News

September 23, 2018

Rachel Marty Pyke, a Ph.D. student in the Bioinformatics and Systems Biology graduate program, has been named a 2019 Siebel Scholar.

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June 14, 2018

Daniela Nachmanson, a Ph.D. student in Bioinformatics & Systems Biology, has been awarded a TRDRP (Tobacco-Related Disease Research Program) predoctoral research fellowship.

April 12, 2018

Journal of Biological Chemistry cover Dec 1, 2017

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.

Article

April 12, 2018

Bioinformatics & Systems Biology graduate student William Greenwald has been awarded an NIH F31 predoctoral fellowship.

August 11, 2017

Bioinformatics & Systems Biology graduate students William Greenwald and Dylan Skola have each been awarded an ARCS Fellowship for 2017-18.

July 27, 2017

Bioinformatics and Systems Biology Ph.D. student Benjamin Kellman organized a bike ride from San Diego to San Francisco to raise money for AAAS.

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Student Publications

Van Nostrand EL, Pratt GA, Shishkin AA, Gelboin-Burkhart C, Fang MY, Sundararaman B, et al. Robust transcriptome-wide discovery of RNA-binding protein binding sites with enhanced CLIP (eCLIP). Nat Methods. 2016;13(6):508-14.
Sauls JT, Li D, Jun S. Adder and a coarse-grained approach to cell size homeostasis in bacteria. Curr Opin Cell Biol. 2016;38:38-44.
Brandler WM, Antaki D, Gujral M, Noor A, Rosanio G, Chapman TR, et al. Frequency and Complexity of De Novo Structural Mutation in Autism. Am J Hum Genet. 2016;98(4):667-79.
Rentas S, Holzapfel NT, Belew MS, Pratt GA, Voisin V, Wilhelm BT, et al. Musashi-2 attenuates AHR signalling to expand human haematopoietic stem cells. Nature. 2016;532(7600):508-11.
Utrilla J, O'Brien EJ, Chen K, McCloskey D, Cheung J, Wang H, et al. Global Rebalancing of Cellular Resources by Pleiotropic Point Mutations Illustrates a Multi-scale Mechanism of Adaptive Evolution. Cell Syst. 2016;2(4):260-71.
Gross AM, Jaeger PA, Kreisberg JF, Licon K, Jepsen KL, Khosroheidari M, et al. Methylome-wide Analysis of Chronic HIV Infection Reveals Five-Year Increase in Biological Age and Epigenetic Targeting of HLA. Mol Cell. 2016;62(2):157-68.
Conway AE, Van Nostrand EL, Pratt GA, Aigner S, Wilbert ML, Sundararaman B, et al. Enhanced CLIP Uncovers IMP Protein-RNA Targets in Human Pluripotent Stem Cells Important for Cell Adhesion and Survival. Cell Rep. 2016;15(3):666-79.
Baker CW, Miller CR, Thaweethai T, Yuan J, Baker MH, Joyce P, et al. Genetically Determined Variation in Lysis Time Variance in the Bacteriophage φX174. G3 (Bethesda). 2016;6(4):939-55.