David Sankoff

ORCID

Publication Activity (10 Years)

Years Active: 1969-2024
Publications (10 Years): 27

Top Venues

RECOMB-CG

BMC Bioinform.

IEEE ACM Trans. Comput. Biol. Bioinform.

ICCABS

Publications

Poly H. da Silva, Arash Jamshidpey, David Sankoff
Sampling Gene Adjacencies and Geodesic Points of Random Genomes. RECOMB-CG (2024)
Haitian Zhong, David Sankoff
Capacity, Collision Avoidance and Shopping Rate under a Social Distancing Regime. Entropy 25 (12) (2023)
Mona Meghdari Miardan, Arash Jamshidpey, David Sankoff
Escape from Parsimony of a Double-Cut-and-Join Genome Evolution Process. J. Comput. Biol. 30 (2) (2023)
Haitian Zhong, David Sankoff
Capacity, Collision Avoidance and Shopping Rate under a Social Distancing Regime. CoRR (2023)
Qiaoji Xu, David Sankoff
Gene Order Phylogeny via Ancestral Genome Reconstruction Under Dollo. RECOMB-CG (2023)
Zhe Yu, David Sankoff
Syntenic Dimensions of Genomic Evolution. RECOMB-CG (2022)
Yue Zhang, Chunfang Zheng, Sindeed Islam, Yong-Min Kim, David Sankoff
Branching Out to Speciation in a Model of Fractionation: The Malvaceae. IEEE ACM Trans. Comput. Biol. Bioinform. 18 (5) (2021)
Qiaoji Xu, Lingling Jin, James H. Leebens-Mack, David Sankoff
Validation of Automated Chromosome Recovery in the Reconstruction of Ancestral Gene Order. Algorithms 14 (6) (2021)
Qiaoji Xu, Xiaomeng Zhang, Yue Zhang, Chunfang Zheng, James H. Leebens-Mack, Lingling Jin, David Sankoff
The monoploid chromosome complement of reconstructed ancestral genomes in a phylogeny. J. Bioinform. Comput. Biol. 19 (6) (2021)
Qiaoji Xu, Lingling Jin, Yue Zhang, Xiaomeng Zhang, Chunfang Zheng, James H. Leebens-Mack, David Sankoff
Ancestral Flowering Plant Chromosomes and Gene Orders Based on Generalized Adjacencies and Chromosomal Gene Co-Occurrences. J. Comput. Biol. 28 (11) (2021)
Louxin Zhang, Shaoliang Peng, Yi-Ping Phoebe Chen, David Sankoff, Guoliang Li, Hong-Yu Zhang
Guest Editorial for the 17th Asia Pacific Bioinformatics Conference. IEEE ACM Trans. Comput. Biol. Bioinform. 18 (6) (2021)
Qiaoji Xu, Lingling Jin, Chunfang Zheng, James H. Leebens-Mack, David Sankoff
RACCROCHE: Ancestral Flowering Plant Chromosomes and Gene Orders Based on Generalized Adjacencies and Chromosomal Gene Co-occurrences. ICCABS (2020)
Zhe Yu, Chunfang Zheng, David Sankoff
Gaps and Runs in Syntenic Alignments. AlCoB (2020)
David Sankoff, Chunfang Zheng, Yue Zhang, Joao Meidanis, Eric Lyons, Haibao Tang
Models for Similarity Distributions of Syntenic Homologs and Applications to Phylogenomics. IEEE ACM Trans. Comput. Biol. Bioinform. 16 (3) (2019)
Yue Zhang, Chunfang Zheng, David Sankoff
Distinguishing successive ancient polyploidy levels based on genome-internal syntenic alignment. BMC Bioinform. (20) (2019)
Yue Zhang, Chunfang Zheng, David Sankoff
A branching process for homology distribution-based inference of polyploidy, speciation and loss. Algorithms Mol. Biol. 14 (1) (2019)
Yue Zhang, Chunfang Zheng, David Sankoff
Speciation and Rate Variation in a Birth-and-Death Account of WGD and Fractionation; the Case of Solanaceae. RECOMB-CG (2018)
Chunfang Zheng, Yuji Jeong, Madisyn Gabrielle Turcotte, David Sankoff
Resolution effects in reconstructing ancestral genomes. BMC Genom. 19 (S2) (2018)
Haitao Jiang, Lianrong Pu, Letu Qingge, David Sankoff, Binhai Zhu
A Randomized FPT Approximation Algorithm for Maximum Alternating-Cycle Decomposition with Applications. COCOON (2018)
Manuel Lafond, Mona Meghdari Miardan, David Sankoff
Accurate prediction of orthologs in the presence of divergence after duplication. Bioinform. 34 (13) (2018)
Yue Zhang, Chunfang Zheng, David Sankoff
Evolutionary Model for the Statistical Divergence of Paralogous and Orthologous Gene Pairs Generated by Whole Genome Duplication and Speciation. IEEE ACM Trans. Comput. Biol. Bioinform. 15 (5) (2018)
Yue Zhang, David Sankoff
The Similarity Distribution of Paralogous Gene Pairs Created by Recurrent Alternation of Polyploidization and Fractionation. RECOMB-CG (2017)
Arash Jamshidpey, David Sankoff
Asymptotic medians of random permutations sampled from reversal random walks. Theor. Comput. Sci. 698 (2017)
Chunfang Zheng, David Sankoff
Locating rearrangement events in a phylogeny based on highly fragmented assemblies. BMC Genom. 17 (S-1) (2016)
Zhe Yu, David Sankoff
A continuous analog of run length distributions reflecting accumulated fractionation events. BMC Bioinform. 17 (S-14) (2016)
Caroline Anne Larlee, Alex Brandts, David Sankoff
Compromise or optimize? The breakpoint anti-median. BMC Bioinform. 17 (S-18) (2016)
David Sankoff, Chunfang Zheng, Eric Lyons, Haibao Tang
The Trees in the Peaks. AlCoB (2016)
Hanadi Alfraidi, Won-Sook Lee, David Sankoff
Literature Visualization and Similarity Measurement Based on Citation Relations. IV (2015)
Eric C. H. Chen, Annie Morin, Jean-Hugues Chauchat, David Sankoff
Statistical analysis of fractionation resistance by functional category and expression level. ICCABS (2015)
Poly H. da Silva, Simone Dantas, Chunfang Zheng, David Sankoff
Graph-Theoretic Modelling of the Domain Chaining Problem. WABI (2015)
David Sankoff, Chunfang Zheng, Baoyong Wang, Carlos Fernando Buen Abad Najar
Structural vs. functional mechanisms of duplicate gene loss following whole genome doubling. BMC Bioinform. 16 (S17) (2015)
David Sankoff, Baoyong Wang, Chunfang Zheng, Carlos Fernando Buen Abad Najar
Structural vs. functional mechanisms of duplicate gene loss following whole genome doubling. ICCABS (2014)
Chunfang Zheng, David Sankoff
Practical halving; the Nelumbo nucifera evidence on early eudicot evolution. Comput. Biol. Chem. 50 (2014)
Chunfang Zheng, David Sankoff
Practical aliquoting of flowering plant genomes. BMC Bioinform. 14 (S-15) (2013)
Arash Jamshidpey, David Sankoff
Phase change for the accuracy of the median value in estimating divergence time. BMC Bioinform. 14 (S-15) (2013)
Eric C. H. Chen, Carlos Fernando Buen Abad Najar, Chunfang Zheng, Alex Brandts, Eric Lyons, Haibao Tang, Lorenzo Carretero-Paulet, Victor A. Albert, David Sankoff
The dynamics of functional classes of plant genes in rediploidized ancient polyploids. BMC Bioinform. 14 (S-15) (2013)
Zhenyu Yang, David Sankoff
Generalized adjacency and the conservation of gene clusters in genetic networks defined by synthetic lethals. BMC Bioinform. 13 (S-9) (2012)
Krister M. Swenson, Eric C. H. Chen, Nicholas D. Pattengale, David Sankoff
The Kernel of Maximum Agreement Subtrees. IEEE ACM Trans. Comput. Biol. Bioinform. 9 (4) (2012)
Haitao Jiang, Chunfang Zheng, David Sankoff, Binhai Zhu
Scaffold Filling under the Breakpoint and Related Distances. IEEE ACM Trans. Comput. Biol. Bioinform. 9 (4) (2012)
Katharina Jahn, Chunfang Zheng, Jakub Kovác, David Sankoff
A consolidation algorithm for genomes fractionated after higher order polyploidization. BMC Bioinform. 13 (S-19) (2012)
Chunfang Zheng, Victor A. Albert, Eric Lyons, David Sankoff
Ancient angiosperm hexaploidy meets ancestral eudicot gene order. ICCABS (2012)
Maryam Haghighi, David Sankoff
Medians seek the corners, and other conjectures. BMC Bioinform. 13 (S-19) (2012)
Vítor Costa, Simone Dantas, David Sankoff, Ximing Xu
Gene clusters as intersections of powers of paths. J. Braz. Comput. Soc. 18 (2) (2012)
Adriana Muñoz, David Sankoff
Detection of gene expression changes at chromosomal rearrangement breakpoints in evolution. BMC Bioinform. 13 (S-3) (2012)
David Sankoff, Chunfang Zheng, Baoyong Wang
A model for biased fractionation after whole genome duplication. BMC Genom. 13 (S-1) (2012)
Chunfang Zheng, David Sankoff
Gene order in rosid phylogeny, inferred from pairwise syntenies among extant genomes. BMC Bioinform. 13 (S-10) (2012)
David Sankoff
Keynote: Aspects of fractionation. ICCABS (2012)
David Sankoff, Chunfang Zheng
Fractionation, rearrangement and subgenome dominance. Bioinform. 28 (18) (2012)
David Sankoff, Chunfang Zheng, Baoyong Wang
A Model for Biased Fractionation after Whole Genome Duplication. RECOMB (2012)
Krister M. Swenson, Eric C. H. Chen, Nicholas D. Pattengale, David Sankoff
The Kernel of Maximum Agreement Subtrees. ISBRA (2011)
Adriana Muñoz, David Sankoff
Changes in gene expression near evolutionary breakpoints. BCB (2011)
Chunfang Zheng, David Sankoff
On the PATHGROUPS approach to rapid small phylogeny. BMC Bioinform. 12 (S-1) (2011)
Baoyong Wang, Chunfang Zheng, David Sankoff
Fractionation statistics. BMC Bioinform. 12 (S-9) (2011)
David Sankoff
OMG! Orthologs for Multiple Genomes - Competing Formulations - (Keynote Talk). ISBRA (2011)
Zhenyu Yang, David Sankoff
Generalized Adjacency in Genetic Networks and the Conservation of Functional Gene Clusters. BIBM (2011)
Chunfang Zheng, David Sankoff
Gene Order in Rosid Phylogeny, Inferred from Pairwise Syntenies among Extant Genomes. ISBRA (2011)
Ghada Badr, Krister M. Swenson, David Sankoff
Listing All Parsimonious Reversal Sequences: New Algorithms and Perspectives. J. Comput. Biol. 18 (9) (2011)
Chunfang Zheng, Krister M. Swenson, Eric Lyons, David Sankoff
OMG! Orthologs in Multiple Genomes - Competing Graph-Theoretical Formulations. WABI (2011)
Robert Warren, David Sankoff
Genome Aliquoting Revisited. J. Comput. Biol. 18 (9) (2011)
Krister M. Swenson, Ghada Badr, David Sankoff
Listing all sorting reversals in quadratic time. Algorithms Mol. Biol. 6 (2011)
Robert Warren, David Sankoff
Genome Aliquoting Revisited. RECOMB-CG (2010)
Zhenyu Yang, David Sankoff
Natural Parameter Values for Generalized Gene Adjacency. J. Comput. Biol. 17 (9) (2010)
Adriana Muñoz, Chunfang Zheng, Qian Zhu, Victor A. Albert, Steve Rounsley, David Sankoff
Scaffold filling, contig fusion and comparative gene order inference. BMC Bioinform. 11 (2010)
Krister M. Swenson, Ghada Badr, David Sankoff
Listing All Sorting Reversals in Quadratic Time. WABI (2010)
Ghada Badr, Krister M. Swenson, David Sankoff
Listing All Parsimonious Reversal Sequences: New Algorithms and Perspectives. RECOMB-CG (2010)
Bernard M. E. Moret, Webb Miller, Pavel A. Pevzner, David Sankoff
Session Introduction. Pacific Symposium on Biocomputing (2010)
Haitao Jiang, Chunfang Zheng, David Sankoff, Binhai Zhu
Scaffold Filling under the Breakpoint Distance. RECOMB-CG (2010)
Adriana Muñoz, David Sankoff
Rearrangement Phylogeny of Genomes in Contig Form. IEEE ACM Trans. Comput. Biol. Bioinform. 7 (4) (2010)
Zaky Adam, David Sankoff
A Statistically Fair Comparison of Ancestral Genome Reconstructions, Based on Breakpoint and Rearrangement Distances. J. Comput. Biol. 17 (9) (2010)
Zhenyu Yang, David Sankoff
Natural Parameter Values for Generalized Gene Adjacency. RECOMB-CG (2009)
Zaky Adam, David Sankoff
A Statistically Fair Comparison of Ancestral Genome Reconstructions, Based on Breakpoint and Rearrangement Distances. RECOMB-CG (2009)
Robert Warren, David Sankoff
Genome aliquoting with double cut and join. BMC Bioinform. 10 (S-1) (2009)
Adriana Muñoz, David Sankoff
Rearrangement Phylogeny of Genomes in Contig Form. ISBRA (2009)
Eric Tannier, Chunfang Zheng, David Sankoff
Multichromosomal median and halving problems under different genomic distances. BMC Bioinform. 10 (2009)
Robert Warren, David Sankoff
Genome Halving with Double Cut and Join. J. Bioinform. Comput. Biol. 7 (2) (2009)
Qian Zhu, Zaky Adam, Vicky Choi, David Sankoff
Generalized Gene Adjacencies, Graph Bandwidth, and Clusters in Yeast Evolution. IEEE ACM Trans. Comput. Biol. Bioinform. 6 (2) (2009)
David Sankoff, Chunfang Zheng, Adriana Muñoz, Zhenyu Yang, Zaky Adam, Robert Warren, Vicky Choi, Qian Zhu
Issues in the Reconstruction of Gene Order Evolution. J. Comput. Sci. Technol. 25 (1) (2009)
Chunfang Zheng, P. Kerr Wall, James H. Leebens-Mack, Claude de Pamphilis, Victor A. Albert, David Sankoff
Gene Loss under Neighborhood Selection Following Whole genome Duplication and the Reconstruction of the Ancestral Populus genome. J. Bioinform. Comput. Biol. 7 (3) (2009)
Bernard M. E. Moret, Webb Miller, Pavel A. Pevzner, David Sankoff
Session Introduction. Pacific Symposium on Biocomputing (2009)
David Sankoff, Chunfang Zheng, P. Kerr Wall, Claude de Pamphilis, James H. Leebens-Mack, Victor A. Albert
Towards Improved Reconstruction of Ancestral Gene Order in Angiosperm Phylogeny. J. Comput. Biol. 16 (10) (2009)
Qian Zhu, Zaky Adam, Vicky Choi, David Sankoff
Generalized Gene Adjacencies, Graph Bandwidth and Clusters in Yeast Evolution. ISBRA (2008)
Robert Warren, David Sankoff
Genome Halving with Double Cut and Join. APBC (2008)
David Sankoff, Chunfang Zheng, P. Kerr Wall, Claude W. dePamphilis, James H. Leebens-Mack, Victor A. Albert
Internal Validation of Ancestral Gene Order Reconstruction in Angiosperm Phylogeny. RECOMB-CG (2008)
Chunfang Zheng, Qian Zhu, David Sankoff
Descendants of Whole Genome Duplication within Gene Order Phylogeny. J. Comput. Biol. 15 (8) (2008)
Chunfang Zheng, Qian Zhu, Zaky Adam, David Sankoff
Guided genome halving: hardness, heuristics and the history of the Hemiascomycetes. ISMB (2008)
Shenggang Li, Miguel A. Andrade-Navarro, David Sankoff
A Customized Class of Functions for Modeling and Clustering Gene Expression Profiles in Embryonic Stem Cells. BSB (2008)
Eric Tannier, Chunfang Zheng, David Sankoff
Multichromosomal Genome Median and Halving Problems. WABI (2008)
Andrew Wei Xu, David Sankoff
Decompositions of Multiple Breakpoint Graphs and Rapid Exact Solutions to the Median Problem. WABI (2008)
Andrew Wei Xu, Benoît Alain, David Sankoff
Poisson adjacency distributions in genome comparison: multichromosomal, circular, signed and unsigned cases. ECCB (2008)
Mariana Kant, Maurice LeBon, David Sankoff
Hierarchical Clustering Using Constraints. ISBRA (2008)
Ximing Xu, David Sankoff
Tests for Gene Clusters Satisfying the Generalized Adjacency Criterion. BSB (2008)
David Sankoff, Lusheng Wang, Francis Y. L. Chin
Preface. APBC (2007)
Chunfang Zheng, Qian Zhu, David Sankoff
Removing Noise and Ambiguities from Comparative Maps in Rearrangement Analysis. IEEE ACM Trans. Comput. Biol. Bioinform. 4 (4) (2007)
Chunfang Zheng, Qian Zhu, David Sankoff
Parts of the Problem of Polyploids in Rearrangement Phylogeny. RECOMB-CG (2007)
Wei Xu, Chunfang Zheng, David Sankoff
Paths and Cycles in Breakpoint Graph of Random Multichromosomal Genomes. J. Comput. Biol. 14 (4) (2007)
Zaky Adam, Monique Turmel, Claude Lemieux, David Sankoff
Common Intervals and Symmetric Difference in a Model-Free Phylogenomics, with an Application to Streptophyte Evolution. J. Comput. Biol. 14 (4) (2007)
David Sankoff, Chunfang Zheng, Qian Zhu
Polyploids, genome halving and phylogeny. ISMB/ECCB (Supplement of Bioinformatics) (2007)
Vicky Choi, Chunfang Zheng, Qian Zhu, David Sankoff
Algorithms for the Extraction of Synteny Blocks from Comparative Maps. WABI (2007)
Chunfang Zheng, David Sankoff
Rearrangement of Noisy Genomes. International Conference on Computational Science (2) (2006)
David Sankoff
Statistical Evaluation of Genome Rearrangement. RECOMB (2006)

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Publication Activity (10 Years)

Top Topics

Top Venues

David Sankoff