Chunfang Zheng

54 papers A 1B 1C 4Misc 2Journal 30Unranked 15

Year	Rank	Type	Title / Venue / Authors
2021	J	`jnl`	Ancestral Flowering Plant Chromosomes and Gene Orders Based on Generalized Adjacencies and Chromosomal Gene Co-Occurrences. J. Comput. Biol. Qiaoji Xu, Lingling Jin, Yue Zhang, Xiaomeng Zhang, Chunfang Zheng, James H. Leebens-Mack, David Sankoff
2021	J	`jnl`	Branching Out to Speciation in a Model of Fractionation: The Malvaceae. IEEE ACM Trans. Comput. Biol. Bioinform. Yue Zhang, Chunfang Zheng, Sindeed Islam, Yong-Min Kim, David Sankoff
2021	J	`jnl`	The monoploid chromosome complement of reconstructed ancestral genomes in a phylogeny. J. Bioinform. Comput. Biol. Qiaoji Xu, Xiaomeng Zhang, Yue Zhang, Chunfang Zheng, James H. Leebens-Mack, Lingling Jin, David Sankoff
2020	—	`conf`	Gaps and Runs in Syntenic Alignments. AlCoB Zhe Yu, Chunfang Zheng, David Sankoff
2020	—	`conf`	RACCROCHE: Ancestral Flowering Plant Chromosomes and Gene Orders Based on Generalized Adjacencies and Chromosomal Gene Co-occurrences. ICCABS Qiaoji Xu, Lingling Jin, Chunfang Zheng, James H. Leebens-Mack, David Sankoff
2019	J	`jnl`	A branching process for homology distribution-based inference of polyploidy, speciation and loss. Algorithms Mol. Biol. Yue Zhang, Chunfang Zheng, David Sankoff
2019	J	`jnl`	Distinguishing successive ancient polyploidy levels based on genome-internal syntenic alignment. BMC Bioinform. Yue Zhang, Chunfang Zheng, David Sankoff
2019	J	`jnl`	Models for Similarity Distributions of Syntenic Homologs and Applications to Phylogenomics. IEEE ACM Trans. Comput. Biol. Bioinform. David Sankoff, Chunfang Zheng, Yue Zhang, Joao Meidanis, Eric Lyons, Haibao Tang
2018	J	`jnl`	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. Yue Zhang, Chunfang Zheng, David Sankoff
2018	J	`jnl`	Resolution effects in reconstructing ancestral genomes. BMC Genom. Chunfang Zheng, Yuji Jeong, Madisyn Gabrielle Turcotte, David Sankoff
2018	—	`conf`	Speciation and Rate Variation in a Birth-and-Death Account of WGD and Fractionation; the Case of Solanaceae. RECOMB-CG Yue Zhang, Chunfang Zheng, David Sankoff
2016	J	`jnl`	Locating rearrangement events in a phylogeny based on highly fragmented assemblies. BMC Genom. Chunfang Zheng, David Sankoff
2016	—	`conf`	The Trees in the Peaks. AlCoB David Sankoff, Chunfang Zheng, Eric Lyons, Haibao Tang
2015	C	`conf`	Graph-Theoretic Modelling of the Domain Chaining Problem. WABI Poly H. da Silva, Simone Dantas, Chunfang Zheng, David Sankoff
2015	J	`jnl`	Structural vs. functional mechanisms of duplicate gene loss following whole genome doubling. BMC Bioinform. David Sankoff, Chunfang Zheng, Baoyong Wang, Carlos Fernando Buen Abad Najar
2014	J	`jnl`	Practical halving; the Nelumbo nucifera evidence on early eudicot evolution. Comput. Biol. Chem. Chunfang Zheng, David Sankoff
2014	—	`conf`	Structural vs. functional mechanisms of duplicate gene loss following whole genome doubling. ICCABS David Sankoff, Baoyong Wang, Chunfang Zheng, Carlos Fernando Buen Abad Najar
2013	—	`ch.`	Fractionation, Rearrangement, Consolidation, Reconstruction. Models and Algorithms for Genome Evolution David Sankoff, Chunfang Zheng
2013	J	`jnl`	Practical aliquoting of flowering plant genomes. BMC Bioinform. Chunfang Zheng, David Sankoff
2013	J	`jnl`	The dynamics of functional classes of plant genes in rediploidized ancient polyploids. BMC Bioinform. 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
2012	B	`conf`	A Model for Biased Fractionation after Whole Genome Duplication. RECOMB David Sankoff, Chunfang Zheng, Baoyong Wang
2012	J	`jnl`	A consolidation algorithm for genomes fractionated after higher order polyploidization. BMC Bioinform. Katharina Jahn, Chunfang Zheng, Jakub Kovác, David Sankoff
2012	J	`jnl`	A model for biased fractionation after whole genome duplication. BMC Genom. David Sankoff, Chunfang Zheng, Baoyong Wang
2012	—	`conf`	Ancient angiosperm hexaploidy meets ancestral eudicot gene order. ICCABS Chunfang Zheng, Victor A. Albert, Eric Lyons, David Sankoff
2012	J	`jnl`	Fractionation, rearrangement and subgenome dominance. Bioinform. David Sankoff, Chunfang Zheng
2012	J	`jnl`	Gene order in rosid phylogeny, inferred from pairwise syntenies among extant genomes. BMC Bioinform. Chunfang Zheng, David Sankoff
2012	J	`jnl`	Scaffold Filling under the Breakpoint and Related Distances. IEEE ACM Trans. Comput. Biol. Bioinform. Haitao Jiang, Chunfang Zheng, David Sankoff, Binhai Zhu
2011	J	`jnl`	Fractionation statistics. BMC Bioinform. Baoyong Wang, Chunfang Zheng, David Sankoff
2011	—	`conf`	Gene Order in Rosid Phylogeny, Inferred from Pairwise Syntenies among Extant Genomes. ISBRA Chunfang Zheng, David Sankoff
2011	C	`conf`	OMG! Orthologs in Multiple Genomes - Competing Graph-Theoretical Formulations. WABI Chunfang Zheng, Krister M. Swenson, Eric Lyons, David Sankoff
2011	J	`jnl`	On the PATHGROUPS approach to rapid small phylogeny. BMC Bioinform. Chunfang Zheng, David Sankoff
2010	—	`conf`	Analysis of Applicability of Strategic Trade Policy to China's Electronics and Information Industry: A Perspective from Market Power. ICEE Chunfang Zheng
2010	J	`jnl`	Pathgroups, a dynamic data structure for genome reconstruction problems. Bioinform. Chunfang Zheng
2010	—	`conf`	Scaffold Filling under the Breakpoint Distance. RECOMB-CG Haitao Jiang, Chunfang Zheng, David Sankoff, Binhai Zhu
2010	J	`jnl`	Scaffold filling, contig fusion and comparative gene order inference. BMC Bioinform. Adriana Muñoz, Chunfang Zheng, Qian Zhu, Victor A. Albert, Steve Rounsley, David Sankoff
2009	J	`jnl`	Gene Loss under Neighborhood Selection Following Whole genome Duplication and the Reconstruction of the Ancestral Populus genome. J. Bioinform. Comput. Biol. Chunfang Zheng, P. Kerr Wall, James H. Leebens-Mack, Claude de Pamphilis, Victor A. Albert, David Sankoff
2009	J	`jnl`	Issues in the Reconstruction of Gene Order Evolution. J. Comput. Sci. Technol. David Sankoff, Chunfang Zheng, Adriana Muñoz, Zhenyu Yang, Zaky Adam, Robert Warren, Vicky Choi, Qian Zhu
2009	J	`jnl`	Multichromosomal median and halving problems under different genomic distances. BMC Bioinform. Eric Tannier, Chunfang Zheng, David Sankoff
2009	J	`jnl`	Towards Improved Reconstruction of Ancestral Gene Order in Angiosperm Phylogeny. J. Comput. Biol. David Sankoff, Chunfang Zheng, P. Kerr Wall, Claude de Pamphilis, James H. Leebens-Mack, Victor A. Albert
2008	J	`jnl`	Descendants of Whole Genome Duplication within Gene Order Phylogeny. J. Comput. Biol. Chunfang Zheng, Qian Zhu, David Sankoff
2008	A	`conf`	Guided genome halving: hardness, heuristics and the history of the Hemiascomycetes. ISMB Chunfang Zheng, Qian Zhu, Zaky Adam, David Sankoff
2008	—	`conf`	Internal Validation of Ancestral Gene Order Reconstruction in Angiosperm Phylogeny. RECOMB-CG David Sankoff, Chunfang Zheng, P. Kerr Wall, Claude W. dePamphilis, James H. Leebens-Mack, Victor A. Albert
2008	C	`conf`	Multichromosomal Genome Median and Halving Problems. WABI Eric Tannier, Chunfang Zheng, David Sankoff
2007	C	`conf`	Algorithms for the Extraction of Synteny Blocks from Comparative Maps. WABI Vicky Choi, Chunfang Zheng, Qian Zhu, David Sankoff
2007	—	`conf`	Parts of the Problem of Polyploids in Rearrangement Phylogeny. RECOMB-CG Chunfang Zheng, Qian Zhu, David Sankoff
2007	J	`jnl`	Paths and Cycles in Breakpoint Graph of Random Multichromosomal Genomes. J. Comput. Biol. Wei Xu, Chunfang Zheng, David Sankoff
2007	—	`conf`	Polyploids, genome halving and phylogeny. ISMB/ECCB (Supplement of Bioinformatics) David Sankoff, Chunfang Zheng, Qian Zhu
2007	J	`jnl`	Removing Noise and Ambiguities from Comparative Maps in Rearrangement Analysis. IEEE ACM Trans. Comput. Biol. Bioinform. Chunfang Zheng, Qian Zhu, David Sankoff
2006	J	`jnl`	Genome rearrangements with partially ordered chromosomes. J. Comb. Optim. Chunfang Zheng, David Sankoff
2006	—	`conf`	Paths and Cycles in Breakpoint Graphs of Random Multichromosomal Genomes. Comparative Genomics Andrew Wei Xu, Chunfang Zheng, David Sankoff
2006	Misc	`conf`	Rearrangement of Noisy Genomes. International Conference on Computational Science (2) Chunfang Zheng, David Sankoff
2005	Misc	`conf`	Genome Rearrangements with Partially Ordered Chromosomes. COCOON Chunfang Zheng, David Sankoff
2005	—	`conf`	Reversal distance for partially ordered genomes. ISMB (Supplement of Bioinformatics) Chunfang Zheng, Aleksander Lenert, David Sankoff
2005	—	`conf`	Reversals of Fortune. Comparative Genomics David Sankoff, Chunfang Zheng, Aleksander Lenert