PathWeigh – Quantifying the Behavior of Biochemical Pathway Cascades

Dani Livne; Sol Efroni

doi:10.1007/978-3-031-07802-6_29

PathWeigh – Quantifying the Behavior of Biochemical Pathway Cascades

Dani Livne, Sol Efroni

Research output: Chapter in Book/Report/Conference proceeding › Conference contribution › peer-review

1 Scopus citations

Abstract

Biochemical pathways analysis is an effective tool for understanding changes in gene expression data and associating such changes with cellular phenotypes. Pathway research aims to identify associated proteins within a cell using pathways and at building new pathways from a group of molecules of interest. Using pathway-based methods we gain insight into different functions of relevant molecules and find direct and indirect relations between them. We present PathWeigh, a Python-based tool for pathway analysis and graph presentation. The tool is open-sourced, extendable and runtime efficient. PathWeigh is available at https://github.org/zurkin1/Pathweigh and is released under MIT license. A sample Python notebook is provided with examples of running the tool.

Original language	English
Title of host publication	Bioinformatics and Biomedical Engineering - 9th International Work-Conference, IWBBIO 2022, Proceedings
Editors	Ignacio Rojas, Olga Valenzuela, Fernando Rojas, Luis Javier Herrera, Francisco Ortuño
Publisher	Springer Science and Business Media Deutschland GmbH
Pages	346-352
Number of pages	7
ISBN (Print)	9783031078019
DOIs	https://doi.org/10.1007/978-3-031-07802-6_29
State	Published - 2022
Event	9th International Work-Conference on Bioinformatics and Biomedical Engineering, IWBBIO 2022 - Gran Canaria, Spain Duration: 27 Jun 2022 → 30 Jun 2022

Publication series

Name	Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)
Volume	13347 LNBI
ISSN (Print)	0302-9743
ISSN (Electronic)	1611-3349

Conference

Conference	9th International Work-Conference on Bioinformatics and Biomedical Engineering, IWBBIO 2022
Country/Territory	Spain
City	Gran Canaria
Period	27/06/22 → 30/06/22

Bibliographical note

Publisher Copyright:
© 2022, Springer Nature Switzerland AG.

Keywords

Machine learning
Pathway analysis
RNA sequencing

Access to Document

10.1007/978-3-031-07802-6_29

Cite this

Livne, D., & Efroni, S. (2022). PathWeigh – Quantifying the Behavior of Biochemical Pathway Cascades. In I. Rojas, O. Valenzuela, F. Rojas, L. J. Herrera, & F. Ortuño (Eds.), Bioinformatics and Biomedical Engineering - 9th International Work-Conference, IWBBIO 2022, Proceedings (pp. 346-352). (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); Vol. 13347 LNBI). Springer Science and Business Media Deutschland GmbH. https://doi.org/10.1007/978-3-031-07802-6_29

Livne, Dani ; Efroni, Sol. / PathWeigh – Quantifying the Behavior of Biochemical Pathway Cascades. Bioinformatics and Biomedical Engineering - 9th International Work-Conference, IWBBIO 2022, Proceedings. editor / Ignacio Rojas ; Olga Valenzuela ; Fernando Rojas ; Luis Javier Herrera ; Francisco Ortuño. Springer Science and Business Media Deutschland GmbH, 2022. pp. 346-352 (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)).

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Livne, D & Efroni, S 2022, PathWeigh – Quantifying the Behavior of Biochemical Pathway Cascades. in I Rojas, O Valenzuela, F Rojas, LJ Herrera & F Ortuño (eds), Bioinformatics and Biomedical Engineering - 9th International Work-Conference, IWBBIO 2022, Proceedings. Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), vol. 13347 LNBI, Springer Science and Business Media Deutschland GmbH, pp. 346-352, 9th International Work-Conference on Bioinformatics and Biomedical Engineering, IWBBIO 2022, Gran Canaria, Spain, 27/06/22. https://doi.org/10.1007/978-3-031-07802-6_29

PathWeigh – Quantifying the Behavior of Biochemical Pathway Cascades. / Livne, Dani; Efroni, Sol.
Bioinformatics and Biomedical Engineering - 9th International Work-Conference, IWBBIO 2022, Proceedings. ed. / Ignacio Rojas; Olga Valenzuela; Fernando Rojas; Luis Javier Herrera; Francisco Ortuño. Springer Science and Business Media Deutschland GmbH, 2022. p. 346-352 (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); Vol. 13347 LNBI).

Research output: Chapter in Book/Report/Conference proceeding › Conference contribution › peer-review

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Livne D, Efroni S. PathWeigh – Quantifying the Behavior of Biochemical Pathway Cascades. In Rojas I, Valenzuela O, Rojas F, Herrera LJ, Ortuño F, editors, Bioinformatics and Biomedical Engineering - 9th International Work-Conference, IWBBIO 2022, Proceedings. Springer Science and Business Media Deutschland GmbH. 2022. p. 346-352. (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)). doi: 10.1007/978-3-031-07802-6_29

PathWeigh – Quantifying the Behavior of Biochemical Pathway Cascades

Abstract

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Keywords

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