Benedict Paten

Affiliations
  • UC Santa Cruz Genomics Institute, Santa Cruz, CA, USA. bpaten@ucsc.edu.
ORCID: http://orcid.org/0000-0001-8863-3539

Publications (91)

Nanopore sequencing and the Shasta toolkit enable efficient de novo assembly of eleven human genomes.

Nature biotechnology
Avec: Kishwar Shafin , Trevor Pesout , Ryan Lorig-Roach , Marina Haukness , Hugh E Olsen , Colleen Bosworth , Joel Armstrong , Kristof Tigyi , Nicholas Maurer , Sergey Koren , Fritz J Sedlazeck , Tobias Marschall , Simon Mayes , Vania Costa , Justin M Zook , Kelvin J Liu , Duncan Kilburn , Melanie Sorensen , Katy M Munson , Mitchell R Vollger , Jean Monlong , Erik Garrison , Evan E Eichler , Sofie Salama , David Haussler , Richard E Green , Mark Akeson , Adam Phillippy , Karen H Miga , Paolo Carnevali , Miten Jain , Benedict Paten

Off Earth Identification of Bacterial Populations Using 16S rDNA Nanopore Sequencing.

Genes
Avec: Aaron S Burton , Sarah E Stahl , Kristen K John , Miten Jain , Sissel Juul , Daniel J Turner , Eoghan D Harrington , David Stoddart , Benedict Paten , Mark Akeson , Sarah L Castro-Wallace

Haplotype-aware diplotyping from noisy long reads.

Genome biology
Avec: Jana Ebler , Marina Haukness , Trevor Pesout , Tobias Marschall , Benedict Paten

A Survey of Rare Epigenetic Variation in 23,116 Human Genomes Identifies Disease-Relevant Epivariations and CGG Expansions.

American journal of human genetics
Avec: Paras Garg , Bharati Jadhav , Oscar L Rodriguez , Nihir Patel , Alejandro Martin-Trujillo , Miten Jain , Sofie Metsu , Hugh Olsen , Benedict Paten , Beate Ritz , R Frank Kooy , Jozef Gecz , Andrew J Sharp

Inverting the model of genomics data sharing with the NHGRI Genomic Data Science Analysis, Visualization, and Informatics Lab-space.

Cell genomics
Avec: Michael C Schatz , Anthony A Philippakis , Enis Afgan , Eric Banks , Vincent J Carey , Robert J Carroll , Alessandro Culotti , Kyle Ellrott , Jeremy Goecks , Robert L Grossman , Ira M Hall , Kasper D Hansen , Jonathan Lawson , Jeffrey T Leek , Anne O'Donnell Luria , Stephen Mosher , Martin Morgan , Anton Nekrutenko , Brian D O'Connor , Kevin Osborn , Benedict Paten , Candace Patterson , Frederick J Tan , Casey Overby Taylor , Jennifer Vessio , Levi Waldron , Ting Wang , Kristin Wuichet

LungMAP Portal Ecosystem: Systems-Level Exploration of the Lung.

American journal of respiratory cell and molecular biology
Avec: Nathan Gaddis , Joshua Fortriede , Minzhe Guo , Eric E Bardes , Michal Kouril , Scott Tabar , Kevin Burns , Maryanne E Ardini-Poleske , Stephanie Loos , Daniel Schnell , Kang Jin , Balaji Iyer , Yina Du , Bing-Xing Huo , Anukana Bhattacharjee , Jeff Korte , Ruchi Munshi , Victoria Smith , Andrew Herbst , Joseph A Kitzmiller , Geremy C Clair , James P Carson , Joshua Adkins , Edward E Morrisey , Gloria S Pryhuber , Ravi Misra , Jeffrey A Whitsett , Xin Sun , Trevor Heathorn , Benedict Paten , V B Surya Prasath , Yan Xu , Tim Tickle , Bruce J Aronow , Nathan Salomonis , Auteur inconnu

Increased mutation and gene conversion within human segmental duplications.

Nature
Avec: Mitchell R Vollger , Philip C Dishuck , William T Harvey , William S DeWitt , Xavi Guitart , Michael E Goldberg , Allison N Rozanski , Julian Lucas , Mobin Asri , Auteur inconnu , Katherine M Munson , Alexandra P Lewis , Kendra Hoekzema , Glennis A Logsdon , David Porubsky , Benedict Paten , Kelley Harris , PingHsun Hsieh , Evan E Eichler

Scalable Nanopore sequencing of human genomes provides a comprehensive view of haplotype-resolved variation and methylation.

bioRxiv : the preprint server for biology
Avec: Mikhail Kolmogorov , Kimberley J Billingsley , Mira Mastoras , Melissa Meredith , Jean Monlong , Ryan Lorig-Roach , Mobin Asri , Pilar Alvarez Jerez , Laksh Malik , Ramita Dewan , Xylena Reed , Rylee M Genner , Kensuke Daida , Sairam Behera , Kishwar Shafin , Trevor Pesout , Jeshuwin Prabakaran , Paolo Carnevali , Auteur inconnu , Jianzhi Yang , Arang Rhie , Sonja W Scholz , Bryan J Traynor , Karen H Miga , Miten Jain , Winston Timp , Adam M Phillippy , Mark Chaisson , Fritz J Sedlazeck , Cornelis Blauwendraat , Benedict Paten

Structurally divergent and recurrently mutated regions of primate genomes.

bioRxiv : the preprint server for biology
Avec: Yafei Mao , William T Harvey , David Porubsky , Katherine M Munson , Kendra Hoekzema , Alexandra P Lewis , Peter A Audano , Allison Rozanski , Xiangyu Yang , Shilong Zhang , David S Gordon , Xiaoxi Wei , Glennis A Logsdon , Marina Haukness , Philip C Dishuck , Hyeonsoo Jeong , Ricardo Del Rosario , Vanessa L Bauer , Will T Fattor , Gregory K Wilkerson , Qing Lu , Benedict Paten , Guoping Feng , Sara L Sawyer , Wesley C Warren , Lucia Carbone , Evan E Eichler

Leveraging Base Pair Mammalian Constraint to Understand Genetic Variation and Human Disease.

bioRxiv : the preprint server for biology
Avec: Patrick F Sullivan , Jennifer R S Meadows , Steven Gazal , BaDoi N Phan , Xue Li , Diane P Genereux , Michael X Dong , Matteo Bianchi , Gregory Andrews , Sharadha Sakthikumar , Jessika Nordin , Ananya Roy , Matthew J Christmas , Voichita D Marinescu , Ola Wallerman , James R Xue , Yun Li , Shuyang Yao , Quan Sun , Jin Szatkiewicz , Jia Wen , Laura M Huckins , Alyssa J Lawler , Kathleen C Keough , Zhili Zheng , Jian Zeng , Naomi R Wray , Jessica Johnson , Jiawen Chen , Auteur inconnu , Benedict Paten , Steven K Reilly , Graham M Hughes , Zhiping Weng , Katherine S Pollard , Andreas R Pfenning , Karin Forsberg-Nilsson , Elinor K Karlsson , Kerstin Lindblad-Toh

Severus: accurate detection and characterization of somatic structural variation in tumor genomes using long reads.

medRxiv : the preprint server for health sciences
Avec: Ayse Keskus , Asher Bryant , Tanveer Ahmad , Byunggil Yoo , Sergey Aganezov , Anton Goretsky , Ataberk Donmez , Lisa A Lansdon , Isabel Rodriguez , Jimin Park , Yuelin Liu , Xiwen Cui , Joshua Gardner , Brandy McNulty , Samuel Sacco , Jyoti Shetty , Yongmei Zhao , Bao Tran , Giuseppe Narzisi , Adrienne Helland , Daniel E Cook , Pi-Chuan Chang , Alexey Kolesnikov , Andrew Carroll , Erin K Molloy , Irina Pushel , Erin Guest , Tomi Pastinen , Kishwar Shafin , Karen H Miga , Salem Malikic , Chi-Ping Day , Nicolas Robine , Cenk Sahinalp , Michael Dean , Midhat S Farooqi , Benedict Paten , Mikhail Kolmogorov

Phased nanopore assembly with Shasta and modular graph phasing with GFAse.

Genome research
Avec: Ryan Lorig-Roach , Melissa Meredith , Jean Monlong , Miten Jain , Hugh Olsen , Brandy McNulty , David Porubsky , Tessa Montague , Julian Lucas , Chris Condon , Jordan M Eizenga , Sissel Juul , Sean McKenzie , Sara E Simmonds , Jimin Park , Mobin Asri , Sergey Koren , Evan Eichler , Richard Axel , Bruce Martin , Paolo Carnevali , Karen Miga , Benedict Paten

Advancing long-read nanopore genome assembly and accurate variant calling for rare disease detection.

medRxiv : the preprint server for health sciences
Avec: Shloka Negi , Sarah L Stenton , Seth I Berger , Brandy McNulty , Ivo Violich , Joshua Gardner , Todd Hillaker , Sara M O'Rourke , Melanie C O'Leary , Elizabeth Carbonell , Christina Austin-Tse , Gabrielle Lemire , Jillian Serrano , Brian Mangilog , Grace VanNoy , Mikhail Kolmogorov , Eric Vilain , Anne O'Donnell-Luria , Emmanuèle Délot , Karen H Miga , Jean Monlong , Benedict Paten

halSynteny: a fast, easy-to-use conserved synteny block construction method for multiple whole-genome alignments.

GigaScience
Avec: Ksenia Krasheninnikova , Mark Diekhans , Joel Armstrong , Aleksei Dievskii , Benedict Paten , Stephen O'Brien

Genotyping structural variants in pangenome graphs using the vg toolkit.

Genome biology
Avec: Glenn Hickey , David Heller , Jean Monlong , Jonas A Sibbesen , Jouni Sirén , Jordan Eizenga , Eric T Dawson , Erik Garrison , Adam M Novak , Benedict Paten

Haplotype-aware graph indexes.

Bioinformatics (Oxford, England)
Avec: Jouni Sirén , Erik Garrison , Adam M Novak , Benedict Paten , Richard Durbin

Bayesian Framework for Detecting Gene Expression Outliers in Individual Samples.

JCO clinical cancer informatics
Avec: John Vivian , Jordan M Eizenga , Holly C Beale , Olena M Vaske , Benedict Paten

Haplotype-aware variant calling with PEPPER-Margin-DeepVariant enables high accuracy in nanopore long-reads.

Nature methods
Avec: Kishwar Shafin , Trevor Pesout , Pi-Chuan Chang , Maria Nattestad , Alexey Kolesnikov , Sidharth Goel , Gunjan Baid , Mikhail Kolmogorov , Jordan M Eizenga , Karen H Miga , Paolo Carnevali , Miten Jain , Andrew Carroll , Benedict Paten

Progressive Cactus is a multiple-genome aligner for the thousand-genome era.

Nature
Avec: Joel Armstrong , Glenn Hickey , Mark Diekhans , Ian T Fiddes , Adam M Novak , Alden Deran , Qi Fang , Duo Xie , Shaohong Feng , Josefin Stiller , Diane Genereux , Jeremy Johnson , Voichita Dana Marinescu , Jessica Alföldi , Robert S Harris , Kerstin Lindblad-Toh , David Haussler , Elinor Karlsson , Erich D Jarvis , Guojie Zhang , Benedict Paten

Dense sampling of bird diversity increases power of comparative genomics.

Nature
Avec: Shaohong Feng , Josefin Stiller , Yuan Deng , Joel Armstrong , Qi Fang , Andrew Hart Reeve , Duo Xie , Guangji Chen , Chunxue Guo , Brant C Faircloth , Bent Petersen , Zongji Wang , Qi Zhou , Mark Diekhans , Wanjun Chen , Sergio Andreu-Sánchez , Ashot Margaryan , Jason Travis Howard , Carole Parent , George Pacheco , Mikkel-Holger S Sinding , Lara Puetz , Emily Cavill , Ângela M Ribeiro , Leopold Eckhart , Jon Fjeldså , Peter A Hosner , Robb T Brumfield , Les Christidis , Mads F Bertelsen , Thomas Sicheritz-Ponten , Dieter Thomas Tietze , Bruce C Robertson , Gang Song , Gerald Borgia , Santiago Claramunt , Irby J Lovette , Saul J Cowen , Peter Njoroge , John Philip Dumbacher , Oliver A Ryder , Jérôme Fuchs , Michael Bunce , David W Burt , Joel Cracraft , Guanliang Meng , Shannon J Hackett , Peter G Ryan , Knud Andreas Jønsson , Ian G Jamieson , Rute R da Fonseca , Edward L Braun , Peter Houde , Siavash Mirarab , Alexander Suh , Bengt Hansson , Suvi Ponnikas , Hanna Sigeman , Martin Stervander , Paul B Frandsen , Henriette van der Zwan , Rencia van der Sluis , Carina Visser , Christopher N Balakrishnan , Andrew G Clark , John W Fitzpatrick , Reed Bowman , Nancy Chen , Alison Cloutier , Timothy B Sackton , Scott V Edwards , Dustin J Foote , Subir B Shakya , Frederick H Sheldon , Alain Vignal , André E R Soares , Beth Shapiro , Jacob González-Solís , Joan Ferrer-Obiol , Julio Rozas , Marta Riutort , Anna Tigano , Vicki Friesen , Love Dalén , Araxi O Urrutia , Tamás Székely , Yang Liu , Michael G Campana , André Corvelo , Robert C Fleischer , Kim M Rutherford , Neil J Gemmell , Nicolas Dussex , Henrik Mouritsen , Nadine Thiele , Kira Delmore , Miriam Liedvogel , Andre Franke , Marc P Hoeppner , Oliver Krone , Adam M Fudickar , Borja Milá , Ellen D Ketterson , Andrew Eric Fidler , Guillermo Friis , Ángela M Parody-Merino , Phil F Battley , Murray P Cox , Nicholas Costa Barroso Lima , Francisco Prosdocimi , Thomas Lee Parchman , Barney A Schlinger , Bette A Loiselle , John G Blake , Haw Chuan Lim , Lainy B Day , Matthew J Fuxjager , Maude W Baldwin , Michael J Braun , Morgan Wirthlin , Rebecca B Dikow , T Brandt Ryder , Glauco Camenisch , Lukas F Keller , Jeffrey M DaCosta , Mark E Hauber , Matthew I M Louder , Christopher C Witt , Jimmy A McGuire , Joann Mudge , Libby C Megna , Matthew D Carling , Biao Wang , Scott A Taylor , Glaucia Del-Rio , Alexandre Aleixo , Ana Tereza Ribeiro Vasconcelos , Claudio V Mello , Jason T Weir , David Haussler , Qiye Li , Huanming Yang , Jian Wang , Fumin Lei , Carsten Rahbek , M Thomas P Gilbert , Gary R Graves , Erich D Jarvis , Benedict Paten , Guojie Zhang

ProTECT-Prediction of T-Cell Epitopes for Cancer Therapy.

Frontiers in immunology
Avec: Arjun A Rao , Ada A Madejska , Jacob Pfeil , Benedict Paten , Sofie R Salama , David Haussler

Efficient dynamic variation graphs.

Bioinformatics (Oxford, England)
Avec: Jordan M Eizenga , Adam M Novak , Emily Kobayashi , Flavia Villani , Cecilia Cisar , Simon Heumos , Glenn Hickey , Vincenza Colonna , Benedict Paten , Erik Garrison

Personalized Pangenome References.

bioRxiv : the preprint server for biology
Avec: Jouni Sirén , Parsa Eskandar , Matteo Tommaso Ungaro , Glenn Hickey , Jordan M Eizenga , Adam M Novak , Xian Chang , Pi-Chuan Chang , Mikhail Kolmogorov , Andrew Carroll , Jean Monlong , Benedict Paten

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

Journal of the American Medical Informatics Association : JAMIA
Avec: Stan Ahalt , Paul Avillach , Rebecca Boyles , Kira Bradford , Steven Cox , Brandi Davis-Dusenbery , Robert L Grossman , Ashok 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 Conomos , Alessandro Culotti , Thomas Desain , Jack Digiovanna , Milan Domazet , Stephanie Gogarten , Alba Gutierrez-Sacristan , 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 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

Leveraging base-pair mammalian constraint to understand genetic variation and human disease.

Science (New York, N.Y.)
Avec: Patrick F Sullivan , Jennifer R S Meadows , Steven Gazal , BaDoi N Phan , Xue Li , Diane P Genereux , Michael X Dong , Matteo Bianchi , Gregory Andrews , Sharadha Sakthikumar , Jessika Nordin , Ananya Roy , Matthew J Christmas , Voichita D Marinescu , Chao Wang , Ola Wallerman , James Xue , Shuyang Yao , Quan Sun , Jin Szatkiewicz , Jia Wen , Laura M Huckins , Alyssa Lawler , Kathleen C Keough , Zhili Zheng , Jian Zeng , Naomi R Wray , Yun Li , Jessica Johnson , Jiawen Chen , Auteur inconnu , Benedict Paten , Steven K Reilly , Graham M Hughes , Zhiping Weng , Katherine S Pollard , Andreas R Pfenning , Karin Forsberg-Nilsson , Elinor K Karlsson , Kerstin Lindblad-Toh

Vocal learning-associated convergent evolution in mammalian proteins and regulatory elements.

Science (New York, N.Y.)
Avec: Morgan E Wirthlin , Tobias A Schmid , Julie E Elie , Xiaomeng Zhang , Amanda Kowalczyk , Ruby Redlich , Varvara A Shvareva , Ashley Rakuljic , Maria B Ji , Ninad S Bhat , Irene M Kaplow , Daniel E Schäffer , Alyssa J Lawler , Andrew Z Wang , BaDoi N Phan , Siddharth Annaldasula , Ashley R Brown , Tianyu Lu , Byung Kook Lim , Eiman Azim , Auteur inconnu , Nathan L Clark , Wynn K Meyer , Sergei L Kosakovsky Pond , Maria Chikina , Michael M Yartsev , Andreas R Pfenning , Gregory Andrews , Joel C Armstrong , Matteo Bianchi , Bruce W Birren , Kevin R Bredemeyer , Ana M Breit , Matthew J Christmas , Hiram Clawson , Joana Damas , Federica Di Palma , Mark Diekhans , Michael X Dong , Eduardo Eizirik , Kaili Fan , Cornelia Fanter , Nicole M Foley , Karin Forsberg-Nilsson , Carlos J Garcia , John Gatesy , Steven Gazal , Diane P Genereux , Linda Goodman , Jenna Grimshaw , Michaela K Halsey , Andrew J Harris , Glenn Hickey , Michael Hiller , Allyson G Hindle , Robert M Hubley , Graham M Hughes , Jeremy Johnson , David Juan , Irene M Kaplow , Elinor K Karlsson , Kathleen C Keough , Bogdan Kirilenko , Klaus-Peter Koepfli , Jennifer M Korstian , Amanda Kowalczyk , Sergey V Kozyrev , Alyssa J Lawler , Colleen Lawless , Thomas Lehmann , Danielle L Levesque , Harris A Lewin , Xue Li , Abigail Lind , Kerstin Lindblad-Toh , Ava Mackay-Smith , Voichita D Marinescu , Tomas Marques-Bonet , Victor C Mason , Jennifer R S Meadows , Wynn K Meyer , Jill E Moore , Lucas R Moreira , Diana D Moreno-Santillan , Kathleen M Morrill , Gerard Muntané , William J Murphy , Arcadi Navarro , Martin Nweeia , Sylvia Ortmann , Austin Osmanski , Benedict Paten , Nicole S Paulat , Andreas R Pfenning , BaDoi N Phan , Katherine S Pollard , Henry E Pratt , David A Ray , Steven K Reilly , Jeb R Rosen , Irina Ruf , Louise Ryan , Oliver A Ryder , Pardis C Sabeti , Daniel E Schäffer , Aitor Serres , Beth Shapiro , Arian F A Smit , Mark Springer , Chaitanya Srinivasan , Cynthia Steiner , Jessica M Storer , Kevin A M Sullivan , Patrick F Sullivan , Elisabeth Sundström , Megan A Supple , Ross Swofford , Joy-El Talbot , Emma Teeling , Jason Turner-Maier , Alejandro Valenzuela , Franziska Wagner , Ola Wallerman , Chao Wang , Juehan Wang , Zhiping Weng , Aryn P Wilder , Morgan E Wirthlin , James R Xue , Xiaomeng Zhang

Beyond the Human Genome Project: The Age of Complete Human Genome Sequences and Pangenome References.

Annual review of genomics and human genetics
Avec: Dylan J Taylor , Jordan M Eizenga , Qiuhui Li , Arun Das , Katharine M Jenike , Eimear E Kenny , Karen H Miga , Jean Monlong , Rajiv C McCoy , Benedict Paten , Michael C Schatz

Personalized pangenome references.

Nature methods
Avec: Jouni Sirén , Parsa Eskandar , Matteo Tommaso Ungaro , Glenn Hickey , Jordan M Eizenga , Adam M Novak , Xian Chang , Pi-Chuan Chang , Mikhail Kolmogorov , Andrew Carroll , Jean Monlong , Benedict Paten

A phenome-wide association study of methylated GC-rich repeats identifies a GCC repeat expansion in AFF3 associated with intellectual disability.

Nature genetics
Avec: Bharati Jadhav , Paras Garg , Joke J F A van Vugt , Kristina Ibanez , Delia Gagliardi , William Lee , Mariya Shadrina , Tom Mokveld , Egor Dolzhenko , Alejandro Martin-Trujillo , Scott J Gies , Gabrielle Altman , Clarissa Rocca , Mafalda Barbosa , Miten Jain , Nayana Lahiri , Katherine Lachlan , Henry Houlden , Benedict Paten , Auteur inconnu , Auteur inconnu , Jan Veldink , Arianna Tucci , Andrew J Sharp

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

Bioinformatics (Oxford, England)
Avec: Hongxu Ding , Andrew D Bailey , Miten Jain , Hugh Olsen , Benedict Paten

Author Correction: Nanopore native RNA sequencing of a human poly(A) transcriptome.

Nature methods
Avec: Rachael E Workman , Alison D Tang , Paul S Tang , Miten Jain , John R Tyson , Roham Razaghi , Philip C Zuzarte , Timothy Gilpatrick , Alexander Payne , Joshua Quick , Norah Sadowski , Nadine Holmes , Jaqueline Goes de Jesus , Karen L Jones , Cameron M Soulette , Terrance P Snutch , Nicholas Loman , Benedict Paten , Matthew Loose , Jared T Simpson , Hugh E Olsen , Angela N Brooks , Mark Akeson , Winston Timp

Fully phased human genome assembly without parental data using single-cell strand sequencing and long reads.

Nature biotechnology
Avec: David Porubsky , Peter Ebert , Peter A Audano , Mitchell R Vollger , William T Harvey , Pierre Marijon , Jana Ebler , Katherine M Munson , Melanie Sorensen , Arvis Sulovari , Marina Haukness , Maryam Ghareghani , Auteur inconnu , Peter M Lansdorp , Benedict Paten , Scott E Devine , Ashley D Sanders , Charles Lee , Mark J P Chaisson , Jan O Korbel , Evan E Eichler , Tobias Marschall

Genus-Wide Characterization of Bumblebee Genomes Provides Insights into Their Evolution and Variation in Ecological and Behavioral Traits.

Molecular biology and evolution
Avec: Cheng Sun , Jiaxing Huang , Yun Wang , Xiaomeng Zhao , Long Su , Gregg W C Thomas , Mengya Zhao , Xingtan Zhang , Irwin Jungreis , Manolis Kellis , Saverio Vicario , Igor V Sharakhov , Semen M Bondarenko , Martin Hasselmann , Chang N Kim , Benedict Paten , Luca Penso-Dolfin , Li Wang , Yuxiao Chang , Qiang Gao , Ling Ma , Lina Ma , Zhang Zhang , Hongbo Zhang , Huahao Zhang , Livio Ruzzante , Hugh M Robertson , Yihui Zhu , Yanjie Liu , Huipeng Yang , Lele Ding , Quangui Wang , Dongna Ma , Weilin Xu , Cheng Liang , Michael W Itgen , Lauren Mee , Gang Cao , Ze Zhang , Ben M Sadd , Matthew W Hahn , Sarah Schaack , Seth M Barribeau , Paul H Williams , Robert M Waterhouse , Rachel Lockridge Mueller

A high-quality bonobo genome refines the analysis of hominid evolution.

Nature
Avec: Yafei Mao , Claudia R Catacchio , LaDeana W Hillier , David Porubsky , Ruiyang Li , Arvis Sulovari , Jason D Fernandes , Francesco Montinaro , David S Gordon , Jessica M Storer , Marina Haukness , Ian T Fiddes , Shwetha Canchi Murali , Philip C Dishuck , PingHsun Hsieh , William T Harvey , Peter A Audano , Ludovica Mercuri , Ilaria Piccolo , Francesca Antonacci , Katherine M Munson , Alexandra P Lewis , Carl Baker , Jason G Underwood , Kendra Hoekzema , Tzu-Hsueh Huang , Melanie Sorensen , Jerilyn A Walker , Jinna Hoffman , Françoise Thibaud-Nissen , Sofie R Salama , Andy W C Pang , Joyce Lee , Alex R Hastie , Benedict Paten , Mark A Batzer , Mark Diekhans , Mario Ventura , Evan E Eichler

Pervasive cis effects of variation in copy number of large tandem repeats on local DNA methylation and gene expression.

American journal of human genetics
Avec: Paras Garg , Alejandro Martin-Trujillo , Oscar L Rodriguez , Scott J Gies , Elina Hadelia , Bharati Jadhav , Miten Jain , Benedict Paten , Andrew J Sharp

Positive selection in noncoding genomic regions of vocal learning birds is associated with genes implicated in vocal learning and speech functions in humans.

Genome research
Avec: James A Cahill , Joel Armstrong , Alden Deran , Carolyn J Khoury , Benedict Paten , David Haussler , Erich D Jarvis

PrecisionFDA Truth Challenge V2: Calling variants from short and long reads in difficult-to-map regions.

Cell genomics
Avec: Nathan D Olson , Justin Wagner , Jennifer McDaniel , Sarah H Stephens , Samuel T Westreich , Anish G Prasanna , Elaine Johanson , Emily Boja , Ezekiel J Maier , Omar Serang , David Jáspez , José M Lorenzo-Salazar , Adrián Muñoz-Barrera , Luis A Rubio-Rodríguez , Carlos Flores , Konstantinos Kyriakidis , Andigoni Malousi , Kishwar Shafin , Trevor Pesout , Miten Jain , Benedict Paten , Pi-Chuan Chang , Alexey Kolesnikov , Maria Nattestad , Gunjan Baid , Sidharth Goel , Howard Yang , Andrew Carroll , Robert Eveleigh , Mathieu Bourgey , Guillaume Bourque , Gen Li , ChouXian Ma , LinQi Tang , YuanPing Du , ShaoWei Zhang , Jordi Morata , Raúl Tonda , Genís Parra , Jean-Rémi Trotta , Christian Brueffer , Sinem Demirkaya-Budak , Duygu Kabakci-Zorlu , Deniz Turgut , Özem Kalay , Gungor Budak , Kübra Narcı , Elif Arslan , Richard Brown , Ivan J Johnson , Alexey Dolgoborodov , Vladimir Semenyuk , Amit Jain , H Serhat Tetikol , Varun Jain , Mike Ruehle , Bryan Lajoie , Cooper Roddey , Severine Catreux , Rami Mehio , Mian Umair Ahsan , Qian Liu , Kai Wang , Sayed Mohammad Ebrahim Sahraeian , Li Tai Fang , Marghoob Mohiyuddin , Calvin Hung , Chirag Jain , Hanying Feng , Zhipan Li , Luoqi Chen , Fritz J Sedlazeck , Justin M Zook

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

Nucleic acids research
Avec: Adam Frankish , Sílvia 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 Berry , Alexandra Bignell , Carles Boix , Ferriol Calvet , Daniel Cerdán-Vélez , Fiona Cunningham , Claire Davidson , Sarah Donaldson , Cagatay Dursun , Reham Fatima , Stefano Giorgetti , Carlos Garcıa Giron , Jose Manuel Gonzalez , Matthew Hardy , Peter W Harrison , Thibaut Hourlier , Zoe Hollis , Toby Hunt , Benjamin James , Yunzhe Jiang , Rory Johnson , Mike 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 Yates , Zahoor Zafrulla , Jyoti S Choudhary , Mark Gerstein , Roderic Guigo , Tim J P Hubbard , Manolis Kellis , Anshul Kundaje , Benedict Paten , Michael L Tress , Paul Flicek

Toward a data infrastructure for the Plant Cell Atlas.

Plant physiology
Avec: Noah Fahlgren , Muskan Kapoor , Galabina Yordanova , Irene Papatheodorou , Jamie Waese , Benjamin Cole , Peter Harrison , Doreen Ware , Timothy Tickle , Benedict Paten , Tony Burdett , Christine G Elsik , Christopher K Tuggle , Nicholas J Provart

Pangenome graph construction from genome alignments with Minigraph-Cactus.

Nature biotechnology
Avec: Glenn Hickey , Jean Monlong , Jana Ebler , Adam M Novak , Jordan M Eizenga , Yan Gao , Auteur inconnu , Tobias Marschall , Heng Li , Benedict Paten

Unraveling Neuronal Identities Using SIMS: A Deep Learning Label Transfer Tool for Single-Cell RNA Sequencing Analysis.

bioRxiv : the preprint server for biology
Avec: Jesus Gonzalez-Ferrer , Julian Lehrer , Ash O'Farrell , Benedict Paten , Mircea Teodorescu , David Haussler , Vanessa D Jonsson , Mohammed A Mostajo-Radji

The Complete Sequence and Comparative Analysis of Ape Sex Chromosomes.

bioRxiv : the preprint server for biology
Avec: Kateryna D Makova , Brandon D Pickett , Robert S Harris , Gabrielle A Hartley , Monika Cechova , Karol Pal , Sergey Nurk , DongAhn Yoo , Qiuhui Li , Prajna Hebbar , Barbara C McGrath , Francesca Antonacci , Margaux Aubel , Arjun Biddanda , Matthew Borchers , Erich Bomberg , Gerard G Bouffard , Shelise Y Brooks , Lucia Carbone , Laura Carrel , Andrew Carroll , Pi-Chuan Chang , Chen-Shan Chin , Daniel E Cook , Sarah J C Craig , Luciana de Gennaro , Mark Diekhans , Amalia Dutra , Gage H Garcia , Patrick G S Grady , Richard E Green , Diana Haddad , Pille Hallast , William T Harvey , Glenn Hickey , David A Hillis , Savannah J Hoyt , Hyeonsoo Jeong , Kaivan Kamali , Sergei L Kosakovsky Pond , Troy M LaPolice , Charles Lee , Alexandra P Lewis , Yong-Hwee E Loh , Patrick Masterson , Rajiv C McCoy , Paul Medvedev , Karen H Miga , Katherine M Munson , Evgenia Pak , Benedict Paten , Brendan J Pinto , Tamara Potapova , Arang Rhie , Joana L Rocha , Fedor Ryabov , Oliver A Ryder , Samuel Sacco , Kishwar Shafin , Valery A Shepelev , Viviane Slon , Steven J Solar , Jessica M Storer , Peter H Sudmant , Sweetalana , Alex Sweeten , Michael G Tassia , Françoise Thibaud-Nissen , Mario Ventura , Melissa A Wilson , Alice C Young , Huiqing Zeng , Xinru Zhang , Zachary A Szpiech , Christian D Huber , Jennifer L Gerton , Soojin V Yi , Michael C Schatz , Ivan A Alexandrov , Sergey Koren , Rachel J O'Neill , Evan Eichler , Adam M Phillippy

PrecisionFDA Truth Challenge V2: Calling variants from short and long reads in difficult-to-map regions.

Cell genomics
Avec: Nathan D Olson , Justin Wagner , Jennifer McDaniel , Sarah H Stephens , Samuel T Westreich , Anish G Prasanna , Elaine Johanson , Emily Boja , Ezekiel J Maier , Omar Serang , David Jáspez , José M Lorenzo-Salazar , Adrián Muñoz-Barrera , Luis A Rubio-Rodríguez , Carlos Flores , Konstantinos Kyriakidis , Andigoni Malousi , Kishwar Shafin , Trevor Pesout , Miten Jain , Benedict Paten , Pi-Chuan Chang , Alexey Kolesnikov , Maria Nattestad , Gunjan Baid , Sidharth Goel , Howard Yang , Andrew Carroll , Robert Eveleigh , Mathieu Bourgey , Guillaume Bourque , Gen Li , ChouXian Ma , LinQi Tang , YuanPing Du , ShaoWei Zhang , Jordi Morata , Raúl Tonda , Genís Parra , Jean-Rémi Trotta , Christian Brueffer , Sinem Demirkaya-Budak , Duygu Kabakci-Zorlu , Deniz Turgut , Özem Kalay , Gungor Budak , Kübra Narcı , Elif Arslan , Richard Brown , Ivan J Johnson , Alexey Dolgoborodov , Vladimir Semenyuk , Amit Jain , H Serhat Tetikol , Varun Jain , Mike Ruehle , Bryan Lajoie , Cooper Roddey , Severine Catreux , Rami Mehio , Mian Umair Ahsan , Qian Liu , Kai Wang , Sayed Mohammad Ebrahim Sahraeian , Li Tai Fang , Marghoob Mohiyuddin , Calvin Hung , Chirag Jain , Hanying Feng , Zhipan Li , Luoqi Chen , Fritz J Sedlazeck , Justin M Zook

The UCSC Genome Browser database: 2024 update.

Nucleic acids research
Avec: Brian J Raney , Galt P Barber , Anna Benet-Pagès , Jonathan Casper , Hiram Clawson , Melissa S Cline , Mark Diekhans , Clayton Fischer , Jairo Navarro Gonzalez , Glenn Hickey , Angie S Hinrichs , Robert M Kuhn , Brian T Lee , Christopher M Lee , Phillipe Le Mercier , Karen H Miga , Luis R Nassar , Parisa Nejad , Benedict Paten , Gerardo Perez , Daniel Schmelter , Matthew L Speir , Brittney D Wick , Ann S Zweig , David Haussler , W James Kent , Maximilian Haeussler

The complete sequence and comparative analysis of ape sex chromosomes.

Nature
Avec: Kateryna D Makova , Brandon D Pickett , Robert S Harris , Gabrielle A Hartley , Monika Cechova , Karol Pal , Sergey Nurk , DongAhn Yoo , Qiuhui Li , Prajna Hebbar , Barbara C McGrath , Francesca Antonacci , Margaux Aubel , Arjun Biddanda , Matthew Borchers , Erich Bornberg-Bauer , Gerard G Bouffard , Shelise Y Brooks , Lucia Carbone , Laura Carrel , Andrew Carroll , Pi-Chuan Chang , Chen-Shan Chin , Daniel E Cook , Sarah J C Craig , Luciana de Gennaro , Mark Diekhans , Amalia Dutra , Gage H Garcia , Patrick G S Grady , Richard E Green , Diana Haddad , Pille Hallast , William T Harvey , Glenn Hickey , David A Hillis , Savannah J Hoyt , Hyeonsoo Jeong , Kaivan Kamali , Sergei L Kosakovsky Pond , Troy M LaPolice , Charles Lee , Alexandra P Lewis , Yong-Hwee E Loh , Patrick Masterson , Kelly M McGarvey , Rajiv C McCoy , Paul Medvedev , Karen H Miga , Katherine M Munson , Evgenia Pak , Benedict Paten , Brendan J Pinto , Tamara Potapova , Arang Rhie , Joana L Rocha , Fedor Ryabov , Oliver A Ryder , Samuel Sacco , Kishwar Shafin , Valery A Shepelev , Viviane Slon , Steven J Solar , Jessica M Storer , Peter H Sudmant , Sweetalana , Alex Sweeten , Michael G Tassia , Françoise Thibaud-Nissen , Mario Ventura , Melissa A Wilson , Alice C Young , Huiqing Zeng , Xinru Zhang , Zachary A Szpiech , Christian D Huber , Jennifer L Gerton , Soojin V Yi , Michael C Schatz , Ivan A Alexandrov , Sergey Koren , Rachel J O'Neill , Evan E Eichler , Adam M Phillippy

Local read haplotagging enables accurate long-read small variant calling.

Nature communications
Avec: Alexey Kolesnikov , Daniel Cook , Maria Nattestad , Lucas Brambrink , Brandy McNulty , John Gorzynski , Sneha Goenka , Euan A Ashley , Miten Jain , Karen H Miga , Benedict Paten , Pi-Chuan Chang , Andrew Carroll , Kishwar Shafin

Development and extensive sequencing of a broadly-consented Genome in a Bottle matched tumor-normal pair for somatic benchmarks.

bioRxiv : the preprint server for biology
Avec: Jennifer H McDaniel , Vaidehi Patel , Nathan D Olson , Hua-Jun He , Zhiyong He , Anthony Schmitt , Kristin Sikkink , Fritz J Sedlazeck , Harsha Doddapaneni , Shalini N Jhangiani , Donna M Muzny , Marie-Claude Gingras , Heer Mehta , Luis F Paulin , Alex R Hastie , Hung-Chun Yu , Victor Weigman , Alison Rojas , Katie Kennedy , Jamie Remington , Isai Gonzalez , Mitch Sudkamp , Kelly Wiseman , Bryan Lajoie , Shawn Levy , Miten Jain , Stuart Akeson , Giuseppe Narzisi , Zoe Steinsnyder , Catherine Reeves , Jennifer Shelton , Sarah B Kingan , Christine Lambert , Primo Bayabyan , Aaron M Wenger , Ian J McLaughlin , Aaron Adamson , Christopher Kingsley , Melanie Wescott , Young Kim , Benedict Paten , Jimin Park , Ivo Violich , Karen H Miga , Joshua Gardner , Brandy McNulty , Gail Rosen , Rajiv McCoy , Lesley Chapman Hannah , Doron Lipson , Hila Benjamin , Nika Iremadze , Ilya Soifer , Stephen Eacker , Mary Wood , Erin Cross , Greg Husar , Stephen Gross , Michael Vernich , Mikhail Kolmogorov , Tanveer Ahmad , Ayse Keskus , Asher Bryant , Francoise Thibaud-Nissen , Jonathan Trow , Justin Wagner , Chunlin Xiao , Andrew S Liss , Justin M Zook , Auteur inconnu

Towards complete and error-free genome assemblies of all vertebrate species.

Nature
Avec: Arang Rhie , Shane A McCarthy , Olivier Fedrigo , Joana Damas , Giulio Formenti , Sergey Koren , Marcela Uliano-Silva , William Chow , Arkarachai Fungtammasan , Juwan Kim , Chul Lee , Byung June Ko , Mark Chaisson , Gregory L Gedman , Lindsey J Cantin , Francoise Thibaud-Nissen , Leanne Haggerty , Iliana Bista , Michelle Smith , Bettina Haase , Jacquelyn Mountcastle , Sylke Winkler , Sadye Paez , Jason Howard , Sonja C Vernes , Tanya M Lama , Frank Grutzner , Wesley C Warren , Christopher N Balakrishnan , Dave Burt , Julia M George , Matthew T Biegler , David Iorns , Andrew Digby , Daryl Eason , Bruce Robertson , Taylor Edwards , Mark Wilkinson , George Turner , Axel Meyer , Andreas F Kautt , Paolo Franchini , H William Detrich , Hannes Svardal , Maximilian Wagner , Gavin J P Naylor , Martin Pippel , Milan Malinsky , Mark Mooney , Maria Simbirsky , Brett T Hannigan , Trevor Pesout , Marlys Houck , Ann Misuraca , Sarah B Kingan , Richard Hall , Zev Kronenberg , Ivan Sović , Christopher Dunn , Zemin Ning , Alex Hastie , Joyce Lee , Siddarth Selvaraj , Richard E Green , Nicholas H Putnam , Ivo Gut , Jay Ghurye , Erik Garrison , Ying Sims , Joanna Collins , Sarah Pelan , James Torrance , Alan Tracey , Jonathan Wood , Robel E Dagnew , Dengfeng Guan , Sarah E London , David F Clayton , Claudio V Mello , Samantha R Friedrich , Peter V Lovell , Ekaterina Osipova , Farooq O Al-Ajli , Simona Secomandi , Heebal Kim , Constantina Theofanopoulou , Michael Hiller , Yang Zhou , Robert S Harris , Kateryna D Makova , Paul Medvedev , Jinna Hoffman , Patrick Masterson , Karen Clark , Fergal Martin , Kevin Howe , Paul Flicek , Brian P Walenz , Woori Kwak , Hiram Clawson , Mark Diekhans , Luis Nassar , Benedict Paten , Robert H S Kraus , Andrew J Crawford , M Thomas P Gilbert , Guojie Zhang , Byrappa Venkatesh , Robert W Murphy , Klaus-Peter Koepfli , Beth Shapiro , Warren E Johnson , Federica Di Palma , Tomas Marques-Bonet , Emma C Teeling , Tandy Warnow , Jennifer Marshall Graves , Oliver A Ryder , David Haussler , Stephen J O'Brien , Jonas Korlach , Harris A Lewin , Kerstin Howe , Eugene W Myers , Richard Durbin , Adam M Phillippy , Erich D Jarvis

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

Nucleic acids research
Avec: 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

GENCODE 2021.

Nucleic acids research
Avec: Adam Frankish , Mark Diekhans , Irwin Jungreis , Julien Lagarde , Jane E Loveland , Jonathan M Mudge , Cristina Sisu , James C Wright , Joel Armstrong , If Barnes , Andrew Berry , Alexandra Bignell , Carles Boix , Silvia Carbonell Sala , Fiona Cunningham , Tomás Di Domenico , Sarah Donaldson , Ian T Fiddes , Carlos García Girón , Jose Manuel 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 , Jinuri Xu , Yucheng T Yang , Andrew Yates , Daniel Zerbino , Yan Zhang , Jyoti S Choudhary , Mark Gerstein , Roderic Guigó , Tim J P Hubbard , Manolis Kellis , Benedict Paten , Michael L Tress , Paul Flicek

Whole-Genome Alignment and Comparative Annotation.

Annual review of animal biosciences
Avec: Joel Armstrong , Ian T Fiddes , Mark Diekhans , Benedict Paten

GENCODE reference annotation for the human and mouse genomes.

Nucleic acids research
Avec: Adam Frankish , Mark Diekhans , Anne-Maud Ferreira , Rory Johnson , Irwin Jungreis , Jane Loveland , Jonathan M Mudge , Cristina Sisu , James Wright , Joel Armstrong , If Barnes , Andrew Berry , Alexandra Bignell , Silvia Carbonell Sala , Jacqueline Chrast , Fiona Cunningham , Tomás Di Domenico , Sarah Donaldson , Ian T Fiddes , Carlos García Girón , Jose Manuel 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 , Jinuri Xu , Andrew Yates , Daniel Zerbino , Yan Zhang , Bronwen Aken , Jyoti S Choudhary , Mark Gerstein , Roderic Guigó , Tim J P Hubbard , Manolis Kellis , Benedict Paten , Alexandre Reymond , Michael L Tress , Paul Flicek

Sequence tube maps: making graph genomes intuitive to commuters.

Bioinformatics (Oxford, England)
Avec: Wolfgang Beyer , Adam M Novak , Glenn Hickey , Jeffrey Chan , Vanessa Tan , Benedict Paten , Daniel R Zerbino

The Genome of C57BL/6J "Eve", the Mother of the Laboratory Mouse Genome Reference Strain.

G3 (Bethesda, Md.)
Avec: Vishal Kumar Sarsani , Narayanan Raghupathy , Ian T Fiddes , Joel Armstrong , Francoise Thibaud-Nissen , Oraya Zinder , Mohan Bolisetty , Kerstin Howe , Doug Hinerfeld , Xiaoan Ruan , Lucy Rowe , Mary Barter , Guruprasad Ananda , Benedict Paten , George M Weinstock , Gary A Churchill , Michael V Wiles , Valerie A Schneider , Anuj Srivastava , Laura G Reinholdt

Nanopore native RNA sequencing of a human poly(A) transcriptome.

Nature methods
Avec: Rachael E Workman , Alison D Tang , Paul S Tang , Miten Jain , John R Tyson , Roham Razaghi , Philip C Zuzarte , Timothy Gilpatrick , Alexander Payne , Joshua Quick , Norah Sadowski , Nadine Holmes , Jaqueline Goes de Jesus , Karen L Jones , Cameron M Soulette , Terrance P Snutch , Nicholas Loman , Benedict Paten , Matthew Loose , Jared T Simpson , Hugh E Olsen , Angela N Brooks , Mark Akeson , Winston Timp

Telomere-to-telomere assembly of a complete human X chromosome.

Nature
Avec: Karen H Miga , Sergey Koren , Arang Rhie , Mitchell R Vollger , Ariel Gershman , Andrey Bzikadze , Shelise Brooks , Edmund Howe , David Porubsky , Glennis A Logsdon , Valerie A Schneider , Tamara Potapova , Jonathan Wood , William Chow , Joel Armstrong , Jeanne Fredrickson , Evgenia Pak , Kristof Tigyi , Milinn Kremitzki , Christopher Markovic , Valerie Maduro , Amalia Dutra , Gerard G Bouffard , Alexander M Chang , Nancy F Hansen , Amy B Wilfert , Françoise Thibaud-Nissen , Anthony D Schmitt , Jon-Matthew Belton , Siddarth Selvaraj , Megan Y Dennis , Daniela C Soto , Ruta Sahasrabudhe , Gulhan Kaya , Josh Quick , Nicholas J Loman , Nadine Holmes , Matthew Loose , Urvashi Surti , Rosa Ana Risques , Tina A Graves Lindsay , Robert Fulton , Ira Hall , Benedict Paten , Kerstin Howe , Winston Timp , Alice Young , James C Mullikin , Pavel A Pevzner , Jennifer L Gerton , Beth A Sullivan , Evan E Eichler , Adam M Phillippy

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

F1000Research
Avec: 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

Accelerated identification of disease-causing variants with ultra-rapid nanopore genome sequencing.

Nature biotechnology
Avec: Sneha D Goenka , John E Gorzynski , Kishwar Shafin , Dianna G Fisk , Trevor Pesout , Tanner D Jensen , Jean Monlong , Pi-Chuan Chang , Gunjan Baid , Jonathan A Bernstein , Jeffrey W Christle , Karen P Dalton , Daniel R Garalde , Megan E Grove , Joseph Guillory , Alexey Kolesnikov , Maria Nattestad , Maura R Z Ruzhnikov , Mehrzad Samadi , Ankit Sethia , Elizabeth Spiteri , Christopher J Wright , Katherine Xiong , Tong Zhu , Miten Jain , Fritz J Sedlazeck , Andrew Carroll , Benedict Paten , Euan A Ashley

The complete sequence of a human genome.

Science (New York, N.Y.)
Avec: Sergey Nurk , Sergey Koren , Arang Rhie , Mikko Rautiainen , Andrey V Bzikadze , Alla Mikheenko , Mitchell R Vollger , Nicolas Altemose , Lev Uralsky , Ariel Gershman , Sergey Aganezov , Savannah J Hoyt , Mark Diekhans , Glennis A Logsdon , Michael Alonge , Stylianos E Antonarakis , Matthew Borchers , Gerard G Bouffard , Shelise Y Brooks , Gina V Caldas , Nae-Chyun Chen , Haoyu Cheng , Chen-Shan Chin , William Chow , Leonardo G de Lima , Philip C Dishuck , Richard Durbin , Tatiana Dvorkina , Ian T Fiddes , Giulio Formenti , Robert S Fulton , Arkarachai Fungtammasan , Erik Garrison , Patrick G S Grady , Tina A Graves-Lindsay , Ira M Hall , Nancy F Hansen , Gabrielle A Hartley , Marina Haukness , Kerstin Howe , Michael W Hunkapiller , Chirag Jain , Miten Jain , Erich D Jarvis , Peter Kerpedjiev , Melanie Kirsche , Mikhail Kolmogorov , Jonas Korlach , Milinn Kremitzki , Heng Li , Valerie V Maduro , Tobias Marschall , Ann M McCartney , Jennifer McDaniel , Danny E Miller , James C Mullikin , Eugene W Myers , Nathan D Olson , Benedict Paten , Paul Peluso , Pavel A Pevzner , David Porubsky , Tamara Potapova , Evgeny I Rogaev , Jeffrey A Rosenfeld , Steven L Salzberg , Valerie A Schneider , Fritz J Sedlazeck , Kishwar Shafin , Colin J Shew , Alaina Shumate , Ying Sims , Arian F A Smit , Daniela C Soto , Ivan Sović , Jessica M Storer , Aaron Streets , Beth A Sullivan , Françoise Thibaud-Nissen , James Torrance , Justin Wagner , Brian P Walenz , Aaron Wenger , Jonathan M D Wood , Chunlin Xiao , Stephanie M Yan , Alice C Young , Samantha Zarate , Urvashi Surti , Rajiv C McCoy , Megan Y Dennis , Ivan A Alexandrov , Jennifer L Gerton , Rachel J O'Neill , Winston Timp , Justin M Zook , Michael C Schatz , Evan E Eichler , Karen H Miga , Adam M Phillippy

A complete reference genome improves analysis of human genetic variation.

Science (New York, N.Y.)
Avec: Sergey Aganezov , Stephanie M Yan , Daniela C Soto , Melanie Kirsche , Samantha Zarate , Pavel Avdeyev , Dylan J Taylor , Kishwar Shafin , Alaina Shumate , Chunlin Xiao , Justin Wagner , Jennifer McDaniel , Nathan D Olson , Michael E G Sauria , Mitchell R Vollger , Arang Rhie , Melissa Meredith , Skylar Martin , Joyce Lee , Sergey Koren , Jeffrey A Rosenfeld , Benedict Paten , Ryan Layer , Chen-Shan Chin , Fritz J Sedlazeck , Nancy F Hansen , Danny E Miller , Adam M Phillippy , Karen H Miga , Rajiv C McCoy , Megan Y Dennis , Justin M Zook , Michael C Schatz

Chasing perfection: validation and polishing strategies for telomere-to-telomere genome assemblies.

Nature methods
Avec: Ann M Mc Cartney , Kishwar Shafin , Michael Alonge , Andrey V Bzikadze , Giulio Formenti , Arkarachai Fungtammasan , Kerstin Howe , Chirag Jain , Sergey Koren , Glennis A Logsdon , Karen H Miga , Alla Mikheenko , Benedict Paten , Alaina Shumate , Daniela C Soto , Ivan Sović , Jonathan M D Wood , Justin M Zook , Adam M Phillippy , Arang Rhie

Concerted modification of nucleotides at functional centers of the ribosome revealed by single-molecule RNA modification profiling.

eLife
Avec: Andrew D Bailey , Jason Talkish , Hongxu Ding , Haller Igel , Alejandra Duran , Shreya Mantripragada , Benedict Paten , Manuel Ares

The Human Pangenome Project: a global resource to map genomic diversity.

Nature
Avec: Ting Wang , Lucinda Antonacci-Fulton , Kerstin Howe , Heather A Lawson , Julian K Lucas , Adam M Phillippy , Alice B Popejoy , Mobin Asri , Caryn Carson , Mark J P Chaisson , Xian Chang , Robert Cook-Deegan , Adam L Felsenfeld , Robert S Fulton , Erik P Garrison , Nanibaa' A Garrison , Tina A Graves-Lindsay , Hanlee Ji , Eimear E Kenny , Barbara A Koenig , Daofeng Li , Tobias Marschall , Joshua F McMichael , Adam M Novak , Deepak Purushotham , Valerie A Schneider , Baergen I Schultz , Michael W Smith , Heidi J Sofia , Tsachy Weissman , Paul Flicek , Heng Li , Karen H Miga , Benedict Paten , Erich D Jarvis , Ira M Hall , Evan E Eichler , David Haussler , Auteur inconnu

Structurally divergent and recurrently mutated regions of primate genomes.

Cell
Avec: Yafei Mao , William T Harvey , David Porubsky , Katherine M Munson , Kendra Hoekzema , Alexandra P Lewis , Peter A Audano , Allison Rozanski , Xiangyu Yang , Shilong Zhang , DongAhn Yoo , David S Gordon , Tyler Fair , Xiaoxi Wei , Glennis A Logsdon , Marina Haukness , Philip C Dishuck , Hyeonsoo Jeong , Ricardo Del Rosario , Vanessa L Bauer , Will T Fattor , Gregory K Wilkerson , Yuxiang Mao , Yongyong Shi , Qiang Sun , Qing Lu , Benedict Paten , Trygve E Bakken , Alex A Pollen , Guoping Feng , Sara L Sawyer , Wesley C Warren , Lucia Carbone , Evan E Eichler

SIMS: A deep-learning label transfer tool for single-cell RNA sequencing analysis.

Cell genomics
Avec: Jesus Gonzalez-Ferrer , Julian Lehrer , Ash O'Farrell , Benedict Paten , Mircea Teodorescu , David Haussler , Vanessa D Jonsson , Mohammed A Mostajo-Radji

Semi-automated assembly of high-quality diploid human reference genomes.

Nature
Avec: Erich D Jarvis , Giulio Formenti , Arang Rhie , Andrea Guarracino , Chentao Yang , Jonathan Wood , Alan Tracey , Francoise Thibaud-Nissen , Mitchell R Vollger , David Porubsky , Haoyu Cheng , Mobin Asri , Glennis A Logsdon , Paolo Carnevali , Mark J P Chaisson , Chen-Shan Chin , Sarah Cody , Joanna Collins , Peter Ebert , Merly Escalona , Olivier Fedrigo , Robert S Fulton , Lucinda L Fulton , Shilpa Garg , Jennifer L Gerton , Jay Ghurye , Anastasiya Granat , Richard E Green , William Harvey , Patrick Hasenfeld , Alex Hastie , Marina Haukness , Erich B Jaeger , Miten Jain , Melanie Kirsche , Mikhail Kolmogorov , Jan O Korbel , Sergey Koren , Jonas Korlach , Joyce Lee , Daofeng Li , Tina Lindsay , Julian Lucas , Feng Luo , Tobias Marschall , Matthew W Mitchell , Jennifer McDaniel , Fan Nie , Hugh E Olsen , Nathan D Olson , Trevor Pesout , Tamara Potapova , Daniela Puiu , Allison Regier , Jue Ruan , Steven L Salzberg , Ashley D Sanders , Michael C Schatz , Anthony Schmitt , Valerie A Schneider , Siddarth Selvaraj , Kishwar Shafin , Alaina Shumate , Nathan O Stitziel , Catherine Stober , James Torrance , Justin Wagner , Jianxin Wang , Aaron Wenger , Chuanle Xiao , Aleksey V Zimin , Guojie Zhang , Ting Wang , Heng Li , Erik Garrison , David Haussler , Ira Hall , Justin M Zook , Evan E Eichler , Adam M Phillippy , Benedict Paten , Kerstin Howe , Karen H Miga , Auteur inconnu

Optimal gap-affine alignment in O(s) space.

Bioinformatics (Oxford, England)
Avec: Santiago Marco-Sola , Jordan M Eizenga , Andrea Guarracino , Benedict Paten , Erik Garrison , Miquel Moreto

Haplotype-aware pantranscriptome analyses using spliced pangenome graphs.

Nature methods
Avec: Jonas A Sibbesen , Jordan M Eizenga , Adam M Novak , Jouni Sirén , Xian Chang , Erik Garrison , Benedict Paten

Phased nanopore assembly with Shasta and modular graph phasing with GFAse.

bioRxiv : the preprint server for biology
Avec: Ryan Lorig-Roach , Melissa Meredith , Jean Monlong , Miten Jain , Hugh Olsen , Brandy McNulty , David Porubsky , Tessa Montague , Julian Lucas , Chris Condon , Jordan Eizenga , Sissel Juul , Sean McKenzie , Sara E Simmonds , Jimin Park , Mobin Asri , Sergey Koren , Evan Eichler , Richard Axel , Bruce Martin , Paolo Carnevali , Karen Miga , Benedict Paten

A draft human pangenome reference.

Nature
Avec: Wen-Wei Liao , Mobin Asri , Jana Ebler , Daniel Doerr , Marina Haukness , Glenn Hickey , Shuangjia Lu , Julian K Lucas , Jean Monlong , Haley J Abel , Silvia Buonaiuto , Xian H Chang , Haoyu Cheng , Justin Chu , Vincenza Colonna , Jordan M Eizenga , Xiaowen Feng , Christian Fischer , Robert S Fulton , Shilpa Garg , Cristian Groza , Andrea Guarracino , William T Harvey , Simon Heumos , Kerstin Howe , Miten Jain , Tsung-Yu Lu , Charles Markello , Fergal J Martin , Matthew W Mitchell , Katherine M Munson , Moses Njagi Mwaniki , Adam M Novak , Hugh E Olsen , Trevor Pesout , David Porubsky , Pjotr Prins , Jonas A Sibbesen , Jouni Sirén , Chad Tomlinson , Flavia Villani , Mitchell R Vollger , Lucinda L Antonacci-Fulton , Gunjan Baid , Carl A Baker , Anastasiya Belyaeva , Konstantinos Billis , Andrew Carroll , Pi-Chuan Chang , Sarah Cody , Daniel E Cook , Robert M Cook-Deegan , Omar E Cornejo , Mark Diekhans , Peter Ebert , Susan Fairley , Olivier Fedrigo , Adam L Felsenfeld , Giulio Formenti , Adam Frankish , Yan Gao , Nanibaa' A Garrison , Carlos Garcia Giron , Richard E Green , Leanne Haggerty , Kendra Hoekzema , Thibaut Hourlier , Hanlee P Ji , Eimear E Kenny , Barbara A Koenig , Alexey Kolesnikov , Jan O Korbel , Jennifer Kordosky , Sergey Koren , HoJoon Lee , Alexandra P Lewis , Hugo Magalhães , Santiago Marco-Sola , Pierre Marijon , Ann McCartney , Jennifer McDaniel , Jacquelyn Mountcastle , Maria Nattestad , Sergey Nurk , Nathan D Olson , Alice B Popejoy , Daniela Puiu , Mikko Rautiainen , Allison A Regier , Arang Rhie , Samuel Sacco , Ashley D Sanders , Valerie A Schneider , Baergen I Schultz , Kishwar Shafin , Michael W Smith , Heidi J Sofia , Ahmad N Abou Tayoun , Françoise Thibaud-Nissen , Francesca Floriana Tricomi , Justin Wagner , Brian Walenz , Jonathan M D Wood , Aleksey V Zimin , Guillaume Bourque , Mark J P Chaisson , Paul Flicek , Adam M Phillippy , Justin M Zook , Evan E Eichler , David Haussler , Ting Wang , Erich D Jarvis , Karen H Miga , Erik Garrison , Tobias Marschall , Ira M Hall , Heng Li , Benedict Paten

Gaps and complex structurally variant loci in phased genome assemblies.

Genome research
Avec: David Porubsky , Mitchell R Vollger , William T Harvey , Allison N Rozanski , Peter Ebert , Glenn Hickey , Patrick Hasenfeld , Ashley D Sanders , Catherine Stober , Auteur inconnu , Jan O Korbel , Benedict Paten , Tobias Marschall , Evan E Eichler

A unified pipeline for FISH spatial transcriptomics.

Cell genomics
Avec: Cecilia Cisar , Nicholas Keener , Mathew Ruffalo , Benedict Paten

Identification of constrained sequence elements across 239 primate genomes.

Nature
Avec: Lukas F K Kuderna , Jacob C Ulirsch , Sabrina Rashid , Mohamed Ameen , Laksshman Sundaram , Glenn Hickey , Anthony J Cox , Hong Gao , Arvind Kumar , Francois Aguet , Matthew J Christmas , Hiram Clawson , Maximilian Haeussler , Mareike C Janiak , Martin Kuhlwilm , Joseph D Orkin , Thomas Bataillon , Shivakumara Manu , Alejandro Valenzuela , Juraj Bergman , Marjolaine Rouselle , Felipe Ennes Silva , Lidia Agueda , Julie Blanc , Marta Gut , Dorien de Vries , Ian Goodhead , R Alan Harris , Muthuswamy Raveendran , Axel Jensen , Idriss S Chuma , Julie E Horvath , Christina Hvilsom , David Juan , Peter Frandsen , Joshua G Schraiber , Fabiano R de Melo , Fabrício Bertuol , Hazel Byrne , Iracilda Sampaio , Izeni Farias , João Valsecchi , Malu Messias , Maria N F da Silva , Mihir Trivedi , Rogerio Rossi , Tomas Hrbek , Nicole Andriaholinirina , Clément J Rabarivola , Alphonse Zaramody , Clifford J Jolly , Jane Phillips-Conroy , Gregory Wilkerson , Christian Abee , Joe H Simmons , Eduardo Fernandez-Duque , Sree Kanthaswamy , Fekadu Shiferaw , Dongdong Wu , Long Zhou , Yong Shao , Guojie Zhang , Julius D Keyyu , Sascha Knauf , Minh D Le , Esther Lizano , Stefan Merker , Arcadi Navarro , Tilo Nadler , Chiea Chuen Khor , Jessica Lee , Patrick Tan , Weng Khong Lim , Andrew C Kitchener , Dietmar Zinner , Ivo Gut , Amanda D Melin , Katerina Guschanski , Mikkel Heide Schierup , Robin M D Beck , Ioannis Karakikes , Kevin C Wang , Govindhaswamy Umapathy , Christian Roos , Jean P Boubli , Adam Siepel , Anshul Kundaje , Benedict Paten , Kerstin Lindblad-Toh , Jeffrey Rogers , Tomas Marques Bonet , Kyle Kai-How Farh

Distance indexing and seed clustering in sequence graphs.

Bioinformatics (Oxford, England)
Avec: Xian Chang , Jordan Eizenga , Adam M Novak , Jouni Sirén , Benedict Paten

Pangenome Graphs.

Annual review of genomics and human genetics
Avec: Jordan M Eizenga , Adam M Novak , Jonas A Sibbesen , Simon Heumos , Ali Ghaffaari , Glenn Hickey , Xian Chang , Josiah D Seaman , Robin Rounthwaite , Jana Ebler , Mikko Rautiainen , Shilpa Garg , Benedict Paten , Tobias Marschall , Jouni Sirén , Erik Garrison

Towards inferring nanopore sequencing ionic currents from nucleotide chemical structures.

Nature communications
Avec: Hongxu Ding , Ioannis Anastopoulos , Andrew D Bailey , Joshua Stuart , Benedict Paten

Sequence diversity analyses of an improved rhesus macaque genome enhance its biomedical utility.

Science (New York, N.Y.)
Avec: Wesley C Warren , R Alan Harris , Marina Haukness , Ian T Fiddes , Shwetha C Murali , Jason Fernandes , Philip C Dishuck , Jessica M Storer , Muthuswamy Raveendran , LaDeana W Hillier , David Porubsky , Yafei Mao , David Gordon , Mitchell R Vollger , Alexandra P Lewis , Katherine M Munson , Elizabeth DeVogelaere , Joel Armstrong , Mark Diekhans , Jerilyn A Walker , Chad Tomlinson , Tina A Graves-Lindsay , Milinn Kremitzki , Sofie R Salama , Peter A Audano , Merly Escalona , Nicholas W Maurer , Francesca Antonacci , Ludovica Mercuri , Flavia A M Maggiolini , Claudia Rita Catacchio , Jason G Underwood , David H O'Connor , Ashley D Sanders , Jan O Korbel , Betsy Ferguson , H Michael Kubisch , Louis Picker , Ned H Kalin , Douglas Rosene , Jon Levine , David H Abbott , Stanton B Gray , Mar M Sanchez , Zsofia A Kovacs-Balint , Joseph W Kemnitz , Sara M Thomasy , Jeffrey A Roberts , Erin L Kinnally , John P Capitanio , J H Pate Skene , Michael Platt , Shelley A Cole , Richard E Green , Mario Ventura , Roger W Wiseman , Benedict Paten , Mark A Batzer , Jeffrey Rogers , Evan E Eichler

Pangenomics enables genotyping of known structural variants in 5202 diverse genomes.

Science (New York, N.Y.)
Avec: Jouni Sirén , Jean Monlong , Xian Chang , Adam M Novak , Jordan M Eizenga , Charles Markello , Jonas A Sibbesen , Glenn Hickey , Pi-Chuan Chang , Andrew Carroll , Namrata Gupta , Stacey Gabriel , Thomas W Blackwell , Aakrosh Ratan , Kent D Taylor , Stephen S Rich , Jerome I Rotter , David Haussler , Erik Garrison , Benedict Paten

Real-Time Culture-Independent Microbial Profiling Onboard the International Space Station Using Nanopore Sequencing.

Genes
Avec: Sarah Stahl-Rommel , Miten Jain , Hang N Nguyen , Richard R Arnold , Serena M Aunon-Chancellor , Gretta Marie Sharp , Christian L Castro , Kristen K John , Sissel Juul , Daniel J Turner , David Stoddart , Benedict Paten , Mark Akeson , Aaron S Burton , Sarah L Castro-Wallace

A strategy for building and using a human reference pangenome.

F1000Research
Avec: 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

Complete genomic and epigenetic maps of human centromeres.

Science (New York, N.Y.)
Avec: Nicolas Altemose , Glennis A Logsdon , Andrey V Bzikadze , Pragya Sidhwani , Sasha A Langley , Gina V Caldas , Savannah J Hoyt , Lev Uralsky , Fedor D Ryabov , Colin J Shew , Michael E G Sauria , Matthew Borchers , Ariel Gershman , Alla Mikheenko , Valery A Shepelev , Tatiana Dvorkina , Olga Kunyavskaya , Mitchell R Vollger , Arang Rhie , Ann M McCartney , Mobin Asri , Ryan Lorig-Roach , Kishwar Shafin , Julian K Lucas , Sergey Aganezov , Daniel Olson , Leonardo Gomes de Lima , Tamara Potapova , Gabrielle A Hartley , Marina Haukness , Peter Kerpedjiev , Fedor Gusev , Kristof Tigyi , Shelise Brooks , Alice Young , Sergey Nurk , Sergey Koren , Sofie R Salama , Benedict Paten , Evgeny I Rogaev , Aaron Streets , Gary H Karpen , Abby F Dernburg , Beth A Sullivan , Aaron F Straight , Travis J Wheeler , Jennifer L Gerton , Evan E Eichler , Adam M Phillippy , Winston Timp , Megan Y Dennis , Rachel J O'Neill , Justin M Zook , Michael C Schatz , Pavel A Pevzner , Mark Diekhans , Charles H Langley , Ivan A Alexandrov , Karen H Miga

A complete pedigree-based graph workflow for rare candidate variant analysis.

Genome research
Avec: Charles Markello , Charles Huang , Alex Rodriguez , Andrew Carroll , Pi-Chuan Chang , Jordan Eizenga , Thomas Markello , David Haussler , Benedict Paten

Inversion polymorphism in a complete human genome assembly.

Genome biology
Avec: David Porubsky , William T Harvey , Allison N Rozanski , Jana Ebler , Wolfram Höps , Hufsah Ashraf , Patrick Hasenfeld , Auteur inconnu , Auteur inconnu , Benedict Paten , Ashley D Sanders , Tobias Marschall , Jan O Korbel , Evan E Eichler

Evolutionary constraint and innovation across hundreds of placental mammals.

Science (New York, N.Y.)
Avec: Matthew J Christmas , Irene M Kaplow , Diane P Genereux , Michael X Dong , Graham M Hughes , Xue Li , Patrick F Sullivan , Allyson G Hindle , Gregory Andrews , Joel C Armstrong , Matteo Bianchi , Ana M Breit , Mark Diekhans , Cornelia Fanter , Nicole M Foley , Daniel B Goodman , Linda Goodman , Kathleen C Keough , Bogdan Kirilenko , Amanda Kowalczyk , Colleen Lawless , Abigail L Lind , Jennifer R S Meadows , Lucas R Moreira , Ruby W Redlich , Louise Ryan , Ross Swofford , Alejandro Valenzuela , Franziska Wagner , Ola Wallerman , Ashley R Brown , Joana Damas , Kaili Fan , John Gatesy , Jenna Grimshaw , Jeremy Johnson , Sergey V Kozyrev , Alyssa J Lawler , Voichita D Marinescu , Kathleen M Morrill , Austin Osmanski , Nicole S Paulat , BaDoi N Phan , Steven K Reilly , Daniel E Schäffer , Cynthia Steiner , Megan A Supple , Aryn P Wilder , Morgan E Wirthlin , James R Xue , Auteur inconnu , Bruce W Birren , Steven Gazal , Robert M Hubley , Klaus-Peter Koepfli , Tomas Marques-Bonet , Wynn K Meyer , Martin Nweeia , Pardis C Sabeti , Beth Shapiro , Arian F A Smit , Mark S Springer , Emma C Teeling , Zhiping Weng , Michael Hiller , Danielle L Levesque , Harris A Lewin , William J Murphy , Arcadi Navarro , Benedict Paten , Katherine S Pollard , David A Ray , Irina Ruf , Oliver A Ryder , Andreas R Pfenning , Kerstin Lindblad-Toh , Elinor K Karlsson

A region of suppressed recombination misleads neoavian phylogenomics.

Proceedings of the National Academy of Sciences of the United States of America
Avec: Siavash Mirarab , Iker Rivas-González , Shaohong Feng , Josefin Stiller , Qi Fang , Uyen Mai , Glenn Hickey , Guangji Chen , Nadolina Brajuka , Olivier Fedrigo , Giulio Formenti , Jochen B W Wolf , Kerstin Howe , Agostinho Antunes , Mikkel H Schierup , Benedict Paten , Erich D Jarvis , Guojie Zhang , Edward L Braun

Assessing methylation detection for primary human tissue using Nanopore sequencing.

bioRxiv : the preprint server for biology
Avec: Rylee Genner , Stuart Akeson , Melissa Meredith , Pilar Alvarez Jerez , Laksh Malik , Breeana Baker , Abigail Miano-Burkhardt , Auteur inconnu , Benedict Paten , Kimberley J Billingsley , Cornelis Blauwendraat , Miten Jain

GBZ file format for pangenome graphs.

Bioinformatics (Oxford, England)
Avec: Jouni Sirén , Benedict Paten

Hydroxymethylation profile of cell-free DNA is a biomarker for early colorectal cancer.

Scientific reports
Avec: Nicolas J Walker , Mamunur Rashid , Shirong Yu , Helen Bignell , Casper K Lumby , Carmen M Livi , Kate Howell , David J Morley , Sandro Morganella , Daniel Barrell , Shabhonam Caim , Walraj Gosal , Jens Füllgrabe , Thomas J Charlesworth , Louella Vasquez , Miika Ahdesmäki , Jordan Eizenga , Parul Prabhat , Vitali Proutski , Marie Laurie Murat-Onana , Catherine J Greenwood , Lisa Kirkwood , Meeta Maisuria-Armer , Mengjie Li , Emma Coats , Victoria Winfield , Lachlan MacBean , Toby Stock , Alice Tomé-Fernandez , Yat Chan , Nasir Sheikh , Paula Golder , Michael Steward , Tobias W B Ost , Douglas Stewart , Albert Vilella , Mojtaba Noursalehi , Benedict Paten , Debora Lucarelli , Joanne Mason , Gareth Ridge , Jason Mellad , Suman Shirodkar , Shankar Balasubaramanian , Joanna D Holbrook

A GCC repeat expansion in

medRxiv : the preprint server for health sciences
Avec: Bharati Jadhav , Paras Garg , Joke J F A van Vugt , Kristina Ibanez Garikano , Delia Gagliardi , William Lee , Alejandro Martin-Trujillo , Scott L Gies , Mafalda Barbosa , Miten Jain , Henry Houlden , Benedict Paten , Auteur inconnu , Auteur inconnu , Jan Veldink , Arianna Tucci , Andrew J Sharp

Scalable Nanopore sequencing of human genomes provides a comprehensive view of haplotype-resolved variation and methylation.

Nature methods
Avec: Mikhail Kolmogorov , Kimberley J Billingsley , Mira Mastoras , Melissa Meredith , Jean Monlong , Ryan Lorig-Roach , Mobin Asri , Pilar Alvarez Jerez , Laksh Malik , Ramita Dewan , Xylena Reed , Rylee M Genner , Kensuke Daida , Sairam Behera , Kishwar Shafin , Trevor Pesout , Jeshuwin Prabakaran , Paolo Carnevali , Jianzhi Yang , Arang Rhie , Sonja W Scholz , Bryan J Traynor , Karen H Miga , Miten Jain , Winston Timp , Adam M Phillippy , Mark Chaisson , Fritz J Sedlazeck , Cornelis Blauwendraat , Benedict Paten

Local read haplotagging enables accurate long-read small variant calling.

bioRxiv : the preprint server for biology
Avec: Alexey Kolesnikov , Daniel Cook , Maria Nattestad , Brandy McNulty , John Gorzynski , Sneha Goenka , Euan A Ashley , Miten Jain , Karen H Miga , Benedict Paten , Pi-Chuan Chang , Andrew Carroll , Kishwar Shafin

Réseau de co-auteurs

Miten Jain 25 collaborations
Karen H Miga 21 collaborations
None None 20 collaborations
Kishwar Shafin 18 collaborations
Mark Diekhans 18 collaborations
Glenn Hickey 18 collaborations
Evan E Eichler 16 collaborations
Jean Monlong 15 collaborations
Adam M Novak 15 collaborations
David Haussler 14 collaborations
David Porubsky 14 collaborations
Pi-Chuan Chang 14 collaborations
Andrew Carroll 14 collaborations
Sergey Koren 13 collaborations
Erik Garrison 13 collaborations
Adam M Phillippy 13 collaborations
Jordan M Eizenga 13 collaborations
Tobias Marschall 12 collaborations
Arang Rhie 12 collaborations
Trevor Pesout 11 collaborations
Marina Haukness 11 collaborations
Joel Armstrong 11 collaborations
Justin M Zook 11 collaborations
Mitchell R Vollger 11 collaborations
Fritz J Sedlazeck 10 collaborations
William T Harvey 10 collaborations
Mikhail Kolmogorov 10 collaborations
Jouni Sirén 10 collaborations
Mobin Asri 9 collaborations
Katherine M Munson 9 collaborations
Erich D Jarvis 9 collaborations
Kerstin Howe 9 collaborations
Michael C Schatz 8 collaborations
Alexandra P Lewis 8 collaborations
Glennis A Logsdon 8 collaborations
Alexey Kolesnikov 8 collaborations
Ian T Fiddes 8 collaborations
Xian Chang 8 collaborations
Justin Wagner 8 collaborations
Richard E Green 7 collaborations
Paolo Carnevali 7 collaborations
Jana Ebler 7 collaborations
Winston Timp 7 collaborations
Brandy McNulty 7 collaborations
Maria Nattestad 7 collaborations
Nathan D Olson 7 collaborations
Ryan Lorig-Roach 6 collaborations
Philip C Dishuck 6 collaborations
Melissa Meredith 6 collaborations
Peter A Audano 6 collaborations
Kerstin Lindblad-Toh 6 collaborations
Jonas A Sibbesen 6 collaborations
Jordan Eizenga 6 collaborations
Guojie Zhang 6 collaborations
Oliver A Ryder 6 collaborations
Jessica M Storer 6 collaborations
Ashley D Sanders 6 collaborations
Jan O Korbel 6 collaborations
Françoise Thibaud-Nissen 6 collaborations
Jennifer McDaniel 6 collaborations
Paul Flicek 6 collaborations
Chen-Shan Chin 6 collaborations
Tamara Potapova 6 collaborations
Jennifer L Gerton 6 collaborations
Giulio Formenti 6 collaborations
Valerie A Schneider 6 collaborations
Hugh E Olsen 5 collaborations
Mark Akeson 5 collaborations
Kendra Hoekzema 5 collaborations
BaDoi N Phan 5 collaborations
Matthew J Christmas 5 collaborations
Andreas R Pfenning 5 collaborations
Gunjan Baid 5 collaborations
Rajiv C McCoy 5 collaborations
Heng Li 5 collaborations
Sergey Nurk 5 collaborations
Sissel Juul 4 collaborations
Paras Garg 4 collaborations
Bharati Jadhav 4 collaborations
Alejandro Martin-Trujillo 4 collaborations
Hugh Olsen 4 collaborations
Andrew J Sharp 4 collaborations
Ira M Hall 4 collaborations
Ting Wang 4 collaborations
Julian Lucas 4 collaborations
Yafei Mao 4 collaborations
Hyeonsoo Jeong 4 collaborations
Wesley C Warren 4 collaborations
Lucia Carbone 4 collaborations
Patrick F Sullivan 4 collaborations
Jennifer R S Meadows 4 collaborations
Steven Gazal 4 collaborations
Xue Li 4 collaborations
Diane P Genereux 4 collaborations
Michael X Dong 4 collaborations
Matteo Bianchi 4 collaborations
Gregory Andrews 4 collaborations
Voichita D Marinescu 4 collaborations
Ola Wallerman 4 collaborations
Alyssa J Lawler 4 collaborations
Kathleen C Keough 4 collaborations
Steven K Reilly 4 collaborations
Graham M Hughes 4 collaborations
Zhiping Weng 4 collaborations
Katherine S Pollard 4 collaborations
Elinor K Karlsson 4 collaborations
Sergey Aganezov 4 collaborations
Jimin Park 4 collaborations
Samuel Sacco 4 collaborations
Daniel E Cook 4 collaborations
Robert S Harris 4 collaborations
Beth Shapiro 4 collaborations
Sofie R Salama 4 collaborations
Hiram Clawson 4 collaborations
Peter Ebert 4 collaborations
Mark J P Chaisson 4 collaborations
Irwin Jungreis 4 collaborations
Manolis Kellis 4 collaborations
Francesca Antonacci 4 collaborations
Joyce Lee 4 collaborations
Mario Ventura 4 collaborations
Chirag Jain 4 collaborations
Adam Frankish 4 collaborations
Thibaut Hourlier 4 collaborations
Fergal J Martin 4 collaborations
Gabrielle A Hartley 4 collaborations
Matthew Borchers 4 collaborations
Gerard G Bouffard 4 collaborations
Savannah J Hoyt 4 collaborations
Ivan A Alexandrov 4 collaborations
Rachel J O'Neill 4 collaborations
Francoise Thibaud-Nissen 4 collaborations
Olivier Fedrigo 4 collaborations
Arkarachai Fungtammasan 4 collaborations
Megan Y Dennis 4 collaborations
Daniela C Soto 4 collaborations
Mikko Rautiainen 4 collaborations
Robert S Fulton 4 collaborations
Alaina Shumate 4 collaborations
Shilpa Garg 4 collaborations
Kristof Tigyi 3 collaborations
Melanie Sorensen 3 collaborations
Allison N Rozanski 3 collaborations
Kimberley J Billingsley 3 collaborations
Pilar Alvarez Jerez 3 collaborations
Laksh Malik 3 collaborations
Mark Chaisson 3 collaborations
Cornelis Blauwendraat 3 collaborations
David S Gordon 3 collaborations
James R Xue 3 collaborations
Karin Forsberg-Nilsson 3 collaborations
Joshua Gardner 3 collaborations
Giuseppe Narzisi 3 collaborations
Evan Eichler 3 collaborations
Richard Durbin 3 collaborations
Sidharth Goel 3 collaborations
Qi Fang 3 collaborations
Shaohong Feng 3 collaborations
Josefin Stiller 3 collaborations
Jeremy Johnson 3 collaborations
Simon Heumos 3 collaborations
Morgan E Wirthlin 3 collaborations
Amanda Kowalczyk 3 collaborations
Irene M Kaplow 3 collaborations
Daniel E Schäffer 3 collaborations
Wynn K Meyer 3 collaborations
Sergei L Kosakovsky Pond 3 collaborations
Joana Damas 3 collaborations
Michael Hiller 3 collaborations
Klaus-Peter Koepfli 3 collaborations
Harris A Lewin 3 collaborations
Tomas Marques-Bonet 3 collaborations
Arcadi Navarro 3 collaborations
Arian F A Smit 3 collaborations
Alejandro Valenzuela 3 collaborations
Qiuhui Li 3 collaborations
Eimear E Kenny 3 collaborations
Hongxu Ding 3 collaborations
Andrew D Bailey 3 collaborations
Nadine Holmes 3 collaborations
Matthew Loose 3 collaborations
Charles Lee 3 collaborations
Guillaume Bourque 3 collaborations
Bryan Lajoie 3 collaborations
Jonathan M Mudge 3 collaborations
Cristina Sisu 3 collaborations
If Barnes 3 collaborations
Andrew Berry 3 collaborations
Alexandra Bignell 3 collaborations
Fiona Cunningham 3 collaborations
Sarah Donaldson 3 collaborations
Jose Manuel Gonzalez 3 collaborations
Matthew Hardy 3 collaborations
Toby Hunt 3 collaborations
Rory Johnson 3 collaborations
Julien Lagarde 3 collaborations
Fernando Pozo 3 collaborations
Magali Ruffier 3 collaborations
Bianca M Schmitt 3 collaborations
Marie-Marthe Suner 3 collaborations
Irina Sycheva 3 collaborations
Barbara Uszczynska-Ratajczak 3 collaborations
Andrew Yates 3 collaborations
Jyoti S Choudhary 3 collaborations
Mark Gerstein 3 collaborations
Tim J P Hubbard 3 collaborations
Michael L Tress 3 collaborations
Ash O'Farrell 3 collaborations
Kateryna D Makova 3 collaborations
DongAhn Yoo 3 collaborations
Shelise Y Brooks 3 collaborations
Amalia Dutra 3 collaborations
Patrick G S Grady 3 collaborations
Patrick Masterson 3 collaborations
Paul Medvedev 3 collaborations
Evgenia Pak 3 collaborations
Valery A Shepelev 3 collaborations
Alice C Young 3 collaborations
Euan A Ashley 3 collaborations
Chunlin Xiao 3 collaborations
William Chow 3 collaborations
Ivan Sović 3 collaborations
Siddarth Selvaraj 3 collaborations
James Torrance 3 collaborations
Jonathan Wood 3 collaborations
Jonas Korlach 3 collaborations
Ariel Gershman 3 collaborations
Milinn Kremitzki 3 collaborations
Nancy F Hansen 3 collaborations
Pavel A Pevzner 3 collaborations
Beth A Sullivan 3 collaborations
Andrey V Bzikadze 3 collaborations
Alla Mikheenko 3 collaborations
Haoyu Cheng 3 collaborations
Tina A Graves-Lindsay 3 collaborations
Melanie Kirsche 3 collaborations
Jonathan M D Wood 3 collaborations
Julian K Lucas 3 collaborations
Andrea Guarracino 3 collaborations
Patrick Hasenfeld 3 collaborations
Charles Markello 3 collaborations
Aaron S Burton 2 collaborations
Kristen K John 2 collaborations
Daniel J Turner 2 collaborations
David Stoddart 2 collaborations
Sarah L Castro-Wallace 2 collaborations
Oscar L Rodriguez 2 collaborations
Alessandro Culotti 2 collaborations
Robert L Grossman 2 collaborations
Brian D O'Connor 2 collaborations
Kevin Osborn 2 collaborations
PingHsun Hsieh 2 collaborations
Mira Mastoras 2 collaborations
Ramita Dewan 2 collaborations
Xylena Reed 2 collaborations
Rylee M Genner 2 collaborations
Kensuke Daida 2 collaborations
Sairam Behera 2 collaborations
Jeshuwin Prabakaran 2 collaborations
Jianzhi Yang 2 collaborations
Sonja W Scholz 2 collaborations
Bryan J Traynor 2 collaborations
Allison Rozanski 2 collaborations
Xiangyu Yang 2 collaborations
Shilong Zhang 2 collaborations
Xiaoxi Wei 2 collaborations
Ricardo Del Rosario 2 collaborations
Vanessa L Bauer 2 collaborations
Will T Fattor 2 collaborations
Gregory K Wilkerson 2 collaborations
Qing Lu 2 collaborations
Guoping Feng 2 collaborations
Sara L Sawyer 2 collaborations
Sharadha Sakthikumar 2 collaborations
Jessika Nordin 2 collaborations
Ananya Roy 2 collaborations
Yun Li 2 collaborations
Shuyang Yao 2 collaborations
Quan Sun 2 collaborations
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Zhili Zheng 2 collaborations
Jian Zeng 2 collaborations
Naomi R Wray 2 collaborations
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Ayse Keskus 2 collaborations
Asher Bryant 2 collaborations
Tanveer Ahmad 2 collaborations
Tessa Montague 2 collaborations
Chris Condon 2 collaborations
Sean McKenzie 2 collaborations
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Richard Axel 2 collaborations
Bruce Martin 2 collaborations
Karen Miga 2 collaborations
Ivo Violich 2 collaborations
Alden Deran 2 collaborations
Duo Xie 2 collaborations
Guangji Chen 2 collaborations
Edward L Braun 2 collaborations
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Christopher N Balakrishnan 2 collaborations
Claudio V Mello 2 collaborations
M Thomas P Gilbert 2 collaborations
Flavia Villani 2 collaborations
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Elizabeth Sheets 2 collaborations
Chao Wang 2 collaborations
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Ashley R Brown 2 collaborations
Joel C Armstrong 2 collaborations
Bruce W Birren 2 collaborations
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Cornelia Fanter 2 collaborations
Nicole M Foley 2 collaborations
John Gatesy 2 collaborations
Linda Goodman 2 collaborations
Jenna Grimshaw 2 collaborations
Allyson G Hindle 2 collaborations
Robert M Hubley 2 collaborations
David Juan 2 collaborations
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Sergey V Kozyrev 2 collaborations
Colleen Lawless 2 collaborations
Danielle L Levesque 2 collaborations
Lucas R Moreira 2 collaborations
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Martin Nweeia 2 collaborations
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Nicole S Paulat 2 collaborations
David A Ray 2 collaborations
Irina Ruf 2 collaborations
Louise Ryan 2 collaborations
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Megan A Supple 2 collaborations
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William Lee 2 collaborations
Scott J Gies 2 collaborations
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Henry Houlden 2 collaborations
Jan Veldink 2 collaborations
Arianna Tucci 2 collaborations
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Paul S Tang 2 collaborations
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Philip C Zuzarte 2 collaborations
Timothy Gilpatrick 2 collaborations
Alexander Payne 2 collaborations
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Pierre Marijon 2 collaborations
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Jason G Underwood 2 collaborations
Jerilyn A Walker 2 collaborations
Jinna Hoffman 2 collaborations
Alex R Hastie 2 collaborations
Mark A Batzer 2 collaborations
Sarah H Stephens 2 collaborations
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Elaine Johanson 2 collaborations
Emily Boja 2 collaborations
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Omar Serang 2 collaborations
David Jáspez 2 collaborations
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Adrián Muñoz-Barrera 2 collaborations
Luis A Rubio-Rodríguez 2 collaborations
Carlos Flores 2 collaborations
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Robert Eveleigh 2 collaborations
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Elif Arslan 2 collaborations
Richard Brown 2 collaborations
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Amit Jain 2 collaborations
H Serhat Tetikol 2 collaborations
Varun Jain 2 collaborations
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Qian Liu 2 collaborations
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Li Tai Fang 2 collaborations
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Jane E Loveland 2 collaborations
James C Wright 2 collaborations
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Vanessa D Jonsson 2 collaborations
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Brandon D Pickett 2 collaborations
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Karol Pal 2 collaborations
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Barbara C McGrath 2 collaborations
Margaux Aubel 2 collaborations
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Steven J Solar 2 collaborations
Peter H Sudmant 2 collaborations
None Sweetalana 2 collaborations
Alex Sweeten 2 collaborations
Michael G Tassia 2 collaborations
Melissa A Wilson 2 collaborations
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Xinru Zhang 2 collaborations
Zachary A Szpiech 2 collaborations
Christian D Huber 2 collaborations
Soojin V Yi 2 collaborations
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Daniel Cook 2 collaborations
John Gorzynski 2 collaborations
Sneha Goenka 2 collaborations
Anthony Schmitt 2 collaborations
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Sarah B Kingan 2 collaborations
Leanne Haggerty 2 collaborations
Jacquelyn Mountcastle 2 collaborations
Mark Wilkinson 2 collaborations
Alex Hastie 2 collaborations
Ivo Gut 2 collaborations
Jay Ghurye 2 collaborations
Ying Sims 2 collaborations
Joanna Collins 2 collaborations
Alan Tracey 2 collaborations
Brian P Walenz 2 collaborations
Emma C Teeling 2 collaborations
Eugene W Myers 2 collaborations
Silvia Carbonell Sala 2 collaborations
Tomás Di Domenico 2 collaborations
Carlos García Girón 2 collaborations
Tiago Grego 2 collaborations
Osagie G Izuogu 2 collaborations
Laura Martínez 2 collaborations
Shamika Mohanan 2 collaborations
Paul Muir 2 collaborations
Fabio C P Navarro 2 collaborations
Anne Parker 2 collaborations
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Jinuri Xu 2 collaborations
Daniel Zerbino 2 collaborations
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Roderic Guigó 2 collaborations
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Urvashi Surti 2 collaborations
Ira Hall 2 collaborations
Alice Young 2 collaborations
James C Mullikin 2 collaborations
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Nicolas Altemose 2 collaborations
Lev Uralsky 2 collaborations
Michael Alonge 2 collaborations
Gina V Caldas 2 collaborations
Tatiana Dvorkina 2 collaborations
Peter Kerpedjiev 2 collaborations
Ann M McCartney 2 collaborations
Danny E Miller 2 collaborations
Evgeny I Rogaev 2 collaborations
Jeffrey A Rosenfeld 2 collaborations
Steven L Salzberg 2 collaborations
Colin J Shew 2 collaborations
Aaron Streets 2 collaborations
Aaron Wenger 2 collaborations
Stephanie M Yan 2 collaborations
Samantha Zarate 2 collaborations
Michael E G Sauria 2 collaborations
Alice B Popejoy 2 collaborations
Adam L Felsenfeld 2 collaborations
Nanibaa' A Garrison 2 collaborations
Barbara A Koenig 2 collaborations
Daofeng Li 2 collaborations
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