e-Newsletter Volume 4 Issue 8 | October 2024
Personal Remarks by Dr. Remo Rohs
Computational Biology is a soaring field. The Nobel Prize in Chemistry 2024 has been awarded to pioneers of computational biology, for protein design and structure prediction. One of the QCB department’s core faculty members, Dr. Helen Berman, was acknowledged by one of the laureates, Dr. John Jumper, in his Nobel Prize press conference for her pivotal contributions that made AlphaFold possible.
I am excited to announce two keynotes of our upcoming QCB retreat. Our opening keynote speaker is Dr. Paul Thompson, the Inaugural Director of the AI in Medicine Collaboratory at the USC Keck School of Medicine. He will speak about ‘ENIGMA’s global studies of brain diseases using imaging, genomics and AI’. Our evening keynote speaker is Dr. Anna Krylov, the USC Associates Chair in Natural Sciences. She will speak about ‘Merit- based science is effective and fair: How such a banal idea has become controversial’.
Remo Rohs, Ph.D.
Department Chair
QCB Staff Welcome
The QCB Department welcomes Ms. Dominique Andrade as Student Services Advisor II for our CBB Ph.D. program and two Master's programs. Coming from an academic advisor position for undergraduate students in USC Dornsife, Ms. Andrade joins us following an extensive search led by Dr. Rokas Oginskis. Graduate students can reach her at dominique.andrade@usc.edu. Welcome, Dominique!
QCB Faculty
QCB faculty Dr. Helen Berman’s key contributions to structural biology that enabled the recent Nobel Prize-winning breakthroughs in AI prediction of protein structures have been acknowledged by this year's Nobel laureates in Chemistry. Dr. Berman co-founded the Protein Data Bank (PDB), a database for protein structures, which served as foundation for AlphaFold. This contribution is highlighted by Nature and Dornsife News.
Dr. Steve Kay was appointed as Acting Director of the Zilkha Neurogenetic Institute and Acting Department Chair of the Department of Physiology & Neuroscience at the Keck School of Medicine of USC.
Dr. Mark Chaisson received new funding from the National Institutes of Health for the project “Identifying and Characterizing the Full Spectrum of Haplotype-resolved Structural Variation in Human Genomes”. Dr. Chaisson will be studying the relationship between genetic variation and genome structure.
Dr. Seva Katritch received a new Maximizing Investigators' Research Award (MIRA) for “Computational approaches to discover ligands with new chemotypes and functional properties” from the National Institute of General Medical Sciences.
QCB Publications
Dr. Jazlyn Mooney published a paper in PNAS titled “Unraveling the genomic diversity and admixture history of captive tigers in the United States”. The study reveals that the captive tiger population contains ancestry from all six extant wild tiger subspecies, similar to what is observed in wild populations. It establishes a reference panel of tiger ancestry assessment using ultralow coverage genomic data, which can be used cost-effectively to support monitoring and management decisions. Read the paper here, and highlights in the NY Times, Science, and USC Today.
QCB research scientist Dr. Joshua Schraiber (left) and faculty members Drs. Doc Edge (right) and Matthew Pennell (bottom) published a paper in PLoS Biology titled "Unifying approaches from statistical genetics and phylogenetics for mapping phenotypes in structured populations." This work brings together two traditions of applied statistical methods that developed separately, paving the way for new techniques for analyzing genetic data, including principled methods for understanding genetic variation within and between species simultaneously." Read the paper here.
CBB students Yuxuan Du (left) and Wenxuan Zuo (right) from Dr. Fengzhu Sun's (bottom) lab published a paper “Imputing Metagenomic Hi-C Contacts Facilitates the Integrative Contig Binning Through Constrained Random Walk with Restart” in the Journal of Computational Biology.” The new approach, ImputeCC, was applied to a genus-level analysis of the sheep gut microbiota, demonstrating its capability to recover key species from dominant genera and identify previously unknown genera. Read the paper here.
Dr. Liang Chen led the publication of a paper titled “Deciphering single-cell gene expression variability and its role in drug response” in Human Molecular Genetics. The study, performed with computer science student Sizhe (Steven) Liu explores the impact of cross-cell and cross-individual pharmacogene expression variation on drug efficacy. Read the paper here.
Dr. Steve Kay led a study “The clock-associated LUX ARRHYTHMO regulates high-affinity nitrate transport in Arabidopsis roots”, published in The Plant journal : for cell and molecular biology. This study uncovers a molecular pathway connecting the root nitrate uptake and circadian clock, with potential agro-chronobiological applications. Read the paper here.
Dr. Antonina Nazarova (left) and Dr. Jordy Homing Lam (right) from Katritch (bottom) lab contributed to the study “A bitopic agonist bound to the dopamine 3 receptor reveals a selectivity site”, published in Nature Communications. Structure-based computational analysis in this study reveals the mechanism of interaction for the subtype-selective bitopic ligand designed by Katritch lab. Read the paper here.
Joint faculty member Dr. Andrei Irimia published a paper “Neuroinformatics and Analysis of Traumatic Brain Injury and Related Conditions” in Neuroinformatics. Read the paper here.
CBB Graduate Students
Dr. Raktim Mitra from the Rohs Lab defended his Ph.D. thesis after publishing three first-author papers with more to come. Raktim will join the lab of one of this year's Nobel Laureates in Chemistry, Dr. David Baker, at the University of Washington. Well done, Raktim!
QBIO Undergraduate Students
QBIO students, graduates, and QCB staff provided insight into our undergraduate programs, the QBIO major and CBB minor, during the USC Dornsife Majors and Minors Fair. Huge thanks to everyone who contributed!
The QCB Department thanks Dr. Morgan Ponder, Academic Advisor and Undergraduate Programs Supervisor, for stepping in as interim academic advisor for our QBIO undergraduate students. He will continue being available remotely for the reminder of the Fall semester. Thanks, Morgan!
Advisors to the Department Chair
Dr. Amy Ross, Trustee of the University of Southern California, Vice Chair of the USC Health System Board, and former cancer researcher at Caltech, visited the QBIO table at the recent Dornsife Majors and Minors Fair after her meeting with QCB Chair Dr. Remo Rohs.
QCB Advisory Board member, Dr. Ming Hsieh, Life Trustee of the University of Southern California and Chairman and CEO of Fulgent Genetics, recently visited the USC campus and gave a pioneer lecture at the Viterbi School of Engineering on his life and career.
Founding QCB Advisory Board member, Dr. Andrew Viterbi, Life Trustee of the University of Southern California and co-founder of Qualcomm, gave a new gift to USC in support of interdisciplinary collaboration within the new School of Advanced Computing. QCB is thankful to Dr. Viterbi for having served on the QCB Advisory Board and for endowing our Ph.D. Program in Computational Biology and Bioinformatics. Read more here.
QCB Advisory Board member, Dr. Bin Yu, Chancellor's Distinguished Professor and Professor of Statistics at the University of California Berkeley, co-published a new book "Veridical Data Science: the practice of responsible data analysis and decision-making". Find the book here.
QCB Advisory Board member, Dr. Barry Honig, Professor of Biochemistry and Molecular Biophysics, Systems Biology, and Medicine at Columbia University will visit the QCB Department and give a lecture "Structure-informed prediction of protein-protein interactions on a genomic scale" on January 9th, 2025.
Upcoming QCB Events
November 7th: Seminar from Dr. Martha Bulyk, Harvard Medical School
November 10th-11th: QCG Departmental Retreat @ Ventura Beach, CA
November 14th: Seminar from Dr. Eran Halperin, UCLA
November 21th: Seminar from Dr. Polly Fordyce, Stanford University
December 5th: Seminar from Dr. Peter Ralph, University of Oregon
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