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Journal

Bioinformatics

Publishes scientific papers and review articles on new developments in bioinformatics and computational biology. Shorter papers report biologically interesting discoveries using computational methods and explore their applications.

Journal

Bioinformatics Advances

Bioinformatics AdvancesÂ is a fully open access journal published by OUP and the International Society for Computational Biology. The journal publishes original research articles, reviews, application notes, opinion, perspective and Society features.

Journal Article

ACCEPTED MANUSCRIPT

High-dimensional Biomarker Identification for Interpretable Disease Prediction via Machine Learning Models

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Yifan Dai and others

in Bioinformatics

Bioinformatics, btaf266, https://doi.org/10.1093/bioinformatics/btaf266

Published: 26 April 2025

Supplementary data

Journal Article

ACCEPTED MANUSCRIPT

RabbitSketch: A High-Performance Sketching Library for Genome Analysis

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Tong Zhang and others

in Bioinformatics

Bioinformatics, btaf249, https://doi.org/10.1093/bioinformatics/btaf249

Published: 26 April 2025

Supplementary data

Journal Article

ACCEPTED MANUSCRIPT

Identifying Core Genes in Keloid and Investigating Immune Infiltration and Pan-Cancer Associations Using eQTL and Machine Learning

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Xiaoyuan He and Yang Song

in Bioinformatics Advances

Bioinformatics Advances, vbaf076, https://doi.org/10.1093/bioadv/vbaf076

Published: 26 April 2025

Journal Article

ACCEPTED MANUSCRIPT

Grape-Pi: Graph-Based Neural Networks for Enhanced Protein Identification in Proteomics Pipelines

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Chunhui Gu and others

in Bioinformatics Advances

Bioinformatics Advances, vbaf095, https://doi.org/10.1093/bioadv/vbaf095

Published: 26 April 2025

Supplementary data

Journal Article

ACCEPTED MANUSCRIPT

Gencube: Centralized retrieval and integration of multi-omics resources from leading databases

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Keun Hong Son and Je-Yoel Cho

in Bioinformatics

Bioinformatics, btaf128, https://doi.org/10.1093/bioinformatics/btaf128

Published: 25 April 2025

Journal Article

ACCEPTED MANUSCRIPT

Popcorn: prediction of short coding and noncoding genomic sequences in prokaryotes

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Alison Kyrouz and others

in Bioinformatics

Bioinformatics, btaf250, https://doi.org/10.1093/bioinformatics/btaf250

Published: 25 April 2025

Supplementary data

Journal Article

ACCEPTED MANUSCRIPT

TissueViewer: A Web-Based Multiplexed Image Viewer

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David Gerardus Pieter van IJzendoorn and others

in Bioinformatics

Bioinformatics, btaf246, https://doi.org/10.1093/bioinformatics/btaf246

Published: 25 April 2025

Journal Article

ACCEPTED MANUSCRIPT

JAX-RNAfold: Scalable Differentiable Folding

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Ryan K Krueger and Max Ward

in Bioinformatics

Bioinformatics, btaf203, https://doi.org/10.1093/bioinformatics/btaf203

Published: 25 April 2025

Supplementary data

Journal Article

ACCEPTED MANUSCRIPT

m2ST: Dual Multi-Scale Graph Clustering for Spatially Resolved Transcriptomics

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Wei Zhang and others

in Bioinformatics

Bioinformatics, btaf221, https://doi.org/10.1093/bioinformatics/btaf221

Published: 24 April 2025

Supplementary data

Journal Article

ACCEPTED MANUSCRIPT

VSOT: Volume-Surface Optimization for Accurate Ultrastructure Analysis of Dendritic Spines

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Boyu Lyu and others

in Bioinformatics

Bioinformatics, btaf220, https://doi.org/10.1093/bioinformatics/btaf220

Published: 24 April 2025

Supplementary data

Journal Article

ACCEPTED MANUSCRIPT

PPIFold: a tool for analysis of Protein-Protein Interaction from AlphaPullDown

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Quentin Rouger and others

in Bioinformatics Advances

Bioinformatics Advances, vbaf090, https://doi.org/10.1093/bioadv/vbaf090

Published: 24 April 2025

Supplementary data

Journal Article

ACCEPTED MANUSCRIPT

AlphaMissenseR: an integrated framework for investigating missense mutations in human protein-coding genes

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Tram N Nguyen and others

in Bioinformatics Advances

Bioinformatics Advances, vbaf093, https://doi.org/10.1093/bioadv/vbaf093

Published: 23 April 2025

Journal Article

ACCEPTED MANUSCRIPT

De novo clustering of large long-read transcriptome datasets with isONclust3

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Alexander J Petri and Kristoffer Sahlin

in Bioinformatics

Bioinformatics, btaf207, https://doi.org/10.1093/bioinformatics/btaf207

Published: 23 April 2025

Supplementary data

Journal Article

The Signed Two-Space Proximity Model for Learning Representations in Protein-Protein Interaction Networks

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Nikolaos Nakis and others

in Bioinformatics

Bioinformatics, btaf204, https://doi.org/10.1093/bioinformatics/btaf204

Published: 23 April 2025

Supplementary data

Journal Article

ACCEPTED MANUSCRIPT

Integration of multi-source gene interaction networks and omics data with graph attention networks to identify novel disease genes

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Kaiyuan Yang and others

in Bioinformatics

Bioinformatics, btaf181, https://doi.org/10.1093/bioinformatics/btaf181

Published: 23 April 2025

Supplementary data

Journal Article

ACCEPTED MANUSCRIPT

Functional protein biomarkers based on distributions of expression levels in single-cell imaging data

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Misung Yi and others

in Bioinformatics

Bioinformatics, btaf182, https://doi.org/10.1093/bioinformatics/btaf182

Published: 21 April 2025

Supplementary data

Image

Flowchart illustrating genome-wide causal gene searches using HORNET. Examp...

in Bioinformatics Advances > HORNET: tools to find genes with causal evidence and their regulatory networks using eQTLs

Published: 18 April 2025

Figure 1. Flowchart illustrating genome-wide causal gene searches using HORNET. Example options given to flags that the command line version of HORNET uses are at the bottom of each panel. In the “Input data” section, ±1 Mb is used because it is standard in many publicly available data such as GTEx (2015) and

Image

This figure illustrates the adjustments for CHP and inflation that are intr...

in Bioinformatics Advances > HORNET: tools to find genes with causal evidence and their regulatory networks using eQTLs

Published: 18 April 2025

Figure 3. This figure illustrates the adjustments for CHP and inflation that are introduced when the eQTLs used in MR are in LD and researchers only have access to relatively small reference panels. (A) The goal of eQTL-MVMR is to estimate θ , which may be subject to bias when Λ and η are eac

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Bioinformatics

Bioinformatics Advances

High-dimensional Biomarker Identification for Interpretable Disease Prediction via Machine Learning Models

RabbitSketch: A High-Performance Sketching Library for Genome Analysis

Identifying Core Genes in Keloid and Investigating Immune Infiltration and Pan-Cancer Associations Using eQTL and Machine Learning

Grape-Pi: Graph-Based Neural Networks for Enhanced Protein Identification in Proteomics Pipelines

Gencube: Centralized retrieval and integration of multi-omics resources from leading databases

Popcorn: prediction of short coding and noncoding genomic sequences in prokaryotes

TissueViewer: A Web-Based Multiplexed Image Viewer

JAX-RNAfold: Scalable Differentiable Folding

m2ST: Dual Multi-Scale Graph Clustering for Spatially Resolved Transcriptomics

VSOT: Volume-Surface Optimization for Accurate Ultrastructure Analysis of Dendritic Spines

PPIFold: a tool for analysis of Protein-Protein Interaction from AlphaPullDown

AlphaMissenseR: an integrated framework for investigating missense mutations in human protein-coding genes

De novo clustering of large long-read transcriptome datasets with isONclust3

The Signed Two-Space Proximity Model for Learning Representations in Protein-Protein Interaction Networks

Integration of multi-source gene interaction networks and omics data with graph attention networks to identify novel disease genes

Functional protein biomarkers based on distributions of expression levels in single-cell imaging data

Flowchart illustrating genome-wide causal gene searches using HORNET. Examp...

This figure illustrates the adjustments for CHP and inflation that are intr...

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