ESR Team


ESR 1: Ulrika Boulund

Ulrika Boulund was born in Sweden and completed her Bachelor degree in Human Life Science Engineering at the Technical University of Denmark (DTU, 2016). During her Bachelor she participated in an exchange programme to Seoul National University in South Korea. She then completed her Master’s degree in Bioinformatics and Systems Biology to obtain a Master of Science in Engineering (DTU, 2018). Her master thesis was focused on analysing RNA-sequencing data, and it was written in collaboration with the pharmaceutical company Lundbeck in Copenhagen. During her studies she was also employed as a student assistant with the bioinformatics company Intomics.
Currently, Ulrika is working as a PhD student at the Academic Medical Center in Amsterdam, where she is conducting various bioinformatic and machine learning analyses to study non-alcoholic fatty liver disease (NAFLD). The main goal of the project is to identify biomarkers for NAFLD in serum and urine, as well as characterising the gut microbiome.

Research domain: Metabolism & endocrinology, Physiology & biochemistry and Computational & systems biology

WP2,3,4: Human cohorts and mice models, Mechanistic studies of microbiome-host interactions and Big data analysis of the gut microbiome

Academic Medical Centre Amsterdam (AMC)

Department of Vascular Medicine

u.boulund@amc.uva.nl


ESR 2: Veera Houttu

Veera is originally from Finland. She holds a Master’s degree in health science with a major in clinical nutrition from the University of Eastern Finland, a degree which entitles her to work as a registered dietitian in Finland. After her degree she gained some clinical experience in health care. Veera did her master’s thesis in the University of Hong Kong focusing on non-alcoholic fatty liver disease (NAFLD) which inspired her to pursue international PhD position.
Veera is interested in an interdisciplinary way of conducting science combining her expertise in nutrition but also going over her comfort-zone outside of her main areas of expertise. Her goal is to gain more knowledge of metabolism and microbiome in NAFLD by conducting a lifestyle intervention study in NAFLD patients. She will use analytical techniques to characterise the metabolic effect and to define exercise-responsive gut microbiome.

Research domain: Metabolism & endocrinology

WP2: Human cohorts and mice models

Academic Medical Centre Amsterdam (AMC)

Department of Vascular Medicine

v.a.houttu@amc.uva.nl


ESR 3: Susanne Csader

Susanne Csader was born in Germany and studied pharmacy at the University of Greifswald. After her second “Staatsexamen”, she gained a postgraduate diploma in pharmacy in the field of clinical pharmacology about transporter proteins at the University of Greifswald. After she gained her license to practise she worked for 1 ½ year as pharmacist. Owing to her high interest in clinical research and especially in Non-alcoholic fatty liver disease (NAFLD), she decided to go back to research and works as a PhD student at University of Eastern Finland (UEF), Kuopio campus, since January 2019.
Susanne's project is “a randomised controlled exercise intervention study in subjects with NAFLD”. She will investigate the effects of high-intensity aerobic interval training in comparison to a sedentary lifestyle. The aim of this study is to find out a link between exercise and the gut-liver axis regarding the stage of liver adiposity and define exercise-responsive gut microbiome in NAFLD patients.

Research domain: Physiology & biochemistry

WP2: Human cohorts and mice models

University of Eastern Finland (UEF)

Institute of Public Health and Clinical Nutrition

susanne.csader@uef.fi


ESR 4: Johnson Lok

Coming from Hong Kong, Johnson obtained his Bachelor of Science degree majoring in biochemistry in 2017 and Master of Science degree in the field of Food Safety and Toxicology in 2018 at the University of Hong Kong. His Master’s thesis was on “Understanding the Mechanisms of the Protective Effect of Schisandrin A and B on Alcohol-Induced Toxicity on Liver Cells”. Currently, he is working as an Early Stage Researcher on the BestTreat project at the University of Eastern Finland under the supervision of Professor Hani El-Nezami.
The title of his project is the metagenomic and metabolomics analysis of microbiota intervention therapies of non-alcoholic fatty liver disease (NADFL) in vivo models. He will look at the influence NAFLD-related hormones have on NAFLD progression. And will study the therapeutic effect of exercise and bacterial strains.

Research domain: Physiology & biochemistry

WP2: Human cohorts and mice models

University of Eastern Finland (UEF)

Institute of Public Health and Clinical Nutrition

johnson.lok@uef.fi


ESR 5: Valeria Iannone

Valeria is from Italy where she obtained a Bachelor of Science in Medical and Pharmaceutical Biotechnology at University Vita-Salute San Raffaele, Milan (Italy) in 2015. At the same University she completed the Master degree in Molecular, Cellular and Medical Biotechnology in 2017. Her thesis project, performed at the Viral Evolution and Transmission Unit of San Raffaele Hospital under the supervision of Doctor Gabriella Scarlatti, focused on the effect of seminal plasma on human colonic mucosa and its possible role in modulating HIV infection. She completed her training as Post Graduated Student for one year on the same project.
Since 2019 she is PhD student and works at the BestTreat project on Mechanisms relating gastrointestinal microbiota with liver and adipose tissue metabolism and inflammation in the development of Non-alcoholic Fatty Liver Disease, under the supervision of Professor Marjukka Kolehmainen at Institute of Public Health and Clinical Nutrition, University of Eastern Finland, Kuopio (Finland).

Research domain: Physiology & biochemistry

WP3: Mechanistic studies of microbiome-host interactions

University of Eastern Finland (UEF)

Institute of Public Health and Clinical Nutrition

valeria.iannone@uef.fi


ESR 6: Ambrin Farizah Babu

Ambrin is originally from India where she studied Biotechnology at Sathyabama University, India, and graduated with honours as the topper of her batch. Briefly after her Bachelors, she moved to Switzerland and earned her Masters in Molecular Life Sciences from the University of Lausanne. She is very keen on the study of microbes, and their interactions in natural communities. As part of her Master thesis, she worked on the microbial degradation of antibiotics at low concentrations and was involved in the development of a novel artificial neural network method for biomass estimation.
Currently, she is a PhD student under the BestTreat project and is working on the functional characterisation of the gut microbiome and microbiome-host interaction. Based at Afekta, her work is mainly focussed on metabolomics and omics-data integration.

Research domain: Computational & systems biology

WP4: Big data analysis of the gut microbiome


ESR 7: Manos Nychas

Manos was born in Greece where he obtained his Bachelor’s degree in Biochemistry and Biotechnology from the University of Thessaly in Greece. He continued his studies at Cranfield University in the United Kingdom in the Applied Bioinformatics Master programme. During this time, he worked on the development of a web based application for NGS data visualisation using circus plots. For his Master’s thesis he developed a Cytoscape plugin for transcription factor enrichment analysis using RNA-Seq data.
Manos now works in the Systems Biology and Bioinformatics group in Hans Knöll Institute in Jena (Germany) being enrolled at the Friedrich Schiller University (Germany).His project is the analysis of meta-omic datasets from human subjects and mice models with the aim to integrate metagenomic, metatranscriptomic and metabolomic data in novel ways for modelling the association of microbial communities and metabolic disease state.

Research domain: Computational & systems biology

WP4: Big data analysis of the gut microbiome

Hans Knöll Institute (HKI)

Systems Biology and Bioinformatics Group

Emmanouil.Nychas@leibniz-hki.de


ESR 8: Howell Leung

Howell moved from his native Hong Kong to Canada where he received his Bachelor’s degree in Honours Science with minors in Biology and Computer Science, from the University of Waterloo, Canada. He then worked in a biotechnology company in Hong Kong, performing toxicity tests with transgenic fish embryos, developing computational tools to analyse experimental data and procedure automation to increase productivity of the laboratory workflow. After 3 years of working, he decided to continue his study enroling in the Genomics and Bioinformatics Master’s program at the Chinese University of Hong Kong, Hong Kong. During his Master’s program he worked on identifying new breast cancer sub-types based on lncRNA expression.
He is currently working on developing a machine-learning framework for identifying bacterial gene clusters critical for the elimination of disease related microbes in gut microbiome at Hans Knöll Institute (Germany) and is enrolled at the Friedrich Schiller University, Jena (Germany).

Research domain: Computational & systems biology

WP4: Big data analysis of the gut microbiome

Hans Knöll Institute (HKI)

Systems Biology and Bioinformatics Group

howell.leung@leibniz-hki.de


ESR 9: Sara Leal Siliceo

Sara is from Spain. Her background is in the field of bioinformatics. She received her Bachelor Degree in Biomedical Engineering with specialisation in Bioengineering from the Polytechnic University of Madrid (UPM). Then, she studied a Master Degree in Bioinformatics and Computational Biology at Autonomous University of Madrid (UAM). During her master, she completed a Swiss-European Mobility Programme (SEMP) internship at Haute Ecole d'Ingénierie et de Gestion du Canton de Vaud in the Computational Intelligence for Computational Biology Group, where she did her master thesis on a project that combined next-generation sequencing, bioinformatics and machine learning as tools to diagnose the quality of soils.
Now, Sara is working at the BestTreat project in the Hans Knöll Institute (Germany) and is PhD student at Friedrich-Schiller-University Jena (Germany). Sara's project is Phages as predators for disease-related bacterial strains. The objective of this project is to develop a computational pipeline for identifying phages in metagenomic data for targeted microbiome manipulation.

Research domain: Computational & systems biology

WP4: Big data analysis of the gut microbiome

Hans Knöll Institute (HKI)

Systems Biology and Bioinformatics Group

sara.lealsiliceo@leibniz-hki.de


ESR 10: Dennis Pohl

Dennis is from Germany. He holds a Master’s degree in Bioinformatics from the University of Tübingen (Germany). For his master thesis he studied if changes in replication rates are correlated to antibiotic administration and whether it provides additional biological insights by estimating bacterial replication rates from microbiome sequencing data. Before this he received a bachelor’s degree in Applied Biology from the University of Applied Sciences Bonn-Rhein-Sieg (Germany). He conducted his bachelor’s thesis at the University of Bonn (Germany) where he evaluated AHRD, a tool which automatically assigns human-readable descriptions to protein sequences.
His objectives in the BestTreat program are to identify keystone species in the human gut microbiome that are critical for the systems diversity, stability or human health. He will develop a framework for estimating microbial persistence / colonisation probabilities and will study the association of the gut microbiome to non-alcoholic fatty liver disease (NAFLD). He works at Clinical Microbiomics in Denmark, a contract research organisation focusing on microbiome research, and is affiliated with the Technical University of Denmark (DTU).

Research domain: Computational & systems biology

WP4: Big data analysis of the gut microbiome

Clinical-Microbiomics (CLIM)

pohl@clinical-microbiomics.com


ESR 11: Jérémy Armetta

Born in France, Jérémy trained in microbiology and molecular biology at different research institutes such as INRA, CNRS or French Army Biomedical Research Institute. In 2018, Jeremy graduated in Systems and Synthetic biology from Paris-Saclay University after completing his Master thesis at the Technical University of Denmark under the supervision of Prof. Morten Sommer. He there specialised in applying synthetic biology tools to study and engineer the gut microbiome using In-vivo Flow-sequencing to assess and predict the behaviour of core regulatory elements from mouse gut microbiome.
Jérémy currently works as a PhD student on innovative methods to find and selectively isolate new probiotic strains displaying notable features. This could provide efficient tools to treat diseases linked to the gut microbiome like NASH and NAFLD, either by finding the appropriate probiotic strain to harness for its native capabilities, or by designing new chassis strains to engineer advanced microbial therapeutics.

Research domain: Microbiology & bioengineering

WP5: Phenotyping, engineering & characterization

Technical University of Denmark (DTU)

DTU Biosustain / Bacterial Synthetic Biology

jerarm@biosustain.dtu.dk


ESR 12: Karl Alex Hedin

Alex is from Sweden where he obtained his Bachelor’s and Master’s degrees in Biotechnology at Chalmers University of Technology (Sweden). For his master’s program, he chose courses with a strong focus in systems biology, where he expanded his knowledge in genome-scale metabolic models, omics technologies and bioinformatics. During his master’s thesis in Professor Jens Nielsen’s lab, his work was laboratory oriented and focused on synthetic biology and metabolic engineering. The title of his thesis was “Development of a Growth-sensitive Malonyl-CoA Platform Strain”, where he developed a novel technique to increase the supply of the highly relevant precursor malonyl-CoA.
Currently, Alex is PhD student in Professor Morten Sommer’s lab at the Technical University of Denmark, working with designing novel microbial therapeutics against human diseases through human gut microbiome engineering.

Research domain: Microbiology & bioengineering

WP5: Phenotyping, engineering & characterization

Technical University of Denmark (DTU)

DTU Biosustain / Bacterial Synthetic Biology


ESR 13: Victoria Fernández Cantos

Originally from Spain Victoria received her Bachelor’s degree in Biology in 2017 from the University of Granada (Spain). During her Bachelor she spent 7 months at the Wilhelms-Universität Münster (Germany), where she had the opportunity to get expertise in different topics such as evolutionary medicine and nanotechnology. Back in Granada, she finished her Master’s degree in Biotechnology in 2018. For her Bachelor and Master’s thesis, she joined Prof. Mohamed Merroun’s research group and worked on the interaction between microorganisms and selenium as part of the EU project “Microbiology In Nuclear waste Disposal (MIND)”.
Currently, Victoria is working as a PhD student at the University of Groningen (The Netherlands). She focuses on the identification of potential antimicrobials against undesirable gut bacterial strains related to Non-Alcoholic Fatty Liver Disease (NAFLD). These antimicrobials will help on the microbiome modulation and, hence, serve as a potential therapy.

Research domain: Microbiology & bioengineering

WP5: Phenotyping, engineering & characterization

University of Groningen (RUG)

Groningen Biomolecular Sciences and Biotechnology Institute

m.v.fernandez.cantos@rug.nl


ESR 14: Diego García de la Morena

Diego is from Spain. He obtained his bachelor in Biology with a mention in Biotechnology at the University Complutense of Madrid in Spain in 2016. Next, he followed a two-years master in Molecular and Cellular Integrative Biology at the Biological Research Centre of the Spanish National Research Council (CIB - CSIC) and International University Menéndez Pelayo (UIMP) in Spain. During his studies he has collaborated with two research laboratories specialised in molecular biology, microbiology, genetic and metabolic engineering.
Currently, he is enrolled as a PhD student at the University of Groningen in The Netherlands. There, at the department of Molecular Genetics, he is studying the interplay between non-alcoholic fatty liver disease (NAFLD) and the gut microbiota. Particularly, he is involved in the engineering of microbial strains aiming at modifying our gut microbiota and, therefore, influence either the onset and/or the progression of the disease.

Research domain: Microbiology & bioengineering

WP5: Phenotyping, engineering & characterization

University of Groningen (RUG)

Groningen Biomolecular Sciences and Biotechnology Institute

d.garcia.de.la.morena@rug.nl


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