December 2025 QCB Newsletter

e-Newsletter Volume 5 Issue 8 | December 2025

Personal Remarks by Dr. Remo Rohs

As the year 2025 winds down, I want to thank all staff, faculty, and students for their hard work, resiliency, and commitment to excellence in education and research. This was a particularly difficult year for our wonderful staff, and I was really impressed with their commitment and work ethic.

This month, the Director of Graduate Studies, Dr. Fengzhu Sun, and I met with the first- and second-year Ph.D. student cohorts. From these meetings and my experience in working with some of them in my laboratory, I know that the QCB department is well-positioned with these fantastic students.

Finally, I want to send a message of gratitude to our donors and philanthropic supporters. This includes long-time QCB friends, parents of QBIO students, and CBB alumni. Without them and their financial support, it would be much harder to maintain both excellence and a welcoming department culture.

With this, I wish everyone Happy Holidays and a happy, healthy, and successful New Year.

Remo Rohs, Ph.D.

Department Chair

QCB Faculty

Keck School of Medicine and Viterbi School of Engineering faculty have recently joined the faculty of the Department of Quantitative and Computational Biology. Our new QCB joint faculty include Dr. Arun Durvasula (Assistant Professor of Population and Public Health Sciences), Dr. Sheng Li (Associate Professor of Cancer Biology), Dr. Ruishan Lui (Gabilan Assistant Professor of Computer Science), and Dr. Chang (April) Shu (Assistant Professor of Population and Public Health Sciences).

QCB Publications

Dr. Maxime Tortora, a QCB postdoc in Dr. Geoffrey Fudenberg’s lab, published a paper in Cell Genomics titled “The physical chemistry of interphase loop extrusion”. The paper describes a kinetic model of how regulatory proteins control the dynamics of the motor protein complexes that organize our genomes. Please read the paper here.

CBB Ph.D. student Obadiah Mulder from Dr. Doc Edge’s lab published a paper titled “An agent-based model of metabolic signaling oscillations in Bacillus subtilis biofilms” in PLoS Computational Biology. The authors built an agent-based model of nutrient consumption and flow in a bacterial biofilm that reproduces oscillatory signaling behavior observed in in vitro Bacillus subtilis biofilms. The model shows how an apparent collective, coordinated behavior can emerge from individual cells' behavior. This work was in collaboration with Dr. Joe Larkin of Boston University, whose lab provided new observations of B. subtilis behavior consistent with the model. Please read the paper here.

QCB faculty Dr. Geoffrey Fudenberg and his former lab members Smit Kadvani and Bozhena Pokorny, contributed to a Science paper titled “Synergy between regulatory elements can render cohesin dispensable for distal enhancer function”. The paper, led by the Nora Lab at UCSF, describes how 3D genome folding impacts gene regulation, with Fudenberg’s lab contributing transcriptomic analyses. Please read the paper here.

QCB faculty Dr. Liang Chen, as the last author, and former CBB Ph.D. student Dr. Wei Jiang, as the first author, published a paper in Nature Communications titled “The implications of alternative splicing regulation for maximum lifespan.” The study identifies conserved, lifespan-associated splicing programs and highlights alternative splicing as a genetically programmed axis of longevity beyond gene expression changes. Please read the paper here.

QCB postdoc Dr. Jordy Homing Lam from Dr. Seva Katritch’s lab published a review in NPJ Drug Discovery titled "Navigating structure-based drug discovery with emerging innovations in physics- and knowledge-based approaches”. Please read the paper here.

QCB faculty Dr Fengzhu Sun contributed to a study published in Communications Biology titled ”ViTrace detects viral signatures in tumor transcriptomes using a hybrid language model”. The method provides a scalable framework for guiding precision oncology and characterizing tumor-associated viruses. This is a joint work with a former visiting scholar at USC, Dr. Ying Wang, from Xiamen University, China. Please read the paper here.

QCB joint faculty Dr. Paul Thomas published a paper in the Journal of Molecular Evolution titled “OrthoGrafter: Rapid Identification of Orthologs from Precomputed Placement in Phylogenetic Trees.” Please read the paper here.

QCB joint faculty Dr. Andrei Irimia published a paper in Geroscience titled  “Deep neural networks and genome-wide associations reveal the polygenic architecture of local brain aging”,  also with a contribution from Dr. Paul Thompson, another QCB joint faculty. Please read the paper here.

QCB Postdocs

Dr. Jordy Homing Lam, a QCB postdoc and Croucher Fellow in Dr. Katritch’s lab, will start the new year 2026 in a new postdoc position at UC Berkeley. Best wishes to Jordy in his new endeavors!

CBB Graduate Students

CBB Ph.D. student Tessa Ferrari from Dr. Jazlyn Mooney's group received the Simons Graduate Fellowships in Ecology and Evolution. Her project will combine genomics and evolutionary simulations to better understand how endangered species survive despite small population sizes and low genetic diversity. She will use Ethiopian wolves as her study system because they have long existed in small populations and remain critically endangered.

CBB Ph.D. student Yingfei Wang (Rohs lab) successfully defended her dissertation, "Understanding Transcription Factor–DNA Binding: From Sequence and Local Shape to DNA Conformation and Flexibility".

CBB Ph.D. student Dallace Francis (Sun lab) successfully defended his dissertation, "Computational Methods for Improving the Generalizability of Microbiome Research".

QBIO Undergraduate Students

The very first student who joined the QBIO major, Nicholas Markarian, a graduate from 2020, defended his dissertation "Interpretable Mixtures of Latent Variable Models for Gene Covariation from Pathways to Transcriptomes" at Caltech this month. Nicholas is an M.D./Ph.D. student in the joint Caltech/Keck School of Medicine program.

QBIO student Matthew Genchev received the Provost Fellowship for Spring 2026. He will be combining analytical and simulation models to better understand how (and when) Channel Island foxes ended up on each of the five islands they inhabit.

QBIO undergraduate students presented their final projects for the research class QBIO 490 in the presence of QCB faculty, including Dr. Jerry Lee and other faculty from the Ellison Medical Institute, and Dr. Lee's collaborators from the federal government's APOLLO program.

Upcoming Events

January 15th (RRI 101 @ 2 pm): Seminar by Dr. Sean Eddy, Harvard University

January 22nd (RRI 101 @ 2 pm): Seminar by Dr. Bogdan Pasaniuc, University of Pennsylvania

January 29th (RRI 101 @ 2 pm): Seminar by Dr. Jeff Ross Ibarra, UC Davis

February 12th (RRI 101 @ 2 pm): Seminar by Dr. Lin Chen, USC

February 19th (RRI 101 @ 2 pm): Seminary by Dr. Elinor Karlsson, Broad Institute

February 27th (MCB 101 & 102): Drug Discovery Innovation Workshop

Please register for the workshop here.

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