Department of Quantitative and Computational Biology
This month's newsletter is a final reminder to register for our upcoming Computational Biology Symposium 2022. The Early Bird Registration ends in a few days on March 31, 2022. Everyone who wants to attend needs to register. There will be no walk ins permitted.
Take a look at the speaker list below - even if you are not directly in the field, it is probably one of the most compelling lineups many of us have seen in our careers. Take this opportunity, attend an in-person conference, and if you are a mentor, give your students the opportunity to attend this conference.
Register at: https://www.qcb-dornsife.usc.edu/qcb40
I am looking forward to seeing many of you on May 19-21, 2022, to celebrate Computational Biology at USC!
Remo Rohs, Ph.D.
QCB Department Chair
Jan Amend USC
Elizabeth Graddy USC
Andrew Viterbi USC Trustee
Yannis Yortsos USC
Bonnie Berger MIT
Barry Honig Columbia University
Mike Levine Princeton University
Ron Shamir Tel Aviv University
Simon Tavaré Columbia University
Bin Yu UC Berkeley
Serafim Batzoglou Stanford University
Mark Chaisson USC
Christina Curtis Stanford University
Michael "Doc" Edge USC
Eleazar Eskin UCLA
Geoffrey Fudenberg USC
Susan Holmes Stanford University
Haiyuan Huang UC Berkeley
Naomi Levine USC
Jingyi Jessica Li UCLA
Xiaole Shirley Liu Harvard University
Adam MacLean USC
Jazlyn Mooney USC
Lior Pachter Caltech
Giulia Palermo UC Riverside
Laxmi Parida IBM
Matt Pennell USC
Pavel Pevzner UC San Diego
Stephan Preibisch HHMI Janelia Research Campus
Teresa Przytycka NIH
Aviv Regev Genentech
Noah Rosenberg Stanford University
Russell Schwartz Carnegie Mellon University
Mona Singh Princeton University
Martin Vingron Max Planck Institute of Berlin
Tandy Warnow U Illinois Urbana-Champaign
Zhiping Weng U Mass Medical School
Jing Zhang UC Irvine
Ming Hsieh USC Trustee
Steve Kay USC
Simon Tavaré Columbia University
Michael Waterman USC
QBIO Undergraduate Students
Sydney Rashid (senior in QBIO) won a Spring 2022 Provost Research Fellowship to continue her research on coronavirus modeling with Professor Peter Calabrese.Dr. Jerry Lee, of the Ellison Institute for Transformational Medicine of USC, spoke to the QBIO 105 class in person on Tuesday, March 1, 2022. Having classes back in person has led to many lively discussions.
QCB Faculty and CBB Graduate Students
Dr. Xin Bai and Dr. Zifan Zhu from Dr. Fengzhu Sun’s group, and Dr. Bo Sun from Dr. Liang Chen’s group successfully defended their dissertations. Xin is going to join Google, and Bo and Zifan are going to join Meta (Facebook).Megan Rommelfanger and Adam MacLean led the computational data analysis of a paper now published in Blood, in which they identify a metabolic signaling pathway as an important regulator of hematopoietic stem cell maintenance and function. (See article here)
Dr. Seva Katritch will be The Rosalie and Harold Rae Brown Center for Cancer Drug Development Seminar Series speaker on Tuesday, March 29, 2022 2:00-3:00 p.m. (See more information here)
CBB student, Yuxuan Du from Dr. Fengzhu Sun’s group, published a paper “HiCBin: binning metagenomic contigs and recovering metagenome-assembled genomes using Hi-C contact maps” in Genome Biology (See paper here). He also published another paper “Normalizing Metagenomic Hi-C Data and Detecting Spurious Contacts Using Zero-Inflated Negative Binomial Regression” in the Journal of Computational Biology (RECOMB2021 special issue) (See paper here).
Dr. Zifan Zhu’s PNAS paper “DeepLINK: Deep learning inference using knockoffs with applications to genomics” was selected as a RECOMB 2022 highlight talk (See paper here).
CBB PhD Student Recruitment
On March 7, 2022, we had PhD student recruitment where we welcomed 14 students to campus. Their day included a tour of campus, hearing research talks from faculty, a poster session with current students, and ended with bowling with current students and faculty.
QCB Faculty Chats
CBB graduate students and postdocs, please join us for a series of informal conversations with our faculty. Every other Thursday for the remainder of spring semester, bring your post-seminar coffee and have a chat with our faculty. Hear how our faculty got interested in science, and how they found their career paths. Ask your questions about their research, careers, and what matters to them and why. This is a great chance to get to know our department’s faculty better.
This semester’s meetings are as follows:
Fengzhu Sun, Thursday March 24th, RRI 421
Jazlyn Mooney, Thursday April 7th, RRI 421
Liang Chen, Thursday April 21st, Zoom
PhD Hooding Ceremony 2022
The Dornsife PhD Hooding Ceremony will be held on Wednesday, May 11, 2022 on Cromwell Field at 11 a.m. A reception will be held at Cromwell Field immediately following the Hooding Ceremony. Please see the Dornsife PhD Hooding Ceremony web page for more information. (Click here)
QBIO Commencement 2022
Commencement will be held Friday, May 13, 2022. Quantitative Biology and Computational Biology and Bioinformatics is part of the Dornsife Group 1 Ceremony which will be held at 11 a.m. on Cromwell Field. A departmental reception will be held at the front entrance of Michelson Hall immediately following the ceremony. Please see the Dornsife Commencement web page for more information. (Click here)
QCB Book Club
Featuring Nonlinear Dynamics and Chaos by Steven Strogatz, this book club will convene once a month to discuss established paradigms and analytic techniques in mathematical modeling, and showcase recent development in methods and applications in addressing key biological questions. Next meeting, Thursday March 31, 2022 11 a.m.-12 p.m., RRI 421 and zoom. All are welcome!
We are excited to return to in-person seminars: Dr. Suhas Diggavi, Professor, Electrical & Computer Engineering, UCLA "An information theoretic approach to nanopore sequencing." April 7, 2022, 2:00-3:00 p.m., RRI 101 Dr. Michael Schatz, Bloomberg Distinguished Professor, Whiting School of Engineering, John Hopkns University "A complete reference genome improves analysis of human genetic variation." April 14, 2022, 2:00-3:00 p.m., RRI 101 Dr. Cenk Sahinalp, Senior Investigator, Cancer Data Science Laboratory, NIH "Tumor subclonal structure inference and neoantigen therapeutic impact assessment via single-cell expressed mutation profiling." April 21, 2022, 2:00-3:00 p.m., RRI 101 Dr. Aaron Quinlan, Professor in the Departments of Human Genetics and Biomedical Informatics, University of Utah "Measurements and mysteries of human germline mutation." April 28, 2022, 2:00-3:00 p.m., RRI 101
Postdoctoral Positions Open
The Edge Lab is accepting postdoctoral applications in evolutionary genetics (https://edgepopgen.github.io/edgelab/vacancies) Postdoctoral positions in 3D genome biology are open in the Fudenberg Research Group (https://fudenberg.team) The Katritch Lab is accepting postdoctoral applications in structural bioinformatics and drug discovery (https://katritch.usc.edu/)
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