Proteogenomic analysis of bacteria and archaea: a 46 organism case study.

Autor: Eli Venter, Richard D Smith, Samuel H Payne

Publikováno v: PLoS ONE, Vol 6, Iss 11, p e27587 (2011)

Experimental evidence is increasingly being used to reassess the quality and accuracy of genome annotation. Proteomics data used for this purpose, called proteogenomics, can alleviate many of the problematic areas of genome annotation, e.g. short pro

Externí odkaz: https://doaj.org/article/e89034d9355545659d8bb0df13a59538

Partial Duplication and Poly(A) Insertion in KCNQ1 Not Detected by Next-Generation Sequencing in Jervell and Lange–Nielsen Syndrome

Autor: Courtney M. Campbell, David Konecki, Wendy K. Chung, Arvindh Kanagasundram, Daniela Macaya, M. Benjamin Shoemaker, Dan M. Roden, Kevin R. Bersell, Jay A. Montgomery, Eli Venter

Publikováno v: Circulation: Arrhythmia and Electrophysiology. 9

Jervell and Lange–Nielsen syndrome is caused by absence of the voltage-gated potassium current I Ks through either homozygous recessive or compound heterozygous mutations in KCNQ1 or KCNE1 . We report here a case of Jervell and Lange–Nielsen synd

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::286aa3ac31f1c8b1f2ada98cbeaea6f5
https://doi.org/10.1161/circep.116.004081

Evolutionary and Biomedical Insights from the Rhesus Macaque Genome

Autor: Carolin Kosiol, Belinda Giardine, Janet A. Hopkins, Andrew G. Clark, Ryan D. Hernandez, Peng Wang, Peter D. Stenson, Yu-Hui Rogers, Aaron L. Halpern, Andrew D. Kern, Webb Miller, Kymberlie H. Pepin, Melissa J. Hubisz, Kimberly D. Delehaunty, Robert E. Palermo, Matthew W. Hahn, Erica Sodergren, Brian P. Walenz, Scott M. Smith, Sandra L. Lee, Xiang Qin, Yucheng Feng, Ewen F. Kirkness, Vandita Joshi, Xiaoqiu Huang, Amanda F. Svatek, Fan Yang, Young Ho Kim, Laura Clarke, John E. Karro, Courtney Sherell White, Jessica Kolb, David Glenn Smith, Clay Davis, Jian Ma, Shobha Patil, Todd Wylie, Arian F.A. Smit, Shalini N. Jhangiani, Michael G. Katze, Edward V. Ball, Jennifer Godfrey, Heather A. Lawson, Brian J. Raney, Michael Holder, Ross C. Hardison, Christian J. Buhay, Zhangwan Li, Alicia Hawes, Eric J. Vallender, David A. Wheeler, James C. Wallace, Galt P. Barber, Jinchuan Xing, Yufeng Shen, Kayla E. Smith, Marvin Diep Dao, Jeffrey Rogers, Evan E. Eichler, Cynthia Pfannkoch, Jireh Santibanez, Kateryna D. Makova, Kashif Hirani, Robert M. Kuhn, Yanru Ren, David Neil Cooper, David Haussler, Carlos Bustamante, Adam Siepel, Mimi N. Chandrabose, Xiaoming Liu, George M. Weinstock, Teresa Utterback, Jarret Glasscock, Tomas Vinar, R. Alan Harris, Anis Karimpour-Fard, San Juana Ruiz, Lucinda Fulton, Asif T. Chinwalla, Aniko Sabo, Xinwei She, Charles Addo-Quaye, David L. Nelson, Lora Lewis, Hui Ke, Eli Venter, Donna M. Muzny, Alison Marklein, Bruce T. Lahn, Grace Pai, Brian W. Schneider, Shannon Dugan-Rocha, Henry Xing-Zhi Song, Jeremiah D. Degenhardt, Kyudong Han, Huaiyang Jiang, Stephanie M. Moore, Ian Schenck, Dinh Ngoc Ngo, Michael J. Cox, Heidie A. Paul, Ann S. Zwieg, Kim C. Worley, Craig Pohl, Rui Chen, Robert L. Strausberg, Ling-Ling Pu, Donna Karolchik, Jonathan R. Pollack, Geoffrey Okwuonu, Jennifer Hume, Elaine R. Mardis, David N. Messina, W. James Kent, William E. O'Brien, Fan Hsu, Andrew R. Jackson, Huyen Dinh, Hui Wang, LaDeana W. Hillier, Richard A. Gibbs, Alexandra Denby, Wesley C. Warren, Brygg Ullmer, Laura J. Dumas, Yih-shin Liu, Tony Attaway, Richard K. Wilson, Patrick Minx, James M. Sikela, Lan Zhang, Sandra Hines, Steven J. M. Jones, Amit Indap, Ze Cheng, Karin A. Remington, Stephanie Bell, Jungnam Lee, Kelly E. Bernard, Sang-Gook Han, Mariano Rocchi, Judith Hernandez, Betsy Ferguson, Hildegard Kehrer-Sawatzki, Ziad Khan, Aleksandar Milosavljevic, Joanne O. Nelson, Jeffery P. Demuth, Richard Burhans, David A. Parker, Lynne V. Nazareth, Roger E. Bumgarner, Marco A. Marra, Robert Baertsch, Andrew Cree, Paul Havlak, J. Craig Venter, Kay Prüfer, Rasmus Nielsen, Ewan Birney, Miriam K. Konkel, Mark A. Batzer, Arthur M. Lesk, Jacqueline E. Schein, Granger G. Sutton, Yan Ding, Yue Liu, Andy Peng Xiang, Miklós Csürös, Selina Vattathil, John W. Wallis, R. Gerald Fowler, Shiaw-Pyng Yang, Ramatu Ayiesha Gabisi, Toni T. Garner

Publikováno v: Science. 316:222-234

The rhesus macaque ( Macaca mulatta ) is an abundant primate species that diverged from the ancestors of Homo sapiens about 25 million years ago. Because they are genetically and physiologically similar to humans, rhesus monkeys are the most widely u

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::529333918462caf3b6ccd4f9829c4752
https://doi.org/10.1126/science.1139247

Proteogenomic Analysis of Bacteria and Archaea: A 46 Organism Case Study

Autor: Richard D. Smith, Samuel H. Payne, Eli Venter

Publikováno v: PLoS ONE
PLoS ONE, Vol 6, Iss 11, p e27587 (2011)

Experimental evidence is increasingly being used to reassess the quality and accuracy of genome annotation. Proteomics data used for this purpose, called proteogenomics, can alleviate many of the problematic areas of genome annotation, e.g. short pro

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::be5abbe92224e1dbbc55ad5942878157
http://europepmc.org/articles/PMC3219674

Evolution of genes and genomes on the Drosophila phylogeny

Autor: Adam M. Phillippy, Edward Grandbois, Pen MacDonald, Iain MacCallum, Laura K. Reed, Wojciech Makalowski, Tracey Honan, Tania Tassinari Rieger, Melissa J. Hubisz, Josep M. Comeron, Douglas Smith, Jennifer Godfrey, Sebastian Strempel, Amr Abdouelleil, Brenton Gravely, Harindra Arachi, Albert J. Vilella, Marc Azer, Sarah A. Teichmann, Roger A. Hoskins, Corbin D. Jones, Keenan Ross, Derek Wilson, Stuart J. Newfeld, John Stalker, Thomas D. Watts, Dennis C. Friedrich, Therese A. Markow, Michael U. Mollenhauer, Tina Goode, Geneva Young, Terry Shea, Krista Lance, Karin A. Remington, Kevin A. Edwards, Lynne Aftuck, Cecil Rise, Sheridon Channer, Matthew D. Rasmussen, Nicole Stange-Thomann, Annie Lui, Robert A. Reenan, Todd Sparrow, Dave Begun, Tamrat Negash, Laura K. Sirot, Adrianne Brand, Adam Brown, Daisuke Yamamoto, Pema Phunkhang, Justin Abreu, Russell Schwartz, Ana Llopart, Abderrahim Farina, Kebede Maru, Chung-I Wu, Allen Alexander, Scott Anderson, So Jeong Lee, Jason Blye, Gary H. Karpen, Wilfried Haerty, Daniel A. Barbash, Peter Rogov, Barry O'Neill, Rachel Mittelman, Jakob Skou Pedersen, Leanne Hughes, Robert K. Bradley, Graziano Pesole, Wyatt W. Anderson, Anthony J. Greenberg, Alejandro Sánchez-Gracia, Julio Rozas, Stephen W. Schaeffer, Yama Thoulutsang, Roger K. Butlin, David H. Ardell, Stuart DeGray, Chris P. Ponting, Deborah E. Stage, Corrado Caggese, Montserrat Aguadé, Casey M. Bergman, Diallo Ferguson, Peili Zhang, Jeffrey R. Powell, Hajime Sato, Xiaohong Liu, Marta Sabariego Puig, Michael Parisi, Passang Dorje, Yoshihiko Tomimura, Adal Abebe, Carlo G. Artieri, Brian Hurhula, Filip Rege, Peter D. Keightley, Andrew Barry, Pablo Alvarez, Tsamla Tsamla, Marvin Wasserman, Santosh Jagadeeshan, Daniel L. Halligan, Chelsea D. Foley, Kim D. Delehaunty, Manfred Grabherr, Sourav Chatterji, Angela N. Brooks, James C. Costello, Mieke Citroen, James A. Yorke, Hsiao Pei Yang, Charles Chapple, Jian Lu, Carlos A. Machado, Norbu Dhargay, Tsering Wangchuk, Anat Caspi, Patrick Cahill, Tashi Bayul, Lisa Levesque, Otero L. Oyono, Atanas Mihalev, Dawa Thoulutsang, Dawn N. Abt, Sujaa Raghuraman, Manyuan Long, Maria Mendez-Lago, Charles Matthews, Kimberly Dooley, Alex Wong, Melanie A. Huntley, William R. Jeck, Ira Topping, Ben Kanga, José P. Abad, Ana Cristina Lauer Garcia, Brikti Abera, Kunsang Gyaltsen, Jonathan Butler, Alicia Franke, Michael C. Schatz, Cheewhye Chin, Charles F. Aquadro, Justin Johnson, Bryant F. McAllister, Georgia Giannoukos, M. Erii Husby, Rod A. Wing, Shangtao Liu, Jean L. Chang, Jennifer Daub, Eiko Kataoka, Leopold Parts, Rakela Lubonja, Margaret Priest, Yoshiko N. Tobari, Teena Mehta, Evgeny M. Zdobnov, Yeshi Lokyitsang, Richard Elong, Matthew J. Parisi, Louis Meneus, Eric S. Lander, Alan Filipski, Gary Gearin, Nabil Hafez, Nicholas Sisneros, David B. Jaffe, Ian Holmes, Marina Sirota, Leonid Boguslavskiy, Lisa Chuda, LaDeana W. Hillier, Meizhong Luo, Phil Batterham, Michael Kleber, Richard K. Wilson, Yama Cheshatsang, Qing Yu, Rebecca Reyes, Matthew W. Hahn, Andreas Heger, Mar Marzo, Patrick Minx, Kerstin Lindblad-Toh, Vera L. S. Valente, Adam Wilson, William C. Jordan, Mohamed A. F. Noor, Chiao-Feng Lin, Asha Kamat, Heather Ebling, Mihai Pop, Frances Letendre, Mariana F. Wolfner, Don Gilbert, Ngawang Sherpa, Riza M. Daza, Oana Mihai, Gabriel C. Wu, Aaron M. Berlin, Ewen F. Kirkness, Monika D. Huard, Robert S. Fulton, Randall H. Brown, Danni Zhong, Sharon Stavropoulos, Venky N. Iyer, Xu Mu, Christina R. Gearin, David M. Rand, Jerry A. Coyne, Dan Hultmark, Jill Falk, Christopher Patti, Montserrat Papaceit, James Meldrim, Valentine Mlenga, Muneo Matsuda, Sven Findeiß, Todd A. Schlenke, Kevin McKernan, Brian P. Walenz, Timothy B. Sackton, Leonardo Koerich, Peter An, Robert Nicol, Chuong B. Do, Dmitry Khazanovich, Carmen Segarra, Maura Costello, St Christophe Acer, Claudia Rohde, Serafim Batzoglou, Hadi Quesneville, Evan Mauceli, Andy Vo, Luciano M. Matzkin, Susan E. Celniker, Patrick M. O’Grady, William M. Gelbart, Lloyd Low, Jamal Abdulkadir, Jessica Spaulding, Brian R. Calvi, Charlotte Henson, Robert David, Jennifer L. Hall, Andrew G. Clark, Anastasia Gardiner, Susan M. Russo, Birhane Hagos, Kerri Topham, Amy Denise Reily, Eli Venter, Jerome Naylor, Sandra W. Clifton, Valer Gotea, Samuel R. Gross, Manolis Kellis, Claude Bonnet, Christopher Strader, Tashi Lokyitsang, Nyima Norbu, Jennifer Baldwin, Stephen M. Mount, Robert L. Strausberg, Shailendra Yadav, Kristipati Ravi Ram, Steven L. Salzberg, Erik Gustafson, David A. Garfield, Eva Freyhult, Arthur L. Delcher, Enrico Blanco, Granger G. Sutton, Jason M. Tsolas, Charles Robin, Angie S. Hinrichs, Christopher D. Smith, Jane Wilkinson, Brendan McKernan, Fritz Pierre, William McCusker, Brian Oliver, Barry E. Garvin, Sudhir Kumar, Peter Kisner, Kunsang Dorjee, A. Bernardo Carvalho, Anna Montmayeur, Andrew Zimmer, Diana Shih, Wei Tao, Shiaw Pyng Yang, Sante Gnerre, Sampath Settipalli, Thu Nguyen, Paolo Barsanti, Brian P. Lazzaro, Sonja J. Prohaska, J. Craig Venter, Senait Tesfaye, Susan McDonough, Kim D. Pruitt, Alexander Stark, Sergio Castrezana, Lucinda Fulton, Richard T. Lapoint, Greg Gibson, John Spieth, Boris Adryan, Georgius De Haan, Sheila Fisher, Daniel A. Pollard, Seva Kashin, Rob J. Kulathinal, Michael B. Eisen, Nathaniel Novod, Christina Demaso, Alan Dupes, Amanda M. Larracuente, Toby Bloom, Alfredo Villasante, Charles H. Langley, Rama S. Singh, Niall J. Lennon, Kristi L. Montooth, Daniel Barker, Wolfgang Stephan, David Sturgill, Ruiqiang Li, Andrew Hollinger, Boris Boukhgalter, Talene Thomson, Patrick Cooke, Zac Zwirko, Nadia D. Singh, Michael Weiand, Lior Pachter, Roderic Guigó, Yu Zhang, Jay D. Evans, Stephanie Bosak, Rosie Levine, Lu Shi, Kiyohito Yoshida, Carolyn S. McBride, Pouya Kheradpour, William Brockman, Alberto Civetta, Hiroshi Akashi, Marcia Lara, Susan Faro, Sam Griffiths-Jones, Michael R. Brent, Thomas H. Eickbush, Gane Ka-Shu Wong, Elizabeth P. Ryan, Erica Anderson, Roberta Kwok, Asif T. Chinwalla, Sahal Osman, Nga Nguyen, Damiano Porcelli, Missole Doricent, Saverio Vicario, Marc Rubenfield, Bárbara Negre, Gillian M. Halter, Erin E. Dooley, Elena R. Lozovsky, William Lee, Alville Collymore, Catherine Stone, Tanya Mihova, Jun Wang, Karsten Kristiansen, Imane Bourzgui, Michael F. Lin, Katie D'Aco, Filipe G. Vieira, Choe Norbu, Yu-Hui Rogers, Aaron L. Halpern, Eugene W. Myers, Sharleen Grewal, Robert T. Good, Alfredo Ruiz, Dave Kudrna, Joseph Graham, Alex Lipovsky, Leonidas Mulrain, Tsering Wangdi, Roman Arguello, Mira V. Han, Arjun Bhutkar, Rasmus Nielsen, David J. Saranga, Aleksey V. Zimin, Vasilia Magnisalis, Helen Vassiliev, Thomas C. Kaufman, Eva Markiewicz, Temple F. Smith, Jinlei Liu, Loryn Gadbois, Michael G. Ritchie, Lisa Zembek, Daniel Bessette, Pasang Bachantsang, Adam Navidi

Publikováno v: Clark, A G, Eisen, M B, Smith, D R, Bergman, C M, Oliver, B, Markow, T A, Kaufman, T C, Kellis, M, Gelbart, W, Iyer, V N, Pollard, D A, Sackton, T B, Larracuente, A M, Singh, N D, Abad, J P, Abt, D N, Adryan, B, Aguade, M, Akashi, H, Anderson, W W, Aquadro, C F, Ardell, D H, Arguello, R, Artieri, C G, Barbash, D A, Barker, D, Barsanti, P, Batterham, P, Batzoglou, S, Begun, D, Bhutkar, A, Blanco, E, Bosak, S A, Bradley, R K, Brand, A D, Brent, M R, Brooks, A N, Brown, R H, Butlin, R K, Caggese, C, Calvi, B R, Bernardo de Carvalho, A, Caspi, A, Castrezana, S, Celniker, S E, Chang, J L, Chapple, C, Chatterji, S, Kristiansen, K, Pedersen, J S & Drosophila 12 Genomes Consortium 2007, ' Evolution of genes and genomes on the Drosophila phylogeny ', Nature, vol. 450, no. 7167, pp. 203-18 . https://doi.org/10.1038/nature06341
Nature
Nature, Nature Publishing Group, 2007, 450 (7167), pp.203-18. ⟨10.1038/nature06341⟩
Clark, A G, Eisen, M B, Smith, D R, Bergman, C M, Oliver, B, Markow, T A, Kaufman, T C, Kellis, M, Gelbart, W, Iyer, V N, Pollard, D A, Sackton, T B, Larracuente, A M, Singh, N D, Abad, J P, Abt, D N, Adryan, B, Aguade, M, Akashi, H, Anderson, W W, Aquadro, C F, Ardell, D H, Arguello, R, Artieri, C G, Barbash, D A, Barker, D, Barsanti, P, Batterham, P, Batzoglou, S, Begun, D, Bhutkar, A, Blanco, E, Bosak, S A, Bradley, R K, Brand, A D, Brent, M R, Brooks, A N, Brown, R H, Butlin, R K, Caggese, C, Calvi, B R, Bernardo de Carvalho, A, Caspi, A, Castrezana, S, Celniker, S E, Chang, J L, Chapple, C, Chatterji, S, Chinwalla, A, Civetta, A, Clifton, S W, Comeron, J M, Costello, J C, Coyne, J A, Daub, J, David, R G, Delcher, A L, Delehaunty, K, Do, C B, Ebling, H, Edwards, K, Eickbush, T, Evans, J D, Filipski, A, Findeiss, S, Freyhult, E, Fulton, L, Fulton, R, Garcia, A C L, Gardiner, A, Garfield, D A, Garvin, B E, Gibson, G, Gilbert, D, Gnerre, S, Godfrey, J, Good, R, Gotea, V, Gravely, B, 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Phillippy, A M, Ponting, C P, Pop, M, Porcelli, D, Powell, J R, Prohaska, S, Pruitt, K, Puig, M, Quesneville, H, Ram, K R, Rand, D, Rasmussen, M D, Reed, L K, Reenan, R, Reily, A, Remington, K A, Rieger, T T, Ritchie, M G, Robin, C, Rogers, Y-H, Rohde, C, Rozas, J, Rubenfield, M J, Ruiz, A, Russo, S, Salzberg, S L, Sanchez-Gracia, A, Saranga, D J, Sato, H, Schaeffer, S W, Schatz, M C, Schlenke, T, Schwartz, R, Segarra, C, Singh, R S, Sirot, L, Sirota, M, Sisneros, N B, Smith, C D, Smith, T F, Spieth, J, Stage, D E, Stark, A, Stephan, W, Strausberg, R L, Strempel, S, Sturgill, D, Sutton, G, Sutton, G G, Tao, W, Teichmann, S, Tobari, Y N, Tomimura, Y, Tsolas, J M, Valente, V L S, Venter, E, Venter, J C, Vicario, S, Vieira, F G, Vilella, A J, Villasante, A, Walenz, B, Wang, J, Wasserman, M, Watts, T, Wilson, D, Wilson, R K, Wing, R A, Wolfner, M F, Wong, A, Wong, G K-S, Wu, C-I, Wu, G, Yamamoto, D, Yang, H-P, Yang, S-P, Yorke, J A, Yoshida, K, Zdobnov, E, Zhang, P, Zhang, Y, Zimin, A V, Baldwin, J, Abdouelleil, A, Abdulkadir, J, Abebe, A, Abera, B, Abreu, J, Acer, S C, Aftuck, L, Alexander, A, An, P, Anderson, E, Anderson, S, Arachi, H, Azer, M, Bachantsang, P, Barry, A, Bayul, T, Berlin, A, Bessette, D, Bloom, T, Blye, J, Boguslavskiy, L, Bonnet, C, Boukhgalter, B, Bourzgui, I, Brown, A, Cahill, P, Channer, S, Cheshatsang, Y, Chuda, L, Citroen, M, Collymore, A, Cooke, P, Costello, M, D'Aco, K, Daza, R, De Haan, G, DeGray, S, DeMaso, C, Dhargay, N, Dooley, K, Dooley, E, Doricent, M, Dorje, P, Dorjee, K, Dupes, A, Elong, R, Falk, J, Farina, A, Faro, S, Ferguson, D, Fisher, S, Foley, C D, Franke, A, Friedrich, D, Gadbois, L, Gearin, G, Gearin, C R, Giannoukos, G, Goode, T, Graham, J, Grandbois, E, Grewal, S, Gyaltsen, K, Hafez, N, Hagos, B, Hall, J, Henson, C, Hollinger, A, Honan, T, Huard, M D, Hughes, L, Hurhula, B, Husby, M E, Kamat, A, Kanga, B, Kashin, S, Khazanovich, D, Kisner, P, Lance, K, Lara, M, Lee, W, Lennon, N, Letendre, F, LeVine, R, Lipovsky, A, Liu, X, Liu, J, Liu, S, Lokyitsang, T, Lokyitsang, Y, Lubonja, R, Lui, A, MacDonald, P, Magnisalis, V, Maru, K, Matthews, C, McCusker, W, McDonough, S, Mehta, T, Meldrim, J, Meneus, L, Mihai, O, Mihalev, A, Mihova, T, Mittelman, R, Mlenga, V, Montmayeur, A, Mulrain, L, Navidi, A, Naylor, J, Negash, T, Nguyen, T, Nguyen, N, Nicol, R, Norbu, C, Norbu, N, Novod, N, O'Neill, B, Osman, S, Markiewicz, E, Oyono, O L, Patti, C, Phunkhang, P, Pierre, F, Priest, M, Raghuraman, S, Rege, F, Reyes, R, Rise, C, Rogov, P, Ross, K, Ryan, E, Settipalli, S, Shea, T, Sherpa, N, Shi, L, Shih, D, Sparrow, T, Spaulding, J, Stalker, J, Stange-Thomann, N, Stavropoulos, S, Stone, C, Strader, C, Tesfaye, S, Thomson, T, Thoulutsang, Y, Thoulutsang, D, Topham, K, Topping, I, Tsamla, T, Vassiliev, H, Vo, A, Wangchuk, T, Wangdi, T, Weiand, M, Wilkinson, J, Wilson, A, Yadav, S, Young, G, Yu, Q, Zembek, L, Zhong, D, Zimmer, A, Zwirko, Z, Jaffe, D B, Alvarez, P, Brockman, W, Butler, J, Chin, C, Gnerre, S, Grabherr, M, Kleber, M, Mauceli, E & MacCallum, I 2007, ' Evolution of genes and genomes on the Drosophila phylogeny ', Nature, vol. 450, no. 7167, pp. 203-218 . https://doi.org/10.1038/nature06341
Nature, Vol. 450, No 7167 (2007) pp. 203-218
ResearcherID

Affiliations des auteurs : cf page 216 de l'article; International audience; Comparative analysis of multiple genomes in a phylogenetic framework dramatically improves the precision and sensitivity of evolutionary inference, producing more robust res

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::185fcef84a75fcef336e3156b9953635
https://resolver.caltech.edu/CaltechAUTHORS:20170307-113900780