e-Newsletter Volume 3 Issue 5 | August 2023
Department of Quantitative and Computational Biology
Welcome back everyone to the academic year 2023-2024!
I hope you all had both a relaxing and productive summer. I was able to submit several research papers and also spent time and travel with my family. I missed the busy campus and of course our QCB newsletters.
Last spring ended strong for QCB – Professor Helen Berman was elected to the National Academy of Sciences. She is the 4th QCB core faculty member in the NAS and the first female faculty member in the Dornsife College who was elected to the Academy. Dean Miller will honor Professor Berman with a reception in two weeks.
The QCB faculty further expanded – Professor Andrew McMahon of the Keck School of Medicine and Professor Peter Yingxiao Wang of the Viterbi School of Engineering joined the QCB joint faculty. Our faculty spans over five different schools highlighting the role of QCB as nexus for computational biology across the entire university.
I wish you all a successful semester and I am looking forward to seeing you all on campus.
Remo Rohs, Ph.D.
QCB Department Chair
QCB Faculty
Dr. Helen Berman, a core faculty member of the Department Of Quantitative and Computational Biology, was elected to the National Academy of Sciences. This achievement was covered by a Dornsife News Story, which can be found here.
Dr. Michael Waterman received the William Benter Prize in Applied Mathematics at the International Conference in Applied Mathematics held in City University of Hongkong, China. A special workshop on computational biology and bioinformatics organized by Dr. Fengzhu Sun and Dr. Xuegong Zhang at Tsinghua University, China, was held at the conference.
Dr. Fengzhu Sun attended the Joint Statistics Meeting (JSM) held in Toronto, Canada. He was officially recognized as an Institute of Mathematical Statistics (IMS) Fellow for “outstanding developments and applications of probability and statistics methods to central biological and biomedical problems, in particular, protein interaction networks and metagenomics”.
Dr. Matt Pennell was awarded an NIH R35 Early Stage Investigator MIRA award from the National Institute of General Medical Sciences for his project entitled “Leveraging phylogenetic approaches to investigate the evolution of gene expression”. Read more about it here.
Dr. Seva Katritch, in collaboration with other PIs from Wash.U and U.Florida, was awarded a new NIH R01 grant titled “Targeting the allosteric sodium site with novel probes for delta opioid receptor”. The project builds upon long-term studies of GPCR functional mechanisms and bitopic ligand design in the Katritch lab. Read about the project here.
Dr. Steve Kay, in collaboration with Dr. Seva Katritch, was awarded a new grant “Targeting circadian clock proteins for novel therapeutics to treat Acute Myeloid Leukemia” from the Ming Hsieh Institute (MHI) for Research on Engineering Medicine for Cancer.
Dr. Stacey Finley was featured in an interview published by the National Cancer Institute. The interview discussed her work in building computational models to better understand cancer, and her goals to identify new drug targets for the disease by exploiting its metabolic dependencies. Read more about the interview here.
QCB Publications
Dr. Mark Chaisson (left) and two of his graduate students, Dr. Jingwen Ren (middle) and Bida Gu (right), published a new method called 'vamos' for the variable-number tandem repeats annotation using efficient motif sets in Genome Biology. Read about their work here.
Dr. Rex Jiang (left), a postdoc in the Pennell (right) Lab, published a paper, “On the Decoupling of Evolutionary Changes in mRNA and Protein Levels”, in the journal Molecular Biology and Evolution. The paper which can be found here, used mathematical modeling to investigate how evolutionary processes shape the relationship between mRNA and protein abundances.
CBB Student Xiaojun Wu (left) of the MacLean (right) Lab published a paper on inferring the dynamics of single-cell responses and mapping them to gene expression states in the Journal of the Royal Society Interface. Read more about Xiaojun's work here.
Dr. Jazlyn Mooney’s work on uncovering the number of African and European genealogical ancestors of an admixed African American individual born between 1960-1965 was published as a cover story in Genetics! This innovative model revealed new important genealogical details about African ancestors of Americans since there are largely no records available to get this information. The article (found here) was also featured by GSA's Genes to Genomes Blog, Axios, Stanford, and USC.
A recent PNAS paper led by Dr. Tsu-Pei Chiu (left), a postdoc in the Rohs (right) Lab, was featured in a Dornsife News article, AI Sheds New Light on the 'Code of Life'. The article cites Dr. Soheil Shams, CIO Emeritus of Bionano Genomics, “The proposed approach is offering a much more complete representation of the DNA sequence that should enable similarly more complete discoveries in interpretation of genetic variants as well as cancer research.”
The Rohs (middle) Lab collaborated on a paper with Dr. Peter Qin (left), Professor and Chair of the Department of Chemistry, in Biochemistry on how CRISPR-Cas9 activities are tuned by target duplex stability in the gene editing complex. This paper combines experimental studies with machine learning approaches. The computational work was performed by Dr. Brendon Cooper (right), a former postdoc in the Rohs Lab.
Dr. Brendon Cooper (left), a former postdoc in the Rohs Lab, published a paper in Nucleic Acids Research (find it here) that uses experimental and computational machine learning approaches to reveal the DNA binding specificities of all four Forkhead transcription factors in yeast. This was a collaboration between the Rohs (middle) Lab and Dr. Oscar Aparicio's (right) lab in the Department of Biological Sciences.
Dr. Steve Kay (left) and PhD Student Yuanzhong Pan (right) published a review article with Frontiers in Oncology about E-box binding transcription factors in cancer, and the potential for E-box transcription factors (EBTFs) to become targeted as a regulatory network in disease treatment. Read more about their work here.
Dr. Steven Gazal recently published an article in Science, about utilizing our knowledge of mammalian evolution to connect genetic variation to disease risk. Read more about his work here.
QBIO Undergraduate Students
Last week, we welcomed our new and returning Quantitative Biology undergraduate students via a series of Ice Cream Social events. Students were able to reconnect with friends and network among themselves, staff, and faculty members, as they adjust to the new academic year!
Calling all QBIO undergraduate students! Are you interested in networking with QBIO alumni, QCB Faculty, and getting more involved with the Quantitative Biology Community at USC? Join our new Quantitative Biology Association (QBA) for undergraduate students, as we explore the fields of bioinformatics, computational methods, and strengthen our community of QBIO students in LA. Fill out this form to join our organization: https://forms.gle/Wf6pnqKdY4phAZh36 -- our first meeting will (tentatively) take place on September 12th @ 6pm (more information to come).
QCB Graduate Students
The PhD Program in Computational Biology and Bioinformatics welcomed their new class to campus and the department with a two-day orientation and a dinner hosted by Dr. Remo Rohs.
The students of the CBB graduate program elected a new student government this summer and we are happy to introduce Katalin Voss (left), Shirin Nataneli (middle), and Ashley Kasem (right) as the newly elected president, vice president, and treasurer, respectively. The Computational Biology and Bioinformatics Graduate Student Association (CBSA) had their first meeting and discussed various social and academic events for the Fall 2023 semester. Among these will be field trips to the Natural History Museum, board-game nights, craft nights, and biological nature walks. They’ve also planned to create a seminar series with computational biologists from industry, to offer networking opportunities and insight into new-cutting edge technologies in the field. In addition to these plans, they have recently introduced a mentoring program for incoming first-year students. This offers our first years a chance to be paired with continuing CBB students, who can support them to thrive in our program. CBSA is hoping to promote the exchange of scientific ideas and create a vibrant community for everyone.
QCB Postdocs
Dr. Antonina Nazarova, a postdoc in the Katritch lab, received the Wiley Computers in Chemistry Outstanding Postdoc Award at the American Chemical Society Meeting, recognizing her work in the development and application of the next generation giga-scale chemical space screening. Read about her accomplishment here.
Upcoming Events
September 1st @ 5pm (RRI 101): QBIO Mentorship Meet & Greet Social for undergraduate students. RSVP link: https://forms.gle/13MBnQrMBwi61oQN9
September 7th @ 2pm (RRI 101): Seminar from Christina Leslie, Memorial Sloan Kettering Cancer Center.
September 14th @ 2pm (RRI 101): Seminar from Arbel Harpak, University of Texas at Austin.
September 21st @ 2pm (RRI 101): Seminar from Elaine Ostrander, National Institute of Health.
September 28th @ 2pm (RRI 101): Seminar from Xiaotu Ma, St. Jude Children's Research Hospital.
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