Functional genomics assays based on high-throughput sequencing greatly expand our
ability to understand the genome. Here, we define the ENCODE blacklist-a comprehensive …

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Background Accurate evaluation of the quality of genomic or proteomic data and
computational methods is vital to our ability to use them for formulating novel biological …

By using genome information to create tools for perturbing gene function, it is now possible
to undertake systematic genome-wide functional screens that examine the contribution of …

Genome-wide sequencing has enabled modern biomedical research to relate more and
more events in healthy as well as disease-affected cells and tissues to the genomic …

Motivation: High-throughput sequencing (HTS) has revolutionized gene regulation studies
and is now fundamental for the detection of protein–DNA and protein–RNA binding, as well …

Comprehensive and accurate detection of variants from whole-genome sequencing (WGS)
is a strong prerequisite for translational genomic medicine; however, low concordance …

Motivation: Sequencing-based assays such as ChIP-seq, DNase-seq and MNase-seq have
become important tools for genome annotation. In these assays, short sequence reads …

Areas of life sciences research that were previously distant from each other in ideology,
analysis practices and toolkits, such as microbial ecology and personalized medicine, have …

Affordable genome sequencing technologies promise to revolutionize the field of human
genetics by enabling comprehensive studies that interrogate all classes of genome …