David Sankoff

According to our database1, David Sankoff authored at least 127 papers between 1969 and 2019.

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Bibliography

2019
Models for Similarity Distributions of Syntenic Homologs and Applications to Phylogenomics.
IEEE/ACM Trans. Comput. Biology Bioinform., 2019

Distinguishing successive ancient polyploidy levels based on genome-internal syntenic alignment.
BMC Bioinformatics, 2019

A branching process for homology distribution-based inference of polyploidy, speciation and loss.
Algorithms for Molecular Biology, 2019

2018
Evolutionary Model for the Statistical Divergence of Paralogous and Orthologous Gene Pairs Generated by Whole Genome Duplication and Speciation.
IEEE/ACM Trans. Comput. Biology Bioinform., 2018

Accurate prediction of orthologs in the presence of divergence after duplication.
Bioinformatics, 2018

Speciation and Rate Variation in a Birth-and-Death Account of WGD and Fractionation; the Case of Solanaceae.
Proceedings of the Comparative Genomics - 16th International Conference, 2018

A Randomized FPT Approximation Algorithm for Maximum Alternating-Cycle Decomposition with Applications.
Proceedings of the Computing and Combinatorics - 24th International Conference, 2018

2017
Asymptotic medians of random permutations sampled from reversal random walks.
Theor. Comput. Sci., 2017

The Similarity Distribution of Paralogous Gene Pairs Created by Recurrent Alternation of Polyploidization and Fractionation.
Proceedings of the Comparative Genomics - 15th International Workshop, 2017

2016
Locating rearrangement events in a phylogeny based on highly fragmented assemblies.
BMC Genomics, 2016

A continuous analog of run length distributions reflecting accumulated fractionation events.
BMC Bioinformatics, 2016

Compromise or optimize? The breakpoint anti-median.
BMC Bioinformatics, 2016

The Trees in the Peaks.
Proceedings of the Algorithms for Computational Biology - Third International Conference, 2016

2015
Graph-Theoretic Modelling of the Domain Chaining Problem.
Proceedings of the Algorithms in Bioinformatics - 15th International Workshop, 2015

Literature Visualization and Similarity Measurement Based on Citation Relations.
Proceedings of the 19th International Conference on Information Visualisation, 2015

Statistical analysis of fractionation resistance by functional category and expression level.
Proceedings of the 5th IEEE International Conference on Computational Advances in Bio and Medical Sciences, 2015

2014
Practical halving; the Nelumbo nucifera evidence on early eudicot evolution.
Comput. Biology Chem., 2014

Structural vs. functional mechanisms of duplicate gene loss following whole genome doubling.
Proceedings of the IEEE 4th International Conference on Computational Advances in Bio and Medical Sciences, 2014

2013
Practical aliquoting of flowering plant genomes.
BMC Bioinformatics, 2013

Phase change for the accuracy of the median value in estimating divergence time.
BMC Bioinformatics, 2013

The dynamics of functional classes of plant genes in rediploidized ancient polyploids.
BMC Bioinformatics, 2013

Fractionation, Rearrangement, Consolidation, Reconstruction.
Proceedings of the Models and Algorithms for Genome Evolution, 2013

2012
The Kernel of Maximum Agreement Subtrees.
IEEE/ACM Trans. Comput. Biology Bioinform., 2012

Scaffold Filling under the Breakpoint and Related Distances.
IEEE/ACM Trans. Comput. Biology Bioinform., 2012

Gene clusters as intersections of powers of paths.
J. Braz. Comp. Soc., 2012

A model for biased fractionation after whole genome duplication.
BMC Genomics, 2012

Gene order in rosid phylogeny, inferred from pairwise syntenies among extant genomes.
BMC Bioinformatics, 2012

Generalized adjacency and the conservation of gene clusters in genetic networks defined by synthetic lethals.
BMC Bioinformatics, 2012

Detection of gene expression changes at chromosomal rearrangement breakpoints in evolution.
BMC Bioinformatics, 2012

A consolidation algorithm for genomes fractionated after higher order polyploidization.
BMC Bioinformatics, 2012

Medians seek the corners, and other conjectures.
BMC Bioinformatics, 2012

Fractionation, rearrangement and subgenome dominance.
Bioinformatics, 2012

Ancient angiosperm hexaploidy meets ancestral eudicot gene order.
Proceedings of the IEEE 2nd International Conference on Computational Advances in Bio and Medical Sciences, 2012

Keynote: Aspects of fractionation.
Proceedings of the IEEE 2nd International Conference on Computational Advances in Bio and Medical Sciences, 2012

2011
Genome Aliquoting Revisited.
Journal of Computational Biology, 2011

Listing All Parsimonious Reversal Sequences: New Algorithms and Perspectives.
Journal of Computational Biology, 2011

On the PATHGROUPS approach to rapid small phylogeny.
BMC Bioinformatics, 2011

Fractionation statistics.
BMC Bioinformatics, 2011

Listing all sorting reversals in quadratic time.
Algorithms for Molecular Biology, 2011

OMG! Orthologs in Multiple Genomes - Competing Graph-Theoretical Formulations.
Proceedings of the Algorithms in Bioinformatics - 11th International Workshop, 2011

OMG! Orthologs for Multiple Genomes - Competing Formulations - (Keynote Talk).
Proceedings of the Bioinformatics Research and Applications - 7th International Symposium, 2011

Generalized Adjacency in Genetic Networks and the Conservation of Functional Gene Clusters.
Proceedings of the IEEE International Conference on Bioinformatics and Biomedicine, 2011

Changes in gene expression near evolutionary breakpoints.
Proceedings of the ACM International Conference on Bioinformatics, 2011

2010
Rearrangement Phylogeny of Genomes in Contig Form.
IEEE/ACM Trans. Comput. Biology Bioinform., 2010

Natural Parameter Values for Generalized Gene Adjacency.
Journal of Computational Biology, 2010

A Statistically Fair Comparison of Ancestral Genome Reconstructions, Based on Breakpoint and Rearrangement Distances.
Journal of Computational Biology, 2010

Scaffold filling, contig fusion and comparative gene order inference.
BMC Bioinformatics, 2010

Scaffold Filling under the Breakpoint Distance.
Proceedings of the Comparative Genomics - International Workshop, 2010

2009
Generalized Gene Adjacencies, Graph Bandwidth, and Clusters in Yeast Evolution.
IEEE/ACM Trans. Comput. Biology Bioinform., 2009

Issues in the Reconstruction of Gene Order Evolution.
J. Comput. Sci. Technol., 2009

Towards Improved Reconstruction of Ancestral Gene Order in Angiosperm Phylogeny.
Journal of Computational Biology, 2009

Gene Loss under Neighborhood Selection Following Whole genome Duplication and the Reconstruction of the Ancestral Populus genome.
J. Bioinformatics and Computational Biology, 2009

Genome Halving with Double Cut and Join.
J. Bioinformatics and Computational Biology, 2009

Genome aliquoting with double cut and join.
BMC Bioinformatics, 2009

Multichromosomal median and halving problems under different genomic distances.
BMC Bioinformatics, 2009

Session Introduction.
Proceedings of the Biocomputing 2009: Proceedings of the Pacific Symposium, 2009

2008
Descendants of Whole Genome Duplication within Gene Order Phylogeny.
Journal of Computational Biology, 2008

Tests for Gene Clusters Satisfying the Generalized Adjacency Criterion.
Proceedings of the Advances in Bioinformatics and Computational Biology, 2008

A Customized Class of Functions for Modeling and Clustering Gene Expression Profiles in Embryonic Stem Cells.
Proceedings of the Advances in Bioinformatics and Computational Biology, 2008

Decompositions of Multiple Breakpoint Graphs and Rapid Exact Solutions to the Median Problem.
Proceedings of the Algorithms in Bioinformatics, 8th International Workshop, 2008

Multichromosomal Genome Median and Halving Problems.
Proceedings of the Algorithms in Bioinformatics, 8th International Workshop, 2008

Internal Validation of Ancestral Gene Order Reconstruction in Angiosperm Phylogeny.
Proceedings of the Comparative Genomics, International Workshop, 2008

Guided genome halving: hardness, heuristics and the history of the Hemiascomycetes.
Proceedings of the Proceedings 16th International Conference on Intelligent Systems for Molecular Biology (ISMB), 2008

Hierarchical Clustering Using Constraints.
Proceedings of the Bioinformatics Research and Applications, 2008

Poisson adjacency distributions in genome comparison: multichromosomal, circular, signed and unsigned cases.
Proceedings of the ECCB'08 Proceedings, 2008

2007
Removing Noise and Ambiguities from Comparative Maps in Rearrangement Analysis.
IEEE/ACM Trans. Comput. Biology Bioinform., 2007

Paths and Cycles in Breakpoint Graph of Random Multichromosomal Genomes.
Journal of Computational Biology, 2007

Common Intervals and Symmetric Difference in a Model-Free Phylogenomics, with an Application to Streptophyte Evolution.
Journal of Computational Biology, 2007

Algorithms for the Extraction of Synteny Blocks from Comparative Maps.
Proceedings of the Algorithms in Bioinformatics, 7th International Workshop, 2007

Parts of the Problem of Polyploids in Rearrangement Phylogeny.
Proceedings of the Comparative Genomics, RECOMB 2007 International Workshop, 2007

Polyploids, genome halving and phylogeny.
Proceedings of the Proceedings 15th International Conference on Intelligent Systems for Molecular Biology (ISMB) & 6th European Conference on Computational Biology (ECCB), 2007

Preface.
Proceedings of 5th Asia-Pacific Bioinformatics Conference, 2007

2006
The Signal in the Genomes.
PLoS Computational Biology, 2006

Genome rearrangements with partially ordered chromosomes.
J. Comb. Optim., 2006

The Distribution of Genomic Distance between Random Genomes.
Journal of Computational Biology, 2006

Stability of Rearrangement Measures in the Comparison of Genome Sequences.
Journal of Computational Biology, 2006

Paths and Cycles in Breakpoint Graphs of Random Multichromosomal Genomes.
Proceedings of the Comparative Genomics, 2006

Statistical Evaluation of Genome Rearrangement.
Proceedings of the Research in Computational Molecular Biology, 2006

Rearrangement of Noisy Genomes.
Proceedings of the Computational Science, 2006

2005
Chromosomal Breakpoint Reuse in Genome Sequence Rearrangement.
Journal of Computational Biology, 2005

The Statistical Analysis of Spatially Clustered Genes under the Maximum Gap Criterion.
Journal of Computational Biology, 2005

Reversals of Fortune.
Proceedings of the Comparative Genomics, 2005

Stability of Rearrangement Measures in the Comparison of Genome Sequences.
Proceedings of the Research in Computational Molecular Biology, 2005

Power Boosts for Cluster Tests.
Proceedings of the Comparative Genomics, 2005

Reversal distance for partially ordered genomes.
Proceedings of the Proceedings Thirteenth International Conference on Intelligent Systems for Molecular Biology 2005, 2005

2004
Editorial: Combinatiorial Pattern Matching.
J. Discrete Algorithms, 2004

Improving Gene Network Inference by Comparing Expression Time-series across Species, Developmental Stages or Tissues.
J. Bioinformatics and Computational Biology, 2004

Chromosomal breakpoint re-use in the inference of genome sequence rearrangement.
Proceedings of the Eighth Annual International Conference on Computational Molecular Biology, 2004

Estimators of Translocations and Inversions in Comparative Maps.
Proceedings of the Comparative Genomics, 2004

The Distribution of Inversion Lengths in Bacteria.
Proceedings of the Comparative Genomics, 2004

The Statistical Significance of Max-Gap Clusters.
Proceedings of the Comparative Genomics, 2004

Genomic features in the breakpoint regions between syntenic blocks.
Proceedings of the Proceedings Twelfth International Conference on Intelligent Systems for Molecular Biology/Third European Conference on Computational Biology 2004, 2004

2003
The Reconstruction of Doubled Genomes.
SIAM J. Comput., 2003

Tests for Gene Clustering.
Journal of Computational Biology, 2003

Detection and validation of single gene inversions.
Proceedings of the Eleventh International Conference on Intelligent Systems for Molecular Biology, June 29, 2003

2002
Short inversions and conserved gene cluster.
Bioinformatics, 2002

Short inversions and conserved gene clusters.
Proceedings of the 2002 ACM Symposium on Applied Computing (SAC), 2002

2000
Early Eukaryote Evolution Based on Mitochondrial Gene Order Breakpoints.
Journal of Computational Biology, 2000

The early introduction of dynamic programming into computational biology.
Bioinformatics, 2000

1999
Phylogenetic Invariants for Genome Rearrangements.
Journal of Computational Biology, 1999

Phylogenetic Reconstruction from Genome Order Data.
Electron. Notes Discret. Math., 1999

Genome rearrangement with gene families.
Bioinformatics, 1999

Generating 3D Virtual Populations from Pictures of a Few Individuals.
Proceedings of the Algorithms and Data Structures, 6th International Workshop, 1999

Probability models for genome rearrangement and linear invariants for phylogenetic inference.
Proceedings of the Third Annual International Conference on Research in Computational Molecular Biology, 1999

Reconstructing the pre-doubling genome.
Proceedings of the Third Annual International Conference on Research in Computational Molecular Biology, 1999

Hybridization and Genome Rearrangement.
Proceedings of the Combinatorial Pattern Matching, 10th Annual Symposium, 1999

1998
Multiple Genome Rearrangement and Breakpoint Phylogeny.
Journal of Computational Biology, 1998

Multiple genome rearrangements.
Proceedings of the Second Annual International Conference on Research in Computational Molecular Biology, 1998

Genome Halving.
Proceedings of the Combinatorial Pattern Matching, 9th Annual Symposium, 1998

The Production of Code-Mixed Discourse.
Proceedings of the 36th Annual Meeting of the Association for Computational Linguistics and 17th International Conference on Computational Linguistics, 1998

1997
Conserved Segment Identification.
Journal of Computational Biology, 1997

On the Nadeau-Taylor Theory of Conserved Chromosome Segments.
Proceedings of the Combinatorial Pattern Matching, 8th Annual Symposium, 1997

The Median Problem for Breakpoints in Comparative Genomics.
Proceedings of the Computing and Combinatorics, Third Annual International Conference, 1997

1996
Steiner Points in the Space of Genome Rearrangements.
Int. J. Found. Comput. Sci., 1996

Conserved Synteny As a Measure of Genomic Distance.
Discret. Appl. Math., 1996

Original Synteny.
Proceedings of the Combinatorial Pattern Matching, 7th Annual Symposium, 1996

1995
Exact and Approximation Algorithms for Sorting by Reversals, with Application to Genome Rearrangement.
Algorithmica, 1995

1994
Skewed Base Compositions, Asymmetric Transition Matrices, and Phylogenetic Invariants.
Journal of Computational Biology, 1994

Efficient Bounds for Oriented Chromosome Inversion Distance.
Proceedings of the Combinatorial Pattern Matching, 5th Annual Symposium, 1994

1993
Exact and Approximation Algorithms for the Inversion Distance Between Two Chromosomes.
Proceedings of the Combinatorial Pattern Matching, 4th Annual Symposium, 1993

1992
Edit Distances for Genome Comparisons Based on Non-Local Operations.
Proceedings of the Combinatorial Pattern Matching, Third Annual Symposium, 1992

1990
Comparison of musical sequences.
Computers and the Humanities, 1990

1982
A strategy for sequence phylogeny research.
Nucleic Acids Research, 1982

1975
Locating the vertices of a steiner tree in an arbitrary metric space.
Math. Program., 1975

1973
Shortcuts, diversions, and maximal chainsin partially ordered sets.
Discret. Math., 1973

1971
Dictionary Structure and Probability Measures
Information and Control, September, 1971

1969
Simulation of Word-Meaning Stochastic Processes.
Proceedings of the Third International Conference on Computational Linguistics, 1969


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