June & July 2024 QCB Newsletter

e-Newsletter Volume 4 Issue 6 | June & July 2024

Personal Remarks by Dr. Remo Rohs

I hope that you are all enjoying your summer break, with increased research productivity or a well-deserved vacation. I also was planning a summer break for the QCB Newsletter, but the papers and news are just not taking a break and merit a combined June/July Newsletter.

I want to share that I have agreed to serve another period of three years until August 2027 as QCB department chair. This wasn’t an easy decision as I was looking forward to returning my full attention to my currently very active research group. However, I also saw the need to stabilize this department a little further, especially given the new opportunities that I see on the horizon for QCB in research and education.

I want to close with welcoming Interim Dean Dr. Moh El-Naggar to his new position and thank him for taking on this important leadership role. I am looking forward to working with him.

Remo Rohs, Ph.D.

Department Chair

QCB Faculty

Professor Michael Waterman received an Honorary Doctorate from Oregon State University as the only recipient this year. Dr. Waterman is an alumnus of OSU, currently serves on its College of Science Board of Advisers and established a scholarship at OSU. The left photo shows OSU's hooding ceremony, and the right photo shows Dr. Waterman with commencement speaker and former NFL player Steven Jackson. Read more here.

Professor Helen Berman was formally inducted into the National Academy of Sciences during their 161st Annual Meeting in Washington, DC. The photo shows Dr. Berman signing the book of NAS membership. Photo credits: National Academy of Sciences.

Dr. Remo Rohs was featured in the Dornsife Magazine Spring/Summer 2024 Health and Well-Being Issue, sharing his vision for the QCB department, the computational biology field in general, and some of his own recent research. Read his feature here.

Dr. Katritch's research on discovery of pain and drug abuse treatments was featured in the Dornsife Magazine Spring/Summer 2024 Health and Well-Being Issue. Read more here.

Additionally, Dr. Katritch and his collaborators from Washington University received a National Institute of Health grant titled “Development of PAC1 receptor antagonists for the treatment of Headache Disorders”.  The project will employ new computational tools developed in the Katritch lab to discover new medicines for migraine disorders. View the grant here.

Dr. Adam MacLean received a National Science Foundation award for his work, “Developmental IGF/growth-signaling induced influences on adult life trajectories of hematopoietic stem cell selection and function." This international collaboration with Dr. KL Rudolph (Leibniz Institute on Aging) will use genetic and dietary interventions together with computational modeling to determine how early-life signaling affects stem cells as we age, and study whether such effects can be reversed. Read more about this award here. 

QCB Publications

A recent paper published by CBB student Raktim Mitra and QBIO graduate Ari Cohen in the Rohs lab was featured on the journal cover of Nucleic Acids Research. The paper is about a new method, RNAscape, for the base pairing and tertiary interaction mapping in RNA structure. Read the paper here.

A second paper in the same issue of Nucleic Acids Research, published by postdoc Dr. Jinsen Li in the Rohs lab, introduces Deep DNAshape for DNA shape prediction considering extended k-mers. Read the paper here. The paper builds on the authors' recently published new deep learning method, published in Nature Communications.

Dr. Geoff Fudenberg’s lab had two papers published in PLoS Computational biology in collaboration with the Open2C team. The first, with contributions from QCB student Yao Xiao, "Cooltools: Enabling high-resolution Hi-C analysis in Python", enables analysis of large sparse 3D genome folding datasets in Python and through the command line (Full article here). The second paper, "Pairtools: From sequencing data to chromosome contacts", discusses a flexible suite of high-performance tools for contact extraction from large-scale sequencing data. (Full article here).

CBB Graduate Dr. Tianqi Tang and Siliangyu Cheng from Dr. Fengzhu Sun's lab published a paper titled, "DeepMicroClass sorts metagenomic contigs into prokaryotes, eukaryotes and viruses.” in NAR Genomics & Bioinformatics. The paper introduces the new a deep-learning based sequence classifier, DeepMicroClass, and describes its application to marine metagenomic datasets. Read their work here. 

CBB student Jiawei Huang and CBB Graduate Dr. Yuxuan Du from Dr. Fengzhu Sun's lab published a paper titled “DeepDecon accurately estimates cancer cell fractions in bulk RNA-seq data" in the journal Patterns. The new deep neural network model leverages single-cell gene expression information to accurately predict the fraction of cancer cells in bulk tissues. Read the paper here. 

Former postdoc Dr. Jared Sagendorf in the Rohs lab published a deep learning method that uses protein structure to predict DNA or RNA binding. The PNAbind method uses graph neural networks and structural and physicochemical protein features to determine nucleic acid binding. Other authors who contributed are CBB students Raktim Mitra and Jiawei Huang and Professor Xiaojiang Chen. Read the paper here.

Dr. Stacey Finley published the paper “Modeling the heterogeneous apoptotic response of caspase-mediated signaling in tumor cells” in the Journal of Theoretical Biology. This work provides quantitative insights for how the apoptotic signaling response can be forecasted, and precisely triggered, amongst heterogeneous cells via extracellular activation. Read her work here. 

QCB Graduate Dr. Yuxuan Du from Dr. Fengzhu Sun's lab presented a paper, "ImputeCC Enhances Integrative Hi-C-Based Metagenomic Binning Through Constrained Random-Walk-Based Imputation" at the RECOMB conference 2024, and published the paper in the selective conference proceedings. Read their work here.

Dr. Helen Berman published with colleagues a paper in Nature Methods on the "Outcomes of the EMDataResource cryo-EM ligand modeling challenge". This paper assesses the reliability and reproducibility of modeling ligands bound to protein and protein–nucleic acid complexes in cryogenic electron microscopy (cryo-EM) maps determined at near-atomic resolution. Read more here. 

Dr. Tsu-Pei Chiu and Dr. Remo Rohs contributed to a paper published in Nucleic Acids Research on "DNA sequence and chromatin differentiate sequence-specific transcription factor binding in the human malaria parasite Plasmodium falciparum". This study was a collaboration with the labs of Drs. Raluca Gordan, Shaun Mahony, and Manuel Llinas. Read the paper here.

Dr. Matt Pennell published with colleagues from other universities a paper in Current Biology, "Maternal investment evolves with larger body size and higher diversification rate in sharks and rays". In this study, the authors investigated the question of how reproductive diversity arose and whether reproductive diversification underlies species diversification. Read more here. 

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

QCB student Ram Ayyala from Dr Sergei Mangul's lab published a paper titled “Analytical code sharing practices in biomedical research” in PeerJ Computer Science. The study shows that only 10% of publications organized their code in a structured and reproducible manner, suggesting that more efforts toward open science practices are needed to ensure that biomedical research can be replicated and built upon by others. Read the paper here.

QCB Postdocs

QCB wishes farewell and best of luck to Dr. Vivian Link from the Edge lab who is moving back to Switzerland for a Bioinformatics position with a Swiss Foundation. Vivian published two first-author papers in the Edge lab, in Am. J. Hum. Genet. and iScience, and contributed to the QCB department in many ways.

QCB welcomes a new postdoc Dr. Xingchi Yan in Dr. Fudenberd's lab. Xingchi received his ScM in applied mathematics and PhD from Brown University. His research focuses on the mathematical, computational, and algorithmic aspects of biochemical and biophysical measurements.

QCB PhD Students

The QCB Department congratulates Dr. Yuxuan Du (recent Ph.D. graduate from Dr. Fengzhu Sun's lab) on starting his tenure-track faculty position as Assistant Professor in the Electrical and Computer Engineering Department at the University of Texas in San Antonio. We wish Yuxuan a great start of his faculty career.

Jianzhi Yang (top left) from Dr. Mark Chaisson’s lab, Jordy Homing Lam (top right) from Dr. Seva Katritch’s lab, Ji Youn Seo (bottom right) from Peter Kuhn's lab and Yuxiang Zhan (bottom left) from Frank Alber’s lab successfully defended their Ph.D. dissertations in the CBB Ph.D. Program. Congratulations!

When CBB students graduate with a Ph.D., it is tradition that they sign the ceiling of the student lounge with their name and date of dissertation defense. Here you see Ji Youn Seo signing the ceiling - all our graduates remain forever part of our QCB family.

Search for Graduate Student Advisor

We are still accepting qualified applications for our position of Graduate Student Services Advisor II for the CBB Program: https://usccareers.usc.edu/job/los-angeles/graduate-student-services-advisor-student-services-advisor-ii/1209/66511949840

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