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.
Organisations
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
Costea PI
(2018)
Publisher Correction: 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
| Title | Additional file 10 of A comprehensive benchmarking study of protocols and sequencing platforms for 16S rRNA community profiling |
| Description | Figure S10. Heatmap of arc heal species in the EM community. (ZIP 9 kb) |
| Type Of Material | Database/Collection of data |
| Year Produced | 2016 |
| Provided To Others? | Yes |
| URL | https://springernature.figshare.com/articles/dataset/Additional_file_10_of_A_comprehensive_benchmark... |
| Title | Additional file 2 of DESMAN: a new tool for de novo extraction of strains from metagenomes |
| Description | Separate text file containing variant prediction results in the complex mock. (TSV 4 kb) |
| Type Of Material | Database/Collection of data |
| Year Produced | 2017 |
| Provided To Others? | Yes |
| URL | https://springernature.figshare.com/articles/dataset/Additional_file_2_of_DESMAN_a_new_tool_for_de_n... |
| Title | Additional file 2 of STRONG: metagenomics strain resolution on assembly graphs |
| Description | Additional file 2 Genomes used in the synthetic communities (Additional file 1: Tables S1 and S2). |
| Type Of Material | Database/Collection of data |
| Year Produced | 2021 |
| Provided To Others? | Yes |
| URL | https://springernature.figshare.com/articles/dataset/Additional_file_2_of_STRONG_metagenomics_strain... |
| Title | Additional file 3 of A comprehensive benchmarking study of protocols and sequencing platforms for 16S rRNA community profiling |
| Description | Figure S3. Error Transition Probabilities for all platforms. (ZIP 34 kb) |
| Type Of Material | Database/Collection of data |
| Year Produced | 2016 |
| Provided To Others? | Yes |
| URL | https://springernature.figshare.com/articles/dataset/Additional_file_3_of_A_comprehensive_benchmarki... |
| Title | Additional file 3 of DESMAN: a new tool for de novo extraction of strains from metagenomes |
| Description | Separate text file containing strains used in the complex mock. (TSV 12 kb) |
| Type Of Material | Database/Collection of data |
| Year Produced | 2017 |
| Provided To Others? | Yes |
| URL | https://springernature.figshare.com/articles/dataset/Additional_file_3_of_DESMAN_a_new_tool_for_de_n... |
| Title | Additional file 4 of A comprehensive benchmarking study of protocols and sequencing platforms for 16S rRNA community profiling |
| Description | Figure S4. Impact of platform and region on entropy. (ZIP 16 kb) |
| Type Of Material | Database/Collection of data |
| Year Produced | 2016 |
| Provided To Others? | Yes |
| URL | https://springernature.figshare.com/articles/dataset/Additional_file_4_of_A_comprehensive_benchmarki... |
| Title | Additional file 9 of A comprehensive benchmarking study of protocols and sequencing platforms for 16S rRNA community profiling |
| Description | Figure S9. Impact of PCR cycles on OTUs. (ZIP 43 kb) |
| Type Of Material | Database/Collection of data |
| Year Produced | 2016 |
| Provided To Others? | Yes |
| URL | https://springernature.figshare.com/articles/dataset/Additional_file_9_of_A_comprehensive_benchmarki... |
| 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 |