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/
2009

  1. Luca Abatangelo, Rosalia Maglietta, Angela Distaso, Annarita D'Addabbo, Teresa Maria Creanza, Sayan Mukherjee, Nicola Ancona (2009), "Comparative study of gene set enrichment methods", BMC Bioinformatics, 10:275
    [abstract]

  2. D Amaratunga, J Cabrera (2009), "A conditional t suite of tests for identifying differentially expressed genes in a DNA microarray experiment with little replication", Statistics in Biopharmaceutical Research, 1:26-38.

  3. Bill Andreopoulos, Aijun An, Xiaogang Wang, Michael Schroeder (2009), "A roadmap of clustering algorithms: finding a match for a biomedical application", Briefings in Bioinformatics, 10(3):297-314.
    [abstract]

  4. Reija Autio, Sami Kilpinen, Matti Saarela, Olli Kallioniemi, Sampsa Hautaniemi, Jaakko Astola (2009), "Comparison of Affymetrix data normalization methods using 6,926 experiments across five array generations", BMC Bioinformatics, 10(suppl 1):S24.
    [ abstract]

  5. Ulrike Bacher, Alexander Kohlmann, and Torsten Haferlach (2009), "Perspectives of gene expression profiling for diagnosis and therapy in haematological malignancies", Briefings in Functional Genomics and Proteomics, 8: 184-193.
    [abstract]

  6. Songjoon Baek, Chen-An Tsai and James J. Chen (2009), "Development of biomarker classifiers from high-dimensional data", Briefings in Bioinformatics, 10(5):537-546
    [abstract]

  7. Harald Binder, Arthur Allignol, Martin Schumacher, Jan Beyersmann (2009), "Boosting for high-dimensional time-to-event data with competing risks", Bioinformatics, 25(7):890-896.
    [abstract]

  8. Andrea Bisognin, Alessandro Coppe, Francesco Ferrari, Davide Risso, Chiara Romualdi, Silvio Bicciato, Stefania Bortoluzzi (2009), "A-MADMAN: Annotation-based microarray data meta-analysis tool", BMC Bioinformatics, 10:201
    [abstract]

  9. Anne-Laure Boulesteix, Martin Slawski (2009), "Stability and aggregation of ranked gene lists", Briefings in Bioinformatics, 10(5):556-568.
    [abstract]

  10. PA Bryant, GK Smyth, R Robins-Browne, N Curtis (2009), "Detection of gene expression in an individual cell type within a cell mixture using microarray analysis", PLoS ONE, 4:e4427.
    [ abstract]

  11. Mônica G Campiteli, Frederico M Soriani, Iran Malavazi, Osame Kinouchi, Carlos AB Pereira, Gustavo H Goldman (2009), "A reliable measure of similarity based on dependency for short time series: an application to gene expression networks", BMC Bioinformatics, 10:270.
    [abstract]

  12. Enrico Capobianco (2009), "Aliasing in gene feature detection by projective methods", Journal of Bioinformatics and Computational Biology, 7(4):685-700.
    [ abstract]

  13. Dustin A. Cartwright, Siobhan M. Brady, David A. Orlando, Bernd Sturmfels, and Philip N. Benfey (2009), "Reconstructing spatiotemporal gene expression data from partial observations", Bioinformatics, 25(19):2581-2587.
    [abstract]

  14. Antonio Carvajal-Rodríguez, Jacobo de Uña-Alvarez, Emilio Rolán-Alvarez (2009), "A new multitest correction (SGoF) that increases its statistical power when increasing the number of tests", BMC Bioinformatics, 10:209.
    [abstract]

  15. Xin Chen (2009), "Curve-based clustering of time course gene expression data using self-organizing maps", Journal of Bioinformatics and Computational Biology, 7(4):645-661.
    [ abstract]

  16. Vivian G Cheung, Richard S Spielman (2009), "Genetics of human gene expression: mapping DNA variants that influence gene expression", Nature Reviews Genetics, 10:595-604.
    [ abstract]

  17. Monica Chiogna, Maria Sofia Massa, Davide Risso, Chiara Romualdi (2009), "A comparison on effects of normalisations in the detection of differentially expressed genes", BMC Bioinformatics, 10:61.
    [abstract]

  18. Li-Yeh Chuang, Cheng-Huei Yang, Cheng-Hong Yang (2009), "Tabu search and binary particle swarm optimization for feature selection using microarray data", Journal of Computational Biology, 16(12):1689-1703.
    [ abstract]

  19. William Cookson, Liming Liang, Gonçalo Abecasis, Miriam Moffatt, Mark Lathrop (2009), "Mapping complex disease traits with global gene expression", Nature Reviews Genetics, 10:184-194.
    [ abstract]

  20. Chad J. Creighton, Jeffrey G. Reid, Preethi H. Gunaratne (2009), "Expression profiling of microRNAs by deep sequencing", Briefings in Bioinformatics, 10:490-497.
    [abstract]

  21. João Pedro De Magalhães, João Curado, George M. Church (2009), "Meta-analysis of age-related gene expression profiles identifies common signatures of aging", Bioinformatics, 25(7):875-881.
    [abstract]

  22. Irina Dinu, John D. Potter, Thomas Mueller, Qi Liu, Adeniyi J. Adewale, Gian S. Jhangri, Gunilla Einecke, Konrad S. Famulski, Philip Halloran, Yutaka Yasui (2009), "Gene-set analysis and reduction", Briefings in Bioinformatics, 10(1):24-34.
    [abstract]

  23. Igor Dozmorov, Ivan Lefkovits (2009), "Internal standard-based analysis of microarray data. Part I: analysis of differential gene expressions", Nucleic Acids Research, 37(19):6323-6339.

  24. Rose Du, Kelan Tantisira, Vincent Carey, Soumyaroop Bhattacharya, Stephanie Metje, Alvin T Kho, Barbara J Klanderman, Roger Gaedigk, Ross Lazarus, Thomas J Mariani, J Steven Leeder, Scott T Weiss (2009), "Platform dependence of inference on gene-wise and gene-set involvement in human lung development", BMC Bioinformatics, 10:189
    [abstract]

  25. Daniela Eggle, Svenja Debey-Pascher, Marc Beyer, Joachim L Schultze (2009), "The development of a comparison approach for Illumina bead chips unravels unexpected challenges applying newest generation microarrays", BMC Bioinformatics, 10:186
    [abstract]

  26. Laura L. Elo, Jukka Hiissa, Jarno Tuimala, Aleksi Kallio, Eija Korpelainen, Tero Aittokallio (2009), "Optimized detection of differential expression in global profiling experiments: case studies in clinical transcriptomic and quantitative proteomic datasets", Briefings in Bioinformatics, 10(5):547-555
    [abstract]

  27. Robert M. Flight and Peter D. Wentzell (2009), "Potential Bias in GO::TermFinder", Briefings in Bioinformatics, 10:289-294.
    [abstract]

  28. Johannes M Freudenberg, Vineet K Joshi, Zhen Hu, Mario Medvedovic (2009), "CLEAN: CLustering Enrichment ANalysis", BMC Bioinformatics, 10:234.
    [abstract]

  29. Andre Fujita, Joao Ricardo Sato, Marcos Angelo Almeida Demasi, Mari Cleide Sogayar, Carlos Eduardo Ferreira, Satoru Miyano (2009), "Comparing Pearon, Spearman and Hoeffding's D measure for gene expression association Analysis", Journal of Bioinformatics and Computational Biology, 7(4):663-684.
    [ abstract]

  30. D Ghosh, AM Chinnaiyan (2009), "Genomic outlier profile analysis: mixture models, null hypotheses, and nonparametric estimation", Biostatistics, 10(1):60-69.

  31. Jesse Gillis, Paul Pavlidis (2009), "A methodology for the analysis of differential coexpression across the human lifespan", BMC Bioinformatics, 10:306.
    [abstract]

  32. Galina V. Glazko and Frank Emmert-Streib (2009), "Unite and conquer: univariate and multivariate approaches for finding differentially expressed gene sets", Bioinformatics, 25(18):2348-2354.
    [abstract]

  33. Daniel Glez-Peña, Fernando Díaz, Jesús M Hernández, Juan M Corchado, Florentino Fdez-Riverola (2009), "geneCBR: a translational tool for multiple-microarray analysis and integrative information retrieval for aiding diagnosis in cancer research", BMC Bioinformatics, 10:187
    [abstract]

  34. Ruth Heller, Elisabetta Manduchi, Gregory R. Grant, Warren J Ewens (2009), "A flexible two-stage procedure for identifying gene sets that are differentially expressed", Bioinformatics, 25(8):1019-1025.
    [abstract]

  35. Ruth Heller, Elisabetta Manduchi, Dylan S. Small (2009), "Matching methods for observational microarray studies", Bioinformatics, 25(7):904-909.
    [abstract]

  36. Jérôme Hennetin, Petri Pehkonen, Michel Bellis (2009), "Construction and use of gene expression covariation matrix", BMC Bioinformatics, 10:214
    [abstract]

  37. Yvonne Hey and Stuart D. Pepper (2009), "Interesting times for microarray expression profiling", Briefings in Functional Genomics and Proteomics, 8(3):170-173.
    [abstract]

  38. Brian E Howard, Beate Sick, Steffen Heber (2009), "Unsupervised assessment of microarray data quality using a Gaussian mixture model", BMC Bioinformatics, 10:191
    [abstract]

  39. Paul J. Hurd and Christopher J. Nelson (2009), "Advantages of next-generation sequencing versus the microarray in epigenetic research", Briefings in Functional Genomics and Proteomics, 8(3):174-183.
    [abstract]

  40. JP Ioannidis, Allison DB, Ball CA, Coulibaly I, Cui X, Culhane AC, Falchi M, Furlanello C, Game L, Jurman G, Mangion J, Mehta T, Nitzberg M, Page GP, Petretto E, van Noort V. (2009), "Repeatability of published microarray gene expression analyses", Nature Genetics, 41(2):149-155.

  41. Natalia Jiménez-Lozano, Joan Segura, José Ramón Macías, Juanjo Vega, and José María Carazo (2009), "aGEM: an integrative system for analyzing spatial-temporal gene-expression information", Bioinformatics, 25(19):2566-2572.
    [abstract]

  42. Eun-Youn Kim, Seon-Young Kim, Daniel Ashlock, Dougu Nam (2009), "MULTI-K: accurate classification of microarray subtypes using ensemble k-means clustering", BMC Bioinformatics, 10:260
    [abstract]

  43. Lee J. Lancashire, Christophe Lemetre and Graham R. Ball (2009), "An introduction to artificial neural networks in bioinformatics -- application to complex microarray and mass spectrometry datasets in cancer studies", Briefings in Bioinformatics, 10(3):315-329.
    [abstract]

  44. William B. Langdon, Graham J. G. Upton, and Andrew P. Harrison (2009), "Probes containing runs of guanines provide insights into the biophysics and bioinformatics of Affymetrix GeneChips", Briefings in Bioinformatics, 10:259-277.
    [abstract]

  45. Z Liu, RB Gartenhaus, XW Chen, CD Howell, M Tan (2009), "Survival prediction and gene identification with penalized global AUC maximization", Journal of Computational Biology, 16(12):1661-1670.
    [ abstract]

  46. A. H. M. Mahbub Latif, Frank Bretz, and Edgar Brunner (2009), "Robustness considerations in selecting efficient two-color microarray designs", Bioinformatics, 25(18):2355-2361.
    [abstract]

  47. Xue Lin, Bahman Afsari, Luigi Marchionni, Leslie Cope, Giovanni Parmigiani, Daniel Naiman, Donald Geman (2009), "The ordering of expression among a few genes can provide simple cancer biomarkers and signal BRCA1 mutations", BMC Bioinformatics, 10:256
    [abstract]

  48. Ke-Shiuan Lynn, Li-Lan Li, Yen-Ju Lin, Chiuen-Huei Wang, Shu-Hui Sheng, Ju-Hwa Lin, Wayne Liao, Wen-Lian Hsu, Wen-Harn Pan (2009), "A neural network model for constructing endophenotypes of common complex diseases: an application to male young-onset hypertension microarray data", Bioinformatics, 25(8):981-988.
    [abstract]

  49. Shuangge Ma, Michael R. Kosorok (2009), "Identification of differential gene pathways with principal component analysis", Bioinformatics, 25(7):882-889.
    [abstract]

  50. Davis J McCarthy, Gordon K Smyth (2009), "Testing significance relative to a fold-change threshold is a TREAT", Bioinformatics, 25(6):765-771.
    [abstract]

  51. Anirban Mukhopadhyay, Ujjwal Maulik, Sanghamitra Bandyopadhyay (2009), "A novel coherence measure for discovering scaling biclusters from gene expression data" Journal of Bioinformatics and Computational Biology, 7(5):853-868.
    [ abstract]

  52. protein
    E Shannon Neeley, Steven M Kornblau, Kevin R Coombes, Keith A Baggerly (2009), "Variable slope normalization of reverse phase protein arrays", Bioinformatics, 25(11):1384-1389.
    [abstract]

  53. L Omberg, J R Meyerson, K Kobayashi, L S Drury, J F X Diffley, O Alter (2009), "Global effects of DNA replication and DNA replication origin activity on eukaryotic gene expression," Nature Molecular Systems Biology, 5:312
    [ abstract]

  54. Richard D Pearson, Xuejun Liu, Guido Sanguinetti, Marta Milo, Neil D Lawrence, Magnus Rattray (2009), "puma: a Bioconductor package for propagating uncertainty in microarray analysis", BMC Bioinformatics, 10:211
    [abstract]

  55. David M Rocke, Trey Ideker, Olga Troyanskaya, John Quackenbush, Joaquin Dopazo (2009), "Papers on normalization, variable selection, classification or clustering of microarray data" (editorial), Bioinformatics, 25(6):701-702.
    [abstract]

  56. Robert A Rubin (2009), "A first principles approach to differential expression in microarray data analysis", BMC Bioinformatics, 10:292
    [abstract]

  57. Ahmet Sacan, Nilgun Ferhatosmanoglu, Hakan Ferhatosmanoglu (2009), "MicroarrayDesigner: an online search tool and repository for near-optimal microarray experimental designs", BMC Bioinformatics, 10:304
    [abstract]

  58. Maureen A Sartor, George D Leikauf, Mario Medvedovic (2009), "LRpath: a logistic regression approach for identifying enriched biological groups in gene expression data", Bioinformatics, 25(2):211-217.
    [ abstract]

  59. Richard S Savage, Katherine Heller, Yang Xu, Zoubin Ghahramani, William M Truman, Murray Grant, Katherine J Denby, David L Wild (2009), "R/BHC: fast Bayesian hierarchical clustering for microarray data", BMC Bioinformatics, 10:242
    [abstract]

  60. Theresa Scharl, Friedrich Leisch (2009), "gcExplorer: interactive exploration of gene clusters", Bioinformatics, 25(8):1089-1090.
    [abstract]

  61. Theresa Scharl, Ingo Voglhuber, Friedrich Leisch (2009), "Exploratory and inferential analysis of gene cluster neighborhood graphs", BMC Bioinformatics, 10:288
    [abstract]

  62. JD Silver, ME Ritchie, GK Smyth (2009), "Microarray background correction: maximum likelihood estimation for the normal-exponential convolution", Biostatistics, 10:352-363.
    [ abstract]

  63. Richard Simon (2009), "Advances in clinical trial designs for predictive biomarker discovery and validation", Current Breast Cancer Reports, 1(4):216-221.
    [ abstract]

  64. Hoicheong Siu, Hua Dong, Li Jin, Momiao Xiong (2009), "New statistics for testing differential expression of pathways from microarray data", in Lecture Notes of the Institute for Computer Sciences, Social Informatics and Telecommunications Engineering, Vol.4, pp.277-285.
    [ abstract]

  65. John R. Stevens and Gabriel Nicholas (2009), "metahdep: meta-analysis of hierarchically dependent gene expression studies", Bioinformatics, 25(19):2619-2620.
    [abstract]

  66. Yunxia Sui, Xiaoyue Zhao, Terence P. Speed, Zhijin Wu (2009), "Background adjustment for DNA microarrays using a database of microarray experiments", Journal of Computational Biology, 16(11): 1501-1515.
    [ abstract]

  67. Youting Sun, Ulisses Braga-Neto, Edward R. Dougherty (2009), "Impact of missing value imputation on classification for DNA microarray gene expression data -- a model-based study", EURASIP Journal on Bioinformatics and Systems Biology, 2009:504069.
    [ abstract]

  68. Chuen Seng Tan, Agus Salim, Alexander Ploner, Janne Lehtiö, Kee Seng Chia, Yudi Pawitan (2009), "Correlating gene and protein expression data using Correlated Factor Analysis", BMC Bioinformatics, 10:272
    [abstract]

  69. Alain B Tchagang, Kevin V Bui, Thomas McGinnis, Panayiotis V Benos (2009), "Extracting biologically significant patterns from short time series gene expression data", BMC Bioinformatics, 10:255
    [abstract]

  70. Terry Therneau (2009), "The perils and promise of high-dimensional biology" (comments from the editors), Hepatology, 49(4):1061-1062.
    [ abstract]

  71. Petri Toronen, Pauli J Ojala, Pekka Marttinen, Liisa Holm (2009), "Robust extraction of functional signals from gene set analysis using a generalized threshold free scoring function", BMC Bioinformatics, 10:307.
    [abstract]

  72. Chen-An Tsai, James J Chen (2009), "Multivariate analysis of variance test for gene set analysis", Bioinformatics, 25(7):897-903.
    [abstract]

  73. affymetrix
    Graham J G Upton, Olivia Sanchez-Graillet, Joanna Rowsell, Jose M Arteaga-Salas, Neil S Graham, Maria A Stalteri, Farhat N Memon, Sean T May, Andrew P Harrison (2009), "On the causes of outliers in Affymetrix GeneChip data", Briefings in Functional Genomics and Proteomics, 8(3):199-212.
    [abstract]

  74. K. Van Deun, H. Hoijtink, L. Thorrez, L. Van Lommel, F. Schuit, and I. Van Mechelen (2009), "Testing the hypothesis of tissue selectivity: the intersection -- union test and a Bayesian approach", Bioinformatics, 25(19):2588-2594.
    [abstract]

  75. Aaron L Vollrath, Adam A Smith, Mark Craven, Christopher A Bradfield (2009), "EDGE3: A web-based solution for management and analysis of Agilent two color microarray experiments", BMC Bioinformatics, 10:280
    [abstract]

  76. Fang-Xiang Wu, Zhonghang Xia, Lei Mu (2009), "Finding Significantly Expressed genes from time-course expression profiles", International Journal of Bioinformatics Research and Applications, 5(1):50-63.
    [abstract]

  77. Xiao-Qin Xia, Michael McClelland, Steffen Porwollik, Wenzhi Song, Xianling Cong, and Yipeng Wang (2009), "WebArrayDB: cross-platform microarray data analysis and public data repository", Bioinformatics, 25(18):2425-2429
    [abstract]

  78. Yang Xie, Xinlei Wang, Michael Story (2009), "Statistical methods of background correction for Illumina BeadArray data", Bioinformatics, 25(6):751-757.
    [abstract]

  79. Tao Xu, JianLei Gu, Yan Zhou, LinFang Du (2009), "Improving detection of differentially expressed gene sets by applying cluster enrichment analysis to Gene Ontology", BMC Bioinformatics, 10:240.
    [abstract]

  80. Phillip D Yates, Mark A Reimers (2009), "RCMAT: a regularized covariance matrix approach to testing gene sets", BMC Bioinformatics, 10:300.
    [abstract]

  81. Ming Yi, Uma Mudunuri, Anney Che, Robert M Stephens (2009), "Seeking unique and common biological themes in multiple gene lists or datasets: pathway pattern extraction pipeline for pathway-level comparative analysis", BMC Bioinformatics, 10:200
    [abstract]

  82. Yao Yu, Kang Tu, Siyuan Zheng, Yun Li, Guohui Ding, Jie Ping, Pei Hao, Yixue Li (2009), "GEOGLE: context mining tool for the correlation between gene expression and the phenotypic distinction", BMC Bioinformatics, 10:264
    [abstract]

  83. Xue-Qiang Zeng, Guo-Zheng Li, Geng-Feng Wu, Jack Y. Yang, Mary Qu Yang (2009), "Irrelevant gene elimination for Partial Least Squares based Dimension Reduction by using feature probes", International Journal of Data Mining and Bioinformatics, 3(1):85-103.
    [ abstract]
2009