Bioengineering Colloquia

The Rice Bioengineering Colloquia is a seminar series that has a long tradition at the Department of Bioengineering at Rice University. Each week, experts from around the world are brought to Rice to present the latest findings and research in the broadly defined bioengineering field. In Fall 2021, the BIOE Colloquia will be held on Tuesdays.

Attendees must register in advance to receive the Zoom Webinar link. Graduate students enrolled in BIOE 699 must register for each event to count their attendance.

Upcoming Fall 2021 Seminars

RESCHEDULED: Tuesday, November 23 | 4:00 pm (ZOOM ONLY)


Adam Arkin

Adam Arkin, Ph.D.

Dean A. Richard Newton Memorial Professor, Bioengineering Senior Faculty Scientist, Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Director, Berkeley Synthetic Biology Institute University of California, Berkeley

"Dissecting mechanisms of metabolism and predation in environmental microbial communities"


Adam is the Dean A. Richard Newton Memorial Professor in the Department of Bioengineering, University of California, Berkeley and Senior Faculty Scientist at the Lawrence Berkeley National Laboratory. He and his laboratory develop experimental and computational technologies for discovery, prediction, control and design of microbial and viral functions and behaviors in environmental contexts. His work spans synthetic and systems biology, genomics, metagenomics, and physiology. He is the chief scientist of the Department of Energy Scientific Focus Area, ENIGMA, designed to understand, at a molecular level, the impact of microbial communities on their ecosystems with specific focus on terrestrial communities in contaminated watersheds. He also directs the Department of Energy Systems Biology Knowledgebase program, an open platform for comparative functional genomics, systems and synthetic biology for microbes, plants and their communities, and for sharing results and methods with other scientists. He is director of the Center for Utilization of Biological Engineering in Space which seeks microbial and plant-based biological solutions for in situ resource utilization that reduce the launch mass and improves reliability and quality of food, pharmaceuticals, fuels and materials for astronauts on a mission to Mars.

Tuesday, November 30


FischbachMichael A. Fischbach, Ph.D.

Associate Professor
Department of Bioengineering Department of Microbiology Immunology
Stanford University

Past Seminars

Tuesday, August 24 | 4:00 pm

Michael Jewett

Michael Jewett, PhD

Walter P. Murphy Professor of Chemical and Biological Engineering and the Director of the Center for Synthetic Biology at Northwestern University

"Bioengineering beyond cells to enable a fair and sustainable 21st bio-century "

Abstract: Synthetic Biology (SB) is one of the most promising fields of research for the 21st century. SB offers powerful new ways to improve human health, build the global economy, manufacture sustainable materials, and address climate change. However, current access to SB-enabled breakthroughs is unequal, largely due to bottlenecks in infrastructure and education. Here, I describe our efforts to re-think the way we engineer biology using cell-free systems to address these bottlenecks. We show how the ability to readily store, distribute, and activate low-cost, freeze-dried cell-free systems by simply adding water has opened new opportunities for on-demand biomanufacturing of vaccines for global health, point-of-care diagnostics for environmental safety, and education for SB literacy and citizenship. By integrating cell-free systems with artificial intelligence (AI), we also show the ability to accelerate the production of carbon-negative platform chemicals. Looking forward, advances in engineering tools and new knowledge underpinning the fundamental science of living matter will ensure that SB helps solve humanity’s most pressing challenges.


Michael Jewett is the Charles Deering McCormick Professor of Teaching Excellence, the Walter P. Murphy Professor of Chemical and Biological Engineering, and Director of the Center for Synthetic Biology at Northwestern University. Dr. Jewett received his PhD in 2005 at Stanford University, completed postdoctoral studies at the Center for Microbial Biotechnology in Denmark and the Harvard Medical School, and was a guest professor at the Swiss Federal Institute of Technology (ETH Zurich). He is the recipient of the NIH Pathway to Independence Award, David and Lucile Packard Fellowship in Science and Engineering, Camille-Dreyfus Teacher-Scholar Award, and a Finalist for the Blavatnik National Awards for Young Scientists, among others. He is the co-founder of SwiftScale Biologics, Stemloop, Inc., Pearl Bio, Induro Therapeutics, and Design Pharmaceuticals. Jewett is a Fellow of AIMBE, AAAS, and NAI.

Tuesday, August 31 | 4:00 pm

Deblina Sarkar

Deblina Sarkar, PhD

Assistant Professor, MIT
AT&T Career Development Chair Professor at MIT Media Lab

"Of Computers, Brain and Neurological Diseases"

Abstract: While the computing demands of Information Technology are ever increasing, the capabilities of electronics have hit fundamental walls due to energy and dimensional unscalability. In this talk, I will demonstrate the quantum mechanical transistor, which beats the fundamental energy limitations. This device is the world's thinnest channel (6 atoms thick) sub-thermal tunnel-transistor. Thus, it has the potential to allow dimensional scalability to beyond Silicon scaling era and thereby to address the long-standing issue of simultaneous dimensional and power scalability.

Going beyond electronic computation, I will discuss about the biological computer: the brain, which can be thought of as an ultimate example of low power computational system. I will introduce the technology, which reveals for the first time, a nanoscale trans-synaptic architecture in brain and the way mother nature has engineered biomolecular organization in the brain to optimize its computing efficiency. This technology can also be used to decipher intriguing biomolecular nanoarchitectures related to neurological diseases, otherwise invisible to existing technologies.

I will conclude with our group’s research vision for how extremely powerful technologies can be built by fusing diverse fields and discuss briefly about the research directions of my new lab at MIT.

[1] D. Sarkar et. al., Nature, 526 (7571), 91, 2015;
[2] D. Sarkar et. al., Nano Lett., 15 (5), 2852, 2015;
[3] D. Sarkar et. al., ACS Nano., 8 (4), 3992, 2014;
[4] D. Sarkar et. al., Appl. Phys. Lett., 100 (14), 143108, 2012;
[5] D. Sarkar et. al., bioRxiv, 2020; doi:10.1101/2020.08.29.273540;


Deblina Sarkar is an assistant professor at MIT and AT&T Career Development Chair Professor at MIT Media Lab. She heads the Nano-Cybernetic Biotrek research group. Her group carries out trans-disciplinary research fusing engineering, applied physics, and biology, aiming to bridge the gap between nanotechnology and synthetic biology to develop disruptive technologies for nanoelectronic devices and create new paradigms for life-machine symbiosis. Her inventions include, among others, a 6-atom thick channel quantum-mechanical transistor overcoming fundamental power limitations, an ultra-sensitive label-free biosensor and technology for nanoscale deciphering of biological building blocks of brain. Her PhD dissertation was honored as one of the top 3 dissertations throughout USA and Canada in the field of Mathematics, Physical sciences and all departments of Engineering. She is the recipient of numerous other awards and recognitions, including the Lancaster Award, Technology Review’s one of the Top 10 Innovators Under 35 from India, NIH K99/R00 Pathway to Independence Award.

Tuesday, September 7 | 4:00 pm

Jamie Spangler

Jamie Spangler, PhD

Assistant Professor, Departments of Biomedical Engineering and Chemical & Biomolecular Engineering, Johns Hopkins University

"Reprogramming the immune response through molecular engineering "

Abstract: The repertoire of naturally occurring proteins is finite and many molecules induce multiple confounding effects, limiting their efficacy as therapeutics. Recently, there has been a growing interest in redesigning existing proteins or engineering entirely new proteins to address the deficiencies of molecules found in nature. Researchers have traditionally taken an unbiased approach to protein engineering, but as our knowledge of protein structure-function relationships advances, we have the exciting opportunity to apply molecular principles to guide engineering. Leveraging cutting-edge tools and technologies in structural biology and molecular design, our lab is pioneering a unique structure-based engineering approach to elucidate the mechanistic determinants of protein activity, in order to inform therapeutic development. Our group is particularly interested in engineering immune proteins, such as cytokines, growth factors, and antibodies, to bias the immune response for targeted disease treatment. Despite the recent explosive growth of protein drugs within the pharmaceutical market, limitations such as delivery, acquired resistance, and toxicity have impeded realization of the full potential of these therapeutics, necessitating new approaches that synergize with existing strategies to address clinically unmet needs. This talk will highlight ongoing work in our lab that spans the discovery, design, and translation of novel molecular immunotherapeutics for applications ranging from cancer to autoimmune disorders to regenerative medicine.


Dr. Jamie Spangler earned a Bachelor of Science degree in Biomedical Engineering at Johns Hopkins University and went on to conduct her Ph.D. research in Biological Engineering in Professor K. Dane Wittrup’s group at MIT, studying antibody-mediated down-regulation of epidermal growth factor receptor as a new mechanism for cancer therapy. She then completed a postdoctoral fellowship in Professor K. Christopher Garcia’s lab in the Molecular & Cellular Physiology and Structural Biology departments at Stanford University School of Medicine, focusing on engineering cytokine systems to bias immune homeostasis. Dr. Spangler launched her independent research group at Johns Hopkins University in July 2017, jointly between the departments of Biomedical Engineering and Chemical & Biomolecular Engineering. Her lab, located in the Translational Tissue Engineering Center at the School of Medicine, applies structural and mechanistic insights to re-engineer existing proteins and design new proteins that therapeutically modulate the immune response.

Tuesday, September 7 | 4:00 pm

Alex Shalek

Alex Shalek, Ph.D.

Associate Professor of Chemistry; Core Member, Institute for Medical Engineering and Science, MIT; Extramural Member, The Koch Institute for Integrative Cancer Research, MIT; Member, Ragon Institute of MGH, MIT, and Harvard Institute Member, Broad Institute of MIT and Harvard

“Identifying and rationally modulating cellular drivers of tumor responses”

Abstract: Recent advances in high throughput genomic sequencing technologies have led to a detailed understanding of the genetic alterations that underlie human tumors. However, evidence increasingly indicates that using mutations alone to assign therapies has its limitations, even for cancers with actionable mutational heterogeneity. The advent of single-cell genomic technologies has confirmed extensive mutational heterogeneity in human tumors but also revealed that the complexity of cancer extends to variation in cell transcriptional state. Deciphering whether transcriptional variation informs treatment response heterogeneity represents a new but poorly understood frontier in cancer therapeutics.

In pancreatic ductal adenocarcinoma (PDAC), clinically relevant RNA expression states exist but our understanding of their drivers, stability, and relationship to therapeutic response is limited. To examine these attributes systematically, we profiled metastatic biopsies and matched organoid models at single-cell resolution. We identify a new intermediate PDAC transcriptional cell state and uncover distinct site- and state-specific tumor microenvironments. Moreover, we reveal strong organoid culture-specific biases in cancer cell transcriptional state representation and nominate critical factors missing from the ex vivo microenvironment. By adding back specific factors, we restore in vivo expression state heterogeneity and show plasticity in culture models, demonstrating that microenvironmental signals are critical regulators of cell state. Importantly, we prove that non-genetic modulation of cell state can significantly influence drug responses and uncover state-specific vulnerabilities. Our work provides a broadly applicable framework for mapping cell states across in vivo and ex vivo settings, identifying drivers of transcriptional plasticity, and manipulating cell state to target its associated vulnerabilities.


Alex K. Shalek, PhD, is a Core Member of the Institute for Medical Engineering and Science (IMES), an Associate Professor of Chemistry, and an Extramural Member of The Koch Institute for Integrative Cancer Research at MIT. He is also an Institute Member of the Broad Institute, a Member of the Ragon Institute, an Assistant in Immunology at MGH, and an Instructor in Health Sciences and Technology at HMS. Dr. Shalek received his bachelor's degree summa cum laude from Columbia University and his Ph.D. from Harvard University in chemical physics under the guidance of Hongkun Park, and performed postdoctoral training under Hongkun Park and Aviv Regev (Broad/MIT). His lab’s research is directed towards the development and application of new approaches to elucidate cellular and molecular features that inform tissue-level function and dysfunction across the spectrum of human health and disease. Dr. Shalek and his work have received numerous honors including a NIH New Innovator Award, a Beckman Young Investigator Award, a Searle Scholar Award, a Pew-Stewart Scholar Award, and an Alfred P. Sloan Research Fellowship in Chemistry, as well as the 2019-2020 Harold E. Edgerton Faculty Achievement Award at MIT.

Tuesday, October 5 | 4:00 pm

Jennifer Elisseeff

Jennifer Elisseeff, Ph.D.

Professor and Director, Translational Tissue Engineering Center
Wilmer Eye Institute and Departments of Biomedical Engineering, Orthopedic Surgery, Chemical and Biological Engineering, and Materials Science and Engineering at Johns Hopkins University

“The immune system in tissue repair and biomaterial response across lifespan”

Abstract: Biomaterial implants have a long history in the clinic but regenerative biomaterials and regenerative medicine therapies have been slow to reach patients. Clinical translation provides a unique and critical opportunity to investigate the key therapeutic drivers of technology efficacy in people. Our clinical translation experiences in orthopedics and plastic surgery yielded the unexpected discovery of adaptive immune cells in the biomaterial response. The immune system is a first responder to trauma and depending on phenotype can orchestrate downstream processes including stem cell activation, vasculogenesis and new matrix production. The immune system can also act as powerful “brakes” to tissue repair as in the case of aging and infection that occurs in parallel with tissue trauma. We are now working to understand the role of the immune system and cellular senescence in the biomaterial response and repair across different tissues. This research now serves as the basis for the design of regenerative immunotherapies and a new therapeutic target in regenerative medicine.


Dr. Elisseeff is the Morton Goldberg Professor and Director of the Translational Tissue Engineering Center at Johns Hopkins Department of Biomedical Engineering and the Wilmer Eye Institute with appointments in Chemical and Biological Engineering, Materials Science and Orthopedic Surgery. She was elected a Fellow of the American Institute of Medical and Biological Engineering, the National Academy of Inventors, a Young Global Leader by World Economic Forum. In 2018, she was elected to the National Academy of Engineering and National Academy of Medicine and in 2019 she received the NIH Directors Pioneer Award.

Jennifer received a bachelor’s degree in chemistry from Carnegie Mellon University and a PhD in Medical Engineering from the Harvard–MIT Division of Health Sciences and Technology. Later she was a Fellow at the National Institute of General Medical Sciences, Pharmacology Research Associate Program, where she worked in the National Institute of Dental and Craniofacial Research. She has published over 200 papers, book chapters, and patent applications and received a number of awards including the Carnegie Young Alumni Award and in 2002 she was named by MIT Technology Review as a top innovator under 35. She is committed to the translation of regenerative biomaterials and has founded several companies and participates in several industry advisory boards including the State of Maryland’s Technology Development Corporation (TEDCO).

Jennifer’s initial research efforts focused on the development of biomaterials for studying stem cells and designing regenerative medicine technologies for application in orthopedics, plastic and reconstructive surgery, and ophthalmology. In clinical translation of these technologies, the group recognized the importance of the immune response in regenerative medicine responses. This led to a significant shift in research efforts to biomaterials-directed regenerative immunology and leveraging the adaptive immune system to promote tissue repair. The group is now characterizing the immune and stromal environments of healing versus non-healing wounds and tumors. Biomaterials are now being applied to model and manipulate tissue environments and studying the impact of systemic and environmental factors such as aging and senescent cells, sex differences, and infection/microbiome on tissue repair and homeostasis.

Tuesday, October 19 | 4:00 pm

Gabe Kwong

Gabe Kwong, Ph.D.

Associate Professor of Biomedical Engineering, Wallace H. Coulter Distinguished Faculty Fellow, Georgia Tech and Emory School of Medicine

“Bioengineering Immunity: From Early Detection to Cell Therapies”

Abstract: The advent of immunotherapies has ushered in a new era in medicine where we can meaningfully change and improve the outcome of patients with serious and life-threatening conditions. My research program is focused on merging engineering approaches with immunology to drive advances in early detection and cell therapies. In this seminar, I will first describe the early detection challenge that motivates our work on synthetic biomarkers – an emerging class of diagnostics that deploy bioengineered sensors inside the body to query tumors and amplify disease signals to levels that could potentially exceed those of shed biomarkers. We are particularly focused on developing protease-activated synthetic biomarkers that report on T cell activity for early detection applications in transplant rejection and checkpoint blockade immunotherapy. The second half of the seminar will be focused on our work on CAR T cell therapies where treatment of solid tumors typically results in poor responses despite the clinical success of anti-CD19 CAR T cells against certain types of hematological cancers. To breakthrough this barrier, we are developing strategies to potentiate therapy including spatial control of CAR T cells to localize production of otherwise systemically toxic adjuvants, and sensitizing tumors through the expression of synthetic antigens to overcome the lack of tumor-specific CAR targets. Our work motivates new bioengineering approaches to drive the next wave of immunotherapies.


Dr. Kwong is an Associate Professor and Wallace H. Coulter Distinguished Faculty Fellow in the Department of Biomedical Engineering at Georgia Tech and Emory. He earned his B.S. in Bioengineering with Highest Honors from University of California at Berkeley, his Ph.D. from Caltech, and conducted postdoctoral studies at MIT. Dr. Kwong directs the Laboratory for Synthetic Immunity where he leads a multidisciplinary team focused on engineering cell therapies and immune sensors for early detection. His research impacts broad arenas in biomedicine including cancer, transplantation medicine, and infectious diseases. His work has been published in leading scientific journals and profiled broadly including coverage in The Economist, NPR, BBC, and WGBH-2, Boston’s PBS station. In recognition of his work, Dr. Kwong was named a "Future Leader in Cancer Research and Translational Medicine" by the Massachusetts General Hospital, and selected by the National Academy of Engineering to the US Frontiers of Engineering. He has been awarded selective distinctions including the Burroughs Wellcome Fund Career Award at the Scientific Interface, NIH Director's New Innovator Award, TEDMED Hive Innovator Award, and the SBUR Don Coffey Lectureship. Dr. Kwong is co-founder of Glympse Bio, which is developing a powerful new paradigm in diagnostics to enable noninvasive and predictive monitoring of multiple human diseases. He holds 25+ issued or pending patents in biomedical technology.

Tuesday, October 26 | 4:00 pm

Scott Medina

Scott Medina, Ph.D.

Associate Professor of Biomedical Engineering, Penn State University

“Building Beyond Biology: Exploiting Abiotic Matter to Create Adaptive Materials”

Abstract: Nature has evolved several elegant strategies to organize inert building blocks into adaptive supramolecular structures. Favored among these is interfacial assembly, where the unique environment of liquid-liquid junctions provides structural, kinetic, thermodynamic, and chemical properties that are distinct from bulk solution. Dr. Medina’s lab exploits these liquid-liquid systems to design supramolecular materials with defined architectures realized through interfacial assembly of organofluorine building blocks. In this talk, he presents three examples demonstrating how antithetical fluorous-water interfaces can be utilized to drive assembly phenomena that yield adaptive molecular networks and living matter. In the first, liquid-liquid assembly of fluorinated amino acids yields mechanomorphogenic crystalline films that alter their macro-morphology depending on exogenous mechanical stimuli. These films are self-supporting, self-healing and show selective permeability, capturing fluorous compounds while allowing the free diffusion of water. These unique capabilities are leveraged to rapidly extract perfluoroalkyl substances from contaminated water samples. In a second example, mechanistic insights gained from the assembly of fluorinated amino acids are used to develop fluoropeptide nanoemulsions that enable synchronous ultrasound imaging and disruption of venous blood clots in real-time. Finally, acoustic nanoemulsions are paired with a fluorous protein masking paradigm developed in the Medina group to permit simultaneous monitoring, guidance and delivery of therapeutic antibodies to the cytoplasm of cancer cells in vitro and in vivo. The Medina group envisions these theranostic technologies will open new opportunities in precision medicine, with on-going efforts focused in oncology, immuno-engineering, and infectious disease.


Dr. Scott H. Medina is an assistant professor of Biomedical Engineering at Penn State University. His group interfaces chemical biology, supramolecular chemistry and nanotechnology to develop new tools to address grand challenges in human health. Dr. Medina is a recipient of the DARPA Young Faculty, NSF CAREER, ACS Early Career Investigator in Biological Chemistry, Controlled Release Society Young Investigator, and the BMES Young Innovator and Rising Star awards. He serves as an editorial board member of the journal Engineered Regeneration, a special content editor of Molecules, and Academic Representative for the Controlled Release Society. In addition to his passion for creating new technologic paradigms in precision medicine, Dr. Medina is an ardent advocate for diversifying the research community and puts this into practice as the graduate recruitment chair for the BME department at Penn State University.

Tuesday, November 2 | 4:00 pm

Stanley Qi

Stanley Qi, Ph.D.

Assistant professor in the Department of Bioengineering
Department of Chemical and Systems Biology
ChEM-H Institute at Stanford University

“Synthetic Genome Engineering for Studying Genomics and Therapy”

Abstract: Precision genome engineering is important for studying genomics and developing therapies. Our research focuses on applying synthetic biology to engineering and designing genomic functions for gene therapy. While gene editing tools are harnessed from naturally occurring CRISPR systems, we expand genome engineering applications beyond editing. By engineering nuclease-dead dCas systems, we address the needs for the precise modulation of gene transcription, epigenetics, and 3D genome in human cells. We apply protein engineering to develop miniature Cas molecule for in vivo research and applications. We further develop CRISPR as antivirals to target broad families of RNA viruses for elimination including SARS-CoV-2 mutant variants and diverse coronaviruses. In this talk, I will cover our efforts on expanding CRISPR as a toolbox for genome editing, regulation, and therapy.


Dr. Stanley Qi is assistant professor in the Department of Bioengineering, Department of Chemical and Systems Biology, and ChEM-H Institute at Stanford University. He obtained B.S. in Physics from Tsinghua University and Ph.D. in Bioengineering from UC Berkeley, where he studied synthetic biology with Dr. Adam Arkin and CRISPR biology with Dr. Jennifer Doudna. He worked as Faculty Fellow at UCSF and joined Stanford faculty in 2014. Dr. Stanley Qi is the developer of dCas9, CRISPR interference (CRISPRi) and CRISPR activation (CRISPRa) technologies. His research expanded the CRISPR toolbox for human genome engineering beyond editing, including transcription modulation, epigenome editing, 3D genome structure organization, live-cell DNA/RNA imaging, and synthetic biology applications. He has won national awards including NIH Director’s Early Independence Award and NSF CAREER Award, and was named a Pew Biomedical Scholar and Alfred. P. Sloan Fellow among other awards.

Tuesday, November 9 | 4:00 pm (ZOOM ONLY)

Mark Anastasio

Mark A Anastasio, Ph.D.

Donald Biggar Willett Professor in Engineering
Head, Department of Bioengineering
University of Illinois at Urbana-Champaign

“Objective assessment of deep learning methods for biomedical image formation”

Abstract: A variety of deep learning-based image restoration and reconstruction methods have been proposed for use with biomedical images. It is widely accepted that the assessment and refinement of biomedical imaging technologies should be performed by objective, i.e., task-based, measures of image quality (IQ). However, the objective evaluation of deep learning-based image formation technologies remains largely lacking, despite the breakneck speed at which they are being developed. As such, there is an ever-growing collection of methods whose utility remains largely unknown. In this work, we report studies in which the performance of deep learning-based image restoration methods is objectively assessed. Specifically, binary signal detection tasks under signal-known-exactly (SKE) with background-known-statistically (BKS) conditions are considered. The performance of the ideal observer (IO) and common linear numerical observers are quantified, and detection efficiencies are computed to assess the impact of the restoration operation on task performance. The numerical results indicate that, in the cases considered, the application of a deep image restoration network can result in a loss of task-relevant information in the image, despite improvement in traditional computer-vision metrics. We also demonstrate that traditional and objective IQ measures can vary in opposite ways as a function of network depth. These results highlight the need for the objective evaluation of IQ for deep image restoration technologies and may suggest future avenues for improving the effectiveness of medical imaging applications. Finally, we present a formal definition of image hallucinations in tomographic imaging and a framework for analyzing them.


Dr. Mark Anastasio is the Donald Biggar Willett Professor in Engineering and the Head of the Department of Bioengineering at the University of Illinois at Urbana-Champaign (UIUC). Before joining UIUC in 2019, he was a Professor of Biomedical Engineering at Washington University in St. Louis, where he established one of the nation’s first stand-alone PhD programs in imaging science. Dr. Anastasio’s research accomplishments to the fields of biomedical imaging and image science have been numerous and impactful and his general interests broadly address the computational aspects of image formation, modern imaging science, and applied machine learning. He has conducted research in the fields of diffraction tomography, X-ray phase-contrast imaging, and ultrasound tomography. He one of the world’s leading authorities on photoacoustic computed tomography (PACT) and has made numerous and important contributions to development of PACT for over fifteen years. He has published over 155 peer-reviewed papers in leading imaging and optical science journals and was the recipient of a National Science Foundation (NSF) CAREER Award to develop image reconstruction methods. He is a Fellow of the American Institute for Medical and Biological Engineering (AIMBE), the International Academy of Medical and Biological Engineering (IAMBE) and the SPIE. He also served as the Chair of the NIH BMIT-B and EITA Study Sections.

Tuesday, November 16 | 4:00 pm (HYBRID - ZOOM AND IN-PERSON)
BioScience Research Collaborative Room 282

Erik Hernandez

Erik Torres Hernandez, Ph.D.

Postdoctoral Scholar
Dr. Matthew B. Francis Lab
Department of Chemistry
College of Chemistry

“Selective Side Chain Modifications Directed Towards Single-Molecule Proteomics, Modular Synthetic Peptides, and Next-Generation Protein Engineering”

Abstract: Selective modifications of protein residues continue to gain importance due to the emergence of new biological and therapeutic technologies. Several techniques focus on genome manipulation to achieve novel peptide or protein constructs. Such methods are indispensable for the development of biomolecules embedded with desired abiotic functionality. A complementary approach relies on chemo-specific strategies aimed for introducing new functionality—but with minimal, to no, disruption of an organism’s genetic milieu. The advantage of using chemical manipulations centers on reducing challenges caused by genomic changes, which complicate the implementation of reliable research tools and therapeutics. In this talk, strategies for modifying side chains selectively for single-molecule proteomics, synthetic peptides, and protein engineering will be discussed. Targeted labeling of amino acids with fluorescent probes enabled a proof-of-concept sequencing and identification of insulin at the single molecule level using TIRF microscopy. This work also spearheaded efforts to expand the number of side chains accessible for multiplexed-based identification of proteins. These chemo-selective transformations inspired methods for introducing complex functionality to synthetic peptides. Recently, efforts to modify intact proteins, under biotic conditions, has led to the development of biorthogonal, oxidative coupling of super hydrophobic cargo using fungal tyrosinase. The applications presented will highlight how chemo-based modifications of biomolecules contribute to significant advancements in the fields of bioengineering, synthetic biology, and biotechnology.


Erik was born and raised in Lubbock, TX. He completed his undergraduate studies at Oberlin College. He earned his PhD in chemistry at The University of Texas at Austin and currently works as a postdoctoral researcher in Dr. Matthew B. Francis’ Lab at the University of California, Berkeley.

Thursday, November 18 | 4:00 pm (HYBRID - ZOOM AND IN-PERSON)
BioScience Research Collaborative Room 282

Changyang Linghu

Changyang Linghu, Ph.D.

McGovern Institute for Brain Research
Massachusetts Institute of Technology

“Tools for Observing and Analyzing Complex Biological Dynamics”

Abstract: Unlike electronic computers that use electrical signal alone to process information, biological systems such as the brain use a collection of interacting biological signals to achieve biological computation and drive biological outcome. These biological signals include ion concentrations, molecular messenger levels, protein activities, and other biophysical dynamics. They form signaling networks in cells and collectively convert cellular inputs into cellular outcomes by interacting in complex ways. Subtle defects in the harmony of signaling network dynamics lead to gene expression abnormalities and are associated with a wide range of diseases. Understanding these complex cellular processes requires systematic observation of signaling network dynamics as well as the ability to track the dynamics of gene expression over time. Here I present a family of new tools for precise and multiplexed recording of signaling network dynamics and gene expression dynamics. These tools are powered by recent breakthroughs in biological, chemical, and optical engineering, to enable systematic studies for biological sciences. We share all these tools freely, and I aim to integrate the use of these tools to enable comprehensive understandings of biological dynamics in healthy and diseased states.


Changyang Linghu is a postdoctoral fellow in the Synthetic Neurobiology Group with Dr. Ed Boyden at Massachusetts Institute of Technology. His work aims to bridge the gap between enduring questions in biology and breakthroughs in the fields of engineering. He has been developing new technologies for precise and multiplexed observations of signaling network dynamics (‘Signaling Reporter Islands’ and ‘SomaGCaMP’) and gene expression dynamics (‘Expression Recording Islands’) in single cells and in cell populations. He was a visiting student at University of Wisconsin-Madison, obtained his bachelor’s degree at Tsinghua University, and obtained his Ph.D. degree at Massachusetts Institute of Technology. He is the recipient of MIT Presidential Fellowship, McGovern Graduate Fellowship, and J. Douglas Tan Postdoctoral Fellowship.