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
Master’s Student
Eryk Kropiwnicki, MS
Training Period in Lab: 2019-2020
Postdoctoral Fellows
Minji Jeon, PhD
Training Period in Lab: 2020-2022
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, Software Engineers, and Data Scientists
Nasheath Ahmed, BS, AB
Training Period in Lab: 2022-2024
Stephanie Olaiya, ScB
Training Period in Lab: 2023-2024
Eden Deng, BS
Training Period in Lab: 2023-2024
Zhuorui (Sherry) Xie, BA
Training Period in Lab: 2020-2024
Juncheng Pan, BS
Training Period in Lab: 2022
Eryk Kropiwnicki, MS
Training Period in Lab: 2020-2022
Megan Wojciechowicz, MS
Training Period in Lab: 2017-2019
Denis Torre, BS
Training Period in Lab: 2016-2019
Shai Magidi, MEng
Training Period in Lab: 2016-2017
Anders Dohlman, BA
Training Period in Lab: 2015-2017
Gregory Gundersen, MA
Training Period in Lab: 2014-2016
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
Alexandra Agris
Training Period in Lab: Summer 2023
Bioengineering (major), Computer Science (minor), Stanford University
Gaurvi Awasthi
Training Period in Lab: Summer 2023
Biology and Society (major), Biometry and Statistics (minor), Cornell University
Rhea Desai
Training Period in Lab: Summer 2023
Biomedical Engineering, Cornell University
Nooha Kawsar
Training Period in Lab: Summer 2023
Molecular Biology, Princeton University
Adam Lalani
Training Period in Lab: Summer 2023
Computer Science and Biology, Brown University
Hannah Lee
Training Period in Lab: Summer 2023
Computer Science (major), Computational Biology and Bioinformatics (minor), Duke University
Lauren Malek
Training Period in Lab: Summer 2023
Electrical and Computer Engineering, Princeton University
Jacob Mayourian
Training Period in Lab: Summer 2023
Computer Science (major), Data Science (minor), Cornell University
Osaiyekemwen Ruth Ogbemudia
Training Period in Lab: Summer 2023
Biomedical Engineering (major), Anthropology (minor), Cornell University
Shriya Rangaswamy
Training Period in Lab: Summer 2023
Biological Engineering (major), Mathematics (minor), Massachusetts Institute of Technology
Abigail Zaroff
Training Period in Lab: Summer 2023
Bioinformatics and Computational Biology, Duke University
Mason Zhang
Training Period in Lab: Summer 2023
Computer Science (major), Philosophy (minor), Brown University
Clara Chen
Training Period in Lab: Summer 2022
Statistics, Harvard University
Sophia Colmenares
Training Period in Lab: Summer 2022
Chemical and Biological Engineering, Princeton University
Eden Deng
Training Period in Lab: Summer 2022
Statistics, Computer Science, Duke University
Lauren Druz
Training Period in Lab: Summer 2022
Biology and Society, Cornell University
Reid Fleishman
Training Period in Lab: Summer 2022
Computer Science, Cornell University
Sophie Goldman
Training Period in Lab: Summer 2022
Computer Science and Information Science, University of Pennsylvania
Jason Han
Training Period in Lab: Summer 2022
Computer Science, Rice University
Cole Heine
Training Period in Lab: Summer 2022
Biochemistry and Molecular Biology, Brown University
David Lewis
Training Period in Lab: Summer 2022
Computation and Cognition, Massachusetts Institute of Technology
Nhi Nguyen
Training Period in Lab: Summer 2022
Neuroscience, Dartmouth College
Hannah Qu
Training Period in Lab: Summer 2022
Biomedical Engineering, Johns Hopkins University
Derek Wang
Training Period in Lab: Summer 2022
Biological Sciences, Computer Science, Carnegie Mellon University
Eric Che
Training Period in Lab: Summer 2021
Computer Science and Pre-Med, Columbia University
Kerwin Chen
Training Period in Lab: Summer 2021
Biometry and Statistics, Cornell University
Sarah Fida
Training Period in Lab: Summer 2021
Computer Science and Biology, Williams College
Sophie Guo
Training Period in Lab: Summer 2021
Biological Engineering and Computer Science, Massachusetts Institute of Technology
Angelina Huang
Training Period in Lab: Summer 2021
Biomedical Engineering and Information Science, Cornell University
Marilyn Meyers
Training Period in Lab: Summer 2021
Electrical Engineering and Computer Science, Massachusetts Institute of Technology
Gabrielle Pile
Training Period in Lab: Summer 2021
Computer Science, Brandeis University
Helen Propson
Training Period in Lab: Summer 2021
Computer Science and Engineering, Massachusetts Institute of Technology
Emily Slobodenyuk
Training Period in Lab: Summer 2021
Biological Sciences and Computer Science, Carnegie Mellon University
Hunter Smith
Training Period in Lab: Summer 2021
Computer Science, University of Chicago
Alexander Tsai
Training Period in Lab: Summer 2021
Molecular Biology, Statistics and Machine Learning, Princeton University
Sophia Vincoff
Training Period in Lab: Summer 2021
Biomedical Engineering and Computer Science, Duke University
Cindy Xiong
Training Period in Lab: Summer 2021
Mathematical Sciences, Carnegie Mellon University
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, Co