CSB 2025 Retreat

Event Description:

The Computational and Systems Biology Ph.D. The program will hold our annual retreat at the Colony Hotel in picturesque Kennebunkport, ME., from Sunday, October 12th, to Monday, October 13th, 2025. Our retreat will feature a poster session, lobster buffet, and talks from CSB students, MIT Faculty, and invited speakers.

Sunday, October 12, 2025 11:15 – 11:30 AM

Yi Hua Chen, CSB student in the lab of Prof. Jonathan Weissman

Title of Talk: High-Throughput Functional Genomics of Pan-Viral Microproteomes Reveals Novel Viral Oncogenes

Bio:

Yi is a PhD student in Jonathan Weissman’s lab at MIT, where she studies gene annotation, function, and evolution. Using a combination of experimental and computational approaches in functional genomics, her research focuses on uncharacterized genes from viral genomes. Yi earned her bachelor’s degree in Chemical and Physical Biology at Harvard, where she developed her interest in genome evolution while studying the yeast cell cycle in Andrew Murray’s lab. She is especially fascinated by the ‘dark proteome’ and loves discussing all things viruses.

Sunday, October 12, 2025, 11:30 am – 12:00 pm

Prof. Harikesh Wong, Assistant Professor, MIT Department of Biology, Core Member, Ragon Institute of Mass General, MIT, and Harvard

Title of Talk: Redefining self versus non-self discrimination

Bio:

Hari completed his PhD in Cell Biology at the University of Toronto, where he used single-molecule imaging techniques to reveal how multimolecular interactions govern early signaling events in individual immune cells. For his postdoctoral research, Hari joined Dr. Ron Germain’s lab at the NIH, working at the interface of Immunology and Systems Biology. During this time, he combined advanced tissue imaging, in vivo manipulations, and computational modeling to uncover a local intercellular feedback circuit that constrains highly self-reactive T cell responses to prevent autoimmunity.

In 2022, Hari launched his independent research program as an Assistant Professor in the Department of Biology at MIT and a Core Member of the Ragon Institute. His lab integrates immunology, advanced imaging, and quantitative approaches to investigate regulatory circuits of the immune system within intact tissues. Much of the lab’s work focuses on T cells as a model system, exploring how subtle shifts in their regulation can drive divergent host outcomes, including homeostasis, autoimmunity, cancer, and chronic infection.

Sunday, October 12, 2025, 12:00 – 12:30 pm

Prof. Sergey Ovchinnikov, Helen and Irwin Sizer Career Development Professor, MIT Biology Department

Title of Talk: Evaluating Language models for Protein Design 

Bio:

Sergey Ovchinnikov uses phylogenetic inference, protein structure prediction/determination, protein design, deep learning, energy-based models, and differentiable programming to tackle evolutionary questions at environmental, organismal, genomic, structural, and molecular scales, with the aim of developing a unified model of protein evolution.

Sunday, October 12, 2025, 1:30 – 2:00 pm

Prof. Sam Peng, Pfizer Gerald D. Laubach Assistant Professor, MIT Department of Chemistry; Core Institute Member, The Broad Institute of MIT and Harvard

Title of Talk: Engineering Photostable Probes for Ultralong-term, Single-Molecule Imaging in Live Cells

Bio:

Sam Peng is a core institute member of the Broad Institute of MIT and Harvard and the Pfizer Gerald D. Laubach Career Development Assistant Professor of Chemistry at MIT. His lab develops optical imaging techniques and nanoprobes to enable long-term single-molecule imaging in living systems and reveal molecular interactions that are responsible for human diseases. Peng earned his B.S. in chemistry from the University of California, Berkeley, and his Ph.D. from MIT in physical chemistry. He completed his postdoctoral research at Stanford University, where he developed long-term single molecule imaging in live cells. He applied this new technique to study axonal transport in neurons and the molecular dynamics of dynein motors.  His work has been recognized by the NIH Pathway to Independence Award, Beckman Young Investigator Award, and the Sloan Matter-to-Life Award.

Sunday, October 12, 2025, 2:00 – 2:30 pm

Prof. Zhiliang Bai, Assistant Professor of Biological Engineering; Intramural Member of the Koch Institute

Title of Talk: Decoding Human Tissue Biology with Spatial Multi-Omics Innovation

Bio:

Dr. Zhiliang Bai is an Assistant Professor in the Department of Biological Engineering and an intramural member of the Koch Institute for Integrative Cancer Research at MIT. He obtained a B.E. in Measuring and Control Technology in 2015 and a Ph.D. in Instrument Science and Technology in 2021, both from Tianjin University. As a visiting graduate student in Dr. Rong Fan’s laboratory at Yale University, he developed microfluidic devices for active single-cell sequencing and established single-cell pipelines to characterize CAR T cells. He subsequently continued as a postdoctoral scholar in the same lab, co-advised by Dr. Mina Xu in Yale Pathology, where he investigated the mechanistic basis of durable cancer immunotherapy and led the development of multiple spatial omics technologies. His lab integrates spatial multi-omics innovation with RNA biology, digital pathology, and AI to advance cancer and aging research. Dr. Bai has received several accolades, including the Joan and Tom Steitz RNA Fellow, SITC Young Investigator Award, FOCIS Clinical Immunology Award, BMES-CMBE Postdoctoral Researcher Award, ASH Abstract Achievement Award, and the Committee of 100 Leadership Scholarship.

Sunday, October 12, 2025, 5:00 – 5:30 pm

Dr. Melody Morris, Scientific Senior Director, Translational Informatics and Predictive Sciences at Bristol Myers Squibb

Title of Talk: A decade of data science in large Pharma: evolution, regression, and inflection points

Bio:

Dr. Melody Morris is a Scientific Senior Director within the Translational Informatics and Predictive Sciences organization at Bristol Myers Squibb, where she leads a team that applies advanced analytics to multi-omic real world and clinical trial patient data to accelerate therapeutic development in neuroscience, immunology, and cardiovascular diseases.

Prior to her current role, Melody held positions in computational research at Novartis and Merck Research Laboratories, contributing to the elucidation of disease mechanisms and the identification of molecularly defined patient sub-populations across complex indications.

Melody earned her Ph.D. in Biological Engineering from the Massachusetts Institute of Technology and her B.S. in Chemical Engineering from the University of Kentucky.

Sunday, October 12, 2025, 5:30 – 6:00 pm

Dr. Mariana Matus Garcia, CEO and Co-founder at Biobot Analytics

Title of Talk: Computational Biology Meets Public Health: The Science of Wastewater Epidemiology

Bio:

Mariana Matus Garcia is a seasoned leader with over 10 years of experience driving the adoption of innovative technology and data products in historically low-tech sectors. As CEO and Co-founder of Biobot Analytics, she has transformed public health surveillance by integrating traditional clinical approaches with near real-time wastewater epidemiology. Today, wastewater intelligence is recognized as a critical technological breakthrough from the COVID-19 pandemic, and Dr. Matus was pivotal in advancing its development and adoption across U.S. public health agencies. Biobot provided vital insights during the pandemic to the CDC, HHS, and hundreds of local communities, designing and scaling the first nationwide wastewater surveillance program. This landmark initiative required coordination across wastewater facilities, public health agencies, federal institutions, and academia.

Biobot has also led innovations in wastewater intelligence within congregate living settings, including assisted-living facilities, university dorms, U.S. military bases, and correctional facilities. Recently, the company has begun piloting its wastewater intelligence platform with top pharmaceutical companies to support vaccine and medical countermeasure development.

Thanks to Dr. Matus’s technological expertise, Biobot continues to expand its platform to monitor additional infectious diseases and high-risk substances of public health concern.

An internationally recognized expert, Dr. Matus has testified before Congress on the value of wastewater data for national biosurveillance and regularly briefed strategic teams at the White House during the COVID-19 pandemic. She holds a PhD in Computational Biology from the Massachusetts Institute of Technology (MIT), where her research focused on fecal biomarkers for clinical and public health applications. Mariana has raised approximately $40 million in venture capital for Biobot and was selected to the prestigious Y Combinator startup accelerator in early 2018.

Dr. Matus’s leadership and entrepreneurial excellence have been recognized through numerous awards. In 2020, she was named a C&EN Trailblazing Woman in Chemistry. She appeared on Newsweek’s lists of America’s 50 Greatest Disruptors (2021) and 50 Enterprising Idealists (2022). Boston Globe ranked her #8 on its inaugural 50 Tech Power Players list in 2022, and TIME100 NEXT recognized her as a 2022 industry innovator. Most recently, she was named a 2023 Henry Crown Fellow in the Aspen Global Leadership Network at the Aspen Institute.

Sunday, October 12, 2025, 7:30 – 7:45 pm

Peter DeWeirdt, CSB student in the lab of Prof. Mike Laub

Title of Talk: DefensePredictor: A Machine Learning Model to Discover Novel Prokaryotic Immune Systems

Bio:

Peter graduated with a bachelor’s in mathematics from Hamilton college in 2018. Before starting at MIT he worked at the Broad Institute for three years, using machine learning to design CRISPR guide RNAs. His current research in the Laub Lab uses machine learning to identify novel bacterial immune systems. Outside of lab Peter enjoys tending to his community garden plot and running along the Charles river.

Sunday, October 12, 2025, 7:45 – 8:00 pm

Jorge Reyes, CSB Student in the lab of Prof. Jörn Dunkel

Title of Talk:  Functional classification of metabolic networks

Bio:

Jorge Reyes is a fifth-year PhD candidate in the group of Jörn Dunkel. He attended Princeton University for undergraduate where he majored in physics. He went on to work at the Columbia University Irving Medical Center in the field of DNA repair. He now focuses on data-driven applied mathematics research in the fields of metabolism and bacterial communities.

Sunday, October 12, 2025, 8:00 – 8:15 pm

Paul Torrillo, CSB student in the lab of Prof. Tami Lieberman

Title of Talk: Predicting the future of bacterial evolution

Bio:

Paul Torrillo is a fifth-year PhD candidate in Tami Lieberman’s lab at MIT. He attended the University of Pittsburgh for undergraduate where he double majored in mathematical biology and molecular biology. Previously, he published theory-driven work on genetic reversions in microbial evolution. He now focuses on machine-learning approaches—building models to predict gene gain/loss in Staphylococcus aureus and developing methods to probe Liberibacter biology, the pathogen behind citrus greening.

Monday, October 13, 2025 9:00 – 9:30 AM

Prof. Jessica Stark, Assistant Professor of Biological Engineering, Chemical Engineering; Underwood-Prescott Career Development Professor; Koch Institute for Integrative Cancer Research, MIT