ORCID Profile
0000-0002-5394-8896
Current Organisation
European Bioinformatics Institute
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Publisher: Oxford University Press (OUP)
Date: 08-11-2018
DOI: 10.1093/NAR/GKY1113
Publisher: Oxford University Press (OUP)
Date: 21-01-2016
DOI: 10.1093/BIOINFORMATICS/BTW022
Abstract: Summary: Transposon insertion sequencing is a high-throughput technique for assaying large libraries of otherwise isogenic transposon mutants providing insight into gene essentiality, gene function and genetic interactions. We previously developed the Transposon Directed Insertion Sequencing (TraDIS) protocol for this purpose, which utilizes shearing of genomic DNA followed by specific PCR lification of transposon-containing fragments and Illumina sequencing. Here we describe an optimized high-yield library preparation and sequencing protocol for TraDIS experiments and a novel software pipeline for analysis of the resulting data. The Bio-Tradis analysis pipeline is implemented as an extensible Perl library which can either be used as is, or as a basis for the development of more advanced analysis tools. This article can serve as a general reference for the application of the TraDIS methodology. Availability and implementation: The optimized sequencing protocol is included as supplementary information. The Bio-Tradis analysis pipeline is available under a GPL license at anger-pathogens/Bio-Tradis Contact: parkhill@sanger.ac.uk Supplementary information: Supplementary data are available at Bioinformatics online.
Publisher: Oxford University Press (OUP)
Date: 02-11-2020
DOI: 10.1093/NAR/GKAA942
Abstract: The Ensembl project (www.ensembl.org) annotates genomes and disseminates genomic data for vertebrate species. We create detailed and comprehensive annotation of gene structures, regulatory elements and variants, and enable comparative genomics by inferring the evolutionary history of genes and genomes. Our integrated genomic data are made available in a variety of ways, including genome browsers, search interfaces, specialist tools such as the Ensembl Variant Effect Predictor, download files and programmatic interfaces. Here, we present recent Ensembl developments including two new website portals. Ensembl Rapid Release (rapid.ensembl.org) is designed to provide core tools and services for genomes as soon as possible and has been deployed to support large bio ersity sequencing projects. Our SARS-CoV-2 genome browser (covid-19.ensembl.org) integrates our own annotation with publicly available genomic data from numerous sources to facilitate the use of genomics in the international scientific response to the COVID-19 pandemic. We also report on other updates to our annotation resources, tools and services. All Ensembl data and software are freely available without restriction.
Publisher: Cold Spring Harbor Laboratory
Date: 08-04-2023
DOI: 10.1101/2023.04.08.536076
Abstract: Whole genome duplications (WGDs) are major events that drastically reshape genome architecture and are causally associated with organismal innovations and radiations 1 . The 2R Hypothesis suggests that two WGD events (1R and 2R) occurred during early vertebrate evolution 2, 3 . However, the veracity and timing of the 2R event relative to the ergence of gnathostomes (jawed vertebrates) and cyclostomes (jawless hagfishes and l reys) is unresolved 4–6 and whether these WGD events underlie vertebrate phenotypic ersification remains elusive 7 . Here we present the genome of the inshore hagfish, Eptatretus burgeri . Through comparative analysis with l rey and gnathostome genomes, we reconstruct the early events in cyclostome genome evolution, leveraging insights into the ancestral vertebrate genome. Genome-wide synteny and phylogenetic analyses support a scenario in which 1R occurred in the vertebrate stem-lineage during the early Cambrian, and the 2R event occurred in the gnathostome stem-lineage in the late Cambrian after its ergence from cyclostomes. We find that the genome of stem-cyclostomes experienced two additional, independent genome duplications (herein CR1 and CR2). Functional genomic and morphospace analyses demonstrate that WGD events generally contribute to developmental evolution with similar changes in the regulatory genome of both vertebrate groups. However, appreciable morphological ersification occurred only after the 2R event, questioning the general expectation that WGDs lead to leaps of morphological complexity 7 .
Location: United Kingdom of Great Britain and Northern Ireland
Location: United Kingdom of Great Britain and Northern Ireland
No related grants have been discovered for Carla Cummins.