March 2025 QCB Newsletter

e-Newsletter Volume 5 Issue 3 | March 2025

Personal Remarks by Dr. Remo Rohs

The QCB Department is excited that we quickly succeeded in recruiting a full cohort of fantastic incoming graduate students who will join us in August for their Ph.D. studies. Welcome all to the QCB family! My thanks go to admissions chair Dr. Mark Chaisson, Dominique Andrade, the admissions committee, and Dr. Rokas Oginskis for their hard work on Ph.D. admissions.

My recent election as Fellow of the International Society for Computational Biology (ISCB) is good news for the QCB Department with now four ISCB Fellows, Drs. Michael Waterman, Helen Berman, and Fengzhu Sun, only matched by Carnegie Mellon University. Receiving recognition from peers is a special honor, and I want to thank my current and former lab members who made this possible.

Remo Rohs, Ph.D.

Department Chair

QCB Faculty

Dr. Remo Rohs has been named a Fellow of the International Society for Computational Biology (ISCB). Lauding Rohs as “world leader in computational biology,” the ISCB recognizes his pioneering research, noting that his computational methods have transformed the understanding of gene regulation by integrating genomics, structural biology and Al-driven modeling. Congratulations, Remo! See the Dornsife announcement here.

Dr. Arieh Warshel, QCB joint faculty and 2013 Nobel Laureate in Chemistry, was elected a Member of the National Academy of Artificial Intelligence (NAAI). Dr. Warshel was also elected an Honorary Member of the Serbian National Academy of Sciences. Mazal Tov, Arieh! See the Dornsife announcement here.

The The Chan-Zuckerberg Initiative (CZI) announced QCB joint faculty Dr. Scott Fraser as the leader of a new Biohub to develop breakthrough imaging technologies to observe cells in action. Under Dr. Fraser's guidance, the CZ Biohub San Francisco and CZ Imaging Institute will join together to achieve this goal. Congrats on this exciting new challenge, Scott! See the CZI announcement here.

QCB Publications

Former QCB PhD student Dr. Caoqi Fan together with QBIO alumna Jordan Cahoon and QCB PhD student Bryan Dinh from QCB joint faculty Dr. Charleston Chiang's lab published a new paper, 'A likelihood-based framework for demographic inference from genealogical trees' in Nature Genetics. This paper presents a substantial advance on a classic problem in evolutionary genetics - estimating the demographic history of a population. The study is based on so-called coalescent trees, which have a long history at QCB, dating back to the work of co-founding faculty member Simon Tavaré. The work featured contributions from QCB joint faculty member Dr. Nicholas Mancuso and QCB faculty member Dr. Doc Edge. Please read the paper here.

CBB graduate students Dandan Peng, Obadiah Mulder, and Janis Liu from Dr. Doc Edge's lab published two papers in the journal Genetics. The first paper by Peng and Mulder is titled "Evaluating ARG-estimation methods in the context of estimating population-mean polygenic score histories". The second paper by Liu is titled "Error rates in Q_ST--F_ST comparisons depend on genetic architecture and estimation procedures". Both papers make contributions to methods for testing hypotheses about natural selection on traits affected by many genes and environmental factors. Please read the papers here and here.

Dr. Raktim Mitra, Ari Cohen, and Wei Yu Tang from Dr. Remo Rohs's lab are the co-first authors of a new paper published in the Journal of Molecular Biology. The paper describes a new webserver, analysis pipeline, database, and highly interactive visualization tool, RNAproDB, designed for protein-RNA interactions, along with a statistical analysis of protein-RNA complexes." Other contributing authors were QBIO undergraduate senior Hirad Hosseini, CBB first-year graduate student Yongchan Hong, and QCB faculty Dr. Helen Berman. Please read the paper here.

Drs. Jordy Lam, Antonina Nazarova, and Saheem Zaidi, current and former members of Dr. Seva Katritch’s lab, contributed to the study “Structure-guided design of partial agonists at an opioid receptor”, published in Nature Communications. They designed and provided a thorough binding and dynamics computational assessment of the new bitopic compounds with potent analgesic activity and reduced side effects. Please read the paper here.

QCB research scientist Dr. Joshua Schraiber from the lab of former QCB faculty Dr. Matt Pennell, in collaboration with Dr. Alexander Cope from Vanderbilt University, published a new study titled “Macroevolutionary divergence of gene expression driven by selection on protein abundance” in Science magazine. Analysis of transcriptomic and proteomic data on ten mammals in this study reveals that evolution primarily acts on protein levels, with gene expression driven to accommodate those optimal levels. Please read the paper here.

CBB Graduate Students

CBB graduate student Wei Yu Tang published a co-first author paper in the Journal of Molecular Biology (please read here) from research entirely completed in his first rotation. Publishing a co-lead author paper this early is a record. Wei Yu made a huge contribution to the paper and handled the revision while also working on a manuscript from his undergraduate research.

Incoming CBB student Dylan Kemmerer is a Barry Goldwater Scholar. This prestigious scholarship is only given to a small group of excellent undergraduate students from all over the country. Only four QCB students have received this honor over the years. Welcome to QCB, Dylan! Please read the announcement here.

QBIO Undergraduate Students

QBIO senior Wade Boohar interviewed QCB faculty Dr. Jazlyn Mooney for the Paradigm Podcast, a series published by Shift SC, a technology ethics club at USC. The 60-minute interview explores ethical considerations when dealing with population genetics and large-scale genomic studies. Please listen to it here!

Undergraduate Student Spotlight

QBIO Senior Brandon Ye received the prestigious Discovery Scholar Award which recognizes ten USC graduating seniors with exceptional academic achievement, research involvement or creative work, and significant promise for future research or creative endeavors. Congratulations, Brandon!

QCB Outreach

In March, QCB faculty member Dr. Adam MacLean hosted a teacher development day as a part of the Joint Educational Project’s (JEP) STEM Education Programs at USC. Teachers from local school districts were invited to campus to tour QCB and the MacLean lab, and taught from the curriculum that Dr. MacLean recently published in the education journal "Connected Science Learning." The workshop and the developed curriculum were funded by an NSF CAREER award with an education component focused on enhancing computational biology and stem cell education. Read more details in the journal article here.

Upcoming Events

April 3rd (RRI 101 @ 2pm): Seminar by Dr. Charles Perou, UNC Chapel Hill

April 17th (RRI 101 @ 2pm): Seminar by Dr. Sohini Ramachandran, Brown University

April 24th (RRI 101 @ 2pm): Seminar by Dr. Jasmine Foo, University of Minnesota

May 1st (RRI 101 @ 2pm): Seminar by Dr. Jonathan Pritchard, Stanford University

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