TP53 copy number expansion is associated w…enhanced DNA damage response in elephants https://elifesciences.org/content/5/e11994 18 p53 retro- & pseudo- genes
Archive for the 'SciLit' Category
Big Data: Astronomical or Genomical?
March 3, 2017#BigData: Astronomical or Genomical?
http://journals.PLOS.org/plosbiology/article?id=10.1371/journal.pbio.1002195 Est. current storage in EB/yr: Astro .1, omics .1, Twitter .001, YouTube .1-1
QT:{{”
“Data storage requirements for all four domains are projected to be enormous. Today, the largest astronomy data center devotes ~100 petabytes to storage, and the completion of the Square Kilometre Array (SKA) project is expected to lead to a storage demand of 1 exabyte per year. YouTube currently requires from 100 petabytes to 1 exabyte for storage and may be projected to require between 1 and 2 exabytes additional storage per year by 2025. Twitter’s storage needs today are estimated at 0.5 petabytes per year, which may increase to 1.5 petabytes in the next ten years. (Our estimates here ignore the “replication factor” that multiplies storage needs by ~4, for redundancy.) For genomics, we have determined more than 100 petabytes of storage are currently used by only 20 of the largest institutions ().”
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FastProject: a tool for low-dimensional analysis of single-cell RNA-Seq data | BMC Bioinformatics | Full Text
March 2, 2017FastProject: A Tool for Low-Dimensional Analysis of #ScRNASeq https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-016-1176-5 Software for many reductions to 2D scatterplots
* FastProject: A Tool for Low-Dimensional Analysis of Single-Cell RNA-Seq Data/ D. DeTomaso, N. Yosef. BMC Bioinformatics
2016.17(1):315. doi: 10.1186/s12859-016-1176-5
FastProject, developed by DeTomaso and Yosef, is a software tool for analyzing and interpreting single-cell RNA-Seq(scRNA-Seq) data. This pipeline utilizes a plethora of dimensionality reduction methods to project the high-dimensional scRNA-Seq data (i.e. the gene expression matrix) to dozens of two-dimensional scatter-plots. By incorporating the signature-based analysis, the biological significance of these two-dimensional representations can be systematically investigated. FastProject was designed using a modular architecture with the aim of serving as a general platform for the development and evaluation of new scRNA-Seq analysis methods.
Inferring chromatin-bound protein complexes from genome-wide binding assays – Genome Research
February 26, 2017Inferring [w. NMF] chromatin-bound protein complexes [of TFs] from [ENCODE ChIP-seq] binding assays, by @ElementoLab
http://genome.cshlp.org/content/23/8/1295.full
Giannopoulou E, Elemento O. 2013. Inferring chromatin-bound
protein complexes from genome-wide binding assays. Genome Research, Published in Advance April 3, 2013, doi: 10.1101/gr.149419.112.
This study uses nonnegative matrix factorization (NMF) of ENCODE CHIP-seq data (transcription
factors and histone modifications) to predict complexes of
transcription factors that bind DNA
together; it then assesses how these predicted complexes regulate gene expression. It goes beyond
previous studies in that it attempts to treat the TFs as complexes rather than individuals. A handful of
the predicted complexes correspond to known regulatory complexes, e.g. PRC2, and overall, the
complexes were enriched for known protein-protein interactions. Linear regression and random forest
models were then used to predict the effects of the complexes on the expression of adjacent genes. In
both models, the complexes performed better than those predicted from a scrambled TF read count
matrix. Overall, this study provides a large set of hypotheses for combinations of TFs that may
function together, as well as potential new components of known complexes.
Detecting overlapping protein complexes in protein-protein interaction networks : Nature Methods : Nature Research
February 24, 2017A Proteome-wide Fission Yeast Interactome Reveals Network Evolution Principles from Yeasts to Human: Cell
February 24, 2017FissionNet: Proteome-wide [pombe] Interactome Reveals #Network Evolution Principles
http://www.Cell.com/cell/abstract/S0092-8674(15)01556-1 Involving ~1300 soluble proteins
Computational tools for cancer immunology : Computational genomics tools for dissecting tumour-immune cell interactions : Nature Reviews Genetics : Nature Research
February 24, 2017http://www.nature.com/nrg/journal/v17/n8/fig_tab/nrg.2016.67_T1.html
Table 1: Computational tools for cancer immunology
FromComputational genomics tools for dissecting tumour–immune cell interactions
Hubert Hackl,
Pornpimol Charoentong,
Francesca Finotello
& Zlatko Trajanoski
Nature Reviews Genetics 17, 441–458 (2016) doi:10.1038/nrg.2016.67
interesting paper
February 22, 2017Partitioning heritability of regulatory…variants across 11 common diseases http://www.Cell.com/ajhg/abstract/S0002-9297(14)00426-1 Almost 80% #noncoding v 10% coding
The paper below claims to find most of the heritability of 11 common diseases in regulatory regions (79% of heritability found in regulatory regions, <10% in protein coding regions).
Partitioning heritability of regulatory and cell-type-specific variants across 11 common
diseases.
Gusev A, Lee SH, Trynka G, Finucane H, Vilhjálmsson BJ, Xu H, Zang C, Ripke S, Bulik-Sullivan B, Stahl E; Schizophrenia Working Group of the Psychiatric Genomics Consortium; SWE-SCZ Consortium, Kähler AK, Hultman CM, Purcell SM, McCarroll SA, Daly M, Pasaniuc B, Sullivan PF, Neale BM, Wray NR, Raychaudhuri S, Price AL; Schizophrenia Working Group of the Psychiatric Genomics Consortium; SWE-SCZ Consortium.
Am J Hum Genet. 2014 Nov 6;95(5):535-52. doi:
10.1016/j.ajhg.2014.10.004. Epub 2014 Nov 6.
JClub papers
February 16, 2017A #circadian gene-expr atlas in mammals by @jbhclock lab
http://www.PNAS.org/content/111/45/16219.abstract 43% of genes have a daily rhythm in at least 1 tissue [1/2]
.@jbhclock Fewest circadian genes in brain; most in liver. Perhaps this more reflects daily feeding cycle than true light-dark cycle? [2/2]
A circadian gene expression atlas in mammals: Implications for biology and medicine
Ray Zhanga,1,
Nicholas F. Lahensa,1,
Heather I. Ballancea,
Michael E. Hughesb,2, and
John B. Hogenescha,2
* Interestingly brain regions have the fewest circ genes(only ~3%), liver has most
* Diseases assoc with circadian genes correlate with NIH funding
* Genes can have up to a 6-hour phase diff. Between diff. organs (eg Vegfa betw. Heart & fat)
* 56 of the top 100 drugs incl. Top 7, targeted the product of a circadian gene. Related to the half-life of drugs.
* Could the liver genes be more reflective of feeding rhythm rather than true circadian clock.
Genome expansion via lineage splitting and genome reduction in the cicada endosymbiont Hodgkinia
February 13, 2017Genome expansion via lineage splitting…in the cicada endosymbiont Hodgkinia http://www.PNAS.org/content/112/33/10192.abstract Host lifecycle partially enables split
linkstream2 microblog 