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Kingsford, C. School of Computer Science H-Index: 26 I. CURRICULUM VITAE CARLETON KINGSFORD EDUCATION Ph.D. in Computer Science (advisor: Mona Singh) Princeton University 2005 M.A. in Computer Science Princeton University 2002 B.S. in Computer Science (second major: Mathematics) Duke University 2000 EMPLOYMENT 2019 – Present Professor, Computational Biology Department, School of Computer Science, Carnegie Mellon University. (Courtesy appointment Department of Biological Sciences.) 2016 – 2019 Associate Professor (with tenure), Computational Biology Department, School of Computer Science, Carnegie Mellon University. (Courtesy appointment Department of Biological Sciences.) 2012 – 2016 Associate Professor (without tenure), Computational Biology Department (formerly the Lane Center for Computational Biology), School of Computer Science, Carnegie Mellon University. 2007 – 2012 Assistant Professor, Computer Science Department, University of Maryland, College Park (Courtesy appointments in Institute for Advanced Computer Studies, Applied Mathematics & Statistics, Biological Sciences Graduate Program, and Department of Bioengineering) 2005 – 2007 Postdoctoral Fellow, Steven L. Salzberg Group, Center for Bioinformatics and Computational Biology, University of Maryland, College Park II. PUBLICATION LIST H-index: 26 CHAPTERS IN BOOKS 1. P. Spealman, H. Wang, G.E. May, C. Kingsford, and C.J. McManus. Exploring ribosome positioning on translating transcripts with ribosome profiling. Methods in Molecular Biology, Springer (2015). 2. H. Lee and C. Kingsford. Accurate assembly and typing of HLA using a graph-guided assembler Kourami. HLA Typing: Methods and Protocols, Sebastian Boegel, editor. (2018). REFEREED JOURNAL PAPERS – PUBLISHED Kingsford, C. School of Computer Science 1. 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). [Cited ≥ 91 times; Conference version appeared as: The side-chain positioning problem: a semidefinite programming formulation with new rounding schemes. In Proceedings of ACM FCRC 2003, Principles of Computing and Knowledge: Paris Kanellakis Memorial Workshop, pages 86-94 (2003).] 2. C. Kingsford, B. Chazelle, and M. Singh. Solving and analyzing side-chain positioning problems using linear and integer programming. Bioinformatics 21:1028-1039 (2005). [Cited ≥ 184 times.] 3. 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). [Cited ≥ 346 times.] 4. S. L. Salzberg, C. Kingsford, G. Cattoli, D. J. Spiro, D. A. Janies, M. Mehrez Aly, I. H. Brown, E. Couacy-Hymann, G. Mario De Mia, D.H. Dung, A. Guercio, T. Joannis, A. S. Maken Ali, A. Osmani, I. Padalino, M. D. Saad, V. Savic, N. A. Sengamalay, S. Yingst, J. Zaborsky, O. Zorman-Rojs, E. Ghedin, and I. Capua. Genome analysis linking recent European and African influenza (H5N1) viruses. Emerging Infectious Diseases 13(5):713-718 (2007). [Cited ≥ 199 times.] 5. C. Kingsford, A. Delcher, and S. L. Salzberg. A unified model explaining the offsets of overlapping and near-overlapping prokaryotic genes. Molecular Biology and Evolution 24:2091-2098 (2007). 6. C. Kingsford and S. L. Salzberg. What are decision trees? (Review), Nature Biotechnology 26(9):1011-1013 (2008). [Cited ≥ 140 times.] 7. S. Navlakha, M. C. Schatz, and C. Kingsford. Revealing biological modules using graph summarization. Journal of Computational Biology 16(2):253-264 (2009). [Presented at RECOMB-SB/RG satellite conference, 2008; cited ≥ 75 times.] 8. C. Kingsford†, N. Nagarajan†, and S. Salzberg. 2009 Swine-Origin Influenza A (H1N1) resembles previous influenza isolates. PLoS ONE 4(7):e6402 (2009). †First two authors contributed equally; C.K. corresponding author. [Cited ≥ 68 times.] 9. S. Navlakha, J. White, N. Nagarajan, M. Pop, and C. Kingsford. Finding biologically accurate clusterings in hierarchical decompositions using the variation of information. Journal of Computational Biology 17(3):503-516 (2010). [Conference version appeared in Proceedings of 13th Annual International Conference on Research in Computational Molecular Biology (RECOMB), pages 400-418 (2009).] 10. C. Kingsford, M. Schatz, M. Pop. Assembly complexity of prokaryotic genomes using short reads. BMC Bioinformatics 11:21 (2010). [Designated highly accessed; top-10 most-viewed articles Jan/Feb 2010; top-10 cited article in BMC Bioinformatics for 2010; cited ≥ 102 times.] 11. S. Navlakha and C. Kingsford. The power of protein interaction networks for associating diseases with genes. Bioinformatics 26 (8):1057-1063 (2010). [Recommended by the Faculty of 1000 (http://f1000.com/3314959); cited ≥ 255 times.] 12. J. White, S. Navlakha, N. Nagarajan, C. Kingsford, and M. Pop. Alignment and clustering of phylogenetic markers – implications for microbial diversity studies. BMC Kingsford, C. School of Computer Science Bioinformatics 11:152 (2010). [Designated highly accessed by the journal; cited ≥ 73 times.] 13. C. Kingsford, E. Zaslavsky, and M. Singh. A cost-aggregating integer linear program for motif finding. Journal of Discrete Algorithms 9(4):326-334 (2011). [Conference version appeared as: A compact mathematical programming formulation for DNA motif finding. In Proceedings of the 17th Annual Symposium on Combinatorial Pattern Matching, LNCS 4009, pages 233-245 (2006).] 14. N. Nagarajan and C. Kingsford. GiRaF: Robust, computational identification of influenza reassortments via graph mining. Nucleic Acids Research 39(6):e34 (2011). [Cited ≥ 39 times.] 15. G. Marçais and C. Kingsford. A fast, lock-free approach for efficient parallel counting of occurrences of k-mers. Bioinformatics 27(6):764-770 (2011). [Cited ≥ 650 times.] 16. D. R. Kelley and C. Kingsford. Extracting between-pathway models from E-MAP interactions using expected graph compression. Journal of Computational Biology 18(3):379-390 (2011). [Conference version appeared in Proceedings of the 14th Annual International Conference on Research in Computational Molecular Biology (RECOMB), pages 248-262 (2010).] 17. S. Navlakha and C. Kingsford. Network archaeology: Uncovering ancient networks from present-day interactions. PLoS Computational Biology 7(4):e1001119. [Selected for oral presentation at the RECOMB-Systems Biology satellite conference, 2010; cited ≥ 57 times.] 18. J. Wetzel, C. Kingsford, and M. Pop. Assessing the benefits of using mate-pairs to resolve repeats in de novo short-read prokaryotic assemblies. BMC Bioinformatics 12:95, 2011. [Cited ≥ 53 times. Designated “Highly Accessed” by the journal.] 19. R. Patro, E. Sefer, J. Malin, G. Marcais, S. Navlakha, and C. Kingsford. Parsimonious reconstruction of network evolution. Algorithms for Molecular Biology 7:25 (2012). [Conference version appeared in Proceedings of the 11th Workshop on Algorithms in Bioinformatics (WABI), pages 237-249 (2011).] 20. R. Patro and C. Kingsford. Global network alignment using multiscale spectral signatures. Bioinformatics 28(23):3105-3114 (2012). [Cited ≥ 104 times.] 21. G. Duggal and C. Kingsford. Graph rigidity reveals well-constrained regions of chromosome conformation embeddings. BMC Bioinformatics 13:241 (2012). 22. D. Filippova, A. Gadani, C. Kingsford. Coral: an integrated suite of visualizations for comparing clusterings. BMC Bioinformatics 13:276 (2012). [Designated “Highly Accessed” by the journal.] 23. G. Duggal, R. Patro, E. Sefer, H. Wang, D. Filippova, S. Khuller and C. Kingsford. Resolving spatial inconsistencies in chromosome conformation measurements. Algorithms for Molecular Biology 8:8 (2013). [Conference version appeared as: Resolving spatial inconsistencies in chromosome conformation data. In Proceedings of 12th Annual Workshop on Algorithms in Bioinformatics (WABI), pp 288-300, 2012.] 24. G. Duggal, H. Wang, and C. Kingsford. Higher-order chromatin domains link eQTLs with the expression of far-away genes. Nucleic Acids Research 42(1):87-96 (2014). Kingsford, C. School of Computer Science 25. R. Patro, S. M. Mount, and C. Kingsford. Sailfish enables alignment-free isoform quantification from RNA-seq reads using lightweight algorithms. Nature Biotechnology 32:462-464 (2014). [Cited ≥ 270 times.] 26. D. Filippova, R. Patro, G. Duggal, and C. Kingsford. Identification of alternative topological domains in chromatin. Algorithms for Molecular Biology 9:14 (2014). [Cited ≥ 79 times; Designated “Highly Accessed” by the journal. Conference version appeared as: Multiscale identification of topological domains in chromatin. In Proceedings of Workshop on Algorithms in Bioinformatics (WABI), pages 300-312 (2013).] 27. H. Xin, J. Greth, J. Emmons, G. Pekhimenko, C. Kingsford, C. Alkan, and O. Mutlu. Shifted Hamming Distance: A fast and accurate SIMD-friendly filter for local alignment in read mapping. Bioinformatics 31(10):1553-60 (2015). 28. C. Kingsford and R. Patro. Compression of short-read sequences using path encoding. Bioinformatics 31(12):1920-1928 (2015). http://dx.doi.org/10.1093/bioinformatics/btv071 29. R. Patro and C. Kingsford. Data-dependent bucketing improves reference-free compression of sequencing reads. Bioinformatics 31(17):2770-2777 (2015). http://dx.doi.org/10.1093/bioinformatics/btv248 30. Hongyi Xin, Richard Zhu, Sunny Nahar, John Emmons, Gennady Pekhimenko, Carl Kingsford, Can Alkan and Onur Mutlu. Optimal seed solver: Optimizing seed selection in read mapping.
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