Université Catholique de Louvain, Belgium
Spiros N. Agathos is Professor Emeritus and Invited Research Professor at the Catholic University of Louvain, Belgium. He served as the Rector and President of the Governing Board of Yachay Tech University, the first research-intensive university in Ecuador and the Andean Region of South America (2019) and as the Inaugural Dean of Biological Sciences and Engineering at Yachay Tech (2015-2019). Before that he was Professor (1993-2015) and Chair of Bioengineering (1998-2010) at the Catholic University of Louvain. He obtained his Diploma in Chemical Engineering from the National Technical University of Athens, his Master’s in the same field from McGill University, and his Ph.D. in Biochemical Engineering from the Massachusetts Institute of Technology (MIT). Professor Agathos was a faculty member at the University of Western Ontario in Canada (1982- 1985) and at Rutgers University in the United States (1985-1993) and has served as a visiting professor in Europe and the Americas. He has published over 200 articles, 5 books and 4 patents. He has received more than 70 competitive grants, is Editor or Editorial Board member of many journals and serves as chair or member of grant panels as well as on international committees for science and technology policy and for institutional accreditation. He is advising governments, agencies, transnational bodies and industry, while his former students and postdocs have significant academic and industrial positions across the globe. Among his many awards, he is an elected Fellow of the American Academy of Microbiology (AAM), the International Water Association (IWA), the American Institute for Medical & Biological Engineering (AIMBE) and the Society for Industrial Microbiology & Biotechnology (SIMB). He is the recipient of the 2019 Waksman Outstanding Teaching Award for his role as mentor and educator. His research interests include fungal, insect and mammalian cell cultures in bioreactors, biocatalyst development, bioprocess optimization, bioreactor design and scale-up, pollutant biodegradation and site bioremediation, microbial ecogenomics, and biotechnology for sustainability.
Technion Israel Institute of Technology, Israel
1993-1998 : Ph. D. degree - Dept. of Biological Chemistry, The Weizmann Institute of Science, Rehovot, Israel.
Thesis title: “Structure and function of Multidrug Resistance protein expressed in Escherichia coli”.
Advisor: Prof. E. Bibi.
1991-1993 : M. Sc. degree - Dept. of Membrane Research and Biophysics, The Weizmann Institute of Science, Rehovot, Israel.
Thesis title: “Protein translocation machinery of the Trypanosomatids”.
Advisor: Prof. S. Michaeli.
1987-1990 : B. Sc. degree with distinction. - Faculty of Agricultural,Food & Environmental Quality Sciences, The Hebrew University of Jerusalem, Israel.
2010 (May)-present Professor, Technion -Israel Institute of Technology, Israel.
2006 (June)-2010 Associate Professor, Technion -Israel Institute of Technology, Israel.
2001-2006 Assistant Professor, Technion -Israel Institute of Technology, Israel.
1998-2001 Postdoctoral fellow (in Prof. Ed DeLong’s lab), Monterey Bay Aquarium Research Institute (MBARI), California, USA.
Microbiology & Virology (undergraduate)
Biology 1 (undergraduate)
Biology 1 for Engineers (undergraduate)
Genetic Engineering lab (undergraduate)
Microbial Ecology (graduate)
Marine Microbiology (IUI, graduate)
1988-2000 EMBO Long Term Fellowship.
2002 New Investigator Award, American Society for Photobiology.
2003 EMBO Young Investigator Award (EMBO-YIP 2003).
2005 The Moshe Shilo Prize, Israel Society for Microbiology.
2007 The Henry Taub Prize, Technion- Israel Institute of Technology.
2008 The Gutwirth Award, Technion-Israel Institute of Technology.
2010 The Ulitzki Prize, Israel Society for Microbiology.
2012 Member of The European Academy of Microbiology (EAM).
2013 F1000 Faculty Member of the Year 2012 in Microbiology.
2014 Louis and Lyra Richmond Chair in Life Sciences
2019 The Henry Taub Prize for Academic Excellence, Technion-Israel Institute of Technology.
Membership in professional societies
International Society for Microbial Ecology Israel Society for Microbiology
Senior Research Scientist, Directeur de Recherche INRA, France
2016/1 – INRAE Senior Research Scientist and group leader, Fungal Biodiversity and Biotechnology, Marseille
2012 – 2015 INRAE First class Research Scientist, Fungal Biodiversity and Biotechnology, Marseille
2008/7 - 2012 INRAE Research scientist, Fungal Biodiversity and Biotechnology, Marseille
Academic and Training Background
2007-2008 Post-doctoral research, CNRS, Marseille, France. Topic: Hydrogen production using biomimetic approaches; Advisor: Dr. M. Reglier
2005-2006 Post-doctoral research, Aix Marseille University, Marseille, France. Topic: Carbohydrate enzymology; Advisor: Dr. Nathalie Juge
2003-2004 Post-doctoral research, CEA, Saint Paul Lez Durance, France. Topic: Plant redox enzymes; Advisor: Dr. A. Vermeglio
2000-2002 Ph.D.: University of East Anglia, Institute of Food Research (IFR), Norwich, U.K. Topic: Carbohydrate enzymology; Advisor: Prof. G. Williamson.
Selected Accomplishments and Honours
2014 Laureate of the foundation Amidex for excellence and innovation, Aix Marseille, University, Marseille, France
2012 Award from INRAE division for scientific excellence
Research coordination activities
2013-2017 Coordinator of the collaborative ANR project Funlock.
2014-2016 Coordinator of the collaborative AMIDEX project FUNCOPPER
2012- Coordinator of the priority programme “Biorefinery of Lignocellulose” of the INRAE division CEPIA (Organization of annual workshops and supervision of internal project calls).
2013/2019 Session chair at the Gordon Research Conference on Cellulases, Cellulosomes, and Other Carbohydrate Modifying Enzymes
2018 – Member, Editorial Board, Biotechnology for Biofuels
2014 – Member, Editorial Board, PLOS One
2014 – Member, Editorial Board, Fungal Biology and Biotechnology
2008-2016 Invited speaker at 3 Gordon Research Conferences, plus ca. 10 others
Peer-Reviewed Publications and patents
As of May 2021, I have published over 95 peer-reviewed articles (Biotech. for Biofuels, Nature Chem. Biol., Nature comm., J. Biol. Chem., …), reviews, and book chapters (>5300 cumulative citations, H-index = 40) and filled 13 patents in the field of carbohydrate enzymology applied to biomass conversion.
University of Padova, Italy
Current position: Associate professor of molecular biology (BIO/11) at the Biology department (University of Padova).
Bibliometric parameters: (orcid 0000-0002-9431-1648) peer-reviewed articles 102; total citations, approx. 5793; h-index, 28.
Area of expertise.
[i] Microbial genomics and metagenomics of food and resource recovery through the anaerobic digestion process;
[ii] gene expression analysis (RNA-seq) of microbial species including for example Saccharomyces cerevisiae, lactic acid bacteria, archaea (Methanococcoides butonii);
[iii] development of software and pipelines for metagenomics (genome-centric metagenomics) and transcriptome analysis.
Institutional responsibilities – Commission of trust.
Director of the Interdepartmental Center for Biotechnologies (CRIBI, UniPD).
Member of the “Frontiers Community” as Review Editor in the journal “Frontiers in Microbiology” (IF 4.2) (January 2018-present).
Guest editor in the special issue “Microorganisms with Probiotic Properties” (Foods - IF 4.1);
Guest editor in the special issue “The complex anaerobic community in wastewater treatment plants and bioreactors” Frontiers in Microbiology (IF – 4.2).
Research in Foreign Institutions.
Invited visting fellow at the UNSW (Sydney, Australia) (2008); from 2014 to 2019 invited as research collaborator in the Bioenergy Group directed by Irini Angelidaki at the Denmark Technical University (five periods for a total of four months).
Coordination/Participation of/to projects.
April 2004-March 2007: Participation to the National research project (FIRB) “Post-genomics of the extremophilic bacterium Photobacterium profundum” granted by MIUR.
March 2009-February 2011: Coordination of the research grant “Genomic characterization, transcriptomics and analysis of the metabolites in Saccharomyces cerevisiae strains of oenological interest” granted by the University of Padova (Italy).
January 2010-December 2012: Participation to the research project “Selection of new grape rootstocks resistant to abiotic stresses through the development and validation of physiological and molecular markers – SERRES”, granted by AGER.
March 2011-February 2014: Participation to the research project “Understanding protein-nucleic-acid interaction networks in cold-adapted archaea” presented as “Discovery-Project” to the Australian Research Council by Prof. Ricardo Cavicchioli (UNSW, Sydney, Australia).
April 2011-March 2013: Participation to the research project “Ankrd2 signaling and gene expression during muscle differentiation” coordinated by Prof. Giorgio Valle (Department of Biology, University of Padova), granted by the University of Padova (Italy).
March 2013 February 2014: Coordinator of the project “Development of new enological starters obtained from autochthonous yeast strains to improve the peculiar characters of the Venetian wines” granted by the Venetian region (Italy) in the framework of the European Social Found.
March 2014-2017: Participation to the strategic research project “Bioinformatics for Personal Genomics – BIOINFOGEN” granted by the University of Padova.
Aug 2018-July 2019: Participation to the project “New strategies for the identification of enological yeasts using genomic and metabolic profiling” granted by the Venetian region (Italy) in the framework of the European Social Found.
January 2019-present: Participation to the research project “Unravelling the Ariadne’s thread into the microbiome of Anaerobic Digestion labyrinth” granted by the “Hellenic Foundation for Research and Innovation”.
October 2020-present: Participation to the research project “Biofermentors: new applications” within the framework of the competitive project supported by Italian MIUR “Development of the innovation in biotechnologies” MIUR ex D.M.738 dd 08/08/19-October 2020.
Research projects with industries and incentives for technology transfer of results.
Founding member of the BMR Genomics spinoff of the University of Padova (http://www.bmr-genomics.it/bmr_it/storia_2010.html). The spinoff raised from the pre-existing DNA sequencing service developed at the Genomics and Bioinformatics research group of CRIBI
(University of Padova).
Funding agreements (2018, 2020) with the company Italiana Biotecnologie for the genome sequencing and bioinformatics variants analysis of S. cerevisiae yeast strain used in winemaking.
Wageningen University, the Netherlands
WORK EXPERIENCE AND EDUCATION
From 11/19 Assistant Professor; Laboratory of Nematology; Wageningen University, the Netherlands
01/18 – 10/19 Junior Group leader and Staff member; Netherland Institute for Ecology (NIOO),
Wageningen, the Netherlands
From 01/18 Guest Researcher; Crowther lab; ETH Zürich, Switzerland
From 11/17 Guest Professor; Nanjing Agricultural University; China
05/17 – 12/17 Post-doctoral fellow; NIOO, Wageningen, the Netherlands
11/16 – 05/17 Post-doctoral fellow; Wageningen University, the Netherlands
04/14 – 10/16 Post-doctoral fellow; NIOO, Wageningen, the Netherlands
04/11 – 03/14 PhD thesis; University of Cologne, Germany (Grade: Summa cum laude)
10/08 – 09/10 Master of Science in Biology; University of Cologne (Grade: Excellent)
01/05 – 07/08 Bachelor of Science in Biology; University of Cologne (Grade: Very good)
• Awardee of a personal VENI grant for 3 years of personal and research funding funded by the Dutch Science
• Published 85 Peer-reviewed papers in international journals (26 first, 16 last, 29 corresponding authorships),
three being highly cited and three highlighted in dedicated articles. 2 book chapters
• Coordinator Dutch top-sector projectinvolving 3 SMEs to characterize and steer soil biodiversity to fight plant
parasitic quarantine nematodes inventorise and Karakterisering en sturing van een zeer gewenst maar
sporadisch bodem fenomeen: biologische onderdrukking van plantparasitaire aaltjes met quarantaine status
• Co-applicant; Application of protozoa as next generation biofertilizer in sustainable agriculture; NWO funded
• Early career award; International society of testate amoeba research (2018)
• Active participation in more than 50 international workshops and conferences, including more than 30 oral,
3 invited and 2 keynote presentations
• Organising and convening 6 sessions at conferences
• Initiator and manager of the Soil Protist Initiative joint with the Global Soil Biodiversity Initiative (GSBI)
• Steering committee member of the global project UniEuk
• Examiner and opponent of 6 PhD theses
• Ad hoc Reviewer for about 50 international journals and 15 funding programmes
• Editor in Chief: European Journal of Soil Biology; Section Editor: Pedobiologa; Editorial Board: Soil Ecology
Letters; Topic & Review editor: Frontiers in Microbiology; Guest editor: Basic and Applied Ecology
• Invited to symposium presentations at 9 Universities
• Participation in professional training courses such as leadership, supervision, presentation, teaching and
• Co-promotor of 2 Postdoc, 5 PhD students, 12 Master thesis and 15 Bachelor students
• Research stays: Nanjing University (2016, 2017, 2019), Hainan and Chongqing University (2016); Natural
history museum London (UK; 2014); INRA Dijon (France; 2013); St. Petersburg State University (Russia; 2012)
• International internships: Lund University (Sweden; 2009), Federal Institute for Hydrology (BfG) (Germany;
2009); Teagasc Research Station (Irland; 2008); Bayer CropScience (Germany; 2007)
Joint Genome Institute, USA
Dr. Kyrpides joined the DOE Joint Genome Institute in 2004 to lead the Genome Biology Program and the development of the data management and comparative analysis platforms for microbial genomes and metagenomes (IMG). He became the Metagenomics Program head in 2010 and leads the Prokaryotic Super Program and the Microbiome Data Science Group since 2011. Prior to joining the DOE Joint Genome Institute, Dr. Kyrpides led the development of the genome analysis and Bioinformatics core at Integrated Genomics Inc. in Chicago, IL. He did his postdoctoral studies with Carl Woese at the University of Illinois at Urbana-Champaign and with Ross Overbeek at the Argonne National Laboratory.
· BA in Biology, Aristotle University of Thessaloniki, Greece;
· PhD in Molecular Biology and Biotechnology, University of Crete, Greece
Awards and Service
Awards: USFCC/J. Roger Porter Award (2018); Honorary Doctorate, Aristotle University of Thessaloniki, Greece (2017); The van Niel International Prize for Studies in Bacterial Systematics (2012-2014); American Academy of Microbiology Fellow (2014); Thomson Reuters Highly Cited Researchers (2014-2017); Academic Excellent Prize Award, Empeirikeion Foundation (2012); Outstanding Performance Award, Lawrence Berkeley National Laboratory (2007)
Administrative Boards: Genomics Standards Consortium. Scientific Advisory Boards: Microbiomes in Transition (MinT), PNNL, EarthCube Oceanography & Geobiology Environmental Omics (ECOGEO) RCN, USA; Biocreative programme, USA; AgreenSkills programme, France; Meta-omics of microbial ecosystems, INRA, France; A Knowledge-Based Bioinformatics Framework for Microbial Pathway Genomics (MICROME), EU; Association for Computing Machinery (ACM) Special Interest Group in Bioinformatics, USA; Metagenomics of the Human Intestinal Tract (MetaHIT), EU; Community Cyber-infrastructure for Advanced Marine Microbial Ecology Research and Analysis (CAMERA), USA. Editorial Board: PeerJ; Environmental Microbiology; BMC Microbiome; Life; Journal of Bacteriology; BMC Standards in Genomic Sciences (SIGS)
Cranfield University , UK
2005-2009 : PhD in Bioinformatics and Systems Biology Cranfield University.
2004-2005 : MSc Bioinformatics, Cranfield University.
1997-2002 : BSc (Hons) - Pharmaceutical Sciences, Cairo University, Egypt.
2011-Present : Bioinformatics Group Leader and Course Director of MSc Applied Bioinformatics.
2019-Present : Reader in Bioinformatics, School Water, Energy and Environment, Cranfield University
2016-2019 : Senior Lecturer in Bioinformatics, School Water, Energy and Environment, Cranfield University
2011-2016 : Lecturer in Bioinformatics, School Water, Energy and Environment (2015-16), School of Engineering (2013-2015) and Cranfield Health School (2011-2013), Cranfield University
2009-2011 : Research Fellow, Cranfield Health - Cranfield University.
2002-2004 : Research Pharmacist, Vacsera Biopharmaceuticals Co., Cairo, Egypt.
I am a Reader in Bioinformatics and Head of Bioinformatics Group at Cranfield University. I have ~14 years of experience in the field, and my research focuses on genome and transcriptome informatics, machine learning, data science, data visualization and cloud technologies. My research mainly focuses on three areas:
1. Next-Generation Sequencing informatics: I am leading the NGS data analysis work at Cranfield University and have been involved in a number of publicly and commercially-funded projects in this research area both as PI and CoI such as “AdRoot” BB/S007970/1, “Nutrishield – H2020/210497548”, “Oats for the future” - BB/P001432/1, “Controlling dormancy and sprouting in potato and onion” - BB/K02065X/, and “Genomics-assisted selection of Solanum chilense introgression lines for enhancing drought resistance in tomatoes” - BB/L011611/11.
2. Machine learning and pattern recognition: I have a long and established track record in the application of machine learning in tandem with rapid and non-invasive techniques for profiling food quality, safety and authentication through major national and international projects such as Nutrishield (H2020/210497548) and DiTECT (H2020/ 861915)- . The advances in this field achieved through my research has been internationally recognized through key publications in the field, keynote talks in a number of high-profile international food conferences.
3. Software Development, data visualisation and cloud computing: My group have developed, and continue to refine and maintain, several standalone and web-based software tools, such as:
i. Vargen (https://github.com/MCorentin/VarGen)
ii. WebCircos (https://github.com/FadyMohareb/webcircos)
iii. Tersect (https://github.com/tomkurowski/tersect)
iv. MapOptics (https://github.com/FadyMohareb/mapoptics)
v. Cramer (https://github.com/-FadyMohareb/cramer)
vi. sorfML (www.sorfml.com).
Hellenic Centre for Marine Research, Greece
Paraskevi N. Polymenakou is Researcher in Environmental Microbiology with specialization in extreme environments at the Institute of Marine Biology, Biotechnology and Aquaculture of the Hellenic Centre for Marine Research. Her research is focused on molecular microbial ecology of extreme environments including submarine volcanoes and hydrothermal vents, on bioprospecting of genomic and metagenomics data and the genomic observation of ecosystems vulnerable to changes. She is the scientific responsible of the Environmental Microbiology Lab at IMBBC. She has also initiated the IMBBC microbial strain collection from extreme environments for biotechnological exploitation. She has been involved as Principal Investigator or Collaborator in 16 international (EU & USA) and national research projects. Her research work has been presented in 45 publications (18 as the first author and 16 as the corresponding author) in peer-reviewed international journals and in 2 Book Chapters. The accumulative journal impact factor corresponding to her publications is 198.243 and the average is 4.506 (ISI impact factors). Her publications so far have received 1857 citations (Scopus– 28 April 2021; h-index: 22).
Scopus ID: 9239758200
University Torino, Italy
Kalliopi Rantsiou graduated from the University of Athens in Greece in 1997 with a degree in Biology and continued her education at the University of Davis, USA obtaining a PhD in Food Science in 2002. She then returned to Greece and from 2003 to 2005 was scientific advisor for the Hellenic Food Safety Authority, regarding microbial hazards. In 2006 she moved to Italy and initiated her researcher career first at the University of Udine and then at the University of Turin. In 2008 she became researcher/lecturer and then in 2016 Associate Professor at the same University. Her main research interest is microbial ecology of foods with particular emphasis on combining culture dependent and culture independent approaches to describe the microbiota and its function in foods.
University of Athens, Greece
Emeritus Prof. Milton A. Typas, received his PhD in Microbial Genetics, London University, Queen Elizabeth College, UK (1975), served as Temporar Lecturer (1975-77) at the same College, and has been a Faculty member of the Dept. Genetics and Biotechnology, National Kapodistrian University of Athens (NKUA) from 1978 to 2016. He became Lecturer (1978-86), Assistant Prof. (1986-92), Assoc. Prof. (1992-2000), Professor 2001- 2016 and served as Head of the Department for 17 years and member of the NKUA Senate (1982-86; 1993-95).
He has been the receiver of several personal scholarships (ARC, EMBO, Royal Society of Britain, British Council, EU mobility, DGF, ESF), 40 competitive research grants, and visiting Professor –sabbatical leaves- of: King’s College, London, UK; Julich, Kernforschungsanlage, Germany; Novartis Research Centre (NIMRI)–U.C. San Diego and Cornell University, NY, USA. He coordinated and taught courses on Genetics, Molecular Genetics, and Biotechnology, to under- and post-graduate students of NKUA as well as several other Universities in Greece and abroad. He supervised 6 Postdocs, 26 Ph.D. theses, has been the examiner of more than 200 Ph.D theses (15 from other countries).and has published over 100 articles and 3 books. He has been Editorial Board member of many journals and has presided more than 30 International and National Conferences. For over 35 years has been independent expert/evaluator of research proposals and grant applications of young investigators in the EU (hundreds of cases, in subjects of Βiotechnology, Molecular-Microbial Genetics, Βiodiversity, Biosafety, Plant Pathology, Plant-microbe interactions, Biocontrol, Biomass, Bioethanol etc) for Programmes like. ΒΙΟΤΕCH, FAIR, COST, INTAS, COPERNICUS, THIRD COUNTRIES, STP, MARIE-CURRIE, FP5, FP6, FP7, Horizon. His research interests are placed in the fields of fungal and bacterial Molecular Genetics and Biotechnology.
Administrative boards: National Hellenic Research Foundation (1982-96, for 6 consecutive terms), Director of the National Documentation Centre, NHRF (1982-88), National Delegate for Science and Technology, U.N. (1982-87), National Representative for the Committee for Science and Technology Programme, EC (1983-86), Advisory Committees for Science and Technology in EU and Expert of National Delegations in Science & Research, Biotechnology, Agriculture and Energy DG’s VI, XII and ΧΙΙI, EU (1986-2005), National Advisory Committee for Research (1996-98), National Council for Research and Technology (2001-04), Chairman Special Advisory Committee in Biotechnology (1996-2004), Research Committee of the National and Kapodistrian University of Athens (2007-2014), National Competent Authority for the control of GMOs (1997-2004), Ad hoc expert-advisor for GMO organisms/products in EU Committees (1996-2010).
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