Spring 2010

Post-Doctoral Fellows & Research Scientists (Current)



Ph.D. Students (Current)


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Justin Jee
Areas: Evolution, Codon Assignent.
Ph.D. student in Medicine, Expected Graduation Date: TBD.

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Ilya Korsunsky
Areas: Machine Learning and Statistical Inference for Cancer Diagnosis and Prognosis.
Ph.D. student in Computer Science, Expected Graduation Date: TBD.


Post-Doctoral Fellows & Research Scientists (Past)


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Andreas Witzel
Areas: Cancer Progression and Therapy Design.
Project: Expedition in Computing (NSF).
2009-2012.

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Samantha Kleinberg
Areas: AITIA; Causal Analysis of Electronic Health Records.
Project: NYU Seed Grant (NYU-Geisinger).
2009-2010.

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Toto Paxia
Areas: Computational Biology and Software Environments.
Project: VALIS.
2004-2007.

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Marco Antoniotti
Areas: Computational Systems Biology and LISP.
Project: GOALIE & Simpathica.
1999-2006.

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Raoul-Sam Daruwala
Areas: Mathematical Biology and Genomics.
Project: Array CGH Data Analysis.
2002-2005.

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Joseph McQuown
Areas: Computational Biology and Genomics.
Project: Multiscaling Algorithms and Data Mining(DOE and NYSTAR).
2002-2004.

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Archisman Rudra
Areas: Computational Biology and Genomics.
Project: Genome Evolution and Cancer Genomics(NYSTAR and PCRP-Army).
2001-2005.

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Saurabh Sinha
Areas: Computational Biology and Genomics.
Project: Learning Algorithms to Understand Genomic Regulatory Mechanisms.(Rockefeller Univ)
2002-2004.

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Nadia Ugel
Areas: System Biology.
Project: Simpathica, a pathways analysis tool(DARPA)
2001-2005.

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William Casey
Areas: Mathematical Biology and Genomic Mapping.
Project: Array Mapping(NYSTAR and NSF ITR).
2002-2003.

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Amy Greenwald
Areas: Computational Games.
Project: Automated Learning in Network Traffic Control.(NSF)
1998-1999.

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Marek Teichman
Areas: Computational Geometry and Robotics.
Project: Reactive Robotics(NSF).
1995-1996.


Ph.D. Students (Past)


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Andrew Sundstrom
"Toward a Computational Solution to the Inverse Problem of How Hypoxia Arises in Metabolically Heterogeneous Cancer Cell Populations," (pdf) 2013.

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Loes Olde Loohuis
"Cancer Progression: Model, Therapy, Extraction," (pdf) 2013.

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Pierre Franquin
"On Populations, Haplotypes and Genome Sequencing," (pdf) 2012.

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Giuseppe Narzisi
"Scoring-and-Unfolding Trimmed Tree Assembler: Algorithms for Assembling Genome Sequences Accurately and Efficiently," (pdf) 2011.

Samantha Kleinberg
"An Algorithmic Enquiry Concerning Causality," (pdf) 2010.

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Antonina Mitrofanova
"Efficient Systems Biology Algorithms for Biological Networks over Multiple Time-Scales: From Evolutionary to Regulatory Time," (pdf) 2009.

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Seongho Ryu
"Hypothesis Testing with Systems Biology and Evolutionary Models," (pdf) 2007.

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Fang Cheng
"Statistical Approaches and Rich Probabilistic Models of Biological Regulation," (pdf) 2007.

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Bing Sun
"Pairwise Comparison between Genomic Sequences and Optical-Maps," (pdf) 2006.

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Ofer Gill
"Finding Your Match: Techniques for Improving Sequence Alignment in DNA and RNA," (pdf) 2006.

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Iuliana Ionita
"Multimarker Genetic Analysis Methods for High Throughput Array Data," (pdf) 2006.

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Mysore Venkatesh
"Algorithmic Algebraic Model Checking: Hybrid Automata and Systems Biology," (pdf) 2006.

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Yi (Joey) Zhou
"Statistical Analyses and Markov Modeling of Duplication in Genome Evolution," (pdf) 2005.

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Toto Paxia
"Rapid Prototyping in Computational Biology:
Multi-scripting Environment, Free-format Databases, Data Manipulation Algorithms and Visualization Widgets in the Valis System
," (pdf) 2003.

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Vera Cherepinsky
"On Mathematical Aspects of Genomic Computing," (pdf) 2003.

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Raoul-Sam Daruwala
"On Computing the Pareto Optimal Solution in Large Scale Dynamic Network," (pdf) 2002.

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William Casey
"Graph Embeddings with Application in Genomic Experiments," (pdf) 2002.

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Gideon Berger
"Knowledge Discovery in Databases for Intrusion Detection, Disease Classification and Beyond," (pdf) 2001.

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Amy Greenwald
"Learning to Play Network Games," (pdf) 1999.

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Ron Even
"Distributed Intelligence with Bounded Rationality: Applications to Economies and Networks," 1998.

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Laxmi Parida
"Algorithmic Techniques in Computational Genomics," (pdf) 1998.

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Marek Teichman
"Grasping and Fixturing: a Geometric Study and an Implementation," (pdf) 1995.

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Marco Antoniotti
"Synthesis and Verification of Controllers for Robotics and Manufacturing Devices with Temporal Logic and the Control-D System," (pdf) 1995.

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Lars Ericson
"GEDANKEN: A Tool for Pondering the Intractability of the Correct Program Technology," (abstract) 1994.

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Gilad Koren
"Competitive Real-time Scheduling," (pdf) 1993.

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Christopher Fernandes
"NonHolonomic Motion Planning: Algorithms and Software," (abstract) 1993.

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Naomi Silver
"Control of Dexterous Hands: Theory, Implementation and Experiments," (abstract) 1992.

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Giovanni Gallo
"Complexity Issues in Computational Algebra," (abstract) 1992.

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Paul Pedersen
"Counting Real Zeros," (abstract) 1991.

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Anne Dinning
"Detecting Nondeterminism in Shared Memory Parallel Programs," 1990.

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Lou Salkind
"SAGE: A Real-Time System for Robotic Supervisory Control," 1990.

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Pasquale Caianiello
"Learning as the Evolution of Representation," 1989.

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Dayton Clark
"Data Communication in Robot Control Systems," 1989.


Recent Master's Students


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Andrew Sundstrom
"Measuring Biomolecules: An Image Processing and Length Estimation Pipeline Using Atomic Force Microscopy to Measure DNA and RNA with High Precision," 2008.

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Kevin Casey
"Information-based Biclustering for the Analysis of Multivariate Time Series Data,"2007.

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Joseph McQuown
"Examining Microarray Experiments,"2002.

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Viloet Chang
"Genome Comparison of Haemophilus influenzae and Helicobacter pylori 26695," 2001.