Martin Kircher

The paper introduces standardized formats and tools for processing MPRA data to improve reproducibility and integration across studies.

The paper characterizes regulatory variants in human neurons using lentiMPRA and shows that variant effects are influenced by regulatory element activity and sequence context, not population frequency.

CADD-SV v2.0 improves variant prioritization by integrating coordinate- and sequence-based features, outperforming previous versions and other tools for structural variant deleteriousness scoring.

The paper introduces varCADD, a method using standing genetic variation to predict variant pathogenicity, showing improved accuracy over existing tools in certain genomic regions.

This paper introduces ccMPRA, a method that combines Capture-C and MPRA to study promoter interactions and regulatory activity, identifying enhancers and silencers.

The paper develops a high-throughput assay to test retrotransposon jumping activity and identifies variants that influence transposition.

The paper identifies functional cis-regulatory elements in three human cell types using lentiMPRAs and develops predictive models for CRE function.

LBFextract extracts transcription factor dynamics from liquid biopsy data to improve reproducibility and subtype classification in prostate cancer.

The paper introduces cfDNA UniFlow, a unified preprocessing pipeline for cell-free DNA data, enabling standardized processing and analysis across different settings.

The paper introduces AlphScore, a pathogenicity prediction score for missense variants using AlphaFold2-derived features, showing improved performance when combined with existing scores.

CADD-SV scores structural variants using annotations and random forest models, correlating with known pathogenic and non-coding variants affecting gene expression.

The paper updates the Regulatory Mendelian Mutation score for GRCh38 and provides a website and API for variant scoring.

This study evaluates how different negative training data affect regulatory sequence prediction models, finding that genomic backgrounds yield better results than shuffled sequences.

This study evaluates how experimental design, orientation, and sequence context affect MPRA results, finding significant differences in regulatory activity measurements.

This study demonstrates concurrent genome and epigenome editing by CRISPR-mediated sequence replacement, showing that promoter methylation can functionally silence gene expression.

The paper performs saturation mutagenesis on disease-associated regulatory elements to assess the functional effects of mutations, revealing variability in transcription factor binding site density and predictive power of conservation scores.

This paper introduces VAMP-seq, a method to assess the abundance of protein variants, and identifies pathogenic variants in PTEN and TPMT.

The paper compares chromosomal and episomal enhancer activity using a novel assay, finding significant differences in activity and predictability.