Wei Wang

Omics-scale decoding of protein N-glycosylation using protein language model embeddings

The paper decodes protein N-glycosylation sites from protein language model embeddings using a zero-shot framework, revealing biological insights and disease associations.

A compact motif vocabulary is differentially interpreted across human cell types

The paper shows that a compact set of regulatory motifs can explain gene expression across diverse human cell types through context-dependent interpretation.

Stable large-scale network architecture and structured individual variability in the awake mouse brain

The paper introduces the Awake Mouse Connectome Project (AMCP), a dataset of 212 awake mice, and presents functional network atlases and analysis tools for studying brain connectivity and variability.

Polyglutamine-expanded TBP rewires neuronal and muscle proteomes beyond transcription in a Drosophila model of SCA17

This study identifies tissue-specific proteomic changes in a Drosophila SCA17 model, showing polyglutamine-expanded TBP affects pathways beyond transcription.

LineageFlow: Growth-Corrected State Dynamics for Probabilistic Cell-Fate Prediction

LineageFlow predicts clonal fate and transcriptional profiles by integrating growth dynamics and state transitions in single-cell lineage data.

HSF1 inhibition potentiates the antifungal activity and proteome instability induced by the fungal Hsp110 inhibitor 2H

This study shows that combining HSF1 inhibition with Hsp110 inhibitor 2H enhances antifungal activity by increasing proteome instability in fungal pathogens.

Monkeypox virus M2 rewires nucleocytoplasmic transport to coordinate host translation suppression and immune evasion

This study identifies M2 as a multifunctional protein in monkeypox virus that blocks host gene expression by disrupting nucleocytoplasmic transport and altering signaling pathways, contributing to host shutoff and immune evasion.

The small molecule inhibitor SU056-mediated targeting of YB1 inhibits the Rb pathway in triple-negative breast cancer tumors

This study shows that SU056, a YB1 inhibitor, suppresses TNBC growth and metastasis by targeting the Rb pathway, with enhanced efficacy when combined with CDK4/6 inhibition.

PalmLab: A Comprehensive Computational Platform for Systematic Annotation and Functional Interrogation of Protein Palmitoylation

PalmLab curates and analyzes palmitoylation data from human and mouse proteomes, providing tools for functional interrogation and cross-cohort comparisons.

Glutamatergic Neuron-Meningioma Synapse Interaction Promotes Brain-Invasive Tumor Growth

The paper identifies functional glutamatergic synapses between meningioma cells and neurons, showing they promote tumor invasion and proliferation.

Pto evolved from malectin-like RLKs phosphorylates AvrPtoB to promote Prf-mediated immunity in Solanum pimpinellifolium

This study shows Pto phosphorylates AvrPtoB to enhance immunity in tomato and identifies evolutionary changes that stabilize Pto.

Systematic In Silico Off-Target Assessment of siRNAs: Integrated Tissue-Specific Scoring and Cross-Species Preclinical Model Selection with TargetSureR

TargetSureR assesses siRNA off-target risks using a seven-dimensional scoring system and enables cross-species model selection for preclinical safety evaluation.

Candida albicans reprograms host inosine metabolism to drive immunosuppressive macrophage polarization and gastric cancer carcinogenesis

SpaCir-VDJ: a broadly compatible circularization strategy for spatial immune repertoire profiling

SpaCir-VDJ enables spatial immune repertoire profiling by integrating spatial barcodes and V(D)J sequences into circular templates, revealing clonal organization and somatic hypermutation patterns in human tissues and gastric cancer.

Epigenetic trajectory predicts development of clinical rheumatoid arthritis in ACPA+ individuals: Targeting Immune Responses for Prevention of Rheumatoid Arthritis (TIP-RA)

The paper identifies epigenetic trajectories in ACPA+ individuals that predict RA development, showing dynamic methylation changes in Pre-RA compared to stable methylomes in non-converters and controls.

Adaptation of the freshwater anaerobic methanotroph 'Ca. Methanoperedens vercellensis' to low pH levels reveals membrane lipid remodelling

This study shows that Ca. Methanoperedens vercellensis adapts to low pH by remodelling membrane lipids, maintaining methane oxidation activity despite increased energy demands.

scLong: A Billion-Parameter Foundation Model for Capturing Long-Range Gene Context in Single-Cell Transcriptomics

scLong is a billion-parameter foundation model that captures long-range gene context in scRNA-seq by modeling all genes and integrating gene knowledge, outperforming existing models in various tasks.

Scalable embedding fusion with protein language models: insights from benchmarking text-integrated representations

The paper benchmarks text-integrated protein language models and introduces embedding fusion to improve performance across diverse tasks.

LISA: A Comprehensive R Package for Lentiviral Integration Site Analysis in Gene Therapy Safety Assessment

LISA is an R package for analyzing lentiviral integration sites in gene therapy to assess safety by identifying risk-associated genomic regions and tracking clonal dynamics.

Minute-scale single-cell transcriptomics enables dynamic modeling of cellular behavior

ChronoSeq enables minute-scale single-cell transcriptomics to model dynamic cellular processes with high temporal resolution.

Spatial transcriptomics reveals distinct inflammatory and adaptive immune properties of rheumatoid arthritis synovial fibroblasts

This study uses spatial transcriptomics to identify distinct gene expression patterns in RA synovial fibroblasts and macrophages, revealing region- and cell-type-specific roles in inflammation and adaptive immunity.

Senescent astrocytic deposits drive cognitive decline by disrupting tripartite synapse in the aging brain

This study identifies Senescent Astrocytic Deposits (SAD) as a mechanism linking astrocyte senescence to synaptic dysfunction and cognitive decline in aging brains.

Nanoscale volumetric fluorescence imaging via photochemical sectioning

The paper develops photochemical sectioning to enable nanoscale volumetric imaging of whole-mount specimens, demonstrating its application in analyzing axon degeneration and myelination in mouse olfactory bulbs.

Qimai: a multi-agent framework for zero-shot DNA-protein interaction prediction

Qimai improves DNA-protein interaction prediction for unseen proteins by integrating deep learning with LLM-based reasoning, achieving higher AUC-PR, AUC-ROC, and MCC than standalone models.

NLRP3 is a thermosensor that is negatively regulated by high temperature

This study shows high temperatures inhibit NLRP3 inflammasome activation, identifying NLRP3 as a thermosensor and revealing a temperature-sensitive conformational change in its C-terminal domain.

Expression screening and functional verification of recombinant hirudin from novel chassis cell Chlamydomonas reinhardtii

This paper produces functional hirudin in Chlamydomonas reinhardtii, demonstrating high thrombin-inhibitory activity and safety in a murine model.

A partner switch from CDS2 to RAB1A redirects MBOAT7 to inhibit DGAT2-mediated lipid droplet growth

The paper shows MBOAT7 redistributes to ER-LD contacts via RAB1 to inhibit DGAT2-mediated lipid droplet growth in response to CDS2 disruption.

Single oocyte full-length isoform sequencing unveils the impact of transposable elements on RNA diversity and stability during oocyte maturation

The paper uses single oocyte full-length isoform sequencing to identify novel transcripts and show that transposable elements contribute to RNA isoform diversity and stability during oocyte maturation.

Multi-lineage transcriptional and cell communication signatures define evolving personalized mechanisms that initiate and perpetuate rheumatoid arthritis

The paper identifies shared transcriptional and cell communication signatures in RA patients and at-risk individuals, showing how multiple pathogenic mechanisms contribute to disease initiation and progression.

The shared genetic architecture and evolution of human language and musical rhythm

This study investigates the shared genetic architecture between rhythm and dyslexia using large-scale genome-wide association studies.