Mona Singh

66 papers A* 3B 7C 1Misc 2Journal 44Unranked 6
YearRankTypeTitle / Venue / Authors
2026 J jnl
Preface.
J. Comput. Biol.
Mona Singh
2026 J jnl
The Imperative for Grand Challenges in Computing.
CoRR
William Regli, Rajmohan Rajaraman, Daniel Lopresti, David Jensen, Mary Lou Maher, Manish Parashar, Mona Singh, Holly A. Yanco
2025 J jnl
Enabling the AI Revolution in Healthcare.
CoRR
Mona Singh, Katie A. Siek, David Danks, Rayid Ghani, Haley Grin, Brian LaMacchia, Daniel Lopresti, Tammy Toscos
2025 J jnl
KINAID: an orthology-based kinase-substrate prediction and analysis tool for phosphoproteomics.
Bioinform.
Javed M. Aman, Audrey W. Zhu, Martin Wühr, Stanislav Y. Shvartsman, Mona Singh
2025 J jnl
Locality-aware pooling enhances protein language model performance across varied applications.
Bioinform.
Minh Hoang, Mona Singh
2024 J jnl
Future of Pandemic Prevention and Response CCC Workshop Report.
CoRR
David Danks, Rada Mihalcea, Katie A. Siek, Mona Singh, Brian Dixon, Haley Griffin
2024 J jnl
RECOMB 2024 Special Issue.
J. Comput. Biol.
Jian Ma, Mona Singh
2023 J jnl
Primate protein-ligand interfaces exhibit significant conservation and unveil human-specific evolutionary drivers.
PLoS Comput. Biol.
Sean B. King, Mona Singh
2022 B conf
Learning Probabilistic Protein-DNA Recognition Codes from DNA-Binding Specificities Using Structural Mappings.
RECOMB
Joshua L. Wetzel, Kaiqian Zhang, Mona Singh
2021 J jnl
Comparative genomic analysis reveals varying levels of mammalian adaptation to coronavirus infections.
PLoS Comput. Biol.
Sean B. King, Mona Singh
2021 J jnl
DeMaSk: a deep mutational scanning substitution matrix and its use for variant impact prediction.
Bioinform.
Daniel Munro, Mona Singh
2021 J jnl
Improved inference of tandem domain duplications.
Bioinform.
Chaitanya Aluru, Mona Singh
2020 B conf
A Guided Network Propagation Approach to Identify Disease Genes that Combines Prior and New Information.
RECOMB
Borislav H. Hristov, Bernard Chazelle, Mona Singh
2020 — conf
Identifying Evolutionary Origins of Repeat Domains in Protein Families.
BCB
Chaitanya Aluru, Mona Singh
2018 — conf
Sequence, Structure and Network Methods to Uncover Cancer Genes.
BCB
Mona Singh
2018 J jnl
Two critical positions in zinc finger domains are heavily mutated in three human cancer types.
PLoS Comput. Biol.
Daniel Munro, Dario Ghersi, Mona Singh
2017 J jnl
Domain prediction with probabilistic directional context.
Bioinform.
Alejandro Ochoa, Mona Singh
2017 B conf
Network-Based Coverage of Mutational Profiles Reveals Cancer Genes.
RECOMB
Borislav H. Hristov, Mona Singh
2017 J jnl
Network-based coverage of mutational profiles reveals cancer genes.
CoRR
Borislav H. Hristov, Mona Singh
2016 B ed.
Research in Computational Molecular Biology - 20th Annual Conference, RECOMB 2016, Santa Monica, CA, USA, April 17-21, 2016, Proceedings
RECOMB
Mona Singh
2015 J jnl
Beyond the
PLoS Comput. Biol.
Alejandro Ochoa, John D. Storey, Manuel Llinás, Mona Singh
2015 J jnl
Genome-Wide Detection and Analysis of Multifunctional Genes.
PLoS Comput. Biol.
Yuri Pritykin, Dario Ghersi, Mona Singh
2014 J jnl
molBLOCKS: decomposing small molecule sets and uncovering enriched fragments.
Bioinform.
Dario Ghersi, Mona Singh
2013 J jnl
Computational Assessment of the Cooperativity between RNA Binding Proteins and MicroRNAs in Transcript Decay.
PLoS Comput. Biol.
Peng Jiang, Mona Singh, Hilary A. Coller
2013 J jnl
Disentangling function from topology to infer the network properties of disease genes.
BMC Syst. Biol.
Dario Ghersi, Mona Singh
2013 J jnl
From Hub Proteins to Hub Modules: The Relationship Between Essentiality and Centrality in the Yeast Interactome at Different Scales of Organization.
PLoS Comput. Biol.
Jimin Song, Mona Singh
2013 J jnl
Guest Editorial for ACM BCB.
IEEE ACM Trans. Comput. Biol. Bioinform.
Tamer Kahveci, Mona Singh
2013 J jnl
Simple Topological Features Reflect Dynamics and Modularity in Protein Interaction Networks.
PLoS Comput. Biol.
Yuri Pritykin, Mona Singh
2012 — ed.
ACM International Conference on Bioinformatics, Computational Biology and Biomedicine, BCB' 12, Orlando, FL, USA - October 08 - 10, 2012
BCB
Sanjay Ranka, Tamer Kahveci, Mona Singh
2011 J jnl
A cost-aggregating integer linear program for motif finding.
J. Discrete Algorithms
Carl Kingsford, Elena Zaslavsky, Mona Singh
2011 J jnl
Using context to improve protein domain identification.
BMC Bioinform.
Alejandro Ochoa, Manuel Llinás, Mona Singh
2010 C ed.
Algorithms in Bioinformatics, 10th International Workshop, WABI 2010, Liverpool, UK, September 6-8, 2010. Proceedings
WABI
Vincent Moulton, Mona Singh
2010 J jnl
G-Quadruplex DNA Sequences Are Evolutionarily Conserved and Associated with Distinct Genomic Features in
PLoS Comput. Biol.
John A. Capra, Katrin Paeschke, Mona Singh, Virginia A. Zakian
2010 — conf
Predicting and Analyzing Cellular Networks.
ISBRA
Mona Singh
2010 J jnl
SPICi: a fast clustering algorithm for large biological networks.
Bioinform.
Peng Jiang, Mona Singh
2010 Misc conf
Session Introduction.
Pacific Symposium on Biocomputing
Tanya Y. Berger-Wolf, Teresa M. Przytycka, Mona Singh, Donna K. Slonim
2010 J jnl
Toward the dynamic interactome: it's about time.
Briefings Bioinform.
Teresa M. Przytycka, Mona Singh, Donna K. Slonim
2009 J jnl
A practical algorithm for finding maximal exact matches in large sequence datasets using sparse suffix arrays.
Bioinform.
Zia Khan, Joshua S. Bloom, Leonid Kruglyak, Mona Singh
2009 — conf
Analyzing and Interrogating Biological Networks (Abstract).
BICoB
Eric Banks, Elena Nabieva, Bernard Chazelle, Ryan Peterson, Mona Singh
2009 J jnl
How and when should interactome-derived clusters be used to predict functional modules and protein function?
Bioinform.
Jimin Song, Mona Singh
2009 J jnl
Predicting DNA recognition by Cys
Bioinform.
Anton V. Persikov, Robert Osada, Mona Singh
2009 J jnl
Predicting Protein Ligand Binding Sites by Combining Evolutionary Sequence Conservation and 3D Structure.
PLoS Comput. Biol.
John A. Capra, Roman A. Laskowski, Janet M. Thornton, Mona Singh, Thomas A. Funkhouser
2009 J jnl
Protein quantification across hundreds of experimental conditions.
Proc. Natl. Acad. Sci. USA
Zia Khan, Joshua S. Bloom, Benjamin A. Garcia, Mona Singh, Leonid Kruglyak
2009 Misc conf
Session Introduction.
Pacific Symposium on Biocomputing
Tanya Y. Berger-Wolf, Teresa M. Przytycka, Mona Singh
2008 J jnl
Characterization and prediction of residues determining protein functional specificity.
Bioinform.
John A. Capra, Mona Singh
2008 — ch.
From Protein Interaction Networks to Protein Function.
Protein-protein Interactions and Networks
Mona Singh
2008 J jnl
Organization of Physical Interactomes as Uncovered by Network Schemas.
PLoS Comput. Biol.
Eric Banks, Elena Nabieva, Bernard Chazelle, Mona Singh
2007 J jnl
Predicting functionally important residues from sequence conservation.
Bioinform.
John A. Capra, Mona Singh
2006 B conf
A Compact Mathematical Programming Formulation for DNA Motif Finding.
CPM
Carl Kingsford, Elena Zaslavsky, Mona Singh
2006 J jnl
A combinatorial optimization approach for diverse motif finding applications.
Algorithms Mol. Biol.
Elena Zaslavsky, Mona Singh
2005 J jnl
Solving and analyzing side-chain positioning problems using linear and integer programming.
Bioinform.
Carleton Kingsford, Bernard Chazelle, Mona Singh
2005 — conf
Whole-proteome prediction of protein function via graph-theoretic analysis of interaction maps.
ISMB (Supplement of Bioinformatics)
Elena Nabieva, Kam Jim, Amit Agarwal, Bernard Chazelle, Mona Singh
2004 J jnl
A Semidefinite Programming Approach to Side Chain Positioning with New Rounding Strategies.
INFORMS J. Comput.
Bernard Chazelle, Carl Kingsford, Mona Singh
2004 J jnl
A novel method for estimating ancestral amino acid composition and its application to proteins of the Last Universal Ancestor.
Bioinform.
Dawn J. Brooks, Jacques R. Fresco, Mona Singh
2004 J jnl
Comparative analysis of methods for representing and searching for transcription factor binding sites.
Bioinform.
Robert Osada, Elena Zaslavsky, Mona Singh
2003 — conf
The Side-Chain Positioning Problem: A Semidefinite Programming Formulation With New Rounding Schemes.
PCK50
Bernard Chazelle, Carl Kingsford, Mona Singh
2001 B conf
Towards predicting coiled-coil protein interactions.
RECOMB
Mona Singh, Peter S. Kim
1999 J jnl
Piecemeal Graph Exploration by a Mobile Robot.
Inf. Comput.
Baruch Awerbuch, Margrit Betke, Ronald L. Rivest, Mona Singh
1998 J jnl
Computational learning reveals coiled coil-like motifs in histidine kinase linker domains.
Proc. Natl. Acad. Sci. USA
Mona Singh, Bonnie Berger, Peter S. Kim, James M. Berger, Andrea G. Cochran
1997 J jnl
An Iterative Method for Improved Protein Structural Motif Recognition.
J. Comput. Biol.
Bonnie Berger, Mona Singh
1997 B conf
An iterative method for improved protein structural motif recognition.
RECOMB
Bonnie Berger, Mona Singh
1995 — —
Learning algorithms with applications to robot navigation and protein folding.
Mona Singh
1995 A* conf
Piecemeal Graph Exploration by a Mobile Robot (Extended Abstract).
COLT
Baruch Awerbuch, Margrit Betke, Ronald L. Rivest, Mona Singh
1995 J jnl
Piecemeal Learning of an Unknown Environment.
Mach. Learn.
Margrit Betke, Ronald L. Rivest, Mona Singh
1993 A* conf
Piecemeal Learning of an Unknown Environment.
COLT
Margrit Betke, Ronald L. Rivest, Mona Singh
1990 A* conf
Learning Functions of
COLT
Avrim Blum, Mona Singh