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
Filters: Author is Singh, Mona [Clear All Filters]
, “An expanded binding model for Cys2His2 zinc finger protein-DNA interfaces.”, Phys Biol, vol. 8, no. 3, p. 035010, 2011.
, “De novo prediction of DNA-binding specificities for Cys2His2 zinc finger proteins.”, Nucleic Acids Res, vol. 42, no. 1, pp. 97-108, 2014.
, “Predicting DNA recognition by Cys2His2 zinc finger proteins.”, Bioinformatics, vol. 25, no. 1, pp. 22-9, 2009.
, “Two critical positions in zinc finger domains are heavily mutated in three human cancer types.”, PLoS Comput Biol, vol. 14, no. 6, p. e1006290, 2018.
, “Deep sequencing of large library selections allows computational discovery of diverse sets of zinc fingers that bind common targets.”, Nucleic Acids Res, vol. 42, no. 3, pp. 1497-508, 2014.
, “G-quadruplex DNA sequences are evolutionarily conserved and associated with distinct genomic features in Saccharomyces cerevisiae.”, PLoS Comput Biol, vol. 6, no. 7, p. e1000861, 2010.
, “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.
, “Two critical positions in zinc finger domains are heavily mutated in three human cancer types.”, PLoS Comput Biol, vol. 14, no. 6, p. e1006290, 2018.
, “Interaction-based discovery of functionally important genes in cancers.”, Nucleic Acids Res, vol. 42, no. 3, p. e18, 2014.
, “A cross-genomic approach for systematic mapping of phenotypic traits to genes.”, Genome Res, vol. 14, no. 1, pp. 109-15, 2004.
, “CCAT: Combinatorial Code Analysis Tool for transcriptional regulation.”, Nucleic Acids Res, vol. 42, no. 5, pp. 2833-47, 2014.
, “The Cutoff protein regulates piRNA cluster expression and piRNA production in the Drosophila germline.”, EMBO J, vol. 30, no. 22, pp. 4601-15, 2011.
, “Two critical positions in zinc finger domains are heavily mutated in three human cancer types.”, PLoS Comput Biol, vol. 14, no. 6, p. e1006290, 2018.
, “CCAT: Combinatorial Code Analysis Tool for transcriptional regulation.”, Nucleic Acids Res, vol. 42, no. 5, pp. 2833-47, 2014.
, “Comparative analysis of methods for representing and searching for transcription factor binding sites.”, Bioinformatics, vol. 20, no. 18, pp. 3516-25, 2004.
, “Interaction-based discovery of functionally important genes in cancers.”, Nucleic Acids Res, vol. 42, no. 3, p. e18, 2014.
, “Deep sequencing of large library selections allows computational discovery of diverse sets of zinc fingers that bind common targets.”, Nucleic Acids Res, vol. 42, no. 3, pp. 1497-508, 2014.
, “Predicting specificity in bZIP coiled-coil protein interactions.”, Genome Biol, vol. 5, no. 2, p. R11, 2004.
, “Evolution of amino acid frequencies in proteins over deep time: inferred order of introduction of amino acids into the genetic code.”, Mol Biol Evol, vol. 19, no. 10, pp. 1645-55, 2002.
, “Protein quantification across hundreds of experimental conditions.”, Proc Natl Acad Sci U S A, vol. 106, no. 37, pp. 15544-8, 2009.
, “Solving and analyzing side-chain positioning problems using linear and integer programming.”, Bioinformatics, vol. 21, no. 7, pp. 1028-36, 2005.
, “Predicting functionally important residues from sequence conservation.”, Bioinformatics, vol. 23, no. 15, pp. 1875-82, 2007.
, “Sharing DNA-binding information across structurally similar proteins enables accurate specificity determination.”, Nucleic Acids Res, vol. 48, no. 2, p. e9, 2020.
, “A cross-genomic approach for systematic mapping of phenotypic traits to genes.”, Genome Res, vol. 14, no. 1, pp. 109-15, 2004.
, “The Cutoff protein regulates piRNA cluster expression and piRNA production in the Drosophila germline.”, EMBO J, vol. 30, no. 22, pp. 4601-15, 2011.
, “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.
, “Predicting specificity in bZIP coiled-coil protein interactions.”, Genome Biol, vol. 5, no. 2, p. R11, 2004.
, “Quantitative measurement of allele-specific protein expression in a diploid yeast hybrid by LC-MS.”, Mol Syst Biol, vol. 8, p. 602, 2012.
, “Comparative analysis of methods for representing and searching for transcription factor binding sites.”, Bioinformatics, vol. 20, no. 18, pp. 3516-25, 2004.
, “SPICi: a fast clustering algorithm for large biological networks.”, Bioinformatics, vol. 26, no. 8, pp. 1105-11, 2010.
, “molBLOCKS: decomposing small molecule sets and uncovering enriched fragments.”, Bioinformatics, vol. 30, no. 14, pp. 2081-3, 2014.
, “Solving and analyzing side-chain positioning problems using linear and integer programming.”, Bioinformatics, vol. 21, no. 7, pp. 1028-36, 2005.
, “CCAT: Combinatorial Code Analysis Tool for transcriptional regulation.”, Nucleic Acids Res, vol. 42, no. 5, pp. 2833-47, 2014.
, “Accurate proteome-wide protein quantification from high-resolution 15N mass spectra.”, Genome Biol, vol. 12, no. 12, p. R122, 2011.
, “Comparative analysis of methods for representing and searching for transcription factor binding sites.”, Bioinformatics, vol. 20, no. 18, pp. 3516-25, 2004.
, “Interaction-based discovery of functionally important genes in cancers.”, Nucleic Acids Res, vol. 42, no. 3, p. e18, 2014.
, “Differential analysis between somatic mutation and germline variation profiles reveals cancer-related genes.”, Genome Med, vol. 9, no. 1, p. 79, 2017.
, “Two critical positions in zinc finger domains are heavily mutated in three human cancer types.”, PLoS Comput Biol, vol. 14, no. 6, p. e1006290, 2018.
, “Predicting functionally important residues from sequence conservation.”, Bioinformatics, vol. 23, no. 15, pp. 1875-82, 2007.
, “Two critical positions in zinc finger domains are heavily mutated in three human cancer types.”, PLoS Comput Biol, vol. 14, no. 6, p. e1006290, 2018.
, “Solving and analyzing side-chain positioning problems using linear and integer programming.”, Bioinformatics, vol. 21, no. 7, pp. 1028-36, 2005.
, “Integrative analysis unveils new functions for the Drosophila Cutoff protein in noncoding RNA biogenesis and gene regulation.”, RNA, vol. 23, no. 7, pp. 1097-1109, 2017.
, “De novo prediction of DNA-binding specificities for Cys2His2 zinc finger proteins.”, Nucleic Acids Res, vol. 42, no. 1, pp. 97-108, 2014.
, “Solving and analyzing side-chain positioning problems using linear and integer programming.”, Bioinformatics, vol. 21, no. 7, pp. 1028-36, 2005.
, “Predicting functionally important residues from sequence conservation.”, Bioinformatics, vol. 23, no. 15, pp. 1875-82, 2007.
, “Using context to improve protein domain identification.”, BMC Bioinformatics, vol. 12, p. 90, 2011.
, “Characterization and prediction of residues determining protein functional specificity.”, Bioinformatics, vol. 24, no. 13, pp. 1473-80, 2008.
, “G-quadruplex DNA sequences are evolutionarily conserved and associated with distinct genomic features in Saccharomyces cerevisiae.”, PLoS Comput Biol, vol. 6, no. 7, p. e1000861, 2010.
, “Measuring differential gene expression by short read sequencing: quantitative comparison to 2-channel gene expression microarrays.”, BMC Genomics, vol. 10, p. 221, 2009.
, “The Cutoff protein regulates piRNA cluster expression and piRNA production in the Drosophila germline.”, EMBO J, vol. 30, no. 22, pp. 4601-15, 2011.
, “A practical algorithm for finding maximal exact matches in large sequence datasets using sparse suffix arrays.”, Bioinformatics, vol. 25, no. 13, pp. 1609-16, 2009.
, “Comparative analysis of methods for representing and searching for transcription factor binding sites.”, Bioinformatics, vol. 20, no. 18, pp. 3516-25, 2004.
, “Solving and analyzing side-chain positioning problems using linear and integer programming.”, Bioinformatics, vol. 21, no. 7, pp. 1028-36, 2005.
, “Measuring differential gene expression by short read sequencing: quantitative comparison to 2-channel gene expression microarrays.”, BMC Genomics, vol. 10, p. 221, 2009.
, “A practical algorithm for finding maximal exact matches in large sequence datasets using sparse suffix arrays.”, Bioinformatics, vol. 25, no. 13, pp. 1609-16, 2009.
, “Predicting functionally important residues from sequence conservation.”, Bioinformatics, vol. 23, no. 15, pp. 1875-82, 2007.
, “Characterization and prediction of residues determining protein functional specificity.”, Bioinformatics, vol. 24, no. 13, pp. 1473-80, 2008.
, “Accurate proteome-wide protein quantification from high-resolution 15N mass spectra.”, Genome Biol, vol. 12, no. 12, p. R122, 2011.
, “Quantitative measurement of allele-specific protein expression in a diploid yeast hybrid by LC-MS.”, Mol Syst Biol, vol. 8, p. 602, 2012.
, “The Cutoff protein regulates piRNA cluster expression and piRNA production in the Drosophila germline.”, EMBO J, vol. 30, no. 22, pp. 4601-15, 2011.
, “Organization of physical interactomes as uncovered by network schemas.”, PLoS Comput Biol, vol. 4, no. 10, p. e1000203, 2008.
, “Quantitative measurement of allele-specific protein expression in a diploid yeast hybrid by LC-MS.”, Mol Syst Biol, vol. 8, p. 602, 2012.
, “Measuring differential gene expression by short read sequencing: quantitative comparison to 2-channel gene expression microarrays.”, BMC Genomics, vol. 10, p. 221, 2009.
, “G-quadruplex DNA sequences are evolutionarily conserved and associated with distinct genomic features in Saccharomyces cerevisiae.”, PLoS Comput Biol, vol. 6, no. 7, p. e1000861, 2010.
, “Organization of physical interactomes as uncovered by network schemas.”, PLoS Comput Biol, vol. 4, no. 10, p. e1000203, 2008.
, “Simple topological features reflect dynamics and modularity in protein interaction networks.”, PLoS Comput Biol, vol. 9, no. 10, p. e1003243, 2013.
, “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.
, “Quantitative measurement of allele-specific protein expression in a diploid yeast hybrid by LC-MS.”, Mol Syst Biol, vol. 8, p. 602, 2012.
, “Computational assessment of the cooperativity between RNA binding proteins and MicroRNAs in Transcript Decay.”, PLoS Comput Biol, vol. 9, no. 5, p. e1003075, 2013.
, “Integrative analysis unveils new functions for the Drosophila Cutoff protein in noncoding RNA biogenesis and gene regulation.”, RNA, vol. 23, no. 7, pp. 1097-1109, 2017.
, “Systematic domain-based aggregation of protein structures highlights DNA-, RNA- and other ligand-binding positions.”, Nucleic Acids Res, vol. 47, no. 2, pp. 582-593, 2019.
, “Integrative analysis unveils new functions for the Drosophila Cutoff protein in noncoding RNA biogenesis and gene regulation.”, RNA, vol. 23, no. 7, pp. 1097-1109, 2017.
, “Integrative analysis unveils new functions for the Drosophila Cutoff protein in noncoding RNA biogenesis and gene regulation.”, RNA, vol. 23, no. 7, pp. 1097-1109, 2017.
, “The Cutoff protein regulates piRNA cluster expression and piRNA production in the Drosophila germline.”, EMBO J, vol. 30, no. 22, pp. 4601-15, 2011.
, “Computational assessment of the cooperativity between RNA binding proteins and MicroRNAs in Transcript Decay.”, PLoS Comput Biol, vol. 9, no. 5, p. e1003075, 2013.
, “Systematic domain-based aggregation of protein structures highlights DNA-, RNA- and other ligand-binding positions.”, Nucleic Acids Res, vol. 47, no. 2, pp. 582-593, 2019.
, “Interaction-based discovery of functionally important genes in cancers.”, Nucleic Acids Res, vol. 42, no. 3, p. e18, 2014.
, “A cross-genomic approach for systematic mapping of phenotypic traits to genes.”, Genome Res, vol. 14, no. 1, pp. 109-15, 2004.
, “Predicting DNA recognition by Cys2His2 zinc finger proteins.”, Bioinformatics, vol. 25, no. 1, pp. 22-9, 2009.
, “Predicting specificity in bZIP coiled-coil protein interactions.”, Genome Biol, vol. 5, no. 2, p. R11, 2004.
, “Two critical positions in zinc finger domains are heavily mutated in three human cancer types.”, PLoS Comput Biol, vol. 14, no. 6, p. e1006290, 2018.
, “CCAT: Combinatorial Code Analysis Tool for transcriptional regulation.”, Nucleic Acids Res, vol. 42, no. 5, pp. 2833-47, 2014.
, “Quantitative measurement of allele-specific protein expression in a diploid yeast hybrid by LC-MS.”, Mol Syst Biol, vol. 8, p. 602, 2012.
, “A cross-genomic approach for systematic mapping of phenotypic traits to genes.”, Genome Res, vol. 14, no. 1, pp. 109-15, 2004.
, “Interaction-based discovery of functionally important genes in cancers.”, Nucleic Acids Res, vol. 42, no. 3, p. e18, 2014.
, “Quantitative measurement of allele-specific protein expression in a diploid yeast hybrid by LC-MS.”, Mol Syst Biol, vol. 8, p. 602, 2012.
, “Accurate proteome-wide protein quantification from high-resolution 15N mass spectra.”, Genome Biol, vol. 12, no. 12, p. R122, 2011.
, “Protein quantification across hundreds of experimental conditions.”, Proc Natl Acad Sci U S A, vol. 106, no. 37, pp. 15544-8, 2009.
, “Whole-proteome prediction of protein function via graph-theoretic analysis of interaction maps.”, Bioinformatics, vol. 21 Suppl 1, pp. i302-10, 2005.
, “Organization of physical interactomes as uncovered by network schemas.”, PLoS Comput Biol, vol. 4, no. 10, p. e1000203, 2008.
, “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.
, “Accurate proteome-wide protein quantification from high-resolution 15N mass spectra.”, Genome Biol, vol. 12, no. 12, p. R122, 2011.
, “molBLOCKS: decomposing small molecule sets and uncovering enriched fragments.”, Bioinformatics, vol. 30, no. 14, pp. 2081-3, 2014.
, “Solving and analyzing side-chain positioning problems using linear and integer programming.”, Bioinformatics, vol. 21, no. 7, pp. 1028-36, 2005.
, “Predicting protein ligand binding sites by combining evolutionary sequence conservation and 3D structure.”, PLoS Comput Biol, vol. 5, no. 12, p. e1000585, 2009.
, “Evolution of amino acid frequencies in proteins over deep time: inferred order of introduction of amino acids into the genetic code.”, Mol Biol Evol, vol. 19, no. 10, pp. 1645-55, 2002.
, “Whole-proteome prediction of protein function via graph-theoretic analysis of interaction maps.”, Bioinformatics, vol. 21 Suppl 1, pp. i302-10, 2005.
, “Protein quantification across hundreds of experimental conditions.”, Proc Natl Acad Sci U S A, vol. 106, no. 37, pp. 15544-8, 2009.
, “Interaction-based discovery of functionally important genes in cancers.”, Nucleic Acids Res, vol. 42, no. 3, p. e18, 2014.
, “Predicting functionally important residues from sequence conservation.”, Bioinformatics, vol. 23, no. 15, pp. 1875-82, 2007.
, “Using context to improve protein domain identification.”, BMC Bioinformatics, vol. 12, p. 90, 2011.
, “Simple topological features reflect dynamics and modularity in protein interaction networks.”, PLoS Comput Biol, vol. 9, no. 10, p. e1003243, 2013.
, “Characterization and prediction of residues determining protein functional specificity.”, Bioinformatics, vol. 24, no. 13, pp. 1473-80, 2008.
, “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.
, “SPICi: a fast clustering algorithm for large biological networks.”, Bioinformatics, vol. 26, no. 8, pp. 1105-11, 2010.
, “Using context to improve protein domain identification.”, BMC Bioinformatics, vol. 12, p. 90, 2011.
, “Solving and analyzing side-chain positioning problems using linear and integer programming.”, Bioinformatics, vol. 21, no. 7, pp. 1028-36, 2005.
, “Predicting specificity in bZIP coiled-coil protein interactions.”, Genome Biol, vol. 5, no. 2, p. R11, 2004.
, “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.
, “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.
, “Whole-proteome prediction of protein function via graph-theoretic analysis of interaction maps.”, Bioinformatics, vol. 21 Suppl 1, pp. i302-10, 2005.
, “Disentangling function from topology to infer the network properties of disease genes.”, BMC Syst Biol, vol. 7, p. 5, 2013.
, “Organization of physical interactomes as uncovered by network schemas.”, PLoS Comput Biol, vol. 4, no. 10, p. e1000203, 2008.
, “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.
, “NetGrep: fast network schema searches in interactomes.”, Genome Biol, vol. 9, no. 9, p. R138, 2008.
, “Organization of physical interactomes as uncovered by network schemas.”, PLoS Comput Biol, vol. 4, no. 10, p. e1000203, 2008.
, “Solving and analyzing side-chain positioning problems using linear and integer programming.”, Bioinformatics, vol. 21, no. 7, pp. 1028-36, 2005.
, “Systematic domain-based aggregation of protein structures highlights DNA-, RNA- and other ligand-binding positions.”, Nucleic Acids Res, vol. 47, no. 2, pp. 582-593, 2019.
, “Predicting protein ligand binding sites by combining evolutionary sequence conservation and 3D structure.”, PLoS Comput Biol, vol. 5, no. 12, p. e1000585, 2009.
, “Predicting protein ligand binding sites by combining evolutionary sequence conservation and 3D structure.”, PLoS Comput Biol, vol. 5, no. 12, p. e1000585, 2009.
, “Sharing DNA-binding information across structurally similar proteins enables accurate specificity determination.”, Nucleic Acids Res, vol. 48, no. 2, p. e9, 2020.
, “Comparative analysis of methods for representing and searching for transcription factor binding sites.”, Bioinformatics, vol. 20, no. 18, pp. 3516-25, 2004.
, “Systematic domain-based aggregation of protein structures highlights DNA-, RNA- and other ligand-binding positions.”, Nucleic Acids Res, vol. 47, no. 2, pp. 582-593, 2019.
, “Predicting specificity in bZIP coiled-coil protein interactions.”, Genome Biol, vol. 5, no. 2, p. R11, 2004.
, “Solving and analyzing side-chain positioning problems using linear and integer programming.”, Bioinformatics, vol. 21, no. 7, pp. 1028-36, 2005.
, “Evolution of amino acid frequencies in proteins over deep time: inferred order of introduction of amino acids into the genetic code.”, Mol Biol Evol, vol. 19, no. 10, pp. 1645-55, 2002.
, “De novo prediction of DNA-binding specificities for Cys2His2 zinc finger proteins.”, Nucleic Acids Res, vol. 42, no. 1, pp. 97-108, 2014.
, “Interaction-based discovery of functionally important genes in cancers.”, Nucleic Acids Res, vol. 42, no. 3, p. e18, 2014.
, “Differential analysis between somatic mutation and germline variation profiles reveals cancer-related genes.”, Genome Med, vol. 9, no. 1, p. 79, 2017.
, “Deep sequencing of large library selections allows computational discovery of diverse sets of zinc fingers that bind common targets.”, Nucleic Acids Res, vol. 42, no. 3, pp. 1497-508, 2014.
, “Using context to improve protein domain identification.”, BMC Bioinformatics, vol. 12, p. 90, 2011.
, “G-quadruplex DNA sequences are evolutionarily conserved and associated with distinct genomic features in Saccharomyces cerevisiae.”, PLoS Comput Biol, vol. 6, no. 7, p. e1000861, 2010.
, “A cross-genomic approach for systematic mapping of phenotypic traits to genes.”, Genome Res, vol. 14, no. 1, pp. 109-15, 2004.
, “Organization of physical interactomes as uncovered by network schemas.”, PLoS Comput Biol, vol. 4, no. 10, p. e1000203, 2008.
, “Characterization and prediction of residues determining protein functional specificity.”, Bioinformatics, vol. 24, no. 13, pp. 1473-80, 2008.
, “Integrative analysis unveils new functions for the Drosophila Cutoff protein in noncoding RNA biogenesis and gene regulation.”, RNA, vol. 23, no. 7, pp. 1097-1109, 2017.
, “Measuring differential gene expression by short read sequencing: quantitative comparison to 2-channel gene expression microarrays.”, BMC Genomics, vol. 10, p. 221, 2009.
, “Predicting DNA recognition by Cys2His2 zinc finger proteins.”, Bioinformatics, vol. 25, no. 1, pp. 22-9, 2009.
, “Solving and analyzing side-chain positioning problems using linear and integer programming.”, Bioinformatics, vol. 21, no. 7, pp. 1028-36, 2005.
, “G-quadruplex DNA sequences are evolutionarily conserved and associated with distinct genomic features in Saccharomyces cerevisiae.”, PLoS Comput Biol, vol. 6, no. 7, p. e1000861, 2010.
, “Disentangling function from topology to infer the network properties of disease genes.”, BMC Syst Biol, vol. 7, p. 5, 2013.
, “The Cutoff protein regulates piRNA cluster expression and piRNA production in the Drosophila germline.”, EMBO J, vol. 30, no. 22, pp. 4601-15, 2011.
, “Accurate proteome-wide protein quantification from high-resolution 15N mass spectra.”, Genome Biol, vol. 12, no. 12, p. R122, 2011.
, “Organization of physical interactomes as uncovered by network schemas.”, PLoS Comput Biol, vol. 4, no. 10, p. e1000203, 2008.
, “Two critical positions in zinc finger domains are heavily mutated in three human cancer types.”, PLoS Comput Biol, vol. 14, no. 6, p. e1006290, 2018.
, “Interaction-based discovery of functionally important genes in cancers.”, Nucleic Acids Res, vol. 42, no. 3, p. e18, 2014.
, “Differential analysis between somatic mutation and germline variation profiles reveals cancer-related genes.”, Genome Med, vol. 9, no. 1, p. 79, 2017.
, “Interaction-based discovery of functionally important genes in cancers.”, Nucleic Acids Res, vol. 42, no. 3, p. e18, 2014.
, “Integrative analysis unveils new functions for the Drosophila Cutoff protein in noncoding RNA biogenesis and gene regulation.”, RNA, vol. 23, no. 7, pp. 1097-1109, 2017.
, “The Cutoff protein regulates piRNA cluster expression and piRNA production in the Drosophila germline.”, EMBO J, vol. 30, no. 22, pp. 4601-15, 2011.
, “Systematic domain-based aggregation of protein structures highlights DNA-, RNA- and other ligand-binding positions.”, Nucleic Acids Res, vol. 47, no. 2, pp. 582-593, 2019.
, “Differential analysis between somatic mutation and germline variation profiles reveals cancer-related genes.”, Genome Med, vol. 9, no. 1, p. 79, 2017.
, “Deep sequencing of large library selections allows computational discovery of diverse sets of zinc fingers that bind common targets.”, Nucleic Acids Res, vol. 42, no. 3, pp. 1497-508, 2014.
, “Solving and analyzing side-chain positioning problems using linear and integer programming.”, Bioinformatics, vol. 21, no. 7, pp. 1028-36, 2005.
, “G-quadruplex DNA sequences are evolutionarily conserved and associated with distinct genomic features in Saccharomyces cerevisiae.”, PLoS Comput Biol, vol. 6, no. 7, p. e1000861, 2010.
, “Accurate proteome-wide protein quantification from high-resolution 15N mass spectra.”, Genome Biol, vol. 12, no. 12, p. R122, 2011.
, “Predicting functionally important residues from sequence conservation.”, Bioinformatics, vol. 23, no. 15, pp. 1875-82, 2007.
, “Characterization and prediction of residues determining protein functional specificity.”, Bioinformatics, vol. 24, no. 13, pp. 1473-80, 2008.
, “Disentangling function from topology to infer the network properties of disease genes.”, BMC Syst Biol, vol. 7, p. 5, 2013.
, “Using context to improve protein domain identification.”, BMC Bioinformatics, vol. 12, p. 90, 2011.
, “Whole-proteome prediction of protein function via graph-theoretic analysis of interaction maps.”, Bioinformatics, vol. 21 Suppl 1, pp. i302-10, 2005.
, “Whole-proteome prediction of protein function via graph-theoretic analysis of interaction maps.”, Bioinformatics, vol. 21 Suppl 1, pp. i302-10, 2005.
, “Predicting protein ligand binding sites by combining evolutionary sequence conservation and 3D structure.”, PLoS Comput Biol, vol. 5, no. 12, p. e1000585, 2009.
, “Systematic domain-based aggregation of protein structures highlights DNA-, RNA- and other ligand-binding positions.”, Nucleic Acids Res, vol. 47, no. 2, pp. 582-593, 2019.
, “Predicting specificity in bZIP coiled-coil protein interactions.”, Genome Biol, vol. 5, no. 2, p. R11, 2004.
, “An expanded binding model for Cys2His2 zinc finger protein-DNA interfaces.”, Phys Biol, vol. 8, no. 3, p. 035010, 2011.
, “Evolution of amino acid frequencies in proteins over deep time: inferred order of introduction of amino acids into the genetic code.”, Mol Biol Evol, vol. 19, no. 10, pp. 1645-55, 2002.
, “Computational assessment of the cooperativity between RNA binding proteins and MicroRNAs in Transcript Decay.”, PLoS Comput Biol, vol. 9, no. 5, p. e1003075, 2013.
, “G-quadruplex DNA sequences are evolutionarily conserved and associated with distinct genomic features in Saccharomyces cerevisiae.”, PLoS Comput Biol, vol. 6, no. 7, p. e1000861, 2010.
, “A cross-genomic approach for systematic mapping of phenotypic traits to genes.”, Genome Res, vol. 14, no. 1, pp. 109-15, 2004.
, “Solving and analyzing side-chain positioning problems using linear and integer programming.”, Bioinformatics, vol. 21, no. 7, pp. 1028-36, 2005.
, “Organization of physical interactomes as uncovered by network schemas.”, PLoS Comput Biol, vol. 4, no. 10, p. e1000203, 2008.
, “An expanded binding model for Cys2His2 zinc finger protein-DNA interfaces.”, Phys Biol, vol. 8, no. 3, p. 035010, 2011.
, “Predicting DNA recognition by Cys2His2 zinc finger proteins.”, Bioinformatics, vol. 25, no. 1, pp. 22-9, 2009.
, “Computational assessment of the cooperativity between RNA binding proteins and MicroRNAs in Transcript Decay.”, PLoS Comput Biol, vol. 9, no. 5, p. e1003075, 2013.
, “Computational assessment of the cooperativity between RNA binding proteins and MicroRNAs in Transcript Decay.”, PLoS Comput Biol, vol. 9, no. 5, p. e1003075, 2013.
, “Protein quantification across hundreds of experimental conditions.”, Proc Natl Acad Sci U S A, vol. 106, no. 37, pp. 15544-8, 2009.
, “SPICi: a fast clustering algorithm for large biological networks.”, Bioinformatics, vol. 26, no. 8, pp. 1105-11, 2010.
, “Quantitative measurement of allele-specific protein expression in a diploid yeast hybrid by LC-MS.”, Mol Syst Biol, vol. 8, p. 602, 2012.
, “Accurate proteome-wide protein quantification from high-resolution 15N mass spectra.”, Genome Biol, vol. 12, no. 12, p. R122, 2011.
, “G-quadruplex DNA sequences are evolutionarily conserved and associated with distinct genomic features in Saccharomyces cerevisiae.”, PLoS Comput Biol, vol. 6, no. 7, p. e1000861, 2010.
, “Differential analysis between somatic mutation and germline variation profiles reveals cancer-related genes.”, Genome Med, vol. 9, no. 1, p. 79, 2017.
, “Two critical positions in zinc finger domains are heavily mutated in three human cancer types.”, PLoS Comput Biol, vol. 14, no. 6, p. e1006290, 2018.
, “molBLOCKS: decomposing small molecule sets and uncovering enriched fragments.”, Bioinformatics, vol. 30, no. 14, pp. 2081-3, 2014.
, “Systematic domain-based aggregation of protein structures highlights DNA-, RNA- and other ligand-binding positions.”, Nucleic Acids Res, vol. 47, no. 2, pp. 582-593, 2019.
, “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.
, “Protein quantification across hundreds of experimental conditions.”, Proc Natl Acad Sci U S A, vol. 106, no. 37, pp. 15544-8, 2009.
, “Accurate proteome-wide protein quantification from high-resolution 15N mass spectra.”, Genome Biol, vol. 12, no. 12, p. R122, 2011.
, “Organization of physical interactomes as uncovered by network schemas.”, PLoS Comput Biol, vol. 4, no. 10, p. e1000203, 2008.
, “Two critical positions in zinc finger domains are heavily mutated in three human cancer types.”, PLoS Comput Biol, vol. 14, no. 6, p. e1006290, 2018.
, “Computational assessment of the cooperativity between RNA binding proteins and MicroRNAs in Transcript Decay.”, PLoS Comput Biol, vol. 9, no. 5, p. e1003075, 2013.
, “Protein quantification across hundreds of experimental conditions.”, Proc Natl Acad Sci U S A, vol. 106, no. 37, pp. 15544-8, 2009.
, “Disentangling function from topology to infer the network properties of disease genes.”, BMC Syst Biol, vol. 7, p. 5, 2013.
, “Interaction-based discovery of functionally important genes in cancers.”, Nucleic Acids Res, vol. 42, no. 3, p. e18, 2014.
, “Organization of physical interactomes as uncovered by network schemas.”, PLoS Comput Biol, vol. 4, no. 10, p. e1000203, 2008.
, “Simple topological features reflect dynamics and modularity in protein interaction networks.”, PLoS Comput Biol, vol. 9, no. 10, p. e1003243, 2013.
, “Systematic domain-based aggregation of protein structures highlights DNA-, RNA- and other ligand-binding positions.”, Nucleic Acids Res, vol. 47, no. 2, pp. 582-593, 2019.