Carl Kingsford

Assistant Professor
3113 Biomolecular Sciences Building
(301) 405-7395
Academic Web Page
Research Group(s): 
Center for Bioinformatics and Computational Biology
Education: 
Ph.D., Princeton University
Special Awards/Honors: 
NSF Career Award
Biography: 

Carl Kingsford is an assistant professor in the Department of Computer Science at the University of Maryland with a joint appointment in the Center for Bioinformatics and Computational Biology (CBCB), part of the University's Institute for Advanced Computer Studies (UMIACS). He received his Ph.D. in Computer Science from Princeton University in 2005 and has been an assistant professor at Maryland since 2007.

His main research interests are the development and application of optimization and graph algorithms to answer biological questions using large collections of biological measurements. He has been exploring key problems within computational systems biology and genomics, such as predicting protein function, reconstructing ancient biological pathways, and improving genome assembly. He has authored or co-authored of over 25 scientific publications, and he and his collaborators have developed several widely-used bioinformatics analysis software packages, including GIRAF (for influenza reassortment detection), JELLYFISH (for fast parallel k-mer counting), and TransTermHP (to identify Rho-independent transcription terminators). In 2011, he won a NSF CAREER award, and he won a CS Department Award for Excellence in Teaching in 2010. In 2008, he was named one of 30 "Tomorrow's PIs" by Genome Technology Magazine.

He has served on the program committees for several major computational biology conferences and served as an area co-chair for the 20th Annual International Conference on Intelligent Systems for Molecular Biology (ISMB) in 2012.

Publications

2011


Kingsford C, Zaslavsky E, Singh M.  2011.  A cost-aggregating integer linear program for motif finding. Journal of Discrete Algorithms. 9(4):326-334.

Kelley DR, Kingsford C.  2011.  Extracting Between-Pathway Models from E-MAP Interactions Using Expected Graph Compression. Journal of Computational Biology. 18(3):379-390.

Wetzel J, Kingsford C, Pop M.  2011.  Assessing the benefits of using mate-pairs to resolve repeats in de novo short-read prokaryotic assemblies. BMC Bioinformatics. 12(1):95-95.

2010


White JR, Navlakha S, Nagarajan N, Ghodsi M-R, Kingsford C, Pop M.  2010.  Alignment and clustering of phylogenetic markers - implications for microbial diversity studies. BMC Bioinformatics. 11(1):152-152.

Kingsford C, Schatz MC, Pop M.  2010.  Assembly complexity of prokaryotic genomes using short reads. BMC Bioinformatics. 11(1):21-21.

Navlakha S, Kingsford C.  2010.  Exploring Biological Network Dynamics with Ensembles of Graph Partitions. Proceedings of the PSB Pacific Symposium on Biocomputing. 15:166-177.

Navlakha S, White J, Nagarajan N, Pop M, Kingsford C.  2010.  Finding Biologically Accurate Clusterings in Hierarchical Tree Decompositions Using the Variation of Information. Journal of Computational Biology. 17(3):503-516.

Navlakha S, Kingsford C.  2010.  The power of protein interaction networks for associating genes with diseases. Bioinformatics. 26(8):1057-1057.

2009


Lapizco-Encinas G, Kingsford C, Reggia JA.  2009.  A cooperative combinatorial Particle Swarm Optimization algorithm for side-chain packing. IEEE Swarm Intelligence Symposium, 2009. SIS '09. :22-29.

Navlakha S, Schatz MC, Kingsford C.  2009.  Revealing biological modules via graph summarization. Journal of Computational Biology. 16(2):253-264.

Kingsford C, Marçais G.  2009.  A synthesis for exactly 3-edge-connected graphs. Arxiv preprint arXiv:0905.1053.

Navlakha S, White JR, Nagarajan N, Pop M, Kingsford C.  2009.  Finding Biologically Accurate Clusterings in Hierarchical Decompositions Using the Variation of Information. Lecture Notes in Computer Science: Research in Computational Molecular Biology. 5541:400-417.

Kingsford C, Nagarajan N, Salzberg SL.  2009.  2009 Swine-Origin Influenza A (H1N1) Resembles Previous Influenza Isolates. PLoS ONEPLoS ONE. 4(7):e6402-e6402.

2008


Nagarajan N, Kingsford C.  2008.  Uncovering Genomic Reassortments among Influenza Strains by Enumerating Maximal Bicliques. IEEE International Conference on Bioinformatics and Biomedicine, 2008. BIBM '08. :223-230.

Kingsford C, Salzberg SL.  2008.  What are decision trees? Nature biotechnology. 26(9):1011-1011.

2007


Salzberg SL, Kingsford C, Cattoli G, Spiro DJ, Janies DA, Aly M M, Brown IH, Couacy-Hymann E, De Mia G M, Dung D H et al..  2007.  Genome Analysis Linking Recent European and African Influenza (H5N1) Viruses. Emerging Infectious DiseasesEmerg Infect Dis. 13(5):713-718.

Kingsford C, Delcher AL, Salzberg SL.  2007.  A unified model explaining the offsets of overlapping and near-overlapping prokaryotic genes. Molecular biology and evolution. 24(9):2091-2091.

2006


Kingsford C, Zaslavsky E, Singh M.  2006.  A compact mathematical programming formulation for DNA motif finding. Combinatorial Pattern Matching. :233-245.

2004


Chazelle B, Kingsford C, Singh M.  2004.  A semidefinite programming approach to side chain positioning with new rounding strategies. INFORMS Journal on Computing. 16(4):380-392.

2002


Reif JH, LaBean TH, Pirrung M, Rana VS, Guo B, Kingsford C, Wickham GS.  2002.  Experimental Construction of Very Large Scale DNA Databases with Associative Search. DNA computing: 7th International Workshop on DNA-Based Computers, DNA 7, Tampa, FL, USA, June 10-13, 2001: revised papers. 7:231-231.