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February 2024 QCB Newsletter

e-Newsletter Volume 4 Issue 2 | February 2024

Personal Remarks by Dr. Remo Rohs

This month began with the shock of the untimely passing of our Divisional Dean for the Life Sciences, Dr. Jan Amend. I will miss Jan, his appreciation of quality and openness to innovative ideas. Jan played a key role in establishing Quantitative and Computational Biology as department.

The new School of Advanced Computing and its inaugural Director, Dr. Gaurav Sukhatme, have been announced. This university has only three departments with “computing” in their name – Computer Science, Electrical and Computer Engineering, and QCB. I am looking forward to an exciting future for Computing at USC.

In a few days, the students admitted to our Ph.D. Program in Computational Biology and Bioinformatics will visit USC. Exceptionally strong students applied to our program in record numbers this year. I want to thank Dr. Liang Chen for leading the admissions process and Christian Robbie for making it all possible.

Remo Rohs, Ph.D.

Department Chair

Tracey and Michael Waterman have endowed the Michael S. Waterman Award in Quantitative and Computational Biology. The QCB Department thanks Tracey and Mike for their generosity to make this new endowment possible. This endowment ensures that the funds will exist in perpetuity. 

QCB Publications

Dr. Jinsen Li, a postdoc in the Rohs lab, published as lead author a new paper in Nature Communications that introduces an innovative AI method for the prediction of DNA structure. Dr. Tsu-Pei Chiu, Visiting Assistant Professor (Teaching) also contributed to the study. The paper can be read here.

Dr. Geoffrey Fudenberg published a paper “Bioframe: Operations on genomic intervals in pandas dataframes” in Bioinformatics. The paper, co-authored with the Open2C group, enables genomic interval analysis in Python/Pandas. Read more here.

Dr. Steve Kay’s new study “The interplay between the circadian clock and abiotic stress responses mediated by ABF3 and CCA1/LHY” was published in Proceedings of the National Academy of Sciences of the United States of America. The study discovered a biological circuit that protects plants from extreme conditions. Read the paper here, and the USC press coverage here.

Dr. Mark Chaisson, together with an international team of researchers from the Morgridge Institute, NOAA, and USC have published a high-quality genome assembly of the Pacific blue whale in the journal Molecular Biology and Evolution.  The comparative analysis of contrasting genomes of the blue whale as the largest cetacean and vaquita as the smallest one shows that the blue whale genome contains significantly more duplicated genes, revealing candidate genes that could influence body size. Read the paper here.

QCB Faculty

QCB joint faculty member Dr. Scott Fraser was appointed Vice President of the Chan Zuckerberg Initiative (CZI). In this role, Dr. Fraser will be responsible for the CZI science grants programs. Read more about Dr. Fraser's new role here.

QCB Graduate Students

QCB student Vardges Tserunyan from Prof. Stacey Finley lab successfully defended his Ph.D. thesis on January 31, 2024! Congratulations, Vardges!

QBIO Undergraduate Students

This semester's QBIO 105 course, taught by Drs. Peter Calabrese and Remo Rohs, is almost entirely devoted to AI in the life sciences. This includes guest lectures from industry. This month, Dr. Matt Michelson, the CEO of Readout AI and a graduate of the Viterbi School, shared his experience in starting several companies using computer science and machine learning for making a difference in health care.

Upcoming Events

QCB Departmental Seminars

March 7th: John Marko, Northwestern University 

March 21st: Jianhua Xing, University of Pittsburgh

March 28th: Hernan Garcia, UC Berkeley

Professor (Research) of Quantitative and Computational Biology, Dr. Helen Berman, is organizing VIZBI 2024, a computational biology conference on the visualization of biological data. Dr. Remo Rohs is one of the invited speakers.

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