Matthew A. Hibbs - Publications

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Manuscripts in Preparation

Hibbs MA, Dunham M, Wallace G, Li K, Troyanskaya OG. A Platform for Integrated, Scalable Analysis and Visualization of Gene Expression Microarray Data Compendia. In preparation, 2008.
Hibbs MA*, Myers CL*, Huttenhower C*, Hess DC, Caudy AA, Li K, Troyanskaya OG. On the Use of Computational Functional Genomics to Discover Novel Biology. In preparation, 2008. *Authors contributed equally
Hess DC, Myers CL*, Huttenhower C*, Hibbs MA*, Hayes A, Paw J, Clore J, Mendoza R, San Luis B, Costanzo M, Boone C, Caudy AA, Troyanskaya OG. Integrating computation and experimentation to discover novel mitochondrial biology. In preparation, 2008. *Authors contributed equally
Huttenhower C*, Myers CL*, Hibbs MA*, Hess DC, Caudy AA, Troyanskaya OG. The impact of incomplete knowledge on gene function prediction. In preparation, 2008. *Authors contributed equally

Published Manuscripts

Hibbs MA, Hess DC, Myers CL, Huttenhower C, Li K, Troyanskaya OG. Exploring the functional landscape of gene expression: directed search of large microarray compendia. Bioinformatics, 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.
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.
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.
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.
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.
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 MA, Myers CL, Troyanskaya OG. A scalable method for integration and functional analysis of multiple microarray data sets. Bioinformatics 22:2890, 2006.
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.
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 MA, 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 MA, Wallace G, Troyanskaya OG. Dynamic Scalable Visualization for Collaborative Scientific Applications. IPDPS 2005 Workshop on Next Generation Software Proceedings, 2005.