2023
Lu, Tsung-Yu, and Mark J. P. Chaisson. “The Motif Composition of Variable-Number Tandem Repeats Impacts Gene Expression.” Genome Research 2023.
Liao, Wen-Wei, 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 Hall, Heng Li, Benedict Paten, and Human Pangenome Reference Consortium. “A Draft Human Pangenome Reference.” Nature 617.7960 (2023): 312-324.
2022
Huishi Toh, Giulio Formenti, Kalpana Raja, Alan Tracey, William Chow, Kirsten Howe, Lucie Bergeron, Guojie Zhang, Bettina Haase, Jacquelyn Mountcastle, John Fogg, Bogdan Kirilenko, Chetan Munegowda, Michael Hiller, Ashish Jain, Diana Kihara, Arang Rhie, Adam M. Phillippy, Scott Swanson, Peng Jiang, Dennis O. Clegg, Erich D. Jarvis, James A. Thomson, Ron Stewart, Mark J.P. Chaisson*, and Yury V. Bukhman. 2021. “A Haplotype-Resolved Genome Assembly of the Nile Rat Facilitates Exploration of the Genetic Basis of Diabetes.” BMC biology 20.1 (2022): 245.
*Co-corresponding author
Yang, Jianzhi, and Mark J. P. Chaisson. 2022. “TT-Mars: Structural Variants Assessment Based on Haplotype-Resolved Assemblies.” Genome Biology 23 (1): 110.
Jarvis, Erich D., Giulio Formenti, Arang Rhie, Andrea Guarracino, Chentao Yang, Jonathan Wood, Alan Tracey, Francoise Thibaud-Nissen, Mitchell R. Vollger, David Porubsky, Haoyu Cheng, Mobin Asri, Glennis A. Logsdon, Paolo Carnevali, Mark J. P. Chaisson, Chen-Shan Chin, Sarah Cody, Joanna Collins, Peter Ebert, Merly Escalona, Olivier Fedrigo, Robert S. Fulton, Lucinda L. Fulton, Shilpa Garg, Jay Ghurye, Ana Granat, Edward Green, Ira Hall, William Harvey, Patrick Hasenfeld, Alex Hastie, Marina Haukness, Erich B. Jaeger, Miten Jain, Melanie Kirsche, Mikhail Kolmogorov, Jan O. Korbel, Sergey Koren, Jonas Korlach, Joyce Lee, Daofeng Li, Tina Lindsay, Julian Lucas, Feng Luo, Tobias Marschall, Jennifer McDaniel, Fan Nie, Hugh E. Olsen, Nathan D. Olson, Trevor Pesout, Daniela Puiu, Allison Regier, Jue Ruan, Steven L. Salzberg, Ashley D. Sanders, Michael C. Schatz, Anthony Schmitt, Valerie A. Schneider, Siddarth Selvaraj, Kishwar Shafin, Alaina Shumate, Catherine Stober, James Torrance, Justin Wagner, Jianxin Wang, Aaron Wenger, Chuanle Xiao, Aleksey V. Zimin, Guojie Zhang, Ting Wang, Heng Li, Erik Garrison, David Haussler, Justin M. Zook, Evan E. Eichler, Adam M. Phillippy, Benedict Paten, Kerstin Howe, Karen H. Miga, and Human Pangenome Reference Consortium. 2022. “Automated Assembly of High-Quality Diploid Human Reference Genomes.” Nature, (2022): 1-13.
Wang, Ting, Lucinda Antonacci-Fulton, Kerstin Howe, Heather A. Lawson, Julian K. Lucas, Adam M. Phillippy, Alice B. Popejoy, Mobin Asri, Caryn Carson, Mark J. P. Chaisson, Xian Chang, Robert Cook-Deegan, Adam L. Felsenfeld, Robert S. Fulton, Erik P. Garrison, Nanibaa’ A. Garrison, Tina A. Graves-Lindsay, Hanlee Ji, Eimear E. Kenny, Barbara A. Koenig, Daofeng Li, Tobias Marschall, Joshua F. McMichael, Adam M. Novak, Deepak Purushotham, Valerie A. Schneider, Baergen I. Schultz, Michael W. Smith, Heidi J. Sofia, Tsachy Weissman, Paul Flicek, Heng Li, Karen H. Miga, Benedict Paten, Erich D. Jarvis, Ira M. Hall, Evan E. Eichler, David Haussler, and the Human Pangenome Reference Consortium. 2022. “The Human Pangenome Project: A Global Resource to Map Genomic Diversity.” Nature. 604(7906), 437-446
2021
Ren, Jingwen, and Mark J. P. Chaisson. 2021. “lra: A Long Read Aligner for Sequences and Contigs.” PLoS Computational Biology 17 (6): e1009078.
Lu, Tsung-Yu, Mark J. P. Chaisson, and The Human Genome Structural Variation Consortium. 2021. “Profiling Variable-Number Tandem Repeat Variation across Populations Using Repeat-Pangenome Graphs.” Nature Communications. doi:10.1038/s41467-021-24378-0.
Ebert, Peter, Peter A. Audano, Qihui Zhu, Bernardo Rodriguez-Martin, David Porubsky, Marc Jan Bonder, Arvis Sulovari, Jana Ebler, Weichen Zhou, Rebecca Serra Mari, Feyza Yilmaz, Xuefang Zhao, Pinghsun Hsieh, Joyce Lee, Sushant Kumar, Jiadong Lin, Tobias Rausch, Yu Chen, Jingwen Ren, Martin Santamarina, Wolfram Höps, Hufsah Ashraf, Nelson T. Chuang, Xiaofei Yang, Katherine M. Munson, Alexandra P. Lewis, Susan Fairley, Luke J. Tallon, Wayne E. Clarke, Anna O. Basile, Marta Byrska-Bishop, André Corvelo, Uday S. Evani, Tsung-Yu Lu, Mark J. P. Chaisson, Junjie Chen, Chong Li, Harrison Brand, Aaron M. Wenger, Maryam Ghareghani, William T. Harvey, Benjamin Raeder, Patrick Hasenfeld, Allison A. Regier, Haley J. Abel, Ira M. Hall, Paul Flicek, Oliver Stegle, Mark B. Gerstein, Jose M. C. Tubio, Zepeng Mu, Yang I. Li, Xinghua Shi, Alex R. Hastie, Kai Ye, Zechen Chong, Ashley D. Sanders, Michael C. Zody, Michael E. Talkowski, Ryan E. Mills, Scott E. Devine, Charles Lee, Jan O. Korbel, Tobias Marschall, and Evan E. Eichler. 2021. “Haplotype-Resolved Diverse Human Genomes and Integrated Analysis of Structural Variation.” Science 372 (6537). doi:10.1126/science.abf7117.
Rhie, Arang, Shane A. McCarthy, Olivier Fedrigo, Joana Damas, Giulio Formenti, Sergey Koren, Marcela Uliano-Silva, William Chow, Arkarachai Fungtammasan, Juwan Kim, Chul Lee, Byung June Ko, Mark Chaisson, Gregory L. Gedman, Lindsey J. Cantin, Francoise Thibaud-Nissen, Leanne Haggerty, Iliana Bista, Michelle Smith, Bettina Haase, Jacquelyn Mountcastle, Sylke Winkler, Sadye Paez, Jason Howard, Sonja C. Vernes, Tanya M. Lama, Frank Grutzner, Wesley C. Warren, Christopher N. Balakrishnan, Dave Burt, Julia M. George, Matthew T. Biegler, David Iorns, Andrew Digby, Daryl Eason, Bruce Robertson, Taylor Edwards, Mark Wilkinson, George Turner, Axel Meyer, Andreas F. Kautt, Paolo Franchini, H. William Detrich 3rd, Hannes Svardal, Maximilian Wagner, Gavin J. P. Naylor, Martin Pippel, Milan Malinsky, Mark Mooney, Maria Simbirsky, Brett T. Hannigan, Trevor Pesout, Marlys Houck, Ann Misuraca, Sarah B. Kingan, Richard Hall, Zev Kronenberg, Ivan Sović, Christopher Dunn, Zemin Ning, Alex Hastie, Joyce Lee, Siddarth Selvaraj, Richard E. Green, Nicholas H. Putnam, Ivo Gut, Jay Ghurye, Erik Garrison, Ying Sims, Joanna Collins, Sarah Pelan, James Torrance, Alan Tracey, Jonathan Wood, Robel E. Dagnew, Dengfeng Guan, Sarah E. London, David F. Clayton, Claudio V. Mello, Samantha R. Friedrich, Peter V. Lovell, Ekaterina Osipova, Farooq O. Al-Ajli, Simona Secomandi, Heebal Kim, Constantina Theofanopoulou, Michael Hiller, Yang Zhou, Robert S. Harris, Kateryna D. Makova, Paul Medvedev, Jinna Hoffman, Patrick Masterson, Karen Clark, Fergal Martin, Kevin Howe, Paul Flicek, Brian P. Walenz, Woori Kwak, Hiram Clawson, Mark Diekhans, Luis Nassar, Benedict Paten, Robert H. S. Kraus, Andrew J. Crawford, M. Thomas P. Gilbert, Guojie Zhang, Byrappa Venkatesh, Robert W. Murphy, Klaus-Peter Koepfli, Beth Shapiro, Warren E. Johnson, Federica Di Palma, Tomas Marques-Bonet, Emma C. Teeling, Tandy Warnow, Jennifer Marshall Graves, Oliver A. Ryder, David Haussler, Stephen J. O’Brien, Jonas Korlach, Harris A. Lewin, Kerstin Howe, Eugene W. Myers, Richard Durbin, Adam M. Phillippy, and Erich D. Jarvis. 2021. “Towards Complete and Error-Free Genome Assemblies of All Vertebrate Species.” Nature 592 (7856): 737–46.
Mc Cartney, Ann M., Medhat Mahmoud, Michael Jochum, Daniel Paiva Agustinho, Barry Zorman, Ahmad Al Khleifat, Fawaz Dabbaghie, Rupesh K Kesharwani, Moritz Smolka, Moez Dawood, Dreycey Albin, Elbay Aliyev, Hakeem Almabrazi, Ahmed Arslan, Advait Balaji, Sairam Behera, Kimberley Billingsley, Daniel L Cameron, Joyjit Daw, Eric T Dawson, Wouter De Coster, Haowei Du, Christopher Dunn, Rocio Esteban, Angad Jolly, Divya Kalra, Chunxiao Liao, Yunxi Liu, Tsung-Yu Lu, James M Havrilla, Michael M Khayat, Maximillian Marin, Jean Monlong, Stephen Price, Alejandro Rafael Gener, Jingwen Ren, Sagayamary Sagayaradj, Nicolae Sapoval, Claude Sinner, Daniela C Soto, Arda Soylev, Arun Subramaniyan, Najeeb Syed, Neha Tadimeti, Pamella Tater, Pankaj Vats, Justin Vaughn, Kimberly Walker, Gaojianyong Wang, Qiandong Zeng, Shangzhe Zhang, Tingting Zhao, Bryce Kille, Evan Biederstedt, Mark Chaisson, Adam English, Zev Kronenberg, Todd J Treangen, Timothy Hefferon, Chen-Shan Chin, Ben Busby, and Fritz J Sedlazeck. 2021. “An International Virtual Hackathon to Build Tools for the Analysis of Structural Variants within Species Ranging from Coronaviruses to Vertebrates.” F1000Research 10 (March): 246.
Zhao, Xuefang, Ryan L. Collins, Wan-Ping Lee, Alexandra M. Weber, Yukyung Jun, Qihui Zhu, Ben Weisburd, Yongqing Huang, Peter A. Audano, Harold Wang, Mark Walker, Chelsea Lowther, Jack Fu, Human Genome Structural Variation Consortium, Mark B. Gerstein, Scott E. Devine, Tobias Marschall, Jan O. Korbel, Evan E. Eichler, Mark J. P. Chaisson, Charles Lee, Ryan E. Mills, Harrison Brand, and Michael E. Talkowski. 2021. “Expectations and Blind Spots for Structural Variation Detection from Long-Read Assemblies and Short-Read Genome Sequencing Technologies.” American Journal of Human Genetics 108 (5): 919–28.
2020
Porubsky, David, Human Genome Structural Variation Consortium, Peter Ebert, Peter A. Audano, Mitchell R. Vollger, William T. Harvey, Pierre Marijon, Jana Ebler, Katherine M. Munson, Melanie Sorensen, Arvis Sulovari, Marina Haukness, Maryam Ghareghani, Peter M. Lansdorp, Benedict Paten, Scott E. Devine, Ashley D. Sanders, Charles Lee, Mark J. P. Chaisson, Jan O. Korbel, Evan E. Eichler, and Tobias Marschall. 2020. “Fully Phased Human Genome Assembly without Parental Data Using Single-Cell Strand Sequencing and Long Reads.” Nature Biotechnology. doi:10.1038/s41587-020-0719-5.
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 Stütz, 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 Huddleston1; Mark 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