Jesse Engreitz, Ph.D.

Principal Investigator

Jesse is currently an Assistant Professor at Stanford University in the Department of Genetics and the Children’s Heart Center Basic Sciences and Engineering (BASE) Initiative, and is a recipient of the NHGRI Genomic Innovator Award. He co-leads a Functional Characterization Center at Stanford for the Impact of Genomic Variation on Function (IGVF) Consortium, a Data Analysis and Validation Center for the NHGRI MorPhiC Consortium, and is an investigator in the Novo Nordisk Foundation Center for Genomic Mechanisms of Disease at the Broad Institute.

Previously, Jesse was a Junior Fellow at the Harvard Society of Fellows and led a research group at the Broad Institute of MIT and Harvard. During his postdoctoral fellowship at the Broad Institute, Jesse developed large-scale CRISPR tools to map enhancer-gene regulation with Eric Lander and Nir Hacohen, and launched the Variants-to-Function (V2F) Initiative to connect genetic disease variants to their molecular and cellular functions. Jesse previously attended Stanford University, where he developed computational algorithms for analyzing gene expression with Russ Altman, and completed his PhD in the Harvard-MIT Division of Health Sciences and Technology, where he studied genome regulation by long noncoding RNAs with Eric Lander and Mitch Guttman. His research has been supported by the National Human Genome Research Institute, National Heart, Lung, and Blood Institute, Additional Ventures, Foundations for the National Institutes of Health, Harvard Society of Fellows, Fannie and John Hertz Foundation, and Department of Defense. Outside the lab, Jesse enjoys playing jazz/rock/funk, testing Chinese recipes, and surfing.

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Dulguun Amgalan, Ph.D.

Postdoctoral Fellow

Dulguun aims to understand how enhancer-gene connections rewire across cell types, cell states, and dynamic cellular trajectories. She is particularly interested in comprehensively mapping the enhancer-gene regulation during cardiac cell differentiation and human heart development in the hopes to discover the genetic basis of heart diseases. Before joining the Engreitz Lab, Dulguun studied the molecular mechanisms of cell death and developed small molecule inhibitors as prototype drugs to prevent cardiac toxicity. Dulguun holds a Ph.D. in Biomedical Sciences from Albert Einstein College of Medicine and a B.S. in Biochemistry from the University of Tokyo.

Hadley Bickford

Administrative Associate

Hadley is originally from the Napa Valley, and attended Iowa State University and received a BS in Animal Science. She returned to the Bay Area after graduation to work at Peninsula Equine Medical Center as a veterinary technician. During her time there, she completed the Veterinary Allied Staff Education Accelerated RVT Program, and received her Registered Veterinary Technician License in 2018. She then took over duties as Lead Technician and Office and Hospital Manager, overseeing all day to day operations of the practice. In her free time, Hadley enjoys travelling, hiking, spending time on the 80 horse ranch where she lives, and showing her own horse in Western Pleasure competitions around the country.

Danila Bredikhin, Ph.D.

Postdoctoral Scholar, Joint with Anshul Kundaje Lab

Danila is focusing on multimodal models that integrate sequence information with gene expression in order to study the enhancer-gene interactions at single-cell and base-pair resolution. He is interested in finding ways to improve the predictive power of the models that determine the functional outcome of genetic variation in cis-regulatory elements. Danila completed his Ph.D. at the European Molecular Biology Laboratory where he worked on statistical integration methods for single-cell multimodal omics in the group of Oliver Stegle. His research includes developing statistical methods and computational instruments for multimodal data integration and devising approaches to identify transcriptional regulators from perturbation screens. Danila is also a co-founder and core developer of scverse, an open-source consortium that aims to drive development and support maintenance of the foundational tools in single-cell genomics. Beyond the lab, Danila enjoys cycling, sailing, music, and tea.

Xiangmeng Shawn Cai, M.S.

PhD Student (Bioengineering), Joint with Lacra Bintu Lab

Shawn aims to understand the functions and dynamics of cis-regulatory elements, with a specific focus on the role of transcription factors (TFs). His research interests encompass exploring how TFs influence the 3D structure of the genome and how the interactions between TFs and their co-factors contribute to the functions of cis-regulatory elements. To do this, he seeks to develop high-throughput tools designed to perturb, re-write and restructure the human genome. Before joining the Engreitz Lab, Shawn obtained a B.S. of Bioengineering and a M.S. of Computer Science from Stanford University. As an undergraduate student, he worked in Dr. Stanley Qi’s lab to develop synthetic biology tools, which enabled him to understand how 3D localization in the nucleus can impact the functionality of genetic elements. Outside of the lab, he enjoys reading, going to concerts, and playing piano.

Stephanie Conley

Lab Manager and Research Associate

Stephanie is interested in the role enhancers and promoters play in heart disease, specifically congenital heart diseases. Before coming to the Engreitz Lab, Stephanie was a researcher in Irving Weissman’s lab at Stanford, where she contributed to single-cell RNA-seq projects focused on building the human and mouse cell atlas. Some of Stephanie’s work includes the identification of the human skeletal stem cell, the molecular cell atlas of human lung and brain, and the mouse single-cell atlas. Stephanie left the California Mojave Desert to complete her undergraduate degree at UC San Diego, where she studied Biochemistry and Cell Biology. Currently, she is studying for her master’s in Computer Science. Outside the lab, she likes to expand her plant collection and explore Bay Area hiking trails.

Ben Doughty

Collaborator, PhD Student (Genetics) in Will Greenleaf Lab

Ben joined the Engreitz Lab at the Broad Institute to develop experimental and computational tools to study enhancers and noncoding GWAS variants at single-cell resolution. He continues to collaborate with the lab as PhD student in the Stanford Genetics program. He is enthusiastic about Bayesian statistics and elegant pipelines. Before joining the Engreitz Lab, Ben completed an undergraduate degree at Brown University, where he studied DNA re-replication and origin mapping with Susan Gerbi. Outside of lab, he enjoys riding his bike and eating feta cheese, and you can often find him swing dancing around Boston.

James Galante

Research Associate, Joint with Lars Steinmetz Lab

James is interested in the mechanisms and determinants of enhancer-gene regulatory interactions. Specifically, he is interested in integrating properties of cis-regulatory elements with ML/AI methods to understand the sequence determinants of enhancer-gene regulation. Before joining the Engreitz lab, James graduated from the University of Notre Dame with a degree in Science-Computing. There, he compared in vivo neural recordings from vision systems with numerical activations from neural networks while also studying the genetics of rare neurodevelopment diseases like Miller-Dieker Syndrome. He is ultimately interested in training ML/AI models on genetic data and probing these models to better understand gene regulation. In his free time, he sings Jazz and Rock and plays piano.

Andreas Gschwind, Ph.D.

Research Scientist, Joint with Lars Steinmetz Lab

Andreas’ main interests lie in understanding how cis-regulatory elements, such as enhancers, shape a cell’s transcriptome and how genetic variation affects these regulatory mechanisms. To this end, he analyzes pooled CRISPR perturbation screens to learn fundamental rules of gene regulation, and to build and evaluate computational methods that predict regulatory connections across the genome and cell types. As part of his postdoc, Andreas led the bioinformatics work for the development of Targeted Perturb-seq (TAP-seq), a novel experimental approach that combines pooled CRISPRi perturbations with targeted single-cell RNA-seq readout. TAP-seq enables identifying effects of perturbed regulatory elements with high sensitivity at low sequencing cost. Before coming to Stanford, Andreas obtained his PhD from the University of Lausanne in Switzerland, where he studied the functional impact of genetic variation on chromatin landscape and gene expression. Outside of work, Andreas likes to explore California’s stunning nature.

Philine Guckelberger, M.S.

Collaborator, Max Planck Institute for Molecular Genetics

Philine aims to understand how 3D chromosome conformation controls enhancer function, and is developing new tools to perturb enhancers in vivo in mice. Philine worked in the Engreitz and Lander Labs at the Broad Institute, and continues to collaborate as a PhD student in the laboratory of Alex Meissner. Previously, Philine completed her undergraduate thesis work at the Max-Planck Institute for Molecular Genetics in the laboratory of Stefan Mundlos studying transcriptional control by enhancers in context of 3D genome architecture during limb development. Philine loves CTCF and big faux fur coats. Outside of the lab you will probably find her in the nearest thrift store playing Lana del Rey.

Jacob Huang

Research Associate, Broad Institute, Joint with Ray Jones Group

Jacob is interested in understanding gene regulatory networks across the human genome. Specifically, he aims to comprehensively map enhancer-gene connections across various cell types and dynamic systems by studying the differentiation of hepatocytes, with the hope of uncovering mechanisms driving genetic diseases. Before joining the Human Gene Regulation Map team at the Broad Institute, Jacob earned a B.A. in Biology from the University of Pennsylvania with a concentration in molecular biology. During his undergraduate studies, Jacob researched cancer-related regulatory proteins linked to neurodegeneration at the Abramson Cancer Research Institute. Outside the lab, Jacob enjoys biking, hiking, cooking, and amateur bartending.

Revant Gupta, Ph.D.

Computational Scientist, Joint with Anshul Kundaje Lab

Revant is interested in identifying the causal impact of genomic variation on phenotypes, mediated via genomic regulatory mechanisms and gene expression, utilizing single-cell multi-omic and perturbation data. He aims to integrate a mechanistic understanding of biological systems into the development of his machine-learning models to enhance their interpretability. Revant has a PhD from the University of Tübingen, where he developed machine-learning models of cell differentiation processes that enabled the data-driven discovery of convergent trajectories and the identification of transitional cell states in CD8+ T-cell differentiation. When he has time, Revant enjoys rock climbing & bouldering or satisfying his intellectual curiosity in science & history.

Helen Kang

Collaborator, PhD student at MIT in Rajat Gupta and Bonnie Berger Labs

Helen is interested in studying gene regulatory networks in cardiovascular disease. Helen worked as a computational research associate in the Engreitz Lab from 2020-2023, where she led the development of the Variant-to-Gene-to-Program method its application to Perturb-seq data. In 2023, she joined the PhD Programs in Computational Systems Biology at MIT. She continues to collaborate with the Engreitz Lab. Previously, Helen worked on information integration in nonlinear systems in the Sommer Lab at the Redwood Center for Theoretical Neuroscience as an undergraduate student. She completed her undergraduate studies in Applied Mathematics and Molecular and Cell Biology with Neurobiology emphasis at UC Berkeley. Outside the lab, she enjoys taking care of her plants and exploring local cafes.

Evelyn Jagoda, Ph.D.

Research Scientist, Broad Institute, Joint with Ray Jones Group

Evelyn aims to create maps of noncoding genomic regulation in diverse human cell types and to connect genetic variants in regulatory elements to disease. Before joining the Human Gene Regulation Map team at the Broad Institute, Evelyn completed a Ph.D. at Harvard in the Evolutionary Biology Department, working on connecting positively-selected genetic variation that entered the human gene pool via interbreeding with Neanderthals to non-coding impacts and phenotypic changes, particularly in immune cells. Prior to this, Evelyn received a M.Phil. in Biological Anthropological Science at the University of Cambridge and a B.A. in Evolutionary Biology of the Human Species at Columbia University.

Yannick Lee-yow

PhD Student (Genetics), Joint with Howard Chang Lab

Yannick is a PhD student and NSF Graduate Research Fellow in the Stanford Genetics program, co-mentored by Jesse Engreitz and Howard Chang. He is interested in understanding the roles and underlying mechanisms of circular RNAs in gene regulation, development, and human disease. Before joining the Engreitz lab, Yannick studied at the University of Colorado Boulder, where he majored in Molecular Biology and Biochemistry, and worked in Ding Xue's lab. His work in the Xue lab involved utilizing the C. elegans model to investigate genes involved in mitochondrial stress response and disease, as well as understand the molecular effects of radiotherapy. Outside of lab, Yannick enjoys playing piano, listening to jazz music, and hanging out with his cat, Sakamoto.

Rosa Ma

PhD Student (Genetics)

Rosa is a PhD student in the Stanford Genetics program. She is interested in understanding the role of non-coding genetic variants in the pathogenesis of congenital heart disease through enhancer-gene mapping at single-cell resolution. Before joining the Engreitz lab, she studied cryptic splicing in neurodegenerative diseases. Rosa completed her undergraduate degree at Cornell University, where she majored in Biological Sciences with a concentration in Computational Biology, and studied the pseudoautosomal regions for her thesis. Outside the lab, she enjoys being food-driven, hiking in the Bay Area mountains, and stressing her fingers on the climbing wall.

Gabriella Martyn, Ph.D.

Postdoctoral Fellow

Gabriella is interested in understanding enhancer biology and the roles of non-coding variants in these genetic elements. She is particularly interested in dissecting the sequence logic behind enhancers and linking variants to functions and disease mechanisms. Gabriella completed her Ph.D. at the University of New South Wales (UNSW) in Sydney, Australia, under the supervision of Professor Merlin Crossley and Dr. Kate Quinlan. During her Ph.D., she investigated the molecular mechanism behind a cluster of naturally occurring mutations which are known to elevate fetal hemoglobin levels and alleviate symptoms of sickle cell disease. Gabriella also holds a Bachelor of Science (Honours) from UNSW. Outside the lab, she loves exploring natural parks, hiking, camping and swimming in the ocean.

Michael Montgomery

PhD Student (Genetics)

Michael is a PhD Student and NSF Graduate Research Fellow in the Stanford Department of Genetics. He is particularly interested in understanding how dynamic interactions between enhancers, transcription factors and target genes orchestrate differentiation and function of complex tissues such as the human heart. Before joining the Engreitz Lab, Michael obtained a B.S. in Microbiology from California State University, Long Beach and spent three years as a researcher in Max Seibold’s Lab at National Jewish Health in Denver, CO. His work in the Seibold Lab included investigating the effects of air pollution on the asthmatic lung and deploying gene-editing methods to identify genes underlying differentiation of lung cell types. Outside of the lab, Michael enjoys backpacking in the Sierra Nevada Mountains, spending time at the dog park, and skateboarding.

Glen Munson

Collaborator, Broad Institute, Joint with Elisa Donnard Group

Glen specializes in high-throughput technologies for engineering cells and performing large-scale perturbation screens. Glen joined what was soon to become the Broad Institute in 2002, and has helped to develop and implement numerous high-throughput genomics technologies.

Tri Nguyen, Ph.D.

Postdoctoral Fellow

Tri is interested in understanding the functions of disease genes and their regulations in tissue homeostasis. He aims to decipher disease-critical cell types, together with cell-autonomous and nonautonomous processes that underlie cardiovascular diseases. Prior to joining the Engreitz lab, Tri completed his Ph.D. in Bioengineering at the University of California, San Diego under the guidance of Professor Sheng Zhong. During his Ph.D., he developed high throughput technologies to map RNA-RNA, and RNA-chromatin interactomes at bulk and single-cell resolution, applying them to discover new molecular mechanisms of vascular endothelial cell dysfunction in diabetes. He also holds a B.Eng. in Bioengineering from the Nanyang Technological University, Singapore. Outside of lab, he enjoys exploring new food fads, reading books short-listed for major prizes, and checking out new musicals at BroadwaySF.

Judhajeet Ray, Ph.D.

Research Scientist, Broad Institute, Joint with Ray Jones Group

Judhajeet is broadly interested in understanding gene regulatory networks in healthy and diseased cells. His current goal is to map enhancer-promoter connections in different cell types and develop genomic tools to dissect the mechanistic details of those interactions. Before joining the Human Gene Regulation Map team at the Broad Institute, Judhajeet was a postdoc with John Lis at Cornell where he investigated transcription-associated changes in chromatin organization of human and Drosophila cells. He has developed RNA aptamer technologies for analysis of macromolecular complexes by mass spectrometry and sequencing, and for perturbing complex interactions to dissect mechanisms of transcriptional pausing. During his PhD in the lab of Marit Nilsen-Hamilton at Iowa State, Judhajeet utilized RNA aptamers to develop a FRET-based method capable to image real-time gene expression. Judhajeet also holds a Master’s and a Bachelor’s degree from University of Calcutta, India.

Oriane Matthys Rubio, Ph.D.

Research Program Manager, BASE Initiative

Oriane works with the BASE Program faculty, administration, and lab members to support research projects and collaborations, secure grant funding, and develop scientific and professional development programming. She holds a Ph.D. in Bioengineering from UC San Francisco/UC Berkeley and a B.S.E. in Biomedical Engineering from Duke University. Oriane found her passion at the niche intersection of science and administration, and is continually inspired by the innovative and collaborative research environment at BASE and Stanford. Outside of work, Oriane enjoys traveling, testing out new recipes in the kitchen, and exploring the outdoors with her two dogs. 

Gavin Schnitzler, Ph.D.

Collaborator, Raj Gupta Lab, Broad Institute

Gavin received his PhD from UCSD in Molecular Biology, and finished a postdoctoral fellowship with Bob Kingston at MGH. Before joining the group, he managed a small group of researchers at Tufts Medical School/Tufts Medical Center, on projects ranging from biochemical mechanisms of transcriptional regulation in chromatin to epigenomic and organismal mechanisms underlying the vasculoprotective effects of estrogen. He is currently spearheading an effort to develop methods to much more rapidly connect noncoding GWAS variants associated with cardiovascular disease to target genes and cellular mechanisms.

Maya Sheth

PhD Student (Bioengineering), Joint with Polly Pordyce Lab

Maya hopes to apply the powerful tools of single-cell sequencing and analytic techniques to tackle the critical challenges of human disease and environmental conservation. She hopes to develop new methods of analysis to construct high-resolution, dynamic maps of biological systems. Before working with the Engreitz Lab, Maya completed her undergraduate studies in Biomedical Engineering at Duke University. While at Duke, she worked with the Comparative Oncology Group, applying ecological and evolutionary approaches to cancer research. Specifically, she studied what cetaceans can teach us about hypoxia tolerance, how phenotypic plasticity contributes to drug resistance in prostate cancer, and how clinical trials for pet dogs with sarcomas can help build more effective drug discovery pipelines for canines and humans alike. Outside the lab, Maya enjoys sunshine, coffee, and playing with her dog, Laguna.

Jason Tan

PhD Student (Computer Science), Joint with Will Greenleaf Lab

Jason is a PhD student and NSF Graduate Research Fellow in the Stanford Computer Science program. He is interested in developing computational and experimental tools to understand the mechanisms of enhancer function. Previously, Jason studied computer science at Rice University and dabbled in epigenome editing and metagenomics. Outside of lab, he’s either dog walking or busy being a foodie.

Sarah Xia

Research Associate

Sarah is interested in better understanding the regulatory elements of the human genome and how non-coding regions affect the expression of various genes, particularly those related to heart disease. Prior to joining the Engreitz lab, Sarah obtained her B.S. in Biomolecular Engineering and Bioinformatics from UC Santa Cruz. While working at the UCSC Genomics Institute, she studied human brain development using cerebral organoid models and contributed to several DEI outreach projects. When she’s not doing science, Sarah enjoys choreographing and practicing modern/contemporary dance and keeping up with her bullet journal.

Tony Zeng

PhD Student (Genetics), Joint with Jonathan Pritchard Lab

Tony aims to apply genetic approaches to understand the molecular and cellular processes that cause disease. He is particularly interested in modeling data from high-throughput and high-content perturbation experiments, with a focus on causal discovery for coronary artery disease. Previously, Tony worked on computational methods to study alternative splicing as an undergraduate at the University of Chicago, where he majored in Computational and Applied Math.

Ronghao Zhou

PhD Student (Genetics), Joint with Tom Rando Lab

Ronghao is a PhD student in the Genetics program, co-mentored by Jesse and Tom Rando. Ronghao is interested in studying the genetic and epigenetic changes of aging, and hopes to find the potential causes of aging. Before joining the Engreitz lab, Ronghao went to Wellesley College, where she majored in Chemistry and Mathematics, and worked in the Keith Joung Lab at MGH on gene editing. Outside of lab, she enjoys exploring the Bay Area.