ITM Probe statistics

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Citations per year

Number of citations per year for the bioinformatics software tool ITM Probe

Tool usage distribution map

This map represents all the scientific publications referring to ITM Probe per scientific context
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Associated diseases


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ITM Probe specifications


Unique identifier OMICS_24196
Name ITM Probe
Interface Web user interface
Restrictions to use None
Output data A list of the top ranking nodes together with an image of the sub-network consisting of these nodes.
Computer skills Basic
Stability Stable
Maintained Yes


  • person_outline Yi-Kuo Yu


Unique identifier OMICS_24196
Name ITM Probe
Software type Application/Script
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Programming languages Python
Computer skills Advanced
Version 1.5.4
Stability Stable
Maintained Yes


No version available


  • person_outline Yi-Kuo Yu

Publications for ITM Probe

ITM Probe citations


Identifying diseases related metabolites using random walk

BMC Bioinformatics
PMCID: 5907145
PMID: 29671398
DOI: 10.1186/s12859-018-2098-1

[…] the similarity of diseases by gene functional network. Gene functional network can provide the information flow which can be used to calculate the disease similarity. To analyze the information flow, ITM Probe [] is employed which included three models: absorbing, emitting and channel. Each disease is a boundary node in the network, besides, each gene is a transient node.Each disease has several r […]


InfAcrOnt: calculating cross ontology term similarities using information flow by a random walk

BMC Genomics
PMCID: 5780854
PMID: 29363423
DOI: 10.1186/s12864-017-4338-6

[…] m walk ends at, emitting model assigns nodes the random walk starts from and channel model integrates both absorbing and emitting models for directed information flow.Information Transduction Module (ITM) Probe [] program has implemented all of these three models. It outputs the expected number of visits to each transient and sink node by random walker originated from every node. The ITM takes an […]


Measuring disease similarity and predicting disease related ncRNAs by a novel method

BMC Med Genomics
PMCID: 5751624
PMID: 29297338
DOI: 10.1186/s12920-017-0315-9

[…] In this study, we designed a novel method to compute disease similarity by modelling the information flow in the comprehensive GFN. In the previous study, a tool called ITM Probe [] was created for analyzing information flow in the network based on random walk with damping. Currently, three models involving absorbing, emitting, and channel were employed in ITM Probe. […]


Using biological networks to integrate, visualize and analyze genomics data

PMCID: 4818439
PMID: 27036106
DOI: 10.1186/s12711-016-0205-1

[…] rmation flow analysis, a computational biology method that uses random walk algorithms to model how signals flow through large networks. One example of software that performs this type of analysis is ITM Probe [], which is also available as a Cytoscape App []. In ITM Probe, the user can define source nodes (nodes that emit information, e.g., receptors) and sink nodes (target nodes that absorb info […]


Perturbation Centrality and Turbine: A Novel Centrality Measure Obtained Using a Versatile Network Dynamics Tool

PLoS One
PMCID: 3804472
PMID: 24205090
DOI: 10.1371/journal.pone.0078059

[…] rk studies , . A number of programs have been developed for the calculation of certain aspects of network dynamics, such as network simulation tools based on Boolean dynamics –, the random-walk based ITM-Probe , the law of mass action-based PerturbationAnalyzer , or the biological system modeling tool, BIOCHAM . However, to our knowledge, no stand-alone program exists, which can easily integrate a […]


CytoITMprobe: a network information flow plugin for Cytoscape

BMC Res Notes
PMCID: 3514294
PMID: 22587372
DOI: 10.1186/1756-0500-5-237

[…] Subnetwork nodes are selected through a ranking attribute, which assigns a numerical value from ITM Probe results to each node. The nodes are listed in descending order of the ranking attribute and top nodes are displayed as the ITM subnetwork. The number of top nodes is determined by specifying […]

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ITM Probe institution(s)
National Center for Biotechnology Information National Library of Medicine National Institutes of Health, Bethesda, MD, USA
ITM Probe funding source(s)
Supported by the Intramural Research Program of the National Library of Medicine at the National Institutes of Health.

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