Benedict Paten

Publication Activity (10 Years)

Years Active: 2009-2023
Publications (10 Years): 36

Top Topics

Gaussian Mixture

Comparative Genomics

Anatomical Landmarks

Top Venues

Nucleic Acids Res.

J. Comput. Biol.

Publications

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, Ben 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
Building a collaborative cloud platform to accelerate heart, lung, blood, and sleep research. J. Am. Medical Informatics Assoc. 30 (7) (2023)
Santiago Marco-Sola, Jordan M. Eizenga, Andrea Guarracino, Benedict Paten, Erik Garrison, Miquel Moretó
) space. Bioinform. 39 (2) (2023)
Deepro Pasha, Yohei Rosen, Maxim Kuznetsov, Benedict Paten
Genetic Site-Aware Three-Dimensional Layout Algorithm for Variation Graphs. BCB (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
GENCODE: reference annotation for the human and mouse genomes in 2023. Nucleic Acids Res. 51 (D1) (2023)
Jouni Sirén, Benedict Paten
GBZ file format for pangenome graphs. Bioinform. 38 (22) (2022)
Jordan M. Eizenga, Adam M. Novak, Emily Kobayashi, Flavia Villani, Cecilia Cisar, Simon Heumos, Glenn Hickey, Vincenza Colonna, Benedict Paten, Erik Garrison
Efficient dynamic variation graphs. Bioinform. 36 (21) (2021)
Denis Yuen, Louise Cabansay, Andrew 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
The Dockstore: enhancing a community platform for sharing reproducible and accessible computational protocols. Nucleic Acids Res. 49 (Webserver-Issue) (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
GENCODE 2021. Nucleic Acids Res. 49 (Database-Issue) (2021)
Jordan M. Eizenga, Ryan Lorig-Roach, Melissa M. Meredith, Benedict Paten
Walk-Preserving Transformation of Overlapped Sequence Graphs into Blunt Sequence Graphs with GetBlunted. CiE (2021)
Maxim Kuznetsov, Aviv Elor, Sri Kurniawan, Colleen M. Bosworth, Yohei Rosen, Nicholas Heyer, Mircea Teodorescu, Benedict Paten, David Haussler
The Immersive Graph Genome Explorer: Navigating Genomics in Immersive Virtual Reality. SEGAH (2021)
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
BioHackathon 2015: Semantics of data for life sciences and reproducible research. F1000Research 9 (2020)
Xian Chang, Jordan Eizenga, Adam M. Novak, Jouni Sirén, Benedict Paten
Distance indexing and seed clustering in sequence graphs. Bioinform. 36 (Supplement-1) (2020)
Hongxu Ding, Andrew D. Bailey, Miten Jain, Hugh Olsen, Benedict Paten
Gaussian mixture model-based unsupervised nucleotide modification number detection using nanopore-sequencing readouts. Bioinform. 36 (19) (2020)
Sneha D. Goenka, Yatish Turakhia, Benedict Paten, Mark Horowitz
SegAlign: a scalable GPU-based whole genome aligner. SC (2020)
Jouni Sirén, Erik Garrison, Adam M. Novak, Benedict Paten, Richard Durbin
Haplotype-aware graph indexes. Bioinform. 36 (2) (2020)
Reihaneh Torkzadehmahani, Peter Kairouz, Benedict Paten
DP-CGAN: Differentially Private Synthetic Data and Label Generation. CoRR (2020)
Wolfgang Beyer, Adam M. Novak, Glenn Hickey, Jeffrey Chan, Vanessa Tan, Benedict Paten, Daniel R. Zerbino
Sequence tube maps: making graph genomes intuitive to commuters. Bioinform. 35 (24) (2019)
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
GENCODE reference annotation for the human and mouse genomes. Nucleic Acids Res. 47 (Database-Issue) (2019)
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 deCaestecker, 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 A. 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
The human body at cellular resolution: the NIH Human Biomolecular Atlas Program. Nat. 574 (7777) (2019)
Reihaneh Torkzadehmahani, Peter Kairouz, Benedict Paten
DP-CGAN: Differentially Private Synthetic Data and Label Generation. CVPR Workshops (2019)
David Haussler, Maciej Smuga-Otto, Jordan M. Eizenga, Benedict Paten, Adam M. Novak, Sergei Nikitin, Maria Zueva, Dmitrii Miagkov
A Flow Procedure for Linearization of Genome Sequence Graphs. J. Comput. Biol. 25 (7) (2018)
Jouni Sirén, Erik Garrison, Adam M. Novak, Benedict Paten, Richard Durbin
Haplotype-aware graph indexes. WABI (2018)
Jouni Sirén, Erik Garrison, Adam M. Novak, Benedict Paten, Richard Durbin
Haplotype-aware graph indexes. CoRR (2018)
Benedict Paten, Jordan M. Eizenga, Yohei M. Rosen, Adam M. Novak, Erik Garrison, Glenn Hickey
Superbubbles, Ultrabubbles, and Cacti. J. Comput. Biol. 25 (7) (2018)
Yohei Rosen, Jordan Eizenga, Benedict Paten
Modelling haplotypes with respect to reference cohort variation graphs. Bioinform. 33 (14) (2017)
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
Developing a framework for digital objects in the Big Data to Knowledge (BD2K) commons: Report from the Commons Framework Pilots workshop. J. Biomed. Informatics 71 (2017)
Xiaoqian Jiang, Claudiu Farcas, Benedict Paten, Mark Diekhans, Paul Avillach, Wallace Wadge, David Haussler, Lucila Ohno-Machado, Ida Sim
Count Everything: Secure Count Query Framework Across Big Data Centers. CRI (2017)
Benedict Paten, Adam M. Novak, Erik Garrison, Glenn Hickey
Superbubbles, Ultrabubbles and Cacti. RECOMB (2017)
David Haussler, Maciej Smuga-Otto, Benedict Paten, Adam M. Novak, Sergei Nikitin, Maria Zueva, Dmitrii Miagkov
A Flow Procedure for the Linearization of Genome Sequence Graphs. RECOMB (2017)
Adam M. Novak, Erik Garrison, Benedict Paten
A graph extension of the positional Burrows-Wheeler transform and its applications. Algorithms Mol. Biol. 12 (1) (2017)
Yohei Rosen, Jordan Eizenga, Benedict Paten
Describing the Local Structure of Sequence Graphs. AlCoB (2017)
Shan Yang, Melissa S. Cline, Can Zhang, Benedict Paten, Stephen E. Lincoln
Data Sharing and Reproducible Clinical Genetic Testing: Successes and Challenges. PSB (2017)
Brian D. O'Connor, Denis Yuen, Vincent Chung, Andrew G. Duncan, Xiangkun Liu, Janice Patricia, Benedict Paten, Lincoln Stein, Vincent Ferretti
The Dockstore: enabling modular, community-focused sharing of Docker-based genomics tools and workflows. F1000Research 6 (2017)
Daniel R. Zerbino, Tracy Ballinger, Benedict Paten, Glenn Hickey, David Haussler
Representing and decomposing genomic structural variants as balanced integer flows on sequence graphs. BMC Bioinform. 17 (2016)
Adam M. Novak, Erik Garrison, Benedict Paten
A Graph Extension of the Positional Burrows-Wheeler Transform and Its Applications. WABI (2016)
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
The UCSC Genome Browser database: 2016 update. Nucleic Acids Res. 44 (Database-Issue) (2016)
Ngan Nguyen, Glenn Hickey, Daniel R. Zerbino, Brian J. Raney, Dent Earl, Joel Armstrong, W. James Kent, David Haussler, Benedict Paten
Building a Pan-Genome Reference for a Population. J. Comput. Biol. 22 (5) (2015)
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
MinION Analysis and Reference Consortium: Phase 1 data release and analysis. F1000Research 4 (2015)
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
The NIH BD2K center for big data in translational genomics. J. Am. Medical Informatics Assoc. 22 (6) (2015)
Adam M. Novak, Yohei Rosen, David Haussler, Benedict Paten
Canonical, stable, general mapping using context schemes. Bioinform. 31 (22) (2015)
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
The UCSC Genome Browser database: 2015 update. Nucleic Acids Res. 43 (Database-Issue) (2015)
Ngan Nguyen, Glenn Hickey, Brian J. Raney, Joel Armstrong, Hiram Clawson, Ann S. Zweig, Donna Karolchik, William James Kent, David Haussler, Benedict Paten
Comparative assembly hubs: Web-accessible browsers for comparative genomics. Bioinform. 30 (23) (2014)
Mikhail Kolmogorov, Brian J. Raney, Benedict Paten, Son K. Pham
Ragout - a reference-assisted assembly tool for bacterial genomes. Bioinform. 30 (12) (2014)
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
Track data hubs enable visualization of user-defined genome-wide annotations on the UCSC Genome Browser. Bioinform. 30 (7) (2014)
Benedict Paten, Daniel R. Zerbino, Glenn Hickey, David Haussler
A unifying model of genome evolution under parsimony. BMC Bioinform. 15 (2014)
Ngan Nguyen, Glenn Hickey, Daniel R. Zerbino, Brian J. Raney, Dent Earl, Joel Armstrong, David Haussler, Benedict Paten
Building a Pangenome Reference for a Population. RECOMB (2014)
Glenn Hickey, Benedict Paten, Dent Earl, Daniel R. Zerbino, David Haussler
HAL: a hierarchical format for storing and analyzing multiple genome alignments. Bioinform. 29 (10) (2013)
Krishna M. Roskin, Benedict Paten, David Haussler
Meta-Alignment with Crumble and Prune: Partitioning very large alignment problems for performance and parallelization. BMC Bioinform. 12 (2011)
Benedict Paten, Mark Diekhans, Dent Earl, John St. John, Jian Ma, Bernard B. Suh, David Haussler
Cactus Graphs for Genome Comparisons. J. Comput. Biol. 18 (3) (2011)
Benedict Paten, Mark Diekhans, Dent Earl, John St. John, Jian Ma, Bernard B. Suh, David Haussler
Cactus Graphs for Genome Comparisons. RECOMB (2010)
Benedict Paten, Javier Herrero, Kathryn Beal, Ewan Birney
Sequence progressive alignment, a framework for practical large-scale probabilistic consistency alignment. Bioinform. 25 (3) (2009)