Posts Tagged ‘csds’

The Pangenome: Are Single Reference Genomes Dead? | The Scientist Magazine(R)

December 17, 2016

The #Pangenome: Are Single Reference Genomes Dead? YES!
http://www.The-Scientist.com/?articles.view/articleNo/47510/title/The-Pangenome–Are-Single-Reference-Genomes-Dead-/ Division into conserved/core & dispensable/variable genes

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smart plugs for heating and light

December 9, 2016

https://www.hivehome.com/us

Genome-wide association study identifies 74 loci associated with educational attainment : Nature : Nature Publishing Group

May 21, 2016

GWAS identifies 74 loci associated w. educational attainment http://www.nature.com/nature/journal/vaop/ncurrent/full/nature17671.html Described in 3 pgs of main text & 146 pgs of supplement

http://www.nature.com/nature/journal/vaop/ncurrent/full/nature17671.html

BMC Genomics | Full text | Pseudogenes transcribed in breast invasive carcinoma show subtype-specific expression and ceRNA potential

July 31, 2015

[440 @GencodeGenes] #Pseudogenes transcribed in breast…carcinoma show subtype-specific expression & ceRNA potential http://www.biomedcentral.com/1471-2164/16/113

Oqtans: the RNA-seq workbench in the cloud for complete and reproducible quantitative transcriptome analysis. – PubMed – NCBI

July 21, 2015

http://Oqtans.org: RNAseq…in the cloud by @gxr http://bioinformatics.oxfordjournals.org/content/30/9/1300.long Distributing a tool in many ways: AMI, GIT, Galaxy workflow, &c
Nice illustration how to distribute a tool in many forms —

AMI, GIT, Galaxy workflow + more.

* Sreedharan et al. Oqtans: the RNA-seq workbench in the cloud for
complete and reproducible quantitative transcriptome analysis.

The authors describe an open source transcriptome analysis software
package, Oqtans. The package contains a variety of existing analysis
tools (from short-read alignment, transcript quantification and
expression analysis) assembled into a comprehensive workflow. The
package can be either run locally or as a virtual machine in the cloud
using the AWS. One innovative feature is the availability of comparing
the efficiency of the integrated tools on the same data set. Oqtans is
a highly modular software package that can be easily extended. It also
offers the possibility to create customized workflows based on the
integrated tools available.

Moore’s law is not that easy to follow anymore

July 16, 2015

http://thenextweb.com/insider/2015/07/16/intel-quietly-admits-that-its-struggling-with-moores-law/

Extensive evolutionary changes in regulatory element activity during human origins are associated with altered gene expression and positive selection. PLoS Genet. 2012

April 12, 2015

Changes in [DHS] #regulatory element activity…[over 3 primates] associated w/ altered…expression & pos. selection
http://journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.1002789

DHS across 3 primates finds species specific sites associated with differential expression & positive selection

Shibata Y, Sheffield NC, Fedrigo O, Babbitt CC, Wortham M, Tewari AK, London D, Song L, Lee BK, Iyer VR, Parker SC, Margulies EH, Wray GA, Furey TS, Crawford GE*. Extensive evolutionary changes in regulatory element activity during human origins are
associated with altered gene expression and positive selection. PLoS Genet. 2012 Jun; 8(6):e1002789. doi: 10.1371/journal.pgen.1002789. Epub 2012 Jun 28. PubMed PMID: 22761590; PubMed Central PMCID: PMC3386175

SUMMARY (from csds):

The study is focused on analyzing genotype-phenotype correlation by looking at the evolution of DHS sites across three primate genomes: human, chimp and macaque. By comparing the data they were able to identify common DHS sites across the three species (sites that show similar DHS levels) and also species-specific sites. All the assays were supported by ChiP experiments. The study identified >2000 regulatory elements that were gained/lost since the divergence of
human and chimp. Looking at DNase and RNAseq data the authors show that the enrichment of regulatory elements next to genes with species-specific expression, suggests that the gain or loss of DHS sites impacts transcript abundance. The human DHS sites were enhanced for chromatin marks predictive of enhancers, while common regions were preferentially associated with promoters and insulators. By looking at species specificity, they found that species-specific DHS gains are cell type specific while both species specific DHS gains and losses are subject to positive selection. The common DHS sites are conserved and are suggested to have roles involving transcription and general housekeeping.

het/hom

March 24, 2014

het/hom ratio = ~1.5
in the sequencing of many Asian individuals (Table 1)

http://www.nature.com/ng/journal/v43/n8/fig_tab/ng.872_T1.html

From
Extensive genomic and transcriptional diversity identified through massively parallel DNA and RNA sequencing of eighteen Korean individuals
Nature Genetics 43, 745-752 (2011) doi:10.1038/ng.872

Bibdesk software

July 20, 2013

http://bibdesk.sourceforge.net

If you download the citations from pubmed in .nbib or .bib format you can open them directly in bib desk (I think it will also work in Mendeley, EndNote and Papers). Also if you look into the file you’ll see that the key words are tagged in OT field.