| 2018 | RECOMB | Speciation and Rate Variation in a Birth-and-Death Account of WGD and Fractionation; the Case of Solanaceae. | Yue Zhang, Chunfang Zheng, David Sankoff |
| 2015 | WABI | Graph-Theoretic Modelling of the Domain Chaining Problem. | Poly H. da Silva, Simone Dantas, Chunfang Zheng, David Sankoff |
| 2012 | RECOMB | A Model for Biased Fractionation after Whole Genome Duplication. | David Sankoff, Chunfang Zheng, Baoyong Wang |
| 2011 | WABI | OMG! Orthologs in Multiple Genomes - Competing Graph-Theoretical Formulations. | Chunfang Zheng, Krister M. Swenson, Eric Lyons, David Sankoff |
| 2010 | RECOMB | Scaffold Filling under the Breakpoint Distance. | Haitao Jiang, Chunfang Zheng, David Sankoff, Binhai Zhu |
| 2008 | ISMB | Guided genome halving: hardness, heuristics and the history of the Hemiascomycetes. | Chunfang Zheng, Qian Zhu, Zaky Adam, David Sankoff |
| 2008 | RECOMB | Internal Validation of Ancestral Gene Order Reconstruction in Angiosperm Phylogeny. | David Sankoff, Chunfang Zheng, P. Kerr Wall, Claude W. dePamphilis, James H. Leebens-Mack, Victor A. Albert |
| 2008 | WABI | Multichromosomal Genome Median and Halving Problems. | Eric Tannier, Chunfang Zheng, David Sankoff |
| 2007 | ISMB | Polyploids, genome halving and phylogeny. | David Sankoff, Chunfang Zheng, Qian Zhu |
| 2007 | RECOMB | Parts of the Problem of Polyploids in Rearrangement Phylogeny. | Chunfang Zheng, Qian Zhu, David Sankoff |
| 2007 | WABI | Algorithms for the Extraction of Synteny Blocks from Comparative Maps. | Vicky Choi, Chunfang Zheng, Qian Zhu, David Sankoff |
| 2006 | ICCS | Rearrangement of Noisy Genomes. | Chunfang Zheng, David Sankoff |
| 2006 | RECOMB | Paths and Cycles in Breakpoint Graphs of Random Multichromosomal Genomes. | Andrew Wei Xu, Chunfang Zheng, David Sankoff |
| 2005 | COCOON | Genome Rearrangements with Partially Ordered Chromosomes. | Chunfang Zheng, David Sankoff |
| 2005 | ISMB | Reversal distance for partially ordered genomes. | Chunfang Zheng, Aleksander Lenert, David Sankoff |
| 2005 | RECOMB | Reversals of Fortune. | David Sankoff, Chunfang Zheng, Aleksander Lenert |