List of Faculty Publications
Below is a list of Faculty publications imported from PubMed or manually added. By default, publications are sorted by year with titles displayed in ascending alphabetical order.
Shortcuts: Wühr, Martin | Wingreen, Ned | Wieschaus, Eric | Troyanskaya, Olga | Tilghman, Shirley | Storey, John | Singh, Mona | Shvartsman, Stanislav | Shaevitz, Joshua | Rabinowitz, Joshua | Murphy, Coleen | Levine, Michael {Levine, Michael S.} | Gregor, Thomas | Botstein, David | Bialek, William | Ayroles, Julien | Andolfatto, Peter | Akey, Joshua
“From hub proteins to hub modules: the relationship between essentiality and centrality in the yeast interactome at different scales of organization.”, PLoS Comput Biol, vol. 9, no. 2, p. e1002910, 2013.
, “Simple topological features reflect dynamics and modularity in protein interaction networks.”, PLoS Comput Biol, vol. 9, no. 10, p. e1003243, 2013.
, “The Gene Ontology in 2010: extensions and refinements.”, Nucleic Acids Res, vol. 38, no. Database issue, pp. D331-5, 2010.
“Saccharomyces Genome Database provides mutant phenotype data.”, Nucleic Acids Res, vol. 38, no. Database issue, pp. D433-6, 2010.
, “SPICi: a fast clustering algorithm for large biological networks.”, Bioinformatics, vol. 26, no. 8, pp. 1105-11, 2010.
, “Computational analysis of the yeast proteome: understanding and exploiting functional specificity in genomic data.”, Methods Mol Biol, vol. 548, pp. 273-93, 2009.
, “Graphle: Interactive exploration of large, dense graphs.”, BMC Bioinformatics, vol. 10, p. 417, 2009.
, “How and when should interactome-derived clusters be used to predict functional modules and protein function?”, Bioinformatics, vol. 25, no. 23, pp. 3143-50, 2009.
, “The impact of incomplete knowledge on evaluation: an experimental benchmark for protein function prediction.”, Bioinformatics, vol. 25, no. 18, pp. 2404-10, 2009.
, “Recurated protein interaction datasets.”, Nat Methods, vol. 6, no. 12, pp. 860-1, 2009.
, “Organization of physical interactomes as uncovered by network schemas.”, PLoS Comput Biol, vol. 4, no. 10, p. e1000203, 2008.
, “Context-sensitive data integration and prediction of biological networks.”, Bioinformatics, vol. 23, no. 17, pp. 2322-30, 2007.
, “Expanded protein information at SGD: new pages and proteome browser.”, Nucleic Acids Res, vol. 35, no. Database issue, pp. D468-71, 2007.
, “Exploring the functional landscape of gene expression: directed search of large microarray compendia.”, Bioinformatics, vol. 23, no. 20, pp. 2692-9, 2007.
, “The Princeton Protein Orthology Database (P-POD): a comparative genomics analysis tool for biologists.”, PLoS One, vol. 2, no. 8, p. e766, 2007.
, “GOLEM: an interactive graph-based gene-ontology navigation and analysis tool.”, BMC Bioinformatics, vol. 7, p. 443, 2006.
, “Hierarchical multi-label prediction of gene function.”, Bioinformatics, vol. 22, no. 7, pp. 830-6, 2006.
, “Gibbs sampling and helix-cap motifs.”, Nucleic Acids Res, vol. 33, no. 16, pp. 5343-53, 2005.
, “Fast accurate evaluation of protein solvent exposure.”, Proteins, vol. 57, no. 3, pp. 565-76, 2004.
, “Flexibility of beta-sheets: principal component analysis of database protein structures.”, Proteins, vol. 55, no. 1, pp. 91-8, 2004.
, “GO::TermFinder--open source software for accessing Gene Ontology information and finding significantly enriched Gene Ontology terms associated with a list of genes.”, Bioinformatics, vol. 20, no. 18, pp. 3710-5, 2004.
, “Flexibility of alpha-helices: results of a statistical analysis of database protein structures.”, J Mol Biol, vol. 327, no. 1, pp. 229-37, 2003.
, “Saccharomyces Genome Database (SGD) provides biochemical and structural information for budding yeast proteins.”, Nucleic Acids Res, vol. 31, no. 1, pp. 216-8, 2003.
, “Designability of alpha-helical proteins.”, Proc Natl Acad Sci U S A, vol. 99, no. 17, pp. 11163-8, 2002.
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