College of Chemical and Life Sciences

College of Computer, Mathematical and Physical Sciences

Institute for Advanced Computer Studies

Carl Kingsford Assistant Professor Department of Computer Science, UM Institute for Advanced Computer Studies, and Center for Bioinformatics and Computational Biology Ph.D., Princeton University, 2005 (advisor: Mona Singh) MA, Princeton University, 2002 BS, Duke University, 2000 carlk [at] umiacs.umd.edu Center for Bioinformatics and Computational Biology Biomolecular Sciences Bldg #296 College Park, MD 20742 301-405-7395

Classes

Office Hours: Mondays 1:00-2:30 in AVW 3223.

Fall 2008 - Design & Analysis of Computer Algorithms (CMSC 451)

Spring 2008 - Data Structures (CMSC 420)

Fall 2007 - Graphs and Networks in Computational Biology (CMSC 858L)

Current Interests

• Protein-protein interaction networks.
• Protein function prediction.
• Protein structure prediction (e.g. using mathematical programming to predict protein structure).

• Overlapping genes in Bacteria.
• Transcription termination in bacteria. See the TransTermHP program for predicting Rho-independent terminators.
• Evolution of the influenza genome.

Partial Research Schematic

Selected Publications

• S. Navlakha, M. Schatz, and C. Kingsford. Revealing Biological Modules via Graph Summarization. To appear in RECOMB-SB/RG/DREAM3 satelite coference, 2008. Journal version to appear in J. Comp. Biol. [Preprint]


• 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. To appear in Proceedings of IEEE International Conference on Bioinformatics and Biomedicine, 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, 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]