Classes
Fall 2007 - Graphs and Networks in Computational Biology (CMSC 858L)
Current Interests
- Protein-protein interaction networks.
- Transcription termination in bacteria. See the
TransTermHP
program for predicting Rho-independent terminators.
- Protein structure prediction (e.g.
using mathematical programming to predict protein structure).
- Overlapping genes in Bacteria.
- Evolution of the influenza genome.
- Motif finding (e.g. transcription factor binding sites,
Rho-independent transcription terminators).
- Protein function prediction.
Partial Research Schematic
Selected Publications
Click on the title of the paper to download a PDF version.
- C. Kingsford, A. Delcher, S. Salzberg,
A Unified Model Explaining the Offsets of Overlapping and Near-Overlapping Prokaryotic Genes
Molecular Biology and Evolution,
24(9):2091–2098 (2007).
(Journal Page)
- S. Salzberg, C. Kingsford, G. Cattoli, D.J. Spiro, D.A. Janies, M.M. Aly
et al., Genome analysis
linking recent European and African influenza (H5N1) viruses. Emerging
Infectious Diseases 13(5), 2007
- C. Kingsford, K. Ayanbule, and S. Salzberg, Rapid, accurate,
computational discovery of Rho-independent transcription terminators
illuminates their relationship to DNA uptake. Genome Biology
8:R22 (2007).
[Preprint]
[Software Download]
- C. Kingsford, E. Zaslavsky, and M. Singh, A compact mathematical programming
formulation for DNA motif finding. In the proceedings of the 17th Annual Symposium on Combinatorial
Pattern Matching (2006). [PDF of Talk
Slides] [Preprint]
- C. Kingsford, Computational
Approaches to Problems in Protein Structure and Function. Ph.D. Thesis,
Princeton University, August 2005.
- C. Kingsford, B. Chazelle, and M. Singh, Solving and
analyzing side-chain positioning problems using linear and integer
programming. Bioinformatics 21(7):1028-1039 (2005). (Advanced
access publication on 11/16/2004.) [Preprint] [Software Download]
- B. Chazelle, C. Kingsford, and M. Singh,
A semidefinite programming approach to side-chain positioning with new rounding
strategies. INFORMS Journal on Computing, Special Issue on
Computational Molecular Biology/Bioinformatics, 16:380-392 (2004). [Preprint]
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