Publications

Genotyping sequence-resolved copy number variation using pangenomes reveals paralog-specific global diversity and expression divergence of duplicated genes. Ma, Walfred, Chaisson, Mark J P, Nature genetics (2025) PMID: 41107550

Long-read sequencing identifies FGF14 repeat expansions in Parkinson’s disease. Akcimen, Fulya, Daida, Kensuke, Lange, Lara M, Moller, Abraham, Miano-Burkhardt, Abigail, Malik, Laksh, Paquette, Kimberly, Jerez, Pilar Alvarez, Mingle, Jackson, Baker, Breeana, Meredith, Melissa, Kouam, Cedric, Jarreau, Paige, Markham, Androo, Anderson, Jessica, Jain, Miten, Chaisson, Mark, Cookson, Mark, Casey, Bradford, Iwaki, Hirotaka, Bandres-Ciga, Sara, Saffie-Awad, Paula, Nalls, Mike, Fang, Zih-Hua, Singleton, Andrew B, Blauwendraat, Cornelis, Billingsley, Kimberley J, medRxiv : the preprint server for health sciences (2025) PMID: 40894141

Complex genetic variation in nearly complete human genomes. Logsdon, Glennis A, Ebert, Peter, Audano, Peter A, Loftus, Mark, Porubsky, David, Ebler, Jana, Yilmaz, Feyza, Hallast, Pille, Prodanov, Timofey, Yoo, DongAhn, Paisie, Carolyn A, Harvey, William T, Zhao, Xuefang, Martino, Gianni V, Henglin, Mir, Munson, Katherine M, Rabbani, Keon, Chin, Chen-Shan, Gu, Bida, Ashraf, Hufsah, Scholz, Stephan, Austine-Orimoloye, Olanrewaju, Balachandran, Parithi, Bonder, Marc Jan, Cheng, Haoyu, Chong, Zechen, Crabtree, Jonathan, Gerstein, Mark, Guethlein, Lisbeth A, Hasenfeld, Patrick, Hickey, Glenn, Hoekzema, Kendra, Hunt, Sarah E, Jensen, Matthew, Jiang, Yunzhe, Koren, Sergey, Kwon, Youngjun, Li, Chong, Li, Heng, Li, Jiaqi, Norman, Paul J, Oshima, Keisuke K, Paten, Benedict, Phillippy, Adam M, Pollock, Nicholas R, Rausch, Tobias, Rautiainen, Mikko, Song, Yuwei, Soylev, Arda, Sulovari, Arvis, Surapaneni, Likhitha, Tsapalou, Vasiliki, Zhou, Weichen, Zhou, Ying, Zhu, Qihui, Zody, Michael C, Mills, Ryan E, Devine, Scott E, Shi, Xinghua, Talkowski, Michael E, Chaisson, Mark J P, Dilthey, Alexander T, Konkel, Miriam K, Korbel, Jan O, Lee, Charles, Beck, Christine R, Eichler, Evan E, Marschall, Tobias, Nature (2025) PMID: 40702183

Identification of GGC Repeat Expansions in ZFHX3 among Chilean Movement Disorder Patients. Saffie-Awad, Paula, Moller, Abraham, Daida, Kensuke, Alvarez Jerez, Pilar, Chen, Zhongbo, Anderson, Zachary B, Isayan, Mariam, Paquette, Kimberly, Gibson, Sophia B, Fulcher, Madison, Miano-Burkhardt, Abigail, Malik, Laksh, Baker, Breeana, Jarreau, Paige, Houlden, Henry, Ryten, Mina, Gu, Bida, Chaisson, Mark J P, Miller, Danny E, Chana-Cuevas, Pedro, Blauwendraat, Cornelis, Singleton, Andrew B, Billingsley, Kimberley J, Movement disorders : official journal of the Movement Disorder Society (2025) PMID: 40459184

Analysis and benchmarking of small and large genomic variants across tandem repeats. English, Adam C, Dolzhenko, Egor, Ziaei Jam, Helyaneh, McKenzie, Sean K, Olson, Nathan D, De Coster, Wouter, Park, Jonghun, Gu, Bida, Wagner, Justin, Eberle, Michael A, Gymrek, Melissa, Chaisson, Mark J P, Zook, Justin M, Sedlazeck, Fritz J, Nature biotechnology (2025) PMID: 38671154

An integrative TAD catalog in lymphoblastoid cell lines discloses the functional impact of deletions and insertions in human genomes. Li, Chong, Bonder, Marc Jan, Syed, Sabriya, Jensen, Matthew, Gerstein, Mark B, Zody, Michael C, Chaisson, Mark J P, Talkowski, Michael E, Marschall, Tobias, Korbel, Jan O, Eichler, Evan E, Lee, Charles, Shi, Xinghua, Genome research (2024) PMID: 39638559

Long-read sequencing of hundreds of diverse brains provides insight into the impact of structural variation on gene expression and DNA methylation. Billingsley, Kimberley J, Meredith, Melissa, Daida, Kensuke, Jerez, Pilar Alvarez, Negi, Shloka, Malik, Laksh, Genner, Rylee M, Moller, Abraham, Zheng, Xinchang, Gibson, Sophia B, Mastoras, Mira, Baker, Breeana, Kouam, Cedric, Paquette, Kimberly, Jarreau, Paige, Makarious, Mary B, Moore, Anni, Hong, Samantha, Vitale, Dan, Shah, Syed, Monlong, Jean, Pantazis, Caroline B, Asri, Mobin, Shafin, Kishwar, Carnevali, Paolo, Marenco, Stefano, Auluck, Pavan, Mandal, Ajeet, Miga, Karen H, Rhie, Arang, Reed, Xylena, Ding, Jinhui, Cookson, Mark R, Nalls, Mike, Singleton, Andrew, Miller, Danny E, Chaisson, Mark, Timp, Winston, Gibbs, J Raphael, Phillippy, Adam M, Kolmogorov, Mikhail, Jain, Miten, Sedlazeck, Fritz J, Paten, Benedict, Blauwendraat, Cornelis, bioRxiv : the preprint server for biology (2024) PMID: 39764002

VISTA: an integrated framework for structural variant discovery. Sarwal, Varuni, Lee, Seungmo, Yang, Jianzhi, Sankararaman, Sriram, Chaisson, Mark, Eskin, Eleazar, Mangul, Serghei, Briefings in bioinformatics (2024) PMID: 39297879

Scalable, accessible and reproducible reference genome assembly and evaluation in Galaxy. Lariviere, Delphine, Abueg, Linelle, Brajuka, Nadolina, Gallardo-Alba, Cristobal, Gruning, Bjorn, Ko, Byung June, Ostrovsky, Alex, Palmada-Flores, Marc, Pickett, Brandon D, Rabbani, Keon, Antunes, Agostinho, Balacco, Jennifer R, Chaisson, Mark J P, Cheng, Haoyu, Collins, Joanna, Couture, Melanie, Denisova, Alexandra, Fedrigo, Olivier, Gallo, Guido Roberto, Giani, Alice Maria, Gooder, Grenville MacDonald, Horan, Kathleen, Jain, Nivesh, Johnson, Cassidy, Kim, Heebal, Lee, Chul, Marques-Bonet, Tomas, O’Toole, Brian, Rhie, Arang, Secomandi, Simona, Sozzoni, Marcella, Tilley, Tatiana, Uliano-Silva, Marcela, van den Beek, Marius, Williams, Robert W, Waterhouse, Robert M, Phillippy, Adam M, Jarvis, Erich D, Schatz, Michael C, Nekrutenko, Anton, Formenti, Giulio, Nature biotechnology (2024) PMID: 38278971

A High-Quality Blue Whale Genome, Segmental Duplications, and Historical Demography. Bukhman, Yury V, Morin, Phillip A, Meyer, Susanne, Chu, Li-Fang, Jacobsen, Jeff K, Antosiewicz-Bourget, Jessica, Mamott, Daniel, Gonzales, Maylie, Argus, Cara, Bolin, Jennifer, Berres, Mark E, Fedrigo, Olivier, Steill, John, Swanson, Scott A, Jiang, Peng, Rhie, Arang, Formenti, Giulio, Phillippy, Adam M, Harris, Robert S, Wood, Jonathan M D, Howe, Kerstin, Kirilenko, Bogdan M, Munegowda, Chetan, Hiller, Michael, Jain, Aashish, Kihara, Daisuke, Johnston, J Spencer, Ionkov, Alexander, Raja, Kalpana, Toh, Huishi, Lang, Aimee, Wolf, Magnus, Jarvis, Erich D, Thomson, James A, Chaisson, Mark J P, Stewart, Ron, Molecular biology and evolution (2024) PMID: 38376487

Chromosome level genome assembly of the Etruscan shrew Suncus etruscus. Bukhman, Yury V, Meyer, Susanne, Chu, Li-Fang, Abueg, Linelle, Antosiewicz-Bourget, Jessica, Balacco, Jennifer, Brecht, Michael, Dinatale, Erica, Fedrigo, Olivier, Formenti, Giulio, Fungtammasan, Arkarachai, Giri, Swagarika Jaharlal, Hiller, Michael, Howe, Kerstin, Kihara, Daisuke, Mamott, Daniel, Mountcastle, Jacquelyn, Pelan, Sarah, Rabbani, Keon, Sims, Ying, Tracey, Alan, Wood, Jonathan M D, Jarvis, Erich D, Thomson, James A, Chaisson, Mark J P, Stewart, Ron, Scientific data (2024) PMID: 38326333

Advances in the discovery and analyses of human tandem repeats. Chaisson, Mark J P, Sulovari, Arvis, Valdmanis, Paul N, Miller, Danny E, Eichler, Evan E, Emerging topics in life sciences (2023) PMID: 37905568

HQAlign: aligning nanopore reads for SV detection using current-level modeling. Joshi, Dhaivat, Diggavi, Suhas, Chaisson, Mark J P, Kannan, Sreeram, Bioinformatics (Oxford, England) (2023) PMID: 37738608

Scalable Nanopore sequencing of human genomes provides a comprehensive view of haplotype-resolved variation and methylation. Kolmogorov, Mikhail, Billingsley, Kimberley J, Mastoras, Mira, Meredith, Melissa, Monlong, Jean, Lorig-Roach, Ryan, Asri, Mobin, Alvarez Jerez, Pilar, Malik, Laksh, Dewan, Ramita, Reed, Xylena, Genner, Rylee M, Daida, Kensuke, Behera, Sairam, Shafin, Kishwar, Pesout, Trevor, Prabakaran, Jeshuwin, Carnevali, Paolo, Yang, Jianzhi, Rhie, Arang, Scholz, Sonja W, Traynor, Bryan J, Miga, Karen H, Jain, Miten, Timp, Winston, Phillippy, Adam M, Chaisson, Mark, Sedlazeck, Fritz J, Blauwendraat, Cornelis, Paten, Benedict, Nature methods (2023) PMID: 37710018

vamos: variable-number tandem repeats annotation using efficient motif sets. Ren, Jingwen, Gu, Bida, Chaisson, Mark J P, Genome biology (2023) PMID: 37501141

A draft human pangenome reference. Liao, Wen-Wei, Asri, Mobin, Ebler, Jana, Doerr, Daniel, Haukness, Marina, Hickey, Glenn, Lu, Shuangjia, Lucas, Julian K, Monlong, Jean, Abel, Haley J, Buonaiuto, Silvia, Chang, Xian H, Cheng, Haoyu, Chu, Justin, Colonna, Vincenza, Eizenga, Jordan M, Feng, Xiaowen, Fischer, Christian, Fulton, Robert S, Garg, Shilpa, Groza, Cristian, Guarracino, Andrea, Harvey, William T, Heumos, Simon, Howe, Kerstin, Jain, Miten, Lu, Tsung-Yu, Markello, Charles, Martin, Fergal J, Mitchell, Matthew W, Munson, Katherine M, Mwaniki, Moses Njagi, Novak, Adam M, Olsen, Hugh E, Pesout, Trevor, Porubsky, David, Prins, Pjotr, Sibbesen, Jonas A, Siren, Jouni, Tomlinson, Chad, Villani, Flavia, Vollger, Mitchell R, Antonacci-Fulton, Lucinda L, Baid, Gunjan, Baker, Carl A, Belyaeva, Anastasiya, Billis, Konstantinos, Carroll, Andrew, Chang, Pi-Chuan, Cody, Sarah, Cook, Daniel E, Cook-Deegan, Robert M, Cornejo, Omar E, Diekhans, Mark, Ebert, Peter, Fairley, Susan, Fedrigo, Olivier, Felsenfeld, Adam L, Formenti, Giulio, Frankish, Adam, Gao, Yan, Garrison, Nanibaa’ A, Giron, Carlos Garcia, Green, Richard E, Haggerty, Leanne, Hoekzema, Kendra, Hourlier, Thibaut, Ji, Hanlee P, Kenny, Eimear E, Koenig, Barbara A, Kolesnikov, Alexey, Korbel, Jan O, Kordosky, Jennifer, Koren, Sergey, Lee, HoJoon, Lewis, Alexandra P, Magalhaes, Hugo, Marco-Sola, Santiago, Marijon, Pierre, McCartney, Ann, McDaniel, Jennifer, Mountcastle, Jacquelyn, Nattestad, Maria, Nurk, Sergey, Olson, Nathan D, Popejoy, Alice B, Puiu, Daniela, Rautiainen, Mikko, Regier, Allison A, Rhie, Arang, Sacco, Samuel, Sanders, Ashley D, Schneider, Valerie A, Schultz, Baergen I, Shafin, Kishwar, Smith, Michael W, Sofia, Heidi J, Abou Tayoun, Ahmad N, Thibaud-Nissen, Francoise, Tricomi, Francesca Floriana, Wagner, Justin, Walenz, Brian, Wood, Jonathan M D, Zimin, Aleksey V, Bourque, Guillaume, Chaisson, Mark J P, Flicek, Paul, Phillippy, Adam M, Zook, Justin M, Eichler, Evan E, Haussler, David, Wang, Ting, Jarvis, Erich D, Miga, Karen H, Garrison, Erik, Marschall, Tobias, Hall, Ira M, Li, Heng, Paten, Benedict, Nature (2023) PMID: 37165242

Inversion polymorphism in a complete human genome assembly. Porubsky, David, Harvey, William T, Rozanski, Allison N, Ebler, Jana, Hops, Wolfram, Ashraf, Hufsah, Hasenfeld, Patrick, Paten, Benedict, Sanders, Ashley D, Marschall, Tobias, Korbel, Jan O, Eichler, Evan E, Genome biology (2023) PMID: 37122002

The motif composition of variable number tandem repeats impacts gene expression. Lu, Tsung-Yu, Smaruj, Paulina N, Fudenberg, Geoffrey, Mancuso, Nicholas, Chaisson, Mark J P, Genome research (2023) PMID: 37037626

Gaps and complex structurally variant loci in phased genome assemblies. Porubsky, David, Vollger, Mitchell R, Harvey, William T, Rozanski, Allison N, Ebert, Peter, Hickey, Glenn, Hasenfeld, Patrick, Sanders, Ashley D, Stober, Catherine, Korbel, Jan O, Paten, Benedict, Marschall, Tobias, Eichler, Evan E, Genome research (2023) PMID: 37164484

Structural variation across 138,134 samples in the TOPMed consortium. Jun, Goo, English, Adam C, Metcalf, Ginger A, Yang, Jianzhi, Chaisson, Mark Jp, Pankratz, Nathan, Menon, Vipin K, Salerno, William J, Krasheninina, Olga, Smith, Albert V, Lane, John A, Blackwell, Tom, Kang, Hyun Min, Salvi, Sejal, Meng, Qingchang, Shen, Hua, Pasham, Divya, Bhamidipati, Sravya, Kottapalli, Kavya, Arnett, Donna K, Ashley-Koch, Allison, Auer, Paul L, Beutel, Kathleen M, Bis, Joshua C, Blangero, John, Bowden, Donald W, Brody, Jennifer A, Cade, Brian E, Chen, Yii-Der Ida, Cho, Michael H, Curran, Joanne E, Fornage, Myriam, Freedman, Barry I, Fingerlin, Tasha, Gelb, Bruce D, Hou, Lifang, Hung, Yi-Jen, Kane, John P, Kaplan, Robert, Kim, Wonji, Loos, Ruth J F, Marcus, Gregory M, Mathias, Rasika A, McGarvey, Stephen T, Montgomery, Courtney, Naseri, Take, Nouraie, S Mehdi, Preuss, Michael H, Palmer, Nicholette D, Peyser, Patricia A, Raffield, Laura M, Ratan, Aakrosh, Redline, Susan, Reupena, Sefuiva, Rotter, Jerome I, Rich, Stephen S, Rienstra, Michiel, Ruczinski, Ingo, Sankaran, Vijay G, Schwartz, David A, Seidman, Christine E, Seidman, Jonathan G, Silverman, Edwin K, Smith, Jennifer A, Stilp, Adrienne, Taylor, Kent D, Telen, Marilyn J, Weiss, Scott T, Williams, L Keoki, Wu, Baojun, Yanek, Lisa R, Zhang, Yingze, Lasky-Su, Jessica, Gingras, Marie Claude, Dutcher, Susan K, Eichler, Evan E, Gabriel, Stacey, Germer, Soren, Kim, Ryan, Viaud-Martinez, Karine A, Nickerson, Deborah A, Luo, James, Reiner, Alex, Gibbs, Richard A, Boerwinkle, Eric, Abecasis, Goncalo, Sedlazeck, Fritz J, Research square (2023) PMID: 36778386

Recurrent inversion polymorphisms in humans associate with genetic instability and genomic disorders. Porubsky, David, Hops, Wolfram, Ashraf, Hufsah, Hsieh, PingHsun, Rodriguez-Martin, Bernardo, Yilmaz, Feyza, Ebler, Jana, Hallast, Pille, Maria Maggiolini, Flavia Angela, Harvey, William T, Henning, Barbara, Audano, Peter A, Gordon, David S, Ebert, Peter, Hasenfeld, Patrick, Benito, Eva, Zhu, Qihui, Lee, Charles, Antonacci, Francesca, Steinrucken, Matthias, Beck, Christine R, Sanders, Ashley D, Marschall, Tobias, Eichler, Evan E, Korbel, Jan O, Cell (2022) PMID: 35525246

TT-Mars: structural variants assessment based on haplotype-resolved assemblies. Yang, Jianzhi, Chaisson, Mark J P, Genome biology (2022) PMID: 35524317

The Human Pangenome Project: a global resource to map genomic diversity. Wang, Ting, Antonacci-Fulton, Lucinda, Howe, Kerstin, Lawson, Heather A, Lucas, Julian K, Phillippy, Adam M, Popejoy, Alice B, Asri, Mobin, Carson, Caryn, Chaisson, Mark J P, Chang, Xian, Cook-Deegan, Robert, Felsenfeld, Adam L, Fulton, Robert S, Garrison, Erik P, Garrison, Nanibaa’ A, Graves-Lindsay, Tina A, Ji, Hanlee, Kenny, Eimear E, Koenig, Barbara A, Li, Daofeng, Marschall, Tobias, McMichael, Joshua F, Novak, Adam M, Purushotham, Deepak, Schneider, Valerie A, Schultz, Baergen I, Smith, Michael W, Sofia, Heidi J, Weissman, Tsachy, Flicek, Paul, Li, Heng, Miga, Karen H, Paten, Benedict, Jarvis, Erich D, Hall, Ira M, Eichler, Evan E, Haussler, David, Nature (2022) PMID: 35444317

Segmental duplications and their variation in a complete human genome. Vollger, Mitchell R, Guitart, Xavi, Dishuck, Philip C, Mercuri, Ludovica, Harvey, William T, Gershman, Ariel, Diekhans, Mark, Sulovari, Arvis, Munson, Katherine M, Lewis, Alexandra P, Hoekzema, Kendra, Porubsky, David, Li, Ruiyang, Nurk, Sergey, Koren, Sergey, Miga, Karen H, Phillippy, Adam M, Timp, Winston, Ventura, Mario, Eichler, Evan E, Science (New York, N.Y.) (2022) PMID: 35357917

Profiling variable-number tandem repeat variation across populations using repeat-pangenome graphs. Lu, Tsung-Yu, Chaisson, Mark J P, Nature communications (2021) PMID: 34253730

lra: A long read aligner for sequences and contigs. Ren, Jingwen, Chaisson, Mark J P, PLoS computational biology (2021) PMID: 34153026

Haplotype-resolved diverse human genomes and integrated analysis of structural variation. Ebert, Peter, Audano, Peter A, Zhu, Qihui, Rodriguez-Martin, Bernardo, Porubsky, David, Bonder, Marc Jan, Sulovari, Arvis, Ebler, Jana, Zhou, Weichen, Serra Mari, Rebecca, Yilmaz, Feyza, Zhao, Xuefang, Hsieh, PingHsun, Lee, Joyce, Kumar, Sushant, Lin, Jiadong, Rausch, Tobias, Chen, Yu, Ren, Jingwen, Santamarina, Martin, Hops, Wolfram, Ashraf, Hufsah, Chuang, Nelson T, Yang, Xiaofei, Munson, Katherine M, Lewis, Alexandra P, Fairley, Susan, Tallon, Luke J, Clarke, Wayne E, Basile, Anna O, Byrska-Bishop, Marta, Corvelo, Andre, Evani, Uday S, Lu, Tsung-Yu, Chaisson, Mark J P, Chen, Junjie, Li, Chong, Brand, Harrison, Wenger, Aaron M, Ghareghani, Maryam, Harvey, William T, Raeder, Benjamin, Hasenfeld, Patrick, Regier, Allison A, Abel, Haley J, Hall, Ira M, Flicek, Paul, Stegle, Oliver, Gerstein, Mark B, Tubio, Jose M C, Mu, Zepeng, Li, Yang I, Shi, Xinghua, Hastie, Alex R, Ye, Kai, Chong, Zechen, Sanders, Ashley D, Zody, Michael C, Talkowski, Michael E, Mills, Ryan E, Devine, Scott E, Lee, Charles, Korbel, Jan O, Marschall, Tobias, Eichler, Evan E, Science (New York, N.Y.) (2021) PMID: 33632895

A robust benchmark for detection of germline large deletions and insertions. Zook, Justin M, Hansen, Nancy F, Olson, Nathan D, Chapman, Lesley, Mullikin, James C, Xiao, Chunlin, Sherry, Stephen, Koren, Sergey, Phillippy, Adam M, Boutros, Paul C, Sahraeian, Sayed Mohammad E, Huang, Vincent, Rouette, Alexandre, Alexander, Noah, Mason, Christopher E, Hajirasouliha, Iman, Ricketts, Camir, Lee, Joyce, Tearle, Rick, Fiddes, Ian T, Barrio, Alvaro Martinez, Wala, Jeremiah, Carroll, Andrew, Ghaffari, Noushin, Rodriguez, Oscar L, Bashir, Ali, Jackman, Shaun, Farrell, John J, Wenger, Aaron M, Alkan, Can, Soylev, Arda, Schatz, Michael C, Garg, Shilpa, Church, George, Marschall, Tobias, Chen, Ken, Fan, Xian, English, Adam C, Rosenfeld, Jeffrey A, Zhou, Weichen, Mills, Ryan E, Sage, Jay M, Davis, Jennifer R, Kaiser, Michael D, Oliver, John S, Catalano, Anthony P, Chaisson, Mark J P, Spies, Noah, Sedlazeck, Fritz J, Salit, Marc, Nature biotechnology (2020) PMID: 32541955

Human-specific tandem repeat expansion and differential gene expression during primate evolution. Sulovari, Arvis, Li, Ruiyang, Audano, Peter A, Porubsky, David, Vollger, Mitchell R, Logsdon, Glennis A, Warren, Wesley C, Pollen, Alex A, Chaisson, Mark J P, Eichler, Evan E, Proceedings of the National Academy of Sciences of the United States of America (2019) PMID: 31659027

Multi-platform discovery of haplotype-resolved structural variation in human genomes. Chaisson, Mark J P, Sanders, Ashley D, Zhao, Xuefang, Malhotra, Ankit, Porubsky, David, Rausch, Tobias, Gardner, Eugene J, Rodriguez, Oscar L, Guo, Li, Collins, Ryan L, Fan, Xian, Wen, Jia, Handsaker, Robert E, Fairley, Susan, Kronenberg, Zev N, Kong, Xiangmeng, Hormozdiari, Fereydoun, Lee, Dillon, Wenger, Aaron M, Hastie, Alex R, Antaki, Danny, Anantharaman, Thomas, Audano, Peter A, Brand, Harrison, Cantsilieris, Stuart, Cao, Han, Cerveira, Eliza, Chen, Chong, Chen, Xintong, Chin, Chen-Shan, Chong, Zechen, Chuang, Nelson T, Lambert, Christine C, Church, Deanna M, Clarke, Laura, Farrell, Andrew, Flores, Joey, Galeev, Timur, Gorkin, David U, Gujral, Madhusudan, Guryev, Victor, Heaton, William Haynes, Korlach, Jonas, Kumar, Sushant, Kwon, Jee Young, Lam, Ernest T, Lee, Jong Eun, Lee, Joyce, Lee, Wan-Ping, Lee, Sau Peng, Li, Shantao, Marks, Patrick, Viaud-Martinez, Karine, Meiers, Sascha, Munson, Katherine M, Navarro, Fabio C P, Nelson, Bradley J, Nodzak, Conor, Noor, Amina, Kyriazopoulou-Panagiotopoulou, Sofia, Pang, Andy W C, Qiu, Yunjiang, Rosanio, Gabriel, Ryan, Mallory, Stutz, Adrian, Spierings, Diana C J, Ward, Alistair, Welch, AnneMarie E, Xiao, Ming, Xu, Wei, Zhang, Chengsheng, Zhu, Qihui, Zheng-Bradley, Xiangqun, Lowy, Ernesto, Yakneen, Sergei, McCarroll, Steven, Jun, Goo, Ding, Li, Koh, Chong Lek, Ren, Bing, Flicek, Paul, Chen, Ken, Gerstein, Mark B, Kwok, Pui-Yan, Lansdorp, Peter M, Marth, Gabor T, Sebat, Jonathan, Shi, Xinghua, Bashir, Ali, Ye, Kai, Devine, Scott E, Talkowski, Michael E, Mills, Ryan E, Marschall, Tobias, Korbel, Jan O, Eichler, Evan E, Lee, Charles, Nature communications (2019) PMID: 30992455

Long-read sequence and assembly of segmental duplications. Vollger, Mitchell R, Dishuck, Philip C, Sorensen, Melanie, Welch, AnneMarie E, Dang, Vy, Dougherty, Max L, Graves-Lindsay, Tina A, Wilson, Richard K, Chaisson, Mark J P, Eichler, Evan E, Nature methods (2019) PMID: 30559433

Deleterious mitochondrial DNA point mutations are overrepresented in Drosophila expressing a proofreading-defective DNA polymerase gamma. Samstag, Colby L, Hoekstra, Jake G, Huang, Chiu-Hui, Chaisson, Mark J, Youle, Richard J, Kennedy, Scott R, Pallanck, Leo J, PLoS genetics (2018) PMID: 30452458

High-resolution comparative analysis of great ape genomes. Kronenberg, Zev N, Fiddes, Ian T, Gordon, David, Murali, Shwetha, Cantsilieris, Stuart, Meyerson, Olivia S, Underwood, Jason G, Nelson, Bradley J, Chaisson, Mark J P, Dougherty, Max L, Munson, Katherine M, Hastie, Alex R, Diekhans, Mark, Hormozdiari, Fereydoun, Lorusso, Nicola, Hoekzema, Kendra, Qiu, Ruolan, Clark, Karen, Raja, Archana, Welch, AnneMarie E, Sorensen, Melanie, Baker, Carl, Fulton, Robert S, Armstrong, Joel, Graves-Lindsay, Tina A, Denli, Ahmet M, Hoppe, Emma R, Hsieh, PingHsun, Hill, Christopher M, Pang, Andy Wing Chun, Lee, Joyce, Lam, Ernest T, Dutcher, Susan K, Gage, Fred H, Warren, Wesley C, Shendure, Jay, Haussler, David, Schneider, Valerie A, Cao, Han, Ventura, Mario, Wilson, Richard K, Paten, Benedict, Pollen, Alex, Eichler, Evan E, Science (New York, N.Y.) (2018) PMID: 29880660

Resolving multicopy duplications de novo using polyploid phasing. Chaisson, Mark J, Mukherjee, Sudipto, Kannan, Sreeram, Eichler, Evan E, Research in computational molecular biology : … Annual International Conference, RECOMB … : proceedings. RECOMB (Conference : 2005- ) (2017) PMID: 28808695

HySA: a Hybrid Structural variant Assembly approach using next-generation and single-molecule sequencing technologies. Fan, Xian, Chaisson, Mark, Nakhleh, Luay, Chen, Ken, Genome research (2017) PMID: 28104618

Assembly of long error-prone reads using de Bruijn graphs. Lin, Yu, Yuan, Jeffrey, Kolmogorov, Mikhail, Shen, Max W, Chaisson, Mark, Pevzner, Pavel A, Proceedings of the National Academy of Sciences of the United States of America (2016) PMID: 27956617

Long-read sequence assembly of the gorilla genome. Gordon, David, Huddleston, John, Chaisson, Mark J P, Hill, Christopher M, Kronenberg, Zev N, Munson, Katherine M, Malig, Maika, Raja, Archana, Fiddes, Ian, Hillier, LaDeana W, Dunn, Christopher, Baker, Carl, Armstrong, Joel, Diekhans, Mark, Paten, Benedict, Shendure, Jay, Wilson, Richard K, Haussler, David, Chin, Chen-Shan, Eichler, Evan E, Science (New York, N.Y.) (2016) PMID: 27034376

Genetic variation and the de novo assembly of human genomes. Chaisson, Mark J P, Wilson, Richard K, Eichler, Evan E, Nature reviews. Genetics (2015) PMID: 26442640

An integrated map of structural variation in 2,504 human genomes. Sudmant, Peter H, Rausch, Tobias, Gardner, Eugene J, Handsaker, Robert E, Abyzov, Alexej, Huddleston, John, Zhang, Yan, Ye, Kai, Jun, Goo, Fritz, Markus Hsi-Yang, Konkel, Miriam K, Malhotra, Ankit, Stutz, Adrian M, Shi, Xinghua, Casale, Francesco Paolo, Chen, Jieming, Hormozdiari, Fereydoun, Dayama, Gargi, Chen, Ken, Malig, Maika, Chaisson, Mark J P, Walter, Klaudia, Meiers, Sascha, Kashin, Seva, Garrison, Erik, Auton, Adam, Lam, Hugo Y K, Mu, Xinmeng Jasmine, Alkan, Can, Antaki, Danny, Bae, Taejeong, Cerveira, Eliza, Chines, Peter, Chong, Zechen, Clarke, Laura, Dal, Elif, Ding, Li, Emery, Sarah, Fan, Xian, Gujral, Madhusudan, Kahveci, Fatma, Kidd, Jeffrey M, Kong, Yu, Lameijer, Eric-Wubbo, McCarthy, Shane, Flicek, Paul, Gibbs, Richard A, Marth, Gabor, Mason, Christopher E, Menelaou, Androniki, Muzny, Donna M, Nelson, Bradley J, Noor, Amina, Parrish, Nicholas F, Pendleton, Matthew, Quitadamo, Andrew, Raeder, Benjamin, Schadt, Eric E, Romanovitch, Mallory, Schlattl, Andreas, Sebra, Robert, Shabalin, Andrey A, Untergasser, Andreas, Walker, Jerilyn A, Wang, Min, Yu, Fuli, Zhang, Chengsheng, Zhang, Jing, Zheng-Bradley, Xiangqun, Zhou, Wanding, Zichner, Thomas, Sebat, Jonathan, Batzer, Mark A, McCarroll, Steven A, Mills, Ryan E, Gerstein, Mark B, Bashir, Ali, Stegle, Oliver, Devine, Scott E, Lee, Charles, Eichler, Evan E, Korbel, Jan O, Nature (2015) PMID: 26432246

Resolving the complexity of the human genome using single-molecule sequencing. Chaisson, Mark J P, Huddleston, John, Dennis, Megan Y, Sudmant, Peter H, Malig, Maika, Hormozdiari, Fereydoun, Antonacci, Francesca, Surti, Urvashi, Sandstrom, Richard, Boitano, Matthew, Landolin, Jane M, Stamatoyannopoulos, John A, Hunkapiller, Michael W, Korlach, Jonas, Eichler, Evan E, Nature (2015) PMID: 25383537

Reconstructing complex regions of genomes using long-read sequencing technology. Huddleston, John, Ranade, Swati, Malig, Maika, Antonacci, Francesca, Chaisson, Mark, Hon, Lawrence, Sudmant, Peter H, Graves, Tina A, Alkan, Can, Dennis, Megan Y, Wilson, Richard K, Turner, Stephen W, Korlach, Jonas, Eichler, Evan E, Genome research (2014) PMID: 24418700

STAR: ultrafast universal RNA-seq aligner. Dobin, Alexander, Davis, Carrie A, Schlesinger, Felix, Drenkow, Jorg, Zaleski, Chris, Jha, Sonali, Batut, Philippe, Chaisson, Mark, Gingeras, Thomas R, Bioinformatics (Oxford, England) (2013) PMID: 23104886

Mapping single molecule sequencing reads using basic local alignment with successive refinement (BLASR): application and theory. Chaisson, Mark J, Tesler, Glenn, BMC bioinformatics (2012) PMID: 22988817

Paired de bruijn graphs: a novel approach for incorporating mate pair information into genome assemblers. Medvedev, Paul, Pham, Son, Chaisson, Mark, Tesler, Glenn, Pevzner, Pavel, Journal of computational biology : a journal of computational molecular cell biology (2011) PMID: 21999285

De novo fragment assembly with short mate-paired reads: Does the read length matter? Chaisson, Mark J, Brinza, Dumitru, Pevzner, Pavel A, Genome research (2009) PMID: 19056694

Short read fragment assembly of bacterial genomes. Chaisson, Mark J, Pevzner, Pavel A, Genome research (2008) PMID: 18083777

Microinversions in mammalian evolution. Chaisson, M J, Raphael, B J, Pevzner, P A, Proceedings of the National Academy of Sciences of the United States of America (2006) PMID: 17189424

Fragment assembly with short reads. Chaisson, Mark, Pevzner, Pavel, Tang, Haixu, Bioinformatics (Oxford, England) (2004) PMID: 15059830

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