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January 2024 QCB Newsletter

e-Newsletter Volume 4 Issue 1 | January 2024

Personal Remarks by Dr. Remo Rohs

Happy Belated 2024! I hope you all had a wonderful start into the New Year and spring semester.

I want to welcome Dr. Tsu-Pei Chiu as our newest QCB core faculty member. Professor Chiu joins us as a Visiting Assistant Professor (Teaching) who will teach a few of our existing courses and a couple new courses on Machine Learning and Artificial Intelligence in Biology and Medicine. Welcome, Tsu-Pei!

This month, we also started interviewing candidates for our Ph.D. Program in Computational Biology and Bioinformatics. I feel that this is a special year where the department has become attractive in many ways. This is the historically first program in computational biology in the world with a well-developed curriculum. The strong research grant funding and our philanthropic efforts allow us to offer a Ph.D. stipend that is 10% or $4,000 above university standard. We're looking forward to welcoming some fantastic individuals to our program.

Remo Rohs, Ph.D.

QCB Department Chair

Faculty Promotions

Dr. Tsu-Pei Chiu was promoted to Visiting Assistant Professor (Teaching) of Quantitative and Computational Biology and became a QCB core faculty member. Dr. Chiu will be teaching classes on machine learning, and AI methods and applications. Congratulations, Tsu-Pei!

Joint faculty member Dr. Christoph Haselwandter was promoted to Full Professor of Physics and Astronomy, and Quantitative and Computational Biology. Congratulations, Christoph!

QCB Publications

Yibei Jiang in the Remo Rohs lab with contributions from Tsu-Pei Chiu and Raktim Mitra published a new paper in Biophysical Journal. All-atom MD simulations uncover insights into histidine’s role in modulating the interaction of DNA with transcription factors, where histidine’s protonation state affected the DNA minor-groove width profile and binding free energy. Read more about their study here.

Yuxuan Du from Dr. Fengzhu Sun lab had a paper “ImputeCC enhances integrative Hi-C-based metagenomic binning through constrained random-walk-based imputation” accepted by RECOMB, one of the top two conferences in the field of computational biology. Only 16% of the submissions were accepted by RECOMB this year.

Keon Rabbani and Mark Chaisson contributed to the paper “Scalable, accessible and reproducible reference genome assembly and evaluation in Galaxy”, just published in Nature Biotechnology. This study presents a platform enabling any researcher to create a high-quality de novo assembly using single-molecule sequencing (SMS) data, which allows to resolve sequences of multicopy genes. Mr. Rabbani developed analysis to determine the accuracy of multicopy gene assemblies. Read their paper here.

Notable QCB Joint Faculty Publications

Dinh BL, Tang E, Taparra K, Nakatsuka N, Chen F, Chiang CWK.Hum Genet. 2024 Jan;143(1):85-99. doi: 10.1007/s00439-023-02625-2. Epub 2023 Dec 29.PMID: 38157018

Jung J, Lu Z, de Smith A, Mancuso N.Hum Mol Genet. 2024 Jan 7;33(2):170-181. doi: 10.1093/hmg/ddad174.PMID: 37824084

Yadav R, Gati C.Cell Res. 2024 Jan 19. doi: 10.1038/s41422-023 00922-z. Online ahead of print. PMID: 38242944

Lewthwaite JMM, Baiotto TM, Brown BV, Cheung YY, Baker AJ, Lehnen C, McGlynn TP, Shirey V, Gonzalez L, Hartop E, Kerr PH, Wood E, Guzman LM.Sci Rep. 2024 Jan 3;14(1):390. doi: 10.1038/s41598-023-50675-3.PMID: 38172148

Lynch KM, Cabeen RP, Toga AW.Hum Brain Mapp. 2024 Jan;45(1):e26528. doi: 10.1002/hbm.26528. Epub 2023 Nov 22.PMID: 37994234

QBIO Undergraduate Students

The Fall semester cohort taking QBIO 490 - Multi-Omic Data Analysis presented their research to a faculty panel in December. The QCB Department wants to thank Nicole Black for being an excellent course director of QBIO 490 for several semesters as well as Wade Boohar and Kayla Xu for their contributions as course instructors.

Dr. Soheil Shams gave a guest lecture in QBIO 105 about 'Artificial Intelligence and bioinformatics – A 30-year personal journey'. Dr. Shams was exposed to computational biology through a class by Professor Michael Waterman and went on to found companies like BioDiscovery (which he sold to Bionano Genomics) and Tesa Research (a new company specialized on AI in health).

Professor Hao Li, co-founder of Pinscreen and now faculty at the Mohamed bin Zayed University of Artificial Intelligence in Abu Dhabi, U.A.E., gave a guest lecture in QBIO 105 on 'Generative AI for human synthesis and world capture' in which he shared his work in computer vision with fascinating applications in the film industry and digital media.

Upcoming Events

QCB Departmental Seminars

February 1st: Dr. T.M. Murali, Virginia Tech

February 8th: Dr. Jinghui Zhang, St. Jude Children's Research Hospital

February 15th: Dr. Smita Krishnaswamy, Yale University

February 22nd: Dr. Noah Zaitlen, UCLA

February 29th: Dr. Andre Levchenko, Yale University

QBIO 543 Seminars

February 2nd: Dr. Jesse Weller (Rohs lab)

February 9th: Jesse Kreger (MacLean lab)

February 16th: Dr. Tony Lu (Chaisson lab)

February 23th: Raktim Mitra & Ari Cohen (Rohs lab)

Organized by CNT3D, MESH Academy, Bridge Institute, and Professors Vsevolod 'Seva' Katritch and Charles McKenna.

FEBRUARY 23rd, 2024, 10AM – 5PM

LOCATION: Michelson Center for Convergent Bioscience, 1st floor

1002 Childs Way, Los Angeles, CA 90089-3502

Copyright © 2024 Department of Quantitative and Computational Biology, University of Southern California. All rights reserved.

Our mailing address is:

1050 Childs Way, RRI 201, Los Angeles, CA 90089-2019


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