Alumni

 

Former Ma’ayan Lab PhD students, postdoctoral fellows, bioinformaticians, and computational systems biologists have authored or co-authored publications in leading journals, including Nature, Science, PNAS, Nature Genetics, Nature Medicine, Bioinformatics and Science Signaling. The Ma’ayan Lab alumni have gone to leadership positions in industry and have also been recruited to academic positions. Several of our bioinformatics and computational systems biology research trainees have entered PhD programs at top tier institutions, including Princeton, MIT, Columbia, Duke and Cornell.

PhD Students

wang_headshot
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


duan_headshot
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


yan_kou.fw
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


h_xu.fw
Huilei Xu, PhD
Training Period in Lab: 2009-2012
Thesis: Analysis of Transcriptional Networks in mESCs
Current Position: Senior Bioinformatics Scientist, Genocea Biosciences


Postdoctoral Fellows


Nicolas Fernandez, PhD
Training Period in Lab: 2013-2017
Current Position: Computational Scientist, Icahn School of Medicine at Mount Sinai

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


clark_headshot
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)


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


a_mazloom.fw
Amin Mazloom, PhD
Training Period in Lab: 2008-2011
Summary of Research: Network Analysis of NURSA HT IP-MS Proteomics
Current Position: Vice President, Bioinformatics and Software, ProdermIQ, Inc.


Bioinformaticians and Software / Database Developers


Anders Dohlman, BA
Training Period in Lab: 2015-2017
Current Position: PhD Student, Duke University


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


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


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


ed_chen.fw
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


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


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


chris_tan.fw
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


caroline_baroukh.fw
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)


Undergraduate and Post-bac Research Trainees

troy_goff.fw
Troy Goff, BS
Training Period in Lab: 2015-2017
Current Position: Master’s Student (Data Science), Columbia University


esther_chen.fw
Esther Chen
Training Period in Lab: Summer 2016
Summary of Research: Cite-D-Lite: Chrome Extension for Data and Paper Citations with Text Importance Highlighting
Current Position: Undergraduate Student (Biomedical Engineering), Cornell University



Axel Feldmann
Training Period in Lab: Summer 2016
Summary of Research: X2K-Web: an Updated Web-based Version of the Expression2Kinases Pipeline
Current Position: Major: Undergraduate Student (Computer Science), Carnegie Mellon University


clarke.fw
Daniel Clarke
Training Period in Lab: Summer 2016
Summary of Research: Project 1) Adhesome 2016: An Updated Adhesome Site with Predictions of New Member Components; Project 2) Genes2WordCloud: A Biology Oriented Interactive Word Cloud Generator
Current Position: Undergraduate Student (Electrical Engineering/Computer Engineering), Fairleigh Dickinson University


lin.fw
Jennifer Lin
Training Period in Lab: Summer 2016
Summary of Research: Predicting Potential Drugs for Diabetic Nephropathy using L1000 Data
Current Position: High School Student, Oceanside High School


katie_lin.fw
Katie Lin, BS, MS
Training Period in Lab: Summer 2016
Summary of Research: Visualization of the Multi-Layered Data from the LINCS MCF10A Dense Cube Project
Current Position: Graduate Student (Computer Science), Columbia University


malyack.fw
Colette Malyack, BS, MS
Training Period in Lab: Summer 2016
Summary of Research: Predicting Experimental Platforms by Examining Gene-Set Content
Current Position: Machine Learning Co-op


sani.fw
Kevin Sani
Training Period in Lab: Summer 2016
Major:
Summary of Research: Dr. Gene Budger: Web App to Predict Drugs to Modulate the Expression of a Specific Gene
Current Position: Undergraduate Student (Chemistry/Economics), Harvard University


b_kaplan.fw
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


emily_k.fw
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


azu_lee.fw
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


aditi.fw
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


komosinski.fw
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


john_z.fw
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


mariola_s.fw
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

mounica.fw
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: Undergraduate Student (Computer Science), Northeastern University


axel.fw
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


jay.fw
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


Visiting Medical Students

barash.fw
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


r_webb.fw
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