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Lactate-binding protein DNMT3A in HRMECs promotes angiogenesis by upregulating VEGFA through HIF-1α lactylation
Lactate-binding protein DNMT3A in HRMECs promotes angiogenesis by upregulating VEGFA through HIF-1α lactylation
Ocular neovascularization is a leading cause of blindness. Hypoxia is associated with retinal angiogenesis. Hypoxia result...
Comprehensive evaluation of diverse massively parallel reporter assays to functionally characterize human enhancers genome-wide
Comprehensive evaluation of diverse massively parallel reporter assays to functionally characterize human enhancers genome-wide
Massively parallel reporter assays (MPRAs) and self-transcribing active regulatory region sequencing (STARR-seq) have revo...
MaskGraphene: an advanced framework for interpretable joint representation for multi-slice, multi-condition spatial transcriptomics
MaskGraphene: an advanced framework for interpretable joint representation for multi-slice, multi-condition spatial transcriptomics
Recent advances in spatial transcriptomics (ST) highlight the need to integrate multiple slices for joint analysis. A key ...
Global profiling of CPL3-mediated alternative splicing reveals regulatory mechanisms of DGK5 in plant immunity and phosphatidic acid homeostasis
Global profiling of CPL3-mediated alternative splicing reveals regulatory mechanisms of DGK5 in plant immunity and phosphatidic acid homeostasis
Alternative splicing of precursor mRNAs serves as a crucial mechanism to enhance gene expression plasticity for organismal...
scVAEDer: integrating deep diffusion models and variational autoencoders for single-cell transcriptomics analysis
scVAEDer: integrating deep diffusion models and variational autoencoders for single-cell transcriptomics analysis
Discovering a lower-dimensional embedding of single-cell data can improve downstream analysis. The embedding should encaps...
ASPM mediates nuclear entrapment of FOXM1 via liquid-liquid phase separation to promote progression of hepatocarcinoma
ASPM mediates nuclear entrapment of FOXM1 via liquid-liquid phase separation to promote progression of hepatocarcinoma
Fork-head box protein M1 (FOXM1) plays critical roles in development and progression of multiple cancers, including hepato...
aurora: a machine learning gwas tool for analyzing microbial habitat adaptation
aurora: a machine learning gwas tool for analyzing microbial habitat adaptation
A primary goal of microbial genome-wide association studies is identifying genomic variants associated with a particular h...
Dissecting the genetic architecture of key agronomic traits in lettuce using a MAGIC population
Dissecting the genetic architecture of key agronomic traits in lettuce using a MAGIC population
Lettuce is a globally important leafy vegetable that exhibits diverse horticultural types and strong population structure,...
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...
TargetRNA3: predicting prokaryotic RNA regulatory targets with machine learning
TargetRNA3: predicting prokaryotic RNA regulatory targets with machine learning
Small regulatory RNAs pervade prokaryotes, with the best-studied family of these non-coding genes corresponding to trans-a...
Hybrid-hybrid correction of errors in long reads with HERO
Hybrid-hybrid correction of errors in long reads with HERO
Although generally superior, hybrid approaches for correcting errors in third-generation sequencing (TGS) reads, using nex...
Comparing methods for constructing and representing human pangenome graphs
Comparing methods for constructing and representing human pangenome graphs
As a single reference genome cannot possibly represent all the variation present across human individuals, pangenome graph...
ConDoR: tumor phylogeny inference with a copy-number constrained mutation loss model
ConDoR: tumor phylogeny inference with a copy-number constrained mutation loss model
A tumor contains a diverse collection of somatic mutations that reflect its past evolutionary history and that range in sc...
STmut: a framework for visualizing somatic alterations in spatial transcriptomics data of cancer
STmut: a framework for visualizing somatic alterations in spatial transcriptomics data of cancer
Spatial transcriptomic technologies, such as the Visium platform, measure gene expression in different regions of tissues....
Methylation-directed regulatory networks determine enhancing and silencing of mutation disease driver genes and explain inter-patient expression variation
Methylation-directed regulatory networks determine enhancing and silencing of mutation disease driver genes and explain inter-patient expression variation
Common diseases manifest differentially between patients, but the genetic origin of this variation remains unclear. To exp...
Quartet DNA reference materials and datasets for comprehensively evaluating germline variant calling performance
Quartet DNA reference materials and datasets for comprehensively evaluating germline variant calling performance
Genomic DNA reference materials are widely recognized as essential for ensuring data quality in omics research. However, r...
Cooperation of MLL1 and Jun in controlling H3K4me3 on enhancers in colorectal cancer
Cooperation of MLL1 and Jun in controlling H3K4me3 on enhancers in colorectal cancer
Enhancer dysregulation is one of the important features for cancer cells. Enhancers enriched with H3K4me3 have been implic...
Single-cell multiomics of the human retina reveals hierarchical transcription factor collaboration in mediating cell type-specific effects of genetic variants on gene regulation
Single-cell multiomics of the human retina reveals hierarchical transcription factor collaboration in mediating cell type-specific effects of genetic variants on gene regulation
Systematic characterization of how  genetic variation modulates gene regulation in a cell type-specific context i...
CREaTor: zero-shot cis-regulatory pattern modeling with attention mechanisms
CREaTor: zero-shot cis-regulatory pattern modeling with attention mechanisms
Linking cis-regulatory sequences to target genes has been a long-standing challenge. In this study, we introduce CREaTor, ...
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