K‐mer counting and curated libraries drive efficient annotation of repeats in plant genomes

por Bruno Contreras‐Moreira, Carla V Filippi, Guy Naamati, Carlos García Girón, James E Allen, Paul Flicek
Publicado 2021

Transcriptional activity and strain-specific history of mouse pseudogenes

por Cristina Sisu, Paul Muir, Adam Frankish, Ian Fiddes, Mark Diekhans, David Thybert, Duncan T. Odom, Paul Flicek, Thomas M. Keane, Tim Hubbard, Jennifer Harrow, Mark Gerstein
Publicado 2020

Interplay of cis and trans mechanisms driving transcription factor binding and gene expression evolution

por Emily S. Wong, Bianca M. Schmitt, Anastasiya Kazachenka, David Thybert, Aisling Redmond, Frances Connor, Tim F. Rayner, Christine Feig, Anne C. Ferguson-Smith, John C. Marioni, Duncan T. Odom, Paul Flicek
Publicado 2017

Haplosaurus computes protein haplotypes for use in precision drug design

por William Spooner, William McLaren, Timothy Slidel, Donna K. Finch, Robin Butler, Jamie Campbell, Laura Eghobamien, David Rider, Christine Mione Kiefer, Matthew J. Robinson, Colin Hardman, Fiona Cunningham, Tristan Vaughan, Paul Flicek, Catherine Chaillan Huntington
Publicado 2018

Functional annotations of three domestic animal genomes provide vital resources for comparative and agricultural research

por Colin Kern, Ying Wang, Xiaoqin Xu, Zhangyuan Pan, Michelle Halstead, Ganrea Chanthavixay, Perot Saelao, Susan Waters, Ruidong Xiang, Amanda Chamberlain, Ian Korf, Mary E. Delany, Hans H. Cheng, Juan F. Medrano, Alison L. Van Eenennaam, Chris K. Tuggle, Catherine Ernst, Paul Flicek, Gerald Quon, Pablo Ross, Huaijun Zhou
Publicado 2021

Genetic perturbation of PU.1 binding and chromatin looping at neutrophil enhancers associates with autoimmune disease

por Stephen Watt, Louella Vasquez, Klaudia Walter, Alice L. Mann, Kousik Kundu, Lu Chen, Ying Sims, Simone Ecker, Frances Burden, Samantha Farrow, Ben Farr, Valentina Iotchkova, Heather Elding, Daniel Mead, Manuel Tardaguila, Hannes Ponstingl, David Richardson, Avik Datta, Paul Flicek, Laura Clarke, Kate Downes, Tomi Pastinen, Peter Fraser, Mattia Frontini, Biola-Maria Javierre, Mikhail Spivakov, Nicole Soranzo
Publicado 2021

Convergent genomic signatures of domestication in sheep and goats

por Florian J. Alberto, Frédéric Boyer, Pablo Orozco-terWengel, Ian Streeter, Bertrand Servin, Pierre de Villemereuil, Badr Benjelloun, Pablo Librado, Filippo Biscarini, Licia Colli, Mario Barbato, Wahid Zamani, Adriana Alberti, Stefan Engelen, Alessandra Stella, Stéphane Joost, Paolo Ajmone-Marsan, Riccardo Negrini, Ludovic Orlando, Hamid Reza Rezaei, Saeid Naderi, Laura Clarke, Paul Flicek, Patrick Wincker, Eric Coissac, James Kijas, Gwenola Tosser-Klopp, Abdelkader Chikhi, Michael W. Bruford, Pierre Taberlet, François Pompanon
Publicado 2018

A spatially resolved brain region- and cell type-specific isoform atlas of the postnatal mouse brain

por Anoushka Joglekar, Andrey Prjibelski, Ahmed Mahfouz, Paul Collier, Susan Lin, Anna Katharina Schlusche, Jordan Marrocco, Stephen R. Williams, Bettina Haase, Ashley Hayes, Jennifer G. Chew, Neil I. Weisenfeld, Man Ying Wong, Alexander N. Stein, Simon A. Hardwick, Toby Hunt, Qi Wang, Christoph Dieterich, Zachary Bent, Olivier Fedrigo, Steven A. Sloan, Davide Risso, Erich D. Jarvis, Paul Flicek, Wenjie Luo, Geoffrey S. Pitt, Adam Frankish, August B. Smit, M. Elizabeth Ross, Hagen U. Tilgner
Publicado 2021

Modernizing reference genome assemblies.

por Deanna M Church, Valerie A Schneider, Tina Graves, Katherine Auger, Fiona Cunningham, Nathan Bouk, Hsiu-Chuan Chen, Richa Agarwala, William M McLaren, Graham R S Ritchie, Derek Albracht, Milinn Kremitzki, Susan Rock, Holland Kotkiewicz, Colin Kremitzki, Aye Wollam, Lee Trani, Lucinda Fulton, Robert Fulton, Lucy Matthews, Siobhan Whitehead, Will Chow, James Torrance, Matthew Dunn, Glenn Harden, Glen Threadgold, Jonathan Wood, Joanna Collins, Paul Heath, Guy Griffiths, Sarah Pelan, Darren Grafham, Evan E Eichler, George Weinstock, Elaine R Mardis, Richard K Wilson, Kerstin Howe, Paul Flicek, Tim Hubbard
Publicado 2011

Increased DNA methylation variability in type 1 diabetes across three immune effector cell types

por Dirk S. Paul, Andrew E. Teschendorff, Mary A.N. Dang, Robert Lowe, Mohammed I. Hawa, Simone Ecker, Huriya Beyan, Stephanie Cunningham, Alexandra R. Fouts, Anita Ramelius, Frances Burden, Samantha Farrow, Sophia Rowlston, Karola Rehnstrom, Mattia Frontini, Kate Downes, Stephan Busche, Warren A. Cheung, Bing Ge, Marie-Michelle Simon, David Bujold, Tony Kwan, Guillaume Bourque, Avik Datta, Ernesto Lowy, Laura Clarke, Paul Flicek, Emanuele Libertini, Simon Heath, Marta Gut, Ivo G Gut, Willem H. Ouwehand, Tomi Pastinen, Nicole Soranzo, Sabine E. Hofer, Beate Karges, Thomas Meissner, Bernhard O. Boehm, Corrado Cilio, Helena Elding Larsson, Åke Lernmark, Andrea K. Steck, Vardhman K. Rakyan, Stephan Beck, R. David Leslie
Publicado 2016

A large scale hearing loss screen reveals an extensive unexplored genetic landscape for auditory dysfunction

por Michael R. Bowl, Michelle M. Simon, Neil J. Ingham, Simon Greenaway, Luis Santos, Heather Cater, Sarah Taylor, Jeremy Mason, Natalja Kurbatova, Selina Pearson, Lynette R. Bower, Dave A. Clary, Hamid Meziane, Patrick Reilly, Osamu Minowa, Lois Kelsey, The International Mouse Phenotyping Consortium, Glauco P. Tocchini-Valentini, Xiang Gao, Allan Bradley, William C. Skarnes, Mark Moore, Arthur L. Beaudet, Monica J. Justice, John Seavitt, Mary E. Dickinson, Wolfgang Wurst, Martin Hrabe de Angelis, Yann Herault, Shigeharu Wakana, Lauryl M. J. Nutter, Ann M. Flenniken, Colin McKerlie, Stephen A. Murray, Karen L. Svenson, Robert E. Braun, David B. West, K. C. Kent Lloyd, David J. Adams, Jacqui White, Natasha Karp, Paul Flicek, Damian Smedley, Terrence F. Meehan, Helen E. Parkinson, Lydia M. Teboul, Sara Wells, Karen P. Steel, Ann-Marie Mallon, Steve D. M. Brown
Publicado 2017

Platelet function is modified by common sequence variation in megakaryocyte super enhancers

por Romina Petersen, John J. Lambourne, Biola M. Javierre, Luigi Grassi, Roman Kreuzhuber, Dace Ruklisa, Isabel M. Rosa, Ana R. Tomé, Heather Elding, Johanna P. van Geffen, Tao Jiang, Samantha Farrow, Jonathan Cairns, Abeer M. Al-Subaie, Sofie Ashford, Antony Attwood, Joana Batista, Heleen Bouman, Frances Burden, Fizzah A. Choudry, Laura Clarke, Paul Flicek, Stephen F. Garner, Matthias Haimel, Carly Kempster, Vasileios Ladopoulos, An-Sofie Lenaerts, Paulina M. Materek, Harriet McKinney, Stuart Meacham, Daniel Mead, Magdolna Nagy, Christopher J. Penkett, Augusto Rendon, Denis Seyres, Benjamin Sun, Salih Tuna, Marie-Elise van der Weide, Steven W. Wingett, Joost H. Martens, Oliver Stegle, Sylvia Richardson, Ludovic Vallier, David J. Roberts, Kathleen Freson, Lorenz Wernisch, Hendrik G. Stunnenberg, John Danesh, Peter Fraser, Nicole Soranzo, Adam S. Butterworth, Johan W. Heemskerk, Ernest Turro, Mikhail Spivakov, Willem H. Ouwehand, William J. Astle, Kate Downes, Myrto Kostadima, Mattia Frontini
Publicado 2017

Identification of genetic elements in metabolism by high-throughput mouse phenotyping

por Jan Rozman, Birgit Rathkolb, Manuela A. Oestereicher, Christine Schütt, Aakash Chavan Ravindranath, Stefanie Leuchtenberger, Sapna Sharma, Martin Kistler, Monja Willershäuser, Robert Brommage, Terrence F. Meehan, Jeremy Mason, Hamed Haselimashhadi, IMPC Consortium, Tertius Hough, Ann-Marie Mallon, Sara Wells, Luis Santos, Christopher J. Lelliott, Jacqueline K. White, Tania Sorg, Marie-France Champy, Lynette R. Bower, Corey L. Reynolds, Ann M. Flenniken, Stephen A. Murray, Lauryl M. J. Nutter, Karen L. Svenson, David West, Glauco P. Tocchini-Valentini, Arthur L. Beaudet, Fatima Bosch, Robert B. Braun, Michael S. Dobbie, Xiang Gao, Yann Herault, Ala Moshiri, Bret A. Moore, K. C. Kent Lloyd, Colin McKerlie, Hiroshi Masuya, Nobuhiko Tanaka, Paul Flicek, Helen E. Parkinson, Radislav Sedlacek, Je Kyung Seong, Chi-Kuang Leo Wang, Mark Moore, Steve D. Brown, Matthias H. Tschöp, Wolfgang Wurst, Martin Klingenspor, Eckhard Wolf, Johannes Beckers, Fausto Machicao, Andreas Peter, Harald Staiger, Hans-Ulrich Häring, Harald Grallert, Monica Campillos, Holger Maier, Helmut Fuchs, Valerie Gailus-Durner, Thomas Werner, Martin Hrabe de Angelis
Publicado 2018

Author Correction: Identification of genes required for eye development by high-throughput screening of mouse knockouts

por Bret A. Moore, Brian C. Leonard, Lionel Sebbag, Sydney G. Edwards, Ann Cooper, Denise M. Imai, Ewan Straiton, Luis Santos, Christopher Reilly, Stephen M. Griffey, Lynette Bower, David Clary, Jeremy Mason, Michel J. Roux, Hamid Meziane, Yann Herault, International Mouse Phenotyping Consortium, Colin McKerlie, Ann M. Flenniken, Lauryl M. J. Nutter, Zorana Berberovic, Celeste Owen, Susan Newbigging, Hibret Adissu, Mohammed Eskandarian, Chih-Wei Hsu, Sowmya Kalaga, Uchechukwu Udensi, Chinwe Asomugha, Ritu Bohat, Juan J. Gallegos, John R. Seavitt, Jason D. Heaney, Arthur L. Beaudet, Mary E. Dickinson, Monica J. Justice, Vivek Philip, Vivek Kumar, Karen L. Svenson, Robert E. Braun, Sara Wells, Heather Cater, Michelle Stewart, Sharon Clementson-Mobbs, Russell Joynson, Xiang Gao, Tomohiro Suzuki, Shigeharu Wakana, Damian Smedley, J. K. Seong, Glauco Tocchini-Valentini, Mark Moore, Colin Fletcher, Natasha Karp, Ramiro Ramirez-Solis, Jacqueline K. White, Martin Hrabe de Angelis, Wolfgang Wurst, Sara M. Thomasy, Paul Flicek, Helen Parkinson, Steve D. M. Brown, Terrence F. Meehan, Patsy M. Nishina, Stephen A. Murray, Mark P. Krebs, Ann-Marie Mallon, K. C. Kent Lloyd, Christopher J. Murphy, Ala Moshiri
Publicado 2019

Multi-platform next-generation sequencing of the domestic turkey (Meleagris gallopavo): genome assembly and analysis.

por Rami A Dalloul, Julie A Long, Aleksey V Zimin, Luqman Aslam, Kathryn Beal, Le Ann Blomberg, Pascal Bouffard, David W Burt, Oswald Crasta, Richard P M A Crooijmans, Kristal Cooper, Roger A Coulombe, Supriyo De, Mary E Delany, Jerry B Dodgson, Jennifer J Dong, Clive Evans, Karin M Frederickson, Paul Flicek, Liliana Florea, Otto Folkerts, Martien A M Groenen, Tim T Harkins, Javier Herrero, Steve Hoffmann, Hendrik-Jan Megens, Andrew Jiang, Pieter de Jong, Pete Kaiser, Heebal Kim, Kyu-Won Kim, Sungwon Kim, David Langenberger, Mi-Kyung Lee, Taeheon Lee, Shrinivasrao Mane, Guillaume Marcais, Manja Marz, Audrey P McElroy, Thero Modise, Mikhail Nefedov, Cédric Notredame, Ian R Paton, William S Payne, Geo Pertea, Dennis Prickett, Daniela Puiu, Dan Qioa, Emanuele Raineri, Magali Ruffier, Steven L Salzberg, Michael C Schatz, Chantel Scheuring, Carl J Schmidt, Steven Schroeder, Stephen M J Searle, Edward J Smith, Jacqueline Smith, Tad S Sonstegard, Peter F Stadler, Hakim Tafer, Zhijian Jake Tu, Curtis P Van Tassell, Albert J Vilella, Kelly P Williams, James A Yorke, Liqing Zhang, Hong-Bin Zhang, Xiaojun Zhang, Yang Zhang, Kent M Reed
Publicado 2010

Multi-platform discovery of haplotype-resolved structural variation in human genomes

por Mark J. P. Chaisson, Ashley D. Sanders, Xuefang Zhao, Ankit Malhotra, David Porubsky, Tobias Rausch, Eugene J. Gardner, Oscar L. Rodriguez, Li Guo, Ryan L. Collins, Xian Fan, Jia Wen, Robert E. Handsaker, Susan Fairley, Zev N. Kronenberg, Xiangmeng Kong, Fereydoun Hormozdiari, Dillon Lee, Aaron M. Wenger, Alex R. Hastie, Danny Antaki, Thomas Anantharaman, Peter A. Audano, Harrison Brand, Stuart Cantsilieris, Han Cao, Eliza Cerveira, Chong Chen, Xintong Chen, Chen-Shan Chin, Zechen Chong, Nelson T. Chuang, Christine C. Lambert, Deanna M. Church, Laura Clarke, Andrew Farrell, Joey Flores, Timur Galeev, David U. Gorkin, Madhusudan Gujral, Victor Guryev, William Haynes Heaton, Jonas Korlach, Sushant Kumar, Jee Young Kwon, Ernest T. Lam, Jong Eun Lee, Joyce Lee, Wan-Ping Lee, Sau Peng Lee, Shantao Li, Patrick Marks, Karine Viaud-Martinez, Sascha Meiers, Katherine M. Munson, Fabio C. P. Navarro, Bradley J. Nelson, Conor Nodzak, Amina Noor, Sofia Kyriazopoulou-Panagiotopoulou, Andy W. C. Pang, Yunjiang Qiu, Gabriel Rosanio, Mallory Ryan, Adrian Stütz, Diana C. J. Spierings, Alistair Ward, AnneMarie E. Welch, Ming Xiao, Wei Xu, Chengsheng Zhang, Qihui Zhu, Xiangqun Zheng-Bradley, Ernesto Lowy, Sergei Yakneen, Steven McCarroll, Goo Jun, Li Ding, Chong Lek Koh, Bing Ren, Paul Flicek, Ken Chen, Mark B. Gerstein, Pui-Yan Kwok, Peter M. Lansdorp, Gabor T. Marth, Jonathan Sebat, Xinghua Shi, Ali Bashir, Kai Ye, Scott E. Devine, Michael E. Talkowski, Ryan E. Mills, Tobias Marschall, Jan O. Korbel, Evan E. Eichler, Charles Lee
Publicado 2019