Laboratory for Bioinformatics and Functional Genomics

Publications

Markowetz F, Kostka D, Troyanskaya OG, Spang R. Nested Effects Models for High-Dimensional Phenotyping Screens. ISMB/ECCB, 2007.
Myers CL, Troyanskaya OG. Context-sensitive data integration and prediction of biological networks. Bioinformatics, In Press, 2007.
Hibbs MA, Wallace G, Dunham M, Li K, Troyanskaya OG. Viewing the Larger Context of Genomic Data through Horizontal Integration. 11th Int. Conf. on Information Visualization (IV07), 2007.
Markowetz F, Spang R. Inferring cellular networks - a review. BMC Bioinformatics, 2007.
Huttenhower C, Flamholz AI, Landis JN, Sahi S, Myers CL, Olszewski KL, Hibbs MA, Siemers NO, Troyanskaya OG, Coller HA. Nearest Neighbor Networks: Clustering Expression Data Based on Gene Neighborhoods. BMC Bioinformatics, In Press, 2007.
Markowetz F, Troyanskaya OG. Computational identification of cellular networks and pathways. Molecular BioSystems, 3(7):478-482, 2007.
Wallace G, Hibbs MA, Dunham M, Sealfon RSG, Troyanskaya OG, Li K. Scalable, Dynamic Analysis and Visualization for Genomic Datasets. IPDPS 2007 Workshop on Next Generation Software Proceedings, 2007.
Guan Y, Dunham MJ, Troyanskaya OG. Functional analysis of gene duplications in Saccharomyces cerevisiae. Genetics Epub ahead of pint doi:10.1534/genetics.106.064329, 2006.
Haarer B, Viggiano S, Hibbs MA, Troyanskaya OG, Amberg DC. Modeling Complex Genetic Interactions in a Simple Eukaryotic Genome: Actin Displays a Rich Spectrum of Complex Haploinsufficiencies. Genes & Development 21, 2006.
Chi A*, Huttenhower CH*, Geer LY, Coon JJ, Syka JEP, Bai1 DL, Shabanowitz1 J, Burke DJ, Troyanskaya OG, Hunt DF. Analysis of phosphorylation sites on proteins from Saccharomyces cerevisiae by electron transfer dissociation (ETD) mass spectrometry. PNAS, 2006 in press.
Sealfon RSG, Hibbs MA, Huttenhower C, Myers CL, Troyanskaya OG. GOLEM: an interactive graph-based gene ontology navigation and analysis tool. BMC Bioinformatics 2006, 7:443.
Bongo LA, Wallace G, Larsen T, Li K, Troyanskaya OG. Systems Support for Remote Visualization of Genomics Applications over Wide Area Networks. Proceedings of the International Workshop on Distributed, High-Performance and Grid Computing in Computational Biology (GCCB), 2006.
Myers CL, Barrett D, Hibbs MA, Huttenhower C, Troyanskaya OG. Finding function: evaluation methods for functional genomic data. BMC Genomics 2006, 7:187.
Huttenhower C, Hibbs M, Myers C, Troyanskaya OG. A scalable method for integration and functional analysis of multiple microarray data sets. Bioinformatics 22:2890, 2006.
Huttenhower C, Troyanskaya OG. Bayesian Data Integration: A Functional Perspective. CSB 4:341, 2006.
Barutcuoglu Z, Schapire RE, Troyanskaya OG. Hierarchical Multi-label Prediction of Gene Function. Bioinformatics, 2006 Jan 12.
Myers CL, Robson D, Wible A, Hibbs MA, Chiriac C, Theesfeld CL, Dolinski K, Troyanskaya OG. Discovery of biological networks from diverse functional genomic data. Genome Biology6(13):R114, 2005.
Reguly T, Breitkreutz A, Boucher L, Breitkreutz B, Hon G, Myers CL, Parsons A, Friesen H, Oughtred R, Tong A, Ho Y, Botstein D, Andrews B, Boone C, Troyanskya OG, Ideker T, Dolinski K, Batada NN, Tyers M. Comprehensive Curation and Analysis of Global Interaction Networks in Saccharomyces cerevisiae. Submitted to Journal of Biology, 2005.
Brown JA, Sherlock G, Myers CL, Burrows NM, Deng C, Wu HI, McCann KE, Troyanskaya OG, Brown MG. Global analysis of gene function in yeast by quantitative phenotypic profiling. Molecular Systems Biology, 17 Jan 2006.
Myers CL, Chen X, Troyanskaya OG. Visualization-based discovery and analysis of genomic abberations in microarray data. BMC Bioinformatics, 6:146, 2005.
Hibbs, MA,Dirksen NC, Li K, Troyanskaya OG. Visualization Methods for Statistical Analysis of Microarray Clusters. BMC Bioinformatics, 6:115, 2005.
Wallace G, Chen H, Chen Y, Liu Z, Samanta R, Bi P, Gupta A, Hibbs M, Li K, Finkelstein A, Funkhouser T, Cook P, Sukthankar R, and Troyanskaya OG. Tools and Applications for Large Scale Display Walls. Special Issue on Large Format Displays, IEEE Computer Graphics and Applications, July/August 2005.
Li K, Hibbs M, Wallace G, Troyanskaya OG. Dynamic Scalable Visualization for Collaborative Scientific Applications. IPDPS 2005 Workshop on Next Generation Software Proceedings, 2005.
Troyanskaya OG. Putting the 'bio' into bioinformatics. Genome Biology, 6(10):351, 2005.
Troyanskaya OG. Unsupervised machine learning to support functional characterization of genes. In: Data analysis and visualization methods in genomics and proteomics, Azuaje F & Dopazo J, Eds. John Wiley & Sons. 2005.
Troyanskaya OG. Putting microarrays in a context: integrated analysis of diverse biological data. Briefings in Bioinformatics, 6(1): 34-43, 2005.
Dolinski K, Troyanksya OG. In: Encyclopedia of Genetics, Genomics, Proteomics and Bioinformatics, Jorde LB, Little PFR, Dunn MJ, Subramaniam S, Eds. John Wiley & Sons. 2005.
Myers CL, Dunham M, Kung SY, Troyanskaya OG. Accurate detection of aneuploidies in array CGH and gene expression microarray data. Bioinformatics, 20:3533-3543, 2004.
Liang MP, Troyanskaya OG, Laederach A, Brutlag DL, Altman RB. Computational Functional Genomics. IEEE Signal Processing, 21(6): 62-69, 2004.
Troyanskaya OG, Dolinski K, Owen AB, Altman RB, and Botstein D. A Bayesian framework for combining heterogeneous data sources for gene function prediction (in S. cerevisiae). Proc Natl Acad Sci USA 100(14): 8348-53, 2003.
Whitfield ML, Finlay DR, Murray JI, Troyanskaya OG, Chi JT, Pergamenschikov A, McCalmont TH, Brown PO, Botstein D, Connolly MK. Systemic and cell type-specific gene expression patterns in scleroderma skin. Proc Natl Acad Sci USA, 100(21):12319-24, 2003.
Chi JT, Chang HY, Haraldsen G, Jahnsen FL, Troyanskaya OG, Chang DS, Wang Z, Rockson SG, van de Rijn M, Botstein D, Brown PO. Endothelial cell diversity revealed by global expression profiling. Proc Natl Acad Sci USA, 100(19):10623-8, 2003.
Chen X, Leung SY, Yuen ST, Chu KM, Ji J, Li R, Chan SY, Law S, Troyanskaya OG, Wong J, Botstein D, So S, Brown PO. Variation in gene expression patterns in human gastric cancers. Mol Biol Cell, 14(8):3208-15, 2003.
Bohen SP, Troyanskaya OG, Alter O, Warnke R, Botstein D, Brown PO, Levy R. Variation in gene expression patterns in follicular lymphoma and the response to rituximab. Proc Natl Acad Sci USA, 100(4): 1926-30, 2003.
Troyanskaya OG, Garber ME, Brown PO, Botstein D, Altman RB. Nonparametric methods for identifying differentially expressed genes in microarray data. Bioinformatics, 18:1454-61, 2002.
Leung SY, Chen X, Chu KM, Yuen ST, Mathy J, Ji J, Chan ASY, Li R, Law S, Troyanskaya OG, Tu IP, Wong J, So S, Botstein D, Brown PO. Phospholipase A2, Group IIA expression in gastric adenocarcinoma is associated with prolonged survival and less frequent metastasis. Proc Natl Acad Sci USA, 99(25):16203-8, 2002.
Troyanskaya OG, Botstein D, Altman RB. Missing value estimation. In: A practical approach to microarray data analysis, D Berrar, W Dubitzky, M Granzow, Eds. Kluwer Academic Publishers, London, pp. 65-75, 2002.
Troyanskaya OG, Arbell O, Koren Y, Landau GM, Bolshoy A. Sequence complexity profiles of prokaryotic genomic sequences: A fast algorithm for calculating linguistic complexity. Bioinformatics, 18:679-88, 2002.
Garber ME, Troyanskaya OG, Schluens K, Petersen S, Thaesler Z, Pacyna-Gengelbach M, van de Rijn M, Rosen GD, Perou CM, Whyte RI, Altman RB, Brown PO, Botstein D, Petersen I. Diversity of gene expression in adenocarcinoma of the lung. Proc Natl Acad Sci USA, 98(24):13784-9, 2001.
Troyanskaya O, Cantor M, Sherlock G, Brown P, Hastie T, Tibshirani R, Botstein D, Altman RB. Missing value estimation methods for DNA microarrays. Bioinformatics, 17:520-5, 2001.