Trainer biographies

Melissa F. Adasme | EMBL-EBI

Dr.-Ing. Melissa F. Adasme is a Data Mining Scientist at the Chemical Biology Services/ ChEMBL team at EMBL-EBI. She holds a degree in Bioinformatics Engineering from the Univerisity of Talca, Chile and a PhD in Computer Science from the Technical University of Dresden, Germany. Her current work involves enhancing data integration between the ChEMBL, PDBe and CCSD databases; machine learning on assay description for automated construction; and a text mining pipeline (sponsored by Open Targets) to deliver evidence linking specific protein targets to disease phenotypes. Before joining EMBL-EBI, she focused her research on structure-based drug repositioning by characterising non-covalent patterns defining the binding mode of drugs. She was a developer of the Protein-Ligand Interaction Profiler (PLIP) tool which supported her past research and many others on structural bioinformatics.

David Armstrong | EMBL-EBI

Hi, I’m David. I received a BSc in biochemistry from the University of Sheffield in 2010. I continued at the University of Sheffield, completing a Ph.D in structural biology in 2014, co-supervised by Prof. Mike Williamson and Prof. C. Neil Hunter FRS, with a focus on using solution NMR for structural determination of proteins in the chlorophyll biosynthesis pathway. I joined Protein Data Bank in Europe (PDBe) in 2015 as a database curator and in 2018 took on the role of outreach and training lead for PDBe. This role involves the coordination of training, outreach and public engagement activities for the PDBe, PDBe-KB and AlphaFold DB resources, as well as contribution towards curation of data for the PDB and EMDB archives.

Alexandre Bonvin | Utrecht University

Alexandre Bonvin (1964) studied Chemistry at Lausanne University, Alexandre Bonvin (1964) studied Chemistry at Lausanne University, Switzerland and obtained his PhD at Utrecht University in the Netherlands (1993). After two post-doc periods at Yale University (USA) and the ETHZ (CH) he joined Utrecht University in 1998 where he was appointed full professor of computational structural biology in 2009. In 2006, he received a prestigious VICI grant from the Dutch Research Council. Since September 2019 he is Scientific Director of the Bijvoet Centre for Biomolecular Research. He is participating to several EU projects including the BioExcel Center of Excellence in Biomolecular Simulations and the European Open Science Cloud EGI-ACE project. His work has resulted in over 275 peer-reviewed publications.

Sara Chuguransky | EMBL-EBI

Sara is a biocurator for the InterPro and Pfam databases at EMBL-EBI, where she checks the accuracy of the biological information included, keeping both databases up to date. In the case of Pfam, she also creates new families and domains to expand its coverage. Last year, she has also joined the training team. In 2010 she graduated as a biochemist from the UNLP and continued with a PhD in diabetes associated bone disease using animal models and cell cultures. Previously joining the EMBL-EBI, she was postdoctoral fellow at the UNLP with a CONICET fellowship, working in in silico models for anti-epileptic drug repurposing.

Alessia David | Imperial College

Dr Alessia David is a Clinical Research Fellow in the Centre for Bioinformatics at Imperial College London. She holds a PhD in Molecular Endocrinology from Queen Mary University London and an MSc in Bioinformatics and System Biology from Imperial College London. She joined Imperial College in 2013 on a prestigious MRC fellowship in Biomedical Informatics. Over the last few years, she has been engaged in identifying the genetic and molecular mechanisms contributing to human diseases by using a range of mathematical and bioinformatics approaches. She is one of the main developers of Missense3D and Missense3D-DB.

Genevieve Evans | EMBL-EBI

Genevieve has worked as researcher in protein science at 4 different labs in 3 different countries, New Zealand, Australia and Belgium. She received her PhD in Biochemistry at the University of Canterbury with supervisor Professor Juliet Gerrard. Dame Juliet Gerrard is now the New Zealand Prime Minister’s Chief Science Advisor.Genevieve’s focus in most of these labs was trying to generate new experimental data for structural biology, as well as using a wide variety of techniques to generate other data to characterize protein:protein or protein:ligand interactions. X-ray crystallography was the primary technique she utilized when trying to determine new protein structures.Genevieve currently works as biocurator at PDBe, one of the members of wwPDB. When new structural data is deposited in the database, Genevieve is part of team of biocurators who processes this data and correspond with the scientists about their data. The PDB is an open-source database that predates the internet.

Sudakshina Ganguly | EMBL-EBI

I am a structural biologist with expertise in the area of Nuclear Magnetic Resonance spectroscopy. Currently, I am working as a Scientific Database Curator with the Protein Data Bank in Europe.

Marco Giulini | University of Utrecht

I am a computational biophysicist with a background in statistical mechanics and information theory, fascinated by the challenges posed by computational structural biology. My main research interest lies in the structural prediction and analysis of protein-protein complexes, with a focus on antibody-antigen structures.

Piraveen Gopalasingam | EMBL-EBI

Piv joined EMBL-EBI in 2017 as a Scientific Training Officer for the Training Team and is primarily responsible for the scientific development and delivery of training within the CABANA project. He is a Train the Trainer instructor, and has an interest in science communication, community building, equality, diversity and inclusion.

Piv gained his BSc in Biomedical sciences at Queen Mary University of London in 2009 before completing his PhD at the University of Birmingham in 2015, investigating the structural biology of cancer-causing phosphatases. Whilst writing his thesis he joined the University of Warwick as a postdoctoral researcher studying receptor-ligand interactions and later took on a teaching position at Kingston University London. During this time, he obtained associate fellowship status from the Higher Education Academy, supervised structural bioinformatics MSc projects, co-organised the local Café Scientifique and co-founded the London chapter of PubhD, a communication platform for researchers to explain their work to the public.

Robbie Joosten | Netherlands Cancer Institute

My research focusses on developing new computational methods to validate and improve the quality and value of macromolecular structure models. Within the PDB-REDO project (pdb-redo.eu) we take experimental data and initial models from crystal diffraction experiments, and improve the fit with the data and remove model errors. This approach delivers high-quality structure model for downstream studies such as drug (lead) discovery and structure-function analyses of proteins. Our AlphaFill project (alphafill.eu) focusses on adding value to structure models by fitting ligands, ions and cofactors on the bases of homology or by AI-based predictions.

Fabio Madeira | EMBL-EBI

Fabio Madeira is Technical Project Lead Software Engineer at the EMBL-EBI and his work focus on providing core Bioinformatics Sequence Analysis Applications available through the EMBL-EBI website, as well as through reliable Web Services. Fabio is also involved in bioinformatics training and external user support. Before joining EMBL-EBI, Fabio worked under the supervision of Professor Geoff Barton at the University of Dundee, where he obtained a PhD in Computational Biology and worked as a Postdoctoral Researcher. His work focused on the development of new methods to predict 14-3-3-binding proteins, on the characterisation of genetic variants in protein families and interaction interfaces, and later on Bioinformatics Web Services.

Nandana Madhusoodanan | EMBL-EBI

Nandana Madhusoodanan is a Documentation and Bioinformatics Support Officer in the Software Development and Operations group. Her main responsibilities include offering bioinformatics sequence analysis applications, providing user support, keeping documentation related to these services up-to-date, and conducting training sessions.

Paulyna Magana | EMBL-EBI

Bioinformatician for the AlphaFold Database at the Protein Data Bank in Europe (PDBe)

Emma Manners | EMBL-EBI

Emma is a Biological Curator in the ChEMBL team and is involved in data depositions, curation of biological entities and database enhancements, she also provides support to ChEMBL users. She has a PhD in Bioorganic Chemistry and a background in molecular biology along with experience in both academic and industry research.

Bálint Mészáros | St. Jude Children’s Research Hospital

Bálint Mészáros is a Principal Bioinformatics Research Scientist at St. Jude Children’s Research Hospital at the Department of Structural Biology. Bálint obtained his Ph.D. in Biophysics at the Eötvös Loránd University in Budapest, Hungary. He later worked as a staff scientist at the Institute of Enzymology and the Research Centre for Natural Sciences in Budapest and at EMBL Heidelberg with an EMBO and a Marie Skłodowska-Curie postdoctoral fellowships before joining St. Jude. Bálint’s main interest is understanding how protein flexibility contributes to cellular functions. He studied intrinsically disordered proteins, developing physics-based methods to predict their presence and functionality based on their sequences. He also focused on how disordered proteins mediate interactions between cells, enable pathogenic interactions, and how are rewired by mutations associated with diseases. His current focus is on understanding the role of biological condensation in tumorigenesis and the identification of various protein-protein interactions mediated by the disordered C-terminal tails of human GPCRs, tying GPCR signaling into various cellular processes and pathways.

Typhaine Paysan-Lafosse | EMBL-EBI

Typhaine is a Senior bioinformatician for the InterPro and Pfam databases at EMBL-EBI, where she is developing tools and workflows to facilitate data treatment and analysis. Typhaine is also involved in bioinformatics training and InterPro/Pfam external communication. Previously she worked on the Genome3D project for InterPro and PDBe databases. Prior to joining EMBL-EBI, Typhaine was a bioinformatician for the international ImMunoGeneTics information system in Montpellier, France where she was managing IMGT/3Dstructure-DB and IMGT/2Dstructure-DB. In 2013 Typhaine graduated from the University of Bordeaux, France with a master’s degree in bioinformatics.

Harry Powell | Imperial College London

PhD in Inorganic Chemistry (synthesis and structure determination) followed by postdocs in synthetic Chemistry and small molecule Crystallography. Then moved to structure solution by X-ray diffraction in protein and DNA crystallography. From 1998 to 2016 developed and maintained software for single crystal diffraction image processing (Mosflm) at MRC-LMB in Cambridge, followed by three years running a crystallographic consultancy. Worked at PDBe for a short while before starting at Imperial College London at the start of 2019 working on Phyre2 (homology modelling of proteins).

Pedro Raposo | EMBL-EBI

Pedro Raposo is a Bioinformatician in the Protein Function Content team of UniProt at EMBL-EBI working on creation of rules for automatic annotation of protein function. After obtaining his MSc in Bioinformatics, he worked at the UK Stem Cell Bank on genomic data, before joining EMBL-EBI.

Isabel Romero Calvo | EMBL

Isabel is a scientific illustrator and animator on the Communications Team of the European Molecular Biology Laboratory (EMBL). She is also the founder and Creative Director of Morphology (www.morphologyvisuals.com), a scientific communications company.
Isabel completed her BS degree in Pharmacology, and earned her PhD from the Biochemistry Department of the University of Granada, Spain. She then completed her postdoctoral reasearch and became a biomedical investigator at the The University of Chicago Medicine. Her interest in scientific illustration led her to the Biomedical Visualization Program at the University of Illinois Chicago (UIC) where she completed her MS. She then joined the UIC faculty. As an instructor she specialized in visualization techniques for molecular biology.

Ian Sillitoe | University College London

I completed a Chemistry Masters degree from Sheffield University before coming to UCL for a PhD in Bioinformatics (using inter-residue protein contacts for protein structure comparison and fold recognition). During my PhD and first Post-doc, I helped recode the CATH classification web site and set up automated workflows. I took a few years away from academia to work in commercial web design and software development before coming back to UCL first as a senior postdoc, then Principal Research Associate.

Janet Thornton | EMBL-EBI

As the Director of EMBL’s European Bioinformatics Institute (EMBL-EBI) between 2001 and 2015, Professor Dame Janet Thornton, led the growth of the Institute from 160 to over 600 people. Janet is one of the world’s pioneers in structural bioinformatics, using computational methods to understand protein structure and function. She currently leads a research group at EMBL-EBI, studying the computational biology of proteins and ageing. Janet is also a leading voice in the scientific community, having undertaken leadership and governance roles in the Royal Society, European Research Council, ELIXIR, UK Natural History Museum and chairing the Board of Trustees at the Earlham Institute.

Jack Turner -EMBL-EBI

I came to EMBL-EBI after completing a PhD at the Francis Crick Institute focusing on understanding viral membrane fusion by cryo-electron tomography. I am now a Biocurator for the EMDB. My day-to-day job involves curating new entries that have been submitted to us through the OneDep system. On-top of this I am involved in Development of the OneDep system, Outreach and attending conferences and workshops to present on behalf of EMDB.