e-Newsletter Volume 4 Issue 7 | August & September 2024
Personal Remarks by Dr. Remo Rohs
I am welcoming you back to the academic year 2024-25, and I welcome warmly our new QBIO undergraduate and CBB graduate students to USC and the QCB department.
I am excited to see the energy and quickly evolving friendships of the largest incoming PhD cohort (pictured below) that our department ever recruited. A huge Thank You goes to the generosity of members of the QCB Advisory Board that allowed us to recruit such a large class and pay stipends that are 10% above the university’s new stipend rate.
I also want to thank the QCB faculty for agreeing to take on important new responsibilities in the QCB ‘cabinet’ and especially Professor Liang Chen for accepting to serve as our new Department Vice Chair.
Remo Rohs, Ph.D.
Department Chair
QCB Faculty
Dr. Liang Chen accepted an appointment as Vice Chair of the Department of Quantitative and Computational Biology for the next three years. Professor Chen led graduate student recruitment in the last few years. We thank her for her very successful work as Admissions Chair, having attracted this year's large cohort of excellent students.
We spent the summer renovating several new offices for our first year graduate student cohort. We started the academic year opening the new spaces that provide 15 desks with a ribbon cutting ceremony by our newly promoted faculty members. We thank Luigi Manna for being the architect and designer of these rooms, and Alfonso D’Onofrio and Sabira Zulcic for making this improvement possible.
On the first day of classes, the QCB Department celebrated faculty promotions of the past academic year: Dr. Mark Chaisson's promotion to Associate Professor with Tenure, Dr. Stacey Finley's promotion to Full Professor, and Dr. Vsevolod 'Seva' Katritch's promotion to Full Professor. Congratulations to Mark, Stacey, and Seva on their achievements and well-deserved promotions!
Dr. Fengzhu Sun presented a one-hour plenary talk at the International Congress of Basic Sciences (ICBS) in Beijing, China, on virus identification and virus-host prediction from microbial communities. The talk is publicly available on YouTube at this link. He also gave a keynote speech on the same topic at the Bioinformatics Workshop at the University of Nebraska-Lincoln.
Dr. Fengzhu Sun was also honored for his recent election as Fellow of the International Society for Computational Biology with a symposium of his former students, postdocs, and mentees in Bejing, China.
QCB Publications
Raktim Mitra as lead author from the Rohs lab published an article in Nature Methods on the new AI method DeepPBS that allows the prediction of protein-DNA binding specificity from experimental or AlphaFold protein structures. Read the paper here, and check out the USC Press Release here.
Jesse Weller as lead author from the Rohs lab published a paper in the J. Chem. Inf. Model. on the new AI method DrugHIVE that enables the design of novel chemical compounds from experimental or AlphaFold protein structures of drug receptors. Jesse also designed a journal cover highlighting this paper. Read the paper here.
Dallace Francis from Dr. Fengzhu Sun’s group published a paper “A comparative analysis of mutual information methods for pairwise relationship detection in metagenomic data” in BMC Bioinformatics. Read the paper here.
QCB student Neel Tangella from Dr. Stacey Finley’s lab published a paper “Integrating mechanism-based T cell phenotypes into a model of tumor-immune cell interactions.” in APL Bioengineering. The study introduces a novel agent-based model of the tumor microenvironment capable of providing a mechanistic understanding of cancer evolution, which can be used to study targeted immunotherapeutic strategies. You can read the paper here.
Dr. Finley also published a paper “Modeling the heterogeneous apoptotic response of caspase-mediated signaling in tumor cells" in the Journal of Theoretical Biology. The paper provides quantitative insights for how the apoptotic signaling response can be forecasted, and precisely triggered, amongst heterogeneous cells via extracellular activation. Read the paper here.
Dr. Adam MacLean published a commentary “Hematopoietic stem cell aging by the niche” in Blood with Prof. K.L. Rudolph (Leibniz Institute on Aging, Jena, Germany). They discuss new work that sheds light on the factors that cause aging to occur in hematopoietic stem cells. Read more here.
Dr. Serghei Mangul, a joint QCB faculty, published a Perspective article in Cell titled “The evolution of computational research in a data-centric world”. The paper discusses the central role of computational biology in the life sciences and demonstrates that computational biologists now take the leadership role in biomedical research projects. Read the article here.
Dr. Christoph Haselwandter, a joint QCB faculty, together with the Scheuring Lab (Weill Cornell Medicine) published a paper in Nature Structural & Molecular Biology titled “The cyanobacterial protein VIPP1 forms ESCRT-III-like structures on lipid bilayers”. Read more here.
QCB joint faculty Dr. Steven Gazal, with contributions from joint faculty Dr. Nicholas Mancuso, published a paper in the American Journal of Human Genetics that found that genes with differential expression across ancestries are enriched in ancestry-specific disease effects by gene-by-environment interactions. Read the paper here.
Joint faculty member Dr. Laura Melissa Guzman led a study on the impact of pesticide use on wild bee distributions across the United States, which was recently published in Nature Sustainability. Read the paper here. The paper was also featured in a USC Dornsife news story, which you can read here.
Joint faculty member Dr. Andrei Irimia led three recent publications: “Neuroanatomical and clinical factors predicting future cognitive impairment” in Geroscience, “Increases in regional brain volume across two native South American male populations” in Geroscience, and “Identification and Connectomic Profiling of Concussion Using Bayesian Machine Learning” in the Journal of Neurotrauma.
Joint faculty member Dr. Andrew McMahon led a publication titled “Comparative single-cell analyses identify shared and divergent features of human and mouse kidney development” in Developmental Cell. Read more here.
QCB Postdocs
A warm welcome (back) to Jordy Homing Lam, who, after successfully obtaining his PhD degree at QCB has returned to Dr. Katritch’s lab as a Croucher Foundation postdoctoral fellow.
CBB Graduate & QBIO Undergraduate Students
USC Dornsife published a news article about QBIO student Brandon Ye's recent selection as Barry Goldwater Scholar. Brandon is USC's only Goldwater Scholar this year. Brandon is the President of the Quantitative Biology Association (QBA) and does research in Dr. Peter Kuhn's laboratory and CSI Cancer institute. Read the news article here. Congrats, Brandon!
The first ever QBIO student Nicholas Markarian BS (QBIO)'20 and former Rohs lab member, now an MD/PhD student at Caltech and the USC Keck School of Medicine was awarded a highly selective F30 fellowship from the NIH for his doctoral studies. Congrats, Nick!
The QCB faculty and students thank the Computational Biology Graduate Student Association's leadership and especially its President for the academic year 2023-24, Katalin Voss, for their contributions to the CBB PhD Program and QCB Department. The officers of the CBB student government have stepped down, and we encourage other students and cohorts to consider taking on this important position. Please email Kat if you are interested in stepping up to fill this role.
Joint QCB faculty Dr. Jerry Lee from the Ellison Institute of Technology talks to the QBIO 490 research class.
Upcoming QCB Events
Seminar Schedule
September 5th: Dr. Alison Feder, University of Washington
September 12th: Dr. Luca Pinello, Harvard University
September 19th: Dr. Adam Siepel, Cold Spring Harbor Laboratory
September 26th: Dr. Ritambhara Singh, Brown University
October 3rd: Dr. Shamil Sunyaev, Harvard Medical School and Brigham and Women's Hospital
QCB Departmental Retreat @ Ventura Beach, November 10th - 11th, 2024
Copyright © 2024 Department of Quantitative and Computational Biology, University of Southern California. All rights reserved.
Our mailing address is:
1050 Childs Way, RRI 201, Los Angeles, CA 90089-2019
Comments