Emmanuel Barillot

Emmanuel Barillot

Dr Emmanuel Barillot has background in Mathematics and Physics. He received his PhD in Bioinformatics in 1992 at Généthon/CEPH in Paris where he headed the bioinformatics group which constructed the first physical map of the human genome.

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In 1995 he created a research group in genomic data integration at Infobiogen (France). Then he joined the National Agricultural Research Institute (INRA) to create a research unit for plant bioinformatics, focusing on heterogeneous omics data integration (Génoplante). In 2002 he joined Institut Curie to create a bioinformatics core facility and a research group in computational systems biology of cancer. Since 2008 he has been heading the Department of Epidemiology, Biostatistics, Bioinformatics, and Computational Systems Biology of Cancer (U900), a joint Institut Curie and INSERM research department, in partnership with Mines ParisTech. The Department employs 90 researches, and Professor Barillot heads one of four research teams, the computational systems biology of cancer team, and one core bioinformatics facility. His research focuses on methodological development and statistical analysis of high-throughput biological data (both for biological and clinical research), integration of heterogeneous biological data, developing methods and tools for biological network analysis and molecular network modeling in the context of cancer (covering the different processes involved in tumor progression, like cell proliferation, cell death and survival, DNA repair, EMT, etc. E. Barillot has published more than 130 papers in the fields of bioinformatics, genomics, systems biology, cancer biology and clinical research, biophysics, and computer science. He has been a coordinator and PI in about 40 projects during the last ten years.

Boeva

Valentina Boeva is a research scientist from the Curie Institute, France. She works on data integration and the development of high throughput sequencing data analysis methods to study regulation in cancer.

Valentina Boeva

Valentina Boeva is a research scientist from the Curie Institute, France. She works on data integration and the development of high throughput sequencing data analysis methods to study regulation in cancer. She with her group has designed and implemented the following high-throughput data analysis methods: Analysis of copy number alterations and structural variants in DNA sequencing data: FREEC/Control-FREEC, SVDetect, SV-Bay, ONCOCNV; Analysis of ChIP-seq data: MICSA, HMCan and Nebula.

Gladyshev

Vadim Gladyshev

Vadim Gladyshev graduated in 1988 and obtained Ph.D. in 1992 from Moscow State University, followed by postdoctoral training at the National Institutes of Health and a faculty position at University of Nebraska — Lincoln in 1998. Dr. Gladyshev served as Director of the Redox Biology Center at University of Nebraska in 2007-2009. Since 2009, he has been Professor of Medicine at Brigham and Women’s Hospital, Harvard Medical School, and Associate Member of the Broad Institute. He is also Director of the Center for Redox Medicine. Dr. Gladyshev’ lab applies high throughput and computational approaches to understand mechanisms of aging, control of lifespan and redox regulation of cellular processes. Dr. Gladyshev has published approximately 300 articles and has been elected as an AAAS fellow. He is the 2013 recipient of the NIH Director’s Pioneer Award.

Nikolai V. Ivanov PhD

Nikolai V. Ivanov PhD

After graduation from Mendeleyev University of Chemical Technology in 1996, Nikolai got his PhD degree in Chemistry at Emory University in 2002. He continued his scientific career with Postdoctoral Fellowship in Bioinformatics at Georgia Institute of Technology, USA (2002-2004), and a position of Research Associate at Wellcome Trust Sanger Institute, UK (2004-2005). In 2005 Dr. Ivanov joined PMI Research & Development Division, Switzerland. He got MBA in Management & Corporate Finance, HEC, Université de Lausanne in 2014. He has been leading a Research Technology department as Manager of Research Technologies at PMI Research & Development, Switzerland, since 2009. The department comprises state-of-the-art experimental and in silico labs generating and handling omics and histological data.

Kanapin

Alexander Kanapin

Alexander graduated from Moscow State University in 1986 (biophysics). He has got his PhD degree in the Institute of Cell Biophysics (Puschino, Russia) in 1997. After a short postdoc in microarray bioinformatics (Jena, Germany) he joined European Bioinformatics Institute (Hinxton, UK) in 1998. Alexander was one of key developers and a manager of two world-renowned biological databases: InterPro and Reactome. His participation in pioneering genome sequencing initiatives was marked by core authorship in mouse genome and human transcriptome publications and membership in FANTOM and H-Inv consortia. After EBI Alexander joined Cold Spring Harbor Laboratory (USA) in 2008. He was developing Next Generation Sequencing data analytical approaches as an active member of modENCODE consortium. Since 2010 Alexander works in University of Oxford where he continues his research in biology of mobile genetic elements and also coordinates and manages development of large-scale *omics data processing infrastructure. Now, Alexander is Computational Genomics Head at the Department of Oncology, University of Oxford. He is one of leading researchers and developers in big data genomics projects: WGS500 (Oxford-Illumina consortium) and “Genomics England”.

Karssen

Lennart C. Karssen

Lennart Karssen obtained his MSc in experimental physics at Utrecht University (The Netherlands), followed by a PhD in experimental atomic and optical physics at the same university in 2008 with a thesis titled “Trapping ultracold atoms with ultrashort laser pulses”. In 2009 he worked at the National University of Rwand as postdoc in the Research Commission and as senior lecturer at the Department of Physics. Upon his return to The Netherlands he worked for some time as a Unix/Linux consultant at a company called Snow. From 2010 – 2013 Lennart Karssen worked as a postdoc in bioinformatics and server guru in the Genetic Epidemiology group of Prof. Cornelia van Duijn at the Erasmus Medical Centre, Rotterdam, The Netherlands. At the Erasmus MC he worked on various projects including the Genome of the Netherlands project which used a parent-offspring design to create a reference set for genomic imputations, and the exome sequencing project of the GRIP study, which sequenced the exomes of ~ 1300 people from an isolated population with more than 3000 deeply phenotyped people within a complex pedigree of more than 23,000 individuals spanning 23 generations. Since late 2013 Lennart works together with Dr. Yurii Aulchenko in their company called PolyOmica, which specialises in (teaching) statistical omics, including the development of statistical methods, open source software implementation thereof, and advice on and maintenance of scientific computer clusters. Currently he is working on several projects, including two EU-funded research projects: MIMOmics which develops methods for integrated analysis of multiple omics datasets, in which PolyOmica leads the work package on “Data Integration and Distributed Computing”; and PainOmics, which takes a multi-dimensional omics approach to stratification of patients with low back pain. Here PolyOmica leads the work package on “Integrated models for identification of biomarkers and potential new therapeutic targets”. The GenABEL project for statistical omics is the main software project Lennart Karssen is involved in. He is one of the founders of the project as it grew from a small collection of software packages (mostly written in R) to an open framework that actively encourages involvement of the community in all stages, from formulation of methodological ideas to application of software to specific data sets. He is currently maintainer of several tools in the GenABEL suite, including ProbABEL, a tool for fast genome-wide association analysis (GWAA) of imputed genetic data. Together with computer scientists, data generators and data analysts he currently works on a tool that speeds up this type of GWAA by several orders of magnitude when using many (e.g. 102 – 105) phenotypes and 106 – 108 genotypes, as currently found in e.g. metabolomics studies. Lennart Karssen’s teaching record ranges from computational topics like scientific software development and “Linux for scientists” to more genetic-epidemiological topics like genome-wide meta-analysis, preparation and conversion of next-generation sequencing data, and reproducible research.

Khaitovich

Philipp Khaitovich

Philipp completed undergraduate studies in molecular biology at Moscow State University in 1995 and PhD in biochemistry at the University of Illinois at Chicago in 1999. From 2000 till 2006 Philipp worked as a postdoctoral researcher at the Max Planck Institute for Evolutionary Anthropology at the department of Evolutionary Genetics headed by Prof. Svante Pääbo. In September 2006, Philipp Khaitovich took a faculty position at the Institute for Computational Biology jointly established by the Chinese Academy of Sciences and the Max Planck Society in Shanghai China. In 2012 Philipp was promoted to the Institute Director position. He further received Full Professor position at ShanghaiTech University in Shanghai and became a fellow member of Max Planck Society. In 2013 Philipp received the Friendship medal – the highest award given to foreigners in China. In 2014 Philipp joined Skoltech University in Moscow, Russia, as a Full Professor.

Kharchenko

Peter Kharchenko

Peter Kharchenko received a PhD in Biophysics from Harvard University, studying gene regulation in metabolic networks under the advisement of George Church. His postdoctoral work, as part of a fellowship with Peter Park at the Harvard Medical School, focused on the computational analysis of chromatin organization and the contribution of basic epigenetic mechanisms to gene regulation. Since 2011 he has formed his own computational biology lab at the Center for Biomedical Informatics at the Harvard Medical School where he is currently an Assistant Professor.

Kondratova

Maria Kondratova

Maria completed undergraduate studies in biochemistry at Kharkov National University in 2000 and PhD in molecular biology at Moscow State Universiry in 2006. Maria worked as a postdoctoral researcher at the Institute of Protein Research (Pushchino, Russia) and in Centre de Recherche de Biochimie Macromoléculaire (CRBM, Montpelier, France). 2009-2014 Maria Kondratova worked in R&D department of Thomson Reuters (MetaCore project, Moscow). Il 2014 Maria joined Curie Institute (Paris, France) as a system biology researcher. Actual area of scientific interests is system biology of cancer and oncoimmunology.

Ekaterina Kotelnikova

Ekaterina Kotelnikova

Ekaterina graduated from biophysical department (Faculty of Physics) of Moscow State University in 2001 and obtained her PhD degree in molecular evolution in 2005 from the same institution. From 2005 till 2012 she worked for the US-based company Ariadne Genomics, starting as a researcher and then as a Principal Research Scientist in the field of pathways analysis, drugs repositioning, and biomarkers discovery. In 2013 Ekaterina started a «Personal Biomedicine» company in Moscow, focused on the NGS-based cancer treatment predictions, with bioinformaticians and systems biologists on board. At the same time she got the personal Marie Curie fellowship and moved to Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona.

kulakovsky

Ivan Kulakovskiy

Ivan got his master’s degree in computer science from Moscow State Forest University (Mytishchi) in 2006. In 2009, he completed the postgraduate program in molecular biology (under supervision of prof. V.G. Tumanyan) in Engelhardt Institute of Molecular Biology (Moscow) and got his PhD in bioinformatics at the Institute of Information Transmission Problems (Moscow). Since 2010, Ivan is working in Engelhardt Institute of Molecular Biology. In 2012, Ivan received postdoctoral fellowship from Dmitry Zimin “Dynasty” Foundation and joined the Department of systems biology and computational genetics headed by Dr. V.J. Makeev in Vavilov Institute of General Genetics (Moscow).

Manja Marz

Manja graduated from the University of Leipzig with Diploma in Biology (2005) and Computer Science (2006). In 2009 she got her PhD degree in Bioinformatics in Prof. Peter Stadlers group in Leipzig. She moved to the Institute for Pharmceutical Chemistry at the University of Marburg to have her own (l)ncRNA Bioinformatics group. In 2012 Manja received a Junior Professorship for High-Throughput Data Analysis at the University of Jena. Currently, Manja started to work in the field of Virology-Bioinformatics and Aging. She is founding and board member of the Aging Research Center Jena (ARCJ) and Michael-Stifel-Center Jena (MSCJ) for Data-Driven and Simulation Science.

Papatsenko

Dmitri Papatsenko

Dmitri completed undergraduate studies in molecular biology at Moscow State University in 1991 and PhD in molecular biology at the Engelgardt Institute of Molecular Biology, Moscow, Russian Academy of Sciences in 1995. From 1995 till 2000 Dmitri worked as a postdoctoral researcher at the Rockefeller University, New York in laboratory of developmental genetics headed by Prof. Claude Desplan. At the Rockefeller University Dmitri developed methods for analysis of fly gene control regions, enhancers. In 2003 Dmitri Papatsenko joined University of California, Berkeley as a research scientist, where he collaborated with Prof. Michael Levine on projects related to systems biology and quantitative modeling of Drosophila development. At UC Berkeley Dmitri developed models describing segmentation of early fly embryo. In 2010 Dmitri joined department of Regenerative and Developmental Biology and the Black Family Stem Cell Institute at Icahn School of Medicine at Mount Sinai, New York as an assistant professor. At Mount Sinai Dmitri investigates global gene expression, structure of gene control regions in embryonic stem cells and quantitative models describing self renewal and pluripotency.

Dmitri’s scientific interests cover the area of developmental and regenerative biology, regulation of spatio-temporal gene expression in development, structure and function of eukaryotic enhancers. Several papers published by Dmitri Papatsenko were selected by Faculty of 1000 prime.

Popova

Tatiana Popova

Tatiana Popova completed undergraduate studies in applied mathematics at the Krasnoyarsk State University in 1992 and PhD in biophysics at the Institute of Biophysics, Krasnoyarsk, Russia in 1997. Tatiana continued as a postdoc in the Institute of Computational modeling, in the department of Neuroinformatics (headed by Prof. Alexander Gorban). In 2002 a small bioinformatics team headed by Tatiana was created within the same department. The main research topic of the group was data analysis technique application to the biological sequences. At the same time Tatiana was working as an assistant Professor in Krasnoyarsk State University, in departments of Psychology and Mathematics. In 2005 Tatiana re-started her carrier as a postdoc in Pharmaceutical Company “Boehringer Ingelheim” in the Genomics group of Research and Development department, Biberach, Germany. Since 2008 Tatiana joint the team Genetics and biology of cancer at Institut Curie, Paris, France, and started working in the cancer genomic filed. Since 2013 Tatiana is a senior researcher of INSERM, French national institution of research in medicine.

Pyatnitskiy

Mikhail Pyatnitskiy

Mikhail received MSc in Medical Biophysics at the Russian State Medical University in 2006. In 2005 he started his research career at the Institute of Biomedical Chemistry where he got his PhD in Bioinformatics in 2009. In 2010-2013 Mikhail was with Ariadne Genomics and later Ariadne Diagnostics. After graduation from Yandex’ Data Analysis School in 2013, Mikhail has been working in the field of personalized biomedicine. He is a lecturer at the Faculty of the Bioinformatics at RSMU. Mikhail’s research interests are personalized medicine, system biology and data mining.

Ravcheev

Dmitry A. Ravcheev

Dmitry completed undergraduate studies in virology at Lomonosov Moscow State University in 2003 and got PhD in bioinformatics at the Institute for Information Transmission Problems in 2009. From 2010 to 2013 Dmitry worked as a Postdoctoral Fellow at the Sanford Burnham Medical Research Institute in the group headed by Prof. Andrei Osterman. In 2013, Dmitry joined the Molecular System Physiology Group at Luxembourg Centre for System Biomedicine as a Research Associate. Dmitry’s scientific interests includes functional and comparative genomics of Prokaryotes, functional annotation of genes and proteins, and reconstruction of metabolic and regulatory networks.

Zinovyev

Andrei Zinovyev

Andrei Zinovyev graduated in Theoretical Physics, Cosmology from the Physics department of Krasnoyarsk State University in 1997, obtained PhD in Computer Science in 2001 at Institute of Computational Modeling SB RAS, and habilitated in Biology at École Normale Supérieure, Paris, in 2014, where he gives lectures as a part of systems biology master course. He was a postdoctoral researcher at Institut des Hautes Etudes Scientifiques, Bures-sur-Yvette, in 2001-2004. From 2005 he co-leads the Computational Systems Biology of Cancer group at Institut Curie, Paris. Author of 3 books and more than 60 publications in computational biology and bioinformatics, cancer biology, mathematical chemistry, machine learning and political sciences.