Posts Tagged ‘encode’

Species-Specific | The Scientist Magazine(R)

September 6, 2015

Scientists uncover striking differences between mouse and human gene expression across a variety of tissues.
By Jyoti Madhusoodanan | November 17, 2014

http://www.the-scientist.com/?articles.view/articleNo/41453/title/Species-Specific/

QT:{{”
The results “go a little against the grain,” said bioinformatician Mark Gerstein of Yale University who was not involved in the study. “We might think that humans and mice are very similar [genetically], but when we compare their transcriptomes, they’re more different than we thought.”
“}}

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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

PLOS Genetics: 8.2% of the Human Genome Is Constrained: Variation in Rates of Turnover across Functional Element Classes in the Human Lineage

August 2, 2015

QT:{{”
While enriched with ENCODE biochemical annotations, much of the short-lived constrained sequences we identify are not detected by models optimized for wider pan-mammalian conservation. Constrained DNase 1 hypersensitivity sites, promoters and untranslated regions have been more evolutionarily stable than long noncoding RNA loci which have turned over especially rapidly. By contrast, protein coding sequence has been highly stable, with an estimated half-life of over a billion years (d1/2 = 2.1–5.0). From extrapolations we estimate that 8.2% (7.1–9.2%) of the human genome is presently subject to negative selection and thus is likely to be functional, while only 2.2% has maintained constraint in both human and mouse since these species diverged.
“}}

http://journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.1004525

Inferring gene regulatory logic from high-throughput measurements of thousands of systematically designed promoters : Nature Biotechnology : Nature Publishing Group

June 10, 2015

Segal cites: Measurements of 1000s of…designed promoters
http://www.nature.com/nbt/journal/v30/n6/full/nbt.2205.html Num. binding sites correlated w/ expr., for 1st few #ICSG2015

Unraveling determinants of transcription factor binding outside the core binding site

June 8, 2015

Segal cites: Determinants of TF binding outside the core binding site http://genome.cshlp.org/content/early/2015/06/05/gr.185033.114.abstract Large-scale measurement of affinity #ICSG2015

Comparative genomics reveals insights into avian genome evolution and adaptation

May 16, 2015

Comparative #genomics reveals insights into avian…#evolution http://www.sciencemag.org/content/346/6215/1311 Less repeats & dups in birds; woodpecker, an exception

Science 12 December 2014:
Vol. 346 no. 6215 pp. 1311-1320
DOI: 10.1126/science.1251385

Comparative genomics reveals insights into avian genome evolution and adaptation

Guojie Zhang1,2,*,†,
Cai Li1,3,*,
….
Avian Genome Consortium§,
Erich D. Jarvis20,†,
M. Thomas P. Gilbert3,56,†,
Jun Wang1,55,57,58,59,†

My notes from ENCODE Consortium Meeting

March 23, 2015

links: https://linkstream2.gerstein.info/tag/i0enc15

http://lectures.gersteinlab.org/summary/thoughts-on-ENCODE-annotations–final-i0enc15/

CRE-Seq paper…

November 24, 2014

High-throughput functional testing of ENCODE segmentation
predictionsGenome Res. October 2014 24: 1595-1602; Published in Advance July 17, 2014,

that can be used for training predicted enhancers

http://genome.cshlp.org/content/24/10/1595.full.pdf

Multi-platform assessment of transcriptome profiling using RNA-seq in the ABRF next-generation sequencing study : Nature Biotechnology : Nature Publishing Group

October 10, 2014

Multiplatform assessment of #transcriptome profiling [w.] RNAseq http://www.nature.com/nbt/journal/v32/n9/full/nbt.2972.html Nice plots showing great effect of poly-A selection

IHEC data matrix

September 18, 2014

http://epigenomesportal.ca/ihec/grid.html