December 2024

Dr. Rosa Ma, Engreitz Lab PhD student in the Genetics Graduate Program, successfully defended her thesis titled “Disease Biology Through The Lens Of Genetic Variation” on December 2, 2024. Congrats to our first BASE Program PhD graduate!!

November 2024

New publication out in Cell from Dr. Xiaojie Qiu and collaborators entitled “Spatiotemporal modeling of molecular holograms”. They developed a “virtual embryo” using computational tools to build a 3D cellular map at single-cell resolution of the developing mouse embryo. Read more about it in the Nature News and Views article here.

October 2024

October 2024 - Newest BASE faculty member Dr. Xiaojie Qiu was selected for the prestigious NIH Director’s New Innovator (DP2) Award, which supports unusually innovative research from early career investigators. His project will focus on “Towards Foundational 3D In Silico Models of Whole Mouse Embryogenesis”. Read more about the program and the awardees here. Congrats, Xiaojie!

August 2024

Dr. Casey Gifford was awarded an Additional Ventures/American Heart Association Collaborative Sciences Award. She will collaborate with Anshul Kundaje (Stanford), Elizabeth Crouch (UCSF), and Christina Theodoris (Gladstone Institutes/UCSF) to correct latent mechanisms that underlie neurodevelopmental disorders associated with congenital heart disease. Read more about the program in the press release here. 

July 2024

Dr. Casey Gifford received an award for Best Talk Given by a Senior Investigator for her presentation on “Cardiac Organoids Provide a Platform for Complex Genetic Studies of 22q11 Deletion Syndrome” at the International 22q11.2 Scientific Conference in Portugal.

June 2024

Dr. Xiaojie Qiu, Dr. Jesse Engreitz, and Dr. Marlene Rabinovitch received a California Institute of Regenerative Medicine grant for their work on “Mapping and modeling endothelial cell fate decisions for pulmonary arterial hypertension”.

May 2024

Congratulations to Dr. Luca Rosalia, a postdoctoral fellow in the Skylar-Scott Lab, who was awarded the prestigious Burroughs Wellcome Foundation Career Award at the Scientific Interface to support his transition into an independent investigator position. His work will focus on “Bio-Fabrication and Mechanobiology: A Biomimetic Approach to Modeling and Understanding Cardiovascular Diseases”.

February 2024

New publication out in Nature from the Engreitz Lab and collaborators at the Broad Institute/Brigham and Women’s Hospital. This study developed a Variant-to-Gene-to-Program (V2G2P) to map how genetic variants affect gene expression and how genes impact biological function, and used this approach to uncover mechanisms underlying coronary artery disease risk. Read more in the Broad/BWH press release here. 

Dr. Casey Gifford was selected as a member of Stanford MCHRI's Inaugural Team Science and Translational Medicine Faculty Development Cohort. She will be leading a project focused on “Identifying gene regulatory networks involved in congenital heart disease amenable to therapeutic intervention”.

January 2024

 Two BASE postdocs were awarded the American Heart Association Postdoctoral Fellowship! Congratulations to Dr. Megha Agarwal, postdoc in the Gifford Lab, who was selected for her work on “Understanding left ventricular non-compaction through myocardial-endocardial crosstalk using human cardiac organoid”, and to Dr. Chongyang Zhang, postdoc in the Rabinovitch Lab, studying the “Mechanism underlying pulmonary arterial hypertension induced by reduced SOX17 in congenital heart disease”.

December 2023 - Warm welcome to the BASE Program’s newest faculty recruit: Dr. Xiaojie Qiu, who also joined the Departments of Genetics and Computer Science. His laboratory will leverage his unique background in single-cell genomics, mathematical modeling, and machine learning to bridge the gap between “big data” from single-cell/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. Check out more on his lab website here.

BASE is honoring Betty Irene Moore, who passed away on December 12, 2023. Her transformative donation to the Lucile Packard Foundation in 2017 established the Betty Irene Moore Children’s Heart Center and enabled the launch of our Basic Science and Engineering (BASE) Program to find a cure for children's heart disease through discovery and innovation. This generous donation led to the recruitment and support of our four world-class scientists currently building an interdisciplinary program in bioengineering, stem cell biology, genetics and computer science. Read more about her legacy here.

November 2023- We are excited to announce that our Director Dr. Marlene Rabinovitch is the recipient of the prestigious American Heart Association 2023 Research Achievement Award, celebrating her monumental discoveries in the treatment of Pulmonary Arterial Hypertension. Congrats, Marlene!

September 2023- Congratulations to Dr. Mark Skylar-Scott and his large multidisciplinary team of Investigators at Stanford University for their Advanced Research Projects Agency for Health (ARPA-H) award to bioprint full-scale functional human hearts! Read more about the HEART project here.

Dr. Jesse Engreitz, Dr. Anshul Kundaje, and Dr. Xiaojie Qiu were selected to lead a Data Analysis and Validation Center for the NIH MorPhiC Consortium, which aims to develop a consistent catalog of molecular and cellular phenotypes for null alleles for every human gene by using in-vitro multicellular systems.

May 2023- Congratulations to our BASE PhD students selected as 2023 Stanford Bio-X Fellows! Danielle Klinger (Bioengineering) from the Skylar-Scott Lab will work on “Engineering organoid models of early cardiac developmental stages” and Benjamin Doughty (Genetics) from the Engreitz and Greenleaf Labs will focus on “Deciphering the mechanisms of non-coding genetic variation in enhancers”. 

April 2023- Gifford Lab undergraduate researcher Ximena Sanchez featured in the Stanford Report story on “what it means – and what it takes – to lead”. Read the article here.

March 2023- BASE students are among the prestigious National Science Foundation Graduate Research Fellows! Gifford Lab Stem Cell PhD student Julie Sanchez will study “Investigating Cardiac Neural Crest Cell Dysfunction in Heart Development”. Skylar-Scott Lab undergraduate student Alana Mermin-Bunnell – a senior in Stanford Bioengineering – also received the NSF GRFP award. Congrats Julie & Alana!

New publication out from Dr. Marlene Rabinovitch’s lab! Dr. Lingli Wang led a research project entitled “Dysregulated Smooth Muscle Cell BMPR2–ARRB2 Axis Causes Pulmonary Hypertension”, which provides important insights into how to potentially prevent or reverse the progression of pulmonary arterial hypertension. Read more about the study in the press release here and the publication in Circulation Research.

January 2023- Two BASE postdocs were awarded the American Heart Association + Children’s Heart Foundation Postdoctoral Fellowship! Congrats to Dr. Nirmal Vadgama from the Gifford Lab whose project will focus on “Defining the neural crest's role in CHD and associated comorbidities using single-cell epigenomics and deep learning” & to Dr. Dulguun Amgalan from the Engreitz Lab whose project on “Regulatory maps of endothelial cell differentiation to connect congenital heart disease risk variants to function” was renewed!

October 2022 - Congratulations to Dr. Mark Skylar-Scott, who was selected as recipient of the NIH New Innovator Award for his lab’s work to realize the dream of 3D-bioprinted organs on-demand!  Read more here.

September 2022 - Engreitz Lab postdoctoral fellow Dr. Gabriella Martyn won the 1st place poster prize at the Impact of Genome Variation (IGVF) Consortium Annual Meeting for her work on “Systematically Characterizing Enhancers and Non-Coding Variants by Pairing CRISPR-Editing with RNA-FlowFISH”. Congrats Gabby!

July 2022 - Skylar-Scott Lab graduate student Jonathan Weiss won a TA award for his outstanding effort building, debugging, and operating eight 3D printers for Stanford course BIOE44. Congrats Jonanthan! 

June 2022 - Thanks to a generous gift from the Alfred E. Mann Family Foundation, Dr. Casey Gifford has established a state-of-the-art Biobank at the Moore Children’s Heart Center at Lucile Packard Children’s Hospital that provides collection and storage of samples related to congenital heart disease. The ultimate goal of the Mann Charities Biobank is to provide high-quality data from heart patients to researchers around the world to finally understand why different forms of congenital heart disease occur and inform the best possible treatments, before a child is even born. 

May 2022 - Congrats to our BASE Trainees who were recently awarded fellowships to support their research projects: Fredrik Solberg, Mechanical Engineering PhD student in Dr. Mark Skylar-Scott's lab was awarded the Stanford Bio-X Bowes Fellowship for his work developing concentric tube robots for advanced in vivo bioprinting applications; Danielle Klinger, Bioengineering PhD student in Dr. Mark Skylar-Scott's lab was selected for the Stanford NIH Graduate Training Program for Biotechnology for her project on engineering complex 3D models of cardiovascular development; and Dr. Tri Nguyen, postdoctoral fellow in the Engreitz Lab received the American Heart Association Postdoctoral Fellowship for his research deciphering congenital heart disease gene function by mapping disease genes to disease-critical cell types and cellular processes.

May 2022 - Dr. Jesse Engreitz and team published a study in Nature, which aims to decipher how the millions of "enhancer" sequences in the human genome regulate specific genes. They find that two types of genes respond differently to enhancers, and that these responses are controlled by specific sequences in gene promoters. Read the publication here.

April 2022 - Dr. Casey Gifford was featured in the Additional Ventures Investigator Spotlight! Read more about her scientific journey and motivations propelling her research forward in this article.

March 2022 -  Dr. Mark Skylar-Scott's lab was featured on the front of Stanford News 'Stanford bioengineers aim to build a heart, one layer at a time'. Read the article  here. 

January 2022 - Big congratulations to Dr. Mark Skylar-Scott on his induction into the esteemed cohort of Chan Zuckerberg Biohub Investigators! His work will advance the engineering of organs at scale. Read more about the program and meet the other Investigators here. 

December 2021 - Dr. Jesse Engreitz was selected as a recipient of the Additional Ventures Single Ventricle Research Fund for his research project "A reference map of enhancers during human fetal heart development to understand the genetic etiology of single ventricle diseases". This work will be performed in collaboration with Dr. William Goodyer (Dept. of Pediatrics - Cardiology) and Dr. William Greenleaf (Genetics Department).

November 2021 - Dr. Mark Skylar-Scott was awarded the Beckman Center for Molecular and Genetic Medicine 2021 Technology Development Grant for his work on the “Development of a photo-enzymatic 3D bioprinter for pediatric tissue engineered vascular grafts”. This project will be performed in collaboration with Dr. Steven Boxer (Dept. of Chemistry) and Dr. Michael Ma (Dept. of Cardiovascular Surgery).

September 2021 - Dr. Jesse Engreitz and Dr. Tom Quertermous were selected to lead a Functional Characterization Center for the inaugural NIH/NHGRI Impact of Genomic Variation on Function (IGVF) consortium. Learn more about consortium efforts here, in a press release by NHGRI.

June 2021 - Engreitz Lab postdoctoral fellow, Dr. Gabriella Martyn, was awarded 2 postdoctoral fellowships for her work on linking variants to their effects on target genes via prime editing mediated mutagenesis. She will be supported by the Stanford School of Medicine Dean’s Postdoctoral Fellowship and the Walter V. and Idun Berry Postdoctoral Scholarship.

June 2021 - BASE Faculty Dr. Mark Skylar-Scott (Dept. of Bioengineering) was selected as a 2021 Baxter Foundation Faculty Scholar for his work on “Laser 3D Printed Human Capillary Models to Study SARS-CoV-2 Entry”. Congrats, Mark!

May 2021 - Two Skylar-Scott Lab graduate students were selected as recipients of the Stanford Bio-X PhD Fellowship. Joshua Sampson, Bioengineering PhD student, will study “Optical Coagulation for 3D Bioprinting In Vitro and Directed Homeostasis In Vivo” (Bio-X co-mentors: Dr. Steven Boxer, Dr. Michael Ma). Jonathan Weiss, Bioengineering PhD student, will work on “Organ-scale Biofabrication: 3D Bioprinting of Engineered Pluripotent Stem Cells to Form a Mature Human Ventricle” (Bio-X co-mentor: Dr. Joe Woo).

April 2021 - Dr. Jesse Engreitz published a study in Nature (read it here) in which he built genome-wide enhancer maps to systematically connect thousands of noncoding disease variants to functions in specific cell types. Using inflammatory bowel disease (IBD) as a testbed, the team accurately predicted which enhancers contain risk variants for IBD and experimentally validated these results by modulating a predicted enhancer in immune cells in vitro. Learn more about the study here, in a story released by the Broad Institute.

March 2021 - Two BASE graduate students were awarded the National Science Foundation Graduate Research Fellowship. Skylar-Scott Lab Bioengineering PhD student Jonathan Weiss will study “Genomic Engineering of Pluripotent Stem Cells to Enable Whole Organ-Scale 3D Bioprinting” and Engreitz Lab Genomics PhD student Michael Montgomery’s project will focus on “Untangling Temporal Dynamics of Enhancer-Gene Interactions In Cardiomyocyte Differentiation”.

January 2021 - Engreitz Lab postdoctoral fellow, Dr. Dulguun Amgalan, was awarded 2 prestigious fellowships for her project “Regulatory maps of endothelial cell differentiation to connect congenital heart disease risk variants to target genes”. Her work will be supported by the American Heart Association + Children’s Heart Foundation Congenital Heart Defect Research Award and the Stanford Maternal and Child Health Research Initiative Postdoctoral Support Award.

November 2020 - Dr. Casey Gifford joins Stanford and BASE as an Assistant Professor in the Departments of Pediatrics and Genetics. Her lab will focus on identifying the complex genetic and molecular mechanisms underlying cardiovascular development and disease.

October 2020 - Dr. Mark Skylar-Scott and Dr. Michael Ma (Dept. of Cardiovascular Surgery) were awarded a 2020 Seed Grant from Stanford’s Cardiovascular Institute & Maternal and Child Health Research Initiative for their proposal “Development of Optogenetic Thrombin for Light-directed Hemostasis During Unifocalization Surgery” in collaboration with Dr. Doff McElhinney (Depts of Pediatrics and Cardiovascular Surgery) and Dr. Steven Boxer (Dept. of Chemistry).

September 2020 - Dr. Jesse Engreitz was selected as a 2020 NHGRI Genomic Innovator for his work to "Apply CRISPR tools to understand gene regulation related to common, complex diseases".