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GENCODE reference annotation for the human and mouse genomes

Adam Frankish, Mark Diekhans, Anne-Maud Ferreira, Rory Johnson, Irwin Jungreis, Jane Loveland, Jonathan M Mudge, Cristina Sisu, James Wright, Joel Armstrong, If Barnes, Andrew Berry (+43 others)
2018 Nucleic Acids Research  
The accurate identification and description of the genes in the human and mouse genomes is a fundamental requirement for high quality analysis of data informing both genome biology and clinical genomics  ...  Over the last 15 years, the GENCODE consortium has been producing reference quality gene annotations to provide this foundational resource.  ...  ACKNOWLEDGEMENTS We thank Tim Hubbard and Jennifer Harrow for their leadership in the GENCODE project from 2003-2016 as well as all groups and group members involved in the GENCODE project since its inception  ... 
doi:10.1093/nar/gky955 pmid:30357393 pmcid:PMC6323946 fatcat:vg5kuecy5rc7xewce5u3xczdba


Adam Frankish, Mark Diekhans, Irwin Jungreis, Julien Lagarde, Jane E Loveland, Jonathan M Mudge, Cristina Sisu, James C Wright, Joel Armstrong, If Barnes, Andrew Berry, Alexandra Bignell (+44 others)
2020 Nucleic Acids Research  
reference annotation databases for the annotation of human and mouse protein-coding genes; and the first GENCODE manually supervised automated annotation of lncRNAs.  ...  The GENCODE project annotates human and mouse genes and transcripts supported by experimental data with high accuracy, providing a foundational resource that supports genome biology and clinical genomics  ...  of the human and mouse reference genomes.  ... 
doi:10.1093/nar/gkaa1087 pmid:33270111 pmcid:PMC7778937 fatcat:eqyplhdexbdchn53omyqjckpge

Creating reference gene annotation for the mouse C57BL6/J genome assembly

Jonathan M. Mudge, Jennifer Harrow
2015 Mammalian Genome  
Annotation on the reference genome of the C57BL6/J mouse has been an ongoing project ever since the draft genome was first published.  ...  Here, we describe the progress of the GENCODE mouse annotation project, which combines manual annotation from the HAVANA group with Ensembl computational annotation, alongside experimental and in silico  ...  , and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made.  ... 
doi:10.1007/s00335-015-9583-x pmid:26187010 pmcid:PMC4602055 fatcat:y5eenrzsdnfr5jdy6wezb6etm4

Comparative Annotation Toolkit (CAT) - simultaneous clade and personal genome annotation [article]

Ian T Fiddes, Joel Armstrong, Mark Diekhans, Stefanie Nachtweide, Zev N Kronenberg, Jason G Underwood, David Gordon, Dent Earl, Thomas Keane, Evan E Eichler, David Haussler, Mario Stanke (+1 others)
2017 bioRxiv   pre-print
We show that CAT can be used to improve annotations on the rat genome, annotate the great apes, annotate a diverse set of mammals, and annotate personal, diploid human genomes.  ...  The result is an explosion of new, ultra-contiguous genome assemblies. To compare these genomes we need robust methods for genome annotation.  ...  Finally, we would like to thank Fergal Martin and Paul Flicek for revising the paper and providing a pre-release of the Ensembl V91 annotations on chimpanzee and gorilla, as well as the whole GENCODE consortium  ... 
doi:10.1101/231118 fatcat:y4acyavz2rgf5ceaxqx7cowoze

Exogean: a framework for annotating protein-coding genes in eukaryotic genomic DNA

Sarah Djebali, Franck Delaplace, Hugues Roest Crollius
2006 Genome Biology  
This is illustrated in the EGASP project, where reference annotations against which all automatic methods are measured are generated by human annotators and experimentally verified.  ...  We discuss current limitations of the method and several avenues for improvement.  ...  Acknowledgments We wish to thank Paul Flicek for kindly providing an updated version of the Eval software, Matthieu Muffato for assistance with engineering aspects and Fiona Francis for critical reading  ... 
doi:10.1186/gb-2006-7-s1-s7 pmid:16925841 pmcid:PMC1810556 fatcat:hmzww44ejfezvgcvamarblbib4

APPRIS 2017: principal isoforms for multiple gene sets

Jose Manuel Rodriguez, Juan Rodriguez-Rivas, Tomás Di Domenico, Jesús Vázquez, Alfonso Valencia, Michael L Tress
2017 Nucleic Acids Research  
In addition AP-PRIS now provides a measure of reliability for individual principal isoforms and updates with each release of the GENCODE/Ensembl and RefSeq reference sets.  ...  The individual GENCODE/Ensembl, Ref-Seq and UniProtKB reference gene sets for six organisms have been merged to produce common sets of splice variants.  ...  For that reason we have extended APPRIS to the RefSeqGene and UniProtKB annotations in the case of vertebrate genomes (human, mouse, zebra-fish, rat, pig and chimpanzee).  ... 
doi:10.1093/nar/gkx997 pmid:29069475 pmcid:PMC5753224 fatcat:dmhn5ropvnbtzoftrf4aoovvoe

Comparative Annotation Toolkit (CAT)—simultaneous clade and personal genome annotation

Ian T. Fiddes, Joel Armstrong, Mark Diekhans, Stefanie Nachtweide, Zev N. Kronenberg, Jason G. Underwood, David Gordon, Dent Earl, Thomas Keane, Evan E. Eichler, David Haussler, Mario Stanke (+1 others)
2018 Genome Research  
We show that CAT can be used to improve annotations on the rat genome, annotate the great apes, annotate a diverse set of mammals, and annotate personal, diploid human genomes.  ...  The result is an explosion of new, ultracontiguous genome assemblies. To compare these genomes, we need robust methods for genome annotation.  ...  Finally, we thank Fergal Martin and Paul Flicek for revising the paper and providing a pre-release of the Ensembl V91 annotations on chimpanzee and gorilla, as well as the whole GENCODE Consortium for  ... 
doi:10.1101/gr.233460.117 pmid:29884752 fatcat:gtgabvlntfgxfg3h3wibuy3t2a

Ensembl 2017

Bronwen L. Aken, Premanand Achuthan, Wasiu Akanni, M. Ridwan Amode, Friederike Bernsdorff, Jyothish Bhai, Konstantinos Billis, Denise Carvalho-Silva, Carla Cummins, Peter Clapham, Laurent Gil, Carlos García Girón (+38 others)
2016 Nucleic Acids Research  
Our extensive data resources include evidence-based gene and regulatory region annotation, genome variation and gene trees.  ...  Among many other developments over the past year, we have improved our resources for gene regulation and comparative genomics, and added CRISPR/Cas9 target sites.  ...  ACKNOWLEDGEMENTS Thank you to the Systems Administration teams at the Wellcome Trust Sanger Institute and at EMBL-EBI for  ... 
doi:10.1093/nar/gkw1104 pmid:27899575 pmcid:PMC5210575 fatcat:hzc4nlutrnfo5obbhqtlljr724

Using several pair-wise informant sequences for de novo prediction of alternatively spliced transcripts

Paul Flicek, Michael R Brent
2006 Genome Biology  
MARS uses the mouse, rat, dog, opossum, chicken, and frog genome sequences as pairwise informant sources for Twinscan and combines the resulting transcript predictions into genes based on coding (CDS)  ...  alternatively spliced transcripts in the GENCODE annotation is relatively small.  ...  MRB and the development of the Twinscan code base were supported in part by HG02278 from the National Human Genome Research Institute.  ... 
doi:10.1186/gb-2006-7-s1-s8 pmid:16925842 pmcid:PMC1810557 fatcat:4gjt2gdnofbvrbzjhusulitm64

The UCSC Genome Browser database: update 2011

P. A. Fujita, B. Rhead, A. S. Zweig, A. S. Hinrichs, D. Karolchik, M. S. Cline, M. Goldman, G. P. Barber, H. Clawson, A. Coelho, M. Diekhans, T. R. Dreszer (+15 others)
2010 Nucleic Acids Research  
Highlights of the past year include the release of a browser for the first new human genome reference assembly in 4 years in December 2013 (GRCh38, UCSC hg38), a watershed comparative genomics annotation  ...  As our user community increasingly adopts the UCSC track hub and assembly hub representations for sharing large-scale genomic annotation data sets and genome sequencing projects, our menu of public data  ...  The GENCODE project provides high-quality manual curation of evidence-based automated gene predictions for human and mouse genomes.  ... 
doi:10.1093/nar/gkq963 pmid:20959295 pmcid:PMC3242726 fatcat:fnemefhmkbc65bmwbfxqlp7lpm

Discovery of high-confidence human protein-coding genes and exons by whole-genome PhyloCSF helps elucidate 118 GWAS loci

Jonathan M. Mudge, Irwin Jungreis, Toby Hunt, Jose Manuel Gonzalez, James C. Wright, Mike Kay, Claire Davidson, Stephen Fitzgerald, Ruth Seal, Susan Tweedie, Liang He, Robert M. Waterhouse (+5 others)
2019 Genome Research  
Here, we present the first whole-genome PhyloCSF prediction tracks for human, mouse, chicken, fly, worm, and mosquito.  ...  The most widely appreciated role of DNA is to encode protein, yet the exact portion of the human genome that is translated remains to be ascertained.  ...  Acknowledgments We thank Jade Vinson for help with splice prediction software, Lel Eory for help with chicken data, and Mike Lin, Clara Chan, Mark Diekhans, John Rinn, and Jennifer Harrow for helpful input  ... 
doi:10.1101/gr.246462.118 pmid:31537640 pmcid:PMC6886504 fatcat:3suhcry5dzfovlerm5f4egv7li

GENCODE: The reference human genome annotation for The ENCODE Project

J. Harrow, A. Frankish, J. M. Gonzalez, E. Tapanari, M. Diekhans, F. Kokocinski, B. L. Aken, D. Barrell, A. Zadissa, S. Searle, I. Barnes, A. Bignell (+29 others)
2012 Genome Research  
The GENCODE Consortium aims to identify all gene features in the human genome using a combination of computational analysis, manual annotation, and experimental validation.  ...  GENCODE 7 is publicly available from and via the Ensembl and UCSC Genome Browsers.  ...  Acknowledgments We thank all of the HAVANA team that contributed to the manual annotation and the Ensembl gene builders, and the VEGA team that produced the release of GENCODE.  ... 
doi:10.1101/gr.135350.111 pmid:22955987 pmcid:PMC3431492 fatcat:qnre6dj4fvbbxluelrhsww4mma

Patterns of gene duplication and intron loss in the ENCODE regions suggest a confounding factor

Sourav Chatterji, Lior Pachter
2007 Genomics  
The exon-intron structure of eukaryotic genes allows for phenomena such as alternative splicing, nonsense-mediated decay, and regulation through untranslated regions.  ...  In this study, we use the phylogenetically diverse sequencing of the ENCODE regions to study gene structure evolution in mammalian genomes.  ...  We also thank the GENCODE and HAVANA teams for organizing the EGASP workshop during which we began work on this project.  ... 
doi:10.1016/j.ygeno.2007.03.008 pmid:17499477 pmcid:PMC2034525 fatcat:ixdlfjlf2bcelczusj7bq6bspm

Multiple evidence strands suggest that there may be as few as 19 000 human protein-coding genes

Iakes Ezkurdia, David Juan, Jose Manuel Rodriguez, Adam Frankish, Mark Diekhans, Jennifer Harrow, Jesus Vazquez, Alfonso Valencia, Michael L. Tress
2014 Human Molecular Genetics  
Here, we mapped peptides detected in seven large-scale proteomics studies to almost 60% of the protein-coding genes in the GENCODE annotation of the human genome.  ...  We believe that their inclusion in the human protein-coding gene catalogue should be revised as part of the ongoing human genome annotation effort.  ...  ACKNOWLEDGEMENTS The authors thank Daniel Rico for suggestions and discussions regarding gene expression and gene family age data. Conflict of Interest statement. None declared.  ... 
doi:10.1093/hmg/ddu309 pmid:24939910 pmcid:PMC4204768 fatcat:mnpjk63imrcffjiciswbdxntzq

High-throughput annotation of full-length long noncoding RNAs with Capture Long-Read Sequencing [article]

Julien Lagarde, Barbara Uszczynska-Ratajczak, Silvia Carbonell, Silvia Perez-Lluch, Amaya Abad, Carrie Davis, Thomas R. Gingeras, Adam Frankish, Jennifer Harrow, Roderic Guigo, Rory Johnson
2017 bioRxiv   pre-print
We present an experimental re-annotation of the GENCODE intergenic lncRNA population in matched human and mouse tissues, resulting in novel transcript models for 3574 / 561 gene loci, respectively.  ...  Accurate annotations of genes and their transcripts is a foundation of genomics, but no annotation technique presently combines throughput and accuracy.  ...  Genome-aligned data were assembled into a public Track Hub, which can be loaded into the UCSC Genome Browser (see URLs).  ... 
doi:10.1101/105064 fatcat:ufwxwaedc5dbhhbhrmneiawl3y
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