Modelling haplotypes with respect to reference cohort variation graphs

por Rosen, Yohei, Eizenga, Jordan, Paten, Benedict
Publicado 2017

Genome graphs and the evolution of genome inference

por Paten, Benedict, Novak, Adam M., Eizenga, Jordan M., Garrison, Erik
Publicado 2017

Distance indexing and seed clustering in sequence graphs

por Chang, Xian, Eizenga, Jordan, Novak, Adam M, Sirén, Jouni, Paten, Benedict
Publicado 2020

Optimal gap-affine alignment in O(s) space

por Marco-Sola, Santiago, Eizenga, Jordan M, Guarracino, Andrea, Paten, Benedict, Garrison, Erik, Moreto, Miquel
Publicado 2023

Mapping DNA Methylation with High Throughput Nanopore Sequencing

por Rand, Arthur C., Jain, Miten, Eizenga, Jordan M., Musselman-Brown, Audrey, Olsen, Hugh E., Akeson, Mark, Paten, Benedict
Publicado 2017

Conserved novel ORFs in the mitochondrial genome of the ctenophore Beroe forskalii

por Schultz, Darrin T., Eizenga, Jordan M., Corbett-Detig, Russell B., Francis, Warren R., Christianson, Lynne M., Haddock, Steven H.D.
Publicado 2020

A complete pedigree-based graph workflow for rare candidate variant analysis

por Markello, Charles, Huang, Charles, Rodriguez, Alex, Carroll, Andrew, Chang, Pi-Chuan, Eizenga, Jordan, Markello, Thomas, Haussler, David, Paten, Benedict
Publicado 2022

Genotyping structural variants in pangenome graphs using the vg toolkit

por Hickey, Glenn, Heller, David, Monlong, Jean, Sibbesen, Jonas A., Sirén, Jouni, Eizenga, Jordan, Dawson, Eric T., Garrison, Erik, Novak, Adam M., Paten, Benedict
Publicado 2020

Variation graph toolkit improves read mapping by representing genetic variation in the reference

por Garrison, Erik, Sirén, Jouni, Novak, Adam M., Hickey, Glenn, Eizenga, Jordan M., Dawson, Eric T., Jones, William, Garg, Shilpa, Markello, Charles, Lin, Michael F., Paten, Benedict, Durbin, Richard
Publicado 2018

Haplotype-aware variant calling with PEPPER-Margin-DeepVariant enables high accuracy in nanopore long-reads

por Shafin, Kishwar, Pesout, Trevor, Chang, Pi-Chuan, Nattestad, Maria, Kolesnikov, Alexey, Goel, Sidharth, Baid, Gunjan, Kolmogorov, Mikhail, Eizenga, Jordan M., Miga, Karen H., Carnevali, Paolo, Jain, Miten, Carroll, Andrew, Paten, Benedict
Publicado 2021

Phased nanopore assembly with Shasta and modular graph phasing with GFAse

por Lorig-Roach, Ryan, Meredith, Melissa, Monlong, Jean, Jain, Miten, Olsen, Hugh, McNulty, Brandy, Porubsky, David, Montague, Tessa, Lucas, Julian, Condon, Chris, Eizenga, Jordan, Juul, Sissel, McKenzie, Sean, Simmonds, Sara E., Park, Jimin, Asri, Mobin, Koren, Sergey, Eichler, Evan, Axel, Richard, Martin, Bruce, Carnevali, Paolo, Miga, Karen, Paten, Benedict
Publicado 2023

A strategy for building and using a human reference pangenome

por Llamas, Bastien, Narzisi, Giuseppe, Schneider, Valerie, Audano, Peter A., Biederstedt, Evan, Blauvelt, Lon, Bradbury, Peter, Chang, Xian, Chin, Chen-Shan, Fungtammasan, Arkarachai, Clarke, Wayne E., Cleary, Alan, Ebler, Jana, Eizenga, Jordan, Sibbesen, Jonas A., Markello, Charles J., Garrison, Erik, Garg, Shilpa, Hickey, Glenn, Lazo, Gerard R., Lin, Michael F., Mahmoud, Medhat, Marschall, Tobias, Minkin, Ilia, Monlong, Jean, Musunuri, Rajeeva L., Sagayaradj, Sagayamary, Novak, Adam M., Rautiainen, Mikko, Regier, Allison, Sedlazeck, Fritz J., Siren, Jouni, Souilmi, Yassine, Wagner, Justin, Wrightsman, Travis, Yokoyama, Toshiyuki T., Zeng, Qiandong, Zook, Justin M., Paten, Benedict, Busby, Ben
Publicado 2021

Hydroxymethylation profile of cell-free DNA is a biomarker for early colorectal cancer

por Walker, Nicolas J., Rashid, Mamunur, Yu, Shirong, Bignell, Helen, Lumby, Casper K., Livi, Carmen M., Howell, Kate, Morley, David J., Morganella, Sandro, Barrell, Daniel, Caim, Shabhonam, Gosal, Walraj, Füllgrabe, Jens, Charlesworth, Thomas J., Vasquez, Louella, Ahdesmäki, Miika, Eizenga, Jordan, Prabhat, Parul, Proutski, Vitali, Murat-Onana, Marie Laurie, Greenwood, Catherine J., Kirkwood, Lisa, Maisuria-Armer, Meeta, Li, Mengjie, Coats, Emma, Winfield, Victoria, MacBean, Lachlan, Stock, Toby, Tomé-Fernandez, Alice, Chan, Yat, Sheikh, Nasir, Golder, Paula, Steward, Michael, Ost, Tobias W. B., Stewart, Douglas, Vilella, Albert, Noursalehi, Mojtaba, Paten, Benedict, Lucarelli, Debora, Mason, Joanne, Ridge, Gareth, Mellad, Jason, Shirodkar, Suman, Balasubaramanian, Shankar, Holbrook, Joanna D.
Publicado 2022

A draft human pangenome reference

por 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., Sirén, 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., Magalhães, 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, Françoise, 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
Publicado 2023