Lab Members

Genevieve Stein-O'Brien, PhD, MHS -- PI

Dr. Stein-O'Brien is an Assistant Professor in the Neuroscience Department at Johns Hopkins University with affiliations in the Brain Science Institute, the Division of Quantitative Sciences in the Department of Oncology, the McKusick-Nathans Department of Genomics Medicine , the Institute for Data Intensive Engineering and Science and the Kavli Neuroscience Discovery Institute . Dr. Stein-O'Brien's research is focused on the stochastic processes underlying gene regulation in dynamic biological systems. Specifically, she develops computational, statistical, and molecular methods for pattern recognition, latent space detection, and data integration in high-throughput omics.

Boris Brenerman, PhD -- Postdoctoral fellow

Boris studied Bioengineering at UC Santa Cruz and wrote his doctoral thesis on the use of Random Forest techniques in the analysis of single-cell data at Johns Hopkins University. Boris is interested in developing analytic techniques that can capture the conditional changes in interactions between biochemical pathways, which he hopes to use in the study of the biology of aging. His current work focuses on extending the results of RF-based analysis of fate and commitment decisions that cells make using transformer-based models, in order to examine the localization of error to particular domains and interactions when systems such as the brain are perturbed.

Chaichontat (Richard) Sriworarat -- PhD Candidate, Neuroscience

Richard is a PhD candidate in the Neuroscience Training Program at Johns Hopkins University. He received his Bachelor of Science in Engineering degree from Duke University. His research focuses on investigating the molecular mechanisms underlying brain development using spatial and high-throughput single-cell transcriptomics methods. He is the lead developer of the Samui browser, a tool for visualizing and analyzing spatial transcriptomics data.

Hunter Giles -- PhD Candidate, Human Genetics and Genomics

Hunter is a PhD candidate in the Human Genetics and Genomics program at Johns Hopkins University. He received his bachelor's degree from Brigham Young University, majoring in Molecular Biology and minoring in Economics. He also graduated with University Honors, completing a thesis project using promoter bashing in zebrafish models to explore cis-regulatory promoters involved with congenital heart disease. Before grad school, he spent a year modeling the accuracy of industry variant classification protocols in hereditary cancer gene panels. His current project applies disentanglement methods to postmortem patient samples of amyotrophic lateral schlerosis (ALS) and frontotemporal dementia disease cases. Outside the lab, he enjoys baking sourdough bread, (sometimes) enjoys custom house repair projects, and loves spending time with his wife and two kids.

Kyla Woyshner -- PhD Candidate, Human Genetics and Genomics

Kyla is a PhD candidate in the Human Genetics and Genomics program at Johns Hopkins University. She completed her bachelor's degree at UC Berkeley, double majoring in Computer Science and Molecular/Cell Biology, with an emphasis in neurobiology. She joined the Stein O'Brien lab in 2022. Her thesis focuses on developing and improving novel algorithms for non-negative matrix factorization methods to uncover biological signatures in neurodegenerative disease pathology.

Ryan Palaganas -- PhD Candidate, BCMB

Ryan is a PhD candidate in the Biology, Cellular and Molecular Biology program at Johns Hopkins University. He completed his bachelor's degree at Rowan University, majoring in Biochemistry. He then became a post-bac IRTA fellow at the National Institute on Drug Abuse. He joined the Stein O'Brien lab in 2023. He is currently developing novel techniques to improve simultaneous spatial gene and protein detection to understand the development of gene and protein signatures related to tauopathies.

Parker Stevenson -- PhD Candidate, BCMB

Parker Stevenson is a PhD candidate in the Biochemistry, Cellular, & Molecular Biology (BCMB) predoctoral training program at the Johns Hopkins University School of Medicine (JHUSOM). She completed her bachelor's degree at the University of Tennessee Knoxville, where she double-majored in Neuroscience and BCMB. During her undergraduate, she conducted cellular-level research on an X-linked neurodevelopmental disease. She was accepted as a Post-baccalaureate IRTA Fellow at the National Institute of Mental Health, where she performed systems-level neuroscience research in the Unit on Functional Neural Circuits. She began her graduate career at JHUSOM in 2022, and she joined the Stein-O'Brien lab for her thesis work investigating gene signatures of collectively invasive mammary epithelial cells -- both in the context of healthy glandular development and early metastasis -- using *in silico* transfer learning, single-cell resolution spatial and sequencing technologies, and *ex vivo* organoid assays.

Danyon Gedris -- PhD candidate, Human Genetics and Genomics

Danyon is a student in the Human Genetics and Genomics PhD program at the Johns Hopkins University School of Medicine. His research focuses on cortical development. He aims to improve the spatiotemporal understanding of human corticogenesis by analyzing murine development using spatial transcriptomics, single-nucleus transcriptomics and agent-based computer modeling. So far he has built on David Zhou's work to make the PhysiCell model biologically accurate for mammals. He believes these models can be a starting point to model how regulation of genomic data results in complex tissue development.

Jon Sundstrom -- PhD student, Human Genetics and Genomics

Jon Sundstrom is a PhD student in the Human Genetics and Genomics predoctoral training program at the Johns Hopkins University School of Medicine. He did his undergraduate studies at the University of Rhode Island where he earned his bachelor's degree in Biotechnology. Post-graduation, Jon worked as a research technician at McLean Hospital where he studied bioenergetic dysregulation in Alzheimer's disease (AD) using iPSC models. Additionally, he worked as a research associate at the UMass Chan Medical school also studying AD using brain organoid models. In the Stein-O'Brien lab, he is interested in continuing research on neurodegeneration, using spatial transcriptomics and multi-omics methods.

Crystal Favorito -- Medical Student

Crystal studies the propogation of tau in Alzheimer's Disease using PhysiCell, a computer modeling platform. She is modeling local and axonal propgation and integrating microglia activation in those contexts.

Spruha Deo -- Junior

Niejeen Abdul-Kadir -- Junior

Anthony Clark -- Sophomore

Minal Mustafa -- Sophomore

Derek Truong -- Sophomore -- BSi SiP intern

Zachary Nicholas -- PhD Candidate, Human Genetics and Genomics

Zachary completed his PhD in 2026 under the supervision of Dr. Stein O'Brien as part of the Human Genetics and Genomics predoctoral training program at the Johns Hopkins University School of Medicine. He did his undergraduate studies at the University of Maryland, Baltimore County (UMBC) where he earned his bachelor's degree in Anthropology. During his time at UMBC, he conducted both anthropological and biological research. He joined Dr. Stein O'Brien's lab in 2020. He was selected as an NIH All of Us Research Scholar for the 2023-2024 cohort and was also selected in 2024 as a NIH Neuroscience DSPAN Scholar. He conducted research investigating genetic variants associated with insomnia, in addition to his thesis work. His thesis focused on investigating how changes to neural progenitor cell cycle dynamics, external signaling, and localization alter fate determination and gene expression in the developing cerebral cortex using molecular biology, transcriptomic, and computational methods. After completing his PhD, he moved to Baylor College of Medicine to work on multi-omic methods for dissecting common and distinct architecture of psychiatric disorders across ancestries.

Jeanette Johnson -- PhD Candidate, Immunology, Current: Postdoctoral fellow, University of Maryland

Jeanette developed pyCoGAPS, a Bayesian nonnegative matrix factorization implemented via Markov Chain Monte Carlo.

Kendall Reid -- Senior Software Engineer

Kendall is an aspiring researcher in machine learning interpretability and disentanglement. He worked on developing methods to probe biological deep learning models internal representations to learn how they are making predictions. He spent time in the lab while working on a Masters of Bioinformatcs at the Johns Hopkins Bloomberg School of Public Health. He left the Stein O'Brien lab to begin a PhD in Computer Science at Johns Hopkins University.

David Zhou -- Undergraduate researcher, Neuroscience, Current: Postbachelor researcher, Johns Hopkins University - Bayview

David developed a computational model of murine cerebrocortical development using PhysiCell as a medium for hypothesis testing alternative to conventional in-vivo methods.

Ashley Tsang -- Undergraduate researcher, Current: Bioinformatics PhD Candidate, University of Michigan

Ashley developed the CellXGene inferface for CoGAPS, a Bayesian nonnegative matrix factorization implemented via Markov Chain Monte Carlo.

Asher Baraban -- Intern, Software Development, Current:

While Asher was an undergraduate student at WashU in St. Louis, MO., he worked on developing scProject, a single cell transfer learning tool for visualization and exploration of latent space utilization.

Stein-O'Brien Lab