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]
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Ubiquitin-Protein Ligases
D. Ghersi and Singh, M., Interaction-based discovery of functionally important genes in cancers., Nucleic Acids Res, vol. 42, no. 3, p. e18, 2014.
Tandem Mass Spectrometry
Z. Khan, Bloom, J. S., Garcia, B. A., Singh, M., and Kruglyak, L., Protein quantification across hundreds of experimental conditions., Proc Natl Acad Sci U S A, vol. 106, no. 37, pp. 15544-8, 2009.
Software
C. L. Kingsford, Chazelle, B., and Singh, M., Solving and analyzing side-chain positioning problems using linear and integer programming., Bioinformatics, vol. 21, no. 7, pp. 1028-36, 2005.
P. Jiang and Singh, M., CCAT: Combinatorial Code Analysis Tool for transcriptional regulation., Nucleic Acids Res, vol. 42, no. 5, pp. 2833-47, 2014.
Z. Khan, Amini, S., Bloom, J. S., Ruse, C., Caudy, A. A., Kruglyak, L., Singh, M., Perlman, D. H., and Tavazoie, S., Accurate proteome-wide protein quantification from high-resolution 15N mass spectra., Genome Biol, vol. 12, no. 12, p. R122, 2011.
D. Ghersi and Singh, M., Interaction-based discovery of functionally important genes in cancers., Nucleic Acids Res, vol. 42, no. 3, p. e18, 2014.
R. Osada, Zaslavsky, E., and Singh, M., Comparative analysis of methods for representing and searching for transcription factor binding sites., Bioinformatics, vol. 20, no. 18, pp. 3516-25, 2004.
P. F. Przytycki and Singh, M., Differential analysis between somatic mutation and germline variation profiles reveals cancer-related genes., Genome Med, vol. 9, no. 1, p. 79, 2017.
P. Jiang and Singh, M., SPICi: a fast clustering algorithm for large biological networks., Bioinformatics, vol. 26, no. 8, pp. 1105-11, 2010.
D. Ghersi and Singh, M., molBLOCKS: decomposing small molecule sets and uncovering enriched fragments., Bioinformatics, vol. 30, no. 14, pp. 2081-3, 2014.
Sequence Homology, Nucleic Acid
J. A. Capra and Singh, M., Predicting functionally important residues from sequence conservation., Bioinformatics, vol. 23, no. 15, pp. 1875-82, 2007.
Ribonuclease III
D. Ghersi and Singh, M., Interaction-based discovery of functionally important genes in cancers., Nucleic Acids Res, vol. 42, no. 3, p. e18, 2014.
Regulatory Elements, Transcriptional
P. Jiang and Singh, M., CCAT: Combinatorial Code Analysis Tool for transcriptional regulation., Nucleic Acids Res, vol. 42, no. 5, pp. 2833-47, 2014.
Proto-Oncogene Proteins c-akt
D. Ghersi and Singh, M., Interaction-based discovery of functionally important genes in cancers., Nucleic Acids Res, vol. 42, no. 3, p. e18, 2014.
Proteins
D. J. Brooks, Fresco, J. R., Lesk, A. M., and Singh, M., 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.
C. L. Kingsford, Chazelle, B., and Singh, M., Solving and analyzing side-chain positioning problems using linear and integer programming., Bioinformatics, vol. 21, no. 7, pp. 1028-36, 2005.
J. A. Capra, Laskowski, R. A., Thornton, J. M., Singh, M., and Funkhouser, T. A., Predicting protein ligand binding sites by combining evolutionary sequence conservation and 3D structure., PLoS Comput Biol, vol. 5, no. 12, p. e1000585, 2009.
E. Nabieva, Jim, K., Agarwal, A., Chazelle, B., and Singh, M., Whole-proteome prediction of protein function via graph-theoretic analysis of interaction maps., Bioinformatics, vol. 21 Suppl 1, pp. i302-10, 2005.
Z. Khan, Bloom, J. S., Garcia, B. A., Singh, M., and Kruglyak, L., Protein quantification across hundreds of experimental conditions., Proc Natl Acad Sci U S A, vol. 106, no. 37, pp. 15544-8, 2009.
D. Ghersi and Singh, M., Interaction-based discovery of functionally important genes in cancers., Nucleic Acids Res, vol. 42, no. 3, p. e18, 2014.
J. A. Capra and Singh, M., Predicting functionally important residues from sequence conservation., Bioinformatics, vol. 23, no. 15, pp. 1875-82, 2007.
A. Ochoa, Llinás, M., and Singh, M., Using context to improve protein domain identification., BMC Bioinformatics, vol. 12, p. 90, 2011.
Y. Pritykin and Singh, M., Simple topological features reflect dynamics and modularity in protein interaction networks., PLoS Comput Biol, vol. 9, no. 10, p. e1003243, 2013.
J. A. Capra and Singh, M., Characterization and prediction of residues determining protein functional specificity., Bioinformatics, vol. 24, no. 13, pp. 1473-80, 2008.
P. Jiang and Singh, M., SPICi: a fast clustering algorithm for large biological networks., Bioinformatics, vol. 26, no. 8, pp. 1105-11, 2010.
J. Song and Singh, M., 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.
D. Ghersi and Singh, M., molBLOCKS: decomposing small molecule sets and uncovering enriched fragments., Bioinformatics, vol. 30, no. 14, pp. 2081-3, 2014.
Protein Structure, Tertiary
A. Ochoa, Llinás, M., and Singh, M., Using context to improve protein domain identification., BMC Bioinformatics, vol. 12, p. 90, 2011.
Protein Interaction Domains and Motifs
E. Banks, Nabieva, E., Chazelle, B., and Singh, M., Organization of physical interactomes as uncovered by network schemas., PLoS Comput Biol, vol. 4, no. 10, p. e1000203, 2008.
Position-Specific Scoring Matrices
A. V. Persikov and Singh, M., De novo prediction of DNA-binding specificities for Cys2His2 zinc finger proteins., Nucleic Acids Res, vol. 42, no. 1, pp. 97-108, 2014.
Plasmodium falciparum
A. Ochoa, Llinás, M., and Singh, M., Using context to improve protein domain identification., BMC Bioinformatics, vol. 12, p. 90, 2011.
Numerical Analysis, Computer-Assisted
C. L. Kingsford, Chazelle, B., and Singh, M., Solving and analyzing side-chain positioning problems using linear and integer programming., Bioinformatics, vol. 21, no. 7, pp. 1028-36, 2005.
Neural Networks (Computer)
E. Banks, Nabieva, E., Chazelle, B., and Singh, M., Organization of physical interactomes as uncovered by network schemas., PLoS Comput Biol, vol. 4, no. 10, p. e1000203, 2008.
Mutation, Missense
D. Ghersi and Singh, M., Interaction-based discovery of functionally important genes in cancers., Nucleic Acids Res, vol. 42, no. 3, p. e18, 2014.
Metabolic Networks and Pathways
P. Jiang and Singh, M., SPICi: a fast clustering algorithm for large biological networks., Bioinformatics, vol. 26, no. 8, pp. 1105-11, 2010.
Intracellular Signaling Peptides and Proteins
E. Banks, Nabieva, E., Chazelle, B., and Singh, M., Organization of physical interactomes as uncovered by network schemas., PLoS Comput Biol, vol. 4, no. 10, p. e1000203, 2008.
Humans
P. Jiang, Singh, M., and Coller, H. A., Computational assessment of the cooperativity between RNA binding proteins and MicroRNAs in Transcript Decay., PLoS Comput Biol, vol. 9, no. 5, p. e1003075, 2013.
Z. Khan, Bloom, J. S., Garcia, B. A., Singh, M., and Kruglyak, L., Protein quantification across hundreds of experimental conditions., Proc Natl Acad Sci U S A, vol. 106, no. 37, pp. 15544-8, 2009.
D. Ghersi and Singh, M., Disentangling function from topology to infer the network properties of disease genes., BMC Syst Biol, vol. 7, p. 5, 2013.
D. Ghersi and Singh, M., Interaction-based discovery of functionally important genes in cancers., Nucleic Acids Res, vol. 42, no. 3, p. e18, 2014.
E. Banks, Nabieva, E., Chazelle, B., and Singh, M., Organization of physical interactomes as uncovered by network schemas., PLoS Comput Biol, vol. 4, no. 10, p. e1000203, 2008.
S. Nadimpalli Kobren and Singh, M., 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.
A. Ochoa, Llinás, M., and Singh, M., Using context to improve protein domain identification., BMC Bioinformatics, vol. 12, p. 90, 2011.
Y. Pritykin and Singh, M., Simple topological features reflect dynamics and modularity in protein interaction networks., PLoS Comput Biol, vol. 9, no. 10, p. e1003243, 2013.

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