Trainer biographies

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 is a team leader in the Technical Services Cluster at EMBL-EBI, running the Software Development and Operations team. 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 – The Francis Crick 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.

Andrew Hercules

Hello! I’m Andrew, a London-based design and strategy expert. With more than 10 years of experience, I’ve designed digital products and services for organisations in the financial services, life sciences, education, housing, and transportation industries. I believe in applying user-centred, collaborative, insights-driven methodologies and guiding organisations as they design transactional or data-driven services for multiple devices and touch-points. And with bespoke research and design strategies, I empower organisations to transform their operations with accessible, inclusive, high-impact digital-first solutions that meet user needs, are technically feasible and sustainable, and achieve key strategic objectives.

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.

Urmi Trivedi – Edinburgh Genomics, The University of Edinburgh

Urmi has been working in as a Bioinformatician in research support role at Edinburgh Genomics, a sequencing facility within The University of Edinburgh, since 15 years. Currently, she leads the Bioinformatics team here. The facility possesses multiple sequencing platforms and delivers more than 100 projects annually. Her team is responsible to provide support for data QC and analysis of the sequencing data produced inhouse and elsewhere. She works at the forefront of genomics and has been associated with the delivery of several large-scale genome projects. She is also involved in planning and providing training in various bioinformatics topics. She enjoys walking and exploring nature; and living in Scotland is a huge benefit for this. She also likes baking and have taken that as a part time profession over the weekends.