Yue Shen

Multimodal AI Decodes Extreme Environment Functional Dark Matter Beyond Homology

The paper develops ACCESS, a multimodal graph neural network to annotate functional dark matter proteins from extreme environments beyond homology-based methods.

Revolutionizing large-scale DNA synthesis with microchip-based massive in parallel synthesis system

This paper introduces a microchip-based DNA synthesis system that significantly improves DNA product concentration and simplifies downstream processes for large-scale gene synthesis.

Synthetic genomes unveil the effects of synonymous recoding

This study uses synthetic genomes to investigate how synonymous codon recoding affects organismal fitness and develops a workflow to overcome lethal effects of codon swaps.

BioInformatics Agent (BIA): Unleashing the Power of Large Language Models to Reshape Bioinformatics Workflow

This paper introduces BIA, an intelligent agent using LLMs to automate bioinformatics tasks, demonstrating its effectiveness with scRNA-seq data and outlining strategies for improvement.

Site saturation mutagenesis of 500 human protein domains reveals the contribution of protein destabilization to genetic disease

The paper performs site saturation mutagenesis on 500 human protein domains to assess the impact of missense variants on protein stability and disease.

A 5' UTR Language Model for Decoding Untranslated Regions of mRNA and Function Predictions

This paper introduces a language model for 5' UTRs that improves predictions of translation efficiency and mRNA expression, and validates novel 5' UTR designs through wet-lab experiments.

High plasticity of ribosomal DNA organization in budding yeast

This study constructs synthetic rDNA arrays in budding yeast and shows that reducing copy numbers or dispersing arrays does not harm cell growth or transcriptomes.

Screening and characterization of aging regulators using synthesized yeast chromosome XIII

The paper constructs a synthetic yeast chromosome and identifies aging regulators through replicative lifespan studies and genome-scale analysis.

Dissecting aneuploidy phenotypes by constructing Sc2.0 chromosome VII and SCRaMbLEing synthetic disomic yeast

The paper constructs a synthetic disomic yeast using SCRaMbLE and a newly synthesized chromosome to study aneuploidy phenotypes, finding that both copy number and specific chromosomal regions affect fitness.

Design, Construction, and Functional Characterization of a tRNA Neochromosome in Yeast

A de novo yeast neochromosome carrying all 275 tRNA genes was built and characterized; it imposes a growth burden, with genome doubling and deletions in haploids possibly reflecting compensation.

Debugging and consolidating multiple synthetic chromosomes reveals combinatorial genetic interactions

The paper uses CRISPR D-BUGS and chromosome swapping to identify and resolve genetic interactions in synthetic chromosomes, revealing unexpected links between transcription, inositol metabolism, and tRNA abundance.

Towards Practical and Robust DNA-based Data Archiving Using "Yin-Yang Codec" System

This paper introduces a DNA-based data archiving system called Yin-Yang Codec, which achieves high recovery rates and physical information density in both in vitro and in vivo storage.

DNB-Based On-Chip Motif Finding (DocMF): a High-Throughput Method to Profile Different Types of Protein-DNA Interactions

The paper introduces DocMF, a high-throughput method to profile protein-DNA interactions, identifying PAM sequences for CRISPR systems and other DNA-binding proteins.

BDdb: a comprehensive platform for exploration and utilization of birth defect multi-omics data

BDdb is a database integrating multi-omics data, cfDNA data, and biomarkers for birth defects, enabling data exploration and analysis for research and clinical applications.

FREQUENT GENE CONVERSION IN HUMAN EMBRYOS INDUCED BY DOUBLE STRAND BREAKS

This study shows that gene conversion and NHEJ are major DNA repair mechanisms in human embryos, with gene conversion potentially useful for gene correction but also causing extensive loss of heterozygosity.

Chamaeleo: a robust library for DNA storage coding schemes

Chamaeleo provides a library for DNA storage coding schemes, offering flexibility and expandability over existing single-scheme implementations.

Derivation and characterization of chimera-competent eXtra-Embryonic eNdoderm 1 (XEN) cells from pig blastocysts

The paper derives and characterizes XEN cells from pig embryos, showing their ability to contribute to chimerism and serve as nuclear donors for cloning.

Enhance genome editing efficiency and specificity by a quick CRISPR/Cas9 system

This study introduces qCas9, a modified CRISPR/Cas9 system that enhances genome editing efficiency and reduces off-target effects in zebrafish and mammalian cells.

Sequencing and comparative analysis of three Chlorella genomes provide insights into strain-specific adaptation to wastewater

The paper sequences and compares three Chlorella genomes to identify genetic factors contributing to wastewater tolerance and nutrient removal.