February 2025 – Duke Center for Quantitative BioDesign

CQB Seminar- Rodrigo Reyes- McGill University

Our third guest speaker for this semester is Dr. Rodrigo Reyes. Dr. Reyes obtained his BSc in Biology from the National Autonomous University of Mexico, followed by an MSc at Concordia University (Montreal) under the supervision of Prof. Elaine Newman, where he studied bacterial cell division. He earned his PhD in Biochemistry from the University of Oxford (UK), working with Prof. David Sherratt studying DNA replication and chromosome segregation in bacteria. He subsequently held a Todd-Bird Junior Research Fellowship (New College, Oxford), allowing him to continue as a postdoctoral researcher for three additional years.

In 2013, Rodrigo joined the Department of Biology at McGill University, where he is currently an Associate Professor. His laboratory focuses on leveraging recent advancements in microscopy to uncover the mechanistic links between DNA replication and genome integrity. Central to his work is the use of live-cell single-molecule microscopy to characterize the dynamic activities of proteins involved in DNA replication, DNA repair and chromosome segregation in bacteria, budding yeast, and human cells.

Abstract: This seminar will explore two themes in cellular regulation and genome integrity. First, I will present findings from single-molecule microscopy studies that reveal the mechanisms and functional advantages of subunit turnover within the bacterial replisome, highlighting its critical role in maintaining genome stability. Second, I will discuss how dynamic interactions between transcription factors and chromatin serve as a sensor for cell size, orchestrating the start of the cell cycle in yeast. Together, these studies shed light on fundamental processes that safeguard genetic information and regulate cell division across domains of life.

CQB Seminar: Shriya Srinivasan, PhD- Harvard University

Join the CQB for our seminar series, featuring our second guest speaker of the semester: Dr. Shriya S. Srinivasan

Dr. Shriya Srinivasan is an assistant professor of bioengineering at Harvard University where she directs the Harvard Biohybrid Organs and Neuroprosthetics (BIONICS) lab. The lab focuses on the development of surgical reconstruction techniques in consort with bidirectional neural implants for improved sensorimotor control.

Shriya graduated from Case Western Reserve University with a BS in biomedical engineering, with a concentration in biomaterials. She then received her doctoral degree in medical engineering and medical physics through the Harvard-MIT Health Sciences and Technology program in January 2020. Her doctoral research focused on the development of novel neural interfaces utilizing tissue engineering to better interface human limbs with prostheses, in the context of amputation and paralysis. She developed the Regenerative Agonist-antagonist Myoneural Interface (AMI) that enables patients to control their prosthesis with native neural signals. She also explored optogenetic techniques to create novel strategies to accelerate and improve neural control.

As a junior fellow at the Harvard Society of Fellows and Schmidt Science Fellow, Shriya worked in the labs of Dr. Giovanni Traverso and Dr. Robert Langer, designing ingestible bioelectronics for gastrointestinal neuromodulation.

Shriya has been awarded the Delsys Prize, the Lemelson-MIT Student Prize for her innovative work, and recognized by Forbes and the MIT Technology Review as one of 30 innovators under 30.

Shriya was a former director of MIT Hacking Medicine, where she led educational and programmatic initiatives for design thinking education and medtech innovation – interfacing with various governmental and corporate entities. She also founded Project Prana, a nonprofit devoted to affordable medical technology innovation- which commercialized a ventilator multiplexer to market during the pandemic. In her spare time, Shriya performs Indian classical dance with the Anubhava Dance Company.

Abstract:

The gut-brain axis is an exciting frontier in science. This complex communication network influences everything from mood and cognition to immune responses, emphasizing our gut’s key role in overall health. For many, diseases like gastroparesis and ileus disrupt the normal digestive process, leading to debilitating symptoms and impacting quality of life. These conditions hamper the natural rhythm of the gut, affecting the body’s energy balance and comfort.

Innovative neural interfaces are reshaping treatment by seamlessly interacting with the gut’s nervous system. These devices use precise electrical and mechanostimulation to engage with specific neural pathways, restoring digestive movements and optimizing organ function. By stimulating the nerves of the GI tract, they can restart peristalsis and even simulate sensations like fullness to modulate hunger and satiety. Explore the design of ingestible neural interfaces to sense, monitor, and treat the gut.

CQB Seminar- Maria Brbic, PhD- EPFL

Join the CQB for our seminar series, featuring our first guest speaker of the semester: Dr. Maria Brbic.

Maria Brbic (https://brbiclab.epfl.ch/) is an Assistant Professor of Computer Science and of Life Sciences at the Swiss Federal Institute of Technology, Lausanne (EPFL). She develops new machine learning methods and applies her methods to advance biology and biomedicine. Her methods have been used by global cell atlas consortia efforts aiming to create reference maps of all cell types with the potential to transform biomedicine, including the Human BioMolecular Atlas Program (HuBMAP) and Fly Cell Atlas consortium. Prior to joining the EPFL faculty in 2022, Maria was a postdoctoral fellow at Stanford University, Department of Computer Science, and was a member of the Chan Zuckerberg Biohub at Stanford. Maria received her Ph.D. from University of Zagreb in 2019 while also researching at Stanford University as a Fulbright Scholar and University of Tokyo. Among other awards and recognitions, she was named a Rising Star in EECS by MIT in 2021, she received the Early Career Bioinformatics Award by SIB in 2023 and she was awarded with the SNSF Starting Grant in 2024.

Abstract:

We are witnessing an AI revolution. At the heart of this revolution are generative AI models that, powered by advanced architectures and large datasets, are transforming AI across a variety of disciplines. But how can AI facilitate and eventually enable groundbreaking discoveries in life sciences? How can it bring us closer to understanding biology – the functions of our cells, their alterations in diseases, and variations across species? In the first part of the talk, I will present AI methods that build upon protein foundation models and enable us to learn cell representations across single-cell RNA-seq datasets from different species. Next, I will demonstrate how generative AI can uncover spatial relationships between cells, enabling the reassembly of tissues from dissociated single cells. Finally, I will discuss the future of discovery in the era of generative AI and foundation models, highlighting the paradigm shift in machine learning required to revolutionize biology.