Publications

Constructing Founder Sets Under Allelic and Non-Allelic Homologous Recombination
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A Draft Human Pangenome Reference
Wen-Wei Liao, Mobin Asri, Jana Ebler, Daniel Doerr, Marina Haukness, Glenn Hickey, Shuangjia Lu, Julian K. Lucas, Jean Monlong, Haley J. Abel, Silvia Buonaiuto, Xian H. Chang, Haoyu Cheng, Justin Chu, Vincenza Colonna, Jordan M. Eizenga, Xiaowen Feng, Christian Fischer, Robert S. Fulton, Shilpa Garg, Cristian Groza, Andrea Guarracino, William T. Harvey, Simon Heumos, Kerstin Howe, Miten Jain, Tsung-Yu Lu, Charles Markello, Fergal J. Martin, Matthew W. Mitchell, Katherine M. Munson, Moses Njagi Mwaniki, Adam M. Novak, Hugh E. Olsen, Trevor Pesout, David Porubsky, Pjotr Prins, Jonas A. Sibbesen, Chad Tomlinson, Flavia Villani, Mitchell R. Vollger, Guillaume Bourque, Mark J. P. Chaisson, Paul Flicek, Adam M. Phillippy, Justin M. Zook, Evan E. Eichler, David Haussler, Erich D. Jarvis, Karen H. Miga, Ting Wang, Erik Garrison, Tobias Marschall, Ira M. Hall, Heng Li, Benedict Paten
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The potential of family-free rearrangements towards gene orthology inference
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Small parsimony for natural genomes in the DCJ-indel model
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Computing the Rearrangement Distance of Natural Genomes.
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Horizontal Gene Transfer Phylogenetics: A Model-Based Approach
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Computing the Rearrangement Distance of Natural Genomes
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Analysis of local genome rearrangement improves resolution of ancestral genomic maps in plants
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Active and repressed biosynthetic gene clusters have spatially distinct chromosome states.
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A Perspective on Comparative and Functional Genomics
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Sequence-Based Synteny Analysis of Multiple Large Genomes
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GraphTeams: a method for discovering spatial gene clusters in Hi-C sequencing data
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Family-Free Genome Comparison
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The gene family-free median of three
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The gene family-free median of three
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New Genome Similarity Measures based on Conserved Gene Adjacencies
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Finding Teams in Graphs and Its Application to Spatial Gene Cluster Discovery
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Comparative scaffolding and gap filling of ancient bacterial genomes applied to two ancient Yersinia pestis genomes
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New genome similarity measures based on conserved gene adjacencies
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Gene family-free genome comparison
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Proactive simulation and detection of outbreaks based on product data
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Orthology detection combining clustering and synteny for very large datasets
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Identifying gene clusters by discovering common intervals in indeterminate strings
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The potential of family-free genome comparison
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Stochastic errors vs. modeling errors in distance based phylogenetic reconstructions
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Gene family assignment-free comparative genomics
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Accelerating investigation of food-borne disease outbreaks using pro-active geospatial modeling of food supply chains
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