About

Introduction

Large, Medium, Small

Nick works as an Independent Research Fellow in the Institute for Microbiology and Infection at the University of Birmingham, sponsored by a seven-year MRC Fellowship in Microbial Genomics Bioinformatics. His research explores the use of cutting-edge genomics and metagenomics approaches to the diagnosis, treatment and surveillance of infectious disease. Nick has so far used high-throughput sequencing to investigate outbreaks of important Gram-negative multi-drug resistant pathogens, and recently helped establish real-time genomic surveillance of Ebola in Guinea and Zika in Brazil. His current work and focuses on the development and evaluation of novel molecular biology, sequencing and bioinformatics methods to aid the interpretation of genome and metagenome scale data generated in clinical and public health microbiology.

MicrobesNG

MicrobesNG is a 5-year, 1.2m BBSRC-funded project to produce a world-leading microbial genome sequencing service and strain archiving resource, which launched at the SGM in March 2015. See the website for further details.

CLIMB

The Cloud Infrastructure for Microbial Genomics (CLIMB) is an 8.4m MRC-funded project to invest in bioinformatics and "big data" capacity building for the UK microbial genomics community. At heart it is four-site (Birmingham, Warwick, Cardiff and Swansea) connected virtual computing infrastructure. It is optimised for specific applications such as microbial genome alignment, de novo assembly and metagenomics. See the website for further details.

Group

With Tim Mitchell, I co-supervise a PhD student, Josh Quick. Josh is investigating the role of microbial communities in wound healing in burns and trauma through the NIHR Centre for Surgical Reconstruction and Microbiology, as well as the spread of nosocomial pathogens in our local patient popluation.

Dr Emily Richardson is working as a microbial bioinformatician on the BBSRC MicrobesNG project.

Dr Pablo Fuentes-Utrilla is working as the sequencing manager on the BBSRC MicrobesNG project.

Past group members

Szymon Calus, Research Technician, now doing a PhD with Ameet Pinto in Glasgow.

The E. coli O104:H4 outbreak in Germany

I was involved with the crowd-sourced analysis of genomics data from the Shiga-toxin producing E. coli O104:H4 outbreak in Germany. This outbreakt caused more than 4,000 cases of disease and 50 deaths. I performed an initial assembly of data from the BGI on the 2nd of June 2011 which helped spark a flurry of crowd-sourced analysis, documented on the Github Wiki. Recently, the BBSRC made a video about this project which can be viewed below.

Bioinformatics projects

In my previous role, I was responsible for the maintenance and development of the comparative bacterial genomics database, xBASE. Although funding for this project has ceased, I still continue to develop the high-throughput sequencing pipeline xBASE-NG to support our local sequencing efforts, as well as the rapid bacterial genome annotation service xBASE Annotation.

In collaboration with Lex Nederbragt, we are developing an open-source repository of sequencing and bioinformatics benchmarking datasets entitled Seqbench.

I aim to publish accompanying Github repositories with manuscripts as an aid to extensible and reproducible research, please see my Github page for details.

With James Hadfield, I built Omicsmaps.com, a map of high-througput sequencing instruments.