As above, so below: Whole transcriptome profiling demonstrates strong molecular similarities between avian dorsal and ventral pallial subdivisions

por Gedman, Gregory, Haase, Bettina, Durieux, Gillian, Biegler, Matthew T., Fedrigo, Olivier, Jarvis, Erich D.
Publicado 2021

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

por Biegler, Matthew T., Fedrigo, Olivier, Collier, Paul, Mountcastle, Jacquelyn, Haase, Bettina, Tilgner, Hagen U., Jarvis, Erich D.
Publicado 2022

A Pipeline to Determine RT-QPCR Control Genes for Evolutionary Studies: Application to Primate Gene Expression across Multiple Tissues

por Fedrigo, Olivier, Warner, Lisa R., Pfefferle, Adam D., Babbitt, Courtney C., Cruz-Gordillo, Peter, Wray, Gregory A.
Publicado 2010

Gfastats: conversion, evaluation and manipulation of genome sequences using assembly graphs

por Formenti, Giulio, Abueg, Linelle, Brajuka, Angelo, Brajuka, Nadolina, Gallardo-Alba, Cristóbal, Giani, Alice, Fedrigo, Olivier, Jarvis, Erich D
Publicado 2022

Both Noncoding and Protein-Coding RNAs Contribute to Gene Expression Evolution in the Primate Brain

por Babbitt, Courtney C., Fedrigo, Olivier, Pfefferle, Adam D., Boyle, Alan P., Horvath, Julie E., Furey, Terrence S., Wray, Gregory A.
Publicado 2010

A high-quality, long-read genome assembly of the endangered ring-tailed lemur (Lemur catta)

por Palmada-Flores, Marc, Orkin, Joseph D, Haase, Bettina, Mountcastle, Jacquelyn, Bertelsen, Mads F, Fedrigo, Olivier, Kuderna, Lukas F K, Jarvis, Erich D, Marques-Bonet, Tomas
Publicado 2022

Reading Frame Correction by Targeted Genome Editing Restores Dystrophin Expression in Cells From Duchenne Muscular Dystrophy Patients

por Ousterout, David G, Perez-Pinera, Pablo, Thakore, Pratiksha I, Kabadi, Ami M, Brown, Matthew T, Qin, Xiaoxia, Fedrigo, Olivier, Mouly, Vincent, Tremblay, Jacques P, Gersbach, Charles A
Publicado 2013

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

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

Single-cell long-read mRNA isoform regulation is pervasive across mammalian brain regions, cell types, and development

por Joglekar, Anoushka, Hu, Wen, Zhang, Bei, Narykov, Oleksandr, Diekhans, Mark, Balacco, Jennifer, Ndhlovu, Lishomwa C, Milner, Teresa A, Fedrigo, Olivier, Jarvis, Erich D, Sheynkman, Gloria, Korkin, Dmitry, Ross, M. Elizabeth, Tilgner, Hagen U.
Publicado 2023

Extensive Evolutionary Changes in Regulatory Element Activity during Human Origins Are Associated with Altered Gene Expression and Positive Selection

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

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

por Kim, Juwan, Lee, Chul, Ko, Byung June, Yoo, Dong Ahn, Won, Sohyoung, Phillippy, Adam M., Fedrigo, Olivier, Zhang, Guojie, Howe, Kerstin, Wood, Jonathan, Durbin, Richard, Formenti, Giulio, Brown, Samara, Cantin, Lindsey, Mello, Claudio V., Cho, Seoae, Rhie, Arang, Kim, Heebal, Jarvis, Erich D.
Publicado 2022

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

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

A high-quality genome and comparison of short- versus long-read transcriptome of the palaearctic duck Aythya fuligula (tufted duck)

por Mueller, Ralf C, Ellström, Patrik, Howe, Kerstin, Uliano-Silva, Marcela, Kuo, Richard I, Miedzinska, Katarzyna, Warr, Amanda, Fedrigo, Olivier, Haase, Bettina, Mountcastle, Jacquelyn, Chow, William, Torrance, James, Wood, Jonathan M D, Järhult, Josef D, Naguib, Mahmoud M, Olsen, Björn, Jarvis, Erich D, Smith, Jacqueline, Eöry, Lél, Kraus, Robert H S
Publicado 2021

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

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

The genome sequence of the brown trout, Salmo trutta Linnaeus 1758

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

Benchmarking ultra-high molecular weight DNA preservation methods for long-read and long-range sequencing

por Dahn, Hollis A, Mountcastle, Jacquelyn, Balacco, Jennifer, Winkler, Sylke, Bista, Iliana, Schmitt, Anthony D, Pettersson, Olga Vinnere, Formenti, Giulio, Oliver, Karen, Smith, Michelle, Tan, Wenhua, Kraus, Anne, Mac, Stephen, Komoroske, Lisa M, Lama, Tanya, Crawford, Andrew J, Murphy, Robert W, Brown, Samara, Scott, Alan F, Morin, Phillip A, Jarvis, Erich D, Fedrigo, Olivier
Publicado 2022

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

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

High-coverage sequencing and annotated assemblies of the budgerigar genome

por Ganapathy, Ganeshkumar, Howard, Jason T, Ward, James M, Li, Jianwen, Li, Bo, Li, Yingrui, Xiong, Yingqi, Zhang, Yong, Zhou, Shiguo, Schwartz, David C, Schatz, Michael, Aboukhalil, Robert, Fedrigo, Olivier, Bukovnik, Lisa, Wang, Ty, Wray, Greg, Rasolonjatovo, Isabelle, Winer, Roger, Knight, James R, Koren, Sergey, Warren, Wesley C, Zhang, Guojie, Phillippy, Adam M, Jarvis, Erich D
Publicado 2014

The genome sequence of the Eurasian red squirrel, Sciurus vulgaris Linnaeus 1758

por Mead, Daniel, Fingland, Kathryn, Cripps, Rachel, Portela Miguez, Roberto, Smith, Michelle, Corton, Craig, Oliver, Karen, Skelton, Jason, Betteridge, Emma, Dolucan, Jale, Dudchenko, Olga, Omer, Arina D., Weisz, David, Lieberman Aiden, Erez, Fedrigo, Olivier, Mountcastle, Jacquelyn, Jarvis, Erich, McCarthy, Shane A., Sims, Ying, Torrance, James, Tracey, Alan, Howe, Kerstin, Challis, Richard, Durbin, Richard, Blaxter, Mark
Publicado 2020

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

por Kronenberg, Zev N., Rhie, Arang, Koren, Sergey, Concepcion, Gregory T., Peluso, Paul, Munson, Katherine M., Porubsky, David, Kuhn, Kristen, Mueller, Kathryn A., Low, Wai Yee, Hiendleder, Stefan, Fedrigo, Olivier, Liachko, Ivan, Hall, Richard J., Phillippy, Adam M., Eichler, Evan E., Williams, John L., Smith, Timothy P. L., Jarvis, Erich D., Sullivan, Shawn T., Kingan, Sarah B.
Publicado 2021