John D. Kececioglu

发表

Ensemble Multiple Alignment

Dan DeBlasio, John D. Kececioglu, 2017 .

The Facet Accuracy Estimator

Dan DeBlasio, John D. Kececioglu, Dan F. DeBlasio, 2017 .

Multiple alignment by aligning alignments

John D. Kececioglu, Travis J. Wheeler, J. Kececioglu, 2007, ISMB/ECCB.

Core column prediction for protein multiple sequence alignments

John D. Kececioglu, Dan F. DeBlasio, 2017, Algorithms for Molecular Biology.

Simple and Fast Inverse Alignment

John D. Kececioglu, Eagu Kim, J. Kececioglu, 2006, RECOMB.

Estimating the Accuracy of Multiple Alignments and its Use in Parameter Advising

John D. Kececioglu, Dan F. DeBlasio, Travis J. Wheeler, 2012, RECOMB.

Steiner Points in the Space of Genome Rearrangements

David Sankoff, John D. Kececioglu, Gopal Sundaram, 1996, Int. J. Found. Comput. Sci..

Computing physical maps of chromosomes with nonoverlapping probes by branch-and-cut

John D. Kececioglu, Thomas Christof, J. Kececioglu, 1999, RECOMB.

Predicting Core Columns of Protein Multiple Sequence Alignments for Improved Parameter Advising

John D. Kececioglu, Dan F. DeBlasio, 2016, WABI.

Computational Complexity of Advising

Dan DeBlasio, John D. Kececioglu, 2017 .

Making the Shortest-Paths Approach to Sum-of-Pairs Multiple Sequence Alignment More Space Efficient in Practice (Extended Abstract)

Sandeep K. Gupta, Alejandro A. Schäffer, John D. Kececioglu, 1995, CPM.

Learning Parameter-Advising Sets for Multiple Sequence Alignment

John D. Kececioglu, Dan F. DeBlasio, J. Kececioglu, 2017, IEEE/ACM Transactions on Computational Biology and Bioinformatics.

Core Column Prediction for Alignments

Dan DeBlasio, John D. Kececioglu, Dan F. DeBlasio, 2017 .

Efficient Bounds for Oriented Chromosome Inversion Distance

David Sankoff, John D. Kececioglu, D. Sankoff, 1994, CPM.

A branch-and-cut algorithm for multiple sequence alignment

Kurt Mehlhorn, Petra Mutzel, Hans-Peter Lenhof, 1997, RECOMB '97.

Computing Maximum-Cardinality Matchings in Sparse General Graphs

John D. Kececioglu, A. Justin Pecqueur, 1998, Algorithm Engineering.

Parameter Advising for the Opal Aligner

Dan DeBlasio, John D. Kececioglu, 2017 .

Inferring a DNA Sequence from Erroneous Copies

John D. Kececioglu, Ming Li, John Tromp, 1997, Theor. Comput. Sci..

Aligning alignments exactly

John D. Kececioglu, Dean Starrett, J. Kececioglu, 2004, RECOMB.

Parameter Advising for Multiple Sequence Alignment

John D. Kececioglu, Dan F. DeBlasio, 2017, Computational Biology.

Boosting Alignment Accuracy by Adaptive Local Realignment

John D. Kececioglu, Dan F. DeBlasio, J. Kececioglu, 2017, RECOMB.

Improving the Practical Space and Time Efficiency of the Shortest-Paths Approach to Sum-of-Pairs Multiple Sequence Alignment

Sandeep K. Gupta, Alejandro A. Schäffer, John D. Kececioglu, 1995, J. Comput. Biol..

Learning parameter sets for alignment advising

John D. Kececioglu, Dan F. DeBlasio, 2014, BCB.

Alignment Accuracy Estimation

Dan DeBlasio, John D. Kececioglu, 2017 .

The Maximum Weight Trace Problem in Multiple Sequence Alignment

John D. Kececioglu, J. Kececioglu, 1993, CPM.

Learning Scoring Schemes for Sequence Alignment from Partial Examples

John D. Kececioglu, Eagu Kim, 2008, IEEE/ACM Transactions on Computational Biology and Bioinformatics.

Learning Models for Aligning Protein Sequences with Predicted Secondary Structure

John D. Kececioglu, Travis J. Wheeler, Eagu Kim, 2009, RECOMB.

Enhancing Software Tamper-Resistance via Stealthy Address Computations

John D. Kececioglu, Saumya K. Debray, Cullen Linn, 2003 .

Approximation Algorithms for Multiple Sequence Alignment Under a Fixed Evolutionary Tree

R. Ravi, John D. Kececioglu, 1995, CPM.

Ensemble multiple sequence alignment via advising

John D. Kececioglu, Dan F. DeBlasio, 2015, BCB.

Exact and approximation algorithms for sorting by reversals, with application to genome rearrangement

David Sankoff, John D. Kececioglu, D. Sankoff, 1995, Algorithmica.

Approximation Algorithms for Multiple Sequence Alignment Under a Fixed Evolutionary Tree

R. Ravi, John D. Kececioglu, J. Kececioglu, 1998, Discret. Appl. Math..

Accuracy Estimation and Parameter Advising for Protein Multiple Sequence Alignment

John D. Kececioglu, Dan F. DeBlasio, J. Kececioglu, 2013, J. Comput. Biol..

Inferring a DNA Sequence from Erroneous Copies (Abstract)

John D. Kececioglu, Ming Li, John Tromp, 1995, ALT.

A branch-and-cut approach to physical mapping with end-probes

Michael Jünger, Gerhard Reinelt, Petra Mutzel, 1997, RECOMB '97.

Reconstructing distances in physical maps of chromosomes with nonoverlapping probes

John D. Kececioglu, Jonathan Arnold, Sanjay Shete, 2000, RECOMB '00.

A Branch-and-Cut Approach to Physical Mapping of Chromosomes by Unique End-Probes

Michael Jünger, Gerhard Reinelt, Petra Mutzel, 1997, J. Comput. Biol..

Dynamic path-based software watermarking

Michael Stepp, Christian S. Collberg, Saumya K. Debray, 2004, PLDI '04.

Adaptive Local Realignment

Dan DeBlasio, John D. Kececioglu, Dan F. DeBlasio, 2017 .

Exact and Approximation Algorithms for the Inversion Distance Between Two Chromosomes

David Sankoff, John D. Kececioglu, D. Sankoff, 1993, CPM.

Aligning Protein Sequences with Predicted Secondary Structure

John D. Kececioglu, Travis J. Wheeler, Eagu Kim, 2010, J. Comput. Biol..

Reconstructing a history of recombinations from a set of sequences

John D. Kececioglu, Dan Gusfield, D. Gusfield, 1994, SODA '94.

Aligning Alignments

John D. Kececioglu, Weiqing Zhang, 1998, CPM.

Inverse Sequence Alignment from Partial Examples

John D. Kececioglu, Eagu Kim, 2007, WABI.

Combinatorial algorithms for DNA sequence assembly

Eugene W. Myers, John D. Kececioglu, E. Myers, 1995, Algorithmica.

EMP: execution time measurement protocol for compute‐bound programs

Richard T. Snodgrass, John D. Kececioglu, Peter J. Downey, 2017, Softw. Pract. Exp..

Of mice and men: algorithms for evolutionary distances between genomes with translocation

R. Ravi, John D. Kececioglu, J. Kececioglu, 1995, SODA '95.

Separating repeats in DNA sequence assembly

John D. Kececioglu, Jun Ju, J. Kececioglu, 2001, RECOMB.

Adaptive Local Realignment via Parameter Advising

John D. Kececioglu, Dan F. DeBlasio, 2016, BCB.

Fast Approximate Shortest Hyperpaths for Inferring Pathways in Cell Signaling Hypergraphs

John D. Kececioglu, Spencer Krieger, 2021, WABI.

Reconstructing Order and Distance in Physical Maps Using Nonoverlapping Probes

John D. Kececioglu, Sanjay Shete, Jonathan Arnold, 1998 .