Curriculum vita

• Address
• Education
• Professional experience
• Honors and awards
• Research interests
• Teaching interests
• Journal papers
• Conference papers
• Technical reports
• Dissertation
• Book reviews
• Software
• Grants
• Professional activities
• Students
• Invited presentations
• References

Here's a version in PDF.

Address

John Kececioglu
Department of Computer Science
The University of Arizona
Box 210077
Tucson, Arizona 85721-0077

(520)  621  4526  (voice)
(520)  621  4246  (fax)
kece@cs.arizona.edu   (email)
www.cs.arizona.edu/~kece   (Web)

Education

• Ph.D. in Computer Science, University of Arizona, December 1991. Gene Myers, thesis advisor.
• M.S. in Computer Science, University of Arizona, December 1986.
• B.S. in Mechanical Engineering, University of Arizona, May 1985.

Professional experience

• Associate Professor, University of Arizona, BIO5 Institute, August 2005 to present.
• Associate Professor, University of Arizona, Department of Computer Science, August 2000 to present.
• Associate Professor, University of Georgia, Department of Computer Science, August 1999 to July 2000.
• Assistant Professor, University of Georgia, Department of Computer Science, January 1995 to July 1999.
• Visiting Fellow, Max-Planck-Institut für Informatik, Saarbrücken, Germany, June-July 1996, June-July 1997.
• Visiting Fellow, DIMACS Center for Discrete Mathematics and Theoretical Computer Science, Rutgers University, October-December 1994.
• Postdoctoral Fellow, University of California at Davis, Department of Computer Science, January 1992 to September 1994. Dan Gusfield, postdoctoral advisor.
• Postdoctoral Fellow, Université de Montréal, Centre de Recherches Mathématiques, Montréal, Canada, January-December 1991. David Sankoff, postdoctoral advisor.

Honors and awards

• National Science Foundation CAREER Award, 1997-2001.
• Lilly Teaching Fellow, University of Georgia, 1997-98.
• Department of Energy Human Genome Distinguished Postdoctoral Fellowship, 1993-94.
• National Science Foundation Postdoctoral Fellowship, Program in Mathematics and Molecular Biology, 1992-93.
• Centre de Recherches Mathématiques Postdoctoral Fellowship, Université de Montréal, 1991.

Research interests

• Computational biology, design and analysis of algorithms, algorithm implementation, combinatorial optimization.

Teaching interests

• Design and analysis of algorithms, data structures, theory of computation, algorithms for computational biology, bioinformatics.

Journal papers

• Kim, E. and J. Kececioglu. "Learning scoring schemes for sequence alignment from partial examples." IEEE/ACM Transactions on Computational Biology and Bioinformatics, to appear 2008.
• Wheeler, T.J. and J.D Kececioglu. "Multiple alignment by aligning alignments." Bioinformatics 23, Proceedings of the 15th ISCB Conference on Intelligent Systems for Molecular Biology (ISMB), i559-i568, 2007.

• Kececioglu, J., H.-P. Lenhof, K. Mehlhorn, P. Mutzel, K. Reinert and M. Vingron. "A polyhedral approach to sequence alignment problems." Discrete Applied Mathematics 104, 143-186, 2000.
• Kececioglu, J. and D. Gusfield. "Reconstructing a history of recombinations from a set of sequences." Discrete Applied Mathematics 88, 239-260, 1998.
• Ravi, R. and J. Kececioglu. "Approximation algorithms for multiple sequence alignment under a fixed evolutionary tree." Discrete Applied Mathematics 88, 355-366, 1998.
• Taylor, E.W., A. Bhat, R.G. Nadimpalli, W. Zhang and J. Kececioglu. "HIV-1 encodes a sequence overlapping env gp41 with highly significant similarity to selenium-dependent glutathione peroxidases." Journal of Acquired Immune Deficiency Syndromes and Human Retrovirology 15:5, 393-394, 1997.
• Christof, T., M. Jünger, J. Kececioglu, P. Mutzel and G. Reinelt. "A branch-and-cut approach to physical mapping of chromosomes by unique end-probes." Journal of Computational Biology 4:4, 433-447, 1997.
• Kececioglu, J., M. Li and J. Tromp. "Inferring a DNA sequence from erroneous copies." Theoretical Computer Science 185:1, 3-13, 1997.
• Sankoff, D., G. Sundaram and J. Kececioglu. "Steiner points in the space of genome rearrangements." International Journal of Foundations of Computer Science  7:1, 1-9, 1996.
• Gupta, S., J. Kececioglu and A. Schäffer. "Improving the practical space and time efficiency of the shortest-paths approach to sum-of-pairs multiple sequence alignment." Journal of Computational Biology 2:3, 459-472, 1995.
• Kececioglu, J. and E. Myers. "Combinatorial algorithms for DNA sequence assembly." Algorithmica 13:1/2, 7-51, 1995.
• Kececioglu, J. and D. Sankoff. "Exact and approximation algorithms for sorting by reversals, with application to genome rearrangement." Algorithmica 13:1/2, 180-210, 1995.
• Lipman, D., S. Altschul and J. Kececioglu. "A tool for multiple sequence alignment." Proceedings of the National Academy of Sciences USA 86, 4412-4415, 1989.

Conference papers

• Kim, E. and J. Kececioglu. "Inverse sequence alignment from partial examples." Proceedings of the 7th EATCS/ISCB Workshop on Algorithms in Bioinformatics (WABI), Springer-Verlag Lecture Notes in Bioinformatics 4645, 359-370, 2007.

• Kececioglu, J. and E. Kim. "Simple and fast inverse alignment." Proceedings of the 10th Conference on Research in Computational Molecular Biology (RECOMB), Springer-Verlag Lecture Notes in Bioinformatics 3909, 441-455, 2006.

• Collberg, C., E. Carter, S. Debray, A. Huntwork, J. Kececioglu, C. Linn and M. Stepp. "Dynamic path-based software watermarking." Proceedings of the 25th ACM Conference on Programmming Language Design and Implementation (PLDI), 107-118, 2004.
• Kececioglu, J. and D. Starrett. "Aligning alignments exactly." Proceedings of the 8th ACM Conference on Research in Computational Molecular Biology (RECOMB), 85-96, 2004.
• Kececioglu, J. and J. Yu. "Separating repeats in DNA sequence assembly." Proceedings of the 5th ACM Conference on Research in Computational Molecular Biology (RECOMB), 176-183, 2001.
• Kececioglu, J., S. Shete and J. Arnold. "Reconstructing distances in physical maps of chromosomes with nonoverlapping probes." Proceedings of the 4th ACM Conference on Research in Computational Molecular Biology (RECOMB), 183-192, 2000.
• Christof, T. and J. Kececioglu. "Computing physical maps of chromosomes with nonoverlapping probes by branch-and-cut." Proceedings of the 3rd ACM Conference on Research in Computational Molecular Biology (RECOMB), 115-123, 1999.
• Kececioglu, J. and J. Pecqueur. "Computing maximum-cardinality matchings in sparse general graphs." Proceedings of the 2nd Workshop on Algorithm Engineering (WAE), 121-132, 1998. http://www.mpi-sb.mpg.de/~wae98/PROCEEDINGS
  
• Kececioglu, J. and W. Zhang. "Aligning alignments." Proceedings of the 9th Symposium on Combinatorial Pattern Matching (CPM), Springer-Verlag Lecture Notes in Computer Science 1448, 189-208, 1998.
• Reinert, K., H.-P. Lenhof, P. Mutzel, K. Mehlhorn and J. Kececioglu. "A branch-and-cut algorithm for multiple sequence alignment." Proceedings of the 1st ACM Conference on Research in Computational Molecular Biology (RECOMB), 241-249, 1997.

• Christof, T., M. Jünger, J. Kececioglu, P. Mutzel and G. Reinelt. "A branch-and-cut approach to physical mapping with end-probes." Proceedings of the 1st ACM Conference on Research in Computational Molecular Biology (RECOMB), 84-92, 1997.

• Ravi, R. and J. Kececioglu. "Approximation algorithms for multiple sequence alignment under a fixed evolutionary tree." Proceedings of the 6th Symposium on Combinatorial Pattern Matching (CPM), Springer-Verlag Lecture Notes in Computer Science 937, 330-339, 1995.

• Gupta, S., J. Kececioglu and A. Schäffer. "Making the shortest-paths approach to sum-of-pairs multiple sequence alignment more space efficient in practice." Proceedings of the 6th Symposium on Combinatorial Pattern Matching (CPM), Springer-Verlag Lecture Notes in Computer Science 937, 128-143, 1995.

• Kececioglu, J. and R. Ravi. "Of mice and men: Algorithms for evolutionary distances between genomes with translocation." Proceedings of the 6th ACM-SIAM Symposium on Discrete Algorithms (SODA), 604-613, 1995.
• Kececioglu, J. and D. Gusfield. "Reconstructing a history of recombinations from a set of sequences." Proceedings of the 5th ACM-SIAM Symposium on Discrete Algorithms (SODA), 471-480, 1994.

• Kececioglu, J. and D. Sankoff. "Efficient bounds for oriented chromosome-inversion distance." Proceedings of the 5th Symposium on Combinatorial Pattern Matching (CPM), Springer-Verlag Lecture Notes in Computer Science 807, 307-325, 1994.
• Kececioglu, J. and D. Sankoff. "Exact and approximation algorithms for the inversion distance between two chromosomes." Proceedings of the 4th Symposium on Combinatorial Pattern Matching (CPM), Springer-Verlag Lecture Notes in Computer Science 684, 87-105, 1993.

• Kececioglu, J. "The maximum trace problem in multiple sequence alignment." Proceedings of the 4th Symposium on Combinatorial Pattern Matching (CPM), Springer-Verlag Lecture Notes in Computer Science 684, 106-119, 1993.

Technical reports

• Zhang, W., J. Kececioglu and E.W. Taylor. "Assessing distant homology between an aligned family and a proposed member through accurate sequence alignment." Technical Report 97-3, Department of Computer Science, The University of Georgia, August 1997.

Dissertation

• Kececioglu, J. Exact and Approximation Algorithms for DNA Sequence Reconstruction. Technical Report 91-26, Department of Computer Science, The University of Arizona, December 1991.

Book reviews

• Review of Sequence Analysis Primer, Michael Gribskov and John Devereux, editors, Stockton Press, New York, 1991. In Journal of Classification 10, 144-148, 1993.

Software

• Wheeler, T. and J. Kececioglu. Opal: forming and polishing multiple sequence alignments by optimally aligning alignments. Version 0.3.7, 2007.

• Kim, E. and J. Kececioglu. Ipa: inverse parametric sequence alignment via linear programming. Version 1.0, 2007.

• D. Starrett, T. Wheeler and J. Kececioglu. AlignAlign: optimal alignment of alignments. Version 0.9.7, 2005.

• J. Kececioglu, A. Schäffer, S. Gupta, S. Altschul and D. Lipman. MSA: sum-of-pairs multiple sequence alignment. Version 2.0, 1995.

Grants

• US Department of Education, Graduate Assistance in Areas of National Need (GAANN) Program, "Graduate Assistance in Computer Science: An Area of National Need," J. Kececioglu (PI), A. Efrat, R. Gupta and S. Westbrook (co-PIs), Grant P200A070545, August 2007-July 2010, $383,643.

• US National Science Foundation, Integrative Graduate Education and Research Traineeship (IGERT) Program, "IGERT Program in Comparative Genomics," M. Nachman (PI), D. Vercelli, J. Kececioglu, N. Moran and V. Chandler (co-PIs), Grant&nvsp;0654435, July 2007-June 2012, $2,999,835.

• US National Science Foundation, Biological Databases and Informatics Program, "Robust Tools for Biological Sequence Analysis," J. Kececioglu (PI), Grant DBI-0317498, August 2003-July 2008, $500,498.
• US National Science Foundation, Plant Genome Research Program, "Cross-Linked Sorghum and Rice Physical Maps as a Foundation for Analyzing Genome Structure, Function and Variation in C₄ Grasses," A. Paterson (PI), L. Pratt, M.-M. Cordonnier-Pratt, S. Bhandarkar, and J. Kececioglu (co-PIs), Grant DBI-9872649, September 1998-August 2001, $3,246,755.
• US National Science Foundation, CAREER Award, Computational Biology Activities Program, "Applied Algorithms for Computational Molecular Biology," J. Kececioglu (PI), Grant DBI-0196202, September 1997-August 2002, $241,111.
• US National Science Foundation, Program in Mathematics and Molecular Biology, Travel support for minisymposium "Discrete Algorithms in Computational Biology II" at the SIAM Conference on Discrete Mathematics, June 1996, $5,000.
• US National Science Foundation, Program in Mathematics and Molecular Biology, Travel support for minisymposium "Discrete Algorithms in Computational Biology I" at the SIAM Annual Meeting, October 1995, $4,000.

Selected professional activities

• Editorial Board, Algorithms for Molecular Biology, 2005 to present.
• Scientific Advisory Board, Max-Planck-Institut für Informatik, Saarbrücken, Germany, 2003-06.
• Conference Chair, RECOMB 2009 (13th Conference on Research in Computational Molecular Biology), Tucson, Arizona.
• Program Committees of RECOMB 2008, 2002, 1999 (Conference on Research in Computational Molecular Biology); ISMB 2008 (Conference on Intelligent Systems for Molecular Biology); WABI 2008, 2001 (Workshop on Algorithms in Bioinformatics); ISBRA 2008, 2007 (International Symposium on Bioinformatics Research and Applications); APBC 2006 (Asia-Pacific Bioinformatics Conference); CPM 2000 (Symposium on Combinatorial Pattern Matching); ALENEX 2000 (Workshop on Algorithm Engineering and Experimentation); SPIRE 2001, 2000 (Symposium on String Processing and Information Retrieval).
• NSF Review Panelist, Biological Databases and Informatics Panel, 2005; Theory of Computing Panel, 2005; Medium ITR Bioinformatics Panel, 2004; Small ITR Bioinformatics Panel, 2003; Computational Biology Activities Panel, 1996.
• NIH Review Panelist, Software Development and Maintenance Panel, 2006.
• Organizing Committee, 4th DIMACS Algorithm Implementation Challenge on Sequence Assembly and Genome Rearrangements, Center for Discrete Mathematics and Theoretical Computer Science, Piscataway, New Jersey, 1995.
• Referee for the Journal of the ACM, SIAM Journal on Computing, Algorithmica, Journal of Algorithms, Discrete Applied Mathematics, Information Processing Letters, Journal of Computational Biology, and Genomics.

Students

Postdoctoral

• Thomas Christof.  Branch-and-Cut Algorithms for Physical Mapping of Chromosomes.  Department of Computer Science, University of Georgia, 1998.

PhD

• Eagu Kim.  Inverse Parametric Alignment for Accurate Biological Sequence Comparison.  PhD dissertation, Department of Computer Science, The University of Arizona, August 2008.
• Dean Starrett.  Optimal Alignment of Multiple Sequence Alignments.  PhD dissertation, Department of Computer Science, The University of Arizona, August 2008.

MS

• Jonathan Myers.  Inferring Fragment Overlaps in DNA Sequence Assembly.  MS thesis, Department of Computer Science, University of Georgia, 2001.
• Jun Yu.  Separating Repeats in DNA Sequence Assembly.  MS thesis, Department of Computer Science, University of Georgia, 2000.
• Justin Pecqueur.  An Experimental Study of Edmonds' Algorithm for Maximum-Cardinality Matching in Sparse General Graphs.  MS thesis, Department of Computer Science, University of Georgia, 1998.
• Yuhua Liu.  An Implementation of the Suffix-Tree Data Structure and its Application to String Matching.  MS thesis, Department of Computer Science, University of Georgia, 1997.

Selected invited presentations

• "How to find optimal alignment parameters." Department of Microbiology, Montana State University, Bozeman, November 4, 2005.
• "Multiple sequence alignment: complexity, approximation, and exact solution." CRM Summer School on the Mathematics of Bioinformatics, Centre de Recherches Mathématiques, Université de Montréal, Canada, August 29, 2003.
• "Computing maps of chromosomes that are provably good." Minisymposium on Computational Challenges in Computational Biology, University of Tennessee, Knoxville, August 17, 2001.
• "Separating repeats in DNA sequence assembly." RECOMB Satellite Meeting on DNA Sequence Assembly, University of Southern California, Los Angeles, May 20, 2001.
• "Computing optimal maps of chromosomes by branch-and-cut." Minisymposium on Computational Genetics, Case Western Reserve University, Cleveland, Ohio, October 20, 2000.
• "Physical mapping of chromosomes with nonoverlapping probes" (2 hour tutorial). PIMS Workshop on Mathematical Genomics, Pacific Institute for the Mathematical Sciences, University of British Columbia, Vancouver, Canada, June 2, 1999.
• "A survey of multiple sequence alignment" (3 hour tutorial). CISM Summer School on Computational Biology, International Center for Mechanical Sciences, Udine, Italy, June 12, 1998.
• "Discrete algorithms on sequences" (1 hour tutorial). Mathematics and Molecular Biology V: Statistics and Inference in Molecular Biology, Santa Fe, New Mexico, January 14, 1997.
• "Computing optimal multiple sequence alignments." 2nd Sandia Workshop on Computational Molecular Biology, DIMACS Special Year on Mathematical Support for Molecular Biology, Albuquerque, New Mexico, March 6, 1996.
• "A tour of multiple sequence alignment theory" (3 hour tutorial). Computational Genomics '95, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, November 2, 1995.
• "Algorithms for evolutionary distances between genomes with translocations." Dagstuhl Seminar on Molecular Bioinformatics, Schloss Dagstuhl, Wadern, Germany, July 10, 1995.
• "Combinatorial algorithms for DNA sequencing and mapping" (4 hour tutorial). 6th Symposium on Combinatorial Pattern Matching, Helsinki, Finland, July 4, 1995.
• "A tour of multiple sequence alignment theory." DIMACS Workshop on Sequence Alignment, Center for Discrete Mathematics and Theoretical Computer Science, Rutgers University, Piscataway, New Jersey, November 11, 1994.
• "DNA sequencing in the presence of errors." IMA Summer Program on Molecular Biology, Institute for Mathematics and its Applications, University of Minnesota, Minneapolis, July 6, 1994.
• "Efficient bounds for oriented chromosome-inversion distance." Minisymposium on Combinatorial Methods for Genome Rearrangements, University of Southern California, Los Angeles, March 18, 1994.

References

• Gene Myers, Professor, Department of Computer Science, The University of Arizona, Tucson, AZ 85721. Tel: (520) 621-6612. Fax: (520) 621-4246. Email: gene@cs.arizona.edu
• David Sankoff, Fellow of the Canadian Institute for Advanced Research; Centre de Recherches Mathématiques; Université de Montréal; C.P. 6128, succ. A; Montréal, Québec H3C 3J7; Canada. Tel: (514) 343-7574. Fax: (514) 343-2254. Email: sankoff@ere.umontreal.ca
• Dan Gusfield, Professor, Department of Computer Science, University of California, Davis, CA 95616. Tel: (916) 752-7131. Fax: (916) 752-4767. Email: gusfield@cs.ucdavis.edu
• Richard Karp, Professor, Department of Computer Science and Engineering, University of Washington, Seattle, WA 98195-2350. Tel: (206) 543-4226. Email: karp@cs.washington.edu