Adam Klie

GenVarLoader: An accelerated dataloader for applying deep learning to personalized genomics

GenVarLoader accelerates deep learning applications in personalized genomics by improving data loading speed and compression.

GAME: Genomic API for Model Evaluation

GAME provides a standardized framework for benchmarking genomics models across tasks, enabling consistent evaluation and community contributions.

VADEr: Vision Transformer-Inspired Framework for Polygenic Risk Reveals Underlying Genetic Heterogeneity in Prostate Cancer

VADEr, a Vision Transformer-inspired framework, improves polygenic risk prediction for prostate cancer by capturing genetic interactions and revealing heterogeneity through DARTH scores.

Target deconvolution using in vitro evolution in haploid human cells

The paper uses in vitro evolution in haploid human cells to identify drug resistance mechanisms and validates them through gene expression experiments.

Epigenetic Germline Variants Predict Cancer Prognosis and Risk and Distribute Uniquely in Topologically Associating Domains

This study shows that epigenetic variants affecting DNA methylation are distributed in chromatin domains and are linked to cancer risk and prognosis.

EUGENe: A Python toolkit for predictive analyses of regulatory sequences

EUGENe is a FAIR Python toolkit for deep learning analysis of regulatory sequences, offering modular tools for data handling, model training, and evaluation.

Affinity-optimizing variants within cardiac enhancers disrupt heart development and contribute to cardiac traits

The paper identifies ETS affinity-optimizing SNVs in heart enhancers that disrupt development and contribute to cardiac traits in Ciona and human iPSC-CMs.

Increasing metadata coverage of SRA BioSample entries using deep learning based Named Entity Recognition

The paper uses deep learning for Named Entity Recognition to predict missing metadata in SRA BioSample entries, achieving high accuracy for species, condition, and strain categories.