Adam M Phillippy

Affiliations
  • Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health, 9000 Rockville Pike, Bethesda, MD 20892, USA.

Publications (79)

A chromosome-scale assembly of the major African malaria vector Anopheles funestus.

GigaScience
Avec: Jay Ghurye , Sergey Koren , Scott T Small , Seth Redmond , Paul Howell , Adam M Phillippy , Nora J Besansky

A robust benchmark for detection of germline large deletions and insertions.

Nature biotechnology
Avec: Justin M Zook , Nancy F Hansen , Nathan D Olson , Lesley Chapman , James C Mullikin , Chunlin Xiao , Stephen Sherry , Sergey Koren , Adam M Phillippy , Paul C Boutros , Sayed Mohammad E Sahraeian , Vincent Huang , Alexandre Rouette , Noah Alexander , Christopher E Mason , Iman Hajirasouliha , Camir Ricketts , Joyce Lee , Rick Tearle , Ian T Fiddes , Alvaro Martinez Barrio , Jeremiah Wala , Andrew Carroll , Noushin Ghaffari , Oscar L Rodriguez , Ali Bashir , Shaun Jackman , John J Farrell , Aaron M Wenger , Can Alkan , Arda Soylev , Michael C Schatz , Shilpa Garg , George Church , Tobias Marschall , Ken Chen , Xian Fan , Adam C English , Jeffrey A Rosenfeld , Weichen Zhou , Ryan E Mills , Jay M Sage , Jennifer R Davis , Michael D Kaiser , John S Oliver , Anthony P Catalano , Mark J P Chaisson , Noah Spies , Fritz J Sedlazeck , Marc Salit

StainedGlass: interactive visualization of massive tandem repeat structures with identity heatmaps.

Bioinformatics (Oxford, England)
Avec: Mitchell R Vollger , Peter Kerpedjiev , Adam M Phillippy , Evan E Eichler

Strategic vision for improving human health at The Forefront of Genomics.

Nature
Avec: Eric D Green , Chris Gunter , Leslie G Biesecker , Valentina Di Francesco , Carla L Easter , Elise A Feingold , Adam L Felsenfeld , David J Kaufman , Elaine A Ostrander , William J Pavan , Adam M Phillippy , Anastasia L Wise , Jyoti Gupta Dayal , Britny J Kish , Allison Mandich , Christopher R Wellington , Kris A Wetterstrand , Sarah A Bates , Darryl Leja , Susan Vasquez , William A Gahl , Bettie J Graham , Daniel L Kastner , Paul Liu , Laura Lyman Rodriguez , Benjamin D Solomon , Vence L Bonham , Lawrence C Brody , Carolyn M Hutter , Teri A Manolio

The structure, function and evolution of a complete human chromosome 8.

Nature
Avec: Glennis A Logsdon , Mitchell R Vollger , PingHsun Hsieh , Yafei Mao , Mikhail A Liskovykh , Sergey Koren , Sergey Nurk , Ludovica Mercuri , Philip C Dishuck , Arang Rhie , Leonardo G de Lima , Tatiana Dvorkina , David Porubsky , William T Harvey , Alla Mikheenko , Andrey V Bzikadze , Milinn Kremitzki , Tina A Graves-Lindsay , Chirag Jain , Kendra Hoekzema , Shwetha C Murali , Katherine M Munson , Carl Baker , Melanie Sorensen , Alexandra M Lewis , Urvashi Surti , Jennifer L Gerton , Vladimir Larionov , Mario Ventura , Karen H Miga , Adam M Phillippy , Evan E Eichler

Improved sequence mapping using a complete reference genome and lift-over.

Nature methods
Avec: Nae-Chyun Chen , Luis F Paulin , Fritz J Sedlazeck , Sergey Koren , Adam M Phillippy , Ben Langmead

Population genomics of the critically endangered kākāpō.

Cell genomics
Avec: Nicolas Dussex , Tom van der Valk , Hernán E Morales , Christopher W Wheat , David Díez-Del-Molino , Johanna von Seth , Yasmin Foster , Verena E Kutschera , Katerina Guschanski , Arang Rhie , Adam M Phillippy , Jonas Korlach , Kerstin Howe , William Chow , Sarah Pelan , Joanna D Mendes Damas , Harris A Lewin , Alex R Hastie , Giulio Formenti , Olivier Fedrigo , Joseph Guhlin , Thomas W R Harrop , Marissa F Le Lec , Peter K Dearden , Leanne Haggerty , Fergal J Martin , Vamsi Kodali , Françoise Thibaud-Nissen , David Iorns , Michael Knapp , Neil J Gemmell , Fiona Robertson , Ron Moorhouse , Andrew Digby , Daryl Eason , Deidre Vercoe , Jason Howard , Erich D Jarvis , Bruce C Robertson , Love Dalén

Telomere-to-telomere assembly of diploid chromosomes with Verkko.

Nature biotechnology
Avec: Mikko Rautiainen , Sergey Nurk , Brian P Walenz , Glennis A Logsdon , David Porubsky , Arang Rhie , Evan E Eichler , Adam M Phillippy , Sergey Koren

Minmers are a generalization of minimizers that enable unbiased local Jaccard estimation.

Bioinformatics (Oxford, England)
Avec: Bryce Kille , Erik Garrison , Todd J Treangen , Adam M Phillippy

ModDotPlot-Rapid and interactive visualization of complex repeats.

bioRxiv : the preprint server for biology
Avec: Alexander P Sweeten , Michael C Schatz , Adam M Phillippy

Parsnp 2.0: Scalable Core-Genome Alignment for Massive Microbial Datasets.

bioRxiv : the preprint server for biology
Avec: Bryce Kille , Michael G Nute , Victor Huang , Eddie Kim , Adam M Phillippy , Todd J Treangen

Weighted minimizer sampling improves long read mapping.

Bioinformatics (Oxford, England)
Avec: Chirag Jain , Arang Rhie , Haowen Zhang , Claudia Chu , Brian P Walenz , Sergey Koren , Adam M Phillippy

An improved pig reference genome sequence to enable pig genetics and genomics research.

GigaScience
Avec: Amanda Warr , Nabeel Affara , Bronwen Aken , Hamid Beiki , Derek M Bickhart , Konstantinos Billis , William Chow , Lel Eory , Heather A Finlayson , Paul Flicek , Carlos G Girón , Darren K Griffin , Richard Hall , Greg Hannum , Thibaut Hourlier , Kerstin Howe , David A Hume , Osagie Izuogu , Kristi Kim , Sergey Koren , Haibou Liu , Nancy Manchanda , Fergal J Martin , Dan J Nonneman , Rebecca E O'Connor , Adam M Phillippy , Gary A Rohrer , Benjamin D Rosen , Laurie A Rund , Carole A Sargent , Lawrence B Schook , Steven G Schroeder , Ariel S Schwartz , Ben M Skinner , Richard Talbot , Elizabeth Tseng , Christopher K Tuggle , Mick Watson , Timothy P L Smith , Alan L Archibald

Continuous chromosome-scale haplotypes assembled from a single interspecies F1 hybrid of yak and cattle.

GigaScience
Avec: Edward S Rice , Sergey Koren , Arang Rhie , Michael P Heaton , Theodore S Kalbfleisch , Timothy Hardy , Peter H Hackett , Derek M Bickhart , Benjamin D Rosen , Brian Vander Ley , Nicholas W Maurer , Richard E Green , Adam M Phillippy , Jessica L Petersen , Timothy P L Smith

Strains used in whole organism Plasmodium falciparum vaccine trials differ in genome structure, sequence, and immunogenic potential.

Genome medicine
Avec: Kara A Moser , Elliott F Drábek , Ankit Dwivedi , Emily M Stucke , Jonathan Crabtree , Antoine Dara , Zalak Shah , Matthew Adams , Tao Li , Priscila T Rodrigues , Sergey Koren , Adam M Phillippy , James B Munro , Amed Ouattara , Benjamin C Sparklin , Julie C Dunning Hotopp , Kirsten E Lyke , Lisa Sadzewicz , Luke J Tallon , Michele D Spring , Krisada Jongsakul , Chanthap Lon , David L Saunders , Marcelo U Ferreira , Myaing M Nyunt , Miriam K Laufer , Mark A Travassos , Robert W Sauerwein , Shannon Takala-Harrison , Claire M Fraser , B Kim Lee Sim , Stephen L Hoffman , Christopher V Plowe , Joana C Silva

Strain-level metagenomic assignment and compositional estimation for long reads with MetaMaps.

Nature communications
Avec: Alexander T Dilthey , Chirag Jain , Sergey Koren , Adam M Phillippy

Extended haplotype-phasing of long-read de novo genome assemblies using Hi-C.

Nature communications
Avec: Zev N Kronenberg , Arang Rhie , Sergey Koren , Gregory T Concepcion , Paul Peluso , Katherine M Munson , David Porubsky , Kristen Kuhn , Kathryn A Mueller , Wai Yee Low , Stefan Hiendleder , Olivier Fedrigo , Ivan Liachko , Richard J Hall , Adam M Phillippy , Evan E Eichler , John L Williams , Timothy P L Smith , Erich D Jarvis , Shawn T Sullivan , Sarah B Kingan

De novo assembly of the cattle reference genome with single-molecule sequencing.

GigaScience
Avec: Benjamin D Rosen , Derek M Bickhart , Robert D Schnabel , Sergey Koren , Christine G Elsik , Elizabeth Tseng , Troy N Rowan , Wai Y Low , Aleksey Zimin , Christine Couldrey , Richard Hall , Wenli Li , Arang Rhie , Jay Ghurye , Stephanie D McKay , Françoise Thibaud-Nissen , Jinna Hoffman , Brenda M Murdoch , Warren M Snelling , Tara G McDaneld , John A Hammond , John C Schwartz , Wilson Nandolo , Darren E Hagen , Christian Dreischer , Sebastian J Schultheiss , Steven G Schroeder , Adam M Phillippy , John B Cole , Curtis P Van Tassell , George Liu , Timothy P L Smith , Juan F Medrano

The whale shark genome reveals patterns of vertebrate gene family evolution.

eLife
Avec: Milton Tan , Anthony K Redmond , Helen Dooley , Ryo Nozu , Keiichi Sato , Shigehiro Kuraku , Sergey Koren , Adam M Phillippy , Alistair Dm Dove , Timothy Read

Epigenetic patterns in a complete human genome.

Science (New York, N.Y.)
Avec: Ariel Gershman , Michael E G Sauria , Xavi Guitart , Mitchell R Vollger , Paul W Hook , Savannah J Hoyt , Miten Jain , Alaina Shumate , Roham Razaghi , Sergey Koren , Nicolas Altemose , Gina V Caldas , Glennis A Logsdon , Arang Rhie , Evan E Eichler , Michael C Schatz , Rachel J O'Neill , Adam M Phillippy , Karen H Miga , Winston Timp

From telomere to telomere: The transcriptional and epigenetic state of human repeat elements.

Science (New York, N.Y.)
Avec: Savannah J Hoyt , Jessica M Storer , Gabrielle A Hartley , Patrick G S Grady , Ariel Gershman , Leonardo G de Lima , Charles Limouse , Reza Halabian , Luke Wojenski , Matias Rodriguez , Nicolas Altemose , Arang Rhie , Leighton J Core , Jennifer L Gerton , Wojciech Makalowski , Daniel Olson , Jeb Rosen , Arian F A Smit , Aaron F Straight , Mitchell R Vollger , Travis J Wheeler , Michael C Schatz , Evan E Eichler , Adam M Phillippy , Winston Timp , Karen H Miga , Rachel J O'Neill

False gene and chromosome losses in genome assemblies caused by GC content variation and repeats.

Genome biology
Avec: Juwan Kim , Chul Lee , Byung June Ko , Dong Ahn Yoo , Sohyoung Won , Adam M Phillippy , Olivier Fedrigo , Guojie Zhang , Kerstin Howe , Jonathan Wood , Richard Durbin , Giulio Formenti , Samara Brown , Lindsey Cantin , Claudio V Mello , Seoae Cho , Arang Rhie , Heebal Kim , Erich D Jarvis

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

A high-quality blue whale genome, segmental duplications, and historical demography.

Molecular biology and evolution
Avec: Yury V Bukhman , Phillip A Morin , Susanne Meyer , Li-Fang Chu , Jeff K Jacobsen , Jessica Antosiewicz-Bourget , Daniel Mamott , Maylie Gonzales , Cara Argus , Jennifer Bolin , Mark E Berres , Olivier Fedrigo , John Steill , Scott A Swanson , Peng Jiang , Arang Rhie , Giulio Formenti , Adam M Phillippy , Robert S Harris , Jonathan M D Wood , Kerstin Howe , Bogdan M Kirilenko , Chetan Munegowda , Michael Hiller , Aashish Jain , Daisuke Kihara , J Spencer Johnston , Alexander Ionkov , Kalpana Raja , Huishi Toh , Aimee Lang , Magnus Wolf , Erich D Jarvis , James A Thomson , Mark J P Chaisson , Ron Stewart

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

The Ruminant Telomere-to-Telomere (RT2T) Consortium.

Nature genetics
Avec: Theodore S Kalbfleisch , Stephanie D McKay , Brenda M Murdoch , David L Adelson , Diego Almansa-Villa , Gabrielle Becker , Linda M Beckett , María José Benítez-Galeano , Fernando Biase , Theresa Casey , Edward Chuong , Emily Clark , Shannon Clarke , Noelle Cockett , Christine Couldrey , Brian W Davis , Christine G Elsik , Thomas Faraut , Yahui Gao , Carine Genet , Patrick Grady , Jonathan Green , Richard Green , Dailu Guan , Darren Hagen , Gabrielle A Hartley , Mike Heaton , Savannah J Hoyt , Wen Huang , Erich Jarvis , Jenna Kalleberg , Hasan Khatib , Klaus-Peter Koepfi , James Koltes , Sergey Koren , Christa Kuehn , Tosso Leeb , Alexander Leonard , George E Liu , Wai Yee Low , Hunter McConnell , Kathryn McRae , Karen Miga , Michelle Mousel , Holly Neibergs , Temitayo Olagunju , Matt Pennell , Bruna Petry , Mirjam Pewsner , Adam M Phillippy , Brandon D Pickett , Paulene Pineda , Tamara Potapova , Satyanarayana Rachagani , Arang Rhie , Monique Rijnkels , Annie Robic , Nelida Rodriguez Osorio , Yana Safonova , Gustavo Schettini , Robert D Schnabel , Nagabhishek Sirpu Natesh , Morgan Stegemiller , Jessica Storer , Paul Stothard , Caleb Stull , Gwenola Tosser-Klopp , Germán M Traglia , Christopher K Tuggle , Curtis P Van Tassell , Corey Watson , Rosemarie Weikard , Klaus Wimmers , Shangqian Xie , Liu Yang , Timothy P L Smith , Rachel J O'Neill , Benjamin D Rosen

HiCanu: accurate assembly of segmental duplications, satellites, and allelic variants from high-fidelity long reads.

Genome research
Avec: Sergey Nurk , Brian P Walenz , Arang Rhie , Mitchell R Vollger , Glennis A Logsdon , Robert Grothe , Karen H Miga , Evan E Eichler , Adam M Phillippy , Sergey Koren

Platypus and echidna genomes reveal mammalian biology and evolution.

Nature
Avec: Yang Zhou , Linda Shearwin-Whyatt , Jing Li , Zhenzhen Song , Takashi Hayakawa , David Stevens , Jane C Fenelon , Emma Peel , Yuanyuan Cheng , Filip Pajpach , Natasha Bradley , Hikoyu Suzuki , Masato Nikaido , Joana Damas , Tasman Daish , Tahlia Perry , Zexian Zhu , Yuncong Geng , Arang Rhie , Ying Sims , Jonathan Wood , Bettina Haase , Jacquelyn Mountcastle , Olivier Fedrigo , Qiye Li , Huanming Yang , Jian Wang , Stephen D Johnston , Adam M Phillippy , Kerstin Howe , Erich D Jarvis , Oliver A Ryder , Henrik Kaessmann , Peter Donnelly , Jonas Korlach , Harris A Lewin , Jennifer Graves , Katherine Belov , Marilyn B Renfree , Frank Grutzner , Qi Zhou , Guojie Zhang

Complete vertebrate mitogenomes reveal widespread repeats and gene duplications.

Genome biology
Avec: Giulio Formenti , Arang Rhie , Jennifer Balacco , Bettina Haase , Jacquelyn Mountcastle , Olivier Fedrigo , Samara Brown , Marco Rosario Capodiferro , Farooq O Al-Ajli , Roberto Ambrosini , Peter Houde , Sergey Koren , Karen Oliver , Michelle Smith , Jason Skelton , Emma Betteridge , Jale Dolucan , Craig Corton , Iliana Bista , James Torrance , Alan Tracey , Jonathan Wood , Marcela Uliano-Silva , Kerstin Howe , Shane McCarthy , Sylke Winkler , Woori Kwak , Jonas Korlach , Arkarachai Fungtammasan , Daniel Fordham , Vania Costa , Simon Mayes , Matteo Chiara , David S Horner , Eugene Myers , Richard Durbin , Alessandro Achilli , Edward L Braun , Adam M Phillippy , Erich D Jarvis , Auteur inconnu

Merfin: improved variant filtering, assembly evaluation and polishing via k-mer validation.

Nature methods
Avec: Giulio Formenti , Arang Rhie , Brian P Walenz , Françoise Thibaud-Nissen , Kishwar Shafin , Sergey Koren , Eugene W Myers , Erich D Jarvis , Adam M Phillippy

Segmental duplications and their variation in a complete human genome.

Science (New York, N.Y.)
Avec: Mitchell R Vollger , Xavi Guitart , Philip C Dishuck , Ludovica Mercuri , William T Harvey , Ariel Gershman , Mark Diekhans , Arvis Sulovari , Katherine M Munson , Alexandra P Lewis , Kendra Hoekzema , David Porubsky , Ruiyang Li , Sergey Nurk , Sergey Koren , Karen H Miga , Adam M Phillippy , Winston Timp , Mario Ventura , Evan E Eichler

A family of unusual immunoglobulin superfamily genes in an invertebrate histocompatibility complex.

Proceedings of the National Academy of Sciences of the United States of America
Avec: Aidan L Huene , Steven M Sanders , Zhiwei Ma , Anh-Dao Nguyen , Sergey Koren , Manuel H Michaca , James C Mullikin , Adam M Phillippy , Christine E Schnitzler , Andreas D Baxevanis , Matthew L Nicotra

A haplotype-resolved genome assembly of the Nile rat facilitates exploration of the genetic basis of diabetes.

BMC biology
Avec: Huishi Toh , Chentao Yang , Giulio Formenti , Kalpana Raja , Lily Yan , Alan Tracey , William Chow , Kerstin Howe , Lucie A Bergeron , Guojie Zhang , Bettina Haase , Jacquelyn Mountcastle , Olivier Fedrigo , John Fogg , Bogdan Kirilenko , Chetan Munegowda , Michael Hiller , Aashish Jain , Daisuke Kihara , Arang Rhie , Adam M Phillippy , Scott A Swanson , Peng Jiang , Dennis O Clegg , Erich D Jarvis , James A Thomson , Ron Stewart , Mark J P Chaisson , Yury V Bukhman

High-quality metagenome assembly from long accurate reads with metaMDBG.

Nature biotechnology
Avec: Gaëtan Benoit , Sébastien Raguideau , Robert James , Adam M Phillippy , Rayan Chikhi , Christopher Quince

Efficient High-Quality Metagenome Assembly from Long Accurate Reads using Minimizer-space de Bruijn Graphs.

bioRxiv : the preprint server for biology
Avec: Gaëtan Benoit , Sébastien Raguideau , Robert James , Adam M Phillippy , Rayan Chikhi , Christopher Quince

The variation and evolution of complete human centromeres.

bioRxiv : the preprint server for biology
Avec: Glennis A Logsdon , Allison N Rozanski , Fedor Ryabov , Tamara Potapova , Valery A Shepelev , Yafei Mao , Mikko Rautiainen , Sergey Koren , Sergey Nurk , David Porubsky , Julian K Lucas , Kendra Hoekzema , Katherine M Munson , Jennifer L Gerton , Adam M Phillippy , Ivan A Alexandrov , 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

Gapless assembly of complete human and plant chromosomes using only nanopore sequencing.

bioRxiv : the preprint server for biology
Avec: Sergey Koren , Zhigui Bao , Andrea Guarracino , Shujun Ou , Sara Goodwin , Katharine M Jenike , Julian Lucas , Brandy McNulty , Jimin Park , Mikko Rautianinen , Arang Rhie , Dick Roelofs , Harrie Schneiders , Ilse Vrijenhoek , Koen Nijbroek , Doreen Ware , Michael C Schatz , Erik Garrison , Sanwen Huang , William Richard McCombie , Karen H Miga , Alexander H J Wittenberg , Adam M Phillippy

The formation and propagation of human Robertsonian chromosomes.

bioRxiv : the preprint server for biology
Avec: Leonardo Gomes de Lima , Andrea Guarracino , Sergey Koren , Tamara Potapova , Sean McKinney , Arang Rhie , Steven J Solar , Chris Seidel , Brandon Fagen , Brian P Walenz , Gerard G Bouffard , Shelise Y Brooks , Michael Peterson , Kate Hall , Juyun Crawford , Alice C Young , Brandon D Pickett , Erik Garrison , Adam M Phillippy , Jennifer L Gerton

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

Assignment of virus and antimicrobial resistance genes to microbial hosts in a complex microbial community by combined long-read assembly and proximity ligation.

Genome biology
Avec: Derek M Bickhart , Mick Watson , Sergey Koren , Kevin Panke-Buisse , Laura M Cersosimo , Maximilian O Press , Curtis P Van Tassell , Jo Ann S Van Kessel , Bradd J Haley , Seon Woo Kim , Cheryl Heiner , Garret Suen , Kiranmayee Bakshy , Ivan Liachko , Shawn T Sullivan , Phillip R Myer , Jay Ghurye , Mihai Pop , Paul J Weimer , Adam M Phillippy , Timothy P L Smith

Mash Screen: high-throughput sequence containment estimation for genome discovery.

Genome biology
Avec: Brian D Ondov , Gabriel J Starrett , Anna Sappington , Aleksandra Kostic , Sergey Koren , Christopher B Buck , Adam M Phillippy

De novo assembly of the goldfish (

Science advances
Avec: Zelin Chen , Yoshihiro Omori , Sergey Koren , Takuya Shirokiya , Takuo Kuroda , Atsushi Miyamoto , Hironori Wada , Asao Fujiyama , Atsushi Toyoda , Suiyuan Zhang , Tyra G Wolfsberg , Koichi Kawakami , Adam M Phillippy , Auteur inconnu , James C Mullikin , Shawn M Burgess

New insights into mammalian sex chromosome structure and evolution using high-quality sequences from bovine X and Y chromosomes.

BMC genomics
Avec: Ruijie Liu , Wai Yee Low , Rick Tearle , Sergey Koren , Jay Ghurye , Arang Rhie , Adam M Phillippy , Benjamin D Rosen , Derek M Bickhart , Timothy P L Smith , Stefan Hiendleder , John L Williams

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

Author Correction: A robust benchmark for detection of germline large deletions and insertions.

Nature biotechnology
Avec: Justin M Zook , Nancy F Hansen , Nathan D Olson , Lesley Chapman , James C Mullikin , Chunlin Xiao , Stephen Sherry , Sergey Koren , Adam M Phillippy , Paul C Boutros , Sayed Mohammad E Sahraeian , Vincent Huang , Alexandre Rouette , Noah Alexander , Christopher E Mason , Iman Hajirasouliha , Camir Ricketts , Joyce Lee , Rick Tearle , Ian T Fiddes , Alvaro Martinez Barrio , Jeremiah Wala , Andrew Carroll , Noushin Ghaffari , Oscar L Rodriguez , Ali Bashir , Shaun Jackman , John J Farrell , Aaron M Wenger , Can Alkan , Arda Soylev , Michael C Schatz , Shilpa Garg , George Church , Tobias Marschall , Ken Chen , Xian Fan , Adam C English , Jeffrey A Rosenfeld , Weichen Zhou , Ryan E Mills , Jay M Sage , Jennifer R Davis , Michael D Kaiser , John S Oliver , Anthony P Catalano , Mark J P Chaisson , Noah Spies , Fritz J Sedlazeck , Marc Salit

Merqury: reference-free quality, completeness, and phasing assessment for genome assemblies.

Genome biology
Avec: Arang Rhie , Brian P Walenz , Sergey Koren , Adam M Phillippy

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

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

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

Recombination between heterologous human acrocentric chromosomes.

Nature
Avec: Andrea Guarracino , Silvia Buonaiuto , Leonardo Gomes de Lima , Tamara Potapova , Arang Rhie , Sergey Koren , Boris Rubinstein , Christian Fischer , Auteur inconnu , Jennifer L Gerton , Adam M Phillippy , Vincenza Colonna , Erik Garrison

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

Minmers are a generalization of minimizers that enable unbiased local Jaccard estimation.

bioRxiv : the preprint server for biology
Avec: Bryce Kille , Erik Garrison , Todd J Treangen , Adam M Phillippy

Scalable, accessible, and reproducible reference genome assembly and evaluation in Galaxy.

bioRxiv : the preprint server for biology
Avec: Delphine Larivière , Linelle Abueg , Nadolina Brajuka , Cristóbal Gallardo-Alba , Bjorn Grüning , Byung June Ko , Alex Ostrovsky , Marc Palmada-Flores , Brandon D Pickett , Keon Rabbani , Jennifer R Balacco , Mark Chaisson , Haoyu Cheng , Joanna Collins , Alexandra Denisova , Olivier Fedrigo , Guido Roberto Gallo , Alice Maria Giani , Grenville MacDonald Gooder , Nivesh Jain , Cassidy Johnson , Heebal Kim , Chul Lee , Tomas Marques-Bonet , Brian O'Toole , Arang Rhie , Simona Secomandi , Marcella Sozzoni , Tatiana Tilley , Marcela Uliano-Silva , Marius van den Beek , Robert M Waterhouse , Adam M Phillippy , Erich D Jarvis , Michael C Schatz , Anton Nekrutenko , Giulio Formenti

The variation and evolution of complete human centromeres.

Nature
Avec: Glennis A Logsdon , Allison N Rozanski , Fedor Ryabov , Tamara Potapova , Valery A Shepelev , Claudia R Catacchio , David Porubsky , Yafei Mao , DongAhn Yoo , Mikko Rautiainen , Sergey Koren , Sergey Nurk , Julian K Lucas , Kendra Hoekzema , Katherine M Munson , Jennifer L Gerton , Adam M Phillippy , Mario Ventura , Ivan A Alexandrov , Evan E Eichler

Epigenetic control and inheritance of rDNA arrays.

bioRxiv : the preprint server for biology
Avec: Tamara Potapova , Paxton Kostos , Sean McKinney , Matthew Borchers , Jeff Haug , Andrea Guarracino , Steven Solar , Madelaine Gogol , Graciela Monfort Anez , Leonardo Gomes de Lima , Yan Wang , Kate Hall , Sophie Hoffman , Erik Garrison , Adam M Phillippy , Jennifer L Gerton

Integrating Hi-C links with assembly graphs for chromosome-scale assembly.

PLoS computational biology
Avec: Jay Ghurye , Arang Rhie , Brian P Walenz , Anthony Schmitt , Siddarth Selvaraj , Mihai Pop , Adam M Phillippy , Sergey Koren

Accurate circular consensus long-read sequencing improves variant detection and assembly of a human genome.

Nature biotechnology
Avec: Aaron M Wenger , Paul Peluso , William J Rowell , Pi-Chuan Chang , Richard J Hall , Gregory T Concepcion , Jana Ebler , Arkarachai Fungtammasan , Alexey Kolesnikov , Nathan D Olson , Armin Töpfer , Michael Alonge , Medhat Mahmoud , Yufeng Qian , Chen-Shan Chin , Adam M Phillippy , Michael C Schatz , Gene Myers , Mark A DePristo , Jue Ruan , Tobias Marschall , Fritz J Sedlazeck , Justin M Zook , Heng Li , Sergey Koren , Andrew Carroll , David R Rank , Michael W Hunkapiller

HLA*LA-HLA typing from linearly projected graph alignments.

Bioinformatics (Oxford, England)
Avec: Alexander T Dilthey , Alexander J Mentzer , Raphael Carapito , Clare Cutland , Nezih Cereb , Shabir A Madhi , Arang Rhie , Sergey Koren , Seiamak Bahram , Gil McVean , Adam M Phillippy

Haplotype-resolved genomes provide insights into structural variation and gene content in Angus and Brahman cattle.

Nature communications
Avec: Wai Yee Low , Rick Tearle , Ruijie Liu , Sergey Koren , Arang Rhie , Derek M Bickhart , Benjamin D Rosen , Zev N Kronenberg , Sarah B Kingan , Elizabeth Tseng , Françoise Thibaud-Nissen , Fergal J Martin , Konstantinos Billis , Jay Ghurye , Alex R Hastie , Joyce Lee , Andy W C Pang , Michael P Heaton , Adam M Phillippy , Stefan Hiendleder , Timothy P L Smith , John L Williams

Effect of sequence depth and length in long-read assembly of the maize inbred NC358.

Nature communications
Avec: Shujun Ou , Jianing Liu , Kapeel M Chougule , Arkarachai Fungtammasan , Arun S Seetharam , Joshua C Stein , Victor Llaca , Nancy Manchanda , Amanda M Gilbert , Sharon Wei , Chen-Shan Chin , David E Hufnagel , Sarah Pedersen , Samantha J Snodgrass , Kevin Fengler , Margaret Woodhouse , Brian P Walenz , Sergey Koren , Adam M Phillippy , Brett T Hannigan , R Kelly Dawe , Candice N Hirsch , Matthew B Hufford , Doreen Ware

Genomic analyses of a livestock pest, the New World screwworm, find potential targets for genetic control programs.

Communications biology
Avec: Maxwell J Scott , Joshua B Benoit , Rebecca J Davis , Samuel T Bailey , Virag Varga , Ellen O Martinson , Paul V Hickner , Zainulabeuddin Syed , Gisele A Cardoso , Tatiana T Torres , Matthew T Weirauch , Elizabeth H Scholl , Adam M Phillippy , Agustin Sagel , Mario Vasquez , Gladys Quintero , Steven R Skoda

Evolutionary superscaffolding and chromosome anchoring to improve Anopheles genome assemblies.

BMC biology
Avec: Robert M Waterhouse , Sergey Aganezov , Yoann Anselmetti , Jiyoung Lee , Livio Ruzzante , Maarten J M F Reijnders , Romain Feron , Sèverine Bérard , Phillip George , Matthew W Hahn , Paul I Howell , Maryam Kamali , Sergey Koren , Daniel Lawson , Gareth Maslen , Ashley Peery , Adam M Phillippy , Maria V Sharakhova , Eric Tannier , Maria F Unger , Simo V Zhang , Max A Alekseyev , Nora J Besansky , Cedric Chauve , Scott J Emrich , Igor V Sharakhov

Improved reference genome of the arboviral vector Aedes albopictus.

Genome biology
Avec: Umberto Palatini , Reem A Masri , Luciano V Cosme , Sergey Koren , Françoise Thibaud-Nissen , James K Biedler , Flavia Krsticevic , J Spencer Johnston , Rebecca Halbach , Jacob E Crawford , Igor Antoshechkin , Anna-Bella Failloux , Elisa Pischedda , Michele Marconcini , Jay Ghurye , Arang Rhie , Atashi Sharma , Dmitry A Karagodin , Jeremy Jenrette , Stephanie Gamez , Pascal Miesen , Patrick Masterson , Adalgisa Caccone , Maria V Sharakhova , Zhijian Tu , Philippos A Papathanos , Ronald P Van Rij , Omar S Akbari , Jeffrey Powell , Adam M Phillippy , Mariangela Bonizzoni

Evolutionary and biomedical insights from a marmoset diploid genome assembly.

Nature
Avec: Chentao Yang , Yang Zhou , Stephanie Marcus , Giulio Formenti , Lucie A Bergeron , Zhenzhen Song , Xupeng Bi , Juraj Bergman , Marjolaine Marie C Rousselle , Chengran Zhou , Long Zhou , Yuan Deng , Miaoquan Fang , Duo Xie , Yuanzhen Zhu , Shangjin Tan , Jacquelyn Mountcastle , Bettina Haase , Jennifer Balacco , Jonathan Wood , William Chow , Arang Rhie , Martin Pippel , Margaret M Fabiszak , Sergey Koren , Olivier Fedrigo , Winrich A Freiwald , Kerstin Howe , Huanming Yang , Adam M Phillippy , Mikkel Heide Schierup , Erich D Jarvis , Guojie Zhang

The genomic structure of a human chromosome 22 nucleolar organizer region determined by TAR cloning.

Scientific reports
Avec: Jung-Hyun Kim , Vladimir N Noskov , Aleksey Y Ogurtsov , Ramaiah Nagaraja , Nikolai Petrov , Mikhail Liskovykh , Brian P Walenz , Hee-Sheung Lee , Natalay Kouprina , Adam M Phillippy , Svetlana A Shabalina , David Schlessinger , Vladimir Larionov

Standards recommendations for the Earth BioGenome Project.

Proceedings of the National Academy of Sciences of the United States of America
Avec: Mara K N Lawniczak , Richard Durbin , Paul Flicek , Kerstin Lindblad-Toh , Xiaofeng Wei , John M Archibald , William J Baker , Katherine Belov , Mark L Blaxter , Tomas Marques Bonet , Anna K Childers , Jonathan A Coddington , Keith A Crandall , Andrew J Crawford , Robert P Davey , Federica Di Palma , Qi Fang , Wilfried Haerty , Neil Hall , Katharina J Hoff , Kerstin Howe , Erich D Jarvis , Warren E Johnson , Rebecca N Johnson , Paul J Kersey , Xin Liu , Jose Victor Lopez , Eugene W Myers , Olga Vinnere Pettersson , Adam M Phillippy , Monica F Poelchau , Kim D Pruitt , Arang Rhie , Juan Carlos Castilla-Rubio , Sunil Kumar Sahu , Nicholas A Salmon , Pamela S Soltis , David Swarbreck , Françoise Thibaud-Nissen , Sibo Wang , Jill L Wegrzyn , Guojie Zhang , He Zhang , Harris A Lewin , Stephen Richards

Balancing openness with Indigenous data sovereignty: An opportunity to leave no one behind in the journey to sequence all of life.

Proceedings of the National Academy of Sciences of the United States of America
Avec: Ann M Mc Cartney , Jane Anderson , Libby Liggins , Maui L Hudson , Matthew Z Anderson , Ben TeAika , Janis Geary , Robert Cook-Deegan , Hardip R Patel , Adam M Phillippy

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

Long-read mapping to repetitive reference sequences using Winnowmap2.

Nature methods
Avec: Chirag Jain , Arang Rhie , Nancy F Hansen , Sergey Koren , Adam M Phillippy

The complete sequence of a human Y chromosome.

Nature
Avec: Arang Rhie , Sergey Nurk , Monika Cechova , Savannah J Hoyt , Dylan J Taylor , Nicolas Altemose , Paul W Hook , Sergey Koren , Mikko Rautiainen , Ivan A Alexandrov , Jamie Allen , Mobin Asri , Andrey V Bzikadze , Nae-Chyun Chen , Chen-Shan Chin , Mark Diekhans , Paul Flicek , Giulio Formenti , Arkarachai Fungtammasan , Carlos Garcia Giron , Erik Garrison , Ariel Gershman , Jennifer L Gerton , Patrick G S Grady , Andrea Guarracino , Leanne Haggerty , Reza Halabian , Nancy F Hansen , Robert Harris , Gabrielle A Hartley , William T Harvey , Marina Haukness , Jakob Heinz , Thibaut Hourlier , Robert M Hubley , Sarah E Hunt , Stephen Hwang , Miten Jain , Rupesh K Kesharwani , Alexandra P Lewis , Heng Li , Glennis A Logsdon , Julian K Lucas , Wojciech Makalowski , Christopher Markovic , Fergal J Martin , Ann M Mc Cartney , Rajiv C McCoy , Jennifer McDaniel , Brandy M McNulty , Paul Medvedev , Alla Mikheenko , Katherine M Munson , Terence D Murphy , Hugh E Olsen , Nathan D Olson , Luis F Paulin , David Porubsky , Tamara Potapova , Fedor Ryabov , Steven L Salzberg , Michael E G Sauria , Fritz J Sedlazeck , Kishwar Shafin , Valery A Shepelev , Alaina Shumate , Jessica M Storer , Likhitha Surapaneni , Angela M Taravella Oill , Françoise Thibaud-Nissen , Winston Timp , Marta Tomaszkiewicz , Mitchell R Vollger , Brian P Walenz , Allison C Watwood , Matthias H Weissensteiner , Aaron M Wenger , Melissa A Wilson , Samantha Zarate , Yiming Zhu , Justin M Zook , Evan E Eichler , Rachel J O'Neill , Michael C Schatz , Karen H Miga , Kateryna D Makova , Adam M Phillippy

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

Comparative genomics of macaques and integrated insights into genetic variation and population history.

bioRxiv : the preprint server for biology
Avec: Shilong Zhang , Ning Xu , Lianting Fu , Xiangyu Yang , Yamei Li , Zikun Yang , Yu Feng , Kaiyue Ma , Xinrui Jiang , Junmin Han , Ruixing Hu , Lu Zhang , Luciana de Gennaro , Fedor Ryabov , Dan Meng , Yaoxi He , Dongya Wu , Chentao Yang , Annalisa Paparella , Yuxiang Mao , Xinyan Bian , Yong Lu , Francesca Antonacci , Mario Ventura , Valery A Shepelev , Karen H Miga , Ivan A Alexandrov , Glennis A Logsdon , Adam M Phillippy , Bing Su , Guojie Zhang , Evan E Eichler , Qing Lu , Yongyong Shi , Qiang Sun , Yafei Mao

Parsnp 2.0: Scalable Core-Genome alignment for massive microbial datasets.

Bioinformatics (Oxford, England)
Avec: Bryce Kille , Michael G Nute , Victor Huang , Eddie Kim , Adam M Phillippy , Todd J Treangen

ModDotPlot-rapid and interactive visualization of tandem repeats.

Bioinformatics (Oxford, England)
Avec: Alexander P Sweeten , Michael C Schatz , Adam M Phillippy

Complete sequencing of ape genomes.

bioRxiv : the preprint server for biology
Avec: DongAhn Yoo , Arang Rhie , Prajna Hebbar , Francesca Antonacci , Glennis A Logsdon , Steven J Solar , Dmitry Antipov , Brandon D Pickett , Yana Safonova , Francesco Montinaro , Yanting Luo , Joanna Malukiewicz , Jessica M Storer , Jiadong Lin , Abigail N Sequeira , Riley J Mangan , Glenn Hickey , Graciela Monfort Anez , Parithi Balachandran , Anton Bankevich , Christine R Beck , Arjun Biddanda , Matthew Borchers , Gerard G Bouffard , Emry Brannan , Shelise Y Brooks , Lucia Carbone , Laura Carrel , Agnes P Chan , Juyun Crawford , Mark Diekhans , Eric Engelbrecht , Cedric Feschotte , Giulio Formenti , Gage H Garcia , Luciana de Gennaro , David Gilbert , Richard E Green , Andrea Guarracino , Ishaan Gupta , Diana Haddad , Junmin Han , Robert S Harris , Gabrielle A Hartley , William T Harvey , Michael Hiller , Kendra Hoekzema , Marlys L Houck , Hyeonsoo Jeong , Kaivan Kamali , Manolis Kellis , Bryce Kille , Chul Lee , Youngho Lee , William Lees , Alexandra P Lewis , Qiuhui Li , Mark Loftus , Yong Hwee Eddie Loh , Hailey Loucks , Jian Ma , Yafei Mao , Juan F I Martinez , Patrick Masterson , Rajiv C McCoy , Barbara McGrath , Sean McKinney , Britta S Meyer , Karen H Miga , Saswat K Mohanty , Katherine M Munson , Karol Pal , Matt Pennell , Pavel A Pevzner , David Porubsky , Tamara Potapova , Francisca R Ringeling , Joana L Rocha , Oliver A Ryder , Samuel Sacco , Swati Saha , Takayo Sasaki , Michael C Schatz , Nicholas J Schork , Cole Shanks , Linnéa Smeds , Dongmin R Son , Cynthia Steiner , Alexander P Sweeten , Michael G Tassia , Françoise Thibaud-Nissen , Edmundo Torres-González , Mihir Trivedi , Wenjie Wei , Julie Wertz , Muyu Yang , Panpan Zhang , Shilong Zhang , Yang Zhang , Zhenmiao Zhang , Sarah A Zhao , Yixin Zhu , Erich D Jarvis , Jennifer L Gerton , Iker Rivas-González , Benedict Paten , Zachary A Szpiech , Christian D Huber , Tobias L Lenz , Miriam K Konkel , Soojin V Yi , Stefan Canzar , Corey T Watson , Peter H Sudmant , Erin Molloy , Erik Garrison , Craig B Lowe , Mario Ventura , Rachel J O'Neill , Sergey Koren , Kateryna D Makova , Adam M Phillippy , Evan E Eichler

Complex genetic variation in nearly complete human genomes.

bioRxiv : the preprint server for biology
Avec: Glennis A Logsdon , Peter Ebert , Peter A Audano , Mark Loftus , David Porubsky , Jana Ebler , Feyza Yilmaz , Pille Hallast , Timofey Prodanov , DongAhn Yoo , Carolyn A Paisie , William T Harvey , Xuefang Zhao , Gianni V Martino , Mir Henglin , Katherine M Munson , Keon Rabbani , Chen-Shan Chin , Bida Gu , Hufsah Ashraf , Olanrewaju Austine-Orimoloye , Parithi Balachandran , Marc Jan Bonder , Haoyu Cheng , Zechen Chong , Jonathan Crabtree , Mark Gerstein , Lisbeth A Guethlein , Patrick Hasenfeld , Glenn Hickey , Kendra Hoekzema , Sarah E Hunt , Matthew Jensen , Yunzhe Jiang , Sergey Koren , Youngjun Kwon , Chong Li , Heng Li , Jiaqi Li , Paul J Norman , Keisuke K Oshima , Benedict Paten , Adam M Phillippy , Nicholas R Pollock , Tobias Rausch , Mikko Rautiainen , Stephan Scholz , Yuwei Song , Arda Soylev , Arvis Sulovari , Likhitha Surapaneni , Vasiliki Tsapalou , Weichen Zhou , Ying Zhou , Qihui Zhu , Michael C Zody , Ryan E Mills , Scott E Devine , Xinghua Shi , Mike E Talkowski , Mark J P Chaisson , Alexander T Dilthey , Miriam K Konkel , Jan O Korbel , Charles Lee , Christine R Beck , Evan E Eichler , Tobias Marschall

Réseau de co-auteurs

Sergey Koren 53 collaborations
Arang Rhie 44 collaborations
Evan E Eichler 21 collaborations
Karen H Miga 21 collaborations
Michael C Schatz 17 collaborations
Erich D Jarvis 17 collaborations
Kerstin Howe 16 collaborations
Glennis A Logsdon 15 collaborations
Jennifer L Gerton 15 collaborations
Giulio Formenti 15 collaborations
Benedict Paten 15 collaborations
Tamara Potapova 14 collaborations
Mitchell R Vollger 13 collaborations
David Porubsky 13 collaborations
Françoise Thibaud-Nissen 13 collaborations
Sergey Nurk 12 collaborations
Olivier Fedrigo 12 collaborations
Brian P Walenz 12 collaborations
Erik Garrison 12 collaborations
Kishwar Shafin 12 collaborations
Katherine M Munson 11 collaborations
Justin M Zook 10 collaborations
Jay Ghurye 9 collaborations
Fritz J Sedlazeck 9 collaborations
Rachel J O'Neill 9 collaborations
Winston Timp 9 collaborations
Chen-Shan Chin 9 collaborations
Mark Diekhans 9 collaborations
Nathan D Olson 8 collaborations
Tobias Marschall 8 collaborations
Mark J P Chaisson 8 collaborations
William T Harvey 8 collaborations
Timothy P L Smith 8 collaborations
Savannah J Hoyt 8 collaborations
Gabrielle A Hartley 8 collaborations
Guojie Zhang 8 collaborations
Ivan A Alexandrov 8 collaborations
Andrea Guarracino 8 collaborations
Nancy F Hansen 7 collaborations
Kendra Hoekzema 7 collaborations
Mario Ventura 7 collaborations
William Chow 7 collaborations
Mikko Rautiainen 7 collaborations
Richard E Green 7 collaborations
Ariel Gershman 7 collaborations
Miten Jain 7 collaborations
Jonathan Wood 7 collaborations
Valery A Shepelev 7 collaborations
Arkarachai Fungtammasan 7 collaborations
Mobin Asri 7 collaborations
Heng Li 7 collaborations
James C Mullikin 6 collaborations
Joyce Lee 6 collaborations
Andrew Carroll 6 collaborations
Chirag Jain 6 collaborations
Jonas Korlach 6 collaborations
Derek M Bickhart 6 collaborations
Paul Flicek 6 collaborations
Benjamin D Rosen 6 collaborations
Alaina Shumate 6 collaborations
Jessica M Storer 6 collaborations
Brandon D Pickett 6 collaborations
Matthew Borchers 6 collaborations
Gerard G Bouffard 6 collaborations
Alexandra P Lewis 6 collaborations
Rajiv C McCoy 6 collaborations
Fedor Ryabov 6 collaborations
Jacquelyn Mountcastle 6 collaborations
None None 6 collaborations
Julian K Lucas 6 collaborations
Yafei Mao 5 collaborations
Alla Mikheenko 5 collaborations
Andrey V Bzikadze 5 collaborations
Fergal J Martin 5 collaborations
Bryce Kille 5 collaborations
Nicolas Altemose 5 collaborations
Patrick G S Grady 5 collaborations
Richard Durbin 5 collaborations
Kateryna D Makova 5 collaborations
Robert S Harris 5 collaborations
DongAhn Yoo 5 collaborations
Shelise Y Brooks 5 collaborations
Glenn Hickey 5 collaborations
Patrick Masterson 5 collaborations
Oliver A Ryder 5 collaborations
Bettina Haase 5 collaborations
Trevor Pesout 5 collaborations
Valerie A Schneider 5 collaborations
Haoyu Cheng 5 collaborations
Marina Haukness 5 collaborations
Jennifer McDaniel 5 collaborations
Chunlin Xiao 4 collaborations
Rick Tearle 4 collaborations
Aaron M Wenger 4 collaborations
Shilpa Garg 4 collaborations
Jeffrey A Rosenfeld 4 collaborations
Harris A Lewin 4 collaborations
Leanne Haggerty 4 collaborations
Todd J Treangen 4 collaborations
Wai Yee Low 4 collaborations
Michael E G Sauria 4 collaborations
Chul Lee 4 collaborations
Francesca Antonacci 4 collaborations
Pi-Chuan Chang 4 collaborations
Luciana de Gennaro 4 collaborations
Paul Medvedev 4 collaborations
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Steven J Solar 4 collaborations
Alice C Young 4 collaborations
Jonathan M D Wood 4 collaborations
Michael Hiller 4 collaborations
James Torrance 4 collaborations
Alan Tracey 4 collaborations
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Chentao Yang 4 collaborations
Mikhail Kolmogorov 4 collaborations
Mark Chaisson 4 collaborations
Leonardo Gomes de Lima 4 collaborations
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David Haussler 4 collaborations
Megan Y Dennis 4 collaborations
Daniela C Soto 4 collaborations
Pavel A Pevzner 4 collaborations
Sergey Aganezov 4 collaborations
Robert S Fulton 4 collaborations
Justin Wagner 4 collaborations
Ian T Fiddes 3 collaborations
Arda Soylev 3 collaborations
Weichen Zhou 3 collaborations
Ryan E Mills 3 collaborations
Peter Kerpedjiev 3 collaborations
Adam L Felsenfeld 3 collaborations
Philip C Dishuck 3 collaborations
Leonardo G de Lima 3 collaborations
Tatiana Dvorkina 3 collaborations
Milinn Kremitzki 3 collaborations
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Alexander P Sweeten 3 collaborations
Konstantinos Billis 3 collaborations
Richard Hall 3 collaborations
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Alexander T Dilthey 3 collaborations
Paul Peluso 3 collaborations
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John L Williams 3 collaborations
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Michael G Tassia 3 collaborations
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Jean Monlong 3 collaborations
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Ting Wang 3 collaborations
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Nora J Besansky 2 collaborations
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Sarah Cody 2 collaborations
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