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Volume 10, Issue 1, 2025
Special Collection: Artificial Intelligence in Biology and Bioinformatics
Methods Articles
Quantification of variegated Drosophila ommatidia with high-resolution image analysis and machine learning
Biology Methods and Protocols, Volume 10, Issue 1, 2025, bpaf002, https://doi.org/10.1093/biomethods/bpaf002
ImmuNet: a segmentation-free machine learning pipeline for immune landscape phenotyping in tumors by multiplex imaging
Biology Methods and Protocols, Volume 10, Issue 1, 2025, bpae094, https://doi.org/10.1093/biomethods/bpae094
MRI-based whole-brain elastography and volumetric measurements to predict brain age
Biology Methods and Protocols, Volume 10, Issue 1, 2025, bpae086, https://doi.org/10.1093/biomethods/bpae086
Development of an optimized cell-based selection system for phage display libraries
Biology Methods and Protocols, Volume 10, Issue 1, 2025, bpaf009, https://doi.org/10.1093/biomethods/bpaf009
Retrieval Augmented Medical Diagnosis System
Biology Methods and Protocols, Volume 10, Issue 1, 2025, bpaf017, https://doi.org/10.1093/biomethods/bpaf017
Digital pathology assessment of kidney glomerular filtration barrier ultrastructure in an animal model of podocytopathy
Biology Methods and Protocols, Volume 10, Issue 1, 2025, bpaf024, https://doi.org/10.1093/biomethods/bpaf024
Innovations
The effectiveness of large language models with RAG for auto-annotating trait and phenotype descriptions
Biology Methods and Protocols, Volume 10, Issue 1, 2025, bpaf016, https://doi.org/10.1093/biomethods/bpaf016
Special Collection: COVID-19 Methods & Protocols
Methods Articles
Evaluation of a surrogate virus neutralization assay for detecting neutralizing antibodies against SARS-CoV-2 in an African population
Biology Methods and Protocols, Volume 10, Issue 1, 2025, bpae095, https://doi.org/10.1093/biomethods/bpae095
Association of cognitive deficits with sociodemographic characteristics among adults with post-COVID conditions: Findings from the United States household pulse survey
Biology Methods and Protocols, Volume 10, Issue 1, 2025, bpaf006, https://doi.org/10.1093/biomethods/bpaf006
RUNCOV: a one-pot triplex real-time RT-LAMP as a point-of-care diagnostic tool for detecting SARS-CoV-2
Biology Methods and Protocols, Volume 10, Issue 1, 2025, bpaf010, https://doi.org/10.1093/biomethods/bpaf010
Methods Article
Real time-PCR a diagnostic tool for reporting copy number variation and relative gene-expression changes in pediatric B-cell acute lymphoblastic leukemia—a pilot study
Biology Methods and Protocols, Volume 10, Issue 1, 2025, bpae098, https://doi.org/10.1093/biomethods/bpae098
Novel method for detection of Aβ and Iso-D7-Aβ N-terminus-specific B cells and Iso-D7-Aβ-specific antibodies
Biology Methods and Protocols, Volume 10, Issue 1, 2025, bpaf001, https://doi.org/10.1093/biomethods/bpaf001
Functional and comparative analysis of the FeII/2-oxoglutarate-dependent dioxygenases without using any substrate
Biology Methods and Protocols, Volume 10, Issue 1, 2025, bpae096, https://doi.org/10.1093/biomethods/bpae096
An improved cell nuclear isolation method
Biology Methods and Protocols, Volume 10, Issue 1, 2025, bpaf007, https://doi.org/10.1093/biomethods/bpaf007
Development of a highly sensitive method to detect translational infidelity
Biology Methods and Protocols, Volume 10, Issue 1, 2025, bpaf008, https://doi.org/10.1093/biomethods/bpaf008
PUPMCR: an R package for image-based identification of color based on Rayner’s (1970) terminology and known fungal pigments
Biology Methods and Protocols, Volume 10, Issue 1, 2025, bpaf004, https://doi.org/10.1093/biomethods/bpaf004
A cost-effective and scalable approach for DNA extraction from FFPE tissues
Biology Methods and Protocols, Volume 10, Issue 1, 2025, bpaf003, https://doi.org/10.1093/biomethods/bpaf003
Simplified and economic measurement of glyoxalase I activity using 2,4-dinitrophenylhydrazine: A valuable tool for researchers
Biology Methods and Protocols, Volume 10, Issue 1, 2025, bpaf013, https://doi.org/10.1093/biomethods/bpaf013
Polysaccharide quantification using microbial enzyme cocktails
Biology Methods and Protocols, Volume 10, Issue 1, 2025, bpaf014, https://doi.org/10.1093/biomethods/bpaf014
Combined fluorescent in situ hybridization and F-ara-EdU staining on whole mount Hymenolepis diminuta
Biology Methods and Protocols, Volume 10, Issue 1, 2025, bpaf011, https://doi.org/10.1093/biomethods/bpaf011
Protocol for isolation and expansion of natural killer cells from human peripheral blood scalable for clinical applications
Biology Methods and Protocols, Volume 10, Issue 1, 2025, bpaf015, https://doi.org/10.1093/biomethods/bpaf015
Optimizing drug sensitivity assays in patient-derived tumor organoids: a comparison of IC50 estimation methods and experimental parameters
Biology Methods and Protocols, Volume 10, Issue 1, 2025, bpaf012, https://doi.org/10.1093/biomethods/bpaf012
A protocol for karyotyping and genetic editing of induced pluripotent stem cells with homology-directed repair mediated CRISPR/Cas9
Biology Methods and Protocols, Volume 10, Issue 1, 2025, bpaf018, https://doi.org/10.1093/biomethods/bpaf018
Flow cytometric procedures for deep characterization of nanoparticles
Biology Methods and Protocols, Volume 10, Issue 1, 2025, bpaf019, https://doi.org/10.1093/biomethods/bpaf019
Mass photometry as a fast, facile characterization tool for direct measurement of mRNA length
Biology Methods and Protocols, Volume 10, Issue 1, 2025, bpaf021, https://doi.org/10.1093/biomethods/bpaf021
A generalized protocol for the induction of M2-like macrophages from mouse and rat bone marrow mononuclear cells
Biology Methods and Protocols, Volume 10, Issue 1, 2025, bpaf020, https://doi.org/10.1093/biomethods/bpaf020
Review
Aptamers as innovative tools for malaria diagnosis and treatment: advances and future perspectives
Biology Methods and Protocols, Volume 10, Issue 1, 2025, bpaf025, https://doi.org/10.1093/biomethods/bpaf025
Protocols Article
Directed evolution of peroxidase DNAzymes by a function-based approach
Biology Methods and Protocols, Volume 10, Issue 1, 2025, bpae088, https://doi.org/10.1093/biomethods/bpae088
Optimized immunofluorescence for liver structure analysis: Enhancing 3D resolution and minimizing tissue autofluorescence
Biology Methods and Protocols, Volume 10, Issue 1, 2025, bpaf023, https://doi.org/10.1093/biomethods/bpaf023
Innovations
Robust RNA secondary structure prediction with a mixture of deep learning and physics-based experts
Biology Methods and Protocols, Volume 10, Issue 1, 2025, bpae097, https://doi.org/10.1093/biomethods/bpae097
Correction
Correction to: Real time-PCR a diagnostic tool for reporting copy number variation and relative gene-expression changes in pediatric B-cell acute lymphoblastic leukemia—a pilot study
Biology Methods and Protocols, Volume 10, Issue 1, 2025, bpaf005, https://doi.org/10.1093/biomethods/bpaf005
