DARTpaths, an in silico platform to investigate molecular mechanisms of compounds

Diksha Bhalla; Marvin N Steijaert; Eefje S Poppelaars; Marc Teunis; Monique van der Voet; Marie Corradi; Elisabeth Dévière; Luke Noothout; Wilco Tomassen; Martijn Rooseboom; Richard A Currie; Cyrille Krul; Raymond Pieters; Vera van Noort; Marjolein Wildwater

doi:10.1093/bioinformatics/btac767

DARTpaths, an in silico platform to investigate molecular mechanisms of compounds

Diksha Bhalla, Marvin N Steijaert, Eefje S Poppelaars, Marc Teunis, Monique van der Voet, Marie Corradi, Elisabeth Dévière, Luke Noothout, Wilco Tomassen, Martijn Rooseboom, Richard A Currie, Cyrille Krul, Raymond Pieters, Vera van Noort^*, Marjolein Wildwater^*

^*Corresponding author for this work

Research output: Contribution to journal › Article › Academic › peer-review

Abstract

SUMMARY: Xpaths is a collection of algorithms that allow for the prediction of compound-induced molecular mechanisms of action by integrating phenotypic endpoints of different species; and proposes follow-up tests for model organisms to validate these pathway predictions. The Xpaths algorithms are applied to predict developmental and reproductive toxicity (DART) and implemented into an in silico platform, called DARTpaths.

AVAILABILITY AND IMPLEMENTATION: All code is available on GitHub https://github.com/Xpaths/dartpaths-app under Apache license 2.0, detailed overview with demo is available at https://www.vivaltes.com/dartpaths/.

SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Original language	English
Article number	btac767
Pages (from-to)	1-3
Number of pages	3
Journal	Bioinformatics
Volume	39
Issue number	1
Early online date	8 Dec 2022
DOIs	https://doi.org/10.1093/bioinformatics/btac767
Publication status	Published - 1 Jan 2023

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btac767Final published version, 228 KBLicence: CC BY

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Bhalla, D., Steijaert, M. N., Poppelaars, E. S., Teunis, M., van der Voet, M., Corradi, M., Dévière, E., Noothout, L., Tomassen, W., Rooseboom, M., Currie, R. A., Krul, C., Pieters, R., van Noort, V., & Wildwater, M. (2023). DARTpaths, an in silico platform to investigate molecular mechanisms of compounds. Bioinformatics, 39(1), 1-3. Article btac767. https://doi.org/10.1093/bioinformatics/btac767

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title = "DARTpaths, an in silico platform to investigate molecular mechanisms of compounds",

abstract = "SUMMARY: Xpaths is a collection of algorithms that allow for the prediction of compound-induced molecular mechanisms of action by integrating phenotypic endpoints of different species; and proposes follow-up tests for model organisms to validate these pathway predictions. The Xpaths algorithms are applied to predict developmental and reproductive toxicity (DART) and implemented into an in silico platform, called DARTpaths.AVAILABILITY AND IMPLEMENTATION: All code is available on GitHub https://github.com/Xpaths/dartpaths-app under Apache license 2.0, detailed overview with demo is available at https://www.vivaltes.com/dartpaths/.SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.",

author = "Diksha Bhalla and Steijaert, {Marvin N} and Poppelaars, {Eefje S} and Marc Teunis and {van der Voet}, Monique and Marie Corradi and Elisabeth D{\'e}vi{\`e}re and Luke Noothout and Wilco Tomassen and Martijn Rooseboom and Currie, {Richard A} and Cyrille Krul and Raymond Pieters and {van Noort}, Vera and Marjolein Wildwater",

note = "Publisher Copyright: {\textcopyright} The Author(s) 2022. Published by Oxford University Press.",

year = "2023",

month = jan,

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doi = "10.1093/bioinformatics/btac767",

language = "English",

volume = "39",

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Bhalla, D, Steijaert, MN, Poppelaars, ES, Teunis, M, van der Voet, M, Corradi, M, Dévière, E, Noothout, L, Tomassen, W, Rooseboom, M, Currie, RA, Krul, C, Pieters, R, van Noort, V & Wildwater, M 2023, 'DARTpaths, an in silico platform to investigate molecular mechanisms of compounds', Bioinformatics, vol. 39, no. 1, btac767, pp. 1-3. https://doi.org/10.1093/bioinformatics/btac767

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T1 - DARTpaths, an in silico platform to investigate molecular mechanisms of compounds

AU - Bhalla, Diksha

AU - Steijaert, Marvin N

AU - Poppelaars, Eefje S

AU - Teunis, Marc

AU - van der Voet, Monique

AU - Corradi, Marie

AU - Dévière, Elisabeth

AU - Noothout, Luke

AU - Tomassen, Wilco

AU - Rooseboom, Martijn

AU - Currie, Richard A

AU - Krul, Cyrille

AU - Pieters, Raymond

AU - van Noort, Vera

AU - Wildwater, Marjolein

PY - 2023/1/1

Y1 - 2023/1/1

N2 - SUMMARY: Xpaths is a collection of algorithms that allow for the prediction of compound-induced molecular mechanisms of action by integrating phenotypic endpoints of different species; and proposes follow-up tests for model organisms to validate these pathway predictions. The Xpaths algorithms are applied to predict developmental and reproductive toxicity (DART) and implemented into an in silico platform, called DARTpaths.AVAILABILITY AND IMPLEMENTATION: All code is available on GitHub https://github.com/Xpaths/dartpaths-app under Apache license 2.0, detailed overview with demo is available at https://www.vivaltes.com/dartpaths/.SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

AB - SUMMARY: Xpaths is a collection of algorithms that allow for the prediction of compound-induced molecular mechanisms of action by integrating phenotypic endpoints of different species; and proposes follow-up tests for model organisms to validate these pathway predictions. The Xpaths algorithms are applied to predict developmental and reproductive toxicity (DART) and implemented into an in silico platform, called DARTpaths.AVAILABILITY AND IMPLEMENTATION: All code is available on GitHub https://github.com/Xpaths/dartpaths-app under Apache license 2.0, detailed overview with demo is available at https://www.vivaltes.com/dartpaths/.SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

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DO - 10.1093/bioinformatics/btac767

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JO - Bioinformatics

JF - Bioinformatics

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ER -

DARTpaths, an in silico platform to investigate molecular mechanisms of compounds

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