Mapping single molecule sequencing reads using basic local alignment with successive refinement (BLASR): application and theory by Chaisson, Mark J, Tesler, Glenn

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lra: A long read aligner for sequences and contigs by Ren, Jingwen, Chaisson, Mark J P

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Resolving the complexity of the human genome using single-molecule sequencing by 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.

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vamos: variable-number tandem repeats annotation using efficient motif sets by Ren, Jingwen, Gu, Bida, Chaisson, Mark J P

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Fully phased human genome assembly without parental data using single-cell strand sequencing and long reads by 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

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Short read fragment assembly of bacterial genomes by Chaisson, Mark J, Pevzner, Pavel A

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Profiling variable-number tandem repeat variation across populations using repeat-pangenome graphs by Lu, Tsung-Yu, Chaisson, Mark J. P.

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The Human Pangenome Project: a global resource to map genomic diversity by 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

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High-resolution comparative analysis of great ape genomes by 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

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Long-read sequence assembly of the gorilla genome by 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.

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Deleterious mitochondrial DNA point mutations are overrepresented in Drosophila expressing a proofreading-defective DNA polymerase γ by Samstag, Colby L, Hoekstra, Jake G, Huang, Chiu-Hui, Chaisson, Mark J, Youle, Richard J, Kennedy, Scott R, Pallanck, Leo J

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Scalable, accessible and reproducible reference genome assembly and evaluation in Galaxy by 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

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A haplotype-resolved genome assembly of the Nile rat facilitates exploration of the genetic basis of diabetes by 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

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Chromosome level genome assembly of the Etruscan shrew Suncus etruscus by 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

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Discovery and genotyping of structural variation from long-read haploid genome sequence data by 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

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TT-Mars: structural variants assessment based on haplotype-resolved assemblies by Yang, Jianzhi, Chaisson, Mark J P

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An integrated map of structural variation in 2,504 human genomes by Sudmant, Peter H., Rausch, Tobias, Gardner, Eugene J., Handsaker, Robert E., Abyzov, Alexej, Huddleston, John, Zhang, Yan, Ye, Kai, Jun, Goo, Hsi-Yang Fritz, Markus, Konkel, Miriam K., Malhotra, Ankit, Stütz, Adrian M., Shi, Xinghua, Paolo Casale, Francesco, 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., Jasmine Mu, Xinmeng, 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.

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HQAlign: aligning nanopore reads for SV detection using current-level modeling by Joshi, Dhaivat, Diggavi, Suhas, Chaisson, Mark J P, Kannan, Sreeram

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Expectations and blind spots for structural variation detection from long-read assemblies and short-read genome sequencing technologies by Zhao, Xuefang, Collins, Ryan L., Lee, Wan-Ping, Weber, Alexandra M., Jun, Yukyung, Zhu, Qihui, Weisburd, Ben, Huang, Yongqing, Audano, Peter A., Wang, Harold, Walker, Mark, Lowther, Chelsea, Fu, Jack, Gerstein, Mark B., Devine, Scott E., Marschall, Tobias, Korbel, Jan O., Eichler, Evan E., Chaisson, Mark J.P., Lee, Charles, Mills, Ryan E., Brand, Harrison, Talkowski, Michael E.

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Multi-platform discovery of haplotype-resolved structural variation in human genomes by 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

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