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 and bioinformatics, 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

• Kececioglu, J., E. Kim and T. Wheeler. "Aligning protein sequences with predicted secondary structure." Journal of Computational Biology 17:3, 561-580, 2010.
  (Selected for Faculty of 1000 Biology, http://f1000biology.com/article/id/3324957)
• Kim, E. and J. Kececioglu. "Learning scoring schemes for sequence alignment from partial examples." IEEE/ACM Transactions on Computational Biology and Bioinformatics 5:4, 546-556, 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., T. Wheeler and J. Kececioglu. "Learning models for aligning protein sequences with predicted secondary structure." Proceedings of the 13th Conference on Research in Computational Molecular Biology (RECOMB), Springer-Verlag Lecture Notes in Bioinformatics 5541, 512-531, 2009.

• 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 National Science Foundation, Information Integration and Informatics Program, "An Exploratory System for Inverse Parametric Optimization," J. Kececioglu (PI), EAGER Grant IIS-1050293, September 2010-August 2011, $59,996.

• 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 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

• Associate Editor, IEEE/ACM Transactions on Computational Biology and Bioinformatics, 2008 to present.
• 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 Committee Co-Chair for Sequence Analysis, ISMB 2011 (19th Conference on Intelligent Systems for Molecular Biology), Vienna, Austria.
• Program Committees of ISMB 2010, 2009, 2008 (Conference on Intelligent Systems for Molecular Biology); RECOMB 2008, 2002, 1999 (Conference on Research in Computational 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 2009, 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

• Travis Wheeler.  Efficient Construction of Accurate Multiple Alignments and Large-Scale Phylogenies.  PhD dissertation, Department of Computer Science, The University of Arizona, August 2009.
  (Co-advised by Michael Sanderson)
  (Postdoctoral Fellow at HHMI Janelia Farm Research Campus with Sean Eddy)
• Eagu Kim.  Inverse Parametric Alignment for Accurate Biological Sequence Comparison.  PhD dissertation, Department of Computer Science, The University of Arizona, August 2008.
  (Postdoctoral Fellow at University of Wisconsin-Madison with Colin Dewey)
• Dean Starrett.  Optimal Alignment of Multiple Sequence Alignments.  PhD dissertation, Department of Computer Science, The University of Arizona, August 2008.
  (Postdoctoral Fellow at University of California at Berkeley with Kimmen Sjölander)

MS

• David Perkins.  Predicting Protein Secondary Structure by Linear and Dynamic Programming.  MS thesis, Department of Computer Science, The University of Arizona, 2009.
• 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.

BS

• Joseph Thomas.  An Adaptive Data Structure for Nearest Neighbor Search in a General Metric Space.  BS honors thesis, Department of Computer Science, The University of Arizona, 2010.

Selected invited presentations

• "Learning models for aligning protein sequences with predicted secondary structure." Department of Mathematics, University of California at Berkeley, September 23, 2009.
• "Learning scoring schemes for sequence alignment from partial examples." INFORMS Annual Meeting, Session on Sequence Analysis in Computational Biology, Washington, DC, October 13, 2008.
• "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