Some Publications

Leveraging protein language models for accurate multiple sequence alignments.
Claire McWhite, Isabel Armour-Garb and Mona Singh. Genome Research (2023) 33:1145--1153. (RECOMB 2023 collection.)

Network-augmented compartmental models to track asymptomatic disease spread.
Devavrat Vivek Dabke, Kritkorn Karntikoon, Chaitanya Aluru, Mona Singh, and Bernard Chazelle. Bioinformatics Advances (2023) 3(1):vbad082.

Primate protein-ligand interfaces exhibit significant conservation and unveil human-specific evolutionary drivers.
Sean King and Mona Singh. PLOS Computational Biology (2023) 19: e1010966.

Learning probabilistic protein-DNA recognition codes from DNA-binding specificities using structural mappings.
Joshua Wetzel, Kaiqian Zhang and Mona Singh. Genome Research (2022) 32: 1776--1786. (RECOMB 2022 Collection.)

Neuronal identities derived by misexpression of the POU IV sensory determinant in a protovertebrate.
Prakriti Paul Chacha, Ryoko Horie, Takehiro Kusakabe, Yansuori Sasakura, Mona Singh, Takeo Horie, and Michael Levine. Proceedings of the National Academy of Sciences (2022) 119: e2118817119.

Comparative genomic analysis reveals varying levels of mammalian adaptation to coronavirus infections.
Sean B. King and Mona Singh. PLOS Computational Biology (2021) 17: e1009560.

Metabolite discovery through global annotation of untargeted metabolomics data.
Li Chen, Wenyun Lu, Lin Wang, Xi Xing, Ziyang Chen, Xin Teng, Xianfeng Zeng, Antonio D. Muscarella, Yihui Shen, Alexis Cowan, Melanie R. McReynolds, Brandon J. Kennedy, Ashley M. Lato, Shawn R. Campagna, Mona Singh, and Joshua Rabinowitz. Nature Methods (2021) 18: 1377--1385.

Improved inference of tandem domain duplications.
Chaitanya Aluru and Mona Singh. Bioinformatics (2021) 37(Suppl_1): i333-i141, ISMB.

dSPRINT: predicting DNA, RNA, ion, peptide, and small molecule interaction sites within protein domains.
Anat Etzion-Fuchs, David A. Todd, and Mona Singh. Nucleic Acids Research (2021) 49:e78.

Molecular mechanisms underlying cellular effects of human MEK1 mutations.
Robert A. Marmion, Liu Yang, Yogesh Goyal, Granton A. Jindal, Joshua L. Wetzel, Mona Singh, Trudi Schüpbach, and Stanislav Y. Shvartsman. Molecular Biology of the Cell (2021) 32: 974.

DeMaSk: a deep mutational scanning substitution matrix and its use for variant impact prediction.
Daniel Munro and Mona Singh. Bioinformatics (2020) 36: 5322-5329.

Identifying Evolutionary Origins of Repeat Domains in Protein Families.
Chaitanya Aluru and Mona Singh. Proceedings of the 11th ACM International Conference on Bioinformatics, Computational Biology and Health Informatics (ACM-BCB); 2020 September; Atlanta, GA. New York, NY: ACM. p 1-11.

PertInInt: An Integrative, Analytical Approach to Rapidly Uncover Cancer Driver Genes with Perturbed Interactions and Functionalities.
Shilpa Nadimpalli Kobren, Bernard Chazelle and Mona Singh. Cell Systems (2020) 11: 63-74

uKIN Combines New and Prior Information with Guided Network Propagation to Accurately Identify Disease Genes.
Borislav Hristov, Bernard Chazelle and Mona Singh. Cell Systems (2020) 10: 47-49. (RECOMB 2020 Collection.)

Differential allele specific expression uncovers breast cancer genes dysregulated by cis noncoding mutations.
Pawel Przytycki and Mona Singh. Cell Systems (2020) 10:193.

Sharing DNA-binding information across structurally similar proteins enables accurate specificity determination .
Joshua Wetzel and Mona Singh. Nucleic Acids Research (2020) 48(2): e9.

Systematic domain-based aggregation of protein structures highlights DNA-, RNA- and other ligand-binding positions.
Shilpa Nadimapalli Kobren and Mona Singh. Nucleic Acids Research (2019) 47: 582-593.

Two critical positions in zinc finger domains are heavily mutated in three human cancer types.
Daniel Munro, Dario Ghersi and Mona Singh. PLOS Computational Biology (2018) 14:e1006290.

Network-based coverage of mutational profiles reveals cancer genes.
Borislav Hristov and Mona Singh. Cell Systems (2017) 5:221. (RECOMB 2017 Collection.)

Differential analysis between somatic mutation and germline variation profiles reveals cancer-related genes.
Pawel Przytycki and Mona Singh. Genome Medicine (2017) 9:79.

Domain prediction with probabilistic directional context.
Alex Ochoa and Mona Singh. Bioinformatics (2017) 33:2471-2478.

Integrative analysis unveils new functions for the Drosophila Cutoff protein in non-coding RNA biogenesis and gene regulation.
Yuri Pritykin, Tarcisio Brito, Trudi Schupbach, Mona Singh and Attilio Pane. RNA (2017) 7:1097-1109.

Beyond the E-value: Stratified statistics for protein domain prediction.
Alex Ochoa, John Storey, Manuel Llinas and Mona Singh. PLOS Computational Biology (2015) 11:e1004509.

Genome-wide detection and analysis of multifunctional genes.
Yuri Pritykin, Dario Ghersi and Mona Singh. PLOS Computational Biology (2015) 11:1004467.

Pervasive variation of transcription factor orthologs contributes to regulatory network evolution.
Shilpa Nadimpalli, Anton Persikov and Mona Singh. PLOS Genetics (2015) 11:1005011.

A systematic survey of the Cys2His2 zinc finger DNA-binding landscape.
Anton Persikov, Joshua Wetzel, Elizabeth Rowland, Benjamin Oakes, Denise Xu, Mona Singh and Marcus Noyes. Nucleic Acids Research (2015) 43: 1965-1984. (Co-corresponding author with Marcus Noyes.)

molBLOCKS: Decomposing small molecule sets and uncovering enriched fragments.
Dario Ghersi and Mona Singh. Bioinformatics (2014) 30(14): 2081-2083.

CCAT: Combinatorial code analysis tool for transcriptional regulation.
Peng Jiang and Mona Singh. Nucleic Acids Research (2014) 42:2833-2847.

Interaction-based discovery of functionally important genes in cancer.
Dario Ghersi and Mona Singh. Nucleic Acids Research (2014) 42: e18.

Deep sequencing of large library selections allows computational discovery of diverse sets of zinc fingers that bind common targets.
Anton Persikov, Elizabeth Rowland, Benjamin Oakes, Mona Singh and Marcus Noyes. Nucleic Acids Research (2014) 42: 1497-1508. (Co-corresponding author with Marcus Noyes.)

De novo prediction of DNA-binding specificities for Cys2His2 zinc finger proteins.
Anton Persikov and Mona Singh. Nucleic Acids Res (2014) 42: 97-108.

Simple topological features reflect dynamics and modularity in protein interaction networks.
Yuri Pritykin and Mona Singh. PLOS Computational Biology (2013) 9:e1003243.

Computational assessment of the cooperativity between RNA binding proteins and microRNAs in transcript decay.
Peng Jiang, Mona Singh and Hilary Coller. PLOS Computational Biology (2013) 9:e1003075.

Computational solutions for omics data.
Bonnie Berger, Jian Peng and Mona Singh. Nature Reviews Genetics (2013) 14:333-346.

From hub proteins to hub modules: the relationship between essentiality and centrality in the yeast interactome at different scales of organization.
Jimin Song and Mona Singh. PLOS Computational Biology (2013) 9:e1002910.

Disentangling function from topology to infer the network properties of disease genes.
Dario Ghersi and Mona Singh. BMC Systems Biology (2013) 7:5.

Quantitative measurement of allele-specific protein expression in a diploid yeast hybrid by LC-MS.
Zia Khan, Josh Bloom, Sasan Amini, Mona Singh, David Perlman, Amy Caudy and Leonid Kruglyak. Molecular Systems Biology (2012) 8:602.

Accurate proteome-wide protein quantification from high-resolution 15N mass spectra.
Zia Khan, Sasan Amini, Josh Bloom, Cristina Ruse, Amy Caudy, Leonid Kruglyak, Mona Singh, David Perlman and Saeed Tavazoie. Genome Biology (2011) 12:R122.

A cost-aggregating integer linear program for motif finding.
Carl Kingsford, Elena Zaslavsky Mona Singh. Journal of Discrete Algorithms (2011) 9:326-334.

The Cutoff protein regulates piRNA cluster expression and piRNA production in the Drosophila germline.
Attilio Pane, Peng Jiang, Dorothy Yanling Zhao, Mona Singh, and Trudi Schupbach. EMBO J (2011) 30:4601-4615.

An expanded binding model for Cys2His2 zinc finger protein-DNA interfaces.
Anton Persikov and Mona Singh. Physical Biology (2011) 8:035010.

Using context to improve protein domain identification.
Alex Ochoa, Manuel Llinas and Mona Singh. BMC Bioinformatics (2011) 12:90. (Co-corresponding author with Manuel Llinas.)

Novel genes exhibit distinct patterns of function acquision and network integration.
John A. Capra, Katherine Pollard and Mona Singh. Genome Biology (2010) 11:R127. (Co-corresponding author with Katherine Pollard.)

G-Quadruplex DNA Sequences Are Evolutionarily Conserved and Associated with Distinct Genomic Features in Saccharomyces cerevisiae.
John A. Capra, Katrin Paeschke, Mona Singh and Virginia Zakian. PLOS Computational Biology (2010) e1000861. (Co-corresponding author with Virginia Zakian.)

SPICi: a fast clustering algorithm for large biological networks.
Peng Jiang and Mona Singh. Bioinformatics (2010) 26:1105-1111.

Towards the dynamic interactome: it's about time
Teresa Przytycka, Mona Singh and Donna Slonim. Briefings in Bioinformatics (2010) 1: 15-29. (All authors co-corresponding.)

Predicting protein ligand binding sites by combining evolutionary sequence conservation and 3D structure
John A. Capra, Roman Laskowski, Janet Thorton, Mona Singh and Tom Funkhouser. PLOS Computational Biology (2009) e1000585. (Co-corresponding author with Tom Funkhouser.)

How and when should interactome-derived clusters be used to predict functional modules and protein function?
Jimin Song and Mona Singh. Bioinformatics (2009) 25(23):3143-3150.

Protein quantification across hundreds of experimental conditions.
Zia Khan, Joshua Bloom, Ben Garcia, Mona Singh and Leonid Kruglyak. Proc. Natl. Acad. Sci. USA (2009) 106:15544-15548.

Measuring differential gene expression by short read sequencing: quantitative comparisons to 2-channel gene expression microarrays
Joshua Bloom, Zia Khan, Leonid Kruglyak, Mona Singh and Amy Caudy. BMC Genomics (2009) 10: 221.

A practical algorithm for finding maximal exact matches in large sequence data sets using sparse suffix arrays
Zia Khan, Joshua Bloom, Leonid Kruglyak and Mona Singh. Bioinformatics (2009) 25: 1609-1616.

M are better than one: an ensemble-based motif finder and its application to regulatory element prediction
Chen Yanover, Mona Singh and Elena Zaslavsky. Bioinformatics (2009) 25: 868-874.

Predicting DNA recognition by Cys2His2 zinc finger proteins
Anton Persikov, Robert Osada and Mona Singh. Bioinformatics (2009) 25: 22-29.

Organization of physical interactomes as uncovered by network schemas
Eric Banks, Elena Nabieva, Bernard Chazelle and Mona Singh. PLOS Computational Biology (2008) 4(10): e1000203. (First two authors equal contribution.)

NetGrep: fast network schema searches in interactomes
Eric Banks, Elena Nabieva, Ryan Peterson and Mona Singh. Genome Biology (2008) 24: 1473-1480.

Characterization and prediction of residues determining protein functional specificity
John A. Capra and Mona Singh. Bioinformatics (2008) 24: 1473-1480.

Predicting functionally important residues from sequence conservation
John A. Capra and Mona Singh. Bioinformatics (2007) 23: 1875-1882.

A combinatorial optimization approach for diverse motif finding applications
Elena Zaslavsky and Mona Singh. Algorithms for Molecular Biology (2006) 1: 13.

A compact mathematical programming formulation for DNA motif finding
Carl Kingsford, Elena Zaslavsky and Mona Singh. Proceedings of 17th Annual Symposium on Combinatorial Pattern Matching (2006) July 5-7; Barcelona, Spain. Berlin, Germany: Springer Lecture Notes in Computer Science. p 233-245.

Predicting protein secondary and supersecondary structure
Mona Singh. Handbook of Computational Molecular Biology, Srinivas Aluru (Editor), Chapman & Hall CRC Computer and Information Science Series, 2005.
Whole-proteome prediction of protein function via graph-theoretic analysis of interaction maps
Elena Nabieva, Kam Jim, Amit Agarwal, Bernard Chazelle and Mona Singh. Bioinformatics (2005) 21 Suppl 1:i302–i310. (ISMB 2005 Best student paper award for Elena Nabieva, 426 papers submitted, 56 accepted, 4 best paper awards.)

Solving and analyzing side-chain positioning problems using linear and integer programming
Carl Kingsford, Bernard Chazelle and Mona Singh. Bioinformatics (2005) 21: 1028–1036. (Advance access publication on 11/16/2004.)

Comparative analysis of methods for representing and searching for transcription factor binding sites
Robert Osada, Elena Zaslavsky and Mona Singh. Bioinformatics (2004) 20: 3516–3525. (Advance access publication on 8/5/2004.)

A novel method for estimating ancestral amino acid composition and its application to proteins of the Last Universal Ancestor
Dawn Brooks, Jacques Fresco and Mona Singh. Bioinformatics (2004) 20(14): 2251–2257. (Advance access publication on 4/8/2004.)

A semidefinite approach to side-chain positioning with new rounding schemes
Bernard Chazelle, Carl Kingsford and Mona Singh. (Authors alphabetized.) INFORMS Journal on Computing, Special Issue on Computational Molecular Biology/Bioinformatics, (2004) 16: 380–392.

A cross-genomic approach for systematic mapping of phenotypic traits to genes
Kam Jim, Kush Parmar, Mona Singh and Saeed Tavazoie. (Authors alphabetized, co-corresponding author with Saeed Tavazoie.) Genome Research (2004) 14: 109–115.

Predicting specificity in bZIP coiled-coil protein interactions
Jessica Fong, Amy Keating and Mona Singh. Genome Biology (2004) 5(2): R11.

Evolution of amino acid frequencies in proteins over deep time: Inferred order of introduction of amino acids into the genetic code
Dawn Brooks, Jacques Fresco, Arthur Lesk and Mona Singh. Molecular Biology and Evolution (2002) 19(10): 1645–1655.

The trimer-of-hairpins motif in viral membrane-fusion proteins: Visna virus
Vladimir Malashkevich, Mona Singh and Peter S. Kim. Proc. Natl. Acad. Sci. USA (2001) 98: 8502–8506.

Towards predicting coiled-coil protein interactions
Mona Singh and Peter S. Kim. Proceedings of the 5th Annual International Conference on Computational Molecular Biology (RECOMB); 2001 Apr 22–25; Montreal, CA. New York, NY: ACM. p 279–286.

Structural characterization of the human respiratory syncytial virus fusion protein core
Xun Zhao, Mona Singh, Vladimir Malashkevich, and Peter S. Kim. Proc. Natl. Acad. Sci. USA (2000) 97: 14172–14177.

LearnCoil-VMF: Computational evidence for coiled-coil-like motifs in many viral membrane-fusion proteins
Mona Singh, Bonnie Berger, Peter S. Kim. J. Mol. Biol. (1999) 290(5): 1031–1041.

Computational learning reveals coiled coil-like motifs in histidine kinase linker domains
Mona Singh, Bonnie Berger, Peter S. Kim, James M. Berger and Andrea G. Cochran. Proc. Natl. Acad. Sci. USA (1998) 95: 2738–2743.

An iterative method for improved protein structural motif recognition
Bonnie Berger and Mona Singh. J. Comput. Biol (1997) 4:261–273. (Authors alphabetized.)