Results 21 to 30 of about 4,660,063 (378)

ModHMM: A Modular Supra-Bayesian Genome Segmentation Method [PDF]

, 2020
Genome segmentation methods are powerful tools to obtain cell type or tissue-specific genome-wide annotations and are frequently used to discover regulatory elements.
Benner, P., Vingron, M.
core   +2 more sources

Tetraodon genome confirms Takifugu findings : most fish are ancient polyploids [PDF]

, 2004
An evolutionary hypothesis suggested by studies of the genome of the tiger pufferfish Takifugu rubripes has now been confirmed by comparison with the genome of a close relative, the spotted green pufferfish Tetraodon nigroviridis.
Van de Peer, Yves
core   +2 more sources

NCBI prokaryotic genome annotation pipeline

Nucleic Acids Research, 2016
Recent technological advances have opened unprecedented opportunities for large-scale sequencing and analysis of populations of pathogenic species in disease outbreaks, as well as for large-scale diversity studies aimed at expanding our knowledge across ...
T. Tatusova, Michael DiCuccio, Azat Badretdin, V. Chetvernin, Eric P. Nawrocki, L. Zaslavsky, A. Lomsadze, K. Pruitt, M. Borodovsky, J. Ostell   +9 more
semanticscholar   +1 more source

Defending the genome from the enemy within:mechanisms of retrotransposon suppression in the mouse germline [PDF]

, 2013
The viability of any species requires that the genome is kept stable as it is transmitted from generation to generation by the germ cells. One of the challenges to transgenerational genome stability is the potential mutagenic activity of transposable ...
A Aravin, A Dupressoir, A Dupressoir, A Dupressoir, A Fadloun, A Inagaki, A Inoue, A Inoue, A Meissner, A Prokhortchouk, A Puech, A Sookdeo, A Tsumura, A Vourekas, AA Aravin, AA Aravin, AA Aravin, AA Zabolotneva, AE Peaston, AR Muotri, AR Muotri, B Hendrich, BH Schrans-Stassen, C Chen, C Lu, C Popp, C-X Song, C-X Song, CE Nestor, CG Lian, CM Davis, CP Walsh, D Bourc’his, D Bourc’his, D Branciforte, D Guallar, D Haig, D Lucifero, D Lucifero, D Reiss, D Ribet, D Ribet, D Ribet, D Sproul, D Wolf, D Wolf, DA Kramerov, DC Hancks, DJ Lees-Murdock, DM Maatouk, Donncha S. Dunican, DS Dunican, DT Ting, E Beyret, E Beyret, E Khazina, E Li, EB Chuong, EL Kuff, ES Lander, F Santos, F Yang, FD Araujo, G Hutvagner, G Velasco, GD Evrony, H Cedar, H Cedar, H Heyn, H Kano, H Khan, H Kobayashi, H Stroud, HJ Cooke, HM Rowe, HM Rowe, HM Rowe, I Cantone, I Martín Caballero, I Suetake, IA Maksakova, Ian R. Adams, J Borgel, J Brennecke, J Chen, J Gimenez, J Lange, J Reichmann, J Reichmann, J Rossant, J Sharif, J Xiol, J-H Ng, JA Hackett, JA Hackett, JA Yoder, James H. Crichton, JD Lewis, JK Baillie, JL Garcia-Perez, JL Goodier, JN Athanikar, JO Kriegs, JP Reddington, JP Reddington, JP Thomson, JP Thomson, JV Moran, K Dennis, K Hata, K Hayashi, K Hisada, K Kurimoto, K Myant, K Zheng, K Zheng, KP Koh, L Jackson-Grusby, L Ma, L Piko, L Shen, L-Q Sun, LK Hutnick, M Abe, M Chotalia, M Denne, M Dewannieux, M Dewannieux, M Dewannieux, M Freitag, M Kaneda, M Kaneda, M Ko, M Ko, M Leeb, M Okano, M Reuter, M Reuter, M Ruggiu, M Saitou, M Shoji, M Tachibana, M Tahiliani, M Weber, M Wiench, M Xu, MA Carmell, Marie MacLennan, MC Ward, MM Dawlaty, MM Dawlaty, MM Karimi, MT Romanish, N Bannert, N Gilbert, N Lane, N Mathioudakis, N Reynolds, N Yang, N Zamudio, OH Tam, P Hajkova, P Hajkova, PJ Skene, Q Feng, Q Yan, R Brunmeir, R Burdick, R Fuente De La, R Illingworth, R Lister, R Rebollo, R Shukla, R Yaman, R Öllinger, RH Waterston, Richard R. Meehan, RJ DeBerardinis, RJA Frost, RR Meehan, S Chuma, S Fazio De, S Guibert, S Ito, S Ito, S Kagiwada, S Kaufmann, S Kuntz, S Kuramochi-Miyagawa, S Kuramochi-Miyagawa, S Kuramochi-Miyagawa, S Kuramochi-Miyagawa, S Mi, S Milutinovic, S Salle La, S Schütt, S Seisenberger, S Solyom, S Takebayashi, S Yamaguchi, S-H Lee, SA Smallwood, SA Trelogan, SB Rothbart, SFC Soper, SK Mahadevaiah, SL Martin, SL Martin, SL Martin, SL Mathias, SP Sripathy, SS Tanaka, ST Grivna, T Matsui, T Singer, T Tanaka, T Watanabe, T Watanabe, T Watanabe, T-P Gu, TS Macfarlan, UM Galli, V Chapman, VV Vagin, W Deng, W Filipowicz, W Seifarth, W Wei, W Yan, WA Pastor, X Cai, X Nan, Y Kato, Y Seki, Y Tao, Y Unhavaithaya, Y Yabuta, Y Yotsuyanagi, Y-Q Su, Z Li, ZD Smith, ZD Smith   +241 more
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RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome

BMC Bioinformatics, 2011
BackgroundRNA-Seq is revolutionizing the way transcript abundances are measured. A key challenge in transcript quantification from RNA-Seq data is the handling of reads that map to multiple genes or isoforms.
Bo Li, Colin N. Dewey
semanticscholar   +1 more source

SPAdes: A New Genome Assembly Algorithm and Its Applications to Single-Cell Sequencing

J. Comput. Biol., 2012
The lion's share of bacteria in various environments cannot be cloned in the laboratory and thus cannot be sequenced using existing technologies. A major goal of single-cell genomics is to complement gene-centric metagenomic data with whole-genome ...
A. Bankevich, S. Nurk, D. Antipov, A. Gurevich, M. Dvorkin, Alexander S. Kulikov, Valery M. Lesin, S. Nikolenko, Son K. Pham, Andrey D. Prjibelski, A. Pyshkin, Alexander Sirotkin, Nikolay Vyahhi, G. Tesler, M. Alekseyev, P. Pevzner   +15 more
semanticscholar   +1 more source

GIVE: portable genome browsers for personal websites. [PDF]

, 2018
Growing popularity and diversity of genomic data demand portable and versatile genome browsers. Here, we present an open source programming library called GIVE that facilitates the creation of personalized genome browsers without requiring a system ...
Alvin Zheng, B Sridhar, B Sridhar, C Tyner, D Barrios, D Comer, E Lieberman-Aiden, E Sharma, F Ozsolak, F Yue, FH Biase, JD Buenrostro, JG Aw, JT Robinson, LD Stein, ME Skinner, MJ Fullwood, Qiuyang Wu, R Bayer, R Li, R Mourad, S Carrere, Sheng Zhong, TC Nguyen, The ENCODE Project Consortium, VW Zhou, WJ Kent, X Li, X Zhou, Xiaoyi Cao, Z Lu, Zhangming Yan   +31 more
core   +2 more sources

The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data.

Genome Research, 2010
Next-generation DNA sequencing (NGS) projects, such as the 1000 Genomes Project, are already revolutionizing our understanding of genetic variation among individuals.
A. McKenna, M. Hanna, E. Banks, A. Sivachenko, K. Cibulskis, A. Kernytsky, K. Garimella, D. Altshuler, S. Gabriel, M. Daly, M. DePristo   +10 more
semanticscholar   +1 more source

Ultrafast and memory-efficient alignment of short DNA sequences to the human genome

Genome Biology, 2009
Bowtie is an ultrafast, memory-efficient alignment program for aligning short DNA sequence reads to large genomes. For the human genome, Burrows-Wheeler indexing allows Bowtie to align more than 25 million reads per CPU hour with a memory footprint of ...
Ben Langmead, C. Trapnell, Mihai Pop, S. Salzberg   +3 more
semanticscholar   +1 more source

Roary: rapid large-scale prokaryote pan genome analysis

bioRxiv, 2015
Summary A typical prokaryote population sequencing study can now consist of hundreds or thousands of isolates. Interrogating these datasets can provide detailed insights into the genetic structure of of prokaryotic genomes.
Andrew J. Page, Carla A. Cummins, Martin Hunt, V. Wong, S. Reuter, M. Holden, Maria Fookes, D. Falush, Jacqueline A. Keane, J. Parkhill   +9 more
semanticscholar   +1 more source