Posts Tagged ‘ah’

paper on geuvadis rna-seq variant calling

February 11, 2017

Calling 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

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Journal Club

July 23, 2016

Basset: #DeepLearning the regulatory code w/…NNs by @noncodarnia lab http://genome.cshlp.org/content/early/2016/05/03/gr.200535.115 Has score for all possible SNVs in the genome

“Basset: learning the regulatory code of the accessible genome with deep convolutional neural networks”

expression patterns in brain

November 18, 2015

Canonical genetic signatures [across 132 structures] of the adult human #brain [in 6 individuals]
http://www.nature.com/neuro/journal/vaop/ncurrent/full/nn.4171.html HT @ozgunharmanci

QT:{{”
We applied a correlation-based metric called differential stability to assess reproducibility of gene expression patterning across 132 structures in six individual brains, revealing mesoscale genetic organization. The genes with the highest differential stability are highly biologically relevant, with enrichment for brain-related annotations, disease associations, drug targets and literature citations.
“}}

Single-cell chromatin accessibility reveals principles of regulatory variation : Nature : Nature Publishing Group

August 28, 2015

#SingleCell chromatin accessibility
http://www.nature.com/nature/journal/v523/n7561/full/nature14590.html >1.6k ATAC-seq expts; many on @ENCODE_NIH cell lines H1, GM12878 & K562

Cost of Reproducibility

July 6, 2015

Cost of #Reproducibility http://journals.plos.org/plosbiology/article?id=10.1371/journal.pbio.1002165 Estimated at almost $30B for life science research, based on 50% of studies not replicating

Pgenes make proteins

January 24, 2015

Bioinformatics (2015) 31 (1): 33-39. doi: 10.1093/bioinformatics/btu615

Making novel proteins from #pseudogenes
http://bioinformatics.oxfordjournals.org/content/31/1/33.short Outcomes in 16 cases where one gets stable & functional translated products

http://bioinformatics.oxfordjournals.org/content/31/1/33.short

twin ASEs

December 15, 2014

http://www.nature.com/ng/journal/vaop/ncurrent/full/ng.3162.html

Gene-gene and gene-environment interactions detected by transcriptome sequence analysis in twins

Alfonso Buil,
Andrew Anand Brown,
Tuuli Lappalainen,
Ana Viñuela,
Matthew N Davies,
Hou-Feng Zheng,
J Brent Richards,
Daniel Glass,
Kerrin S Small,
Richard Durbin,
Timothy D Spector
& Emmanouil T Dermitzakis

cancer mutation rates versus chromatin

June 14, 2014

Chromatin organization is a major influence on regional mutation rates in human cancer cells
Benjamin Schuster-Böckler & Ben Lehner

http://www.nature.com/nature/journal/vaop/ncurrent/abs/nature11273.html

cell free DNA circulating for cancer

May 12, 2014

NYT recently ran an article as well:
http://www.nytimes.com/2014/04/08/business/cancer-analysis-tools-circumvent-biopsies.html

http://www.nature.com/nm/journal/v20/n4/abs/nm.3511.html

An ultrasensitive method for quantitating circulating tumor DNA with broad patient coverage
http://www.nature.com/nm/journal/vaop/ncurrent/abs/nm.3519.html

http://stm.sciencemag.org/content/6/224/224ra24
http://www.nejm.org/doi/full/10.1056/NEJMoa1213261

http://stm.sciencemag.org/content/4/162/162ra154.full
DIAGNOSTICS: Detection of Chromosomal Alterations in the Circulation of Cancer Patients with Whole-Genome Sequencing

Three-Dimensional Genome Architecture Influences Partner Selection for Chromosomal Translocations in Human Disease

April 10, 2014

QT:"We show that many translocation-prone pairs of regions genome-wide, including the cancer translocation partners BCR-ABL and MYC-IGH, display elevated Hi-C contact frequencies in normal human cells."

Overlap of Hi-C & gene fusions

http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0044196