Free Unix & Perl Course Aimed at Biologists

It is increasingly common that biologists have to deal with vast amounts of in silico data as part of their research, often in the form of many large text files that are the output from research equipment or computer programs. To help biology grad students at UC Davis deal with this data, Keith Bradnam and Ian Korf teach a course that helps them to learn the essential aspects of the Perl programming language. The course is very much aimed at people with no prior experience in either programming or Unix. Feedback from this course has been very positive and so they have decided that the course should be available to anyone who is interested. The course material is available at:

http://korflab.ucdavis.edu/Unix_and_Perl/

There is also a Google Group tied to this course so people can ask questions and get help as they work their way through the course:

http://groups.google.com/group/unix-and-perl-for-biologists

Forefronts of Genomics: 2008/2009 Schedule
All Seminars at 11:00 am in the GBSF Auditorium unless otherwise noted.

Sept 26, 2008 Note: 10:00 am	Drew Endy
	Biological Engineering Division Massachusetts Institute of Technology Seminar Flier
Oct 17, 2008	Bob Jernigan
	L.H. Baker Center for Bioinformatics and Biological Statistics Iowa State University
Nov 21, 2008	David Schwartz
	Professor of Genetics and Chemistry University of Wisconsin
Dec 19 2008	No Seminar
Jan 16 2009	TBA
Feb 20 2009	Gail Mandel (host: Farnham)
	Vollum Institute Oregon Health and Science University
Mar 20 2009	Xianlin Han
	Associate Professor of Medicine Washington University School of Medicine
April 17 2009	Joe Ecker
	Plant Molecular and Cellular Biology Laboratory Salk Institute
May 15 2009	Karen Usdin
	Laboratory of Molecular and Cellular Biology NIDDK, National Institutes of Health
June 12 2009	Genome Center Research Day
Sept 18 2009	Jay Keasling
	Berkeley Center for Synthetic Biology University of California, Berkeley
Oct 16 2009	Mark Vidal
	Center for Cancer Systems Biology (CCSB) and Department of Cancer Biology Dana-Farber Cancer Institute
Jan 15 2010	Steve Jacobsen
	Howard Hughes Medical Institute and the Department of MCD Biology UCLA
Mar 19 2010	Graham Coop
	Evolution and Ecology UCD
May 26 2010	Mark Gerstein
	Albert L Williams Prof Biomedical Informatics & Prof Mol Biophys & Biochem and Computer Science Yale University

For more information about the series, please contact Angela Cummins (530) 754-4986.

Upcoming Seminars

Bi-weekly Bioinformatics Tech Forums - Tuesdays 11:00am-12:00pm, Room 4202

The purpose of the Tuesday Bioinformatics Technology Forum (BTF) meeting series at the Genome Center is to provide a campus-wide venue to show and tell how bioinformatics tools or related information technology actually work. To present your practical problems and ask bioinformatics help is also an appropriate thing to do. In the meeting, people are encouraged to do live demonstrations as well as brief introductions of their work or problems. All talks are informal (although introduction slides are often helpful) and active interactions are expected. BTF is operating by a committee, which consists of Kyoungmi Kim and Dawei Lin. If you want to talk at BTF, please send an email to lhslin@ucdavis.edu to schedule your talk. BTF meetings are usually held at 11:00am-12:00pm every other Tuesday in room 4202, GBSF.

ENCYCLOPEDIA OF DNA PUBLISHED

A consortium of U.S. and international researchers, including a team led by Peggy Farnham, Professor of Pharmacology and Associate Director at the Genome Center, has completed a detailed study of a piece of the human genome. The study, which was carried out by 35 groups from 80 organizations around the world, was published in the June 14 issue of Nature and in 28 companion papers published in the June issue of Genome Research.

Recent Publications from the Genome Center

CEGMA: a pipeline to accurately annotate core genes in eukaryotic genomes, 2007, Bioinformatics, 23, 9, Genis Parra, Keith Bradnam, and Ian Korf The numbers of finished and ongoing genome projects are increasing at a rapid rate, and providing the catalog of genes for these new genomes is a key challenge.. read more ...

Structure- based redesign of the dimerization interface reduces the toxicity of zinc-finger nucleases Nature Biotechnology, 25:786-793. Cover article
The Segal Lab, with collaborator Toni Cathomen at Charite´ Medical School in Berlin, Germany, describe an important advance in methods for editing the genomes of living cells. read more...

Genome-Wide Analysis of KAP1 Binding Suggests Autoregulation of KRAB-ZNFs
We performed a genome-scale chromatin immunoprecipitation (ChIP)-chip comparison of two modifications (trimethylation of lysine 9 [H3me3K9] and trimethylation of lysine 27 [H3me3K27]) of histone H3 in Ntera2 testicular carcinoma cells and in three different anatomical sources of primary human fibroblasts.read more...

Folding free-energy landscape of villin headpiece subdomain from molecular dynamics simulations. PNAS, in-press (published online)
Lei et al studied the folding process of a protein called villin headpiece (HP35) using molecular dynamics simulation and achieved high accuracy ab initio folding to as close as 0.46 Å. The achievement marks the first time that ab initio simulations can reach this level. The simulation demonstrated a comprehensive picture on the kinetics and thermodynamics of HP35 folding. read more ...

Forces Shaping the Fastest Evolving Regions in the Human Genome. PLoS Genetics, 2: e168.
Katherine Pollard and colleagues identified 202 genome sequences that are highly conserved between chimpanzee and other vertebrates, but changed significantly in the human lineage since divergence from the chimp-human ancestor. These Human Accelerated Regions (HARs) are mostly in non-coding DNA, often nearby proteins involved in transcription. There is some evidence of positive selection in the most accelerated HARs. In addition, the human-specific changes show a strong bias for AT to GC nucleotide changes, suggesting either biased gene conversion or isochore selection. read more ...

"Macronuclear Genome Sequence of the Ciliate Tetrahymena thermophila, a Model Eukaryote." PLoS Biol. 2006 Aug 29;4(9).
In the September issue of PLoS Biology, Jonathan Eisen and colleagues report on the sequencing and
analysis of the macronuclear genome of the ciliate Tetrahymena thermophila. read more ...

"An RNA gene expressed during cortical development evolved rapidly in humans." Nature. 2006 Aug 16.
Pollard and colleagues scanned the human genome for DNA sequences that have been nearly frozen throughout vertebrate evolution but changed rapidly in the human lineage since the chimp-human ancestor. read more ...

"Structure of Aart, a Designed Six-Finger Zinc Finger Peptide, bound to DNA" J. Mol. Biol. Aug 2006. doi:10.1016/j.jmb.2006.08.016
The Segal Lab, in collaboration with crystallographer Nancy Horton at U. Arizona, present the first crystal structure of an engineered, 6-zinc finger DNA-binding protein bound to DNA. read more ...

"Suz12 binds to silenced regions of the genome in a cell-type-specific manner." Genome Res. published online Jun 2, 2006.
In this manuscript, Squazzo and colleagues use the technique of genome-wide ChIP-chip to identify thousands of promoters that are silenced by Polycomb Group Repression Complexes (PRCs). read more ...