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

Yurkovich JT, Palsson BO. Solving Puzzles With Missing Pieces: The Power of Systems Biology. Proceedings of the IEEE. 2016;104(1):2-7. URL 
Wu J, Okamura D, Li M, Suzuki K, Luo C, Ma L, et al. An alternative pluripotent state confers interspecies chimaeric competency. Nature. 2015;521(7552):316-21.
Friedmann-Morvinski D, Bhargava V, Gupta S, Verma IM, Subramaniam S. Identification of therapeutic targets for glioblastoma by network analysis. Oncogene. 2015.
Murrell B, Weaver S, Smith MD, Wertheim JO, Murrell S, Aylward A, et al. Gene-wide identification of episodic selection. Mol Biol Evol. 2015;32(5):1365-71.
DeBoever C, Ghia EM, Shepard PJ, Rassenti L, Barrett CL, Jepsen K, et al. Transcriptome sequencing reveals potential mechanism of cryptic 3' splice site selection in SF3B1-mutated cancers. PLoS Comput Biol. 2015;11(3):e1004105.
He Y, Ecker JR. Non-CG Methylation in the Human Genome. Annu Rev Genomics Hum Genet. 2015.
Taheri-Araghi S, Brown SD, Sauls JT, McIntosh DB, Jun S. Single-Cell Physiology. Annu Rev Biophys. 2015;44:123-42.