Pioneering the Bioengineering field through cutting-edge research and dedicated mentorship.

Daniela Valdez-Jasso, PhD

Assistant Professor of Bioengineering

National Science Foundation Awardees

The Faculty Early Career Development (CAREER) Program Award 2020 -2021

This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.

Ester Kwon, PhD

Assistant Professor of Bioengineering
A multiscale approach to pulmonary arterial hypertension

Mechanical and Structural Adaptations of Blood Vessels in Pulmonary Arterial Hypertension

A new Faculty Early Career Development (CAREER) award to Asst. Prof. Daniela Valdez-Jasso will focus on improving our understanding of the adverse changes that occur in the arteries of the lung during pulmonary arterial hypertension, a serious disease with high mortality rates and no cure other than a lung transplantation.

The new research will build on the lab’s discovery that accumulation of fibrous tissue in the pulmonary arteries during disease progression is accompanied by an increase in their mechanical stiffness that impairs lung blood flow. Dr. Valdez-Jasso’s team will investigate the biological mechanisms by which the diseased arteries respond to increased blood pressure and how the structural changes in the vessel wall affect their mechanical properties using novel in-vivo physiological measurements, ex-vivo biomechanics, in-vitro cell biology and mathematical modeling.

The research will be complemented by an outreach program that teaches students how skills in biology, mathematics and engineering can be combined to find solutions to chronic health problems. Undergraduate students will gain hands-on access to the laboratory facilities used in this research.

BioE faculty gets award to advance tools for sensing traumatic brain injury damage

Traumatic brain injury (TBI) affects millions of Americans a year and there are currently no therapeutics available that address the long-term impairments observed in the majority of TBI survivors. One major challenge is the lack of sensors that can stage the severity of injury and predict long-term outcomes after TBI. In order to address this challenge, Asst. Prof. Ester Kwon received an NSF CAREER Award

in April 2021 to develop a new sensor that can measure the action of disease-causative proteins called proteases. In order to do so, she is leveraging the ability of nanometer-scaled materials or “nanomaterials” to enter into the injured brain across the damaged blood-brain barrier. She will combine these nanomaterials with synthetic peptides that are engineered as a switch to turn “on” in the presence of proteases that have elevated activity in TBI. The result will be a sensor that can detect protease activity after TBI in the living brain, which can be used to answer fundamental questions about proteases and TBI or developed as rapid diagnostic for TBI patients.

The award also supports Prof. Kwon to share with classrooms in the San Diego community that cool engineering can come in small packages. In partnership with high school teachers, she will be developing lesson plans to teach students about nanoscale materials in our daily lives, such as integrated circuits in mobile phones, nanoparticles in personal hygiene products, and microbial-resistant textiles.

Sensor activation (red) in a mouse model of TBI

ACHIEVEMENTS

Karen Christman, PhD

Professor of Bioengineering

2021 Clemson Award for Applied Research

Biomaterials Society acknowledges Professor Christman's pioneering vision in biomaterials

This is awarded to an individual whose accomplishments include significant utilization or application of basic knowledge in science to achieve a specific goal in the field of biomaterials.

“Karen has pioneered the use of injectable biomaterials to treat tissue after myocardial infarction (MI),” wrote nominator Jason Burdick, PhD. “This is an area that has grown greatly in the biomaterials community in the past decade, where biomaterials have been developed to deliver various biological and mechanical signals to the myocardium to improve outcomes of tissue remodeling.”

About the research >>

Stephanie Fraley, PhD

Associate Professor of Bioengineering

2021 UC San Diego Integrity Champion

"Courage is the Key"

The UC San Diego Integrity Champion reward is intended to recognize actions or activities that are above and beyond those normally expected based on the individual's role within the University.

Quickly moving to Remote Instruction at the end of WI20 caused many integrity challenges for the entire community. For this 11th Annual Integrity Awards Nomination process, nominations that recognized the challenging environment and how community members rose to those challenges were included.

LEADERSHIP

Andrew McCulloch, PhD

Distinguished Professor of Bioengineering

Bernard Palsson, PhD

Distinguished Professor of Bioengineeirng

Kun Zhang, PhD

Professor and Chair of Bioengineeirng

Professor Andrew McCulloch

chosen for the inaugural

Shu Chien Chancellor's Endowed Chair in Engineering and Medicine

The stated purpose of this chair, established in 2018, is to recognize an individual with a primary appointment in the Department of Bioengineering and a joint appointment with the School of Medicine. The endowment will support the teaching and research activities of the chairholder. The chair holder should be an internationally recognized leader in research, education and service.

Professor Andrew McCulloch was appointed as Director of the Institute of Engineering in Medicine (IEM), an Organized Research Unit at UC San Diego, effective November 1, 2019 by Vice Chancellor Sandra Brown. He was chosen as the inaugural candidate for the Shu Chien Chair. Dr. McCulloch is a Fellow of the American Physiological Society, Cardiovascular Section, a Fellow of the American Institute for Medical and Biological Engineering, as well as a Fellow of the International Association of Medical and Biological Engineering. His consistent service to the department and university are exemplary and Dr. McCulloch remains one of the most valued senior members of the Department of Bioengineering. Dr. McCulloch is widely regarded as an international leader in modeling the biomechanics and electrical signaling of the heart. His approach is the most advanced form of precision medicine in cardiology today. Dr. McCulloch teaches both undergraduate and graduate courses, with consistently high CAPE scores. Dr. McCulloch continues to direct the direct the UC San Diego Interfaces Graduate Training program that administers the Interdisciplinary PhD Specialization in Multi-Scale Biology that offers seven laboratory-based courses and is supported by an NIH T32 that was renewed recently with an impact score of 10. Dr. McCulloch continues to serve as the Editor in Chief of Drug Discovery Today: Disease Models, the Associate Editor of PLoS Computational Biology, and an Editorial Board Member of the Biophysical Journal. Dr. McCulloch supports our diversity mission by serving on the Diversity Outreach Collaboration, by serving as a member of the IRACDA (NIH’s Institutional Research and Academic Career Development Awards) program and has successfully recruited URM students into two of his NIH supported training grants.

Professor Bernhard Palsson

chosen for

Y-C Fung Endowed Chair


The stated purpose of this chair, named in honor of the founder of Bioengineering at UCSD and the undisputed “father of biomechanics” is “to retain outstanding faculty who will carry Dr. Fung’s grand vision into the future.” The chair holder should be an internationally recognized leader in research, education and service. Professor Palsson was unanimously chosen as the candidate to succeed Professor Shu Chien, the inaugural Y-C Fung Endowed Chair.

Professor Palsson is the Primary Investigator for the Systems Biology Research Group at UCSD, and in partnership with the Norvo Nordisk Foundation, also leads the Center for Biosustainability which has raised just under $500M in funding from private foundations. His own group, the SBRG has brought in almost $100M of research funding to the Bioengineering Department. Professor Palsson has over 500 publications, 4 textbooks and has 89,695 citations (Google Scholar 08.17.2020) and was recently recognized in the Web of Science “2019 Highly Cited Researchers list”. He was selected by Thomson Reuters as one of “The World’s Most Influential Scientific Minds” in 2015 and was awarded the International Metabolic Engineering Award in 2016. Professor Palsson is a member of the National Academy of Engineering (2006), and a Fellow of the American Association for the Advancement of Science (2010). Educationally, Professor Palsson has developed new course content in the field of data science for both our undergraduate and graduate courses, serves on average 50 thesis and exam committees per review period and has mentored hundreds of students, postdocs and visiting scholars in his UCSD lab. Outside the University, Dr. Palsson has an amazing record of service to the scientific community. He given over 200 invited talks and keynote speeches, serves as a reviewer on many numerous publications including: AIChE Journal, AIDS Research and Human Retroviruses, Annals of Bioengineering, Applied and Environmental Microbiology, Bioinformatics, Biophysical Journal, Biotechniques, Biotechnology and Bioengineering, Biotechnology Progress, BMC Central, Cellular Engineering, Chemical Engineering Science, Experimental Hematology, Human Gene Therapy, Journal of Biotechnology, Journal of Hematotherapy, Journal of Theoretical Biology, NASA, Nature, Nature Biotechnology, Nature Medicine, Nature Communications, NIH, NSF, Science, Trends in Biotechnology to name a few.

Professor Kun Zhang

chosen for

Leo and Trude Szilard Chancellor's Endowed Chair

Transforming how we understand and treat disease.

The Leo and Trude Szilard Chancellor’s Endowed Chair was established by Joan and Irwin Jacobs as part of the Chancellor’s Endowed Chair Challenge, created to support teaching and research of quality tenured faculty.

Professor Kun Zhang, Chair of the Department of Bioengineering was selected as the inaugural Chair-holder for his exceptional academic accomplishments and outstanding contributions to teaching, diversity and service. Regarded internationally as one of the pioneers in genomic technology and a major leader in single cell research, his research focuses on developing molecular techniques and engineering platforms for building single-cell maps of multiple human organs; analyzing the genome, epigenome and transcriptome; and applying cell imaging and lineage tracing — all with an eye toward potentially transforming how we understand and treat disease.

A leader in the single cell and high-throughput sequencing field, Dr. Zhang has made outstanding contributions to innovative and pace-setting research on single-cell genomics and its application to several human organs and tissues. He and his laboratory have pioneered several technologies, including a “single-nucleus RNA sequence” method that has transformed the field by making it feasible to study a large number of human neurons at single-cell resolution.

In addition, Dr. Zhang has made major contributions to teaching through his excellent classroom and laboratory education as well as his wonderful mentoring of graduate students and postdoctoral fellows. As co-chair and then the chair of the Graduate Studies Committee (GSC) of the Department of Bioengineering, Dr. Zhang has made important contributions to different aspects of graduate education. He has greatly improved the outcome of graduate student recruitment, and his dedicated work has led to an improvement of the acceptance rate by the students who have been offered admission and enhanced the diversity of our graduate students. Besides his service as GSC chair and department chair, Dr. Zhang has served on several campus/JSOE committees during this review period, i.e., High-Throughput Genomics Steering Committee, Institute of Engineering in Medicine Academic Personnel Committee, and JSOE E4 committee. He has served as Director of the JSOE Cell Engineering Research Center core facility director. He also served on three NIH review panels (two for Genomics, Computational Biology and Technology and one for Re-Building a Kidney).

Dr. Shu Chien Celebrates his 90th Birthday

Happy 90th birthday to pioneering bioengineer Shu Chien. Chien made many foundational scientific discoveries over the course of his 62-year academic career, and was a galvanizing force in the creation of our UC San Diego Department of Bioengineering, which has consistently been top-ranked globally.

Bruce Wheeler, PhD

Adjunct Professor of Bioengineering

Endowed Student Awards Fund Created by Faculty Philanthropy

Seeing the importance and need to properly recognize our top undergraduate students, Bioengineering faculty kickstarted a fundraising campaign to create an Endowed Student Awards Fund. As faculty gathered to review award nominees this spring, they saw that not all awards came with a financial prize. This imbalance inspired Professor Bruce Wheeler to explore the creation of a fundraising campaign.

“This initiative creates an endowed fund to provide financial prizes to complement the annual year-end recognition awards,” stated Prof. Bruce Wheeler. “This will allow awards like the Anushka Michailova Memorial Award, Eugene H. Mead Award for Engineering Excellence, Best Senior Design Project and Outstanding Contributions to Diversity to be funded in perpetuity.”

As of July 2021, faculty have contributed $16,000 toward the $25,000 goal. The BE department aspires to achieve the fundraising goal by the end of 2021 with gifts being received by faculty, alumni and industry leaders. Gifts can be made online here.

SPOTLIGHT ON RESEARCH

Interviews

Trey Ideker, PhD

Affiliate Professor

Using Systems Biology to Advance Genomic Medicine

An Interview with Professor Trey Ideker : A Founder of Systems Biology

Dr. Trey ldeker is a Professor of Medicine, Bioengineering, and Computer Science at UCSD. He received his 8.5 and M.5. in Computer Science and Electrical Engineering from MIT. and later his PhD in Biology at UWash with Dr. Leroy Hood. It was during his doctoral work that Dr. ldeker helped lay the foundation for the field of systems biology as we know it today, through the creation of Cytoscape. By applying quantitative approaches to solve complex biological problems, Dr. ldeker now leads a team that aims to advance our understanding of gene regulatory networks in the domains of cancer. CRISPR-Cas9 screens, and more recently, the mechanisms behind COVID-19 infection.

Read more...

Advancing the Frontiers of Brain-Machine Interfaces

Research at the crossroads of silicon and biology

The Integrated Systems Neuroengineering (ISN) Lab, run by Dr. Gert Cauwenberghs, aims to advance the frontiers of both neuromorphic engineering and silicon neural interfaces through the creation of large-scale systems integrated circuits that mimic the structures found within the nervous system.

As a dedicated group of project scientists, postdoctoral fellows, graduate and undergraduate students, the ISN lab exemplifies teamwork and innovation. Dr. Cauwenberghs notes, “Our lab is quite dry, literally. There are no chemicals in the lab besides some solder paste in the fume hood. Our wet lab experiments are then through collaborations, and it has really been thriving and productive.” ISN lab is highly interdisciplinary, and interacts regularly with neuroscientists, biologists, physicists, and device fabrication engineers.

Read more...

Prof. Gert Cauwenberghs and members of the Integrated Systems Neuroengineering (ISN ) Lab.

PROMOTIONS

Meet our Faculty

Xioahua Huang

ProfessorBioengineering

Professor Xiaohua Huang

Huang Lab: Digital Molecular Biotechnology and Nanodevice Engineering

Our research focuses on developing digital molecular, micro and nano technologies to decode the molecular circuitry and operating systems (OS) of living systems.


Applying the fundamental principles and state-of-the-art tools of molecular biology, chemistry, physics, mathematics, computer science, electrical engineering and materials science, we aim to develop technologies and engineer devices for single-molecule sequencing and digital counting of DNA/RNA and proteins in single cells, or any biological/clinical samples. These precise digital measurements will enable better computational modeling and deterministic understanding of living systems, and human physiology and diseases for basic research and biomedical applications. Our current research areas:

· Molecular and nano technologies for single-molecule DNA/RNA and protein sequencing

· Genomics, proteomics and medical diagnostics

· Lab-on-a-chip microfluidics, protein and nano device engineering

· DNA data storage and molecular computing

· Physical modeling, numerical simulations and deep machine learning

Stephanie Fraley, PhD

Associate ProfessorBioengineering

Associate Professor Stephanie Fraley

Fraley Lab: Contechtual Bioengineering

The Fraley Lab's vision is to contribute to the development of a new scientific framework for bridging knowledge between in vitro studies and clinical diseases. In vitro model systems, which are necessary for studying the molecular mechanisms of disease, often fail to represent critical pathophysiological features of human disease.

This incoherence originates from the context and time dependent nature of biological phenomena. As a result, findings from in vitro studies rarely translate directly into impact for patients. It remains a major challenge to identify critical disease features and capture them “in a dish”. Diseases that involve complex microenvironmental deregulation, rather than a causal genetic mutation, are especially challenging. Linking in vitro and clinical information across temporal and spatial scales requires engineering innovation in two major areas, on which the Fraley Lab focuses: I.) quantitative, time-dependent, and integrative measurements of disease processes in humans to identify dominant features, and II.) recapitulating these key features in three-dimensional (3D) human tissue system mimics to study causal relationships.

Prashant Mali, PhD

Associate ProfessorBioengineering

Associate Professor Prashant Mali

Mali Lab: Understanding and progressively engineering biology towards enabling gene & cell based human therapeutics.

The major research thrusts in the laboratory are two-fold: one, development of molecular toolsets for genome, transcriptome, and proteome engineering and their application to systematic genome interpretation and gene therapy applications; and two, study and engineering of cell fate specification during development utilizing human pluripotent stem cells as the core model system. Given the parallels in phenotypes (such as self-renewal and tumor forming ability) between pluripotent stem cells and cancer cells, a key research thrust is also in dissecting aberrant cellular transformation processes such as during tumorigenesis.

Our research approach is curiosity-driven, integrating core expertise in genome engineering and stem cell engineering, with synthetic biology and materials science, and we are passionate about understanding and progressively engineering biology towards enabling gene & cell based human therapeutics.