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Ensembl Genomes 2013: scaling up access to genome-wide data

Paul Julian Kersey, James E. Allen, Mikkel Christensen, Paul Davis, Lee J. Falin, Christoph Grabmueller, Daniel Seth Toney Hughes, Jay Humphrey, Arnaud Kerhornou, Julia Khobova, Nicholas Langridge, Mark D. McDowall (+21 others)
2013 Nucleic Acids Research  
ACKNOWLEDGEMENTS The authors would also like to acknowledge the contributions of all our collaborators and of all colleagues working on the Ensembl project.  ...  In addition, the resource has scaled up its representation of bacterial genomes, and now includes the genomes of over 9000 bacteria.  ...  The overall suite of Ensembl Genomes interfaces mirrors the interfaces provided for vertebrate genomes in Ensembl, and allows users access to genomic data from across the tree of life in a consistent manner  ... 
doi:10.1093/nar/gkt979 pmid:24163254 pmcid:PMC3965094 fatcat:bzydx6qowvdunnkte5sioqgk5y

The Ensembl Genome Browser: Strategies for Accessing Eukaryotic Genome Data [chapter]

Victoria Newman, Benjamin Moore, Helen Sparrow, Emily Perry
2018 Msphere  
The Ensembl Genome Browser provides a wealth of freely available genomic data that can be accessed for many purposes by genetics, genomics, and molecular biology researchers.  ...  These workflows illustrate a subset of the data types available through the Ensembl Browser, and can be considered a springboard for further exploration.  ...  Data from Ensembl can be accessed at multiple scales.  ... 
doi:10.1007/978-1-4939-7737-6_6 pmid:29761458 fatcat:eehmfjjfrveyppuanp5fw7n7sq

The Ensembl Variant Effect Predictor

William McLaren, Laurent Gil, Sarah E. Hunt, Harpreet Singh Riat, Graham R. S. Ritchie, Anja Thormann, Paul Flicek, Fiona Cunningham
2016 Genome Biology  
It provides access to an extensive collection of genomic annotation, with a variety of interfaces to suit different requirements, and simple options for configuring and extending analysis.  ...  It is open source, free to use, and supports full reproducibility of results. The Ensembl Variant Effect Predictor can simplify and accelerate variant interpretation in a wide range of study designs.  ...  access to the latest annotation data.  ... 
doi:10.1186/s13059-016-0974-4 pmid:27268795 pmcid:PMC4893825 fatcat:lziduun2xnhpteudwo3utn4nyi

TIARA genome database: update 2013

D. Hong, J. Lee, T. Bleazard, H. Jung, Y. S. Ju, S.-b. Yu, S. Kim, S.-S. Park, J.-I. Kim, J.-S. Seo
2013 Database: The Journal of Biological Databases and Curation  
Improvements to the TIARA genome browser include the intuitive display of new complex and large-scale data sets.  ...  Following TIARA's fundamentally integrative approach, new transcriptome sequencing data are matched with whole-genome sequencing data in the genome browser.  ...  As the use of genome-wide sequencing increases, so also do the challenges of efficiently managing and retrieving these large-scale data structures.  ... 
doi:10.1093/database/bat003 pmid:23515433 pmcid:PMC3602786 fatcat:5m22dpcuyngnfkfg2jmmypkxem

Gramene 2013: comparative plant genomics resources

Marcela K. Monaco, Joshua Stein, Sushma Naithani, Sharon Wei, Palitha Dharmawardhana, Sunita Kumari, Vindhya Amarasinghe, Ken Youens-Clark, James Thomason, Justin Preece, Shiran Pasternak, Andrew Olson (+14 others)
2013 Nucleic Acids Research  
Its strength derives from the application of a phylogenetic framework for genome comparison and the use of ontologies to integrate structural and functional annotation data.  ...  Genetic variation data, sequences and genome mappings available for 10 species, including Arabidopsis, rice and maize, help infer putative variant effects on genes and transcripts.  ...  We acknowledge our fellow researchers, and their respective organizations for sharing genomic-scale datasets.  ... 
doi:10.1093/nar/gkt1110 pmid:24217918 pmcid:PMC3964986 fatcat:lcgbm3znjnaptk4vprqeoowt34

NetMiner-an ensemble pipeline for building genome-wide and high-quality gene co-expression network using massive-scale RNA-seq samples

Hua Yu, Bingke Jiao, Lu Lu, Pengfei Wang, Shuangcheng Chen, Chengzhi Liang, Wei Liu, Yun Zheng
2018 PLoS ONE  
C, et al. (2018) NetMiner-an ensemble pipeline for building genome-wide and high-quality gene coexpression network using massive-scale RNA-seq samples. PLoS ONE 13(2): e0192613. https://doi.  ...  Using massive-scale RNA-seq samples, we have designed an ensemble pipeline, called NetMiner, for building genome-scale and high-quality Gene Co-expression Network (GCN) by integrating three frequently  ...  The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.  ... 
doi:10.1371/journal.pone.0192613 pmid:29425247 pmcid:PMC5806890 fatcat:k33ho27l3fdqde4pyqviyldjg4

Linear-time cluster ensembles of large-scale single-cell RNA-seq and multimodal data

Van Hoan Do, Francisca Rojas Ringeling, Stefan Canzar
2021 Genome Research  
Its linear time complexity allows Specter to scale to millions of cells and leads to fast computation times in practice.  ...  We exploit Specter's speed in a cluster ensemble scheme that achieves a substantial improvement in accuracy over existing methods and that is sensitive to rare cell types.  ...  profiling genome-wide expression for hundreds of thousands of cells at once.  ... 
doi:10.1101/gr.267906.120 pmid:33627473 pmcid:PMC8015854 fatcat:iyaka44c6zauxkrhra5ayg7q4q

BioUML Genome Browser

Tagir Valeev, Ivan Yevshin, Fedor Kolpakov
2013 Virtual Biology  
Motivation: The BioUML platform contains a number of analysis tools to process genomic data. Visualization of such data can be performed using genome browsers.  ...  Using external genome browsers is inconvenient as it requires exporting data from BioUML and importing it into a genome browser. Thus creation of an internal BioUML genome browser was considered.  ...  As you can see, the genome browser is capable of displaying this track in any scale from per-nucleotide to chromosome-wide.  ... 
doi:10.12704/vb/e8 fatcat:ly6lixmulvfubmt436dfhnkgje

BioHackathon series in 2013 and 2014: improvements of semantic interoperability in life science data and services

Toshiaki Katayama, Shuichi Kawashima, Gos Micklem, Shin Kawano, Jin-Dong Kim, Simon Kocbek, Shinobu Okamoto, Yue Wang, Hongyan Wu, Atsuko Yamaguchi, Yasunori Yamamoto, Erick Antezana (+64 others)
2019 F1000Research  
Publishing databases in the Resource Description Framework (RDF) model is becoming widely accepted to maximize the syntactic and semantic interoperability of open data in life sciences.  ...  The first section describes how we developed RDF data, ontologies and tools in genomics, proteomics, metabolomics, glycomics and by literature text mining.  ...  Acknowledgements BioHackathon 2013 and 2014 are supported by the Integrated Database Project (Ministry of Education, Culture, Sports, Science and Technology of Japan) and hosted by the National Bioscience  ... 
doi:10.12688/f1000research.18238.1 fatcat:mdt6bijqlveanplh4bmca5towu

Database tools in genetic diseases research

Anna Monica Bianco, Annalisa Marcuzzi, Valentina Zanin, Martina Girardelli, Josef Vuch, Sergio Crovella
2013 Genomics  
In relation to data sets available from genome-wide association studies, we describe databases that could be the starting point for developing studies in the field of complex diseases, particularly those  ...  The knowledge of the human genome is in continuous progression: a large number of databases have been developed to make meaningful connections among worldwide scientific discoveries.  ...  It plays a central role in bioinformatics by offering access to a wide variety of biological access.  ... 
doi:10.1016/j.ygeno.2012.11.001 pmid:23147677 fatcat:axmspbxbkzavnduisji4e37ilm

HTS-DB: an online resource to publish and query data from functional genomics high-throughput siRNA screening projects

Rebecca E. Saunders, Rachael Instrell, Rossella Rispoli, Ming Jiang, Michael Howell
2013 Database: The Journal of Biological Databases and Curation  
., HTS-DB: an online resource to publish and query data from functional genomics highthroughput siRNA screening projects.  ...  High-throughput screening (HTS) uses technologies such as RNA interference to generate loss-of-function phenotypes on a genomic scale.  ...  Acknowledgements The authors thank their colleagues at the LRI for allowing to make their hard-won data public before publication, and Ilaria Gori and Nicholas McGranahan for helpful comments on the manuscript  ... 
doi:10.1093/database/bat072 pmid:24122843 pmcid:PMC3796064 fatcat:jqb6t7zjdzcq3pri6r462fyku4

EASER: Ensembl Easy Sequence Retriever

Emanuel Maldonado, Imran Khan, Siby Philip, Vítor Vasconcelos, Agostinho Antunes
2013 Evolutionary Bioinformatics  
This script retrieves Ensembl defined genomic features, associated with a given Ensembl identifier.  ...  The rapid advances in genome sequencing technologies have increased the pace at which biological sequence databases are becoming available to the broad scientific community.  ...  Acknowledgements We are thankful to the anonymous reviewers for their valuable comments and suggestions which lead to the improvement of the manuscript.  ... 
doi:10.4137/ebo.s11335 pmid:24324324 pmcid:PMC3855309 fatcat:73ktr6rgyrhsxoihnmkq6eqhwe

ArkMAP: integrating genomic maps across species and data sources

Trevor Paterson, Andy Law
2013 BMC Bioinformatics  
Conclusions: ArkMAP allows users to draw and interactively explore gene and variation maps for any version of any annotated genome curated in the Ensembl data sources, and to integrate local mapping data  ...  Maps can be retrieved from our public map database ArkDB or from any Ensembl data source (i.e. Ensembl and Ensembl Genomes).  ...  Acknowledgements The authors would like to acknowledge the contributions of previous members of the ArkDB project, particularly Fahad Ifthkar, Paul Martin and Phil Devall.  ... 
doi:10.1186/1471-2105-14-246 pmid:23941167 pmcid:PMC3751345 fatcat:4qsprll4zjesfjdffsfp762aee

GenomeRNAi: a database for cell-based and in vivo RNAi phenotypes, 2013 update

Esther E. Schmidt, Oliver Pelz, Svetlana Buhlmann, Grainne Kerr, Thomas Horn, Michael Boutros
2012 Nucleic Acids Research  
RNA interference (RNAi) represents a powerful method to systematically study loss-of-function phenotypes on a large scale with a wide variety of biological assays, constituting a rich source for the assignment  ...  Structured annotation guidelines have been established to facilitate consistent curation, and a submission template for direct submission by data producers is available for download.  ...  They are grateful to Marco Breinig for critical comments on the manuscript.  ... 
doi:10.1093/nar/gks1170 pmid:23193271 pmcid:PMC3531141 fatcat:5dp6n47pdjcnphy73jmqtl2qgy

TASUKE: a web-based visualization program for large-scale resequencing data

M. Kumagai, J. Kim, R. Itoh, T. Itoh
2013 Bioinformatics  
TASUKE is a web application that visualizes large-scale resequencing data generated by next-generation sequencing technologies and is suitable for rapid data release to the public on the web.  ...  The variation and read depths of multiple genomes, as well as annotations, can be shown simultaneously at various scales.  ...  TASUKE helps bioinformatics researchers of genome-wide resequencing projects to visualize a large amount of polymorphisms on multiple genomes and to release the data to the public.  ... 
doi:10.1093/bioinformatics/btt295 pmid:23749962 pmcid:PMC3702261 fatcat:6zbvhaigb5dwlivw6g23te2uo4
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