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September 2023 QCB Newsletter

e-Newsletter Volume 3 Issue 6 | September 2023


Department of Quantitative and Computational Biology


In this month’s newsletter we are looking back at graduation and include the placement of our most recently graduated undergraduate class. When we started the QBIO major, we needed to decide between an easy major that would have grown much faster or a smaller major that provides meaningful skills for the students. We decided for the latter, to provide training for the 21st century.


The QBIO major is now a major with more than 100 students. Despite the challenging courses that we require, all students complete the program on time, and the success of the students is impressive. The Medical School acceptance rate is 100% and the MD/PhD Program acceptance rate is 100% too. QBIO students get accepted to the best graduate schools in the country, or find excellent jobs in industry.


In faculty news, Dr. Matt Pennell and colleagues were successful in establishing the new Center for Ecological and Evolutionary Dynamics (CEED), and Dr. Seva Katritch and colleagues were successful in expanding the Center for New Technologies for Drug Discovery and Development (CNT3D). These centers link QCB directly with other departments and schools through new seminar series and collaborations.


I want to end with an invitation for everyone to attend Dr. Mark Chaisson’s Tenure Talk entitled ‘Computational tools for individual and population-scale discovery of complex genetic variation from single-molecule sequencing’ this Thursday, October 5th, at 2 pm, in RRI 101, or on Zoom.

Remo Rohs, Ph.D.

QCB Department Chair



QCB PhD Program Applications

Please see the flyer above for QCB PhD Program Applications. We will be accepting applications until December 15th, 2023. Contact Christian Robbie at crobbie@usc.edu for any questions. You can also directly apply through this website: https://www.qcb-dornsife.usc.edu/application


QCB PhD Hooding



QCB Graduation Reception Photos




Annual QCB Awards (2022-2023)

USC QCB Google Alumni Awards are given to highly accomplished graduating Seniors in Quantitative Biology based on research and contributions to the program, as determined by the faculty in the Department of Quantitative and Computational Biology. This award was started by Alumni of the Computational Biology and Bioinformatics Graduate Program, Tianyin Zhou and Lin Yang, who were joined by Xuele Wu, Jie Jessie Ren, Nan Hua, Haifeng Cheng, Dazhe Meng, Weili Wang, Kujing Tang, Yichao Dong, and Xin Bai. All are current Google Employees who want to recognize the outstanding students in QCB. The award carries a cash stipend and a certificate of recognition. Our 2023 QCB Google Alumni Scholar Awardees were: Sanjana Paye, Vamsi Chavali, Leon Zha, Kayla Xu, and Dottie Yu.

The John Petruska Memorial Award is given to the most accomplished undergraduate student majoring in Biological Sciences or Quantitative Biology with research contributions. The awardee is determined by the faculty in the Department of Quantitative and Computational BIology. The award was established by Mark and Wendy Petruska (pictured, bottom right) to honor Mark’s father, Dr. John Petruska. The late Dr. Petruska was a DNA and protein structure expert and a fixture at USC since September 1968, when he joined USC as a faculty member. Dr. Petruska loved to teach and found great joy in watching students flourish at their studies and research. The award carries a cash stipend and a certificate of recognition. Our 2023 QCB John Petruska Memorial Awardee was: Colin Yeo.

The Michael S. Waterman Award is given to the most accomplished graduating Ph.D. Student in Computational Biology and Bioinformatics based on research and contributions to the program, as determined by the faculty in the Department of Quantitative and Computational Biology. This award was started in 2022 in honor of Emeritus University Professor Michael S. Waterman and his contributions to starting Computational Biology at USC in 1982. The award was established by his students, colleagues, and friends, and has recently been endowed -- more about this in a forthcoming newsletter. The award carries a cash stipend and a certificate of recognition. Our 2023 QCB Michael S. Waterman Awardee was: Dr. Tsung-Yu “Tony” Lu.


QBIO Undergraduate Outcomes (c/o 2023)

This year, we congratulated 17 QBIO undergraduates, making up the QBIO Class of 2023, for earning their bachelor degrees and entering the next stage of their academic & professional lives. Read more about each of their journeys and what they're all up to below:


Shannon Brownlee: I will be working full-time on my startup, Valence Vibrations, where I work at the intersection of machine learning, voice tech, neuroscience, and affective computing. I will also graduate with a master's degree in Electrical Engineering next spring. More about Shannon here.


Mengdi Chai: I will go to Yale to continue my master degree in biostatistics, as I found my interest in the combination of biology and data, which led me to pursue biostatistics. After that, I may go into industry or pursue a PhD degree. I found my interest in the combination of biology and data, which leads me to pursue biostatistics in my master degree.


Vamsi Chavali: I am currently a Business Analyst at McKinsey & Company. I joined the QBIO program my freshman year and have appreciated the flexibility and opportunities it has enabled me to pursue.


Tessa Ferrari: I am doing research with Dr. Jazlyn Mooney, implementing spatial simulations to model genetic diversity through time in populations of conservation concern.


Carolyn Kaleta: After graduation, I moved to New York to pursue a career in biotechnology. I am particularly interested in cancer treatment and diagnostics, and hope to attend grad school in the future.


Fangyun Liu: I will be pursuing my PhD degree in the QBIO CBB program, so see you around campus next year!”


Sankalp Mrutyunjaya: I am applying to medical school.


Sanjana Paye: I am interested in the applications of computational biology to medicine and started my MD/PhD program after graduating. I am pursuing research in statistical genetics.


Grace Scheg: I am taking a gap year and applying to medical school. I hope to work in clinical research or health advocacy and education.


Echo Tang: I am continuing my education at USC and will be graduating with my Masters in Public Health Data Science in December.


Brian Tinsley: I am staying at USC to get a master’s in Applied Data Science and will hopefully start my own software company someday.


Judy Wang: I am attending the Columbia Journalism School with an emphasis in science journalism and investigative journalism.


Kayla Xu: I'm currently working as a bioinformatics specialist at the City of Hope Beckman Research Institute, and will be applying for bioinformatics PhD programs in the future. I am also a senior advisor for the new Quantitative Biology Assocation (QBA) for our undergraduate students.


Colin Yeo: I am currently an MS-1 at the Keck School of Medicine, with a primary interest in anesthesiology. I am also continuing in my role of QBIO Undergraduate Student Liaison and the director of the QBIO Mentorship Program. I'm excited to see where the next few years take me!


Dottie Yu: I’m applying to med school with an interest in women’s fertility and reproductive health.


Leon Zha: I am currently working for Chevron in Houston.


Sabrina Zhong: I am completing my PDP in Applied Biostatistics and Epidemiology. I am also interested in careers related to cancer, biotechnology, and data science.


QCB Faculty

Dr. Naomi Levine published a study in Science Advances introducing a new proteome allocation model to investigate the relationships between temperature, size and metabolism among marine phytoplankton. They applied the model to decipher the mechanisms behind both short-term (acclimation) and long-term (adaptation) responses, providing insights into the metabolic trade-offs that a cell faces while managing stress, space and energetic constraints. These results have implications for rates of carbon sequestration and export in a warmer ocean.


Dr. Matt Pennell (left), Dr. Melissa Guzman, and Dr. Jazlyn Mooney, with colleagues from Biological Sciences, Keck, and Viterbi, founded a new Center for Ecological and Evolutionary Dynamics (CEED). Phase 1 funding from the Dornsife College will support a seminar series, establish a CEED community at USC and beyond, and enable the hosting of the Southern California Evolutionary Genomics meeting at USC.


Dr. Seva Katritch (QCB) and Dr. Charles McKenna (CHEM) received Phase 2 funding from the Dornsife College to expand the Center for New Technologies for Drug Discovery and Development. In addition to the CNT3D seminar series and short courses, the funding will support student co-advising between CNT3D member labs, as well as pilot computer-driven drug discovery projects in collaboration with groups across both USC campuses.


Dr. Remo Rohs is co-PI of a new center together with colleagues from the Viterbi School of Engineering and the Price School of Public Policy. This center is led by Dr. Urbashi Mitra, with the goal of developing methods and technology to study emerging infectious diseases and pandemic spillover events.


Dr. Serghei Mangul received a new NSF grant for undergraduate education. This collaborative project aims to equip undergraduate students with essential skills in big data analytics, bridging an educational gap at community colleges and minority-serving institutions (read here). Dr. Mangul also published a new paper “Scientists without borders: lessons from Ukraine” on how to help the scientific community in Ukraine by reaching out, providing accessible training opportunities, and developing collaborations that increase inclusion and connectivity (read here).


QCB Graduate Students

This month, the Computational Biology Student Association (CBSA) organized multiple events for graduate students and postdocs to engage the student body. One of the highlights was a cozy crafting night, where students created collages based on their happy place. In addition, the student government organized an educational trip to the Natural History Museum with a special tour about entomology by Austin Baker Ph.D. His enthusiasm for entomology was infectious, as he shared his experiences from years of fieldwork, offering fascinating anecdotes and knowledge about insect behavior and conservation efforts. The highlight of the tour was the chance to examine a wide array of insect specimens up close, from rare butterflies to bizarre beetles.


Anna Nadtochiy, a CBB PhD student in Dr. Scott Fraser's lab, published a first-author Bioinformatics paper (link here) for the time annotation and management of volumetric functional imaging data. Anna also defended her PhD thesis on September 29th and becomes Dr. Fraser's first graduate from the CBB Program.


QBIO Undergraduate Students

QBIO student leaders, along with Dr. Remo Rohs, represented the QCB Department at a student career event at La Cañada High School. This group presented the QBIO major to students and parents, shared their experiences within the department, and ultimately encouraged them to apply to USC and QBIO. The representatives pictured are: Karen Lee, Wade Boohar, Brandon Ye, and Colin Yeo.


The undergraduate Quantitative Biology Association (QBA) had a successful first meeting as a student organization in September. The event introduced the QBA executive board and focused on student networking, giving organization members a chance to connect with their peers as they approach the new academic semester together.


Jordan Cahoon, a QCB Department junior who completed a minor in Computational Biology and Bioinformatics, was named a Goldwater Scholar. Jordan is interested in genetics and computational biology, and hopes to pursue a PhD in one of these topics after she graduates. Read more about her accomplishment here.


Upcoming Events

October 4th @ 3:30pm (RRI 101): CEED Seminar from Dr. Findley Finseth, Claremont College.


October 5th @ 2pm (RRI 101): QCB Seminar from Dr. Mark Chaisson, USC, who will present his Tenure Talk.


October 10th @ 6pm (RRI 101): Quantitative Biology Association (QBA) General Meeting #2.


October 18th @ 3:30pm (RRI 101): CEED Seminar from Dr. Josh Shraiber, USC QCB.


October 19th @ 2pm (RRI 101): QCB Seminar from Dr. Josh Plotkin, University of Pennsylvania.


October 26th @ 2pm (RRI 101): QCB Seminar from Sui Huang, Institute for Systems Biology, Seattle.



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Our mailing address is:

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

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