SPR Distance Computation for Unrooted Trees

gan Hickey, Glenn, Dehne, Frank, Rau-Chaplin, Andrew, Blouin, Christian
Cyhoeddwyd 2008

A unifying model of genome evolution under parsimony

gan Paten, Benedict, Zerbino, Daniel R, Hickey, Glenn, Haussler, David
Cyhoeddwyd 2014

HAL: a hierarchical format for storing and analyzing multiple genome alignments

gan Hickey, Glenn, Paten, Benedict, Earl, Dent, Zerbino, Daniel, Haussler, David
Cyhoeddwyd 2013

Representing and decomposing genomic structural variants as balanced integer flows on sequence graphs

gan Zerbino, Daniel R., Ballinger, Tracy, Paten, Benedict, Hickey, Glenn, Haussler, David
Cyhoeddwyd 2016

Sequence tube maps: making graph genomes intuitive to commuters

gan Beyer, Wolfgang, Novak, Adam M, Hickey, Glenn, Chan, Jeffrey, Tan, Vanessa, Paten, Benedict, Zerbino, Daniel R
Cyhoeddwyd 2019

Genotyping structural variants in pangenome graphs using the vg toolkit

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

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

gan 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
Cyhoeddwyd 2018

Gaps and complex structurally variant loci in phased genome assemblies

gan 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.
Cyhoeddwyd 2023

A call for benchmarking transposable element annotation methods

gan Hoen, Douglas R., Hickey, Glenn, Bourque, Guillaume, Casacuberta, Josep, Cordaux, Richard, Feschotte, Cédric, Fiston-Lavier, Anna-Sophie, Hua-Van, Aurélie, Hubley, Robert, Kapusta, Aurélie, Lerat, Emmanuelle, Maumus, Florian, Pollock, David D., Quesneville, Hadi, Smit, Arian, Wheeler, Travis J., Bureau, Thomas E., Blanchette, Mathieu
Cyhoeddwyd 2015

Progressive Cactus is a multiple-genome aligner for the thousand-genome era

gan Armstrong, Joel, Hickey, Glenn, Diekhans, Mark, Fiddes, Ian T., Novak, Adam M., Deran, Alden, Fang, Qi, Xie, Duo, Feng, Shaohong, Stiller, Josefin, Genereux, Diane, Johnson, Jeremy, Marinescu, Voichita Dana, Alföldi, Jessica, Harris, Robert S., Lindblad-Toh, Kerstin, Haussler, David, Karlsson, Elinor, Jarvis, Erich D., Zhang, Guojie, Paten, Benedict
Cyhoeddwyd 2020

Alignathon: a competitive assessment of whole-genome alignment methods

gan Earl, Dent, Nguyen, Ngan, Hickey, Glenn, Harris, Robert S., Fitzgerald, Stephen, Beal, Kathryn, Seledtsov, Igor, Molodtsov, Vladimir, Raney, Brian J., Clawson, Hiram, Kim, Jaebum, Kemena, Carsten, Chang, Jia-Ming, Erb, Ionas, Poliakov, Alexander, Hou, Minmei, Herrero, Javier, Kent, William James, Solovyev, Victor, Darling, Aaron E., Ma, Jian, Notredame, Cedric, Brudno, Michael, Dubchak, Inna, Haussler, David, Paten, Benedict
Cyhoeddwyd 2014

Improved genome assembly of American alligator genome reveals conserved architecture of estrogen signaling

gan Rice, Edward S., Kohno, Satomi, John, John St., Pham, Son, Howard, Jonathan, Lareau, Liana F., O'Connell, Brendan L., Hickey, Glenn, Armstrong, Joel, Deran, Alden, Fiddes, Ian, Platt, Roy N., Gresham, Cathy, McCarthy, Fiona, Kern, Colin, Haan, David, Phan, Tan, Schmidt, Carl, Sanford, Jeremy R., Ray, David A., Paten, Benedict, Guillette, Louis J., Green, Richard E.
Cyhoeddwyd 2017

The UCSC Genome Browser database: 2015 update

gan Rosenbloom, Kate R., Armstrong, Joel, Barber, Galt P., Casper, Jonathan, Clawson, Hiram, Diekhans, Mark, Dreszer, Timothy R., Fujita, Pauline A., Guruvadoo, Luvina, Haeussler, Maximilian, Harte, Rachel A., Heitner, Steve, Hickey, Glenn, Hinrichs, Angie S., Hubley, Robert, Karolchik, Donna, Learned, Katrina, Lee, Brian T., Li, Chin H., Miga, Karen H., Nguyen, Ngan, Paten, Benedict, Raney, Brian J., Smit, Arian F. A., Speir, Matthew L., Zweig, Ann S., Haussler, David, Kuhn, Robert M., Kent, W. James
Cyhoeddwyd 2014

A strategy for building and using a human reference pangenome

gan 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
Cyhoeddwyd 2021

A draft human pangenome reference

gan 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
Cyhoeddwyd 2023