Geometric Interpretation of Gene Expression by Sparse Reconstruction of Transcript Profiles

Yosef Prat; Menachem Fromer; Michal Linial; Nathan Linial

doi:10.1007/978-3-642-20036-6_33

Geometric Interpretation of Gene Expression by Sparse Reconstruction of Transcript Profiles

Yosef Prat
, Menachem Fromer
, Michal Linial^*
, Nathan Linial

^*Corresponding author for this work

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

Abstract

Large-scale data collection technologies have come to play a central role in biological and biomedical research in the last decade. Consequently, it has become a major goal of functional genomics to develop, based on such data, a comprehensive description of the functions and interactions of all genes and proteins in a genome. Most large-scale biological data, including gene expression profiles, are usually represented by a matrix, where n genes are examined in d experiments. Here, we view such data as a set of n points (vectors) in d-dimensional space, each of which represents the profile of a given gene over d different experimental conditions. Many known methods that have yielded meaningful biological insights seek geometric or algebraic features of these vectors.

Original language	English
Title of host publication	Research in Computational Molecular Biology - 15th Annual International Conference, RECOMB 2011, Proceedings
Editors	Vineet Bafna, S. Cenk Sahinalp
Publisher	Springer Verlag
Pages	355-357
Number of pages	3
ISBN (Print)	9783642200359
DOIs	https://doi.org/10.1007/978-3-642-20036-6_33
State	Published - 2011
Event	15th Annual International Conference on Research in Computational Molecular Biology, RECOMB 2011 - Vancouver, Canada Duration: 28 Mar 2011 → 31 Mar 2011

Publication series

Name	Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)
Volume	6577 LNBI
ISSN (Print)	0302-9743
ISSN (Electronic)	1611-3349

Conference

Conference	15th Annual International Conference on Research in Computational Molecular Biology, RECOMB 2011
Country/Territory	Canada
City	Vancouver
Period	28/03/11 → 31/03/11

Bibliographical note

Publisher Copyright:
© 2011, Springer-Verlag Berlin Heidelberg.

Access to Document

10.1007/978-3-642-20036-6_33

Cite this

Prat, Y., Fromer, M., Linial, M., & Linial, N. (2011). Geometric Interpretation of Gene Expression by Sparse Reconstruction of Transcript Profiles. In V. Bafna, & S. C. Sahinalp (Eds.), Research in Computational Molecular Biology - 15th Annual International Conference, RECOMB 2011, Proceedings (pp. 355-357). (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); Vol. 6577 LNBI). Springer Verlag. https://doi.org/10.1007/978-3-642-20036-6_33

Prat, Yosef ; Fromer, Menachem ; Linial, Michal et al. / Geometric Interpretation of Gene Expression by Sparse Reconstruction of Transcript Profiles. Research in Computational Molecular Biology - 15th Annual International Conference, RECOMB 2011, Proceedings. editor / Vineet Bafna ; S. Cenk Sahinalp. Springer Verlag, 2011. pp. 355-357 (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)).

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abstract = "Large-scale data collection technologies have come to play a central role in biological and biomedical research in the last decade. Consequently, it has become a major goal of functional genomics to develop, based on such data, a comprehensive description of the functions and interactions of all genes and proteins in a genome. Most large-scale biological data, including gene expression profiles, are usually represented by a matrix, where n genes are examined in d experiments. Here, we view such data as a set of n points (vectors) in d-dimensional space, each of which represents the profile of a given gene over d different experimental conditions. Many known methods that have yielded meaningful biological insights seek geometric or algebraic features of these vectors.",

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Prat, Y, Fromer, M, Linial, M & Linial, N 2011, Geometric Interpretation of Gene Expression by Sparse Reconstruction of Transcript Profiles. in V Bafna & SC Sahinalp (eds), Research in Computational Molecular Biology - 15th Annual International Conference, RECOMB 2011, Proceedings. Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), vol. 6577 LNBI, Springer Verlag, pp. 355-357, 15th Annual International Conference on Research in Computational Molecular Biology, RECOMB 2011, Vancouver, Canada, 28/03/11. https://doi.org/10.1007/978-3-642-20036-6_33

Geometric Interpretation of Gene Expression by Sparse Reconstruction of Transcript Profiles. / Prat, Yosef; Fromer, Menachem; Linial, Michal et al.
Research in Computational Molecular Biology - 15th Annual International Conference, RECOMB 2011, Proceedings. ed. / Vineet Bafna; S. Cenk Sahinalp. Springer Verlag, 2011. p. 355-357 (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); Vol. 6577 LNBI).

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

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AB - Large-scale data collection technologies have come to play a central role in biological and biomedical research in the last decade. Consequently, it has become a major goal of functional genomics to develop, based on such data, a comprehensive description of the functions and interactions of all genes and proteins in a genome. Most large-scale biological data, including gene expression profiles, are usually represented by a matrix, where n genes are examined in d experiments. Here, we view such data as a set of n points (vectors) in d-dimensional space, each of which represents the profile of a given gene over d different experimental conditions. Many known methods that have yielded meaningful biological insights seek geometric or algebraic features of these vectors.

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Prat Y, Fromer M, Linial M , Linial N. Geometric Interpretation of Gene Expression by Sparse Reconstruction of Transcript Profiles. In Bafna V, Sahinalp SC, editors, Research in Computational Molecular Biology - 15th Annual International Conference, RECOMB 2011, Proceedings. Springer Verlag. 2011. p. 355-357. (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)). doi: 10.1007/978-3-642-20036-6_33

Geometric Interpretation of Gene Expression by Sparse Reconstruction of Transcript Profiles

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