Predicting DNA recognition by Cys2His2 zinc finger
proteins
Anton Persikov, Robert Osada and
Mona Singh.
Bioinformatics (2008) in press.
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, in press.
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.)
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.)