Ryne C. Ramaker

Long-read genome sequencing for the diagnosis of neurodevelopmental disorders

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

Pooled CRISPR screening in pancreatic cancer cells implicates co-repressor complexes as a cause of multiple drug resistance via regulation of epithelial-to-mesenchymal transition

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

Dissecting the regulatory activity and sequence content of loci with exceptional numbers of transcription factor associations

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

CRISPR/Cas9-targeted removal of unwanted sequences from small-RNA sequencing libraries

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.

De novo mutations in the GTP/GDP-binding region of RALA, a RAS-like small GTPase, cause intellectual disability and developmental delay

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.

Occupancy patterns of 208 DNA-associated proteins in a single human cell type

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: Threshold-free peak alignment and identification for 2D gas chromatography mass spectrometry in R

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

A genome-wide interactome of DNA-associated proteins in the human liver

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.

Post-mortem molecular profiling of three psychiatric disorders

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.

RNA sequencing-based cell proliferation analysis across 19 cancers identifies a subset of proliferation-informative cancers with a common survival signature

aRNApipe: A balanced, efficient and distributed pipeline for processing RNA-seq data in high performance computing environments

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