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Ensembl Genomes 2018: an integrated omics infrastructure for non-vertebrate species

Paul Julian Kersey, James E Allen, Alexis Allot, Matthieu Barba, Sanjay Boddu, Bruce J Bolt, Denise Carvalho-Silva, Mikkel Christensen, Paul Davis, Christoph Grabmueller, Navin Kumar, Zicheng Liu (+34 others)
2017 Nucleic Acids Research  
Ensembl Genomes (http://www.ensemblgenomes. org) is an integrating resource for genome-scale data from non-vertebrate species, complementing the resources for vertebrate genomics developed in the Ensembl  ...  These include the incorporation of almost 20 000 additional genome sequences and over 35 000 tracks of RNA-Seq data, which have been aligned to genomic sequence and made available for visualization.  ...  Vertebrate metazoa are the focus of the Ensembl project (1); Ensembl Genomes provides a complementary set of interfaces for non-vertebrate species.  ... 
doi:10.1093/nar/gkx1011 pmid:29092050 pmcid:PMC5753204 fatcat:mmgammsp3fcrpdfrwprhsxl4g4

Ensembl 2018

Daniel R Zerbino, Premanand Achuthan, Wasiu Akanni, M Ridwan Amode, Daniel Barrell, Jyothish Bhai, Konstantinos Billis, Carla Cummins, Astrid Gall, Carlos García Girón, Laurent Gil, Leo Gordon (+45 others)
2017 Nucleic Acids Research  
The Ensembl project has been aggregating, processing, integrating and redistributing genomic datasets since the initial releases of the draft human genome, with the aim of accelerating genomics research  ...  We present here the latest developments of the Ensembl project, with a focus on managing an increasing number of assemblies, supporting efforts in genome interpretation and improving our browser.  ...  For their assistance with the Ensembl infrastructure and hardware mi-  ... 
doi:10.1093/nar/gkx1098 pmid:29155950 pmcid:PMC5753206 fatcat:g7pg5j5vpfgilgtr2bflfiqyei

New perspectives: systems medicine in cardiovascular disease

Frank Kramer, Steffen Just, Tanja Zeller
2018 BMC Systems Biology  
Conclusion: In this review, we provide an overview of the current molecular-experimental, epidemiological and bioinformatical tools applied in systems medicine in the cardiovascular field.  ... [ 59] Ensembl A genome browser for vertebrate genomes that supports cross-species research in genomics, evolution, sequence variation and transcriptional regulation.  ...  Nowadays, large biobanks are an integral part of a cohort's infrastructure [48, 49] and build the basis for a large part of the biomedical research.  ... 
doi:10.1186/s12918-018-0579-5 pmid:29699591 pmcid:PMC5921396 fatcat:lefbtc4x3zcghi4gzqlv3y5xxm

Ensembl 2019

Fiona Cunningham, Premanand Achuthan, Wasiu Akanni, James Allen, M Ridwan Amode, Irina M Armean, Ruth Bennett, Jyothish Bhai, Konstantinos Billis, Sanjay Boddu, Carla Cummins, Claire Davidson (+56 others)
2018 Nucleic Acids Research  
This year we describe our new and expanded gene, variant and comparative annotation capabilities, which led to a 50% increase in the number of vertebrate genomes we support.  ...  Ensembl seeks to be a fundamental resource driving scientific progress by creating, maintaining and updating reference genome annotation and comparative genomics resources.  ...  For their assistance with the Ensembl infrastructure we acknowledge Simone Badoer, Jonathan Barker, Andy Bryant, Liz Beresford, Andy Cafferkey, Andrea Cristofori, Ray Coetzee, Salvatore Di Nardo, Pete  ... 
doi:10.1093/nar/gky1113 pmid:30407521 fatcat:q2roq24hdjaqrlqc6r52kemvzi

Abstracts from the Human Genome Meeting 2018

2018 Human Genomics  
We would also like to thank GeNAS for data production. Acknowledgements  ...  Acknowledgments We are grateful to all members of the Laboratory for Autoimmune Diseases for their expert technical assistance Acknowledgements The study was supported by the Russian Science Foundation  ...  Here we present the automatic genome annotation pipeline that integrates the RNA-seq and protein sequences derived from various species.  ... 
doi:10.1186/s40246-018-0138-6 fatcat:nl6xhsuchzgbxik4pjwjvbbkie

A tutorial of diverse genome analysis tools found in the CoGe web-platform using Plasmodium spp. as a model

Andreina I Castillo, Andrew D L Nelson, Asher K Haug-Baltzell, Eric Lyons
2018 Database: The Journal of Biological Databases and Curation  
Acknowledgements The authors thank CyVerse (NSF DBI-0735191 and DBI-1265383) for sharing best practices and providing data and computational infrastructure for CoGe (NSF IOS-1339156 and IOS-1444490).  ...  They are also grateful to Blake Joyce for his helpful comments and Sean Davey for providing assistance with CoGe's resources.  ...  Database, Vol. 2018, Article ID bay030  ... 
doi:10.1093/database/bay030 fatcat:hol35dkaqzaldfucbovzp6ppxe

Loss of stomach, loss of appetite? Sequencing of the ballan wrasse (Labrus bergylta) genome and intestinal transcriptomic profiling illuminate the evolution of loss of stomach function in fish

Kai K. Lie, Ole K. Tørresen, Monica Hongrø Solbakken, Ivar Rønnestad, Ave Tooming-Klunderud, Alexander J. Nederbragt, Sissel Jentoft, Øystein Sæle
2018 BMC Genomics  
gastric species.  ...  Analysis of the genome and transcriptome assemblies confirmed the absence of genes that code for proteins involved in gastric function.  ...  The NSC is a national technology platform hosted by the University of Oslo and supported by the "Functional Genomics" and "Infrastructure" programs of the Research Council of Norway and the South-eastern  ... 
doi:10.1186/s12864-018-4570-8 pmid:29510660 pmcid:PMC5840709 fatcat:jmlguipe6nfjrmvdhwhflaf5ve

BarleyNet: A Network-Based Functional Omics Analysis Server for Cultivated Barley, Hordeum vulgare L

Sungho Lee, Tak Lee, Sunmo Yang, Insuk Lee
2020 Frontiers in Plant Science  
Barley is an important crop species not only as a food source, but also in plant genetics because it harbors numerous stress response alleles in its genome that can be exploited for crop engineering.  ...  Moreover, bioinformatics tools for system-wide analyses of omics data from barley are not yet available.  ...  Ensembl Genomes 2018: an integrated omics infrastructure for non-vertebrate species.  ... 
doi:10.3389/fpls.2020.00098 pmid:32133024 pmcid:PMC7040090 fatcat:7laysai2sjgdzpukrlkuctdici

Vision, challenges and opportunities for a Plant Cell Atlas

Plant Cell Atlas Consortium, Jahed Ahmed, Oluwafemi Alaba, Gazala Ameen, Vaishali Arora, Mario A Arteaga-Vazquez, Alok Arun, Julia Bailey-Serres, Laura E Bartley, George W Bassel, Dominique C Bergmann, Edoardo Bertolini (+137 others)
2021 eLife  
This framework, called the Plant Cell Atlas (PCA), will be critical for understanding and engineering plant development, physiology and environmental responses.  ...  A workshop was convened to discuss the purpose and utility of such an initiative, resulting in a roadmap that acknowledges the current knowledge gaps and technical challenges, and underscores how the PCA  ...  Lack of well-characterized, cell-type-specific marker genes in non-model species.  ... 
doi:10.7554/elife.66877 pmid:34491200 pmcid:PMC8423441 fatcat:xq6vypwp4rbbjfkhtl5l2ty35q

Contents list

2018 Soft Matter  
Each of the 55 IRCS carries up to seven SEG/Pas chromosomal segments with an average size of 13.4 Mb, totalizing 1.26% of the genome. The complete series covers 38% of the SEG/Pas genome.  ...  In particular, inbred strains of several mouse species show substantial morphological differences.  ...  Center for Vertebrate Genomics, Dept Biomed.  ... 
doi:10.1039/c8sm90107d fatcat:tko5byj5izccvgfzmdsssx4mgm

AgBioData consortium recommendations for sustainable genomics and genetics databases for agriculture

Lisa Harper, Jacqueline Campbell, Ethalinda K S Cannon, Sook Jung, Monica Poelchau, Ramona Walls, Carson Andorf, Elizabeth Arnaud, Tanya Z Berardini, Clayton Birkett, Steve Cannon, James Carson (+40 others)
2018 Database: The Journal of Biological Databases and Curation  
Furthermore, the value of data increases exponentially when they are properly stored, described, integrated and shared, so that they can be easily utilized in future analyses.  ...  Governmental agencies, publishers and science funders require data management plans for publicly funded research.  ...  Acknowledgements We acknowledge with thanks The National Science Foundation Plant Genome Research Program Award # 1444573 for funding the AgBioData Workshop and development and hosting of the AgBio-Data  ... 
doi:10.1093/database/bay088 pmid:30239679 pmcid:PMC6146126 fatcat:spcxmd66qrgdnos4larqfvf6ai

Livestock genome annotation: transcriptome and chromatin structure profiling in cattle, goat, chicken and pig [article]

Sylvain Foissac, Sarah Djebali, Kylie Munyard, Nathalie Vialaneix, Andrea Rau, Kevin Muret, Diane Esquerre, Matthias Zytnicki, Thomas Derrien, Philippe Bardou, Fany Blanc, Cedric Cabau (+23 others)
2018 bioRxiv   pre-print
Standardized protocols were applied to produce transcriptome and chromatin datasets for the four species.  ...  We report the first multi-species and multi-assay genome annotation results obtained by a FAANG pilot project.  ...  the integrative analysis of 'omics data and the importance of future metanalysis of several datasets.  ... 
doi:10.1101/316091 fatcat:rbkdh72ecrcljduc7dhwm3bq3i

Abstracts for the 42nd Human Genetics Society of Australasia Annual Scientific Meeting Sydney, New South Wales August 4–7, 2018

2018 Twin Research and Human Genetics  
In this talk I will describe work done as part of the Genome Aggregation Database (gnomAD) project and its predecessor, the Exome Aggregation Consortium (ExAC), to harmonize exome and genome sequencing  ...  More than two million humans have now had their exomes or genomes sequenced, but the underlying data are typically heavily siloed by project and generated using inconsistent sequencing and analysis technologies  ...  Three ml of blood specimen was collected for genomic DNA isolation and amplification of TPO gene (Exon 8 to Exon 14) by PCR followed by Sanger Sequencing.  ... 
doi:10.1017/thg.2018.51 pmid:30284531 fatcat:2fzkr56iwndxfhcpcuuwtxymkm

dbAMP: an integrated resource for exploring antimicrobial peptides with functional activities and physicochemical properties on transcriptome and proteome data

Jhih-Hua Jhong, Yu-Hsiang Chi, Wen-Chi Li, Tsai-Hsuan Lin, Kai-Yao Huang, Tzong-Yi Lee
2018 Nucleic Acids Research  
Additionally, a Docker container has been developed as a downloadable package for discovering known and novel AMPs on high-throughput omics data.  ...  Significant improvements available in dbAMP include the information of AMP-protein interactions, antimicrobial potency analysis for 'cryptic' region detection, annotations of AMP target species, as well  ...  ACKNOWLEDGEMENTS The authors sincerely appreciate the Warshel Institute for Computational Biology.  ... 
doi:10.1093/nar/gky1030 pmid:30380085 pmcid:PMC6323920 fatcat:caefwxw6pfgfzhb2uhxotzyoom

Artificial Intelligence Based Approaches to Identify Molecular Determinants of Exceptional Health and Life Span-An Interdisciplinary Workshop at the National Institute on Aging

Jason H. Moore, Nalini Raghavachari, Workshop Speakers
2019 Frontiers in Artificial Intelligence  
Artificial intelligence (AI) has emerged as a powerful approach for integrated analysis of the rapidly growing volume of multi-omics data, including many research and clinical tasks such as prediction  ...  Span and Life Span" in August 2018.  ...  William La Cava for his valuable input in this manuscript.  ... 
doi:10.3389/frai.2019.00012 pmid:33733101 pmcid:PMC7861312 fatcat:bcksleryynb3vermp64tceheti
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