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Subject: Computational Methods
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Journal Article

Digital pathology assessment of kidney glomerular filtration barrier ultrastructure in an animal model of podocytopathy

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Aksel Laudon and others
Biology Methods and Protocols, Volume 10, Issue 1, 2025, bpaf024, https://doi.org/10.1093/biomethods/bpaf024
Published: 28 March 2025
Journal Article

The effectiveness of large language models with RAG for auto-annotating trait and phenotype descriptions

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David Kainer
Biology Methods and Protocols, Volume 10, Issue 1, 2025, bpaf016, https://doi.org/10.1093/biomethods/bpaf016
Published: 26 February 2025
Journal Article

Retrieval Augmented Medical Diagnosis System

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Ethan Thomas Johnson and others
Biology Methods and Protocols, Volume 10, Issue 1, 2025, bpaf017, https://doi.org/10.1093/biomethods/bpaf017
Published: 25 February 2025
Journal Article

Deep learning and transfer learning for brain tumor detection and classification

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Faris Rustom and others
Biology Methods and Protocols, Volume 9, Issue 1, 2024, bpae080, https://doi.org/10.1093/biomethods/bpae080
Published: 19 November 2024
Journal Article

Cluster analysis identifies long COVID subtypes in Belgian patients

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Pamela Mfouth Kemajou and others
Biology Methods and Protocols, Volume 9, Issue 1, 2024, bpae076, https://doi.org/10.1093/biomethods/bpae076
Published: 09 October 2024
Journal Article

Unpacking unstructured data: A pilot study on extracting insights from neuropathological reports of Parkinson’s Disease patients using large language models

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Oleg Stroganov and others
Biology Methods and Protocols, Volume 9, Issue 1, 2024, bpae072, https://doi.org/10.1093/biomethods/bpae072
Published: 04 October 2024
Journal Article

Digital approaches in post-COVID healthcare: a systematic review of technological innovations in disease management

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Pamela Mfouth Kemajou and others
Biology Methods and Protocols, Volume 9, Issue 1, 2024, bpae070, https://doi.org/10.1093/biomethods/bpae070
Published: 01 October 2024
Journal Article

Graph neural networks are promising for phenotypic virtual screening on cancer cell lines

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Sachin Vishwakarma and others
Biology Methods and Protocols, Volume 9, Issue 1, 2024, bpae065, https://doi.org/10.1093/biomethods/bpae065
Published: 03 September 2024
Journal Article

Deep learning image analysis for filamentous fungi taxonomic classification: Dealing with small datasets with class imbalance and hierarchical grouping

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Stefan Stiller and others
Biology Methods and Protocols, Volume 9, Issue 1, 2024, bpae063, https://doi.org/10.1093/biomethods/bpae063
Published: 27 August 2024
Journal Article

DLKcat cannot predict meaningful kcat values for mutants and unfamiliar enzymes

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Alexander Kroll and Martin J Lercher
Biology Methods and Protocols, Volume 9, Issue 1, 2024, bpae061, https://doi.org/10.1093/biomethods/bpae061
Published: 24 August 2024
Journal Article

Advancing age grading techniques for Glossina morsitans morsitans, vectors of African trypanosomiasis, through mid-infrared spectroscopy and machine learning

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Mauro Pazmiño-Betancourth and others
Biology Methods and Protocols, Volume 9, Issue 1, 2024, bpae058, https://doi.org/10.1093/biomethods/bpae058
Published: 17 August 2024
Journal Article

Early detection and diagnosis of cancer with interpretable machine learning to uncover cancer-specific DNA methylation patterns

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Izzy Newsham and others
Biology Methods and Protocols, Volume 9, Issue 1, 2024, bpae028, https://doi.org/10.1093/biomethods/bpae028
Published: 20 June 2024
Journal Article

Mapping adipocyte interactome networks by HaloTag-enrichment-mass spectrometry

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Junshi Yazaki and others
Biology Methods and Protocols, Volume 9, Issue 1, 2024, bpae039, https://doi.org/10.1093/biomethods/bpae039
Published: 29 May 2024
Journal Article

IntelliGenes: Interactive and user-friendly multimodal AI/ML application for biomarker discovery and predictive medicine

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Rishabh Narayanan and others
Biology Methods and Protocols, Volume 9, Issue 1, 2024, bpae040, https://doi.org/10.1093/biomethods/bpae040
Published: 29 May 2024
Journal Article

Macro-based collagen quantification and segmentation in picrosirius red-stained heart sections using light microscopy

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Julian Kammerer and others
Biology Methods and Protocols, Volume 9, Issue 1, 2024, bpae027, https://doi.org/10.1093/biomethods/bpae027
Published: 27 April 2024
Journal Article

An extended multiplicative error model of allometry: Incorporating systematic components, non-normal distributions, and piecewise heteroscedasticity

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Héctor Echavarría-Heras and others
Biology Methods and Protocols, Volume 9, Issue 1, 2024, bpae024, https://doi.org/10.1093/biomethods/bpae024
Published: 18 April 2024
Journal Article

A semi-automated spectral approach to analyzing cyclical growth patterns using fish scales

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Julien A Chaput and Gérald Chaput
Biology Methods and Protocols, Volume 9, Issue 1, 2024, bpae018, https://doi.org/10.1093/biomethods/bpae018
Published: 18 March 2024
Journal Article

Pairing a bioinformatics-focused course-based undergraduate research experience with specifications grading in an introductory biology classroom

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Melinda A Yang and Kylie Korsnack
Biology Methods and Protocols, Volume 9, Issue 1, 2024, bpae013, https://doi.org/10.1093/biomethods/bpae013
Published: 28 February 2024
Journal Article

Protocol for transcriptome assembly by the TransBorrow algorithm

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Dengyi Zhao and others
Biology Methods and Protocols, Volume 8, Issue 1, 2023, bpad028, https://doi.org/10.1093/biomethods/bpad028
Published: 01 November 2023
Journal Article

Robustness of quantifying mediating effects of genetically regulated expression on complex traits with mediated expression score regression

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Chen Lin and others
Biology Methods and Protocols, Volume 8, Issue 1, 2023, bpad024, https://doi.org/10.1093/biomethods/bpad024
Published: 17 October 2023