O Dudchenko

Publications (49)

The gene-rich genome of the scallop Pecten maximus.

GigaScience
Avec: Nathan J Kenny , Shane A McCarthy , Olga Dudchenko , Katherine James , Emma Betteridge , Craig Corton , Jale Dolucan , Dan Mead , Karen Oliver , Arina D Omer , Sarah Pelan , Yan Ryan , Ying Sims , Jason Skelton , Michelle Smith , James Torrance , David Weisz , Anil Wipat , Erez L Aiden , Kerstin Howe , Suzanne T Williams

The swan genome and transcriptome, it is not all black and white.

Genome biology
Avec: Anjana C Karawita , Yuanyuan Cheng , Keng Yih Chew , Arjun Challagulla , Robert Kraus , Ralf C Mueller , Marcus Z W Tong , Katina D Hulme , Helle Bielefeldt-Ohmann , Lauren E Steele , Melanie Wu , Julian Sng , Ellesandra Noye , Timothy J Bruxner , Gough G Au , Suzanne Lowther , Julie Blommaert , Alexander Suh , Alexander J McCauley , Parwinder Kaur , Olga Dudchenko , Erez Aiden , Olivier Fedrigo , Giulio Formenti , Jacquelyn Mountcastle , William Chow , Fergal J Martin , Denye N Ogeh , Françoise Thiaud-Nissen , Kerstin Howe , Alan Tracey , Jacqueline Smith , Richard I Kuo , Marilyn B Renfree , Takashi Kimura , Yoshihiro Sakoda , Mathew McDougall , Hamish G Spencer , Michael Pyne , Conny Tolf , Jonas Waldenström , Erich D Jarvis , Michelle L Baker , David W Burt , Kirsty R Short

GigaByte (Hong Kong, China)
Avec: Sydney Lamb , Adam M Taylor , Tabitha A Hughes , Brock R McMillan , Randy T Larsen , Ruqayya Khan , David Weisz , Olga Dudchenko , Erez Lieberman Aiden , Nathaniel B Edelman , Paul B Frandsen

The ENCODE Uniform Analysis Pipelines.

Research square
Avec: Benjamin C Hitz , Jin-Wook Lee , Otto Jolanki , Meenakshi S Kagda , Keenan Graham , Paul Sud , Idan Gabdank , J Seth Strattan , Cricket A Sloan , Timothy Dreszer , Laurence D Rowe , Nikhil R Podduturi , Venkat S Malladi , Esther T Chan , Jean M Davidson , Marcus Ho , Stuart Miyasato , Matt Simison , Forrest Tanaka , Yunhai Luo , Ian Whaling , Eurie L Hong , Brian T Lee , Richard Sandstrom , Eric Rynes , Jemma Nelson , Andrew Nishida , Alyssa Ingersoll , Michael Buckley , Mark Frerker , Daniel S Kim , Nathan Boley , Diane Trout , Alex Dobin , Sorena Rahmanian , Dana Wyman , Gabriela Balderrama-Gutierrez , Fairlie Reese , Neva C Durand , Olga Dudchenko , David Weisz , Suhas S P Rao , Alyssa Blackburn , Dimos Gkountaroulis , Mahdi Sadr , Moshe Olshansky , Yossi Eliaz , Dat Nguyen , Ivan Bochkov , Muhammad Saad Shamim , Ragini Mahajan , Erez Aiden , Tom Gingeras , Simon Heath , Martin Hirst , W James Kent , Anshul Kundaje , Ali Mortazavi , Barbara Wold , J Michael Cherry

Delineating the

International journal of molecular sciences
Avec: Parwinder Kaur , Christopher Lui , Olga Dudchenko , Raja Sekhar Nandety , Bhavna Hurgobin , Melanie Pham , Erez Lieberman Aiden , Jiangqi Wen , Kirankumar Mysore

Chromosome size affects sequence divergence between species through the interplay of recombination and selection.

Evolution; international journal of organic evolution
Avec: Anna Tigano , Ruqayya Khan , Arina D Omer , David Weisz , Olga Dudchenko , Asha S Multani , Sen Pathak , Richard R Behringer , Erez L Aiden , Heidi Fisher , Matthew D MacManes

Transcriptional and functional consequences of alterations to MEF2C and its topological organization in neuronal models.

American journal of human genetics
Avec: Kiana Mohajeri , Rachita Yadav , Eva D'haene , Philip M Boone , Serkan Erdin , Dadi Gao , Mariana Moyses-Oliveira , Riya Bhavsar , Benjamin B Currall , Kathryn O'Keefe , Nicholas D Burt , Chelsea Lowther , Diane Lucente , Monica Salani , Mathew Larson , Claire Redin , Olga Dudchenko , Erez Lieberman Aiden , Björn Menten , Derek J C Tai , James F Gusella , Sarah Vergult , Michael E Talkowski

The Australasian dingo archetype:

bioRxiv : the preprint server for biology
Avec: J William O Ballard , Matt A Field , Richard J Edwards , Laura A B Wilson , Loukas G Koungoulos , Benjamin D Rosen , Barry Chernoff , Olga Dudchenko , Arina Omer , Jens Keilwagen , Ksenia Skvortsova , Ozren Bogdanovic , Eva Chan , Robert Zammit , Vanessa Hayes , Erez Lieberman Aiden

A Chromosome-length Assembly of the Black Petaltail (Tanypteryx hageni) Dragonfly.

Genome biology and evolution
Avec: Ethan R Tolman , Christopher D Beatty , Jonas Bush , Manpreet Kohli , Carlos M Moreno , Jessica L Ware , K Scott Weber , Ruqayya Khan , Chirag Maheshwari , David Weisz , Olga Dudchenko , Erez Lieberman Aiden , Paul B Frandsen

The genome of the Australian water dragon (Intellagama lesueurii), an agamid model for urban adaptation.

The Journal of heredity
Avec: Daniel Powell , Nicola Jackson , Parwinder Kaur , Olga Dudchenko , Erez Lieberman Aiden , Arthur Georges , Céline H Frère

The genome sequence of segmental allotetraploid peanut Arachis hypogaea.

Nature genetics
Avec: David J Bertioli , Jerry Jenkins , Josh Clevenger , Olga Dudchenko , Dongying Gao , Guillermo Seijo , Soraya C M Leal-Bertioli , Longhui Ren , Andrew D Farmer , Manish K Pandey , Sergio S Samoluk , Brian Abernathy , Gaurav Agarwal , Carolina Ballén-Taborda , Connor Cameron , Jacqueline Campbell , Carolina Chavarro , Annapurna Chitikineni , Ye Chu , Sudhansu Dash , Moaine El Baidouri , Baozhu Guo , Wei Huang , Kyung Do Kim , Walid Korani , Sophie Lanciano , Christopher G Lui , Marie Mirouze , Márcio C Moretzsohn , Melanie Pham , Jin Hee Shin , Kenta Shirasawa , Senjuti Sinharoy , Avinash Sreedasyam , Nathan T Weeks , Xinyou Zhang , Zheng Zheng , Ziqi Sun , Lutz Froenicke , Erez L Aiden , Richard Michelmore , Rajeev K Varshney , C Corley Holbrook , Ethalinda K S Cannon , Brian E Scheffler , Jane Grimwood , Peggy Ozias-Akins , Steven B Cannon , Scott A Jackson , Jeremy Schmutz

Chromosomal-level genome assembly of the scimitar-horned oryx: Insights into diversity and demography of a species extinct in the wild.

Molecular ecology resources
Avec: Emily Humble , Pavel Dobrynin , Helen Senn , Justin Chuven , Alan F Scott , David W Mohr , Olga Dudchenko , Arina D Omer , Zane Colaric , Erez Lieberman Aiden , Shaikha Salem Al Dhaheri , David Wildt , Shireen Oliaji , Gaik Tamazian , Budhan Pukazhenthi , Rob Ogden , Klaus-Peter Koepfli

3D genomics across the tree of life reveals condensin II as a determinant of architecture type.

Science (New York, N.Y.)
Avec: Claire Hoencamp , Olga Dudchenko , Ahmed M O Elbatsh , Sumitabha Brahmachari , Jonne A Raaijmakers , Tom van Schaik , Ángela Sedeño Cacciatore , Vinícius G Contessoto , Roy G H P van Heesbeen , Bram van den Broek , Aditya N Mhaskar , Hans Teunissen , Brian Glenn St Hilaire , David Weisz , Arina D Omer , Melanie Pham , Zane Colaric , Zhenzhen Yang , Suhas S P Rao , Namita Mitra , Christopher Lui , Weijie Yao , Ruqayya Khan , Leonid L Moroz , Andrea Kohn , Judy St Leger , Alexandria Mena , Karen Holcroft , Maria Cristina Gambetta , Fabian Lim , Emma Farley , Nils Stein , Alexander Haddad , Daniel Chauss , Ayse Sena Mutlu , Meng C Wang , Neil D Young , Evin Hildebrandt , Hans H Cheng , Christopher J Knight , Theresa L U Burnham , Kevin A Hovel , Andrew J Beel , Pierre-Jean Mattei , Roger D Kornberg , Wesley C Warren , Gregory Cary , José Luis Gómez-Skarmeta , Veronica Hinman , Kerstin Lindblad-Toh , Federica Di Palma , Kazuhiro Maeshima , Asha S Multani , Sen Pathak , Liesl Nel-Themaat , Richard R Behringer , Parwinder Kaur , René H Medema , Bas van Steensel , Elzo de Wit , José N Onuchic , Michele Di Pierro , Erez Lieberman Aiden , Benjamin D Rowland

Chromosome-length genome assembly and structural variations of the primal Basenji dog (Canis lupus familiaris) genome.

BMC genomics
Avec: Richard J Edwards , Matt A Field , James M Ferguson , Olga Dudchenko , Jens Keilwagen , Benjamin D Rosen , Gary S Johnson , Edward S Rice , La Deanna Hillier , Jillian M Hammond , Samuel G Towarnicki , Arina Omer , Ruqayya Khan , Ksenia Skvortsova , Ozren Bogdanovic , Robert A Zammit , Erez Lieberman Aiden , Wesley C Warren , J William O Ballard

Limited Evidence for Parallel Evolution Among Desert-Adapted Peromyscus Deer Mice.

The Journal of heredity
Avec: Jocelyn P Colella , Anna Tigano , Olga Dudchenko , Arina D Omer , Ruqayya Khan , Ivan D Bochkov , Erez L Aiden , Matthew D MacManes

Chromosome Level Genome Assembly and Annotation of a Periodical Cicada Species: Magicicada septendecula.

Genome biology and evolution
Avec: Jonas Bush , Cynthia Webster , Jill Wegrzyn , Chris Simon , Edward Wilcox , Ruqayya Khan , David Weisz , Olga Dudchenko , Erez Lieberman Aiden , Paul Frandsen

Chromosome-length genome assembly and karyotype of the endangered black-footed ferret (Mustela nigripes).

The Journal of heredity
Avec: Sergei Kliver , Marlys L Houck , Polina L Perelman , Azamat Totikov , Andrey Tomarovsky , Olga Dudchenko , Arina D Omer , Zane Colaric , David Weisz , Erez Lieberman Aiden , Saki Chan , Alex Hastie , Aleksey Komissarov , Oliver A Ryder , Alexander Graphodatsky , Warren E Johnson , Jesús E Maldonado , Budhan S Pukazhenthi , Paul E Marinari , David E Wildt , Klaus-Peter Koepfli

A rapid, low-cost, and highly sensitive SARS-CoV-2 diagnostic based on whole-genome sequencing.

PloS one
Avec: Per A Adastra , Neva C Durand , Namita Mitra , Saul Godinez Pulido , Ragini Mahajan , Alyssa Blackburn , Zane L Colaric , Joshua W M Theisen , David Weisz , Olga Dudchenko , Andreas Gnirke , Suhas S P Rao , Parwinder Kaur , Erez Lieberman Aiden , Aviva Presser Aiden

The sensory shark: high-quality morphological, genomic and transcriptomic data for the small-spotted catshark

bioRxiv : the preprint server for biology
Avec: H Mayeur , J Leyhr , J Mulley , N Leurs , L Michel , K Sharma , R Lagadec , J-M Aury , O G Osborne , P Mulhair , J Poulain , S Mangenot , D Mead , M Smith , C Corton , K Oliver , J Skelton , E Betteridge , J Dolucan , O Dudchenko , A D Omer , D Weisz , E L Aiden , S McCarthy , Y Sims , J Torrance , A Tracey , K Howe , T Baril , A Hayward , C Martinand-Mari , S Sanchez , T Haitina , K Martin , S I Korsching , S Mazan , M Debiais-Thibaud

The genome sequence of the Eurasian river otter, Lutra lutra Linnaeus 1758.

Wellcome open research
Avec: Dan Mead , Frank Hailer , Elisabeth Chadwick , Roberto Portela Miguez , Michelle Smith , Craig Corton , Karen Oliver , Jason Skelton , Emma Betteridge , Jale Doulcan Doulcan , Olga Dudchenko , Arina Omer , David Weisz , Erez Lieberman Aiden , Shane McCarthy , Kerstin Howe , Ying Sims , James Torrance , Alan Tracey , Richard Challis , Richard Durbin , Mark Blaxter

Genome-wide diversity in the California condor tracks its prehistoric abundance and decline.

Current biology : CB
Avec: Jacqueline A Robinson , Rauri C K Bowie , Olga Dudchenko , Erez Lieberman Aiden , Sher L Hendrickson , Cynthia C Steiner , Oliver A Ryder , David P Mindell , Jeffrey D Wall

Chromosome-level genome of Schistosoma haematobium underpins genome-wide explorations of molecular variation.

PLoS pathogens
Avec: Andreas J Stroehlein , Pasi K Korhonen , V Vern Lee , Stuart A Ralph , Margaret Mentink-Kane , Hong You , Donald P McManus , Louis-Albert Tchuem Tchuenté , J Russell Stothard , Parwinder Kaur , Olga Dudchenko , Erez Lieberman Aiden , Bicheng Yang , Huanming Yang , Aidan M Emery , Bonnie L Webster , Paul J Brindley , David Rollinson , Bill C H Chang , Robin B Gasser , Neil D Young

Chromosome-length genome assembly and linkage map of a critically endangered Australian bird: the helmeted honeyeater.

GigaScience
Avec: Diana A Robledo-Ruiz , Han Ming Gan , Parwinder Kaur , Olga Dudchenko , David Weisz , Ruqayya Khan , Erez Lieberman Aiden , Ekaterina Osipova , Michael Hiller , Hernán E Morales , Michael J L Magrath , Rohan H Clarke , Paul Sunnucks , Alexandra Pavlova

The Australian dingo is an early offshoot of modern breed dogs.

Science advances
Avec: Matt A Field , Sonu Yadav , Olga Dudchenko , Meera Esvaran , Benjamin D Rosen , Ksenia Skvortsova , Richard J Edwards , Jens Keilwagen , Blake J Cochran , Bikash Manandhar , Sonia Bustamante , Jacob Agerbo Rasmussen , Richard G Melvin , Barry Chernoff , Arina Omer , Zane Colaric , Eva K F Chan , Andre E Minoche , Timothy P L Smith , M Thomas P Gilbert , Ozren Bogdanovic , Robert A Zammit , Torsten Thomas , Erez L Aiden , J William O Ballard

A Chromosome-Length Reference Genome for the Endangered Pacific Pocket Mouse Reveals Recent Inbreeding in a Historically Large Population.

Genome biology and evolution
Avec: Aryn P Wilder , Olga Dudchenko , Caitlin Curry , Marisa Korody , Sheela P Turbek , Mark Daly , Ann Misuraca , Gaojianyong Wang , Ruqayya Khan , David Weisz , Julie Fronczek , Erez Lieberman Aiden , Marlys L Houck , Debra M Shier , Oliver A Ryder , Cynthia C Steiner

Chromosome-length genome assemblies of six legume species provide insights into genome organization, evolution, and agronomic traits for crop improvement.

Journal of advanced research
Avec: Vanika Garg , Olga Dudchenko , Jinpeng Wang , Aamir W Khan , Saurabh Gupta , Parwinder Kaur , Kai Han , Rachit K Saxena , Sandip M Kale , Melanie Pham , Jigao Yu , Annapurna Chitikineni , Zhikang Zhang , Guangyi Fan , Christopher Lui , Vinodkumar Valluri , Fanbo Meng , Aditi Bhandari , Xiaochuan Liu , Tao Yang , Hua Chen , Babu Valliyodan , Manish Roorkiwal , Chengcheng Shi , Hong Bin Yang , Neva C Durand , Manish K Pandey , Guowei Li , Rutwik Barmukh , Xingjun Wang , Xiaoping Chen , Hon-Ming Lam , Huifang Jiang , Xuxiao Zong , Xuanqiang Liang , Xin Liu , Boshou Liao , Baozhu Guo , Scott Jackson , Henry T Nguyen , Weijian Zhuang , Wan Shubo , Xiyin Wang , Erez Lieberman Aiden , Jeffrey L Bennetzen , Rajeev K Varshney

Convergent and complementary selection shaped gains and losses of eusociality in sweat bees.

Nature ecology & evolution
Avec: Beryl M Jones , Benjamin E R Rubin , Olga Dudchenko , Callum J Kingwell , Ian M Traniello , Z Yan Wang , Karen M Kapheim , Eli S Wyman , Per A Adastra , Weijie Liu , Lance R Parsons , S RaElle Jackson , Katharine Goodwin , Shawn M Davidson , Matthew J McBride , Andrew E Webb , Kennedy S Omufwoko , Nikki Van Dorp , Mauricio Fernández Otárola , Melanie Pham , Arina D Omer , David Weisz , Joshua Schraiber , Fernando Villanea , William T Wcislo , Robert J Paxton , Brendan G Hunt , Erez Lieberman Aiden , Sarah D Kocher

Chromosome-length genome assembly of Teladorsagia circumcincta - a globally important helminth parasite in livestock.

BMC genomics
Avec: Shamshad Ul Hassan , Eng Guan Chua , Erwin A Paz , Chin Yen Tay , Johan C Greeff , Dieter G Palmer , Olga Dudchenko , Erez Lieberman Aiden , Graeme B Martin , Parwinder Kaur

The ENCODE Uniform Analysis Pipelines.

bioRxiv : the preprint server for biology
Avec: Benjamin C Hitz , Lee Jin-Wook , Otto Jolanki , Meenakshi S Kagda , Keenan Graham , Paul Sud , Idan Gabdank , J Seth Strattan , Cricket A Sloan , Timothy Dreszer , Laurence D Rowe , Nikhil R Podduturi , Venkat S Malladi , Esther T Chan , Jean M Davidson , Marcus Ho , Stuart Miyasato , Matt Simison , Forrest Tanaka , Yunhai Luo , Ian Whaling , Eurie L Hong , Brian T Lee , Richard Sandstrom , Eric Rynes , Jemma Nelson , Andrew Nishida , Alyssa Ingersoll , Michael Buckley , Mark Frerker , Daniel S Kim , Nathan Boley , Diane Trout , Alex Dobin , Sorena Rahmanian , Dana Wyman , Gabriela Balderrama-Gutierrez , Fairlie Reese , Neva C Durand , Olga Dudchenko , David Weisz , Suhas S P Rao , Alyssa Blackburn , Dimos Gkountaroulis , Mahdi Sadr , Moshe Olshansky , Yossi Eliaz , Dat Nguyen , Ivan Bochkov , Muhammad Saad Shamim , Ragini Mahajan , Erez Aiden , Tom Gingeras , Simon Heath , Martin Hirst , W James Kent , Anshul Kundaje , Ali Mortazavi , Barbara Wold , J Michael Cherry

Respiratory epithelial cell types, states and fates in the era of single-cell RNA-sequencing.

The Biochemical journal
Avec: Oleksandr Dudchenko , Jose Ordovas-Montanes , Colin D Bingle

Emx2 underlies the development and evolution of marsupial gliding membranes.

Nature
Avec: Jorge A Moreno , Olga Dudchenko , Charles Y Feigin , Sarah A Mereby , Zhuoxin Chen , Raul Ramos , Axel A Almet , Harsha Sen , Benjamin J Brack , Matthew R Johnson , Sha Li , Wei Wang , Jenna M Gaska , Alexander Ploss , David Weisz , Arina D Omer , Weijie Yao , Zane Colaric , Parwinder Kaur , Judy St Leger , Qing Nie , Alexandria Mena , Joseph P Flanagan , Greta Keller , Thomas Sanger , Bruce Ostrow , Maksim V Plikus , Evgeny Z Kvon , Erez Lieberman Aiden , Ricardo Mallarino

Cicer super-pangenome provides insights into species evolution and agronomic trait loci for crop improvement in chickpea.

Nature genetics
Avec: Aamir W Khan , Vanika Garg , Shuai Sun , Saurabh Gupta , Olga Dudchenko , Manish Roorkiwal , Annapurna Chitikineni , Philipp E Bayer , Chengcheng Shi , Hari D Upadhyaya , Abhishek Bohra , Chellapilla Bharadwaj , Reyazul Rouf Mir , Kobi Baruch , Bicheng Yang , Clarice J Coyne , Kailash C Bansal , Henry T Nguyen , Gil Ronen , Erez Lieberman Aiden , Erik Veneklaas , Kadambot H M Siddique , Xin Liu , David Edwards , Rajeev K Varshney

Improved high quality sand fly assemblies enabled by ultra low input long read sequencing.

Scientific data
Avec: Michelle Huang , Sarah Kingan , Douglas Shoue , Oanh Nguyen , Lutz Froenicke , Brendan Galvin , Christine Lambert , Ruqayya Khan , Chirag Maheshwari , David Weisz , Gareth Maslen , Helen Davison , Erez Lieberman Aiden , Jonas Korlach , Olga Dudchenko , Mary Ann McDowell , Stephen Richards

High-quality reference genome for Clonorchis sinensis.

Genomics
Avec: Neil D Young , Andreas J Stroehlein , Liina Kinkar , Tao Wang , Woon-Mok Sohn , Bill C H Chang , Parwinder Kaur , David Weisz , Olga Dudchenko , Erez Lieberman Aiden , Pasi K Korhonen , Robin B Gasser

Canfam_GSD: De novo chromosome-length genome assembly of the German Shepherd Dog (Canis lupus familiaris) using a combination of long reads, optical mapping, and Hi-C.

GigaScience
Avec: Matt A Field , Benjamin D Rosen , Olga Dudchenko , Eva K F Chan , Andre E Minoche , Richard J Edwards , Kirston Barton , Ruth J Lyons , Daniel Enosi Tuipulotu , Vanessa M Hayes , Arina D Omer , Zane Colaric , Jens Keilwagen , Ksenia Skvortsova , Ozren Bogdanovic , Martin A Smith , Erez Lieberman Aiden , Timothy P L Smith , Robert A Zammit , J William O Ballard

The genome sequence of the Eurasian red squirrel,

Wellcome open research
Avec: Daniel Mead , Kathryn Fingland , Rachel Cripps , Roberto Portela Miguez , Michelle Smith , Craig Corton , Karen Oliver , Jason Skelton , Emma Betteridge , Jale Dolucan , Olga Dudchenko , Arina D Omer , David Weisz , Erez Lieberman Aiden , Olivier Fedrigo , Jacquelyn Mountcastle , Erich Jarvis , Shane A McCarthy , Ying Sims , James Torrance , Alan Tracey , Kerstin Howe , Richard Challis , Richard Durbin , Mark Blaxter

The Easter Egg Weevil (Pachyrhynchus) genome reveals syntenic patterns in Coleoptera across 200 million years of evolution.

PLoS genetics
Avec: Matthew H Van Dam , Analyn Anzano Cabras , James B Henderson , Andrew J Rominger , Cynthia Pérez Estrada , Arina D Omer , Olga Dudchenko , Erez Lieberman Aiden , Athena W Lam

A chromosome-level genome sequence assembly of the red raspberry (Rubus idaeus L.).

PloS one
Avec: Jahn Davik , Dag Røen , Erik Lysøe , Matteo Buti , Simeon Rossman , Muath Alsheikh , Erez Lieberman Aiden , Olga Dudchenko , Daniel James Sargent

Response to Bakker et al.

Current biology : CB
Avec: Jacqueline A Robinson , Rauri C K Bowie , Olga Dudchenko , Erez Lieberman Aiden , Sher L Hendrickson , Cynthia C Steiner , Oliver A Ryder , David P Mindell , Jeffrey D Wall

A pan-genome and chromosome-length reference genome of narrow-leafed lupin (Lupinus angustifolius) reveals genomic diversity and insights into key industry and biological traits.

The Plant journal : for cell and molecular biology
Avec: Gagan Garg , Lars G Kamphuis , Philipp E Bayer , Parwinder Kaur , Olga Dudchenko , Candy M Taylor , Karen M Frick , Rhonda C Foley , Ling-Ling Gao , Erez Lieberman Aiden , David Edwards , Karam B Singh

An unusually large genome from an unusually large stonefly: a chromosome-length genome assembly for the giant salmonfly, Pteronarcys californica (Plecoptera: Pteronarcyidae).

The Journal of heredity
Avec: Anna Eichert , John Sproul , Ethan R Tolman , Jackson Birrell , Jared Meek , Jacqueline Heckenhauer , C Riley Nelson , Olga Dudchenko , Jiyun Jeong , David Weisz , Erez Lieberman Aiden , Scott Hotaling , Jessica L Ware , Paul B Frandsen

A Chromosome-Length Assembly of the Hawaiian Monk Seal (

Genes
Avec: David W Mohr , Stephen J Gaughran , Justin Paschall , Ahmed Naguib , Andy Wing Chun Pang , Olga Dudchenko , Erez Lieberman Aiden , Deanna M Church , Alan F Scott

Three-dimensional genome architecture persists in a 52,000-year-old woolly mammoth skin sample.

Cell
Avec: Marcela Sandoval-Velasco , Olga Dudchenko , Juan Antonio Rodríguez , Cynthia Pérez Estrada , Marianne Dehasque , Claudia Fontsere , Sarah S T Mak , Ruqayya Khan , Vinícius G Contessoto , Antonio B Oliveira Junior , Achyuth Kalluchi , Bernardo J Zubillaga Herrera , Jiyun Jeong , Renata P Roy , Ishawnia Christopher , David Weisz , Arina D Omer , Sanjit S Batra , Muhammad S Shamim , Neva C Durand , Brendan O'Connell , Alfred L Roca , Maksim V Plikus , Mariya A Kusliy , Svetlana A Romanenko , Natalya A Lemskaya , Natalya A Serdyukova , Svetlana A Modina , Polina L Perelman , Elena A Kizilova , Sergei I Baiborodin , Nikolai B Rubtsov , Gur Machol , Krisha Rath , Ragini Mahajan , Parwinder Kaur , Andreas Gnirke , Isabel Garcia-Treviño , Rob Coke , Joseph P Flanagan , Kelcie Pletch , Aurora Ruiz-Herrera , Valerii Plotnikov , Innokentiy S Pavlov , Naryya I Pavlova , Albert V Protopopov , Michele Di Pierro , Alexander S Graphodatsky , Eric S Lander , M Jordan Rowley , Peter G Wolynes , José N Onuchic , Love Dalén , Marc A Marti-Renom , M Thomas P Gilbert , Erez Lieberman Aiden

A chromosome-length genome assembly and annotation of blackberry (Rubus argutus, cv. "Hillquist").

G3 (Bethesda, Md.)
Avec: Tomáš Brůna , Rishi Aryal , Olga Dudchenko , Daniel James Sargent , Daniel Mead , Matteo Buti , Andrea Cavallini , Timo Hytönen , Javier Andrés , Melanie Pham , David Weisz , Flavia Mascagni , Gabriele Usai , Lucia Natali , Nahla Bassil , Gina E Fernandez , Alexandre Lomsadze , Mitchell Armour , Bode Olukolu , Thomas Poorten , Caitlin Britton , Jahn Davik , Hamid Ashrafi , Erez Lieberman Aiden , Mark Borodovsky , Margaret Worthington

Interphase chromosomes of the Aedes aegypti mosquito are liquid crystalline and can sense mechanical cues.

Nature communications
Avec: Vinícius G Contessoto , Olga Dudchenko , Erez Lieberman Aiden , Peter G Wolynes , José N Onuchic , Michele Di Pierro

Whole genome analysis of clouded leopard species reveals an ancient divergence and distinct demographic histories.

iScience
Avec: Madeline G Bursell , Rebecca B Dikow , Henrique V Figueiró , Olga Dudchenko , Joseph P Flanagan , Erez Lieberman Aiden , Benoit Goossens , Senthilvel K S S Nathan , Warren E Johnson , Klaus-Peter Koepfli , Paul B Frandsen

Chromosome-length genome assemblies and cytogenomic analyses of pangolins reveal remarkable chromosome counts and plasticity.

Chromosome research : an international journal on the molecular, supramolecular and evolutionary aspects of chromosome biology
Avec: Marlys L Houck , Klaus-Peter Koepfli , Taylor Hains , Ruqayya Khan , Suellen J Charter , Julie A Fronczek , Ann C Misuraca , Sergei Kliver , Polina L Perelman , Violetta Beklemisheva , Alexander Graphodatsky , Shu-Jin Luo , Stephen J O'Brien , Norman T-L Lim , Jason S C Chin , Vanessa Guerra , Gaik Tamazian , Arina Omer , David Weisz , Kenneth Kaemmerer , Ginger Sturgeon , Joseph Gaspard , Alicia Hahn , Mark McDonough , Isabel Garcia-Treviño , Jordan Gentry , Rob L Coke , Jan E Janecka , Ryan J Harrigan , Jen Tinsman , Thomas B Smith , Erez Lieberman Aiden , Olga Dudchenko

The Australasian dingo archetype: de novo chromosome-length genome assembly, DNA methylome, and cranial morphology.

GigaScience
Avec: J William O Ballard , Matt A Field , Richard J Edwards , Laura A B Wilson , Loukas G Koungoulos , Benjamin D Rosen , Barry Chernoff , Olga Dudchenko , Arina Omer , Jens Keilwagen , Ksenia Skvortsova , Ozren Bogdanovic , Eva Chan , Robert Zammit , Vanessa Hayes , Erez Lieberman Aiden

Chromatin alternates between A and B compartments at kilobase scale for subgenic organization.

Nature communications
Avec: Hannah L Harris , Huiya Gu , Moshe Olshansky , Ailun Wang , Irene Farabella , Yossi Eliaz , Achyuth Kalluchi , Akshay Krishna , Mozes Jacobs , Gesine Cauer , Melanie Pham , Suhas S P Rao , Olga Dudchenko , Arina Omer , Kiana Mohajeri , Sungjae Kim , Michael H Nichols , Eric S Davis , Dimos Gkountaroulis , Devika Udupa , Aviva Presser Aiden , Victor G Corces , Douglas H Phanstiel , William Stafford Noble , Guy Nir , Michele Di Pierro , Jeong-Sun Seo , Michael E Talkowski , Erez Lieberman Aiden , M Jordan Rowley

Réseau de co-auteurs

Olga Dudchenko 47 collaborations
Erez Lieberman Aiden 39 collaborations
David Weisz 22 collaborations
Parwinder Kaur 13 collaborations
Arina D Omer 12 collaborations
Ruqayya Khan 12 collaborations
Melanie Pham 7 collaborations
Arina Omer 7 collaborations
Zane Colaric 6 collaborations
Erez L Aiden 5 collaborations
Neva C Durand 5 collaborations
Suhas S P Rao 5 collaborations
J William O Ballard 5 collaborations
Matt A Field 5 collaborations
Richard J Edwards 5 collaborations
Benjamin D Rosen 5 collaborations
Jens Keilwagen 5 collaborations
Ksenia Skvortsova 5 collaborations
Ozren Bogdanovic 5 collaborations
Kerstin Howe 4 collaborations
Paul B Frandsen 4 collaborations
Ragini Mahajan 4 collaborations
Klaus-Peter Koepfli 4 collaborations
Michele Di Pierro 4 collaborations
Oliver A Ryder 4 collaborations
Emma Betteridge 3 collaborations
Craig Corton 3 collaborations
Karen Oliver 3 collaborations
Ying Sims 3 collaborations
Jason Skelton 3 collaborations
Michelle Smith 3 collaborations
James Torrance 3 collaborations
Erez Aiden 3 collaborations
Alan Tracey 3 collaborations
Alyssa Blackburn 3 collaborations
Dimos Gkountaroulis 3 collaborations
Moshe Olshansky 3 collaborations
Yossi Eliaz 3 collaborations
Christopher Lui 3 collaborations
Barry Chernoff 3 collaborations
Annapurna Chitikineni 3 collaborations
Rajeev K Varshney 3 collaborations
Vinícius G Contessoto 3 collaborations
Neil D Young 3 collaborations
José N Onuchic 3 collaborations
Robert A Zammit 3 collaborations
Marlys L Houck 3 collaborations
Polina L Perelman 3 collaborations
Cynthia C Steiner 3 collaborations
Joseph P Flanagan 3 collaborations
Shane A McCarthy 2 collaborations
Jale Dolucan 2 collaborations
Dan Mead 2 collaborations
Olivier Fedrigo 2 collaborations
Jacquelyn Mountcastle 2 collaborations
Benjamin C Hitz 2 collaborations
Otto Jolanki 2 collaborations
Meenakshi S Kagda 2 collaborations
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Paul Sud 2 collaborations
Idan Gabdank 2 collaborations
J Seth Strattan 2 collaborations
Cricket A Sloan 2 collaborations
Timothy Dreszer 2 collaborations
Laurence D Rowe 2 collaborations
Nikhil R Podduturi 2 collaborations
Venkat S Malladi 2 collaborations
Esther T Chan 2 collaborations
Jean M Davidson 2 collaborations
Marcus Ho 2 collaborations
Stuart Miyasato 2 collaborations
Matt Simison 2 collaborations
Forrest Tanaka 2 collaborations
Yunhai Luo 2 collaborations
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Eurie L Hong 2 collaborations
Brian T Lee 2 collaborations
Richard Sandstrom 2 collaborations
Eric Rynes 2 collaborations
Jemma Nelson 2 collaborations
Andrew Nishida 2 collaborations
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Michael Buckley 2 collaborations
Mark Frerker 2 collaborations
Daniel S Kim 2 collaborations
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Alex Dobin 2 collaborations
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Dana Wyman 2 collaborations
Gabriela Balderrama-Gutierrez 2 collaborations
Fairlie Reese 2 collaborations
Mahdi Sadr 2 collaborations
Dat Nguyen 2 collaborations
Ivan Bochkov 2 collaborations
Muhammad Saad Shamim 2 collaborations
Tom Gingeras 2 collaborations
Simon Heath 2 collaborations
Martin Hirst 2 collaborations
W James Kent 2 collaborations
Anshul Kundaje 2 collaborations
Ali Mortazavi 2 collaborations
Barbara Wold 2 collaborations
J Michael Cherry 2 collaborations
Anna Tigano 2 collaborations
Asha S Multani 2 collaborations
Sen Pathak 2 collaborations
Richard R Behringer 2 collaborations
Matthew D MacManes 2 collaborations
Kiana Mohajeri 2 collaborations
Michael E Talkowski 2 collaborations
Laura A B Wilson 2 collaborations
Loukas G Koungoulos 2 collaborations
Eva Chan 2 collaborations
Robert Zammit 2 collaborations
Vanessa Hayes 2 collaborations
Ethan R Tolman 2 collaborations
Jonas Bush 2 collaborations
Jessica L Ware 2 collaborations
Chirag Maheshwari 2 collaborations
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Baozhu Guo 2 collaborations
Lutz Froenicke 2 collaborations
Alan F Scott 2 collaborations
David W Mohr 2 collaborations
Gaik Tamazian 2 collaborations
Namita Mitra 2 collaborations
Weijie Yao 2 collaborations
Judy St Leger 2 collaborations
Alexandria Mena 2 collaborations
Wesley C Warren 2 collaborations
Sergei Kliver 2 collaborations
Alexander Graphodatsky 2 collaborations
Warren E Johnson 2 collaborations
Per A Adastra 2 collaborations
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Aviva Presser Aiden 2 collaborations
Roberto Portela Miguez 2 collaborations
Richard Challis 2 collaborations
Richard Durbin 2 collaborations
Mark Blaxter 2 collaborations
Jacqueline A Robinson 2 collaborations
Rauri C K Bowie 2 collaborations
Sher L Hendrickson 2 collaborations
David P Mindell 2 collaborations
Jeffrey D Wall 2 collaborations
Andreas J Stroehlein 2 collaborations
Pasi K Korhonen 2 collaborations
Bicheng Yang 2 collaborations
Bill C H Chang 2 collaborations
Robin B Gasser 2 collaborations
Eva K F Chan 2 collaborations
Andre E Minoche 2 collaborations
Timothy P L Smith 2 collaborations
M Thomas P Gilbert 2 collaborations
Vanika Garg 2 collaborations
Aamir W Khan 2 collaborations
Saurabh Gupta 2 collaborations
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Chengcheng Shi 2 collaborations
Xin Liu 2 collaborations
Henry T Nguyen 2 collaborations
Maksim V Plikus 2 collaborations
Philipp E Bayer 2 collaborations
David Edwards 2 collaborations
Daniel Mead 2 collaborations
Cynthia Pérez Estrada 2 collaborations
Jahn Davik 2 collaborations
Matteo Buti 2 collaborations
Daniel James Sargent 2 collaborations
Jiyun Jeong 2 collaborations
Achyuth Kalluchi 2 collaborations
Isabel Garcia-Treviño 2 collaborations
M Jordan Rowley 2 collaborations
Peter G Wolynes 2 collaborations
Nathan J Kenny 1 collaboration
Katherine James 1 collaboration
Sarah Pelan 1 collaboration
Yan Ryan 1 collaboration
Anil Wipat 1 collaboration
Suzanne T Williams 1 collaboration
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Yuanyuan Cheng 1 collaboration
Keng Yih Chew 1 collaboration
Arjun Challagulla 1 collaboration
Robert Kraus 1 collaboration
Ralf C Mueller 1 collaboration
Marcus Z W Tong 1 collaboration
Katina D Hulme 1 collaboration
Helle Bielefeldt-Ohmann 1 collaboration
Lauren E Steele 1 collaboration
Melanie Wu 1 collaboration
Julian Sng 1 collaboration
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Gough G Au 1 collaboration
Suzanne Lowther 1 collaboration
Julie Blommaert 1 collaboration
Alexander Suh 1 collaboration
Alexander J McCauley 1 collaboration
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William Chow 1 collaboration
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Denye N Ogeh 1 collaboration
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Jacqueline Smith 1 collaboration
Richard I Kuo 1 collaboration
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Takashi Kimura 1 collaboration
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Mathew McDougall 1 collaboration
Hamish G Spencer 1 collaboration
Michael Pyne 1 collaboration
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Kirsty R Short 1 collaboration
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Adam M Taylor 1 collaboration
Tabitha A Hughes 1 collaboration
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Randy T Larsen 1 collaboration
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Jin-Wook Lee 1 collaboration
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Philip M Boone 1 collaboration
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K Scott Weber 1 collaboration
Daniel Powell 1 collaboration
Nicola Jackson 1 collaboration
Arthur Georges 1 collaboration
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David J Bertioli 1 collaboration
Jerry Jenkins 1 collaboration
Josh Clevenger 1 collaboration
Dongying Gao 1 collaboration
Guillermo Seijo 1 collaboration
Soraya C M Leal-Bertioli 1 collaboration
Longhui Ren 1 collaboration
Andrew D Farmer 1 collaboration
Sergio S Samoluk 1 collaboration
Brian Abernathy 1 collaboration
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Carolina Ballén-Taborda 1 collaboration
Connor Cameron 1 collaboration
Jacqueline Campbell 1 collaboration
Carolina Chavarro 1 collaboration
Ye Chu 1 collaboration
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Marie Mirouze 1 collaboration
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Xinyou Zhang 1 collaboration
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Ziqi Sun 1 collaboration
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Brian E Scheffler 1 collaboration
Jane Grimwood 1 collaboration
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Steven B Cannon 1 collaboration
Scott A Jackson 1 collaboration
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Rob Ogden 1 collaboration
Claire Hoencamp 1 collaboration
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Sumitabha Brahmachari 1 collaboration
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Ángela Sedeño Cacciatore 1 collaboration
Roy G H P van Heesbeen 1 collaboration
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Zhenzhen Yang 1 collaboration
Leonid L Moroz 1 collaboration
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Karen Holcroft 1 collaboration
Maria Cristina Gambetta 1 collaboration
Fabian Lim 1 collaboration
Emma Farley 1 collaboration
Nils Stein 1 collaboration
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Daniel Chauss 1 collaboration
Ayse Sena Mutlu 1 collaboration
Meng C Wang 1 collaboration
Evin Hildebrandt 1 collaboration
Hans H Cheng 1 collaboration
Christopher J Knight 1 collaboration
Theresa L U Burnham 1 collaboration
Kevin A Hovel 1 collaboration
Andrew J Beel 1 collaboration
Pierre-Jean Mattei 1 collaboration
Roger D Kornberg 1 collaboration
Gregory Cary 1 collaboration
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Veronica Hinman 1 collaboration
Kerstin Lindblad-Toh 1 collaboration
Federica Di Palma 1 collaboration
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Liesl Nel-Themaat 1 collaboration
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Bas van Steensel 1 collaboration
Elzo de Wit 1 collaboration
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James M Ferguson 1 collaboration
Gary S Johnson 1 collaboration
Edward S Rice 1 collaboration
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Edward Wilcox 1 collaboration
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Azamat Totikov 1 collaboration
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Saki Chan 1 collaboration
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Budhan S Pukazhenthi 1 collaboration
Paul E Marinari 1 collaboration
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L Michel 1 collaboration
K Sharma 1 collaboration
R Lagadec 1 collaboration
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O G Osborne 1 collaboration
P Mulhair 1 collaboration
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D Mead 1 collaboration
M Smith 1 collaboration
C Corton 1 collaboration
K Oliver 1 collaboration
J Skelton 1 collaboration
E Betteridge 1 collaboration
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A D Omer 1 collaboration
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E L Aiden 1 collaboration
S McCarthy 1 collaboration
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A Tracey 1 collaboration
K Howe 1 collaboration
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S Sanchez 1 collaboration
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K Martin 1 collaboration
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Frank Hailer 1 collaboration
Elisabeth Chadwick 1 collaboration
Jale Doulcan Doulcan 1 collaboration
Shane McCarthy 1 collaboration
V Vern Lee 1 collaboration
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Huanming Yang 1 collaboration
Aidan M Emery 1 collaboration
Bonnie L Webster 1 collaboration
Paul J Brindley 1 collaboration
David Rollinson 1 collaboration
Diana A Robledo-Ruiz 1 collaboration
Han Ming Gan 1 collaboration
Ekaterina Osipova 1 collaboration
Michael Hiller 1 collaboration
Hernán E Morales 1 collaboration
Michael J L Magrath 1 collaboration
Rohan H Clarke 1 collaboration
Paul Sunnucks 1 collaboration
Alexandra Pavlova 1 collaboration
Sonu Yadav 1 collaboration
Meera Esvaran 1 collaboration
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Jacob Agerbo Rasmussen 1 collaboration
Richard G Melvin 1 collaboration
Torsten Thomas 1 collaboration
Aryn P Wilder 1 collaboration
Caitlin Curry 1 collaboration
Marisa Korody 1 collaboration
Sheela P Turbek 1 collaboration
Mark Daly 1 collaboration
Ann Misuraca 1 collaboration
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Debra M Shier 1 collaboration
Jinpeng Wang 1 collaboration
Kai Han 1 collaboration
Rachit K Saxena 1 collaboration
Sandip M Kale 1 collaboration
Jigao Yu 1 collaboration
Zhikang Zhang 1 collaboration
Guangyi Fan 1 collaboration
Vinodkumar Valluri 1 collaboration
Fanbo Meng 1 collaboration
Aditi Bhandari 1 collaboration
Xiaochuan Liu 1 collaboration
Tao Yang 1 collaboration
Hua Chen 1 collaboration
Babu Valliyodan 1 collaboration
Hong Bin Yang 1 collaboration
Guowei Li 1 collaboration
Rutwik Barmukh 1 collaboration
Xingjun Wang 1 collaboration
Xiaoping Chen 1 collaboration
Hon-Ming Lam 1 collaboration
Huifang Jiang 1 collaboration
Xuxiao Zong 1 collaboration
Xuanqiang Liang 1 collaboration
Boshou Liao 1 collaboration
Scott Jackson 1 collaboration
Weijian Zhuang 1 collaboration
Wan Shubo 1 collaboration
Xiyin Wang 1 collaboration
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Beryl M Jones 1 collaboration
Benjamin E R Rubin 1 collaboration
Callum J Kingwell 1 collaboration
Ian M Traniello 1 collaboration
Z Yan Wang 1 collaboration
Karen M Kapheim 1 collaboration
Eli S Wyman 1 collaboration
Weijie Liu 1 collaboration
Lance R Parsons 1 collaboration
S RaElle Jackson 1 collaboration
Katharine Goodwin 1 collaboration
Shawn M Davidson 1 collaboration
Matthew J McBride 1 collaboration
Andrew E Webb 1 collaboration
Kennedy S Omufwoko 1 collaboration
Nikki Van Dorp 1 collaboration
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Fernando Villanea 1 collaboration
William T Wcislo 1 collaboration
Robert J Paxton 1 collaboration
Brendan G Hunt 1 collaboration
Sarah D Kocher 1 collaboration
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Eng Guan Chua 1 collaboration
Erwin A Paz 1 collaboration
Chin Yen Tay 1 collaboration
Johan C Greeff 1 collaboration
Dieter G Palmer 1 collaboration
Graeme B Martin 1 collaboration
Lee Jin-Wook 1 collaboration
Oleksandr Dudchenko 1 collaboration
Jose Ordovas-Montanes 1 collaboration
Colin D Bingle 1 collaboration
Jorge A Moreno 1 collaboration
Charles Y Feigin 1 collaboration
Sarah A Mereby 1 collaboration
Zhuoxin Chen 1 collaboration
Raul Ramos 1 collaboration
Axel A Almet 1 collaboration
Harsha Sen 1 collaboration
Benjamin J Brack 1 collaboration
Matthew R Johnson 1 collaboration
Sha Li 1 collaboration
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Jenna M Gaska 1 collaboration
Alexander Ploss 1 collaboration
Qing Nie 1 collaboration
Greta Keller 1 collaboration
Thomas Sanger 1 collaboration
Bruce Ostrow 1 collaboration
Evgeny Z Kvon 1 collaboration
Ricardo Mallarino 1 collaboration
Shuai Sun 1 collaboration
Hari D Upadhyaya 1 collaboration
Abhishek Bohra 1 collaboration
Chellapilla Bharadwaj 1 collaboration
Reyazul Rouf Mir 1 collaboration
Kobi Baruch 1 collaboration
Clarice J Coyne 1 collaboration
Kailash C Bansal 1 collaboration
Gil Ronen 1 collaboration
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Kadambot H M Siddique 1 collaboration
Michelle Huang 1 collaboration
Sarah Kingan 1 collaboration
Douglas Shoue 1 collaboration
Oanh Nguyen 1 collaboration
Brendan Galvin 1 collaboration
Christine Lambert 1 collaboration
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Helen Davison 1 collaboration
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Mary Ann McDowell 1 collaboration
Stephen Richards 1 collaboration
Liina Kinkar 1 collaboration
Tao Wang 1 collaboration
Woon-Mok Sohn 1 collaboration
Kirston Barton 1 collaboration
Ruth J Lyons 1 collaboration
Daniel Enosi Tuipulotu 1 collaboration
Vanessa M Hayes 1 collaboration
Martin A Smith 1 collaboration
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Rachel Cripps 1 collaboration
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Matthew H Van Dam 1 collaboration
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Andrew J Rominger 1 collaboration
Athena W Lam 1 collaboration
Dag Røen 1 collaboration
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Muath Alsheikh 1 collaboration
Gagan Garg 1 collaboration
Lars G Kamphuis 1 collaboration
Candy M Taylor 1 collaboration
Karen M Frick 1 collaboration
Rhonda C Foley 1 collaboration
Ling-Ling Gao 1 collaboration
Karam B Singh 1 collaboration
Anna Eichert 1 collaboration
John Sproul 1 collaboration
Jackson Birrell 1 collaboration
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C Riley Nelson 1 collaboration
Scott Hotaling 1 collaboration
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Ahmed Naguib 1 collaboration
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Marianne Dehasque 1 collaboration
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Sarah S T Mak 1 collaboration
Antonio B Oliveira Junior 1 collaboration
Bernardo J Zubillaga Herrera 1 collaboration
Renata P Roy 1 collaboration
Ishawnia Christopher 1 collaboration
Sanjit S Batra 1 collaboration
Muhammad S Shamim 1 collaboration
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Alfred L Roca 1 collaboration
Mariya A Kusliy 1 collaboration
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Rob Coke 1 collaboration
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Alexander S Graphodatsky 1 collaboration
Eric S Lander 1 collaboration
Love Dalén 1 collaboration
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Taylor Hains 1 collaboration
Suellen J Charter 1 collaboration
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Ann C Misuraca 1 collaboration
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Jason S C Chin 1 collaboration
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Jordan Gentry 1 collaboration
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Jen Tinsman 1 collaboration
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Michael H Nichols 1 collaboration
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