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GET TO KNOW YOUR NEIGHBOR ; SDEE 2015 Year End Social on Dec 8th in San Diego ; Must Attend 5-Day Event in San Diego Starting Tomorrow! -- CDW on Cells, Sensors, and Sysems, with Updates on Stem Cells ; SDEE October 2015 Event - Financings: Tales from the Tranches ; Allele Biotech Takes Major Step into Nano Antibody Leadership Position
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NexGen Sequencing, Epigenetics, and Editing
Genomics: Zebrafish earns its stripes
Friday, 04.19.2013, 09:29am
The reported sequence of the zebrafish genome, together with the production of mutant strains representing more than one-third of all its protein-coding regions, will accelerate the characterization of human genes.
A CRISPR/Cas system mediates bacterial innate immune evasion and virulence
Wednesday, 04.17.2013, 08:50am
CRISPR/Cas (clustered regularly interspaced palindromic repeats/CRISPR-associated) systems are a bacterial defense against invading foreign nucleic acids derived from bacteriophages or exogenous plasmids. These systems use an array of small CRISPR RNAs (crRNAs) consisting of repetitive sequences flanking unique spacers to recognize their targets, and conserved Cas proteins to mediate target degradation. Recent studies have suggested that these systems may have broader functions in bacterial physiology, and it is unknown if they regulate expression of endogenous genes. Here we demonstrate that the Cas protein Cas9 of Francisella novicida uses a unique, small, CRISPR/Cas-associated RNA (scaRNA) to repress an endogenous transcript encoding a bacterial lipoprotein. As bacterial lipoproteins trigger a proinflammatory innate immune response aimed at combating pathogens, CRISPR/Cas-mediated repression of bacterial lipoprotein expression is critical for F. novicida to dampen this host response and promote virulence. Because Cas9 proteins are highly enriched in pathogenic and commensal bacteria, our work indicates that CRISPR/Cas-mediated gene regulation may broadly contribute to the regulation of endogenous bacterial genes, particularly during the interaction of such bacteria with eukaryotic hosts.
Genome-wide mapping of RNA structure using nuclease digestion and high-throughput sequencing
Thursday, 04.11.2013, 08:55am
RNA structure is important for RNA function and regulation, and there is growing interest in determining the RNA structure of many transcripts. Here we provide a detailed protocol for the parallel analysis of RNA structure (PARS) for probing RNA secondary structures genome-wide. In this method,
[Report] Inhibition of PRC2 Activity by a Gain-of-Function H3 Mutation Found in Pediatric Glioblastoma
Wednesday, 04.03.2013, 09:07am
Mutations of histones in some cancers results in inhibition of enzymes that lay down epigenetic marks on chromatin.Authors: Peter W. Lewis, Manuel M. Müller, Matthew S. Koletsky, Francisco Cordero, Shu Lin, Laura A. Banaszynski, Benjamin A. Garcia, Tom W. Muir, Oren J. Becher, C. David Allis
Predicting the influence of common variants
Tuesday, 04.02.2013, 09:26am
An ever-larger proportion of the liability to common and complex disease can be obtained by progressively larger studies. However, for most diseases, the sample sizes required to gain usable predictions will be out of reach of sequencing technologies for the foreseeable future. Array-based genotyping genome-wide association studies (GWAS) still offer a reliable harvest of biological hypotheses for many diseases, together with the secondary benefit of slowly improving prediction.
Aegilops tauschii draft genome sequence reveals a gene repertoire for wheat adaptation
Monday, 03.25.2013, 08:50am
About 8,000 years ago in the Fertile Crescent, a spontaneous hybridization of the wild diploid grass Aegilops tauschii (2n = 14; DD) with the cultivated tetraploid wheat Triticum turgidum (2n = 4x = 28; AABB) resulted in hexaploid wheat (T. aestivum; 2n = 6x = 42; AABBDD). Wheat has since become a primary staple crop worldwide as a result of its enhanced adaptability to a wide range of climates and improved grain quality for the production of baker’s flour. Here we describe sequencing the Ae. tauschii genome and obtaining a roughly 90-fold depth of short reads from libraries with various insert sizes, to gain a better understanding of this genetically complex plant. The assembled scaffolds represented 83.4% of the genome, of which 65.9% comprised transposable elements. We generated comprehensive RNA-Seq data and used it to identify 43,150 protein-coding genes, of which 30,697 (71.1%) were uniquely anchored to chromosomes with an integrated high-density genetic map. Whole-genome analysis revealed gene family expansion in Ae. tauschii of agronomically relevant gene families that were associated with disease resistance, abiotic stress tolerance and grain quality. This draft genome sequence provides insight into the environmental adaptation of bread wheat and can aid in defining the large and complicated genomes of wheat species.
  » Epigenetic control of female puberty
  » TALENs and ZFNs are associated with different mutation signatures
  » Tracking recent adaptive evolution in microbial species using TimeZone
  » Interlaboratory reproducibility of large-scale human protein-complex analysis by standardized AP-MS
  » How much coverage do you need when doing deep sequencing?
  » Identifying RNA editing sites using RNA sequencing data alone
  » Epigenetics: Reading methylated genomes
  » Epigenetic inheritance of a cocaine-resistance phenotype
  » Impaired adult myelination in the prefrontal cortex of socially isolated mice
  » Kits herald new wave of genomics diagnostics for cancer

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::| Hot News
Analysis of five years of controlled access and data sharing compliance at the International Cancer Genome Consortium
Analysis of computational footprinting methods for DNase sequencing experiments
Mammalian NET-seq analysis defines nascent RNA profiles and associated RNA processing genome-wide
Co-occurrence of MYC amplification and TP53 mutations in human cancer
Quantification of private information leakage from phenotype-genotype data: linking attacks
Improving databases for human variation
A diamond in the ruff
Microbiomes: Curating communities from plants
Small island, big genetic discoveries
TARDIS, a targeted RNA directional sequencing method for rare RNA discovery