Benedict Paten

According to our database, Benedict Paten authored at least 48 papers between 2009 and 2023.

Collaborative distances:

• Dijkstra number of four.
• Erdős number of three.

2023

Building a collaborative cloud platform to accelerate heart, lung, blood, and sleep research.

Stan Ahalt, Paul Avillach, Rebecca R. Boyles, Kira Bradford, Steven Cox, Brandi Davis-Dusenbery, Robert L. Grossman, Ashok K. Krishnamurthy, Alisa Manning, Benedict Paten, Anthony Philippakis, Ingrid Borecki, Shu Hui Chen, Jon Kaltman, Sweta Ladwa, Chip Schwartz, Alastair Thomson, Sarah Davis, Alison Leaf, Jessica Lyons, Elizabeth Sheets, Joshua C. Bis, Matthew P. Conomos, Alessandro Culotti, Thomas N. Desain, Jack DiGiovanna, Milan Domazet, Stephanie M. Gogarten, Alba Gutiérrez-Sacristán, Tim Harris, Benjamin D. Heavner, Deepti Jain, Brian O'Connor, Kevin Osborn, Danielle Pillion, Jacob Pleiness, Ken Rice, Garrett Rupp, Arnaud Serret-Larmande, Albert Smith, Jason P. Stedman, Adrienne Stilp, Teresa Barsanti, John B. Cheadle, Christopher Erdmann, Brandy Farlow, Allie Gartland-Gray, Julie Hayes, Hannah Hiles, Paul Kerr, Chris Lenhardt, Tom Madden, Joanna O. Mieczkowska, Amanda Miller, Patrick Patton, Marcie Rathbun, Stephanie Suber, Joe Asare

J. Am. Medical Informatics Assoc., June, 2023

Optimal gap-affine alignment in <i>O</i>(<i>s</i>) space.

Santiago Marco-Sola, Jordan M. Eizenga, Andrea Guarracino, Benedict Paten, Erik Garrison, Miquel Moretó

Bioinform., February, 2023

GENCODE: reference annotation for the human and mouse genomes in 2023.

Adam Frankish, Silvia Carbonell Sala, Mark Diekhans, Irwin Jungreis, Jane E. Loveland, Jonathan M. Mudge, Cristina Sisu, James C. Wright, Carme Arnan, If Barnes, Abhimanyu Banerjee, Ruth Bennett, Andrew E. Berry, Alexandra Bignell, Carles Boix, Ferriol Calvet Riera, Daniel Cerdán-Vélez, Fiona Cunningham, Claire Davidson, Sarah M. Donaldson, Cagatay Dursun, Reham Fatima, Stefano Giorgetti, Carlos García-Girón, Jose M. Gonzalez, Matthew Hardy, Peter W. Harrison, Thibaut Hourlier, Zoe Hollis, Toby Hunt, Benjamin James, Yunzhe Jiang, Rory Johnson, Mike P. Kay, Julien Lagarde, Fergal J. Martin, Laura Martínez Gómez, Surag Nair, Pengyu Ni, Fernando Pozo, Vivek Ramalingam, Magali Ruffier, Bianca M. Schmitt, Jacob M. Schreiber, Emily Steed, Marie-Marthe Suner, Dulika Sumathipala, Irina Sycheva, Barbara Uszczynska-Ratajczak, Elizabeth Wass, Yucheng T. Yang, Andrew D. Yates, Zahoor Zafrulla, Jyoti Choudhary, Mark Gerstein, Roderic Guigó, Tim J. P. Hubbard, Manolis Kellis, Anshul Kundaje, Benedict Paten, Michael L. Tress, Paul Flicek

Nucleic Acids Res., January, 2023

Genetic Site-Aware Three-Dimensional Layout Algorithm for Variation Graphs.

Deepro Pasha, Yohei Rosen, Maxim Kuznetsov, Benedict Paten

Proceedings of the 14th ACM International Conference on Bioinformatics, 2023

2022

GBZ file format for pangenome graphs.

Jouni Sirén, Benedict Paten

Bioinform., November, 2022

2021

The Dockstore: enhancing a community platform for sharing reproducible and accessible computational protocols.

Denis Yuen, Louise Cabansay, Andrew G. Duncan, Gary Luu, Gregory Hogue, Charles Overbeck, Natalie Perez, Walt Shands, David Steinberg, Chaz Reid, Nneka Olunwa, Richard Hansen, Elizabeth Sheets, Ash O'farrell, Kim Cullion, Brian D. O'Connor, Benedict Paten, Lincoln Stein

Nucleic Acids Res., 2021

GENCODE 2021.

Adam Frankish, Mark Diekhans, Irwin Jungreis, Julien Lagarde, Jane E. Loveland, Jonathan M. Mudge, Cristina Sisu, James C. Wright, Joel Armstrong, If Barnes, Andrew E. Berry, Alexandra Bignell, Carles Boix, Silvia Carbonell Sala, Fiona Cunningham, Tomás Di Domenico, Sarah M. Donaldson, Ian T. Fiddes, Carlos García-Girón, Jose M. Gonzalez, Tiago Grego, Matthew Hardy, Thibaut Hourlier, Kevin L. Howe, Toby Hunt, Osagie G. Izuogu, Rory Johnson, Fergal J. Martin, Laura Martínez, Shamika Mohanan, Paul Muir, Fabio C. P. Navarro, Anne Parker, Baikang Pei, Fernando Pozo, Ferriol Calvet Riera, Magali Ruffier, Bianca M. Schmitt, Eloise Stapleton, Marie-Marthe Suner, Irina Sycheva, Barbara Uszczynska-Ratajczak, Maxim Y. Wolf, Jinrui Xu, Yucheng T. Yang, Andrew D. Yates, Daniel R. Zerbino, Yan Zhang, Jyoti Choudhary, Mark Gerstein, Roderic Guigó, Tim J. P. Hubbard, Manolis Kellis, Benedict Paten, Michael L. Tress, Paul Flicek

Nucleic Acids Res., 2021

Efficient dynamic variation graphs.

Jordan M. Eizenga, Adam M. Novak, Emily Kobayashi, Flavia Villani, Cecilia Cisar, Simon Heumos, Glenn Hickey, Vincenza Colonna, Benedict Paten, Erik Garrison

Bioinform., 2021

The Immersive Graph Genome Explorer: Navigating Genomics in Immersive Virtual Reality.

Maxim Kuznetsov, Aviv Elor, Sri Kurniawan, Colleen M. Bosworth, Yohei Rosen, Nicholas Heyer, Mircea Teodorescu, Benedict Paten, David Haussler

Proceedings of the 9th IEEE International Conference on Serious Games and Applications for Health, 2021

Walk-Preserving Transformation of Overlapped Sequence Graphs into Blunt Sequence Graphs with GetBlunted.

Jordan M. Eizenga, Ryan Lorig-Roach, Melissa M. Meredith, Benedict Paten

Proceedings of the Connecting with Computability, 2021

2020

BioHackathon 2015: Semantics of data for life sciences and reproducible research.

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 E. Bolton, Raoul Jean Pierre Bonnal, Hidemasa Bono, Kees Burger, Hirokazu Chiba, Kevin Bretonnel Cohen, Eric W. Deutsch, Jesualdo Tomás Fernández-Breis, Gang Fu, Takatomo Fujisawa, Atsushi Fukushima, Alexander García Castro, Naohisa Goto, Tudor Groza, Colin Hercus, Robert Hoehndorf, Kotone Itaya, Nick S. 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 NguyenXuan, 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 R. Taylor, Mark Thompson, Ikuo Uchiyama, Bruno Vieira, Chih-Hsuan Wei, Mark D. Wilkinson, Issaku Yamada, Ryota Yamanaka, Kazutoshi Yoshitake, Akiyasu C. Yoshizawa, Michel Dumontier, Kenjiro Kosaki, Toshihisa Takagi

F1000Research, 2020

Haplotype-aware graph indexes.

Jouni Sirén, Erik Garrison, Adam M. Novak, Benedict Paten, Richard Durbin

Bioinform., 2020

Gaussian mixture model-based unsupervised nucleotide modification number detection using nanopore-sequencing readouts.

Hongxu Ding, Andrew D. Bailey, Miten Jain, Hugh E. Olsen, Benedict Paten

Bioinform., 2020

Distance indexing and seed clustering in sequence graphs.

Xian Chang, Jordan Eizenga, Adam M. Novak, Jouni Sirén, Benedict Paten

Bioinform., 2020

SegAlign: a scalable GPU-based whole genome aligner.

Sneha D. Goenka, Yatish Turakhia, Benedict Paten, Mark Horowitz

Proceedings of the International Conference for High Performance Computing, 2020

2019

The human body at cellular resolution: the NIH Human Biomolecular Atlas Program.

Michael P. Snyder, Shin Lin, Amanda Posgai, Mark Atkinson, Aviv Regev, Jennifer Rood, Orit Rozenblatt-Rosen, Leslie Gaffney, Anna Hupalowska, Rahul Satija, Nils Gehlenborg, Jay Shendure, Julia Laskin, Pehr Harbury, Nicholas A. Nystrom, Jonathan C. Silverstein, Ziv Bar-Joseph, Kun Zhang, Katy Börner, Yiing Lin, Richard Conroy, Dena Procaccini, Ananda L. Roy, Ajay Pillai, Marishka Brown, Zorina S. Galis, Long Cai, Cole Trapnell, Dana Jackson, Garry P. Nolan, William James Greenleaf, Sylvia K. Plevritis, Sara Ahadi, Stephanie A. Nevins, Hayan Lee, Christian Martijn Schuerch, Sarah Black, Vishal Gautham Venkataraaman, Ed Esplin, Aaron Horning, Amir Bahmani, Xin Sun, Sanjay Jain, James S. Hagood, Gloria Pryhuber, Peter V. Kharchenko, Bernd Bodenmiller, Todd Brusko, Michael Clare-Salzler, Harry Nick, Kevin Otto, Clive Wasserfall, Marda Jorgensen, Maigan Brusko, Sergio Maffioletti, Richard M. Caprioli, Jeffrey M. Spraggins, Danielle Gutierrez, Nathan Heath Patterson, Elizabeth K. Neumann, Raymond Harris, Mark P. de Caestecker, Agnes B. Fogo, Raf Van de Plas, Ken Lau, Guo-Cheng Yuan, Qian Zhu, Ruben Dries, Peng Yin, Sinem K. Saka, Jocelyn Y. Kishi, Yu Wang, Isabel Goldaracena, Dong Hye Ye, Kristin E. Burnum-Johnson, Paul D. Piehowski, Charles Ansong, Ying Zhu, Tushar Desai, Jay Mulye, Peter Chou, Monica Nagendran, Sarah A. Teichmann, Benedict Paten, Robert F. Murphy, Jian Ma, Vladimir Yu. Kiselev, Carl Kingsford, Allyson Ricarte, Maria Keays, Sushma Anand Akoju, Matthew Ruffalo, Margaret Vella, Chuck McCallum, Leonard E. Cross, Samuel H. Friedman, Randy W. Heiland, Bruce William Herr II, Paul Macklin, Ellen M. Quardokus, Lisel Record, James P. Sluka, Griffin M. Weber, Philip D. Blood, Alexander Ropelewski, William Shirey, Robin M. Scibek, Paula M. Mabee, W. Christopher Lenhardt, Kimberly Robasky, Stavros Michailidis, John C. Marioni, Andrew Butler, Tim Stuart, Eyal Fisher, Shila Ghazanfar, Gökcen Eraslan, Tommaso Biancalani, Eeshit D. Vaishnav, Pothur Srinivas, Aaron Pawlyk, Salvatore Sechi, Elizabeth L. Wilder, James Anderson

Nat., 2019

GENCODE reference annotation for the human and mouse genomes.

Adam Frankish, Mark Diekhans, Anne-Maud Ferreira, Rory Johnson, Irwin Jungreis, Jane E. Loveland, Jonathan M. Mudge, Cristina Sisu, James C. Wright, Joel Armstrong, If Barnes, Andrew E. Berry, Alexandra Bignell, Silvia Carbonell Sala, Jacqueline Chrast, Fiona Cunningham, Tomás Di Domenico, Sarah M. Donaldson, Ian T. Fiddes, Carlos García-Girón, Jose M. Gonzalez, Tiago Grego, Matthew Hardy, Thibaut Hourlier, Toby Hunt, Osagie G. Izuogu, Julien Lagarde, Fergal J. Martin, Laura Martínez, Shamika Mohanan, Paul Muir, Fabio C. P. Navarro, Anne Parker, Baikang Pei, Fernando Pozo, Magali Ruffier, Bianca M. Schmitt, Eloise Stapleton, Marie-Marthe Suner, Irina Sycheva, Barbara Uszczynska-Ratajczak, Jinrui Xu, Andrew D. Yates, Daniel R. Zerbino, Yan Zhang, Bronwen L. Aken, Jyoti Choudhary, Mark Gerstein, Roderic Guigó, Tim J. P. Hubbard, Manolis Kellis, Benedict Paten, Alexandre Reymond, Michael L. Tress, Paul Flicek

Nucleic Acids Res., 2019

Sequence tube maps: making graph genomes intuitive to commuters.

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

Bioinform., 2019

An average-case sublinear forward algorithm for the haploid Li and Stephens model.

Yohei M. Rosen, Benedict J. Paten

Algorithms Mol. Biol., 2019

DP-CGAN: Differentially Private Synthetic Data and Label Generation.

Reihaneh Torkzadehmahani, Peter Kairouz, Benedict Paten

Proceedings of the IEEE Conference on Computer Vision and Pattern Recognition Workshops, 2019

2018

Superbubbles, Ultrabubbles, and Cacti.

Benedict Paten, Jordan M. Eizenga, Yohei M. Rosen, Adam M. Novak, Erik Garrison, Glenn Hickey

J. Comput. Biol., 2018

A Flow Procedure for Linearization of Genome Sequence Graphs.

David Haussler, Maciej Smuga-Otto, Jordan M. Eizenga, Benedict Paten, Adam M. Novak, Sergei Nikitin, Maria Zueva, Dmitrii Miagkov

J. Comput. Biol., 2018

An Average-Case Sublinear Exact Li and Stephens Forward Algorithm.

Yohei M. Rosen, Benedict J. Paten

Proceedings of the 18th International Workshop on Algorithms in Bioinformatics, 2018

2017

Developing a framework for digital objects in the Big Data to Knowledge (BD2K) commons: Report from the Commons Framework Pilots workshop.

Kathleen M. Jagodnik, Simon Koplev, Sherry L. Jenkins, Lucila Ohno-Machado, Benedict Paten, Stephan C. Schürer, Michel Dumontier, Ruben Verborgh, Alex Bui, Peipei Ping, Neil J. McKenna, Ravi K. Madduri, Ajay Pillai, Avi Ma'ayan

J. Biomed. Informatics, 2017

The Dockstore: enabling modular, community-focused sharing of Docker-based genomics tools and workflows.

Brian D. O'Connor, Denis Yuen, Vincent Chung, Andrew G. Duncan, Xiangkun Liu, Janice Patricia, Benedict Paten, Lincoln Stein, Vincent Ferretti

F1000Research, 2017

Modelling haplotypes with respect to reference cohort variation graphs.

Yohei Rosen, Jordan Eizenga, Benedict Paten

Bioinform., 2017

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

Adam M. Novak, Erik Garrison, Benedict Paten

Algorithms Mol. Biol., 2017

Superbubbles, Ultrabubbles and Cacti.

Benedict Paten, Adam M. Novak, Erik Garrison, Glenn Hickey

Proceedings of the Research in Computational Molecular Biology, 2017

A Flow Procedure for the Linearization of Genome Sequence Graphs.

David Haussler, Maciej Smuga-Otto, Benedict Paten, Adam M. Novak, Sergei Nikitin, Maria Zueva, Dmitrii Miagkov

Proceedings of the Research in Computational Molecular Biology, 2017

Data Sharing and Reproducible Clinical Genetic Testing: Successes and Challenges.

Shan Yang, Melissa S. Cline, Can Zhang, Benedict Paten, Stephen E. Lincoln

Proceedings of the Biocomputing 2017: Proceedings of the Pacific Symposium, 2017

Count Everything: Secure Count Query Framework Across Big Data Centers.

Xiaoqian Jiang, Claudiu Farcas, Benedict Paten, Mark Diekhans, Paul Avillach, Wallace Wadge, David Haussler, Lucila Ohno-Machado, Ida Sim

Proceedings of the Summit on Clinical Research Informatics, 2017

Describing the Local Structure of Sequence Graphs.

Yohei Rosen, Jordan Eizenga, Benedict Paten

Proceedings of the Algorithms for Computational Biology, 2017

2016

The UCSC Genome Browser database: 2016 update.

Matthew L. Speir, Ann S. Zweig, Kate R. Rosenbloom, Brian J. Raney, Benedict Paten, Parisa Nejad, Brian T. Lee, Katrina Learned, Donna Karolchik, Angie S. Hinrichs, Steven G. Heitner, Rachel A. Harte, Maximilian Haeussler, Luvina Guruvadoo, Pauline A. Fujita, Christopher Eisenhart, Mark Diekhans, Hiram Clawson, Jonathan Casper, Galt P. Barber, David Haussler, Robert M. Kuhn, W. James Kent

Nucleic Acids Res., 2016

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

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

BMC Bioinform., 2016

2015

The UCSC Genome Browser database: 2015 update.

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

Nucleic Acids Res., 2015

Building a Pan-Genome Reference for a Population.

Ngan Nguyen, Glenn Hickey, Daniel R. Zerbino, Brian J. Raney, Dent Earl, Joel Armstrong, W. James Kent, David Haussler, Benedict Paten

J. Comput. Biol., 2015

The NIH BD2K center for big data in translational genomics.

Benedict Paten, Mark Diekhans, Brian J. Druker, Stephen H. Friend, Justin Guinney, Nadine Gassner, Mitchell Guttman, W. James Kent, Patrick Mantey, Adam A. Margolin, Matt Massie, Adam M. Novak, Frank A. Nothaft, Lior Pachter, David A. Patterson, Maciej Smuga-Otto, Joshua M. Stuart, Laura J. van't Veer, Barbara J. Wold, David Haussler

J. Am. Medical Informatics Assoc., 2015

MinION Analysis and Reference Consortium: Phase 1 data release and analysis.

Camilla L. C. Ip, Matthew Loose, John R. Tyson, Mariateresa de Cesare, Bonnie L. Brown, Miten Jain, Richard M. Leggett, David A. Eccles, Vadim Zalunin, John M. Urban, Paolo Piazza, Rory J. Bowden, Benedict Paten, Solomon Mwaigwisya, Elizabeth M. Batty, Jared T. Simpson, Terrance P. Snutch, Ewan Birney, David Buck, Sara Goodwin, Hans J. Jansen, Justin O'Grady, Hugh E. Olsen, MinION Analysis, Reference Consortium

F1000Research, 2015

Canonical, stable, general mapping using context schemes.

Adam M. Novak, Yohei Rosen, David Haussler, Benedict Paten

Bioinform., 2015

2014

A unifying model of genome evolution under parsimony.

Benedict Paten, Daniel R. Zerbino, Glenn Hickey, David Haussler

BMC Bioinform., 2014

Track data hubs enable visualization of user-defined genome-wide annotations on the UCSC Genome Browser.

Brian J. Raney, Timothy R. Dreszer, Galt P. Barber, Hiram Clawson, Pauline A. Fujita, Ting Wang, Ngan Nguyen, Benedict Paten, Ann S. Zweig, Donna Karolchik, W. James Kent

Bioinform., 2014

Comparative assembly hubs: Web-accessible browsers for comparative genomics.

Ngan Nguyen, Glenn Hickey, Brian J. Raney, Joel Armstrong, Hiram Clawson, Ann S. Zweig, Donna Karolchik, William James Kent, David Haussler, Benedict Paten

Bioinform., 2014

Ragout - a reference-assisted assembly tool for bacterial genomes.

Mikhail Kolmogorov, Brian J. Raney, Benedict Paten, Son K. Pham

Bioinform., 2014

Building a Pangenome Reference for a Population.

Ngan Nguyen, Glenn Hickey, Daniel R. Zerbino, Brian J. Raney, Dent Earl, Joel Armstrong, David Haussler, Benedict Paten

Proceedings of the Research in Computational Molecular Biology, 2014

2013

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

Glenn Hickey, Benedict Paten, Dent Earl, Daniel R. Zerbino, David Haussler

Bioinform., 2013

2011

Cactus Graphs for Genome Comparisons.

Benedict Paten, Mark Diekhans, Dent Earl, John St. John, Jian Ma, Bernard B. Suh, David Haussler

J. Comput. Biol., 2011

Meta-Alignment with Crumble and Prune: Partitioning very large alignment problems for performance and parallelization.

Krishna M. Roskin, Benedict Paten, David Haussler

BMC Bioinform., 2011

2009

Sequence progressive alignment, a framework for practical large-scale probabilistic consistency alignment.

Benedict Paten, Javier Herrero, Kathryn Beal, Ewan Birney

Bioinform., 2009