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.”

Full story

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.

Full story

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

Today

  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:

      Digital Epigenomics to Study Transcriptional Dynamics

      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

      Abstract:
      Eukaryotic gene expression occurs in the context of chromatin, and maintaining a region accessible to DNA-binding proteins for transcriptional regulation requires active processes that mobilize nucleosomes. However, most technologies applied to genome-wide mapping of chromatin features have serious limitations, and so we have endeavored to develop new strategies that would allow us to better explore nucleosome dynamics. These include genome-wide high- resolution methods for profiling nucleosome turnover dynamics, nucleosome substructures, RNA polymerase stalling and DNA torsional strain, and for precisely mapping components of the epigenome, including transcription factors, chromatin complexes and remodelers. I will describe applications of these methods, for example to understand the interaction between RNA polymerase and nucleosomes in vivo.

Monday, April 28th

  1. Ph.D. Defense: Winston Chen
    • Start time: 10:00am
    • End date: Monday, April 28th
    • End time: 11:30am
    • Where: Fung Auditorium, PFBH
    • Description:

      UCSD Bioinformatics and Systems Biology Graduate Program
      Ph.D. Dissertation Defense Announcement

      Winston Chen

      "Deciphering Molecular Mechanism of Adverse Reactions of Drugs"

      Monday, April 28, 2014
      10 AM
      Fung Auditorium, Powell-Focht Bioengineering Hall

      Dissertation Committee:
      Committee Chair: Dr. Ruben Abagyan
      Co-Chair: Dr. Grace M. Kuo

      Abstract:
      Some drugs result in severe side effects. Here we explore two different routes to attack this problem: one from the point of view of structural chemistry and human proteome and another from the improved statistical analysis of patient reports

      1. Therapeutic molecules and their metabolites interact with multiple protein targets in human body. Some protein target modulation events due to this poly-pharmacology are desirable for therapeutic effect, some are neutral, and some cause serious adverse reactions. The identification of drug poly-pharmacological targets in advance remains one of the major challenges in drug development. To address this problem, we developed a drug target profiling system using a hybrid chemoinformatics and structural approach that predicts biological activity of any chemical. The two approaches compliment each other since the first one is strongly dependent on the known chemical structures of the compounds while the approach based on three dimensional docking and pharmacophoric field matching depends on the previous knowledge to a lesser degree. The performance of the profiling system was assessed by a carefully designed benchmark that includes a large number of chemicals with experimental annotation of biological activity. The profiling system not only proved to be efficient for retrospective prediction but also enables the discovery of previously unknown drug targets that may lead to side effects.

      2. Independently, unexpected adverse reactions are revealed in clinical trials and, in some unfortunate cases, only in post-marketing surveillance by the FDA many years later. The FDA post-marketing data, however, have not been properly analyzed and used for quantitative characterization of the risks of severe side effects. Here we develop a profiling system - the Early Drug Alerts, EDA - in which we separated the drug-dependent rates of adverse effects from the disease-dependent rates. The Early Drug Alerts also improved signal- to-noise ratio by aggregating related adverse reactions in order to overcome the issues of data fragmentation, data scarcity and multiple ways in which the underlying problem may manifest itself. Many of the established risk signals were confirmed by clinical studies while some safety alerts revealed by the EDA analysis need immediate attention.

      3. Finally, by integrating off-target profile, adverse reaction profile, and gene-phenotype relationship, we discovered a reason why raloxifene, an anti-breast-cancer modulator of estrogen receptor, may cause thromboembolism and confirmed its binding to thrombin. This emerging profiling pipeline could be applied to raise alerts about drug-associated adverse reactions in new drug candidates, explain observed adverse effects, discover novel anti-targets explaining side effects, repurpose drugs for new indications, and expedite the rational design of more effective, but less toxic drug.

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.