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Your search keyword '"Yuri Kapustin"' showing total 3 results
Start Over Author "Yuri Kapustin" Topic 030304 developmental biology
3 results on '"Yuri Kapustin"'

1. Database resources of the National Center for Biotechnology Information

Author

Eric W. Sayers, Tanya Barrett, Dennis A. Benson, Evan Bolton, Stephen H. Bryant, Kathi Canese, Vyacheslav Chetvernin, Deanna M. Church, Michael DiCuccio, Scott Federhen, Michael Feolo, Lewis Y. Geer, Wolfgang Helmberg, Yuri Kapustin, David Landsman, David J. Lipman, Zhiyong Lu, Thomas L. Madden, Tom Madej, Donna R. Maglott, Aron Marchler-Bauer, Vadim Miller, Ilene Mizrachi, James Ostell, Anna Panchenko, Kim D. Pruitt, Gregory D. Schuler, Edwin Sequeira, Stephen T. Sherry, Martin Shumway, Karl Sirotkin, Douglas Slotta, Alexandre Souvorov, Grigory Starchenko, Tatiana A. Tatusova, Lukas Wagner, Yanli Wang, W. John Wilbur, Eugene Yaschenko, and Jian Ye

Subjects
Internet, 0303 health sciences, National Library of Medicine (U.S.), Computational Biology, Information Storage and Retrieval, Genome, Viral, Articles, United States, 3. Good health, 03 medical and health sciences, 0302 clinical medicine, National Institutes of Health (U.S.), 030220 oncology & carcinogenesis, Databases, Genetic, Genetics, Animals, Humans, natural sciences, Databases, Nucleic Acid, Databases, Protein, Algorithms, Genome, Bacterial, Software, 030304 developmental biology
Abstract

In addition to maintaining the GenBank® nucleic acid sequence database, the National Center for Biotechnology Information (NCBI) provides analysis and retrieval resources for the data in GenBank and other biological data made available through the NCBI web site. NCBI resources include Entrez, the Entrez Programming Utilities, MyNCBI, PubMed, PubMed Central, Entrez Gene, the NCBI Taxonomy Browser, BLAST, BLAST Link (BLink), Electronic PCR, OrfFinder, Spidey, Splign, Reference Sequence, UniGene, HomoloGene, ProtEST, dbMHC, dbSNP, Cancer Chromosomes, Entrez Genomes and related tools, the Map Viewer, Model Maker, Evidence Viewer, Trace Archive, Sequence Read Archive, Retroviral Genotyping Tools, HIV-1/Human Protein Interaction Database, Gene Expression Omnibus, Entrez Probe, GENSAT, Online Mendelian Inheritance in Man, Online Mendelian Inheritance in Animals, the Molecular Modeling Database, the Conserved Domain Database, the Conserved Domain Architecture Retrieval Tool, Biosystems, Peptidome, Protein Clusters and the PubChem suite of small molecule databases. Augmenting many of the web applications are custom implementations of the BLAST program optimized to search specialized data sets. All these resources can be accessed through the NCBI home page at www.ncbi.nlm.nih.gov.

Published
2009
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2. Lineage-specific biology revealed by a finished genome assembly of the mouse

Author

Kerstin Lindblad-Toh, Dan Forrest, David C. Schwartz, Ana C. Marques, Chris P. Ponting, Donna Maglott, Shiguo Zhou, Carol J. Bult, James M. Amos-Landgraf, Christopher Churas, Tina Graves, Deanna M. Church, Ron Runnheim, Yuri Kapustin, Joshua L. Cherry, Zoë Birtle, LaDeana W. Hillier, Michael C. Zody, Michael Place, Ze Cheng, Wratko Hlavina, Steve Goldstein, Richa Agarwala, Konstantinos Potamousis, Jill Herschleb, Evan E. Eichler, Xinwe She, Leo Goodstadt, Brian Teague, Peter Meric, and Michael DiCuccio

Subjects
QH301-705.5, Population, Sequence assembly, Computational biology, Biology, Genome, General Biochemistry, Genetics and Molecular Biology, Mice, 03 medical and health sciences, 0302 clinical medicine, Gene Duplication, Databases, Genetic, Animals, Humans, Gene family, Genetics and Genomics/Genomics, Biology (General), education, Gene, Genetics and Genomics/Plant Genomes and Evolution, 030304 developmental biology, Whole genome sequencing, Comparative genomics, Genetics, 0303 health sciences, education.field_of_study, General Immunology and Microbiology, General Neuroscience, Computational Biology, Genetics and Genomics/Bioinformatics, Genetics and Genomics/Genome Projects, Human genome, General Agricultural and Biological Sciences, 030217 neurology & neurosurgery, Research Article
Abstract

A finished clone-based assembly of the mouse genome reveals extensive recent sequence duplication during recent evolution and rodent-specific expansion of certain gene families. Newly assembled duplications contain protein-coding genes that are mostly involved in reproductive function., The mouse (Mus musculus) is the premier animal model for understanding human disease and development. Here we show that a comprehensive understanding of mouse biology is only possible with the availability of a finished, high-quality genome assembly. The finished clone-based assembly of the mouse strain C57BL/6J reported here has over 175,000 fewer gaps and over 139 Mb more of novel sequence, compared with the earlier MGSCv3 draft genome assembly. In a comprehensive analysis of this revised genome sequence, we are now able to define 20,210 protein-coding genes, over a thousand more than predicted in the human genome (19,042 genes). In addition, we identified 439 long, non–protein-coding RNAs with evidence for transcribed orthologs in human. We analyzed the complex and repetitive landscape of 267 Mb of sequence that was missing or misassembled in the previously published assembly, and we provide insights into the reasons for its resistance to sequencing and assembly by whole-genome shotgun approaches. Duplicated regions within newly assembled sequence tend to be of more recent ancestry than duplicates in the published draft, correcting our initial understanding of recent evolution on the mouse lineage. These duplicates appear to be largely composed of sequence regions containing transposable elements and duplicated protein-coding genes; of these, some may be fixed in the mouse population, but at least 40% of segmentally duplicated sequences are copy number variable even among laboratory mouse strains. Mouse lineage-specific regions contain 3,767 genes drawn mainly from rapidly-changing gene families associated with reproductive functions. The finished mouse genome assembly, therefore, greatly improves our understanding of rodent-specific biology and allows the delineation of ancestral biological functions that are shared with human from derived functions that are not., Author Summary The availability of an accurate genome sequence provides the bedrock upon which modern biomedical research is based. Here we describe a high-quality assembly, Build 36, of the mouse genome. This assembly was put together by aligning overlapping individual clones representing parts of the genome, and it provides a more complete picture than previous assemblies, because it adds much rodent-specific sequence that was previously unavailable. The addition of these sequences provides insight into both the genomic architecture and the gene complement of the mouse. In particular, it highlights recent gene duplications and the expansion of certain gene families during rodent evolution. An improved understanding of the mouse genome and thus mouse biology will enhance the utility of the mouse as a model for human disease.

Published
2009
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3. The genome sequence of taurine cattle: A window to ruminant biology and evolution

Author

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

Subjects
Male, genome sequence, [SDV]Life Sciences [q-bio], ved/biology.organism_classification_rank.species, Genome, Genética y Herencia, Segmental duplication, 2. Zero hunger, Genetics, ddc:616, 0303 health sciences, Multidisciplinary, 04 agricultural and veterinary sciences, Bovine genome, Animals, Domestic, Proteins/genetics, Female, CIENCIAS NATURALES Y EXACTAS, Sequence analysis, Evolution, Biotecnología Agropecuaria, Molecular Sequence Data, Tecnología GM, clonación de ganado, selección asistida, diagnósticos, tecnología de producción de biomasa, etc, Biology, Synteny, Article, Ciencias Biológicas, Evolution, Molecular, 03 medical and health sciences, Species Specificity, Animals, Humans, General, Gene, 030304 developmental biology, Whole genome sequencing, ved/biology, Taurine cattle, 0402 animal and dairy science, Genetic Variation, Sequence Analysis, DNA, 040201 dairy & animal science, Bos taurus, Alternative Splicing, MicroRNAs/genetics, CIENCIAS AGRÍCOLAS, cattle, Cattle, genetic
Abstract

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. Fil: Bovine Genome Sequencing and Analysis Consortium. Bovine Genome Sequencing And Analysis Consortium; Estados Unidos Fil: Amadio, Ariel Fernando. Instituto Nacional de Tecnología Agropecuaria. Centro Regional Santa Fe. Estación Experimental Agropecuaria Rafaela; Argentina Fil: Poli, Mario Andres. Instituto Nacional de Tecnología Agropecuaria. Centro de Investigación en Ciencias Veterinarias y Agronómicas. Instituto de Genética; Argentina

Published
2009
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