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