Sequence progressive alignment, a framework for practical large-scale probabilistic consistency alignment. - Benedict Paten; Javier Herrero; Kathryn Beal; Ewan Birney (Bioinform., 2009)

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)

Cactus Graphs for Genome Comparisons. - Benedict Paten; Mark Diekhans; Dent Earl; John St. John; Jian Ma 004; Bernard B. Suh; David Haussler (J. Comput. Biol., 2011)

HAL: a hierarchical format for storing and analyzing multiple genome alignments. - Glenn Hickey; Benedict Paten; Dent Earl; Daniel R. Zerbino; David Haussler (Bioinform., 2013)

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 (RECOMB, 2014)

Ragout - a reference-assisted assembly tool for bacterial genomes. - Mikhail Kolmogorov; Brian J. Raney; Benedict Paten; Son K. Pham (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)

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 032; Ngan Nguyen; Benedict Paten; Ann S. Zweig; Donna Karolchik; W. James Kent (Bioinform., 2014)

A unifying model of genome evolution under parsimony. - Benedict Paten; Daniel R. Zerbino; Glenn Hickey; David Haussler (BMC Bioinform., 2014)

Canonical, stable, general mapping using context schemes. - Adam M. Novak; Yohei Rosen; David Haussler; Benedict Paten (Bioinform., 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; et al. (F1000Research, 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; et al. (J. Am. Medical Informatics Assoc., 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 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; et al. (Nucleic Acids Res., 2015)

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)

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; et al. (Nucleic Acids Res., 2016)

Describing the Local Structure of Sequence Graphs. - Yohei Rosen; Jordan Eizenga; Benedict Paten (AlCoB, 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 (CRI, 2017)

Data Sharing and Reproducible Clinical Genetic Testing: Successes and Challenges. - Shan Yang; Melissa S. Cline; Can Zhang; Benedict Paten; Stephen E. Lincoln (PSB, 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 (RECOMB, 2017)

Superbubbles, Ultrabubbles and Cacti. - Benedict Paten; Adam M. Novak; Erik Garrison; Glenn Hickey (RECOMB, 2017)

A graph extension of the positional Burrows-Wheeler transform and its applications. - Adam M. Novak; Erik Garrison; Benedict Paten (Algorithms Mol. Biol., 2017)

Modelling haplotypes with respect to reference cohort variation graphs. - Yohei Rosen; Jordan Eizenga; Benedict Paten (Bioinform., 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)

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 A. T. Bui; Peipei Ping; Neil J. McKenna; Ravi K. Madduri; et al. (J. Biomed. Informatics, 2017)

An Average-Case Sublinear Exact Li and Stephens Forward Algorithm. - Yohei M. Rosen; Benedict J. Paten (WABI, 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)

Superbubbles, Ultrabubbles, and Cacti. - Benedict Paten; Jordan M. Eizenga; Yohei M. Rosen; Adam M. Novak; Erik Garrison; Glenn Hickey (J. Comput. Biol., 2018)

DP-CGAN: Differentially Private Synthetic Data and Label Generation. - Reihaneh Torkzadehmahani; Peter Kairouz; Benedict Paten (CVPR Workshops, 2019)

An average-case sublinear forward algorithm for the haploid Li and Stephens model. - Yohei M. Rosen; Benedict J. Paten (Algorithms Mol. Biol., 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)

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; et al. (Nucleic Acids Res., 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; et al. (Nat., 2019)

SegAlign: a scalable GPU-based whole genome aligner. - Sneha D. Goenka; Yatish Turakhia; Benedict Paten; Mark Horowitz (SC, 2020)

Distance indexing and seed clustering in sequence graphs. - Xian Chang; Jordan Eizenga; Adam M. Novak; Jouni Sirén; Benedict Paten (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)

Haplotype-aware graph indexes. - Jouni Sirén; Erik Garrison; Adam M. Novak; Benedict Paten; Richard Durbin (Bioinform., 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; et al. (F1000Research, 2020)

Walk-Preserving Transformation of Overlapped Sequence Graphs into Blunt Sequence Graphs with GetBlunted. - Jordan M. Eizenga; Ryan Lorig-Roach; Melissa M. Meredith; Benedict Paten (CiE, 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 (SEGAH, 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)

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; et al. (Nucleic Acids Res., 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; et al. (Nucleic Acids Res., 2021)

GBZ file format for pangenome graphs. - Jouni Sirén; Benedict Paten (Bioinform., 2022)

Genetic Site-Aware Three-Dimensional Layout Algorithm for Variation Graphs. - Deepro Pasha; Yohei Rosen; Maxim Kuznetsov; Benedict Paten (BCB, 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; et al. (Nucleic Acids Res., 2023)

Optimal gap-affine alignment in O(s) space. - Santiago Marco-Sola; Jordan M. Eizenga; Andrea Guarracino; Benedict Paten; Erik Garrison; Miquel Moretó (Bioinform., 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 001; Brandi Davis-Dusenbery; Robert L. Grossman; Ashok K. Krishnamurthy 001; Alisa Manning; Benedict Paten; Anthony Philippakis; Ingrid Borecki; et al. (J. Am. Medical Informatics Assoc., 2023)

Lossless Pangenome Indexing Using Tag Arrays. - Parsa Eskandar; Benedict Paten; Jouni Sirén (WABI, 2025)