Volume 9, Issue 1, 2024
Special Collection: Covid-19 Methods & Protocols
Methods Articles
tANCHOR cell-based ELISA approach as a surrogate for antigen-coated plates to monitor specific IgG directed to the SARS-CoV-2 receptor-binding domain
Biology Methods and Protocols, Volume 9, Issue 1, 2024, bpae001, https://doi.org/10.1093/biomethods/bpae001
A one-step low-cost molecular test for SARS-CoV-2 detection suitable for community testing using minimally processed saliva
Biology Methods and Protocols, Volume 9, Issue 1, 2024, bpae035, https://doi.org/10.1093/biomethods/bpae035
Detection of SARS-CoV-2 B.1.1.529 (Omicron) variant by SYBR Green-based RT-qPCR
Biology Methods and Protocols, Volume 9, Issue 1, 2024, bpae020, https://doi.org/10.1093/biomethods/bpae020
KCL TEST: an open-source inspired asymptomatic SARS-CoV-2 surveillance programme in an academic institution
Biology Methods and Protocols, Volume 9, Issue 1, 2024, bpae046, https://doi.org/10.1093/biomethods/bpae046
Optimization and application of digital droplet PCR for the detection of SARS-CoV-2 in saliva specimen using commercially available kit
Biology Methods and Protocols, Volume 9, Issue 1, 2024, bpae068, https://doi.org/10.1093/biomethods/bpae068
Cluster analysis identifies long COVID subtypes in Belgian patients
Biology Methods and Protocols, Volume 9, Issue 1, 2024, bpae076, https://doi.org/10.1093/biomethods/bpae076
Development of a large-scale rapid LAMP diagnostic testing platform for pandemic preparedness and outbreak response
Biology Methods and Protocols, Volume 9, Issue 1, 2024, bpae090, https://doi.org/10.1093/biomethods/bpae090
Reviews
Baricitinib statistically significantly reduced COVID-19-related mortality: a systematic review and meta-analysis of five phase III randomized, blinded and placebo-controlled clinical trials
Biology Methods and Protocols, Volume 9, Issue 1, 2024, bpae002, https://doi.org/10.1093/biomethods/bpae002
Meaning and prediction of ‘excess mortality’: a comparison of Covid-19 and pre-Covid-19 mortality data in 31 Eurostat countries from 1965 to 2021
Biology Methods and Protocols, Volume 9, Issue 1, 2024, bpae031, https://doi.org/10.1093/biomethods/bpae031
Digital approaches in post-COVID healthcare: a systematic review of technological innovations in disease management
Biology Methods and Protocols, Volume 9, Issue 1, 2024, bpae070, https://doi.org/10.1093/biomethods/bpae070
Special Collection - Teaching and Outreach in Molecular Biology and Evolution Guest Editors: Tugce Bilgin & Debora Monego
Teaching New Methods
Teaching at the intersection of science and society: An activity on healthcare disparities
Biology Methods and Protocols, Volume 9, Issue 1, 2024, bpad041, https://doi.org/10.1093/biomethods/bpad041
Pairing a bioinformatics-focused course-based undergraduate research experience with specifications grading in an introductory biology classroom
Biology Methods and Protocols, Volume 9, Issue 1, 2024, bpae013, https://doi.org/10.1093/biomethods/bpae013
A cognitive and sensory approach based on workshops using the zebrafish model promotes the discovery of life sciences in the classroom
Biology Methods and Protocols, Volume 9, Issue 1, 2024, bpae092, https://doi.org/10.1093/biomethods/bpae092
Opinion Article
Teaching scientific evidence and critical thinking for policy making
Biology Methods and Protocols, Volume 9, Issue 1, 2024, bpae023, https://doi.org/10.1093/biomethods/bpae023
Special Collection: Artificial Intelligence in Biology and Bioinformatics
Methods Articles
IntelliGenes: Interactive and user-friendly multimodal AI/ML application for biomarker discovery and predictive medicine
Biology Methods and Protocols, Volume 9, Issue 1, 2024, bpae040, https://doi.org/10.1093/biomethods/bpae040
Mapping adipocyte interactome networks by HaloTag-enrichment-mass spectrometry
Biology Methods and Protocols, Volume 9, Issue 1, 2024, bpae039, https://doi.org/10.1093/biomethods/bpae039
Early detection and diagnosis of cancer with interpretable machine learning to uncover cancer-specific DNA methylation patterns
Biology Methods and Protocols, Volume 9, Issue 1, 2024, bpae028, https://doi.org/10.1093/biomethods/bpae028
Multimodal pretraining for unsupervised protein representation learning
Biology Methods and Protocols, Volume 9, Issue 1, 2024, bpae043, https://doi.org/10.1093/biomethods/bpae043
Machine learning of cellular metabolic rewiring
Biology Methods and Protocols, Volume 9, Issue 1, 2024, bpae048, https://doi.org/10.1093/biomethods/bpae048
Deep learning pipeline reveals key moments in human embryonic development predictive of live birth after in vitro fertilization
Biology Methods and Protocols, Volume 9, Issue 1, 2024, bpae052, https://doi.org/10.1093/biomethods/bpae052
Automatic detection of fish scale circuli using deep learning
Biology Methods and Protocols, Volume 9, Issue 1, 2024, bpae056, https://doi.org/10.1093/biomethods/bpae056
Advanced image generation for cancer using diffusion models
Biology Methods and Protocols, Volume 9, Issue 1, 2024, bpae062, https://doi.org/10.1093/biomethods/bpae062
Deep learning image analysis for filamentous fungi taxonomic classification: Dealing with small datasets with class imbalance and hierarchical grouping
Biology Methods and Protocols, Volume 9, Issue 1, 2024, bpae063, https://doi.org/10.1093/biomethods/bpae063
Graph neural networks are promising for phenotypic virtual screening on cancer cell lines
Biology Methods and Protocols, Volume 9, Issue 1, 2024, bpae065, https://doi.org/10.1093/biomethods/bpae065
Advancing age grading techniques for Glossina morsitans morsitans, vectors of African trypanosomiasis, through mid-infrared spectroscopy and machine learning
Biology Methods and Protocols, Volume 9, Issue 1, 2024, bpae058, https://doi.org/10.1093/biomethods/bpae058
Harmonizing immune cell sequences for computational analysis with large language models
Biology Methods and Protocols, Volume 9, Issue 1, 2024, bpae055, https://doi.org/10.1093/biomethods/bpae055
Unpacking unstructured data: A pilot study on extracting insights from neuropathological reports of Parkinson’s Disease patients using large language models
Biology Methods and Protocols, Volume 9, Issue 1, 2024, bpae072, https://doi.org/10.1093/biomethods/bpae072
Deep learning and transfer learning for brain tumor detection and classification
Biology Methods and Protocols, Volume 9, Issue 1, 2024, bpae080, https://doi.org/10.1093/biomethods/bpae080
Spontaneous breaking of symmetry in overlapping cell instance segmentation using diffusion models
Biology Methods and Protocols, Volume 9, Issue 1, 2024, bpae084, https://doi.org/10.1093/biomethods/bpae084
iHDSel software: The price equation and the population stability index to detect genomic patterns compatible with selective sweeps. An example with SARS-CoV-2
Biology Methods and Protocols, Volume 9, Issue 1, 2024, bpae089, https://doi.org/10.1093/biomethods/bpae089
Review
The landscape of RNA 3D structure modeling with transformer networks
Biology Methods and Protocols, Volume 9, Issue 1, 2024, bpae047, https://doi.org/10.1093/biomethods/bpae047
Commentary
DLKcat cannot predict meaningful kcat values for mutants and unfamiliar enzymes
Biology Methods and Protocols, Volume 9, Issue 1, 2024, bpae061, https://doi.org/10.1093/biomethods/bpae061
Methods Articles
Serum metallomics reveals insights into the associations of elements with the progression of preleukemic diseases toward acute leukemia
Biology Methods and Protocols, Volume 9, Issue 1, 2024, bpad027, https://doi.org/10.1093/biomethods/bpad027
Long amplicon nanopore sequencing of Botrytis cinerea and other fungal species present in infected grapevine leaf samples
Biology Methods and Protocols, Volume 9, Issue 1, 2024, bpad042, https://doi.org/10.1093/biomethods/bpad042
An amplicon-based protocol for whole-genome sequencing of human respiratory syncytial virus subgroup A
Biology Methods and Protocols, Volume 9, Issue 1, 2024, bpae007, https://doi.org/10.1093/biomethods/bpae007
Identification and quantitation of multiple variants in RNA virus genomes
Biology Methods and Protocols, Volume 9, Issue 1, 2024, bpae004, https://doi.org/10.1093/biomethods/bpae004
Establishment of new transurethral catheterization methods for male mice
Biology Methods and Protocols, Volume 9, Issue 1, 2024, bpae005, https://doi.org/10.1093/biomethods/bpae005
A methodological primer of extracellular vesicles isolation and characterization via different techniques
Biology Methods and Protocols, Volume 9, Issue 1, 2024, bpae009, https://doi.org/10.1093/biomethods/bpae009
Development of a highly sensitive TaqMan method based on multi-probe strategy: its application in ASFV detection
Biology Methods and Protocols, Volume 9, Issue 1, 2024, bpae011, https://doi.org/10.1093/biomethods/bpae011
An improved method for measuring catalase activity in biological samples
Biology Methods and Protocols, Volume 9, Issue 1, 2024, bpae015, https://doi.org/10.1093/biomethods/bpae015
A rapid and accurate method for evaluating the degradation of pan-Akt in cells by PROTACs using NanoLuc luciferase
Biology Methods and Protocols, Volume 9, Issue 1, 2024, bpae014, https://doi.org/10.1093/biomethods/bpae014
Protocol for preliminary, multicenteric validation of “PoCOsteo device”: A point of care tool for proteomic and genomic study of osteoporosis
Biology Methods and Protocols, Volume 9, Issue 1, 2024, bpae006, https://doi.org/10.1093/biomethods/bpae006
Rapid IDH1-R132 genotyping panel utilizing locked nucleic acid loop-mediated isothermal amplification
Biology Methods and Protocols, Volume 9, Issue 1, 2024, bpae012, https://doi.org/10.1093/biomethods/bpae012
TypeTaxonScript: sugarifying and enhancing data structures in biological systematics and biodiversity research
Biology Methods and Protocols, Volume 9, Issue 1, 2024, bpae017, https://doi.org/10.1093/biomethods/bpae017
A semi-automated spectral approach to analyzing cyclical growth patterns using fish scales
Biology Methods and Protocols, Volume 9, Issue 1, 2024, bpae018, https://doi.org/10.1093/biomethods/bpae018
Intra-arterial delivery of neurospheres into isolated perfused porcine colons: a proof of concept
Biology Methods and Protocols, Volume 9, Issue 1, 2024, bpae022, https://doi.org/10.1093/biomethods/bpae022
Multiparameter flow cytometric detection and analysis of rare cells in in vivo models of cancer metastasis
Biology Methods and Protocols, Volume 9, Issue 1, 2024, bpae026, https://doi.org/10.1093/biomethods/bpae026
An extended multiplicative error model of allometry: Incorporating systematic components, non-normal distributions, and piecewise heteroscedasticity
Biology Methods and Protocols, Volume 9, Issue 1, 2024, bpae024, https://doi.org/10.1093/biomethods/bpae024
A highly sensitive stem-loop RT-qPCR method to study siRNA intracellular pharmacokinetics and pharmacodynamics
Biology Methods and Protocols, Volume 9, Issue 1, 2024, bpae029, https://doi.org/10.1093/biomethods/bpae029
Macro-based collagen quantification and segmentation in picrosirius red-stained heart sections using light microscopy
Biology Methods and Protocols, Volume 9, Issue 1, 2024, bpae027, https://doi.org/10.1093/biomethods/bpae027
Comparing skin swabs, buccal swabs, and toe clips for amphibian genetic sampling, a case study with a small anuran (Acris blanchardi)
Biology Methods and Protocols, Volume 9, Issue 1, 2024, bpae030, https://doi.org/10.1093/biomethods/bpae030
An optimized ligation-mediated PCR method for chromosome walking and fusion gene chromosomal breakpoints identification
Biology Methods and Protocols, Volume 9, Issue 1, 2024, bpae037, https://doi.org/10.1093/biomethods/bpae037
Northern blotting of endogenous full-length human-specific LINE-1 RNA
Biology Methods and Protocols, Volume 9, Issue 1, 2024, bpae036, https://doi.org/10.1093/biomethods/bpae036
PROMER technology: A new real-time PCR tool enabling multiplex detection of point mutation with high specificity and sensitivity
Biology Methods and Protocols, Volume 9, Issue 1, 2024, bpae041, https://doi.org/10.1093/biomethods/bpae041
High-throughput evaluation of hemolytic activity through precise measurement of colony and hemolytic zone sizes of engineered Bacillus subtilis on blood agar
Biology Methods and Protocols, Volume 9, Issue 1, 2024, bpae044, https://doi.org/10.1093/biomethods/bpae044
Two methods of isolation of rat aortic smooth muscle cells with high yield
Biology Methods and Protocols, Volume 9, Issue 1, 2024, bpae038, https://doi.org/10.1093/biomethods/bpae038
Molecular identification of polymorphic transposable elements in populations of the invasive ant Cardiocondyla obscurior
Biology Methods and Protocols, Volume 9, Issue 1, 2024, bpae050, https://doi.org/10.1093/biomethods/bpae050
A modified dual preparatory method for improved isolation of nucleic acids from laser microdissected fresh-frozen human cancer tissue specimens
Biology Methods and Protocols, Volume 9, Issue 1, 2024, bpae066, https://doi.org/10.1093/biomethods/bpae066
High-throughput surface epitope immunoaffinity isolation of extracellular vesicles and downstream analysis
Biology Methods and Protocols, Volume 9, Issue 1, 2024, bpae032, https://doi.org/10.1093/biomethods/bpae032
Assessing RNA integrity by digital RT-PCR: Influence of extraction, storage, and matrices
Biology Methods and Protocols, Volume 9, Issue 1, 2024, bpae053, https://doi.org/10.1093/biomethods/bpae053
Simple protocol for combined extraction of exocrine secretions and RNA in small arthropods
Biology Methods and Protocols, Volume 9, Issue 1, 2024, bpae054, https://doi.org/10.1093/biomethods/bpae054
Circular PCR as an efficient and precise umbrella of methods for the generation of circular dsDNA with staggered nicks: Mechanism and types
Biology Methods and Protocols, Volume 9, Issue 1, 2024, bpae051, https://doi.org/10.1093/biomethods/bpae051
Generating CRISPR-edited clonal lines of cultured Drosophila S2 cells
Biology Methods and Protocols, Volume 9, Issue 1, 2024, bpae059, https://doi.org/10.1093/biomethods/bpae059
Methods in cancer research: Assessing therapy response of spheroid cultures by life cell imaging using a cost-effective live-dead staining protocol
Biology Methods and Protocols, Volume 9, Issue 1, 2024, bpae060, https://doi.org/10.1093/biomethods/bpae060
NanoMGT: Marker gene typing of low complexity mono-species metagenomic samples using noisy long reads
Biology Methods and Protocols, Volume 9, Issue 1, 2024, bpae057, https://doi.org/10.1093/biomethods/bpae057
An efficient protocol for the extraction of pigment-free active polyphenol oxidase and soluble proteins from plant cells
Biology Methods and Protocols, Volume 9, Issue 1, 2024, bpae067, https://doi.org/10.1093/biomethods/bpae067
A new method for quantifying glyoxalase II activity in biological samples
Biology Methods and Protocols, Volume 9, Issue 1, 2024, bpae069, https://doi.org/10.1093/biomethods/bpae069
Oligoribonucleotide interference-PCR-based methods for the sensitive and accurate detection of KRAS mutations
Biology Methods and Protocols, Volume 9, Issue 1, 2024, bpae071, https://doi.org/10.1093/biomethods/bpae071
Development and characterization of human T-cell receptor (TCR) alpha and beta clones’ library as biological standards and resources for TCR sequencing and engineering
Biology Methods and Protocols, Volume 9, Issue 1, 2024, bpae064, https://doi.org/10.1093/biomethods/bpae064
Modified throughput ninhydrin method for the qualitative assessment of dietary protein absorption in pig plasma
Biology Methods and Protocols, Volume 9, Issue 1, 2024, bpae078, https://doi.org/10.1093/biomethods/bpae078
Implementation of plate reader-based indooxine and Nessler protocols for monitoring L-asparaginase serum activity in childhood acute lymphoblastic leukaemia
Biology Methods and Protocols, Volume 9, Issue 1, 2024, bpae042, https://doi.org/10.1093/biomethods/bpae042
Efficient protocol for isolating human fibroblast from primary skin cell cultures: application to keloid, hypertrophic scar, and normal skin biopsies
Biology Methods and Protocols, Volume 9, Issue 1, 2024, bpae082, https://doi.org/10.1093/biomethods/bpae082
Enhancing negative control selection: A comparative analysis of random and targeted sampling techniques for obtaining High-Quality RNA from normal breast tissue
Biology Methods and Protocols, Volume 9, Issue 1, 2024, bpae083, https://doi.org/10.1093/biomethods/bpae083
Practical application of PMA–qPCR assay for determination of viable cells of inter-species biofilm of Candida albicans–Staphylococcus aureus
Biology Methods and Protocols, Volume 9, Issue 1, 2024, bpae081, https://doi.org/10.1093/biomethods/bpae081
Development of a new breath collection method for analyzing volatile organic compounds from intubated mouse models
Biology Methods and Protocols, Volume 9, Issue 1, 2024, bpae087, https://doi.org/10.1093/biomethods/bpae087
A rapid and inexpensive 96-well DNA-extraction method from blood using silicon dioxide powder (Glassmilk)
Biology Methods and Protocols, Volume 9, Issue 1, 2024, bpae079, https://doi.org/10.1093/biomethods/bpae079
An efficient injection protocol for Drosophila larvae
Biology Methods and Protocols, Volume 9, Issue 1, 2024, bpae093, https://doi.org/10.1093/biomethods/bpae093
Reviews
Pyrimethamine reduced tumour growth in pre-clinical cancer models: a systematic review to identify potential pre-clinical studies for subsequent human clinical trials
Biology Methods and Protocols, Volume 9, Issue 1, 2024, bpae021, https://doi.org/10.1093/biomethods/bpae021
Point-of-care potentials of lateral flow-based field screening for Mycoplasma bovis infections: a literature review
Biology Methods and Protocols, Volume 9, Issue 1, 2024, bpae034, https://doi.org/10.1093/biomethods/bpae034
The use of droplet-based microfluidic technologies for accelerated selection of Yarrowia lipolytica and Phaffia rhodozyma yeast mutants
Biology Methods and Protocols, Volume 9, Issue 1, 2024, bpae049, https://doi.org/10.1093/biomethods/bpae049
Pre-registered study protocols
Alternative community-led intervention to improve uptake of cataract surgery services in rural Tanzania—The Dodoma Community Cataract Acceptance Trial (DoCCAT): a protocol for intervention co-designing and implementation in a cluster-randomized controlled trial
Biology Methods and Protocols, Volume 9, Issue 1, 2024, bpae016, https://doi.org/10.1093/biomethods/bpae016
Protocols
Optimized protocol for shotgun label-free proteomic analysis of pancreatic islets
Biology Methods and Protocols, Volume 9, Issue 1, 2024, bpae003, https://doi.org/10.1093/biomethods/bpae003
Efficient regeneration of protoplasts from Solanum lycopersicum cultivar Micro-Tom
Biology Methods and Protocols, Volume 9, Issue 1, 2024, bpae008, https://doi.org/10.1093/biomethods/bpae008
An optimized protocol for generating appendage-bearing skin organoids from human-induced pluripotent stem cells
Biology Methods and Protocols, Volume 9, Issue 1, 2024, bpae019, https://doi.org/10.1093/biomethods/bpae019
A protocol to isolate, identify, and verify glucose- or carbohydrate-binding receptors
Biology Methods and Protocols, Volume 9, Issue 1, 2024, bpae045, https://doi.org/10.1093/biomethods/bpae045
A reproducible method to study traumatic injury-induced zebrafish brain regeneration
Biology Methods and Protocols, Volume 9, Issue 1, 2024, bpae073, https://doi.org/10.1093/biomethods/bpae073
SMaRT M-Seq: an optimized step-by-step protocol for M protein sequencing in monoclonal gammopathies
Biology Methods and Protocols, Volume 9, Issue 1, 2024, bpae074, https://doi.org/10.1093/biomethods/bpae074
Live cell fluorescence microscopy—an end-to-end workflow for high-throughput image and data analysis
Biology Methods and Protocols, Volume 9, Issue 1, 2024, bpae075, https://doi.org/10.1093/biomethods/bpae075
Protocol for obtaining doubled haploids in isolated microspore culture in vitro for poorly responsive genotypes of brassicaceae family
Biology Methods and Protocols, Volume 9, Issue 1, 2024, bpae091, https://doi.org/10.1093/biomethods/bpae091
Innovations
Isolation of short RNAs with homogeneous 3′-ends using quaternary-amine anion exchange chromatography
Biology Methods and Protocols, Volume 9, Issue 1, 2024, bpae033, https://doi.org/10.1093/biomethods/bpae033
Optimizing Western blotting immunodetection: Streamlining antibody cocktails for reduced protocol time and enhanced multiplexing applications
Biology Methods and Protocols, Volume 9, Issue 1, 2024, bpae077, https://doi.org/10.1093/biomethods/bpae077
Corrections
Correction to: Long amplicon nanopore sequencing of Botrytis cinerea and other fungal species present in infected grapevine leaf samples
Biology Methods and Protocols, Volume 9, Issue 1, 2024, bpae010, https://doi.org/10.1093/biomethods/bpae010
Correction to: An improved method for measuring catalase activity in biological samples
Biology Methods and Protocols, Volume 9, Issue 1, 2024, bpae025, https://doi.org/10.1093/biomethods/bpae025
Correction to: Heterozygous KCNH2 variant phenotyping using Flp-In HEK293 and high-throughput automated patch clamp electrophysiology
Biology Methods and Protocols, Volume 9, Issue 1, 2024, bpae085, https://doi.org/10.1093/biomethods/bpae085
