SCI时时刷

search
+
Transcription of a centromere-enriched retroelement and local retention of its RNA are significant features of the CENP-A chromatin landscape
Transcription of a centromere-enriched retroelement and local retention of its RNA are significant features of the CENP-A chromatin landscape
Centromeres depend on chromatin containing the conserved histone H3 variant CENP-A for function and inheritance, while the...
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...
Cohesin distribution alone predicts chromatin organization in yeast via conserved-current loop extrusion
Cohesin distribution alone predicts chromatin organization in yeast via conserved-current loop extrusion
Inhomogeneous patterns of chromatin-chromatin contacts within 10–100-kb-sized regions of the genome are a generic fe...
VI-VS: calibrated identification of feature dependencies in single-cell multiomics
VI-VS: calibrated identification of feature dependencies in single-cell multiomics
Unveiling functional relationships between various molecular cell phenotypes from data using machine learning models is a ...
Adenine base editors induce off-target structure variations in mouse embryos and primary human T cells
Adenine base editors induce off-target structure variations in mouse embryos and primary human T cells
The safety of CRISPR-based gene editing methods is of the utmost priority in clinical applications. Previous studies have ...
SpottedPy quantifies relationships between spatial transcriptomic hotspots and uncovers environmental cues of epithelial-mesenchymal plasticity in breast cancer
SpottedPy quantifies relationships between spatial transcriptomic hotspots and uncovers environmental cues of epithelial-mesenchymal plasticity in breast cancer
Spatial transcriptomics is revolutionizing the exploration of intratissue heterogeneity in cancer, yet capturing cellular ...
IAMSAM: image-based analysis of molecular signatures using the Segment Anything Model
IAMSAM: image-based analysis of molecular signatures using the Segment Anything Model
Spatial transcriptomics is a cutting-edge technique that combines gene expression with spatial information, allowing resea...
GraphPCA: a fast and interpretable dimension reduction algorithm for spatial transcriptomics data
GraphPCA: a fast and interpretable dimension reduction algorithm for spatial transcriptomics data
The rapid advancement of spatial transcriptomics technologies has revolutionized our understanding of cell heterogeneity a...
scDOT: optimal transport for mapping senescent cells in spatial transcriptomics
scDOT: optimal transport for mapping senescent cells in spatial transcriptomics
The low resolution of spatial transcriptomics data necessitates additional information for optimal use. We developed scDOT...
TDFPS-Designer: an efficient toolkit for barcode design and selection in nanopore sequencing
TDFPS-Designer: an efficient toolkit for barcode design and selection in nanopore sequencing
Oxford Nanopore Technologies (ONT) offers ultrahigh-throughput multi-sample sequencing but only provides barcode kits that...
CaClust: linking genotype to transcriptional heterogeneity of follicular lymphoma using BCR and exomic variants
CaClust: linking genotype to transcriptional heterogeneity of follicular lymphoma using BCR and exomic variants
Tumours exhibit high genotypic and transcriptional heterogeneity. Both affect cancer progression and treatment, but have b...
Response to "Neglecting normalization impact in semi-synthetic RNA-seq data simulation generates artificial false positives" and "Winsorization greatly reduces false positives by popular differential expression methods when analyzing human population samples"
Response to "Neglecting normalization impact in semi-synthetic RNA-seq data simulation generates artificial false positives" and "Winsorization greatly reduces false positives by popular differential expression methods when analyzing human population samples"
Two correspondences raised concerns or comments about our analyses regarding exaggerated false positives found by differen...
Winsorization greatly reduces false positives by popular differential expression methods when analyzing human population samples
Winsorization greatly reduces false positives by popular differential expression methods when analyzing human population samples
A recent study found severely inflated type I error rates for DESeq2 and edgeR, two dominant tools used for differential e...
Neglecting the impact of normalization in semi-synthetic RNA-seq data simulations generates artificial false positives
Neglecting the impact of normalization in semi-synthetic RNA-seq data simulations generates artificial false positives
A recent study reported exaggerated false positives by popular differential expression methods when analyzing large popula...
Benchmarking and building DNA binding affinity models using allele-specific and allele-agnostic transcription factor binding data
Benchmarking and building DNA binding affinity models using allele-specific and allele-agnostic transcription factor binding data
Transcription factors (TFs) bind to DNA in a highly sequence-specific manner. This specificity manifests itself in vivo as...
Mapping lineage-traced cells across time points with moslin
Mapping lineage-traced cells across time points with moslin
Simultaneous profiling of single-cell gene expression and lineage history holds enormous potential for studying cellular d...
STASCAN deciphers fine-resolution cell distribution maps in spatial transcriptomics by deep learning
STASCAN deciphers fine-resolution cell distribution maps in spatial transcriptomics by deep learning
Spatial transcriptomics technologies have been widely applied to decode cellular distribution by resolving gene expression...
Plant conservation in the age of genome editing: opportunities and challenges
Plant conservation in the age of genome editing: opportunities and challenges
Numerous plant taxa are threatened by habitat destruction or overexploitation. To overcome these threats, new methods are ...
pan-Draft: automated reconstruction of species-representative metabolic models from multiple genomes
pan-Draft: automated reconstruction of species-representative metabolic models from multiple genomes
The accurate reconstruction of genome-scale metabolic models (GEMs) for unculturable species poses challenges due to the i...
Scalable identification of lineage-specific gene regulatory networks from metacells with NetID
Scalable identification of lineage-specific gene regulatory networks from metacells with NetID
The identification of gene regulatory networks (GRNs) is crucial for understanding cellular differentiation. Single-cell R...
A comprehensive study of genetic regulation and disease associations of plasma circulatory microRNAs using population-level data
A comprehensive study of genetic regulation and disease associations of plasma circulatory microRNAs using population-level data
MicroRNAs (miRNAs) are small non-coding RNAs that post-transcriptionally regulate gene expression. Perturbations in plasma...
SDePER: a hybrid machine learning and regression method for cell-type deconvolution of spatial barcoding-based transcriptomic data
SDePER: a hybrid machine learning and regression method for cell-type deconvolution of spatial barcoding-based transcriptomic data
Spatial barcoding-based transcriptomic (ST) data require deconvolution for cellular-level downstream analysis. Here we pre...
scCTS: identifying the cell type-specific marker genes from population-level single-cell RNA-seq
scCTS: identifying the cell type-specific marker genes from population-level single-cell RNA-seq
Single-cell RNA-sequencing (scRNA-seq) provides gene expression profiles of individual cells from complex samples, facilit...
zMAP toolset: model-based analysis of large-scale proteomic data via a variance stabilizing z-transformation
zMAP toolset: model-based analysis of large-scale proteomic data via a variance stabilizing z-transformation
Isobaric labeling-based mass spectrometry (ILMS) has been widely used to quantify, on a proteome-wide scale, the relative ...
HBI: a hierarchical Bayesian interaction model to estimate cell-type-specific methylation quantitative trait loci incorporating priors from cell-sorted bisulfite sequencing data
HBI: a hierarchical Bayesian interaction model to estimate cell-type-specific methylation quantitative trait loci incorporating priors from cell-sorted bisulfite sequencing data
Methylation quantitative trait loci (meQTLs) quantify the effects of genetic variants on DNA methylation levels. However, ...
Multi-omics reveals lactylation-driven regulatory mechanisms promoting tumor progression in oral squamous cell carcinoma
Multi-omics reveals lactylation-driven regulatory mechanisms promoting tumor progression in oral squamous cell carcinoma
Lactylation, a post-translational modification, is increasingly recognized for its role in cancer progression. This study ...
Transipedia.org: k-mer-based exploration of large RNA sequencing datasets and application to cancer data
Transipedia.org: k-mer-based exploration of large RNA sequencing datasets and application to cancer data
Indexing techniques relying on k-mers have proven effective in searching for RNA sequences across thousands of RNA-seq lib...
Spatiotemporal modeling reveals high-resolution invasion states in glioblastoma
Spatiotemporal modeling reveals high-resolution invasion states in glioblastoma
Diffuse invasion of glioblastoma cells through normal brain tissue is a key contributor to tumor aggressiveness, resistanc...
Graphasing: phasing diploid genome assembly graphs with single-cell strand sequencing
Graphasing: phasing diploid genome assembly graphs with single-cell strand sequencing
Haplotype information is crucial for biomedical and population genetics research. However, current strategies to produce d...
Drought-responsive dynamics of H3K9ac-marked 3D chromatin interactions are integrated by OsbZIP23-associated super-enhancer-like promoter regions in rice
Drought-responsive dynamics of H3K9ac-marked 3D chromatin interactions are integrated by OsbZIP23-associated super-enhancer-like promoter regions in rice
In response to drought stress (DS), plants undergo complex processes that entail significant transcriptome reprogramming. ...
阅读更多
format_indent_increase