#SingleCell #RNASeq Reveals Dynamic, Random Monoallelic Gene Expression, occurring in ~20% of genes in mice cells
http://science.sciencemag.org/content/343/6167/193.abstract
perhaps useful for workflow viz
https://www.mindmeister.com/
Tumor genome simulation w/ #crowdsourcing to benchmark…SNV detection http://www.nature.com/nmeth/journal/v12/n7/full/nmeth.3407.html Addresses lack of gold standards & privacy
Ewing, Houlahan…..Stuart, Boutros (2015) “Combining accurate
tumour genome simulation with crowd-sourcing to benchmark somatic
single nucleotide variant detection” Nature Methods 12(7):623-630
(PMID: 25984700)
A crowdsourced benchmark of somatic mutation detection algorithms was
introduced for the ICGC-TCGA DREAM challenge. This has the advantage
of dealing with the lack of gold standard data and the issue of
sharing private genomic data. All groups worked on three different
simulated tumor-normal pairs generated with BAMSurgeon, by directly
adding synthetic mutations to existing reads. An ensemble of
pipelines outperforms the best individual pipeline in all cases,
assessed on the basis of recall, precision and F-score.
Parameterization and genomic localization both have an effect on
pipeline performance, while characteristics of prediction errors
differed for most pipelines.
Bias from removing read duplication [eg from PCR amplification] in ultra-deep #sequencing
http://bioinformatics.oxfordjournals.org/content/early/2014/01/02/bioinformatics.btt771 pot. overcorrection issues
Zhou et al.
Bias from removing read duplication in ultra-deep sequencing experiments
Estimating variant allele frequency and copy number variations can be approached by counting reads. In practice, read counting is
complicated by bias from PCR amplification and from sampling coincidence. This paper assessed the overcorrection introduced while removing read duplicates. The overcorrection is a particular concern when the sequencing is ultra-deep and the insert size is short and non-variant.
Your coffee maker is a #bacterial breeding ground http://qz.com/564102/your-coffee-maker-is-a-bacterial-breeding-ground/ Bugs love the warm water but it appears cleaning is effective
QT:{{"
“The researchers only counted the number of different bacteria types in their samples, not the total cells. A CBS investigation earlier this year found bacteria including staphylococcus and E. coli on the Keurig machines it swabbed. More than half were harboring millions of bacteria cells.
Bacteria appear to thrive in the high temperatures and chemical makeup of the coffee making process itself. Neither user behavior, the type of coffee brewed, nor frequency of the machine’s use seemed to affect the composition of the bacteria present.”
"}}
Celltype & region–resolved mouse brain proteome
http://www.nature.com/neuro/journal/v18/n12/full/nn.4160.html proteins enriched there v liver & in specific regions (eg NCX v STR)
http://www.nature.com/neuro/journal/v18/n12/full/nn.4160.html
works w/ ipad & outlook but not gcal
Discussion about listing babies & cats as co-authors on scientific
manuscriptshttp://academia.stackexchange.com/questions/57120/can-i-add-a-baby-as-a-co-author-of-a-scientific-paper via @bornalibran #authorship
#Enhancer Evolution across 20 Mammal[s is faster than for promoters] by @PaulFlicek lab http://www.cell.com/cell/abstract/S0092-8674(15)00007-0 H3K27ac & H3K4me3 #chipseq