Database Resources of the National Genomics Data Center in 2020 DOI Creative Commons
Zhang Zhang, Wenming Zhao, Jingfa Xiao

et al.

Nucleic Acids Research, Journal Year: 2019, Volume and Issue: unknown

Published: Oct. 2, 2019

The National Genomics Data Center (NGDC) provides a suite of database resources to support worldwide research activities in both academia and industry. With the rapid advancements higher-throughput lower-cost sequencing technologies accordingly huge volume multi-omics data generated at exponential scales rates, NGDC is continually expanding, updating enriching its core through big integration value-added curation. In past year, efforts for update have been mainly devoted BioProject, BioSample, GSA, GWH, GVM, NONCODE, LncBook, EWAS Atlas IC4R. Newly released include three human genome databases (PGG.SNV, PGG.Han CGVD), eLMSG, Hub, GWAS Atlas, iSheep PADS Arsenal. addition, four web services, namely, eGPS Cloud, BIG Search, Submission SSO, significantly improved enhanced. All these along with their services are publicly accessible https://bigd.big.ac.cn.

Language: Английский

COSMIC: somatic cancer genetics at high-resolution DOI Creative Commons

Simon Forbes,

David Beare,

Harry Boutselakis

et al.

Nucleic Acids Research, Journal Year: 2016, Volume and Issue: 45(D1), P. D777 - D783

Published: Oct. 27, 2016

COSMIC, the Catalogue of Somatic Mutations in Cancer (http://cancer.sanger.ac.uk) is a high-resolution resource for exploring targets and trends genetics human cancer. Currently broadest database mutations cancer, information COSMIC curated by expert scientists, primarily scrutinizing large numbers scientific publications. Over 4 million coding are described v78 (September 2016), combining genome-wide sequencing results from 28 366 tumours with complete manual curation 23 489 individual publications focused on 186 key genes 286 fusion pairs across all cancers. Molecular profiling tumour has also allowed annotation more than 13 non-coding mutations, 18 029 gene fusions, 187 429 genome rearrangements, 1 271 436 abnormal copy number segments, 9 175 462 expression variants 7 879 142 differentially methylated CpG dinucleotides. now details drug resistance, novel somatic which allow to evade therapeutic cancer drugs. Focusing initially highly characterized drugs genes, contains wide resistance mutation profiles 20 drugs, detailing recurrence 301 unique alleles 1934 drug-resistant tumours. All available freely website.

Language: Английский

Citations

1852
FlyBase 2.0: the next generation DOI Creative Commons
Jim Thurmond, Joshua L. Goodman,

Victor Strelets

et al.

Nucleic Acids Research, Journal Year: 2018, Volume and Issue: 47(D1), P. D759 - D765

Published: Oct. 9, 2018

FlyBase (flybase.org) is a knowledge base that supports the community of researchers use fruit fly, Drosophila melanogaster, as model organism. The team curates and organizes diverse array genetic, molecular, genomic, developmental information about Drosophila. At beginning 2018, 'FlyBase 2.0' was released with significantly improved user interface new tools. Among these important changes are organization search results into interactive lists or tables (hitlists), enhanced reference lists, protein domain graphics. An data class called 'experimental tools' consolidates on useful fly strains other resources related to specific gene, which enhances ability researcher design carry out experiments. With release 2.0, there has also been restructuring backend architecture continued development application programming interfaces (APIs) for programmatic access data. In this review, we describe major features functionalities 2.0 site how they support organism biological discovery translational research.

Language: Английский

Citations

772
Prediction of acute myeloid leukaemia risk in healthy individuals DOI
Sagi Abelson, Grace Collord,

Stanley Ng

et al.

Nature, Journal Year: 2018, Volume and Issue: 559(7714), P. 400 - 404

Published: July 1, 2018

Language: Английский

Citations

741
The landscape of somatic mutation in normal colorectal epithelial cells DOI
Henry Lee-Six, Sigurgeir Ólafsson, Peter Ellis

et al.

Nature, Journal Year: 2019, Volume and Issue: 574(7779), P. 532 - 537

Published: Oct. 23, 2019

Language: Английский

Citations

619
Introducing the Bacterial and Viral Bioinformatics Resource Center (BV-BRC): a resource combining PATRIC, IRD and ViPR DOI Creative Commons
Robert Olson,

Rida Assaf,

Thomas Brettin

et al.

Nucleic Acids Research, Journal Year: 2022, Volume and Issue: 51(D1), P. D678 - D689

Published: Nov. 9, 2022

Abstract The National Institute of Allergy and Infectious Diseases (NIAID) established the Bioinformatics Resource Center (BRC) program to assist researchers with analyzing growing body genome sequence other omics-related data. In this report, we describe merger PAThosystems Integration (PATRIC), Influenza Research Database (IRD) Virus Pathogen Analysis (ViPR) BRCs form Bacterial Viral (BV-BRC) https://www.bv-brc.org/. combined BV-BRC leverages functionality bacterial viral resources provide a unified data model, enhanced web-based visualization analysis tools, bioinformatics services, powerful suite command line tools that benefit research communities.

Language: Английский

Citations

611
JBrowse 2: a modular genome browser with views of synteny and structural variation DOI Creative Commons
Colin Diesh, Garrett J Stevens,

Peter Xie

et al.

Genome biology, Journal Year: 2023, Volume and Issue: 24(1)

Published: April 17, 2023

Abstract We present JBrowse 2, a general-purpose genome annotation browser offering enhanced visualization of complex structural variation and evolutionary relationships. It retains core features while adding new views for synteny, dotplots, breakpoints, gene fusions, whole-genome overviews. allows users to share sessions, open multiple genomes, navigate between views. can be embedded in web page, used as standalone application, or run from Jupyter notebooks R sessions. These improvements are enabled by ground-up redesign using modern technology. describe application functionality, use cases, performance benchmarks, implementation notes administrators developers.

Language: Английский

Citations

590
Allele-defined genome of the autopolyploid sugarcane Saccharum spontaneum L. DOI Creative Commons
Jisen Zhang, Xingtan Zhang, Haibao Tang

et al.

Nature Genetics, Journal Year: 2018, Volume and Issue: 50(11), P. 1565 - 1573

Published: Oct. 8, 2018

Modern sugarcanes are polyploid interspecific hybrids, combining high sugar content from Saccharum officinarum with hardiness, disease resistance and ratooning of spontaneum. Sequencing a haploid S. spontaneum, AP85-441, facilitated the assembly 32 pseudo-chromosomes comprising 8 homologous groups 4 members each, bearing 35,525 genes alleles defined. The reduction basic chromosome number 10 to in spontaneum was caused by fissions 2 ancestral chromosomes followed translocations chromosomes. Surprisingly, 80% nucleotide binding site-encoding associated located rearranged 51% those regions. Resequencing 64 genomes identified balancing selection regions, maintaining their diversity. Introgressed modern randomly distributed AP85-441 genome, indicating random recombination among homologs different accessions. allele-defined genome offers new knowledge resources accelerate sugarcane improvement. sugarcane, allows prototypical version set. This reference will serve as resource

Language: Английский

Citations

571
FlyBase: a guided tour of highlighted features DOI Creative Commons
L. Sian Gramates,

Julie Agapite,

Helen Attrill

et al.

Genetics, Journal Year: 2022, Volume and Issue: 220(4)

Published: March 10, 2022

FlyBase provides a centralized resource for the genetic and genomic data of Drosophila melanogaster. As enters our fourth decade service to research community, we reflect on unique aspects look forward continued collaboration with larger model organism communities. In this study, emphasize dedicated reports tools have constructed meet specialized needs fly researchers but also facilitate use by other We highlight ways that support including an external resources page, help resources, multiple avenues which can interact FlyBase.

Language: Английский

Citations

464
New Insights into Human Nostril Microbiome from the Expanded Human Oral Microbiome Database (eHOMD): a Resource for the Microbiome of the Human Aerodigestive Tract DOI Creative Commons
Isabel F. Escapa, Tsute Chen, Yanmei Huang

et al.

mSystems, Journal Year: 2018, Volume and Issue: 3(6)

Published: Oct. 30, 2018

The eHOMD ( http://www.ehomd.org ) is a valuable resource for researchers, from basic to clinical, who study the microbiomes and individual microbes in body sites human aerodigestive tract, which includes nasal passages, sinuses, throat, esophagus, mouth, lower respiratory health disease. an actively curated, web-based, open-access resource. provides following: (i) species-level taxonomy based on grouping 16S rRNA gene sequences at 98.5% identity, (ii) systematic naming scheme unnamed and/or uncultivated microbial taxa, (iii) reference genomes facilitate metagenomic, metatranscriptomic, proteomic studies (iv) convenient cross-links other databases (e.g., PubMed Entrez). By facilitating assignment of species names sequences, vital enhancing clinical relevance gene-based microbiome studies, as well metagenomic studies.

Language: Английский

Citations

460
The UCSC Genome Browser database: 2023 update DOI Creative Commons
Luis R Nassar,

Galt P Barber,

Anna Benet‐Pagès

et al.

Nucleic Acids Research, Journal Year: 2022, Volume and Issue: 51(D1), P. D1188 - D1195

Published: Oct. 25, 2022

Abstract The UCSC Genome Browser (https://genome.ucsc.edu) is an omics data consolidator, graphical viewer, and general bioinformatics resource that continues to serve the community as it enters its 23rd year. This year has seen emphasis in clinical data, with new tracks expanded Recommended Track Sets feature on hg38 well addition of a single cell track group. SARS-CoV-2 remain focus, regular annotation updates browser continued curation our phylogenetic sequence placing tool, hgPhyloPlace, whose tree now reached over 12M sequences. Our GenArk also grown, offering 2500 hubs system for users request any absent assemblies. We have bigBarChart display type created ways visualize via bigRmsk dynseq display. Displaying custom annotations easier due chromAlias which eliminates requirement renaming names standard. Users involved generation may be interested tools trackDb settings facilitate creation their annotations.

Language: Английский

Citations

453