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 Icahn School of Medicine at Mount Sinai, Princeton, MIT, Columbia, Duke, Cornell, and University of Pennsylvania.
MD/PhD Student
Alexandra Keenan, PhD
Training Period in Lab: 2017-2019
Thesis: Inferring Transcriptional Regulation by Data Integration
PhD Students
Zichen Wang, PhD
Training Period in Lab: 2013-2016
Thesis: Methods for Collecting, Improving and Exploring Mammalian Gene Expression Signatures
Qiaonan Duan, PhD
Training Period in Lab: 2012-2016
Thesis: Harnessing the LINCS L1000 Data for Drug Discovery and Drug Response Analysis
Yan Kou, PhD
Training Period in Lab: 2011-2015
Thesis: Big Data Analytics for Understanding Mechanism of Human Disease
Huilei Xu, PhD
Training Period in Lab: 2009-2012
Thesis: Analysis of Transcriptional Networks in mESCs
Postdoctoral Fellows
Kathleen Jagodnik, PhD
Training Period in Lab: 2016-2021
Nicolas Fernandez, PhD
Training Period in Lab: 2013-2017
Andrew Rouillard, PhD
Training Period in Lab: 2013-2016
Research Focus: Inferring Cell Signaling Pathways from LINCS
Neil Clark, PhD
Training Period in Lab: 2011-2015
Research Focus: Statistical Methods for Network Analysis in Systems Biology
Ben MacArthur, PhD
Training Period in Lab: 2008-2011
Research Focus: Systems Biology of mESCs
Amin Mazloom, PhD
Training Period in Lab: 2008-2011
Research Focus: Network Analysis of NURSA HT IP-MS Proteomics
Bioinformaticians and Software / Database Developers
Eryk Kropiwnicki, MS
Training Period in Lab: 2020-2021
Megan Wojciechowicz, MS
Training Period in Lab: 2017-2019
Current Position: PhD Student, Ma’ayan Laboratory, Icahn School of Medicine at Mount Sinai
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
Anders Dohlman, BA
Training Period in Lab: 2015-2017
Current Position: PhD Student, Duke University
Gregory Gundersen, MA
Training Period in Lab: 2014-2016
Current Position: PhD Student, Princeton University
Michael McDermott, BS
Training Period in Lab: 2014-2016
Matthew Jones, BS
Training Period in Lab: 2014-2015
Edward Chen, MS
Training Period in Lab: 2010-2013
Research Focus: Enrichr – Interactive and Collaborative HTML5 Gene List Enrichment Analysis Tool
Ruth Dannenfelser, MSE
Training Period in Lab: 2010-2012
Research Focus: Software Tools for Systems Biology
Simon Gordonov, PhD
Training Period in Lab: 2011-2012
Research Focus: Software Tools for Systems Biology
Christopher Tan, MD
Training Period in Lab: 2011-2012
Research Focus: Software Tools for Systems Biology
Caroline Baroukh, PhD
Training Period in Lab: 2010-2011
Research Focus: Embryonic Stem Cells Atlas of Pluripotency Evidence (ESCAPE) Database
Undergraduate and Post-bac Research Trainees
Tahmid Ahamed
Training Period in Lab: Summer 2020
Undergraduate, University of Pennsylvania
Project: Tracing Single Human and Mouse Gene Expression with Age
Samantha Bhuiyan
Training Period in Lab: Summer 2020
Undergraduate, Barnard College, Columbia University
Project: Functional Predictions for Undiagnosed Disease Network (UDN) Genes
Jessie Cheng
Training Period in Lab: Summer 2020
Undergraduate, Carnegie Mellon University
Project: Analysis and Visualization of SARS-CoV-2 Gene Expression Signatures
Charles Dai
Training Period in Lab: Summer 2020
Undergraduate, Cornell University
Project: Appyters to Extract, Transform, and Load (ETL) Data for the Harmonizome
Lucas Goldman
Training Period in Lab: Summer 2020
Undergraduate, Vanderbilt University
Project: L1000KD2: Analysis and Visualization of the LINCS L1000 shRNA Gene Knock-Down Dataset
Jason Hom
Training Period in Lab: Summer 2020
Undergraduate, University of Pennsylvania
Project: Gene Set Comparison Appyter
Julie Karam
Training Period in Lab: Summer 2020
Undergraduate, Brown University
Project: GeneBot and DrugBot – Slack Applications to Discover Knowledge about Genes and Drugs
Skylar Litz
Training Period in Lab: Summer 2020
Undergraduate, Harvey Mudd College
Project: Enrichr Visualization Appyters
Nicole Moiseyev
Training Period in Lab: Summer 2020
Undergraduate, Duke University
Project: An Appyter for the Visualization and Characterization of Cancer Patient Clusters based on RNA-Seq Profiles
Daniel Stein
Training Period in Lab: Summer 2020
Undergraduate, Massachusetts Institute of Technology
Project: Drugmonizome-ML: An Appyter for Predicting Drug Indications
Christine Yoon
Training Period in Lab: Summer 2020
Undergraduate, Duke University
Project: RNA-seq Co-Expression for Functional Prediction of Non-Coding Genes
Serena Zhang
Training Period in Lab: Summer 2020
Undergraduate, University of Pennsylvania
Project: The KINOMEscan and KEA3 Appyters
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
Current Position: Medical Student, Icahn School of Medicine at Mount Sinai
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, Genomics and Computational Biology, University of Pennsylvania Perelman School of Medicine
Vivian Utti
Training Period in Lab: Summer 2018
Undergraduate, Cornell University
Project: ChEA3: Transcription Factor Enrichment Analysis
Current Position: Medical Student, Icahn School of Medicine at Mount Sinai
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
Current Position: PhD Student, Bioinformatics and Integrative Genomics, Harvard University
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
Current Position: Bioinformatician, Ma’ayan Laboratory, Icahn School of Medicine at Mount Sinai
Patrycja Krawczuk
Training Period in Lab: Summer 2017
Undergraduate, Hunter College
Project: Automated Indexing of Bioinformatics Tools
Current Position: PhD Student, Computer Science, 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
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
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
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
Colette Malyack, BS, MS
Training Period in Lab: Summer 2016
Undergraduate, Fairleigh Dickinson University
Project: Predicting Experimental Platforms by Examining Gene-Set Content
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
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
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
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
Aditi Dandapani, PhD
Training Period in Lab: 2009-2010
Project: Dynamical Model of Viral DI Particles
Michael Komosinski, BS
Training Period in Lab: Summer 2011
Undergraduate, Colgate University
Project: Integrating, Predicting, and Visualizing Mammalian Protein-Protein Interaction Networks
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
Mariola Szenk, PhD
Training Period in Lab: 2009
Undergraduate, Hunter College
Project: PathwayGenerator2: Automated Visualization of Signaling Pathways using Flash and ActionScript 3
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
Jennifer Lin
Training Period in Lab: Summer 2016
Oceanside High School
Project: Predicting Potential Drugs for Diabetic Nephropathy using L1000 Data
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
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
Jayanath Krishnan
Training Period in Lab: Summer 2010
Mahopac High School
Project: Regulatory Signatures of Cancer Cell Lines Inferred from Expression Data
Visiting Medical Students
Andrew Warburton
Training Period in Lab: Summer 2019
Project: D2S2 – Collections of Disease and Drug Centric Gene Sets
Alexander Barash, MD
Training Period in Lab: 2007-2008
Research Focus: Systems Pharmacology
Ryan Logan Webb, MD
Training Period in Lab: 2007-2008
Research Focus: Software Tools for Systems Biology