Trainer biographies

Simon Andrews | Babraham Institute

Simon heads the bioinformatics group at the Babraham Institute in Cambridge. His group provides bioinformatics support for the researchers at the institute as well as a wide variety of companies on the Babraham Research Campus. Simon’s group have interests in a wide variety of different bioinformatics areas, but have been particularly focused on the QC, processing and analysis of high-throughput sequencing data. They maintain a number of processing and analysis tools which are widely used in this area. The Babraham Bioinformatics group run an extensive range of training courses covering core programming and statistics concepts, specific experimental data types, data visualisation and biological interpretation.

Vladimír Beneš | EMBL-EBI

Vladimír Beneš, PhD, Head of EMBL GeneCore, born & studied in Prague, the Czech Republic. He has been at EMBL since 1994 when he came as a postdoc to Ansorge group in the Biochemical Instrumentation Unit. Vladimir worked on development of methodology supporting genome-wide high-throughput sequencing, mainly in the sample processing part. In 2001 he was appointed to build EMBL Genomics Core Facility, a technology orientated service laboratory founded to assist researchers with functional genomics projects. This facility is currently utilizing mainly massively parallel sequencing in its both short as well as long form and supporting technologies, such as qPCR, for example. Most recently, Vladimír’s expertise has enhanced by adding single-cell genomic approaches. Among Vladimír’s tasks belong also assessment of new technologies and their applications in functional genomics, in particular their suitability for implementation in the environment of core facilities. He is also strongly involved in teaching of methods applied in this field.

Sarah Butcher | EMBL-EBI

Sarah was a team leader in the Technical Services Cluster at EMBL-EBI, running the Software Development and Operations team but is now retired. While she was in service, the team develops and runs inwards-facing software, collaborates on external grants requiring software development and operate several large resources for EMBL-EBI including the multi-petabyte file replication system that underpins ENA, EGA, EMPIAR and others, and the centrally managed File Transfer services that underpin file upload and download for EBI data resources.

Previously, she set up and led the Imperial College Bioinformatics Support Service for 16 years, following 3 years managing the Oxford University Bioinformatics Centre, although originating from a wet-lab background in Virology. As well as being a grant holder, she has participated on review panels for several funding bodies, and experienced running core facilities with Having made the transitions from wet-lab scientist to bioinformatics support, to running a core facility, she is interested in understanding how different knowledge-sets and differing local circumstances can shape the approaches to bioinformatics facilities, whilst many of the challenges remain common to all.

Philip East | Gustave Roussy Institute

I am a bioinformatician with over 25 years of bioinformatics and data analysis experience. I have recently taken up a Data Science Lead position at Gustave Roussy in France where I am looking after the bioinformatics and data science for the large genomic and AI clinical programs run at the hospital. Previous to this new position, I ran the Bioinformatics and Biostatistics core facility at the Francis Crick Institute, both as interim head and deputy head. We were a team of twenty analysts with heterogeneous skills providing bioinformatics expertise to Crick scientists across a broad range of research fields, genomic applications and data analysis questions. During my time at the Crick, I was involved in building robust project management tools and automated analysis pipelines to address the challenges of delivering bioinformatics to a large and busy medical research institute. I am also interested in building the right environment so bioinformaticians and data analysts can work effectively, be happy in their work and realise their career ambitions. On the bioinformatics side, I have a background in cancer genomics and transcriptomics and, more recently, have been involved in developing and delivering single-cell analysis approaches.

Kim Gurwitz | EMBL-EBI

Kim joined EMBL-EBI Training in June 2022 and leads the team’s portfolio of grant funded projects. She has led training, career development, and impact assessment initiatives across Africa, Europe, and the UK for consortia such as H3ABioNet and ELIXIR. She has a background in bioinformatics and medical biochemistry.

Shannan Ho Sui | Harvard University

Shannan is a Principal Research Scientist in Biostatistics at the Harvard Chan School of Public Health and the Director of the Harvard Chan Bioinformatics Core. She has a BSc in Biochemistry followed by a PhD in Genetics from the University of British Columbia where she focused on computational approaches for inferring gene regulatory networks. Her postdoctoral work includes work in pathogen genomics and infectious diseases as well as stem cell research and large-scale data management and integration. Shannan has led the Harvard Chan Bioinformatics Core as its Director for almost 10 years. Her team focuses on applications of high-throughput sequencing analysis, providing analysis consulting, training and platform services to the Harvard community. Her research focuses on applying multimodal single cell analysis approaches to understand cellular heterogeneity and the signaling and regulatory networks underlying development and disease.

Adam Reid | University of Cambridge

Adam has been Head of Bioinformatics at the Gurdon Institute, University of Cambridge since 2021. His team provides bioinformatics support both within the institute and across the School of Biological Sciences. He is passionate about tackling complex data analysis problems, teaching bioinformatics and mentoring junior bioinformaticians. Adam’s undergraduate degree was in Genetics at the University of Sheffield, after which he completed an MRes in Bioinformatics at the University of York. He worked at AstraZeneca as a Proteomics Bioinformatician, before going on to a PhD at University College London with Professor Christine Orengo. His thesis explored the evolution and functions of protein domain families. He then spent a productive 12 years as postdoc and staff scientist in the Parasite Genomics group at the Wellcome Sanger Institute with Dr Matthew Berriman. There he studied the evolution and function of parasite genomes, using bioinformatics applied to whole genome sequencing, bulk and single-cell RNA-seq technologies. During this time he generated and analysed genome sequences for a wide range of species, identified the role of pir genes in establishing chronic infections in malaria parasites and published the first single-cell RNA-seq dataset for these parasites.

Ajay Mishra | EMBL-EBI

 Ajay has DPhil in Biochemistry from University of Oxford where he studied the mechanisms underlying the regulation of chromosome segregation during cell division. For his post-doctoral research at Cancer Research UK, Cambridge Institute and King’s College London, Ajay investigated the molecular mechanisms regulating the stem cell differentiation in human skin using multi-omics, imaging and organotypic culture approaches. After post-doctoral research, Ajay headed a biology team at Cambridge Infinitus Research Centre (CIRCE) in the Department of Chemical Engineering and Biotechnology at the University of Cambridge where the key focus was to elucidate the mechanistic insight of the activity of traditional Chinese medicine in ageing and age-related human disorders such as neurodegeneration. Ajay joined EMBL-EBI Training team as a Scientific Training Officer in July 2019, and is now jointly responsible for managing EMBL-EBI’s e-learning programme.

Hugo Tavares | University of Cambridge

Hugo is an Associate Teaching Professor in Bioinformatics at the University of Cambridge. He is responsible for coordinating a curriculum of Bioinformatics courses aimed at postgraduate and researcher audiences.

Daniel Thomas López

Daniel joined the Training team in September 2020 as Scientific Project Manager, working on several EU-funded projects, mainly PerMedCoE, EOSC-Life, and BioExcel. He organises and facilitates face-to-face as well as online training based on competency frameworks and training needs analyses that he develops. In his activities, he engages with partners and new collaborators, and coordinates stakeholders involved to ensure high quality outputs.

He studied Veterinary Medicine at the Complutense University of Madrid, Spain. He holds a PhD in Molecular Biology, Biochemistry, and Biomedicine, and he completed the ECDC-EUPHEM fellowship (the Public Health Microbiology path of the European Centre for Disease Prevention and Control Programme). Over the course of his career he has worked on a variety of topics in microbiology, antimicrobial resistance, and infectious diseases.

Daniel has delivered undergraduate as well as postgraduate teaching and training at different universities. He has organised several scientific conferences and events, and he is an active collaborator in science dissemination.