UC Davis Bioinformatics Training Program

Bioinformatics workshops presented by the University of California, Davis Bioinformatics Core

Bioinformatics Short Course 2012

Sponsored in part by:

We are happy to announce the 2012 Bioinformatics Short Course will be held September 10-14, 2012. This will be our 5th year offering our Bioinformatics Short Course (visit our year 2010 and 2011 sites). Each year has provided us opportunity to expand the course from previous years, and this year is no different. The course includes a rich collection of lectures and hands-on sessions. In morning sessions, leading experts in each field will introduce basic concepts as well as present real world practical examples. During the afternoons, students will have a chance to walk through software and protocols for handling next-generation data analysis. While biological and medical knowledge are helpful, students do not need to have prior programming skills to participate in the course.

To register for the 2012 Bioinformatics Short Course on Next-Generation Sequencing, please click here.

Our panel of lecturers and guests will touch on the following topics: sequencing technologies (Illumina, SOLiD, 454, Ion Torrent, Pacific Biosciences, Oxford Nanopore), read quality assessment and improvement (adapter and quality trimming), de novo genome and transcriptome assembly, variant discovery (SNPs, indels), RNA-Seq (differential gene expression, isoform discovery), ChIP-Seq, miRNA discovery, data visualization (genome browsers, alignment viewers), metagenomics, bioinformatics IT issues and infrastructure.

Here are just some of the hands-on classes offered as part of the course:

  • read QC
  • genome assembly
  • variant discovery
  • RNA-Seq analysis
  • ChIP-Seq analysis
  • data visualization

All exercises will use the Galaxy platform (http://usegalaxy.org), and we will focus on Illumina read data.

Course seating is limited to stimulate an effective learning environment and ensure sufficient one-on-one attention is provided. Course registration will be $1,300, while students, professors, and other academic professionals receive a $200 discount. Pre-registration is now open, so click here to sign up now to ensure your spot in the course.

Update – 2012/09/04 : Course map

View 2012 Bioinformatics Short Course Map (201209BSC – September 10-14, 2012) in a larger map

Update – 2012/08/21 : Full schedule now live

Update – 2012/08/15 : Registration is now open!

Registration is now open for this course as well as the fall workshops: Cloud Computing for Bioinformatics and Data Analysis & Visualization using R. To register for these courses, click here.

Update – 2012/08/13 : Preregistration closed. General Registration opens this week

Preregistration is closed, but we’ll be opening up general registration this week, so stay tuned!

Update – 2012/06/27 : Pre-registration now open

We’re taking signups for the 2012 Bioinformatics Short Course, happening September 10-14, 2012 held at the University of California, Davis. When registration opens, those that have applied will be notified with the update and moved to the top of the list. Seating is limited as we strive to deliver a stellar learning environment with full access to course presenters, industry professionals, and plenty of one-on-one help. Because of this limited space, we urge you to pre-register below to save a seat for this week-long intensive course.

Click here to preregister.

Course Speakers

lin-daweiDawei Lin

Dawei Lin is currently the Bioinformatics Core Director. He received his Ph.D. from Peking
University, China in Computational and Structural Biology in 1996. He created China’s
first Bioinformatics server in 1995. He started his career at the Protein Data Bank (PDB) at
Brookhaven National Laboratory, a worldwide repository for macromolecular structures.
In his current position, he is leading his team to provide expertise and infrastructure to
carry out acquisition, curation, and distribution of complex data sets as well as to develop
and perform computations, analyses and simulations addressing a wide variety of biological
questions from genomics to network biology.


bingham-jonathanJonathan Bingham

Jonathan Bingham is Product Manager for informatics at Pacific Biosciences, where he leads
the informatics, software and hardware roadmap for working with single-molecule real-time
sequencing data. He’s also a coder and startup co-founder who got going in bioinformatics
with a year at Los Alamos National Lab in theoretical and computational biology.


monica-brittonMonica Britton

Monica Britton joined the Bioinformatics Core in 2009 after working in the UC Davis
Plant Sciences Dept. for seven years. There she earned her Ph.D. in Genetics, studying the
interactions between walnut roots and plant parasitic nematodes. Previously, she received a
BSc in Horticulture from Cal Poly San Luis Obispo. In the Bioinformatics Core, Monica uses
here knowledge of biology in the analysis of data, and has shown that a biologist can learn
some Linux and Perl.


luca-comaiLuca Comai

Luca Comai obtained his Ph.D. from UC Davis, worked for several years at Calgene Inc, one of
the first plant biotech companies, and then joined the faculty at the University of Washington, in
Seattle. Since 2006 he is a professor of Plant Biology working at the UC Davis Genome Center.
He studies the effect of gene and chromosomal dosage on interspecific hybridization, phenotype
and evolution. He is a co-developer of TILLING, a functional genomic tool for mutation


de-la-vega-franciscoFrancisco de la Vega

Francisco De La Vega is Vice President of Genome Science at Real Time Genomics, a startup
company providing bioinformatics tools for the large-scale analysis of high-throughput
sequencing data. Previously he spent 13 years at Applied Biosystems (currently Life
Technologies), where he was the Distinguished Scientific Fellow, Vice President of Next-
Generation Sequencing Applications, a distinguished inventor, and a founding member of
the Life Technologies’ i2 (Invention x Innovation) Society. He was member of the steering
committee of the 1000 Genomes Project Consortium, an international collaboration that is
sequencing the genomes of thousands of diverse people around the world. Francisco earned
his Doctor of Science degree in Genetics and Molecular Biology at CINVESTAV (Mexico),
studying the genetic regulation of protein biosynthesis in the bacteria/bacteriophage system
with emphasis in the computational analysis.


durbin-johnson-blytheBlythe Durbin-Johnson

Blythe Durbin-Johnson is a biostatistician with multiple years of experience in statistics
related to clinical and translational research. Her dissertation work at UC Davis focused on
data transformations for gene expression microarrays. She spent two years at UC Berkeley
as an NSF Postdoctoral Fellow in Interdisciplinary Informatics, followed by four years in the
pharmaceutical industry. She returned to UC Davis in 2009 in order to be able to bike to work
and because she missed the smell of cows. When not working with the UCD Genome Center
Bioinformatics Core, she analyzes data for a dizzying array of projects as part of the Biostatistics
Core at the Clinical and Translational Science Center.


facciotti-marcMarc Facciotti

Marc Facciotti is an Assistant Professor in the Department of Biomedical Engineering at the
UC Davis Genome Center. Before this, he worked in the Institute for Systems Biology in Seattle,
WA after finishing a postdoctoral fellowship there. He earned his Ph.D. in biophysics from UC
Berkeley and did his undergraduate in biochemistry at UC Davis.


joe-fassJoe Fass

Joseph Fass joined the UC Davis Bioinformatics Core in 2007 after wandering through the fields
of Chemical Engineering, Cell Biology, Molecular Biology, and Scientific Computing. He has
spent the past two years dabbling in sequence assembly, microarray analysis, SNP discovery, and
other meat n’ potatoes bioinformatics tools.


gepts-paulPaul Gepts

Paul Gepts is a plant geneticist and breeder, primarily interested in the study of crop
biodiversity and its utilization in the development of improved varieties. To achieve his
research and development goals, he combines botanical explorations, field studies, and
laboratory analyses to better understand the processes that have shaped geographic and
ecological patterns of genetic diversity and to determine the inheritance of agronomic
traits. One of the specific activities of his program is the development of PhaseolusGenes,
a genome database set up in collaboration with the Bioinformatics Core of the UC Davis
Genome Center. The PhaseolusGenes database is set up specifically to assist bean breeders
in the development new markers to facilitate marker-assisted selection as a tool in breeding.


nikhil-joshiNik Joshi

Nikhil Joshi is a bioinformatics programming, database delving, salsa dancing, scrabble
playing genius. He has a Master’s degree in Computer Science and a Ph.D. in sheer chutzpah.



kim-ryanRyan Kim

Ryan Kim is the Director of the DNA Technology at UC Davis Genome Center. He, along
with the core, are leading the implementation of second and third generation sequencing
technology (Illumina, 454, and PacBio), genotyping applications, and other emerging
technologies for large scale genome study. Among the sequencing projects he’s been involved
include personal genome projects (sequencing the genomes of twins and Korean male), de
novo sequencing of cotton, cacao medicago, legumes, major pathogens of chili (P. capsici)
and citrus (Huanglongbing), and numerous de novo, re-sequencing, and comparative
genome sequencing projects.


ian-korfIan Korf

  • Assistant Professor: Molecular & Cellular Biology, Genome Center
  • email: ifkorf@ucdavis.edu

Ian Korf has had a keen interest in biology and computers since he was 15. It wasn’t until he was
a post-doc at the Washington University Genome Sequencing Center that he realized that he
could combine these two interests in the emerging field of bioinformatics. Dr. Korf specializes
in sequence analysis algorithms (alignment, gene prediction, etc.) and their applications. He is
currently an Assistant Professor at UC Davis.


teri-muellerTeri Mueller

Teri Mueller received her BS in Biology and Marine Science at The University of Alabama. Prior
to joining Roche in 2007, she worked nine years at the Clemson University Genomics Institute
and The University of Arizona Genomics Institute with a concentration in finishing.


gary-schrothGary Schroth

Gary Schroth is a Senior Director of Expression Applications R&D at Illumina. Before joining
Illumina, he previously held research positions at Solexa, Applied Biosystems, Genelabs
Technologies and Gen-Probe. Gary obtained his Ph.D. in Biochemistry from the University of
California, Davis. Following graduation, he was awarded an American Cancer Society postdoctoral
fellowship grant to study at Oregon State University. During his career, Gary has
published more than 35 peer-reviewed research papers and holds 15 United States patents. His
main research interests are in the areas of gene expression, epigenetics, and genome structure
and function.


wang-zhongZhong Wang

Zhong Wang is the Genome Analysis Group Lead at JGI, as well as a professor at Fudan University in China  and as an editor for Nature Scientific Reports and BMC Cell & BioSciences. He also serves as a scientist at the Lawrence Berkeley National Lab in Berkeley, California. He’s done work at Yale and Duke universities as well as served as the Director of Bioinformatics at the Yale Stem Cell Center.