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: Tuesday 2:30-3:30 in CBCB 3113.

Spring 2009 - Graphs and Networks in Computational Biology (CMSC 858L)

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

Click on the title of the paper to download a PDF version.
* indicates that the authors are alphabetized.

• C. Kingsford, G. Marçais.* A synthesis for exactly 3-edge-connected graphs. In submission. [Preprint]


• C. Kingsford, G. Marçais.* Vertices of degree k in edge-minimal, k-edge-connected graphs. In submission. [Preprint]


• S. Navlakha, J. White, N. Nagarajan, M. Pop, and C. Kingsford. Finding Biologically Accurate Clusterings in Hierarchical Tree Decompositions Using the Variation of Information. To appear in Proceedings of RECOMB 2009. [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. [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, 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]