Volume 40, Issue 11, November 2024

Original Paper

Genome analysis

Generative haplotype prediction outperforms statistical methods for small variant detection in next-generation sequencing data

Brendan O’Fallon and others

Bioinformatics, Volume 40, Issue 11, November 2024, btae565, https://doi.org/10.1093/bioinformatics/btae565

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GCI: a continuity inspector for complete genome assembly

Quanyu Chen and others

Bioinformatics, Volume 40, Issue 11, November 2024, btae633, https://doi.org/10.1093/bioinformatics/btae633

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GEEES: inferring cell-specific gene–enhancer interactions from multi-modal single-cell data

Shuyang Chen and Sündüz Keleş

Bioinformatics, Volume 40, Issue 11, November 2024, btae638, https://doi.org/10.1093/bioinformatics/btae638

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BS-clock, advancing epigenetic age prediction with high-resolution DNA methylation bisulfite sequencing data

Congcong Hu and others

Bioinformatics, Volume 40, Issue 11, November 2024, btae656, https://doi.org/10.1093/bioinformatics/btae656

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ADAPT: Analysis of Microbiome Differential Abundance by Pooling Tobit Models

Mukai Wang and others

Bioinformatics, Volume 40, Issue 11, November 2024, btae661, https://doi.org/10.1093/bioinformatics/btae661

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Detecting transposable elements in long-read genomes using sTELLeR

Kristine Bilgrav Saether and Jesper Eisfeldt

Bioinformatics, Volume 40, Issue 11, November 2024, btae686, https://doi.org/10.1093/bioinformatics/btae686

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Sequence analysis

Addressing the antibody germline bias and its effect on language models for improved antibody design

Tobias H Olsen and others

Bioinformatics, Volume 40, Issue 11, November 2024, btae618, https://doi.org/10.1093/bioinformatics/btae618

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DPNN-ac4C: a dual-path neural network with self-attention mechanism for identification of N4-acetylcytidine (ac4C) in mRNA

Jiahao Yuan and others

Bioinformatics, Volume 40, Issue 11, November 2024, btae625, https://doi.org/10.1093/bioinformatics/btae625

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Sitetack: a deep learning model that improves PTM prediction by using known PTMs

Clair S Gutierrez and others

Bioinformatics, Volume 40, Issue 11, November 2024, btae602, https://doi.org/10.1093/bioinformatics/btae602

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InterLabelGO+: unraveling label correlations in protein function prediction

Quancheng Liu and others

Bioinformatics, Volume 40, Issue 11, November 2024, btae655, https://doi.org/10.1093/bioinformatics/btae655

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BIMSA: accelerating long sequence alignment using processing-in-memory

Alejandro Alonso-Marín and others

Bioinformatics, Volume 40, Issue 11, November 2024, btae631, https://doi.org/10.1093/bioinformatics/btae631

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p-IgGen: a paired antibody generative language model

Oliver M Turnbull and others

Bioinformatics, Volume 40, Issue 11, November 2024, btae659, https://doi.org/10.1093/bioinformatics/btae659

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CompariPSSM: a PSSM–PSSM comparison tool for motif-binding determinant analysis

Ifigenia Tsitsa and others

Bioinformatics, Volume 40, Issue 11, November 2024, btae644, https://doi.org/10.1093/bioinformatics/btae644

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Expert-guided protein language models enable accurate and blazingly fast fitness prediction

Céline Marquet and others

Bioinformatics, Volume 40, Issue 11, November 2024, btae621, https://doi.org/10.1093/bioinformatics/btae621

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Structural bioinformatics

Weighted families of contact maps to characterize conformational ensembles of (highly-)flexible proteins

Javier González-Delgado and others

Bioinformatics, Volume 40, Issue 11, November 2024, btae627, https://doi.org/10.1093/bioinformatics/btae627

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EuDockScore: Euclidean graph neural networks for scoring protein–protein interfaces

Matthew McFee and others

Bioinformatics, Volume 40, Issue 11, November 2024, btae636, https://doi.org/10.1093/bioinformatics/btae636

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OpenDock: a pytorch-based open-source framework for protein–ligand docking and modelling

Qiuyue Hu and others

Bioinformatics, Volume 40, Issue 11, November 2024, btae628, https://doi.org/10.1093/bioinformatics/btae628

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Protein structure alignment by Reseek improves sensitivity to remote homologs

Robert C Edgar

Bioinformatics, Volume 40, Issue 11, November 2024, btae687, https://doi.org/10.1093/bioinformatics/btae687

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Gene expression

PONYTA: prioritization of phenotype-related genes from mouse KO events using PU learning on a biological network

Jun Hyeong Kim and others

Bioinformatics, Volume 40, Issue 11, November 2024, btae634, https://doi.org/10.1093/bioinformatics/btae634

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A deep learning method to integrate extracelluar miRNA with mRNA for cancer studies

Tasbiraha Athaya and others

Bioinformatics, Volume 40, Issue 11, November 2024, btae653, https://doi.org/10.1093/bioinformatics/btae653

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A signal-diffusion-based unsupervised contrastive representation learning for spatial transcriptomics analysis

Nan Chen and others

Bioinformatics, Volume 40, Issue 11, November 2024, btae663, https://doi.org/10.1093/bioinformatics/btae663

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Systems biology

PhenoMultiOmics: an enzymatic reaction inferred multi-omics network visualization web server

Yuying Shi and others

Bioinformatics, Volume 40, Issue 11, November 2024, btae623, https://doi.org/10.1093/bioinformatics/btae623

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q2-metnet: QIIME2 package to analyse 16S rRNA data via high-quality metabolic reconstructions of the human gut microbiota

Francesco Balzerani and others

Bioinformatics, Volume 40, Issue 11, November 2024, btae455, https://doi.org/10.1093/bioinformatics/btae455

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Differential expression and co-expression reveal cell types relevant to genetic disorder phenotypes

Sergio Alías-Segura and others

Bioinformatics, Volume 40, Issue 11, November 2024, btae646, https://doi.org/10.1093/bioinformatics/btae646

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Graphlet-based hyperbolic embeddings capture evolutionary dynamics in genetic networks

Sam F L Windels and others

Bioinformatics, Volume 40, Issue 11, November 2024, btae650, https://doi.org/10.1093/bioinformatics/btae650

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Target controllability: a feed-forward greedy algorithm in complex networks, meeting Kalman’s rank condition

Seyedeh Fatemeh Khezri and others

Bioinformatics, Volume 40, Issue 11, November 2024, btae630, https://doi.org/10.1093/bioinformatics/btae630

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Optimizing multi-omics data imputation with NMF and GAN synergy

Md Istiaq Ansari and others

Bioinformatics, Volume 40, Issue 11, November 2024, btae674, https://doi.org/10.1093/bioinformatics/btae674

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RUCova: Removal of Unwanted Covariance in mass cytometry data

Rosario Astaburuaga-García and others

Bioinformatics, Volume 40, Issue 11, November 2024, btae669, https://doi.org/10.1093/bioinformatics/btae669

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Genetics and population analysis

Detection and quantification of introgression using Bayesian inference based on conjugate priors

Bastian Pfeifer and others

Bioinformatics, Volume 40, Issue 11, November 2024, btae642, https://doi.org/10.1093/bioinformatics/btae642

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Quantifying defective and wild-type viruses from high-throughput RNA sequencing

Juan C Muñoz-Sánchez and others

Bioinformatics, Volume 40, Issue 11, November 2024, btae651, https://doi.org/10.1093/bioinformatics/btae651

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Data and text mining

Lifestyle factors in the biomedical literature: an ontology and comprehensive resources for named entity recognition

Esmaeil Nourani and others

Bioinformatics, Volume 40, Issue 11, November 2024, btae613, https://doi.org/10.1093/bioinformatics/btae613

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k-nonical space: sketching with reverse complements

Guillaume Marçais and others

Bioinformatics, Volume 40, Issue 11, November 2024, btae629, https://doi.org/10.1093/bioinformatics/btae629

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Improving ncRNA family prediction using multi-modal contrastive learning of sequence and structure

Ruiting Xu and others

Bioinformatics, Volume 40, Issue 11, November 2024, btae640, https://doi.org/10.1093/bioinformatics/btae640

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Causal relationships between diseases mined from the literature improve the use of polygenic risk scores

Sumyyah Toonsi and others

Bioinformatics, Volume 40, Issue 11, November 2024, btae639, https://doi.org/10.1093/bioinformatics/btae639

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Bioimage informatics

Deep coupled registration and segmentation of multimodal whole-brain images

Tingting Han and others

Bioinformatics, Volume 40, Issue 11, November 2024, btae606, https://doi.org/10.1093/bioinformatics/btae606

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Deep learning-based enhancement of fluorescence labeling for accurate cell lineage tracing during embryogenesis

Zelin Li and others

Bioinformatics, Volume 40, Issue 11, November 2024, btae626, https://doi.org/10.1093/bioinformatics/btae626

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TRAITER: transformer-guided diagnosis and prognosis of heart failure using cell nuclear morphology and DNA damage marker

Hiromu Hayashi and others

Bioinformatics, Volume 40, Issue 11, November 2024, btae610, https://doi.org/10.1093/bioinformatics/btae610

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Prediction of human O-linked glycosylation sites using stacked generalization and embeddings from pre-trained protein language model

Subash Chandra Pakhrin and others

Bioinformatics, Volume 40, Issue 11, November 2024, btae643, https://doi.org/10.1093/bioinformatics/btae643

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Applications Note

Genome analysis

Biologically-informed killer cell immunoglobulin-like receptor gene annotation tool

Michael K B Ford and others

Bioinformatics, Volume 40, Issue 11, November 2024, btae622, https://doi.org/10.1093/bioinformatics/btae622

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findGSEP: estimating genome size of polyploid species using k-mer frequencies

Laiyi Fu and others

Bioinformatics, Volume 40, Issue 11, November 2024, btae647, https://doi.org/10.1093/bioinformatics/btae647

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Cluster-efficient pangenome graph construction with nf-core/pangenome

Simon Heumos and others

Bioinformatics, Volume 40, Issue 11, November 2024, btae609, https://doi.org/10.1093/bioinformatics/btae609

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Xenomake: a pipeline for processing and sorting xenograft reads from spatial transcriptomic experiments

Benjamin S Strope and others

Bioinformatics, Volume 40, Issue 11, November 2024, btae608, https://doi.org/10.1093/bioinformatics/btae608

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BindCompare: a novel integrated protein–nucleic acid binding analysis platform

Pranav Mahableshwarkar and others

Bioinformatics, Volume 40, Issue 11, November 2024, btae668, https://doi.org/10.1093/bioinformatics/btae668

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Sequence analysis

quaqc: efficient and quick ATAC-seq quality control and filtering

Benjamin J M Tremblay and Julia I Qüesta

Bioinformatics, Volume 40, Issue 11, November 2024, btae649, https://doi.org/10.1093/bioinformatics/btae649

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Structural bioinformatics

Memprot.GPCR-ModSim: modelling and simulation of membrane proteins in a nutshell

Remco L van den Broek and others

Bioinformatics, Volume 40, Issue 11, November 2024, btae662, https://doi.org/10.1093/bioinformatics/btae662

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R3DMCS: a web server for visualizing structural variation in RNA motifs across experimental 3D structures from the same organism or across species

Sri Devan Appasamy and Craig L Zirbel

Bioinformatics, Volume 40, Issue 11, November 2024, btae682, https://doi.org/10.1093/bioinformatics/btae682

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Gene expression

Collapsible tree: interactive web app to present collapsible hierarchies

Yuan Gao and others

Bioinformatics, Volume 40, Issue 11, November 2024, btae645, https://doi.org/10.1093/bioinformatics/btae645

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ADTGP: correcting single-cell antibody sequencing data using Gaussian process regression

Alex C H Liu and Steven M Chan

Bioinformatics, Volume 40, Issue 11, November 2024, btae660, https://doi.org/10.1093/bioinformatics/btae660

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APAtizer: a tool for alternative polyadenylation analysis of RNA-Seq data

Bruno Sousa and others

Bioinformatics, Volume 40, Issue 11, November 2024, btae689, https://doi.org/10.1093/bioinformatics/btae689

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Genetics and population analysis

AncestryGrapher toolkit: Python command-line pipelines to visualize global- and local- ancestry inferences from the RFMIX version 2 software

Alessandro Lisi and Michael C Campbell

Bioinformatics, Volume 40, Issue 11, November 2024, btae616, https://doi.org/10.1093/bioinformatics/btae616

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MR Corge: sensitivity analysis of Mendelian randomization based on the core gene hypothesis for polygenic exposures

Wenmin Zhang and others

Bioinformatics, Volume 40, Issue 11, November 2024, btae666, https://doi.org/10.1093/bioinformatics/btae666

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Pf-HaploAtlas: an interactive web app for spatiotemporal analysis of Plasmodium falciparum genes

Chiyun Lee and others

Bioinformatics, Volume 40, Issue 11, November 2024, btae673, https://doi.org/10.1093/bioinformatics/btae673

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Systems biology

ENKIE: a package for predicting enzyme kinetic parameter values and their uncertainties

Mattia G Gollub and others

Bioinformatics, Volume 40, Issue 11, November 2024, btae652, https://doi.org/10.1093/bioinformatics/btae652

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Data and text mining

iSeq: an integrated tool to fetch public sequencing data

Haoyu Chao and others

Bioinformatics, Volume 40, Issue 11, November 2024, btae641, https://doi.org/10.1093/bioinformatics/btae641

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PubMed Computed Authors in 2024: an open resource of disambiguated author names in biomedical literature

Shubo Tian and others

Bioinformatics, Volume 40, Issue 11, November 2024, btae672, https://doi.org/10.1093/bioinformatics/btae672

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M²ara: unraveling metabolomic drug responses in whole-cell MALDI mass spectrometry bioassays

Thomas Enzlein and others

Bioinformatics, Volume 40, Issue 11, November 2024, btae694, https://doi.org/10.1093/bioinformatics/btae694

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PRONA: an R-package for Patient Reported Outcomes Network Analysis

Brandon H Bergsneider and Orieta Celiku

Bioinformatics, Volume 40, Issue 11, November 2024, btae671, https://doi.org/10.1093/bioinformatics/btae671

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Databases and ontologies

scToppR: a coding-friendly R interface to ToppGene

Bryan Granger and Stefano Berto

Bioinformatics, Volume 40, Issue 11, November 2024, btae582, https://doi.org/10.1093/bioinformatics/btae582

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ViralPrimer: a web server to monitor viral nucleic acid amplification tests’ primer efficiency during pandemics, with emphasis on SARS-CoV-2 and Mpox

Norbert Deutsch and others

Bioinformatics, Volume 40, Issue 11, November 2024, btae657, https://doi.org/10.1093/bioinformatics/btae657

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FungiFun3: systemic gene set enrichment analysis for fungal species

Albert Garcia Lopez and others

Bioinformatics, Volume 40, Issue 11, November 2024, btae620, https://doi.org/10.1093/bioinformatics/btae620

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Bioimage informatics

MSIreg: an R package for unsupervised coregistration of mass spectrometry and H&E images

Sai Srikanth Lakkimsetty and others

Bioinformatics, Volume 40, Issue 11, November 2024, btae624, https://doi.org/10.1093/bioinformatics/btae624

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Letter to the Editor

Genome analysis

Improving bioinformatics software quality through teamwork

Katalin Ferenc and others

Bioinformatics, Volume 40, Issue 11, November 2024, btae632, https://doi.org/10.1093/bioinformatics/btae632

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