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N6-methyladenosine writer METTL16-mediated alternative splicing and translation control are essential for murine spermatogenesis
N6-methyladenosine writer METTL16-mediated alternative splicing and translation control are essential for murine spermatogenesis
The mitosis-to-meiosis switch during spermatogenesis requires dynamic changes in gene expression. However, the regulation ...
A benchmark of computational methods for correcting biases of established and unknown origin in CRISPR-Cas9 screening data
A benchmark of computational methods for correcting biases of established and unknown origin in CRISPR-Cas9 screening data
CRISPR-Cas9 dropout screens are formidable tools for investigating biology with unprecedented precision and scale. However...
Single-cell decoding of drug induced transcriptomic reprogramming in triple negative breast cancers
Single-cell decoding of drug induced transcriptomic reprogramming in triple negative breast cancers
The encoding of cell intrinsic drug resistance states in breast cancer reflects the contributions of genomic and non-genom...
Leveraging neighborhood representations of single-cell data to achieve sensitive DE testing with miloDE
Leveraging neighborhood representations of single-cell data to achieve sensitive DE testing with miloDE
Single-cell RNA-sequencing enables testing for differential expression (DE) between conditions at a cell type level. While...
Non-coding variants impact cis-regulatory coordination in a cell type-specific manner
Non-coding variants impact cis-regulatory coordination in a cell type-specific manner
Interactions among cis-regulatory elements (CREs) play a crucial role in gene regulation. Various approaches have been dev...
TFscope: systematic analysis of the sequence features involved in the binding preferences of transcription factors
TFscope: systematic analysis of the sequence features involved in the binding preferences of transcription factors
Characterizing the binding preferences of transcription factors (TFs) in different cell types and conditions is key to und...
sciMET-cap: high-throughput single-cell methylation analysis with a reduced sequencing burden
sciMET-cap: high-throughput single-cell methylation analysis with a reduced sequencing burden
DNA methylation is a key component of the mammalian epigenome, playing a regulatory role in development, disease, and othe...
Comprehensive and deep evaluation of structural variation detection pipelines with third-generation sequencing data
Comprehensive and deep evaluation of structural variation detection pipelines with third-generation sequencing data
Structural variation (SV) detection methods using third-generation sequencing data are widely employed, yet accurately det...
Systemic interindividual DNA methylation variants in cattle share major hallmarks with those in humans
Systemic interindividual DNA methylation variants in cattle share major hallmarks with those in humans
We recently identified ~ 10,000 correlated regions of systemic interindividual epigenetic variation (CoRSIVs) ...
scHolography: a computational method for single-cell spatial neighborhood reconstruction and analysis
scHolography: a computational method for single-cell spatial neighborhood reconstruction and analysis
Spatial transcriptomics has transformed our ability to study tissue complexity. However, it remains challenging to accurat...
A feedback loop driven by H3K9 lactylation and HDAC2 in endothelial cells regulates VEGF-induced angiogenesis
A feedback loop driven by H3K9 lactylation and HDAC2 in endothelial cells regulates VEGF-induced angiogenesis
Vascular endothelial growth factor (VEGF) is one of the most powerful proangiogenic factors and plays an important role in...
Immune evasion impacts the landscape of driver genes during cancer evolution
Immune evasion impacts the landscape of driver genes during cancer evolution
Carcinogenesis is driven by interactions between genetic mutations and the local tumor microenvironment. Recent research h...
Resolving intra-repeat variation in medically relevant VNTRs from short-read sequencing data using the cardiovascular risk gene LPA as a model
Resolving intra-repeat variation in medically relevant VNTRs from short-read sequencing data using the cardiovascular risk gene LPA as a model
Variable number tandem repeats (VNTRs) are highly polymorphic DNA regions harboring many potentially disease-causing varia...
An integrated single-cell RNA-seq map of human neuroblastoma tumors and preclinical models uncovers divergent mesenchymal-like gene expression programs
An integrated single-cell RNA-seq map of human neuroblastoma tumors and preclinical models uncovers divergent mesenchymal-like gene expression programs
Neuroblastoma is a common pediatric cancer, where preclinical studies suggest that a mesenchymal-like gene expression prog...
Evaluation of somatic copy number variation detection by NGS technologies and bioinformatics tools on a hyper-diploid cancer genome
Evaluation of somatic copy number variation detection by NGS technologies and bioinformatics tools on a hyper-diploid cancer genome
Copy number variation (CNV) is a key genetic characteristic for cancer diagnostics and can be used as a biomarker for the ...
Alternative splicing coupled to nonsense-mediated decay coordinates downregulation of non-neuronal genes in developing mouse neurons
Alternative splicing coupled to nonsense-mediated decay coordinates downregulation of non-neuronal genes in developing mouse neurons
The functional coupling between alternative pre-mRNA splicing (AS) and the mRNA quality control mechanism called nonsense-...
Beyond benchmarking and towards predictive models of dataset-specific single-cell RNA-seq pipeline performance
Beyond benchmarking and towards predictive models of dataset-specific single-cell RNA-seq pipeline performance
The advent of single-cell RNA-sequencing (scRNA-seq) has driven significant computational methods development for all step...
DNA methylation variations underlie lettuce domestication and divergence
DNA methylation variations underlie lettuce domestication and divergence
Lettuce (Lactuca sativa L.) is an economically important vegetable crop worldwide. Lettuce is believed to be domesticated ...
CpG island turnover events predict evolutionary changes in enhancer activity
CpG island turnover events predict evolutionary changes in enhancer activity
Genetic changes that modify the function of transcriptional enhancers have been linked to the evolution of biological dive...
Leaf: an ultrafast filter for population-scale long-read SV detection
Leaf: an ultrafast filter for population-scale long-read SV detection
Advances in sequencing technology have facilitated population-scale long-read structural variant (SV) detection. Arguably,...
Legal aspects of privacy-enhancing technologies in genome-wide association studies and their impact on performance and feasibility
Legal aspects of privacy-enhancing technologies in genome-wide association studies and their impact on performance and feasibility
Genomic data holds huge potential for medical progress but requires strict safety measures due to its sensitive nature to ...
LABS: linear amplification-based bisulfite sequencing for ultrasensitive cancer detection from cell-free DNA
LABS: linear amplification-based bisulfite sequencing for ultrasensitive cancer detection from cell-free DNA
Methylation-based liquid biopsies show promises in detecting cancer using circulating cell-free DNA; however, current limi...
Gene count normalization in single-cell imaging-based spatially resolved transcriptomics
Gene count normalization in single-cell imaging-based spatially resolved transcriptomics
Recent advances in imaging-based spatially resolved transcriptomics (im-SRT) technologies now enable high-throughput profi...
CelFiE-ISH: a probabilistic model for multi-cell type deconvolution from single-molecule DNA methylation haplotypes
CelFiE-ISH: a probabilistic model for multi-cell type deconvolution from single-molecule DNA methylation haplotypes
Deconvolution methods infer quantitative cell type estimates from bulk measurement of mixed samples including blood and ti...
Author Correction: The senescent methylome and its relationship with cancer, ageing and germline genetic variation in humans
Author Correction: The senescent methylome and its relationship with cancer, ageing and germline genetic variation in humans
Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, whi...
FoldPAthreader: predicting protein folding pathway using a novel folding force field model derived from known protein universe
FoldPAthreader: predicting protein folding pathway using a novel folding force field model derived from known protein universe
Protein folding has become a tractable problem with the significant advances in deep learning-driven protein structure pre...
TMO-Net: an explainable pretrained multi-omics model for multi-task learning in oncology
TMO-Net: an explainable pretrained multi-omics model for multi-task learning in oncology
Cancer is a complex disease composing systemic alterations in multiple scales. In this study, we develop the Tumor Multi-O...
iIMPACT: integrating image and molecular profiles for spatial transcriptomics analysis
iIMPACT: integrating image and molecular profiles for spatial transcriptomics analysis
Current clustering analysis of spatial transcriptomics data primarily relies on molecular information and fails to fully e...
Structural variant landscapes reveal convergent signatures of evolution in sheep and goats
Structural variant landscapes reveal convergent signatures of evolution in sheep and goats
Sheep and goats have undergone domestication and improvement to produce similar phenotypes, which have been greatly impact...
DNA methylation patterns of transcription factor binding regions characterize their functional and evolutionary contexts
DNA methylation patterns of transcription factor binding regions characterize their functional and evolutionary contexts
DNA methylation is an important epigenetic modification which has numerous roles in modulating genome function. Its levels...
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