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Hypoxia-inducible factor (HIF)-prolyl hydroxylase 3 (PHD3) maintains high HIF2A mRNA levels in clear cell renal cell carcinoma
Most clear cell renal cell carcinomas (ccRCCs) have inactivation of the von Hippel-Lindau tumor suppressor protein (pVHL), resulting in the accumulation of hypoxia-inducible factor -subunits (HIF-) and their downstream ...
Differential ATAC-seq and ChIP-seq peak detection using ROTS
<p> Changes in cellular chromatin states fine-tune transcriptional output and ultimately lead to phenotypic changes. Here we propose a novel application of our reproducibility-optimized test statistics (ROTS) to detect ...
An Unbiased Functional Genetics Screen Identifies Rare Activating ERBB4 Mutations
<p>Despite the relatively high frequency of somatic <i>ERBB4</i> mutations in various cancer types, only a few activating <i>ERBB4</i> mutations have been characterized, primarily due to lack of mutational hotspots in ...
Computational strategies for single-cell multi-omics integration
<p>Single-cell omics technologies are currently solving biological and medical problems that earlier have remained elusive, such as discovery of new cell types, cellular differentiation trajectories and communication ...
Computational deconvolution to estimate cell type-specific gene expression from bulk data
<p>Computational deconvolution is a time and cost-efficient approach to obtain cell type-specific information from bulk gene expression of heterogeneous tissues like blood. Deconvolution can aim to either estimate cell ...