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.)