BASE Faculty
Jesse Engreitz, PhD
Assistant Professor
Jesse is currently in the Department of Genetics and the Children’s Heart Center Basic Science and Engineering (BASE) Initiative.
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, 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.
Casey Gifford, PhD
Assistant Professor
Casey is currently an Assistant Professor in the Department of Pediatrics and, by courtesy, of Genetics. Prior to joining Stanford, she was an HHMI fellow of the Damon Runyon Cancer Research Foundation at the Gladstone Institutes and UCSF in the lab of Deepak Srivastava, M.D. While at the Gladstone Institutes, she employed recent advances in gene editing and gene expression technologies to study cardiovascular development and disease. She earned her B.S. in Biochemistry from Simmons University and her Ph.D. from Harvard University and the Broad Institute where she studied the epigenomic mechanisms that underlie pluripotent stem cell differentiation in the lab of Alex Meissner. Research in her lab is focused on defining the complex genetic and molecular mechanisms associated with congenital heart disease using both rodent and stem cell experimental models. Ultimately, she hopes to make personalized medicine a reality for those that suffer from cardiovascular anomalies.
Xiaojie Qiu, PhD
Assistant Professor
Dr. Xiaojie Qiu is currently an assistant professor at the Department of Genetics, the BASE program, and the Department of Computer Science at Stanford. Xiaojie’s Ph.D. work at University of Washington with Dr. Cole Trapnell made critical contributions to the field of single-cell genomics, exemplified by the development of Monocle ⅔ (monocle 2 & monocle 3) for pseudotemporal trajectory analysis of scRNA-seq data. In his post-doc at Whitehead Institute and MIT with Dr. Jonathan Weissman, Xiaojie developed Dynamo (aristoteleo/dynamo-release) to reconstruct RNA velocity vector field and make reprogramming and in silico perturbation predictions with metabolic labeling enabled single-cell RNA-seq. Recently he also leaded the development of a powerful toolkit, Spateo (aristoteleo/spateo-release), for advanced multi-dimensional spatiotemporal modeling of high definition spatial transcriptomics.
The Qiu lab at Stanford started on Dec. 16, 2023.. Xiaojie will continue leveraging his unique background in single-cell genomics, mathematical modeling, and machine learning to lead a research team that bridges the gap between the “big data” from single-cell and spatial genomics and quantitative/predictive modeling in order to address fundamental questions in mammalian cell fate transitions, especially those of heart evolution, development and disease. His research has been supported by the National Human Genome Research Institute, Chan Zuckerberg Institute, Impetus longevity grant, Arc institute and others.
Mark Skylar-Scott, PhD
Assistant Professor
Mark joined Stanford Unversity's Bioengineering Department in July 2020. Previously, he was a research fellow in Jennifer Lewis' group in the John A. Paulson School of Engineering & Applied Sciences as well as the Wyss Institute for Biologically Inspired Engineering at Harvard University. He obtained his B.A. and M.Eng. degrees from Cambridge University, and his Ph.D. in Medical and Electrical Engineering from the Department of Health Science & Technology at the Massachusetts Institute of Technology, focusing on high-resolution multiphoton microfabrication of capillary networks.
Mark's research focuses on cardiovascular tissue biomanufacturing, seeking to push the complexity and scale at which tissue can be designed and manufactured on demand. By integrating high-throughput culture of designer organoids with new machines and methods for advanced 3D bioprinting, his laboratory seeks to enhance the maturation and function of vascularized cardiac tissues in vitro and in vivo.
BASE Director
Marlene Rabinovitch, MD
Dwight and Vera Dunlevie Professor of Pediatrics (Cardiology)
Marlene joined the Stanford Faculty in 2002 having trained in pediatric cardiology at Boston Children’s Hospital (Harvard) and following a 20-year career at the Hospital for Sick Children in Toronto (University of Toronto) where she established a world class vascular cellular and molecular biology program leading to new paradigms in the treatment of pulmonary hypertension that are applicable to other cardiovascular diseases. At Stanford, her research uses high-throughput genomic technologies, a variety of cell biology platforms including confocal and videomicroscopy, genetically modified mouse models of human disease, human tissue samples from lung and blood and induced pluripotent stem cells differentiated to vascular cells to learn how we can activate molecular programs to regenerate lost microvessels and to reverse the obliterative changes in pulmonary hypertension and other vascular diseases. Over the past decade our research has led to two novel compounds, the elastase inhibitor human recombinant elafin, for which a Phase I clinical trial has been completed, and low dose FK-506 that is positioned for a Phase II clinical trial. Since the initiation of the BASE program, her collaborative research with the BASE faculty is resulting in strategies to build blood vessels with Dr. Skylar Scott, map changes in the chromatin landscape with Dr. Engreitz, and identify the cause of penetrance of mutations in causing vascular pathologies with Dr. Gifford.