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Protocols

GIMME specifications

Information


Unique identifier OMICS_06819
Name GIMME
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

Versioning


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Publication for Gene Inactivity Moderated by Metabolism and Expression

GIMME citations

 (79)
library_books

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

2018
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 […]

library_books

Bilingual Contexts Modulate the Inhibitory Control Network

2018
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 […]

library_books

Perspectives on Systems Modeling of Human Peripheral Blood Mononuclear Cells

2018
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 […]

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

2017
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 […]

call_split

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

2017
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 […]

library_books

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

2017
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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