NDLI: <italic>PreProPath</italic>: An Uncertainty-Aware Algorithm for Identifying Predictable Profitable Pathways in Biochemical Networks

Content Provider	IEEE Xplore Digital Library
Author	Ullah, E. Walker, M. Kyongbum Lee Hassoun, S.
Copyright Year	2004
Abstract	Pathway analysis is a powerful approach to enable rational design or redesign of biochemical networks for optimizing metabolic engineering and synthetic biology objectives such as production of desired chemicals or biomolecules from specific nutrients. While experimental methods can be quite successful, computational approaches can enhance discovery and guide experimentation by efficiently exploring very large design spaces. We present a computational algorithm, Predictably Profitable Path (PreProPath), to identify target pathways best suited for engineering modifications. The algorithm utilizes uncertainties about the metabolic networks operating state inherent in the underdetermined linear equations representing the stoichiometric model. Flux Variability Analysis is used to determine the operational flux range. PreProPath identifies a path that is predictable in behavior, exhibiting small flux ranges, and profitable, containing the least restrictive flux-limiting reaction in the network. The algorithm is computationally efficient because it does not require enumeration of pathways. The results of case studies show that PreProPath can efficiently analyze variances in metabolic states and model uncertainties to suggest pathway engineering strategies that have been previously supported by experimental data.
Sponsorship	IEEE Computer Society
Starting Page	1405
Ending Page	1415
Page Count	11
File Size	1149207
File Format	PDF
ISSN	15455963
Volume Number	12
Issue Number	6
Language	English
Publisher	Institute of Electrical and Electronics Engineers, Inc. (IEEE)
Publisher Date	2015-11-01
Publisher Place	U.S.A.
Access Restriction	One Nation One Subscription (ONOS)
Rights Holder	Institute of Electrical and Electronics Engineers, Inc. (IEEE)
Subject Keyword	Prediction algorithms Computational biology Bioinformatics Algorithm design and analysis Biochemistry Uncertainty Flux Balance Analysis Flux Variability Analysis Metabolic Networks uncertainty Flux balance analysis flux variability analysis metabolic networks
Content Type	Text
Resource Type	Article
Subject	Applied Mathematics Genetics Biotechnology

Sl.	Authority	Responsibilities	Communication Details
1	Ministry of Education (GoI), Department of Higher Education	Sanctioning Authority	https://www.education.gov.in/ict-initiatives
2	Indian Institute of Technology Kharagpur	Host Institute of the Project: The host institute of the project is responsible for providing infrastructure support and hosting the project	https://www.iitkgp.ac.in
3	National Digital Library of India Office, Indian Institute of Technology Kharagpur	The administrative and infrastructural headquarters of the project	Dr. B. Sutradhar bsutra@ndl.gov.in
4	Project PI / Joint PI	Principal Investigator and Joint Principal Investigators of the project	Dr. B. Sutradhar bsutra@ndl.gov.in Prof. Saswat Chakrabarti will be added soon
5	Website/Portal (Helpdesk)	Queries regarding NDLI and its services	support@ndl.gov.in
6	Contents and Copyright Issues	Queries related to content curation and copyright issues	content@ndl.gov.in
7	National Digital Library of India Club (NDLI Club)	Queries related to NDLI Club formation, support, user awareness program, seminar/symposium, collaboration, social media, promotion, and outreach	clubsupport@ndl.gov.in
8	Digital Preservation Centre (DPC)	Assistance with digitizing and archiving copyright-free printed books	dpc@ndl.gov.in
9	IDR Setup or Support	Queries related to establishment and support of Institutional Digital Repository (IDR) and IDR workshops	idr@ndl.gov.in

gEFM: An Algorithm for Computing Elementary Flux Modes Using Graph Traversal

Robust flux balance analysis of multiscale biochemical reaction networks

Computationally efficient flux variability analysis

An in silico platform for the design of heterologous pathways in nonnative metabolite production

Decomposition of Flux Distributions into Metabolic Pathways

FASIMU: flexible software for flux-balance computation series in large metabolic networks

Sensitivity Analysis of Genome-Scale Metabolic Flux Prediction.

CiliateGEM: an open-project and a tool for predictions of ciliate metabolic variations and experimental condition design

An improved algorithm for flux variability analysis

PreProPath: An Uncertainty-Aware Algorithm for Identifying Predictable Profitable Pathways in Biochemical Networks

Similar Documents

gEFM: An Algorithm for Computing Elementary Flux Modes Using Graph Traversal

Robust flux balance analysis of multiscale biochemical reaction networks

Computationally efficient flux variability analysis

An in silico platform for the design of heterologous pathways in nonnative metabolite production

Decomposition of Flux Distributions into Metabolic Pathways

FASIMU: flexible software for flux-balance computation series in large metabolic networks

Sensitivity Analysis of Genome-Scale Metabolic Flux Prediction.

CiliateGEM: an open-project and a tool for predictions of ciliate metabolic variations and experimental condition design

An improved algorithm for flux variability analysis

PreProPath: An Uncertainty-Aware Algorithm for Identifying Predictable Profitable Pathways in Biochemical Networks