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MoCHI: neural networks to fit interpretable models and quantify energies, energetic couplings, epistasis, and allostery from deep mutational scanning data
MoCHI: neural networks to fit interpretable models and quantify energies, energetic couplings, epistasis, and allostery from deep mutational scanning data
We present MoCHI, a tool to fit interpretable models using deep mutational scanning data. MoCHI infers free energy changes...
Chromatin loops gather targets of upstream regulators together for efficient gene transcription regulation during vernalization in wheat
Chromatin loops gather targets of upstream regulators together for efficient gene transcription regulation during vernalization in wheat
Plants respond to environmental stimuli by altering gene transcription that is highly related with chromatin status, inclu...
EpiCHAOS: a metric to quantify epigenomic heterogeneity in single-cell data
EpiCHAOS: a metric to quantify epigenomic heterogeneity in single-cell data
Epigenetic heterogeneity is a fundamental property of biological systems and is recognized as a potential driver of tumor ...
Increased spatial coupling of integrin and collagen IV in the immunoresistant clear-cell renal-cell carcinoma tumor microenvironment
Increased spatial coupling of integrin and collagen IV in the immunoresistant clear-cell renal-cell carcinoma tumor microenvironment
Immunotherapy has improved survival for patients with advanced clear cell renal cell carcinoma (ccRCC), but resistance to ...
Systemic evaluation of various CRISPR/Cas13 orthologs for knockdown of targeted transcripts in plants
Systemic evaluation of various CRISPR/Cas13 orthologs for knockdown of targeted transcripts in plants
CRISPR/Cas13 system, recognized for its compact size and specificity in targeting RNA, is currently employed for RNA degra...
Benchmarking bioinformatic virus identification tools using real-world metagenomic data across biomes
Benchmarking bioinformatic virus identification tools using real-world metagenomic data across biomes
As most viruses remain uncultivated, metagenomics is currently the main method for virus discovery. Detecting viruses in m...
Powerful and accurate detection of temporal gene expression patterns from multi-sample multi-stage single-cell transcriptomics data with TDEseq
Powerful and accurate detection of temporal gene expression patterns from multi-sample multi-stage single-cell transcriptomics data with TDEseq
We present a non-parametric statistical method called TDEseq that takes full advantage of smoothing splines basis function...
Machine-learning analysis reveals an important role for negative selection in shaping cancer aneuploidy landscapes
Machine-learning analysis reveals an important role for negative selection in shaping cancer aneuploidy landscapes
Aneuploidy, an abnormal number of chromosomes within a cell, is a hallmark of cancer. Patterns of aneuploidy differ across...
Characterizing glucokinase variant mechanisms using a multiplexed abundance assay
Characterizing glucokinase variant mechanisms using a multiplexed abundance assay
Amino acid substitutions can perturb protein activity in multiple ways. Understanding their mechanistic basis may pinpoint...
Library size confounds biology in spatial transcriptomics data
Library size confounds biology in spatial transcriptomics data
Spatial molecular data has transformed the study of disease microenvironments, though, larger datasets pose an analytics c...
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...
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