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ORCIDDavid Sankoff
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- affiliation: University of Ottawa, Ontario, Canada
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2020 – today
- 2024
[c78]Poly H. da Silva, Arash Jamshidpey, David Sankoff:
Sampling Gene Adjacencies and Geodesic Points of Random Genomes. RECOMB-CG 2024: 189-210- 2023
- [j79]Haitian Zhong
, David Sankoff:
Capacity, Collision Avoidance and Shopping Rate under a Social Distancing Regime. Entropy 25(12): 1668 (2023) - [j78]Mona Meghdari Miardan, Arash Jamshidpey, David Sankoff:
Escape from Parsimony of a Double-Cut-and-Join Genome Evolution Process. J. Comput. Biol. 30(2): 118-130 (2023) - [c77]Qiaoji Xu, David Sankoff:
Gene Order Phylogeny via Ancestral Genome Reconstruction Under Dollo. RECOMB-CG 2023: 100-111 - [i1]Haitian Zhong, David Sankoff:
Capacity, Collision Avoidance and Shopping Rate under a Social Distancing Regime. CoRR abs/2310.18480 (2023) - 2022
- [c76]Zhe Yu, David Sankoff:
Syntenic Dimensions of Genomic Evolution. RECOMB-CG 2022: 21-30 - 2021
- [j77]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): 160 (2021) - [j76]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): 2140008:1-2140008:17 (2021) - [j75]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): 1156-1179 (2021) - [j74]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): 1875-1884 (2021) - [j73]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): 2123-2124 (2021) - 2020
- [c75]Zhe Yu, Chunfang Zheng, David Sankoff:
Gaps and Runs in Syntenic Alignments. AlCoB 2020: 49-60 - [c74]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: 97-115
2010 – 2019
- 2019
- [j72]Yue Zhang, Chunfang Zheng, David Sankoff:
A branching process for homology distribution-based inference of polyploidy, speciation and loss. Algorithms Mol. Biol. 14(1): 18:1-18:13 (2019) - [j71]Yue Zhang, Chunfang Zheng, David Sankoff:
Distinguishing successive ancient polyploidy levels based on genome-internal syntenic alignment. BMC Bioinform. 20-S(20): 635 (2019) - [j70]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): 727-737 (2019) - 2018
- [j69]Manuel Lafond, Mona Meghdari Miardan, David Sankoff:
Accurate prediction of orthologs in the presence of divergence after duplication. Bioinform. 34(13): i366-i375 (2018) - [j68]Chunfang Zheng, Yuji Jeong, Madisyn Gabrielle Turcotte, David Sankoff:
Resolution effects in reconstructing ancestral genomes. BMC Genom. 19(S2) (2018) - [j67]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): 1579-1584 (2018) - [c73]Haitao Jiang, Lianrong Pu, Letu Qingge, David Sankoff, Binhai Zhu:
A Randomized FPT Approximation Algorithm for Maximum Alternating-Cycle Decomposition with Applications. COCOON 2018: 26-38 - [c72]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: 146-160 - [e5]Gonzalo Navarro, David Sankoff, Binhai Zhu:
Annual Symposium on Combinatorial Pattern Matching, CPM 2018, July 2-4, 2018 - Qingdao, China. LIPIcs 105, Schloss Dagstuhl - Leibniz-Zentrum für Informatik 2018, ISBN 978-3-95977-074-3 [contents] - 2017
- [j66]Arash Jamshidpey, David Sankoff:
Asymptotic medians of random permutations sampled from reversal random walks. Theor. Comput. Sci. 698: 9-13 (2017) - [c71]Yue Zhang, David Sankoff:
The Similarity Distribution of Paralogous Gene Pairs Created by Recurrent Alternation of Polyploidization and Fractionation. RECOMB-CG 2017: 1-13 - 2016
- [j65]Zhe Yu, David Sankoff:
A continuous analog of run length distributions reflecting accumulated fractionation events. BMC Bioinform. 17(S-14): 233-240 (2016) - [j64]Caroline Anne Larlee, Alex Brandts, David Sankoff:
Compromise or optimize? The breakpoint anti-median. BMC Bioinform. 17(S-18): 19-23 (2016) - [j63]Chunfang Zheng, David Sankoff:
Locating rearrangement events in a phylogeny based on highly fragmented assemblies. BMC Genom. 17(S-1): 1 (2016) - [c70]David Sankoff, Chunfang Zheng, Eric Lyons, Haibao Tang:
The Trees in the Peaks. AlCoB 2016: 3-14 - 2015
- [j62]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): S9 (2015) - [c69]Eric C. H. Chen, Annie Morin, Jean-Hugues Chauchat, David Sankoff:
Statistical analysis of fractionation resistance by functional category and expression level. ICCABS 2015: 1 - [c68]Hanadi Alfraidi, Won-Sook Lee, David Sankoff:
Literature Visualization and Similarity Measurement Based on Citation Relations. IV 2015: 217-222 - [c67]Poly H. da Silva, Simone Dantas, Chunfang Zheng, David Sankoff:
Graph-Theoretic Modelling of the Domain Chaining Problem. WABI 2015: 296-307 - 2014
- [j61]Chunfang Zheng, David Sankoff:
Practical halving; the Nelumbo nucifera evidence on early eudicot evolution. Comput. Biol. Chem. 50: 75-81 (2014) - [c66]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: 1-2 - 2013
- [j60]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): S19 (2013) - [j59]Arash Jamshidpey, David Sankoff:
Phase change for the accuracy of the median value in estimating divergence time. BMC Bioinform. 14(S-15): S7 (2013) - [j58]Chunfang Zheng, David Sankoff:
Practical aliquoting of flowering plant genomes. BMC Bioinform. 14(S-15): S8 (2013) - [p2]David Sankoff, Chunfang Zheng:
Fractionation, Rearrangement, Consolidation, Reconstruction. Models and Algorithms for Genome Evolution 2013: 247-260 - 2012
- [j57]David Sankoff, Chunfang Zheng:
Fractionation, rearrangement and subgenome dominance. Bioinform. 28(18): 402-408 (2012) - [j56]Chunfang Zheng, David Sankoff:
Gene order in rosid phylogeny, inferred from pairwise syntenies among extant genomes. BMC Bioinform. 13(S-10): S9 (2012) - [j55]Maryam Haghighi, David Sankoff:
Medians seek the corners, and other conjectures. BMC Bioinform. 13(S-19): S5 (2012) - [j54]Katharina Jahn, Chunfang Zheng, Jakub Kovác, David Sankoff:
A consolidation algorithm for genomes fractionated after higher order polyploidization. BMC Bioinform. 13(S-19): S8 (2012) - [j53]Adriana Muñoz, David Sankoff:
Detection of gene expression changes at chromosomal rearrangement breakpoints in evolution. BMC Bioinform. 13(S-3): S6 (2012) - [j52]Zhenyu Yang, David Sankoff:
Generalized adjacency and the conservation of gene clusters in genetic networks defined by synthetic lethals. BMC Bioinform. 13(S-9): S8 (2012) - [j51]David Sankoff, Chunfang Zheng, Baoyong Wang:
A model for biased fractionation after whole genome duplication. BMC Genom. 13(S-1): S8 (2012) - [j50]Vítor Costa, Simone Dantas, David Sankoff, Ximing Xu:
Gene clusters as intersections of powers of paths. J. Braz. Comput. Soc. 18(2): 129-136 (2012) - [j49]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): 1023-1031 (2012) - [j48]Haitao Jiang, Chunfang Zheng, David Sankoff, Binhai Zhu:
Scaffold Filling under the Breakpoint and Related Distances. IEEE ACM Trans. Comput. Biol. Bioinform. 9(4): 1220-1229 (2012) - [c65]David Sankoff:
Keynote: Aspects of fractionation. ICCABS 2012: 1 - [c64]Chunfang Zheng, Victor A. Albert, Eric Lyons, David Sankoff:
Ancient angiosperm hexaploidy meets ancestral eudicot gene order. ICCABS 2012: 1-6 - [c63]David Sankoff, Chunfang Zheng, Baoyong Wang:
A Model for Biased Fractionation after Whole Genome Duplication. RECOMB 2012: 244 - 2011
- [j47]Krister M. Swenson, Ghada Badr, David Sankoff:
Listing all sorting reversals in quadratic time. Algorithms Mol. Biol. 6: 11 (2011) - [j46]Chunfang Zheng, David Sankoff:
On the PATHGROUPS approach to rapid small phylogeny. BMC Bioinform. 12(S-1): S4 (2011) - [j45]Baoyong Wang, Chunfang Zheng, David Sankoff:
Fractionation statistics. BMC Bioinform. 12(S-9): S5 (2011) - [j44]Robert Warren, David Sankoff:
Genome Aliquoting Revisited. J. Comput. Biol. 18(9): 1065-1075 (2011) - [j43]Ghada Badr, Krister M. Swenson, David Sankoff:
Listing All Parsimonious Reversal Sequences: New Algorithms and Perspectives. J. Comput. Biol. 18(9): 1201-1210 (2011) - [c62]Adriana Muñoz, David Sankoff:
Changes in gene expression near evolutionary breakpoints. BCB 2011: 393-398 - [c61]Zhenyu Yang, David Sankoff:
Generalized Adjacency in Genetic Networks and the Conservation of Functional Gene Clusters. BIBM 2011: 173-178 - [c60]David Sankoff:
OMG! Orthologs for Multiple Genomes - Competing Formulations - (Keynote Talk). ISBRA 2011: 2-3 - [c59]Chunfang Zheng, David Sankoff:
Gene Order in Rosid Phylogeny, Inferred from Pairwise Syntenies among Extant Genomes. ISBRA 2011: 99-110 - [c58]Krister M. Swenson, Eric C. H. Chen, Nicholas D. Pattengale, David Sankoff:
The Kernel of Maximum Agreement Subtrees. ISBRA 2011: 123-135 - [c57]Chunfang Zheng, Krister M. Swenson, Eric Lyons, David Sankoff:
OMG! Orthologs in Multiple Genomes - Competing Graph-Theoretical Formulations. WABI 2011: 364-375 - 2010
- [j42]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: 304 (2010) - [j41]Zhenyu Yang, David Sankoff:
Natural Parameter Values for Generalized Gene Adjacency. J. Comput. Biol. 17(9): 1113-1128 (2010) - [j40]Zaky Adam, David Sankoff:
A Statistically Fair Comparison of Ancestral Genome Reconstructions, Based on Breakpoint and Rearrangement Distances. J. Comput. Biol. 17(9): 1299-1314 (2010) - [j39]Adriana Muñoz, David Sankoff:
Rearrangement Phylogeny of Genomes in Contig Form. IEEE ACM Trans. Comput. Biol. Bioinform. 7(4): 579-587 (2010) - [c56]Bernard M. E. Moret, Webb Miller, Pavel A. Pevzner, David Sankoff:
Session Introduction. Pacific Symposium on Biocomputing 2010: 1-2 - [c55]Robert Warren, David Sankoff:
Genome Aliquoting Revisited. RECOMB-CG 2010: 1-12 - [c54]Ghada Badr, Krister M. Swenson, David Sankoff:
Listing All Parsimonious Reversal Sequences: New Algorithms and Perspectives. RECOMB-CG 2010: 39-49 - [c53]Haitao Jiang, Chunfang Zheng, David Sankoff, Binhai Zhu:
Scaffold Filling under the Breakpoint Distance. RECOMB-CG 2010: 83-92 - [c52]Krister M. Swenson, Ghada Badr, David Sankoff:
Listing All Sorting Reversals in Quadratic Time. WABI 2010: 102-110
2000 – 2009
- 2009
- [j38]Eric Tannier, Chunfang Zheng, David Sankoff:
Multichromosomal median and halving problems under different genomic distances. BMC Bioinform. 10 (2009) - [j37]Robert Warren, David Sankoff:
Genome aliquoting with double cut and join. BMC Bioinform. 10(S-1) (2009) - [j36]Robert Warren, David Sankoff:
Genome Halving with Double Cut and Join. J. Bioinform. Comput. Biol. 7(2): 357-371 (2009) - [j35]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): 499-520 (2009) - [j34]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): 1353-1367 (2009) - [j33]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): 10-25 (2009) - [j32]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): 213-220 (2009) - [c51]Adriana Muñoz, David Sankoff:
Rearrangement Phylogeny of Genomes in Contig Form. ISBRA 2009: 160-172 - [c50]Bernard M. E. Moret, Webb Miller, Pavel A. Pevzner, David Sankoff:
Session Introduction. Pacific Symposium on Biocomputing 2009: 111-113 - [c49]Zhenyu Yang, David Sankoff:
Natural Parameter Values for Generalized Gene Adjacency. RECOMB-CG 2009: 13-23 - [c48]Zaky Adam, David Sankoff:
A Statistically Fair Comparison of Ancestral Genome Reconstructions, Based on Breakpoint and Rearrangement Distances. RECOMB-CG 2009: 193-204 - 2008
- [j31]Chunfang Zheng, Qian Zhu, David Sankoff:
Descendants of Whole Genome Duplication within Gene Order Phylogeny. J. Comput. Biol. 15(8): 947-964 (2008) - [c47]Robert Warren, David Sankoff:
Genome Halving with Double Cut and Join. APBC 2008: 231-240 - [c46]Andrew Wei Xu, Benoît Alain, David Sankoff:
Poisson adjacency distributions in genome comparison: multichromosomal, circular, signed and unsigned cases. ECCB 2008: 146-152 - [c45]Mariana Kant, Maurice LeBon, David Sankoff:
Hierarchical Clustering Using Constraints. ISBRA 2008: 2-13 - [c44]Qian Zhu, Zaky Adam, Vicky Choi, David Sankoff:
Generalized Gene Adjacencies, Graph Bandwidth and Clusters in Yeast Evolution. ISBRA 2008: 134-145 - [c43]Chunfang Zheng, Qian Zhu, Zaky Adam, David Sankoff:
Guided genome halving: hardness, heuristics and the history of the Hemiascomycetes. ISMB 2008: 96-104 - [c42]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: 252-264 - [c41]Eric Tannier, Chunfang Zheng, David Sankoff:
Multichromosomal Genome Median and Halving Problems. WABI 2008: 1-13 - [c40]Andrew Wei Xu, David Sankoff:
Decompositions of Multiple Breakpoint Graphs and Rapid Exact Solutions to the Median Problem. WABI 2008: 25-37 - [c39]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: 92-103 - [c38]Ximing Xu, David Sankoff:
Tests for Gene Clusters Satisfying the Generalized Adjacency Criterion. BSB 2008: 152-160 - 2007
- [j30]Wei Xu, Chunfang Zheng, David Sankoff:
Paths and Cycles in Breakpoint Graph of Random Multichromosomal Genomes. J. Comput. Biol. 14(4): 423-435 (2007) - [j29]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): 436-445 (2007) - [j28]Chunfang Zheng, Qian Zhu, David Sankoff:
Removing Noise and Ambiguities from Comparative Maps in Rearrangement Analysis. IEEE ACM Trans. Comput. Biol. Bioinform. 4(4): 515-522 (2007) - [c37]David Sankoff, Lusheng Wang, Francis Y. L. Chin:
Preface. APBC 2007 - [c36]David Sankoff, Chunfang Zheng, Qian Zhu:
Polyploids, genome halving and phylogeny. ISMB/ECCB (Supplement of Bioinformatics) 2007: 433-439 - [c35]Chunfang Zheng, Qian Zhu, David Sankoff:
Parts of the Problem of Polyploids in Rearrangement Phylogeny. RECOMB-CG 2007: 162-176 - [c34]Vicky Choi, Chunfang Zheng, Qian Zhu, David Sankoff:
Algorithms for the Extraction of Synteny Blocks from Comparative Maps. WABI 2007: 277-288 - [p1]David Sankoff:
Conserved segment statistics and rearrangement inferences in comparative genomics. Mathematics of Evolution and Phylogeny 2007 - [e4]David Sankoff, Lusheng Wang, Francis Y. L. Chin:
Proceedings of 5th Asia-Pacific Bioinformatics Conference, APBC 2007, 15-17 January 2007, Hong Kong, China. Advances in Bioinformatics and Computational Biology 5, Imperial College Press 2007, ISBN 978-1-86094-783-4 [contents] - 2006
- [j27]Matthew Mazowita, Lani Haque, David Sankoff:
Stability of Rearrangement Measures in the Comparison of Genome Sequences. J. Comput. Biol. 13(2): 554-566 (2006) - [j26]David Sankoff, Lani Haque:
The Distribution of Genomic Distance between Random Genomes. J. Comput. Biol. 13(5): 1005-1012 (2006) - [j25]Chunfang Zheng, David Sankoff:
Genome rearrangements with partially ordered chromosomes. J. Comb. Optim. 11(2): 133-144 (2006) - [j24]David Sankoff:
The Signal in the Genomes. PLoS Comput. Biol. 2(4) (2006) - [c33]Chunfang Zheng, David Sankoff:
Rearrangement of Noisy Genomes. International Conference on Computational Science (2) 2006: 791-798 - [c32]Andrew Wei Xu, Chunfang Zheng, David Sankoff:
Paths and Cycles in Breakpoint Graphs of Random Multichromosomal Genomes. Comparative Genomics 2006: 51-62 - [c31]Zaky Adam, Monique Turmel, Claude Lemieux, David Sankoff:
Common Intervals and Symmetric Difference in a Model-Free Phylogenomics, with an Application to Streptophyte Evolution. Comparative Genomics 2006: 63-74 - [c30]David Sankoff:
Statistical Evaluation of Genome Rearrangement. RECOMB 2006: 84-84 - 2005
- [j23]David Sankoff, Phil Trinh:
Chromosomal Breakpoint Reuse in Genome Sequence Rearrangement. J. Comput. Biol. 12(6): 812-821 (2005) - [j22]Rose Hoberman, David Sankoff, Dannie Durand:
The Statistical Analysis of Spatially Clustered Genes under the Maximum Gap Criterion. J. Comput. Biol. 12(8): 1083-1102 (2005) - [c29]Chunfang Zheng, David Sankoff:
Genome Rearrangements with Partially Ordered Chromosomes. COCOON 2005: 52-62 - [c28]Chunfang Zheng, Aleksander Lenert, David Sankoff:
Reversal distance for partially ordered genomes. ISMB (Supplement of Bioinformatics) 2005: 502-508 - [c27]David Sankoff, Lani Haque:
Power Boosts for Cluster Tests. Comparative Genomics 2005: 121-130 - [c26]David Sankoff, Chunfang Zheng, Aleksander Lenert:
Reversals of Fortune. Comparative Genomics 2005: 131-141 - [c25]David Sankoff, Matthew Mazowita:
Stability of Rearrangement Measures in the Comparison of Genome Sequences. RECOMB 2005: 603-614 - 2004
- [j21]Guillaume Bourque, David Sankoff:
Improving Gene Network Inference by Comparing Expression Time-series across Species, Developmental Stages or Tissues. J. Bioinform. Comput. Biol. 2(4): 765-784 (2004) - [j20]Raffaele Giancarlo, David Sankoff:
Editorial: Combinatiorial Pattern Matching. J. Discrete Algorithms 2(2): 135-136 (2004) - [c24]Phil Trinh, Aoife McLysaght, David Sankoff:
Genomic features in the breakpoint regions between syntenic blocks. ISMB/ECCB (Supplement of Bioinformatics) 2004: 318-325 - [c23]David Sankoff, Phil Trinh:
Chromosomal breakpoint re-use in the inference of genome sequence rearrangement.