Bioinformatics Advances
@bioinfoadv.bsky.social
A fully open access, peer-reviewed journal published jointly by Oxford University Press and the International Society for Computational Biology.
💻 Now published in Bioinformatics Advances: “Prompt-based bioinformatic pipeline generation for a multi-step metaviral workflow.”
Explore the full study: https://doi.org/10.1093/bioadv/vbaf308
Authors include: @rocknmicrobe.bsky.social
Explore the full study: https://doi.org/10.1093/bioadv/vbaf308
Authors include: @rocknmicrobe.bsky.social
December 23, 2025 at 11:01 AM
💻 Now published in Bioinformatics Advances: “Prompt-based bioinformatic pipeline generation for a multi-step metaviral workflow.”
Explore the full study: https://doi.org/10.1093/bioadv/vbaf308
Authors include: @rocknmicrobe.bsky.social
Explore the full study: https://doi.org/10.1093/bioadv/vbaf308
Authors include: @rocknmicrobe.bsky.social
Season’s greetings from Bioinformatics Advances!
This has been a year of growth, with more than 600 submissions. We’re grateful to our editors, authors, and reviewers for their contributions and look forward to advancing computational biology together in 2026.
This has been a year of growth, with more than 600 submissions. We’re grateful to our editors, authors, and reviewers for their contributions and look forward to advancing computational biology together in 2026.
December 22, 2025 at 11:30 AM
Season’s greetings from Bioinformatics Advances!
This has been a year of growth, with more than 600 submissions. We’re grateful to our editors, authors, and reviewers for their contributions and look forward to advancing computational biology together in 2026.
This has been a year of growth, with more than 600 submissions. We’re grateful to our editors, authors, and reviewers for their contributions and look forward to advancing computational biology together in 2026.
🧬 Just out in Bioinformatics Advances: “Omics BioAnalytics: An RShiny application for multimodal biomarker panel discovery and assessment”
Full article available at https://doi.org/10.1093/bioadv/vbaf307
Full article available at https://doi.org/10.1093/bioadv/vbaf307
December 22, 2025 at 10:01 AM
🧬 Just out in Bioinformatics Advances: “Omics BioAnalytics: An RShiny application for multimodal biomarker panel discovery and assessment”
Full article available at https://doi.org/10.1093/bioadv/vbaf307
Full article available at https://doi.org/10.1093/bioadv/vbaf307
📊 Now published in Bioinformatics Advances: “Integrative analysis and imputation of multiple data streams via deep Gaussian processes.”
Explore the full study at https://doi.org/10.1093/bioadv/vbaf305
Authors include: @aliakbars.id, @drsamray.bsky.social
Explore the full study at https://doi.org/10.1093/bioadv/vbaf305
Authors include: @aliakbars.id, @drsamray.bsky.social
December 19, 2025 at 11:01 AM
📊 Now published in Bioinformatics Advances: “Integrative analysis and imputation of multiple data streams via deep Gaussian processes.”
Explore the full study at https://doi.org/10.1093/bioadv/vbaf305
Authors include: @aliakbars.id, @drsamray.bsky.social
Explore the full study at https://doi.org/10.1093/bioadv/vbaf305
Authors include: @aliakbars.id, @drsamray.bsky.social
🧪 Now published in Bioinformatics Advances: “Colony: A framework for reproducible and easy-to-use data analysis pipelines for biomedical research with Singularity containers.”
Explore the full study at https://doi.org/10.1093/bioadv/vbaf304
Explore the full study at https://doi.org/10.1093/bioadv/vbaf304
December 19, 2025 at 10:02 AM
🧪 Now published in Bioinformatics Advances: “Colony: A framework for reproducible and easy-to-use data analysis pipelines for biomedical research with Singularity containers.”
Explore the full study at https://doi.org/10.1093/bioadv/vbaf304
Explore the full study at https://doi.org/10.1093/bioadv/vbaf304
🦠 Now published in Bioinformatics Advances: “AI-powered rapid detection of multidrug-resistant Klebsiella pneumoniae with informative peaks of MALDI-TOF MS”
Read the full paper here: https://doi.org/10.1093/bioadv/vbaf303
Read the full paper here: https://doi.org/10.1093/bioadv/vbaf303
December 18, 2025 at 11:01 AM
🦠 Now published in Bioinformatics Advances: “AI-powered rapid detection of multidrug-resistant Klebsiella pneumoniae with informative peaks of MALDI-TOF MS”
Read the full paper here: https://doi.org/10.1093/bioadv/vbaf303
Read the full paper here: https://doi.org/10.1093/bioadv/vbaf303
🧬 Just out in Bioinformatics Advances: “tskit arg visualizer: Interactive plotting of ancestral recombination graphs.”
Read the full paper here: https://doi.org/10.1093/bioadv/vbaf302
Authors include: @kitchensjn.bsky.social, @yanwong.bsky.social
Read the full paper here: https://doi.org/10.1093/bioadv/vbaf302
Authors include: @kitchensjn.bsky.social, @yanwong.bsky.social
December 18, 2025 at 10:02 AM
🧬 Just out in Bioinformatics Advances: “tskit arg visualizer: Interactive plotting of ancestral recombination graphs.”
Read the full paper here: https://doi.org/10.1093/bioadv/vbaf302
Authors include: @kitchensjn.bsky.social, @yanwong.bsky.social
Read the full paper here: https://doi.org/10.1093/bioadv/vbaf302
Authors include: @kitchensjn.bsky.social, @yanwong.bsky.social
🧬 Explore the latest from Bioinformatics Advances: "geomeTriD: A Bioconductor package for interactive and integrative visualization of 3D structural model with multi-omics data"
Full article available: https://doi.org/10.1093/bioadv/vbaf299
Full article available: https://doi.org/10.1093/bioadv/vbaf299
December 17, 2025 at 11:01 AM
🧬 Explore the latest from Bioinformatics Advances: "geomeTriD: A Bioconductor package for interactive and integrative visualization of 3D structural model with multi-omics data"
Full article available: https://doi.org/10.1093/bioadv/vbaf299
Full article available: https://doi.org/10.1093/bioadv/vbaf299
🌳 Now published in Bioinformatics Advances: "Performance assessment of phylogenetic inference tools using PhyloSmew"
Explore the full study: https://doi.org/10.1093/bioadv/vbaf300
Explore the full study: https://doi.org/10.1093/bioadv/vbaf300
December 17, 2025 at 10:02 AM
🌳 Now published in Bioinformatics Advances: "Performance assessment of phylogenetic inference tools using PhyloSmew"
Explore the full study: https://doi.org/10.1093/bioadv/vbaf300
Explore the full study: https://doi.org/10.1093/bioadv/vbaf300
🔒 Just out in Bioinformatics Advances: "Integrating differential privacy into federated multi-task learning algorithms in dsMTL"
Full article available: https://doi.org/10.1093/bioadv/vbaf298
Full article available: https://doi.org/10.1093/bioadv/vbaf298
December 16, 2025 at 11:03 AM
🔒 Just out in Bioinformatics Advances: "Integrating differential privacy into federated multi-task learning algorithms in dsMTL"
Full article available: https://doi.org/10.1093/bioadv/vbaf298
Full article available: https://doi.org/10.1093/bioadv/vbaf298
🧬 Explore the latest from Bioinformatics Advances: "PseudoChecker2 and PseudoViz: Automation and visualization of gene loss in the Genome Era”
Read the full paper here: https://doi.org/10.1093/bioadv/vbaf202
Read the full paper here: https://doi.org/10.1093/bioadv/vbaf202
December 16, 2025 at 10:02 AM
🧬 Explore the latest from Bioinformatics Advances: "PseudoChecker2 and PseudoViz: Automation and visualization of gene loss in the Genome Era”
Read the full paper here: https://doi.org/10.1093/bioadv/vbaf202
Read the full paper here: https://doi.org/10.1093/bioadv/vbaf202
🔬 Just out in Bioinformatics Advances: "SNPraefentia: A toolkit to prioritize microbial genome variants linked to health and disease”
Read the full paper here: https://doi.org/10.1093/bioadv/vbaf297
Read the full paper here: https://doi.org/10.1093/bioadv/vbaf297
December 15, 2025 at 11:02 AM
🔬 Just out in Bioinformatics Advances: "SNPraefentia: A toolkit to prioritize microbial genome variants linked to health and disease”
Read the full paper here: https://doi.org/10.1093/bioadv/vbaf297
Read the full paper here: https://doi.org/10.1093/bioadv/vbaf297
🧬 Now published in Bioinformatics Advances: "Snappy: Fast identification of DNA methylation motifs based on Oxford Nanopore reads"
Full article available: https://doi.org/10.1093/bioadv/vbaf296
Full article available: https://doi.org/10.1093/bioadv/vbaf296
December 15, 2025 at 10:02 AM
🧬 Now published in Bioinformatics Advances: "Snappy: Fast identification of DNA methylation motifs based on Oxford Nanopore reads"
Full article available: https://doi.org/10.1093/bioadv/vbaf296
Full article available: https://doi.org/10.1093/bioadv/vbaf296
🔬 Now published in Bioinformatics Advances: “Adding highly variable genes to spatially variable genes can improve cell type clustering performance in spatial transcriptomics data”
Read the full paper here: https://doi.org/10.1093/bioadv/vbaf285
Authors include: @lgarmire.bsky.social
Read the full paper here: https://doi.org/10.1093/bioadv/vbaf285
Authors include: @lgarmire.bsky.social
December 12, 2025 at 11:02 AM
🔬 Now published in Bioinformatics Advances: “Adding highly variable genes to spatially variable genes can improve cell type clustering performance in spatial transcriptomics data”
Read the full paper here: https://doi.org/10.1093/bioadv/vbaf285
Authors include: @lgarmire.bsky.social
Read the full paper here: https://doi.org/10.1093/bioadv/vbaf285
Authors include: @lgarmire.bsky.social
🧬 Now published in Bioinformatics Advances: “PSQAN: A pipeline to prioritise novel and biologically relevant transcripts from long-read RNA sequencing”
Explore the full study at https://doi.org/10.1093/bioadv/vbaf293
Explore the full study at https://doi.org/10.1093/bioadv/vbaf293
December 12, 2025 at 10:02 AM
🧬 Now published in Bioinformatics Advances: “PSQAN: A pipeline to prioritise novel and biologically relevant transcripts from long-read RNA sequencing”
Explore the full study at https://doi.org/10.1093/bioadv/vbaf293
Explore the full study at https://doi.org/10.1093/bioadv/vbaf293
🧪 Now published in Bioinformatics Advances: “SiaScoreNet: A Siamese neural network-based model integrating prediction scores for HLA-peptide interaction prediction.”
Read the full paper at https://doi.org/10.1093/bioadv/vbaf248
Read the full paper at https://doi.org/10.1093/bioadv/vbaf248
December 11, 2025 at 11:02 AM
🧪 Now published in Bioinformatics Advances: “SiaScoreNet: A Siamese neural network-based model integrating prediction scores for HLA-peptide interaction prediction.”
Read the full paper at https://doi.org/10.1093/bioadv/vbaf248
Read the full paper at https://doi.org/10.1093/bioadv/vbaf248
🧬 Just out in Bioinformatics Advances: “SurprisalAnalysis: An open-source software for information-theoretic analysis of gene expression.”
Explore the full study at https://doi.org/10.1093/bioadv/vbaf291
Explore the full study at https://doi.org/10.1093/bioadv/vbaf291
December 11, 2025 at 10:03 AM
🧬 Just out in Bioinformatics Advances: “SurprisalAnalysis: An open-source software for information-theoretic analysis of gene expression.”
Explore the full study at https://doi.org/10.1093/bioadv/vbaf291
Explore the full study at https://doi.org/10.1093/bioadv/vbaf291
🌱 Explore the latest from Bioinformatics Advances: “MxlPy: Python package for mechanistic learning and hybrid modelling in life science.”
Full article available at https://doi.org/10.1093/bioadv/vbaf294
Full article available at https://doi.org/10.1093/bioadv/vbaf294
December 10, 2025 at 11:02 AM
🌱 Explore the latest from Bioinformatics Advances: “MxlPy: Python package for mechanistic learning and hybrid modelling in life science.”
Full article available at https://doi.org/10.1093/bioadv/vbaf294
Full article available at https://doi.org/10.1093/bioadv/vbaf294
🧪 Now published in Bioinformatics Advances: “GDC cohort copilot: An AI copilot for curating cohorts from the Genomic Data Commons.”
Read the full paper here: https://doi.org/10.1093/bioadv/vbaf295
Read the full paper here: https://doi.org/10.1093/bioadv/vbaf295
December 10, 2025 at 10:01 AM
🧪 Now published in Bioinformatics Advances: “GDC cohort copilot: An AI copilot for curating cohorts from the Genomic Data Commons.”
Read the full paper here: https://doi.org/10.1093/bioadv/vbaf295
Read the full paper here: https://doi.org/10.1093/bioadv/vbaf295
🧬Explore the latest from Bioinformatics Advances: “Ish: SIMD and GPU accelerated local and semi-global alignment as a CLI filtering tool.”
Read the full paper here: https://doi.org/10.1093/bioadv/vbaf292
Author: @ducktapeprogrammer.bsky.social
Read the full paper here: https://doi.org/10.1093/bioadv/vbaf292
Author: @ducktapeprogrammer.bsky.social
December 9, 2025 at 10:01 AM
🧬Explore the latest from Bioinformatics Advances: “Ish: SIMD and GPU accelerated local and semi-global alignment as a CLI filtering tool.”
Read the full paper here: https://doi.org/10.1093/bioadv/vbaf292
Author: @ducktapeprogrammer.bsky.social
Read the full paper here: https://doi.org/10.1093/bioadv/vbaf292
Author: @ducktapeprogrammer.bsky.social
🗂️ Explore the latest from Bioinformatics Advances: “SeqManager: A web-based tool for efficient sequencing data storage management and duplicate detection.”
Explore the full study: https://doi.org/10.1093/bioadv/vbaf282
Authors include: @serialchiper.bsky.social
Explore the full study: https://doi.org/10.1093/bioadv/vbaf282
Authors include: @serialchiper.bsky.social
December 8, 2025 at 10:01 AM
🗂️ Explore the latest from Bioinformatics Advances: “SeqManager: A web-based tool for efficient sequencing data storage management and duplicate detection.”
Explore the full study: https://doi.org/10.1093/bioadv/vbaf282
Authors include: @serialchiper.bsky.social
Explore the full study: https://doi.org/10.1093/bioadv/vbaf282
Authors include: @serialchiper.bsky.social
🧮 Just out in Bioinformatics Advances: “FroM Superstring to Indexing: A space-efficient index for unconstrained k-mer sets using the Masked Burrows-Wheeler Transform (MBWT)”
Full article available: https://doi.org/10.1093/bioadv/vbaf290
Authors include: @pavelvesely.bsky.social, @brinda.eu
Full article available: https://doi.org/10.1093/bioadv/vbaf290
Authors include: @pavelvesely.bsky.social, @brinda.eu
December 5, 2025 at 10:01 AM
🧮 Just out in Bioinformatics Advances: “FroM Superstring to Indexing: A space-efficient index for unconstrained k-mer sets using the Masked Burrows-Wheeler Transform (MBWT)”
Full article available: https://doi.org/10.1093/bioadv/vbaf290
Authors include: @pavelvesely.bsky.social, @brinda.eu
Full article available: https://doi.org/10.1093/bioadv/vbaf290
Authors include: @pavelvesely.bsky.social, @brinda.eu
💊 Explore the latest from Bioinformatics Advances: “Unveiling novel drug-target couples: An empowered automated pipeline for enhanced virtual screening using AutoDock Vina.”
Read the full paper here: https://doi.org/10.1093/bioadv/vbaf267
Read the full paper here: https://doi.org/10.1093/bioadv/vbaf267
December 4, 2025 at 10:03 AM
💊 Explore the latest from Bioinformatics Advances: “Unveiling novel drug-target couples: An empowered automated pipeline for enhanced virtual screening using AutoDock Vina.”
Read the full paper here: https://doi.org/10.1093/bioadv/vbaf267
Read the full paper here: https://doi.org/10.1093/bioadv/vbaf267
🧬 Just out in Bioinformatics Advances: “Exploring SARS-CoV-2 spike protein mutations through genetic algorithm-driven structural modeling.”
Full article available: https://doi.org/10.1093/bioadv/vbaf288
Full article available: https://doi.org/10.1093/bioadv/vbaf288
December 3, 2025 at 10:02 AM
🧬 Just out in Bioinformatics Advances: “Exploring SARS-CoV-2 spike protein mutations through genetic algorithm-driven structural modeling.”
Full article available: https://doi.org/10.1093/bioadv/vbaf288
Full article available: https://doi.org/10.1093/bioadv/vbaf288
🔬Now published in Bioinformatics Advances: “KSMoFinder: Knowledge graph embedding of proteins and motifs for predicting kinases of human phosphosites.”
Read the full paper here: https://doi.org/10.1093/bioadv/vbaf289
Read the full paper here: https://doi.org/10.1093/bioadv/vbaf289
December 2, 2025 at 10:02 AM
🔬Now published in Bioinformatics Advances: “KSMoFinder: Knowledge graph embedding of proteins and motifs for predicting kinases of human phosphosites.”
Read the full paper here: https://doi.org/10.1093/bioadv/vbaf289
Read the full paper here: https://doi.org/10.1093/bioadv/vbaf289