Towards equitable MHC binding predictions: computational strategies to assess and reduce data bias.
Eric Glynn, Dario Ghersi, and
Mona Singh.
bioRxiv (2024) doi:10.1101/2024.01.30.578103.
How has the AI boom impacted algorithmic biology?
Mona Singh, Cenk Sahinalp, Jianyang Zeng, Wei Vivian Li, Carl Kingsford, Qiangfeng Zhang, Teresa Przytycka, Joshua Welch, Jian Ma, Bonnie Berger.
Cell Systems (2024) 15:483--487.
Current and future directions in network biology
Marinka Zitnik, Michelle M Li, Aydin Wells, Kimberly Glass, Deisy Morselli Gysi, Arjun Krishnan, TM Murali, Predrag Radivojac, Sushmita Roy, Anaïs Baudot, Serdar Bozdag, Danny Z Chen, Lenore Cowen, Kapil Devkota, Anthony Gitter, Sara Gosline, Pengfei Gu, Pietro H Guzzi, Heng Huang, Meng Jiang, Ziynet Nesibe Kesimoglu, Mehmet Koyuturk, Jian Ma, Alexander R Pico, Nataša Pržulj, Teresa M Przytycka, Benjamin J Raphael, Anna Ritz, Roded Sharan, Yang Shen,
Mona Singh, Donna K Slonim, Hanghang Tong, Xinan Holly Yang, Byung-Jun Yoon, Haiyuan Yu, Tijana Milenković.
Bioinformatics Advances (2024) 4: vbae099.
A benchmarked, high-efficiency prime editing platform for multiplexed dropout screening
Ann Cirincione, Danny Simpson, Purnima Ravisankar, Sabrina C Solley, Jun Yan,
Mona Singh, Britt Adamson.
Accepted in principle.
ERK synchronizes embryonic cleavages in Drosophila.
Liu Yang, Audrey Zhu, Javed M Aman, David Denberg, Marcus D Kilwein, Robert A Marmion, Alex NT Johnson, Alexey Veraksa,
Mona Singh, Martin Wuhr, Stanislav Shvartsman.
Developmental Cell (2024) doi: 10.1016/j.devcel.2024.08.004.
Computational Methods for Predicting Key Interactions in T Cell–Mediated Adaptive Immunity.
Ryan Ehrlich, Eric Glynn,
Mona Singh, and Dario Ghersi.
Annual Review of Biomedical Data Science (2024) 7:295--316. (Co-corresponding with Dario Ghersi.)
Ensemble Detection of DNA Engineering Signatures.
Aaron Adler, Joel S Bader, Brian Basnight, Benjamin W Booth, Jitong Cai, Elizabeth Cho, Joseph H Collins, Yuchen Ge, John Grothendieck, Kevin Keating, Tyler Marshall, Anton Persikov, Helen Scott, Roy Siegelmann,
Mona Singh, Allison Taggart, Benjamin Toll, Kenneth H Wan, Daniel Wyschogrod, Fusun Yaman, Eric M Young, Susan E Celniker, Nicholas Roehner.
ACS Synthetic Biology (2024) 4: 1105--1115.
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.)
