Trainer biographies
Alex Bateman | EMBL-EBI
Alex Bateman is a computational biologist and Head of Protein Sequence Resources at the European Bioinformatics Institute (EBI), part of the European Molecular Biology Laboratory (EMBL). He has led the development of the Pfam biological database and introduced the Rfam database of RNA families. His team also delivers the InterPro and RNAcentral resource. He is PI for the UniProt project at EMBL-EBI. He is currently Editor-in-Chief of Bioinformatics Advances.
Amanda M. Saravia-Butler | NASA
Dr. Amanda Saravia-Butler is a molecular biologist turned bioinformatician currently working on the GeneLab project at NASA Ames Research Center (ARC) as the Data Processing Lead. Originally from upstate New York, Amanda received her Bachelor’s degrees in Biology, Chemistry, and Mathematics from Utica College in Utica, NY. As an undergraduate student, she performed microbiology research to help discover a new species of bacteria. Amanda earned her Ph.D. in Biochemistry and Molecular Biology with a concentration in Cancer Biology from the Mayo Clinic, where she identified and characterized novel molecular targets to treat pancreatic cancer. After graduate school, Amanda worked as a postdoctoral associate at the University of Miami studying early germ line development. In September 2017 she started at NASA ARC as a Mission Scientist on the Rodent Research project. Amanda transitioned to GeneLab in May 2018 and has been working on the GeneLab project full time since then. In 2020, Amanda helped initiate, and currently leads, GeneLab for Colleges and Universities (GL4U), which provides space biology-relevant training in bioinformatics to both students and educators. Outside of work, Amanda volunteers her time to serve as the Ames Early Career Network president and chair of the seminar series and outreach committees.
Aleena Mushtaq | EMBL-EBI
Group project: Genome variation across human populations
Aleena studied Molecular and Biomedical Sciences at King’s College London. She joined the Quadram Institute Biosciences, UK to pursue her PhD in the field of Molecular Biology. Her PhD investigated the molecular and microbial changes in the gut-liver axis in response to the high-fibre and low-fibre Western diets. Aleena joined EMBL-EBI as an Ensembl Outreach Officer in 2021 and delivers training on Ensembl resources.
Anna Swan | EMBL-EBI
Anna has a PhD in Bioinformatics from the University of Nottingham, where she focused on the bioinformatic identification of biomarkers of osteoarthritis. Following her PhD, Anna worked as a medical writer, spanning many therapeutic areas and working both on promotional and educational content for clinicians. Returning to bioinformatics, Anna worked as a data wrangler for the International Mouse Phenotyping Consortium at the project’s data coordination centre based in the Medical Research Council’s Harwell Institute. Anna joined the Training Team at EMBL-EBI in March 2019 and is now a Senior Scientific Training Officer, Digital Learning.
Anna Vathrakokoili-Pournara | EMBL-EBI
Group project: Single cell RNA-seq analysis using Python
I am a Predoctoral fellow at Papatheodorou Group at EBI and during my PhD I have been working on cell-type deconvolution of bulk expression data, exploring the contribution of cell composition in various phenotypes. I am focusing on investigating the contribution of immune cells in cancer outcomes and my goal is to apply machine learning models utilising omics data to predict patient outcomes. I am passionate about making bioinformatic analyses and tools more accessible to the community and reproducible. Beyond bioinformatics I enjoy going for long walks with friends and exploring new cafés in town.
Anu Shivalikanjli | EMBL-EBI
Group project: Genome variation across human populations
Anu Shivalikanjli has a background in bioinformatic data analysis. She holds a PhD in Human Molecular Genetics from the University of Barcelona, where she investigated the genetic risk factors in the manifestation of ADHD and comorbid conditions through GWAS, association studies and bioinformatic analysis applied to population cohorts. Anu began working as a postdoctoral researcher with the Mouse Genomes Project at the European Bioinformatics Institute (EMBL-EBI) in 2019. She carried out comparative genomic analysis using NGS data from multiple mouse strains in order to better understand the genetic variables involved in immune and behavioural responses in mice. She is now developing FAIR (Findable, Accessible, Interoperable, and Reusable) technology to support omics data management for initiatives including Human Cell Atlas (HCA) Data Coordination Platform and MorPhiC. Anu has been assisting with NGS Bioinformatics courses at EBI and is actively involved in scientific dissemination and outreach programmes for both school students and the wider community.
Aybuke Kupcu Yoldas | EMBL-EBI
Group project: Improving AI-based bioimage analysis
Aybuke is a senior bioinformatician for the BioImage Archive at EMBL-EBI. Her background is on physics and astronomy, with the recent edition of biological imaging data. Prior to joining EBI she was a postdoctoral researcher at the University of Cambridge Institute of Astronomy, and before that at the European Southern Observatory in Germany. After her PhD, Aybuke’s focus has been on image analysis and data management. During that time she has worked on many astronomy projects as well as biological imaging data as part of a Cancer Research Grand Challenge project and a Covid-19 project.
Craig Russell | EMBL-EBI
Group project: Improving AI-based bioimage analysis
Craig is a staff scientist at the European BioInformatics Institute – EMBL. His main interests are large biological imaging data analysis, cloud computing and infrastructure, and using machine learning for developing new image analysis tools. He obtained his PhD in microscope development from the University of Cambridge.
Joseph Ellaway | EMBL-EBI
Group project: Interpreting functional information from large scale protein structure data
Hi all! My name is Joseph and I’m a bioinformatician for the Protein Data Bank in Europe. I joined EMBL-EBI in 2022 to work on classifying protein conformational states, developing new algorithms to identify and characterise distinct protein conformers. I’ve been involved with several training events and conferences since joining EMBL-EBI and I’m looking forward to meeting you all! My background is in bioinformatics and biochemistry – graduating with a master’s degree from Imperial College London in 2021. I worked on cryoEM and X-ray model refinement, solving the structures of several protein complexes. Between 2018-2019, I joined a group at UCL as a research assistant during a placement year, performing protein biochemistry and molecular biology research into the mechanisms of neuropathic pain. My post-graduate research spanned investigations of differential equations Turing patterns in development, 3D chromosomal interactions in the nucleus and agent-based models for studying aberrant stem cell growth. I have also been involved with Imperial College’s Computational Biology Society, helping to found it in 2020 and organising seminars, an online conference and numerous educational programming sessions. I look forward to meeting you all and please don’t hesitate to ask for assistance!
Dayane Araujo | EMBL-EBI
Dayane completed her PhD in Microbiology at the Ludwig Maximilian University of Munich where she studied bacterial ECF sigma factors in order to design and implement orthogonal genetic switches in Bacillus subtilis. She also studied the mechanisms of resistance against antimicrobial peptides in Streptomyces venezuelae.
In 2019, Dayane joined the database of life sciences publications Europe PMC which is hosted at EMBL-EBI. At Europe PMC, Dayane worked as a Technical Outreach Officer engaging with programmatic users including researchers, curators, developers, policymakers and funders. She has recently joined EMBL-EBI training team as a Scientific Training Officer where she works on the development and delivery of a range of bioinformatics-focused courses for the life science community.
Hedi Peterson | University of Tartu, Estonia
Jenny Cook is a Senior Scientist at the medical research charity; LifeArc. With Uppsala University and later pursued postdoctoral studies at the University of Geneva. Upon returning to Estonia from Geneva, Peterson took on the role of leading the bioinformatics team at Quretec Ltd. At the same time, she collaborated with Prof. Jaak Vilo to establish ELIXIR Estonia at the University of Tartu. Peterson’s research interests mainly lie in data integration and biological networks. She has applied her expertise to study various diseases and the regulation of stem cells. Her team has developed numerous bioinformatics tools that are openly accessible to the research community. During the COVID-19 pandemic, Peterson’s team played a significant role in supporting multiple SARS-CoV-2 studies in Estonia. They developed both public and restricted access dashboards, as well as performed data wrangling and sharing, to aid in the monitoring and understanding of the virus’s impact.
Jenny Cook | LifeArc
Jenny Cook is a Senior Scientist at the medical research charity; LifeArc. With more than 10 year’s experience in the drug discovery industry as a lab-based cellular biologist, she has worked in a variety of therapeutic areas. After several years of part time learning, she transitioned to the bioinformatics team, where her current role focusses on enabling data-driven drug discovery.
Krishna Tiwari | EMBL-EBI
Group project: Modelling cell signalling pathways
Krishna currently works as Scientific Database Curator for Molecular connections group focusing primarily on pathway curation and mathematical models curation related to Immune-oncology, Cancer signalling etc. Krishna brings a vast experience in pathway modelling/analysis and translational research.
Lee Larcombe | Amphimatic
Lee Lee Larcombe (PhD) provides expert bioinformatics and data analytics support to biotech, pharma and FMCG clients through APEXOMIC (Founded in 2012). He has a research background spanning wet-lab and bioinformatics, with particular expertise in functional genetics, biomolecular modelling and data integration for immunology and oncology. After spending 10 years in academia conducting collaborative industry research projects, he has spent the last decade supporting in silico target discovery and (bio)therapeutic development in industry. Lee also has broad experience of teaching and training in bioinformatics, including development of training strategy. He led development of the UK Level 7 Bioinformatics Scientist Apprenticeship standard, has supported several consortium projects, and continues to support skills projects in industry, academia and national institutes. He is an invited organiser of the EMBL European Bioinformatics Institute international summer school, and leads on bioinformatics apprenticeship assessment with the NHS National School of Health Care Science.
Loïc Lannelongue | University of Cambridge
Loïc is a Research Associate in Biomedical Data Science in the Cardiovascular Epidemiology Unit at the University of Cambridge. He leads the Green Algorithms project, an initiative promoting more environmentally sustainable computational science. His research interests also include combining medical imaging and genetic information with machine learning to better understand and treat cardiovascular diseases. He obtained an MSc from ENSAE, the French National School of Statistics, and an MSc from the University of Oxford, before doing his PhD at the University of Cambridge as part of the Cambridge-Baker Systems Genomics Initiative. He is a Software Sustainability Institute Fellow, a Post-doctoral Associate at Jesus College, Cambridge, and an Associate Fellow of Advance HE.
Marcus Bage | EMBL-EBI
Group project: Interpreting functional information from large scale protein structure data
Marcus joined EMBL-EBI in 2022 as a Bioinformatician in the PDBe Team, where he is responsible for standardising the representation of protein modifications in the PDB archive. In 2021, he completed a PhD in Computational Biology at the University of Dundee, studying the mammalian mRNA Capping enzymes using molecular dynamics simulations. Marcus has a background in structural bioinformatics and holds a Masters degree in Biochemistry from University College London.
Priit Adler | University of Tartu, Estonia
Group project: Networks and pathways
Priit Adler is a researcher at the Institute of Computer Science at the University of Tartu. With experience in gene expression data analysis, he has recently shifted his focus to studying antibody repertoire and sequence analysis. Priit has led the development of bioinformatics tools such as MEM and KEGGanim and contributed to others like g:Profiler. As a trainer in ELIXIR-EE and a member of the ELIXIR Data Steward Interest Group, Priit actively engages in the responsible use of life sciences data. His professional work emphasizes continuous growth in bioinformatics, data management, and community involvement. Priit enjoys chess and archery in his leisure time, which allows him to develop strategic thinking, concentration, and patience.
Rahuman Sheriff | EMBL-EBI
Group project: Modelling cell signalling pathways
Dr. Sheriff is a Senior Project Leader at EMBL-EBI, Cambridge, UK. He develops tools and resources for chemoinformatics & systems biology modelling and is interested in developing ‘Digital Twin’ of the human immune system and cancer. He leads the BioModels repository, and is an editorial board member of SBML. He has over 13 years of research experience working at EMBL-EBI, MRC-LMS, UK, & MPI, DE.
Yuyao Song | EMBL-EBI
Group project: Single-cell RNA-sequencing analysis with Python
Yuyao is a PhD candidate from the Papatheodorou group at EMBL-EBI. Her primary research lies in cross-species comparison of cell types using scRNA-seq data. She has been developing packages and workflows to tackle the conservation and divergence of cell type expression profiles across species, from the perspective of evolution and functional genomics. She is enthusiastic about exploring nature and culture across the globe and theatre.