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Estimating the accuracy of multiple alignments and its use in parameter advising
Dan F. DeBlasio
,
Travis J. Wheeler
,
John D. Kececioglu
Lecture Notes in Computer Science
7262
, 2012, pp. 45-59
Learning models for aligning protein sequences with predicted secondary structure
Eagu Kim
,
Travis Wheeler
,
John Kececioglu
LNCS/LNBI
5541
, 2009, pp. 512-531
Multiple alignment by aligning alignments
Travis J. Wheeler
,
John D. Kececioglu
Bioinformatics
23
(13), 2007, pp. 559-568
Simple and fast inverse alignment
John Kececioglu
,
Eagu Kim
LNCS/LNBI
3909
, 2006, pp. 441-455
Aligning alignments exactly
John Kececioglu
,
Dean Starrett
Proceedings of the 8th Annual International Conference on Research in Computational Molecular Biology, RECOMB'2004 (San Diego, CA, USA, March 27-31, 2004)
, 2004, pp. 85-96
A polyhedral approach to sequence alignment problems
John D. Kececioglu
,
Hans-Peter Lenhof
,
Kurt Mehlhorn
,
Petra Mutzel
,
Knut Reinert
,
Martin Vingron
Discrete Applied Mathematics
104
(1-3), 2000, pp. 143-186
Reconstructing distances in physical maps of chromosomes with nonoverlapping probes
John Kececioglu
,
Sanjay Shete
,
Jonathan Arnold
Proceedings of the 4th Annual International Conference on Computational Molecular Biology, RECOMB'2000 (Tokyo, Japan, April 8-11, 2000)
, 2000, pp. 183-192
Computing physical maps of chromosomes with nonoverlapping probes by branch-and-cut
Thomas Christof
,
John Kececioglu
Proceedings of the 3rd Annual International Conference on Computational Molecular Biology, RECOMB'99 (Lyon, France, April 11-14, 1999)
, 1999, pp. 115-123
Reconstructing a history of recombinations from a set of sequences
John Kececioglu
,
Dan Gusfield
Discrete Applied Mathematics
88
(1-3), 1998, pp. 239-260
Computing maximum-cardinality matchings in sparse general graphs
John D. Kececioglu
,
A. Justin Pecqueur
Proceedings of the 2nd Workshop on Algorithm Engineering, WAE'98 (Saarbrücken, Germany, August 20-22, 1998)
(MPI-I-98-1-019), 1998, pp. 121-132
Aligning alignments
John D. Kececioglu
,
Weiqing Zhang
Lecture Notes in Computer Science
1448
, 1998, pp. 189-208
Approximation algorithms for multiple sequence alignment under a fixed evolutionary tree
R. Ravi
,
John D. Kececioglu
Discrete Applied Mathematics
88
(1-3), 1998, pp. 355-366
A branch-and-cut approach to physical mapping with end-probes
Thomas Christof
,
Michael Jünger
,
John Kececioglu
,
Petra Mutzel
,
Gerhard Reinelt
Proceedings of the 1st Annual International Conference on Computational Molecular Biology, RECOMB'97 (Santa Fe, New Mexico, January 20-23, 1997)
, 1997, pp. 84-92
Iferring a DNA sequence from erroneous copies
John Kececioglu
,
Ming Li
,
John Tromp
Theoretical Computer Science
185
(1), 1997, pp. 3-13
Steiner points in the space of genome rearrrangements
David Sankoff
,
Gopalakrishnan Sundaram
,
John Kececioglu
International Journal of Foundations of Computer Science
7
(1), 1996, pp. 1-9
Making the shortest-paths approach to sum-of-pairs multiple sequence alignment more space efficient in practice
Sandeep K. Gupta
,
John D. Kececioglu
,
Alejandro A. Schäffer
Lecture Notes in Computer Science
937
, 1995, pp. 128-143
Of mice and men: Algorithms for evolutionary distances between genomes with translocation
John D. Kececioglu
,
R. Ravi
Proceedings of the 6th Annual ACM-SIAM Symposium on Discrete Algorithms, SODA'95 (San Francisdo, California, January 22-24, 1995)
, 1995, pp. 604-613
Approximation algorithms for multiple sequence alignment under a fixed evolutionary tree
R. Ravi
,
John D. Kececioglu
Lecture Notes in Computer Science
937
, 1995, pp. 330-339
Reconstructing a history of recombinations from a set of sequences
John Kececioglu
,
Dan Gusfield
Proceedings of the 5th Annual ACM-SIAM Symposium on Discrete Algorithms, SODA'94 (Arlington, Virginia, January 23-25, 1994)
, 1994, pp. 471-480
Efficient bounds for oriented chromosome inversion distance
John Kececioglu
,
David Sankoff
Lecture Notes in Computer Science
807
, 1994, pp. 307-325
Exact and approximation algorithms for the inversion distance between two chromosomes
John Kececioglu
,
David Sankoff
Lecture Notes in Computer Science
684
, 1993, pp. 87-105
The maximum weight trace problem in multiple sequence alignment
John Kececioglu
Lecture Notes in Computer Science
684
, 1993, pp. 106-119
Separating repeats in DNA sequence assembly
John Kececioglu
,
Jun Yu
Proceedings of the 5th Annual International Conference on Computational Molecular Biology, RECOMB'2001 (Montreal, Canada, April 22-25, 2001)
, pp. 176-183