Qiangfeng Cliff Zhang

Programmable design of functional RNAs through multimodal generative learning

RNAverse, a multimodal generative model, designs functional RNAs with high performance across tasks, outperforming existing methods and enabling applications in gene therapy and vaccine development.

CryoSeek identification of glycofibrils with diverse compositions and structural assemblies

The paper characterizes five new glycofibrils isolated from Tsinghua Lotus Pond using cryo-EM and AI, revealing structural diversity in their central protein components and glycans.

Polymerization of Tetraspanin 7 into Helical Transmembrane Skeletons for Tubular Membrane Stabilization

The paper identifies TSPAN7's role in forming helical transmembrane structures that stabilize tubular membrane protrusions by sensing curvature and resisting mechanical stress.

Structural RNA components supervise the sequential DNA cleavage in R2 retrotransposon

The paper determines the cryo-EM structure of R2 retrotransposon with RNA and reveals DNA regions and RNA roles in DNA cleavage and reverse transcription.

Online single-cell data integration through projecting heterogeneous datasets into a common cell-embedding space

SCALEX integrates single-cell data into a common embedding space without retraining, outperforming existing methods on diverse datasets and enabling expandable atlases.

Differential Analysis of RNA Structure Probing Experiments at Nucleotide Resolution: Uncovering Regulatory Functions of RNA Structure

DiffScan identifies structurally variable regions in RNA structure probing data with improved accuracy across multiple platforms.

rG4-seq 2.0: enhanced transcriptome-wide RNA G-quadruplex structure sequencing for low RNA input samples

This study introduces rG4-seq 2.0, an improved method for detecting RNA G-quadruplexes with lower RNA input requirements and better library quality.

The chromatin-remodeling enzyme Smarca5 regulates erythrocyte aggregation via Keap1-Nrf2 signaling

This study shows that Smarca5 regulates erythrocyte aggregation through Keap1-Nrf2 signaling in zebrafish, leading to venous thrombosis-like phenotypes.

In vivo structural characterization of the whole SARS-CoV-2 RNA genome identifies host cell target proteins vulnerable to re-purposed drugs

The paper maps the in vivo structure of SARS-CoV-2 RNA, identifies novel structural features, and predicts host proteins interacting with the RNA using deep learning.

VRmol: an Integrative Cloud-Based Virtual Reality System to Explore Macromolecular Structure

VRmol provides a cloud-based VR system for exploring macromolecular structures with integrated genomic and drug information.

U1 snRNP regulates chromatin retention of noncoding RNAs

The paper identifies a U1 snRNP recognition motif that regulates chromatin retention of noncoding RNAs through experimental and computational methods.

The identification of mecciRNAs and their roles in mitochondrial entry of proteins

The paper identifies mecciRNAs, circular RNAs from the mitochondrial genome that assist in the mitochondrial import of nuclear-encoded proteins by acting as molecular chaperones.

Dynamic Regulation of RNA Structure in Mammalian Cells

The paper maps RNA structuromes in three subcellular compartments and identifies LIN28A as an m6A anti-reader, revealing dynamic RNA structure regulation.

Integrative analysis of Zika virus genome RNA structure reveals critical determinants of viral infectivity

This study identifies RNA structural elements in ZIKV strains that influence infectivity through comparative in vivo analysis.