Landscape of allele-specific transcription factor binding in the human genome
Sequence variants in gene regulatory regions alter gene expression and contribute to
phenotypes of individual cells and the whole organism, including disease susceptibility and …
phenotypes of individual cells and the whole organism, including disease susceptibility and …
Integrative analysis of '‐omics' data using penalty functions
In the analysis of omics data, integrative analysis provides an effective way of pooling
information across multiple datasets or multiple correlated responses, and can be more …
information across multiple datasets or multiple correlated responses, and can be more …
Toward integrative Bayesian analysis in molecular biology
In the postgenome era, multiple types of molecular data for the same set of samples are
often available and should be analyzed jointly in an integrative analysis in order to maximize …
often available and should be analyzed jointly in an integrative analysis in order to maximize …
BaalChIP: Bayesian analysis of allele-specific transcription factor binding in cancer genomes
I de Santiago, W Liu, K Yuan, M O'Reilly… - Genome biology, 2017 - Springer
Allele-specific measurements of transcription factor binding from ChIP-seq data are key to
dissecting the allelic effects of non-coding variants and their contribution to phenotypic …
dissecting the allelic effects of non-coding variants and their contribution to phenotypic …
Allele specific chromatin signals, 3D interactions, and motif predictions for immune and B cell related diseases
Abstract Several Genome Wide Association Studies (GWAS) have reported variants
associated to immune diseases. However, the identified variants are rarely the drivers of the …
associated to immune diseases. However, the identified variants are rarely the drivers of the …
HycDemux: a hybrid unsupervised approach for accurate barcoded sample demultiplexing in nanopore sequencing
DNA barcodes enable Oxford Nanopore sequencing to sequence multiple barcoded DNA
samples on a single flow cell. DNA sequences with the same barcode need to be grouped …
samples on a single flow cell. DNA sequences with the same barcode need to be grouped …
[HTML][HTML] Allele-specific transcription factor binding in liver and cervix cells unveils many likely drivers of GWAS signals
M Cavalli, G Pan, H Nord, EW Arzt, O Wallerman… - Genomics, 2016 - Elsevier
Genome-wide association studies (GWAS) point to regions with associated genetic variants
but rarely to a specific gene and therefore detailed knowledge regarding the genes …
but rarely to a specific gene and therefore detailed knowledge regarding the genes …
SignalSpider: probabilistic pattern discovery on multiple normalized ChIP-Seq signal profiles
Abstract Motivation: Chromatin immunoprecipitation (ChIP) followed by high-throughput
sequencing (ChIP-Seq) measures the genome-wide occupancy of transcription factors in …
sequencing (ChIP-Seq) measures the genome-wide occupancy of transcription factors in …
Allele-specific transcription factor binding as a benchmark for assessing variant impact predictors
Genetic variation has long been known to alter transcription factor binding sites, resulting in
sometimes major phenotypic consequences. While the performance for current binding site …
sometimes major phenotypic consequences. While the performance for current binding site …
ALEA: a toolbox for allele-specific epigenomics analysis
The assessment of expression and epigenomic status using sequencing based methods
provides an unprecedented opportunity to identify and correlate allelic differences with …
provides an unprecedented opportunity to identify and correlate allelic differences with …