Publications
Publications, organized by subject.
Also available are abstracts,
and links to collaborators.
John has an
Erdös number of three,
by the path
Kececioglu, Sankoff, Chvátal, Erdös.
Subjects
Sequence comparison
Multiple alignment
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"Multiple alignment by
aligning alignments,"
Travis Wheeler and John Kececioglu,
Proceedings of the 15th ISCB
Conference on Intelligent Systems for Molecular Biology,
Bioinformatics 23,
i559-i568, 2007.
The conference talk presenting this paper is available
here.
Software implementing the algorithm in this paper is available at
opal.cs.arizona.edu.
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"Aligning alignments
exactly,"
John Kececioglu and Dean Starrett,
Proceedings of the 8th ACM
Conference on Research in Computational Molecular Biology, 85-96, 2004.
Software implementing the algorithm in this paper is available at
alignalign.cs.arizona.edu.
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"A polyhedral
approach to sequence alignment problems,"
John Kececioglu, Hans-Peter Lenhof,
Kurt Mehlhorn, Petra Mutzel, Knut Reinert and Martin Vingron,
Discrete Applied Mathematics 104, 143-186, 2000.
An earlier version appeared as
K. Reinert, 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, 241-249,
1997.
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"Aligning alignments,"
John Kececioglu and Weiqing Zhang,
Proceedings of the 9th Symposium on Combinatorial Pattern Matching,
Springer-Verlag Lecture Notes in Computer Science 1448, 189-208, 1998.
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"Approximation algorithms for
multiple sequence
alignment under a fixed evolutionary tree,"
R. Ravi and John Kececioglu,
Discrete Applied Mathematics 88, 355-366, 1998.
An earlier version appeared as
R. Ravi and J. Kececioglu,
"Approximation algorithms for multiple sequence alignment
under a fixed evolutionary tree,"
Proceedings of the
6th Symposium on Combinatorial Pattern Matching,
Springer-Verlag Lecture Notes in Computer Science 937, 330-339,
1995.
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"Improving the practical space and time
efficiency of the shortest-paths approach to sum-of-pairs multiple sequence
alignment,"
Sandeep Gupta, John Kececioglu and Alejandro Schäffer,
Journal of Computational Biology 2:3, 459-472, 1995.
An earlier version appeared as
S. Gupta, 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,
Springer-Verlag Lecture Notes in Computer Science 937, 128-43, 1995.
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"The maximum weight trace problem in multiple
sequence alignment,"
John Kececioglu,
Proceedings of the 4th Symposium on Combinatorial Pattern Matching,
Springer-Verlag Lecture Notes in Computer Science 684, 106-119, 1993.
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"A tool for multiple sequence
alignment,"
David Lipman, Stephen Altschul and John Kececioglu,
Proceedings of the National Academy
of Science USA 86, 4412-4415, 1989.
Sequence assembly
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"Separating repeats in
DNA sequence assembly,"
John Kececioglu and Jun Yu,
Proceedings of the 5th ACM
Conference on Research in Computational Molecular Biology, 176-183,
2001.
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"Inferring a DNA sequence from erroneous
copies,"
John Kececioglu, Ming Li and John Tromp,
Theoretical Computer Science 185:1, 3-13, 1997.
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"Combinatorial algorithms
for DNA sequence assembly,"
John Kececioglu and Eugene Myers,
Algorithmica 13:1/2, 7-51, 1995.
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Exact and Approximation Algorithms for DNA
Sequence Reconstruction,
John Kececioglu,
PhD dissertation,
Technical Report 91-26, Department of Computer Science,
University of Arizona, December 1991.
Physical mapping
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"Reconstructing distances
in physical maps of chromosomes with nonoverlapping probes,"
John Kececioglu, Sanjay Shete and Jonathan Arnold,
Proceedings of the 4th ACM
Conference on Research in Computational Molecular Biology, 183-192,
2000.
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"Computing physical maps
of chromosomes with
nonoverlapping probes by branch-and-cut,"
Thomas Christof and John Kececioglu,
Proceedings of the 3rd ACM
Conference on Research in Computational Molecular Biology, 115-123,
1999.
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"A branch-and-cut
approach to physical
mapping of chromosomes by unique end-probes,"
Thomas Christof, Michael Jünger,
John Kececioglu, Petra Mutzel and Gerhard Reinelt,
Journal of Computational Biology 4:4, 433-447, 1997.
An earlier version appeared as
T. Christof,
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, 84-92, 1997.
Genome rearrangement
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"Steiner points in the space of genome
rearrangements,"
David Sankoff, Gopal Sundaram and John Kececioglu,
International Journal of Foundations of Computer Science 7:1,
1-9, 1996.
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"Exact and approximation
algorithms for sorting by reversals, with application to genome
rearrangement,"
John Kececioglu and David Sankoff,
Algorithmica 13:1/2,
180-210, 1995.
An earlier version appeared as
J. Kececioglu and D. Sankoff,
"Exact and approximation algorithms for the inversion distance
between two chromosomes,"
Proceedings of the 4th
Symposium on Combinatorial Pattern Matching,
Springer-Verlag Lecture Notes in Computer Science 684, 87-105, 1993.
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"Of mice and men: Algorithms
for evolutionary distances between genomes with translocation,"
John Kececioglu and R. Ravi,
Proceedings of the 6th ACM-SIAM Symposium on Discrete Algorithms,
604-613, 1995.
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"Efficient bounds for oriented
chromosome-inversion distance,"
John Kececioglu and David Sankoff,
Proceedings of the 5th Symposium on Combinatorial
Pattern Matching, Springer-Verlag Lecture Notes in Computer
Science 807, 307-325, 1994.
Recombinations
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"Reconstructing a history of
recombinations from a set of sequences,"
John Kececioglu and Dan Gusfield,
Discrete Applied Mathematics 88, 239-260, 1998.
An earlier version appeared as
J. Kececioglu and D. Gusfield,
"Reconstructing a history of recombinations from a set of sequences,"
Proceedings of the 5th ACM-SIAM
Symposium on Discrete Algorithms, 471-480, 1994.
Biology
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"HIV-1 encodes a
sequence overlapping env gp41 with highly significant similarity
to selenium-dependent glutathione peroxidases,"
Ethan Will Taylor, Ajita Bhat,
Ram Nadimpalli, Weiqing Zhang and John Kececioglu,
Journal of Acquired Immune Deficiency Syndromes and Human
Retrovirology 15:5, 393-394, 1997.
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"Assessing distant homology
between an aligned family and a proposed member through accurate sequence
alignment,"
Weiqing Zhang, John Kececioglu and Ethan Will Taylor,
Technical Report 97-3, Department of Computer Science,
University of Georgia, August 1997.
Matchings
Systems
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"Dynamic path-based
software watermarking,"
Christian Collberg, Edward Carter, Saumya Debray, Andrew Huntwork,
John Kececioglu, Cullen Linn and Martin Stepp,
Proceedings of the 25th ACM
Conference on Programmming Language Design and Implementation,
107-118, 2004.
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"Enhancing software
tamper-resistance via stealthy address computations,"
Cullen Linn, Saumya Debray and John Kececioglu,
Presented as work in progress at the
19th Computer Security Applications Conference, 2003.
Reviews
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Review of Sequence Analysis Primer,
Michael Gribskov and John Devereux editors,
Stockton Press, New York, 1991;
John Kececioglu,
Journal of Classification 10, 144-148, 1993.
Collaborators
Research