César de la Fuente on AIChE’s 35 Under 35 List

César de la Fuente, PhD

César de la Fuente, Presidential Assistant Professor in Psychiatry, Microbiology, and Bioengineering, was named one of the American Institute of Chemical Engineers’ (AIChE) 35 members under 35 for 2020.

“The AIChE 35 Under 35 Award was founded to recognize young chemical engineers who have achieved greatness in their fields,” reads the 2020 award announcement. “The winners are a group of driven, engaged, and socially active professionals, representing the breadth and diversity that chemical engineering exemplifies.”

De la Fuente was named in the list’s “Bioengineering” category for his his lab’s work in machine biology. Their goal is to develop computer-made tools and medicines that will combat antibiotic resistance. De la Fuente has already been featured on several other young innovators lists, including MIT Technology Review’s 35 under 35 and GEN’s Top 10 under 40, both in 2019. His research in antibiotic resistance has been profiled in Penn Today and Penn Engineering Today, and he was recently awarded Penn Health-Tech’s inaugural NEMO Prize for his proposal to develop paper-based COVID diagnostic system that could capture viral particles on a person’s breath.

In addition to being named on the 2020 list, the honorees will receive a $500 prize and will be celebrated at the 2020 AIChE Annual Meeting this November.

Learn more about de la Fuente’s pioneering research on his lab website.

‘The Self-Organized Movement to Create an Inclusive Computational Neuroscience School’

When the COVID-19 pandemic began taking hold in the United States, one of the first “superspreader” events was an academic conference. Such conferences have long been a primary way for researchers to share new findings and launch collaborations, but with thousands of people from around the world, indoors and in close proximity, it quickly became clear that the traditional format for these events would need to radically change.

Konrad Kording
Konrad Kording

Konrad Kording, a Penn Integrates Knowledge Professor with appointments in the departments of Bioengineering and Computer and Information Science in Penn Engineering and the Department of Neuroscience at Penn’s Perelman School of Medicine, was ahead of the curve on this shift. With the issues of prohibitive costs and environmental impact of travel in mind, Kording had already started brainstorming ways of reinventing the traditional conference format when the pandemic made it a necessity.

The resulting event, Neuromatch, involved algorithmically analyzing participants’ work in order to connect researchers who might not otherwise meet. Building on the success of that “unconference,” Kording and his colleagues launched the Neuromatch Academy, a free-ranging online summer school organized around the same principles.

Ashley Juavinett writing for The Simons Collaboration on the Global Brain, recently dug into how Neuromatch was able to pull together 1,750 students from 70 countries in a matter of months:

Kording already had experience quickly pulling together online events. Early in the pandemic, together with Dan Goodman, Titipat Achakulvisut and Brad Wyble, he developed an online ‘unconference,’ which featured both lectures and a virtual networking component designed to mimic the in-person interactions that make conferences so valuable. (For more, see “Designing a Virtual Neuroscience Conference.”) Soon after, they decided to spin that success into a full-fledged summer school offering live lectures with top computational neuroscientists, guided coding exercises to teach mathematical approaches to neural modeling and analysis, and community support from mentors and teaching assistants (TAs).

The result was a summer school with well-designed content, a diverse student body, including participants from U.S.-sanctioned Iran, and a determined group of organizers who managed to pull off the most inclusive computational neuroscience school yet. NMA now has its eye on a future with even broader representation across countries, languages and skill levels. This year has been incredibly difficult for many, but NMA has provided an important precedent for how to collaborate across, and even dismantle, all sorts of barriers.

Continue reading “The Self-Organized Movement to Create an Inclusive Computational Neuroscience School” at The Simons Collaboration on the Global Brain.

Originally posted on the SEAS blog. Media contact Evan Lerner.

BE Seminar: “Imaging and Sequencing Single Cells” (Aaron Streets, UC Berkeley)

The Penn Bioengineering virtual seminar series continues on October 8th.

Aaron Streets, PhD


Speaker: Aaron Streets, Ph.D.
Associate Professor of Bioengineering
University of California, Berkeley

Date: Thursday, October 8, 2020
Time: 2:00-3:00 pm (note the change from our regular seminar time)
Zoom – check email for link or contact ksas@seas.upenn.edu

Title: “Imaging and Sequencing Single Cells”


Recent advances in microfluidics and high-throughput sequencing technology have enabled rapid profiling of genomic material in single cells. Valve- and droplet-based microfluidic platforms can precisely and efficiently manipulate, sort, and process cells to generate indexed sequencing libraries, allowing for high-throughput single-cell analysis of the genome, transcriptome, proteome, and epigenome. Such technology has been instrumental in the global effort to create a human cell atlas, with the ambitious goal of identifying and cataloging all human cell types and cell states in health and disease. However, not all cell phenotypes are directly encoded in the genome and high-throughput sequencing cannot probe the full space of cellular identity. Therefore, microscopy remains one of the most powerful and versatile tools for characterizing cells. Fluorescent imaging and quantitative non-linear optical imaging can reveal morphological characteristics, protein localization, chromatin organization, and chemical composition in single cells. Both single-cell genomics and microscopy can uncover heterogeneity in cellular populations that would otherwise be obscured in ensemble measurement. In this talk, I will discuss a suite of new microfluidic platforms for coupling genomic measurements and optical measurements of the same single cell, and some novel computational approaches to grapple with these new datasets. With a combination of new hardware and software, our goal is to converge on a quantitative and comprehensive understanding of cellular identity.


Aaron received a Bachelor of Science in Physics and a Bachelor of Arts in Art at UCLA. He completed his PhD in Applied Physics at Stanford with Dr. Stephen Quake. Aaron then went to Beijing, China as a Whitaker International Postdoctoral Fellow and a Ford postdoctoral fellow and worked with Dr. Yanyi Huang in the Biodynamic Optical Imaging Center (BIOPIC) at Peking University. Aaron joined the faculty of UC Berkeley as an Assistant Professor in Bioengineering in 2016 and is currently a core member of the Biophysics Program and the Center for Computational Biology and he is a Chan Zuckerberg Biohub investigator. Aaron has received the NSF Early Career award and was recently named a Pew Biomedical Scholar.

See the full list of upcoming Penn Bioengineering fall seminars here.

Postdoctoral Fellow Linden Parkes Wins BBRF Young Investigator Grant

Linden Parkes, PhD

The Department of Bioengineering at Penn is thrilled to congratulate Linden Parkes on receiving a Brain & Behavior Research Foundation (BBRF) Young Investigator Grant for 2021-2022. This grant will support Parkes’ continued postdoctoral research under the supervision of Danielle S. Bassett, J. Peter Skirkanich Professor of Bioengineering and Electrical and Systems Engineering in the School of Engineering and Applied Science (SEAS),  Theodore D. Satterthwaite, Associate Professor of Psychiatry in the Perelman School of Medicine (PSOM), and Raquel E. Gur, the Karl and Linda Rickels Professor of Psychiatry in PSOM.

Originally from Australia, Parkes did his undergraduate B.Sc. (Hons.) in Psychology and Psychophysiology at the Swinburne University of Technology in Melbourne. He went on to receive his Ph.D. in Neuroscience from the Turner Institute for Brain and Mental Health at Monash University (also in Melbourne) under the supervision of Murat Yucel, Professor of Psychology, Alex Fornito, Professor of Psychology, and Ben Fulcher, Senior Lecturer in the School of Physics at the University of Sydney. After finishing his doctorate, Parkes moved to Philadelphia to take up a position as a postdoctoral fellow in Danielle Bassett’s Complex Systems Lab.

Parkes will use the BBRF’s support to continue his research examining the link between the symptoms of mental illness and the brain. In particular, he seeks to uncover how individual patterns of abnormal neurodevelopment link to, and predict, the emergence of psychosis symptoms through childhood and adolescence using longitudinal data. In turn, Parkes’ work will discover prognostic biomarkers for the psychosis spectrum that will help inform clinical outcome tracking.

“I am honored to have been selected for a Young Investigator Grant from the BBRF this year,” Parkes says. “This award will support me to conduct research that I believe will make real inroads into understanding the pathways that link abnormalities in neurodevelopment to the symptoms of psychosis. I feel grateful for the opportunity to complete my postdoctoral training at Penn. Penn has connected me with wonderful people who I’m sure will be lifelong mentors, colleagues, and peers.”

The BBRF Young Investigator Grants are valued at more than $10.3 million and are awarded annually to 150 of the world’s most promising young scientists to support the work of early career investigators with innovative ideas for groundbreaking neurobiological research seeking to identify causes, improve treatments, and develop prevention strategies for psychiatric disorders.

Read more about the BBRF 2020 Young Investigators here.

BE Seminar: “Predicting the Effects of Engineering Immune Cells Using Systems Biology Modeling” (Stacey Finley, USC)

The Penn Bioengineering virtual seminar series continues on October 1st.

Stacey Finley, PhD


Speaker: Stacey Finley, Ph.D.
Gordon S. Marshall Early Career Chair and Associate Professor of Biomedical Engineering and Biological Sciences
University of Southern California


Date: Thursday, October 1, 2020
Time: 3:00-4:00 pm
Zoom – check email for link or contact ksas@seas.upenn.edu

Title: “Predicting the Effects of Engineering Immune Cells Using Systems Biology Modeling”


Systems biology approaches, including computational models, provide a framework to test biological hypotheses and optimize effective therapeutic strategies to treat human diseases. In this talk, I present recent work in modeling signaling in cancer-targeting immune cells, including CAR T cells at Natural Killer cells. Chimeric antigen receptors (CARs) are comprised of a variety of different activating domains and co-stimulatory domains that initiate signaling required for T cell activation. There is a lack of understanding of the mechanisms by which activation occurs. We apply mathematical modeling to investigate how CAR structure influences downstream T cell signaling and develop new hypotheses for the optimal design of CAR-engineered T cell systems. Natural Killer cells also provide a useful platform for targeting cancer cells. However, NK cells have been shown to exhibit reduced killing ability with prolonged stimulation by cancer cells. We use a combination of mechanistic model, optimal control theory and in silico synthetic biology to investigate strategies to enhance NK cell-mediated killing.


Stacey D. Finley is the Gordon S. Marshall Early Career Chair and Associate Professor of Biomedical Engineering at the University of Southern California. Dr. Finley received her B.S. in Chemical Engineering from Florida A & M University and obtained her Ph.D. in Chemical Engineering from Northwestern University. She completed postdoctoral training at Johns Hopkins University in the Department of Biomedical Engineering. Dr. Finley joined the faculty at USC in 2013, and she leads the Computational Systems Biology Laboratory. Dr. Finley has joint appointments in the Departments of Chemical Engineering and Materials Science and Biological Science, and she is a member of the USC Norris Comprehensive Cancer Center. Dr. Finley is also the Director of the Center for Computational Modeling of Cancer at USC. Her research is supported by grants from NSF, NIH, and the American Cancer Society.

Selected honors: 2016 NSF Faculty Early CAREER Award; 2016 Young Innovator by the Cellular and Molecular Bioengineering journal; Leah Edelstein-Keshet Prize from the Society of Mathematical Biology; Junior Research Award from the USC Viterbi School of Engineering; the Hanna Reisler Mentorship Award; 2018 AACR NextGen Star; 2018 Orange County Engineering Council Outstanding Young Engineer

See the full list of upcoming Penn Bioengineering fall seminars here.

Gardening in Costa Rica Yields Inspiration During Quarantine


María Suarez in her garden.

When the coronavirus pandemic began in March, María Suarez, junior in bioengineering, left Penn’s campus and returned home to Costa Rica. What should have been the final weeks of club activities, social events and end-of-year celebrations shifted to months spent at home, far away from Philadelphia. But Suarez, like many others, wanted to do something productive with her time in quarantine. Drawing on her bucolic roots, she decided to start a garden.

“I was born and raised in a very rural area,” Suarez says. “There is a huge river in my backyard where I learned how to count by throwing pebbles in the river with my mother and sister. Nature is a big part of my life, and it’s really shaped my personality. As a child, I planted herbs, like basil, mint and oregano, with my parents. When you are close to the land like this, gardening was something that grew naturally out of our lifestyle.”

As the spring semester shifted into summer, Suarez returned to her love of planting and embarked on an ambitious project to grow a vegetable garden in her backyard. Unlike the smaller herb gardens she had grown as a child, this vegetable garden required deeper horticultural knowledge as well as intense work under the hot sun.

“To begin the garden, I had to clear the land I wanted to use and remove all the grass and stones from the soil,” Suarez shares. “It was the dry season in Costa Rica and the ground was very difficult to work with.”

After clearing the land, Suarez had to bring nutrients back into the soil of her garden plot. Luckily, her family has been maintaining a natural compost pile for many years.

“Basically, the compost pile is a hole in the ground where we put our natural food waste. There are worms and animals there that help us naturally decompose the waste and they produce a very nutrient rich soil.” Suarez explains. “The compost is a five-minute walk from my garden, and I had to take at least ten trips with a wheelbarrow to bring enough back. It was a great arm workout.”

Once the soil was placed and watered, Suarez was finally able to plant her seeds. After a few days, she saw celery and zucchini plants beginning to sprout. Throughout the summer, Suarez’s crops grew well, and she was able to harvest the vegetables and share them with her family.

“It was very fulfilling to see the products of my efforts,” Suarez says.

Read the full story on the Penn Engineering blog.

BE Seminar: “Patients, Providers and Data: How the EMR and Data Science are Changing Clinical Care” (Kevin Johnson, Vanderbilt)

The Penn Bioengineering virtual seminar series continues on September 24th.

Kevin Johnson, MD, MS

Speaker: Kevin Johnson, M.D., M.S.
Cornelius Vanderbilt Professor and Chair
Department of Biomedical Informatics
Vanderbilt University Medical Center

Date: Thursday, September 24, 2020
Time: 3:00-4:00 pm
Zoom – check email for link or contact ksas@seas.upenn.edu

Title: “Patients, Providers and Data: How the EMR and Data Science are Changing Clinical Care”


The electronic health record (EHR) is a powerful application of Systems Engineering to healthcare. It is a byproduct of a host of pressures including cost, consolidation of providers into networks, uniform drivers of quality, and the need for timely care across disparate socioeconomic and geographic landscapes within health systems. The EHR is also a fulcrum for innovation and one of the most tangible examples of how data science affects our health and health care. In this talk I will showcase projects from my lab that demonstrate the multi-disciplinary nature of biomedical informatics/data science research and translation using the EHR, and our current understanding of its potential from my perspective as a pediatrician, a researcher in biomedical informatics, a Chief Information Officer, an educator, and an advisor to local and international policy. I will describe advances in applying human factors engineering to support medical documentation and generic prescribing, approaches to improve medication safety, and innovations to support precision medicine and interoperability. I will present our efforts to integrate EHR-enabled data science into the Vanderbilt health system and provide a vision for what this could mean for our future.


Kevin B. Johnson, M.D., M.S. is Informatician-in-Chief, Cornelius Vanderbilt Professor and Chair of Biomedical Informatics, and Professor Pediatrics at Vanderbilt University Medical Center. He received his M.D. from Johns Hopkins Hospital in Baltimore and his M.S. in Medical Informatics from Stanford University. In 1992 he returned to Johns Hopkins where he served as a Pediatric Chief Resident. He was a member of the faculty in both Pediatrics and Biomedical Information Sciences at Johns Hopkins until 2002, when he was recruited to Vanderbilt University. He also is a Board-Certified Pediatrician.

Dr. Johnson is an internationally respected developer and evaluator of clinical information technology. His research interests have been related to developing and encouraging the adoption of clinical information systems to improve patient safety and compliance with practice guidelines; the uses of advanced computer technologies, including the Worldwide Web, personal digital assistants, and pen-based computers in medicine; and the development of computer-based documentation systems for the point of care. In the early phases of his career, he directed the development and evaluation of evidence-based pediatric care guidelines for the Johns Hopkins Hospital. He has been principal investigator on numerous grants and has been an invited speaker at most major medical informatics and pediatrics conferences. He also was the Chief Informatics Officer at Vanderbilt University Medical Center from 2015-2019.

See the full list of upcoming Penn Bioengineering fall seminars here.

MINS/BE Seminar: “Mapping emotions: discovering structure in mesoscale electrical brain recordings” (Kafui Dzirasa, Duke University)

The Mahoney Institute for Neurosciences (MINS) and Department of Bioengineering will co-host a seminar on September 16. Details and registration information are below. We hope you will join us to hear this upcoming talk.

Title: “Mapping emotions: discovering structure in mesoscale electrical brain recordings”

Kafui Dzirasa, MD, PhD

Speaker: Kafui Dzirasa,MD, PhD
K. Ranga Rama Krishnan Endowed Associate Professor
Department of Psychiatry and Behavioral Sciences
Duke University Medical Center




Date: Wednesday, September 16, 2020
Time: 4:00-5:30 PM Eastern Time
This event will be held virtually via Bluejeans (link here)

Hosted by Danielle Bassett and Joshua Gold