Time-window analysis of developmental gene expression data with multiple genetic backgrounds

Tamir Tuller; Efrat Oron; Erez Makavy; Daniel A. Chamovitz; Benny Chor

doi:10.1007/11557067_5

Time-window analysis of developmental gene expression data with multiple genetic backgrounds

Tamir Tuller, Efrat Oron, Erez Makavy, Daniel A. Chamovitz, Benny Chor

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

2 Scopus citations

Abstract

We study gene expression data, derived from developing tissues, under multiple genetic backgrounds (mutations). Motivated by the perceived behavior under these background, our main goals are to explore time windows questions: 1. Find a large set of genes that have a similar behavior in two different genetic backgrounds, under an appropriate time shift. 2. Find a model that approximates the dynamics of a gene network in developing tissues at different continuous time windows. We first explain the biological significance of these problems, and then explore their computational complexity, which ranges from polynomial to NP-hard. We developed algorithms and heuristics for the different problems, and ran those on synthetic and biological data, with very encouraging results.

Original language	English
Title of host publication	Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)
Pages	53-64
Number of pages	12
DOIs	https://doi.org/10.1007/11557067_5
State	Published - 1 Dec 2005
Externally published	Yes
Event	5th International Workshop on Algorithms in Bioinformatics, WABI 2005 - Mallorca, Spain Duration: 3 Oct 2005 → 6 Oct 2005

Publication series

Name	Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)
Volume	3692 LNBI
ISSN (Print)	0302-9743
ISSN (Electronic)	1611-3349

Conference

Conference	5th International Workshop on Algorithms in Bioinformatics, WABI 2005
Country/Territory	Spain
City	Mallorca
Period	3/10/05 → 6/10/05

ASJC Scopus subject areas

Theoretical Computer Science
General Computer Science

Access to Document

10.1007/11557067_5

Cite this

Tuller, T., Oron, E., Makavy, E., Chamovitz, D. A., & Chor, B. (2005). Time-window analysis of developmental gene expression data with multiple genetic backgrounds. In Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics) (pp. 53-64). (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); Vol. 3692 LNBI). https://doi.org/10.1007/11557067_5

Tuller, Tamir ; Oron, Efrat ; Makavy, Erez et al. / Time-window analysis of developmental gene expression data with multiple genetic backgrounds. Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). 2005. pp. 53-64 (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)).

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title = "Time-window analysis of developmental gene expression data with multiple genetic backgrounds",

abstract = "We study gene expression data, derived from developing tissues, under multiple genetic backgrounds (mutations). Motivated by the perceived behavior under these background, our main goals are to explore time windows questions: 1. Find a large set of genes that have a similar behavior in two different genetic backgrounds, under an appropriate time shift. 2. Find a model that approximates the dynamics of a gene network in developing tissues at different continuous time windows. We first explain the biological significance of these problems, and then explore their computational complexity, which ranges from polynomial to NP-hard. We developed algorithms and heuristics for the different problems, and ran those on synthetic and biological data, with very encouraging results.",

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Tuller, T, Oron, E, Makavy, E, Chamovitz, DA & Chor, B 2005, Time-window analysis of developmental gene expression data with multiple genetic backgrounds. in Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), vol. 3692 LNBI, pp. 53-64, 5th International Workshop on Algorithms in Bioinformatics, WABI 2005, Mallorca, Spain, 3/10/05. https://doi.org/10.1007/11557067_5

Time-window analysis of developmental gene expression data with multiple genetic backgrounds. / Tuller, Tamir; Oron, Efrat; Makavy, Erez et al.
Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). 2005. p. 53-64 (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); Vol. 3692 LNBI).

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

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Tuller T, Oron E, Makavy E, Chamovitz DA, Chor B. Time-window analysis of developmental gene expression data with multiple genetic backgrounds. In Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). 2005. p. 53-64. (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)). doi: 10.1007/11557067_5

Time-window analysis of developmental gene expression data with multiple genetic backgrounds

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