Induction of an immortalized songbird cell line allows for gene characterization and knockout by CRISPR-Cas9

by Matthew T. Biegler, Olivier Fedrigo, Paul Collier, Jacquelyn Mountcastle, Bettina Haase, Hagen U. Tilgner, Erich D. Jarvis
Published 2022-03-01

A pipeline to determine RT-QPCR control genes for evolutionary studies: application to primate gene expression across multiple tissues.

by Olivier Fedrigo, Lisa R Warner, Adam D Pfefferle, Courtney C Babbitt, Peter Cruz-Gordillo, Gregory A Wray
Published 2010-01-01

Prioritizing Endangered Species in Genome Sequencing: Conservation Genomics in Action with the First Platinum-Standard Reference-Quality Genome of the Critically Endangered Europea...

by Jakub Skorupski, Florian Brandes, Christian Seebass, Wolfgang Festl, Przemysław Śmietana, Jennifer Balacco, Nivesh Jain, Tatiana Tilley, Linelle Abueg, Jonathan Wood, Ying Sims, Giulio Formenti, Olivier Fedrigo, Erich D. Jarvis
Published 2023-10-01

Extensive evolutionary changes in regulatory element activity during human origins are associated with altered gene expression and positive selection.

by Yoichiro Shibata, Nathan C Sheffield, Olivier Fedrigo, Courtney C Babbitt, Matthew Wortham, Alok K Tewari, Darin London, Lingyun Song, Bum-Kyu Lee, Vishwanath R Iyer, Stephen C J Parker, Elliott H Margulies, Gregory A Wray, Terrence S Furey, Gregory E Crawford
Published 2012-06-01

Sex-specific changes in autosomal methylation rate in ageing common terns

by Britta S. Meyer, Maria Moiron, Calvinna Caswara, William Chow, Olivier Fedrigo, Giulio Formenti, Bettina Haase, Kerstin Howe, Jacquelyn Mountcastle, Marcela Uliano-Silva, Marcela Uliano-Silva, Marcela Uliano-Silva, Jonathan Wood, Erich D. Jarvis, Erich D. Jarvis, Miriam Liedvogel, Miriam Liedvogel, Sandra Bouwhuis
Published 2023-01-01

Chromosome-level genome assembly of chub mackerel (Scomber japonicus) from the Indo-Pacific Ocean

by Young Ho Lee, Linelle Abueg, Jin-Koo Kim, Young Wook Kim, Olivier Fedrigo, Jennifer Balacco, Giulio Formenti, Kerstin Howe, Alan Tracey, Jonathan Wood, Françoise Thibaud-Nissen, Bo Hye Nam, Eun Soo No, Hye Ran Kim, Chul Lee, Erich D. Jarvis, Heebal Kim
Published 2023-12-01

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

by 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
Published 2022-09-01

A genomic basis of vocal rhythm in birds

by Matteo Sebastianelli, Sifiso M. Lukhele, Simona Secomandi, Stacey G. de Souza, Bettina Haase, Michaella Moysi, Christos Nikiforou, Alexander Hutfluss, Jacquelyn Mountcastle, Jennifer Balacco, Sarah Pelan, William Chow, Olivier Fedrigo, Colleen T. Downs, Ara Monadjem, Niels J. Dingemanse, Erich D. Jarvis, Alan Brelsford, Bridgett M. vonHoldt, Alexander N. G. Kirschel
Published 2024-04-01

Comprehensive identification of mRNA isoforms reveals the diversity of neural cell-surface molecules with roles in retinal development and disease

by Thomas A. Ray, Kelly Cochran, Chris Kozlowski, Jingjing Wang, Graham Alexander, Martha A. Cady, William J. Spencer, Philip A. Ruzycki, Brian S. Clark, Annelies Laeremans, Ming-Xiao He, Xiaoming Wang, Emily Park, Ying Hao, Alessandro Iannaccone, Gary Hu, Olivier Fedrigo, Nikolai P. Skiba, Vadim Y. Arshavsky, Jeremy N. Kay
Published 2020-07-01

Low mutation rate in epaulette sharks is consistent with a slow rate of evolution in sharks

by Ashley T. Sendell-Price, Frank J. Tulenko, Mats Pettersson, Du Kang, Margo Montandon, Sylke Winkler, Kathleen Kulb, Gavin P. Naylor, Adam Phillippy, Olivier Fedrigo, Jacquelyn Mountcastle, Jennifer R. Balacco, Amalia Dutra, Rebecca E. Dale, Bettina Haase, Erich D. Jarvis, Gene Myers, Shawn M. Burgess, Peter D. Currie, Leif Andersson, Manfred Schartl
Published 2023-10-01

The genome sequence of the brown trout, Salmo trutta Linnaeus 1758 [version 1; peer review: 2 approved]

by Tom Hansen, Per Gunnar Fjelldal, Sigbjørn Lien, Michelle Smith, Craig Corton, Karen Oliver, Jason Skelton, Emma Betteridge, Jale Doulcan, Olivier Fedrigo, Jacquelyn Mountcastle, Erich Jarvis, Shane A. McCarthy, William Chow, Kerstin Howe, James Torrance, Jonathan Wood, Ying Sims, Leanne Haggerty, Richard Challis, Jonathan Threlfall, Daniel Mead, Richard Durbin, Mark Blaxter
Published 2021-05-01

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

by 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
Published 2021-04-01

The genome sequence of the Eurasian red squirrel, Sciurus vulgaris Linnaeus 1758 [version 1; peer review: 2 approved]

by 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
Published 2020-02-01

A pangenome graph reference of 30 chicken genomes allows genotyping of large and complex structural variants

by Edward S. Rice, Antton Alberdi, James Alfieri, Giridhar Athrey, Jennifer R. Balacco, Philippe Bardou, Heath Blackmon, Mathieu Charles, Hans H. Cheng, Olivier Fedrigo, Steven R. Fiddaman, Giulio Formenti, Laurent A. F. Frantz, M. Thomas P. Gilbert, Cari J. Hearn, Erich D. Jarvis, Christophe Klopp, Sofia Marcos, Andrew S. Mason, Deborah Velez-Irizarry, Luohao Xu, Wesley C. Warren
Published 2023-11-01

Chromosome level genome assembly of the Etruscan shrew Suncus etruscus

by Yury V. Bukhman, Susanne Meyer, Li-Fang Chu, Linelle Abueg, Jessica Antosiewicz-Bourget, Jennifer Balacco, Michael Brecht, Erica Dinatale, Olivier Fedrigo, Giulio Formenti, Arkarachai Fungtammasan, Swagarika Jaharlal Giri, Michael Hiller, Kerstin Howe, Daisuke Kihara, Daniel Mamott, Jacquelyn Mountcastle, Sarah Pelan, Keon Rabbani, Ying Sims, Alan Tracey, Jonathan M. D. Wood, Erich D. Jarvis, James A. Thomson, Mark J. P. Chaisson, Ron Stewart
Published 2024-02-01

An improved germline genome assembly for the sea lamprey Petromyzon marinus illuminates the evolution of germline-specific chromosomes

by Nataliya Timoshevskaya, Kaan İ. Eşkut, Vladimir A. Timoshevskiy, Sofia M.C. Robb, Carson Holt, Jon E. Hess, Hugo J. Parker, Cindy F. Baker, Allison K. Miller, Cody Saraceno, Mark Yandell, Robb Krumlauf, Shawn R. Narum, Ralph T. Lampman, Neil J. Gemmell, Jacquelyn Mountcastle, Bettina Haase, Jennifer R. Balacco, Giulio Formenti, Sarah Pelan, Ying Sims, Kerstin Howe, Olivier Fedrigo, Erich D. Jarvis, Jeramiah J. Smith
Published 2023-03-01

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

by 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
Published 2022-11-01

The admixed brushtail possum genome reveals invasion history in New Zealand and novel imprinted genes

by Donna M. Bond, Oscar Ortega-Recalde, Melanie K. Laird, Takashi Hayakawa, Kyle S. Richardson, Finlay.C. B. Reese, Bruce Kyle, Brooke E. McIsaac-Williams, Bruce C. Robertson, Yolanda van Heezik, Amy L. Adams, Wei-Shan Chang, Bettina Haase, Jacquelyn Mountcastle, Maximilian Driller, Joanna Collins, Kerstin Howe, Yasuhiro Go, Francoise Thibaud-Nissen, Nicholas C. Lister, Paul D. Waters, Olivier Fedrigo, Erich D. Jarvis, Neil J. Gemmell, Alana Alexander, Timothy A. Hore
Published 2023-10-01

Optical genome mapping identifies rare structural variations as predisposition factors associated with severe COVID-19

by Nikhil Shri Sahajpal, Chi-Yu Jill Lai, Alex Hastie, Ashis K. Mondal, Siavash Raeisi Dehkordi, Caspar I. van der Made, Olivier Fedrigo, Farooq Al-Ajli, Sawan Jalnapurkar, Marta Byrska-Bishop, Rashmi Kanagal-Shamanna, Brynn Levy, Maximilian Schieck, Thomas Illig, Silviu-Alin Bacanu, Janet S. Chou, Adrienne G. Randolph, Amyn M. Rojiani, Michael C. Zody, Catherine A. Brownstein, Alan H. Beggs, Vineet Bafna, Erich D. Jarvis, Alexander Hoischen, Alka Chaubey, Ravindra Kolhe
Published 2022-02-01

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

by 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
Published 2021-01-01