Persikov, Anton, V, Joshua L Wetzel, Elizabeth F Rowland, Benjamin L Oakes, Denise J Xu, Mona Singh, and Marcus B Noyes. (2015) 2015. “A Systematic Survey of the Cys2His2 Zinc Finger DNA-Binding Landscape.”. Nucleic Acids Res 43 (3): 1965-84.

Ghersi, Dario, and Mona Singh. (2014) 2014. “Interaction-Based Discovery of Functionally Important Genes in Cancers.”. Nucleic Acids Res 42 (3): e18.

Khan, Zia, Sasan Amini, Joshua S Bloom, Cristian Ruse, Amy A Caudy, Leonid Kruglyak, Mona Singh, David H Perlman, and Saeed Tavazoie. 2011. “Accurate Proteome-Wide Protein Quantification from High-Resolution 15N Mass Spectra.”. Genome Biol 12 (12): R122.

Jiang, Peng, and Mona Singh. (2010) 2010. “SPICi: A Fast Clustering Algorithm for Large Biological Networks.”. Bioinformatics 26 (8): 1105-11.

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.

Pritykin, Yuri, Dario Ghersi, and Mona Singh. (2015) 2015. “Genome-Wide Detection and Analysis of Multifunctional Genes.”. PLoS Comput Biol 11 (10): e1004467.

Kingsford, Carleton L, Bernard Chazelle, and Mona Singh. (2005) 2005. “Solving and Analyzing Side-Chain Positioning Problems Using Linear and Integer Programming.”. Bioinformatics 21 (7): 1028-36.

Capra, John A, Katrin Paeschke, Mona Singh, and Virginia A Zakian. 2010. “G-Quadruplex DNA Sequences Are Evolutionarily Conserved and Associated With Distinct Genomic Features in Saccharomyces Cerevisiae.”. PLoS Comput Biol 6 (7): e1000861.

Ochoa, Alejandro, John D Storey, Manuel Llinás, and Mona Singh. (2015) 2015. “Beyond the E-Value: Stratified Statistics for Protein Domain Prediction.”. PLoS Comput Biol 11 (11): e1004509.

Pritykin, Yuri, and Mona Singh. 2013. “Simple Topological Features Reflect Dynamics and Modularity in Protein Interaction Networks.”. PLoS Comput Biol 9 (10): e1003243.

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.

Ochoa, Alejandro, and Mona Singh. (2017) 2017. “Domain Prediction With Probabilistic Directional Context.”. Bioinformatics 33 (16): 2471-78. doi:10.1093/bioinformatics/btx221.

Khan, Zia, Joshua S Bloom, Sasan Amini, Mona Singh, David H Perlman, Amy A Caudy, and Leonid Kruglyak. 2012. “Quantitative Measurement of Allele-Specific Protein Expression in a Diploid Yeast Hybrid by LC-MS.”. Mol Syst Biol 8: 602.

Persikov, Anton, V, and Mona Singh. (2011) 2011. “An Expanded Binding Model for Cys2His2 Zinc Finger Protein-DNA Interfaces.”. Phys Biol 8 (3): 035010.

Przytycki, Pawel F, and Mona Singh. (2017) 2017. “Differential Analysis Between Somatic Mutation and Germline Variation Profiles Reveals Cancer-Related Genes.”. Genome Med 9 (1): 79. doi:10.1186/s13073-017-0465-6.

Khan, Zia, Joshua S Bloom, Benjamin A Garcia, Mona Singh, and Leonid Kruglyak. (2009) 2009. “Protein Quantification across Hundreds of Experimental Conditions.”. Proc Natl Acad Sci U S A 106 (37): 15544-8.

Brooks, Dawn J, Jacques R Fresco, Arthur M Lesk, and Mona Singh. (2002) 2002. “Evolution of Amino Acid Frequencies in Proteins over Deep Time: Inferred Order of Introduction of Amino Acids into the Genetic Code.”. Mol Biol Evol 19 (10): 1645-55.

Pritykin, Yuri, Tarcisio Brito, Trudi Schüpbach, Mona Singh, and Attilio Pane. (2017) 2017. “Integrative Analysis Unveils New Functions for the Drosophila Cutoff Protein in Noncoding RNA Biogenesis and Gene Regulation.”. RNA 23 (7): 1097-1109. doi:10.1261/rna.058594.116.

Fong, Jessica H, Amy E Keating, and Mona Singh. 2004. “Predicting Specificity in BZIP Coiled-Coil Protein Interactions.”. Genome Biol 5 (2): R11.

Ghersi, Dario, and Mona Singh. 2013. “Disentangling Function from Topology to Infer the Network Properties of Disease Genes.”. BMC Syst Biol 7: 5.

Hristov, Borislav H, and Mona Singh. (2017) 2017. “Network-Based Coverage of Mutational Profiles Reveals Cancer Genes.”. Cell Syst 5 (3): 221-229.e4. doi:10.1016/j.cels.2017.09.003.

Capra, John A, Roman A Laskowski, Janet M Thornton, Mona Singh, and Thomas A Funkhouser. (2009) 2009. “Predicting Protein Ligand Binding Sites by Combining Evolutionary Sequence Conservation and 3D Structure.”. PLoS Comput Biol 5 (12): e1000585.

Persikov, Anton, V, Elizabeth F Rowland, Benjamin L Oakes, Mona Singh, and Marcus B Noyes. (2014) 2014. “Deep Sequencing of Large Library Selections Allows Computational Discovery of Diverse Sets of Zinc Fingers That Bind Common Targets.”. Nucleic Acids Res 42 (3): 1497-508.

Kobren, Shilpa Nadimpalli, and Mona Singh. (2019) 2019. “Systematic Domain-Based Aggregation of Protein Structures Highlights DNA-, RNA- and Other Ligand-Binding Positions.”. Nucleic Acids Res 47 (2): 582-93. doi:10.1093/nar/gky1224.

Capra, John A, and Mona Singh. (2007) 2007. “Predicting Functionally Important Residues from Sequence Conservation.”. Bioinformatics 23 (15): 1875-82.

Persikov, Anton, V, and Mona Singh. (2014) 2014. “De Novo Prediction of DNA-Binding Specificities for Cys2His2 Zinc Finger Proteins.”. Nucleic Acids Res 42 (1): 97-108.

Munro, Daniel, Dario Ghersi, and Mona Singh. (2018) 2018. “Two Critical Positions in Zinc Finger Domains Are Heavily Mutated in Three Human Cancer Types.”. PLoS Comput Biol 14 (6): e1006290. doi:10.1371/journal.pcbi.1006290.

Persikov, Anton, V, Robert Osada, and Mona Singh. (2009) 2009. “Predicting DNA Recognition by Cys2His2 Zinc Finger Proteins.”. Bioinformatics 25 (1): 22-9.

Pane, Attilio, Peng Jiang, Dorothy Yanling Zhao, Mona Singh, and Trudi Schüpbach. (2011) 2011. “The Cutoff Protein Regulates PiRNA Cluster Expression and PiRNA Production in the Drosophila Germline.”. EMBO J 30 (22): 4601-15.

Wetzel, Joshua L, and Mona Singh. (2020) 2020. “Sharing DNA-Binding Information across Structurally Similar Proteins Enables Accurate Specificity Determination.”. Nucleic Acids Res 48 (2): e9. doi:10.1093/nar/gkz1087.

Khan, Zia, Joshua S Bloom, Leonid Kruglyak, and Mona Singh. (2009) 2009. “A Practical Algorithm for Finding Maximal Exact Matches in Large Sequence Datasets Using Sparse Suffix Arrays.”. Bioinformatics 25 (13): 1609-16.

Jim, Kam, Kush Parmar, Mona Singh, and Saeed Tavazoie. (2004) 2004. “A Cross-Genomic Approach for Systematic Mapping of Phenotypic Traits to Genes.”. Genome Res 14 (1): 109-15.

Przytycki, Pawel F, and Mona Singh. (2020) 2020. “Differential Allele-Specific Expression Uncovers Breast Cancer Genes Dysregulated by Cis Noncoding Mutations.”. Cell Syst 10 (2): 193-203.e4. doi:10.1016/j.cels.2020.01.002.

Nadimpalli, Shilpa, Anton Persikov V, and Mona Singh. (2015) 2015. “Pervasive Variation of Transcription Factor Orthologs Contributes to Regulatory Network Evolution.”. PLoS Genet 11 (3): e1005011.

Jiang, Peng, Mona Singh, and Hilary A Coller. 2013. “Computational Assessment of the Cooperativity Between RNA Binding Proteins and MicroRNAs in Transcript Decay.”. PLoS Comput Biol 9 (5): e1003075.

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.

Osada, Robert, Elena Zaslavsky, and Mona Singh. (2004) 2004. “Comparative Analysis of Methods for Representing and Searching for Transcription Factor Binding Sites.”. Bioinformatics 20 (18): 3516-25.

Banks, Eric, Elena Nabieva, Ryan Peterson, and Mona Singh. 2008. “NetGrep: Fast Network Schema Searches in Interactomes.”. Genome Biol 9 (9): R138.

Zaslavsky, Elena, and Mona Singh. 2006. “A Combinatorial Optimization Approach for Diverse Motif Finding Applications.”. Algorithms Mol Biol 1: 13.

Nabieva, Elena, Kam Jim, Amit Agarwal, Bernard Chazelle, and Mona Singh. (2005) 2005. “Whole-Proteome Prediction of Protein Function via Graph-Theoretic Analysis of Interaction Maps.”. Bioinformatics 21 Suppl 1.

Ghersi, Dario, and Mona Singh. (2014) 2014. “MolBLOCKS: Decomposing Small Molecule Sets and Uncovering Enriched Fragments.”. Bioinformatics 30 (14): 2081-3.

Capra, John A, and Mona Singh. (2008) 2008. “Characterization and Prediction of Residues Determining Protein Functional Specificity.”. Bioinformatics 24 (13): 1473-80.

Ochoa, Alejandro, Manuel Llinás, and Mona Singh. 2011. “Using Context to Improve Protein Domain Identification.”. BMC Bioinformatics 12: 90.

Bloom, Joshua S, Zia Khan, Leonid Kruglyak, Mona Singh, and Amy A Caudy. 2009. “Measuring Differential Gene Expression by Short Read Sequencing: Quantitative Comparison to 2-Channel Gene Expression Microarrays.”. BMC Genomics 10: 221.

Jiang, Peng, and Mona Singh. (2014) 2014. “CCAT: Combinatorial Code Analysis Tool for Transcriptional Regulation.”. Nucleic Acids Res 42 (5): 2833-47.