exome score and annotation
https://sites.google.com/site/jpopgen/dbNSFP
whole genome score and annotation
https://sites.google.com/site/jpopgen/wgsa
Posts Tagged ‘funseq’
annotation score
May 18, 2019Fast, scalable prediction of deleterious noncoding variants from functional and population genomic data | Nature Genetics
March 18, 2018Fast, scalable prediction of deleterious #noncoding variants from functional & population genomic data
https://www.Nature.com/articles/ng.3810 LINSIGHT, by @ASiepel et al., combines DNAse & conservation information
Yi-Fei Huang, Brad Gulko & Adam Siepel
Nature Genetics 49, 618–624 (2017)
doi:10.1038/ng.3810
Published online:
13 March 2017
Recurrent noncoding regulatory mutations in pancreatic ductal adenocarcinoma | Nature Genetics
February 11, 2018Journal Club Paper
June 18, 2017Zhou, J. and Troyanskaya, O.G. (2015). Predicting effects of noncoding variants with deep learning–based sequence model. Nature Methods, 12, 931–934.
Predicting (& prioritizing) effects of noncoding variants w. [DeepSEA] #DeepLearning…model
https://www.Nature.com/nmeth/journal/v12/n10/full/nmeth.3547.html Trained w #ENCODE data
PLOS Computational Biology: PredictSNP2: A Unified Platform for Accurately Evaluating SNP Effects by Exploiting the Different Characteristics of Variants in Distinct Genomic Regions
October 9, 2016PredictSNP2: A Unified Platform http://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1004962 Ensembles many scores for the impact of non-coding variants, including #FunSeq
PETModule: a motif module based approach for enhancer target gene prediction : Scientific Reports
September 17, 2016PETModule…enhancer-target-gene prediction
http://www.nature.com/articles/srep30043 Compares activity
correlations against a Hi-C/ChIA-PET gold std.
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
Journal Club
July 23, 2016Basset: #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”
GERV: a statistical method for generative evaluation of regulatory variants for transcription factor binding
June 21, 2016http://bioinformatics.oxfordjournals.org/content/early/2015/11/05/bioinformatics.btv565
GERV: a statistical method for generative evaluation of regulatory variants for transcription factor binding
Haoyang Zeng
Tatsunori Hashimoto
Daniel D. Kang
David K. Gifford
Topology of the human and mouse m6A RNA methylomes revealed by m6A-seq
February 21, 2015Human & mouse [mRNA] #methylomes revealed by m6A-seq http://www.nature.com/nature/journal/v485/n7397/full/nature11112.html Conservation across species & conditions (for most sites)
Dan Dominissini,
Sharon Moshitch-Moshkovitz,
Schraga Schwartz,
…
Rotem Sorek
& Gideon Rechavi
Nature 485, 201–206 (10 May 2012) doi:10.1038/nature11112
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