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Master of Science in
Computational Biology and Biomedicine

Biomedical signal and image analysis
Modeling in neuroscience

Nice Sophia Antipolis University, France

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"Modeling in Computational Biology and Biomedicine: A Multidisciplinary Endeavor"
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» Class of » 2010/2011

2010/2011 program was sponsored by I3S, INRIA and the following project teams from INRIA Sophia Antipolis Méditerranée: ABS (Algorithms Biology Structure), Ariana (Earth observation and cartography, image processing) Asclepios (Medical Image Analysis, Biological Image Analysis, Computational Anatomy, Computational Physiology), Comore (Modelling and control of renewable resources), NeuroMathComp (Mathematical and Computational Neuroscience), Athena (Computational Brain Anatomical and Functional Imaging).

Deepesh AGARWAL recently completed Master of Technology and Bachelor of Technology in Biochemical Engineering and Biotechnology under the dual degree program at Indian Institute of Technology (IIT), Delhi, India. I did a summer internship at INRA, Nantes, France where I studied the thermal denaturation of one of the milk proteins, beta-lactoglobulin and the work is published in Journal of Agricultural and food Chemistry ( 2009, 57, 4974-4982 ). I was a summer trainee at Research Innovation labs, TCS, Hyderabad where I worked on structure-function relationship of a malarial parasite protein using Molecular Dynamics simulation of protein. My final year thesis work was on development of reliable tool for Eukaryotic Gene prediction based on physico-chemical properties of DNA. My research interests include Mathematical modeling of Biological systems from Systems Biology perspective.
Internship supervised by Karen lipkow (Cambridge Systems Biology Centre, University of Cambridge, UK): Study of Bacterial Chemotaxis phenomenon using SMOLDYN simulator
In 2011... PhD at INRIA EPI ABS, under the supervision of Frederic Cazals. Title: Towards nano-molecular design : advanced algorithms for modeling large protein assemblies

Rodrigo COFRE, Chilean Mathematical Engineer from Pontificia Universidad Católica de Chile (PUC). My thesis was on a stochastic process for gating of calcium ion channels in collaboration with Center of Neuroscience of Valparaiso (CNV) and the stochastic analysis laboratory (LAE-PUC). I worked on research at the School of Economics and Business Administration (FACEA-PUC) in Data Base and statistical methods for analysis and at (LAE-PUC) in stochastic processes. My main area of interest is stochastic processes in neuroscience and biophysics . I am well acquainted with MATLAB, R, SPSS, SQL. Eventually, I would like to pursue a Phd.
Internship supervised by Bruno Cessac (INRIA, Neuromathcomp): From statistical analysis of spike trains to network structure
In 2011... PhD at INRIA EPI Neuromathcomp, under the supervision of Bruno Cessac. Title: Statistics of action potential and neural structures

Vikash GUPTA is from INDIA and holds a M.S. in Mechanical Engineering from Vanderbilt University, US. He Completed his Bachelors in Mechanical Engineering from National Institute of Technology Karnataka, Surathkal. After completing his undergraduate degree he worked as research assistant at Center for Robotics, Indian Institute of Technology, Kanpur. He has worked on volumetric parameterization of 3D non convex domains under Dr. Bhaskar Dasgupta. During his masters he has worked on kinematic analysis of an exoskeleton for post-stroke thumb rehabilitation at Robotics and Autonomous Systems Laboratory, Vanderbilt University. He has studied advanced dynamics, nonlinear control, nonlinear optimization, robotics and probability. He has a proficiency in various 3D modelling softwares, Matlab and C. He is presently a masters student in Computational Biology at UNSA.
Internship supervised by Xavier Pennec (INRIA, Asclepios): Statistical Atlases for Diffusion Tensor Images of the brain
In 2011... PhD at INRIA EPI Asclepios, under the supervision of Xavier Pennec. Title: Statistical atlases of diffusion tensor imaging

Alejandro MOTTINI is an Electrical Engineer from Uruguay. He graduated from the Universidad de la República (Uruguay) in 2009. During his five year degree program he acquired abilities in math, programming, signal processing and telecommunications. For 9 months he worked as a Research Assistant in the Signal and Image Processing Department of the Electrical Engineering Institute of the Universidad de la República. As part of his activities he collaborated in an interdisciplinary project between the Signal and Image Processing Department and the National Center of Nuclear Medicine. He also worked for over a year in Ericsson (Uruguay), where he gained significant experience in the field of Telecommunications. He is now a graduated student in the Computational Biology master at Polytech Nice / UNSA.
Internship supervised by Xavier Descombes (INRIA, Ariana): Detection and tracking of axons in neuronal images
In 2011... PhD at INRIA, under the supervision of Xavier Descombes and Laure Blanc-Feraud. Title: Detecting, Tracking and Classifying axons from neuronal images

Siyamalan MANIVANNAN is from Sri Lanka. He completed his special degree in Computer Science at the University of Jaffna with a first class. He followed his Masters degree in Computer Science at the University of Moratuwa, awaiting results. He worked at the University of Jaffna as an Instructor and later on as an Assistant Lecturer for one year and then he worked as a Research and Development Software Engineer at a multinational company in Sri Lanka for more than two years where he did many research work on 3D Computer Graphics. His undergraduate project is "Character Recognition using Artificial Neural Networks" and his master thesis is "An image processing based ECG signal delineation". He is interested in doing further research leading to PhD on Computational Biology, Medical Image Processing, Computer Vision, or Artificial Neural Networks.
Internship supervised by Nicholas Ayache and Olivier Clatz (INRIA, Asclepios): Medical image segmentation via non local matches
In 2011... PhD in Image processing under the European project "Colonic Disease Investigation by Robotic Hydro-colonoscopy (CODIR)" at the Computer Vision and Image Processing group, School of Computing, University of Dundee, UK under the supervision of Prof Emanuele Trucco.

Alexandra NADASAN: I am a Romanian student with a Master 1 degree in the field of Networks and Telecommunications. During the first 2 years of university I studied Electronics, Telecommunications and IT at the Technical University of Cluj-Napoca, Romania. The courses were held in english and they revolved around mathematics, computer science and electronics. For my third year I had the opportunity to come in France with an Erasmus scholarship, where I further obtained my bachelor degree in Networks and Telecommunications. Throughout my studies at the University of Savoie I chose subjects with a focus on computer science, such as object programming, database management and distributed computing. I've done my final year internship (5 months) at Euriware Company, my project being the development of an intranet application.
Internship supervised by Enrico Formenti (UNS): Gene regulatory networks: the role of distances between genes
In 2011: M2 Bioinformatique et Biostatistiques, Paris-Sud 11

Elzbieta RAUS graduated from Electronics and Telecommunication at Silesian University of Technology in Gliwice in Poland. Her graduation project was Speaker verification in Matlab environment. She has strong background in the signal processing, algorithm analysis and implementation, statistical design of experiments and data modeling fields. While working as a Research and Teaching Assistant at AGH University of Science and Technology in Krakow she was engaged in the project Micro- and Nanosystem in Chemistry and Medical Diagnostics which included designing cytometric data acquisition electronics compatible with photon-counting device. The aim of the project was to construct fluorescence-based scanning cytometer for monitoring changes in cell population. Her responsibilities encompassed electronic design and development combined with scientific research carried out in various fields. Elzbieta had also exciting opportunity to participate in Implantable / Wearable System for on-line Monitoring of Human Metabolic Condition Implantable-IRONIC during her internship at L'Ecole Polytechnique Fédéral de Lausanne where she was responsible for designing Multiplexing System Interface compatible with implantable sensors. While working on the projects, Elzbieta Raus gained some knowledge of biomedical sensor technologies and experience with biological detection system.
Viateur TUYISENGE, from Rwanda. I have completed postgraduate diploma in Mathematical Sciences from AIMS/Stellenbosch University, Cape town in South Africa, June 2010. I have bachelor of Science in Computer Science from Kigali Institute of Education, Kigali, Rwanda, 2007. After my bachelor degree, I served as tutorial assistant in computer science department, Kigali Institute of Education for two years. I start a MSc computational Biology, Polytech'Nice, UNSA, September, 2010. My ambition is to pursue my studies up PhD level.
Internship supervised by Maxime Sermesant (INRIA, Asclepios): Prediction of Cardiac Electrophysiology Signal Characteristics from Image Features
In 2011... PhD in Computer Science:Cooperation between segmentation and movement for 3D regional myocardial tracking ISIT Lab:Université d'Auvergne Clermont1, supervised by Adélaïde Albouy-Kissi

Master d'Informatique: Fondements et Ingénierie
Parcours de Biologie Computationnelle et Biomedecine
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