Evaluation of GRCh38 and de novo haploid genome assemblies demonstrates the enduring quality of the reference assembly

Autor: Valerie A. Schneider, Adam M. Phillippy, Chen-Shan Chin, Glen Threadgold, Deanna M. Church, Sergey Koren, Jared T. Simpson, Evan E. Eichler, Chris Markovic, Matthew Boitano, Milinn Kremitzki, William Chow, Jonathan Wood, Kate Auger, Tim Hubbard, Françoise Thibaud-Nissen, Richard Durbin, Karyn Meltz Steinberg, Terence Murphy, Heng Li, Joanna Collins, Kerstin Howe, Laura Clarke, Paul Flicek, Glenn Harden, Richard K. Wilson, Nathan Bouk, Paul Kitts, James Torrance, Kim D. Pruitt, Hsiu-Chuan Chen, Robert S. Fulton, Paul Peluso, Sarah Pelan, Sean McGrath, Vincent Magrini, Tina A. Graves-Lindsay, Derek Albracht

Publikováno v: Genome Research. 27:849-864

The human reference genome assembly plays a central role in nearly all aspects of today's basic and clinical research. GRCh38 is the first coordinate-changing assembly update since 2009; it reflects the resolution of roughly 1000 issues and encompass

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::1fc8b3738169c24f6928cef473f32ede
https://doi.org/10.1101/gr.213611.116

Reference sequence (RefSeq) database at NCBI: current status, taxonomic expansion, and functional annotation

Autor: Barbara Robbertse, Patrick Masterson, Jinna Choi, Sanjida H. Rangwala, Vyacheslav Brover, Olga Blinkova, Stacy Ciufo, Kim D. Pruitt, Conrad L. Schoch, Daniel H. Haft, Kelly M. McGarvey, Richard McVeigh, Raymond E. Tully, Bhanu Rajput, Alexander Astashyn, Vinita Joardar, Wratko Hlavina, Vamsi K. Kodali, Kathleen O'Neill, Danso Ako-adjei, Hanzhen Sun, Craig Wallin, Mathew W. Wright, Michael DiCuccio, Daniel Rausch, Catherine M. Farrell, Susan S. Storz, Avi Kimchi, Terence Murphy, Tripti Gupta, Eneida L. Hatcher, Donna Maglott, Shashikant Pujar, Brian Smith-White, David Webb, Nuala A. O'Leary, Wenjun Li, Michael R. Murphy, Igor Tolstoy, Françoise Thibaud-Nissen, Diana Haddad, Olga Ermolaeva, Azat Badretdin, Andrei Shkeda, Lillian D. Riddick, Tatiana Tatusova, Wendy Wu, Melissa J. Landrum, Vyacheslav Chetvernin, Tamara Goldfarb, Anjana R. Vatsan, Paul Kitts, J. Rodney Brister, Yiming Bao, Eric Cox

Publikováno v: Nucleic Acids Research

The RefSeq project at the National Center for Biotechnology Information (NCBI) maintains and curates a publicly available database of annotated genomic, transcript, and protein sequence records (http://www.ncbi.nlm.nih.gov/refseq/). The RefSeq projec

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::7fa63f34080e34e61b5a99d6a1c2b83d

Meeting report: GenBank microbial genomic taxonomy workshop (12-13 May, 2015)

Autor: Rita R. Colwell, James Ostell, Aidan Parte, Richa Agarwala, William B. Whitman, Avi Kimchi, Richard McVeigh, Brian J. Tindall, Scott Federhen, Kim D. Pruitt, Brittany Goldberg, David P. Labeda, Sean Turner, William Klimke, Thomas L. Madden, Tatiana Tatusova, Ramon Rosselló-Móra, Karen Clark, Joerg Graf, Hans-Peter Klenk, Ilene Karsch-Mizrachi, Daniel R. Brown, Michael DiCuccio, Heike Sichtig, Konstantinos T. Konstantinidis, Robert B. Falk, Paul Kitts, Pablo Yarza, George M. Garrity, David W. Ussery, Nur A. Hasan

Publikováno v: Digital.CSIC. Repositorio Institucional del CSIC
instname
Standards in Genomic Sciences

Many genomes are incorrectly identified at GenBank. We developed a plan to find and correct misidentified genomes using genomic comparison statistics together with a scaffold of reliably identified genomes from type. A workshop was organized with bro

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::6dd196299fe368a66b45c9ddc358d299
http://hdl.handle.net/10261/152554

Human adenovirus serotype 3 (Ad3) and the AD fiber protein bind to a 130-kDa membrane protein on HeLa cells

Autor: Anne Marie Di Guilmi, Evelyne Gout, Jadwiga Chroboczek, Paul Kitts, Annie Barge

Publikováno v: Virus Research. 38:71-81

The fiber protein of adenovirus mediates the interaction of adenovirus with cell membrane receptors. We have produced the Ad3 fiber protein in the baculovirus expression system. Biochemical, morphological and functional analyses showed that the recom

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_________::1b5d359f0101eeacf562549eca5c65f6
https://doi.org/10.1016/0168-1702(95)00043-p

The genome sequence of taurine cattle: A window to ruminant biology and evolution

Autor: Heather M Deobald, Gerald R. Fowler, Clay Davis, Judith Herdandez, Donna Maglott, Lin Chen, Gonzalo Rincon, Darren E. Hagen, James T. Warren, Evgenia V. Kriventseva, Ingrid Olsaker, Debora L. Hamernik, Charles Moen, Oliver C. Jann, Yuri Kapustin, Erdogan Memili, Timothy Connelley, Ling Ling Pu, Terhi Iso-Touru, Gemma Marie Payne, Ye Cheng, Amy Egan, Alexandre Reymond, Aniko Sabo, J. Bruce German, Jason R. Grant, Joseph Chacko, Ronnie D. Green, Isabel Kinney Ferreira de Miranda Santos, Raffaele Mazza, A.J. Molenaar, Richard A. Moore, Christian J. Buhay, Henry Song, Cham G. Kumar, Marion L. Greaser, Hasan Khatib, Harris A. Lewin, Olga Ermolaeva, Jonathan V. Sweedler, Steven J.M. Jones, Rosemeire Conceição Parra Pastor, Paul Stothard, Adam J. Colley, Antti Livanainen, Francesca Panzitta, Dan Graur, Aaron Ingham, David L. Adelson, Timothy P. L. Smith, Shirley A. Ellis, Andy Cree, Jingkun Zhang, Carolyn T.A. Herzig, Jason Goodell, Colette A. Abbey, Feng-Qi Zhao, Mimi M. Chandrabose, Ross L. Tellam, Alex Astashyn, Yanru Ren, Laura Elnitski, Bella Mayurkumar Patel, Sem Genini, Lassudara G. Almeida, Jacqueline E. Schein, Theresa Casey, Hanni Salih, José Fernando Garcia, Zhiquan Wang, Carolyn Fitzsimmons, Evan E. Eichler, Ngoc Nguyen, Kaitlin E. Donohue, Ariel Fernando Amadio, Clayton R. Boldt, John C. McEwan, Juan Manuel Anzola, Francisco Câmara, Shoba Ranganathan, Eran Elhaik, Stefan Hiendleder, George M. Weinstock, Lora Lewis, Jeremy F. Taylor, Dimos Kapetis, Andrew J. Roberts, Lee Alexander, Nelida Rodriguez-Osorio, Alexandre Souvorov, Justin C. Lee, Bruce R. Southey, Boris Kiryutin, Michael Holder, Xiang Qin, Warren M. Snelling, Abhirami Ratnakumar, Marcelo Fábio Gouveia Nogueira, Angela K. Walker, Hatam A. Hakimov, Fernando H. Biase, Roderic Guigó, Shannon Dugan-Rocha, Sean McWilliam, Rex Lee Williams, Jacqueline Chrast, Huyen Dinh, Robert C. Edgar, Huaiyang Jiang, Justin T. Reese, John W. Keele, George E. Liu, Yufeng Shen, Jireh Santibanez, Kim C. Worley, Sandra L. Lee, Sari S. Khalil, Marta Hernández, Stephen N. White, Suria M. Bahadue, Changxi Li, Kim D. Pruitt, Kirsty Jensen, C. Michael Dickens, Jung-Woo Choi, Jennifer Harrow, Tatiana A. DeCampos, Richard A. Gibbs, Ryan J. Lozado, Yoshikazu Sugimoto, Sigbjam Lien, Anna K. Bennett, Curtis P. Van Tassell, Eve Devinoy, Gustavo Garcia, R. Baxter, Satyanarayana Rachagani, Kevin K. Lahmers, Stylianos E. Antonarakis, D. Kolbehdari, Cynthia L. Baldwin, Lillian Sando, Darryl L. Hadsell, Elen Anatriello, Ze Cheng, Richard C. Waterman, Paul Havlak, Peter Dove, Laura Sherman, Wes Barris, Imke Tammen, Geoffrey Okwuonu, Jennifer Hume, Denis M. Larkin, Robert D. Schnabel, Zhi-Liang Hu, Evgeny M. Zdobnov, Danielle G. Lemay, Stephanie Bell, Roberto Malinverni, Jiuzhou Song, David Steffen, James M. Reecy, Lynne V. Nazareth, Carlo José Freire de Oliveira, E. Marques, Cody J. Gladney, Donna M. Muzny, Candice L. Brinkmeyer-Larigford, Lakshmi K. Matukumalli, Jan Aerts, Stephen S. Moore, Margaret Morgan, Kim L. McLean, Juan F. Medrano, Felix Kokocinski, Marco A. Marra, Gregory P. Harhay, Frank W. Nicholas, Loren C. Skow, Fiona S. L. Brinkman, Tovah Kerr, Krista L. Fritz, Stacey M. Curry, Charlotte N. Henrichsen, Catherine Ucla, David J. Lynn, Victor V. Solovyev, Natasha E. Romero, Sandra Hines, Joy M. Raison, Alessandra Mara Franzin, Selina Vattathil, Jeffery A. Carroll, Brian P. Dalrymple, Katarzyna Wilczek-Boney, Seongwon Seo, Richard J. Leach, Mireya Plass, Paul Kitts, Kris R. Wunderlich, Bhanu Prakash V.L. Telugu, Gary L. Bennett, Ramatu Ayiesha Gabisi, Ravikiran Donthu, Shalini N. Jhangiani, Rita A. Wright, Mary Qu Yang, Nauman J. Maqbool, W. A. Carvalho, Monique Rijnkels, Yuri Tani Utsunomiya, Charles E. Chappie, John L. Williams, Rob Halgren, Stephen M. J. Searle, A.R.R. Abatepaulo, Thomas Junier, Stephanie D. McKay, Anne G. Rosenwald, David A. Wheeler, Rosemarie Weikard, N. Hastings, Roger T. Stone, Eduardo Eyras, Cerissa Hamilton, Wendy C. Brown, Yan Ding, Ylva Strandberg Lutzow, Matthew Hobbs, Annett Eberlein, Carine Wyss, Jennifer M. Urbanski, Matthew Peter Kent, Lilian P.L. Lau, Dinesh Kumar, Penny K. Riggs, Lawrence B. Schook, Matthew Hitchens, Vandita Joshi, Melissa J. Landrum, Tyler Alioto, Nathan Poslusny, Thomas T. Wheeler, Victor Sapojnikov, Natália F. Martins, San Juana Ruiz, Michael D. MacNeil, Alexandre Rodrigues Caetano, Mario Andres Poli, Catherine Jamis, Masaaki Taniguchi, James E. Womack, William F. Martin, Andrej Razpet, James G. R. Gilbert, Daniel G. Bradley, Readman Chiu, Thomas H. Welsh, Clare A. Gill, Erica Sodergren, Carol G. Chitko-McKown, Hari Prasad Nandakumar, Virpi Ahola, Steve M. Kappes, Jennifer E. Chapin, Sandra Regina Maruyama, John Lopez, Krystin M. Logan, Jonathan A. Green, Laurens G. Wilming, Yue Liu, Antti Iivanainen, Robert A. Holt, Barbara T. Moreno, Marcos De Donato, Christie Kovar, Angela Jolivet Johnson, Carl T. Muntean, Robert Ward, K. James Durbin, Matthew D. Whiteside, Christopher P. Childers, Tad S. Sonstegard, Yin Shin Liu, Bin Zhu, Sameer D. Pant, Ashley J. Waardenberg, André Eggen, D.M. Spurlock, Hsiu Chuan Chen, Le Luo Guan, Sandra L. Rodriguez-Zas, Akiko Takasuga, Daniela D. Moré, Jianqi Yang, Wratko Hlavina, Sheila M. Schmutz, Michael J. Brownstein, Christine G. Elsik, Marvin Diep Dao, Daniel Gerlach, E. Hart, Elsa Chacko, Elizabeth Glass, Libing Shen, Chris P. Verschoor, Eliane P. Cervelatti

Publikováno v: Science
Science, American Association for the Advancement of Science, 2009, 324 (5926), pp.522-528. ⟨10.1126/science.1169588⟩
Science, Vol. 324, No 5926 (2009) pp. 522-528
Science (New York N.Y.)
Elsik, C G, Tellam, R L, Worley, K C, Gibbs, R A, Abatepaulo, A R R, Abbey, C A, Adelson, D L, Aerts, J, Ahola, V, Alexander, L, Alioto, T, Almeida, I G, Amadio, A F, Anatriello, E, Antonarakis, S E, Anzola, J M, Astashyn, A, Bahadue, S M, Baldwin, C L, Barris, W, Baxter, R, Bell, S N, Bennett, A K, Bennett, G L, Biase, F H, Boldt, C R, Bradley, D G, Brinkman, F S L, Brinkmeyer-Langford, C L, Brown, W C, Brownstein, M J, Buhay, C, Caetano, A R, Camara, F, Carroll, J A, Carvalho, W A, Casey, T, Cervelatti, E P, Chack, J, Chacko, E, Chandrabose, M M, Chapin, J E, Chapple, C E, Chen, H-C, Chen, L, Cheng, Y, Cheng, Z, Childers, C P & Glass, E J & Jensen, K 2009, ' The Genome Sequence of Taurine Cattle: A Window to Ruminant Biology and Evolution ', Science, vol. 324, no. 5926, pp. 522-528 . https://doi.org/10.1126/science.1169588
ResearcherID

To understand the biology and evolution of ruminants, the cattle genome was sequenced to about sevenfold coverage. The cattle genome contains a minimum of 22,000 genes, with a core set of 14,345 orthologs shared among seven mammalian species of which

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::3d69a948882238dc144c14e55e77459d
https://hal.inrae.fr/hal-02667039