Ryne C. Ramaker

This paper uses long-read genome sequencing to identify pathogenic variants in neurodevelopmental disorders, finding clinically relevant structural variants in two of six probands.

The paper uses CRISPR screens to identify co-repressor complexes as mediators of drug resistance in pancreatic cancer by regulating epithelial-to-mesenchymal transition.

The paper identifies and characterizes HOT loci with high DAP associations, finds driver motifs, and shows their regulatory importance through mutagenesis.

The paper introduces MAD-DASH, a CRISPR/Cas9-based method to remove adapter dimers and highly expressed smRNAs from small RNA sequencing libraries, improving quantification of low-abundance species.

The paper identifies de novo mutations in RALA, a RAS-like GTPase, as a cause of intellectual disability and developmental delay, showing their functional impact on GTP binding and effector interactions.

The paper presents ChIP-seq data for 208 DNA-associated proteins in HepG2 cells, revealing occupancy patterns and DNA motifs, and distinguishing promoters from enhancers.

R2DGC aligns and identifies peaks in 2D gas chromatography-mass spectrometry data without thresholds, using R.

The paper presents a genome-wide interactome of DNA-associated proteins in human liver tissue, revealing binding patterns more consistent with liver biology than cell lines and highlighting non-coding variation impacts.

The paper compares transcriptomes and metabolomes of postmortem brain samples from schizophrenia, bipolar disorder, major depressive disorder, and controls to identify molecular differences and potential therapeutic targets.

aRNApipe is a modular RNA-seq processing pipeline designed for HPC environments, offering efficient workflow management and customizable analysis modules.