News

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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July 31, 2013

A biology and physics professor at UC San Diego has received a $1.15 million grant from the National Science Foundation to establish a series of annual “boot camps” that will educate San Diego-area high school and college students about an emerging field at the intersection of physics and biology called “quantitative biology.”

"Quantitative biology is more than adding numbers to what biologists already know,” says Suckjoon Jun, an assistant professor of physics and molecular biology, who received the five-year Faculty Early Career Development (CAREER) grant, awarded by the foundation to promising young scholar-researchers, and will work with a biology professor at San Diego State University to start the first of the boot camps next summer. “The power of the approach is to bring quantitative rigor from physical sciences to identify and solve important and interesting problems in biology.”

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June 13, 2013

Two early-career scientists at UC San Diego are among 22 of the nation’s most enterprising researchers named Pew Scholars in the Biomedical Sciences by The Pew Charitable Trusts.

These scholars will each receive $240,000 over the next four years to pursue research projects without restriction that are focused on solving some of the nation’s most perplexing health problems—including diabetes, autism, Parkinson’s disease and cancer.

Andrew Huberman, an assistant professor of neurosciences, neurobiology and ophthalmology, and Suckjoon Jun, an assistant professor of physics and molecular biology, join a prestigious community of Nobel laureates, MacArthur Fellows, Albert Lasker Basic Medical Research Award winners and hundreds of other pioneers who earned Pew grants at the start of their careers.

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June 6, 2013

The American Statistical Association (ASA) announced that Professor Lily Xu is being honored as a 2013 ASA Fellow. Honorees are recognized for their outstanding professional contributions to and leadership in the field of statistical science.

May 8, 2013

The National Science Foundation has awarded Graduate Research Fellowships to Ph.D. students Gabriel Pratt and Kunal Bhutani in the Bioinformatics Graduate Program.

Upcoming Events

Thursday, April 17th

  1. Genetics, Bioinformatics and Systems Biology Colloquium: Lucy Shapiro, PhD
    • Start time: 12:00pm
    • End date: Thursday, April 17th
    • End time: 1:00pm
    • Where: Leichtag Auditorium (Leichtag Biomedical Research Building, Room 107)
    • Description:

      PLEASE NOTE: Spring Quarter Series is being held in Leichtag Building

      Genetics, Bioinformatics, and Systems Biology Colloquium

      presents:

      Title TBA

      Leichtag Auditorium (Leichtag Biomedical Research Building, Room 107)
      Thursday, April 17 ~ NOON - 1:00PM

      Speaker:
      Lucy Shapiro, PhD
      Professor of Developmental Biology
      Stanford University

Thursday, April 24th

  1. Genetics, Bioinformatics and Systems Biology Colloquium: Steve Henikoff, PhD
    • Start time: 12:00pm
    • End date: Thursday, April 24th
    • End time: 1:00pm
    • Where: Leichtag Auditorium (Leichtag Biomedical Research Building, Room 107)
    • Description:

      PLEASE NOTE: Spring Quarter Series is being held in Leichtag Building

      Genetics, Bioinformatics, and Systems Biology Colloquium

      presents:

      Title TBA

      Leichtag Auditorium (Leichtag Biomedical Research Building, Room 107)
      Thursday, April 24 ~ NOON - 1:00PM

      Speaker:
      Steve Henikoff, PhD
      Principal Investigator
      Fred Hutchinson Cancer Research Center

Thursday, May 1st

  1. Genetics, Bioinformatics and Systems Biology Colloquium: Marian Walhout, PhD
    • Start time: 12:00pm
    • End date: Thursday, May 1st
    • End time: 1:00pm
    • Where: Leichtag Auditorium (Leichtag Biomedical Research Building, Room 107)
    • Description:

      PLEASE NOTE: Spring Quarter Series is being held in Leichtag Building

      Genetics, Bioinformatics, and Systems Biology Colloquium

      presents:

      Title TBA

      Leichtag Auditorium (Leichtag Biomedical Research Building, Room 107)
      Thursday, May 1 ~ NOON - 1:00PM

      Speaker:
      Marian Walhout, PhD
      Professor of Program in Molecular Medicine
      Co-Chair of Program in Systems Biology
      University of Massachusetts Medical School

Thursday, May 8th

  1. Genetics, Bioinformatics and Systems Biology Colloquium: Arthur Lander, MD, PhD
    • Start time: 12:00pm
    • End date: Thursday, May 8th
    • End time: 1:00pm
    • Where: Leichtag Auditorium (Leichtag Biomedical Research Building, Room 107)
    • Description:

      PLEASE NOTE: Spring Quarter Series is being held in Leichtag Building

      Genetics, Bioinformatics, and Systems Biology Colloquium

      presents:

      Title TBA

      Leichtag Auditorium (Leichtag Biomedical Research Building, Room 107)
      Thursday, May 8 ~ NOON - 1:00PM

      Speaker:
      Arthur Lander, MD, PhD
      Donald Bren Professor of Developmental and Cell Biology
      Professor of Biomedical Engineering
      University of California, Irvine

Thursday, May 15th

  1. Genetics, Bioinformatics and Systems Biology Colloquium: Hana El-Samad, PhD
    • Start time: 12:00pm
    • End date: Thursday, May 15th
    • End time: 1:00pm
    • Where: Leichtag Auditorium (Leichtag Biomedical Research Building, Room 107)
    • Description:

      PLEASE NOTE: Spring Quarter Series is being held in Leichtag Building

      Genetics, Bioinformatics, and Systems Biology Colloquium

      presents:

      Title TBA

      Leichtag Auditorium (Leichtag Biomedical Research Building, Room 107)
      Thursday, May 15 ~ NOON - 1:00PM

      Speaker:
      Hana El-Samad, PhD
      Associate Professor of Biochemistry and Biophysics
      UCSF School of Medicine

Thursday, May 22nd

  1. Genetics, Bioinformatics and Systems Biology Colloquium: Andre Levchenko, Eng.Sc.D.
    • Start time: 12:00pm
    • End date: Thursday, May 22nd
    • End time: 1:00pm
    • Where: Leichtag Auditorium (Leichtag Biomedical Research Building, Room 107)
    • Description:

      PLEASE NOTE: Spring Quarter Series is being held in Leichtag Building

      Genetics, Bioinformatics, and Systems Biology Colloquium

      presents:

      Title TBA

      Leichtag Auditorium (Leichtag Biomedical Research Building, Room 107)
      Thursday, May 22 ~ NOON - 1:00PM

      Speaker:
      Andre Levchenko, Eng.Sc.D.
      John C. Malone Professor of Biomedical Engineering
      Yale University

Student Publications

Wang C-, Bajikar SS, Jamal L, Atkins KA, Janes KA. A time- and matrix-dependent TGFBR3-JUND-KRT5 regulatory circuit in single breast epithelial cells and basal-like premalignancies. Nat Cell Biol. 2014.
Bean GJ, Jaeger PA, Bahr S, Ideker T. Development of ultra-high-density screening tools for microbial "omics". PLoS ONE. 2014;9(1):e85177. PMC 
Sauls JT, Buescher JM. Assimilating genome-scale metabolic reconstructions with modelBorgifier. Bioinformatics. 2014.
Bhargava V, Head SR, Ordoukhanian P, Mercola M, Subramaniam S. Technical Variations in Low-Input RNA-seq Methodologies. Sci Rep. 2014;4:3678.
Zhou D, Udpa N, Ronen R, Stobdan T, Liang J, Appenzeller O, Zhao HW, Yin Y, Du Y, Guo L, Cao R, Wang Y, Jin X, Huang C, Jia W, Cao D, Guo G, Gamboa JL, Villafuerte F, Callacondo D, Xue J, Liu S, Frazer KA, Li Y, Bafna V, Haddad GG. Whole-genome sequencing uncovers the genetic basis of chronic mountain sickness in Andean highlanders. Am J Hum Genet. 2013;93(3):452-62. PMC 
Doan S, Lin K-, Conway M, Ohno-Machado L, Hsieh A, Feupe S , Garland A, Ross MK, Jiang X, Farzaneh S, Walker R, Alipanah N, Zhang J, Xu H, Kim H-. PhenDisco: phenotype discovery system for the database of genotypes and phenotypes. J Am Med Inform Assoc. 2013.
Ronen R, Udpa N, Halperin E, Bafna V. Learning natural selection from the site frequency spectrum. Genetics. 2013;195(1):181-93. PMC 
Jung H, Bleazard T, Lee J, Hong D. Systematic investigation of cancer-associated somatic point mutations in SNP databases. Nat Biotechnol. 2013;31(9):787-9.