PIK Professor Kevin Johnson named University Professor

Johnson, who has appointments in the Perelman School of Medicine and the School of Engineering and Applied Science, and a secondary appointment in the Annenberg School for Communication, will become the David L. Cohen University Professor.

Penn Integrates Knowledge Professor Kevin Johnson, a pediatrician who has pioneered the use of clinical information systems and artificial intelligence to improve medical research and patient care, has received a named University professorship.

Kevin Johnson, a Penn Integrates Knowledge University Professor whose work as a physician-scientist has led to medical information technologies that improve patient safety, has been named the David L. Cohen University Professor. The announcement was made today by President Amy Gutmann.

“David Cohen’s extraordinary leadership at the University and Penn Medicine, and longtime dedication to Philadelphia, has without a doubt shaped the booming campus, health system, and city we so much enjoy today,” says Gutmann. “His dedication is mirrored by the extraordinarily influential, innovative, and committed Dr. Kevin Johnson, whose university professorship will now bear Ambassador Cohen’s name.”

Johnson joined Penn this year from the Vanderbilt University School of Medicine. A board-certified pediatrician and leading medical informaticist, he holds faculty appointments in the Department of Biostatistics, Epidemiology, and Informatics in the Perelman School of Medicine and the Department of Computer and Information Science in the School of Engineering and Applied Science. He is also vice president for applied informatics at the University of Pennsylvania Health System and has secondary faculty appointments in the Perelman School of Medicine’s Department of Pediatrics and in the Annenberg School for Communication.

Cohen has served for two decades on Penn’s Board of Trustees and recently concluded a 12-year term as chair. He was confirmed by the U.S. Senate last month as United States Ambassador to Canada, bringing to the role decades of experience as a senior executive at Comcast Corp., chair of the Ballard Spahr law firm, chief of staff to Philadelphia Mayor Ed Rendell, trustee chair at Penn, and major player in a number of other business, civic, political, and philanthropic venues.

In addition to serving as a Trustee, Cohen is a Penn alum, having graduated from what is now the University of Pennsylvania Carey School of Law in 1981. His wife and son also attended the Law School. Cohen’s leadership in the University has been credited with helping guide the growth and advancement of both the University and Health System, in close partnership with both President Gutmann and her predecessor, Judith Rodin.

“It’s an honor to hold a professorship named after Mr. Cohen,” Johnson says. “Throughout his career, he has provided inspired leadership across Penn and our city and region. He is a passionate believer in uniting the public, private, and nonprofit sectors to tackle complex challenges and strengthen communities. Those who know me know that I’ve played a similar role as a pediatrician who works with technology, and who uses digital media to communicate to lay audiences about both. His passion for this city and our University’s educational mission are inspiring.”

N.B.: Johnson also holds a secondary appointment in the Department of Bioengineering. Read his full appointment announcement here.

Single-cell Cancer Detection Project Wins 2021 NEMO Prize

This scProteome-seq array shows separated protein biomarkers (green and magenta spots) from thousands of single cells.

Penn Health-Tech’s Nemirovsky Engineering and Medicine Opportunity (NEMO) Prize awards $80,000 to support early-stage ideas joining engineering and medicine. The goal of the prize is to encourage collaboration between the University of Pennsylvania’s Perelman School of Medicine and the School of Engineering and Applied Science by supporting innovative ideas that might not receive funding from traditional sources.

This year, the NEMO Prize has been awarded to a team of researchers from Penn Engineering’s Department of Bioengineering. Their project aims to develop a technology that can detect multiple cancer biomarkers in single cells from tumor biopsy samples.

As cancer cells grow in the body, one of the characteristics that influences tumor growth and response to treatment is cancer cell state heterogeneity, or differences in cell states. Methods that rapidly catalogue cell heterogeneity may be able to detect rare cells responsible for tumor growth and drug resistance.

Single-cell transcriptomics (scRNA-seq) is the standard method for studying cell states; by amplifying and analyzing the cell’s complement of RNA sequences at a given time, researchers can get a snapshot of what proteins the cell is in the process of making. However, this method does not fully capture the function of the cell. The field of proteomics, which captures the actual protein content of cells along with post-translational modifications, provides a better picture of the cell’s function, but single-cell proteomic methods with the same sensitivity as scRNA-seq do not currently exist.

Alex Hughes, Lukasz Bugaj and Andrew Tsourkas

This collaborative project, which joins Assistant Professors Alex Hughes and Lukasz Bugaj, as well as Professor Andrew Tsourkas, aims to change that by developing multiplexed, sensitive and highly specific single-cell proteomics technologies to advance our understanding of cancer, its detection and its treatment.

This new technology, called scProteome-seq, builds from Hughes’s previous work.

“My specific expertise here is as an inventor of single-cell western blotting, which is the core technology that our team is building on,” says Hughes. “Single-cell proteomics technologies of this type have a track-record of commercial translation for applications in basic science and clinical automation, so our approach has a high potential for real-world impact.”

The current technology from Hughes’ lab separates proteins in cells by their molecular weight and “blots” them on a piece of paper. Improvements to this technology included in this project will remove the limitation of using light-emitting dyes to detect different proteins and instead use DNA barcodes to differentiate them.

Read the full story in Penn Engineering Today.

Jenny Jiang on T Cell Diversity and Cancer Immunotherapy

by Melissa Pappas

Jenny Jiang, Ph.D.

Our body’s natural line of defense against infection and disease, as well as cancer, is our immune system equipped with T cells, a type of white blood cell that determines how we react to foreign substances, or antigens, in the body. While we have an arsenal of T cells to protect us from these various infections, some people lack certain T cells or simply do not have enough to fight off infections, such as the flu or HIV, or defend against the body’s own mutated cancer cells.

Understanding the diversity of T cells and which antigens they target can provide insight into developing personalized immunotherapy to help those patients with weak spots or gaps in their T cell community. Jenny Jiang, Peter and Geri Skirkanich Associate Professor of Innovation in Bioengineering, is characterizing this diversity.

Jiang recently received a Cancer Research Institute’s (CRI) Lloyd J. Old STAR grant to support her research on this topic. The CRI STAR grant identifies mid-career “Scientists TAking Risks” in innovative cancer immunotherapy research areas, providing freedom and flexibility to pursue high-risk, high-reward research with financial support of $1.25 Million over the course of five years.

Jiang spoke with CRI science writer Arthur Brodsky about her research and how the STAR grant will support it.

“In our studies of healthy individuals, who have some natural immune protection against commonly encountered viruses like the flu, we noticed that not everyone has T cells that cover all the possible antigens,” says Jiang. “There are differences in the number and types of flu-targeting T cells that each individual has. For some “exotic” antigens, like those of HIV for example, although the general population doesn’t actually have exposure to them, they should still have a very low level of minimum T cells that can offer some protection from possible future infection. So that part of our T cell arsenal acts as a safety net. But some individuals may completely lack those T cells. In those cases, as you can imagine, those people will have a hard time overcoming a future infection.”

Jiang describes how this is similar to how our bodies prevent cancerous tumor growth.

Read the full story in Penn Engineering Today.

Investing in Penn’s Data Science Ecosystem

by Erica K. Brockmeier

As part of a major University-wide investment in science, engineering, and medicine, the Innovation in Data Engineering and Science Initiative aims to help Penn become a leader in developing data-driven approaches that can transform scientific discovery, engineering research, and technological innovation.

From smartphones and fitness trackers to social media posts and COVID-19 cases, the past few years have seen an explosion in the amount and types of data that are generated daily. To help make sense of these large, complex datasets, the field of data science has grown, providing methodologies, tools, and perspectives across a wide range of academic disciplines.

But the challenges that lie ahead for data scientists and engineers, from developing algorithms that don’t exacerbate biases to ensuring privacy protections, are equally complex and, in some instances, require entirely new ways of thinking.

As part of its $750 million investment in science, engineering, and medicine, the University has committed to supporting the future needs of this field. To this end, the Innovation in Data Engineering and Science (IDEAS) initiative will help Penn become a leader in developing data-driven approaches that can transform scientific discovery, engineering research, and technological innovation.

“The IDEAS initiative is game-changing for our University,” says President Amy Gutmann. “This new investment allows us to boost our interdisciplinary efforts across campus, recruit phenomenal additional team members, and generate an even more sound foundation for discovery, experimentation, and design. This initiative is a clear statement that Penn is committed to taking data science head-on.”

Building on a foundation of existing expertise

Led by the School of Engineering and Applied Science, the IDEAS initiative builds upon the steadily gathering momentum of its data-centric research. The Warren Center for Network and Data Sciences has been a major catalyst for this type of work, generating foundational research on ethical algorithms and data privacy, as well as collaborations that have drawn in faculty from the Wharton School, Law School, Perelman School of Medicine, and beyond. In addition, Wharton’s Department of Statistics and Data Science is an active partner in research and teaching initiatives that apply statistical modeling across a wide variety of fields.

“One of the unique things about data science and data engineering is that it’s a very horizontal technology, one that is going to be impacting every department on campus,” says George Pappas, Electrical and Systems Engineering Department chair. “When you have a horizontal technology in a competitive area, we have to figure out specific areas where Penn can become a worldwide leader.”

To do this, IDEAS aims to recruit new faculty across three research areas: artificial intelligence (AI) to transform scientific discovery, trustworthy AI for autonomous systems, and understanding connections between the human brain and AI.

Penn already has a strong foundation in using AI for scientific discovery thanks in part to investments in basic research facilities such as the Singh Center for Nanotechnology and the Laboratory for Research on the Structure of Matter. Additionally, there are centers focused on connecting researchers from different fields to address complex scientific questions, including the Center for Soft and Living Matter, Center for Engineering Mechanobiology, and Penn Institute for Computational Science.

Developing “trustworthy” algorithms, ones that work reliably outside of situations in which they are trained, is another key component of the IDEAS initiative. Ongoing research at the Penn Research in Embedded Computing and Integrated Systems Engineering (PRECISE) Center, the General Robotics, Automation, Sensing & Perception (GRASP) Lab, and DARPA-funded projects on the safety of AI-based aircraft control provide a starting point for furthering Penn’s research portfolio on safe, explainable, and trustworthy autonomous systems.

In the area of neuroscience and how the human brain is similar to AI and machine learning approaches, research from PIK Professor Konrad Kording and Dani Bassett’s Complex Systems lab exemplifies the types of cross-disciplinary efforts that are essential for addressing complex questions. By recruiting additional faculty in this area, IDEAS will help Penn make strides in bio-inspired computing and in future life-changing discoveries that could address cognitive disorders and nervous system diseases.

Read the full story in Penn Today.

Penn Bioengineering Celebrates Five Researchers on Highly Cited Researchers 2021 List

The Department of Bioengineering is proud to announce that five of our faculty have been named on the annual Highly Cited Researchers™ 2021 list from Clarivate:

Dani Bassett, Ph.D.

Dani S. Bassett, J. Peter Skirkanich Professor in Bioengineering and in Electrical and Systems Engineering
Bassett runs the Complex Systems lab which tackles problems at the intersection of science, engineering, and medicine using systems-level approaches, exploring fields such as curiosity, dynamic networks in neuroscience, and psychiatric disease. They are a pioneer in the emerging field of network science which combines mathematics, physics, biology and systems engineering to better understand how the overall shape of connections between individual neurons influences cognitive traits.

Robert D. Bent Chair
Jason Burdick, Ph.D.

Jason A. Burdick, Robert D. Bent Professor in Bioengineering
Burdick runs the Polymeric Biomaterials Laboratory which develops polymer networks for fundamental and applied studies with biomedical applications with a specific emphasis on tissue regeneration and drug delivery. The specific targets of his research include: scaffolding for cartilage regeneration, controlling stem cell differentiation through material signals, electrospinning and 3D printing for scaffold fabrication, and injectable hydrogels for therapies after a heart attack.

César de la Fuente, Ph.D.

César de la Fuente, Presidential Assistant Professor in Bioengineering and Chemical & Biomedical Engineering in Penn Engineering and in Microbiology and Psychiatry in the Perelman School of Medicine
De la Fuente runs the Machine Biology Group which combines the power of machines and biology to prevent, detect, and treat infectious diseases. He pioneered the development of the first antibiotic designed by a computer with efficacy in animals, designed algorithms for antibiotic discovery, and invented rapid low-cost diagnostics for COVID-19 and other infections.

Carl June, M.D.

Carl H. June, Richard W. Vague Professor in Immunotherapy in the Perelman School of Medicine and member of the Bioengineering Graduate Group
June is the Director for the Center for Cellular Immunotherapies and the Parker Institute for Cancer Therapy and runs the June Lab which develops new forms of T cell based therapies. June’s pioneering research in gene therapy led to the FDA approval for CAR T therapy for treating acute lymphoblastic leukemia (ALL), one of the most common childhood cancers.

Vivek Shenoy, Ph.D.

Vivek Shenoy, Eduardo D. Glandt President’s Distinguished Professor in Bioengineering, Mechanical Engineering and Applied Mechanics (MEAM), and in Materials Science and Engineering (MSE)
Shenoy runs the Theoretical Mechanobiology and Materials Lab which develops theoretical concepts and numerical principles for understanding engineering and biological systems. His analytical methods and multiscale modeling techniques gain insight into a myriad of problems in materials science and biomechanics.

The highly anticipated annual list identifies researchers who demonstrated significant influence in their chosen field or fields through the publication of multiple highly cited papers during the last decade. Their names are drawn from the publications that rank in the top 1% by citations for field and publication year in the Web of Science™ citation index.

Bassett and Burdick were both on the Highly Cited Researchers list in 2019 and 2020.

The methodology that determines the “who’s who” of influential researchers draws on the data and analysis performed by bibliometric experts and data scientists at the Institute for Scientific Information™ at Clarivate. It also uses the tallies to identify the countries and research institutions where these scientific elite are based.

David Pendlebury, Senior Citation Analyst at the Institute for Scientific Information at Clarivate, said: “In the race for knowledge, it is human capital that is fundamental and this list identifies and celebrates exceptional individual researchers who are having a great impact on the research community as measured by the rate at which their work is being cited by others.”

The full 2021 Highly Cited Researchers list and executive summary can be found online here.

César de La Fuente Uses AI to Discover Germ-fighting Peptides

César de la Fuente, PhD

The impending danger of bacterial resistance to antibiotics is well-documented within the scientific community. Bacteria are the most efficient evolvers, and their ability to develop tolerance to drugs, in addition to antibiotic overuse and misuse, means that researchers have had to get particularly resourceful to ensure the future of modern medicine.  

Presidential Assistant Professor in Bioengineering, Microbiology, Psychiatry, and Chemical and Biomolecular Engineering César de la Fuente and his team are using an algorithm to search the human genome for microbe-fighting peptides. So far, the team has synthesized roughly 55 peptides that, when tested against popular drug-resistant microbes such as the germ responsible for staph infections, have proven to prevent bacteria from replicating.  

WIRED’s Max G. Levy recently spoke with de la Fuente and postdoctoral researcher and study collaborator Marcelo Torres about the urgency of the team’s work, and why developing these solutions is critical to the survival of civilization as we know it. The team’s algorithm, based on pattern recognition software used to analyze images, makes an otherwise insurmountable feat tangible.  

De la Fuente’s lab specializes in using AI to discover and design new drugs. Rather than making some all-new peptide molecules that fit the bill, they hypothesized that an algorithm could use machine learning to winnow down the huge repository of natural peptide sequences in the human proteome into a select few candidates.

“We know those patterns—the multiple patterns—that we’re looking for,” says de la Fuente. “So that allows us to use the algorithm as a search function.”

Read Max G. Levy’s An AI Finds Superbug-Killing Potential in Human Proteins” at WIRED. 

This story previously appeared in Penn Engineering Today.

Konrad Kording Receives Named University Professorship

Konrad Kording (Photo by Eric Sucar)

President Amy Gutmann has recently announced that two Penn Integrates Knowledge Professors, one of which is Penn Engineering’s own Konrad Kording, have received named University Professorships.  

Kording, who holds joint appointments in the Department of Neuroscience in the Perelman School of Medicine and the Department of Bioengineering in the School of Engineering and Applied Science, will become the Nathan Francis Mossell University Professor. 

When Nathan Francis Mossell graduated in 1882, he became the first African American to earn a medical degree from Penn. He soon became a prominent African American physician, the first to be elected to the Philadelphia County Medical Society. He helped found the Frederick Douglass Memorial Hospital and Training School, which treated Black patients and helped train the next generation of Black doctors and nurses.  

“Dr. Mossell was truly inspiring. He had to fight for everything, yet never reneged on his principles. He pretty much started a hospital and was a major champion for the advancement of equality for African Americans,” Kording said. “In my research, where I study how intelligence works, I am inspired by scholars like him who combine many different insights. He was a wonderful man, and I will be proud to carry his name.” 

Read more in Penn Today.

“You get what you put in”: A First-generation Penn Bioengineering Graduate Student Discusses His Journey

Joseph Lance Casila

Joseph Lance Casila, a doctoral student and Fontaine Fellow in Bioengineering, was profiled by his alma mater, the University of Guam (UOG. Casila was the first person in his family to graduate from a U.S.-accredited university and is now studying tissue engineering and regenerative medicine in the Bioengineering and Biomaterials Laboratory of Riccardo Gottardi, Assistant Professor in Bioengineering in Penn Engineering and Pediatrics in Penn Medicine and the Children’s Hospital of Philadelphia (CHOP). His research in the Gottardi lab employs “tissue engineering and drug delivery for biomedical problems relating to knees, ears, nose, and throat but specifically to pediatric airway disorders.” The article discusses Casila’s journey from valedictorian of his high school, to a first-generation undergraduate interested bioengineering, and now a graduate student studying at Penn on a full scholarship. After completing his degree, Casila hopes to bring what he’s learned back home to advance health care in Guam.

“My mentors, and especially my friends, helped me make the most of what UOG had to offer, and it paid off rewardingly,” he said. “You get what you put in.”

Read “A first-generation student’s path to an Ivy League Ph.D. program” in the University of Guam News & Announcements.

Penn’s 2021 iGEM Team Takes Home Multiple Prizes

Four of Penn’s 2021 iGEM team (left to right): Juliette Hooper, Grace Qian, Saachi Datta, and Gloria Lee.

The University of Pennsylvania’s 2021 iGEM team has been awarded several distinctions in this year’s highly competitive iGEM Competition. The International Genetically Engineered Machine Competition is the largest synthetic biology community and the premiere synthetic biology competition for both university and high school level students from around the world. Each year, hundreds of interdisciplinary teams of students combine molecular biology techniques and engineering concepts to create novel biological systems and compete for prizes and awards through oral presentations and poster sessions.

The Penn team’s project, “OptoReader,” is a combined light-simulation device and plate reader, which makes optogenetic experiments more powerful and accessible. The abstract reads:

“Metabolic engineering has the potential to change the world, and optogenetic tools can make metabolic engineering research easier by providing spatiotemporal control over cells. However, current optogenetic experiments are low-throughput, expensive, and laborious, which makes them inaccessible to many. To tackle this problem, we combined a light-stimulation device with a plate reader, creating our OptoReader. This device allows us to automate ~100 complex optogenetic experiments at the same time. Because it is open source and inexpensive, our device would make optogenetic experiments more efficient and available to all.”

Watch the team’s presentation on OptoReader here.

This year’s Penn team was mentored by Lukasz Bugaj, Assistant Professor in Bioengineering. In addition, the team was supported by Brian Chow, Associate Professor in Bioengineering. Chow has supported previous undergraduate iGEM teams at Penn, and was involved in the creation of the iGEM program during his time as a graduate student at MIT.

OptoReader took home the top prizes in three of the four categories in which it was nominated. These prizes include:

  • Best Foundational Advance (best in track)
  • Best Hardware (best from all undergraduate teams)
  • Best Presentation (best from all undergraduate teams)

They were also awarded a Gold Medal Distinction and were included in the Top 10 Overall (from all undergraduate teams, and the only team from the United States to make the top 10) and Top 10 Websites (from all undergraduate teams).

The awards were announced during iGEM’s online Jamboree Award Ceremony on November 14, 2021 (watch the full award ceremony here).

In addition to the outstanding awards recognition, OptoReader was also selected for an iGEM Impact Grant which awards teams $2,500 to continue development of their projects. This new initiative from the iGEM Foundation was announced earlier this year, and with the support of the Frederick Gardner Cottrell Foundation, is distributing a total of $225,000 in grant funds to 90 iGEM teams during the 2021 competition season. Learn more about the Impact Grant and read the full list of winning teams here.

Penn’s 2021 iGEM team was made up of an interdisciplinary group of women undergraduates from the School of Engineering and Applied Science (SEAS) and the School of Arts and Sciences (SAS):

  • Saachi Datta (B.A. in Biology and Religious Studies 2021)
  • Juliette Hooper (B.S.E. and M.S.E. in Bioengineering 2022)
  • Gabrielle Leavitt (B.S.E. in Bioengineering 2021 and current Master’s student in Bioengineering)
  • Gloria Lee (B.A. in Physics and B.S.E. in Bioengineering 2023)
  • Grace Qian (B.S.E. in Bioengineering 2023)
  • Lana Salloum (B.A. in Neuroscience 2022)

They were mentored by three doctoral students in Bioengineering: Will Benman (Bugaj Lab), David Gonzalez Martinez (Bugaj Lab), Gabrielle Ho (Chow Lab). Saurabh Malani, a graduate student in the Avalos Lab at Prince University, was also very involved in mentoring the team.

OptoReader

The graduate mentors were instrumental in quickly bringing the undergraduates up to speed on a diverse array of skills needed to accomplish this project including circuit design, optics, optogenetics, programming, and additive manufacturing. They then coached the team through building and testing prototypes, as well as accomplishing other objectives required for success at iGEM. These other objectives included establishing collaborations with other iGEM teams, performing outreach, and effectively communicating their project through a website and online presentations.

“This team and their work is outstanding,” said William Benman. “Not only did they sweep several awards, but they did it all with a small team and while working with technology they had no prior experience with. They created a device that not only increases accessibility to optogenetics but also allows optogenetic systems to interface directly with computer programs, allowing for completely new research avenues within the field. They are truly a remarkable group.”

Due to the COVID pandemic, the team operated virtually through the summer of 2020, and then continued in person in the summer of 2021 as the project progressed and more students returned to Penn’s campus. Upon return to campus, the work was conducted in both the Bugaj lab in the Stephenson Foundation Educational Laboratory & Bio-MakerSpace, the primary teaching laboratory in Penn Bioengineering and an interdisciplinary makerspace open to anyone at Penn. The team also collaborated with the Avalos Lab at Princeton University, which conducts research in the application of optogenetics to optimize production of valuable  chemicals in microbes.

“I’m beyond excited about this phenomenal showing from team Penn at the iGEM Jamboree awards ceremony,” said faculty mentor Lukasz Bugaj. “This is truly outstanding recognition for what the team has accomplished, and it wouldn’t have happened without essential contributions from everyone on the team.”

Brian Chow added that this achievement is “no small feat,” especially for a hardware project. “The iGEM competition leans toward genetic strain engineering, but the advances in the field made by these incredible students were undeniable,” he said.

Going forward, the team plans to publish a scientific article and file a patent application describing their device. “It’s clear that there is excitement in the scientific community for what our students created, and we’re excited to share the details and designs of their work,” said Bugaj.

Congratulations to all the team members and mentors of OptoReader on this incredible achievement! Check out the OptoReader project website and Instagram to learn more about their project.

This project was supported by the Department of Bioengineering, the School of Engineering and Applied Science, and the Office of the Vice Provost for Research (OVPR). 

Yogesh Goyal Selected as 2021 STAT Wunderkind

Yogesh Goyal, Ph.D.

Yogesh Goyal, Ph.D.,  a postdoctoral researcher in Genetics and Bioengineering, has been selected as a 2021 STAT Wunderkind, which honors the “next generation of scientific superstars.” Goyal’s research is centered around developing novel mathematical and experimental frameworks to study how a rare subpopulation of cancer cells are able to survive drug therapy and develop resistance, resulting in relapse in patients. In particular, his work provides a view of different paths that single cancer cells take when becoming resistant, at unprecedented resolution and scale. This research aims to help devise novel therapeutic strategies to combat the challenge of drug resistance in cancer.

Goyal is a Jane Coffin Childs Postdoctoral Fellow in the systems biology lab of Arjun Raj, Professor in Bioengineering and Genetics at Penn. He will begin an appointment as Assistant Professor in the Department of Cell and Developmental Biology (CDB) in the Feinberg School of Medicine at Northwestern University in spring 2022.

Read the announcement in Penn Medicine News.