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November 2023 QCB Newsletter

e-Newsletter Volume 3 Issue 8 | November 2023

Personal Remarks by Dr. Remo Rohs

This past month saw many highlights for the QCB Department. We had our best departmental retreat ever, the fourth QCB retreat. A huge difference made the keynote speaker, Dr. Mike Levine (Princeton University). It was also wonderful to see QBIO undergraduate students actively participate in the sessions. Thanks to our staff and students for organizing the retreat.

Another highlight were the promotions of Dr. Seva Katritch and Dr. Stacey Finley to Full Professors of Quantitative and Computational Biology. Becoming a Full Professor is a huge achievement. We are proud of their trajectories and contributions to science and to QCB.

Our department is recruiting a new cohort of Ph.D. students in Computational Biology and Bioinformatics. We will offer a competitive stipend that we will soon announce. Come join us. We are one of the top-ranked programs if you seek a training in computational biology.

Remo Rohs, Ph.D.

QCB Department Chair

QCB PhD Program Applications

Please see the flyer above for QCB PhD Program Applications and spread the word! We will be accepting applications until December 15th, 2023. Contact Christian Robbie at for any questions. You can also directly apply through this website:

QCB Department Retreat

Thank you to everyone who attended our QCB Departmental Retreat this year, and to all of the staff, faculty, and students who worked hard to make it a success!

QCB Homecoming Thank-You

This year's homecoming weekend, QCB alumni Drs. Lin Yang and Xiaofei Wang visited the USC campus. Dr. Yang, together with Dr. Tianyin Zhou, ensure that the USC QCB Google Alumni Awards remain funded by our Google alumni. We are thankful for their support.

QCB Publications

Dr. Michael "Doc" Edge lab postdoc Dr. Vivian Link published a new paper in iScience, "Microsatellites used in forensics are in regions enriched for trait-associated variants." Vivian found that, contrary to assumptions sometimes adopted in forensic science, the genetic markers used in forensics are more likely than comparable markers to be near trait-associated variants identified in genome-wide association studies and previously identified pathogenic variants. Read more here.

The Pennell group published a new paper “Evaluating the Performance of Widely Used Phylogenetic Models for Gene Expression Evolution” in Genome Biology and Evolution. The study analyses previously published multi-species gene expression datasets to evaluate both the relative fit of alternative trait models as well as the absolute fit of the best of the set. Read more about this study here.

Dr. Matt Pennell also published a News and Views article in Nature. In this perspective, he discusses emerging statistical discoveries that may confound estimates for when major groups of organisms originated. Read the paper here.

Dr. Lingyun (Ivy) Xiong, a postdoc working in the Dr. Adam MacLean and Dr. Andy McMahon labs, published a paper with co-first author Jing Liu, in which they employed single-cell multiomics to discover that androgen plays the key role in regulating gene expression and sexual dimorphism in the mouse kidney. Read more about their work here.

Dr. Steve Kay's lab published a comprehensive review titled “Watching the clock in glioblastoma” on the role of circadian genes in brain cancer and strategies for targeting them in drug discovery. Read the review here.

Dr. Jingwen Ren and Bida Gu published a paper on a new approach for annotating variable-number tandem repeats (VNTRs) in population scale sequencing studies that use long reads, with Dr. Mark Chaisson. This approach is currently being used in a large-scale study to find associations between tandem repeat variation and Alzheimers. Read more here.

Dr. Mark Chaisson published a review on tandem repeats, and discusses genomic distribution of repeats, algorithms to analyze and visualize tandem repeat variation, and diseases with tandem repeat etiology. Read the review here.

Dr. Chaisson also published a paper with Dhaivat Joshi that used a novel treatment of nanopore sequencing data to translate bases into signal quantiles, and to detect variation in quantile space instead of base space. When combined with standard alignment, this approach improves specificity and sensitivity of variant discovery. Read the paper here.

QCB joint faculty Drs. Nichola Mancuso (top), Andrew McMahon (left), Paul Thompson (bottom-left), Arthur Toga (bottom-right), and Arieh Warshel (right) published nine research papers in major peer reviewed journals, which can be found here.

QCB Faculty

Dr. Remo Rohs presented a Keynote Lecture "Deep Learning Reveals Mechanisms of Protein-DNA Binding" at the RECOMB/ISCB Conference on Regulatory & Systems Genomics on November 29, 2023, held at UCLA.

President Carol Folt celebrated Dr. Helen Berman and other new members of the National Academies at the National Academies Inductees Dinner, with Dr. Berman being USC's only inductee this year of the National Academy of Sciences.

In November, QCB hosted a celebration in honor of Dr. Helen Berman for her election to the National Academy of Sciences. Photos of this event will follow in the December Newsletter.

QCB Graduate Students

This month, the Computational Biology Student Association (CBSA) hosted a Friendsgiving before the holidays. The event was a true community effort, with graduate students, undergraduate students as well as staff contributing a dish to the potluck. Attendees also enjoyed a crafting session, creating turkeys and pumpkins that added a creative and fun element to the celebration.

Yilin Gao from Dr. Fengzhu Sun’s lab successfully defended her dissertation “Enhancing Phenotype Prediction through Integrative Analysis of Heterogeneous Microbiome Studies”. She will join Adobe as a data scientist. Congratulations, Yilin!

QBIO Undergraduate Students

The Quantitative Biology Association (QBA) held their third general meeting in November. This event brought in a panel consisting of industry professionals at Pacific Biosciences, Elemnt Bio, Seagen, Cajal Neurosciences, Protillion, and Bristol Myers Squibb. A special thanks to Dr. Mark Chaisson & Dr. Jazlyn Mooney for helping to coordinate these wonderful speakers!

Upcoming Events

Join the Computational Biology Student Association (CBSA) for a fun night of Holiday-themed Karaoke on December 5th at 5 pm in RRI 421!

Copyright © 2023 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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