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Volume 41, Issue 1, January 2025
Original Paper
Genome analysis
SCARAP: scalable cross-species comparative genomics of prokaryotes
Bioinformatics, Volume 41, Issue 1, January 2025, btae735, https://doi.org/10.1093/bioinformatics/btae735
CrossIsoFun: predicting isoform functions using the integration of multi-omics data
Bioinformatics, Volume 41, Issue 1, January 2025, btae742, https://doi.org/10.1093/bioinformatics/btae742
End-to-end simulation of nanopore sequencing signals with feed-forward transformers
Bioinformatics, Volume 41, Issue 1, January 2025, btae744, https://doi.org/10.1093/bioinformatics/btae744
Integrating single-cell multimodal epigenomic data using 1D convolutional neural networks
Bioinformatics, Volume 41, Issue 1, January 2025, btae705, https://doi.org/10.1093/bioinformatics/btae705
Fast and exact gap-affine partial order alignment with POASTA
Bioinformatics, Volume 41, Issue 1, January 2025, btae757, https://doi.org/10.1093/bioinformatics/btae757
Sequence analysis
DiffPaSS—high-performance differentiable pairing of protein sequences using soft scores
Bioinformatics, Volume 41, Issue 1, January 2025, btae738, https://doi.org/10.1093/bioinformatics/btae738
A near-tight lower bound on the density of forward sampling schemes
Bioinformatics, Volume 41, Issue 1, January 2025, btae736, https://doi.org/10.1093/bioinformatics/btae736
m5c-iEnsem: 5-methylcytosine sites identification through ensemble models
Bioinformatics, Volume 41, Issue 1, January 2025, btae722, https://doi.org/10.1093/bioinformatics/btae722
Nanopore decoding with speed and versatility for data storage
Bioinformatics, Volume 41, Issue 1, January 2025, btaf006, https://doi.org/10.1093/bioinformatics/btaf006
PHIStruct: improving phage–host interaction prediction at low sequence similarity settings using structure-aware protein embeddings
Bioinformatics, Volume 41, Issue 1, January 2025, btaf016, https://doi.org/10.1093/bioinformatics/btaf016
EnrichRBP: an automated and interpretable computational platform for predicting and analysing RNA-binding protein events
Bioinformatics, Volume 41, Issue 1, January 2025, btaf018, https://doi.org/10.1093/bioinformatics/btaf018
DDGemb: predicting protein stability change upon single- and multi-point variations with embeddings and deep learning
Bioinformatics, Volume 41, Issue 1, January 2025, btaf019, https://doi.org/10.1093/bioinformatics/btaf019
TPepRet: a deep learning model for characterizing T-cell receptors–antigen binding patterns
Bioinformatics, Volume 41, Issue 1, January 2025, btaf022, https://doi.org/10.1093/bioinformatics/btaf022
Phylogenetics
BetaAlign: a deep learning approach for multiple sequence alignment
Bioinformatics, Volume 41, Issue 1, January 2025, btaf009, https://doi.org/10.1093/bioinformatics/btaf009
Structural Bioinformatics
TargetSA: adaptive simulated annealing for target-specific drug design
Bioinformatics, Volume 41, Issue 1, January 2025, btae730, https://doi.org/10.1093/bioinformatics/btae730
TPepPro: a deep learning model for predicting peptide–protein interactions
Bioinformatics, Volume 41, Issue 1, January 2025, btae708, https://doi.org/10.1093/bioinformatics/btae708
Ligand identification in CryoEM and X-ray maps using deep learning
Bioinformatics, Volume 41, Issue 1, January 2025, btae749, https://doi.org/10.1093/bioinformatics/btae749
CParty: hierarchically constrained partition function of RNA pseudoknots
Bioinformatics, Volume 41, Issue 1, January 2025, btae748, https://doi.org/10.1093/bioinformatics/btae748
DPAM-AI: a domain parser for AlphaFold models powered by artificial intelligence
Bioinformatics, Volume 41, Issue 1, January 2025, btae740, https://doi.org/10.1093/bioinformatics/btae740
CryptoBench: cryptic protein–ligand binding sites dataset and benchmark
Bioinformatics, Volume 41, Issue 1, January 2025, btae745, https://doi.org/10.1093/bioinformatics/btae745
RNA-TorsionBERT: leveraging language models for RNA 3D torsion angles prediction
Bioinformatics, Volume 41, Issue 1, January 2025, btaf004, https://doi.org/10.1093/bioinformatics/btaf004
Transcription factor prediction using protein 3D secondary structures
Bioinformatics, Volume 41, Issue 1, January 2025, btae762, https://doi.org/10.1093/bioinformatics/btae762
Gene expression
VarNMF: non-negative probabilistic factorization with source variation
Bioinformatics, Volume 41, Issue 1, January 2025, btae758, https://doi.org/10.1093/bioinformatics/btae758
Bayesian gene set benchmark dose estimation for “omic” responses
Bioinformatics, Volume 41, Issue 1, January 2025, btaf008, https://doi.org/10.1093/bioinformatics/btaf008
Genetics and population analysis
The scalable variant call representation: enabling genetic analysis beyond one million genomes
Bioinformatics, Volume 41, Issue 1, January 2025, btae746, https://doi.org/10.1093/bioinformatics/btae746
Funmap: integrating high-dimensional functional annotations to improve fine-mapping
Bioinformatics, Volume 41, Issue 1, January 2025, btaf017, https://doi.org/10.1093/bioinformatics/btaf017
Systems biology
IMPACT: interpretable microbial phenotype analysis via microbial characteristic traits
Bioinformatics, Volume 41, Issue 1, January 2025, btae702, https://doi.org/10.1093/bioinformatics/btae702
Accelerated enumeration of extreme rays through a positive-definite elementarity test
Bioinformatics, Volume 41, Issue 1, January 2025, btae723, https://doi.org/10.1093/bioinformatics/btae723
QuICSeedR: an R package for analyzing fluorophore-assisted seed amplification assay data
Bioinformatics, Volume 41, Issue 1, January 2025, btae752, https://doi.org/10.1093/bioinformatics/btae752
PCA-based spatial domain identification with state-of-the-art performance
Bioinformatics, Volume 41, Issue 1, January 2025, btaf005, https://doi.org/10.1093/bioinformatics/btaf005
PredCMB: predicting changes in microbial metabolites based on the gene–metabolite network analysis of shotgun metagenome data
Bioinformatics, Volume 41, Issue 1, January 2025, btaf020, https://doi.org/10.1093/bioinformatics/btaf020
Data and text mining
MMOSurv: meta-learning for few-shot survival analysis with multi-omics data
Bioinformatics, Volume 41, Issue 1, January 2025, btae684, https://doi.org/10.1093/bioinformatics/btae684
FuncFetch: an LLM-assisted workflow enables mining thousands of enzyme–substrate interactions from published manuscripts
Bioinformatics, Volume 41, Issue 1, January 2025, btae756, https://doi.org/10.1093/bioinformatics/btae756
Heterogeneous entity representation for medicinal synergy prediction
Bioinformatics, Volume 41, Issue 1, January 2025, btae750, https://doi.org/10.1093/bioinformatics/btae750
Improving generalizability of drug–target binding prediction by pre-trained multi-view molecular representations
Bioinformatics, Volume 41, Issue 1, January 2025, btaf002, https://doi.org/10.1093/bioinformatics/btaf002
Bioimage informatics
Quantitative analysis of the dexamethasone side effect on human-derived young and aged skeletal muscle by myotube and nuclei segmentation using deep learning
Bioinformatics, Volume 41, Issue 1, January 2025, btae658, https://doi.org/10.1093/bioinformatics/btae658
Modeling multi-stage disease progression and identifying genetic risk factors via a novel collaborative learning method
Bioinformatics, Volume 41, Issue 1, January 2025, btae728, https://doi.org/10.1093/bioinformatics/btae728
Autoencoder-based phenotyping of ophthalmic images highlights genetic loci influencing retinal morphology and provides informative biomarkers
Bioinformatics, Volume 41, Issue 1, January 2025, btae732, https://doi.org/10.1093/bioinformatics/btae732
A semi-supervised fracture-attention model for segmenting tubular objects with improved topological connectivity
Bioinformatics, Volume 41, Issue 1, January 2025, btaf013, https://doi.org/10.1093/bioinformatics/btaf013
Applications Note
Genome analysis
Gretl—variation GRaph Evaluation TooLkit
Bioinformatics, Volume 41, Issue 1, January 2025, btae755, https://doi.org/10.1093/bioinformatics/btae755
Rnalib: a Python library for custom transcriptomics analyses
Bioinformatics, Volume 41, Issue 1, January 2025, btae751, https://doi.org/10.1093/bioinformatics/btae751
Crypt4GH-JS: securely storing sensitive data online with client-side encryption
Bioinformatics, Volume 41, Issue 1, January 2025, btae763, https://doi.org/10.1093/bioinformatics/btae763
Sequence analysis
The Naïve Bayes classifier++ for metagenomic taxonomic classification—query evaluation
Bioinformatics, Volume 41, Issue 1, January 2025, btae743, https://doi.org/10.1093/bioinformatics/btae743
Semblans: automated assembly and processing of RNA-seq data
Bioinformatics, Volume 41, Issue 1, January 2025, btaf003, https://doi.org/10.1093/bioinformatics/btaf003
MeSS and assembly_finder: a toolkit for in silico metagenomic sample generation
Bioinformatics, Volume 41, Issue 1, January 2025, btae760, https://doi.org/10.1093/bioinformatics/btae760
Proteoform identification and quantification based on alignment graphs
Bioinformatics, Volume 41, Issue 1, January 2025, btaf007, https://doi.org/10.1093/bioinformatics/btaf007
Structural bioinformatics
MapTurns: mapping the structure, H-bonding, and contexts of beta turns in proteins
Bioinformatics, Volume 41, Issue 1, January 2025, btae741, https://doi.org/10.1093/bioinformatics/btae741
MOLGENIS Armadillo: a lightweight server for federated analysis using DataSHIELD
Bioinformatics, Volume 41, Issue 1, January 2025, btae726, https://doi.org/10.1093/bioinformatics/btae726
Gene expression
NLSDeconv: an efficient cell-type deconvolution method for spatial transcriptomics data
Bioinformatics, Volume 41, Issue 1, January 2025, btae747, https://doi.org/10.1093/bioinformatics/btae747
SuperSpot: coarse graining spatial transcriptomics data into metaspots
Bioinformatics, Volume 41, Issue 1, January 2025, btae734, https://doi.org/10.1093/bioinformatics/btae734
Scope+: an open source generalizable architecture for single-cell RNA-seq atlases at sample and cell levels
Bioinformatics, Volume 41, Issue 1, January 2025, btae727, https://doi.org/10.1093/bioinformatics/btae727
Genetics and population analysis
A hypercubic Mk model framework for capturing reversibility in disease, cancer, and evolutionary accumulation modelling
Bioinformatics, Volume 41, Issue 1, January 2025, btae737, https://doi.org/10.1093/bioinformatics/btae737
PheWAS analysis on large-scale biobank data with PheTK
Bioinformatics, Volume 41, Issue 1, January 2025, btae719, https://doi.org/10.1093/bioinformatics/btae719
FlexLMM: a Nextflow linear mixed model framework for GWAS
Bioinformatics, Volume 41, Issue 1, January 2025, btaf021, https://doi.org/10.1093/bioinformatics/btaf021
Systems biology
The FunCoup Cytoscape App: multi-species network analysis and visualization
Bioinformatics, Volume 41, Issue 1, January 2025, btae739, https://doi.org/10.1093/bioinformatics/btae739
Data and text mining
SampleExplorer: using language models to discover relevant transcriptome data
Bioinformatics, Volume 41, Issue 1, January 2025, btae759, https://doi.org/10.1093/bioinformatics/btae759
nipalsMCIA: flexible multi-block dimensionality reduction in R via nonlinear iterative partial least squares
Bioinformatics, Volume 41, Issue 1, January 2025, btaf015, https://doi.org/10.1093/bioinformatics/btaf015
Bioimage informatics
Open Chrono-Morph Viewer: visualize big bioimage time series containing heterogeneous volumes
Bioinformatics, Volume 41, Issue 1, January 2025, btae761, https://doi.org/10.1093/bioinformatics/btae761
Correction
Correction to: Damsel: analysis and visualisation of DamID sequencing in R
Bioinformatics, Volume 41, Issue 1, January 2025, btae753, https://doi.org/10.1093/bioinformatics/btae753
Expression of Concern
Expression of Concern: Cleavage-Stage Embryo Segmentation Using SAM-Based Dual Branch Pipeline: Development and Evaluation with the CleavageEmbryo Dataset
Bioinformatics, Volume 41, Issue 1, January 2025, btaf001, https://doi.org/10.1093/bioinformatics/btaf001
