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
Parameter advising
The following publications on parameter advising also fall within
the subject area of multiple sequence alignment.

Parameter
Advising for Multiple Sequence Alignment.
Dan DeBlasio and John Kececioglu.
Springer, New York, Computational Biology Series Volume 26,
xiv+152 pages, 2017.

"Learning parameteradvising
sets for multiple sequence alignment,"
Dan DeBlasio and John Kececioglu,
IEEE/ACM Transactions on Computational Biology and
Bioinformatics 14:5, 10281041, 2017.
An earlier version appeared as
D. DeBlasio and J. Kececioglu,
"Learning parameter sets for alignment advising,"
Proceedings of the 5th ACM Conference on Bioinformatics,
Computational Biology, and Health Informatics (ACMBCB),
230239, 2014.
The conference talk presenting this paper is available
here.

"Core column prediction for
protein multiple sequence alignments,"
Dan DeBlasio and John Kececioglu,
Algorithms for Molecular Biology 12:11, 16 pages, 2017.
An earlier version appeared as
D. DeBlasio and J. Kececioglu,
"Predicting core columns of protein multiple sequence alignments for
improved parameter advising,"
Proceedings of the 16th EATCS/ISCB Workshop on Algorithms in
Bioinformatics (WABI),
Springer Lecture Notes in Bioinformatics 9838, 7789, 2016.

"Accuracy estimation
and parameter advising for protein multiple sequence alignment,"
John Kececioglu and Dan DeBlasio,
Journal of Computational Biology 20:4, 259279, 2013.
An earlier version appeared as
D. DeBlasio, T. Wheeler and J. Kececioglu,
"Estimating the accuracy of multiple alignments and its use in parameter
advising,"
Proceedings of the 16th Conference on Research in Computational Molecular
Biology (RECOMB), Springer Lecture Notes in
Bioinformatics 7262, 4559, 2012.
The conference talk presenting this paper is available
here.
Software implementing the algorithm in this paper is available at
facet.cs.arizona.edu.
Multiple sequence alignment

"Boosting alignment accuracy
by adaptive local realignment,"
Dan DeBlasio and John Kececioglu,
Proceedings of the 21st Conference on Research in Computational
Molecular Biology (RECOMB),
Springer Lecture Notes in Bioinformatics 10229, 117, 2017.

"Ensemble multiple sequence
alignment via advising,"
Dan DeBlasio and John Kececioglu,
Proceedings of the 6th ACM
Conference on Bioinformatics, Computational Biology, and Health
Informatics (ACMBCB), 452461, 2015.

"Aligning protein sequences
with predicted secondary structure,"
John Kececioglu, Eagu Kim and Travis Wheeler,
Journal of Computational Biology 17:3, 561580, 2010.
This paper was selected for Faculty of 1000 Biology,
factor 3.0,
http://f1000biology.com/article/id/3324957.

"Multiple alignment by
aligning alignments,"
Travis Wheeler and John Kececioglu,
Proceedings of the 15th ISCB
Conference on Intelligent Systems for Molecular Biology (ISMB),
Bioinformatics 23,
i559i568, 2007.
The conference talk presenting this paper is available
here.
Software implementing the algorithm in this paper is available at
opal.cs.arizona.edu.

"Aligning alignments
exactly,"
John Kececioglu and Dean Starrett,
Proceedings of the 8th ACM
Conference on Research in Computational Molecular Biology (RECOMB),
8596, 2004.
Software implementing the algorithm in this paper is available at
alignalign.cs.arizona.edu.

"A polyhedral
approach to sequence alignment problems,"
John Kececioglu, HansPeter Lenhof,
Kurt Mehlhorn, Petra Mutzel, Knut Reinert and Martin Vingron,
Discrete Applied Mathematics 104, 143186, 2000.
An earlier version appeared as
K. Reinert, H.P. Lenhof,
P. Mutzel, K. Mehlhorn and J. Kececioglu,
"A branchandcut algorithm for multiple sequence alignment,"
Proceedings of the 1st ACM
Conference on Research in Computational Molecular Biology (RECOMB),
241249,
1997.

"Aligning alignments,"
John Kececioglu and Weiqing Zhang,
Proceedings of the 9th Symposium on Combinatorial Pattern
Matching (CPM),
Springer Lecture Notes in Computer Science 1448, 189208, 1998.

"Approximation algorithms for
multiple sequence
alignment under a fixed evolutionary tree,"
R. Ravi and John Kececioglu,
Discrete Applied Mathematics 88, 355366, 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 (CPM),
Springer Lecture Notes in Computer Science 937, 330339,
1995.

"Improving the practical space and time
efficiency of the shortestpaths approach to sumofpairs multiple sequence
alignment,"
Sandeep Gupta, John Kececioglu and Alejandro Schäffer,
Journal of Computational Biology 2:3, 459472, 1995.
An earlier version appeared as
S. Gupta, J. Kececioglu and A. Schäffer,
"Making the shortestpaths approach to sumofpairs multiple sequence
alignment more space efficient in practice,"
Proceedings of the 6th Symposium on Combinatorial Pattern
Matching (CPM),
Springer Lecture Notes in Computer Science 937, 12843, 1995.

"The maximum weight trace problem in multiple
sequence alignment,"
John Kececioglu,
Proceedings of the 4th Symposium on Combinatorial Pattern
Matching (CPM),
Springer Lecture Notes in Computer Science 684, 106119, 1993.

"A tool for multiple sequence
alignment,"
David Lipman, Stephen Altschul and John Kececioglu,
Proceedings of the National Academy
of Sciences USA 86, 44124415, 1989.
Inverse parametric alignment

"Learning models for
aligning protein sequences with predicted secondary structure,"
Eagu Kim, Travis Wheeler and John Kececioglu,
Proceedings of the 13th Conference on Research in Computational Molecular
Biology (RECOMB),
Springer Lecture Notes in Bioinformatics 5541, 512531, 2009.

"Learning scoring schemes
for sequence alignment from partial examples,"
Eagu Kim and John Kececioglu,
IEEE/ACM
Transactions on Computational Biology and Bioinformatics 5:4,
546556, 2008.

"Inverse sequence alignment
from partial examples,"
Eagu Kim and John Kececioglu,
Proceedings of the 7th EATCS/ISCB
Workshop on Algorithms in Bioinformatics (WABI),
Springer Lecture Notes in Bioinformatics 4645,
359370, 2007.
Software implementing the algorithm in this paper is available at
inversealign.cs.arizona.edu.

"Simple and fast inverse
alignment,"
John Kececioglu and Eagu Kim,
Proceedings of the 10th
Conference on Research in Computational Molecular Biology (RECOMB),
441455, 2006.
Sequence assembly

"Separating repeats in
DNA sequence assembly,"
John Kececioglu and Jun Yu,
Proceedings of the 5th ACM
Conference on Research in Computational Molecular Biology (RECOMB),
176183, 2001.

"Inferring a DNA sequence from erroneous
copies,"
John Kececioglu, Ming Li and John Tromp,
Theoretical Computer Science 185:1, 313, 1997.

"Combinatorial algorithms
for DNA sequence assembly,"
John Kececioglu and Eugene Myers,
Algorithmica 13:1/2, 751, 1995.

Exact and Approximation Algorithms for DNA
Sequence Reconstruction,
John Kececioglu,
PhD dissertation,
Technical Report 9126, Department of Computer Science,
University of Arizona, December 1991.
Physical mapping

"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 (RECOMB),
183192, 2000.

"Computing physical maps
of chromosomes with
nonoverlapping probes by branchandcut,"
Thomas Christof and John Kececioglu,
Proceedings of the 3rd ACM
Conference on Research in Computational Molecular Biology (RECOMB),
115123, 1999.

"A branchandcut
approach to physical
mapping of chromosomes by unique endprobes,"
Thomas Christof, Michael Jünger,
John Kececioglu, Petra Mutzel and Gerhard Reinelt,
Journal of Computational Biology 4:4, 433447, 1997.
An earlier version appeared as
T. Christof,
M. Jünger,
J. Kececioglu,
P. Mutzel,
and
G. Reinelt,
"A branchandcut approach to physical mapping with endprobes,"
Proceedings of the 1st ACM
Conference on Research in Computational Molecular Biology (RECOMB),
8492, 1997.
Genome rearrangements

"Steiner points in the space of genome
rearrangements,"
David Sankoff, Gopal Sundaram and John Kececioglu,
International Journal of Foundations of Computer Science 7:1,
19, 1996.

"Exact and approximation
algorithms for sorting by reversals, with application to genome
rearrangement,"
John Kececioglu and David Sankoff,
Algorithmica 13:1/2,
180210, 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 (CPM),
Springer Lecture Notes in Computer Science 684, 87105, 1993.

"Of mice and men: Algorithms
for evolutionary distances between genomes with translocation,"
John Kececioglu and R. Ravi,
Proceedings of the 6th ACMSIAM Symposium on Discrete
Algorithms (SODA),
604613, 1995.

"Efficient bounds for oriented
chromosomeinversion distance,"
John Kececioglu and David Sankoff,
Proceedings of the 5th Symposium on Combinatorial
Pattern Matching (CPM), Springer Lecture Notes in Computer
Science 807, 307325, 1994.
Recombination networks

"Reconstructing a history of
recombinations from a set of sequences,"
John Kececioglu and Dan Gusfield,
Discrete Applied Mathematics 88, 239260, 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 ACMSIAM
Symposium on Discrete Algorithms (SODA), 471480, 1994.
Synthetic biology

"Automatic design of
synthetic gene circuits
through mixed integer nonlinear programming,"
Linh Huynh, John Kececioglu, Matthias Köppe and
Ilias Tagkopoulos,
Public Library of Science One (PLoS One) 7:4, e35529, 2012.

"Automated design of
synthetic gene circuits
through linear approximation and mixed integer optimization,"
Linh Huynh, John Kececioglu and Ilias Tagkopoulos,
Proceedings of the 3rd
International Workshop on BioDesign Automation (IWBDA),
4849, 2011.
Molecular biology

"HIV1 encodes a
sequence overlapping env gp41 with highly significant similarity
to seleniumdependent 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, 393394, 1997.

"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 973, Department of Computer Science,
University of Georgia, August 1997.
Computational astronomy

"ANTARES:
progress towards building a broker of timedomain alerts,"
Abhijit Saha, Zhe Wang, Thomas Matheson, Gautham Narayan, Richard Snodgrass,
John Kececioglu, Carlos Scheidegger, Tim Axelrod, Tim Jenness, Stephen Ridgway,
Robert Seaman, Clark Taylor, Jackson Toeniskoetter, Eric Welch, Shuo Yang
and Tayeb Zaidi,
Proceedings of SPIE 9910 (Observatory Operations: Strategies,
Processes, and Systems VI), 8 pages, 2016.

"ANTARES:
a prototype transient broker system,"
Abhijit Saha, Thomas Matheson, Richard Snodgrass, John Kececioglu,
Gautham Narayan, Robert Seaman, Tim Jenness, and Tim Axelrod,
Proceedings of SPIE 9149 (Observatory Operations: Strategies,
Processes, and Systems V), 8 pages, 2014.

"ANTARES:
the ArizonaNOAO temporal analysis and response to events system,"
Thomas Matheson, Abhijit Saha, Richard Snodgrass and John Kececioglu,
Proceedings of the 3rd HotWiring the Transient Universe Workshop,
145150, 2014.
Graph matchings
Software security

"Dynamic pathbased
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 (PLDI),
107118, 2004.

"Enhancing software
tamperresistance via stealthy address computations,"
Cullen Linn, Saumya Debray and John Kececioglu,
Proceedings of the 19th Computer Security Applications
Conference (CSA), 3 pages, 2003.
Software runtime measurement
Reviews

Review of Sequence Analysis Primer,
Michael Gribskov and John Devereux editors,
Stockton Press, New York, 1991;
John Kececioglu,
Journal of Classification 10, 144148, 1993.
Collaborators
Research