Trainer biographies

Ananth Prakash – EMBL-EBI

Ananth Prakash is a bioinformatician and data analyst at the PRIDE proteomics team at the European Bioinformatics Institute. He has a PhD from the University of Cambridge and his research work was carried out at EBI. His doctoral thesis was on protein bioinformatics where he studied evolution and interaction of protein domains and RNAs. He did his postdoctoral work at the John Innes Centre in Norwich, where he investigated folding of RNA secondary structures in different species of rice using SHAPE RNA-seq technology. At present his work involves developing methodologies for large-scale reanalysis of mass spectrometry proteomics datasets in PRIDE database, especially to generate an atlas of protein expression across various tissues and organs from normal healthy samples in human, mouse and rat. He is also interested in studying differential protein expression in brain in patients diagnosed with Alzheimer’s and Parkinson’s disease. Apart from research, he is an amateur astronomer and member of the Cambridge University Astronomical Society, he also enjoys gardening and reading books.

Andy Jones – University of Liverpool

I am a Professor of Bioinformatics and Director of the Computational Biology Facility at the University of Liverpool. In our research group, we work extensively with developing and applying computational methods for proteomics, as well as using data science techniques across multi-omics. I have previously contributed also to the development of data standards for proteomics.

Carlo de Nart – Max Planck Institute of Biochemistry, Germany

I am a biologist with a master degree in neuroscience. During the bachelor degree I started learning computational biology and in particular omics data analysis. Initially I worked with genomics data, then after the master I switched to transcriptomics. I am a PhD student at the Max Planck Institute of Biochemistry, where I am currently focusing on Proteomics. In particular I am working at Jürgen Cox’s laboratory, where MaxQuant and Perseus were developed.

Deepti Jaiswal Kundu – EMBL-EBI

I am Deepti Jaiswal Kundu, work as a Scientific Curator at EMBL-EBI, Cambridge. I studied botany, psychology, and bioinformatics in India, before doing my Ph.D. in Cheminformatics in the Czech Republic in 2015. I joined EMBL-EBI in 2018. As a Scientific Curator, I check and validate new datasets submitted to the PRoteomics IDEntifications Database (PRIDE) – the world’s largest public database dedicated to mass spectrometry-based proteomics. Also, I curate the datasets for further reanalysis and integration into other bioinformatics resources in EBI.

Eliot Ragueneau – EMBL-EBI

Software Engineer in Reactome team. Specialised in network knowledge base and the creation of their interface, I developed IntAct App during my internship in IntAct team.

Dr James Wright is a bioinformatician with over a decade of experience in genomics and proteomics research and has published widely in top research journals, including Science and Nature. James specialises in proteogenomics and personal proteomics, using advanced computational and machine learning techniques in the investigation of multi-omics datasets to explore cancer development and the impact of novel cancer therapies. In 2017, James joined Professor Jyoti Choudhary’s Functional Proteomics team at the ICR. Previously, he held positions as principal bioinformatician at the Wellcome Trust Sanger Institute, bioinformatician at AstraZeneca, and was a member of the GENCODE Project which led and was responsible for the comprehensive annotation of the human and mouse genomes. James was awarded a PhD in Techniques for Cross Species Proteomics jointly by the University of Manchester and University of Liverpool in 2010.

Juan A. Vizcaíno – EMBL-EBI

Juan Antonio Vizcaino, Proteomics Team Leader, EMBL-European Bioinformatics Institute Dr. Juan Antonio Vizcaíno’s team is responsible of the PRIDE database (https://www.ebi.ac.uk/pride/), the world-leading public repository for mass spectrometry (MS) proteomics data, and related tools and resources. In addition, he co-founded and is coordinating the ProteomeXchange Consortium, aiming to standardize data submission and dissemination of proteomics data worldwide. Over the years, he has heavily contributed to the development of open proteomics data standard formats (e.g. mzIdentML, mzTab, Universal Spectrum Identifier, ProForma, etc) and related software, as part of his contribution to the Proteomics Standards Initiative. He is is also co-leading the ELIXIR Proteomics Community (https://elixir-europe.org/communities/proteomics). He actively promotes open data policies in the field and has led several studies where public proteomics datasets are reused for different purposes. He has been the leading author of highly-cited publications in journals such as Nature Biotechnology, Nature Methods, Nucleic Acids Research, Genome Biology and Molecular and Cellular Proteomics, among others. He has published >145 articles with >25,000 citations, largely in computational MS and bioinformatics. He earned undergraduate degrees in Pharmacy (1997) and Biochemistry (2000), a Master’s degree in Microbiology (1998), and a doctoral degree in Molecular Biology (2005), from the University of Salamanca (Spain).

Juan Jose Medina Reyes – EMBL-EBI

I’m a software engineer with a few years of experience that started working at EMBL-EBI on September 2022, as part of the Molecular Networks group.

Jyoti Choudhary – The Institute of Cancer Research, UK

Professor Jyoti Choudhary leads the Functional Proteomics Unit at The Institute of Cancer Research, London. She received her PhD in biological mass spectrometry under the guidance of Professor Howard Morris (FRS) at Imperial College London. In subsequent positions in pharma and biotech sectors, her research focused on developing and applying mass spectrometry based methods to address biological and structural problems. She was a founding member of Cellzome UK, a globally recognised proteomics company. She joined the Wellcome Trust Sanger Institute, to pursue her research in interaction proteomics and proteogenomics. Her group implemented methods to systematically study native protein complexes in a range of cell types and tissues. They also developed open access computational tools and data analysis pipelines to integrate proteomics data with genomics. At the Institute of Cancer Research, Dr Jyoti Choudhary’s research focuses on applying quantitative proteomics approaches to investigate the impact of mutations and genetic variation on the protein attributes, and to understand how the organisation and signalling of cellular networks are rewired during cancer progression and resistance.

Kalpana Panneerselvam – EMBL-EBI

I am Kalpana Panneerselvam – IntAct project lead at EBI. In IntAct, we work closely with the researchers on their direct submissions and focus on generating tissue/cell specific, disease centric interactomes. We are also interested in perturbants of molecular interactions – mutations, agonist, antagonists. Previously, I have been handling genetic variant data for commercial databases and other custom curation projects.

Kathryn Lilley – University of Cambridge

Kathryn received her PhD in Biochemistry from the University of Sheffield. After being a laboratory manager for eleven years, she established the Cambridge Centre for Proteomics, University of Cambridge in 2001. She became the Professor in Cellular Dynamics in Department of Biochemistry University of Cambridge in 2012. She directs a research programme focused on the development and application of technologies to map RNA and protein subcellular localization on a cell-wide scale. Her research looks at the effect of post transcriptional and post translational processing on location, and the extent of re-localization in response to cellular stress and disease. She is a recipient of a Wellcome Trust Investigator Award and a partner in EPIC-XS, a pan European proteomics infrastructure consortium. She is the recipient of the Juan Pablo Albar Proteome Pioneer Award from the European Proteomics Association the HUPO Distinguished Achievements in Proteomics award. She was elected as a member of EMBO in July 2020.

Kerry Ramsbottom – University of Liverpool

Kerry is a PDRA currently working on the “DIA-eXchange” project, aiming to reanalyse Data Independent Acquisition (DIA) proteomics datasets and has previously worked on the “PTMeXchange” project, a large scale reanalysis of post-translational modification data. She completed her PhD at the University of Liverpool in 2019. This work used informatics investigations to explore the involvement of Human Leukocyte Antigens (HLA) with adverse drug reactions, in order to further the understanding of the associations and the mechanisms involved.

Krishna Kumar Tiwari – EMBL-EBI

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.

Lennart Martens – Ghent University and VIB, Belgium

Lennart Martens is Senior Full Professor of Systems Biology at Ghent University, Group Leader of the Computational Omics and Systems Biology (CompOmics) group at VIB, and Associate Director of the VIB-UGent Center for Medical Biotechnology, all in Ghent, Belgium. He has been working in proteomics bioinformatics since his Master’s degree, which focused on the computational interpretation of peptide mass spectra, and the sequence-dependent fragmentation of peptides. He then worked as a software developer and framework architect for a software company for a few years, before returning to Ghent University to pursue a Ph.D. in proteomics and proteomics informatics. During this time, he worked on the development of high-throughput peptide centric proteomics techniques and on bioinformatics tools to support these new approaches. In 2003 he designed and built the PRIDE repository for global dissemination of proteomics data. After obtaining his Ph.D., he rejoined EMBL-EBI to coordinate PRIDE for the next three years, establishing the system as the world’s foremost public proteomics data repository. He moved back to Ghent University and VIB in 2009, in where he focuses on novel machine learning algorithms for mass spectrometry data analysis, and their application to the large-scale orthogonal reprocessing of public proteomics data.

Lieven Clement – Ghent University and VIB, Belgium

Lieven Clement is an Associate Professor of Statistical Genomics at Ghent University. He is an expert in developing statistical methods and open source tools for differential omics data analysis. His research efforts resulted in numerous publications on novel methods and tools for, and applied research in omics data analysis. His lab is built around two strategic research pillars each connected to an omics domain: (single cell) transcriptomics and proteomics and he also has a strong interest in leveraging his expertise to translational research.

Lisa Breckels – University of Cambridge

Since November 2010, Lisa has worked in the Cambridge Centre for Proteomics in spatial proteomics as a Computational Biologist. Her main area of research focuses on computational analysis of high-throughput quantitative spatial proteomics data and development of new machine learning tools and R packages, contributing to the Bioconductor project. She is particularly interested in visualisation and developing robust and reproducible pipelines. Prior to working in Cambridge she received a BSc (Hons) in Mathematics from the University of Essex and went on to complete a PhD in Computational Biology. Working in structure-based drug-design she used molecular modelling and molecular dynamics simulation techniques to gain an insight into the structural and functional properties of GPCRs in their multiple states.

Megan Hasoon | University of Liverpool

Megan works as a Data Scientist at University of Liverpool as part of their Computational Biology Facility (CBF). Her role at the CBF primarily involves performing analysis for academic and industry collaborators. Megan also demonstrates on a range of CBF-led courses, including ‘R for Beginners’ and ‘R for Data Science’. Prior to joining the CBF, Megan completed a PhD in Evolutionary Ecology at the University of York (2020) investigating host-symbiont interactions in the pea aphid, with a particular focus on host defence and immunity. Megan’s PhD involved both wet lab and computational work and this where she first embarked on her bioinformatics journey, building and analysing novel genomes of newly discovered symbiotic bacterial species. Following her PhD, Megan worked for two years as a Bioinformatician within the Bioinformatics Support Unit at Newcastle University, where she grew her Bioinformatics and data science skillset further working on a diverse range of research projects. Megan is also passionate about public engagement and widening participation – in particular, helping create opportunities which aim to break down some of the barriers for under-represented groups in biology and data science.

Pelagia Kyriakidou – Max Planck Institute of Biochemistry, Germany

I have studied Biochemistry & Biotechnology at the University of Thessaly in Greece. I continued my studies at the same university to get my Master’s Degree in “Applications of Molecular Biology – Genetics – Diagnostic Biomarkers». During my Master’s Degree I shifted my focus to bioinformatics and chose my thesis to be on bioinformatics analysis of phosphoproteomics data. To develop and improve my bioinformatics skills and proteomics knowledge I visited Prof. Dr. Juergen Cox’s research group: “Computational Systems Biochemistry” in Max Planck Institute of Biochemistry as an Erasmus+ intern. Currently I am a PhD student at Juergen Cox’s lab working on Computational Palaeoproteomics. This project is part of the PUSHH program which is a Marie Skłodowska-Curie European Training Network (ETN) providing international doctoral training on palaeoproteomics applied to palaeontology, palaeoanthropology and archaeology.

Sreejan Bandyopadhyay – The Institute of Cancer Research, UK

Sreejan is a Scientific Officer in the Functional Proteomics group at the Institute of Cancer Research (ICR). He has successfully led various proteogenomics projects. Sreejan has designed and developed a range of novel genomic pipelines to create personalised databases from variants and alternative splicing events in RNA sequencing data. He has also developed software to search for such events in proteomics and immunopeptidomics data. Sreejan work is currently focused on using these tools to understand translation and antigen presentation rates of non-coding regions of the genome, particularly in the context of cancer.

Shengbo Wang – EMBL-EBI

Shengbo Wang is a bioinformatician working in the Proteomics group (PRIDE group) at the European Bioinformatics Institute (EMBL-EBI, Cambridge). He currently working on reanalysis of Metaproteomics datasets as well mass spectrometry datasets from DDA. He graduated with a joint MSc in Bioinformatics from the University of Amsterdam and Vrije University of Amsterdam. He interned at the Institute of Data Science, Imperial College London, working on Multi-Omics Data based Classification and Survival Prediction of Pan-Cancer with Variational Autoencoders. This was then followed by another internship at the Robert Koch Institute, Germany, working on Deep Learning Prediction and Interpreting of Phosphorylated Peptides from Tandem Mass Spectra.

Yasset Perez Riverol – EMBL-EBI

Dr Yasset Perez-Riverol obtained a BSc degree in Software Engineering in 2006 with the development of a high-performance algorithm for conformational search of small molecules. Between 2006-2014, he worked at the Center for Genetic Engineering and Biotechnology (CIGB), Havana, Cuba, as a Group Leader in the Proteomics Department. During this period, he developed new machine learning algorithms and tools for peptide and protein identification using mass spectrometry data.

In 2014, he achieved a PhD in Biochemistry at Havana University and joined EMBL-EBI as Bioinformatian in the PRIDE team. Between 2014-2015, he led and developed PRIDE Inspector Toolsuite, Protein inference toolbox (PIA), PRIDE Cluster and a set of libraries and tools for visualisation, quality assessment and protein inference of proteomics experiments.

Recently, he has led the development of Omics Discovery Index, an open source platform to facilitate the access and dissemination of omics datasets coming from multiple omics studies. In addition, he has lead the BioContainers, a community for bioinformatics software containers. In 2019, he was appointed Proteomics Team Coordinator, including PRIDE Archive, PRIDE Cluster and Proteogenomics resources.