Invited speakers and Tutorials contributors

Invited speakers

Systems Biology:

Olivier Elemento, Weill Cornell Medical College, US
Dr Elemento initially trained as a mechanical enginneer at INSA Toulouse in France. He then obtained a master in Intelligent Sytems from University of Paris, and a PhD in Computational Biology from the CNRS.
He was then a postdoctoral fellow and lecturer at Princeton University, working on unravelling and characterizing transcriptional and posttranscriptional networks using computational genomic approaches.
In 2009, he joined Weill Cornell Medical College as Assistant Professor.
  At Weill Cornell, Dr Elemento directs the Laboratory of Cancer Systems Biology. The Elemento lab at Weill Cornell uses ultrafast genome and DNA sequencing, high-performance computing, mathematical modeling, Big Data and machine learning techniques to develop entirely new ways to help prevent, diagnose, treat and ultimately cure cancer. In addition, Dr Elemento oversees the development of analytic pipelines for clinical sequencing at Weill Cornell's Institute for Precision Medicine. Dr Elemento is the recipient of several awards including the NSF CAREER award, the Hirschl trust Career Scientist Award and the Starr Cancer Consortium award or organizes several educational activities such as the the NIH-funded Summer Course on Statistical Methods for Functional Genomics at Cold Spring Harbor Laboratories.

 

 

 
Jeroen Raes, VIB, Belgium
Prof. Raes obtained  a PhD  at  Ghent University, Ghent, Belgium in 2003. He obtained a Post-Doc researcher position first at Department of Plant Systems Biology of  VIB, from 2003 to 2005 and then at EMBL, Heidelberg, Germany, from 2005 to 2007. From 2007 to 2009 he held the  Scientist position at EMBL, Heidelberg, Germany.
From 2009 Prof. Raes is a group leader at VIB, a life sciences research institute in Flanders, Belgium with more than 1300 scientists from over 60 countries employed in basic research into the molecular foundations of life.  The Raes lab combines large-scale, next-generation sequencing with novel computational approaches to investigate the functioning and variability of the healthy human microbiome at the systems level and study its alteration in disease. In this context, Raes lab recently discovered the existence of discrete gut flora types (enterotypes), that are independent of host properties such as nationality, sex or race and are studying the predictive power of microbial markers for various intestinal diseases. In addition, Raes lab focuses on the development of computational methods for the analysis of (next-generation) sequence data and the investigation of community properties from metagenomics,  metatranscriptomics and meta-metabolomics data, which are applied in a wide range of natural environments.

 

 

 

Synthetic Biology:

 

Jean-Loop Faulon, (Head of) Institute of Systems and Synthetic Biology, University of Evry, France
Prof. Jean-Loup Faulon is currently a tenured full Professor in the Biology Department at the University of Evry Val-d’Essonne in France. He is also the director of the institute of Systems and Synthetic Biology (a CNRS research unit) and the course director of the mSSB master program in Systems and Synthetic Biology. Jean-Loup Faulon obtained his PhD in 1991 in computational chemistry at Ecole des Mines, Paris and a Habilitation in 2007 in theoretical chemistry from the University of Strasbourg. Prior holding a faculty position, from 1991 to 2009, Jean-Loup Faulon was a research associate at Penn Sate University and then a senior and distinguished scientist at Sandia a US national laboratory. While in the US, he was the PI or co-PI of a dozen of projects funded by the US National Institute of Health, Chevron, Exxon, and the US DOE Genome To Life, Math Information, and Joint Bioenergy Institute programs. Jean-Loup Faulon’s main research interest is the development of computational methods at the interface between chemistry and biology. He is the author of about 100 peer reviewed publications and book chapters in systems biology, metabolic engineering and synthetic biology. Jean-Loup Faulon research is currently being funded by the ANR, the CNRS, and Genopole.

 

 

 

Semantics Biology:

Andrea Splendiani
Andrea Splendiani is an independent professional (intelliLeaf ltd) specialized in the application ofsemantic technologies and data modelling in the Life Sciences.
Andrea Splendiani earned a Laurea Degree in Information Technology from the Politecnico di Milano, and a PhD in Computer Science from the University of Milano-Bicocca. He has been working in functional genomics for immunology (Genopolis) and Systems Biology (Institut Pasteur) where he has been an active contributor to the BioPAX standard. He has then worked on biomedical ontologies (University of Rennes 1), Knowledge Management (Leaf Bioscience s.r.l.) and data integration (Rothamsted Research, BBSRC).
He is co-chair and organizer of SWAT4LS (Semantic Web Applications and Tools for Life Sciences) and Guest Editor of the Journal of Biomedical Semantics.
He is currently collaborating with different companies on data modelling and ontology developmentfor healthcare and life sciences, spanning pharmaceutical research, clinical trials and nutrition.

 

 

 

 

 

 

Tutorials contributors

 

Mikel Egaña Aranguren, Genomic Resources, UPV-EHU , Euskal Herriko Unibertsitatea (UPV/EHU)
Mikel Egaña Aranguren's research is focused on the exploitation of Semantic Web technology (RDF, OWL, automated reasoning, ... ) to improve knowledge management in Life Sciences. The realisation of this interest involves the development of semantic resources (Ontologies, Knowledge Bases, Linked Data datasets, Semantic Web Services, ... ) and the creation of tools for exploiting such resources. He obtained a Computer Science PhD (2009) at the University of Manchester, UK. This included a Marie Curie EST placement at the Vlaams Institute for Biotechnology (VIB) in Belgium, and a placement at the European Bioinformatics Institute (EBI), UK. He then undertook a post-doctoral Marie Curie Cofund fellowship at the Universidad Politecnica Madrid (UPM), Spain, in the Biological Informatics Group of the Centre for Plant Biotechnology and Genomics, lead by Mark Wilkinson. He is currently a post-doc at the Genomic Resources Group of the University of Basque Country (UPV/EHU), Spain
 

 

 

 

Pablo Carbonell, ISSB, Genopole, France
Dr. Pablo Carbonell is a Research Associate at the Institute of Systems and Synthetic Biology, University of Evry/Genopole, CNRS, France. He received his Ph.D. degree in 1999 in control and computing engineering from Polytechnic University of Valencia, Spain, where he was appointed Associate Professor. He was visiting scholar from 2000 to 2002 at New York University Polytechnic School of Engineering (NYU-Poly). From 2006 to 2008, he joined as Staff Researcher the bioinformatics unit of Fujirebio Inc., Tokyo, Japan. In 2010, he received his Habilitation in Computational Biology. Dr. Carbonell has coauthored more than 70 scientific papers in systems biology and bioinformatics, serving as Associate Editor for several scientific journals, including Frontiers in Bioengineering and Biotechnology. His scientific interests lie at the interface between biology and engineering, where he has proposed new approaches to analyze determinants of specificity in protein-mediated interactions, with applications to metabolic pathway design and synthetic biology of cell factories, as well as other advanced topics on biological and bio-inspired complex network analysis and prediction.

 

 

 

Karoline Faust, VIB Belgium
Karoline Faust is a biologist turned bioinformatician who graduated at the Humboldt University in Berlin and earned her PhD at the Université Libre de Bruxelles under the supervision of Prof. Jacques van Helden. She is currently working as a postdoctoral researcher at the Vrije Universiteit Brussel and the VIB in the group of Prof. Jeroen Raes. Her main research interests include  inference and analysis of biological networks (metabolic and microbial association networks) and more recently the modeling of microbial communities. Her work on metabolic pathway detection and microbial association network inference and analysis has resulted in 13 publications in peer-reviewed journals including Nature, Nature Reviews Microbiology, Genome Research, Nature protocols, Nucleic Acids Research, PLoS Computational Biology and Bioinformatics. In addition, Karoline has contributed to the network analysis tool suite NeAT and is the main developer of CoNet, a popular network generation Cytoscape plugin.