HCV quasispecies assembly using network flows

Kelly Westbrooks; Irina Astrovskaya; David Campo; Yury Khudyakov; Piotr Berman; Alex Zelikovsky

doi:10.1007/978-3-540-79450-9_15

HCV quasispecies assembly using network flows

Kelly Westbrooks
, Irina Astrovskaya
, David Campo
, Yury Khudyakov
, Piotr Berman
, Alex Zelikovsky

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

36 Scopus citations

Abstract

Understanding how the genomes of viruses mutate and evolve within infected individuals is critically important in epidemiology. By exploiting knowledge of the forces that guide viral microevolution, researchers can design drugs and treatments that are effective against newly evolved strains. Therefore, it is critical to develop a method for typing the genomes of all of the variants of a virus (quasispecies) inside an infected individual cell. In this paper, we focus on sequence assembly of Hepatitis C Virus (HCV) based on 454 Lifesciences system that produces around 250K reads each 100-400 base long. We introduce several formulations of the quasispecies assembly problem and a measure of the assembly quality. We also propose a novel scalable assembling method for quasispecies based on a novel network flow formulation. Finally, we report the results of assembling 44 quasispecies from the 1700 bp long E1E2 region of HCV.

Original language	English (US)
Title of host publication	Bioinformatics Research and Applications - Fourth International Symposium, ISBRA 2008, Proceedings
Pages	159-170
Number of pages	12
DOIs	https://doi.org/10.1007/978-3-540-79450-9_15
State	Published - 2008
Event	4th International Symposium on Bioinformatics Research and Applications, ISBRA 2008 - Atlanta, GA, United States Duration: May 6 2008 → May 9 2008

Publication series

Name	Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)
Volume	4983 LNBI
ISSN (Print)	0302-9743
ISSN (Electronic)	1611-3349

Other

Other	4th International Symposium on Bioinformatics Research and Applications, ISBRA 2008
Country/Territory	United States
City	Atlanta, GA
Period	5/6/08 → 5/9/08

UN SDGs

This output contributes to the following UN Sustainable Development Goals (SDGs)

SDG 3 Good Health and Well-being

All Science Journal Classification (ASJC) codes

Theoretical Computer Science
General Computer Science

Access to Document

10.1007/978-3-540-79450-9_15

Cite this

Westbrooks, K., Astrovskaya, I., Campo, D., Khudyakov, Y., Berman, P., & Zelikovsky, A. (2008). HCV quasispecies assembly using network flows. In Bioinformatics Research and Applications - Fourth International Symposium, ISBRA 2008, Proceedings (pp. 159-170). (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); Vol. 4983 LNBI). https://doi.org/10.1007/978-3-540-79450-9_15

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title = "HCV quasispecies assembly using network flows",

abstract = "Understanding how the genomes of viruses mutate and evolve within infected individuals is critically important in epidemiology. By exploiting knowledge of the forces that guide viral microevolution, researchers can design drugs and treatments that are effective against newly evolved strains. Therefore, it is critical to develop a method for typing the genomes of all of the variants of a virus (quasispecies) inside an infected individual cell. In this paper, we focus on sequence assembly of Hepatitis C Virus (HCV) based on 454 Lifesciences system that produces around 250K reads each 100-400 base long. We introduce several formulations of the quasispecies assembly problem and a measure of the assembly quality. We also propose a novel scalable assembling method for quasispecies based on a novel network flow formulation. Finally, we report the results of assembling 44 quasispecies from the 1700 bp long E1E2 region of HCV.",

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Westbrooks, K, Astrovskaya, I, Campo, D, Khudyakov, Y, Berman, P & Zelikovsky, A 2008, HCV quasispecies assembly using network flows. in Bioinformatics Research and Applications - Fourth International Symposium, ISBRA 2008, Proceedings. Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), vol. 4983 LNBI, pp. 159-170, 4th International Symposium on Bioinformatics Research and Applications, ISBRA 2008, Atlanta, GA, United States, 5/6/08. https://doi.org/10.1007/978-3-540-79450-9_15

HCV quasispecies assembly using network flows. / Westbrooks, Kelly; Astrovskaya, Irina; Campo, David et al.
Bioinformatics Research and Applications - Fourth International Symposium, ISBRA 2008, Proceedings. 2008. p. 159-170 (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); Vol. 4983 LNBI).

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

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AU - Berman, Piotr

AU - Zelikovsky, Alex

PY - 2008

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AB - Understanding how the genomes of viruses mutate and evolve within infected individuals is critically important in epidemiology. By exploiting knowledge of the forces that guide viral microevolution, researchers can design drugs and treatments that are effective against newly evolved strains. Therefore, it is critical to develop a method for typing the genomes of all of the variants of a virus (quasispecies) inside an infected individual cell. In this paper, we focus on sequence assembly of Hepatitis C Virus (HCV) based on 454 Lifesciences system that produces around 250K reads each 100-400 base long. We introduce several formulations of the quasispecies assembly problem and a measure of the assembly quality. We also propose a novel scalable assembling method for quasispecies based on a novel network flow formulation. Finally, we report the results of assembling 44 quasispecies from the 1700 bp long E1E2 region of HCV.

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Westbrooks K, Astrovskaya I, Campo D, Khudyakov Y, Berman P, Zelikovsky A. HCV quasispecies assembly using network flows. In Bioinformatics Research and Applications - Fourth International Symposium, ISBRA 2008, Proceedings. 2008. p. 159-170. (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)). doi: 10.1007/978-3-540-79450-9_15

HCV quasispecies assembly using network flows

Abstract

Publication series

Other

UN SDGs

All Science Journal Classification (ASJC) codes

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