The MRC Consortium for Medical Microbial Bioinformatics Fellowship 2
Lead Research Organisation:
University of Warwick
Department Name: Sch of Engineering
Abstract
Abstracts are not currently available in GtR for all funded research. This is normally because the abstract was not required at the time of proposal submission, but may be because it included sensitive information such as personal details.
People |
ORCID iD |
| Christopher Quince (Principal Investigator / Fellow) |
Publications
Connelly S
(2017)
Bioreactor Scalability: Laboratory-Scale Bioreactor Design Influences Performance, Ecology, and Community Physiology in Expanded Granular Sludge Bed Bioreactors.
in Frontiers in microbiology
Costea PI
(2018)
Enterotypes in the landscape of gut microbial community composition.
in Nature microbiology
D'Amore R
(2016)
A comprehensive benchmarking study of protocols and sequencing platforms for 16S rRNA community profiling.
in BMC genomics
Delmont TO
(2018)
Nitrogen-fixing populations of Planctomycetes and Proteobacteria are abundant in surface ocean metagenomes.
in Nature microbiology
Eren AM
(2015)
Anvi'o: an advanced analysis and visualization platform for 'omics data.
in PeerJ
Gerasimidis K
(2016)
Response to Kaakoush et al.
in The American journal of gastroenterology
Gerasimidis K
(2019)
Reply.
in Gastroenterology
Gerasimidis K
(2016)
The effect of DNA extraction methodology on gut microbiota research applications.
in BMC research notes
| Title | CONCOCT: Clustering cONtigs with COverage and ComposiTion |
| Description | A program for unsupervised binning of metagenomic contigs by using nucleotide composition, coverage data in multiple samples and linkage data from paired end reads. |
| Type Of Technology | Software |
| Year Produced | 2014 |
| Open Source License? | Yes |
| Impact | 55 citations and use in numerous studies. |
| URL | https://github.com/BinPro/CONCOCT |
| Title | DESMAN De novo Extraction of Strains from MetAgeNomes |
| Description | We introduce DESMAN for De novo Extraction of Strains from MetAgeNomes. Metagenome sequencing generates short reads from throughout the genomes of a microbial community. Increasingly large, multi-sample metagenomes, stratified in space and time are being generated from communities with thousands of species. Repeats result in fragmentary co-assemblies with potentially millions of contigs. Contigs can be binned into metagenome assembled genomes (MAGs) but strain level variation will remain. DESMAN identifies variants on core genes, then uses co-occurrence across samples to link variants into strain sequences and abundance profiles. These strain profiles are then searched for on non-core genes to determine the accessory genes present in each strain. |
| Type Of Technology | Software |
| Year Produced | 2016 |
| Open Source License? | Yes |
| Impact | Used to resolve E coli strains in pediatric Crohn's disease patients. |
| URL | https://github.com/chrisquince/DESMAN |