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2020 – today
- 2021
[j30]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)- [j29]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) - [j28]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) - 2020
- [c23]Zhe Yu, Chunfang Zheng, David Sankoff:
Gaps and Runs in Syntenic Alignments. AlCoB 2020: 49-60 - [c22]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
- [j27]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) - [j26]Yue Zhang, Chunfang Zheng, David Sankoff:
Distinguishing successive ancient polyploidy levels based on genome-internal syntenic alignment. BMC Bioinform. 20-S(20): 635 (2019) - [j25]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
- [j24]Chunfang Zheng, Yuji Jeong, Madisyn Gabrielle Turcotte, David Sankoff:
Resolution effects in reconstructing ancestral genomes. BMC Genom. 19(S2) (2018) - [j23]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) - [c21]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 - 2016
- [j22]Chunfang Zheng, David Sankoff:
Locating rearrangement events in a phylogeny based on highly fragmented assemblies. BMC Genom. 17(S-1): 1 (2016) - [c20]David Sankoff, Chunfang Zheng, Eric Lyons, Haibao Tang:
The Trees in the Peaks. AlCoB 2016: 3-14 - 2015
- [j21]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) - [c19]Poly H. da Silva, Simone Dantas, Chunfang Zheng, David Sankoff:
Graph-Theoretic Modelling of the Domain Chaining Problem. WABI 2015: 296-307 - 2014
- [j20]Chunfang Zheng, David Sankoff:
Practical halving; the Nelumbo nucifera evidence on early eudicot evolution. Comput. Biol. Chem. 50: 75-81 (2014) - [c18]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
- [j19]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) - [j18]Chunfang Zheng, David Sankoff:
Practical aliquoting of flowering plant genomes. BMC Bioinform. 14(S-15): S8 (2013) - [p1]David Sankoff, Chunfang Zheng:
Fractionation, Rearrangement, Consolidation, Reconstruction. Models and Algorithms for Genome Evolution 2013: 247-260 - 2012
- [j17]David Sankoff, Chunfang Zheng:
Fractionation, rearrangement and subgenome dominance. Bioinform. 28(18): 402-408 (2012) - [j16]Chunfang Zheng, David Sankoff:
Gene order in rosid phylogeny, inferred from pairwise syntenies among extant genomes. BMC Bioinform. 13(S-10): S9 (2012) - [j15]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) - [j14]David Sankoff, Chunfang Zheng, Baoyong Wang:
A model for biased fractionation after whole genome duplication. BMC Genom. 13(S-1): S8 (2012) - [j13]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) - [c17]Chunfang Zheng, Victor A. Albert, Eric Lyons, David Sankoff:
Ancient angiosperm hexaploidy meets ancestral eudicot gene order. ICCABS 2012: 1-6 - [c16]David Sankoff, Chunfang Zheng, Baoyong Wang:
A Model for Biased Fractionation after Whole Genome Duplication. RECOMB 2012: 244 - 2011
- [j12]Chunfang Zheng, David Sankoff:
On the PATHGROUPS approach to rapid small phylogeny. BMC Bioinform. 12(S-1): S4 (2011) - [j11]Baoyong Wang, Chunfang Zheng, David Sankoff:
Fractionation statistics. BMC Bioinform. 12(S-9): S5 (2011) - [c15]Chunfang Zheng, David Sankoff:
Gene Order in Rosid Phylogeny, Inferred from Pairwise Syntenies among Extant Genomes. ISBRA 2011: 99-110 - [c14]Chunfang Zheng, Krister M. Swenson, Eric Lyons, David Sankoff:
OMG! Orthologs in Multiple Genomes - Competing Graph-Theoretical Formulations. WABI 2011: 364-375 - 2010
- [j10]Chunfang Zheng:
Pathgroups, a dynamic data structure for genome reconstruction problems. Bioinform. 26(13): 1587-1594 (2010) - [j9]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) - [c13]Chunfang Zheng:
Analysis of Applicability of Strategic Trade Policy to China's Electronics and Information Industry: A Perspective from Market Power. ICEE 2010: 3695-3698 - [c12]Haitao Jiang, Chunfang Zheng, David Sankoff, Binhai Zhu:
Scaffold Filling under the Breakpoint Distance. RECOMB-CG 2010: 83-92
2000 – 2009
- 2009
- [j8]Eric Tannier, Chunfang Zheng, David Sankoff:
Multichromosomal median and halving problems under different genomic distances. BMC Bioinform. 10 (2009) - [j7]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) - [j6]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) - [j5]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) - 2008
- [j4]Chunfang Zheng, Qian Zhu, David Sankoff:
Descendants of Whole Genome Duplication within Gene Order Phylogeny. J. Comput. Biol. 15(8): 947-964 (2008) - [c11]Chunfang Zheng, Qian Zhu, Zaky Adam, David Sankoff:
Guided genome halving: hardness, heuristics and the history of the Hemiascomycetes. ISMB 2008: 96-104 - [c10]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 - [c9]Eric Tannier, Chunfang Zheng, David Sankoff:
Multichromosomal Genome Median and Halving Problems. WABI 2008: 1-13 - 2007
- [j3]Wei Xu, Chunfang Zheng, David Sankoff:
Paths and Cycles in Breakpoint Graph of Random Multichromosomal Genomes. J. Comput. Biol. 14(4): 423-435 (2007) - [j2]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) - [c8]David Sankoff, Chunfang Zheng, Qian Zhu:
Polyploids, genome halving and phylogeny. ISMB/ECCB (Supplement of Bioinformatics) 2007: 433-439 - [c7]Chunfang Zheng, Qian Zhu, David Sankoff:
Parts of the Problem of Polyploids in Rearrangement Phylogeny. RECOMB-CG 2007: 162-176 - [c6]Vicky Choi, Chunfang Zheng, Qian Zhu, David Sankoff:
Algorithms for the Extraction of Synteny Blocks from Comparative Maps. WABI 2007: 277-288 - 2006
- [j1]Chunfang Zheng, David Sankoff:
Genome rearrangements with partially ordered chromosomes. J. Comb. Optim. 11(2): 133-144 (2006) - [c5]Chunfang Zheng, David Sankoff:
Rearrangement of Noisy Genomes. International Conference on Computational Science (2) 2006: 791-798 - [c4]Andrew Wei Xu, Chunfang Zheng, David Sankoff:
Paths and Cycles in Breakpoint Graphs of Random Multichromosomal Genomes. Comparative Genomics 2006: 51-62 - 2005
- [c3]Chunfang Zheng, David Sankoff:
Genome Rearrangements with Partially Ordered Chromosomes. COCOON 2005: 52-62 - [c2]Chunfang Zheng, Aleksander Lenert, David Sankoff:
Reversal distance for partially ordered genomes. ISMB (Supplement of Bioinformatics) 2005: 502-508 - [c1]David Sankoff, Chunfang Zheng, Aleksander Lenert:
Reversals of Fortune. Comparative Genomics 2005: 131-141
Coauthor Index
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