Andrew Delong

Transcriptome-Wide Off-Target Effects of Steric-Blocking Oligonucleotides

This study evaluates off-target effects of steric-blocking oligonucleotides using RNA-seq and finds that in silico methods have limited utility for predicting these effects.

cDeepbind: A context sensitive deep learning model of RNA-protein binding

The paper introduces cDeepbind, a deep learning model that incorporates RNA secondary structure to improve RBP binding predictions, achieving better performance on both in-vitro and in-vivo data.

Inference Of The Human Polyadenylation Code

The paper develops a deep learning model to predict tissue-specific polyadenylation site selection using genomic features and 3-end sequencing data.

Allele-specific transcription factor binding as a benchmark for assessing variant impact predictors

The paper benchmarks variant impact predictors using allele-specific binding ChIP-seq data, finding deep learning methods perform best but have room for improvement.