Alumni

 

PhD Students

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Zichen Wang, PhD
Training Period in Lab: 2013-2016
Thesis: Methods for Collecting, Improving and Exploring Mammalian Gene Expression Signatures
Current Position: Assistant Professor, Icahn School of Medicine at Mount Sinai


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Qiaonan Duan, PhD
Training Period in Lab: 2012-2016
Thesis: Harnessing the LINCS L1000 Data for Drug Discovery and Drug Response Analysis
Current Position: Computational Biology Scientist, NuMedii


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Yan Kou, PhD
Training Period in Lab: 2011-2015
Thesis: Big Data Analytics for Understanding Mechanism of Human Disease
Current Position: Program Director, Insight Data Science


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Huilei Xu, PhD
Training Period in Lab: 2009-2012
Thesis: Analysis of Transcriptional Networks in mESCs
Current Position: Bioinformatics Scientist, Alnylam Pharmaceuticals


Postdoctoral Fellows

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Andrew Rouillard, PhD
Training Period in Lab: 2013-2016
Summary of Research: Inferring Cell Signaling Pathways from LINCS
Current Position: Bioinformatics Scientist, GlaxoSmithKline


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Neil Clark, PhD
Training Period in Lab: 2011-2015
Summary of Research: Statistical Methods for Network Analysis in Systems Biology
Current Position: Research Fellow, University of Edinburgh (UK)


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Ben MacArthur, PhD
Training Period in Lab: 2008-2011
Summary of Research: Systems Biology of mESCs
Current Position: Associate Professor, University of Southampton (UK)


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Amin Mazloom, PhD
Training Period in Lab: 2008-2011
Summary of Research: Network Analysis of NURSA HT IP-MS Proteomics
Current Position: Director of Bioinformatics, Sequenom Inc.


Visiting Medical Students

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Alexander Barash, MD
Training Period in Lab: 2007-2008
Summary of Research: Systems Pharmacology
Current Position: Vitreoretinal Fellow, New York Eye and Ear Infirmary of Mount Sinai


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Ryan Logan Webb, MD
Training Period in Lab: 2007-2008
Summary of Research: Software Tools for Systems Biology
Current Position: Radiology Resident, Staten Island University Hospital


Bioinformaticians and Software / Database Developers

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Gregory Gundersen, MA
Training Period in Lab: 2014-2016
Current Position: PhD Student, Princeton University


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Michael McDermott, BS
Training Period in Lab: 2014-2016
Current Position: Software Engineer, Lifion


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Matthew Jones, BS
Training Period in Lab: 2014-2015
Current Position: Software Engineer, Orion Health (Auckland, New Zealand)


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Edward Chen, MS
Training Period in Lab: 2010-2013
Summary of Research: Enrichr: Interactive and Collaborative HTML5 Gene List Enrichment Analysis Tool
Current Position: Software Engineer, Spotify


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Ruth Dannenfelser, MSE
Training Period in Lab: 2010-2012
Summary of Research: Software Tools for Systems Biology
Current Position: PhD Student, Princeton University


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Simon Gordonov, MS
Training Period in Lab: 2011-2012
Summary of Research: Software Tools for Systems Biology
Current Position: PhD Student, MIT


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Christopher Tan, BS
Training Period in Lab: 2011-2012
Summary of Research: Software Tools for Systems Biology
Current Position: Medical Student, Saint Louis University School of Medicine


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Caroline Baroukh, PhD
Training Period in Lab: 2010-2011
Summary of Research: Embryonic Stem Cells Atlas of Pluripotency Evidence (ESCAPE) Database
Current Position: Postdoctoral Fellow, INRIA (France)


Visiting Undergraduate Students

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Benjamin Kaplan
Training Period in Lab: Summer 2015
Summary of Research: Integrative Analysis and Visualization of Gene Expression Signatures toward the Repurposing of FDA Approved Drugs as Antiviral Medications
Current Position: Undergraduate Student (Computer Science), Carnegie Mellon University


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Emily Kuang
Training Period in Lab: Summer 2015
Summary of Research: Assessing the Dimensionality of MCF7 Cells Response to Perturbations
Current Position: Undergraduate Student (Biomedical Informatics), New York City College of Technology


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Azu Lee, MS
Training Period in Lab: Summer 2015
Summary of Research: Interactive Mobile App Game for Deconvolution of Gene Set Modules from Gene Set Enrichment Analyses
Current Position: Software Development Engineer, Amazon


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Aditi Dandapani, BS
Training Period in Lab: 2009-2010
Summary of Research: Dynamical Model of Viral DI Particles
Current Position: PhD Student (Applied Mathematics), Columbia University


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Michael Komosinski, BS
Training Period in Lab: Summer 2011
Summary of Research: Integrating, Predicting, and Visualizing Mammalian Protein-Protein Interaction Networks
Current Position: Software Developer, Google


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John Zhuang, BS
Training Period in Lab: 2010
Summary of Research: Regulatory Network Created from Loss of Function and Gain of Function Studies of Mouse Embryonic Stem Cells
Current Position: MD/PhD Student, Cornell


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Mariola Szenk, BS
Training Period in Lab: 2009
Summary of Research: PathwayGenerator2: Automated Visualization of Signaling Pathways using Flash and ActionScript 3
Current Position: PhD Student, Stony Brook University


Visiting High School Students

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Mounica Kamesam
Training Period in Lab: Summer 2014 and 2015
Summary of Research: Automated Data Integration and Data Mining to Improve Breast Cancer Classification
Current Position: High School Student, Yorktown High School


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Axel Feldmann
Training Period in Lab: Summer 2014 and 2016
Summary of Research: Hepatocellular Carcinoma Patient Classification with Enrichment Vectors
Current Position: Undergraduate Student (Computer Science), Carnegie Mellon University


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Jayanath Krishnan
Training Period in Lab: Summer 2010
Summary of Research: Regulatory Signatures of Cancer Cell Lines Inferred from Expression Data
Current Position: Undergraduate (Biology), Yale University