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Databases, Protein

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  • Huttenhower, Curtis, Matthew A Hibbs, Chad L Myers, Amy A Caudy, David C Hess, and Olga G Troyanskaya. (2009) 2009. “The Impact of Incomplete Knowledge on Evaluation: An Experimental Benchmark for Protein Function Prediction.”. Bioinformatics 25 (18): 2404-10.
    Reference Link
  • Huttenhower, Curtis, Chad L Myers, Matthew A Hibbs, and Olga G Troyanskaya. 2009. “Computational Analysis of the Yeast Proteome: Understanding and Exploiting Functional Specificity in Genomic Data.”. Methods Mol Biol 548: 273-93.
    Reference Link
  • Song, Jimin, and Mona Singh. (2009) 2009. “How and When Should Interactome-Derived Clusters Be Used to Predict Functional Modules and Protein Function?”. Bioinformatics 25 (23): 3143-50.
    Reference Link
  • Barutcuoglu, Zafer, Robert E Schapire, and Olga G Troyanskaya. (2006) 2006. “Hierarchical Multi-Label Prediction of Gene Function.”. Bioinformatics 22 (7): 830-6.
    Reference Link
  • Huttenhower, Curtis, Sajid O Mehmood, and Olga G Troyanskaya. 2009. “Graphle: Interactive Exploration of Large, Dense Graphs.”. BMC Bioinformatics 10: 417.
    Reference Link
  • Boyle, Elizabeth I, Shuai Weng, Jeremy Gollub, Heng Jin, David Botstein, Michael Cherry, and Gavin Sherlock. (2004) 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 20 (18): 3710-5.
    Reference Link
  • Sealfon, Rachel S G, Matthew A Hibbs, Curtis Huttenhower, Chad L Myers, and Olga G Troyanskaya. 2006. “GOLEM: An Interactive Graph-Based Gene-Ontology Navigation and Analysis Tool.”. BMC Bioinformatics 7: 443.
    Reference Link
  • Kruus, Erik, Peter Thumfort, Chao Tang, and Ned S Wingreen. 2005. “Gibbs Sampling and Helix-Cap Motifs.”. Nucleic Acids Res 33 (16): 5343-53.
    Reference Link
  • Consortium, Gene Ontology. (2010) 2010. “The Gene Ontology in 2010: Extensions and Refinements.”. Nucleic Acids Res 38 (Database issue).
    Reference Link
  • Song, Jimin, and Mona Singh. 2013. “From Hub Proteins to Hub Modules: The Relationship Between Essentiality and Centrality in the Yeast Interactome at Different Scales of Organization.”. PLoS Comput Biol 9 (2): e1002910.
    Reference Link
  • Jiang, Peng, and Mona Singh. (2010) 2010. “SPICi: A Fast Clustering Algorithm for Large Biological Networks.”. Bioinformatics 26 (8): 1105-11.
    Reference Link
  • Emberly, Eldon G, Ranjan Mukhopadhyay, Chao Tang, and Ned S Wingreen. (2004) 2004. “Flexibility of Beta-Sheets: Principal Component Analysis of Database Protein Structures.”. Proteins 55 (1): 91-8.
    Reference Link
  • Pritykin, Yuri, and Mona Singh. 2013. “Simple Topological Features Reflect Dynamics and Modularity in Protein Interaction Networks.”. PLoS Comput Biol 9 (10): e1003243.
    Reference Link
  • Emberly, Eldon G, Ranjan Mukhopadhyay, Ned S Wingreen, and Chao Tang. (2003) 2003. “Flexibility of Alpha-Helices: Results of a Statistical Analysis of Database Protein Structures.”. J Mol Biol 327 (1): 229-37.
    Reference Link
  • Weng, Shuai, Qing Dong, Rama Balakrishnan, Karen R Christie, Maria Costanzo, Kara Dolinski, Selina S Dwight, et al. (2003) 2003. “Saccharomyces Genome Database (SGD) Provides Biochemical and Structural Information for Budding Yeast Proteins.”. Nucleic Acids Res 31 (1): 216-8.
    Reference Link
  • Zhang, Naigong, Chen Zeng, and Ned S Wingreen. (2004) 2004. “Fast Accurate Evaluation of Protein Solvent Exposure.”. Proteins 57 (3): 565-76.
    Reference Link
  • Engel, Stacia R, Rama Balakrishnan, Gail Binkley, Karen R Christie, Maria C Costanzo, Selina S Dwight, Dianna G Fisk, et al. (2010) 2010. “Saccharomyces Genome Database Provides Mutant Phenotype Data.”. Nucleic Acids Res 38 (Database issue).
    Reference Link
  • Hibbs, Matthew A, David C Hess, Chad L Myers, Curtis Huttenhower, Kai Li, and Olga G Troyanskaya. (2007) 2007. “Exploring the Functional Landscape of Gene Expression: Directed Search of Large Microarray Compendia.”. Bioinformatics 23 (20): 2692-9.
    Reference Link
  • Salwinski, Lukasz, Luana Licata, Andrew Winter, David Thorneycroft, Jyoti Khadake, Arnaud Ceol, Andrew Chatr Aryamontri, et al. (2009) 2009. “Recurated Protein Interaction Datasets.”. Nat Methods 6 (12): 860-1.
    Reference Link
  • Nash, Robert, Shuai Weng, Ben Hitz, Rama Balakrishnan, Karen R Christie, Maria C Costanzo, Selina S Dwight, et al. (2007) 2007. “Expanded Protein Information at SGD: New Pages and Proteome Browser.”. Nucleic Acids Res 35 (Database issue).
    Reference Link
  • Heinicke, Sven, Michael S Livstone, Charles Lu, Rose Oughtred, Fan Kang, Samuel Angiuoli V, Owen White, David Botstein, and Kara Dolinski. 2007. “The Princeton Protein Orthology Database (P-POD): A Comparative Genomics Analysis Tool for Biologists.”. PLoS One 2 (8): e766.
    Reference Link
  • Emberly, Eldon G, Ned S Wingreen, and Chao Tang. (2002) 2002. “Designability of Alpha-Helical Proteins.”. Proc Natl Acad Sci U S A 99 (17): 11163-8.
    Reference Link
  • Banks, Eric, Elena Nabieva, Bernard Chazelle, and Mona Singh. (2008) 2008. “Organization of Physical Interactomes As Uncovered by Network Schemas.”. PLoS Comput Biol 4 (10): e1000203.
    Reference Link
  • Myers, Chad L, and Olga G Troyanskaya. (2007) 2007. “Context-Sensitive Data Integration and Prediction of Biological Networks.”. Bioinformatics 23 (17): 2322-30.
    Reference Link

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