David Yu Zhang

The paper introduces BIRT, a method for RNA sequencing that integrates barcoding and 3'-end capture during reverse transcription, improving accuracy and efficiency for low-input samples.

The paper introduces DIMPLE, a scalable qPCR primer design algorithm that enables 10,000+ primers in a single reaction, achieving low VAF detection and multiplex applications.

The paper develops ensemble models using PBMC RNAseq data to discriminate early MS from healthy individuals, differentiate MS from NMO, and subtype RRMS from progressive MS, achieving high AUC scores.

This paper introduces a gene expression transfer learning model that enables cross-species gene mapping using reactome profiles, improving functional gene understanding and drug response prediction.

The paper measures gene expression responses to drugs in mouse and rat genomes across organs and finds that reactomes do not correlate with structural similarity, proposing a new cross-species mapping approach based on expression patterns.

The paper introduces BIOFORMERS, a transformer-based framework for analyzing biological systems, demonstrating its ability to capture biological insights from single-cell transcriptomics data.

This study uses longitudinal RNAseq in rats to identify temporally variable genes and recovery trajectories after chemical exposure.

The paper identifies ultra-short single-stranded DNA (ussDNA) in biofluids, showing its presence across species and potential as a DNA biomarker.

OCEANS improves nanopore sequencing for detecting low VAF somatic mutations with high accuracy and sensitivity in clinical samples.

This paper introduces MLB-seq, a method to profile DNA secondary structures using bisulfite sequencing, and finds that 84% of studied human genome subsequences adopt multiple structures.

This paper introduces BDA, a temperature-robust PCR method that selectively amplifies rare DNA variants, enabling their detection and quantitation across a range of annealing temperatures.