WG4 Leader and Member of the STSM Commission for CA18131. Researcher (molecular biologist and bioinformatician) at the CNR Institute for Biomedical Technologies with research interest in human gut microbiome and nutrition and their relationship with human health and diseases.
WG1 & WG3
STSM coordinator for CA18131 Associate professor at Faculty of Technical Sciences, University of Novi Sad. Interests in CA18131: Performance evaluation of different machine learning methods on microbiome data. Evaluation of supervised, unsupervised and semi-supervised approaches.
WG1 & WG4
I hold a BSc in Physics (1996) and PhD (2004) in Biological Sciences from the National and Kapodistrian University of Athens. My main field of research is computational biology and bioinformatics; interested in microbiome analysis and in machine learning in bioinformatics.
WG2 & WG3
MC for CA18131 & Professor at University of Agricultural Sciences and Veterinary Medicine of Cluj-Napoca, Romania, Life Sciences Institutes Cluj, Head of Molecular Nutrition (Gen&Proteomics) Lab https://erris.gov.ro/Molecular-Nutrition-and-omics ProBone Project (marine microbiome), Interested in integration of metagenomics, metaproteomics and metametabolomics data in microbiome assessment; interested in the preterm newborn gut microbiome and link with ADHD, autism, NIC/ microbiome food modulation/interaction.
Professor at Faculty of Computer Science and Engineering, “Ss. Cyril and Methodius” University in Skopje, R.N. Macedonia. Main research focus: Connected Health.
Prof. Vladimir Trajkovik, PhD has participated in more than 60 national and international ICT projects related to providing novel ICT-based services. He has coordinated 27 of those projects. He is a co-founder or partner in four ICT companies, has done management consultancy in five ICT companies and has been mentor of nine ICT companies in the last 15 years. He is a co-founder of two NGOs that promote digital education and the usage of ICT in education. He has organized or participated as an invited lecturer, mentor or judge in more than 60 events related to the promotion of novel ICT services, Education and Entrepreneurship in the last 5 years.
WG2 & WG3
Alberto Tonda received his Ph.D. degree in Computer Science Engineering from Politecnico di Torino, Italy, in 2011. Currently, he is a permanent Researcher (CRCN) at Université Paris-Saclay and the National Institute of Agronomic Research (INRA), France. His research interests include semi-supervised modeling of complex systems, evolutionary optimization and machine learning, with main applications in food science and biology. He is currently chair of COST Action CA15118 FoodMC, a 4-year European networking project on in-silico modelling in food science.
WG2 & WG4
Head of the Infectious Diseases, Microbiota and Metabolism Unit at the Center for Biomedical Research of La Rioja (CIBIR) and Hospital San Pedro. Interested in the study of intestinal microbiota in different pathologies; specially in infectious diseases, such as HIV infection or Hepatitis C virus infection, but also in other disorders whose origin is still unknown such as Chronic Fatigue Syndrome, Multiple Sclerosis or Obesity. The role of current treatments for these pathologies on the intestinal bacterial and virome composition is also of interest.
We are looking for collaborations in the field of virome.
WG2 & WG3
Michelangelo Ceci Ph.D., is an associate professor at the Dept. of Computer Science, University of Bari, Italy. His research interests are in data mining and machine learning. He has published more than 170 papers in reviewed journals and conferences. He has been the unit coordinator of EU and national projects. He has been in the Program Committee of many conferences, including: IEEE ICDM, SIGKDD, AAAI, IJCAI, ECML-PKDD, SIAM SDM, DS and ISMIS. He is in the editorial board of DMKD, MLJ, JIIS, IJDSN, IJSNM and ``Intelligenza Artificiale''. He was program (co-)Chair of SEBD2007, Discovery Science 2016, ECML-PKDD2017, ISMIS 2018 and General Chair of ECML-PKDD2017.
Researcher at Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, Portugal. I am interested in the development of computational tools based on data mining and machine learning to extract meaningful information from high-dimensional biomedical data.
Aldert Zomer is an Assistant Professor at the Faculty of Veterinary Medicine of Utrecht University. He focuses on analysis of bacterial metagenomes for comparative genomics, molecular epidemiology and linking bacterial genotype to phenotype. Furthermore he is staff member of the WHO-Collaborating Center for Campylobacter, WHO consultant on genomics for antimicrobial resistance detection and bioinformatics consultant for Janssen Pharmaceuticals on bacterial vaccine development.
WG1 & WG3
Full professor at the Faculty of Computer Science and Engineering in Skopje. Head of the Intelligent Systems institute at FCSE, working in the Machine learning group. Coordinator of several European projects. Interested in developing data driven Intelligent systems, Bioinformatics and Microbiome, the brain-gut connection.
I am interested in hosting STSM applicants.
Prof. Victor Moreno is a cancer epidemiologist with expertise in biostatistics and bioinformatics. His main line of research is about the interaction and causality between colorectal cancer (CRC, 3rd most common cancer in the world) and intestinal and oral microbiome. Prof. Victor Moreno and his team are studying in detail these interactions to identify new biomarkers of diagnosis, prediction of progression, prognosis and response to chemotherapy in colorectal cancer. Additionally, the genetic polymorphism, metabolism and lifestyle of patients are included in the analysis.
I am a senior researcher at the Cellular and Molecular Endocrinology Unit, Biomedical research Institute of Málaga (IBIMA). I am interested in the role of gut microbiome in metabolic diseases, especially Obesity. We study different strategies to fight obesity changing gut microbiome: diet (MedDiet, KetoDiet, Intermittent fasting), drugs, FMTs, bariatric surgery. As a translational researcher, I am interested in friendly tools to apply ML techniques in my microbiome data, to search for biomarkers and feature targets.
Bosnia and Herzegovina
WG1 & WG3
Professor at the Faculty of Electrical Engineering Sarajevo - PhD studies, covering field of Artificial Intelligence and Bioinformatics. I worked for 20 years as a researcher in development of algorithms for ship systems control. At the Faculty of Electrical Engineering, I founded the research group for the Artificial Intelligence, Bioinformatics & Biomedical Engineering in 2007. In addition to many grants (WUS, DAAD, SOROS and UNESCO), in 2001 I was awarded the Fulbright scholarship for research: Applying Genetic Algorithms I Control Engineering.
Focus of my latest research is on fusion of artificial intelligence methods into:
1) biomarker discovering based on microarray gene expression profiling and
2) microscopy plant nucleus and cells image processing.
I am interested in cooperation and writing scientific papers for publications.
Wolfram Brück studied microbiology at St. Cloud State University in Minnesota, USA before pursuing a M.Sc. in medical and molecular microbiology at the University of Manchester, UK. In 2003, he finished his Ph.D. at the University of Reading, UK in the laboratory of Prof. Glenn Gibson on the influence of prebiotic milk peptides on infant health. Throughout his professional career, Wolfram Brück has developed a strong international perspective in food and health microbiology and biotechnology through academic and industrial posts in Denmark, USA, Ireland, the UK and Switzerland. His primary research interests is the modulation of the infant gut microbiota with focus on the following questions:
1. What are the intrinsic and extrinsic factors that influence speed of progression through colonization stages at different points? How do they interact?
2. How factors such as delivery mode and maternal microbiome affect rate of progression? What are the consequences for future health (metabolic disorders, protection from invasion and infection)?
3. Is it beneficial to progress through some stages fast and others more slowly?
4. How is the progression of gut re-colonization after disruption by diarrheal pathogens? 5. Is bacterial infection promoted by gut dysbiosis / altered colonization profiles?
WG1 & WG3
I am the head of the Computational Biology Group at IMDEA Food Institute. Our group aims to develop and apply integrative bioinformatic analyses to study complex molecular relationships between nutrition and chronic diseases. This will allow us to develop precision nutrition strategies to complement patient oriented treatments based on individual molecular background. Our research is focused on:
1.The study of the nutrition-disease interaction through epigenetics, transcriptional and interindividual variability.
2.The study of the relationships between microbiome and epithelial cells and its potential as a modular system through nutrition for the prevention and treatment of complex diseases.
3.The development of bioinformatic tools to integrate large genomic, epigenomic and clinical datasets.
The group is active in the TransBioNet network associated to the Spanish National Bioinformatic Institute, Food Nutrition and Security Cloud project and COST Action CA18131 (“Statistical and machine learning techniques in human microbiome studies”). The group members participate in innovation and education activities of EIT Food for future food entrepreneurs. I am interested in hosting STSM applicants I am interested in participate in European innititatives.
WG1 & WG3
1995 Diploma Biology University of Heidelberg, Germany 1995 – 2007 German Cancer Research Center Heidelberg (DKFZ) PhD Student, PostDoc/Researcher, Deputy Department Head 2002 PhD (Dr. sc. hum.) from the Medical Faculty Heidelberg 2007 Professor for Molecular Biology at Technical University of Wildau Germany Foundation of the Division Molecular Biotechnology and Functional Genomics since 2012 Research Professor The department works in various fields of applied research in biomedicine/pharma, food/agriculture and environment. We follow the mission and vision “Add application to academia and innovation to industry.” Insofar we work at the crosspoint with other universities/institutes and commercial partners. An important aspect is also the transfer enabled with patenting, StartUp foundations and standardisation and citizen science.
We operate several NGS-sequencers in the department and analyse several hundred microbiomes per week with our StartUp BIOMES. The department works in various aspekts of genomics, functional genomics and bioanalytics mainly with the aim to develop new technologies. In parallel to NGS we operate MALDI-TOF MS for bacteria identification. Since the division has also some competence in bioinformatics we started recently a project aiming at the development of deep learning algorithms for microbiome analysis. For various techniques we particpated in standardisation activities with industry and academic partners. We have experience in ISO-standardisation and participate in an international project on the harmonisation of standardisation in systems biology. We mainly approach these aspects from the wet-lab side.
The University of Aarhus currently has two major research projects (one in collaboration with the University of Copenhagen) are running, dealing with microbiome research and the use of FMT treatment for incurable diseases. I am a partner in one of the projects where I lead a work package focusing on fundraising, networking and dissemination. Both projects are funded by the Danish Innovation Fund. We have recently sought funding from the Novo Nordisk Foundation to hold for the first time ever in Denmark a large international conference on microbiome research and FMT. I want to anchor the two Danish projects in this Cost Action and to uncover opportunities to integrate the Danish research activities into a European context. In addition, the keys to statistical and machine learning techniques will certainly open up some unprecedented opportunities for Danish research. I am leading fundraising activities at AU and have been involved in attracting more than 65 M EUR. Danish, Nordic and H2020 sources.
Group leader at the University of Ljubljana, Slovenia (Biotechnical Faculty; Faculty of Civil and Geodetic Engineering) and Jozef Stefan Institute (Department for Automation, Biocybernetics and Robotics), interested in microbiome research, focusing on the systemic view of the human, plant and environmental microbiomes: metagenomics, metabolomics, environmental metadata.
Christian Jansen is the leader of ML4Microbiome WG3 from July 2022 onwards as well as the lead bioinformatician and data scientist at Biome Diagnostics GmbH. His responsibilities in the company are the development of bioinformatic pipelines, as well as microbiome-based biomarkers using diverse machine learning techniques. The main focus of Biome Diagnostics GmbH is the development of microbiome-based solutions for immune checkpoint inhibitor (ICI) cancer therapy, colorectal cancer (CRC) and faecal microbiota transplants (FMT).
We are looking for collaboration partners in clinical studies and other research projects, in particular in the Fields of ICI, CRC and FMT.
WG3 & WG4
Assistant professor in biostatistics at the Department of Biology, University of Tirana, Albania, working on statistical and machine learning modelling of biological and health data. Her current project is focused on the role of the microbiome in colorectal cancer. She is also interested in and works on statistical modelling for conservation biology.
Assoc. Prof. Dr Onder Aydemir graduated from Electrical-Electronics Engineering Department at Karadeniz Technical University (KTU) with a B.Sc. degree in 2005 and from Electrical-Electronics Engineering Department at KTU University with M.Sc. degree in 2008. I completed my PhD degree in Electrical and Electronic Engineering at KTU in 2013. I completed my post-doctoral degree in the Department of Electrical and Computer Engineering at the Medical University of Vienna between the years 2014-2015. In my post-doctoral work, I explored whether probabilistic models of the microstructure of sleep reveal more information about the subjectively experienced quality of sleep than the traditional macrostructure based on sleep stages. I am now working as Assoc. Professor in the Electrical and Electronic Engineering Department, Engineering of Faculty, Karadeniz Technical University.
Alper Ozcan is currently an Assistant Professor of Computer Engineering in the Department of Computer Engineering at Akdeniz University. He is teaching undergraduate and graduate-level courses. Dr Alper Ozcan received an M.S. and PhD in Computer Engineering from Istanbul Technical University, Istanbul, Turkey. Dr Alper Ozcan's research interests are data mining and deep learning. In these fields, he is a reviewer and co-author of various publications in prestigious journals and conferences.
Prof. Malik Y. Yousef is a data scientist, with a focus on bioinformatics with applications to various biomedical/biological problems. He has published more than 60 peer‐reviewed articles in top journals and proceedings with over 3700 citations and an H-index of 23 and i10-index of 33 (based on Google scholar). His international experience includes 3 years as a postdoc at The Wistar Institute, Cancer Center, USA [Prof Louise Showe Cancer Biology lab] and one year at the University of Pennsylvania [UPENN-Bioinformatics Center]. Currently, he is an Associate Professor at the Zefat Academic College in Israel and Pranab K. Sen Distinguished Visiting Professor at the University of North Carolina at Chapel Hill in the Department of Biostatistics at the Gillings School of Global Public Health.
Recently he has developed, along with his team, a machine learning tool named MicroBiomeNet based on pre-existing biological knowledge about the association of the features and their taxonomic features at different levels, such as genus, species, and order.
Erik Bongcam-Rudloff is a Professor of Bioinformatics and the head of the Swedish University of Agricultural Sciences (SLU).
Prof. Bongcam-Rudloff’s work concerns bioinformatics, the analysis of large amounts of biological and genetic data. His research mainly deals with the development of bioinformatics solutions for the life sciences community. Prof. Bongcam-Rudloff’s applications are found within research areas such as animal breeding, computing in mathematics, natural science, engineering and medicine. He develops and manages complex multidisciplinary network projects both in and outside Europe. Prof.Bongcam-Rudloff has coordinated EU and National projects like the EU-Horizon2020 B3Africa project and the EU COST project SeqAhead: “Next Generation Sequencing Data Analysis Network”.
ML4MICROBIOME ECI MEMBERS
WG2 & WG3
Assistant Professor at the University of Bari Aldo Moro (Italy). Research interests: Data Mining and Knowledge Discovery, Bioinformatics, Social Network Analysis, Clustering/Co-Clustering and Multi-relational Data Mining, Big Data Analytics. Read Gianvito's post below.
WG2 & WG3
I’m a group leader and ERA Chair holder in Synthetic Biology at the University of Tartu, Estonia. In my research I study yeasts, next generation probiotics and other consortia using integrative data analysis (transcriptome, proteome, fluxome) and modeling to gain insights into the fundamentals of cellular metabolism and consortia behaviour.
WG1 & WG3
Sonia Tarazona has a PhD in Statistics and Optimization and works as Full Time Lecturer at the Universitat Politècnica de València. She has developed her research in the bioinformatics field for more than 10 years, mainly in transcriptomics and multi-omics integration.
MC member for CA18131 & professor at the Faculty of Natural Sciences, University of Tirana. Interested in mathematical models through Monte-Carlo simulations and complex network analysis.
I am interested in using spectral properties for the analysis of complex networks. Interested in research collaborations.
PhD student and researcher at Institute of Public Health of the University of Porto (ISPUP). Interested in the human (skin, gut) microbiome (bacteria) in asthma and also in the effect of environment in microbiome.
I am interested in hosting STSM applicants I am looking for new partnerships in future microbiome projects and also for a future postdoctoral job.
Bioinformatics Analyst and Team Lead at SevenBridges Belgrade office, Serbia, with long academic experience at University of Belgrade. Holds PhD in Computer Science. Designing and developing workflows for processing NGS data related to microbiome on cloud-based infrastructure.
WG2, WG3 & WG4
Postdoctoral researcher at the Laboratory of Human Genetics, Erasmus Medical Center University, Rotterdam, The Netherlands. Interested in genetics and -omics research of the musculoskeletal system with emphasis in genome-wide association studies and microbiome effect.
WG1 & WG4
Chief Scientist in Institute for Digestive Research, Lithuanian University of Health Sciences. (Kaunas, Lithuania) Involved in microbiome research of malignant and premalignant gastrointestinal diseases, gut microbiome modification and functional microbiome studies.
Invited Assistant Professor at NOVA Medical School│Faculdade de Ciências Médicas, Universidade NOVA de Lisboa and CINTESIS - Center for Health Technology and Services Research. MC Substitute for CA18131. Interested in clinical studies to evaluate the impact of dietary components on the modulation of human gut microbiota.
Interested in the development of new microbiota-based therapeutic strategies.
Bioinformatics Research Unit Leader at the Riga Stradins University (RSU) in Latvia. Interested in multi-omics data such as genome, transcriptome, and (gut) microbiome analysis and integration for personalized health care, mainly related to nutrition, oncology and cariology.
I am looking for Bsc, Msc, PhD students and Post-Docs in bioinformatics.
Bosnia and Herzegovina
Assist. Prof. Dr. Kanita Karađuzović-Hadžiabdic, received her PhD from International University of Sarajevo, BiH in 2016. In 2001 she obtained her Master degree at Oxford University. From 2017 Dr. Kanita Karađuzović-Hadžiabdic is working as Assistant Professor and Program coordinator of Computer Sciences and Engineering (CSE) study program at the International University of Sarajevo. Her research interests include applications of machine learning and computational photography (i.e. high dynamic range imaging).
WG2 & WG4
I lead the darkDNA team (http://darkdna.gr) at the Genetics Laboratory, Biotechnology Dept at the Agricultural University of Athens. Our research interests revolve around three distinct, yet intersecting, areas: i) The functional role of long non-coding RNAs, ii) Stress mechanisms and homeostasis via nuclear receptors & iii) Microbiome (Human and Agricultural Approaches). In our lab we use a wide spectrum of methodologies ranging from state-of-the-art bioinformatics, molecular modelling and hypercomputing pipelines to traditional genetic and biochemistry in vitro and in vivo techniques. On one hand, we have developed our own software for machine learning, deep learning and data mining for multimodal fusion of information from genetic, structural and physicochemical analyses. On the other hand, we use DNA engineering, SDM, cloning, expression and protein purification techniques to biologically test and evaluate the validity and reliability of our models.
I am interested in hosting STSM applicants.