Trainer biographies

Craig Russell

Data Scientist on Biological Imaging at the Brazma research group, EMBL-EBI.

Alvis Brazma

Dr Alvis Brazma oversees the development and services for several major resources, including ArrayExpress, the Gene Expression Atlas and the BioStudies Database. His main research interests concern integrative data analysis to reveal patterns of gene and protein expression in normal and diseased state. He has over 100 scientific publications and is a Principal Investigator on several large collaborative genomics and biomedical projects, including the kidney cancer project of the International Cancer Genome Consortium. Dr Brazma studied mathematics at the University of Latvia, Riga, before obtaining his PhD in computer science from the Moscow State University. He was a lecturer at the University of Latvia and a visiting Researcher at Helsinki University before joining EMBL-EBI in 1997. Dr Brazma was among the first scientists to use microarray data to study gene regulation. In 1999 he founded the Microarray Gene Expression Data society was instrumental in starting ArrayExpress, one of the major international repositories for functional genomics data.

Virginie Uhlmann

Virginie Uhlmann is joining EMBL-EBI as a Research Group Leader in September 2018. Her research focuses on bioimage analysis, specifically continuous representations for image analysis. Virginie’s group works on collaborative, interdisciplinary projects with biologists and software developers. She holds a PhD in Electrical Engineering from the Swiss Federal Institute of Technology in Lausanne (EPFL), and is an associate member in the Bio Imaging and Signal Processing Technical Committee of IEEE Signal Processing Society (2018-2020).

Jason Swedlow

Jason Swedlow earned a BA in Chemistry from Brandeis University in 1982 and PhD in Biophysics from UCSF in 1994. After a postdoctoral fellowship with Dr T. J. Mitchison at UCSF and then Harvard Medical School, Dr Swedlow established his own laboratory in 1998 at the Wellcome Trust Biocentre, University of Dundee, as a Wellcome Trust Career Development Fellow. He was awarded a Wellcome Trust Senior Research Fellowship in 2002 and named Professor of Quantitative Cell Biology in 2007. His lab focuses on studies of mitotic chromosome structure and dynamics and has published numerous leading papers in the field. He is co-founder of the Open Microscopy Environment (OME), a community-led open source software project that develops specifications and tools for biological imaging. In 2005, he founded Glencoe Software, Inc., a commercial start-up that provides commercial licenses and customization for OME Software. In 2011, Prof Swedlow and the OME Consortium were named BBSRC’s Social Innovator of the Year and Overall Innovator of the Year. In 2012, he was named Fellow of the Royal Society of Edinburgh and appointed an Honorary OBE by Her Majesty the Queen in 2021.
Prof Swedlow has organized or directed several courses in quantitative
microscopy at the Marine Biological Laboratory, Woods Hole, USA, Cold Spring Harbor Laboratory, USA and the National Centre for Biological Science, Bangalore, India.

Matthew Hartley

Matthew is Team Leader for the BioImage Archive at EMBL-EBI. Prior to joining EBI, he led the Informatics team at the John Innes Centre, a research institute focussing on plant and microbial sciences. Matthew’s background is in image analysis, numerical and statistical modelling and scientific data infrastructure.

Ugis Sarkans

Dr Ugis Sarkans leads the Functional Genomics Software Development team. Ugis has been at EMBL-EBI since 2000, involved in the development of ArrayExpress, a public gene expression data resource (and currently an ELIXIR core resource) and the associated community standards. Ugis’ team now develops and runs the BioStudies database, a resourse for aggregation of heterogeneous biomedical data linked to publication. The team also maintains ArrayExpress and is involved in building the BioImage Archive (with light microscopy data currently managed in the BioStudies database) and collaborates on a number of European ‘multi-omics’ projects in a data-management capacity. Prior to joining EBI Ugis was a postdoc at the University of Wales. His main scientific interests are related to knowledge and data management.

Awais Athar

Awais Athar is a Software Development Project Leader at the European Bioinformatics Institute, working on the BioStudies database as well as ArrayExpress. His research interests include Information Retrieval, Speech Processing and Natural Language Processing. He has more than 20 years of experience in a diverse set of domains including bioinformatics, machine learning, data storage, e-Commerce, ERP, industrial automation, 3D graphics, and mobile apps. He holds a PhD in Computer Science and an MPhil in Computer Speech, Text, and Internet Technology from the University of Cambridge.

Gerard Kleywegt

Gerard is the Team Leader of the Molecular and Cellular Structure group at EMBL-EBI. Prof. Gerard Kleywegt leads the Protein Data Bank in Europe (PDBe), the European partner in the Worldwide Protein Data Bank organisation (wwPDB), which maintains the single international archive for biomacromolecular structure data.

Osman Salih

My post-doctoral, Ph.D. and M.Res. research involved the structural analysis of macromolecular complexes by transmission electron microscopy (EM), single-particle image analysis and the computational interpretation of the resulting 3D EM maps through atomic model building, modelling and energy minimisation. After completing my B.Sc. in Molecular Biology at Queen Mary, I attained my M.Res. and Ph.D. in Structural Molecular Biology from UCL/Birkbeck for projects on the relaxosome complex and the Saf pilus, respectively. My experience and skills led to two post-doctoral research posts; one at the University of Oxford on ribosomal frameshifting and the other at Imperial College London on Type VI secretion system sub-complexes. In 2018, I joined the Cellular Structure and 3D Bioimaging (CS3DB) team at the European Bioinformatics Institute (EMBL-EBI) where I work as a scientific database curator for the Protein Data Bank in Europe (PDBe), the Electron Microscopy Data Bank (EMDB) and the Electron Microscopy Public Image Archive (EMPIAR).

Simone Weyand

Studied Biochemistry at University of Bremen, Germany. PhD at EMBL in X-Ray crystallography, postdoc at Imperial College London and Diamond Light Source Ltd, Oxford, postdoc at MRC-LMB, Sir Henry Dale Fellow and Young Investigator at University of Cambridge, U.K. and Data Curator at EMBL-EBI.

Jean Marie Burel

Jean-Marie Burel joined the staff of the Swedlow lab in 2003. Since then, he’s been contributing to the development of OME. He received his PhD in mathematics from the University of Brest in 2000. His research interests lie in the area of harmonic maps, harmonic morphisms and geometric structure. After his PhD, he worked in a private company as developer then moved (September 2001) to Lund University, Sweden, where he held a post-doctoral research position. Jean-Marie now enjoys the muddy rugby pitches of Scotland.

Beth Cimini

Dr. Beth Cimini is a Senior Group Leader in the Imaging Platform at the Broad Institute in Cambridge, MA and a CZI Imaging Scientist.  After doing research in visual neuroscience with Dr. William Eldred at Boston University as an undergraduate, she obtained a PhD in Biochemistry and Molecular Biology with Dr. Elizabeth Blackburn at UCSF, studying the difference between splicing variants of the telomere master scaffolding protein TIN2.  These projects honed her interests in image analysis, leading her to join Dr. Anne Carpenter’s lab at the Broad, where she now leads an independent team collaborating with approximately 30 outside scientists per year on their own custom image analysis projects.  She co-maintains the lab’s main software tool, CellProfiler, and directs the Broad efforts towards community engagement and driving biological projects for the Center for Open Bioimage Analysis (COBA).  

Wei Ouyang

I am currently a researcher at Science for Life Laboratory and KTH Royal Insitute of Technology, Stockholm, Sweden. I joined the Cell Profiling group since Jan. 2019, mainly working on developing new methods for image analysis and modeling, mostly based on deep learning.

I obtained my Ph.D at Institut Pasteur, Paris where I developed deep learning based methods for advanced microscopy imaging.

Esti Gomez de Mariscal

Ph.D. student of Mathematical Engineering at Universidad Carlos III de Madrid and part of the deepImageJ team. I have experience with biostatistics, machine learning methods, and biomedical image analysis, especially for the study of cancer cell motility and communication. Big defender of open-source and reproducible tools.

Fynn Beuttenmüller

Fynn studied Physics at University of Heidelberg and joined Anna Kreshuk’s lab as a PreDoc in 2018.

Petr Walczysko

Petr Walczysko joined the OME project in October 2012 as a software specialist for testing and
quality assurance. He studied at Charles University of Prague where he received Master of
Science degree in Physics and the University of Freiburg in Germany where he received PhD in
Biology. Throughout his PhD studies and his further career as a researcher he was intensively
using conventional, confocal and multiphoton fluorescence microscopy applications on
biological systems. He was adapting these optical microscopy techniques for particular
biological problems, and also worked on the subsequent image analysis of microscopic images
in a range of image analysis programs. He enjoys yoga, reading and chess.

Frances Wong

Frances Wong leads the Image Data Resource (IDR) project and is the scientific curator for the IDR.  She received her PhD in Developmental Biology from the University of Edinburgh.  She then carried out post-doctoral research in molecular biology, genetics, genomics, neuroscience and biomedical imaging.  She has also worked on atlas-based gene expression databases and created new online scientific resources.

Barbara Diaz-Rohrer

I am a postdoctoral researcher in the image analyst team. I have a background in biochemistry and cell biology. I am passionate about using objective quantitative methods to obtain meaningful data from biological images.

Guillaume Jacquemet

Andrii Iudin

Soham Mandal

Anna Kreshuk

David Stirling

• Martin Weigert
• Ricardo Henriques
• Romain Laine
• Dominik Kutra
• Nasim Jamali