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GIMME specifications


Unique identifier OMICS_06819
Alternative name Gene Inactivity Moderated by Metabolism and Expression
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages MATLAB
Computer skills Advanced
Stability Stable
Maintained Yes


No version available

Publication for Gene Inactivity Moderated by Metabolism and Expression

GIMME citations


Chromatin Accessibility Based Characterization of the Gene Regulatory Network Underlying Plasmodium falciparum Blood Stage Development

PMCID: 5899830
PMID: 29649445
DOI: 10.1016/j.chom.2018.03.007

[…] For de novo motif identification we used gimme motifs from the GimmeMotifs package (v0.11.0; ). Numerous de novo motif searches were performed on individual time points and using different number of clusters ranging from 4 to 16 in regions o […]


Bilingual Contexts Modulate the Inhibitory Control Network

Front Psychol
PMCID: 5881103
PMID: 29636713
DOI: 10.3389/fpsyg.2018.00395

[…] linguals, we made use of recent advances in connectivity modeling (extended unified structural equation modeling, euSEM) (; , ; ; ) and a recently developed Group Iterative Multiple Model Estimation (GIMME), an automatic and freely distributed MATLAB-based program.The euSEM approach has provided a flexible and efficient method for analyzing the causal interactions of brain regions for cognitive fu […]


Perspectives on Systems Modeling of Human Peripheral Blood Mononuclear Cells

Front Mol Biosci
PMCID: 5767226
PMID: 29376056
DOI: 10.3389/fmolb.2017.00096

[…] data such as transcriptome, proteome and metabolome/fluxome (Blazier and Papin, ). Several algorithms were designed that allow integration and contextualization of GEMs based on expression datasets. GIMME designed by Becker and Palsson considers a single gene expression dataset and compares it to a certain threshold, it subsequently lists active and inactive reactions within a GEM model (Becker a […]


Low Concentrations of Vitamin C Reduce the Synthesis of Extracellular Polymers and Destabilize Bacterial Biofilms

Front Microbiol
PMCID: 5748153
PMID: 29317857
DOI: 10.3389/fmicb.2017.02599
call_split See protocol

[…] intensities from biological replicates (three replicates for each sodium ascorbate concentration and 2 for the control) were averaged and used to constrain the fluxes in the associated reaction using Gene Inactivity Moderated by Metabolism and Expression (GIMME) (). GIMME was run using 90% of the objective function threshold and 50th percentile of proteins expression level. Since properly constrai […]


An integrated computational and experimental study uncovers FUT9 as a metabolic driver of colorectal cancer

Mol Syst Biol
PMCID: 5740504
PMID: 29196508
DOI: 10.15252/msb.20177739
call_split See protocol

[…] FUT9 inactivation, we performed a Minimization Of Metabolic Adjustment (MOMA) (Segrè et al, ) analysis to predict the metabolic state after FUT9 KD in late‐stage colorectal cancers, simulated by the Gene Inactivity Moderated by Metabolism and Expression (GIMME) algorithm (Becker & Palsson, ) (). This pinpoints reactions whose flux is predicted to be most afflicted by FUT9 inactivation in advanced […]


In silico gene essentiality analysis of polyamine biosynthesis reveals APRT as a potential target in cancer

Sci Rep
PMCID: 5662602
PMID: 29084986
DOI: 10.1038/s41598-017-14067-8

[…] nly based on gene expression data. In essence, these methods aim to select the consistent subset of reactions active for a given cancer sample. A non-exhaustive list of this type of methods includes: GIMME, iMAT, FastCore and others. With these approaches, the construction of different cancer-specific metabolic networks is now possible.However, less work has been directed to contextualize and enri […]


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GIMME institution(s)
Department of Bioengineering, University of California San Diego, La Jolla, CA, USA

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