e-Newsletter Volume 4 Issue 9 | November & December 2024
Personal Remarks by Dr. Remo Rohs
As the year 2024 is ending, I want to thank everyone in the department and friends and supporters of the department. I want to give a special shout out to the staff who is the glue in the department, keeping it all together.
I want to commend our hard-working and resilient first-year Ph.D. students. Seeing this year’s cohort in the building contributed much to my happiness. I also want to thank my own students and lab members who excelled in productivity and impactful publications.
I wish everyone Happy Holidays and a successful, healthy, and Happy New Year!
Remo Rohs, Ph.D.
Department Chair
QCB Faculty
Drs. Remo Rohs and Fengzhu Sun were elected as Fellows of the Asia-Pacific Artificial Intelligence Association (AAIA). The AAIA is an organization founded by scholars worldwide with a focus on advancing artificial intelligence. Together with Drs. Arieh Warshel and Michael Waterman, QCB is now home to four AAIA Fellows.
The QCB Department came together to celebrate Dr. Naomi Levine's promotion to Full Professor of Biological Sciences and Quantitative and Computational Biology and to say Farewell to Dr. Matt Pennell who accepted a tenured appointment as Associate Professor of Computational Biology at Cornell University in Ithaca, NY. Congratulations, Naomi! Best wishes, Matt, and thanks for everything you did for QCB!
Three QCB faculty members, Drs. Seva Katritch, Arthur Toga, and Paul Thomas, were recognized as 2024 Clarivate Highly Cited Researchers. The list identifies scientists and social scientists who have demonstrated significant influence through publication of multiple highly cited papers during the last decade. Full list can be found here.
Dr. Stacey Finley received a faculty chair from Dean Yannis Yortsos of the Viterbi School of Engineering at her recent installation as the Nichole A. and Thuan Q. Pham Professor, celebrated here by her department chairs, Dr. Remo Rohs (QCB) and Dr. Peter Wang (BME, also QCB joint faculty).
Dr. Remo Rohs was included in a feature story highlighting 23 key players involved in the making of USC's newest school, the School of Advanced Computing. He was quoted “I believe that all fields of biology will become increasingly reliant on computers, databases, mathematics and statistics. That’s why I call our department ‘a biology department of the 21st century.’ And from a different perspective: ‘an engineering+ department where the + encompasses biology and medicine.’" Read the article here.
Drs. Remo Rohs (PI) and Steve Kay (co-PI) received an SBIR/STTR planning grant, "AI-driven discovery of novel BMAL1 modulators for the treatment of Circadian dysregulation and cancer", from the Office of Research and Innovation. A goal of this award is the commercialization of the AI-based design of drug-like molecules and their validation. This work is led by Jesse Weller, a Ph.D. student in the Rohs Lab.
The Head of Machine Learning at Chemspace, a leading drug library provider, published a blog post reporting on their company's evaluation of DrugHIVE, an AI drug design method developed by Jesse Weller (left) in the Rohs Lab (right). Read the blog here.
QCB Publications
CBB Postdoc Dr. Jesse Kreger from Dr. MacLean’s lab, in collaboration with Drs. Jazlyn Mooney (QCB) and Darryl Shibata (USC Keck) published a paper in Nature Communications titled “Developmental hematopoietic stem cell variation explains clonal hematopoiesis later in life”. The theory and data analysis in the study reveals that stem cell variants are most likely present before birth, even though their effects only become apparent later in life. Please read the paper here.
QCB postdoc Dr. My Nguyen from Dr. Katritch’s lab contributed design and modeling studies to the paper “Structure-guided design of a peripherally restricted chemogenetic system” published in Cell. Read the paper here.
QBIO graduates Chenyang (Julie) Li and Tessa Ferrari from Dr. Jazlyn Mooney’s lab published a resource article titled “A Pipeline and Recommendations for Population and Individual Diagnostic SNP Selection in Non‐Model Species” in Molecular Ecology Resources. The method provides the user with marker set for individual and population identification in species of interest. Please read the paper here.
QCB postdocs Dr. Anastasiia Sadybekov and Dr. Jordy Lam from the Katritch lab contributed comprehensive modeling, docking, and MD simulations to the structure-function study of GPR6 orphan receptor in collaboration with Cherezov lab, published in Science Signaling. Read the paper here.
Dr. Raktim Mitra and Ari Cohen published, as co-first authors, in collaboration between Dr. Helen Berman and the Rohs Lab a new paper in Nucleic Acids Research about an interactive database, DNAproDB, for the structural analysis of protein-DNA complexes. Read the article here.
CBB student Katalin Voss from Dr. Pennell’s lab was lead author on a new paper “Applying phylogenetic methods for species delimitation to distinguish B-cell clonal families”, published in Frontiers in Immunology. The study shows that phylogenetics statistical techniques could be used to identify B-cells that descended from the same somatic recombination event, providing a new tool for characterizing the antibody repertoire evolution in response to an infection. Please read the paper here.
Dr. Stacey Finley published a profile of a female Black scientist and administrator combined with a personal perspective in the journal Current Biology. Read the profile "Jewel Plummer Cobb: A trailblazing life of impact" here.
CBB Graduate Students
CBB graduate Dr. Raktim Mitra was on his drive to his new home in Seattle, WA, when he received a phone call from USC that he is one of only four winners of this year's Phi Kappa Phi Student Recognition Award. He will accept this prestigious award at the university's Academic Honors Convocation in spring 2025. He receives this award for his research in the Rohs lab, about which his future advisor Nobel Laureate David Baker said: "Raktim's PhD work is very impressive". Way to go, Raktim!
Jiawei Huang from Dr. Sun’s group successfully defended his dissertation “Malignant Cell Fraction Prediction Using Deep Learning: From Point Estimate to Uncertainty Quantification” on December 10, 2024. He will join Google Inc in Spring 2025.
CBB student Walfred Ma from Dr. Chaisson’s Lab gave a talk at the American Society of Human Genetics 2024 meeting in Denver. The talk was titled "Pangenome-derived copy number variation maps with global diversity and association analysis in BioBank scale data with ctyper"
CBB student Handan Cetin from Dr. Stacey Finley’s lab, presented her research at the 2024 Annual Meeting of the Biomedical Engineering Society, held in October in Baltimore, MD. The title of the poster was “Metabolic reprogramming drives melanoma differentiation: Genome-scale modeling perspective”.
QBIO Undergraduate Students
Each semester, the Office of the Provost awards a small number of fellowships to undergraduate students doing research in their respective academic fields. These awards are given based on the quality of applicants' research proposals and quality of research. This semester, we want to congratulate Andrew Wilk (Senior, mentor: Dr. Remo Rohs) for receiving this competitive fellowship honor.
The student-led section of QBIO 490 concluded with research presentations of the student projects to the department. We thank QBIO students Wade Boohar and Mahija Mogalipuvvu for their leadership this semester and QCB joint faculty Dr. Jerry Lee for his invested mentorship and enthusiastic support of the class.
Upcoming Events
January 9th (RRI 101 @ 2pm): Seminar by Dr. Barry Honig, Columbia University
January 14th (RRI 101 @ 2pm): Seminar by Dr. Xuegong Zhang, Tsinghua University
January 16th (RRI 101 @ 2pm): Seminar by Dr. Guy Sella, Columbia University
January 23rd (RRI 101 @ 2pm): Seminar by Dr. Andre Levchenko, Yale University
January 30th (RRI 101 @ 2pm): Seminar by Dr. Kishwar Shafin, Google
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