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Agenda Day 1

Presentations, Speaker Biographies, and Webcasts

Speaker Biographies

Michael Brady

Keynote: Health and Wellbeing

Cancer Image Analysis

Mike BradyMike Brady

 

 

 

 

 

 

Professor Sir Michael Brady is Professor of Information Engineering at the University of Oxford, and author of nearly 500 articles and 24 patents in computer vision, robotics, medical image analysis, and artificial intelligence, and ten books, including Mammographic Image Analysis. He is a Fellow of the Royal Academy of Engineering, a Fellow of the Royal Society, and most recently a Fellow of the Academy of Medical Science. He was awarded the IEE Faraday Medal for 2000 and the IEEE Third Millennium Medal, as well as the Henry Dale Prize by the Royal Institution in 2005. Mike has a strong commitment to entrepreneurial activity, and serves as Deputy Chairman of Oxford Instruments and director of Isis Innovation. Mike is a Director of the start-up companies Guidance and Mirada Solutions, and is Senior Independent Director of Ixico, which provides image analysis services to the pharmaceutical industry, and is also Director of Dexela, which is developing a novel 3-D mammography system for more reliable and early detection of breast cancer.

Amelio Vázquez-Reina

The Connectome Project: Discovering the Wiring Diagram of the Brain

Amelio Vázquez-Reina Amelio Vázquez-Reina

 

 

 

 

 

 

 

Amelio Vázquez-Reina is a Ph.D. candidate at the Laboratory for Imaging Science Research at Tufts University under the direction of Professor Eric Miller. Prior to attending Tufts, he obtained his M.Sc. in Electrical Engineering with honors from The University of Alcalá in Spain. There he received one of thefive Best National M.Sc Thesis awards from the National Association of Spanish Electrical Engineers (AEIT/COIT). Amelio’s research interests include variational methods for image processing and computer vision. He currently focuses on the study of geometrically constrained deformable models based on level set methods. Amelio is working on the Connectome Project at the Initiative in Innovative Computing (IIC) at Harvard University with Professor Hanspeter Pfister (Computer Science) and Professor Jeff Lichtman (Molecular and Cellular Biology). As part of the project, Amelio is researching segmentation and tracking algorithms for the extraction of the neural circuitry of mammalians in electron and confocal microscopy.

Dan Geiger and Assaf Schuster

Software System for Genetic Linkage Analysis of SNP Data

Dan GeigerDan Geiger

 

 

 

 

Professor Dan Geiger's main research is focused on the study of probabilistic models for intelligent systems, in particular, the study of Bayesian networks and their applications in bioinformatics and in other domains. His main contributions have focused on several aspects of Bayesian networks, including, (1) Foundation – which independence assumptions are encoded in a Bayesian efficiently by using a Bayesian network, (3) Learning – how to learn Bayesian networks from data, and (4) Applications – building effective intelligent systems based on Bayesian networks. Currently, Geiger focuses on building state-of-the-art software packages that help geneticists map genes for diseases by linkage studies, association studies, and other methods. Geiger earned a PhD degree under the guidance of Judea Pearl in 1990, and since then he is a member of the academic staff at the Technion Israel Institute of Technology.

 

Assaf SchusterAssaf Schuster 

 

 

 

 

  

Professor Assaf Schuster established the Distributed Systems Laboratory (DSL), which CS faculty see as the primary means for hosting their applied and systems research. DSL is supported by Intel, Microsoft, Sun, IBM, and other interested partners. Professor Schuster is well known in the area of parallel, distributed, high-performance, and grid computing, has published more than 160 papers in those areas, and consults the hi-tech industry on related issues. He serves as an associate editor of the Journal of Parallel and Distributed Computing, and IEEE Transactions on Computers, and takes part in large national andEuropean Unionprojects as an expert on grid and distributed computing. His research group focuses on distributed knowledge discovery, and large-scale distributed data mining, and has published papers on distributed highly-scalable knowledge discovery for SIGMOD, ICDM, KDD, SDM, Data Mining and Knowledge Discovery, the IEEE Transaction series, and Knowledge and Information Systems and Transactions On Database Systems. The group has developed novel approaches for data-mining in large-scale distributed systems, including multi-party collaborative environments such as grid, peer-to-peer, sensor networks, Internet routers, large mobile systems, and high-performance parallel databases. Recently, the group published several award-winning new approaches and algorithmic breakthroughs for efficient knowledge discovery in such systems, related to local algorithms, hierarchical framework, geometric approaches, and other techniques.

Corrado Priami

Algorithmic Systems Biology 

Corrado PriamiCorrado Priami

 

 

 

 

 

Corrado Priami obtained his Bachelor’s and PhD degrees in Computer Science at the University of Pisa, and was visiting researcher at the laboratory LIX, École Politechnique, Paris (1995) and the École Normale Supérieure, Paris under an EC Marie Curie TMR grant, and was also a researcher and associate professor at the University of Verona. Currently, he is professor of Computer Science at the University of Trento. The results of his PhD thesis on stochastic pi-calculus were the basis for the foundation of the Microsoft Research – University of Trento Centre for Computational and Systems Biology (CoSBi), of which he is the President and CEO. Those same results are recognized as fundamental in the field of systems biology by an expanding international community, which is using them to model the behavior of biological systems (the CMSB conference is a milestone of this). Professor Priami was member of the expert group on the EU 7th FP of the CRUI and participated in many projects promoted by the European Commission. He regularly serves on evaluation committees for projects presented by the European Commission, is a reviewer for many international journals, and serves in the review panels of the Science Foundation Ireland for institutes of systems biology and of the Netherlands Organisation for Scientific Research. His research covers computational methods for the modeling, analysis, and simulation of biological systems, programming languages, and formal computational theories. Professor Priami has published more than 120 papers, delivered 40 invited talks and lectures at conferences and universities worldwide, participated on program committees for 21 international conferences, is a member of three steering committees of international conferences, is editor-in-chief of Transactions on Computational Systems Biology and is a member of the editorial board of the journal Bioinformatics Research and Applications. He founded the international conferences "Computational Methods in Systems Biology (CMSB)," and “Converging Sciences,” whose success has been described by many international journals. Professor Priami is currently a member of ISTAG (Information Society Technologies Advisory Group) of the European Commission.

Frédérique Lisacek

Saving Patients Using Mass Spectrometry

Frederique LisacekFrederique Lisacek

 

 

 

 

 

 

Frédérique Lisacek received a PhD in Computer Science (Artificial Intelligence) from the University Pierre and Marie Curie, Paris, France, in 1984. Since then, she has held research positions in bioinformatics in France, Japan, and Australia working on knowledge representation and sequence analysis in various fields of biology. She has been involved in proteomics projects since 1999 through work with companies such as Proteome Systems Ltd in Sydney, Australia, as a visiting researcher, and Geneva Bioinformatics (GeneBio) S.A, where she acted as CSO until 2005. She currently manages the Proteome Informatics Group of the Swiss Institute of Bioinformatics in Geneva, while on leave from a tenured position in bioinformatics at the University of Versailles-Saint-Quentin, France.

Mark Knobel

Computational Neuropsychology of Visual Perception and Imagery 

Mark KnobelMark Knobel

 

 

 

 

 

 

 

Mark Knobel is currently a doctoral candidate in the department of Psychology at Harvard University. He has SBs in Brain and Cognitive Sciences and Philosophy from MIT and an MA in Psychology from Harvard. Mark works with Professor Stephen Kosslyn and is interested in modeling cognitive functions based on insights from both normal and brain-injured patient performance. His work has focused on the domains of mental imagery and language production.

Lynn Gladden

Keynote: Earth, Energy, and the Environment

Fighting Emissions with Nuclear Magnetic Resonance

 

Lynn GladdenLynn Gladden

 

 

 

 

 

 

 

 

 

 

Professor Lynn Gladden is currently Shell Professor and Head of the Department of Chemical Engineering and Biotechnology at the University of Cambridge; she is also Director of the Magnetic Resonance Research Centre at Cambridge. Prior to moving into the field of chemical engineering, Lynn graduated in Chemical Physics at the University of Bristol and studied for a PhD in the Department of Physical Chemistry at Cambridge. Currently, her major research interests lie in the development and application of magnetic resonance techniques in chemical engineering, with a particular interest in applied catalysis, oil recovery, and pharmaceutical delivery systems. She also has an emerging interest in THz and its use alongside magnetic resonance techniques. In 1996, she was awarded a Miller Visiting Professorship at the University of California, Berkeley, and in 2000, the Tilden lectureship and silver medal of the Royal Society of Chemistry. She is a member of the International Advisory Board of the MacDiarmid Institute for Advanced Materials and Nanotechnology, New Zealand.

Alyssa Goodman

Seamless Astronomy

Alyssa GoodmanAlyssa Goodman

 

 

 

 

 

 

Alyssa Goodman is Professor of Astronomy at Harvard University, and Research Associate at the Smithsonian. Her research group at the Harvard-Smithsonian Center for Astrophysics in Cambridge, Massachusetts, studies dense gas between the stars, and how interstellar gas arranges itself into new stars, using techniques covering the spectral range from X-ray to radio. Goodman is P.I. of The COMPLETE Survey of Star-Forming Regions, which mapped out three very large star-forming regions in our Galaxy in their entirety. The COMPLETE Survey represents a data set of unparalleled diversity and is one thousand times larger than what was available a decade ago, and enables astrophysicists to address questions about how many stars like the Sun can form from a given mass of gas. Goodman co-founded and directed The Initiative in Innovative Computing (IIC) at Harvard, a multi-disciplinary center fostering new work at the boundary between computing and science. Presently, she is working closely with colleagues at Microsoft Research, helping to expand the use of the Worldwide Telescope program. Goodman received her undergraduate degree in Physics from MIT and a Ph.D. in Physics from Harvard. She held a President's Fellowship at the University of California at Berkeley, after which she took up a post as Assistant Professor of Astronomy at Harvard. She also received the Newton Lacy Pierce Prize from the American Astronomical Society for her work on interstellar matter. She currently serves as Chair of the Astronomy Section of the American Association for the Advancement of Science.

Eric Salathé

A Regional climateprediction.net Experiment for the Western United States

Eric SalathéEric Salathé

 

 

 

 

Dr. Eric Salathé is a Senior Research Scientist at the Joint Institute for the Study of the Atmosphere and Ocean, a Principal with the Climate Impacts Group (CIG), and an Affiliate Assistant Professor of Atmospheric Sciences at the University of Washington. Dr. Salathé leads the regional climate modeling and downscaling team for the CIG, supporting climate impact applications in many fields including air quality, hydrology, agriculture, and human health. His current research focuses on how local weather and land-surface processes can affect the regional response to climate change. Dr. Salathé received a PhD in Geology and Geophysics from Yale University and a BA in Physics from Swarthmore College.

Simon Wilson

Regional Climate Modeling Using Distributed Computing

Simon WilsonSimon Wilson

 

 

 

 

 

 

Simon Wilson has been working at the UK Met Office for 10 years. His main area of expertise is the porting and optimization of numerical climate models on a variety of computing platforms from supercomputers to home PCs. His current activities include PRECIS (Providing Regional Climates for Impacts Studies) which was developed in order to help generate high-resolution climate change information for as many regions of the world as possible andwhich can be installed on any home PC; climateprediction.net, a distributed computing system; the installation of the Met Office's climate modeling system on supercomputers and clusters of scientific partners; and investigating various code optimization schemes for climate models on all platforms.

Abdul Alabri

Health–e-Waterways: Data Integration for Smarter, Collaborative Whole-of-Water Cycle Management

Abdul AlabriAbdul Alabri

 

Abdul Alabri, BE (UQ), ME (QUT) is a research assistant working at the eResearch lab at The University of Queensland. Abdul is also a PhD candidate working in spatio-temporal querying and visualization services for understanding and modeling ecosystems under the supervision of Professor Jane Hunter. He has been working on a number of key research projects, including Modeling and Analysis of Biological Network Activity (BioMANTA), Australian Research Enabling Environment (ARCHER) and Annotex. Notably, Abdul has previously been employed by the Department of Natural Resources and Water working on software development and maintenance of water-quality data-collection systems. Abdul is a key researcher on the Health–e-Waterways project, which aims to develop cyber-infrastructure to address new management and decision-making challenges concerning Queensland's water supply. In particular, it aims to enable and promote the sharing and collaborative integration and analysis of high quality information concerning water.

John McGee

Data Interoperability for Cross Domain Modeling

John McGeeJohn McGee

 

 

 

 

 

 

John McGee is the manager for cyber infrastructure development for the Renaissance Computing Institute (RENCI), leading a team of researchers and software developers to design and implement solutions that advance scientific research and discovery. Prior to joining RENCI, McGee was co-executive director of the GRIDS Center at USC’s Information Sciences Institute as part of the NSF Middleware Initiative. He has also served in technical and managerial roles in academia and the private sector, with experience in software development, director of information technology, and as vice president of business development for a small high-tech firm. Mr. McGee holds a bachelor of science degree in mathematics from the University of Maryland, College Park.

 

Mikhail Zhizhin

Storage, Mining, and Visualization of Environmental Data Archives 

Mikhail ZhizhinMikhail Zhizhin

 

 

 

 

 

 

Mikhail Zhizhin is Head of the Grid laboratories at the Geophysical Center and the Space Research Institute in Moscow. Born in 1962 in Moscow, Russia, Zhizhin graduated with honors in 1984 from Mathematical Department of the Moscow State University, MS in Functional Analysis. From 1984 to 1988, he did postgraduate studies in mathematics at MSU and Russian Academy of Sciences. Later, he was a researcher at the Institute of Physics of the Earth and International Institute of Earthquake Prediction Theory. In 1991, he receivedaPhD in databases and syntactic recognition of seismic signals. From 1990–1998, hedeveloped databases and data processing algorithms in seismology and geophysics under several research grants with the French Atomic Energy Commission. From 1997 to the present, he develops Internet applications with NASA Space Science Internet, MirNet, GLORIAD for Space Physics, Remote Sensing and Climatology with the World Data Centers System under research grants from the Russian Academy, NOAA, NASA, EGEE, Microsoft, and the World Bank.

James Hunt

Data Mining for the Development of Scaling Laws in Hydrology

James R. HuntJames R. Hunt

 

 

 

 

 

 

James Hunt has been a professor of civil and environmental engineering at University of California, Berkeley, since 1980. His education has been in environmental engineering starting at UC Irvine for a bachelor's degree, a master's degree at Stanford University, and a PhD at the California Institute of Technology. His teaching and research efforts are focused on contaminant transport processes and water resources engineering. Current research efforts include an analysis of contaminant transport pathways using a combination of conceptual modeling, analytical measurements, and the synthesis of field data. He is evaluating the ability of models based on laboratory experiments to describe contaminant migration at much larger spatial scales encountered at hazardous waste sites using monitoring data recorded at these sites. Another project is testing a model for the isotopic fractionation of mercury atoms during smelting to better understand the contribution of various sources of mercury to fish found within the San Francisco Bay. In the area of watershed-scale processes, he is developing environmental data management tools to assess ecosystem change within complex hydrologic systems, such as coastal California streams, to identify why there are declines in migratory salmonid fish.

Michael Lehning

Swiss Experiment: Advanced Technologies for Collaborative Environmental Research

Michael LehningMichael Lehning

 

 

 

 

 

 

 

 

 

 

 

 

 

Michael Lehning is the Head of the “Snow and Permafrost” Research Unit at WSL—the Swiss Institute for Forest, Snow and Landscape Research, SLF, Davos. He holds a PhD in Atmospheric Physics, and degrees in Meteorology, Hydrology, Atmospheric Sciences, and Atmospheric Physics. His major research areas include Interaction Snow—Atmosphere; Natural Hazards Warning and Forecasting; Turbulence and Boundary Layer Flows over Alpine Terrain; Mountain Hydrology and Permafrost Modeling; and High Performance Computing. He is currently responsible for the development of the “Swiss Experiment,” an ETH CCES activity to install a large and common platform for environmental science including a cyber-collaboratory and data assimilation for better understanding the Alpine environment and for an improved ability to predict natural hazards.