Learning Functions of k Terms. - Avrim Blum; Mona Singh 001 (COLT, 1990)

Piecemeal Graph Exploration by a Mobile Robot (Extended Abstract). - Baruch Awerbuch; Margrit Betke; Ronald L. Rivest; Mona Singh 001 (COLT, 1995)

Piecemeal Learning of an Unknown Environment. - Margrit Betke; Ronald L. Rivest; Mona Singh 001 (Mach. Learn., 1995)

Learning algorithms with applications to robot navigation and protein folding. - Mona Singh 001 (1995)

An Iterative Method for Improved Protein Structural Motif Recognition. - Bonnie Berger; Mona Singh 001 (J. Comput. Biol., 1997)

Computational learning reveals coiled coil-like motifs in histidine kinase linker domains. - Mona Singh 001; Bonnie Berger; Peter S. Kim; James M. Berger; Andrea G. Cochran (Proc. Natl. Acad. Sci. USA, 1998)

Piecemeal Graph Exploration by a Mobile Robot. - Baruch Awerbuch; Margrit Betke; Ronald L. Rivest; Mona Singh 001 (Inf. Comput., 1999)

Towards predicting coiled-coil protein interactions. - Mona Singh 001; Peter S. Kim (RECOMB, 2001)

The Side-Chain Positioning Problem: A Semidefinite Programming Formulation With New Rounding Schemes. - Bernard Chazelle; Carl Kingsford; Mona Singh 001 (PCK50, 2003)

A novel method for estimating ancestral amino acid composition and its application to proteins of the Last Universal Ancestor. - Dawn J. Brooks; Jacques R. Fresco; Mona Singh 001 (Bioinform., 2004)

Comparative analysis of methods for representing and searching for transcription factor binding sites. - Robert Osada; Elena Zaslavsky; Mona Singh 001 (Bioinform., 2004)

A Semidefinite Programming Approach to Side Chain Positioning with New Rounding Strategies. - Bernard Chazelle; Carl Kingsford; Mona Singh 001 (INFORMS J. Comput., 2004)

Whole-proteome prediction of protein function via graph-theoretic analysis of interaction maps. - Elena Nabieva; Kam Jim; Amit Agarwal 008; Bernard Chazelle; Mona Singh 001 (ISMB (Supplement of Bioinformatics), 2005)

Solving and analyzing side-chain positioning problems using linear and integer programming. - Carleton Kingsford; Bernard Chazelle; Mona Singh 001 (Bioinform., 2005)

A Compact Mathematical Programming Formulation for DNA Motif Finding. - Carl Kingsford; Elena Zaslavsky; Mona Singh 001 (CPM, 2006)

A combinatorial optimization approach for diverse motif finding applications. - Elena Zaslavsky; Mona Singh 001 (Algorithms Mol. Biol., 2006)

Predicting functionally important residues from sequence conservation. - John A. Capra; Mona Singh 001 (Bioinform., 2007)

From Protein Interaction Networks to Protein Function. - Mona Singh 001 (Protein-protein Interactions and Networks, 2008)

Characterization and prediction of residues determining protein functional specificity. - John A. Capra; Mona Singh 001 (Bioinform., 2008)

Organization of Physical Interactomes as Uncovered by Network Schemas. - Eric Banks; Elena Nabieva; Bernard Chazelle; Mona Singh 001 (PLoS Comput. Biol., 2008)

Analyzing and Interrogating Biological Networks (Abstract). - Eric Banks; Elena Nabieva; Bernard Chazelle; Ryan Peterson 003; Mona Singh 001 (BICoB, 2009)

Session Introduction. - Tanya Y. Berger-Wolf; Teresa M. Przytycka; Mona Singh 001 (Pacific Symposium on Biocomputing, 2009)

A practical algorithm for finding maximal exact matches in large sequence datasets using sparse suffix arrays. - Zia Khan; Joshua S. Bloom; Leonid Kruglyak; Mona Singh 001 (Bioinform., 2009)

Predicting DNA recognition by Cys2His2 zinc finger proteins. - Anton V. Persikov; Robert Osada; Mona Singh 001 (Bioinform., 2009)

How and when should interactome-derived clusters be used to predict functional modules and protein function? - Jimin Song; Mona Singh 001 (Bioinform., 2009)

M are better than one: an ensemble-based motif finder and its application to regulatory element prediction. - Chen Yanover; Mona Singh 001; Elena Zaslavsky (Bioinform., 2009)

Predicting Protein Ligand Binding Sites by Combining Evolutionary Sequence Conservation and 3D Structure. - John A. Capra; Roman A. Laskowski; Janet M. Thornton; Mona Singh 001; Thomas A. Funkhouser (PLoS Comput. Biol., 2009)

Protein quantification across hundreds of experimental conditions. - Zia Khan; Joshua S. Bloom; Benjamin A. Garcia; Mona Singh 001; Leonid Kruglyak (Proc. Natl. Acad. Sci. USA, 2009)

Predicting and Analyzing Cellular Networks. - Mona Singh 001 (ISBRA, 2010)

Session Introduction. - Tanya Y. Berger-Wolf; Teresa M. Przytycka; Mona Singh 001; Donna K. Slonim (Pacific Symposium on Biocomputing, 2010)

Toward the dynamic interactome: it's about time. - Teresa M. Przytycka; Mona Singh 001; Donna K. Slonim (Briefings Bioinform., 2010)

SPICi: a fast clustering algorithm for large biological networks. - Peng Jiang 006; Mona Singh 001 (Bioinform., 2010)

G-Quadruplex DNA Sequences Are Evolutionarily Conserved and Associated with Distinct Genomic Features in Saccharomyces cerevisiae. - John A. Capra; Katrin Paeschke; Mona Singh 001; Virginia A. Zakian (PLoS Comput. Biol., 2010)

Using context to improve protein domain identification. - Alejandro Ochoa; Manuel Llinás; Mona Singh 001 (BMC Bioinform., 2011)

A cost-aggregating integer linear program for motif finding. - Carl Kingsford; Elena Zaslavsky; Mona Singh 001 (J. Discrete Algorithms, 2011)

Disentangling function from topology to infer the network properties of disease genes. - Dario Ghersi; Mona Singh 001 (BMC Syst. Biol., 2013)

Computational Assessment of the Cooperativity between RNA Binding Proteins and MicroRNAs in Transcript Decay. - Peng Jiang 006; Mona Singh 001; Hilary A. Coller (PLoS Comput. Biol., 2013)

Simple Topological Features Reflect Dynamics and Modularity in Protein Interaction Networks. - Yuri Pritykin; Mona Singh 001 (PLoS Comput. Biol., 2013)

From Hub Proteins to Hub Modules: The Relationship Between Essentiality and Centrality in the Yeast Interactome at Different Scales of Organization. - Jimin Song; Mona Singh 001 (PLoS Comput. Biol., 2013)

Guest Editorial for ACM BCB. - Tamer Kahveci; Mona Singh 001 (IEEE ACM Trans. Comput. Biol. Bioinform., 2013)

molBLOCKS: decomposing small molecule sets and uncovering enriched fragments. - Dario Ghersi; Mona Singh 001 (Bioinform., 2014)

Beyond the E-Value: Stratified Statistics for Protein Domain Prediction. - Alejandro Ochoa; John D. Storey; Manuel Llinás; Mona Singh 001 (PLoS Comput. Biol., 2015)

Genome-Wide Detection and Analysis of Multifunctional Genes. - Yuri Pritykin; Dario Ghersi; Mona Singh 001 (PLoS Comput. Biol., 2015)

Network-Based Coverage of Mutational Profiles Reveals Cancer Genes. - Borislav H. Hristov; Mona Singh 001 (RECOMB, 2017)

Domain prediction with probabilistic directional context. - Alejandro Ochoa; Mona Singh 001 (Bioinform., 2017)

Sequence, Structure and Network Methods to Uncover Cancer Genes. - Mona Singh 001 (BCB, 2018)

Two critical positions in zinc finger domains are heavily mutated in three human cancer types. - Daniel Munro; Dario Ghersi; Mona Singh 001 (PLoS Comput. Biol., 2018)

Identifying Evolutionary Origins of Repeat Domains in Protein Families. - Chaitanya Aluru; Mona Singh 001 (BCB, 2020)

A Guided Network Propagation Approach to Identify Disease Genes that Combines Prior and New Information. - Borislav H. Hristov; Bernard Chazelle; Mona Singh 001 (RECOMB, 2020)

Improved inference of tandem domain duplications. - Chaitanya Aluru; Mona Singh 001 (Bioinform., 2021)

DeMaSk: a deep mutational scanning substitution matrix and its use for variant impact prediction. - Daniel Munro; Mona Singh 001 (Bioinform., 2021)

Comparative genomic analysis reveals varying levels of mammalian adaptation to coronavirus infections. - Sean B. King; Mona Singh 001 (PLoS Comput. Biol., 2021)

Learning Probabilistic Protein-DNA Recognition Codes from DNA-Binding Specificities Using Structural Mappings. - Joshua L. Wetzel; Kaiqian Zhang; Mona Singh 001 (RECOMB, 2022)

Primate protein-ligand interfaces exhibit significant conservation and unveil human-specific evolutionary drivers. - Sean B. King; Mona Singh 001 (PLoS Comput. Biol., 2023)

Future of Pandemic Prevention and Response CCC Workshop Report. - David Danks; Rada Mihalcea; Katie A. Siek; Mona Singh 001; Brian Dixon; Haley Griffin (CoRR, 2024)

RECOMB 2024 Special Issue. - Jian Ma 004; Mona Singh 001 (J. Comput. Biol., 2024)

Enabling the AI Revolution in Healthcare. - Mona Singh 001; Katie A. Siek; David Danks; Rayid Ghani; Haley Grin; Brian LaMacchia; Daniel Lopresti; Tammy Toscos (CoRR, 2025)