e-Newsletter Volume 5 Issue 2 | February 2025
Personal Remarks by Dr. Remo Rohs
This month, the QCB Department is focused on Ph.D. student recruitment. Our Ph.D. Program in Computational Biology and Bioinformatics saw a record number of applications this year. We received more applications than in any prior year.
We are now working on convincing the selected candidates to join. They will visit in the next few weeks. I add that the QCB Department will once again be able to add 10% to the 2025-26 Dornsife stipend rate thanks to generous philanthropists and supporters of the department as well as strong research grant funding.
Remo Rohs, Ph.D.
Department Chair
QCB Faculty
Dr. Helen Berman has been appointed as Distinguished Professor of Quantitative and Computational Biology at USC. This is fantastic news and the most appropriate recognition of Dr. Berman’s contributions to both the field and the QCB department. Please read the announcement here. Congratulations, Helen!
Dr. Andrew McMahon has been appointed University Professor Emeritus of Stem Cell Biology and Regenerative Medicine, and Quantitative and Computational Biology. This is a great honor and reflects Dr. McMahon's many outstanding contributions to USC. Through his continued affiliation with QCB, Dr. McMahon will provide advice and collaborate with our faculty. Congratulations, Andy!
QCB joint faculty Dr. Rosa Di Felice has recently received recognition in the 2024 Airbus Quantum Computing Challenge for a computational protocol that will benefit from the development of quantum technologies and quantum theory. Please read more about the award here.
QCB Publications
CBB graduate student Paulina Smaruj from Dr. Geoffrey Fudenberg's lab published a paper titled “Interpreting the CTCF-mediated sequence grammar of genome folding with AkitaV2” in PLoS Computational Biology. The study employs neural network models to understand genome folding. Please read the paper here.
CBB graduate student Yingfei Wang in Dr. Remo Rohs lab published a paper in Bioinformatics with contributions from Drs. Jinsen Li and Tsu-Pei Chiu that introduces DNAdesign, a method for the design of DNA based on various properties. The paper was accepted without revision, in the editor's words, as easily the first in over 1000 manuscripts. Please read the paper here.
QCB faculty Dr. Geoffrey Fudenberg, jointly with Dr. Vijay Ramani from UCSF, published a perspective article in Science Magazine titled “Relating DNA sequence, organization, and function”. The article discusses new approaches to synthetic genome reconstitutions and their role in better understanding chromatin function. Please read the paper here.
Chemistry graduate student Aleique Allen in Dr. Peter Qin's lab published a paper on the CRISPR gene editing system in Scientific Reports with contributions from QCB alumn Dr. Brendon Cooper in Dr. Remo Rohs lab. The paper shows that DNA conformational flexibility affects the gene editing properties of Cas12a. Please read the paper here.
QCB joint faculty Dr. Paul Thomas published as lead senior author a Nature article describing a comprehensive, computable representation of the functional repertoire of all macromolecules encoded within the human genome as a major resource for the field. The paper, which is part of the Gene Ontology Consortium, can be read here. It was highlighted by a Keck School of Medicine press release - please read here.
QCB faculty Dr. Fengzhu Sun contributed to the paper “Estimated size of the total genome and protein space of viruses” published in ASM journal mSpheres. Please read the paper here.
Dr. Andrei Irimia, QCB joint faculty, published a paper “Deep learning to quantify the pace of brain aging in relation to neurocognitive changes” in PNAS. Please read the paper here and the USC School of Gerontology news here.
CBB Graduate Students
First year student Zijin Xiang and her path to the QCB Department were recently featured by her former institution, the Herbert and Florence Irving Institute for Cancer Dynamics, directed by QCB Emeritus Professor Simon Tavaré, at Columbia University. Please read the profile here.
QBIO Undergraduate Students
QCB joint faculty Dr. Jerry Lee recently visited and spoke with the student-led QBIO-490 course. Thank you, Jerry, for your continued support of the QBIO undergraduates, and QBIO Student Mahija Mogalipuvvu for organizing the opportunity!
The Quantitative Biology Association and Quantitative Biology Mentorship Program hosted a social event this month to foster community among the undergraduate students. We hope that the 26 new mentorship pairings provide more peer support to the undergraduates!
The QCB Department recently donated several boxes of personal protective equipment to Blueprints for Pangaea, a USC nonprofit organization that several QBIO undergraduates are involved in. The QCB donations were included in their recent shipment of medical supplies to several Los Angeles area nonprofits, which was featured by Fox 11 Los Angeles here.
Upcoming Events
March 13th (RRI 101 @ 2 pm): Seminar by Dr. Ben Raphael, Princeton University
March 18th (RRI 101 @ 2 pm): Seminar by Dr. Nicolas Gompel, University of Bonn
March 20th (RRI 101 @ 2 pm): Seminar by Dr. Ruishan Liu, University of Southern California
March 27th (RRI 101 @ 2 pm): Seminar by Dr. Andrew Clark, Cornell University
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
Register here: https://usc.qualtrics.com/jfe/form/SV_8GsUjQif89EMe7I
The School of Advanced Computing is hosting a USC Symposium on the Future of Computing with Bioinformatics speakers including Dr. Wei Wang (UCLA) and Dr. Rose Yu (UCSD).
March 13-14, Ginsburg Hall
More information and registration: https://sac.usc.edu/usc-symposium-on-the-future-of-computing/
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