Mark Pallen started academic life as a medical microbiologist, with training in medicine (BA from Cambridge MBBS, MD from London) and laboratory research (PhD in Gordon Dougan’s lab at Imperial College, during which he captained the winning team in University Challenge). He is currently a Research Leader at the Quadram Institute and Professor of Microbial Genomics at the University of East Anglia. Pallen has a track record of over fifteen years of research council funding for a research programme that spans bioinformatics and bench-based research.

His research interests have included bacterial protein secretion and gene regulation (particularly in E. coli); the evolution of domains, proteins and bacterial flagella; and microbial pathogenomics. In recent years, he has turned his attention to the genomic epidemiology of bacterial pathogens of humans and animals (particularly multi-drug resistant Acinetobacter baumannii) and to pioneering new applications of metagenomics, including the characterisation of complex microbial communities (particularly gut microbiomes), the detection of pathogens in contemporary and historical samples (includes recovery of a medieval Brucella genome) and sedimentary ancient DNA studies on submerged palaeosols (shedding light on the Neolithic transition).

Pallen’s standing in the field is evidenced by research publications in high-impact journals including JAMA, Nature Biotechnology, NEJM, PNAS, EMBO J, Lancet, Nucleic Acids Research, Science and Nature, together with invited reviews in Nature, Nature Biotechnology, Nature Reviews Microbiology, Genome Medicine and Current Opinion in Microbiology.

I am Professor and director of Bioinformatics (Milner Centre for Evolution) at the University of Bath and Co-I of CLIMB-BIG-DATA.
Research in my group centres on the use of genetics/genomics and phenotypic studies to address complex questions in the ecology, epidemiology and evolution of microbes. Our most recent interests focus upon comparative genome analyses to describe the core and flexible genome of pathogenic bacteria (Campylobacter, Staphylococcus, Helicobacter and Escherichia coli) and how this is related to population genetic structuring, the maintenance of species, and the evolution of host/niche adaptation and virulence.

In June 2016 I was promoted to Assistant Professor at Warwick Medical School. I then moved to the University of Leicester in September 2017 to a setup a lectureship. Broadly my research interests are centred around increasing our understanding of phage-host interactions. Much of my previous work has focused on phage-host interactions in the marine environment. Having been involved in the isolation, genome sequencing and annotation of a number of phages capable of infecting cyanobacteria. Much of my research had focused on using the model system of S-PM2 and Synechococcus sp WH7803 to understand how cyanophages interact with their host. I identified the first ‘photosynthetic genes’ in a cyanophage genome and more recently identified an antisense RNA that may have a role in the regulation of these genes.

Professor Busby has performed ground-breaking research on the molecular mechanisms that control gene expression in bacteria, particularly the regulation of transcription initiation in Escherichia coli. In recent years, Busby has pioneered the adoption of powerful new functional genomics approaches to the study of bacterial gene regulation, including adapting chromatin capture to monitor the distribution in vivo of RNA polymerase, transcription factors and nucleoid-shaping proteins (21-24). After validation in model organisms, these techniques are now ready to be rolled out to pathogen biology. However, widespread adoption of these techniques will generate “big data” challenges in data analysis, visualisation and integration, which will benefit from Busby’s involvement in this project.

Tom is a Professor at Cardiff University. He is a Big Data Biologist who has a background in the population genomics and molecular epidemiology of pathogenic bacteria. He obtained his PhD at Imperial, and was Postdoctoral Fellow at the Wellcome Trust Sanger Institute from 2010 to 2012. He joined Cardiff in 2012 and since then has developed his research portfolio to cover a wide spectrum of activities, based around the application of computational approaches to answer biological questions about bacterial pathogens, using next generation sequencing data. His research has taken in work at multiple scales; from the analysis of local outbreaks of Shigella sonnei, up to pathogenicity across the entire genus of Yersinia. He is currently working on projects examining the pathogenomics of (amongst others) Escherichia coli, Salmonella enterica, Clostridium difficile, Shigella flexneri and Clostridium difficile. More generally Tom has additional research interests around making data and approaches more portable, searchable, and easily shared; challenges that CLIMB has the potential to begin to address for microbial researchers.

Walsh is Professor of Medical Microbiology and Antimicrobial Resistance at Cardiff University. His research focuses on the mechanisms, mobilization and spread of antimicrobial resistance, and his recent focus is on blending clinical and molecular epidemiology in low-middle income countries. His group first described NDM1 and has written and spoken widely on this topic. He has published over 170 papers, with funding from numerous sources including MRC, Wellcome Trust, European Union, BBSRC and Gates Foundation. He brings expert knowledge in antimicrobial resistance mechanisms and insights into clinical microbiology to this initiative.

Falush has performed pioneering work on statistical approaches to understand genetic variation within populations, aimed at elucidating evolutionary and historical processes. He has worked extensively with Sheppard and Achtman, with a research portfolio that spans diverse organisms, including many different kinds of bacteria. Falush has a superb track record in statistical and evolutionary genetics with many highly cited publications, including first/last-author papers in Science and PNAS, and a paper on inferring populations with nearly 3000 citations.

Nick is Professor of Microbial Genomics and Bioinformatics at the University of Birmingham. 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 such as Pseudomonas aeruginosa, Acinetobacter baumannii and Shiga-toxin producing Escherichia coli. His current work focuses on the genetic diversity of Pseudomonas aeruginosa infection in chronic lung diseases such as cystic fibrosis as a diagnostic and prognostic marker. A more general aim is to develop bioinformatics tools to aid the interpretation of genome and metagenome-scale data in routine clinical practice.

Quince comes from a physical-sciences background, with a PhD in theoretical physics. In recent years he has successfully turned his attention to bioinformatics problems in sequence-based analyses of microbial communities, with two highly cited papers on removing noise from pyrosequenced amplicons. He held a five-year EPSRC Career Acceleration Fellowship (2009-2014) entitled ‘Pioneering the new genomics era in environmental microbiology for engineering design.’ Quince and has an interest in Bayesian statistical approaches in microbial bioinformatics.

Andrew Page is the Head of Informatics at the Quadram Institute where his group provides support for Informatics and Bioinformatics. He has an interest in high performance computing and high throughput bioinformatics sequence analysis pipelines. Andrew has a BSc in Software Engineering and a PhD in Computer Science on the topic of Distributed Computing Systems. He was a Post-Doctoral research fellow at the National College of Ireland working on machine learning. After moving to the Wellcome Trust Sanger Institute, he worked on Laboratory Information Systems. In 2011 he became the Principal Computer Programmer in the Pathogen Informatics group supporting the Infection Genomics group at Sanger. His work focused on building and managing bioinformatics sequence analysis pipelines for pathogenic organisms using both short and long read sequencing technologies. In 2018 he moved to the Quadram Institute.

Martin Antonio is Unit Molecular Biologist and Principal Investigator at the Medical Research Council Unit The Gambia at London School of Hygiene and Tropical Medicine, Fajara, The Gambia. He serves as the Director, the WHO collaborating Centre for New Vaccines Surveillance and Heads the WHO Regional Reference Laboratory for Invasive Bacterial Diseases (IBD) for West and Central Africa. Martin also holds the position of Honorary Professor at Warwick Medical School, University of Warwick, UK. He is a Fellow of the Royal College of Pathologists (London, UK) and Honorary Fellow of the Royal College of Physicians (London, UK). His research is focused on the leverage of new molecular technologies in diagnosis of tropical infections, investigation of microbial transmission and clinical trials. Martin's group has led and participated in a growing number of large-scale international research projects, serving as the WHO reference laboratory for pneumococcal disease and establishing large disease surveillance platforms for bacterial infections across Africa.

Head of IT-Data Science, University of Swansea

Anna has a background in the physical sciences, earning an MPhys in theoretical physics and a PhD in NEGF simulations of nanotransistors. Since 2017, she has been working as a Research Software Engineer in biosciences and medicine. She has an interest in developing open-source software for bioinformatics and big data problems in microbiology. In her role as a Research Software Engineer for CLIMB-BIG-DATA, she aims to create a repository of software and tools for microbial bioinformatics to support the CLIMB-BIG-DATA community.

Andrew Smith is Research Software Engineer for CLIMB-BIG-DATA, working at the University of Birmingham. He is currently working on the user interface (Bryn), on the ticketing system and on the S3 object storage.

Lisa has a BSc and an MSc in Molecular Biology, and a PhD in Epigenomics. In 2014 she became a project manager for the 70-partner Italian EPIGEN-CNR Flagship Project, ended in summer 2019. She moved to the Quadram in 2017 to manage the MRC-CLIMB project. She has a solid experience in the coordination, follow-up and reporting of the administrative, financial and scientific aspects of a Project, as well as in the organization and follow-up of scientific and dissemination events.

Michaela is a bioinformaticians working at QIB. She joined the CLIMB-BIG-DATA team on April 2022.

Nabil is a the Interim Head of Informatics at the Quadram Institute (Norwich) and a Bioinformatics Scientific Programmer within the Core Bioinformatics at the QIB. He has dedicated his professional life to improving bioinformatic analyses and then using these improvements to find new insight into microbial pathogens. His current duties include developing bioinformatics infrastructure and novel algorithms.

Anmol Hemrom is CLIMB-BIG-DATA Cloud Computing Manager in Warwick. He has a background in bioinformatics and cyber-infrastructure. He has interests in cloud technologies and infrastrcuture, infrastructure as a code, and DevOps methodologies.

Mavis joined the CLIMB-BIG-DATA team in October 2021 as a Project Manager (part-time) with a focus on finance and project administration. Before joining the team, she worked as a project manager at the MRC Unit the Gambia at London School of Hygiene and Tropical Medicine for over six years, where she garnered extensive proficiency in the management and administration of a diverse portfolio of research projects from the grant application stage to successful research completion.

Simon Thompson works in research computing at the University of Birmingham. He has interests in high-performance computing, research data management. He set up the Birmingham node of the CLIMB system and blogs about his experiences and frustrations with OpenStack on his personal blog, RoamingZebra.

Ewan has a BSc in Computing Science from the University of East Anglia. He has interests in web development and project management.