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Vispro improves imaging analysis for Visium spatial transcriptomics
Vispro improves imaging analysis for Visium spatial transcriptomics
Spatial transcriptomics enables spatially resolved gene expression analysis, but accompanying histology images are often d...
k-mer-based GWAS in a wheat collection reveals novel and diverse sources of powdery mildew resistance
k-mer-based GWAS in a wheat collection reveals novel and diverse sources of powdery mildew resistance
Wheat genetic resources hold the diversity required to mitigate agricultural challenges from climate change and reduced in...
scExtract: leveraging large language models for fully automated single-cell RNA-seq data annotation and prior-informed multi-dataset integration
scExtract: leveraging large language models for fully automated single-cell RNA-seq data annotation and prior-informed multi-dataset integration
Single-cell RNA sequencing has revolutionized cellular heterogeneity research, but analyzing the abundance of unannotated ...
Comparison of spatial transcriptomics technologies using tumor cryosections
Comparison of spatial transcriptomics technologies using tumor cryosections
Spatial transcriptomics technologies are revolutionizing our understanding of intra-tumor heterogeneity and the tumor micr...
Loop Catalog: a comprehensive HiChIP database of human and mouse samples
Loop Catalog: a comprehensive HiChIP database of human and mouse samples
HiChIP enables cost-effective and high-resolution profiling of chromatin loops. To leverage the increasing number of HiChI...
Considerations in the search for epistasis
Considerations in the search for epistasis
Epistasis refers to changes in the effect on phenotype of a unit of genetic information, such as a single nucleotide polym...
scStateDynamics: deciphering the drug-responsive tumor cell state dynamics by modeling single-cell level expression changes
scStateDynamics: deciphering the drug-responsive tumor cell state dynamics by modeling single-cell level expression changes
Understanding tumor cell heterogeneity and plasticity is crucial for overcoming drug resistance. Single-cell technologies ...
The genomic portrait of the Picene culture provides new insights into the Italic Iron Age and the legacy of the Roman Empire in Central Italy
The genomic portrait of the Picene culture provides new insights into the Italic Iron Age and the legacy of the Roman Empire in Central Italy
The Italic Iron Age is characterized by the presence of various ethnic groups partially examined from a genomic perspectiv...
Hierarchical annotation of eQTLs by H-eQTL enables identification of genes with cell type-divergent regulation
Hierarchical annotation of eQTLs by H-eQTL enables identification of genes with cell type-divergent regulation
While context-type-specific regulation of genes is largely determined by cis-regulatory regions, attempts to identify cell...
Contribution of homoeologous exchange to domestication of polyploid Brassica
Contribution of homoeologous exchange to domestication of polyploid Brassica
Polyploidy is widely recognized as a significant evolutionary force in the plant kingdom, contributing to the diversificat...
Gut microbiota contributes to high-altitude hypoxia acclimatization of human populations
Gut microbiota contributes to high-altitude hypoxia acclimatization of human populations
The relationship between human gut microbiota and high-altitude hypoxia acclimatization remains highly controversial. This...
Dissecting the genetic basis of UV-B responsive metabolites in rice
Dissecting the genetic basis of UV-B responsive metabolites in rice
UV-B, an important environmental factor, has been shown to affect the yield and quality of rice (Oryza sativa) worldwide. ...
Enhlink infers distal and context-specific enhancer–promoter linkages
Enhlink infers distal and context-specific enhancer–promoter linkages
Enhlink is a computational tool for scATAC-seq data analysis, facilitating precise interrogation of enhancer function at t...
hadge: a comprehensive pipeline for donor deconvolution in single-cell studies
hadge: a comprehensive pipeline for donor deconvolution in single-cell studies
Single-cell multiplexing techniques (cell hashing and genetic multiplexing) combine multiple samples, optimizing sample pr...
Differences in 5'untranslated regions highlight the importance of translational regulation of dosage sensitive genes
Differences in 5'untranslated regions highlight the importance of translational regulation of dosage sensitive genes
Untranslated regions (UTRs) are important mediators of post-transcriptional regulation. The length of UTRs and the composi...
Disruption of metazoan gene regulatory networks in cancer alters the balance of co-expression between genes of unicellular and multicellular origins
Disruption of metazoan gene regulatory networks in cancer alters the balance of co-expression between genes of unicellular and multicellular origins
Metazoans inherited genes from unicellular ancestors that perform essential biological processes such as cell division, me...
DISSECT: deep semi-supervised consistency regularization for accurate cell type fraction and gene expression estimation
DISSECT: deep semi-supervised consistency regularization for accurate cell type fraction and gene expression estimation
Cell deconvolution is the estimation of cell type fractions and cell type-specific gene expression from mixed data. An unm...
mi-Mic: a novel multi-layer statistical test for microbiota-disease associations
mi-Mic: a novel multi-layer statistical test for microbiota-disease associations
mi-Mic, a novel approach for microbiome differential abundance analysis, tackles the key challenges of such statistical te...
SQANTI-SIM: a simulator of controlled transcript novelty for lrRNA-seq benchmark
SQANTI-SIM: a simulator of controlled transcript novelty for lrRNA-seq benchmark
Long-read RNA sequencing has emerged as a powerful tool for transcript discovery, even in well-annotated organisms. Howeve...
DNA methylation modulated genetic variant effect on gene transcriptional regulation
DNA methylation modulated genetic variant effect on gene transcriptional regulation
Expression quantitative trait locus (eQTL) analysis has emerged as an important tool in elucidating the link between genet...
Turnover of strain-level diversity modulates functional traits in the honeybee gut microbiome between nurses and foragers
Turnover of strain-level diversity modulates functional traits in the honeybee gut microbiome between nurses and foragers
Strain-level diversity is widespread among bacterial species and can expand the functional potential of natural microbial ...
Pediatric glioma histone H3.3 K27M/G34R mutations drive abnormalities in PML nuclear bodies
Pediatric glioma histone H3.3 K27M/G34R mutations drive abnormalities in PML nuclear bodies
Point mutations in histone variant H3.3 (H3.3K27M, H3.3G34R) and the H3.3-specific ATRX/DAXX chaperone complex are frequen...
Cotton pedigree genome reveals restriction of cultivar-driven strategy in cotton breeding
Cotton pedigree genome reveals restriction of cultivar-driven strategy in cotton breeding
Many elite genes have been identified from the available cotton genomic data, providing various genetic resources for gene...
GCLiPP: global crosslinking and protein purification method for constructing high-resolution occupancy maps for RNA binding proteins
GCLiPP: global crosslinking and protein purification method for constructing high-resolution occupancy maps for RNA binding proteins
GCLiPP is a global RNA interactome capture method that detects RNA-binding protein (RBP) occupancy transcriptome-wide. GCL...
Meiosis in an asymmetric dikaryotic genome of Tremella fuciformis Tr01 facilitates new chromosome formation
Meiosis in an asymmetric dikaryotic genome of Tremella fuciformis Tr01 facilitates new chromosome formation
The dikaryotic stage dominates most of the life cycle in basidiomycetes, and each cell carries two different haploid nucle...
Dengue and Zika RNA-RNA interactomes reveal pro- and anti-viral RNA in human cells
Dengue and Zika RNA-RNA interactomes reveal pro- and anti-viral RNA in human cells
Identifying host factors is key to understanding RNA virus pathogenicity. Besides proteins, RNAs can interact with virus g...
Integration of datasets for individual prediction of DNA methylation-based biomarkers
Integration of datasets for individual prediction of DNA methylation-based biomarkers
Epigenetic scores (EpiScores) can provide biomarkers of lifestyle and disease risk. Projecting new datasets onto a referen...
A large-scale genomically predicted protein mass database enables rapid and broad-spectrum identification of bacterial and archaeal isolates by mass spectrometry
A large-scale genomically predicted protein mass database enables rapid and broad-spectrum identification of bacterial and archaeal isolates by mass spectrometry
MALDI-TOF MS-based microbial identification relies on reference spectral libraries, which limits the screening of diverse ...
Reconstruction of private genomes through reference-based genotype imputation
Reconstruction of private genomes through reference-based genotype imputation
Genotype imputation is an essential step in genetic studies to improve data quality and statistical power. Public imputati...
Haplotype-resolved assemblies and variant benchmark of a Chinese Quartet
Haplotype-resolved assemblies and variant benchmark of a Chinese Quartet
Recent state-of-the-art sequencing technologies enable the investigation of challenging regions in the human genome and ex...
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