Trainer biographies

Maria Zimmermann-Kogadeeva

I am an interdisciplinary scientist interested in the fundamental question of how the complex properties of a biological system emerge from the interactions of its members. I combine multiomics data integration and mathematical modelling to investigate molecular interactions inside the cell, microbial community interactions, and community interactions with the environment.

I strongly believe that interdisciplinary and collaborative projects are the driving force of modern life sciences. After finishing my studies in computer science, I joined an interdisciplinary systems biology lab for my PhD project, where I developed machine learning-based methods for metabolic flux analysis and multiomics integration approaches to investigate metabolic adaptation in pathogenic bacteria. For my postdoctoral training, I moved to the human microbiome field to investigate the molecular mechanisms of host-microbiome interactions in vivo. In collaboration with experimentalists, I developed computational strategies to analyze high-throughput genetic and untargeted metabolomics datasets to systematically identify and quantify microbiome-host interactions, and to assess the interplay between microbial and metabolic biomarkers in large human disease cohorts.

In October 2021, I started my research group in Genome Biology Unit at EMBL Heidelberg to investigate microbial ecosystems with a combination of computational and experimental approaches. My group combines computational modelling and multi-omics data integration to investigate how microbes adapt to their surroundings, and how metabolic adaptations of individual bacteria shape the functional outcome of microbial communities and their interactions with the environment.

Vladimir Benes

Vladimír Beneš, PhD, Head of EMBL GeneCore, born & studied in Prague, the Czech Republic. He has been at EMBL since 1994 when he came as a postdoc to Ansorge group in the Biochemical Instrumentation Unit. Vladimír worked on development of methodology supporting genome-wide high-throughput sequencing, mainly in the sample processing part. In 2001 he was appointed to build EMBL Genomics Core Facility, a technology orientated service laboratory founded to assist researchers with functional genomics projects. This facility is currently utilizing mainly massively parallel sequencing and supporting technologies, such as qPCR, for example. Most recently, Vladimír’s expertise has enlarged by adding single-cell genomic approaches. Among Vladimír’s tasks belong also assessment of new technologies and their applications in functional genomics, in particular their suitability for implementation in the environment of core facilities. He is also strongly involved in teaching of methods applied in this field.

Kiran Raosaheb Patil

MRC Investigator
ERC Investigator

Kiran studied Chemical Engineering at the Indian Institute of Technology (Mumbai, India). He moved to the Technical University of Denmark (DTU) to work with Prof. Jens Nielsen and obtained his PhD in Systems Biology. Kiran was then appointed as Assistant Professor at DTU where he worked on transcriptional regulation and metabolic engineering. In 2010, Kiran joined the Structural and Computational Biology Unit at the European Molecular Biology Laboratory (EMBL-Heidelberg, Germany). He was appointed Director of Research at the MRC Toxicology Unit (University of Cambridge) in 2019. The Patil lab has developed novel tools and model systems to decipher metabolic interactions in complex microbial communities.

Francisco Zorrilla

Francisco graduated from the University of California, Davis in 2017 with a B.Sc. in Biological Systems Engineering. In 2019 he obtained his M.Sc. in Biotechnology from Chalmers University of Technology in Gothenburg, Sweden. He then spent a year at EMBL Heidelberg with Kiran Patil, where they continued development of the metaGEM pipeline . Francisco began his PhD at the University of Cambridge MRC Toxicology Unit in 2021, where his research focuses the complex metabolism that occurs within networks of microbial communities, such as those found in the human gut microbiome.

Relevant bibliography:

Francisco Zorrilla, Filip Buric, Kiran R Patil, Aleksej Zelezniak, metaGEM: reconstruction of genome scale metabolic models directly from metagenomes, Nucleic Acids Research, Volume 49, Issue 21, 2 December 2021, Page e126, https://doi.org/10.1093/nar/gkab815

Zrimec J, Kokina M, Jonasson S, Zorrilla F, Zelezniak A. Plastic-Degrading Potential across the Global Microbiome Correlates with Recent Pollution Trends. mBio. 2021 Oct 26;12(5):e0215521. doi: 10.1128/mBio.02155-21

Social media:

GitHub: @franciscozorrilla

Twitter: @metagenomez

LinkedIn: @fzorrilla94

Eva Geissen

I received my first degree in Electrical Engineering before I studied Technical Biology in Stuttgart (DE). I did my PhD in Systems Biology at the University of Stuttgart on mechanistic modelling of mitotic checkpoint signalling. Since April 2017 I run the Centre for Biological Modelling (CBM) at EMBL Heidelberg. My job is to support EMBL scientists in adopting mathematical modelling into their workflow.

Julijana Ivanisevic

Julijana Ivanisevic is a Metabolomics and Lipidomics group leader and Senior Lecturer at the Faculty of Biology and Medicine, University of Lausanne, Switzerland. Julijana joined UNIL in 2015 following a postdoctoral training at The Center for Metabolomics and Mass Spectrometry at The Scripps Research Institute in La Jolla, California (led by Prof. Gary Siuzdak). She received her PhD in chemical biology at the Aix-Marseille University, France, in 2011.

The focus of Metabolomics team at UNIL is to advance the knowledge on molecular mechanisms that underlie metabolic health and onset and progression of acquired cardiometabolic disorders. To this end, the team is applying high-coverage quantitative MS-based approaches to metabolic phenotyping of human populations (CoLaus, Complete Health and Heart cohort) in collaboration with clinicians and statistical geneticists. Longitudinal metabolome-wide association studies with cardiometabolic risk factors as health outcomes and gene variants as instrumental variables, are applied to provide insights into metabolite role in disease etiology.

Juan Caballero

Juan Caballero completed his bachelor studies in Biochemistry Engineering and his graduate studies in Plant Genetics and Biotechnology and Biochemistry. He has participated in many research projects for plant, animal, bacteria, fungi and viruses applying his bioinformatics skills and expertise in more than 30 publications. Currently is part of the Microbiome Informatics team at EMBL-EBI as a Software Developer working on pipeline development and automation.

Tatiana Gurbich

Tatiana Gurbich is a bioinformatician on the MGnify team at EMBL-EBI. In this role, she works on generating and maintaining catalogs of metagenome-assembled genomes.

Prior to joining EMBL-EBI, Tatiana worked as a bioinformatician at a clinical genomics start-up, where she analysed next-generation sequencing data and developed a computational pipeline to identify and annotate copy-number variants in clinical samples.

Tatiana’s academic background is in computational evolutionary genomics. She holds a PhD in Integrative Biology from the University of California, Berkeley, where her research focused on the evolution of gene content on the X chromosome in Drosophila. Tatiana’s teaching experience includes working as a lecturer for an introductory biology course at the University of California, Berkeley.

Sara Saheb Kashaf

Sara is an MD PhD candidate pursuing research on the human skin microbiome.

Alejandra Escobar

Alejandra has a PhD in Biochemistry from the National Autonomous University of Mexico. She is a chemist and a microbiologist with bioinformatics education and has experience analysing data from high-throughput sequencing of microbial communities from a variety of biomes as fermented foods, marine environments, and host-associated microbiotas. Her currently role as postdoctoral researcher at the EBI-Sanger Postdoctoral (ESPOD) programme, gives her the opportunity to explore the mobilome of the gut microbiome through high-quality hybrid assemblies of bacterial isolates.

Sandy Rogers

Sandy Rogers is a software developer for MGnify, EMBL-EBI’s
metagenomics resource. He works on the website, API, and analysis packages that surface the metagenomic datasets gathered and analysed by MGnify.

Sandy’s academic background is in Astrophysics, with a PhD in observational astronomy from Edinburgh University at the
Royal Observatory Edinburgh. His doctoral research used image analysis pipelines, ground- and space-based multi-wavelength images, and
modelling to determine the star-formation properties of the Universe’s first-forming galaxies.

Sandy joined EMBL-EBI from a founding-team role at a technology
startup, where he worked on web app development and led the data science programme

Denise Medeiros Selegato

Denise M. Selegato has a bachelor’s degree in Pharmacy and Biochemistry from São Paulo State University, UNESP (2008-2013), and a Ph.D. in Chemistry from the same University (2014-2019). In 2019-2020, she was a postdoctoral fellow at the Centre of Magnetic Resonance (CERM) from the University of Florence (Italy), working with scientific programming to facilitate the analysis of integrative structural biology and NMR-metabolomics. In 2020-2021, she was a postdoctoral researcher at Fundación MEDINA (Spain), where her research focuses on the discovery of new potential antibiotics by MS high throughput screening of microbial species.

Currently, she is a Metabolomics Specialist in the Zimmermann Group (Metabolic host-microbiome interactions) from the European Laboratory of Molecular Biology (EMBL) in Heidelberg. Her main work focus on the development of high throughput screenings and MS-based metabolomics to the study of clinical and microbiome data.

Dayane  Araújo

Dayane completed her PhD in Microbiology at the Ludwig Maximilian University of Munich, with part of her research conducted at the Technical University of Dresden. Her research involved the study of (1) bacterial ECF sigma factors in order to design and implement orthogonal genetic switches in Bacillus subtilis; and (2) 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, policy makers and funders. 

Dayane joined the training team at EMBL-EBI in February 2021 as a Scientific Training Officer, working on the development and delivery of a range of bioinformatics focused courses for the life science community.