The MRC Consortium for Medical Microbial Bioinformatics Fellowship 3
Lead Research Organisation:
University of Birmingham
Department Name: Sch of Biosciences
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 |
| Nicholas Loman (Principal Investigator / Fellow) |
Publications
Abrahams KA
(2016)
Identification of KasA as the cellular target of an anti-tubercular scaffold.
in Nature communications
Abrahams KA
(2017)
Inhibiting mycobacterial tryptophan synthase by targeting the inter-subunit interface.
in Scientific reports
Amit I
(2016)
Voices of biotech.
in Nature biotechnology
Anikeeva P
(2019)
Voices in methods development.
in Nature methods
Azevedo Antunes C
(2018)
Complete Closed Genome Sequence of Nontoxigenic Invasive Corynebacterium diphtheriae bv. mitis Strain ISS 3319.
in Genome announcements
Buckland MS
(2020)
Treatment of COVID-19 with remdesivir in the absence of humoral immunity: a case report.
in Nature communications
Candido DS
(2020)
Evolution and epidemic spread of SARS-CoV-2 in Brazil.
in Science (New York, N.Y.)
Connor TR
(2016)
CLIMB (the Cloud Infrastructure for Microbial Bioinformatics): an online resource for the medical microbiology community.
in Microbial genomics
Cox MJ
(2020)
Co-infections: potentially lethal and unexplored in COVID-19.
in The Lancet. Microbe
Diallo B
(2016)
Resurgence of Ebola Virus Disease in Guinea Linked to a Survivor With Virus Persistence in Seminal Fluid for More Than 500 Days.
in Clinical infectious diseases : an official publication of the Infectious Diseases Society of America
| Description | Invitation to present at Bill Gates private learning session on next-generation sequencing in infection |
| Geographic Reach | Multiple continents/international |
| Policy Influence Type | Participation in a guidance/advisory committee |
| Description | Member of WHO Technical Working Group on Pathogen Genome Data Sharing During Public Health Emergencies |
| Geographic Reach | Multiple continents/international |
| Policy Influence Type | Participation in a guidance/advisory committee |
| Title | Ultra long read protocol for nanopore |
| Description | Sequencing applications such as de novo assembly and detection of structural variation in genomes is limited by read lengths. Traditional Sanger sequencing can sequence reads up to 1000 bases long, and 'next-generation approaches' are more typically between 75 and 300 bases long. We developed a new protocol for the Oxford Nanopore platform that enables sequencing reads up to and above one megabase. This technique relies on keeping DNA fragments intact by reducing manipulation steps (pipetting, clean-ups) and a novel use of transposase in order to only cut molecules a single time. This protocol was developed openly and initially demonstrated on E. coli, then formed the basis of a study of the human genome (Jain et al. Nature Biotechnology 2017). It is now maintained on the open protocols.io website. |
| Type Of Material | Technology assay or reagent |
| Year Produced | 2017 |
| Provided To Others? | Yes |
| Impact | Use of this protocol to sequence the human genome permitted the closing of several gaps in the human genome reference, including clinically relevant regions. |
| URL | https://www.protocols.io/view/ultra-long-read-sequencing-protocol-for-rad004-mrxc57n |
| Title | Supporting data for "Ultra-deep, long-read nanopore sequencing of mock microbial community standards" |
| Description | Long sequencing reads are information-rich: aiding de novo assembly and reference mapping, and consequently have great potential for the study of microbial communities. However, the best approaches for analysis of long-read metagenomic data are unknown. Additionally, rigorous evaluation of bioinformatics tools is hindered by a lack of long-read data from validated samples with known composition.
We sequenced two commercially-available mock communities containing ten microbial species (ZymoBIOMICS Microbial Community Standards) with Oxford Nanopore GridION and PromethION. Both communities and the ten individual species isolates were also sequenced with Illumina technology. We generated 14 and 16 Gbp from two GridION flowcells and 150 and 153 Gbp from two PromethION flowcells for the evenly-distributed and log-distributed communities respectively. Read length N50 ranged between 5.3 Kbp and 5.4 Kbp over the four sequencing runs. Basecalls and corresponding signal data are made available (4.2 TB in total). Alignment to Illumina-sequenced isolates demonstrated the expected microbial species at anticipated abundances, with the limit of detection for the lowest abundance species below 50 cells (GridION). De novo assembly of metagenomes recovered long contiguous sequences without the need for pre-processing techniques such as binning. We present ultra-deep, long-read nanopore datasets from a well-defined mock community. These datasets will be useful for those developing bioinformatics methods for long-read metagenomics and for the validation and comparison of current aboratory and software pipelines. |
| Type Of Material | Database/Collection of data |
| Year Produced | 2019 |
| Provided To Others? | Yes |
| Description | World Health Organization Global Advisory Alert and Response Network - Technical Expert/Outbreak Response Participation |
| Organisation | World Health Organization (WHO) |
| Department | WHO Global Outbreak Alert and Response Network |
| Country | France |
| Sector | Charity/Non Profit |
| PI Contribution | We have been included as technical experts on next-generation molecular diagnostics (by sequencing) to assist the WHO in outbreak and epidemic response when required in-country. |
| Collaborator Contribution | WHO are the recognised international agency responsible for the management and containment of outbreaks and epidemics. |
| Impact | In the past weeks this has included serving in an advisory function to support an outbreak of necrotising cellulitis in Sao Tome. We provided rapid response sequencing facility, in collaboration with Ian Goodfellow (University of Cambridge) to the island and provided real-time pathogen diagnostics and epidemiology using nanopore sequencing. |
| Start Year | 2016 |
| Title | The Zibra Pipeline |
| Description | The Zibra Pipeline provides the bioinformatics component of the Zika real-time sequencing project. This open source package was designed to simplify the process of bioinformatics analysis using standard laptops when performing in-field sequencing. It supports both nanopore and Illumina platforms. It is packaged as a Docker container which means it can run on Windows, Linux and Mac computers. |
| Type Of Technology | Software |
| Year Produced | 2017 |
| Open Source License? | Yes |
| Impact | This software was pivotal in the ability to give local stakeholders in Brazil the ability to generate their own sequences with limited bioinformatics support. |
| URL | https://github.com/zibraproject/zika-pipeline |
| Title | poredb |
| Description | Poredb was designed to manage the very large number of read files generated by the Oxford Nanopore platforms. Its use was demonstrated on the analysis of a whole-human genome sequencing on nanopore which required the tracking of metadata for tens of millions of read files. |
| Type Of Technology | Software |
| Year Produced | 2017 |
| Open Source License? | Yes |
| Impact | This software was pivotal in the successful analysis of a large nanopore human genome dataset generated by a consortium (Jain et al. Nature Biotechnology 2017). |
| URL | http://github.com/nickloman/poredb |