Publications

2020

Justin M Zook, Nancy F Hansen, Nathan D Olson, Lesley Chapman, James C Mullikin, Chunlin Xiao, Stephen Sherry, Sergey Koren, Adam M Phillippy, Paul C Boutros, Sayed Mohammad E Sahraeian, Vincent Huang, Alexandre Rouette, Noah Alexander, Christopher E Mason, Iman Hajirasouliha, Camir Ricketts, Joyce Lee, Rick Tearle, Ian T Fiddes, Alvaro Martinez Barrio, Jeremiah Wala, Andrew Carroll, Noushin Ghaffari, Oscar L Rodriguez, Ali Bashir, Shaun Jackman, John J Farrell, Aaron M Wenger, Can Alkan, Arda Soylev, Michael C Schatz, Shilpa Garg, George Church, Tobias Marschall, Ken Chen, Xian Fan, Adam C English, Jeffrey A Rosenfeld, Weichen Zhou, Ryan E Mills, Jay M Sage, Jennifer R Davis, Michael D Kaiser, John S Oliver, Anthony P Catalano, Mark JP Chaisson, Noah Spies, Fritz J Sedlazeck, Marc Salit; A robust benchmark for detection of germline large deletions and insertions, Nature Biotechnology, 1-9

2019

Arvis Sulovari, Ruiyang Li, Peter A Audano, David Porubsky, Mitchell R Vollger, Glennis A Logsdon, Wesley C Warren, Alex A Pollen, Mark JP Chaisson, Evan E Eichler, Human Genome Structural Variation Consortium; Human-specific tandem repeat expansion and differential gene expression during primate evolution, Proceedings of the National Academy of Sciences 116 (46), 23243-23253

Mark JP Chaisson, Ashley D Sanders, Xuefang Zhao, Ankit Malhotra, David Porubsky, Tobias Rausch, Eugene J Gardner, Oscar L Rodriguez, Li Guo, Ryan L Collins, Xian Fan, Jia Wen, Robert E Handsaker, Susan Fairley, Zev N Kronenberg, Xiangmeng Kong, Fereydoun Hormozdiari, Dillon Lee, Aaron M Wenger, Alex R Hastie, Danny Antaki, Thomas Anantharaman, Peter A Audano, Harrison Brand, Stuart Cantsilieris, Han Cao, Eliza Cerveira, Chong Chen, Xintong Chen, Chen-Shan Chin, Zechen Chong, Nelson T Chuang, Christine C Lambert, Deanna M Church, Laura Clarke, Andrew Farrell, Joey Flores, Timur Galeev, David U Gorkin, Madhusudan Gujral, Victor Guryev, William Haynes Heaton, Jonas Korlach, Sushant Kumar, Jee Young Kwon, Ernest T Lam, Jong Eun Lee, Joyce Lee, Wan-Ping Lee, Sau Peng Lee, Shantao Li, Patrick Marks, Karine Viaud-Martinez, Sascha Meiers, Katherine M Munson, Fabio CP Navarro, Bradley J Nelson, Conor Nodzak, Amina Noor, Sofia Kyriazopoulou-Panagiotopoulou, Andy WC Pang, Yunjiang Qiu, Gabriel Rosanio, Mallory Ryan, Adrian St├╝tz, Diana CJ Spierings, Alistair Ward, AnneMarie E Welch, Ming Xiao, Wei Xu, Chengsheng Zhang, Qihui Zhu, Xiangqun Zheng-Bradley, Ernesto Lowy, Sergei Yakneen, Steven McCarroll, Goo Jun, Li Ding, Chong Lek Koh, Bing Ren, Paul Flicek, Ken Chen, Mark B Gerstein, Pui-Yan Kwok, Peter M Lansdorp, Gabor T Marth, Jonathan Sebat, Xinghua Shi, Ali Bashir, Kai Ye, Scott E Devine, Michael E Talkowski, Ryan E Mills, Tobias Marschall, Jan O Korbel, Evan E Eichler, Charles Lee; Multi-platform discovery of haplotype-resolved structural variation in human genomes, Nature communications 10 (1), 1-16

Mitchell R Vollger, Philip C Dishuck, Melanie Sorensen, AnneMarie E Welch, Vy Dang, Max L Dougherty, Tina A Graves-Lindsay, Richard K Wilson, Mark JP Chaisson, Evan E Eichler; Long-read sequence and assembly of segmental duplications, Nature methods 16 (1), 88-94

2018

Zev N Kronenberg, Ian T Fiddes, David Gordon, Shwetha Murali, Stuart Cantsilieris, Olivia S Meyerson, Jason G Underwood, Bradley J Nelson, Mark JP Chaisson, Max L Dougherty, Katherine M Munson, Alex R Hastie, Mark Diekhans, Fereydoun Hormozdiari, Nicola Lorusso, Kendra Hoekzema, Ruolan Qiu, Karen Clark, Archana Raja, AnneMarie E Welch, Melanie Sorensen, Carl Baker, Robert S Fulton, Joel Armstrong, Tina A Graves-Lindsay, Ahmet M Denli, Emma R Hoppe, PingHsun Hsieh, Christopher M Hill, Andy Wing Chun Pang, Joyce Lee, Ernest T Lam, Susan K Dutcher, Fred H Gage, Wesley C Warren, Jay Shendure, David Haussler, Valerie A Schneider, Han Cao, Mario Ventura, Richard K Wilson, Benedict Paten, Alex Pollen, Evan E Eichler; High-resolution comparative analysis of great ape genomes, Science 360 (6393)

2017

John Huddleston, Mark JP Chaisson, Karyn Meltz Steinberg, Wes Warren, Kendra Hoekzema, David Gordon, Tina A Graves-Lindsay, Katherine M Munson, Zev N Kronenberg, Laura Vives, Paul Peluso, Matthew Boitano, Chen-Shin Chin, Jonas Korlach, Richard K Wilson, Evan E Eichler; Discovery and genotyping of structural variation from long-read haploid genome sequence data, Genome research 27 (5), 677-685

X Fan, M Chaisson, L Nakhleh, K Chen; HySA: a Hybrid Structural variant Assembly approach using next-generation and single-molecule sequencing technologies, Genome research 27 (5), 793-800

2016

Y Lin, J Yuan, M Kolmogorov, MW Shen, M Chaisson, PA Pevzner; Assembly of long error-prone reads using de Bruijn graphs, Proceedings of the National Academy of Sciences 113 (52), E8396-E8405

David Gordon1; John Huddleston1Mark J.P. Chaisson1; Christopher M. Hill1; Zev N. Kronenberg1; Katherine M. Munson; Maika Malig; Archana Raja; Ian Fiddes; LaDeana W. Hillier; Carl Baker; Joel Armstrong; Mark Diekhans; Benedict Paten; Richard K. Wilson; David Haussler; Chen-Shan Chin; and Evan E. Eichler; Long-read sequence assembly of the gorilla genome, Science 352.6281 (2016) 1co-first authors.

2015


Chaisson, Mark JP; Wilson, Richard K; Eichler, Evan E; Genetic variation and the de novo assembly of human genomes, Nature Reviews Genetics 2015

Chaisson, Mark JP ; Huddleston, John; Dennis, Megan Y; Sudmant, Peter H; Malig, Maika; Hormozdiari, Fereydoun; Antonacci, Francesca; Surti, Urvashi; Sandstrom, Richard; Boitano, Matthew; Resolving the complexity of the human genome using single-molecule sequencing, Nature, 517, 7536, 608-611, 2015

Sudmant, Peter H; The 1000 Genomes Project Consortium, An integrated map of structural variation in 2,504 human genomes Nature, 526, 7571, 75-81, 2015

2014


Huddleston, John; Ranade, Swati; Malig, Maika; Antonacci, Francesca; Chaisson, Mark ; Hon, Lawrence; Sudmant, Peter H; Graves, Tina A; Alkan, Can; Dennis, Megan Y; Reconstructing complex regions of genomes using long-read sequencing technology, Genome Research, 24, 4, 688-696, 2014

2013

Dobin, Alexander; Davis, Carrie A; Schlesinger, Felix; Drenkow, Jorg; Zaleski, Chris; Jha, Sonali; Batut, Philippe; Chaisson, Mark; Gingeras, Thomas R; STAR: ultrafast universal RNA-seq aligner, Bioinformatics, 29, 1, 15-21, 2013

2012

Chaisson, Mark J; Tesler, Glenn; Mapping single molecule sequencing reads using basic local alignment with successive refinement (BLASR): application and theory, BMC Bioinformatics, 13,1,238,2012

2011

Medvedev, Paul; Pham, Son; Chaisson, Mark; Tesler, Glenn; Pevzner, Pavel; Paired de bruijn graphs: a novel approach for incorporating mate pair information into genome assemblers Journal of Computational Biology ,18,11,1625-1634,2011

2010 and earlier

Chaisson, Mark J; Brinza, Dumitru; Pevzner, Pavel A; De novo fragment assembly with short mate-paired reads: Does the read length matter? Genome Research 19, 2, 336-346, 2009
Chaisson, Mark J; Pevzner, Pavel A; Short read fragment assembly of bacterial genomes, Genome Research18,2,324-330,2008
Chaisson, Mark J; Raphael, Benjamin J; Pevzner, Pavel A; Microinversions in mammalian evolution, Proceedings of the National Academy of Sciences 103, 52, 19824-19829, 2006
Chaisson, Mark; Pevzner, Pavel; Tang, Haixu; Fragment assembly with short reads, Bioinformatics 20, 13, 2067-2074, 2004