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Bioinformatics Advances|December 22, 2025
Perspectives in computational mass spectrometry: recent developments and key challengesTimo Sachsenberg, Lindsay K Pino, Marie Brunet, et al.Bioinformatics Advances|December 15, 2025
An overview of computational methods for gene prediction in eukaryotes: strengths, limitations, and future directionsAbigail Djossou, Wend Yam D D Ouedraogo, Aida OuangraouaBioinformatics Advances|December 4, 2025
SNPraefentia: a toolkit to prioritize microbial genome variants linked to health and diseaseNadeem Khan, Muhammad Muneeb Nasir, Ammar Mushtaq, et al.Bioinformatics Advances|December 1, 2025
NifFinder: improved Nif protein prediction using SWeeP vectors and neural networksBruno Thiago de Lima Nichio, Roxana Beatriz Ribeiro Chaves, Jeroniza Nunes Marchaukoski, et al.Bioinformatics Advances|November 26, 2025
SiaScoreNet: a siamese neural network-based model integrating prediction scores for HLA-peptide interaction predictionMahsa Saadat, Fatemeh Zare-Mirakabad, Milad BesharatifardBioinformatics Advances|November 26, 2025
Retention order prediction of peptides containing non-proteinogenic amino acidsShohei Nakamukai, Eisuke Hayakawa, Tetsuya Mori, et al.Bioinformatics Advances|January 9, 2026
mhn: a Python package for analyzing cancer progression with Mutual Hazard NetworksStefan Vocht, Yanren Linda Hu, Andreas Lösch, et al.Bioinformatics Advances|January 16, 2026
ggplotAgent: a self-debugging multi-modal agent for robust and reproducible scientific visualizationZelin Wang, Yuanyuan Yin, Jien Wang, et al.Bioinformatics Advances|January 23, 2026
The nutrition toolbox permits in silico generation, analysis, and optimization of personalized diets through metabolic modellingBram Nap, Bronson Weston, Annette Brandt, et al.Bioinformatics Advances|November 24, 2025
SUMO: an R package for simulating multi-omics data for methods development and testingBernard Isekah Osang'ir, Surya Gupta, Ziv Shkedy, et al.Pageof 115