The Epigenetic Consensus Problem

Sabrina Rashid; Gadi Taubenfeld; Ziv Bar-Joseph

doi:10.1007/978-3-030-79527-6_9

The Epigenetic Consensus Problem

Sabrina Rashid, Gadi Taubenfeld, Ziv Bar-Joseph

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

Abstract

A distributed computing system is a collection of processors that communicate either by reading and writing from shared memory or by sending messages over some communication network. Most prior biologically inspired distributed computing algorithms rely on message passing as the communication model. Here we show that in the process of genome-wide epigenetic modifications, cells utilize their DNA as a shared memory system. We formulate a particular consensus problem, called the epigenetic consensus problem, that cells attempt to solve using this shared memory model and then present algorithms, derive expected run time and discuss, analyze and simulate improved methods for solving this problem. Analysis of real biological data indicates that the computational methods indeed reflect aspects of the biological process for genome-wide epigenetic modifications.

Original language	English
Title of host publication	Structural Information and Communication Complexity - 28th International Colloquium, SIROCCO 2021, Proceedings
Editors	Tomasz Jurdziński, Stefan Schmid
Publisher	Springer Science and Business Media Deutschland GmbH
Pages	146-163
Number of pages	18
ISBN (Print)	9783030795269
DOIs	https://doi.org/10.1007/978-3-030-79527-6_9
State	Published - 2021
Externally published	Yes
Event	28th International Colloquium on Structural Information and Communication Complexity, SIROCCO 2021 - Virtual, Online Duration: 28 Jun 2021 → 1 Jul 2021

Publication series

Name	Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)
Volume	12810 LNCS
ISSN (Print)	0302-9743
ISSN (Electronic)	1611-3349

Conference

Conference	28th International Colloquium on Structural Information and Communication Complexity, SIROCCO 2021
City	Virtual, Online
Period	28/06/21 → 1/07/21

Bibliographical note

Publisher Copyright:
© 2021, Springer Nature Switzerland AG.

Access to Document

10.1007/978-3-030-79527-6_9

Cite this

Rashid, S., Taubenfeld, G., & Bar-Joseph, Z. (2021). The Epigenetic Consensus Problem. In T. Jurdziński, & S. Schmid (Eds.), Structural Information and Communication Complexity - 28th International Colloquium, SIROCCO 2021, Proceedings (pp. 146-163). (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); Vol. 12810 LNCS). Springer Science and Business Media Deutschland GmbH. https://doi.org/10.1007/978-3-030-79527-6_9

Rashid, Sabrina ; Taubenfeld, Gadi ; Bar-Joseph, Ziv. / The Epigenetic Consensus Problem. Structural Information and Communication Complexity - 28th International Colloquium, SIROCCO 2021, Proceedings. editor / Tomasz Jurdziński ; Stefan Schmid. Springer Science and Business Media Deutschland GmbH, 2021. pp. 146-163 (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)).

@inproceedings{2541bed52cc8487db868d8738a363a8b,

title = "The Epigenetic Consensus Problem",

abstract = "A distributed computing system is a collection of processors that communicate either by reading and writing from shared memory or by sending messages over some communication network. Most prior biologically inspired distributed computing algorithms rely on message passing as the communication model. Here we show that in the process of genome-wide epigenetic modifications, cells utilize their DNA as a shared memory system. We formulate a particular consensus problem, called the epigenetic consensus problem, that cells attempt to solve using this shared memory model and then present algorithms, derive expected run time and discuss, analyze and simulate improved methods for solving this problem. Analysis of real biological data indicates that the computational methods indeed reflect aspects of the biological process for genome-wide epigenetic modifications.",

author = "Sabrina Rashid and Gadi Taubenfeld and Ziv Bar-Joseph",

note = "Publisher Copyright: {\textcopyright} 2021, Springer Nature Switzerland AG.; 28th International Colloquium on Structural Information and Communication Complexity, SIROCCO 2021 ; Conference date: 28-06-2021 Through 01-07-2021",

year = "2021",

doi = "10.1007/978-3-030-79527-6_9",

language = "אנגלית",

isbn = "9783030795269",

series = "Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)",

publisher = "Springer Science and Business Media Deutschland GmbH",

pages = "146--163",

editor = "Tomasz Jurdzi{\'n}ski and Stefan Schmid",

booktitle = "Structural Information and Communication Complexity - 28th International Colloquium, SIROCCO 2021, Proceedings",

address = "גרמניה",

}

Rashid, S, Taubenfeld, G & Bar-Joseph, Z 2021, The Epigenetic Consensus Problem. in T Jurdziński & S Schmid (eds), Structural Information and Communication Complexity - 28th International Colloquium, SIROCCO 2021, Proceedings. Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), vol. 12810 LNCS, Springer Science and Business Media Deutschland GmbH, pp. 146-163, 28th International Colloquium on Structural Information and Communication Complexity, SIROCCO 2021, Virtual, Online, 28/06/21. https://doi.org/10.1007/978-3-030-79527-6_9

The Epigenetic Consensus Problem. / Rashid, Sabrina; Taubenfeld, Gadi; Bar-Joseph, Ziv.
Structural Information and Communication Complexity - 28th International Colloquium, SIROCCO 2021, Proceedings. ed. / Tomasz Jurdziński; Stefan Schmid. Springer Science and Business Media Deutschland GmbH, 2021. p. 146-163 (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); Vol. 12810 LNCS).

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

TY - GEN

T1 - The Epigenetic Consensus Problem

AU - Rashid, Sabrina

AU - Taubenfeld, Gadi

AU - Bar-Joseph, Ziv

PY - 2021

Y1 - 2021

N2 - A distributed computing system is a collection of processors that communicate either by reading and writing from shared memory or by sending messages over some communication network. Most prior biologically inspired distributed computing algorithms rely on message passing as the communication model. Here we show that in the process of genome-wide epigenetic modifications, cells utilize their DNA as a shared memory system. We formulate a particular consensus problem, called the epigenetic consensus problem, that cells attempt to solve using this shared memory model and then present algorithms, derive expected run time and discuss, analyze and simulate improved methods for solving this problem. Analysis of real biological data indicates that the computational methods indeed reflect aspects of the biological process for genome-wide epigenetic modifications.

AB - A distributed computing system is a collection of processors that communicate either by reading and writing from shared memory or by sending messages over some communication network. Most prior biologically inspired distributed computing algorithms rely on message passing as the communication model. Here we show that in the process of genome-wide epigenetic modifications, cells utilize their DNA as a shared memory system. We formulate a particular consensus problem, called the epigenetic consensus problem, that cells attempt to solve using this shared memory model and then present algorithms, derive expected run time and discuss, analyze and simulate improved methods for solving this problem. Analysis of real biological data indicates that the computational methods indeed reflect aspects of the biological process for genome-wide epigenetic modifications.

UR - http://www.scopus.com/inward/record.url?scp=85111450203&partnerID=8YFLogxK

U2 - 10.1007/978-3-030-79527-6_9

DO - 10.1007/978-3-030-79527-6_9

M3 - ???researchoutput.researchoutputtypes.contributiontobookanthology.conference???

AN - SCOPUS:85111450203

SN - 9783030795269

T3 - Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)

SP - 146

EP - 163

BT - Structural Information and Communication Complexity - 28th International Colloquium, SIROCCO 2021, Proceedings

A2 - Jurdziński, Tomasz

A2 - Schmid, Stefan

PB - Springer Science and Business Media Deutschland GmbH

T2 - 28th International Colloquium on Structural Information and Communication Complexity, SIROCCO 2021

Y2 - 28 June 2021 through 1 July 2021

ER -

Rashid S, Taubenfeld G, Bar-Joseph Z. The Epigenetic Consensus Problem. In Jurdziński T, Schmid S, editors, Structural Information and Communication Complexity - 28th International Colloquium, SIROCCO 2021, Proceedings. Springer Science and Business Media Deutschland GmbH. 2021. p. 146-163. (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)). doi: 10.1007/978-3-030-79527-6_9

The Epigenetic Consensus Problem

Abstract

Publication series

Conference

Bibliographical note

Access to Document

Other files and links

Fingerprint

Cite this