August 2026 
New publication out in Nature Genetics from the Engreitz Lab and collaborators in Robin Andersson’s lab at the University of Copenhagen, titled “Mapping enhancer–gene regulatory interactions from single-cell data.” This study developed scE2G, a family of machine learning models trained on CRISPR perturbation data that predict which enhancers regulate which genes directly from single-cell ATAC-seq or multiomic data. The authors applied scE2G across 45 cell types, including immune cells and pancreatic islets, to show that cell-type-resolved enhancer maps reveal regulatory interactions missed by pooled or bulk-tissue data, providing a resource for interpreting the function of noncoding genetic variants linked to common diseases. Read more in the publication here.

July 2026
New publication out in Nature from the Engreitz Lab and collaborators at Stanford and across the ENCODE Consortium, titled "An encyclopedia of human enhancer–gene regulatory interactions." This study developed ENCODE-rE2G, a machine learning model trained on large-scale CRISPR perturbation data, and used it to build a genome-wide atlas of over 92 million enhancer–gene regulatory interactions across 1,458 cell types, tissues, and contexts. This provides a foundational resource for understanding the functions of DNA variants associated with risk for diseases of the heart and other organs. Read more in the publication here.

April 2026
Dr. Xiaojie Qiu was selected as a recipient of the Laude Institute Moonshot program. He is collaborating with Stanford Profs. Emily Fox and James Zhou, as well as Harvard Prof. Marinka Zitnik, to pioneer “The Virtual Embryo Moonshot: Predictive Modeling of Human Development and Congenital Defects”.

March 2026
Congratulations to Bioengineering PhD student Sophie Clarke in the Skylar-Scott Lab, for being awarded the prestigious National Science Foundation Graduate Research Fellowship!

Dr. Jesse Engreitz was awarded an NIH R01 for working on “Genome-wide maps of enhancer-gene regulation to link variants to functions” in collaboration with Dr. Casey Gifford and Dr. Anshul Kundaje.

January 2026
New publication from the Engreitz Lab and Chang Lab led by PhD student Yannick Lee-Yow was published in Nucleic Acids Research. Read their study about “Junction-targeting designs limit the application of CRISPR-Cas13d in circular RNA perturbation studies” here.

Two BASE PhD students were awarded the 2026 AHA Predoctoral Fellowship! Congratulations to Annie Nguyen in the Skylar-Scott Lab for her project “High-Resolution 3D-Printed Vascularized and Aligned in vitro Cardiac Tissue” and to Tony Zeng in the Engreitz Lab, who was selected for his work on “Perturb-seq to Infer Causal Pathways for Vascular Diseases”. One BASE postdoctoral fellow, Naoki Konno, was also awarded the 2026 AHA Postdoctoral Fellowship for his work "Deciphering Congenital Heart Defects Through Single-Cell Evolution and in silico Perturbation" in the Qiu Lab.

October 2025 
BASE Affiliate Faculty Member Dr. Matteo Molè and Dr. Xiaojie Qiu received a California Institute for Regenerative Medicine DISC0 grant for their work on “Dissecting the cellular and molecular interactions between embryo and endometrium during human implantation”. Read more about the CIRM Discovery Research awards here. 

 Dr. Xiaojie Qiu is part of a team that received the Wu Tsai Big Ideas in Neuroscience award. He will be working with Stanford Profs. Thomas Clandinin and Will Allen on “In Vivo Functional Genomics and Foundational Virtual Models of Brain Homeostasis and Resilience”.

September 2025
BASE Affiliate Faculty Member Dr. Matteo Molè and Dr. Xiaojie Qiu were selected for the ISCBRM Stinehart-Reed Collaborative Investigator seed grant program, to support their work on “A Spatial Transcriptomic Atlas of Embryo-Endometrial Crosstalk During Human Implantation”.

July 2025
Computer Science PhD student Peter Pao-Huang in the Qiu Lab, had a paper accepted to the International Conference on Machine Learning (ICML) entitled “Geometric Generative Modeling with Noise-Conditioned Graph Networks”. Read it here. Congrats, Peter!

Dr. Jesse Engreitz was awarded a Single Ventricle Research Fund award from the Additional Ventures Foundation for his project entitled “Regulatory Map of the Human Fetal Heart to Understand the Etiology of Single Ventricle Defects”. He will be collaborating with Drs. William Goodyer, Casey Gifford, and Xiaojie Qiu to build a foundational map of enhancer-gene regulation during heart development and disease in order to better understand the genetic causes of single ventricle disease. Read more about the program here. 

June 2025 
 New publication out in Cell from Dr. Jesse Engreitz and collaborators entitled “Rewriting regulatory DNA to dissect and reprogram gene expression”.

BASE welcomes their new Research Project Manager, Nicole Navarro!  A Bay Area native and Boston College alumnus, Nicole began her career as a health technologies research engineer at Apple. She then earned her Chemical Biology PhD from UC Berkeley, where she developed carbon nanotube-based nanosensors for brain imaging and viral detection applications in Dr. Markita Landry’s lab. After graduate school, she returned to industry research at Thermo Fisher Scientific where she developed bespoke surface chemistries to improve high-throughput genomic sequencing platforms. Nicole currently lives by Ocean Beach with her partner, Alex, and Karl, the San Francisco fog. Nicole loves hiking, camping, roller skating poorly, and reading horror novels.

New publication out in Science from Dr. Mark Skylar-Scott and collaborators entitled “Rapid model-guided design of organ-scale synthetic vasculature for biomanufacturing”. They developed complex new computational and bioprinting tools to design and 3D print the complex vascular networks found throughout the body. Read more about their study in the Stanford Report article here.

Celebrating another PhD graduate, Dr. Michael Montgomery, an Engreitz Lab PhD student in the Genetics Graduate Program, who successfully defended his thesis titled “Rewriting Regulatory DNA to Dissect and Reprogram Gene Expression” on June 13, 2025!

May 2025
Congratulations to our newest PhD graduate, Dr. Jonathan Weiss, Skylar-Scott Lab PhD student in the Bioengineering Graduate Program, who successfully defended his thesis titled “Low-Cost, Open-Source, and High-Throughput 3D Printing: A Multi-Cellular Spheroid Approach” on May 30, 2025!

Two BASE PhD students were awarded the Bio-X Interdisciplinary Graduate Fellowship! Congratulations to Lucy Zhang in the Gifford Lab, who was selected for her work on “Linking Inflammation and Congenital Heart Disease using a Cardioimmune Organoid System”, and to Yi Yi Du in the Skylar-Scott Lab, for his project “Organ-scale Multicellular Continuous Bioprinting”. 

March 2025 
Dr. Mauro Lago Docampo, postdoc in the Rabinovitch Lab, presented on Loss of TBX4 Alters Smooth Muscle Contractility and Induces Endothelial Dysfunction in Pulmonary Arterial Hypertension at the TBX4-Life Scientific conference in San Francisco. This event brings together scientists and clinicians interested in TBX4 related pathways and diseases.

All News