Mona Singh

发表

Using context to improve protein domain identification

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

Predicting DNA recognition by Cys2His2 zinc finger proteins

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

Analyzing and Interrogating Biological Networks (Abstract)

Mona Singh, Bernard Chazelle, Eric Banks, 2009, BICoB.

Domain prediction with probabilistic directional context

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

Sequence, Structure and Network Methods to Uncover Cancer Genes

Mona Singh, 2018, BCB.

Simple Topological Features Reflect Dynamics and Modularity in Protein Interaction Networks

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

Deconstructing the "any" Key.

Mona Singh, Munindar P. Singh, 2000 .

An Iterative Method for Improved Protein Structural Motif Recognition

Mona Singh, Bonnie Berger, 1997, J. Comput. Biol..

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

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

Piecemeal graph exploration by a mobile robot (extended abstract)

Mona Singh, Margrit Betke, Baruch Awerbuch, 1995, COLT '95.

Toward the dynamic interactome: it's about time

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

Piecemeal learning of an unknown environment

Mona Singh, Margrit Betke, Ronald L. Rivest, 1995, Mach. Learn..

Supplementary Methods

Alejandro Ochoa, Manuel Llinás, Mona Singh, 2005 .

Computational solutions for omics data

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

Learning algorithms with applications to robot navigation and protein folding

Mona Singh, Mona Singh, 1996 .

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..

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

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

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

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

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..

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

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

From Protein Interaction Networks to Protein Function

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

Genome-Wide Detection and Analysis of Multifunctional Genes

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

molBLOCKS: decomposing small molecule sets and uncovering enriched fragments

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

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..

A Semidefinite Programming Approach to Side Chain Positioning with New Rounding Strategies

Mona Singh, Bernard Chazelle, Carl Kingsford, 2004, INFORMS J. Comput..

Session Introduction

Mona Singh, Donna K. Slonim, Tanya Y. Berger-Wolf, 2009, Pacific Symposium on Biocomputing.

Algorithms for analyzing and interrogating protein interaction networks

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

Protein quantification across hundreds of experimental conditions

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

Predicting Protein Secondary and Supersecondary Structure

Mona Singh, Mona Singh, 2005 .

Predicting and Analyzing Cellular Networks

Mona Singh, 2010, ISBRA.

SPICi: a fast clustering algorithm for large biological networks

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

Piecemeal Graph Exploration by a Mobile Robot

Mona Singh, Margrit Betke, Baruch Awerbuch, 1999, Inf. Comput..

Organization of Physical Interactomes as Uncovered by Network Schemas

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

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

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

Towards predicting coiled-coil protein interactions

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

Predicting functionally important residues from sequence conservation

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

Characterization and prediction of residues determining protein functional specificity

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

The side-chain positioning problem: a semidefinite programming formulation with new rounding schemes

Mona Singh, Bernard Chazelle, Carl Kingsford, 2003, PCK50.

Guest Editorial for ACM BCB

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

An iterative method for improved protein structural motif recognition

Mona Singh, Bonnie Berger, 1997, RECOMB '97.

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..

A Compact Mathematical Programming Formulation for DNA Motif Finding

Mona Singh, Carl Kingsford, Elena Zaslavsky, 2006, CPM.

A combinatorial optimization approach for diverse motif finding applications

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

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.

The Perfective Paradox: Or How to Eat Your Cake and Have it Too

Mona Singh, Mona Singh, 1991 .

Learning functions of k terms

Mona Singh, Avrim Blum, A. Blum, 1990, COLT '90.

Perfectivity, definiteness, and specificity : a classification of verbal predicates in Hindi

Mona Singh, 1994 .

Piecemeal Learning of an Unknown Environment

Mona Singh, Margrit Betke, Ronald L. Rivest, 1993, COLT.

A cost-aggregating integer linear program for motif finding

Mona Singh, Carl Kingsford, Elena Zaslavsky, 2011, J. Discrete Algorithms.

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..

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..

Organization of Physical Interactomes as Uncovered by

Mona Singh, Bernard Chazelle, Mona Singh, 2008 .

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

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

Improved inference of tandem domain duplications

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

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

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

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

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

The Inapproximability of Side-Chain Positioning

Mona Singh, Bernard Chazelle, Carl Kingsford, .

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.

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.

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

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

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

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

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

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

Interaction-based discovery of functionally important genes in cancers

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

Novel genes exhibit distinct patterns of function acquisition and network integration

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

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

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