Department of Quantitative and Computational Biology
The summer was a busy time for the QCB department – we had our first in-person graduation as a department. Our Vice Provost for Academic Programs and Dean of the Graduate School, Dr. Andrew Stott, and a proud parent of a QBIO graduate, Dr. Hassan Zamat, helped us to send off our graduates in this year’s departmental ceremony.
Our department hosted a three-day conference to celebrate 40 years of Computational Biology at USC, our founder Professor Michael Waterman’s 80th birthday, and announced our new Department of Quantitative and Computational Biology to the world. The invited speakers, half of them women, included several members of the National Academies and many Fellows of the International Society for Computational Biology. Many participants said that this was the best scientific conference they ever attended in their career. The conference was opened by QCB Board Member Dr. Andrew Viterbi and ended with a Banquet where the Provost, Dr. Charles Zukoski, and QCB Board Member, Dr. Ming Hsieh, spoke about QCB and Dr. Waterman.
We are looking forward to a fantastic new academic year. We welcomed more graduate students in our Ph.D. Program in Computational Biology and Bioinformatics than ever before. We just doubled the number of our joint faculty. Quantitative and Computational Biology is growing to satisfy the undeniable demand in this era of data-driven life sciences.
I wish everyone a successful, enjoyable, and healthy academic year 2022-23!
Remo Rohs, Ph.D.
QCB Department Chair
QBIO, QCB and CBB Commencement 2022
On Wednesday, May 11, 2022, we celebrated six Computational Biology and Bioinformatics graduate students getting hooded and completing their Ph.D. Bo Sun from the Chen Lab; Joe Larsen from the Kuhn Lab; Brendon Cooper and Jinsen Li from the Rohs Lab; and Xin Bai and Zifan Zhu from the Sun Lab. On Friday, May 13, 2022, we celebrated the graduation of our QBIO undergraduates and our QCB Master's students. Please help us congratulate our following QBIO undergraduate students: Jaehyung Choi, Ari Cohen, Patrick Condie, Alexander Hill, Jared Kahn, Jonathan Le, Sunny (Hyo Sun) Lee, Harinarayana Mellacheruvu, Chris Neely, Sophia Pei, Rithik Rajani, Sydney Rashid, Christopher Simmons, Jena Tran, David Wen, Eric Yang, and Dana Zamat. And our QCB Master's students: Bryson Choy, Harinarayana Mellacheruvu, Sophia Pei, Jaclyn Ready, Darius Scott, Christopher Simmons, and Sydney Suzuki.
40 Years of Computational Biology at USC Symposium
To celebrate 40 Years of Computational Biology at USC, we hosted a very successful three day conference for over two hundred people. We had outstanding speakers, exceptional posters presented by students, and lots of opportunity for collaboration and community. We also celebrated Dr. Michael Waterman's 80th birthday, announced the creation of the Department of Quantitative and Computational Biology, and awarded the inaugural Michael S. Waterman Awards, the John Petruska Memorial Awards, and the QCB Alumni Google Awards.
Dr. Adam MacLean wrote a spotlight article in Cell Reports Methods on new computational tools for profiling single cells: to predict what state they are in and where they are going. (See article here).
Dr. Matt Pennellreceived a Canada Research Chair in Adapting Biosystems. (See announcement here). Dr. Matt Pennell published a new paper in the journal Evolution titled: The scaling of diversification rates with age is likely explained by sampling bias. (See article here).
Dr. Antonina Nazarova,a postdoc in the Katritch Lab, was awarded 2nd place in LABEST poster competition.
CBB Graduate Students
CBB Graduate student, Jordy Lam, from the Katritch Lab,in collaboration with Cornelius Gati lab, published a study on Structural basis of GABA reuptake inhibition in Nature. (See article here).CBB student, Tianqi Tang, from the Sun Lab, presented his paper “Phage–bacterial contig association prediction with a convolutional neural network” at ISMB 2022 which was also published recently in Bioinformatics. (See article here).
Dr. Yang Lu, a former student from the Sun Lab, accepted a tenure track assistant professor position from the Cheriton School of Computer Science, University of Waterloo, Canada.
QCB Book Club
Featuring Nonlinear Dynamics and Chaos by Steven Strogatz, this book club will convene once a month to discuss established paradigms and analytic techniques in mathematical modeling, and showcase recent development in methods and applications in addressing key biological questions. Next meeting, Thursday August 11, 2022 11 a.m.-11:45 a.m., RRI 421 and zoom. All are welcome!On June 9, 2022, the Dynamics Club welcomed their first external speaker, Dr. Katherine Sheu from UCLA.On June 16, 2022 the club welcomed Mr. Yuhang Fan from Stanford University.
Dr. Simon Levin, Professor, Princeton University
"COVID-19 and Challenges to the Classical Theory of Epidemics."
September 1, 2022, 2-3 pm, RRI 101/ Virtual
Dr. Michael Zhang, Professor, University of Texas at Dallas
"Single Cell Metabolomics Technology for Dissecting Tissue Microenvironment."
September 8, 2022, 2-3 pm, RRI 101
Dr. Wei Li, Assistant Professor, University of California, Los Angeles
"Computational Biomedicine: Cancer Liquid Biopsy, Alternative Polyadenylation Therapy, and a Large-sample Crisis in anti-PD-1 Trials."
September 15, 2022, 2-3 pm, RRI 101
Postdoctoral Positions Open
The Edge Lab is accepting postdoctoral applications in evolutionary genetics (https://edgepopgen.github.io/edgelab/vacancies) Postdoctoral positions in 3D genome biology are open in the Fudenberg Research Group (https://fudenberg.team) The Katritch Lab is accepting postdoctoral applications in structural bioinformatics and drug discovery (https://katritch.usc.edu/people.html https://katritch.usc.edu/people.html)
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