Publications
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2007. Analysis of phosphorylation sites on proteins from Saccharomyces cerevisiae by electron transfer dissociation (ETD) mass spectrometry.. Proceedings of the National Academy of Sciences of the United States of America. 104(7):2193-8. Abstract
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2006. Bayesian data integration: a functional perspective.. Computational systems bioinformatics / Life Sciences Society. Computational Systems Bioinformatics Conference. :341-51. Abstract
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2009. Computational analysis of the yeast proteome: understanding and exploiting functional specificity in genomic data.. Methods in molecular biology (Clifton, N.J.). 548:273-93. Abstract
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2011. Computational biology: plus c'est la même chose, plus ça change.. Genome biology. 12(8):307. Abstract
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2009. Computationally driven, quantitative experiments discover genes required for mitochondrial biogenesis.. PLoS genetics. 5(3):e1000407. Abstract
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2008. Coordination of growth rate, cell cycle, stress response, and metabolic activity in yeast.. Molecular biology of the cell. 19(1):352-67. Abstract
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2011. Current concepts of the intestinal microbiota and the pathogenesis of infection.. Current infectious disease reports. 13(1):28-34. Abstract
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2009. Detailing regulatory networks through large scale data integration.. Bioinformatics (Oxford, England). 25(24):3267-74. Abstract
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2009. Directing experimental biology: a case study in mitochondrial biogenesis.. PLoS computational biology. 5(3):e1000322. Abstract
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2010. Epigenomic diversity of colorectal cancer indicated by LINE-1 methylation in a database of 869 tumors.. Molecular cancer. 9:125. Abstract
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2007. Exploring the functional landscape of gene expression: directed search of large microarray compendia.. Bioinformatics (Oxford, England). 23(20):2692-9. Abstract
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2009. Exploring the human genome with functional maps.. Genome research. 19(6):1093-106. Abstract
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2006. Finding function: evaluation methods for functional genomic data.. BMC genomics. 7:187. Abstract
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2011. The genome of Th17 cell-inducing segmented filamentous bacteria reveals extensive auxotrophy and adaptations to the intestinal environment.. Cell host & microbe. 10(3):260-72. Abstract
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2011. Genomic analysis identifies association of Fusobacterium with colorectal carcinoma.. Genome research. Abstract
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2011. Genomics in 2011: challenges and opportunities.. Genome biology. 12(12):137. Abstract
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2009. Global prediction of tissue-specific gene expression and context-dependent gene networks in Caenorhabditis elegans.. PLoS computational biology. 5(6):e1000417. Abstract
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2006. GOLEM: an interactive graph-based gene-ontology navigation and analysis tool.. BMC bioinformatics. 7:443. Abstract
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2009. Graphle: Interactive exploration of large, dense graphs.. BMC bioinformatics. 10:417. Abstract
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2011. Host and gut microbiota symbiotic factors: lessons from inflammatory bowel disease and successful symbionts.. Cellular microbiology. Abstract
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2009. The impact of incomplete knowledge on evaluation: an experimental benchmark for protein function prediction.. Bioinformatics (Oxford, England). 25(18):2404-10. Abstract
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2011. Inferring protein function from homology using the Princeton Protein Orthology Database (P-POD).. Current protocols in bioinformatics / editoral board, Andreas D. Baxevanis ... [et al.]. Chapter 6:Unit6.11. Abstract
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2010. Integrated functional networks of process, tissue, and developmental stage specific interactions in Arabidopsis thaliana.. BMC systems biology. 4:180. Abstract
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2012. Integrative approaches for microarray data analysis.. Methods in molecular biology (Clifton, N.J.). 802:157-82. Abstract