Z. Zhang

GeneEmbedLLM: Harnessing Large Language Models for Gene Functional Embedding and Association Prediction

This paper introduces GeneEmbedLLM, a framework using large language models to generate gene embeddings from multi-source textual annotations, achieving competitive performance in various downstream tasks.

STEVE: Single-cell Transcriptomics Expression Visualization and Evaluation

STEVE evaluates cell-type annotation robustness in scRNA-seq datasets through subsampling, novel cell detection, and benchmarking against ground-truth labels.

Amyloid precursor protein interacts with the mitochondrial phosphatase PGAM5 and regulates mitochondrial respiration

This study identifies an interaction between APP and PGAM5, showing that APP regulates mitochondrial respiration by modulating Keap1-Nrf2 signaling.

Ultrasound-Driven Programmable Artificial Muscles

This paper introduces programmable artificial muscles using ultrasound-activated microbubbles, achieving high compactness, low weight, and fast response for applications in soft robotics and biomedical devices.

New structural features of the APC/C revealed by high resolution cryo-EM structures of apo-APC/C and the APC/C CDH1:EMI1 complex

This study uses cryo-EM to determine high-resolution structures of apo-APC/C and APC/C CDH1:EMI1, revealing new structural features and regulatory mechanisms.

Comprehensive Identification of Pathogenic Microbes and Antimicrobial Resistance Genes in Food Products Using Nanopore Sequencing-Based Metagenomics

This study uses nanopore sequencing to identify pathogens and antimicrobial resistance genes in food products, finding high prevalence of certain bacteria and resistance genes in specific food types.

Multiple Unfolded Protein Response pathways cooperate to link cytosolic dsDNA release to Stimulator of Interferon Gene (STING) activation

This study identifies multiple UPR pathways that cooperate to link cytosolic dsDNA release to STING activation and IFN-β induction in response to ER stress.

The mechanistic rules for species coexistence

The paper uses a mechanistic consumer-resource model to predict phytoplankton community composition across resource conditions and species richness, finding that competition for essential resources reduces diversity.

An in-depth analysis and exploreation with focus on the biofilm in Staphylococcus aureus

This study analyzes RNA sequencing data on Staphylococcus aureus biofilm formation using machine learning and co-expression analysis to identify functional modules and novel protein interactions, and develops a database for storing and analyzing the data.

MIPDB: A maize image-phenotype database with multi-angle and multi-time characteristics

The paper introduces MIPDB, a maize image-phenotype database with multi-angle and multi-time images, providing a high-quality dataset for deep learning-based phenomics research.

Matrix Vesicles from Osteoblasts Promote Atherosclerotic Calcification

This study shows osteoblast-derived matrix vesicles (Ost-MVs) contribute to atherosclerotic calcification by being released into circulation and transported to plaques, where they exacerbate calcification through the Ras-Raf-ERK pathway.

FLASH Irradiation Regulates IFN-β induction by mtDNA via Cytochrome c Leakage

This study shows FLASH irradiation increases cytochrome c leakage from mitochondria in normal cells, reducing mtDNA accumulation and IFN-β secretion, while having the opposite effect in cancer cells.

The Class III peroxidase OsPrx20 is a key regulator of stress response and growth in rice

This study identifies OsPrx20 as a key regulator of stress response and growth in rice, showing its dual role in osmotic stress tolerance and blast resistance.

Neuropeptide Bursicon and its receptor mediated the transition from summer-form to winter-form of Cacopsylla chinensis

This study identifies Bursicon and its receptor as key regulators of the summer-to-winter form transition in Cacopsylla chinensis by modulating cuticle properties.

Timing of treatment shapes the path to androgen receptor signaling inhibitor resistance in prostate cancer

This study shows that treatment timing affects the path to androgen receptor signaling inhibitor resistance in prostate cancer, with resistance arising through different mechanisms depending on the tumor context.

Deep learning based genomic breeding of pest-resistant grapevine

This study uses deep learning and genome-wide association studies to identify pest-resistant genes in grapevine, achieving high accuracy in predicting pest damage.

A change in cis-regulatory logic underlying obligate versus facultative muscle multinucleation in chordates

This study identifies cis-regulatory differences in the Mymk promoter that explain divergent muscle multinucleation patterns between vertebrates and tunicates.

Molecular mechanism of Mad2 conformational conversion promoted by the Mad2-interaction motif of Cdc20

This study elucidates how the Cdc20MIM induces Mad2 conformational conversion by transiently exposing a binding site and facilitating structural changes.

Brain-wide neuronal circuit connectome of human glioblastoma

This study shows human glioblastoma cells integrate into brain-wide neuronal circuits, exhibit diverse connectivity, and respond to neuromodulatory inputs like acetylcholine, which promotes invasion and survival.

Engineering an Escherichia coli strain for production of long single-stranded DNA

This paper describes an engineered E. coli strain that produces long single-stranded DNA efficiently, validated for use in genome editing and DNA origami.

Shallow-water chemosymbiotic clams are a globally significant and previously overlooked carbon sink

This study identifies shallow-water chemosymbiotic clams as a significant, previously overlooked carbon sink in the Yellow Sea, contributing 43% of the region's sedimental carbon burial.

Dysregulation of mitochondrial function by PLK1-mediated PDHA1 phosphorylation promotes Cr(VI)-associated lung cancer progression

This study shows that PLK1-mediated PDHA1 phosphorylation impairs mitochondrial function and promotes Cr(VI)-induced lung cancer progression by disrupting energy metabolism and apoptosis.

Neurotensin-Neurotensin Receptor 2 signaling in adipocytes regulates food intake through ceramide metabolism

This study shows that NTS-NTSR2 signaling in white adipocytes regulates food intake by modulating ceramide metabolism and GDF15 production.

Comparative Metagenomics Provide Mechanistic Insights into the Biodegradation of the Non-hydrolysable Plastic Polyvinyl Chloride in Gut Microbiota of Insect Larvae

This study identifies a potent PVC-dechlorinating activity in gut microbiota of insect larvae using comparative metagenomics.

Morroniside promotes skin wound re-epithelialization by facilitating epidermal stem cell proliferation through GLP-1R-mediated upregulation of β-catenin expression

This study shows that morroniside promotes skin wound healing by enhancing epidermal stem cell proliferation through GLP-1R-mediated upregulation of β-catenin and downstream targets.

A nox2 / cybb zebrafish mutant with defective neutrophil ROS production displays normal initial neutrophil recruitment to sterile tail injuries

ATM-Mediated Translocation of RanBPM Regulates DNA Damage Response by Stabilizing p21 in Non-Small Cell Lung Cancer Cells

The paper identifies a novel mechanism where RanBPM stabilizes p21 via deubiquitination, regulating DNA damage response in NSCLC cells.

Oligomeric HIV-1 Integrase Structures Reveal Functional Plasticity for Intasome Assembly and RNA Binding

This study determines cryo-EM structures of HIV-1 integrase tetramers and intasome hexadecamers, revealing structural plasticity and functional roles in viral integration and RNA binding.

Mechanical stability and unfolding pathways of parallel tetrameric G-quadruplexes probed by pulling simulations

This study uses pulling simulations to analyze the mechanical stability and unfolding pathways of tetrameric parallel G-quadruplexes, identifying key factors like vertical force components and unfolding transitions.

Predicting assembly/disassembly orders of protein complexes using coarse-grained simulations

This study develops computational protocols to predict protein complex assembly/disassembly orders using coarse-grained simulations, validated against experimental data.