March 2022 QCB Newsletter




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





OPENING SPEAKERS

Jan Amend USC

Elizabeth Graddy USC

Andrew Viterbi USC Trustee

Yannis Yortsos USC


KEYNOTE SPEAKERS

Bonnie Berger MIT

Barry Honig Columbia University

Mike Levine Princeton University

Ron Shamir Tel Aviv University

Simon Tavaré Columbia University

Bin Yu UC Berkeley


INVITED SPEAKERS

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


DINNER SPEAKERS

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!


Departmental Seminars

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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