%0 Journal Article %J Genome Res %D 2009 %T The completion of the Mammalian Gene Collection (MGC). %A Temple, Gary %A Gerhard, Daniela S %A Rasooly, Rebekah %A Feingold, Elise A %A Good, Peter J %A Robinson, Cristen %A Mandich, Allison %A Derge, Jeffrey G %A Lewis, Jeanne %A Shoaf, Debonny %A Collins, Francis S %A Jang, Wonhee %A Wagner, Lukas %A Shenmen, Carolyn M %A Misquitta, Leonie %A Schaefer, Carl F %A Buetow, Kenneth H %A Bonner, Tom I %A Yankie, Linda %A Ward, Ming %A Phan, Lon %A Astashyn, Alex %A Brown, Garth %A Farrell, Catherine %A Hart, Jennifer %A Landrum, Melissa %A Maidak, Bonnie L %A Murphy, Michael %A Murphy, Terence %A Rajput, Bhanu %A Riddick, Lillian %A Webb, David %A Weber, Janet %A Wu, Wendy %A Pruitt, Kim D %A Maglott, Donna %A Siepel, Adam %A Brejova, Brona %A Diekhans, Mark %A Harte, Rachel %A Baertsch, Robert %A Kent, Jim %A Haussler, David %A Brent, Michael %A Langton, Laura %A Comstock, Charles L G %A Stevens, Michael %A Wei, Chaochun %A van Baren, Marijke J %A Salehi-Ashtiani, Kourosh %A Murray, Ryan R %A Ghamsari, Lila %A Mello, Elizabeth %A Lin, Chenwei %A Pennacchio, Christa %A Schreiber, Kirsten %A Shapiro, Nicole %A Marsh, Amber %A Pardes, Elizabeth %A Moore, Troy %A Lebeau, Anita %A Muratet, Mike %A Simmons, Blake %A Kloske, David %A Sieja, Stephanie %A Hudson, James %A Sethupathy, Praveen %A Brownstein, Michael %A Bhat, Narayan %A Lazar, Joseph %A Jacob, Howard %A Gruber, Chris E %A Smith, Mark R %A McPherson, John %A Garcia, Angela M %A Gunaratne, Preethi H %A Wu, Jiaqian %A Muzny, Donna %A Gibbs, Richard A %A Young, Alice C %A Bouffard, Gerard G %A Blakesley, Robert W %A Mullikin, Jim %A Green, Eric D %A Dickson, Mark C %A Rodriguez, Alex C %A Grimwood, Jane %A Schmutz, Jeremy %A Myers, Richard M %A Hirst, Martin %A Zeng, Thomas %A Tse, Kane %A Moksa, Michelle %A Deng, Merinda %A Ma, Kevin %A Mah, Diana %A Pang, Johnson %A Taylor, Greg %A Chuah, Eric %A Deng, Athena %A Fichter, Keith %A Go, Anne %A Lee, Stephanie %A Wang, Jing %A Griffith, Malachi %A Morin, Ryan %A Moore, Richard A %A Mayo, Michael %A Munro, Sarah %A Wagner, Susan %A Jones, Steven J M %A Holt, Robert A %A Marra, Marco A %A Lu, Sun %A Yang, Shuwei %A Hartigan, James %A Graf, Marcus %A Wagner, Ralf %A Letovksy, Stanley %A Pulido, Jacqueline C %A Robison, Keith %A Esposito, Dominic %A Hartley, James %A Wall, Vanessa E %A Hopkins, Ralph F %A Ohara, Osamu %A Wiemann, Stefan %K Animals %K Cloning, Molecular %K Computational Biology %K DNA %K DNA, Complementary %K Gene Library %K Genes %K Humans %K Mammals %K Mice %K National Institutes of Health (U.S.) %K Rats %K Reverse Transcriptase Polymerase Chain Reaction %K United States %X

Since its start, the Mammalian Gene Collection (MGC) has sought to provide at least one full-protein-coding sequence cDNA clone for every human and mouse gene with a RefSeq transcript, and at least 6200 rat genes. The MGC cloning effort initially relied on random expressed sequence tag screening of cDNA libraries. Here, we summarize our recent progress using directed RT-PCR cloning and DNA synthesis. The MGC now contains clones with the entire protein-coding sequence for 92% of human and 89% of mouse genes with curated RefSeq (NM-accession) transcripts, and for 97% of human and 96% of mouse genes with curated RefSeq transcripts that have one or more PubMed publications, in addition to clones for more than 6300 rat genes. These high-quality MGC clones and their sequences are accessible without restriction to researchers worldwide.

%B Genome Res %V 19 %P 2324-33 %8 2009 Dec %G eng %N 12 %1 https://www.ncbi.nlm.nih.gov/pubmed/19767417?dopt=Abstract %R 10.1101/gr.095976.109 %0 Journal Article %J Genome Res %D 2007 %T 28-way vertebrate alignment and conservation track in the UCSC Genome Browser. %A Miller, Webb %A Rosenbloom, Kate %A Hardison, Ross C %A Hou, Minmei %A Taylor, James %A Raney, Brian %A Burhans, Richard %A King, David C %A Baertsch, Robert %A Blankenberg, Daniel %A Kosakovsky Pond, Sergei L %A Nekrutenko, Anton %A Giardine, Belinda %A Harris, Robert S %A Tyekucheva, Svitlana %A Diekhans, Mark %A Pringle, Thomas H %A Murphy, William J %A Lesk, Arthur %A Weinstock, George M %A Lindblad-Toh, Kerstin %A Gibbs, Richard A %A Lander, Eric S %A Siepel, Adam %A Haussler, David %A Kent, W James %K Animals %K Base Sequence %K Cats %K Cattle %K Codon, Initiator %K Codon, Terminator %K Conserved Sequence %K Databases, Genetic %K Dogs %K Genome, Human %K Guinea Pigs %K Humans %K Mice %K Molecular Sequence Data %K Mutagenesis, Insertional %K Rabbits %K Rats %K Sequence Alignment %K Sequence Deletion %X

This article describes a set of alignments of 28 vertebrate genome sequences that is provided by the UCSC Genome Browser. The alignments can be viewed on the Human Genome Browser (March 2006 assembly) at http://genome.ucsc.edu, downloaded in bulk by anonymous FTP from http://hgdownload.cse.ucsc.edu/goldenPath/hg18/multiz28way, or analyzed with the Galaxy server at http://g2.bx.psu.edu. This article illustrates the power of this resource for exploring vertebrate and mammalian evolution, using three examples. First, we present several vignettes involving insertions and deletions within protein-coding regions, including a look at some human-specific indels. Then we study the extent to which start codons and stop codons in the human sequence are conserved in other species, showing that start codons are in general more poorly conserved than stop codons. Finally, an investigation of the phylogenetic depth of conservation for several classes of functional elements in the human genome reveals striking differences in the rates and modes of decay in alignability. Each functional class has a distinctive period of stringent constraint, followed by decays that allow (for the case of regulatory regions) or reject (for coding regions and ultraconserved elements) insertions and deletions.

%B Genome Res %V 17 %P 1797-808 %8 2007 Dec %G eng %N 12 %1 https://www.ncbi.nlm.nih.gov/pubmed/17984227?dopt=Abstract %R 10.1101/gr.6761107 %0 Journal Article %J Science %D 2007 %T Evolutionary and biomedical insights from the rhesus macaque genome. %A Richard A Gibbs %A Jeffrey Rogers %A Katze, Michael G %A Bumgarner, Roger %A Weinstock, George M %A Mardis, Elaine R %A Remington, Karin A %A Strausberg, Robert L %A Venter, J Craig %A Wilson, Richard K %A Batzer, Mark A %A Bustamante, Carlos D %A Eichler, Evan E %A Hahn, Matthew W %A Hardison, Ross C %A Makova, Kateryna D %A Miller, Webb %A Milosavljevic, Aleksandar %A Palermo, Robert E %A Siepel, Adam %A Sikela, James M %A Attaway, Tony %A Bell, Stephanie %A Bernard, Kelly E %A Buhay, Christian J %A Chandrabose, Mimi N %A Dao, Marvin %A Davis, Clay %A Delehaunty, Kimberly D %A Ding, Yan %A Dinh, Huyen H %A Dugan-Rocha, Shannon %A Fulton, Lucinda A %A Gabisi, Ramatu Ayiesha %A Garner, Toni T %A Godfrey, Jennifer %A Hawes, Alicia C %A Hernandez, Judith %A Hines, Sandra %A Holder, Michael %A Hume, Jennifer %A Jhangiani, Shalini N %A Joshi, Vandita %A Ziad Khan %A Kirkness, Ewen F %A Cree, Andrew %A Fowler, R Gerald %A Lee, Sandra %A Lewis, Lora R %A Li, Zhangwan %A Liu, Yih-Shin %A Moore, Stephanie M %A Donna M Muzny %A Nazareth, Lynne V %A Ngo, Dinh Ngoc %A Okwuonu, Geoffrey O %A Pai, Grace %A Parker, David %A Paul, Heidie A %A Pfannkoch, Cynthia %A Pohl, Craig S %A Rogers, Yu-Hui %A Ruiz, San Juana %A Aniko Sabo %A Santibanez, Jireh %A Schneider, Brian W %A Smith, Scott M %A Sodergren, Erica %A Svatek, Amanda F %A Utterback, Teresa R %A Vattathil, Selina %A Warren, Wesley %A White, Courtney Sherell %A Chinwalla, Asif T %A Feng, Yucheng %A Halpern, Aaron L %A Hillier, LaDeana W %A Huang, Xiaoqiu %A Minx, Pat %A Nelson, Joanne O %A Pepin, Kymberlie H %A Xiang Qin %A Sutton, Granger G %A Venter, Eli %A Walenz, Brian P %A Wallis, John W %A Kim C Worley %A Yang, Shiaw-Pyng %A Jones, Steven M %A Marra, Marco A %A Rocchi, Mariano %A Schein, Jacqueline E %A Baertsch, Robert %A Clarke, Laura %A Csuros, Miklos %A Glasscock, Jarret %A R. Alan Harris %A Havlak, Paul %A Jackson, Andrew R %A Jiang, Huaiyang %A Liu, Yue %A Messina, David N %A Shen, Yufeng %A Song, Henry Xing-Zhi %A Wylie, Todd %A Zhang, Lan %A Birney, Ewan %A Han, Kyudong %A Konkel, Miriam K %A Lee, Jungnam %A Smit, Arian F A %A Ullmer, Brygg %A Wang, Hui %A Xing, Jinchuan %A Burhans, Richard %A Cheng, Ze %A Karro, John E %A Ma, Jian %A Raney, Brian %A She, Xinwei %A Cox, Michael J %A Demuth, Jeffery P %A Dumas, Laura J %A Han, Sang-Gook %A Hopkins, Janet %A Karimpour-Fard, Anis %A Kim, Young H %A Pollack, Jonathan R %A Vinar, Tomas %A Addo-Quaye, Charles %A Degenhardt, Jeremiah %A Denby, Alexandra %A Hubisz, Melissa J %A Indap, Amit %A Kosiol, Carolin %A Lahn, Bruce T %A Lawson, Heather A %A Marklein, Alison %A Nielsen, Rasmus %A Vallender, Eric J %A Clark, Andrew G %A Ferguson, Betsy %A Hernandez, Ryan D %A Hirani, Kashif %A Kehrer-Sawatzki, Hildegard %A Kolb, Jessica %A Patil, Shobha %A Pu, Ling-Ling %A Ren, Yanru %A Smith, David Glenn %A David A Wheeler %A Schenck, Ian %A Ball, Edward V %A Rui Chen %A Cooper, David N %A Giardine, Belinda %A Hsu, Fan %A Kent, W James %A Lesk, Arthur %A Nelson, David L %A O'brien, William E %A Prüfer, Kay %A Stenson, Peter D %A Wallace, James C %A Ke, Hui %A Liu, Xiao-Ming %A Wang, Peng %A Xiang, Andy Peng %A Yang, Fan %A Barber, Galt P %A Haussler, David %A Karolchik, Donna %A Kern, Andy D %A Kuhn, Robert M %A Smith, Kayla E %A Zwieg, Ann S %K Animals %K Biomedical Research %K Evolution, Molecular %K Female %K Gene Duplication %K Gene Rearrangement %K Genetic Diseases, Inborn %K Genetic Variation %K Genome %K Humans %K Macaca mulatta %K Male %K Multigene Family %K Mutation %K Pan troglodytes %K Sequence Analysis, DNA %K Species Specificity %X

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.

%B Science %V 316 %P 222-34 %8 2007 Apr 13 %G eng %N 5822 %1 https://www.ncbi.nlm.nih.gov/pubmed/17431167?dopt=Abstract %R 10.1126/science.1139247 %0 Journal Article %J Nature %D 2007 %T Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. %A Birney, Ewan %A Stamatoyannopoulos, John A %A Dutta, Anindya %A Guigó, Roderic %A Gingeras, Thomas R %A Margulies, Elliott H %A Weng, Zhiping %A Snyder, Michael %A Dermitzakis, Emmanouil T %A Thurman, Robert E %A Kuehn, Michael S %A Taylor, Christopher M %A Neph, Shane %A Koch, Christoph M %A Asthana, Saurabh %A Malhotra, Ankit %A Adzhubei, Ivan %A Greenbaum, Jason A %A Andrews, Robert M %A Flicek, Paul %A Boyle, Patrick J %A Cao, Hua %A Carter, Nigel P %A Clelland, Gayle K %A Davis, Sean %A Day, Nathan %A Dhami, Pawandeep %A Dillon, Shane C %A Dorschner, Michael O %A Fiegler, Heike %A Giresi, Paul G %A Goldy, Jeff %A Hawrylycz, Michael %A Haydock, Andrew %A Humbert, Richard %A James, Keith D %A Johnson, Brett E %A Johnson, Ericka M %A Frum, Tristan T %A Rosenzweig, Elizabeth R %A Karnani, Neerja %A Lee, Kirsten %A Lefebvre, Gregory C %A Navas, Patrick A %A Neri, Fidencio %A Parker, Stephen C J %A Sabo, Peter J %A Sandstrom, Richard %A Shafer, Anthony %A Vetrie, David %A Weaver, Molly %A Wilcox, Sarah %A Yu, Man %A Collins, Francis S %A Dekker, Job %A Lieb, Jason D %A Tullius, Thomas D %A Crawford, Gregory E %A Sunyaev, Shamil %A Noble, William S %A Dunham, Ian %A Denoeud, France %A Reymond, Alexandre %A Kapranov, Philipp %A Rozowsky, Joel %A Zheng, Deyou %A Castelo, Robert %A Frankish, Adam %A Harrow, Jennifer %A Ghosh, Srinka %A Sandelin, Albin %A Hofacker, Ivo L %A Baertsch, Robert %A Keefe, Damian %A Dike, Sujit %A Cheng, Jill %A Hirsch, Heather A %A Sekinger, Edward A %A Lagarde, Julien %A Abril, Josep F %A Shahab, Atif %A Flamm, Christoph %A Fried, Claudia %A Hackermüller, Jörg %A Hertel, Jana %A Lindemeyer, Manja %A Missal, Kristin %A Tanzer, Andrea %A Washietl, Stefan %A Korbel, Jan %A Emanuelsson, Olof %A Pedersen, Jakob S %A Holroyd, Nancy %A Taylor, Ruth %A Swarbreck, David %A Matthews, Nicholas %A Dickson, Mark C %A Thomas, Daryl J %A Weirauch, Matthew T %A Gilbert, James %A Drenkow, Jorg %A Bell, Ian %A Zhao, XiaoDong %A Srinivasan, K G %A Sung, Wing-Kin %A Ooi, Hong Sain %A Chiu, Kuo Ping %A Foissac, Sylvain %A Alioto, Tyler %A Brent, Michael %A Pachter, Lior %A Tress, Michael L %A Valencia, Alfonso %A Choo, Siew Woh %A Choo, Chiou Yu %A Ucla, Catherine %A Manzano, Caroline %A Wyss, Carine %A Cheung, Evelyn %A Clark, Taane G %A Brown, James B %A Ganesh, Madhavan %A Patel, Sandeep %A Tammana, Hari %A Chrast, Jacqueline %A Henrichsen, Charlotte N %A Kai, Chikatoshi %A Kawai, Jun %A Nagalakshmi, Ugrappa %A Wu, Jiaqian %A Lian, Zheng %A Lian, Jin %A Newburger, Peter %A Zhang, Xueqing %A Bickel, Peter %A Mattick, John S %A Carninci, Piero %A Hayashizaki, Yoshihide %A Weissman, Sherman %A Hubbard, Tim %A Myers, Richard M %A Rogers, Jane %A Stadler, Peter F %A Lowe, Todd M %A Wei, Chia-Lin %A Ruan, Yijun %A Struhl, Kevin %A Gerstein, Mark %A Antonarakis, Stylianos E %A Fu, Yutao %A Green, Eric D %A Karaöz, Ulaş %A Siepel, Adam %A Taylor, James %A Liefer, Laura A %A Wetterstrand, Kris A %A Good, Peter J %A Feingold, Elise A %A Guyer, Mark S %A Cooper, Gregory M %A Asimenos, George %A Dewey, Colin N %A Hou, Minmei %A Nikolaev, Sergey %A Montoya-Burgos, Juan I %A Löytynoja, Ari %A Whelan, Simon %A Pardi, Fabio %A Massingham, Tim %A Huang, Haiyan %A Zhang, Nancy R %A Holmes, Ian %A Mullikin, James C %A Ureta-Vidal, Abel %A Paten, Benedict %A Seringhaus, Michael %A Church, Deanna %A Rosenbloom, Kate %A Kent, W James %A Stone, Eric A %A Batzoglou, Serafim %A Goldman, Nick %A Hardison, Ross C %A Haussler, David %A Miller, Webb %A Sidow, Arend %A Trinklein, Nathan D %A Zhang, Zhengdong D %A Barrera, Leah %A Stuart, Rhona %A King, David C %A Ameur, Adam %A Enroth, Stefan %A Bieda, Mark C %A Kim, Jonghwan %A Bhinge, Akshay A %A Jiang, Nan %A Liu, Jun %A Yao, Fei %A Vega, Vinsensius B %A Lee, Charlie W H %A Ng, Patrick %A Shahab, Atif %A Yang, Annie %A Moqtaderi, Zarmik %A Zhu, Zhou %A Xu, Xiaoqin %A Squazzo, Sharon %A Oberley, Matthew J %A Inman, David %A Singer, Michael A %A Richmond, Todd A %A Munn, Kyle J %A Rada-Iglesias, Alvaro %A Wallerman, Ola %A Komorowski, Jan %A Fowler, Joanna C %A Couttet, Phillippe %A Bruce, Alexander W %A Dovey, Oliver M %A Ellis, Peter D %A Langford, Cordelia F %A Nix, David A %A Euskirchen, Ghia %A Hartman, Stephen %A Urban, Alexander E %A Kraus, Peter %A Van Calcar, Sara %A Heintzman, Nate %A Kim, Tae Hoon %A Wang, Kun %A Qu, Chunxu %A Hon, Gary %A Luna, Rosa %A Glass, Christopher K %A Rosenfeld, M Geoff %A Aldred, Shelley Force %A Cooper, Sara J %A Halees, Anason %A Lin, Jane M %A Shulha, Hennady P %A Zhang, Xiaoling %A Xu, Mousheng %A Haidar, Jaafar N S %A Yu, Yong %A Ruan, Yijun %A Iyer, Vishwanath R %A Green, Roland D %A Wadelius, Claes %A Farnham, Peggy J %A Ren, Bing %A Harte, Rachel A %A Hinrichs, Angie S %A Trumbower, Heather %A Clawson, Hiram %A Hillman-Jackson, Jennifer %A Zweig, Ann S %A Smith, Kayla %A Thakkapallayil, Archana %A Barber, Galt %A Kuhn, Robert M %A Karolchik, Donna %A Armengol, Lluis %A Bird, Christine P %A de Bakker, Paul I W %A Kern, Andrew D %A Lopez-Bigas, Nuria %A Martin, Joel D %A Stranger, Barbara E %A Woodroffe, Abigail %A Davydov, Eugene %A Dimas, Antigone %A Eyras, Eduardo %A Hallgrímsdóttir, Ingileif B %A Huppert, Julian %A Zody, Michael C %A Abecasis, Gonçalo R %A Estivill, Xavier %A Bouffard, Gerard G %A Guan, Xiaobin %A Hansen, Nancy F %A Idol, Jacquelyn R %A Maduro, Valerie V B %A Maskeri, Baishali %A McDowell, Jennifer C %A Park, Morgan %A Thomas, Pamela J %A Young, Alice C %A Blakesley, Robert W %A Muzny, Donna M %A Sodergren, Erica %A Wheeler, David A %A Worley, Kim C %A Jiang, Huaiyang %A Weinstock, George M %A Gibbs, Richard A %A Graves, Tina %A Fulton, Robert %A Mardis, Elaine R %A Wilson, Richard K %A Clamp, Michele %A Cuff, James %A Gnerre, Sante %A Jaffe, David B %A Chang, Jean L %A Lindblad-Toh, Kerstin %A Lander, Eric S %A Koriabine, Maxim %A Nefedov, Mikhail %A Osoegawa, Kazutoyo %A Yoshinaga, Yuko %A Zhu, Baoli %A De Jong, Pieter J %K Chromatin %K Chromatin Immunoprecipitation %K Conserved Sequence %K DNA Replication %K Evolution, Molecular %K Exons %K Genetic Variation %K Genome, Human %K Genomics %K Heterozygote %K Histones %K Humans %K Pilot Projects %K Protein Binding %K Regulatory Sequences, Nucleic Acid %K RNA, Messenger %K RNA, Untranslated %K Transcription Factors %K Transcription Initiation Site %K Transcription, Genetic %X

We report the generation and analysis of functional data from multiple, diverse experiments performed on a targeted 1% of the human genome as part of the pilot phase of the ENCODE Project. These data have been further integrated and augmented by a number of evolutionary and computational analyses. Together, our results advance the collective knowledge about human genome function in several major areas. First, our studies provide convincing evidence that the genome is pervasively transcribed, such that the majority of its bases can be found in primary transcripts, including non-protein-coding transcripts, and those that extensively overlap one another. Second, systematic examination of transcriptional regulation has yielded new understanding about transcription start sites, including their relationship to specific regulatory sequences and features of chromatin accessibility and histone modification. Third, a more sophisticated view of chromatin structure has emerged, including its inter-relationship with DNA replication and transcriptional regulation. Finally, integration of these new sources of information, in particular with respect to mammalian evolution based on inter- and intra-species sequence comparisons, has yielded new mechanistic and evolutionary insights concerning the functional landscape of the human genome. Together, these studies are defining a path for pursuit of a more comprehensive characterization of human genome function.

%B Nature %V 447 %P 799-816 %8 2007 Jun 14 %G eng %N 7146 %1 https://www.ncbi.nlm.nih.gov/pubmed/17571346?dopt=Abstract %R 10.1038/nature05874 %0 Journal Article %J Nature %D 2004 %T Genome sequence of the Brown Norway rat yields insights into mammalian evolution. %A Gibbs, Richard A %A Weinstock, George M %A Metzker, Michael L %A Muzny, Donna M %A Sodergren, Erica J %A Scherer, Steven %A Scott, Graham %A Steffen, David %A Worley, Kim C %A Burch, Paula E %A Okwuonu, Geoffrey %A Hines, Sandra %A Lewis, Lora %A DeRamo, Christine %A Delgado, Oliver %A Dugan-Rocha, Shannon %A Miner, George %A Morgan, Margaret %A Hawes, Alicia %A Gill, Rachel %A Holt, Robert A %A Adams, Mark D %A Amanatides, Peter G %A Baden-Tillson, Holly %A Barnstead, Mary %A Chin, Soo %A Evans, Cheryl A %A Ferriera, Steve %A Fosler, Carl %A Glodek, Anna %A Gu, Zhiping %A Jennings, Don %A Kraft, Cheryl L %A Nguyen, Trixie %A Pfannkoch, Cynthia M %A Sitter, Cynthia %A Sutton, Granger G %A Venter, J Craig %A Woodage, Trevor %A Smith, Douglas %A Lee, Hong-Mei %A Gustafson, Erik %A Cahill, Patrick %A Kana, Arnold %A Doucette-Stamm, Lynn %A Weinstock, Keith %A Fechtel, Kim %A Weiss, Robert B %A Dunn, Diane M %A Green, Eric D %A Blakesley, Robert W %A Bouffard, Gerard G %A De Jong, Pieter J %A Osoegawa, Kazutoyo %A Zhu, Baoli %A Marra, Marco %A Schein, Jacqueline %A Bosdet, Ian %A Fjell, Chris %A Jones, Steven %A Krzywinski, Martin %A Mathewson, Carrie %A Siddiqui, Asim %A Wye, Natasja %A McPherson, John %A Zhao, Shaying %A Fraser, Claire M %A Shetty, Jyoti %A Shatsman, Sofiya %A Geer, Keita %A Chen, Yixin %A Abramzon, Sofyia %A Nierman, William C %A Havlak, Paul H %A Chen, Rui %A Durbin, K James %A Simons, Rain %A Ren, Yanru %A Song, Xing-Zhi %A Li, Bingshan %A Liu, Yue %A Qin, Xiang %A Cawley, Simon %A Worley, Kim C %A Cooney, A J %A D'Souza, Lisa M %A Martin, Kirt %A Wu, Jia Qian %A Gonzalez-Garay, Manuel L %A Jackson, Andrew R %A Kalafus, Kenneth J %A McLeod, Michael P %A Milosavljevic, Aleksandar %A Virk, Davinder %A Volkov, Andrei %A Wheeler, David A %A Zhang, Zhengdong %A Bailey, Jeffrey A %A Eichler, Evan E %A Tuzun, Eray %A Birney, Ewan %A Mongin, Emmanuel %A Ureta-Vidal, Abel %A Woodwark, Cara %A Zdobnov, Evgeny %A Bork, Peer %A Suyama, Mikita %A Torrents, David %A Alexandersson, Marina %A Trask, Barbara J %A Young, Janet M %A Huang, Hui %A Wang, Huajun %A Xing, Heming %A Daniels, Sue %A Gietzen, Darryl %A Schmidt, Jeanette %A Stevens, Kristian %A Vitt, Ursula %A Wingrove, Jim %A Camara, Francisco %A Mar Albà, M %A Abril, Josep F %A Guigó, Roderic %A Smit, Arian %A Dubchak, Inna %A Rubin, Edward M %A Couronne, Olivier %A Poliakov, Alexander %A Hübner, Norbert %A Ganten, Detlev %A Goesele, Claudia %A Hummel, Oliver %A Kreitler, Thomas %A Lee, Young-Ae %A Monti, Jan %A Schulz, Herbert %A Zimdahl, Heike %A Himmelbauer, Heinz %A Lehrach, Hans %A Jacob, Howard J %A Bromberg, Susan %A Gullings-Handley, Jo %A Jensen-Seaman, Michael I %A Kwitek, Anne E %A Lazar, Jozef %A Pasko, Dean %A Tonellato, Peter J %A Twigger, Simon %A Ponting, Chris P %A Duarte, Jose M %A Rice, Stephen %A Goodstadt, Leo %A Beatson, Scott A %A Emes, Richard D %A Winter, Eitan E %A Webber, Caleb %A Brandt, Petra %A Nyakatura, Gerald %A Adetobi, Margaret %A Chiaromonte, Francesca %A Elnitski, Laura %A Eswara, Pallavi %A Hardison, Ross C %A Hou, Minmei %A Kolbe, Diana %A Makova, Kateryna %A Miller, Webb %A Nekrutenko, Anton %A Riemer, Cathy %A Schwartz, Scott %A Taylor, James %A Yang, Shan %A Zhang, Yi %A Lindpaintner, Klaus %A Andrews, T Dan %A Caccamo, Mario %A Clamp, Michele %A Clarke, Laura %A Curwen, Valerie %A Durbin, Richard %A Eyras, Eduardo %A Searle, Stephen M %A Cooper, Gregory M %A Batzoglou, Serafim %A Brudno, Michael %A Sidow, Arend %A Stone, Eric A %A Venter, J Craig %A Payseur, Bret A %A Bourque, Guillaume %A López-Otín, Carlos %A Puente, Xose S %A Chakrabarti, Kushal %A Chatterji, Sourav %A Dewey, Colin %A Pachter, Lior %A Bray, Nicolas %A Yap, Von Bing %A Caspi, Anat %A Tesler, Glenn %A Pevzner, Pavel A %A Haussler, David %A Roskin, Krishna M %A Baertsch, Robert %A Clawson, Hiram %A Furey, Terrence S %A Hinrichs, Angie S %A Karolchik, Donna %A Kent, William J %A Rosenbloom, Kate R %A Trumbower, Heather %A Weirauch, Matt %A Cooper, David N %A Stenson, Peter D %A Ma, Bin %A Brent, Michael %A Arumugam, Manimozhiyan %A Shteynberg, David %A Copley, Richard R %A Taylor, Martin S %A Riethman, Harold %A Mudunuri, Uma %A Peterson, Jane %A Guyer, Mark %A Felsenfeld, Adam %A Old, Susan %A Mockrin, Stephen %A Collins, Francis %K Animals %K Base Composition %K Centromere %K Chromosomes, Mammalian %K CpG Islands %K DNA Transposable Elements %K DNA, Mitochondrial %K Evolution, Molecular %K Gene Duplication %K Genome %K Genomics %K Humans %K Introns %K Male %K Mice %K Models, Molecular %K Mutagenesis %K Polymorphism, Single Nucleotide %K Rats %K Rats, Inbred BN %K Regulatory Sequences, Nucleic Acid %K Retroelements %K RNA Splice Sites %K RNA, Untranslated %K Sequence Analysis, DNA %K Telomere %X

The laboratory rat (Rattus norvegicus) is an indispensable tool in experimental medicine and drug development, having made inestimable contributions to human health. We report here the genome sequence of the Brown Norway (BN) rat strain. The sequence represents a high-quality 'draft' covering over 90% of the genome. The BN rat sequence is the third complete mammalian genome to be deciphered, and three-way comparisons with the human and mouse genomes resolve details of mammalian evolution. This first comprehensive analysis includes genes and proteins and their relation to human disease, repeated sequences, comparative genome-wide studies of mammalian orthologous chromosomal regions and rearrangement breakpoints, reconstruction of ancestral karyotypes and the events leading to existing species, rates of variation, and lineage-specific and lineage-independent evolutionary events such as expansion of gene families, orthology relations and protein evolution.

%B Nature %V 428 %P 493-521 %8 2004 Apr 01 %G eng %N 6982 %1 https://www.ncbi.nlm.nih.gov/pubmed/15057822?dopt=Abstract %R 10.1038/nature02426 %0 Journal Article %J Nature %D 2002 %T Initial sequencing and comparative analysis of the mouse genome. %A Waterston, Robert H %A Lindblad-Toh, Kerstin %A Birney, Ewan %A Rogers, Jane %A Abril, Josep F %A Agarwal, Pankaj %A Agarwala, Richa %A Ainscough, Rachel %A Alexandersson, Marina %A An, Peter %A Antonarakis, Stylianos E %A Attwood, John %A Baertsch, Robert %A Bailey, Jonathon %A Barlow, Karen %A Beck, Stephan %A Berry, Eric %A Birren, Bruce %A Bloom, Toby %A Bork, Peer %A Botcherby, Marc %A Bray, Nicolas %A Brent, Michael R %A Brown, Daniel G %A Brown, Stephen D %A Bult, Carol %A Burton, John %A Butler, Jonathan %A Campbell, Robert D %A Carninci, Piero %A Cawley, Simon %A Chiaromonte, Francesca %A Chinwalla, Asif T %A Church, Deanna M %A Clamp, Michele %A Clee, Christopher %A Collins, Francis S %A Cook, Lisa L %A Copley, Richard R %A Coulson, Alan %A Couronne, Olivier %A Cuff, James %A Curwen, Val %A Cutts, Tim %A Daly, Mark %A David, Robert %A Davies, Joy %A Delehaunty, Kimberly D %A Deri, Justin %A Dermitzakis, Emmanouil T %A Dewey, Colin %A Dickens, Nicholas J %A Diekhans, Mark %A Dodge, Sheila %A Dubchak, Inna %A Dunn, Diane M %A Eddy, Sean R %A Elnitski, Laura %A Emes, Richard D %A Eswara, Pallavi %A Eyras, Eduardo %A Felsenfeld, Adam %A Fewell, Ginger A %A Flicek, Paul %A Foley, Karen %A Frankel, Wayne N %A Fulton, Lucinda A %A Fulton, Robert S %A Furey, Terrence S %A Gage, Diane %A Gibbs, Richard A %A Glusman, Gustavo %A Gnerre, Sante %A Goldman, Nick %A Goodstadt, Leo %A Grafham, Darren %A Graves, Tina A %A Green, Eric D %A Gregory, Simon %A Guigó, Roderic %A Guyer, Mark %A Hardison, Ross C %A Haussler, David %A Hayashizaki, Yoshihide %A Hillier, LaDeana W %A Hinrichs, Angela %A Hlavina, Wratko %A Holzer, Timothy %A Hsu, Fan %A Hua, Axin %A Hubbard, Tim %A Hunt, Adrienne %A Jackson, Ian %A Jaffe, David B %A Johnson, L Steven %A Jones, Matthew %A Jones, Thomas A %A Joy, Ann %A Kamal, Michael %A Karlsson, Elinor K %A Karolchik, Donna %A Kasprzyk, Arkadiusz %A Kawai, Jun %A Keibler, Evan %A Kells, Cristyn %A Kent, W James %A Kirby, Andrew %A Kolbe, Diana L %A Korf, Ian %A Kucherlapati, Raju S %A Kulbokas, Edward J %A Kulp, David %A Landers, Tom %A Leger, J P %A Leonard, Steven %A Letunic, Ivica %A Levine, Rosie %A Li, Jia %A Li, Ming %A Lloyd, Christine %A Lucas, Susan %A Ma, Bin %A Maglott, Donna R %A Mardis, Elaine R %A Matthews, Lucy %A Mauceli, Evan %A Mayer, John H %A McCarthy, Megan %A McCombie, W Richard %A McLaren, Stuart %A McLay, Kirsten %A McPherson, John D %A Meldrim, Jim %A Meredith, Beverley %A Mesirov, Jill P %A Miller, Webb %A Miner, Tracie L %A Mongin, Emmanuel %A Montgomery, Kate T %A Morgan, Michael %A Mott, Richard %A Mullikin, James C %A Muzny, Donna M %A Nash, William E %A Nelson, Joanne O %A Nhan, Michael N %A Nicol, Robert %A Ning, Zemin %A Nusbaum, Chad %A O'Connor, Michael J %A Okazaki, Yasushi %A Oliver, Karen %A Overton-Larty, Emma %A Pachter, Lior %A Parra, Genís %A Pepin, Kymberlie H %A Peterson, Jane %A Pevzner, Pavel %A Plumb, Robert %A Pohl, Craig S %A Poliakov, Alex %A Ponce, Tracy C %A Ponting, Chris P %A Potter, Simon %A Quail, Michael %A Reymond, Alexandre %A Roe, Bruce A %A Roskin, Krishna M %A Rubin, Edward M %A Rust, Alistair G %A Santos, Ralph %A Sapojnikov, Victor %A Schultz, Brian %A Schultz, Jörg %A Schwartz, Matthias S %A Schwartz, Scott %A Scott, Carol %A Seaman, Steven %A Searle, Steve %A Sharpe, Ted %A Sheridan, Andrew %A Shownkeen, Ratna %A Sims, Sarah %A Singer, Jonathan B %A Slater, Guy %A Smit, Arian %A Smith, Douglas R %A Spencer, Brian %A Stabenau, Arne %A Stange-Thomann, Nicole %A Sugnet, Charles %A Suyama, Mikita %A Tesler, Glenn %A Thompson, Johanna %A Torrents, David %A Trevaskis, Evanne %A Tromp, John %A Ucla, Catherine %A Ureta-Vidal, Abel %A Vinson, Jade P %A Von Niederhausern, Andrew C %A Wade, Claire M %A Wall, Melanie %A Weber, Ryan J %A Weiss, Robert B %A Wendl, Michael C %A West, Anthony P %A Wetterstrand, Kris %A Wheeler, Raymond %A Whelan, Simon %A Wierzbowski, Jamey %A Willey, David %A Williams, Sophie %A Wilson, Richard K %A Winter, Eitan %A Worley, Kim C %A Wyman, Dudley %A Yang, Shan %A Yang, Shiaw-Pyng %A Zdobnov, Evgeny M %A Zody, Michael C %A Lander, Eric S %K Animals %K Base Composition %K Chromosomes, Mammalian %K Conserved Sequence %K CpG Islands %K Evolution, Molecular %K Gene Expression Regulation %K Genes %K Genetic Variation %K Genome %K Genome, Human %K Genomics %K Humans %K Mice %K Mice, Knockout %K Mice, Transgenic %K Models, Animal %K Multigene Family %K Mutagenesis %K Neoplasms %K Physical Chromosome Mapping %K Proteome %K Pseudogenes %K Quantitative Trait Loci %K Repetitive Sequences, Nucleic Acid %K RNA, Untranslated %K Selection, Genetic %K Sequence Analysis, DNA %K Sex Chromosomes %K Species Specificity %K Synteny %X

The sequence of the mouse genome is a key informational tool for understanding the contents of the human genome and a key experimental tool for biomedical research. Here, we report the results of an international collaboration to produce a high-quality draft sequence of the mouse genome. We also present an initial comparative analysis of the mouse and human genomes, describing some of the insights that can be gleaned from the two sequences. We discuss topics including the analysis of the evolutionary forces shaping the size, structure and sequence of the genomes; the conservation of large-scale synteny across most of the genomes; the much lower extent of sequence orthology covering less than half of the genomes; the proportions of the genomes under selection; the number of protein-coding genes; the expansion of gene families related to reproduction and immunity; the evolution of proteins; and the identification of intraspecies polymorphism.

%B Nature %V 420 %P 520-62 %8 2002 Dec 05 %G eng %N 6915 %1 https://www.ncbi.nlm.nih.gov/pubmed/12466850?dopt=Abstract %R 10.1038/nature01262