April 2024 QCB Newsletter

e-Newsletter Volume 4 Issue 4 | April 2024

Personal Remarks by Dr. Remo Rohs

With the April Newsletter, I want to welcome our new Divisional Dean for the Life Sciences, Dr. Ian Ehrenreich, who has already moved his first mountains for QCB. I am really looking forward to working with Ian. I want to also thank the Divisional Dean for the Physical Sciences and Mathematics, Dr. Moh El-Naggar, for his availability and support of QCB in the interim.

This year, QCB had a strong year in graduate recruiting. We were able to triple last year’s PhD class for this year and recruited exceptionally strong students. I want to thank Dr. Liang Chen who led the recruitment effort. A huge thank you goes to Dr. Andrew Viterbi whose endowment of our Ph.D. program made the strong class size possible.

It is also the season of awards. I am proud of all our students who are honored through different awards – QBIO major Brandon Ye receives the only Barry Goldwater Scholarship this year at USC. Yuxuan Du receives the CAMS Prize and the Waterman Award, Jordy Lam receives an ACS and the Waterman Award, and Raktim Mitra also receives the Waterman Award.

Remo Rohs, Ph.D.

Department Chair

QCB Faculty

Dr. Paul K. Newton, professor of aerospace, mechanical engineering, mathematics and QCB, was named a Guggenheim Fellow for using game theory to study and develop cancer evolution models. Guggenheim Fellowships are awarded to a distinguished and diverse group of culture-creators working across 52 disciplines including Artists, Scholars, Photographers, Novelists, Essayists, Poets, Historians, Choreographers, Environmentalists, and Data Scientists, selected on the basis of career achievement and exceptional promise. Read more here.

Dr. Serghei Mangul, assistant professor of clinical pharmacy and QCB, was selected as a Fulbright U.S. Scholar for 2024-25 for Moldova. Fulbright Fellowships are prestigious and competitive awards that provide unique opportunities for scholars to teach and conduct research abroad. Fulbright scholars also play a critical role in U.S. public diplomacy, establishing long-term relationships between people and nations.

Visiting Assistant Professor (Teaching), Dr. Tsu-Pei Chiu finished his first semester teaching. Professor Chiu taught two classes with 34 students this semester and developed a new class on AI and Machine Learning in Biology and Medicine.

QCB Publications

Jordy Homing Lam (Katritch lab), in collaboration with Dr. Aiichiro Nakano, was the first-author on the paper “Scalable computation of anisotropic vibrations for large macromolecular assemblies” in Nature Communications. The study introduces INCHING, the first vibration mode analysis algorithm designed to work on GPUs with >250 acceleration and scalability to >20M atoms. The work has many potential applications, e.g. capturing dynamics in cryoEM/cryoET 3D reconstructions. Read the paper here.

PhD candidate Raktim Mitra and QBIO graduate Ari Cohen in the Rohs lab published a co-first author paper in Nucleic Acids Research in which they propose a new method for the mapping and visualization of RNA structure. Read their paper here.

Undergraduate QCB student and first author Jordan Cahoon and Charleston Chiang (Keck and QCB) published a paper titled “Imputation accuracy across global human populations” in the American Journal of Human Genetics. Two former QBIO students are co-authors. The study identifies continuing disparity in imputation accuracy for diverse global populations, stressing the importance of improving inclusion of diverse reference individuals to promote equity within genetics research. Read more here.

PhD candidate Bida Gu and Dr. Mark Chaisson contributed to a paper published in Nature Biotechnology titled “Analysis and benchmarking of small and large genomic variants across tandem repeats”. Read more here.

Dr. Anastasiia Sadybekov (Katritch lab) co-first authored a paper titled “Virtual Screening of a Chemically Diverse Superscaffold Library Enables Ligand Discovery for a Key GPCR Target” in ACS Chemical Biology. This is a study in collaboration with Fokin Lab (CHEM) showing how a single super scaffold can dramatically expand on-demand virtual screening space and yield novel lead compounds. Read more here.

A paper titled “Packaging and containerization of computational methods” from Dr. Mangul's lab was published in Nature Protocols, with a contribution from QCB PhD student Ram Ayyala. The review compares packaging and containerization platforms, evaluating features and proposing principles for sustainable distribution to strengthen reproducibility in biomedical research. Read this paper here.

Dr. Michael Waterman has published a new memoir, “Outside Passages” which contains chapters about Los Alamos Scientific Laboratory and USC (including brief discussions of aspects of QCB and QBIO). Read more here.

QBIO Undergraduate Students

The QBIO 490 Directed Research course by Wade Boohar, Kayla Xu, and Mahija Mogalipuvvu, with instructional oversight by Professors Jerry Lee, Peter Calabrese, and Remo Rohs, met on April 26, 2024, for their final presentations. Thanks to the faculty panel for the finals, Professors Jazlyn Mooney and Peter Calabrese.

Several QBIO students, some of whom will be graduating this May, are pictured here on the last day of school -- looking forward to our departmental commencement and reception!

External Accolades and Achievements

Brandon Ye (QBIO student with research in CSI Cancer) was selected for a 2024 Barry Goldwater Scholarship, one of the oldest and most prestigious national scholarships in the natural sciences, engineering, and mathematics in the United States, which seeks to identify, encourage, and financially support college sophomores and juniors who show exceptional promise of becoming this Nation’s next generation of research leaders in these fields.

Dr. Yuxuan Du (Sun lab) was awarded a Center for Applied Mathematical Sciences (CAMS) Prize for his doctoral research by CAMS Director, Professor Susan Friedlander at the award ceremony in the USC Mathematics Department.

Jordy Homing Lam’s (Katritch lab) application was selected as a winner for the Chemical Computing Group Excellence Award, to be presented at the Fall 2024 ACS national meeting.

Andrew Wilk (QBIO student) received a summer 2024 Provost Fellowship for research in the Rohs Lab on using machine learning and AI to infer which protein family binds to genomic target sites.

QCB Departmental Awards

2023-2024 Recipients of the Michael S. Waterman Award in Quantitative and Computational Biology (left to right):

Yuxuan Du (Mentor: Professor Fengzhu Sun)

Ho Ming (Jordy) Lam (Mentor: Professor Vsevolod Katritch)

Raktim Mitra (Mentor: Professor Remo Rohs)

2023-2024 Recipients of the QCB Award for Excellence in Teaching in Quantitative and Computational Biology (left to right):

Dallace Francis (Mentor: Professor Fengzhu Sun)

Yibei Jiang, PhD (Mentor: Professor Remo Rohs)

2023-2024 Recipient of the John Petruska Memorial Award in Quantitative Biology:

Nicole Black, QBIO

2023-2024 Recipients of the USC QCB Google Alumni Award in Quantitative Biology (counterclockwise from top):

Wade Boohar, Jordan L. Cahoon, Karen Lee, Andrew Wilk, Brandon Ye

Upcoming Events

Graduation Ceremonies

Ph.D. Hooding Ceremony: May 8th, Allyson Felix Field @11am

Dornsife Commencement (including QCB): May 10th, Allyson Felix Field @11am

QCB Department Reception: May 10th, Michelson Center & Irani Hall (RRI) Courtyard @1pm

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