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Classes
Office Hours: Tuesday 2:00-3:30 in AVW 3223.
Current Interests
In general, we are interested in designing graph algorithms to extract
insight from biological data.
Protein interactions and networks:
Bacterial & viral genome analysis:
- Overlapping genes in Bacteria.
- Transcription termination in bacteria. See the
TransTermHP
program for predicting Rho-independent terminators.
- Reassortment in the influenza genome.
This work is partially funded by NSF grant 0849899 and by
NSF grant
IIS-0812111.
Selected Publications
Click on the title of the paper to download a PDF version.
* indicates that the authors are alphabetized.
† indicates equal contribution.
- S. Navlakha and C. Kingsford. Exploring Biological Network
Dynamics with Ensembles of Graph Partitions. To appear in Pac. Symp.
Biocomp. 2010.
- C. Kingsford* and G. Marçais.* A synthesis for exactly
3-edge-connected graphs. In submission. [Preprint]
- C. Kingsford* and G. Marçais.* Vertices of degree
k in edge-minimal, k-edge-connected graphs. In submission. [Preprint]
- C. Kingsford†, N. Nagarajan†, and S. L. Salzberg.
2009
Swine-Origin Influenza A (H1N1) Resembles Previous Influenza Isolates.
PLoS ONE 4(7):e6402, 2009.
- S. Navlakha, J. White, N. Nagarajan, M. Pop, and C. Kingsford.
Finding Biologically
Accurate Clusterings in Hierarchical Tree Decompositions Using the Variation of
Information. In Proceedings of RECOMB 2009, Lectures Notes in
Computer Science 5541, pages 400-417. [Preprint]
- G. Lapizco-Encinas, C. Kingsford, and J. Reggia. A Cooperative Combinatorial
Particle Swarm Optimization for Side-chain Packing. Proceedings of IEEE
Swarm Intelligence Symposium 2009, pages 22-29. [Preprint]
- S. Navlakha, M. Schatz, and C. Kingsford. Revealing Biological Modules via
Graph Summarization. Presented at RECOMB-SB/RG/DREAM3 satellite conference,
2008. Journal version J. Comp. Biol. 16(2):253-264, 2009. [Preprint]
[Video of
RECOMB-SB Talk]
- C. Kingsford and S. L. Salzberg. What are
decision trees? Nature Biotechnology 26:1011-1013
(2008).
- N. Nagarajan and C. Kingsford. Uncovering
Genomic Reassortments Among Influenza Strains by Enumerating Maximal
Bicliques. In Proceedings of IEEE International Conference on
Bioinformatics and Biomedicine, pages 223-230, 2008. [Preprint]
- 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, 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]
Students
Current:
- Guillaume Marçais (co-advised with Jim Yorke)
- Saket Navlakha
Former Students:
- Grecia Lapizco-Encinas (co-advised with Jim Reggia; now a postdoc in Dept. of Computer Science at the Universidad Carlos III de Madrid)
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