# List of research methods in biology

This list of research methods in biology is an index to articles about research methodologies used in various branches of biology.

## Research design and analysis
### Research designs

| Research design | Utility | Potential analysis |
| Between-group design | Experiment that has two or more groups of subjects each being tested by a different testing factor simultaneously | Student's t-test, Analysis of variance, Mann–Whitney U test |
| Repeated measures design | A research design that involves multiple measures of the same variable taken on the same or matched subjects either under different conditions or over two or more time periods. | Paired t-test, Wilcoxon signed-rank test |

### Charts and diagrams

| Analysis | Utility | Branch |
| Dose–response curves | Graph that shows the magnitude of the response of an organism, as a function of exposure (or doses) to a stimulus or stressor (usually a chemical) after a certain exposure time | Physiology |
| Electroencephalogram | Graph that shows voltage fluctuations resulting from ionic current within the neurons of the brain | Neuroscience |
| Electrocardiogram | Graph of voltage versus time of the electrical activity of the heart using electrodes placed on the skin | Physiology |
| Identification key | Used to identify a specimen organism from a set of known taxa. | Systematics, Taxonomy |
| Manhattan plot | Used to display data with a large number of data-points, many of non-zero amplitude, and with a distribution of higher-magnitude values. The plot is commonly used in genome-wide association studies (GWAS) to display significant SNPs. | Genetics |
| Pedigree chart | Used to show the occurrence of phenotypes of a particular gene or organism and its ancestors from one generation to the next, most commonly humans, show dogs, and race horses | Genetics |
| Phylogenetic tree | Used to show the evolutionary relationships among various biological species or other entities based upon similarities and differences in their physical or genetic characteristics | Systematics, Evolutionary biology |
| Population pyramid | Used to illustrate the distribution of a population (typically that of a country or region of the world) by age groups and sex; it typically forms the shape of a pyramid when the population is growing | Population ecology |
| Punnett square | Used to predict the genotypes of a particular cross or breeding experiment | Genetics |

### Statistical analyses

| Analysis | Utility | Type |
| Analysis of variance | A collection of statistical models and their associated estimation procedures (such as the "variation" among and between groups) used to analyze the differences among means | Statistical model |
| Chi-squared test | A statistical hypothesis test that is valid to perform when the test statistic is chi-squared distributed under the null hypothesis, specifically Pearson's chi-squared test and variants thereof | Statistical hypothesis test |
| Mann–Whitney U test | A statistical hypothesis test of the null hypothesis that, for randomly selected values X and Y from two populations, the probability of X being greater than Y is equal to the probability of Y being greater than X | Nonparametric statistics |
| Student's t-test | Any statistical hypothesis test in which the test statistic follows a Student's t-distribution under the null hypothesis | Parametric statistics |

## Laboratory techniques

| Method | Utility | Branches |
| Agarose gel electrophoresis | Used to separate a mixed population of macromolecules such as DNA or proteins in a matrix of agarose, one of the two main components of agar | Biochemistry, Molecular biology, Genetics |
| Animal Model | Used for researching diseases and disorders in humans. Some animals may have human-like traits, such as mice, while others may have traits that are ideal for research, such as the squid giant axon | Biochemistry, Neuroscience, Physiology |
| Biological ablation | Used to remove a biological structure or functionality | Genetics, Physiology |
| Calcium imaging | Used to optically measure the status of calcium ions (Ca$^{2+}$) in an isolated cell, tissue or medium | Physiology |
| Cell isolation | Process of separating individual living cells from a solid block of tissue or cell suspension | Cell biology |
| Centrifugation | Use of centrifugal force to separate particles from a solution according to their size, shape, density, medium viscosity, and rotor speed | Cell biology, Biochemistry |
| CRISPR gene editing | Used to modify the genomes of living organisms based on a simplified version of the bacterial CRISPR-Cas9 antiviral defense system | Molecular biology |
| DNA sequencer | Used to automate the DNA sequencing process | Genetics, Molecular biology |
| Enzyme-linked immunosorbent assay (ELISA) | Used to detect the presence of a ligand (commonly a protein) in a liquid sample using antibodies directed against the protein to be measure | Biochemistry, Molecular biology |
| Gene knockout | Used to make one of an organism's genes inoperative ("knocked out" of the organism) | Molecular biology, Genetics |
| Immunostaining | Used of an antibody-based method to detect a specific protein in a sample | Molecular biology, Biochemistry |
| Intracellular recording | Used to measure the voltage across a cell membrane | Neuroscience, Electrophysiology |
| Microarray | Assays (tests) large amounts of biological material using high-throughput screening miniaturized, multiplexed and parallel processing and detection methods | Genetics, Molecular biology |
| Microelectrode array | Devices that contain multiple (tens to thousands) microelectrodes through which neural signals are obtained or delivered, essentially serving as neural interfaces that connect neurons to electronic circuitry | Neuroscience |
| Microscope | Used to examine objects that are too small to be seen by the naked eye | Cell biology |
| Molecular cloning | Used to assemble recombinant DNA molecules and to direct their replication within host organisms. | Molecular biology |
| Northern blot | Used to study gene expression by detection of RNA (or isolated mRNA) in a sample. | Molecular biology |
| Optogenetics | Uses light to control neurons that have been genetically modified to express light-sensitive ion channels | Neuroscience |
| Oscilloscope | Used to graphically displays varying signal voltages, usually as a calibrated two-dimensional plot of one or more signals as a function of time | Neuroscience, Physiology |
| Paper chromatography | Used to separate coloured chemicals or substances. | Molecular biology |
| Patch clamp | Used to study ionic currents in individual isolated living cells, tissue sections, or patches of cell membrane | Electrophysiology, Neuroscience |
| Polymerase chain reaction (PCR) | Used to rapidly make millions to billions of copies (complete copies or partial copies) of a specific DNA sample, allowing scientists to take a very small sample of DNA and amplify it (or a part of it) to a large enough amount to study in detail | Genetics, Molecular biology |
| Somatic cell nuclear transfer | Used for creating a viable embryo from a body cell and an egg cell | Developmental biology |
| Southern blot | Used to detect specific DNA sequence in DNA samples | Molecular biology |
| Test cross | Used to determine whether an individual is homozygous or heterozygous dominant | Genetics |
| Voltage clamp | Used to measure the ion currents through the membranes of excitable cells, such as neurons, while holding the membrane voltage at a set level. | Physiology, Neuroscience |
| Western blot | Used analytical technique in molecular biology and immunogenetics to detect specific proteins in a sample of tissue homogenate or extract | Molecular biology |
| X-ray crystallography | Used to determine the atomic and molecular structure of a crystal, in which the crystalline structure causes a beam of incident X-rays to diffract into many specific directions | Structural biology |

## Field techniques

| Method | Utility | Branches |
| Distance sampling | Used for estimating the density and/or abundance of populations | Ecology |
| Mark and recapture | Used to estimate an animal population's size where it is impractical to count every individual. | Ecology |

## Computational tools
### Mathematical models

| Model | Utility | Branches |
| Exponential integrate-and-fire | Describes compact and computationally efficient nonlinear spiking neuron models with one or two variables | Neuroscience |
| FitzHugh–Nagumo model | Describes a prototype of an excitable system (e.g., a neuron) | Neuroscience |
| Hardy–Weinberg principle | States that allele and genotype frequencies in a population will remain constant from generation to generation in the absence of other evolutionary influences | Genetics, Evolutionary biology |
| Hodgkin–Huxley model | Describes how action potentials in neurons are initiated and propagated | Neuroscience |
| Infinite sites model | Allows for the calculation of heterozygosity, or genetic diversity, in a finite population and for the estimation of genetic distances between populations of interest | Evolutionary biology |
| Logistic growth | Describes the growth of a population as exponential, followed by a decrease in growth, and bound by a carrying capacity due to environmental pressures. | Ecology |
| Lotka–Volterra equations | Describe the dynamics of biological systems in which two species interact, one as a predator and the other as prey | Ecology |
| Moran process | Stochastic process that describes finite populations | Genetics |
| Species–area relationship | describes the relationship between the area of a habitat, or of part of a habitat, and the number of species found within that area | Ecology |

### Algorithms

| Algorithm | Utility | Branches |
| Evolutionary algorithm | Uses mechanisms inspired by biological evolution. Candidate solutions to the optimization problem play the role of individuals in a population, and the fitness function determines the quality of the solutions. | Neuroscience |