Dinghai Zheng

Optimizing Bispecific Antibody Expression via Multi-Omics Analysis and Vector Redesign

This study improves bispecific antibody expression by analyzing multi-omics data and redesigning vectors, resulting in an 11-fold increase in stable titers.

Predicting the translation efficiency of messenger RNA in mammalian cells

The paper predicts translation efficiency (TE) of mRNA in mammalian cells using a deep learning model trained on ribosomal profiling data across multiple cell types.

Translation efficiency covariation across cell types is a conserved organizing principle of mammalian transcriptomes

The paper analyzes ribosome profiling data to show translation efficiency covariation (TEC) is conserved across human and mouse cells, revealing gene functions not evident from RNA or protein co-expression.

Light regulates widespread plant alternative polyadenylation through the chloroplast

The paper investigates how light regulates alternative polyadenylation (APA) in Arabidopsis thaliana, finding that light affects APA in 30% of genes and involves chloroplasts and mitochondrial activity.

CodonBERT: Large Language Models for mRNA Design and Optimization

CodonBERT is a large language model for mRNA design and optimization that outperforms previous methods on a flu vaccine dataset.

MAAPER: model-based analysis of alternative polyadenylation using 3' end-linked reads

MAAPER analyzes alternative polyadenylation using nearSite reads, accurately predicting PASs and examining APA events with robust statistics across bulk and single-cell RNA samples.