Trainer biographies

Cecilia Domínguez Conde – Human Technopole

Cecilia Domínguez Conde is a Group Leader at the Population & Medical Genomics programme of the Genomics Centre. After training as a pharmacist in the University of Seville, Cecilia went on to do a PhD in Immunology at the Research Centre for Molecular Medicine (CeMM) in Vienna where her work focused on dissecting the genetic cause of molecularly undiagnosed primary immunodeficiencies using exome sequencing. In 2019 Cecilia joined the Teichmann lab at the Wellcome Sanger Institute where her focus has been to dissect the diversity of human immune cell types across lymphoid and non-lymphoid tissues as part of the Human Cell Atlas initiative. Her research group at HT uses cutting-edge genomic technologies to study developmental immunology.

Artuur Couckuyt – VIB – IRC – University Ghent

Artuur Couckuyt obtained his Master’s degree in Biochemistry and biotechnology in 2019 at Ghent University. Afterwards, he started his PhD at the VIB-UGent Data Mining and Modeling for Biomedicine group headed by Yvan Saeys. His main project focuses on the analysis of high-dimensional flow cytometry data from patients suffering from acute myeloid leukemia where the main goal is to improve diagnosis and prognosis. He also works on the correspondence between the protein data in CITE-seq and flow cytometry, where on the one hand he is researching transformations for both kinds of data. On the other hand, he is investigating possibilities to extract a flow cytometry panel out of the CITE-seq data.

Gaurhari Dass – EMBL-EBI

Gaurhari Dass is a Senior Cloud Architect in OmicsDI from past 5.5 years. He has very strong expertise in IT sector. He has worked on different technologies during his career and now working on development of OmicsDI from infrastructure deployment to coding.

Rasa Elmentaite – Wellcome Sanger Institute

I am a staff scientist in Sarah Teichmann’s team at Wellcome Sanger Institute.

Nancy George – EMBL-EBI

Scientific Curator – Papatheodorou team: Gene Expression

Read more about Nancy’s team and their research here.

Matthew Hall – EMBL-EBI

Matt is a Senior Scientific Officer in the Industry Partnerships team at EMBL’s European Bioinformatics Institute (EMBL-EBI). The team is responsible for overall strategy development, planning and partnership activities within EMBL-EBI. This includes development of research-related activities with industry, as well as delivery of EMBL-EBI’s Industry Programme. Matt has primary responsibility for the day-to-day management of the Industry Programme. Prior to joining EMBL-EBI, Matt had a 25-year career in the pharmaceutical industry as a bioinformatician, clinical scientist, and molecular biologist. Matt held various scientific management and leadership roles, primarily in the Bioinformatics and Computational Biology departments at GSK. He gained experience as a Clinical Director in GSK’s Africa NCD Open Lab. Matt started his career in industry with Parke-Davis/Pfizer in 1993. Matt has skills in bioinformatics, clinical research, molecular biology, project management, relationship building and working with external partners. He is a member of the Industrial Advisory Board, Faculty of Biological Sciences, University of Leeds. He gained his PhD in Molecular Biology from the University of Leeds in 1991.

Maira Ihsan – EMBL-EBI

Maira joined the ENA as a User Support Bioinformatician in December 2021. She’s happy to assist with any queries regarding data submission or retrieval at the ENA. Her educational background is in Bioinformatics and Biomedical Sciences.

Tamás Korcsmáros – Imperial College London / Earlham Institute

As a PhD student, Tamas developed a signalling network database, SignaLink, which filled a vital niche in the landscape of bioinformatics tools, and by now it has become one of the most used signalling network resources for human and model organism studies. In Budapest, he established and led the “NetBiol” Network Biology group, which has developed additional novel databases to meet key scientific community needs. In March 2014, he moved to the UKand received a special 5-year BBSRC fellowship to work in the computational biology and sequencing focused Earlham Institute and in the gut microbiome centred Quadram Institute. This fellowship allowed him to establish a multi-disciplinary group that combines computational and experimental approaches, including gut organoids. Tamas was the systems genomics workpackage lead of the UKRI-BBSRC funded institute strategic programme of the Earlham Institute. In 2019, he was appointed as a Tenure-track group leader, and in 2021, Tamas moved to Imperial College London as a Senior Lecturer. His group has carried out multiple projects to predict, analyse and validate host-microbe interactions in the gut, especially in relation to the regulation of autophagy by microbes and upon disease conditions such as inflammatory bowel disease (IBD) and cancer.

Anna Lorenc – Wellcome Sanger Institute

Anna is a computational biologist in Gosia Trynka’s lab of Immune Genomics at Wellcome Sanger Institute, which she joined after 7 years at Kings College London in the Adrian Hayday and Mark Peakman labs. Her scientific interests are T cell receptors in the context of autoimmune diabetes. She has experience in analysing diverse immunological datasets, from high throughput flow cytometry to scRNAseq and bulk TCR sequencing. She is a big fan of R, Bioconductor, open science and wet lab scientists developing computational skills.

Elena Lukyanova – Wellcome Sanger Institute

I am a computational postdoctoral fellow at Wellcome Sanger Institute in immune genomics group. The main focus of my research is trying to gain an insight into the immune system biology of patients with rare form of primary immunodeficiency – Omenn Syndrome – using multi-omics single cell technologies and trying to reveal undisclosed mechanisms underlying the disease development and progression. I am particularly passionate about genomics, immunology and cancer biology.

Matthew Madgwick – Earlham Institute

Matthew is a final year PhD student within the Korcsmáros group. With industrial partner BenevolentAI, he is developing machine learning (ML), and systems biology approaches to integrate longitudinal multi-omic data. These approaches identify prognostic indicators from multi-omic data in Inflammatory Bowel Disease to improve our understanding of how the microbiota contributes to our health. Matthew started his research in the second year of his undergraduate studies in Natural Sciences (majoring in Computer Science and minoring in Biological Sciences) at the University of East Anglia. As an intern within the Korcsmáros Group, he developed an algorithm to identify and contextualise autophagy-related proteins within a molecular interaction network. More recently, Matthew has focused his research on Single-cell RNA-seq data. He contributes and develops several computational tools for working with Single-cell RNA-seq data, with projects focusing on investigating immune cells’ role in IBD, SARS-CoV-2 and Breast Cancer.

Maaly Nassar – SciBite

Maaly Nassar is a senior data scientist at Elsevier (SciBite team). She works on developing knowledge and drug discovery machine learning algorithms for pharmaceutical companies. Before moving to SciBite, Maaly worked as a machine learning scientist for the EMERALD project at EMBL- EBI. She developed and integrated machine learning frameworks and pipelines that automatically enrich/annotate metagenomics and biosynthetic gene clusters sequences with data from literature. The metagenomics annotations pipeline is currently integrated into Europe PMC to continuously enrich up-to-date MGnify’s metagenomics studies with data from literature. Before moving to EBI/UK, Maaly was a senior research scientist at the Free University of Berlin in the fields of veterinary medicine, semantic computing and cognitive neuroscience. In Berlin, she investigated perinatal temperature stimulation on brain deiodinase expression using immunohistochemistry, developed semantic search interfaces for 1914-1918-online-encyclopedia, designed and developed a serious game, named Equine Virtual Fram during her PhD and further investigated the brain activities and connectivities of diagnostic reasoning while playing veterinarian in the Equine Virtual Farm. Maaly also is a veterinarian. She had bachelor, master degree (Cairo University) and PhD degree in veterinary medicine (Free University Berlin) and an extra master degree in cognitive neuroscience (Humboldt University Berlin)

Marta Perez Alcantara – Wellcome Sanger Institute

I am a postdoctoral fellow in the immune genomics group. I study the genetics of neurodegenerative disease (particularly Alzheimer’s disease) and how it affects microglial and macrophage function. For this, I analyse the effects of genetic variation on the phenotype and the transcriptome of iPSC-derived microglia, using single cell eQTL and phenotypic QTL analysis and CRISPR screens. During my DPhil I studied the role of islet development in type 2 diabetes (T2D) susceptibility, performing genomics analyses (RNA-seq, ATAC-seq, methylation, ChIP-seq) in an iPSC-derived model of pancreatic beta cells. 

Katrien Quintelier – Ghent University

Katrien Quintelier is a fourth year PhD student in the VIB-UGent Data Mining and Modeling for Biomedicine group (Ghent, Belgium) and the Department of Pulmonary Diseases of the Erasmus Medical Center (Rotterdam, The Netherlands). She is working on a computational pipeline to analyze high-dimensional flow cytometry data of lung cancer patients and to predict response to immunotherapy. Since she is working with clinical data, her main research focus is on the preprocessing of the data including quality control, batch detection and normalization.

Eliot Ragueneau – EMBL-EBI

Software Engineer for Reactome and IntAct.
Author of IntAct App, contributor of IntAct Portal and Reactome website.

Craig Russell – EMBL-EBI

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.

Blagoje Soskic – Human Technopole

Blagoje Soskic is a Research Group Leader at Fondazione Human Technopole. Blagoje uses a wide range of genomic and immunological technologies to study variation in the human immune system and understand how disease variants affect cellular processes and cell-cell interactions. One of the major focuses of his group is understanding the crosstalk between T and B cells, which is central to protective immunity and has been implicated in a wide range of diseases. By studying variation in gene expression, chromatin activity and cellular phenotypes he aims to gain fundamental insights into the molecular and genetic control of cellular processes and immune effector functions. From 2016-2021, Blagoje Soskic was a postdoctoral fellow at Wellcome Sanger Institute, applying immunogenomic approaches to study T cell activation and their role in immune diseases. Blagoje graduated from the University College London with a PhD in Infection and Immunity.