Mona Singh

发表

Predicting specificity in bZIP coiled-coil protein interactions

Jessica H. Fong, J. Fong, A. Keating, 2004, Genome Biology.

NetGrep: fast network schema searches in interactomes

E. Banks, Mona Singh, E. Nabieva, 2008, Genome Biology.

Predicting functionally important residues from sequence conservation

Mona Singh, John A. Capra, Mona Singh, 2007, Bioinform..

An integrative approach uncovers genes with perturbed interactions in cancers

Mona Singh, B. Chazelle, S. N. Kobren, 2019, bioRxiv.

Pervasive Variation of Transcription Factor Orthologs Contributes to Regulatory Network Evolution

Mona Singh, Shilpa Nadimpalli, A. Persikov, 2014, PLoS genetics.

CCAT: Combinatorial Code Analysis Tool for transcriptional regulation

Mona Singh, P. Jiang, Peng Jiang, 2013, Nucleic acids research.

De novo prediction of DNA-binding specificities for Cys2His2 zinc finger proteins

Mona Singh, A. Persikov, Anton V. Persikov, 2013, Nucleic acids research.

Integrative analysis unveils new functions for the Drosophila Cutoff protein in noncoding RNA biogenesis and gene regulation

Mona Singh, A. Pane, Y. Pritykin, 2017, RNA.

Protein Function Prediction via Analysis of Interactomes

Mona Singh, E. Nabieva, 2008 .

A systematic survey of the Cys2His2 zinc finger DNA-binding landscape

Benjamin L. Oakes, Mona Singh, M. Noyes, 2015, Nucleic acids research.

Characterization and Prediction of Residues Determining Functional Specificity-Supplementary Material

Mona Singh, J. Capra, 2008 .

Interaction-based discovery of functionally important genes in cancers

Mona Singh, Dario Ghersi, Mona Singh, 2013, Nucleic acids research.

Evolution of amino acid frequencies in proteins over deep time: inferred order of introduction of amino acids into the genetic code.

Mona Singh, Arthur M Lesk, A. Lesk, 2002, Molecular biology and evolution.

Computational approaches to problems in protein structure and function

Mona Singh, Carl Kingsford, 2005 .

Deep sequencing of large library selections allows computational discovery of diverse sets of zinc fingers that bind common targets

Benjamin L. Oakes, Mona Singh, M. Noyes, 2013, Nucleic acids research.

Accurate proteome-wide protein quantification from high-resolution 15N mass spectra

Mona Singh, Leonid Kruglyak, Saeed Tavazoie, 2011, Genome Biology.

Quantitative measurement of allele-specific protein expression in a diploid yeast hybrid by LC-MS

David H Perlman, Sasan Amini, Mona Singh, 2012, Molecular systems biology.

Differential Allele-Specific Expression Uncovers Breast Cancer Genes Dysregulated by Cis Noncoding Mutations.

Pawel F. Przytycki, Mona Singh, 2020, Cell systems.

Systematic domain-based aggregation of protein structures highlights DNA-, RNA-, and other ligand-binding positions

Mona Singh, S. N. Kobren, 2018, bioRxiv.

Computational methods for predicting transcription factor binding sites

Mona Singh, R. Osada, 2006 .

Sharing DNA-binding information across structurally similar proteins enables accurate specificity determination

Mona Singh, Joshua L. Wetzel, 2019, Nucleic acids research.

A systematic survey of the Cys 2 His 2 zinc ﬁnger DNA-binding landscape

Benjamin L. Oakes, Mona Singh, M. Noyes, 2015 .

Sequence analysis Predicting functionally important residues from sequence conservation

Mona Singh, J. Capra, 2007 .

Improving Mathematical Programming Approaches for Motif Finding

Mona Singh, E. Zaslavsky, Carl Kingsford, 2005 .

S 1 for Simple topological features reflect dynamics and modularity in protein interaction networks

Mona Singh, Y. Pritykin, 2013 .

BIOINFORMATICS ORIGINAL A practical algorithm for ﬁnding maximal exact matches in large sequence datasets using sparse sufﬁx arrays

Mona Singh, L. Kruglyak, J. Bloom, 2009 .

Vector-clustering Multiple Sequence Alignment: Aligning into the twilight zone of protein sequence similarity with protein language models

Claire D. McWhite, Mona Singh, 2022, bioRxiv.

G-Quadruplex DNA Sequences Are Evolutionarily Conserved and Associated with Distinct Genomic Features in Saccharomyces cerevisiae

Mona Singh, John A. Capra, Katrin Paeschke, 2010, PLoS Comput. Biol..

Sequence analysis Domain prediction with probabilistic directional context

Mona Singh, Alejandro Ochoa, 2017 .

Novel genes exhibit distinct patterns of function acquisition and network integration

Mona Singh, Katherine S Pollard, John A Capra, 2010, Genome Biology.

Computational learning reveals coiled coil-like motifs in histidine kinase linker domains

M Singh, B Berger, P S Kim, 1998, Proc. Natl. Acad. Sci. USA.

M are better than one: an ensemble-based motif finder and its application to regulatory element prediction

Mona Singh, Chen Yanover, Elena Zaslavsky, 2009, Bioinform..

Toward the dynamic interactome: it's about time

Mona Singh, Donna K. Slonim, Teresa M. Przytycka, 2010, Briefings Bioinform..

Metabolite discovery through global annotation of untargeted metabolomics data

Mona Singh, J. Rabinowitz, W. Lu, 2021, Nature Methods.

SPICi: a fast clustering algorithm for large biological networks

Peng Jiang, Mona Singh, Mona Singh, 2010, Bioinform..

How and when should interactome-derived clusters be used to predict functional modules and protein function?

Mona Singh, Jimin Song, Mona Singh, 2009, Bioinform..

Network-Based Coverage of Mutational Profiles Reveals Cancer Genes

Borislav H. Hristov, Mona Singh, 2017, RECOMB.

Computational Assessment of the Cooperativity between RNA Binding Proteins and MicroRNAs in Transcript Decay

Peng Jiang, Mona Singh, Hilary A. Coller, 2013, PLoS Comput. Biol..

From Hub Proteins to Hub Modules: The Relationship Between Essentiality and Centrality in the Yeast Interactome at Different Scales of Organization

Mona Singh, Jimin Song, 2013, PLoS Comput. Biol..

Computational solutions for omics data

Mona Singh, Bonnie Berger, Jian Peng, 2013, Nature Reviews Genetics.

The Cutoff protein regulates piRNA cluster expression and piRNA production in the Drosophila germline

Mona Singh, T. Schüpbach, A. Pane, 2011, The EMBO journal.

Learning probabilistic protein–DNA recognition codes from DNA-binding specificities using structural mappings

Mona Singh, Joshua L. Wetzel, Kaiqi Zhang, 2022, bioRxiv.

Differential analysis between somatic mutation and germline variation profiles reveals cancer-related genes

Mona Singh, Pawel F. Przytycki, Mona Singh, 2017, Genome Medicine.

DeMaSk: a deep mutational scanning substitution matrix and its use for variant impact prediction

Mona Singh, Daniel Munro, Mona Singh, 2020, Bioinform..

Neuronal identities derived by misexpression of the POU IV sensory determinant in a protovertebrate

Mona Singh, M. Levine, Y. Sasakura, 2022, Proceedings of the National Academy of Sciences.

Measuring differential gene expression by short read sequencing: quantitative comparison to 2-channel gene expression microarrays

Mona Singh, Leonid Kruglyak, Joshua S Bloom, 2009, BMC Genomics.

Predicting Protein Ligand Binding Sites by Combining Evolutionary Sequence Conservation and 3D Structure

Mona Singh, Thomas A. Funkhouser, Janet M. Thornton, 2009, PLoS Comput. Biol..

Beyond the E-Value: Stratified Statistics for Protein Domain Prediction

John D. Storey, Mona Singh, M. Llinás, 2014, PLoS Comput. Biol..

A novel method for estimating ancestral amino acid composition and its application to proteins of the Last Universal Ancestor

Mona Singh, Dawn J. Brooks, Jacques R. Fresco, 2004, Bioinform..

Comparative analysis of methods for representing and searching for transcription factor binding sites

Mona Singh, Robert Osada, Elena Zaslavsky, 2004, Bioinform..

Algorithms for analyzing and interrogating protein interaction networks

Mona Singh, Eric Banks, E. Banks, 2009 .

Organization of Physical Interactomes as Uncovered by Network Schemas

Mona Singh, Bernard Chazelle, Eric Banks, 2008, PLoS Comput. Biol..

Organization of Physical Interactomes as Uncovered by

Mona Singh, Bernard Chazelle, Mona Singh, 2008 .

molBLOCKS: decomposing small molecule sets and uncovering enriched fragments

Mona Singh, Dario Ghersi, Mona Singh, 2014, Bioinform..

A Guided Network Propagation Approach to Identify Disease Genes that Combines Prior and New Information

Mona Singh, Bernard Chazelle, Borislav H. Hristov, 2020, RECOMB.

Disentangling function from topology to infer the network properties of disease genes

Mona Singh, Dario Ghersi, Mona Singh, 2013, BMC Systems Biology.

Differential Allele-Specific Expression Uncovers Breast Cancer Genes Dysregulated By Cis Noncoding Mutations

Mona Singh, Mona Singh, Pawel F Przytycki, 2019, bioRxiv.

Genome-Wide Detection and Analysis of Multifunctional Genes

Mona Singh, Dario Ghersi, Yuri Pritykin, 2015, PLoS Comput. Biol..

Comparative genomic analysis reveals varying levels of mammalian adaptation to coronavirus infections

Sean King, Mona Singh, Sean King, 2021, PLoS Comput. Biol..

Solving and analyzing side-chain positioning problems using linear and integer programming

Mona Singh, Bernard Chazelle, Carleton L. Kingsford, 2005, Bioinform..

Proceedings of the 10th international conference on Algorithms in bioinformatics

Vincent Moulton, Mona Singh, Mona Singh, 2010 .

dSPRINT: predicting DNA, RNA, ion, peptide and small molecule interaction sites within protein domains

Mona Singh, Anat Etzion-Fuchs, David A Todd, 2021, Nucleic acids research.

Using context to improve protein domain identification

Alejandro Ochoa, Manuel Llinás, Mona Singh, 2011, BMC Bioinformatics.

Towards predicting coiled-coil protein interactions

Mona Singh, Peter S. Kim, P. S. Kim, 2001, RECOMB.

uKIN Combines New and Prior Information with Guided Network Propagation to Accurately Identify Disease Genes.

Mona Singh, Bernard Chazelle, Borislav H. Hristov, 2020, Cell systems.

Systematic domain-based aggregation of protein structures highlights DNA-, RNA- and other ligand-binding positions

Mona Singh, Shilpa Nadimpalli Kobren, Mona Singh, 2018, bioRxiv.

Predicting DNA recognition by Cys2His2 zinc finger proteins

Mona Singh, Anton V. Persikov, Robert Osada, 2009, Bioinform..

PertInInt: An Integrative, Analytical Approach to Rapidly Uncover Cancer Driver Genes with Perturbed Interactions and Functionalities

Mona Singh, Bernard Chazelle, Shilpa Nadimpalli Kobren, 2020, Cell systems.

A practical algorithm for finding maximal exact matches in large sequence datasets using sparse suffix arrays

Mona Singh, Zia Khan, Leonid Kruglyak, 2009, Bioinform..

Protein quantification across hundreds of experimental conditions

Mona Singh, Zia Khan, Leonid Kruglyak, 2009, Proceedings of the National Academy of Sciences.

Whole-proteome prediction of protein function via graph-theoretic analysis of interaction maps

Mona Singh, Bernard Chazelle, Elena Nabieva, 2005, ISMB.

A cross-genomic approach for systematic mapping of phenotypic traits to genes.

Mona Singh, Saeed Tavazoie, Mona Singh, 2003, Genome research.

Traits to Genes A Cross-Genomic Approach for Systematic Mapping of Phenotypic data

Mona Singh, Saeed Tavazoie, K. Parmar, 2003 .

Domain prediction with probabilistic directional context

Alejandro Ochoa, Mona Singh, Mona Singh, 2016, bioRxiv.

Algorithms in Bioinformatics

Mona Singh, Vincent Moulton, Mona Singh, 2014, Lecture Notes in Computer Science.

Two critical positions in zinc finger domains are heavily mutated in three human cancer types

Mona Singh, Dario Ghersi, Daniel Munro, 2018, PLoS Comput. Biol..

Characterization and prediction of residues determining protein functional specificity

Mona Singh, John A. Capra, Mona Singh, 2008, Bioinform..

Molecular mechanisms underlying cellular effects of human MEK1 mutations

Mona Singh, S. Shvartsman, T. Schüpbach, 2021, Molecular biology of the cell.

From Protein Interaction Networks to Protein Function

Mona Singh, Mona Singh, 2008, Protein-protein Interactions and Networks.

ISMB 2014 Proceedings Papers Committee

William Stafford Noble, Noah M. Daniels, D. Heckerman, 2014, Bioinformatics.

Vector-clustering Multiple Sequence Alignment: Aligning into the twilight zone of protein sequence similarity with protein language models

Mona Singh, C. McWhite, 2023, bioRxiv.

Network-augmented compartmental models to track asymptomatic disease spread

Mona Singh, B. Chazelle, Chaitanya Aluru, 2023, Bioinformatics advances.

Guest Editorial for ACM BCB

Mona Singh, Tamer Kahveci, Mona Singh, 2013, TCBB.

Simple Topological Features Reflect Dynamics and Modularity in Protein Interaction Networks

Mona Singh, Yuri Pritykin, Mona Singh, 2013, PLoS Comput. Biol..

Primate protein-ligand interfaces exhibit significant conservation and unveil human-specific evolutionary drivers

Mona Singh, Sean B King, 2023, PLoS Comput. Biol..

A combinatorial optimization approach for diverse motif finding applications

Mona Singh, Elena Zaslavsky, Mona Singh, 2006, Algorithms for Molecular Biology.

Quantitative measurement of allele‐specific protein expression in a diploid yeast hybrid by LC‐MS

David H Perlman, Sasan Amini, Mona Singh, 2013 .

PertInInt: An Integrative, Analytical Approach to Rapidly Uncover Cancer Driver Genes with Perturbed Interactions and Functionalities.

Mona Singh, B. Chazelle, S. Kobren, 2020, Cell systems.

Improved inference of tandem domain duplications

Mona Singh, Chaitanya Aluru, Mona Singh, 2021, Bioinform..

Quantitative measurement of allele‐specific protein expression in a diploid yeast hybrid by LC‐MS

David H Perlman, Sasan Amini, Mona Singh, 2012 .

Two critical positions in zinc finger domains are heavily mutated in three human cancer types

Mona Singh, Daniel Munro, D. Ghersi, 2018, PLoS Comput. Biol..

An expanded binding model for Cys2His2 zinc finger protein–DNA interfaces

Mona Singh, Mona Singh, Anton V Persikov, 2011, Physical biology.

Network-Based Coverage of Mutational Profiles Reveals Cancer Genes

Mona Singh, B. Hristov, 2017, Cell systems.

CCAT: Combinatorial Code Analysis Tool for transcriptional regulation

Mona Singh, Peng Jiang, 2013, Nucleic acids research.