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Methods
Techniques used, canonicalised from 109 raw strings to 43.
| Name | Papers | Appears in |
|---|---|---|
| AlphaFold structure prediction AlphaFold3 Multimer modelling, AlphaFold2 modelling, AlphaFold3 modelling, multi-seed prediction replication | 9 | gao gomezdelacruz guo ibrahim madhuprakash pai seager toghani toghani |
| cell death and HR assays ion leakage assays, HR and DAB staining, cell death assays, trypan blue and DAB staining | 9 | gao gomezdelacruz guo ibrahim madhuprakash pai seager toghani toghani |
| phylogenomics phylogenetics, codon-based sequence alignment, phylogenetic analysis of an allelic series, multiple sequence alignment | 9 | gao gomezdelacruz guo ibrahim madhuprakash marques pai toghani toghani |
| site-directed and structure-guided mutagenesis site-directed mutagenesis of splice sites and start codons, site-directed mutagenesis, saturating single-residue substitution, site-directed interface mutagenesis | 9 | gao gomezdelacruz guo ibrahim madhuprakash pai seager toghani toghani |
| transient expression in N. benthamiana | 8 | gomezdelacruz guo ibrahim madhuprakash pai seager toghani toghani |
| comparative genomics and genome annotation comparative genomics of MADA-NLRs, BLAST similarity searching, comparative genomics, NLR identification and classification against RefPlantNLR | 6 | gao madhuprakash marques pai toghani toghani |
| interface analysis PISA interface analysis, electrostatic potential analysis, interface and buried-surface-area analysis, interface contact classification | 6 | gomezdelacruz ibrahim madhuprakash seager toghani toghani |
| BN-PAGE | 4 | gao guo ibrahim seager |
| CRISPR knockout lines CRISPR knockout lines (nrg1, nrg1/adr1, epss), CRISPR nrc2/3/4 knockout lines, CRISPR nrc2/3/4 knockout complementation lines | 4 | ibrahim madhuprakash seager toghani |
| co-immunoprecipitation | 4 | gao gomezdelacruz madhuprakash toghani |
| protein purification tandem affinity purification, size exclusion chromatography, SEC-MALS, tandem affinity purification from N. benthamiana | 4 | guo madhuprakash seager toghani |
| structural superposition and RMSD analysis structural superposition and interface analysis, structural superposition, structural superposition (ChimeraX matchmaker) | 4 | gomezdelacruz madhuprakash toghani toghani |
| transcriptomics RNA-seq, RT-PCR, transcriptome analysis, qRT-PCR | 4 | gao gomezdelacruz guo marques |
| domain swapping and chimera construction domain swapping and chimeric receptor construction, domain chimera construction, domain swapping | 3 | gomezdelacruz madhuprakash seager |
| genetically encoded calcium imaging cell-based calcium influx assays, GCaMP3 calcium imaging, genetically encoded calcium imaging (GCaMP6s, RCaMP1h, jRGECO1a) | 3 | gao guo ibrahim |
| negative-stain EM immunoprecipitation-electron microscopy (IP-EM), 2D class averaging | 3 | guo seager toghani |
| stable plant transformation stable potato transformation, barley transformation, Agrobacterium-mediated wheat transformation | 3 | gao gomezdelacruz guo |
| cryo-EM | 2 | guo seager |
| pathogen infection assays P. infestans infection assays, pathogen infection assays (spot and spray inoculation) | 2 | gao gomezdelacruz |
| selection analysis positive selection analysis (CodeML, PAML v4.10.7, M8 vs M8a), Bayes Empirical Bayes site identification, sequence conservation analysis | 2 | pai seager |
| EMS mutagenesis | 1 | guo |
| Golden Gate MoClo cloning | 1 | seager |
| HMM profile searching (MADA) | 1 | pai |
| N-terminal motif searching | 1 | ibrahim |
| PVX-mediated gene silencing | 1 | gao |
| PoreAnalyzer pore analysis | 1 | guo |
| Structural Novelty Index (SNI) scoring | 1 | toghani |
| X-ray crystallography | 1 | madhuprakash |
| bootstrap statistical analysis (BestHR) | 1 | madhuprakash |
| chloroplast purification | 1 | ibrahim |
| co-scientist AI feature generation | 1 | toghani |
| confocal live-cell imaging organelle marker colocalisation, time-lapse imaging | 1 | ibrahim |
| copper-inducible transcriptional activation | 1 | seager |
| dexamethasone-inducible expression | 1 | gao |
| hierarchical clustering | 1 | toghani |
| iTOL v6 visualisation | 1 | marques |
| immunoblotting | 1 | toghani |
| map-based cloning | 1 | guo |
| nanobody-mediated relocalisation | 1 | ibrahim |
| parallel reaction monitoring mass spectrometry | 1 | gao |
| patch-clamp electrophysiology | 1 | guo |
| splicing reporter construction (YSR) | 1 | gao |
| yeast two-hybrid | 1 | gomezdelacruz |
Sources
- Built from
data/entities.jsonbyscripts/build_entities.py - Merges and refused merges logged in
notes/alias-decisions.md