An article in Nature announces the release of Phase III of the ENCODE (Encyclopedia of DNA Elements) Project, the most complete catalog to-date of the functional elements in the human and mouse genomes. This international collaboration with hundreds of authors includes a number of BISB faculty (Joe Ecker, Graham McVicker, Bing Ren, Wei Wang, and Gene Yeo) and BISB students (Yupeng He, Vu Ngo, Gabriel Pratt, Mengchi Wang, Kai Zhang, and Yuan Zhao).
Professor Trey Ideker's lab has developed a new epigenetic clock method to compare aging between multiple mammalian species.
Press release and journal article
The UC San Diego Bioinformatics and Systems Biology community has led multiple efforts to address the challenges introduced by the COVID-19 pandemic.
Prof. Ben Smarr became the technical lead on TemPredict, "a global collaboration combining physiological data, symptom reports, and diagnostic testing, seeking to build data models capable of early-onset detection, severity prediction, and recovery monitoring" (Mobile in Clinical Trials 2020), which was featured in The Washington Post.
Profs. Rob Knight, Louise Laurent, and Gene Yeo are members of the core research team of the San Diego Epidemiology and Research for COVID Health (SEARCH) alliance, which received a $350,000 gift from Jean and Gary Shekhter and was featured in PR Newswire and Times of San Diego.
Prof. Niema Moshiri received a $200,000 NSF COVID-19 RAPID grant to develop faster tools for analyzing the evolution of SARS-CoV-2.
Rachel Marty Pyke, a Ph.D. student in the Bioinformatics and Systems Biology graduate program, will receive the 2019 Chancellor's Dissertation Medal at commencement for her dissertation “The Role of MHC Variation in Tumor Progression.” Six graduating Ph.D. students in different disciplines were selected for this honor.
Ileena Mitra, a Ph.D. student in Bioinformatics & Systems Biology, has been awarded the Autism Science Foundation predoctoral fellowship for researching de novo short tandem repeats in Autism.
Carlos Guzman, a Ph.D. student in the Bioinformatics and Systems Biology graduate program, has been awarded a 2019 Ford Foundation Predoctoral Fellowship. The competition is administered by the National Academies on behalf of the Ford Foundation.
Jessica Zhou, a Ph.D. student in Bioinformatics and Systems Biology, has been awarded a Fulbright Research Award to study in Germany 2019-20. She will be doing research at the University of Potsdam and the Max Delbrück Center for Molecular Medicine.
Rachel Marty Pyke, a Ph.D. student in the Bioinformatics and Systems Biology graduate program, has been named a 2019 Siebel Scholar.
Daniela Nachmanson, a Ph.D. student in Bioinformatics & Systems Biology, has been awarded a TRDRP (Tobacco-Related Disease Research Program) predoctoral research fellowship.
James Yurkovich, a Ph.D. student in the Bioinformatics and Systems Biology graduate program, is the lead author of a cover story in the Journal of Biological Chemistry.
Summary: In this study, we examined the temperature dependence of the human red blood cell metabolic network. The temperature dependence of biological functions had been previously studied at the levels of individual biochemical reactions and organism physiology (e.g., basal metabolic rates). Biology is inherently multi-scale, and there existed a gap between observing temperature dependence at the scale of an individual reaction and at the physiological level. We used a systems biology approach to define the temperature dependence of individual metabolite profiles, metabolic reaction fluxes, and the entire metabolic network. Our results provided an ex vivo characterization of temperature dependence, which is in contrast to previous studies of individual reactions that are determined through in vitro assays. Further, we provided a baseline characterization of a biochemical network given no transcriptional or translational regulation that can be used to explore the temperature dependence of metabolism. This paper was featured on the cover of the December 1, 2017 issue (Vol. 292, Num. 48); cover artwork by Rockford Penn, Technicity, LLC.
