June, July & August 2025 QCB Newsletter

e-Newsletter Volume 5 Issue 5 | June, July, & August 2025

Personal Remarks by Dr. Remo Rohs

It feels good to see life back on campus. I traveled a lot this summer. One theme was noticeable in various places and at conferences: Our department is internationally highly recognized, our research is top-ranked, and our innovative education is becoming a gold standard for institutions and universities across the world.

The new academic year started with a lot of excitement and also uncertainty. While we already spent a lot of time to navigate new administrative regulations and know that more is coming our way, we are excited to welcome a full cohort of 12 first-year PhD students (pictured below) in our CBB program and many new QBIO undergraduate students.

We also welcome our new Dean Dr. James Bullock who has already spent time to meet the chair and make himself familiar with the unique features that the QCB department brings to this university. I am looking forward to working with him. Welcome, Dean Bullock!

Remo Rohs, Ph.D.

Department Chair

QCB Faculty

Dornsife faculty Dr. Don Arnold (Biological Sciences), Dr. Peter Foster (Physics), Dr. Judith Kribelbauer (Biological Sciences), Dr. Julia Schwartzman (Biological Sciences), and Dr. Kate White (Chemistry) have recently joined the faculty of the QCB Department as Professor (Dr. Arnold) or Assistant Professors (all others) of Quantitative and Computational Biology. Welcome all! Additional joint appointments with other schools are awaiting university approval.

Dr. Jazlyn Mooney received an Early-Stage Investigator R35 MIRA award from the National Institute of General Medical Sciences. The proposed studies are bridging the fields of evolution, genetics, and statistics by developing novel computational methods that accurately infer complex admixture and population histories, and deepen our understanding of the distribution of variation that contributes to disease. Congratulations, Jazlyn!

Dr. Remo Rohs was named Fellow of the International Society for Computational Biology (ISCB) during the International Systems for Molecular Biology (ISMB)/European Conference on Computational Biology (ECCB) this summer in Liverpool, UK, where he also gave a lecture. The ISCB recognized him as "a world leader in computational biology" and for "pioneering research on DNA shape readout and protein-DNA interactions".

Dr. Remo Rohs was elected this summer as a Member of the National Academy of Artificial Intelligence (NAAI). The Academy recognized Dr. Rohs for his "pioneering work in statistical machine learning, high-throughput DNA shape prediction, Monte Carlo simulations, and geometric deep learning for protein-DNA specificity" and said that his work "significantly advanced both theory and biomedical applications" and that his "leadership is invaluable to our community".

Dr. Seva Katritch is a part of a multi-PI team receiving a 5-year U01 grant award from the National Institute on Aging. The team led by Dr. Hussein Yassine at USC Keck School of Medicine will continue the development of lead compounds discovered using Katritch’s lab computational platform for the treatment and prevention of Alzheimer’s disease. More details can be found here.

Dr. Seva Katritch received a major UG3/UH3 grant award from the National Institute of Neurological Disorders and Stroke to continue the development of AT2 receptor inhibitor as a preclinical candidate for neuropathic pain treatment. The drug candidate was discovered and optimized using the computer-driven platform developed in the lab. More details can be found here.

Dr. Remo Rohs spent time in his home country this summer and gave lectures at the Max Planck Institute for Molecular Genetics in Berlin, the Max Planck Institute for Biochemistry in Munich, and the Max Planck Institute for Molecular Plant Physiology in Potsdam. He is pictured with QCB alum Dr. Martin Vingron who directs the Computational Molecular Biology Department of the Max Planck Society.

Dr. Fengzhu Sun presented a one-hour plenary talk at the 2025 International Congress of Basic Sciences (ICBS) in Beijing, China, on the analysis of metagenomic Hi-C data. The talk is publicly available on YouTube here. He also gave an invited talk on DeepDeconUQ: a computational method for uncertainty quantification of bulk gene expression deconvolution based on single-cell data at the International Workshop on Systems Learning of Single Cells.

Our ”Top-ranked Department of Quantitative and Computational Biology” was prominently featured in the Dornsife Brochure “Mind the Machine (Harnessing AI for Good). This includes recognition of both undergraduate and graduate QCB programs in advancing the field of AI at USC, as well as examples of pioneering AI research in the labs of Drs. Helen Berman, Seva Katritch, and Remo Rohs in biomedicine and drug discovery. The brochure can be found using the "AI For Good" button.

QCB Publications

QCB postdoc Anupam Dey from Dr. MacLean’s lab published a paper “Transition paths across the epithelial-mesenchymal transition landscape are dictated by network logic” in the journal Development. The study investigates the role of logic in gene regulatory network (GRN) models. The study revealed that the choice of network logic (AND vs OR) profoundly impacts cell fate, highlighting the caution that ought to be exercised in constructing models, and enabling prediction of experimental designs sufficient to infer the logic of GRNs in live cells. Please read the paper here.

Dr. Christopher Riccardi, visiting student from the University of Florence, and Rachel Yuqiu Wang from Dr. Sun’s group published a co-first author paper, “Bidirectional subsethood of shared marker profiles enables accurate virus classification” in Microbiome. They developed a program, Virgo, for taxonomy assignment of viruses using different versions of ICTV (International Committee on Taxonomy of Viruses) database. Please read the paper here.

Dr. Jiawei Huang, a former student from Dr. Sun’s group, published a paper, “DeepDeconUQ estimates malignant cell fraction prediction intervals in bulk RNA-seq tissue” in PLoS Computational Biology. DeepDeconUQ provides a computational method for uncertainty quantification of bulk gene expression deconvolution based on single cell data using deep learning. Please read the paper here.

QCB postdoc Dr. Hadi Rahmaninejad from Dr. Geoffrey Fudenberg’s group, with contributions from group members Dr. Maxime Tortora and Yao Xiao, published a paper titled “Dynamic barriers modulate cohesin positioning and genome folding at fixed occupancy" in Genome Research. While previous models had only effectively considered static probabilistic barriers, the study shows that several features of genome folding require dynamic barriers for their explanation. Please read the paper here.

QCB Research Scientist Dr. Josh Schraiber and Professor Doc Edge have published a new paper “Estimation of demography and mutation rates from one million haploid genomes” in the American Journal of Human Genetics. They developed a branching-process approximation to models used for estimating demographic history from genetic data, allowing population-genetic analyses of sequencing datasets for a million chromosomal copies. Please read the paper here.

QCB student Shirin Nataneli, as a co-first author, and Dr. Jazlyn Mooney, as corresponding author, published a perspective in Genetics titled “Echoes of eugenics: confronting its effects in indigenous genomics.” The study explores how science is intertwined with eugenics and how eugenic ideologies continue to negatively impact Indigenous communities and science today. Read the paper here.

QCB student Tessa Ferrari from Dr. Jazlyn Mooney's lab published a paper titled “Parameter Scaling in Population Genetics Simulations may Introduce Unintended Background Selection: Considerations for Scaled Simulation Design” in the journal Genome Biology and Evolution. The study reveals that strongly scaled simulations may introduce major biases in the models and offer potential strategies for the mitigation of scaling effects. Read the paper here.

QCB student Feriel Ouerghi from Dr. Doc Edge's lab published a study titled “On forensic likelihood ratios from low-coverage sequencing” in Forensic Science International Genetics. The study reveals that the likelihood ratios produced by a popular analysis software IBDGem are testing a null hypothesis different from the traditional one used in a forensic genetics context and suggest ways to correct this. Read the paper here.

QCB joint faculty Dr. Naomi Levine published a paper titled “Functional biogeography of marine microbial heterotrophs” in Science. Read the paper here.

QCB joint faculty Drs. Steven Gazal and Nicholas Mancuso, as the last author, published a paper titled “Improved multiancestry fine-mapping identifies cis-regulatory variants underlying molecular traits and disease risk” in Nature Genetics. Read the paper here.

QCB joint faculty Dr. Charleston Chiang published a paper titled “A genealogy-based approach for revealing ancestry-specific structures in admixed populations” in the American Journal of Human Genetics. Read the paper here.

QCB joint faculty Dr. Paul Newton published a paper titled “Gaming the cancer–immunity cycle by synchronizing the dose schedules” in Proceedings of the National Academy of Science.  Please read the paper here.

QCB Postdocs

QCB postdoc Dr. Roshni Patel from Dr. Edge lab starts a new position as Assistant Professor of Data Science at the University of Oregon. Her new departmental colleagues include former QCB professor Peter Ralph. Congratulations to Dr. Patel, who will be missed!

CBB Graduate Students

A QCB team, research specialist and lecturer Dr. Jinsen Li, CBB student Lexi Shewchuk, Dr. Remo Rohs, CBB student Wei Yu Tang, and faculty members Dr. Tsu-Pei Chiu and Dr. Peter Calabrese, attended this year’s ISMB/ECCB conference in Liverpool, UK, from July 20-24, 2025. Jinsen, Lexi, and Wei Yu presented their research in the Rohs Lab, and Drs. Chiu and Calabrese presented educational approaches developed in this department.

Last week, we held a Ph.D. Program orientation for our new graduate students. This important event was organized and run by our fantastic staff. We also thank Vice Chair Dr. Liang Chen, Director of Graduate Studies Dr. Fengzhu Sun, all other faculty and graduate students for their contributions.

The Ph.D. Student Handbook for the CBB Ph.D. Program has been substantially revised. At the request of the Graduate School, the previously separate Handbooks issued by the Graduate School and the Department Handbook were combined into one Handbook that received formal approval by the Graduate School. A few clarifications that have been added include text about minimum expectations and a clarification of RA/TA appointments versus research for progress towards a degree. The document can be found using the "CBB PhD Handbook" button.

QBIO Undergraduate Students

There have been many recent white-coat ceremonies for QBIO graduates entering Medical School. Shown here are Ari S. Cohen from the Rohs Lab with Dean Carolyn Meltzer, Dean of the Keck School of Medicine of USC, and Hirad Hosseini (also from the Rohs Lab) and Kenneth Nguyen. These are only a small fraction of QBIO graduates entering Medical School this fall. The Michal S. Waterman Awardee Brandon Ye (from the Kuhn lab) started Medical School at Johns Hopkins University.

QCB Staff Spotlight

As the new academic year begins, the QCB faculty and students want to send a huge shout out to the staff members that are directly reporting to the department, Dominique Andrade (graduate student advisor), Tanya Moore (administrative assistant), Luigi Manna (director of high-performance computing), and Dr. Rokas Oginskis (program manager and head of the administration). Without any of them, we would not be able to achieve excellence. Thank you for everything you do!

Upcoming Events

October 2nd (RRI 101 @ 2pm): Tenure talk by Dr. Doc Edge

October 9th (RRI 101 @ 2pm): Tenure talk by Dr. Adam MacLean

September 4th (RRI 101 @ 2pm): Seminar by Dr. Graham McVicker, Salk Institute for Biological Studies

September 11th (RRI 101 @ 2pm): Seminar by Dr. Eric Siggia, The Rockefeller University

September 18th (RRI 101 @ 2pm): Seminar by Dr. Krishna Garikipati, USC Viterbi School of Engineering

September 25th (RRI 101 @ 2pm): Seminar by Dr. Kirk Lohmueller, University of California, Los Angeles

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