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January 2025 QCB Newsletter

e-Newsletter Volume 5 Issue 1 | January 2025


Personal Remarks by Dr. Remo Rohs


Welcome back to the Spring Semester!


The year 2025 started with unimaginable tragedy. Too many colleagues and friends lost their

homes, schools, and houses of worship in Altadena, Pasadena, and Pacific Palisades. Please be

extra kind to each other during this challenging time and offer your support.


Lots is also happening on campus. I wouldn’t be writing this letter as department chair if I

wasn’t an optimist most of the time. In this spirit, I am looking forward with enthusiasm to what

the year 2025 might bring for all of us. For a start, here is the first QCB newsletter.


Remo Rohs, Ph.D.

Department Chair


QCB Faculty

The School of Advanced Computing's newly formed Advanced Computing Affinity Groups have been announced, with several QCB faculty members (Dr. Naomi Levine, left; Dr. Vsevolod “Seva” Katritch, right; Dr. Paul Thomspon, bottom) representing our department. The Affinity Groups play an important role in the hiring of new faculty members through the School of Advanced Computing. Please read the article here.


Dr. Remo Rohs received a joint appointment as Professor of Medicine in the Department of Medicine's Division of Medical Oncology at the Keck School of Medicine of USC. Dr. Rohs is looking forward to collaborating with these academic units and form strong connections between the Keck School of Medicine and the QCB department.


The Viterbi Magazine discusses how we got to the USC School of Advanced Computing. Note the time entry for 2021 - The founding of the Department of Quantitative and Computational Biology (QCB). Please read more here.


The QCB department hosted Professor Jingyi Jessica Li this week. Dr. Li gave an excellent talk about two recent statistical methods developed in her lab for evaluating single cell RNA-seq and bulk RNA-seq. Alongside of her research, she also won the ISCB Overton Prize in 2023. Dr. Li has interacted with many members of our department over the years. She was even an instructor for two of our faculty members while they were in graduate school, Jazlyn and Doc; and worked with current graduate student MeiLu McDermott from the MacLean Lab.


Dr. Xuegong Zhang, a professor at Tsinghua University, a pioneer in Bioinformatics, and Fellow of the International Society for Computational Biology, visited QCB this month and gave a departmental seminar.


QCB Publications

Dr. Remo Rohs published a brief article in Molecular Cell, "Artificial Intelligence in Molecular Biology", with leaders in the field including Anshul Kundaje, Katie Pollard, and Jian Ma. The researchers discuss how AI tools address biological questions and explore current implications and future possibilities. Please read the paper here.


QCB students Paulina Smaruj (left) and Yao Xiao (right) as co-first authors and Dr. Geoff Fudenberg (bottom) as the corresponding author published a review article in Current Opinion in Genetics & Development: "Recipes and ingredients for deep learning models of 3D genome folding". The review compares and contrasts recent deep learning models for predicting genome contact maps. Please read the paper here.


QCB postdoc Dr. Xiaojun Wu (first author, left) and CBB student MeiLu McDermott (right) from Dr. Adam MacLean’s (bottom) lab published a paper in PLOS Computational Biology, "Data-driven model discovery and model selection for noisy biological systems". The study uses neural networks to learn unknown model equations from data, providing a practical framework for model discovery in biology in cases where data are noisy and sparse, and the underlying biological mechanisms are only partially known. Please read the paper here.


Joint QCB faculty Dr. Christoph Haselwandter published a paper in Proceedings of the National Academy of Sciences USA titled “Higher-order transient membrane protein structures”, in collaboration with MacKinnon Lab (Rockefeller) and the Sondoghdar Lab (Max Planck Institute for the Science of Light). Please read the paper here.


Joint QCB faculty Dr. Cornelius Gati published a paper in Nature Chemical Biology titled “Molecular mechanisms of inverse agonism via κ-opioid receptor-G protein complexes”. Please read the article here.


Joint QCB Faculty Dr. Paul Thompson published a paper titled “Microstructural mapping of neural pathways in Alzheimer's disease using macrostructure-informed normative tractometry” in the journal Alzheimer’s and Dementia. Please read the paper here.


CBB Graduate Students

Dr. Fengzhu Sun (photo) stepped into the role as Director of Graduate Studies (DGS) for the CBB program. The DGS is the point person for all questions and inquiries from CBB Ph.D. students. The department thanks Dr. Andrew Smith (who started his sabbatical) for his service as DGS over several years.


QBIO Undergraduate Students

The QCB department welcomes Karen Lee (photo) as the new undergraduate liaison for the QBIO program. Karen organizes the peer-mentorship program, is part of the Quantitative Biology Association, and helps with the newsletter. The department thanks Colin Yeo for his contributions as the liaison over the last year.


Upcoming Events

February 6th (RRI 101 @ 2 pm): Seminar by Dr. Kishwar Shafin, Google

February 13th (RRI 101 @ 2 pm): Seminar by Dr. Mark Alber, UC Riverside

February 20th (RRI 101 @ 2 pm): Seminar by Dr. Guy Sella, Columbia University

February 27th (RRI 101 @ 2 pm): Seminar by Dr. Jasmine Foo, University of Minnesota, Twin Cities

3rd Drug Discovery Innovation Workshop

Organized by CNT3D, MESH Academy, Bridge Institute, and Professors Vsevolod 'Seva' Katritch and Charles McKenna.

February 28th, 2025, 10 am – 5 pm,  MCB 1st floor



Copyright © 2025 Department of Quantitative and Computational Biology, University of Southern California. All rights reserved.


Our mailing address is:

1050 Childs Way, RRI 201, Los Angeles, CA 90089-2019

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