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
Published in Nature (London) (29.01.2015)
Published in Nature (London) (29.01.2015)
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Journal Article
Genetic variation and the de novo assembly of human genomes
Chaisson, Mark J P, Wilson, Richard K, Eichler, Evan E
Published in Nature reviews. Genetics (01.11.2015)
Published in Nature reviews. Genetics (01.11.2015)
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Journal Article
A haplotype-resolved genome assembly of the Nile rat facilitates exploration of the genetic basis of diabetes
Toh, Huishi, Yang, Chentao, Formenti, Giulio, Raja, Kalpana, Yan, Lily, Tracey, Alan, Chow, William, Howe, Kerstin, Bergeron, Lucie A, Zhang, Guojie, Haase, Bettina, Mountcastle, Jacquelyn, Fedrigo, Olivier, Fogg, John, Kirilenko, Bogdan, Munegowda, Chetan, Hiller, Michael, Jain, Aashish, Kihara, Daisuke, Rhie, Arang, Phillippy, Adam M, Swanson, Scott A, Jiang, Peng, Clegg, Dennis O, Jarvis, Erich D, Thomson, James A, Stewart, Ron, Chaisson, Mark J. P, Bukhman, Yury V
Published in BMC biology (08.11.2022)
Published in BMC biology (08.11.2022)
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Journal Article
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
Published in Scientific data (07.02.2024)
Published in Scientific data (07.02.2024)
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Journal Article
Fully phased human genome assembly without parental data using single-cell strand sequencing and long reads
Porubsky, David, Ebert, Peter, Audano, Peter A, Vollger, Mitchell R, Harvey, William T, Marijon, Pierre, Ebler, Jana, Munson, Katherine M, Sorensen, Melanie, Sulovari, Arvis, Haukness, Marina, Ghareghani, Maryam, Lansdorp, Peter M, Paten, Benedict, Devine, Scott E, Sanders, Ashley D, Lee, Charles, Chaisson, Mark J P, Korbel, Jan O, Eichler, Evan E, Marschall, Tobias
Published in Nature biotechnology (01.03.2021)
Published in Nature biotechnology (01.03.2021)
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Journal Article
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
Published in Nature (London) (01.04.2022)
Published in Nature (London) (01.04.2022)
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Journal Article
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
Published in Science (American Association for the Advancement of Science) (08.06.2018)
Published in Science (American Association for the Advancement of Science) (08.06.2018)
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Journal Article
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.
Published in Science (American Association for the Advancement of Science) (01.04.2016)
Published in Science (American Association for the Advancement of Science) (01.04.2016)
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Journal Article
Scalable, accessible and reproducible reference genome assembly and evaluation in Galaxy
Larivière, Delphine, Abueg, Linelle, Brajuka, Nadolina, Gallardo-Alba, Cristóbal, Grüning, 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
Published in Nature biotechnology (01.03.2024)
Published in Nature biotechnology (01.03.2024)
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Journal Article
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, Höps, 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, André, 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
Published in Science (American Association for the Advancement of Science) (02.04.2021)
Published in Science (American Association for the Advancement of Science) (02.04.2021)
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Journal Article
HQAlign: aligning nanopore reads for SV detection using current-level modeling
Joshi, Dhaivat, Diggavi, Suhas, Chaisson, Mark J P, Kannan, Sreeram
Published in Bioinformatics (Oxford, England) (03.10.2023)
Published in Bioinformatics (Oxford, England) (03.10.2023)
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Journal Article
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, Stütz, 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
Published in Nature communications (16.04.2019)
Published in Nature communications (16.04.2019)
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Journal Article
Discovery and genotyping of structural variation from long-read haploid genome sequence data
Huddleston, John, Chaisson, Mark J P, Steinberg, Karyn Meltz, Warren, Wes, Hoekzema, Kendra, Gordon, David, Graves-Lindsay, Tina A, Munson, Katherine M, Kronenberg, Zev N, Vives, Laura, Peluso, Paul, Boitano, Matthew, Chin, Chen-Shin, Korlach, Jonas, Wilson, Richard K, Eichler, Evan E
Published in Genome research (01.05.2017)
Published in Genome research (01.05.2017)
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Journal Article
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
Published in Nature methods (01.01.2019)
Published in Nature methods (01.01.2019)
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Journal Article
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, Stütz, 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
Published in Nature (London) (01.10.2015)
Published in Nature (London) (01.10.2015)
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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
Published in Nature biotechnology (01.11.2020)
Published in Nature biotechnology (01.11.2020)
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