (2007), "GEOquery: a bridge between the Gene Expression Omnibus (GEO) and BioConductor", Bioinformatics, 23:1846-1847.
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  244. Nigam H Shah, Daniel L Rubin, Inigo Espinosa, Kelli Montgomery, Mark A Musen (2007), "Annotation and query of tissue microarray data using the NCI Thesaurus", BMC Bioinformatics, 8:296.
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  245. Jahangheer S Shaik, Mohammed Yeasin (2007), "A unified framework for finding differentially expressed genes from microarray experiments", BMC Bioinformatics, 8:347.
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  246. BT Sherman, DW Huang, Q Tan, Y Guo, S Bour, D Liu, R Stephens, MW Baseler, HC Lane, RA Lempicki (2007), "DAVID Knowledgebase: a gene-centered database integrating heterogeneous gene annotation resources to facilitate high-throughput gene functional analysis", BMC Bioinformatics, 8:426.

  247. 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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  248. 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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  249. Anders Sjogren, Erik Kristiansson, Mats Rudemo, Olle Nerman (2007), "Weighted analysis of general microarray experiments", BMC Bioinformatics, 8:387.
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  250. Joon Jin Song, Ho-Jin Lee, Jeffrey S. Morris, Sanghoon Kang (2007), "Clustering of time-course gene expression data using functional data analysis", Computational Biology and Chemistry, 31(4):265-274.
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  251. JZ Song, KM Duan, T Ware, M Surette (2007), "The wavelet-based cluster analysis for temporal gene expression data", EURASIP Journal on Bioinformatics and Systems Biology, article ID 39382.

  252. 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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  253. protein
    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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  254. 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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  255. 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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  256. Phillip Stafford, Marcel Brun (2007), "Three methods for optimization of cross-laboratory and cross-platform microarray expression data", Nucleic Acids Research, 35(10):e72.
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  257. affymetrix
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2007