This page lists a summary of the ten most recent news stories that concern the UC Davis Genome Center. Click on the title of each news item or on the ‘Read more…’ links that follow to see the full story. A feed with all news stories is also available.

The next Bioinformatics Core training workshop will be on ‘RNA-Seq and ChIP-Seq Analysis with Galaxy’, December 16–19

October 13, 2014

Bioinformatics Core (center aligned)

Details are now available on the next workshop to be run by the Genome Center’s Bioinformatics Core. The workshop, which will be held between December 16–19 this year, will instruct participants in how to use Galaxy for analysis of RNA-Seq and ... Read more...

Video from Justin Siegel’s talk at ‘An Evening with the Genome Center’

October 8, 2014

Last Saturday (October 4th), the Genome Center reached out to the community and hosted another An Evening with the Genome Center event. This time, the event featured Assistant Professor Justin Siegel, who gave an engaging talk on the following subject:

A Winning Combination: Video Games + Science: A unique strategy for training the next generation of ... Read more...

DNA Technologies and Expression Analysis Cores News Bulletin: September 2014

October 5, 2014

New Recharge Rates

The recharge rates at our Core Labs have stayed unchanged for the last three years while reagent prices have increased annually. Thus, we have to adjust the rates to be able to continue offering at–cost sequencing services. Details of the the new rates — which went into effect on October 1st — are ... Read more...

C. Titus Brown is recipient of new Data-Driven Discovery Award from Gordon and Betty Moore Foundation

October 2, 2014



C. Titus Brown is one of 14 researchers who have been selected for the new Moore Investigators in Data-Driven Discovery award. These awards are part of a $60 million, five-year Data-Driven Discovery Initiative within the Gordon and Betty Moore Foundation’s Science Program. Titus’s talk and proposal regarding ... Read more...

Beautiful images of Arabidopsis made freely available by Alex Kozik and the Comai Lab

September 26, 2014

The photographic talents of Alex Kozik and the supply of many Arabidopsis plants from the Comai Lab have combined to produce a set of beautiful macro photos that they have generously made freely available to anyone. A few samples are shown below, but you can see all of the many other amazing images on ... Read more...

10 things you may not know about the new Genome Center website

September 25, 2014

GC web update

The new website has been up and running for about six weeks now. Time for a quick update:

  1. We’ve had nearly 7,000 hits from 66 different countries
  2. In the contiguous 48 states, we’ve had visits from everywhere except North Dakota, New Hampshire, and Vermont
  3. The People ...

    Justin Siegel will present at the next ‘Evening with the Genome Center’ on October 4th

    September 24, 2014

    The next event will be on October 4th, and will feature Justin Siegel. His presentation is titled:

    A Winning Combination: Video Games + Science: A unique strategy for training the next generation of scientists to build novel therapeutics and bio-based products.

    This event is scheduled for 7:30–8:30 and ...

    New: PacBio office hours at the DNA Technologies Core

    September 22, 2014

    We are pleased to announce monthly PacBio office hours at the Core Labs. Pacific Biosciences Field Applications Scientist Nicole Rapicavoli will be answering your questions and assisting with the design of experiments every third Tuesday of the month (starting Tuesday, August 19th) from 1 to 4 ... Read more...

    RNA-seq library preparation workshop being organized by the DNA Technologies and Expression Analysis Cores

    September 22, 2014

    The DNA Tech and Expression Analysis cores are offering a three day library preparation workshop from October 22nd to 24th.  You can bring your own RNA-sample, generate your first RNA-seq library, and generate your first data during the course.  The course will cover the technical details ... Read more...

    Dr. Charlie Gersbach to speak at the Genome Center about editing the human genome with the CRISPR/CAS system

    September 19, 2014

    Charles_GersbachDr. Gersbach is a leader in genome engineering and is based in the Biomedical Engineering and Center for Genomics and Computational Biology at Duke University. He is the 2014 recipient of the Outstanding Young Investigator Award by the American Society for Gene and ... Read more...




More news…

Upcoming Talks and Events

  • October 17, 2014
    • David Rocke — Differential Expression Analysis with RNA-SEQ: Review and Critique
      Starts: 9:00 am
      Ends: October 17, 2014 - 10:00 am
      Location: GBSF 4202
      Description: Structural & functional genomics focus group meeting

      Speaker: David Rocke, Public Health Sciences and Biomedical Engineering.


      RNA-Seq data are increasingly used for whole-genome differential mRNA expression analysis in lieu of gene expression arrays such as those from Affymetrix and Illumina. We review commonly used methods for this type of analysis, including DESeq, edgeR, and Cuffdiff2, by placing them within a common framework that allows comparisons of components of the methods as well as of the overall results. We also review a number of recent studies comparing these methods in terms of false positives and sensitivity, and add additional results of our own. We show that none of the existing methods is fully satisfactory, with most identifying large numbers of genes as differentially expressed even when there are none, but some will lead to better, more reliable results than others. This area is still early in its intellectual development and is changing rapidly. This has important implications for how applied researchers should approach the analysis of their RNA-Seq data and how these analyses should be documented.
    • Dr. Nissim Hay— The Role of Akt Isoforms in Cancer and Diabetes: Lessons from Akt KO Mice
      Starts: 9:00 am
      Ends: October 17, 2014 - 10:00 am
      Location: UCDMC Cancer Center Auditorium, Sacramento
      Description: Cancer Center Biology Seminars
    • Daniela Barile — Milk bioactive compounds: prebiotic effect and beyond
      Starts: 12:10 pm
      Ends: October 17, 2014 - 1:00 pm
      Location: GBSF 1005
      Description: MMI 291 Seminar Series: "Emerging Challenges in M
      icrobiology and Immunology"

      Speaker: Daniela Barile, Ph.D., Assistant Professor, Food Science and Technology, University of California, Davis
    • Dr Sriram Subramaniam — Applications to HIV/AIDS and signal transduction: cryo-electron microscopy comes of age
      Starts: 2:00 pm
      Ends: October 17, 2014 - 3:00 pm
      Location: LSA 1022
      Description: Dr Sriram Subramaniam is from the National Cancer Institute, NIH, Bethesda

      Abstract: Recent breakthroughs in the field of cryo-electron microscopy provide new opportunities for determination of the structures of a variety of macromolecular assemblies and small dynamic protein complexes that are not amenable to analysis by X-ray crystallography or NMR spectroscopy. In addition, advances in technologies for imaging whole cells and tissues in 3D at high resolution have opened up new vistas for 3D structural imaging. The long-term mission of our research program is to obtain an integrated molecular understanding of viral and cellular architecture by combining advanced technology development for 3D imaging with novel methods for image segmentation and computational analysis. Specific areas of current interest that I will discuss include: structural biology of HIV entry, mechanisms of membrane transport, and assembly of protein complexes involved in metabolism.
  • October 20, 2014
    • Dr. Charlie Gersbach — Editing the Human Genome and Epigenome with the CRISPR/Cas9 System to Correct Genetic Disease and Program Cell Phenotype
      Starts: 10:00 am
      Ends: October 20, 2014 - 11:00 am
      Location: GBSF 1005
      Description: Dr. Gersbach (Duke University) is a leader in genome engineering. He is the 2014 recipient of the Outstanding Young Investigator Award by the American Society for Gene and Cell Therapy (ASGCT), largely for this work with Duchenne Muscular Dystrophy.
    • Marty Usrey — Dynamic Properties of Neural Circuits for Vision
      Starts: 12:10 pm
      Ends: October 20, 2014 - 1:00 pm
      Location: 1022 Life Sciences
      Description: Neurobiology, Physiology & Behavior 2014 Fall Faculty Seminar Series.