Genome expansion via lineage splitting…in the cicada endosymbiont Hodgkinia http://www.PNAS.org/content/112/33/10192.abstract Host lifecycle partially enables split
Archive for the 'SciLit' Category
Genome expansion via lineage splitting and genome reduction in the cicada endosymbiont Hodgkinia
February 13, 2017paper on geuvadis rna-seq variant calling
February 11, 2017Calling genotypes from public RNA-sequencing data enables
identification of genetic variants that affect gene-expression levels
Patrick Deelen†,
Daria V Zhernakova†,
Mark de Haan,
Marijke van der Sijde,
Marc Jan Bonder,
Juha Karjalainen,
K Joeri van der Velde,
Kristin M Abbott,
Jingyuan Fu,
Cisca Wijmenga,
Richard J Sinke,
Morris A Swertz† and
Lude Franke†
Genotypes from…#RNAseq…enables identification of…variants, related to ASE & eQTLs
https://GenomeMedicine.biomedcentral.com/articles/10.1186/s13073-015-0152-4 Validation w/ #Geuvadis
Best Practices for Scientific Computing
February 5, 2017also from ’14:
https://plus.google.com/+MarkGerstein/posts/D8kYoqiWL1P
Best Practices for Sci Computing
http://journals.PLOS.org/plosbiology/article?id=10.1371/journal.pbio.1001745 Usual stuff (GitHub, profilers, assertions) + some gems (turn bugs into test cases)
Exploiting Temporal Collateral Sensitivity in Tumor Clonal Evolution: Cell
February 4, 2017Temporal Collateral Sensitivity in Tumor…Evolution
http://www.cell.com/cell/abstract/S0092-8674(16)30059-9 Drug-fitness landscape illuminates transiently vulnerable state
Exploiting Temporal Collateral Sensitivity in Tumor Clonal Evolution
Boyang Zhao
Joseph C. Sedlak
Raja Srinivas
Pau Creixell
Justin R. Pritchard
Bruce Tidor
Douglas A. Lauffenburger
Michael T. Hemann
LongISLND: in silico sequencing of lengthy and noisy datatypes
January 30, 2017LongISLND: in silico sequencing of lengthy & noisy datatypes https://www.ncbi.nlm.nih.gov/pubmed/27667791 @PacBio sim. software (NB: was advisor to @binaTechs)
Jclub Paper
January 28, 2017#RNA Struc. Determinants of Optimal Codons…by MAGESeq
http://www.cell.com/cell-systems/fulltext/S2405-4712(16)30368-4 Probing effect of synonymous changes; towards a better dN/dS
RNA Structural Determinants of Optimal Codons Revealed by MAGE-Seq http://www.cell.com/cell-systems/fulltext/S2405-4712(16)30368-4
Genome-wide, integrative analysis implicates microRNA dysregulation in autism spectrum disorder : Nature Neuroscience : Nature Research
January 28, 2017Genome-wide…analysis implicates miRNA dysregulation in #ASD http://www.nature.com/neuro/journal/v19/n11/full/nn.4373.html 58 diff. expr. miRNAs incl 17 strongly down in cases
http://www.nature.com/neuro/journal/v19/n11/full/nn.4373.html
QT:{{”
The miRNA expression profiles were very similar between the frontal and temporal cortex, but were distinct in the cerebellum
(Supplementary Fig. 2a–f), consistent with previous observations for mRNAs11, 12. We therefore combined 95 covariate-matched samples (47 samples from 28 ASD cases and 48 samples from 28 controls;
Supplementary Fig. 1c and Supplementary Table 1) from the FC and TC for differential gene expression (DGE) analysis, comparing ASD and CTL using a linear mixed-effects regression framework to control for potential confounders (Online Methods). We identified 58 miRNAs showing significant (false discovery rate (FDR) < 0.05) expression changes between ASD and CTL: 17 were downregulated and 41 were upregulated in ASD cortex (Fig. 1b and Supplementary Table 2). The fold changes for the differentially expressed miRNAs were highly concordant between the FC and TC (Pearson correlation coefficient R = 0.96, P < 2.2 × 10−16; Fig. 1c).
“}}
Best Practices for Scientific Computing
January 22, 2017Best Practices for Sci Computing
http://journals.PLOS.org/plosbiology/article?id=10.1371/journal.pbio.1001745 Usual stuff (GitHub, profilers, assertions) + some gems (turn bugs into test cases)
Jclub paper
January 16, 2017The impact of #SVs on…gene expression
http://biorxiv.org/content/early/2016/06/09/055962 24k in 147 people in GTEx pilot act as causal variants in 3-7% of ~25k eQTLs
The impact of structural variation on human gene expression
Colby Chiang, Alexandra J Scott, Joe R Davis, Emily
K Tsang, Xin Li, Yungil Kim, Farhan N Damani, Liron Ganel, GTEx Consortium, Stephen B Montgomery, Alexis Battle, Donald F Conrad, Ira M Hall
doi: https://doi.org/10.1101/055962
A gradient of childhood self-control predicts health, wealth, and public safety
January 14, 2017A gradient of childhood #selfcontrol predicts health, wealth & public safety http://www.PNAS.org/content/108/7/2693.full From following 1K kids from 0 to 32 yrs
linkstream2 microblog 