Mapping single molecule sequencing reads using basic local alignment with successive refinement (BLASR): application and theory

por Chaisson, Mark J, Tesler, Glenn
Publicado 2012

lra: A long read aligner for sequences and contigs

por Ren, Jingwen, Chaisson, Mark J. P.
Publicado 2021

TT-Mars: structural variants assessment based on haplotype-resolved assemblies

por Yang, Jianzhi, Chaisson, Mark J.P.
Publicado 2022

Profiling variable-number tandem repeat variation across populations using repeat-pangenome graphs

por Lu, Tsung-Yu, Chaisson, Mark J. P.
Publicado 2021

vamos: variable-number tandem repeats annotation using efficient motif sets

por Ren, Jingwen, Gu, Bida, Chaisson, Mark J. P.
Publicado 2023

HySA: a Hybrid Structural variant Assembly approach using next-generation and single-molecule sequencing technologies

por Fan, Xian, Chaisson, Mark, Nakhleh, Luay, Chen, Ken
Publicado 2017

HQAlign: Aligning nanopore reads for SV detection using current-level modeling

por Joshi, Dhaivat, Diggavi, Suhas, Chaisson, Mark J.P., Kannan, Sreeram
Publicado 2023

HQAlign: Aligning nanopore reads for SV detection using current-level modeling

por Joshi, Dhaivat, Diggavi, Suhas, Chaisson, Mark J.P., Kannan, Sreeram
Publicado 2023

The motif composition of variable number tandem repeats impacts gene expression

por Lu, Tsung-Yu, Smaruj, Paulina N., Fudenberg, Geoffrey, Mancuso, Nicholas, Chaisson, Mark J.P.
Publicado 2023

Deleterious mitochondrial DNA point mutations are overrepresented in Drosophila expressing a proofreading-defective DNA polymerase γ

por Samstag, Colby L., Hoekstra, Jake G., Huang, Chiu-Hui, Chaisson, Mark J., Youle, Richard J., Kennedy, Scott R., Pallanck, Leo J.
Publicado 2018

Long-read sequence and assembly of segmental duplications

por 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.
Publicado 2018

Reconstructing complex regions of genomes using long-read sequencing technology

por 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.
Publicado 2014

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

por 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.
Publicado 2017

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

por 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
Publicado 2020

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

por 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.
Publicado 2022

Scalable Nanopore sequencing of human genomes provides a comprehensive view of haplotype-resolved variation and methylation

por Kolmogorov, Mikhail, Billingsley, Kimberley J., Mastoras, Mira, Meredith, Melissa, Monlong, Jean, Lorig-Roach, Ryan, Asri, Mobin, Jerez, Pilar Alvarez, 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
Publicado 2023

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

por Larivière, Delphine, Abueg, Linelle, Brajuka, Nadolina, Gallardo-Alba, Cristóbal, Grüning, Bjorn, Ko, Byung June, Ostrovsky, Alex, Palmada-Flores, Marc, Pickett, Brandon D., Rabbani, Keon, Balacco, Jennifer R., Chaisson, Mark, Cheng, Haoyu, Collins, Joanna, Denisova, Alexandra, Fedrigo, Olivier, Gallo, Guido Roberto, Giani, Alice Maria, Gooder, Grenville MacDonald, 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, Waterhouse, Robert M., Phillippy, Adam M., Jarvis, Erich D., Schatz, Michael C., Nekrutenko, Anton, Formenti, Giulio
Publicado 2023

Extensive sequencing of seven human genomes to characterize benchmark reference materials

por Zook, Justin M., Catoe, David, McDaniel, Jennifer, Vang, Lindsay, Spies, Noah, Sidow, Arend, Weng, Ziming, Liu, Yuling, Mason, Christopher E., Alexander, Noah, Henaff, Elizabeth, McIntyre, Alexa B.R., Chandramohan, Dhruva, Chen, Feng, Jaeger, Erich, Moshrefi, Ali, Pham, Khoa, Stedman, William, Liang, Tiffany, Saghbini, Michael, Dzakula, Zeljko, Hastie, Alex, Cao, Han, Deikus, Gintaras, Schadt, Eric, Sebra, Robert, Bashir, Ali, Truty, Rebecca M., Chang, Christopher C., Gulbahce, Natali, Zhao, Keyan, Ghosh, Srinka, Hyland, Fiona, Fu, Yutao, Chaisson, Mark, Xiao, Chunlin, Trow, Jonathan, Sherry, Stephen T., Zaranek, Alexander W., Ball, Madeleine, Bobe, Jason, Estep, Preston, Church, George M., Marks, Patrick, Kyriazopoulou-Panagiotopoulou, Sofia, Zheng, Grace X.Y., Schnall-Levin, Michael, Ordonez, Heather S., Mudivarti, Patrice A., Giorda, Kristina, Sheng, Ying, Rypdal, Karoline Bjarnesdatter, Salit, Marc
Publicado 2016

A robust benchmark for detection of germline large deletions and insertions

por Zook, Justin M., Hansen, Nancy F., Olson, Nathan D., Chapman, Lesley M., 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 JP, Spies, Noah, Sedlazeck, Fritz J., Salit, Marc
Publicado 2020

An international virtual hackathon to build tools for the analysis of structural variants within species ranging from coronaviruses to vertebrates

por Mc Cartney, Ann M., Mahmoud, Medhat, Jochum, Michael, Agustinho, Daniel Paiva, Zorman, Barry, Al Khleifat, Ahmad, Dabbaghie, Fawaz, K Kesharwani, Rupesh, Smolka, Moritz, Dawood, Moez, Albin, Dreycey, Aliyev, Elbay, Almabrazi, Hakeem, Arslan, Ahmed, Balaji, Advait, Behera, Sairam, Billingsley, Kimberley, L Cameron, Daniel, Daw, Joyjit, T. Dawson, Eric, De Coster, Wouter, Du, Haowei, Dunn, Christopher, Esteban, Rocio, Jolly, Angad, Kalra, Divya, Liao, Chunxiao, Liu, Yunxi, Lu, Tsung-Yu, M Havrilla, James, M Khayat, Michael, Marin, Maximillian, Monlong, Jean, Price, Stephen, Rafael Gener, Alejandro, Ren, Jingwen, Sagayaradj, Sagayamary, Sapoval, Nicolae, Sinner, Claude, C. Soto, Daniela, Soylev, Arda, Subramaniyan, Arun, Syed, Najeeb, Tadimeti, Neha, Tater, Pamella, Vats, Pankaj, Vaughn, Justin, Walker, Kimberly, Wang, Gaojianyong, Zeng, Qiandong, Zhang, Shangzhe, Zhao, Tingting, Kille, Bryce, Biederstedt, Evan, Chaisson, Mark, English, Adam, Kronenberg, Zev, J. Treangen, Todd, Hefferon, Timothy, Chin, Chen-Shan, Busby, Ben, J Sedlazeck, Fritz
Publicado 2021