A graph extension of the positional Burrows–Wheeler transform and its applications

by Adam M. Novak, Erik Garrison, Benedict Paten
Published 2017-07-01

Removing reference bias and improving indel calling in ancient DNA data analysis by mapping to a sequence variation graph

by Rui Martiniano, Erik Garrison, Eppie R. Jones, Andrea Manica, Richard Durbin
Published 2020-09-01

Genotyping structural variants in pangenome graphs using the vg toolkit

by Glenn Hickey, David Heller, Jean Monlong, Jonas A. Sibbesen, Jouni Sirén, Jordan Eizenga, Eric T. Dawson, Erik Garrison, Adam M. Novak, Benedict Paten
Published 2020-02-01

Viral coinfection analysis using a MinHash toolkit

by Eric T. Dawson, Sarah Wagner, David Roberson, Meredith Yeager, Joseph Boland, Erik Garrison, Stephen Chanock, Mark Schiffman, Tina Raine-Bennett, Thomas Lorey, Phillip E. Castle, Lisa Mirabello, Richard Durbin
Published 2019-07-01

478 Translation of a therapeutic neoantigen vaccine workflow to SARS-CoV-2 vaccine development

by Benjamin Vincent, Timothy O’Donnell, Maria Sambade, Julia Kodysh, Steven Vensko, Wolfgang Beck, Christof Smith, Sarah Entwistle, Caryn Willis, Jason Garness, Eric Routh, Kelly Olsen, Brandon Carpenter, Kaylee Gentry, Maria Fadri, Misha Fini, Amber Washington, Carsten Haber, Kirsten Heiss, Volker Stadler, Erik Garrison, Oliver Grant, Robert Woods, Mark Heise, Alexander Rubinsteyn
Published 2020-11-01

A comprehensive map of mobile element insertion polymorphisms in humans.

by Chip Stewart, Deniz Kural, Michael P Strömberg, Jerilyn A Walker, Miriam K Konkel, Adrian M Stütz, Alexander E Urban, Fabian Grubert, Hugo Y K Lam, Wan-Ping Lee, Michele Busby, Amit R Indap, Erik Garrison, Chad Huff, Jinchuan Xing, Michael P Snyder, Lynn B Jorde, Mark A Batzer, Jan O Korbel, Gabor T Marth, 1000 Genomes Project
Published 2011-08-01

A diploid assembly-based benchmark for variants in the major histocompatibility complex

by Chen-Shan Chin, Justin Wagner, Qiandong Zeng, Erik Garrison, Shilpa Garg, Arkarachai Fungtammasan, Mikko Rautiainen, Sergey Aganezov, Melanie Kirsche, Samantha Zarate, Michael C. Schatz, Chunlin Xiao, William J. Rowell, Charles Markello, Jesse Farek, Fritz J. Sedlazeck, Vikas Bansal, Byunggil Yoo, Neil Miller, Xin Zhou, Andrew Carroll, Alvaro Martinez Barrio, Marc Salit, Tobias Marschall, Alexander T. Dilthey, Justin M. Zook
Published 2020-09-01

Landscape and selection of vaccine epitopes in SARS-CoV-2

by Christof C. Smith, Kelly S. Olsen, Kaylee M. Gentry, Maria Sambade, Wolfgang Beck, Jason Garness, Sarah Entwistle, Caryn Willis, Steven Vensko, Allison Woods, Misha Fini, Brandon Carpenter, Eric Routh, Julia Kodysh, Timothy O’Donnell, Carsten Haber, Kirsten Heiss, Volker Stadler, Erik Garrison, Adam M. Sandor, Jenny P. Y. Ting, Jared Weiss, Krzysztof Krajewski, Oliver C. Grant, Robert J. Woods, Mark Heise, Benjamin G. Vincent, Alex Rubinsteyn
Published 2021-06-01

A strategy for building and using a human reference pangenome [version 2; peer review: 2 approved]

by Bastien Llamas, Giuseppe Narzisi, Valerie Schneider, Peter A. Audano, Evan Biederstedt, Lon Blauvelt, Peter Bradbury, Xian Chang, Chen-Shan Chin, Arkarachai Fungtammasan, Wayne E. Clarke, Alan Cleary, Jana Ebler, Jordan Eizenga, Jonas A. Sibbesen, Charles J. Markello, Erik Garrison, Shilpa Garg, Glenn Hickey, Gerard R. Lazo, Michael F. Lin, Medhat Mahmoud, Tobias Marschall, Ilia Minkin, Jean Monlong, Rajeeva L. Musunuri, Sagayamary Sagayaradj, Adam M. Novak, Mikko Rautiainen, Allison Regier, Fritz J. Sedlazeck, Jouni Siren, Yassine Souilmi, Justin Wagner, Travis Wrightsman, Toshiyuki T. Yokoyama, Qiandong Zeng, Justin M. Zook, Benedict Paten, Ben Busby
Published 2021-07-01