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  • Humans  (1,092)
  • 2005-2009  (1,092)
  • 1950-1954
  • 1
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    The genome sequence of taurine cattle: a window to ruminant biology and evolution (2009)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2009-04-25
    Description: 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 1217 are absent or undetected in noneutherian (marsupial or monotreme) genomes. Cattle-specific evolutionary breakpoint regions in chromosomes have a higher density of segmental duplications, enrichment of repetitive elements, and species-specific variations in genes associated with lactation and immune responsiveness. Genes involved in metabolism are generally highly conserved, although five metabolic genes are deleted or extensively diverged from their human orthologs. The cattle genome sequence thus provides a resource for understanding mammalian evolution and accelerating livestock genetic improvement for milk and meat production.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2943200/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2943200/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Bovine Genome Sequencing and Analysis Consortium -- Elsik, Christine G -- Tellam, Ross L -- Worley, Kim C -- Gibbs, Richard A -- Muzny, Donna M -- Weinstock, George M -- Adelson, David L -- Eichler, Evan E -- Elnitski, Laura -- Guigo, Roderic -- Hamernik, Debora L -- Kappes, Steve M -- Lewin, Harris A -- Lynn, David J -- Nicholas, Frank W -- Reymond, Alexandre -- Rijnkels, Monique -- Skow, Loren C -- Zdobnov, Evgeny M -- Schook, Lawrence -- Womack, James -- Alioto, Tyler -- Antonarakis, Stylianos E -- Astashyn, Alex -- Chapple, Charles E -- Chen, Hsiu-Chuan -- Chrast, Jacqueline -- Camara, Francisco -- Ermolaeva, Olga -- Henrichsen, Charlotte N -- Hlavina, Wratko -- Kapustin, Yuri -- Kiryutin, Boris -- Kitts, Paul -- Kokocinski, Felix -- Landrum, Melissa -- Maglott, Donna -- Pruitt, Kim -- Sapojnikov, Victor -- Searle, Stephen M -- Solovyev, Victor -- Souvorov, Alexandre -- Ucla, Catherine -- Wyss, Carine -- Anzola, Juan M -- Gerlach, Daniel -- Elhaik, Eran -- Graur, Dan -- Reese, Justin T -- Edgar, Robert C -- McEwan, John C -- Payne, Gemma M -- Raison, Joy M -- Junier, Thomas -- Kriventseva, Evgenia V -- Eyras, Eduardo -- Plass, Mireya -- Donthu, Ravikiran -- Larkin, Denis M -- Reecy, James -- Yang, Mary Q -- Chen, Lin -- Cheng, Ze -- Chitko-McKown, Carol G -- Liu, George E -- Matukumalli, Lakshmi K -- Song, Jiuzhou -- Zhu, Bin -- Bradley, Daniel G -- Brinkman, Fiona S L -- Lau, Lilian P L -- Whiteside, Matthew D -- Walker, Angela -- Wheeler, Thomas T -- Casey, Theresa -- German, J Bruce -- Lemay, Danielle G -- Maqbool, Nauman J -- Molenaar, Adrian J -- Seo, Seongwon -- Stothard, Paul -- Baldwin, Cynthia L -- Baxter, Rebecca -- Brinkmeyer-Langford, Candice L -- Brown, Wendy C -- Childers, Christopher P -- Connelley, Timothy -- Ellis, Shirley A -- Fritz, Krista -- Glass, Elizabeth J -- Herzig, Carolyn T A -- Iivanainen, Antti -- Lahmers, Kevin K -- Bennett, Anna K -- Dickens, C Michael -- Gilbert, James G R -- Hagen, Darren E -- Salih, Hanni -- Aerts, Jan -- Caetano, Alexandre R -- Dalrymple, Brian -- Garcia, Jose Fernando -- Gill, Clare A -- Hiendleder, Stefan G -- Memili, Erdogan -- Spurlock, Diane -- Williams, John L -- Alexander, Lee -- Brownstein, Michael J -- Guan, Leluo -- Holt, Robert A -- Jones, Steven J M -- Marra, Marco A -- Moore, Richard -- Moore, Stephen S -- Roberts, Andy -- Taniguchi, Masaaki -- Waterman, Richard C -- Chacko, Joseph -- Chandrabose, Mimi M -- Cree, Andy -- Dao, Marvin Diep -- Dinh, Huyen H -- Gabisi, Ramatu Ayiesha -- Hines, Sandra -- Hume, Jennifer -- Jhangiani, Shalini N -- Joshi, Vandita -- Kovar, Christie L -- Lewis, Lora R -- Liu, Yih-Shin -- Lopez, John -- Morgan, Margaret B -- Nguyen, Ngoc Bich -- Okwuonu, Geoffrey O -- Ruiz, San Juana -- Santibanez, Jireh -- Wright, Rita A -- Buhay, Christian -- Ding, Yan -- Dugan-Rocha, Shannon -- Herdandez, Judith -- Holder, Michael -- Sabo, Aniko -- Egan, Amy -- Goodell, Jason -- Wilczek-Boney, Katarzyna -- Fowler, Gerald R -- Hitchens, Matthew Edward -- Lozado, Ryan J -- Moen, Charles -- Steffen, David -- Warren, James T -- Zhang, Jingkun -- Chiu, Readman -- Schein, Jacqueline E -- Durbin, K James -- Havlak, Paul -- Jiang, Huaiyang -- Liu, Yue -- Qin, Xiang -- Ren, Yanru -- Shen, Yufeng -- Song, Henry -- Bell, Stephanie Nicole -- Davis, Clay -- Johnson, Angela Jolivet -- Lee, Sandra -- Nazareth, Lynne V -- Patel, Bella Mayurkumar -- Pu, Ling-Ling -- Vattathil, Selina -- Williams, Rex Lee Jr -- Curry, Stacey -- Hamilton, Cerissa -- Sodergren, Erica -- Wheeler, David A -- Barris, Wes -- Bennett, Gary L -- Eggen, Andre -- Green, Ronnie D -- Harhay, Gregory P -- Hobbs, Matthew -- Jann, Oliver -- Keele, John W -- Kent, Matthew P -- Lien, Sigbjorn -- McKay, Stephanie D -- McWilliam, Sean -- Ratnakumar, Abhirami -- Schnabel, Robert D -- Smith, Timothy -- Snelling, Warren M -- Sonstegard, Tad S -- Stone, Roger T -- Sugimoto, Yoshikazu -- Takasuga, Akiko -- Taylor, Jeremy F -- Van Tassell, Curtis P -- Macneil, Michael D -- Abatepaulo, Antonio R R -- Abbey, Colette A -- Ahola, Virpi -- Almeida, Iassudara G -- Amadio, Ariel F -- Anatriello, Elen -- Bahadue, Suria M -- Biase, Fernando H -- Boldt, Clayton R -- Carroll, Jeffery A -- Carvalho, Wanessa A -- Cervelatti, Eliane P -- Chacko, Elsa -- Chapin, Jennifer E -- Cheng, Ye -- Choi, Jungwoo -- Colley, Adam J -- de Campos, Tatiana A -- De Donato, Marcos -- Santos, Isabel K F de Miranda -- de Oliveira, Carlo J F -- Deobald, Heather -- Devinoy, Eve -- Donohue, Kaitlin E -- Dovc, Peter -- Eberlein, Annett -- Fitzsimmons, Carolyn J -- Franzin, Alessandra M -- Garcia, Gustavo R -- Genini, Sem -- Gladney, Cody J -- Grant, Jason R -- Greaser, Marion L -- Green, Jonathan A -- Hadsell, Darryl L -- Hakimov, Hatam A -- Halgren, Rob -- Harrow, Jennifer L -- Hart, Elizabeth A -- Hastings, Nicola -- Hernandez, Marta -- Hu, Zhi-Liang -- Ingham, Aaron -- Iso-Touru, Terhi -- Jamis, Catherine -- Jensen, Kirsty -- Kapetis, Dimos -- Kerr, Tovah -- Khalil, Sari S -- Khatib, Hasan -- Kolbehdari, Davood -- Kumar, Charu G -- Kumar, Dinesh -- Leach, Richard -- Lee, Justin C-M -- Li, Changxi -- Logan, Krystin M -- Malinverni, Roberto -- Marques, Elisa -- Martin, William F -- Martins, Natalia F -- Maruyama, Sandra R -- Mazza, Raffaele -- McLean, Kim L -- Medrano, Juan F -- Moreno, Barbara T -- More, Daniela D -- Muntean, Carl T -- Nandakumar, Hari P -- Nogueira, Marcelo F G -- Olsaker, Ingrid -- Pant, Sameer D -- Panzitta, Francesca -- Pastor, Rosemeire C P -- Poli, Mario A -- Poslusny, Nathan -- Rachagani, Satyanarayana -- Ranganathan, Shoba -- Razpet, Andrej -- Riggs, Penny K -- Rincon, Gonzalo -- Rodriguez-Osorio, Nelida -- Rodriguez-Zas, Sandra L -- Romero, Natasha E -- Rosenwald, Anne -- Sando, Lillian -- Schmutz, Sheila M -- Shen, Libing -- Sherman, Laura -- Southey, Bruce R -- Lutzow, Ylva Strandberg -- Sweedler, Jonathan V -- Tammen, Imke -- Telugu, Bhanu Prakash V L -- Urbanski, Jennifer M -- Utsunomiya, Yuri T -- Verschoor, Chris P -- Waardenberg, Ashley J -- Wang, Zhiquan -- Ward, Robert -- Weikard, Rosemarie -- Welsh, Thomas H Jr -- White, Stephen N -- Wilming, Laurens G -- Wunderlich, Kris R -- Yang, Jianqi -- Zhao, Feng-Qi -- 062023/Wellcome Trust/United Kingdom -- 077198/Wellcome Trust/United Kingdom -- BBS/B/13438/Biotechnology and Biological Sciences Research Council/United Kingdom -- BBS/B/13446/Biotechnology and Biological Sciences Research Council/United Kingdom -- P30 DA018310/DA/NIDA NIH HHS/ -- U54 HG003273/HG/NHGRI NIH HHS/ -- U54 HG003273-04/HG/NHGRI NIH HHS/ -- U54 HG003273-04S1/HG/NHGRI NIH HHS/ -- U54 HG003273-05/HG/NHGRI NIH HHS/ -- U54 HG003273-05S1/HG/NHGRI NIH HHS/ -- U54 HG003273-05S2/HG/NHGRI NIH HHS/ -- U54 HG003273-06/HG/NHGRI NIH HHS/ -- U54 HG003273-06S1/HG/NHGRI NIH HHS/ -- U54 HG003273-06S2/HG/NHGRI NIH HHS/ -- U54 HG003273-07/HG/NHGRI NIH HHS/ -- U54 HG003273-08/HG/NHGRI NIH HHS/ -- New York, N.Y. -- Science. 2009 Apr 24;324(5926):522-8. doi: 10.1126/science.1169588.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19390049" target="_blank"〉PubMed〈/a〉
    Keywords: Alternative Splicing ; Animals ; Animals, Domestic ; *Biological Evolution ; Cattle ; Evolution, Molecular ; Female ; Genetic Variation ; *Genome ; Humans ; Male ; MicroRNAs/genetics ; Molecular Sequence Data ; Proteins/genetics ; Sequence Analysis, DNA ; Species Specificity ; Synteny
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
    Published by American Association for the Advancement of Science (AAAS)
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  • 2
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    Accurate whole human genome sequencing using reversible terminator chemistry (2008)
    Nature Publishing Group (NPG)
    Details
    Publication Date: 2008-11-07
    Description: DNA sequence information underpins genetic research, enabling discoveries of important biological or medical benefit. Sequencing projects have traditionally used long (400-800 base pair) reads, but the existence of reference sequences for the human and many other genomes makes it possible to develop new, fast approaches to re-sequencing, whereby shorter reads are compared to a reference to identify intraspecies genetic variation. Here we report an approach that generates several billion bases of accurate nucleotide sequence per experiment at low cost. Single molecules of DNA are attached to a flat surface, amplified in situ and used as templates for synthetic sequencing with fluorescent reversible terminator deoxyribonucleotides. Images of the surface are analysed to generate high-quality sequence. We demonstrate application of this approach to human genome sequencing on flow-sorted X chromosomes and then scale the approach to determine the genome sequence of a male Yoruba from Ibadan, Nigeria. We build an accurate consensus sequence from 〉30x average depth of paired 35-base reads. We characterize four million single-nucleotide polymorphisms and four hundred thousand structural variants, many of which were previously unknown. Our approach is effective for accurate, rapid and economical whole-genome re-sequencing and many other biomedical applications.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2581791/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2581791/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Bentley, David R -- Balasubramanian, Shankar -- Swerdlow, Harold P -- Smith, Geoffrey P -- Milton, John -- Brown, Clive G -- Hall, Kevin P -- Evers, Dirk J -- Barnes, Colin L -- Bignell, Helen R -- Boutell, Jonathan M -- Bryant, Jason -- Carter, Richard J -- Keira Cheetham, R -- Cox, Anthony J -- Ellis, Darren J -- Flatbush, Michael R -- Gormley, Niall A -- Humphray, Sean J -- Irving, Leslie J -- Karbelashvili, Mirian S -- Kirk, Scott M -- Li, Heng -- Liu, Xiaohai -- Maisinger, Klaus S -- Murray, Lisa J -- Obradovic, Bojan -- Ost, Tobias -- Parkinson, Michael L -- Pratt, Mark R -- Rasolonjatovo, Isabelle M J -- Reed, Mark T -- Rigatti, Roberto -- Rodighiero, Chiara -- Ross, Mark T -- Sabot, Andrea -- Sankar, Subramanian V -- Scally, Aylwyn -- Schroth, Gary P -- Smith, Mark E -- Smith, Vincent P -- Spiridou, Anastassia -- Torrance, Peta E -- Tzonev, Svilen S -- Vermaas, Eric H -- Walter, Klaudia -- Wu, Xiaolin -- Zhang, Lu -- Alam, Mohammed D -- Anastasi, Carole -- Aniebo, Ify C -- Bailey, David M D -- Bancarz, Iain R -- Banerjee, Saibal -- Barbour, Selena G -- Baybayan, Primo A -- Benoit, Vincent A -- Benson, Kevin F -- Bevis, Claire -- Black, Phillip J -- Boodhun, Asha -- Brennan, Joe S -- Bridgham, John A -- Brown, Rob C -- Brown, Andrew A -- Buermann, Dale H -- Bundu, Abass A -- Burrows, James C -- Carter, Nigel P -- Castillo, Nestor -- Chiara E Catenazzi, Maria -- Chang, Simon -- Neil Cooley, R -- Crake, Natasha R -- Dada, Olubunmi O -- Diakoumakos, Konstantinos D -- Dominguez-Fernandez, Belen -- Earnshaw, David J -- Egbujor, Ugonna C -- Elmore, David W -- Etchin, Sergey S -- Ewan, Mark R -- Fedurco, Milan -- Fraser, Louise J -- Fuentes Fajardo, Karin V -- Scott Furey, W -- George, David -- Gietzen, Kimberley J -- Goddard, Colin P -- Golda, George S -- Granieri, Philip A -- Green, David E -- Gustafson, David L -- Hansen, Nancy F -- Harnish, Kevin -- Haudenschild, Christian D -- Heyer, Narinder I -- Hims, Matthew M -- Ho, Johnny T -- Horgan, Adrian M -- Hoschler, Katya -- Hurwitz, Steve -- Ivanov, Denis V -- Johnson, Maria Q -- James, Terena -- Huw Jones, T A -- Kang, Gyoung-Dong -- Kerelska, Tzvetana H -- Kersey, Alan D -- Khrebtukova, Irina -- Kindwall, Alex P -- Kingsbury, Zoya -- Kokko-Gonzales, Paula I -- Kumar, Anil -- Laurent, Marc A -- Lawley, Cynthia T -- Lee, Sarah E -- Lee, Xavier -- Liao, Arnold K -- Loch, Jennifer A -- Lok, Mitch -- Luo, Shujun -- Mammen, Radhika M -- Martin, John W -- McCauley, Patrick G -- McNitt, Paul -- Mehta, Parul -- Moon, Keith W -- Mullens, Joe W -- Newington, Taksina -- Ning, Zemin -- Ling Ng, Bee -- Novo, Sonia M -- O'Neill, Michael J -- Osborne, Mark A -- Osnowski, Andrew -- Ostadan, Omead -- Paraschos, Lambros L -- Pickering, Lea -- Pike, Andrew C -- Pike, Alger C -- Chris Pinkard, D -- Pliskin, Daniel P -- Podhasky, Joe -- Quijano, Victor J -- Raczy, Come -- Rae, Vicki H -- Rawlings, Stephen R -- Chiva Rodriguez, Ana -- Roe, Phyllida M -- Rogers, John -- Rogert Bacigalupo, Maria C -- Romanov, Nikolai -- Romieu, Anthony -- Roth, Rithy K -- Rourke, Natalie J -- Ruediger, Silke T -- Rusman, Eli -- Sanches-Kuiper, Raquel M -- Schenker, Martin R -- Seoane, Josefina M -- Shaw, Richard J -- Shiver, Mitch K -- Short, Steven W -- Sizto, Ning L -- Sluis, Johannes P -- Smith, Melanie A -- Ernest Sohna Sohna, Jean -- Spence, Eric J -- Stevens, Kim -- Sutton, Neil -- Szajkowski, Lukasz -- Tregidgo, Carolyn L -- Turcatti, Gerardo -- Vandevondele, Stephanie -- Verhovsky, Yuli -- Virk, Selene M -- Wakelin, Suzanne -- Walcott, Gregory C -- Wang, Jingwen -- Worsley, Graham J -- Yan, Juying -- Yau, Ling -- Zuerlein, Mike -- Rogers, Jane -- Mullikin, James C -- Hurles, Matthew E -- McCooke, Nick J -- West, John S -- Oaks, Frank L -- Lundberg, Peter L -- Klenerman, David -- Durbin, Richard -- Smith, Anthony J -- B05823/Biotechnology and Biological Sciences Research Council/United Kingdom -- G0701805/Medical Research Council/United Kingdom -- MOL04534/Biotechnology and Biological Sciences Research Council/United Kingdom -- Z01 HG200330-03/Intramural NIH HHS/ -- Biotechnology and Biological Sciences Research Council/United Kingdom -- Wellcome Trust/United Kingdom -- England -- Nature. 2008 Nov 6;456(7218):53-9. doi: 10.1038/nature07517.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Illumina Cambridge Ltd. (Formerly Solexa Ltd), Chesterford Research Park, Little Chesterford, Nr Saffron Walden, Essex CB10 1XL, UK. dbentley@illumina.com〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18987734" target="_blank"〉PubMed〈/a〉
    Keywords: Chromosomes, Human, X/genetics ; Consensus Sequence/genetics ; Genome, Human/*genetics ; Genomics/economics/*methods ; Genotype ; Humans ; Male ; Nigeria ; Polymorphism, Single Nucleotide/genetics ; Sensitivity and Specificity ; Sequence Analysis, DNA/economics/*methods
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
    Published by Nature Publishing Group (NPG)
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  • 3
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    The genome of the model beetle and pest Tribolium castaneum (2008)
    Nature Publishing Group (NPG)
    Details
    Publication Date: 2008-03-26
    Description: Tribolium castaneum is a member of the most species-rich eukaryotic order, a powerful model organism for the study of generalized insect development, and an important pest of stored agricultural products. We describe its genome sequence here. This omnivorous beetle has evolved the ability to interact with a diverse chemical environment, as shown by large expansions in odorant and gustatory receptors, as well as P450 and other detoxification enzymes. Development in Tribolium is more representative of other insects than is Drosophila, a fact reflected in gene content and function. For example, Tribolium has retained more ancestral genes involved in cell-cell communication than Drosophila, some being expressed in the growth zone crucial for axial elongation in short-germ development. Systemic RNA interference in T. castaneum functions differently from that in Caenorhabditis elegans, but nevertheless offers similar power for the elucidation of gene function and identification of targets for selective insect control.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Tribolium Genome Sequencing Consortium -- Richards, Stephen -- Gibbs, Richard A -- Weinstock, George M -- Brown, Susan J -- Denell, Robin -- Beeman, Richard W -- Gibbs, Richard -- Bucher, Gregor -- Friedrich, Markus -- Grimmelikhuijzen, Cornelis J P -- Klingler, Martin -- Lorenzen, Marce -- Roth, Siegfried -- Schroder, Reinhard -- Tautz, Diethard -- Zdobnov, Evgeny M -- Muzny, Donna -- Attaway, Tony -- Bell, Stephanie -- Buhay, Christian J -- Chandrabose, Mimi N -- Chavez, Dean -- Clerk-Blankenburg, Kerstin P -- Cree, Andrew -- Dao, Marvin -- Davis, Clay -- Chacko, Joseph -- Dinh, Huyen -- Dugan-Rocha, Shannon -- Fowler, Gerald -- Garner, Toni T -- Garnes, Jeffrey -- Gnirke, Andreas -- Hawes, Alica -- Hernandez, Judith -- Hines, Sandra -- Holder, Michael -- Hume, Jennifer -- Jhangiani, Shalini N -- Joshi, Vandita -- Khan, Ziad Mohid -- Jackson, LaRonda -- Kovar, Christie -- Kowis, Andrea -- Lee, Sandra -- Lewis, Lora R -- Margolis, Jon -- Morgan, Margaret -- Nazareth, Lynne V -- Nguyen, Ngoc -- Okwuonu, Geoffrey -- Parker, David -- Ruiz, San-Juana -- Santibanez, Jireh -- Savard, Joel -- Scherer, Steven E -- Schneider, Brian -- Sodergren, Erica -- Vattahil, Selina -- Villasana, Donna -- White, Courtney S -- Wright, Rita -- Park, Yoonseong -- Lord, Jeff -- Oppert, Brenda -- Brown, Susan -- Wang, Liangjiang -- Weinstock, George -- Liu, Yue -- Worley, Kim -- Elsik, Christine G -- Reese, Justin T -- Elhaik, Eran -- Landan, Giddy -- Graur, Dan -- Arensburger, Peter -- Atkinson, Peter -- Beidler, Jim -- Demuth, Jeffery P -- Drury, Douglas W -- Du, Yu-Zhou -- Fujiwara, Haruhiko -- Maselli, Vincenza -- Osanai, Mizuko -- Robertson, Hugh M -- Tu, Zhijian -- Wang, Jian-jun -- Wang, Suzhi -- Song, Henry -- Zhang, Lan -- Werner, Doreen -- Stanke, Mario -- Morgenstern, Burkhard -- Solovyev, Victor -- Kosarev, Peter -- Brown, Garth -- Chen, Hsiu-Chuan -- Ermolaeva, Olga -- Hlavina, Wratko -- Kapustin, Yuri -- Kiryutin, Boris -- Kitts, Paul -- Maglott, Donna -- Pruitt, Kim -- Sapojnikov, Victor -- Souvorov, Alexandre -- Mackey, Aaron J -- Waterhouse, Robert M -- Wyder, Stefan -- Kriventseva, Evgenia V -- Kadowaki, Tatsuhiko -- Bork, Peer -- Aranda, Manuel -- Bao, Riyue -- Beermann, Anke -- Berns, Nicola -- Bolognesi, Renata -- Bonneton, Francois -- Bopp, Daniel -- Butts, Thomas -- Chaumot, Arnaud -- Denell, Robin E -- Ferrier, David E K -- Gordon, Cassondra M -- Jindra, Marek -- Lan, Que -- Lattorff, H Michael G -- Laudet, Vincent -- von Levetsow, Cornelia -- Liu, Zhenyi -- Lutz, Rebekka -- Lynch, Jeremy A -- da Fonseca, Rodrigo Nunes -- Posnien, Nico -- Reuter, Rolf -- Schinko, Johannes B -- Schmitt, Christian -- Schoppmeier, Michael -- Shippy, Teresa D -- Simonnet, Franck -- Marques-Souza, Henrique -- Tomoyasu, Yoshinori -- Trauner, Jochen -- Van der Zee, Maurijn -- Vervoort, Michel -- Wittkopp, Nadine -- Wimmer, Ernst A -- Yang, Xiaoyun -- Jones, Andrew K -- Sattelle, David B -- Ebert, Paul R -- Nelson, David -- Scott, Jeffrey G -- Muthukrishnan, Subbaratnam -- Kramer, Karl J -- Arakane, Yasuyuki -- Zhu, Qingsong -- Hogenkamp, David -- Dixit, Radhika -- Jiang, Haobo -- Zou, Zhen -- Marshall, Jeremy -- Elpidina, Elena -- Vinokurov, Konstantin -- Oppert, Cris -- Evans, Jay -- Lu, Zhiqiang -- Zhao, Picheng -- Sumathipala, Niranji -- Altincicek, Boran -- Vilcinskas, Andreas -- Williams, Michael -- Hultmark, Dan -- Hetru, Charles -- Hauser, Frank -- Cazzamali, Giuseppe -- Williamson, Michael -- Li, Bin -- Tanaka, Yoshiaki -- Predel, Reinhard -- Neupert, Susanne -- Schachtner, Joachim -- Verleyen, Peter -- Raible, Florian -- Walden, Kimberly K O -- Angeli, Sergio -- Foret, Sylvain -- Schuetz, Stefan -- Maleszka, Ryszard -- Miller, Sherry C -- Grossmann, Daniela -- BBS/B/12067/Biotechnology and Biological Sciences Research Council/United Kingdom -- BBS/B/12067/2/Biotechnology and Biological Sciences Research Council/United Kingdom -- R01 GM058634/GM/NIGMS NIH HHS/ -- R01 HD029594/HD/NICHD NIH HHS/ -- R01 HD029594-16/HD/NICHD NIH HHS/ -- U54 HG003273/HG/NHGRI NIH HHS/ -- Intramural NIH HHS/ -- England -- Nature. 2008 Apr 24;452(7190):949-55. doi: 10.1038/nature06784. Epub 2008 Mar 23.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Human Genome Sequencing Center, Baylor College of Medicine, One Baylor Plaza, Houston, Texas 77030, USA. stephenr@bcm.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18362917" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Base Composition ; Body Patterning/genetics ; Cytochrome P-450 Enzyme System/genetics ; DNA Transposable Elements/genetics ; Genes, Insect/*genetics ; Genome, Insect/*genetics ; Growth and Development/genetics ; Humans ; Insecticides/pharmacology ; Neurotransmitter Agents/genetics ; Oogenesis/genetics ; Phylogeny ; Proteome/genetics ; RNA Interference ; Receptors, G-Protein-Coupled/genetics ; Receptors, Odorant/genetics ; Repetitive Sequences, Nucleic Acid/genetics ; Taste/genetics ; Telomere/genetics ; Tribolium/classification/embryology/*genetics/physiology ; Vision, Ocular/genetics
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
    Published by Nature Publishing Group (NPG)
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  • 4
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    Evolutionary and biomedical insights from the rhesus macaque genome (2007)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2007-04-14
    Description: 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 used nonhuman primate in basic and applied biomedical research. We determined the genome sequence of an Indian-origin Macaca mulatta female and compared the data with chimpanzees and humans to reveal the structure of ancestral primate genomes and to identify evidence for positive selection and lineage-specific expansions and contractions of gene families. A comparison of sequences from individual animals was used to investigate their underlying genetic diversity. The complete description of the macaque genome blueprint enhances the utility of this animal model for biomedical research and improves our understanding of the basic biology of the species.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Rhesus Macaque Genome Sequencing and Analysis Consortium -- Gibbs, Richard A -- Rogers, Jeffrey -- Katze, Michael G -- Bumgarner, Roger -- Weinstock, George M -- Mardis, Elaine R -- Remington, Karin A -- Strausberg, Robert L -- Venter, J Craig -- Wilson, Richard K -- Batzer, Mark A -- Bustamante, Carlos D -- Eichler, Evan E -- Hahn, Matthew W -- Hardison, Ross C -- Makova, Kateryna D -- Miller, Webb -- Milosavljevic, Aleksandar -- Palermo, Robert E -- Siepel, Adam -- Sikela, James M -- Attaway, Tony -- Bell, Stephanie -- Bernard, Kelly E -- Buhay, Christian J -- Chandrabose, Mimi N -- Dao, Marvin -- Davis, Clay -- Delehaunty, Kimberly D -- Ding, Yan -- Dinh, Huyen H -- Dugan-Rocha, Shannon -- Fulton, Lucinda A -- Gabisi, Ramatu Ayiesha -- Garner, Toni T -- Godfrey, Jennifer -- Hawes, Alicia C -- Hernandez, Judith -- Hines, Sandra -- Holder, Michael -- Hume, Jennifer -- Jhangiani, Shalini N -- Joshi, Vandita -- Khan, Ziad Mohid -- Kirkness, Ewen F -- Cree, Andrew -- Fowler, R Gerald -- Lee, Sandra -- Lewis, Lora R -- Li, Zhangwan -- Liu, Yih-Shin -- Moore, Stephanie M -- Muzny, Donna -- Nazareth, Lynne V -- Ngo, Dinh Ngoc -- Okwuonu, Geoffrey O -- Pai, Grace -- Parker, David -- Paul, Heidie A -- Pfannkoch, Cynthia -- Pohl, Craig S -- Rogers, Yu-Hui -- Ruiz, San Juana -- Sabo, Aniko -- Santibanez, Jireh -- Schneider, Brian W -- Smith, Scott M -- Sodergren, Erica -- Svatek, Amanda F -- Utterback, Teresa R -- Vattathil, Selina -- Warren, Wesley -- White, Courtney Sherell -- Chinwalla, Asif T -- Feng, Yucheng -- Halpern, Aaron L -- Hillier, Ladeana W -- Huang, Xiaoqiu -- Minx, Pat -- Nelson, Joanne O -- Pepin, Kymberlie H -- Qin, Xiang -- Sutton, Granger G -- Venter, Eli -- Walenz, Brian P -- Wallis, John W -- Worley, Kim C -- Yang, Shiaw-Pyng -- Jones, Steven M -- Marra, Marco A -- Rocchi, Mariano -- Schein, Jacqueline E -- Baertsch, Robert -- Clarke, Laura -- Csuros, Miklos -- Glasscock, Jarret -- Harris, R Alan -- Havlak, Paul -- Jackson, Andrew R -- Jiang, Huaiyang -- Liu, Yue -- Messina, David N -- Shen, Yufeng -- Song, Henry Xing-Zhi -- Wylie, Todd -- Zhang, Lan -- Birney, Ewan -- Han, Kyudong -- Konkel, Miriam K -- Lee, Jungnam -- Smit, Arian F A -- Ullmer, Brygg -- Wang, Hui -- Xing, Jinchuan -- Burhans, Richard -- Cheng, Ze -- Karro, John E -- Ma, Jian -- Raney, Brian -- She, Xinwei -- Cox, Michael J -- Demuth, Jeffery P -- Dumas, Laura J -- Han, Sang-Gook -- Hopkins, Janet -- Karimpour-Fard, Anis -- Kim, Young H -- Pollack, Jonathan R -- Vinar, Tomas -- Addo-Quaye, Charles -- Degenhardt, Jeremiah -- Denby, Alexandra -- Hubisz, Melissa J -- Indap, Amit -- Kosiol, Carolin -- Lahn, Bruce T -- Lawson, Heather A -- Marklein, Alison -- Nielsen, Rasmus -- Vallender, Eric J -- Clark, Andrew G -- Ferguson, Betsy -- Hernandez, Ryan D -- Hirani, Kashif -- Kehrer-Sawatzki, Hildegard -- Kolb, Jessica -- Patil, Shobha -- Pu, Ling-Ling -- Ren, Yanru -- Smith, David Glenn -- Wheeler, David A -- Schenck, Ian -- Ball, Edward V -- Chen, Rui -- Cooper, David N -- Giardine, Belinda -- Hsu, Fan -- Kent, W James -- Lesk, Arthur -- Nelson, David L -- O'brien, William E -- Prufer, Kay -- Stenson, Peter D -- Wallace, James C -- Ke, Hui -- Liu, Xiao-Ming -- Wang, Peng -- Xiang, Andy Peng -- Yang, Fan -- Barber, Galt P -- Haussler, David -- Karolchik, Donna -- Kern, Andy D -- Kuhn, Robert M -- Smith, Kayla E -- Zwieg, Ann S -- 062023/Wellcome Trust/United Kingdom -- R01 HG002939/HG/NHGRI NIH HHS/ -- U54 HG003068/HG/NHGRI NIH HHS/ -- U54 HG003079/HG/NHGRI NIH HHS/ -- U54 HG003273/HG/NHGRI NIH HHS/ -- New York, N.Y. -- Science. 2007 Apr 13;316(5822):222-34.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA. agibbs@bcm.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/17431167" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Biomedical Research ; *Evolution, Molecular ; Female ; Gene Duplication ; Gene Rearrangement ; Genetic Diseases, Inborn ; Genetic Variation ; *Genome ; Humans ; Macaca mulatta/*genetics ; Male ; Multigene Family ; Mutation ; Pan troglodytes/genetics ; Sequence Analysis, DNA ; Species Specificity
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
    Published by American Association for the Advancement of Science (AAAS)
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  • 5
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    Gender differences and performance in science (2005)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2005-02-19
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Muller, Carol B -- Ride, Sally M -- Fouke, Janie -- Whitney, Telle -- Denton, Denice D -- Cantor, Nancy -- Nelson, Donna J -- Plummer, Jim -- Busch-Vishniac, Ilene -- Meyers, Carolyn -- Rosser, Sue V -- Schiebinger, Londa -- Roberts, Eric -- Burgess, David -- Beeson, Craig -- Metz, Susan Staffin -- Sanders, Lucinda -- Watford, Bevlee A -- Ivey, Elizabeth S -- Frank Fox, Mary -- Wettack, Sheldon -- Klawe, Maria -- Wulf, William A -- Girgus, Joan -- Leboy, Phoebe S -- Babco, Eleanor L -- Shanahan, Betty -- Didion, Catherine -- Chubin, Daryl E -- Frize, Monique -- Ganter, Susan L -- Nalley, E Ann -- Franz, Judy -- Abruna, Hector D -- Strober, Myra H -- Zimmer Daniels, Jane -- Carter, Emily A -- Rhodes, Jean H -- Schrijver, Iris -- Zakian, Virginia A -- Simons, Barbara -- Martin, Ursula -- Boaler, Jo -- Jolluck, Katherine Rose -- Mankekar, Purnima -- Gray, Robert M -- Conkey, Margaret W -- Stansky, Peter -- Xie, Aihua -- Martin, Pino -- Katehi, Linda P B -- Miller, Jo Anne -- Tess Thornton, Amelia -- Lapaugh, Andrea -- Rhode, Deborah L -- Gelpi, Barbara C -- Harrold, Mary Jean -- Spencer, Cherrill M -- Schlatter Ellis, Carla -- Lord, Susan -- Quinn, Helen -- Murnane, Margaret -- Jones, Patricia P -- Hellman, Frances -- Wight, Gail -- O'hara, Ruth -- Pickering, Mary -- Sheppard, Sheri -- Leith, David -- Paytan, Adina -- Sommer, Matthew H -- Shafer, Audrey -- Grusky, David -- Yennello, Sherry -- Madan, Ashima -- Johnson, Denise L -- Yanagisako, Sylvia -- Chou-Green, Jennifer M -- Robinson, Sandra -- New York, N.Y. -- Science. 2005 Feb 18;307(5712):1043.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/15718449" target="_blank"〉PubMed〈/a〉
    Keywords: *Career Choice ; Female ; Humans ; Male ; *Science ; *Sex Characteristics ; Social Change
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
    Published by American Association for the Advancement of Science (AAAS)
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  • 6
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    Genome sequence of Aedes aegypti, a major arbovirus vector (2007)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2007-05-19
    Description: We present a draft sequence of the genome of Aedes aegypti, the primary vector for yellow fever and dengue fever, which at approximately 1376 million base pairs is about 5 times the size of the genome of the malaria vector Anopheles gambiae. Nearly 50% of the Ae. aegypti genome consists of transposable elements. These contribute to a factor of approximately 4 to 6 increase in average gene length and in sizes of intergenic regions relative to An. gambiae and Drosophila melanogaster. Nonetheless, chromosomal synteny is generally maintained among all three insects, although conservation of orthologous gene order is higher (by a factor of approximately 2) between the mosquito species than between either of them and the fruit fly. An increase in genes encoding odorant binding, cytochrome P450, and cuticle domains relative to An. gambiae suggests that members of these protein families underpin some of the biological differences between the two mosquito species.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2868357/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2868357/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Nene, Vishvanath -- Wortman, Jennifer R -- Lawson, Daniel -- Haas, Brian -- Kodira, Chinnappa -- Tu, Zhijian Jake -- Loftus, Brendan -- Xi, Zhiyong -- Megy, Karyn -- Grabherr, Manfred -- Ren, Quinghu -- Zdobnov, Evgeny M -- Lobo, Neil F -- Campbell, Kathryn S -- Brown, Susan E -- Bonaldo, Maria F -- Zhu, Jingsong -- Sinkins, Steven P -- Hogenkamp, David G -- Amedeo, Paolo -- Arensburger, Peter -- Atkinson, Peter W -- Bidwell, Shelby -- Biedler, Jim -- Birney, Ewan -- Bruggner, Robert V -- Costas, Javier -- Coy, Monique R -- Crabtree, Jonathan -- Crawford, Matt -- Debruyn, Becky -- Decaprio, David -- Eiglmeier, Karin -- Eisenstadt, Eric -- El-Dorry, Hamza -- Gelbart, William M -- Gomes, Suely L -- Hammond, Martin -- Hannick, Linda I -- Hogan, James R -- Holmes, Michael H -- Jaffe, David -- Johnston, J Spencer -- Kennedy, Ryan C -- Koo, Hean -- Kravitz, Saul -- Kriventseva, Evgenia V -- Kulp, David -- Labutti, Kurt -- Lee, Eduardo -- Li, Song -- Lovin, Diane D -- Mao, Chunhong -- Mauceli, Evan -- Menck, Carlos F M -- Miller, Jason R -- Montgomery, Philip -- Mori, Akio -- Nascimento, Ana L -- Naveira, Horacio F -- Nusbaum, Chad -- O'leary, Sinead -- Orvis, Joshua -- Pertea, Mihaela -- Quesneville, Hadi -- Reidenbach, Kyanne R -- Rogers, Yu-Hui -- Roth, Charles W -- Schneider, Jennifer R -- Schatz, Michael -- Shumway, Martin -- Stanke, Mario -- Stinson, Eric O -- Tubio, Jose M C -- Vanzee, Janice P -- Verjovski-Almeida, Sergio -- Werner, Doreen -- White, Owen -- Wyder, Stefan -- Zeng, Qiandong -- Zhao, Qi -- Zhao, Yongmei -- Hill, Catherine A -- Raikhel, Alexander S -- Soares, Marcelo B -- Knudson, Dennis L -- Lee, Norman H -- Galagan, James -- Salzberg, Steven L -- Paulsen, Ian T -- Dimopoulos, George -- Collins, Frank H -- Birren, Bruce -- Fraser-Liggett, Claire M -- Severson, David W -- 079059/Wellcome Trust/United Kingdom -- 5 R01 AI61576-2/AI/NIAID NIH HHS/ -- R01 AI059492/AI/NIAID NIH HHS/ -- R01 LM006845/LM/NLM NIH HHS/ -- R01 LM006845-08/LM/NLM NIH HHS/ -- R37 AI024716/AI/NIAID NIH HHS/ -- UO1 AI50936/AI/NIAID NIH HHS/ -- New York, N.Y. -- Science. 2007 Jun 22;316(5832):1718-23. Epub 2007 May 17.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Institute for Genomic Research, 9712 Medical Center Drive, Rockville, MD 20850, USA. nene@tigr.org〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/17510324" target="_blank"〉PubMed〈/a〉
    Keywords: Aedes/*genetics/metabolism ; Animals ; Anopheles gambiae/genetics/metabolism ; Arboviruses ; Base Sequence ; DNA Transposable Elements ; Dengue/prevention & control/transmission ; Drosophila melanogaster/genetics ; Female ; Genes, Insect ; *Genome, Insect ; Humans ; Insect Proteins/genetics ; Insect Vectors/*genetics/metabolism ; Male ; Membrane Transport Proteins/genetics ; Molecular Sequence Data ; Multigene Family ; Protein Structure, Tertiary/genetics ; Sequence Analysis, DNA ; Sex Characteristics ; Sex Determination Processes ; Species Specificity ; Synteny ; Transcription, Genetic ; Yellow Fever/prevention & control/transmission
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
    Published by American Association for the Advancement of Science (AAAS)
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  • 7
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    Somatic mutations affect key pathways in lung adenocarcinoma (2008)
    Nature Publishing Group (NPG)
    Details
    Publication Date: 2008-10-25
    Description: Determining the genetic basis of cancer requires comprehensive analyses of large collections of histopathologically well-classified primary tumours. Here we report the results of a collaborative study to discover somatic mutations in 188 human lung adenocarcinomas. DNA sequencing of 623 genes with known or potential relationships to cancer revealed more than 1,000 somatic mutations across the samples. Our analysis identified 26 genes that are mutated at significantly high frequencies and thus are probably involved in carcinogenesis. The frequently mutated genes include tyrosine kinases, among them the EGFR homologue ERBB4; multiple ephrin receptor genes, notably EPHA3; vascular endothelial growth factor receptor KDR; and NTRK genes. These data provide evidence of somatic mutations in primary lung adenocarcinoma for several tumour suppressor genes involved in other cancers--including NF1, APC, RB1 and ATM--and for sequence changes in PTPRD as well as the frequently deleted gene LRP1B. The observed mutational profiles correlate with clinical features, smoking status and DNA repair defects. These results are reinforced by data integration including single nucleotide polymorphism array and gene expression array. Our findings shed further light on several important signalling pathways involved in lung adenocarcinoma, and suggest new molecular targets for treatment.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2694412/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2694412/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Ding, Li -- Getz, Gad -- Wheeler, David A -- Mardis, Elaine R -- McLellan, Michael D -- Cibulskis, Kristian -- Sougnez, Carrie -- Greulich, Heidi -- Muzny, Donna M -- Morgan, Margaret B -- Fulton, Lucinda -- Fulton, Robert S -- Zhang, Qunyuan -- Wendl, Michael C -- Lawrence, Michael S -- Larson, David E -- Chen, Ken -- Dooling, David J -- Sabo, Aniko -- Hawes, Alicia C -- Shen, Hua -- Jhangiani, Shalini N -- Lewis, Lora R -- Hall, Otis -- Zhu, Yiming -- Mathew, Tittu -- Ren, Yanru -- Yao, Jiqiang -- Scherer, Steven E -- Clerc, Kerstin -- Metcalf, Ginger A -- Ng, Brian -- Milosavljevic, Aleksandar -- Gonzalez-Garay, Manuel L -- Osborne, John R -- Meyer, Rick -- Shi, Xiaoqi -- Tang, Yuzhu -- Koboldt, Daniel C -- Lin, Ling -- Abbott, Rachel -- Miner, Tracie L -- Pohl, Craig -- Fewell, Ginger -- Haipek, Carrie -- Schmidt, Heather -- Dunford-Shore, Brian H -- Kraja, Aldi -- Crosby, Seth D -- Sawyer, Christopher S -- Vickery, Tammi -- Sander, Sacha -- Robinson, Jody -- Winckler, Wendy -- Baldwin, Jennifer -- Chirieac, Lucian R -- Dutt, Amit -- Fennell, Tim -- Hanna, Megan -- Johnson, Bruce E -- Onofrio, Robert C -- Thomas, Roman K -- Tonon, Giovanni -- Weir, Barbara A -- Zhao, Xiaojun -- Ziaugra, Liuda -- Zody, Michael C -- Giordano, Thomas -- Orringer, Mark B -- Roth, Jack A -- Spitz, Margaret R -- Wistuba, Ignacio I -- Ozenberger, Bradley -- Good, Peter J -- Chang, Andrew C -- Beer, David G -- Watson, Mark A -- Ladanyi, Marc -- Broderick, Stephen -- Yoshizawa, Akihiko -- Travis, William D -- Pao, William -- Province, Michael A -- Weinstock, George M -- Varmus, Harold E -- Gabriel, Stacey B -- Lander, Eric S -- Gibbs, Richard A -- Meyerson, Matthew -- Wilson, Richard K -- P50 CA070907/CA/NCI NIH HHS/ -- R01 CA154365/CA/NCI NIH HHS/ -- U19 CA084953/CA/NCI NIH HHS/ -- U19 CA084953-050003/CA/NCI NIH HHS/ -- U54 HG003067/HG/NHGRI NIH HHS/ -- U54 HG003067-04/HG/NHGRI NIH HHS/ -- U54 HG003273/HG/NHGRI NIH HHS/ -- England -- Nature. 2008 Oct 23;455(7216):1069-75. doi: 10.1038/nature07423.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉The Genome Center at Washington University, Department of Genetics, Washington University School of Medicine, St Louis, Missouri 63108, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18948947" target="_blank"〉PubMed〈/a〉
    Keywords: Adenocarcinoma, Bronchiolo-Alveolar/*genetics ; Female ; Gene Dosage ; Gene Expression Regulation, Neoplastic ; Genes, Tumor Suppressor ; Humans ; Lung Neoplasms/*genetics ; Male ; Mutation/*genetics ; Proto-Oncogenes/genetics
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
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  • 8
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    The genome of the African trypanosome Trypanosoma brucei (2005)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2005-07-16
    Description: African trypanosomes cause human sleeping sickness and livestock trypanosomiasis in sub-Saharan Africa. We present the sequence and analysis of the 11 megabase-sized chromosomes of Trypanosoma brucei. The 26-megabase genome contains 9068 predicted genes, including approximately 900 pseudogenes and approximately 1700 T. brucei-specific genes. Large subtelomeric arrays contain an archive of 806 variant surface glycoprotein (VSG) genes used by the parasite to evade the mammalian immune system. Most VSG genes are pseudogenes, which may be used to generate expressed mosaic genes by ectopic recombination. Comparisons of the cytoskeleton and endocytic trafficking systems with those of humans and other eukaryotic organisms reveal major differences. A comparison of metabolic pathways encoded by the genomes of T. brucei, T. cruzi, and Leishmania major reveals the least overall metabolic capability in T. brucei and the greatest in L. major. Horizontal transfer of genes of bacterial origin has contributed to some of the metabolic differences in these parasites, and a number of novel potential drug targets have been identified.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Berriman, Matthew -- Ghedin, Elodie -- Hertz-Fowler, Christiane -- Blandin, Gaelle -- Renauld, Hubert -- Bartholomeu, Daniella C -- Lennard, Nicola J -- Caler, Elisabet -- Hamlin, Nancy E -- Haas, Brian -- Bohme, Ulrike -- Hannick, Linda -- Aslett, Martin A -- Shallom, Joshua -- Marcello, Lucio -- Hou, Lihua -- Wickstead, Bill -- Alsmark, U Cecilia M -- Arrowsmith, Claire -- Atkin, Rebecca J -- Barron, Andrew J -- Bringaud, Frederic -- Brooks, Karen -- Carrington, Mark -- Cherevach, Inna -- Chillingworth, Tracey-Jane -- Churcher, Carol -- Clark, Louise N -- Corton, Craig H -- Cronin, Ann -- Davies, Rob M -- Doggett, Jonathon -- Djikeng, Appolinaire -- Feldblyum, Tamara -- Field, Mark C -- Fraser, Audrey -- Goodhead, Ian -- Hance, Zahra -- Harper, David -- Harris, Barbara R -- Hauser, Heidi -- Hostetler, Jessica -- Ivens, Al -- Jagels, Kay -- Johnson, David -- Johnson, Justin -- Jones, Kristine -- Kerhornou, Arnaud X -- Koo, Hean -- Larke, Natasha -- Landfear, Scott -- Larkin, Christopher -- Leech, Vanessa -- Line, Alexandra -- Lord, Angela -- Macleod, Annette -- Mooney, Paul J -- Moule, Sharon -- Martin, David M A -- Morgan, Gareth W -- Mungall, Karen -- Norbertczak, Halina -- Ormond, Doug -- Pai, Grace -- Peacock, Chris S -- Peterson, Jeremy -- Quail, Michael A -- Rabbinowitsch, Ester -- Rajandream, Marie-Adele -- Reitter, Chris -- Salzberg, Steven L -- Sanders, Mandy -- Schobel, Seth -- Sharp, Sarah -- Simmonds, Mark -- Simpson, Anjana J -- Tallon, Luke -- Turner, C Michael R -- Tait, Andrew -- Tivey, Adrian R -- Van Aken, Susan -- Walker, Danielle -- Wanless, David -- Wang, Shiliang -- White, Brian -- White, Owen -- Whitehead, Sally -- Woodward, John -- Wortman, Jennifer -- Adams, Mark D -- Embley, T Martin -- Gull, Keith -- Ullu, Elisabetta -- Barry, J David -- Fairlamb, Alan H -- Opperdoes, Fred -- Barrell, Barclay G -- Donelson, John E -- Hall, Neil -- Fraser, Claire M -- Melville, Sara E -- El-Sayed, Najib M -- AI43062/AI/NIAID NIH HHS/ -- R01 AI043062/AI/NIAID NIH HHS/ -- U01 AI043062/AI/NIAID NIH HHS/ -- Wellcome Trust/United Kingdom -- New York, N.Y. -- Science. 2005 Jul 15;309(5733):416-22.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton CB10 1SA, UK. mb4@sanger.ac.uk〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/16020726" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acids/metabolism ; Animals ; Antigenic Variation ; Antigens, Protozoan/chemistry/genetics/immunology ; Carbohydrate Metabolism ; Chromosomes/genetics ; Cytoskeleton/chemistry/genetics/physiology ; Ergosterol/biosynthesis ; Genes, Protozoan ; *Genome, Protozoan ; Glutathione/*analogs & derivatives/metabolism ; Glycosylphosphatidylinositols/biosynthesis ; Humans ; Lipid Metabolism ; Molecular Sequence Data ; Protein Transport ; Protozoan Proteins/chemistry/*genetics/metabolism ; Pseudogenes ; Purines/metabolism ; Pyrimidines/biosynthesis ; Recombination, Genetic ; *Sequence Analysis, DNA ; Spermidine/*analogs & derivatives/metabolism ; Trypanosoma brucei brucei/chemistry/*genetics/immunology/metabolism ; Trypanosomiasis, African/parasitology
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 9
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    DNA sequencing of a cytogenetically normal acute myeloid leukaemia genome (2008)
    Nature Publishing Group (NPG)
    Details
    Publication Date: 2008-11-07
    Description: Acute myeloid leukaemia is a highly malignant haematopoietic tumour that affects about 13,000 adults in the United States each year. The treatment of this disease has changed little in the past two decades, because most of the genetic events that initiate the disease remain undiscovered. Whole-genome sequencing is now possible at a reasonable cost and timeframe to use this approach for the unbiased discovery of tumour-specific somatic mutations that alter the protein-coding genes. Here we present the results obtained from sequencing a typical acute myeloid leukaemia genome, and its matched normal counterpart obtained from the same patient's skin. We discovered ten genes with acquired mutations; two were previously described mutations that are thought to contribute to tumour progression, and eight were new mutations present in virtually all tumour cells at presentation and relapse, the function of which is not yet known. Our study establishes whole-genome sequencing as an unbiased method for discovering cancer-initiating mutations in previously unidentified genes that may respond to targeted therapies.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2603574/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2603574/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Ley, Timothy J -- Mardis, Elaine R -- Ding, Li -- Fulton, Bob -- McLellan, Michael D -- Chen, Ken -- Dooling, David -- Dunford-Shore, Brian H -- McGrath, Sean -- Hickenbotham, Matthew -- Cook, Lisa -- Abbott, Rachel -- Larson, David E -- Koboldt, Dan C -- Pohl, Craig -- Smith, Scott -- Hawkins, Amy -- Abbott, Scott -- Locke, Devin -- Hillier, Ladeana W -- Miner, Tracie -- Fulton, Lucinda -- Magrini, Vincent -- Wylie, Todd -- Glasscock, Jarret -- Conyers, Joshua -- Sander, Nathan -- Shi, Xiaoqi -- Osborne, John R -- Minx, Patrick -- Gordon, David -- Chinwalla, Asif -- Zhao, Yu -- Ries, Rhonda E -- Payton, Jacqueline E -- Westervelt, Peter -- Tomasson, Michael H -- Watson, Mark -- Baty, Jack -- Ivanovich, Jennifer -- Heath, Sharon -- Shannon, William D -- Nagarajan, Rakesh -- Walter, Matthew J -- Link, Daniel C -- Graubert, Timothy A -- DiPersio, John F -- Wilson, Richard K -- U54 HG002042/HG/NHGRI NIH HHS/ -- U54 HG002042-05/HG/NHGRI NIH HHS/ -- England -- Nature. 2008 Nov 6;456(7218):66-72. doi: 10.1038/nature07485.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Medicine, Washington University School of Medicine, St. Louis, Missouri 63108, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18987736" target="_blank"〉PubMed〈/a〉
    Keywords: Case-Control Studies ; Disease Progression ; Gene Expression Profiling ; Gene Expression Regulation, Neoplastic/*genetics ; Genome, Human/*genetics ; Genomics ; Humans ; Leukemia, Myeloid, Acute/*genetics ; Mutagenesis, Insertional ; Mutation ; Polymorphism, Single Nucleotide ; Recurrence ; Sequence Analysis, DNA ; Sequence Deletion ; Skin/metabolism
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
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  • 10
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    Unknown
    The transcriptional landscape of the mammalian genome (2005)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2005-09-06
    Description: This study describes comprehensive polling of transcription start and termination sites and analysis of previously unidentified full-length complementary DNAs derived from the mouse genome. We identify the 5' and 3' boundaries of 181,047 transcripts with extensive variation in transcripts arising from alternative promoter usage, splicing, and polyadenylation. There are 16,247 new mouse protein-coding transcripts, including 5154 encoding previously unidentified proteins. Genomic mapping of the transcriptome reveals transcriptional forests, with overlapping transcription on both strands, separated by deserts in which few transcripts are observed. The data provide a comprehensive platform for the comparative analysis of mammalian transcriptional regulation in differentiation and development.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Carninci, P -- Kasukawa, T -- Katayama, S -- Gough, J -- Frith, M C -- Maeda, N -- Oyama, R -- Ravasi, T -- Lenhard, B -- Wells, C -- Kodzius, R -- Shimokawa, K -- Bajic, V B -- Brenner, S E -- Batalov, S -- Forrest, A R R -- Zavolan, M -- Davis, M J -- Wilming, L G -- Aidinis, V -- Allen, J E -- Ambesi-Impiombato, A -- Apweiler, R -- Aturaliya, R N -- Bailey, T L -- Bansal, M -- Baxter, L -- Beisel, K W -- Bersano, T -- Bono, H -- Chalk, A M -- Chiu, K P -- Choudhary, V -- Christoffels, A -- Clutterbuck, D R -- Crowe, M L -- Dalla, E -- Dalrymple, B P -- de Bono, B -- Della Gatta, G -- di Bernardo, D -- Down, T -- Engstrom, P -- Fagiolini, M -- Faulkner, G -- Fletcher, C F -- Fukushima, T -- Furuno, M -- Futaki, S -- Gariboldi, M -- Georgii-Hemming, P -- Gingeras, T R -- Gojobori, T -- Green, R E -- Gustincich, S -- Harbers, M -- Hayashi, Y -- Hensch, T K -- Hirokawa, N -- Hill, D -- Huminiecki, L -- Iacono, M -- Ikeo, K -- Iwama, A -- Ishikawa, T -- Jakt, M -- Kanapin, A -- Katoh, M -- Kawasawa, Y -- Kelso, J -- Kitamura, H -- Kitano, H -- Kollias, G -- Krishnan, S P T -- Kruger, A -- Kummerfeld, S K -- Kurochkin, I V -- Lareau, L F -- Lazarevic, D -- Lipovich, L -- Liu, J -- Liuni, S -- McWilliam, S -- Madan Babu, M -- Madera, M -- Marchionni, L -- Matsuda, H -- Matsuzawa, S -- Miki, H -- Mignone, F -- Miyake, S -- Morris, K -- Mottagui-Tabar, S -- Mulder, N -- Nakano, N -- Nakauchi, H -- Ng, P -- Nilsson, R -- Nishiguchi, S -- Nishikawa, S -- Nori, F -- Ohara, O -- Okazaki, Y -- Orlando, V -- Pang, K C -- Pavan, W J -- Pavesi, G -- Pesole, G -- Petrovsky, N -- Piazza, S -- Reed, J -- Reid, J F -- Ring, B Z -- Ringwald, M -- Rost, B -- Ruan, Y -- Salzberg, S L -- Sandelin, A -- Schneider, C -- Schonbach, C -- Sekiguchi, K -- Semple, C A M -- Seno, S -- Sessa, L -- Sheng, Y -- Shibata, Y -- Shimada, H -- Shimada, K -- Silva, D -- Sinclair, B -- Sperling, S -- Stupka, E -- Sugiura, K -- Sultana, R -- Takenaka, Y -- Taki, K -- Tammoja, K -- Tan, S L -- Tang, S -- Taylor, M S -- Tegner, J -- Teichmann, S A -- Ueda, H R -- van Nimwegen, E -- Verardo, R -- Wei, C L -- Yagi, K -- Yamanishi, H -- Zabarovsky, E -- Zhu, S -- Zimmer, A -- Hide, W -- Bult, C -- Grimmond, S M -- Teasdale, R D -- Liu, E T -- Brusic, V -- Quackenbush, J -- Wahlestedt, C -- Mattick, J S -- Hume, D A -- Kai, C -- Sasaki, D -- Tomaru, Y -- Fukuda, S -- Kanamori-Katayama, M -- Suzuki, M -- Aoki, J -- Arakawa, T -- Iida, J -- Imamura, K -- Itoh, M -- Kato, T -- Kawaji, H -- Kawagashira, N -- Kawashima, T -- Kojima, M -- Kondo, S -- Konno, H -- Nakano, K -- Ninomiya, N -- Nishio, T -- Okada, M -- Plessy, C -- Shibata, K -- Shiraki, T -- Suzuki, S -- Tagami, M -- Waki, K -- Watahiki, A -- Okamura-Oho, Y -- Suzuki, H -- Kawai, J -- Hayashizaki, Y -- FANTOM Consortium -- RIKEN Genome Exploration Research Group and Genome Science Group (Genome Network Project Core Group) -- TGM03P17/Telethon/Italy -- TGM06S01/Telethon/Italy -- New York, N.Y. -- Science. 2005 Sep 2;309(5740):1559-63.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/16141072" target="_blank"〉PubMed〈/a〉
    Keywords: 3' Untranslated Regions ; Animals ; Base Sequence ; Conserved Sequence ; DNA, Complementary/chemistry ; *Genome ; Genome, Human ; Genomics ; Humans ; Mice/*genetics ; Promoter Regions, Genetic ; Proteins/genetics ; RNA/chemistry/classification ; RNA Splicing ; RNA, Untranslated/chemistry ; Regulatory Sequences, Ribonucleic Acid ; *Terminator Regions, Genetic ; *Transcription Initiation Site ; *Transcription, Genetic
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
    Published by American Association for the Advancement of Science (AAAS)
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