October & November 2025 QCB Newsletter

QCB at USC
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e-Newsletter Volume 5 Issue 7 | October & November 2025

Personal Remarks by Dr. Remo Rohs

The QCB Department’s meeting with parents and families of current and prospective QBIO students on Trojan Family Weekend is one of my favorite events in the Fall semester. One theme has always been that a biology education requires quantitative training. A result of this is that our acceptance rate for Medical School and MD/PhD programs is still 100%.

This year, parents were acutely aware that the success of students depends on the integration of computing skills with domain knowledge in a different discipline, such as biology. This is what the QBIO degree offers and, therefore, our graduates remain desirable on the job market.

Meeting parents and families is an opportunity for us to communicate with the public. In my view, there was no better message to the audience than that the QCB department’s only mission is excellence in quantitative and computational biology research and education.

Remo Rohs, Ph.D.

Department Chair

QCB Faculty

QCB joint faculty, Dr. Paul Thomas, has been appointed at the Swiss Institute of Bioinformatics (SIB) in Basel, Switzerland, on a part-time basis effective October 1, 2025. During his appointment at this world-class bioinformatics program, he will maintain his appointment at USC with the plan to return full-time. At SIB, Dr. Thomas will be helping to run the Swiss-Prot group. This appointment is a great opportunity for QCB to initiate new collaborations. Congratulations, Paul.

QCB Staff

The QCB department congratulates our wonderful Administrative Assistant, Tanya Moore, now Tanya McReynolds, and her husband on their recent marriage. We wish them many happy years together and thank Tanya for everything she does for QCB.

QCB Publications

QCB faculty Adam MacLean and a former CBB Ph.D. student Megan Rommelfanger (now a research scientist at Altos Labs) published a paper in iScience titled “Gene regulatory network inference with popInfer reveals dynamic regulation of hematopoietic stem cell quiescence”. The method, popinfer, developed in this study, was used to discover a network of gene regulation that controls quiescence in blood stem cells, potentially contributing to healthier aging phenotypes. This work was also co-authored by current CBB Ph.D. students Jonathan Martinez and Zijin Xiang, and the group of K. L. Rudolph at the Leibniz Institute on Aging. Please read the paper here.

CBB Ph.D. student Walfred Ma from Dr. Mark Chaisson's group published a paper in Nature Genetics titled “Genotyping sequence-resolved copy number variation using pangenomes reveals paralog-specific global diversity and expression divergence of duplicated genes”. The study describes a new approach, ctyper, which links short read sequencing data in biobanks to complex variation resolved in human pangenome assemblies. This method improves genotyping for biomedically relevant genes and provides new insight to the functional roles and evolutionary history of copy-number variable genes. Please read the paper here.

QCB postdocs Drs. Woojin Lee and Jordy Homing Lam from Dr. Katritch’s lab, in collaboration with Dr. Cherezov's lab in the Chemistry Department, published a paper titled “Structural insights into the mechanism of activation and inhibition of the prostaglandin D2 receptor 1” in Nature Communications. The study discovered a new functional mechanism in GPCRs, using a combination of cryo-EM and extensive molecular dynamics characterization of the protein-ligand complexes. Please read the paper here.

CBB Ph.D. student Will Yue Huang from Dr. Fengzhu Sun’s group published a paper “Quantifying microbial interactions based on compositional data using an iterative approach for solving generalized Lotka-Volterra equations” in PLoS Computational Biology. The method developed in this study, iLV, uses an iterative approach to accurately estimate parameters in the Lotka-Volterra model based on compositional data in microbiome datasets. Please read the paper here.

QCB joint faculty Dr. Christoph Haselwandter, in collaboration with Dr. Roderick MacKinnon (Rockefeller University), published a paper titled “The configurational length scale in the self-assembly and modulation of higher-order transient protein structures” in PNAS. Please read the paper here.

QCB joint faculty Dr. Paul Thompson led a paper titled “Classification of major depressive disorder using vertex-wise brain sulcal depth, curvature, and thickness with a deep and a shallow learning model.”, published in Molecular Psychiatry. Please read the paper here.

QCB joint faculty Peter (Yingxiao) Wang published a paper titled “Tumour priming by ultrasound mechanogenetics for CAR T therapy” in Nature Materials. Please read the paper here and the Viterbi School of Engineering press release here.

QCB joint faculty Dr. Kate White published a paper titled “Secretory stimuli distinctly regulate insulin secretory granule maturation through structural remodeling” in Structure. Please read the paper here.

QCB joint faculty Dr. Cornelius Gati published a paper titled “Structural snapshots capture nucleotide release at the μ-opioid receptor” in Nature. Please read the paper here.

QCB Postdocs

QCB postdoc Dr. Priscilla Chan from Dr. Steve A. Kay’s lab was awarded the prestigious John H. Richardson Endowed Postdoctoral Fellowship to support her postdoctoral research project on investigating the effects of circadian clock compounds on the glioblastoma tumor microenvironment and synergy with chemoradiation. Dr. Chan gave a poster presentation to the Achievement Rewards for Collegiate Scientists (ARCS) Foundation members at the annual luncheon at the California Club on November 7th.

CBB Graduate Students

CBB Ph.D. student Yibei Jiang (Rohs lab) successfully defended her dissertation "Understanding the Structural Basis Transcription Factor-DNA Binding through Molecular Dynamics" and joined Illumina, Inc. in San Diego.

CBB Ph.D. student George Wang (Rohs lab) successfully defended his dissertation titled “Analysis of Extended DNA Binding Domains of Forkhead Transcription Factors".

QBIO Undergraduate Students

The Quantitative Biology Association's president, Karen Lee, and vice president, Richard Zhang, along with QCB department chair Dr. Remo Rohs, spoke to parents of current and prospective QBIO students at Trojan Family Weekend.

QBIO graduate Samantha Graham defended her dissertation at the University of Minnesota. Her Ph.D. advisor was Dr. Ran Blekhman from the University of Chicago. Samantha, who was in the first cohort of QBIO students, is now a postdoc at Brigham and Women's Hospital in Boston.

Upcoming Events

November 25th (RRI 101 @ 1 pm): Dissertation Defense by Yingfei Wang (Rohs Lab)

December 2nd (RRI 101 @ 9 am): Dissertation Defense by Dallace Francis (Sun Lab)

December 4th (RRI 101 @ 2pm): Seminar by Dr. Hannah Carter, UCSD, hosted by Dr. Jazlyn Mooney

The QCB Department wishes everyone safe travels and a wonderful Thanksgiving holiday!

Our mailing address is:

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