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.

MD/PhD Student


Alexandra Keenan, PhD 
Training Period in Lab: 2017-2019
Thesis: Inferring Transcriptional Regulation by Data Integration
Current Position: Clinical training at ISMMS


PhD Students


Zichen Wang, PhD
Training Period in Lab: 2013-2016
Thesis: Methods for Collecting, Improving and Exploring Mammalian Gene Expression Signatures


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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: Vice President of Clinical Data Science, Xbiome


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Huilei Xu, PhD
Training Period in Lab: 2009-2012
Thesis: Analysis of Transcriptional Networks in mESCs
Current Position: Investigator III, Novartis Institutes for BioMedical Research (NIBR)


Postdoctoral Fellows


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


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


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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: 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: Senior Director, Discovery Bioinformatics, Progenity, Inc.


Bioinformaticians and Software / Database Developers


Megan Wojciechowicz, MS
Training Period in Lab: 2017-2019
Current Position: PhD Student, Icahn School of Medicine at Mount Sinai


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Denis Torre, BS
Training Period in Lab: 2016-2019
Current Position: PhD Student, Icahn School of Medicine at Mount Sinai



Shai Magidi, MEng
Training Period in Lab: 2016-2017
Current Position: PhD Student, Tulane University



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


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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: Lead Platform Engineer, Lifion


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Matthew Jones, BS
Training Period in Lab: 2014-2015
Current Position: Software Engineer, Market2x (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: Staff 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, PhD
Training Period in Lab: 2011-2012
Summary of Research: Software Tools for Systems Biology
Current Position: Scientist, Vertex Pharmaceuticals


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Christopher Tan, MD
Training Period in Lab: 2011-2012
Summary of Research: Software Tools for Systems Biology
Current Position: Resident Physician, 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: Research Manager, INRA (France)


Undergraduate and Post-bac Research Trainees


Zaire Bryant
Training Period in Lab: Summer 2019
Undergraduate, Rutgers University
Project: Global Analysis of Gene Sets and Signatures Associated with Senescence



Elizabeth Jung
Training Period in Lab: Summer 2019
Undergraduate, Cornell University
Project: FAIRification of NIH Common Fund Programs’ Datasets



Alessandra LaRocco
Training Period in Lab: Summer 2019
Undergraduate, Yale University
Project: Predicting Novel Targets and Drugs to Induce Autophagy



Damon Pham
Training Period in Lab: Summer 2017, Fall 2017, Summer 2019
Undergraduate, Indiana University Bloomington
Projects: Gencodr – Gene Set Enrichment Analysis with Deep Learning and Developing Novel Gene Set Enrichment Analysis Algorithms



Samuel Maltz
Training Period in Lab: Summer 2019
Undergraduate, The Cooper Union
Project: Gene Expression Imputations with the Latent Space of RNA-seq Data from ARCHS4



Kaeli Rizzo
Training Period in Lab: Summer 2019
Undergraduate, Georgia Institute of Technology
Project: Predicting the Function and Disease Associations of Under-Studied GPCRs, Ion Channels, and Protein Kinases



Allison Seiden
Training Period in Lab: Summer 2019
Undergraduate, Johns Hopkins University
Project: Analysis of Gene Sets Extracted from a GWAS of the UK Biobank



Ingrid Shu
Training Period in Lab: Summer 2019
Undergraduate, Amherst College
Project: KEA3: Kinase Enrichment Analysis Version 3



David Szanto
Training Period in Lab: Summer 2019
Undergraduate, Harvard University
Project: PALM2A – Mobile and Web App for Predicting Physiological Age from Lab Tests and Vital Signs



Justin Williams
Training Period in Lab: Summer 2019
Undergraduate, Cornell University
Projects: Drug Repurposing Strategies for Alzheimer’s Disease
and PeerShake – A System to Transform the Scientific Review Process



Katherine Chew
Training Period in Lab: Summer 2018
Undergraduate, Massachusetts Institute of Technology
Project: Predicting Gene Signatures for Understudied Small Molecules



Zachary Flamholz
Training Period in Lab: Summer 2018
Undergraduate, Princeton University
Project: modEnrichr: Gene List Enrichment Analysis Tools for Fish, Fly, Worm, and Yeast
Current Position: MD/PhD Student, Albert Einstein College of Medicine



Hannah Freid
Training Period in Lab: Summer 2018
Undergraduate, Princeton University
Project: Integrative Analysis to Suggest Combination Therapies for Ovarian Cancer



Kevin Moses
Training Period in Lab: Summer 2018
Undergraduate, Yale University
Project: JOIN: The Journal of Interactive Notebooks



Vivek Sriram
Training Period in Lab: Summer 2018
Undergraduate, Duke University
Project: Predicting Diabetes Risk from Labs and Vitals with Machine Learning
Current Position: PhD Student, University of Pennsylvania Perelman School of Medicine



Vivian Utti
Training Period in Lab: Summer 2018
Undergraduate, Cornell University
Project: ChEA3: Transcription Factor Enrichment Analysis



Lily Wang
Training Period in Lab: Summer 2017, Fall 2018, Summer 2018
Undergraduate, Cornell University
Projects: FAIRshake: Digital Objects Evaluation System and FAIRshake: Toolkit to Assess the FAIRness of Biomedical Digital Objects



Sherry Xie
Training Period in Lab: Summer 2018
Undergraduate, Cornell University
Project: Standard API to Enable Semantic Integration of the Tools Developed by the Ma’ayan Lab



Patrycja Krawczuk
Training Period in Lab: Summer 2017
Undergraduate, Hunter College
Project: Automated Indexing of Bioinformatics Tools
Current Position: PhD Student, University of Southern California



Marina Latif
Training Period in Lab: Summer 2017
Undergraduate, Princeton University
Project: Mining the Human Kinome



Joyce (Hyojin) Lee
Training Period in Lab: Summer 2017
Undergraduate, Princeton University
Project: Predicting Gene Function and PPIs with Co-Expression Data



Ariel Leong
Training Period in Lab: Summer 2017
Undergraduate, Stanford University
Project: ChEA3 – Improving Transcription Factor Enrichment Analysis by Data Integration



Christopher Tseng
Training Period in Lab: Summer 2017
Undergraduate, Emory University
Project: Analysis and Visualization of MCF10A Data for the LINCS Common Project
Current Position: Medical Student, Rutgers New Jersey Medical School



Charlotte Zuber
Training Period in Lab: Summer 2017
Undergraduate, Rutgers University
Project: Visualization of the Space of 200,000 Annotated Gene Sets


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Esther Chen
Training Period in Lab: Summer 2016
Undergraduate, Cornell University
Project: Cite-D-Lite: Chrome Extension for Data and Paper Citations with Text Importance Highlighting
Current Position: Medical Student, SUNY Downstate Medical Center College of Medicine



Axel Feldmann
Training Period in Lab: Summer 2016
Undergraduate, Carnegie Mellon University
Project: X2K-Web: an Updated Web-based Version of the Expression2Kinases Pipeline
Current Position: PhD Student, Massachusetts Institute of Technology


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Daniel Clarke
Training Period in Lab: Summer 2016
Undergraduate, Fairleigh Dickinson University
Projects: Adhesome 2016: An Updated Adhesome Site with Predictions of New Member Components and Genes2WordCloud: A Biology Oriented Interactive Word Cloud Generator
Current Position: Data Science Analyst II, Ma’ayan Laboratory, Icahn School of Medicine at Mount Sinai


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Katie Lin, BS, MS
Training Period in Lab: Summer 2016
Undergraduate, Columbia University
Project: Visualization of the Multi-Layered Data from the LINCS MCF10A Dense Cube Project
Current Position: Analyst, Brigham and Women’s Hospital


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Colette Malyack, BS, MS
Training Period in Lab: Summer 2016
Undergraduate, Fairleigh Dickinson University
Project: Predicting Experimental Platforms by Examining Gene-Set Content
Current Position: PhD Student, New Jersey Institute of Technology


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Kevin Sani
Training Period in Lab: Summer 2016
Undergraduate, Harvard University
Project: Dr. Gene Budger: Web App to Predict Drugs to Modulate the Expression of a Specific Gene
Current Position: Senior Associate Consultant, Bain & Company


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Benjamin Kaplan
Training Period in Lab: Summer 2015
Undergraduate, Carnegie Mellon University
Project: Integrative Analysis and Visualization of Gene Expression Signatures toward the Repurposing of FDA Approved Drugs as Antiviral Medications
Current Position: Cancer Genomics Research Associate, Foundation Medicine


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Emily Kuang
Training Period in Lab: Summer 2015
Undergraduate, New York City College of Technology
Project: Assessing the Dimensionality of MCF7 Cells Response to Perturbations


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


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Aditi Dandapani, PhD
Training Period in Lab: 2009-2010
Project: Dynamical Model of Viral DI Particles
Current Position: Postdoctoral Fellow, Ecole Polytechnique


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Michael Komosinski, BS
Training Period in Lab: Summer 2011
Undergraduate, Colgate University
Project: 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
Undergraduate, Columbia University
Project: Regulatory Network Created from Loss of Function and Gain of Function Studies of Mouse Embryonic Stem Cells


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Mariola Szenk, PhD
Training Period in Lab: 2009
Undergraduate, Hunter College
Project: PathwayGenerator2: Automated Visualization of Signaling Pathways using Flash and ActionScript 3
Current Position: Postdoctoral Researcher, Stony Brook University


Visiting High School Students


Inko Bovenzi
Training Period in Lab: Summer 2019
Hunter College High School
Project: Crossing Gene Sets Across Libraries to Discover Novel Pathways



Derek Wang
Training Period in Lab: Summer 2018
East Brunswick High School
Project: GTEx2BioJupies: Jupyter Notebook Analysis Reports from Interactive Selection of GTEx Portal Samples
Current Position: Undergraduate, Carnegie Mellon University


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Jennifer Lin
Training Period in Lab: Summer 2016
Oceanside High School
Project: Predicting Potential Drugs for Diabetic Nephropathy using L1000 Data


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Mounica Kamesam
Training Period in Lab: Summer 2014 and 2015
Yorktown High School
Project: Automated Data Integration and Data Mining to Improve Breast Cancer Classification
Current Position: Undergraduate, Northeastern University


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Axel Feldmann
Training Period in Lab: Summer 2014 and 2016
Hunter College High School
Project: Hepatocellular Carcinoma Patient Classification with Enrichment Vectors
Current Position: PhD Student, Massachusetts Institute of Technology


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Jayanath Krishnan
Training Period in Lab: Summer 2010
Mahopac High School
Project: Regulatory Signatures of Cancer Cell Lines Inferred from Expression Data
Current Position: Researcher, IBM Watson Health


Visiting Medical Students


Andrew Warburton
Training Period in Lab: Summer 2019
Project: D2S2 – Collections of Disease and Drug Centric Gene Sets
Current Position: Medical Student, Icahn School of Medicine at Mount Sinai


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Alexander Barash, MD
Training Period in Lab: 2007-2008
Research Focus: Systems Pharmacology
Current Position: Vitreoretinal Surgeon, New York Retina Care


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