News

May 25, 2016

Olga Botvinnik, a Ph.D. student in the Bioinformatics and Systems Biology graduate program, is featured in a story about women in the open source software community.

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June 19, 2015

The National Science Foundation has awarded Graduate Research Fellowships to Ph.D. student Rachel Marty in the graduate Bioinformatics and Systems Biology program and to Max Shen in the undergraduate Bioinformatics program.

November 26, 2014

Trey Ideker has been selected as a Fellow of the American Association for the Advancement of Science.

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July 7, 2014

Olga Botvinnik, a Ph.D. student in the Bioinformatics and Systems Biology graduate program, has been awarded the 2014 John Hunter Fellowship. The focus of her Fellowship will be to create open source analysis software for the single-cell and biology communities, and to pioneer data, code sharing, and computational reproducibility within the single-cell and RNA biology communities.

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April 1, 2014

The National Science Foundation has awarded Graduate Research Fellowships to Ph.D. students Leen Jamal and Jeffrey Yuan in the graduate Bioinformatics and Systems Biology program, and to students Robin Betz and Christopher Probert in the undergraduate Bioinformatics program.

August 7, 2013

One of the most basic and intensively studied processes in biology—one which has been detailed in biology textbooks for decades—has gained a new level of understanding, thanks to the application of simple math to a problem that scientists never before thought could benefit from mathematics.

The scientists who made the discovery, published in this week's advance online publication of Nature, found that the process bacteria use to quickly adapt to metabolize preferred energy sources such as glucose—a process called “catabolite repression”—is controlled not just by glucose, as had long been known and taught, but just as much by other essential nutrients, such as nitrogen and sulfur, available to bacteria in their growth medium.

“This is one of the most studied processes in molecular biology; it’s in every textbook,” says Terence Hwa, a professor of physics and biology at UC San Diego, who headed the team of scientists. “We showed that this process doesn’t work the way most people thought it did for the past several decades, and its purpose is different from what had generally been assumed.”

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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.