Definitions
Auto-generated glossary of 214 terms.
accuracy: A measure of how closely estimates produced by a statistical method agree with true or observed values.
adaptive radiations: Rapid diversification of a clade into multiple species that occupy a variety of ecological niches.
adjuvant therapy: Treatment administered after primary treatment to eliminate remaining disease and reduce the risk of recurrence.
algorithms: Step-by-step computational procedures for performing a specific task or solving a problem.
anaphase: The stage of mitosis during which sister chromatids separate and move toward opposite poles of the cell.
aneuploid: Definition Having an abnormal number of chromosomes that deviates from the typical diploid complement. A condition characterized by an abnormal number of chromosomes, either more or fewer than the normal diploid number.
aneuploid cells: Definition Cells that contain an abnormal number of chromosomes, deviating from the normal diploid number.
aneuploid yeast: Yeast cells containing an abnormal number of chromosomes, typically with one or more extra or missing chromosomes.
aneuploidy induced stress: A cellular state characterized by molecular and physiological disruption due to an imbalance in gene dosage.
approximate bayesian computation (abc): A method for parameter inference and model selection that bypasses exact likelihood calculations by comparing summary statistics of observed data with those of simulated data generated from a model.
asexual population: A population of organisms that reproduce without sexual recombination, such that all genetic variation is accumulated through mutations in a single lineage of descent.
basic reproduction number: The average number of secondary infections produced by a single infected individual in a completely susceptible population, typically denoted R₀.
bayesian analysis: A statistical framework for inference that integrates prior beliefs with observed data to obtain posterior distributions of parameters, often including model comparison as an integral component.
bijective mapping: A one-to-one correspondence between two sets where each element in one set maps to exactly one unique element in the other set and vice versa.
binary tree: A tree structure where each internal node has exactly two child nodes.
biogeographical causes: Factors related to the geographic distribution of organisms and spatial patterns of biodiversity that influence evolutionary processes.
biological mechanism: A specific molecular or cellular process that operates in living systems and is hypothesized to be relevant to disease development or progression.
bipolar cell division: A cell division process in which two poles organize the spindle apparatus, resulting in the formation of two daughter cells.
bipolar spindle assembly: The formation of a mitotic spindle with two opposing poles that organize microtubules for chromosome segregation.
birth death process: A stochastic process in which individuals in a population give birth and die at specified rates, modeled as a continuous-time Markov chain.
branch lengths: The temporal duration or evolutionary distance represented by individual lineages in a phylogenetic tree.
branching pattern: The topological structure of a genealogical tree that describes how lineages diverge from common ancestors.
breast cancer outcome: The clinical result or prognosis of breast cancer patients, typically measured as disease recurrence, survival, or other disease-related events.
cancer: A disease characterized by uncontrolled proliferation of abnormal cells that can invade and spread to other tissues.
cancer stem cells: A subset of tumor cells with stem cell-like properties including self-renewal capacity and the ability to differentiate into multiple cell types within the tumor.
cell cycle defects: Abnormalities or malfunctions in the orderly progression and execution of events that comprise the cell cycle.
cell cycle genes: Genes whose expression is directly involved in the regulation and progression of cell cycle phases.
cell cycle progression: The orderly advancement through the sequential phases and checkpoints of the cell cycle.
cell proliferation: Definition The process of cell division and growth resulting in an increase in cell number. The process of cell division and multiplication resulting in an increase in cell number.
cellular fitness: The relative capacity of a cell to survive and maintain normal functional properties under given conditions.
CENP-E: A mitosis-specific motor protein that is linked to the centromere and functions to organize kinetochore-microtubule attachments and chromosome segregation during cell division.
centromere: A specialized chromosomal region that serves as the primary attachment site for spindle microtubules during cell division.
centrosome clustering: The process by which extra centrosomes in a cell aggregate together to form fewer functional spindle poles prior to or during cell division.
centrosomes: Cellular organelles that serve as the main microtubule-organizing centers (MTOCs) in animal cells, nucleating and organizing microtubules that form the mitotic spindle.
chemical carcinogens: Chemical agents capable of causing malignant transformation in cells and tissues.
cherry: A pair of sister tips (leaf nodes) that share an immediate common ancestor in a phylogenetic tree.
chromosomal imbalance: A condition in which the normal proportion or copy number of chromosomes is disrupted.
chromosomal instability: Definition An elevated per-division rate of chromosome missegregation resulting in ongoing changes to chromosome number in daughter cells.
chromosomal position: The physical location or coordinates of a gene or DNA sequence along a chromosome.
chromosomally unstable tumors: Tumors exhibiting elevated rates of chromosome mis-segregation and aneuploidy during cell division.
chromosome duplication: The process by which a chromosome is copied, resulting in the presence of an additional identical copy of that chromosome.
chromosome loss: The loss or elimination of an entire chromosome from a cell during division.
chromosome missegregation: Definition The failure of chromosomes to segregate properly during cell division, resulting in unequal distribution to daughter cells.
chromosome number: The total count of chromosomes present in a cell or organism.
circulating: Present and actively existing within a population at a given time, typically used to describe viral or pathogenic variants that are currently in circulation.
clade: A group of organisms comprising an ancestor and all of its descendants.
clinical trial: A research study conducted on human subjects to evaluate the safety, efficacy, or effectiveness of medical treatments or interventions.
complement: A system of proteins involved in immune responses that work together to enhance the immune system’s ability to clear pathogens and damaged cells.
complex models: Statistical models where the likelihood function is computationally prohibitive or intractable to evaluate directly, but for which data simulation is feasible.
complex phenotypes: Observable characteristics or traits that result from the combined effects of multiple genetic and environmental factors.
confounding: definition pending
confounding effect: The bias introduced into an analysis when a confounding variable influences the observed association between a predictor and outcome.
confounding variables: Variables that correlate with both an independent variable and an outcome variable in a study.
copy number: Definition The number of copies of a specific DNA sequence or chromosome present in a cell.
copy number variations (CNVs): Differences in the number of copies of DNA segments between individuals, resulting in variable quantities of genomic sequences.
cross validation: A statistical technique for evaluating the performance and accuracy of a model by partitioning data and testing the model on held-out portions.
data simulation: The process of generating artificial data according to the assumptions and parameters of a statistical model.
diploid: A cell or organism containing two complete sets of chromosomes, one from each parent.
disease susceptibility: The genetic predisposition or likelihood of an individual to develop a particular disease.
disomic strains: Yeast strains that contain two copies of a particular chromosome instead of the normal one, resulting in trisomy for that chromosome.
disseminated tumour cells: Tumor cells that have spread from the primary tumor site to distant tissues and organs.
driver events: Genetic or molecular alterations that confer selective advantages to cancer cells and actively contribute to tumor development and progression.
driver mutations: Specific mutations in genes that actively promote cancer development and progression by conferring growth advantages to tumor cells.
duplicated chromosomes: Chromosomes that are present in two copies within a cell instead of the normal single copy.
ecological causes: Factors related to interactions between organisms and their environment that influence evolutionary processes.
epithelial markers: Molecular markers characteristic of epithelial cells used to identify and detect epithelial-derived cells in tissue samples.
euploid: Having a balanced set of chromosomes in which each chromosome is present in the normal, expected number of copies for that organism.
euploid cells: Cells that contain the normal, balanced complement of chromosomes characteristic of the species.
evolution: Definition The process of cumulative change in the genetic composition of populations over time.
evolutionary divergences: The splitting of lineages from a common ancestor resulting in the formation of distinct evolutionary lineages.
evolutionary prediction: An inference about the future trajectory or successful variants of a population based on analysis of current genetic and evolutionary patterns.
expression states: Distinct configurations of gene expression patterns that cells can occupy, reflecting different functional or developmental conditions.
extant taxa: Organisms or species that are currently living or in existence.
extinction rates: The per-lineage probability or frequency at which species cease to exist over time.
fitness: Definition The relative ability of an organism or variant to survive and reproduce in a given environment.
fitness variation: Differences in the relative ability to survive and reproduce among individuals or variants within a population.
fossil record: The historical collection of preserved remains and traces of organisms from past geological time periods.
gene dosage: Definition The number of copies of a particular gene or genes present in a cell, which affects the amount of gene product produced.
gene expression: Definition The process by which information encoded in a gene is used to synthesize functional gene products, typically measured as mRNA or protein levels.
gene expression marker: A measurable pattern or level of gene expression used as an indicator or proxy for a biological state or mechanism.
gene expression variability: Heterogeneity in the level or pattern of transcript abundance across cells or populations of cells.
genealogical pattern: The structure and distribution of ancestral relationships within a population as represented by patterns of descent.
genetic alterations: Changes in DNA sequence or chromosome structure that modify genetic material.
genetic variation: Differences in DNA sequences and structure among individuals in a population.
glioblastoma subtype classifiers: Molecular features or gene signatures used to categorize glioblastomas into distinct biological subtypes based on their expression profiles.
glucose uptake: The process by which glucose is transported into cells from the extracellular environment.
growth medium: A nutrient-containing substance used to cultivate and maintain cells in culture.
haploid yeast: A yeast organism or strain containing a single complete set of chromosomes, with one copy of each chromosome.
hazard ratio: A statistical measure comparing the instantaneous rate of an outcome occurrence in one group relative to another group.
hypoxia: A condition of insufficient oxygen availability within tissue or cells.
immortalization: The acquisition by a cell or cell line of the ability to undergo unlimited proliferation.
immune cell infiltration: The presence and accumulation of immune cells within tumor tissue.
immune response: The collective biological mechanisms by which an organism defends itself against pathogens and abnormal cells.
immune surveillance: The process by which immune cells monitor and respond to abnormal or foreign cells in tissue.
in vitro: Biological processes or experiments conducted in a controlled environment outside a living organism, typically in cells or tissue cultures.
in vivo: Biological processes or experiments conducted within a living organism.
inference: The process of drawing conclusions about unknown parameters or models based on observed data using statistical methods.
influenza A/H3N2 virus: A subtype of influenza A virus characterized by specific hemagglutinin (H3) and neuraminidase (N2) surface proteins.
influenza season: A period of elevated influenza transmission in a population, typically occurring annually during winter months in temperate regions.
International HapMap project: A collaborative research project that catalogued human genetic variation and haplotype patterns across diverse populations worldwide.
intratumoral heterogeneity: Definition The presence of phenotypic, genotypic, and epigenetic variation among cells within a single tumor. The genetic, epigenetic, and phenotypic variation among cancer cells within a single tumor.
kinetochore: A protein structure assembled at the centromere of a chromosome that attaches to spindle microtubules during mitosis.
lagging chromosomes: Chromosomes that fail to migrate normally to spindle poles during anaphase, remaining positioned away from the poles and often becoming segregated abnormally.
likelihood function: A mathematical function that expresses the probability of observing the given data as a function of model parameters.
lineage: A sequence of organisms or genetic variants descending in a direct line of ancestry from a common ancestor.
liquid chromatography—tandem mass spectrometry: An analytical technique that combines liquid chromatography for separation with tandem mass spectrometry for identification and quantification of proteins or peptides.
local treatment: Therapeutic intervention directed at the primary tumor or localized disease site.
log2 ratios: The base-2 logarithm of the ratio between the abundance of a protein in one sample compared to another, used to represent relative fold changes.
longitudinal dynamics: The temporal changes and evolution of populations or systems observed over time through sequential measurements or observations.
lymphomas: Malignant tumors arising from lymphoid cells in the immune system.
macroevolutionary phenomena: Large-scale evolutionary events and patterns, such as the origin of major groups and changes in biodiversity over geological time.
macroevolutionary processes: The mechanisms and dynamics operating over long timescales that generate large-scale evolutionary change and patterns of biodiversity.
malignancy: The quality or state of being malignant; the characteristic of being capable of uncontrolled growth and invasion.
mass extinctions: Rapid, large-scale extinction events eliminating a substantial proportion of species across multiple lineages.
merotely: An abnormal microtubule–chromosome attachment in which a single kinetochore is attached to microtubules from both spindle poles. An erroneous kinetochore-microtubule attachment in which a single kinetochore is attached to microtubules originating from both spindle poles.
mesenchymal tissues: Non-epithelial connective tissues derived from mesoderm that form the structural framework of organs.
metabolic properties: The characteristic biochemical processes and metabolic functions of a cell or organism.
metagene: A composite variable derived by aggregating or combining the expression values of multiple individual genes into a single metric.
metastasis: The process by which tumor cells spread from the primary tumor to distant sites and establish new tumors.
metastatic relapse: The reappearance of cancer at distant sites after initial treatment of the primary tumor.
metric: A mathematical function that assigns a distance value between any two objects in a set, satisfying properties of non-negativity, identity, symmetry, and the triangle inequality.
microenvironment: The local cellular and acellular environment surrounding tumor cells, including stromal cells, immune cells, and extracellular matrix components.
microtubule: A structural polymer composed of α- and β-tubulin dimers that forms part of the cellular cytoskeleton and organizes the mitotic spindle.
microtubule chromosome attachment: The connection between spindle microtubules and kinetochores that mediates chromosome movement during mitosis.
minimal residual disease: Small numbers of tumor cells or micrometastases remaining in the body after treatment of the primary tumor.
mitosis: The process of nuclear division in which replicated chromosomes are separated to produce two daughter nuclei with identical genetic content.
model selection: The process of comparing and choosing among different candidate models to determine which best fits the observed data.
models: Definition Mathematical or statistical representations of the relationships among variables in a system or process.
molecular subtypes: Distinct categories of tumors defined by their characteristic patterns of gene expression or molecular alterations.
motor protein: A protein that uses energy from ATP hydrolysis to generate mechanical force and movement along cytoskeletal filaments.
multidimensional scaling: A statistical technique that maps high-dimensional distance data into a lower-dimensional space while preserving the relative distances between objects.
multipolar cell division: A cell division process in which three or more spindle poles organize simultaneously, resulting in the formation of three or more daughter cells with abnormal chromosome numbers.
multipolar spindle intermediate: A transient stage during cell division with multiple centrosomes in which the cell transiently exhibits a multipolar spindle configuration before centrosome clustering reduces it to a bipolar arrangement.
multipolar spindles: Abnormal mitotic spindles containing more than two poles, resulting in disorganized chromosome segregation.
mutation: A change in the nucleotide sequence of DNA that can be inherited by descendant organisms.
myc activation: The increased expression or activity of the Myc proto-oncogene, a transcription factor that promotes cell proliferation.
node label: A numerical or symbolic identifier assigned to a node in a tree that encodes structural information about the subtree rooted at that node.
node labeling: The process of assigning labels to nodes in a tree according to a systematic scheme that uniquely characterizes tree topology.
nonlinear heteroscedastic regression: A regression method that models nonlinear relationships between variables where the variance of the response changes as a function of the predictors.
oncogenic: Capable of inducing or promoting the transformation of cells into a malignant cancerous state.
oncogenic signaling: Cell signaling pathways that promote abnormal cell growth, survival, and proliferation characteristic of cancer.
open reading frames: Continuous sequences of DNA codons between start and stop signals that potentially encode proteins.
organismal fitness: The relative capacity of an organism to survive and reproduce under given conditions.
outcome association: The statistical relationship or correlation between a predictor variable (such as gene expression) and a defined clinical outcome.
outcome predictor: A variable or marker whose values can be used to forecast or estimate the probability of a particular clinical outcome.
p53 inactivation: Loss or reduction of function of the p53 tumor suppressor protein.
parameter estimation: The statistical process of inferring the values of parameters of a model based on observed data. Computed values or approximations of unknown parameters or quantities derived from data and a statistical model.
phenotype: Definition The observable physical and biochemical characteristics of an organism or cell that result from the interaction of its genotype with the environment. The observable physical and biochemical characteristics of organisms or cells that result from the interaction of their genotypes with the environment. Observable characteristics or properties of a cell or organism determined by its genotype and environment.
phenotypic changes: Alterations in the observable physical or biochemical characteristics of a cell or organism.
phylogenetic metric: A distance measure defined on the space of phylogenetic trees based on topological or structural properties.
phylogenetic tree: A branching diagram depicting the evolutionary relationships and common ancestry among a set of organisms or taxa.
precision medicine: An approach to medical treatment that tailors therapeutic interventions based on individual patient characteristics, including genetic and molecular profiles.
primary glioblastoma: A glioblastoma that develops de novo without progression from a pre-existing lower-grade tumor.
primary tumour: The original tumor from which cancer cells originate and first appear in the body.
progenitor lineage: The ancestral lineage that gives rise to a successful or dominant population of variants in a subsequent time period.
prognostic implications: The clinical significance of biological or molecular features in predicting patient outcomes or disease course.
proliferation marker: A molecular indicator whose expression level reflects the rate or extent of cell division and growth.
proliferative disadvantage: A reduction in the ability of cells to divide and increase in number compared to normal cells.
protein abundance: The quantity or concentration of a specific protein present in a cell or sample.
protein composition: The relative amounts and types of proteins present in a cell or cellular compartment.
protein folding: The process by which a protein molecule assumes its three-dimensional structure, guided by chemical and physical laws.
protein production: The synthesis and generation of proteins within cells through translation of mRNA. The process by which cells build proteins through translation of messenger RNA using ribosomes and transfer RNAs.
proteome: The complete set of all proteins expressed by a cell, tissue, or organism.
putative regulators: Genes or proteins that are presumed or inferred to control the activity or expression of other genes or cellular processes.
random signature: A gene expression signature constructed by random selection of genes without regard to their biological relevance or functional relationship to any particular process.
relative fitness: The fitness of one variant or organism measured relative to other variants or organisms in the same population.
replicative senescence: A state of permanent cell cycle arrest in which cells lose the capacity to divide after a limited number of divisions.
root node: The single node in a rooted tree that serves as the starting point with no parent node, representing the most recent common ancestor.
seasonal influenza: Influenza that occurs in a predictable, recurring seasonal pattern.
selection pressure: Differential environmental conditions in which some variants have higher fitness than others.
sensitivity: The degree of responsiveness or susceptibility of cells to external stimuli, conditions, or treatments.
sequence: In genomics, the linear order of nucleotides in a DNA or RNA molecule.
silac: A quantitative proteomic technique that uses stable isotope labeling of amino acids in cell culture to measure relative protein abundance between samples.
single cell rna seq: A molecular technique that measures gene expression in individual cells rather than in bulk tissue, allowing quantification of transcript abundance across single-cell genomes.
single nucleotide polymorphisms (SNPs): Locations in the genome where a single nucleotide varies between individuals in a population.
small effect mutations: Mutations that individually produce minimal changes in fitness or phenotype compared to the cumulative effects of all mutations.
spatial distribution: The arrangement and localization of entities or properties across physical space within a defined region or structure.
spatial heterogeneity: Variation in genetic, molecular, or phenotypic characteristics of cancer cells across different physical locations within a tumor.
speciation rates: The per-lineage probability or frequency at which populations diverge to form new species over time.
spindle assembly checkpoint: A cell cycle control mechanism that delays anaphase progression until all chromosomes are properly attached to spindle microtubules.
spontaneous tumor formation: The development of malignant tumors arising without intentional external induction or experimental manipulation.
stat1 inactivation: Loss or reduction of function of the Stat1 signaling molecule, a transcription factor in interferon response pathways.
stat1 signaling: The signal transduction pathway initiated by Stat1, a transcription factor activated by interferon and other cytokine signals.
statistical association: A measurable relationship or correlation between two variables that can be quantified through statistical analysis.
statistical significance: A determination that an observed association or difference is unlikely to have occurred by chance alone, typically assessed using a predefined probability threshold.
stemness: The quality or state of possessing properties characteristic of stem cells, including self-renewal capacity and multipotency.
strain: A subpopulation or variant of a species distinguished by particular genetic, phenotypic, or antigenic characteristics.
subclone: A population of cancer cells within a tumor that shares a common genetic origin but possesses distinct mutations or alterations relative to other subpopulations.
subtree: A connected subgraph of a tree that consists of a node and all of its descendants.
summary statistics: Reduced summaries of data that capture key information relevant to inference, used in ABC to compare observed and simulated data without calculating full likelihoods.
symmetric configuration: A tree structure possessing symmetry properties, such as balanced branching patterns or identical topology on left and right subtrees.
systemic treatment: Therapeutic intervention that targets the entire body to treat cancer cells throughout the organism.
temporal distribution: The arrangement and occurrence of entities or events across time.
temporal heterogeneity: Variation in genetic, molecular, or phenotypic characteristics among cancer cells that arises or changes over different time periods.
therapy response: The reaction or outcome of cancer cells and tumors following exposure to therapeutic treatment.
tmt mass spectrometry: A quantitative mass spectrometry technique using isobaric tandem mass tags to label and measure relative protein abundance across multiple samples.
transcript: An RNA molecule produced by transcription of a DNA gene, serving as the intermediate between genetic information and protein synthesis.
transcriptional programs: Coordinated sets of genes that are regulated together to implement specific cellular functions or responses.
transcriptome: The complete set of mRNA molecules expressed in a particular cell, tissue, or organism at a given time.
tree asymmetry: A measure of the degree to which a tree deviates from balanced or symmetric branching patterns.
tree balance: The relative evenness or symmetry in the branching patterns of a phylogenetic tree, reflecting how splits are distributed across lineages.
tree imbalance: A quantitative measure of how unequally the descendants are distributed across different branches of a tree.
tree isomorphism: A bijective mapping between the nodes of two trees that preserves their structural relationships, indicating the trees have identical topology.
tree shape: Definition The overall geometric structure and branching pattern of a phylogenetic tree determined by its topology, branch lengths, and balance.
trisomic cells: Cells containing three copies of a particular chromosome instead of the normal two. Cell lines or populations consisting of cells that carry three copies of a specific chromosome.
tumor: Definition An abnormal growth of cells resulting from uncontrolled cell proliferation.
tumor cells: Cells that have acquired the ability to divide uncontrollably and form malignant neoplasms.
tumor evolution: The process by which cancer cells within a tumor accumulate genetic and epigenetic changes over time, leading to the emergence of diverse subclones and altered characteristics.
tumor suppression: The inhibition or prevention of malignant tumor development and progression.
tumor suppressor: A gene or gene product that inhibits cell proliferation and prevents the development of malignant tumors.
tumorigenesis: The process of malignant tumor formation and development.
tumors: Definition Abnormal growths of tissue composed of cells that have lost normal growth control, characterized by uncontrolled proliferation.
wild type cells: Cells with the normal, unmutated genotype that serve as a reference or control against which variant strains are compared.
yule model: A stochastic branching process model where new lineages arise from existing lineages at a constant rate with no extinction.