April 2022 QCB Newsletter



Department of Quantitative and Computational Biology

Spring is the time when undergraduate students decide where they go to graduate or medical school. Tenure and promotion decisions are announced, and the campus prepares for commencement. It is a busy time - and it is not any different for the QCB Department.


Our Quantitative Biology (QBIO) undergraduate students received offers from many of the very best places in the country, both for graduate and medical school. These included, among others, MIT, Northwestern University, Princeton University, UC Berkeley, UCLA, UC Santa Cruz, UCSD, UCSF, University of Washington, and USC.


In our own recruitment to the Computational Biology and Bioinformatics (CBB) PhD Program, we were able get a class that is 50% larger than the number of slots given to us. This was important to support our new faculty colleagues. We were able to recruit additional students and offer competitive stipends that are comparable with peer institutions and programs. This is possible only thanks to the generosity of our advisory board members and key supporters. Thanks!


Remo Rohs, Ph.D.

QCB Department Chair


Tenure for Dr. Naomi Levine

Naomi Levine was promoted to Associate Professor of Biological Sciences, Quantitative and Computational Biology, and Earth Sciences. Congratulations, Naomi!


QBIO Undergraduate Students

QBIO Senior, David Wen, received the prestigious NSF Graduate Research Fellowship Program award. Congratulations and way to go, David! This Fall, David will join UCSF for his graduate studies. We will for sure follow your path in science. Keep in touch with your QBIO family!


QBIO student, Dottie Yu, was a co-author on a paper published in ACS Synthetic Biology entitled "Parameterized Computational Framework for the Description and Design of Genetic Circuits of Morphogenesis Based on Contact-Dependent Signaling and Changes in Cell-Cell Adhesion ". (See paper here)


The QBIO 490 "Directed Research" class has been meeting this semester weekly and they have been working together and learning from each other. The students are peer mentored in class by fellow QBIO students.


QCB Faculty and CBB Graduate Students

CBB Student, Xin Bai, from Dr. Fengzhu Sun’s group, published a paper “MLR-OOD: a Markov chain based Likelihood Ratio method for Out-Of-Distribution detection of genomic sequences” in the Journal of Molecular Biology (See paper here).


Dr. Doc Edge co-edited a special issue of Philosophical Transactions of the Royal Society, Series B entitled "Celebrating 50 years since Lewontin’s apportionment of human diversity" (See review here). The issue celebrates the 50th anniversary of a landmark work in human population genetics, which established that the proportion of genetic variation between continental populations of humans is small compared with the within-population diversity.


CBB student, Caoqi Fan, published a paper in American Journal of Human Genetics with QCB joint faculty Drs. Nicolas Mancuso and Charleston Chiang looking at a genealogical estimate of genetic relationships (See paper here).


Dr. Peter Calabrese wrote an article in the Journal of Computational Biology about the Quantitative Biology (QBIO) major on how it started, how it has evolved, where graduates have gone to continue their education, and about the QBIO community (See paper here).


Clinical and Translational Medicine published an editorial by Drs. Nazarova and Katritch on computational approaches to drug discovery (See paper here).


Dr. Naomi Levine published a paper in Nature Communications about how Micro-scale microbial community dynamics can substantially alter the fate of sinking particulates in the ocean thus playing a key role in setting the vertical flux of particulate carbon in the ocean (See paper here as well as additional press here and from Dornsife News here).


PhD Hooding Ceremony 2022

The Ph.D. students of the Computational Biology and Bioinformatics (CBB) program will be hooded at the Dornsife Ph.D. Hooding Ceremony on Wednesday, May 11, 2022, Cromwell Field at 11 a.m. A reception will be held at Cromwell Field immediately following the Hooding Ceremony. Please see the Dornsife Ph.D. Hooding Ceremony web page for more information (Click here).


QBIO and CBB Commencement 2022

Commencement will be held on Friday, May 13, 2022. The Department of Quantitative and Computational Biology (QCB) will celebrate the graduates in Quantitative Biology and Computational Biology and Bioinformatics as part of the Dornsife Group 1 Ceremony which will be held at 11 a.m. on Cromwell Field. We will hold our QCB Departmental celebration and reception in the courtyard between Michelson Hall and Ray R. Irani Hall immediately following the ceremony. Please see the Dornsife Commencement web page for more information. (Click here)


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 April 21, 2022 11 a.m.-11:45 a.m., RRI 421 and zoom. All are welcome!


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://jobrxiv.org/job/university-of-southern-california-dept-of-quantitative-computational-biology-27778-computational-structural-biology-and-computer-aided-drug-discovery-at-usc/)


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