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December 2022 QCB Newsletter

Department of Quantitative and Computational Biology

The year 2022 was a successful year for our department. Two tenure-track faculty members joined us, we saw a rapid growth in our QBIO undergraduate program, we started an important reorganization of our administrative structure, and we celebrated the first birthday of our department together with the 40 year-long legacy of computational biology at USC and our founder Professor Michael Waterman's 80th birthday. To support our talented students, both in the graduate and undergraduate programs, we are ending this year 2022 with a fundraising campaign that will benefit exclusively our students. We are asking everyone who is able to contribute and support our mission of excellence in combining education and research, to directly contribute to the newly established Michael S. Waterman Awards in Quantitative and Computational Biology for graduate and undergraduate students. Please contribute at: Every contribution counts and will be acknowledged. I want to also thank everyone who helped me to end this year successfully. This is our Program Manager Rokas Oginskis, the members of my own lab who often stepped in when departmental staff asked them to help out throughout the year, and all students, staff, and faculty of our department. And finally, I want to warmly welcome Christian Robbie, our new Graduate Student Services Adviser.

Remo Rohs, Ph.D.

QCB Department Chair

CBB PhD Program

This is the final call to complete your applications to the QCB Department's PhD Program in Computational Biology and Bioinformatics. More information is available at Students need to apply by December 15, 2022, at The GRE is waived for all applicants, and we will review applications that are incomplete if applicants are unable to schedule TOEFL exams in time to submit test results with the application. The stipend level for 2023-24 in the CBB Program will as always be competitive with peer programs in our field.

QBIO Undergraduate Students

Pictured: Students in one section of QBIO 490 this fall semester, with Dr. Anna Barker, Chief Strategy Officer of the Ellison Institute.

The students who took the QBIO 490 section "Multi-Omic Data Analysis" gave their final presentations at the Lawrence J. Ellison Institute for Transformative Medicine on Monday, December 5th, 2022. They showcased their work throughout this semester learning multi-omic research methods, scientific programming, and analysis of cancer data. The presentation was attended by QCB core faculty members Dr. Peter Calabrese and Dr. Matthew Pennell.

CBB Graduate Students

CBB student Xiaojun Wu from the MacLean lab gave a talk at the ICSB/RECOMB conference in Las Vegas, presenting his recent work developing parameter inference methods for single-cell dynamic informed by spatial transcriptomics.

QCB Faculty

Dr. Scott Fraser was a recipient of the 2022 Outstanding Researcher Award from Southern California Biomedical Council. Dr. Fraser was honored for "his work on imaging and molecular analyses of intact biological systems aimed at creating new medical diagnostics", also recognizing his "long-standing commitment to quantitative biology which fueled many advancements through the application of chemistry, engineering, and physics."

Dr. Cornelius Gati and his lab led a major study on the structure-function of human GABA transporter-1 (GAT-1), recently published in Nature. The cryo-EM structure of GAT-1 was determined in complex with anticonvulsant tiagabine, opening new venues for drug discovery. Read about it here.

A Gattaca article written by Dr. 'Doc' Edge, highlighted in last month's QCB Newsletter, was chosen for the cover of Genetics! Take a closer look at it here.

The Katritch lab developed a new molecular design concept to discover new bitopic ligands that target sodium pockets, specifically in Opioid GPCRs. This study demonstrated the unique functional profile of mu-opioid bitopics, including side effect-free analgesia in-vivo, and has been published in Nature (link to article) and highlighted in USC News (link to publication).

Dr. Matt Pennell published a review in Trends in Immunology, titled, "The Evolutionary and Functional Significance of Germline Immunoglobulin Gene Variation." Understanding of previously undocumented variation among individuals in the antigen-recognition sequence of antibodies is important for vaccine design and other therapeutics. Read his review here.

Dr. Peter Calabrese (QCB), Dr. Seva Katritch (QCB), and Dr. Norm Arnheim (MCB) recently published a paper in Human Mutation on germline selection, Noonan Syndrome, and a surprising connection to cancer. Read more about their findings here.

Dr. Adam MacLean visited an elementary school local to USC to work with kids, presenting a newly developed "Stem Cell" curriculum that conveys how computational modeling can be used to study stem cell dynamics. The curriculum is a collaboration between the MacLean lab and JEP at USC, funded by an NSF CAREER award. Read about his work here.

QCB Book Club

The Dynamics Club is having a guest lecture featuring Dr. Steven Haase, Thursday, December 15, 2022 at 11am PDT/2pm EST., Zoom Meeting ID: 939 3172 2166 Passcode: 972585. All are welcome!

Postdoctoral Positions Open

Postdoctoral positions in 3D genome biology are open in the Fudenberg Research Group ( The Katritch Lab is accepting postdoctoral applications in structural bioinformatics and drug discovery (

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