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.)
