研究手法をまとめたひとつのカタログ — 各手法の仕組み、使いどころ、そしてできないことを学べます。
Gas Chromatography-Olfactometry (GC-O) combines the separation power of gas chromatography with human olfactory perception to identify which volatile compounds in a food sample contribute to its aroma. Developed by Acree and colleagues in the 1990s, GC-O allows researchers to bypass the human nose's inability to consci
Machine learning-assisted gene set enrichment analysis (ML-GSEA) extends the classical GSEA framework by incorporating supervised or unsupervised ML models — such as random forests, neural networks, or deep learning architectures — to improve the detection, ranking, and biological interpretation of enriched gene sets f
Accelerated Shelf-Life Testing (ASLT) uses elevated temperature and controlled storage conditions to rapidly assess product degradation and predict realistic shelf-life without waiting months. By measuring quality parameters (moisture, acidity, nutrient levels, microbial growth) at accelerated conditions and applying k
Acoustic telemetry is a remote tracking method in which small electronic transmitters attached to or implanted in animals emit unique acoustic signals detectable by underwater or terrestrial receiver networks, enabling real-time monitoring of animal movements, positions, and behavior over extended distances and times.
Admixture analysis is a population genetics method that infers population structure and individual ancestry from multilocus genotype data. Originally developed by Pritchard, Stephens, and Donnelly (2000) and refined by Alexander, Novembre, and Lange (2009), admixture analysis reveals how genetic variation is distribute
An agrometeorological yield model is a quantitative framework that relates observed or forecasted weather variables — temperature, precipitation, solar radiation, humidity — to the final grain or biomass yield of a crop. Grounded in plant physiology and agricultural climatology, the approach is used worldwide in food s
Allometric equations predict tree above-ground or total biomass from easily measured tree dimensions—typically diameter at breast height (DBH), height, and wood density. Grounded in biological allometry (scaling laws) and codified by Chave, Niklas, and others, allometric equations are essential tools for rapid biomass
Ancestral state reconstruction (ASR) is a phylogenetic method that infers the character states (trait values or evolutionary features) of extinct ancestors by analyzing patterns of variation in extant (living) species. Developed by Wayne Maddison and colleagues in the 1990s, ASR uses the phylogenetic tree and observed
Animal BLUP (Best Linear Unbiased Predictor) is a statistical method for estimating the genetic merit (breeding values) of livestock based on their own performance and the performance of their relatives. Developed by Charles R. Henderson in 1949 and refined continuously since, Animal BLUP accounts for pedigree relation
Apparent Total Tract Digestibility (ATTD) is a measure of the proportion of a nutrient consumed in feed that is absorbed by the animal, calculated from the difference between dietary intake and fecal excretion. Standardized since the 1970s, ATTD is essential for quantifying the bioavailability of nutrients in feedstuff
ATAC-seq (Assay for Transposase-Accessible Chromatin using sequencing) is a method for profiling the landscape of chromatin accessibility genome-wide. Developed by Buenrostro and colleagues in 2013, ATAC-seq uses hyperactive transposase to tag open, accessible chromatin regions, enabling rapid and sensitive identificat
Bayesian ChIP-seq peak calling applies probabilistic models — typically Poisson, negative binomial, or hidden Markov models with Bayesian inference — to detect genomic regions enriched for a protein of interest in chromatin immunoprecipitation followed by sequencing experiments. By explicitly modelling read-count noise
Bayesian copy number variation (CNV) analysis is a probabilistic framework for detecting genomic segments where an individual's DNA copy count deviates from the diploid norm. By placing prior distributions over copy-number states and updating them with array CGH, SNP array, or sequencing read-depth evidence, the approa
A Bayesian EWAS is a genome-scale association analysis that links epigenetic marks — most commonly CpG-site DNA methylation — to a phenotype or trait of interest, replacing or supplementing the classical frequentist p-value framework with a Bayesian probabilistic model. It yields posterior probabilities of association
A Bayesian epigenome-wide association study (Bayesian EWAS) scans hundreds of thousands of DNA methylation sites across the genome to identify those statistically associated with an educational outcome — such as cognitive ability, attainment, or socioeconomic exposure during schooling. Unlike classical frequentist EWAS
Bayesian eQTL analysis identifies genetic variants (eQTLs) that regulate gene expression by combining genotype and RNA-seq data within a probabilistic framework. Unlike frequentist approaches that rely on p-value thresholds, the Bayesian formulation produces posterior probabilities of association, enabling principled f
Bayesian gene set enrichment analysis (Bayesian GSEA) applies a probabilistic framework to determine whether predefined sets of genes — representing biological pathways, cellular processes, or functional categories — are collectively more differentially expressed than expected by chance. Unlike classical frequentist GS
Bayesian genome-wide association study (Bayesian GWAS) applies Bayesian statistical models to millions of single-nucleotide polymorphisms (SNPs) to identify genetic variants associated with educational outcomes such as years of schooling or cognitive test scores. Unlike classical frequentist GWAS, Bayesian approaches a
Bayesian GWAS applies Bayesian statistical inference to genome-wide association studies, replacing classical p-value thresholds with Bayes factors and posterior probabilities. This framework naturally incorporates prior knowledge about effect sizes and variant frequencies, quantifies evidence for association on a conti
Bayesian metabolomics analysis applies probabilistic inference to metabolite abundance data — typically from mass spectrometry or NMR spectroscopy — to identify differentially abundant metabolites, annotate spectral features, and integrate pathway knowledge. By encoding prior biological knowledge into prior distributio
Bayesian microbiome diversity analysis applies probabilistic models — chiefly Dirichlet-Multinomial and related hierarchical frameworks — to 16S rRNA or shotgun metagenomic count data to estimate alpha-diversity (within-sample richness and evenness) and beta-diversity (between-sample compositional differences) while pr
Bayesian pathway enrichment analysis tests whether a predefined set of genes — a biological pathway — is systematically overrepresented among genes that show evidence of differential activity in an experiment. Unlike classical over-representation tests, it encodes prior biological knowledge as a prior distribution and
Bayesian phylogenetic analysis uses Bayes' theorem and Markov chain Monte Carlo (MCMC) sampling to estimate the posterior probability distribution over phylogenetic trees and model parameters given observed sequence data. Unlike bootstrapped maximum-likelihood methods that return a single best tree, Bayesian inference
Bayesian proteomics analysis applies probabilistic models to mass spectrometry data to identify peptides, infer protein presence, and quantify differential protein abundance across conditions. By encoding prior knowledge and propagating uncertainty through each step of the pipeline, Bayesian approaches produce calibrat
Bayesian RNA-seq differential expression analysis applies hierarchical Bayesian models to RNA sequencing read-count data to identify genes whose expression levels differ significantly between biological conditions. Rather than relying solely on p-values, these methods quantify the posterior probability that a gene is d
Bayesian sequence alignment treats the alignment of biological sequences (DNA, RNA, or protein) as a probabilistic inference problem rather than a deterministic optimization. Instead of returning a single best alignment, it samples from a posterior distribution over all plausible alignments given a substitution model a
Bayesian single-cell RNA-seq analysis applies probabilistic generative models to the sparse, overdispersed count matrices produced by single-cell RNA sequencing. By placing prior distributions over latent biological variables — cell state, batch effects, dropout — the framework propagates uncertainty through every down
Bayesian variant calling is a computational pipeline that uses probabilistic inference to identify single-nucleotide polymorphisms (SNPs), insertions, and deletions in a genome by treating sequencing data as evidence and computing posterior probabilities over candidate genotypes. Unlike deterministic threshold-based ca
Beta diversity partitioning quantifies how species composition differs among sites, decomposing community dissimilarity into two components: species turnover (replacement of species across sites) and nestedness (loss of species from species-rich sites). Developed by Baselga (2010), this framework reveals whether sites
Bioaccumulation models predict how chemical contaminants accumulate in organisms from environmental exposure (water, food, sediment). Developed by Gobas and colleagues (2006), these models quantify the kinetics of chemical uptake, metabolism, and clearance. Bioaccumulation factors (BAF) and bioconcentration factors (BC
Forest biodiversity indices quantify species richness, evenness, and overall diversity in forest ecosystems. Rooted in information theory (Shannon) and statistical ecology (Simpson, Magurran), these indices compress complex multispecies data into interpretable metrics. Applied to forest inventory data, biodiversity ind
Biomass allometric equations are regression models that predict tree or stand aboveground biomass from easily measurable variables such as diameter at breast height (DBH) and height. These equations embody the principle of allometry: the scaling relationship between body parts or organisms. In forestry, allometric equa
Body Condition Scoring (BCS) is a semi-quantitative visual and palpation assessment method used to evaluate the nutritional status and adipose tissue reserves of livestock, particularly dairy cattle, beef cattle, and small ruminants. Developed systematically in the 1980s, BCS provides a practical, non-invasive tool for
Brix measurement quantifies the dissolved solids (primarily sugars) in fruit juice using refractometry, a non-destructive optical technique. Introduced by Carl Zeiss in the 19th century and standardized by AOAC, it is the universal industry standard for assessing fruit ripeness and quality in horticulture and postharve
Burn severity is a quantitative measure of fire-induced changes in vegetation and soil, assessed using satellite-based spectral indices. The Normalized Burn Ratio (NBR) and its delta (dNBR) compare pre-fire and post-fire spectral reflectance in the near-infrared and shortwave-infrared bands to detect fire-caused vegeta
Canopy cover, or canopy closure, is the proportion of ground area covered by tree crowns when viewed from above, typically expressed as a percentage. Formalized by Jennings and colleagues in pioneering work on tropical forest structure, canopy cover estimation employs multiple methods—from field-based ocular assessment
Canopy gap fraction quantifies the proportion of sky visible through the forest canopy, expressed as a percentage. Developed to measure light availability in the understory, it is a standard metric in forest ecology for characterizing canopy structure and microhabitat conditions. This measure is essential for understan
Canopy interception modeling quantifies the fraction of rainfall captured by plant canopies and subsequently evaporated back to the atmosphere before reaching the soil. Applied across agronomy, forestry, and hydrology, it partitions gross precipitation into throughfall, stemflow, and interception loss. By linking veget
Forest carbon stock estimation quantifies the amount of carbon stored in tree biomass and other forest components, typically expressed in tonnes of carbon per hectare. Formalized by Brown, Chave, and international bodies such as the IPCC and FAO, this method is foundational for climate change mitigation accounting, car
Carbon-13 Discrimination Analysis quantifies the degree to which C3 plants preferentially fix the lighter carbon isotope (12C) over the heavier 13C during photosynthesis. The resulting discrimination value (Delta) is closely linked to the ratio of internal to ambient CO2 concentration, making it a reliable, integrative
Cation exchange capacity (CEC) is a fundamental soil property that measures the soil's ability to hold and release positively charged nutrient ions (cations: K⁺, Ca²⁺, Mg²⁺, Na⁺, H⁺, Al³⁺) in forms available to plant roots. CEC reflects the amount and type of clay minerals and organic matter in the soil—compounds with
Cellulose crystallinity refers to the degree of structural order in cellulose molecules: highly crystalline cellulose has organized, tightly packed chains; amorphous cellulose has disordered chains. Measured using X-ray diffraction, cellulose crystallinity influences wood strength, stiffness, and digestibility in pulpi
ChIP-seq peak calling is a computational pipeline that identifies genomic regions where a protein of interest — a transcription factor or histone modification — is enriched, based on sequencing reads from chromatin immunoprecipitation experiments. It converts raw sequencing data into a set of high-confidence binding or
Chlorophyll fluorescence is a non-invasive optical measurement of how efficiently the photosynthetic machinery converts absorbed light into chemical energy (photosynthesis) or heat and light (fluorescence). When photosynthesis is inhibited by stress (drought, cold, salt, pests), chlorophyll fluorescence increases becau
Circuitscape, developed by Brad McRae (2008), applies circuit theory from electrical engineering to predict organism movement and genetic connectivity across landscapes. The method treats landscapes as electrical networks where habitat quality is resistance and organism movement is electrical current. By analogy, organ
Coalescent theory is a probabilistic framework that traces the genealogical history of DNA sequences backward in time to their most recent common ancestor. Developed by John Kingman in 1982, this method forms the foundation of modern population genetics, enabling researchers to understand demographic events, estimate g
Cold storage protocol establishes optimal temperature, humidity, and duration guidelines for preserving fruit and vegetable quality during extended storage. By maintaining precise refrigeration conditions and monitoring produce condition, growers and distributors can extend shelf life from days to weeks or months, enab
Controlled atmosphere (CA) storage extends fruit shelf life beyond cold storage alone by actively regulating oxygen (O₂) and carbon dioxide (CO₂) concentrations during storage. By reducing respiration and ethylene production rates, CA storage can maintain fruit quality for months. This advanced technique is expensive b
Copy number variation (CNV) analysis is a genomic pipeline for detecting regions where individuals carry fewer or more copies of a DNA segment than the reference genome. CNVs span kilobases to megabases and are a major class of structural variation implicated in cancer, neurodevelopmental disorders, and population dive
CRISPR screen analysis processes data from pooled genetic screens using CRISPR-Cas9 to identify genes required for cell growth, survival, or phenotype in specific conditions. Developed by Zhang, Sanjana, and others, this computational pipeline transforms sequencing readouts of guide RNA abundances into ranked lists of
Crop growth models are mechanistic simulation systems designed to predict crop development, biomass accumulation, and yield under varying environmental and management conditions. DSSAT (Decision Support System for Agrotechnology Transfer) and APSIM (Agricultural Production Systems Simulator) are the most widely used pl
Crop Growth Simulation is a computational pipeline for predicting daily or seasonal crop development, biomass accumulation, and yield under varying environmental conditions. Developed by Jones and colleagues in the DSSAT framework, this method integrates agronomic knowledge with process-based modeling to enable decisio
Crop load management uses quantitative assessment of fruit number and tree vigor to optimize yields and fruit quality through selective thinning and load balancing. This method combines visual assessment of fruitlet density, calculation of target fruit number based on tree age and vigor, physical or chemical thinning,
Crop Yield Estimation is an analytical and predictive pipeline for forecasting final crop yield before harvest or monitoring yield accumulation during the growing season. Developed by agronomic research centers (CIMMYT, ICRISAT, IRRI), this method combines field observations, environmental data, and statistical models
The Van Wagner crown fire model predicts the conditions under which surface fires will transition to active crown fires and the rate of crown fire spread. Developed by Cornelius Van Wagner in the 1970s–1990s, the model is grounded in the physics of heat transfer from the surface flame to the canopy and the rate of vert
Cryo-electron microscopy (cryo-EM) determines three-dimensional macromolecular structures at atomic or near-atomic resolution by imaging proteins frozen in vitreous ice. Pioneered by Frank, Henderson, and others, this technique has revolutionized structural biology by enabling visualization of large, non-crystallizable
D-value (decimal reduction time) and Z-value characterize the thermal resistance of microorganisms in food. D-value is the time required at a specific temperature to reduce microbial population by 90% (one log unit). Z-value is the temperature change needed to reduce the D-value tenfold. Together, they enable food proc
De novo transcriptome assembly reconstructs full-length messenger RNA sequences directly from sequencing reads without requiring a reference genome. Pioneered by Regev, Haas, and colleagues, this pipeline enables transcript discovery in non-model organisms and detection of novel isoforms, fusion genes, and splice varia
Dendrochronology is the science of dating and interpreting wood and climate from tree rings. Each annual ring records the tree's growth response to weather during that year: wide rings indicate favorable conditions (adequate water, warmth, light); narrow rings indicate stress (drought, cold, shade). By crossmatching ri
Dendrochronology is the science of dating and analyzing tree rings to reconstruct past climatic conditions, chronologies, and tree growth patterns. Pioneered by Andrew Ellicott Douglass in the early twentieth century and formalized by Fritts and colleagues, dendrochronology enables precise dating of historical wood sam