ATP	adenosine triphosphate
BOF	biomass objective function
CCLE	Cancer Cell Line Encyclopedia
COBRA	constraint-based reconstruction and analysis
CORDA	cost optimization reaction dependency assessment
COVID	coronavirus disease
EBI	European Bioinformatics Institute
EGA	European Genome-Phenome Archive
ENA	European Nucleotide Archive
FANTOM5	Functional Annotation of the Mammalian Genome 5
FASTCC	fast consistency checking
FBA	flux balance analysis
FVA	flux variability analysis
GEM	genome-scale metabolic model
GEO	Genome Expression Omnibus
GIM3E	gene inactivation moderated by metabolism, metabolomics and expression
GIMME	gene inactivity moderated by metabolism and expression
GIMMEp	gene inactivity moderated by metabolism and expression by proteome
GPR	gene-protein-reaction
GTEx	Genotype-Tissue Expression database
HPA	Human Protein Atlas
iMAT	integrative metabolic analysis tool
INIT	integrative network inference for tissues
LP	linear programming
MADE	metabolic adjustment by differential expression
MBA	model building algorithm
mCADRE	metabolic context-specificity assessed by deterministic reaction evaluation
METRADE	MEtabolic and TRanscriptomics ADaptation Estimator
MILP	mixed integer linear programming
MIQP	mixed integer quadratic programming
MTA	metabolic transformation algorithm
NCBI	National Center for Biotechnology Information
NGS	next-generation sequencing
NHBE	normal human bronchial epithelial
PCA	principal component analysis
PDC	Proteomic Data Commons
pFBA	parsimonious flux balance analysis
PRIME	personalized reconstructIon of metabolic models
QP	quadratic programming
RegrEx	regularized context-specific model extraction method
RIPTide	reaction inclusion by parsimony and transcript distribution
RMetD2	relative metabolic differences version 2
RMF	required metabolic function
RNA-seq	RNA sequencing
SARS-CoV-2	Severe acute respiratory syndrome coronavirus 2
scRNA-seq	single cell RNA sequencing
SRA	Sequence Read Archive
TCGA	The Cancer Genome Atlas
TIGER	toolbox for integrating genome-scale metabolism, expression, and regulation
tINIT	task-driven integrative network inference for tissues
TPM	transcripts per million
VBOF	viral biomass objective function
WBM	whole-body model