Willet E Cali et al., Empirical assessment of competitive hybridization and noise in ultra high density canine tiling arrays Transcriptome analysis. BMC Bioinformatics (2013) doi:10.1186/1471-2105-14-231 Li Sheng et al., An optimized algorithm for detecting and annotating regional differential methylation Proceedings of the Third Annual RECOMB Satellite Workshop on Massively Parallel Sequencing (RECOMB-seq 2013) RECOMB-seq: Third Annual Recomb Satellite Workshop on Massively Parallel Sequencing. BMC Bioinformatics (2013) doi:10.1186/1471-2105-14-S5-S10 The UCSC Genome Browser Introduction
Biotechnology Annual Review - UCSC Genome Browser: Deep support for molecular biomedical research Abstract The volume and complexity of genomic sequence data, and the additional experimental data required for annotation of the genomic context, pose a major challenge for display and access for biomedical researchers. Genome browsers organize this data and make it available in various ways to extract useful information to advance research projects. The UCSC Genome Browser is one of these resources. The official sequence data for a given species forms the framework to display many other types of data such as expression, variation, cross-species comparisons, and more. Visual representations of the data are available for exploration.
For beginners in the field, this review highlights the key features of the genome browser at UCSC for data display, and provides nearly step-by-step procedures for creating publication quality maps. The browser offers an engine (Blat) for searching a known genomic DNA for correspondence with protein and DNA sequences specified by the user. The results provide links to graphical displays, known as maps. Users can create “designer maps” by adding Tracks to view various types of data and specific landmarks. The browser offers an extensive list of options. They include the position of annotated genes, the position of reference cDNA sequences (RefSeq from GenBank), the position of alternatively spliced mRNA species, and predictions derived from computational models to identify potential transcription start sites and potential protein binding elements in genomic DNA. Molecular Biotechnology, Volume 38, Number 3
To receive announcements of new genome assembly releases, new software features, updates and training seminars by email, subscribe to the genome-announce mailing list. 06 March 2014 - The new GRCh38 Human Genome Browser is here! In the final days of 2013, the Genome Reference Consortium (GRC) released the eagerly awaited GRCh38 human genome assembly, the first major revision of the human genome in more than four years. During the past two months, the UCSC team has been hard at work building a browser that will let our users explore the new assembly using their favorite Genome Browser features and tools. Today we're announcing the release of a preliminary browser on the GRCh38 assembly. Although we still have plenty of work ahead of us in constructing the rich feature set that our users have come to expect, this early release will allow you to take a peek at what's new.
Genome Browsers - Tyra Wolfsberg (2012)
BITs: Genome browsers and interpretation of gene lists.
BITS: UCSC genome browser - Part 1 1,471 views These are the first lecture slides of the BITS bioinformatics training session on the UCSC Genome Browser. ... These are the first lecture slides of the BITS bioinformatics training session on the UCSC Genome Browser. See http://www.bits.vib.be/index.php?option=com_content&view=article&id=17203990:orange-genome-browsers-ucsc-training&catid=81:training-pages&Itemid=190
BITS training - UCSC Genome Browser - Part 2 876 views These is the second part of the lecture slides of the BITS bioinformatics training session on the UCSC Genome Browser. ... These is the second part of the lecture slides of the BITS bioinformatics training session on the UCSC Genome Browser. See http://www.bits.vib.be/index.php?
rnomics Twitter timeline / dna limits Filter your results @ GenoScapeGC GenoScapeGC GenoScapeGC Excellent piece by @ Erika_Check DNA has limits, but so does study questioning its value, geneticists say http://t.co/maZQWwfa DNA has limits, but so does study questioning its value, geneticists say : Nature News Blog Scientists are irked over a paper claiming, as The New York Times reported on Monday, that " DNA's power to predict illness is limited."
What the ‘limits of DNA’ story reveals about the challenges of science journalism in the ‘big data’ age By Erika Check Hayden | April 6, 2012 | 30 Comments As a science journalist, I sympathize with book reviewers who wrestle with the question of whether to write negative reviews. It seems a waste of time to write about a dog of a book when there are so many other worthy ones; but readers deserve to know if Oprah is touting a real stinker. On 2 April, Science Translational Medicine published a study on DNA’s shortcomings in predicting disease. My editors and I had decided not to cover the study last week after we saw it in the journal’s embargoed press packet, because my sources offered heavy critiques of its methods.
All genomes are dysfunctional: broken genes in healthy individuals Breakdown of the number of loss-of-function variants in a "typical" genome I don’t normally blog here about my own research, but I’m making an exception for this paper. There are a few reasons to single this paper out: firstly, it’s in Science (!); and secondly, no fewer than five Genomes Unzipped members (me, Luke, Joe, Don and Jeff) are co-authors. For me it also represents the culmination of a fantastic postdoc position at the Wellcome Trust Sanger Institute (for those who haven’t heard on Twitter, I’ll be starting up a new research group at Massachusetts General Hospital in Boston next month). Readers who don’t have a Science subscription can access a pre-formatted version of the manuscript here.
Background Cryptic genetic variation (CGV) is defined as “standing genetic variation that does not contribute to the normal range of phenotypes observed in a population, but that is available to modify a phenotype that arises after environmental change or the introduction of novel alleles” [Gibson & Dworkin, 2004]. As such, CGV fills the gap between : 1. expressed genetic variation, defined as genetic variation that contributes to the normal range of phenotypes actually present in a population ; 2. neutral genetic variation, that does not contribute to phenotypes under any likely genetic or environmental conditions ; a typical example of neutral genetic variation would be synonymous substitutions in protein coding sequences. Cryptic genetic variation promotes rapid evolutionary adaptation in an RNA enzyme (Hayden et al, Nature, 2011)
NIH VideoCasting and Podcasting
VideoCasting - Cancer Genomes Analysis: Computational Challenges and Approaches Dr. Getz will discuss how the recent revolution in sequencing technologies has enabled comprehensive characterization of many thousands of cancer genomes, for example from The Cancer Genome Atlas (TCGA) and the International Cancer Genome Consortium (ICGC). These resulting data pose new computational challenges in detecting the various genomic alterations in the cancer genomes from sequencing data, understanding the mechanisms that create them, and dealing with heterogeneous samples. In addition, he will discuss the greatest challenge is how to introduce these findings to clinical trials and standard practice. The revolution in sequencing technologies in recent years has enabled comprehensive characterization of many thousands of cancer genomes (e.g.
HGM 2012 • Scientific Program
We Are Data : Evan Anthony
Here is a Twitter chat…with Misha Angrist
Introduction to automatic gene annotation (Cold Spring Harbor, NY, US) | Ensembl Training Events
Chromosome Diagrams in Biopython | O|B|F News
Online lecture series on genomics and bioinformatics | Code for Life
Juan Enriquez on genomics and our future
Introduction to The 'Omics Age | Learn Science at Scitable
Podcast : Frontiers in genetics and genomics
Guide to the UCSC Genome Browser | Learn Science at Scitable
De novo genome assembly: what every biologist should know : Nature Methods
transcriptomes, bioinformatics, and light regulated genes « Fungal Evolutionary Genomics
The Human Genome: A Decade of Discovery, Creating a Healthy Future: Agenda, Videos and Presentation Slides
1000 Genomes Project data available on Amazon Cloud, March 29
Current Topics in Genome Analysis 2012
Genomics Q & A: Insights and Impacts
Personal Cancer Genomics