Posts Tagged ‘alleledb’
Gencode Transcriptome variation in human tissues revealed by long-read sequencing | Nature
August 8, 2022Interpretation of allele-specific chromatin accessibility using cell state-aware deep learning
May 18, 2021Mapping the mouse Allelome reveals tissue-specific regulation of allelic expression | eLife
April 21, 2018Mapping the mouse Allelome reveals tissue-specific regulation of allelic expression https://eLifeSciences.org/articles/25125 More noncoding than coding #allelic activity. Also, finding windows of allelic activity for chromatin
Daniel Andergassen,
Christoph P Dotter,
Daniel Wenzel,
Verena Sigl,
Philipp C Bammer,
Markus Muckenhuber,
Daniela Mayer,
Tomasz M Kulinski,
Hans-Christian Theussl,
Josef M Penninger,
Christoph Bock,
Denise P Barlow ,
Florian M Pauler ,
Quanah J Hudson
Research Center for Molecular Medicine of the Austrian Academy of Sciences, Austria;
Institute of Molecular Biotechnology of the Austrian Academy of Sciences, Austria;
Institute of Molecular Pathology, Austria
Genome sequence-independent identification of RNA editing sites : Nature Methods : Nature Research
August 27, 2017http://www.nature.com/nmeth/journal/v12/n4/full/nmeth.3314.html
Genome seq–independent Identification of #RNAediting http://www.Nature.com/nmeth/journal/v12/n4/full/nmeth.3314.html Accurate sites from uncorrelated SNV pair, spanned by reads
CATO score
May 28, 2017Seq. variants influencing…TF occupancy
http://www.Nature.com/ng/journal/v47/n12/full/ng.3432.html Uses allelic analysis to develop the CATO score, how variants alter binding
QT:{{”
This approach resulted in a simple scoring scheme, termed contextual analysis of transcription factor occupancy (CATO), that provides a recalibrated probability of affecting the binding of any transcription factor, as well as a quantitatively ranked list of transcription factor families whose binding might be altered.
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illumina platinum genomes paper
January 10, 2017Set of 5.4M phased…variants…from seq. a 3-gen. 17-member [CEPH] pedigree, centered on #NA12878
http://genome.cshlp.org/content/early/2016/11/25/gr.210500.116 $ILMN Pt genomes
A reference data set of 5.4 million phased human
variants validated by genetic inheritance from
sequencing a three-generation 17-member pedigree
Michael A. Eberle,1 Epameinondas Fritzilas,2 Peter Krusche,2 Morten Källberg,2 Benjamin L. Moore,2 Mitchell A. Bekritsky,2 Zamin Iqbal,3 Han-Yu Chuang,1 Sean J. Humphray,2 Aaron L. Halpern,1 Semyon Kruglyak,1 Elliott H. Margulies,1 Gil McVean,3,4 and David R. Bentley2
http://genome.cshlp.org/content/early/2016/11/25/gr.210500.116
Scientists are assembling a new picture of humanity
December 4, 2016Assembling a new picture of humanity by @CarlZimmer
https://www.statnews.com/2016/10/07/dna-genome-sequencing-new-maps/ 1 graph to represent everyone, counterpoint to #personalgenomes
IHEC Consortium Papers (Cell + other journals)
November 28, 2016#IHECpapers rollout http://www.Cell.com/consortium/ihec Gr8 work! incl. #privacy, normal breast epigenetics, ETG links, deconvolution, #allelic activity
Allele-specific transcription factor binding in liver and cervix cells unveils many likely drivers of GWAS signals. – PubMed – NCBI
August 7, 2016Allele-specific TF binding in liver & cervix cells [HepG2 & HeLa] unveils many likely drivers of GWAS [SNP] signals
http://www.sciencedirect.com/science/article/pii/S0888754316300271
GERV: a statis,tical method for generative evaluation of regulatory variants for transcription factor binding
July 23, 2016GERV: stats method for generative evaluation of regulatory variants
for TF binding http://bioinformatics.oxfordjournals.org/content/early/2015/11/05/bioinformatics.btv565 Predicts effect of #allelic SNPs
GERV: a statistical method for generative evaluation of regulatory ariants for transcription factor binding
> Haoyang Zeng
> Tatsunori Hashimoto
> Daniel D. Kang
> David K. Gifford
linkstream2 microblog 