Yang Yang

Centered cross-context perturbation transfer on the public 2025 Virtual Cell Challenge benchmark

The paper develops a method for cross-context perturbation transfer and differential-expression ranking, achieving competitive results on a benchmark challenge.

Gap-free telomere-to-telomere haplotypes assembly of the hybrid grouper 'Yushuban' (Cromileptes altivelis female x Epinephelus fuscoguttatus male)

The paper presents gap-free telomere-to-telomere haplotype assemblies for a hybrid grouper, enabling genetic analysis and breeding applications.

Oxaloacetate damages mitochondria by perturbing MIC60-dependent membrane remodeling

The paper identifies oxaloacetate accumulation as a cause of mitochondrial damage by inhibiting MIC60-dependent membrane remodeling in C. elegans and mammalian cells.

Loss of mitochondrial co-chaperone GRPEL2 protects mice from age- and diet-induced obesity

This study shows that loss of GRPEL2 in mice protects against age- and diet-induced obesity and improves metabolic health without affecting mitochondrial protein import.

Bone Lymphatic Endothelial Cells Form a Distinct Skeletal Population and Drive Skeletal Repair

The paper identifies bone lymphatic endothelial cells as a distinct population that drives skeletal repair and shows that their dysfunction contributes to mandibular diseases.

Examining the Role of Extrachromosomal DNA in Lung Cancer

This study examines ecDNA in lung cancer, finding it in 18.9% of patients and associating it with worse survival and genomic instability.

Brassinosteroid-auxin crosstalk shapes rice flag leaf angle to boost dense planting yield

OsBZR1 represses OsYUC8 to reduce auxin biosynthesis, modulating secondary cell wall formation and optimizing flag leaf architecture for higher yield in dense planting.

The Proposed Bone Post-Arterial Type R Capillaries Resolve into Venous and Fatty Acid-Handling Endothelial Cells

The paper redefines skeletal endothelial heterogeneity by showing the proposed type R population is part of a venous continuum and includes fatty acid-handling endothelial cells.

The Thermodynamics of Biomolecular CO2 Capture:Disentangling Equilibria in Amino-Acid-based Systems

This study uses isothermal titration calorimetry to analyze the thermodynamics of CO2 capture by amino acids and peptides, revealing distinct optimization strategies for carbamate formation.

Patient-derived tau-seeded human neuronal chimeras recapitulate mature Alzheimer's tau pathology and uncover human-specific neuronal vulnerability

This study develops a human neuronal chimera model to study Alzheimer's tau pathology, showing human-specific vulnerability and recapitulating mature AD features in vivo.

Benchmarking the translational potential of AI-based drug-resistance prediction from Mycobacterium tuberculosis whole-genome sequencing data

This paper benchmarks AI-based drug-resistance prediction models for Mycobacterium tuberculosis using a large unified dataset, finding XGBoost performs best in precision-recall and F1 metrics, while neural models excel in AUROC.

Fibroblast-encoded inflammatory memory orchestrates recurrent skin inflammation via NNMT-dependent metabolic remodeling

This paper identifies NNMT as a metabolic-epigenetic regulator in fibroblasts that sustains inflammatory memory and drives recurrent skin inflammation by maintaining a pro-inflammatory niche.

Dimerisation and twist reversal of the Lewy fold in α-synuclein mutants with Parkinson's disease and dementia

The paper reports the structures of α-synuclein filaments from individuals with Parkinson's disease and dementia, revealing differences in dimerisation and twist reversal between pathogenic and non-pathogenic variants.

OpenStride: an inexpensive, open-source force plate actometry system for quantification of rodent motor activity and behaviour

OpenStride is an open-source, low-cost force plate actometry system for quantifying rodent motor activity and behaviour, offering reliable tracking and analysis of various movement metrics.

Roles of spoVF operon subunits A and B in regulating cell morphology and biofilm formation in the biocontrol agent Bacillus subtilis

This study examines the role of spoVF operon subunits A and B in regulating cell morphology, biofilm formation, and biocontrol ability in Bacillus subtilis, finding that their knockout reduces DPA biosynthesis and biocontrol efficacy.

Synergizing Bayesian and Heuristic Approaches: D-BPP Uncovers Ghost Introgression in Panthera and Thuja

D-BPP detects ghost introgression in Panthera and Thuja by combining heuristic D-statistic with Bayesian phylogenomic inference.

Revealing the Drivers Underlying Distinct Evolutionary Trajectories in Lung Adenocarcinoma

This study identifies three distinct evolutionary trajectories in lung adenocarcinomas using whole-genome sequencing, revealing that some never-smoking tumors follow smoking-like paths driven by KRAS mutations.

Learning universal knowledge graph embedding for predicting biomedical pairwise interactions

This paper introduces LukePi, a self-supervised pre-training framework for GNNs on biomedical knowledge graphs, which improves link prediction in low-data and distribution-shift scenarios.

Functional diversification of the MADS-box gene family in fine-tuning the dimorphic transition of Talaromyces marneffei

The paper identifies functional diversification of MADS-box genes in Talaromyces marneffei, showing mads9 inhibits hyphal-to-yeast transition while mads10 does not.

Cryo-EM structures of Aβ40 filaments from the leptomeninges of individuals with Alzheimer's disease and cerebral amyloid angiopathy

The paper determines cryo-EM structures of Aβ40 filaments from Alzheimer's and cerebral amyloid angiopathy samples, revealing structural differences at higher resolution.

Cryo-EM structures of amyloid-beta filaments with the Arctic mutation (E22G) from human and mouse brains

The paper reports cryo-EM structures of amyloid-beta filaments with the Arctic mutation from human and mouse brains, revealing structural differences and conformational changes.

Transcriptome analysis reveals hepatotoxicity in zebrafish induced by cyhalofop-butyl

The paper investigates hepatotoxicity in zebrafish caused by cyhalofop-butyl but has been retracted due to concerns about the manuscript's validity and author identity.

Cryo-EM Structures of Amyloid-β 42 Filaments from Human Brain

Cryo-EM shows brain-derived Aβ42 filaments adopt two related S-shaped protofilament folds: Type I dominates sporadic Alzheimer's, Type II familial Alzheimer's, other disorders and App^NL-F knock-in mice.

GenomegaMap: within-species genome-wide dN/dS estimation from over 10,000 genomes

GenomegaMap estimates genome-wide dN/dS ratios across 10,209 tuberculosis genomes to identify selection pressures shaping the pathogen's evolution.

Mid-Infrared Spectroscopy Study of Effects of Neonicotinoids on Forager Honey Bee (Apis mellifera) Fat Bodies and Their Connection to Colony Collapse Disorder

This study uses mid-infrared spectroscopy to analyze neonicotinoid effects on honey bee fat bodies, finding changes in protein structure linked to Colony Collapse Disorder.

Recurrently deregulated lncRNAs associated with HCC tumorigenesis and metastasis revealed by genomic, epigenomic and transcriptomic profiling in paired primary tumor and PVTT samples

The paper identifies recurrently deregulated lncRNAs in HCC and PVTT samples, linking them to metastasis and prognosis using multi-omics data.

The Epidemiology and Transmissibility of Zika Virus in Girardot and San Andres Island, Colombia

This study estimates the basic reproductive number (R0) and attack rates of Zika virus outbreaks in San Andres and Girardot, Colombia, finding higher transmission in Girardot and significant gender disparities in case detection.

Comprehensive mapping of mammalian transcriptomes identifies conserved genes associated with different cell differentiation states

The paper integrates RNA-seq data from four mammals to map cell states, identifies conserved genes, and finds distinct evolutionary signatures in neural and testis tissues.