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

Nanopore long-read RNAseq reveals widespread transcriptional variation among the surface receptors of individual B cells

by Ashley Byrne, Anna E. Beaudin, Hugh E. Olsen, Miten Jain, Charles Cole, Theron Palmer, Rebecca M. DuBois, E. Camilla Forsberg, Mark Akeson, Christopher Vollmers
Published 2017-07-01

Haplotype-aware diplotyping from noisy long reads

by Jana Ebler, Marina Haukness, Trevor Pesout, Tobias Marschall, Benedict Paten
Published 2019-06-01

ProTECT—Prediction of T-Cell Epitopes for Cancer Therapy

by Arjun A. Rao, Arjun A. Rao, Arjun A. Rao, Ada A. Madejska, Ada A. Madejska, Jacob Pfeil, Jacob Pfeil, Jacob Pfeil, Benedict Paten, Benedict Paten, Benedict Paten, Sofie R. Salama, Sofie R. Salama, Sofie R. Salama, David Haussler, David Haussler, David Haussler, David Haussler
Published 2020-11-01

Transcriptional activity and strain-specific history of mouse pseudogenes

by Cristina Sisu, Paul Muir, Adam Frankish, Ian Fiddes, Mark Diekhans, David Thybert, Duncan T. Odom, Paul Flicek, Thomas M. Keane, Tim Hubbard, Jennifer Harrow, Mark Gerstein
Published 2020-07-01

CRISPRi-based radiation modifier screen identifies long non-coding RNA therapeutic targets in glioma

by S. John Liu, Martina Malatesta, Brian V. Lien, Parna Saha, Shivani S. Thombare, Sung Jun Hong, Leslie Pedraza, Mark Koontz, Kyounghee Seo, Max A. Horlbeck, Daniel He, Harjus S. Birk, Miten Jain, Hugh E. Olsen, Mark Akeson, Jonathan S. Weissman, Michelle Monje, Nalin Gupta, David R. Raleigh, Erik M. Ullian, Daniel A. Lim
Published 2020-03-01

Common and cell-type specific responses to anti-cancer drugs revealed by high throughput transcript profiling

by Mario Niepel, Marc Hafner, Qiaonan Duan, Zichen Wang, Evan O. Paull, Mirra Chung, Xiaodong Lu, Joshua M. Stuart, Todd R. Golub, Aravind Subramanian, Avi Ma’ayan, Peter K. Sorger
Published 2017-10-01

A user guide for the online exploration and visualization of PCAWG data

by Mary J. Goldman, Junjun Zhang, Nuno A. Fonseca, Isidro Cortés-Ciriano, Qian Xiang, Brian Craft, Elena Piñeiro-Yáñez, Brian D. O’Connor, Wojciech Bazant, Elisabet Barrera, Alfonso Muñoz-Pomer, Robert Petryszak, Anja Füllgrabe, Fatima Al-Shahrour, Maria Keays, David Haussler, John N. Weinstein, Wolfgang Huber, Alfonso Valencia, Peter J. Park, Irene Papatheodorou, Jingchun Zhu, Vincent Ferretti, Miguel Vazquez
Published 2020-07-01

Pathway and network analysis of more than 2500 whole cancer genomes

by Matthew A. Reyna, David Haan, Marta Paczkowska, Lieven P. C. Verbeke, Miguel Vazquez, Abdullah Kahraman, Sergio Pulido-Tamayo, Jonathan Barenboim, Lina Wadi, Priyanka Dhingra, Raunak Shrestha, Gad Getz, Michael S. Lawrence, Jakob Skou Pedersen, Mark A. Rubin, David A. Wheeler, Søren Brunak, Jose M. G. Izarzugaza, Ekta Khurana, Kathleen Marchal, Christian von Mering, S. Cenk Sahinalp, Alfonso Valencia, PCAWG Drivers and Functional Interpretation Working Group, Jüri Reimand, Joshua M. Stuart, Benjamin J. Raphael, PCAWG Consortium
Published 2020-02-01

The Dockstore: enabling modular, community-focused sharing of Docker-based genomics tools and workflows [version 1; referees: 2 approved]

by Brian D. O'Connor, Denis Yuen, Vincent Chung, Andrew G. Duncan, Xiang Kun Liu, Janice Patricia, Benedict Paten, Lincoln Stein, Vincent Ferretti
Published 2017-01-01

Centromeric Satellite DNAs: Hidden Sequence Variation in the Human Population

by Karen H. Miga
Published 2019-05-01

Haplotypes spanning centromeric regions reveal persistence of large blocks of archaic DNA

by Sasha A Langley, Karen H Miga, Gary H Karpen, Charles H Langley
Published 2019-06-01

Alpha-satellite RNA transcripts are repressed by centromere–nucleolus associations

by Leah Bury, Brittania Moodie, Jimmy Ly, Liliana S McKay, Karen HH Miga, Iain M Cheeseman
Published 2020-11-01

Recommendations for the packaging and containerizing of bioinformatics software [version 2; peer review: 2 approved, 1 approved with reservations]

by Bjorn Gruening, Olivier Sallou, Pablo Moreno, Felipe da Veiga Leprevost, Hervé Ménager, Dan Søndergaard, Hannes Röst, Timo Sachsenberg, Brian O'Connor, Fábio Madeira, Victoria Dominguez Del Angel, Michael R. Crusoe, Susheel Varma, Daniel Blankenberg, Rafael C. Jimenez, BioContainers Community, Yasset Perez-Riverol
Published 2019-03-01

TrawlerWeb: an online de novo motif discovery tool for next-generation sequencing datasets

by Louis T. Dang, Markus Tondl, Man Ho H. Chiu, Jerico Revote, Benedict Paten, Vincent Tano, Alex Tokolyi, Florence Besse, Greg Quaife-Ryan, Helen Cumming, Mark J. Drvodelic, Michael P. Eichenlaub, Jeannette C. Hallab, Julian S. Stolper, Fernando J. Rossello, Marie A. Bogoyevitch, David A. Jans, Hieu T. Nim, Enzo R. Porrello, James E. Hudson, Mirana Ramialison
Published 2018-04-01

BioHackathon 2015: Semantics of data for life sciences and reproducible research [version 1; peer review: 2 approved]

by Rutger A. Vos, Toshiaki Katayama, Hiroyuki Mishima, Shin Kawano, Shuichi Kawashima, Jin-Dong Kim, Yuki Moriya, Toshiaki Tokimatsu, Atsuko Yamaguchi, Yasunori Yamamoto, Hongyan Wu, Peter Amstutz, Erick Antezana, Nobuyuki P. Aoki, Kazuharu Arakawa, Jerven T. Bolleman, Evan Bolton, Raoul J. P. Bonnal, Hidemasa Bono, Kees Burger, Hirokazu Chiba, Kevin B. Cohen, Eric W. Deutsch, Jesualdo T. Fernández-Breis, Gang Fu, Takatomo Fujisawa, Atsushi Fukushima, Alexander García, Naohisa Goto, Tudor Groza, Colin Hercus, Robert Hoehndorf, Kotone Itaya, Nick Juty, Takeshi Kawashima, Jee-Hyub Kim, Akira R. Kinjo, Masaaki Kotera, Kouji Kozaki, Sadahiro Kumagai, Tatsuya Kushida, Thomas Lütteke, Masaaki Matsubara, Joe Miyamoto, Attayeb Mohsen, Hiroshi Mori, Yuki Naito, Takeru Nakazato, Jeremy Nguyen-Xuan, Kozo Nishida, Naoki Nishida, Hiroyo Nishide, Soichi Ogishima, Tazro Ohta, Shujiro Okuda, Benedict Paten, Jean-Luc Perret, Philip Prathipati, Pjotr Prins, Núria Queralt-Rosinach, Daisuke Shinmachi, Shinya Suzuki, Tsuyosi Tabata, Terue Takatsuki, Kieron Taylor, Mark Thompson, Ikuo Uchiyama, Bruno Vieira, Chih-Hsuan Wei, Mark Wilkinson, Issaku Yamada, Ryota Yamanaka, Kazutoshi Yoshitake, Akiyasu C. Yoshizawa, Michel Dumontier, Kenjiro Kosaki, Toshihisa Takagi
Published 2020-02-01

Genomic Profiling of Childhood Tumor Patient-Derived Xenograft Models to Enable Rational Clinical Trial Design

by Jo Lynne Rokita, Komal S. Rathi, Maria F. Cardenas, Kristen A. Upton, Joy Jayaseelan, Katherine L. Cross, Jacob Pfeil, Laura E. Egolf, Gregory P. Way, Alvin Farrel, Nathan M. Kendsersky, Khushbu Patel, Krutika S. Gaonkar, Apexa Modi, Esther R. Berko, Gonzalo Lopez, Zalman Vaksman, Chelsea Mayoh, Jonas Nance, Kristyn McCoy, Michelle Haber, Kathryn Evans, Hannah McCalmont, Katerina Bendak, Julia W. Böhm, Glenn M. Marshall, Vanessa Tyrrell, Karthik Kalletla, Frank K. Braun, Lin Qi, Yunchen Du, Huiyuan Zhang, Holly B. Lindsay, Sibo Zhao, Jack Shu, Patricia Baxter, Christopher Morton, Dias Kurmashev, Siyuan Zheng, Yidong Chen, Jay Bowen, Anthony C. Bryan, Kristen M. Leraas, Sara E. Coppens, HarshaVardhan Doddapaneni, Zeineen Momin, Wendong Zhang, Gregory I. Sacks, Lori S. Hart, Kateryna Krytska, Yael P. Mosse, Gregory J. Gatto, Yolanda Sanchez, Casey S. Greene, Sharon J. Diskin, Olena Morozova Vaske, David Haussler, Julie M. Gastier-Foster, E. Anders Kolb, Richard Gorlick, Xiao-Nan Li, C. Patrick Reynolds, Raushan T. Kurmasheva, Peter J. Houghton, Malcolm A. Smith, Richard B. Lock, Pichai Raman, David A. Wheeler, John M. Maris
Published 2019-11-01