This Program is supported through a National Heart, Lung, and Blood Institute (NHLBI) T32 Graduate Research Training Grant and is titled and focused on:
“Training in Bioengineering Research and Technology Development in
Cardiovascular and Cardiopulmonary Health and Disease.”
The training grant was awarded in March, 2022 and is a novel bioengineering predoctoral training program at UC San Diego in cardiopulmonary science and technology. It takes advantage of UC San Diego’s leadership as a top-ranked bioengineering doctoral program focused on basic research and technology development together with world-leading, NHLBI-supported, basic and clinical science in cardiovascular and cardiopulmonary disease and healthcare.
About the Program
- FOCUS & AIM
The focus of this program is to train predoctoral bioengineering students in applying quantitative and integrative interdisciplinary approaches to basic and translational research in cardiac, pulmonary, vascular, blood, and sleep pathophysiology, and developing novel technologies for the diagnosis, treatment, and clinical management of cardiovascular and cardiopulmonary diseases.
This is the only graduate program on campus to provide bioengineering predoctoral students with interdisciplinary, co-mentored training to apply four key technology themes to problems in cardiac, vascular, blood, and lung health. The themes are: biomechanics and mechanobiology; biomaterials, cell and tissue engineering; computational and systems biology; and imaging and biophotonics. Engineering approaches at the interfaces between these four areas will be applied by trainees to research that includes new areas such as pulmonary hypertension, remote monitoring, heart valve and congenital heart diseases, neurovascular injury, metabolic diseases, and infectious and microvascular disease.
Our overall philosophy is to provide co-mentored training in applying rigorous, quantitative and integrative engineering approaches to important interdisciplinary problems in cardiovascular and cardiopulmonary science. The new research training curriculum, themes, and faculty of this program reflect the broadened cardiovascular research activity of Bioengineering graduate research at UC San Diego and the successes of Bioengineering labs in finding engineering solutions to important clinical and translational problems. They also reflect new bioengineering research directions prompted by the COVID-19 pandemic, the rapid adoption of machine learning by many program faculty, advanced understanding of pathophysiological processes in medicine, and the recent opening of the Herbert Wertheim School of Public Health and Human Longevity Science School.
Graduates of this training program will be the next-generation interdisciplinary researchers skilled at developing and using engineering technologies and analysis for research that improves the understanding, prevention, and treatment of cardiovascular and cardiopulmonary diseases.
This training program aligns with its participating departments and graduate programs in the belief that as one community we must work together to embrace and celebrate differences for positive impact, positive change, and for the greater good. This work ultimately impacts society and requires a commitment from us all to be change-makers. Specifically, this training program aligns with the NIH commitment to the value of enhancing trainee equity, diversity, and inclusion (EDI) through proactive outreach, recruitment, retention, and advancement with the goal of impacting the biomedical research field, locally and more broadly. See the NIH commitment to equity, diversity, and inclusion at https://oir.nih.gov/about/
- TRAINEE SELECTION
Trainees will be selected from predoctoral candidates admitted to our highly-ranked and competitive Bioengineering doctoral program.
Selected trainees will take courses on cardiovascular biology and engineering technologies specific to the proposed program, have a clinical immersion experience, and conduct laboratory research in cardiovascular science with interdisciplinary co-mentors.
Students accepted into the training program may be eligible to receive support through the National Institutes of Health (NIH) NHLBI T32 Graduate Research Training Grant which was officially awarded in March, 2022. Training grant fellowships often have the following citizenship information requirements:
Kirschstein-NRSA trainees and institutional career development scholars must be U.S. citizens, non-citizen nationals, or permanent residents of the United States. Individuals on temporary or student visas are not eligible. Trainees or scholars in these programs who are permanent residents of the U.S. must submit a notary’s signed statement with this appointment form certifying that they have (1) A Permanent Resident Card (USCIS Form I - 551), or (2) other legal verification of such status.
- PARTICIPATING DEPARTMENTS
Halıcıoğlu Data Science Institute
La Jolla Institute for Allergy and Immunology
Mechanical and Aerospace Engineering
School of Medicine
Skaggs School of Pharmacy and Pharmaceutical Sciences
- PROGRAM FACULTY
Brian Aguado, PhD is an Assistant Professor who joined UCSD in 2021. His research develops precision biomaterials for studying patient-specific biology as a function of sex, age, or ancestry. He is currently focused on exploring sex differences in cardiovascular diseases (aortic valve stenosis, cardiac fibrosis) at multiple length scales using precision biomaterial tools. Dr. Aguado is pursuing collaboration with Drs. Christman, Engler, Fraley, Valdez-Jasso, Kwon, King, and Reeves.
Pedro Cabrales, PhD analyzes cardiovascular transport and regulation using engineering principles and methods. Recent trainees worked on assessing cardiac function during oxidative stress and blood substitutes, co-mentored with other training faculty, including Drs. Kwon, Christman, Contijoch and Haddad. Trainees develop new techniques to understand in-vivo transport, and quantify organ and tissue function in anemia, hemorrhagic shock, brain injury, polycythemia, malaria and sickle cell disease.
Karen Christman, PhD develops injectable biomaterials for tissue engineering and regenerative medicine as minimally invasive therapies for myocardial infarction, congenital heart defects, peripheral artery disease and COVID-19. She collaborates with many training faculty, including Drs. Engler, Evans, Kwon, Contijoch, Sheikh, and Reeves and has co-mentored many trainees. She will serve as a program Co-Director.
Francisco Contijoch, PhD (Bioengineering and Radiology) develops imaging techniques for cardiovascular assessment. Trainees develop advanced MR and CT analysis techniques for assessing right ventricular and pulmonary vascular function in patients with pulmonary hypertension, congenital heart disease, or mechanical circulatory support. He co-mentors trainees with Drs. Christman, Malhotra, and McVeigh.
Adam Engler, PhD works on mechanobiology in heart disease and cancer. His trainees use novel biomaterials and tissue engineering to study how physical and chemical properties of the extracellular niche influence or misregulate cell function and modify genetic mechanisms of disease. He has co-mentored trainees with Drs. Chi, Fraley, Ross, McCulloch, Christman, Hsaio, Kwon, and Mali.
Stephanie Fraley, PhD studies the systems biology of extracellular matrix regulation of epithelial-to-endothelial transition and collective cell migration. The ability of adult differentiated cells to regain plasticity and transdifferentiate down distinct lineages is leading to new regenerative strategies. She collaborates with Drs. Engler, McCulloch and Valdez-Jasso and is the department Diversity Chair.
Kevin King, MD, PhD (Bioengineering and Medicine-Cardiovascular Medicine) is a clinical cardiologist and bioengineer studying inflammation and tissue remodeling in myocardial infarction. His trainees use single cell transcriptomics to understand how the immune system responds to injury and influences repair. They also develop tools for in-home monitoring of heart failure patients. He collaborates with Drs. Brown, Christman, and Engler.
Ester Kwon, PhD works on nanotechnology and bioinspired materials. Her trainees develop new biomaterial technologies for treating traumatic brain injury by discovering new ways to interact with and repair the damaged blood vessels in the brain. She collaborates with Drs. Christman, Engler, Mali and Contijoch.
Klaus Ley, MD (Bioengineering and La Jolla Institute for Allergy and Immunology) studies the adaptive immune response in atherosclerosis in humans and mouse models. His trainees use advanced imaging and in-vivo models of inflammation as a defense reaction to tissue injury. They are also testing a vaccine against atherosclerosis that is effective in mice. He collaborates with Dr. Mali.
Prashant Mali, PhD works on understanding cell fate specification during early development and disease modeling with vascularized organoids. His trainees develop new technologies for cell engineering and genome editing and use systems biology to enable high resolution, high throughput deciphering of the genetic code in human stem cells. He collaborates with Drs. Christman, Fraley, Wang, Engler and Ley.
Andrew McCulloch, PhD (Bioengineering and Medicine) uses experimental and computational modeling to investigate cardiac biomechanics, electrophysiology and regulatory mechanisms. Recent trainees worked on molecular modeling of myofilament dynamics, network analysis of myocyte mechanosignaling and patient-specific modeling of heart failure, atrial fibrillation and congenital heart diseases, and are co-mentored by many other training faculty including Drs. Brown, Evans, Chen, Sheikh, Ross, Engler and Haddad.
Elliot McVeigh, PhD (Bioengineering, Medicine and Radiology) develops novel cardiovascular imaging techniques using MRI and CT. His trainees develop scanning and image analysis techniques for individualized analysis of patients by applying advanced engineering concepts to address unmet needs. He collaborates with Drs. Hsaio, Contijoch, Reeves and Kahn.
Geert Schmid-Schoenbein, PhD studies microvascular mechanics and physiology in inflammatory disease. His trainees develop new molecular technologies for detection of cardiovascular organ failure in hypertension, heart failure and hemorrhagic shock, and for preventing it by targeting proteolytic degradation by digestive enzymes. He collaborates with Drs. Christman and McVeigh.
Lingyan Shi, PhD develops novel optical imaging techniques to visualize structural dynamics and metabolism of the vascular system in vivo. Her trainees develop multimodal optical imaging of vasculature dynamics and their relationship to neural activity-regulated signaling in vascular endothelial cells.
Daniela Valdez-Jasso, PhD works on soft-tissue biomechanics, mechanobiology and multi-scale modeling of right ventricular and pulmonary arterial adaptations to pulmonary arterial hypertension. She incorporates organ-, tissue-, and cellular-level experimental findings into mechanistic mathematical models. Her trainees use in-vitro, in-vivo and computational models and are co-mentored with Drs. McCulloch and Malhotra. She will be the T32 Diversity Coordinator.
Yingxiao Wang, PhD works on molecular engineering for cellular imaging and reprogramming. His trainees design and use molecular FRET biosensors for visualizing signaling dynamics and microdomains in live cardiovascular cells. Immune cells are engineered cells to control cellular function. He is collaborating with Drs. Engler and Fraley.
Kun Zhang, PhD develops novel genomics and imaging approaches and applications to stem cells and human adult tissues. He leads an NIH HuBMAP U54 center for building 3D single-cell maps for human lungs and other organs. He collaborates with Drs. Mali and Chi.
Sheng Zhong, PhD studies the relationship between gene regulatory networks and cellular behavior. The primary goal of his trainees is to develop new technologies to reveal RNA-participating molecular networks, including the RNA-RNA interactome. He collaborates with Dr. Chen.
Sonya Neal, PhD works on understanding protein quality control pathways, especially those that detect and destroy toxic misfolded proteins. This allows her trainees to define the mechanisms that protect the proteome in health and disease, and devise methods to harness cellular quality control to modify the proteome in the lab and clinic. She is a faculty member of the NHLBI FOCUS program with Drs. Contijoch and Valdez-Jasso and runs a program to promote success in URM trainees.
MECHANICAL AND AEROSPACE ENGINEERING
Stephanie Lindsey, PhD (Mechanical and Aerospace Engineering and Bioengineering) studies how hemodynamic forces affect cardiovascular development. Her trainees use experimental and computational models to discriminate effects of hemodynamic versus genetic alterations in aberrant cardiogenesis and congenital heart defects.
Sylvia Evans, PhD (Medicine, Skaggs School of Pharmacy and Pharmaceutical Sciences) studies cardiac development and its application to heart disease in mouse models. Her trainees study pathways regulating how mesodermal precursors become committed to cardiac progenitors, specified into lineages, and assemble the heart. She co-mentors trainees with Drs. Chen, Brown, McCulloch and Christman.
Emma Farley, PhD (Medicine and Biological Sciences) studies how enhancers encode the patterns of gene expression required for successful cardiovascular development and the mutations within enhancers that lead to developmental defects and evolutionary adaptations. Her trainees’ research is highly multidisciplinary. She is pursuing collaboration with Dr. Christman and Evans.
Mark Ginsberg, MD works on vascular biology and hemostasis-thrombosis, signal transduction, gene regulation, hematopoiesis, angiogenesis, and the molecular and cell biology of blood and vessel walls. He also directs the UC San Diego Physician-Scientist Training Pathway and has collaborated with Dr. Ley.
Atul Malhotra, MD conducts research to understand why patients with respiratory diseases such as obstructive sleep apnea, chronic obstructive pulmonary disease and COVID-19 have cardiovascular complications. His trainees focus on the pathogenesis of sleep apnea and its complications. He has a successful track record of mentoring and collaborates with Drs. Contijoch and Valdez-Jasso.
Ju Chen, PhD is a leading expert in molecular cardiology and genetically engineered mouse models of cardiac and skeletal myopathies. He has co-mentored trainees with Drs. Brown, Chi, Sheikh, McCulloch, Ross and Zhong.
Neil Chi, MD focuses on discovering the fundamental basis of how diverse cardiovascular lineages are created and assembled to form and repair the functioning heart and cardiovascular system. He co-mentors trainees with Drs. Chen, Engler, McCulloch and Evans on cardiovascular stem cells, genetics and systems biology.
Andrew Kahn, MD works on image-based analysis of cardiac hemodynamics. His research focuses on using clinical cardiac CT, MRI, and echocardiography imaging to measure and analyze intra-cardiac flows and create patient-specific computational fluid dynamics simulations. He has collaborated with Drs. Contijoch, McVeigh, and Reeves.
Ryan Reeves, MD is an interventional cardiovascular clinician and researcher. His interests include coronary physiology, acute and chronic heart failure, post-heart transplantation complications, and therapies for coronary and structural heart disease. He co-mentors Bioengineering trainees with Drs. Christman and Contijoch.
Robert Ross, MD works on understanding the mechanisms of cardiac hypertrophy and heart failure, with a focus on cell-matrix and cell-cell interactions in the myocardium. He co-mentors Bioengineering predoctoral trainees with Drs. McCulloch, Engler, Wang, Chen, and Brown.
Farah Sheikh, PhD investigates mechanisms and therapeutics for arrhythmogenic right ventricular cardiomyopathy. Her trainees are focused on understanding pathways driving biomechanical stress responses in cardiac muscle and on mutations in desmosomes associated with ARVC. She has co-mentored bioengineering predoctoral trainees with Drs. Chrstiman, Evans and McCulloch.
John Shyy, PhD investigates molecular mechanisms by which fluid shear stress and pro-inflammatory cues activate gene expression in vascular endothelial cells. His trainees have designed and engineered devices to subject a monolayer of cultured endothelial cells to well-defined mechanical forces. He collaborates with Drs. Brown, Chen and Wang.
Gabriel Haddad, MD studies the effects of hypoxia and hypercapnia on cell function and development with the goal of improving children’s health. His trainees study mechanisms in hypoxia that lead to cellular injury or protect against it, focusing on human genetic evolution at high altitude, especially in relation to erythropoiesis. He has collaborated with Drs. Malhotra, McCulloch and Cabrales.
Joan Heller Brown, PhD works on understanding the mechanisms by which heart failure develops following a myocardial infarction or in response to hypertension. Her current work focuses on the discovery that cardiomyocytes signal through CaMKII to initiate inflammatory activation, macrophage recruitment and fibrosis. Her trainees are testing whether genetic or pharmacologic blockade of these processes attenuates heart failure. She has collaborated with Drs. Chen and Gustafsson.
Jin Zhang, PhD (Pharmacology, Bioengineering, and Chemistry and Biochemistry) works on understanding how cells sense changing environments. Her trainees use FRET sensors, computational models, biochemistry and live cell imaging to reconstruct the dynamic spatiotemporal regulation of protein kinase signaling networks in cardiac and other cells. She has co-mentored trainees with Drs. Wang, McCulloch and Brown.
Albert Hsiao, MD, PhD a radiologist and bioengineer, works on enhancing MRI & CT image acquisition and diagnosis using technologies including 4D Flow MRI and deep learning. His research focuses on structural heart disease, chronic thromboembolic pulmonary hypertension, chronic obstructive pulmonary disease and Covid-19. He collaborates with Drs. Contijoch, McVeigh, Reeves, McCulloch and Engler.
SKAGGS SCHOOL OF PHARMACY AND PHARMACEUTICAL SCIENCES
Asa Gustafsson, PhD works on the molecular pathways that regulate the life and death of cardiac myocytes and their roles in heart disease. Her trainees use systems biology to study the genetic, molecular and physiological interactions of various pathways in heart disease regulating mitochondrial function and apoptosis. She collaborates with Dr. Heller Brown.
Frequently Asked Questions
- What is the NHLBI Graduate Training Program?
UC San Diego’s Bioengineering Department received an NHLBI training grant entitled Training in Bioengineering Research and Technology Development in Cardiovascular and Cardiopulmonary Health and Disease for bioengineering pre-doctoral students in cardiopulmonary science and technology.
The focus of the program is to educate bioengineering students in the application of quantitative and integrative interdisciplinary approaches to basic and translational research in cardiopulmonary, vascular, blood, and sleep pathophysiology, and the development of novel technologies for the diagnosis, treatment, and clinical management of cardiovascular and cardiopulmonary diseases.
Students’ research will need to support at least two areas of the following key themes of the training grant: biomechanics and mechanobiology; biomaterials, cell and tissue engineering; computational and systems biology; and imaging and biophotonics.
Selected trainees will take courses on cardiovascular biology and engineering technologies specific to the program, have a clinical immersion experience, and conduct laboratory research in cardiovascular science with interdisciplinary co-mentors.
- Who is eligible to apply for the Training Program/grant?
Trainees must be U.S. citizens, non-citizen nationals, or permanent residents of the United States. Individuals on temporary or student visas are not eligible. Trainees or scholars in these programs who are permanent residents of the U.S. must submit a notary’s signed statement with this appointment form certifying that they have (1) A Permanent Resident Card (USCIS Form I - 551), or (2) other legal verification of such status.
- What are the eligibility criteria?
Applicant requirements are that the student must:
- Be a 1st or 2nd-year (at the time of application) Bioengineering PhD student, MS to PhD transfer, or Medical Scientist Training Program (MSTP) student
- Have passed the PhD qualifying examination (i.e., departmental exam)
- Have completed (or will complete) training program-specific courses BENG 230C Cardiovascular Physiology and BENG 238 Molecular Biology of the Cardiovascular System
- Provide a written commitment and a written recommendation from each of two interdisciplinary co-mentors on the training grant faculty, one in Bioengineering and one from Health Sciences. Please choose co-mentors from the Program Faculty section of this website. Applicants who do not yet have co-mentors can still submit an application. Please consult with the Training Grants Program Coordinator Kelley Raymond, email@example.com.
- Possess appropriate research experience and academic background.
- Propose research goals within the scope of the program, i.e., how does your research support one of the key technology themes of the program: 1) biomechanics and mechanobiology; 2) biomaterials, cell and tissue engineering; 3) computational and systems biology; or 4) imaging and biophotonics in the diagnosis, treatment, and clinical management of cardiac, vascular, blood and lung health.
Exceptions may be permitted upon petition; however, students who best meet the eligibility criteria will be prioritized.
Note: Applicants with a disadvantaged social, educational, or economic background, and/or who demonstrate a commitment to diversity and/or are committed to increasing educational access for underrepresented students are encouraged to apply and will be considered for funding from the UC San Diego Fellowship Match to this T32 via the same application form on this website (see Apply Here button below).
- What are the training requirements?
- At least two of these courses will be taken before the end of the second year and the remainder by the end of the third year.
- BENG 294A Patient-Centered Clinical Medicine for Bioengineers, offered every Fall Quarter
- BENG 238 Molecular Biology of the Cardiovascular System, offered every Winter Quarter
- BENG 230C Cardiovascular Physiology, offered every Spring Quarter
- BENG 219 Data Science for Multiscale Biology, offered every Spring Quarter
- Responsible conduct of research
- Participate in Med-into-Grad program
- Complete a structured, co-mentored, rotation program
- Maintain Good Academic Standing as defined by the UC San Diego Graduate Division
- Participate in training program activities as requested, e.g., planning and attending Symposium and Seminars
- Complete reporting requirements as requested, e.g., annual progress reports and evaluations
Exceptions to the trainee requirements may be permitted upon petition to the Training Program Executive Committee.
- At least two of these courses will be taken before the end of the second year and the remainder by the end of the third year.
- How do I apply for the Training Program/grant?
The Admissions cycle for AY 23-24 is now complete. If you have any questions, please contact the Training Grants Program Coordinator, Kelley Raymond, at firstname.lastname@example.org.
- PROGRAM DIRECTORS
Andrew McCulloch, PhD - Dr. Andrew McCulloch is the Shu Chien Chancellor’s Endowed Chair in Engineering and Medicine, and the Director of the Institute for Engineering in Medicine (IEM), at UC San Diego. He earned his bachelor and PhD degrees in Engineering Science at the University of Auckland and joined the UC San Diego faculty in 1987. He directs the UC San Diego Interfaces Graduate Training Program and the interdisciplinary PhD Specialization in Multi-Scale Biology. Dr. McCulloch served as Vice Chair of the Bioengineering Department from 2002 to 2005 and Chair from 2005 to 2008. He is also a member of the Qualcomm Institute, a Senior Fellow of the San Diego Supercomputer Center, and Leader of the Wu-Tsai Human Performance Alliance at UC San Diego.
Karen Christman, PhD - Dr. Karen Christman has been with the Bioengineering department since 2007. Her research on biomaterials for cardiovascular regenerative medicine has resulted in the development of novel hydrogels derived from extracellular matrices that promote healing after injury. Recently, she successfully conducted a first-in-human, FDA-approved Phase 1 clinical trial of a hydrogel for post-MI tissue repair. She is a member of the IEM and the Sanford Consortium for Regenerative Medicine, and a fellow of the AHA, BMES, and AIMBE. She received NIH Director’s New Innovator and Transformative Research Awards, the Wallace H. Coulter Foundation Early Career Translational Research Award, the AHA Western States Innovative Sciences Award, and the Tissue Engineering and Regenerative Medicine Society’s Young Investigator and Senior Scientist Awards. She currently serves as the Associate Dean for Faculty in the Jacobs School of Engineering. Dr. McCulloch has served as her formal faculty mentor since she was recruited. He will help prepare her transition to serve as the next lead Program Director. She will also take advantage of the National Center for Leadership in Academic Medicine.
Geert W. Schmid-Schönbein, PhD - Dr. Schmid-Schönbein has been on the Bioengineering faculty since 1979, and is Distinguished Professor and past department chair. He is a past President of the Biomedical Engineering Society, the Microcirculatory Society, and North American Society for Biorheology and past chair of the US National Committee for Biomechanics. He served on or chaired NIH Study Sections on Renal, Cardiovascular, Microcirculation and Hypertension, Systems Biology and Lymphatics Biology. His awards include the Kurt Wiederhielm Award, the Landis Award of the Microcirculatory Society, Fellowships and Honorary Professorships. He was elected to the National Academy of Engineering (NAE) in 2005 and has trained 20 PhD students in microcirculation, lymphatics, cellular and molecular biomechanics, transport modeling and mechanotransduction applied to inflammation, diabetes, hypertension, shock and sepsis. His new treatment for autodigestion is currently in clinical trials.
- PROGRAM CONTACT
Training Grants Program Coordinator