Eric Czech

PlantCAD2: a DNA foundation model for interpreting genomes across flowering plants

PlantCAD2 is a DNA foundation model pre-trained on 65 angiosperm genomes, showing improved performance in evolutionary conservation and chromatin accessible region prediction compared to existing models.

GeneCAD: Plant Genome Annotation with a DNA Foundation Model

GeneCAD improves gene annotation in plant genomes using a DNA foundation model, achieving higher accuracy than existing tools across diverse species.

Analysis-ready VCF at Biobank scale using Zarr

The paper introduces VCF Zarr, a format for efficiently storing and processing large-scale genetic variation data, demonstrating improved performance and scalability over traditional VCF formats.

Clinical Advancement Forecasting

This paper develops a statistical learning framework to predict clinical trial success for target-disease pairs using longitudinal evidence, outperforming existing scores and identifying high-potential targets.

Cytokit: A single-cell analysis toolkit for high dimensional fluorescent microscopy imaging

Cytokit processes and analyzes large-scale fluorescent microscopy data to quantify cell properties, validated through experiments and public datasets.