Finding Minimum Reaction Cuts of Metabolic Networks Under a Boolean Model Using Integer Programming and Feedback Vertex Sets

No abstract is available for this paper.

• Publication year

  2010

• Venue

  International Journal of Knowledge Discovery in Bioinformatics

• Publication date

  Unknown publication date

• Fields of study

  Biology, Computer Science

• Identifiers
  DOI 10.4018/jkdb.2010100202
• External record

  Open on Semantic Scholar

• Source metadata

  Semantic Scholar

• No claims are published for this paper.

• No concepts are published for this paper.

• Kansei Engineering and Soft Computing : Theory and Practice

  2012cited by this paper
• Coupled Matrix Factorization with Sparse Factors to Identify Potential Biomarkers in Metabolomics

  2012cited by this paper
• Sharing Usability Information: A Communication Paradox

  2012cited by this paper
• Improved Feature Selection by Incorporating Gene Similarity Into the LASSO

  2012cited by this paper
• Agile and Lean Service-Oriented Development: Foundations, Theory, and Practice

  2012cited by this paper
• Association Rule Mining Based HotSpot Analysis on SEER Lung Cancer Data

  2011cited by this paper
• MINOTAUR: A Web-Based Annotator-Assistant Tool

  2011cited by this paper
• Handbook of Research on Computational Science and Engineering: Theory and Practice

  2011cited by this paper
• Built-In Self Repair for Logic Structures

  2011cited by this paper
• Natural Language Processing Techniques in Requirements Engineering

  2011cited by this paper
• Fuzzy Logic for Non-Smooth Dynamical Systems

  2011cited by this paper
• Feature Selection and Ensemble Methods for Bioinformatics: Algorithmic Classification and Implementations

  2011cited by this paper
• Interest and Performance When Learning Online: Providing Utility Value Information can be Important for Both Novice and Experienced Students

  2011cited by this paper
• Design and Test Technology for Dependable Systems-on-Chip

  2010cited by this paper
• Synthesis of Flexible Fault-Tolerant Schedules for Embedded Systems with Soft and Hard Timing Constraints

  2010cited by this paper
• Wave-SOM: A Novel Wavelet-Based Clustering Algorithm for Analysis of Gene Expression Patterns

  2010cited by this paper
• Mapping short reads to a genomic sequence with circular structure

  2010cited by this paper
• Enhanced Speech-Enabled Tools for Intelligent and Mobile E-Learning Applications

  2010cited by this paper
• Interdisciplinary Research and Applications in Bioinformatics, Computational Biology, and Environmental Sciences

  2010cited by this paper
• Compensatory ability to null mutation in metabolic networks

  2009cited by this paper
• Measuring Structural Robustness of Metabolic Networks under a Boolean Model Using Integer Programming and Feedback Vertex Sets

  2009cited by this paper
• Biological Data Mining in Protein Interaction Networks

  2009cited by this paper
• Modes and cuts in metabolic networks: Complexity and algorithms

  2009cited by this paper
• Structural robustness of metabolic networks with respect to multiple knockouts.

  2008cited by this paper
• An environmental perspective on metabolism.

  2008cited by this paper
• Evolution and dynamics of protein interactions and networks.

  2008cited by this paper
• Multidimensional annotation of the Escherichia coli K-12 genome

  2007cited by this paper
• Mining Metabolic Networks for Optimal Drug Targets

  2007cited by this paper
• Computing Knock-Out Strategies in Metabolic Networks

  2007cited by this paper
• KEGG for linking genomes to life and the environment

  2007cited by this paper
• A computational framework for the topological analysis and targeted disruption of signal transduction networks.

  2006cited by this paper
• Systems biology Metatool 5.0: fast and flexible elementary modes analysis

  2006cited by this paper
• Transcription control reprogramming in genetic backup circuits

  2005cited by this paper
• Expanding Metabolic Networks: Scopes of Compounds, Robustness, and Evolution

  2005cited by this paper
• Combinatorial Complexity of Pathway Analysis in Metabolic Networks

  2004cited by this paper
• Cancer as a robust system: implications for anticancer therapy

  2004cited by this paper
• Minimal cut sets in biochemical reaction networks

  2004cited by this paper
• Metabolic pathways in the post-genome era.

  2003cited by this paper
• Optknock: A bilevel programming framework for identifying gene knockout strategies for microbial strain optimization

  2003cited by this paper
• Network motifs: simple building blocks of complex networks.

  2002cited by this paper
• Metabolic network structure determines key aspects of functionality and regulation

  2002cited by this paper
• Supporting Modeling Structured Analysis and Design

  2001cited by this paper
• Computer-Aided Method Engineering : Designing CASE Repositories for the 21st Century

  2001cited by this paper
• The small world inside large metabolic networks

  2000cited by this paper
• The large-scale organization of metabolic networks

  2000cited by this paper
• Detection of elementary flux modes in biochemical networks: a promising tool for pathway analysis and metabolic engineering.

  1999cited by this paper
• Approximation Algorithms for the Feedback Vertex Set Problem with Applications to Constraint Satisfaction and Bayesian Inference

  1998cited by this paper
• Approximating Minimum Feedback Sets and Multicuts in Directed Graphs

  1998cited by this paper
• International Journal of Knowledge Discovery in Bioinformatics

  year unknowncited by this paper
• BIOINFORMATICS ORIGINAL PAPER doi:10.1093/bioinformatics/btm150 Systems biology

  year unknowncited by this paper

• QuTIE: quantum optimization for target identification by enzymes.

  2023influential citation
• More String and Sequence Problems Solved by ILP

  2019cites this paper
• Bibliography

  2019cites this paper
• Tanglegrams and Coevolution

  2019cites this paper
• A Flyover Introduction to Integer Linear Programming

  2019cites this paper
• Integer Programming in Molecular Sequence Analysis

  2019cites this paper
• Near Cliques, Dense Subgraphs, and Motifs in Biological Networks

  2019cites this paper
• Communities, Cuts, and High-Density Subgraphs

  2019cites this paper
• More Tanglegrams, More Trees, More ILPs

  2019cites this paper
• Metabolic Networks and Metabolic Engineering

  2019cites this paper
• Biological Networks, Graphs, and High-Density Subgraphs

  2019cites this paper
• Index

  2019cites this paper
• Exploiting and Leveraging Protein Networks

  2019cites this paper
• Protein Problems Solved By Integer Programming

  2019cites this paper
• Maximum Likelihood Pedigree Reconstruction

  2019cites this paper
• Convergent and Maximum Parsimony Problems in Phylogenetics

  2019cites this paper
• Introduction

  2019cites this paper
• More Extended Exercises

  2019cites this paper
• Maximum Character Compatibility in Phylogenetics

  2019cites this paper
• Two DNA Haplotyping Problems

  2019cites this paper
• Epilogue: Some Very Opinionated Comments for Advanced Readers

  2019cites this paper
• Return to Steiner Trees and Maximum Parsimony

  2019cites this paper
• Traveling Salesman Problems in Genomics

  2019cites this paper
• Character Compatibility with Corrupted Data and Generalized Phylogenetic Models

  2019cites this paper
• The RNA-Folding Problem

  2019cites this paper
• Network controllability analysis of intracellular signalling reveals viruses are actively controlling molecular systems

  2019cites this paper
• Integer Linear Programming in Computational and Systems Biology: Tutorial

  2019cites this paper
• Title Computing smallest intervention strategies for multiplemetabolic networks in a boolean model

  2019influential citation
• Part II

  2019cites this paper
• ILP Idioms

  2019cites this paper
• Title Discovery of Boolean Metabolic Networks : Integer LinearProgramming Based Approach

  2018cites this paper
• Discovery of Boolean metabolic networks: integer linear programming based approach

  2018cites this paper
• Computing Minimum Reaction Modifications in a Boolean Metabolic Network

  2018influential citation
• What’s Next?

  2017cites this paper
• A mixed-integer linear programming approach to the reduction of genome-scale metabolic networks

  2017cites this paper
• Finding Influential Genes Using Gene Expression Data and Boolean Models of Metabolic Networks

  2016cites this paper
• Computing Smallest Intervention Strategies for Multiple Metabolic Networks in a Boolean Model

  2015influential citation
• Computational Methods for Modification of Metabolic Networks

  2015influential citation
• High-Performance Computing for Theoretical Study of Nanoscale and Molecular Interconnects

  2014cites this paper
• Integer Programming-Based Method for Designing Synthetic Metabolic Networks by Minimum Reaction Insertion in a Boolean Model

  2014influential citation
• Computational Methods for Analyzing Chemical Graphs and Biological Networks

  2014cites this paper
• Flux balance impact degree: a new definition of impact degree to properly treat reversible reactions in metabolic networks

  2013cites this paper
• Theoretical estimation of metabolic network robustness against multiple reaction knockouts using branching process approximation

  2013influential citation
• Dynamics and control at feedback vertex sets. II: a faithful monitor to determine the diversity of molecular activities in regulatory networks.

  2013cites this paper
• The State of Development of CSE

  2012cites this paper
• Analysis of the impact degree distribution in metabolic networks using branching process approximation

  2011cites this paper
• The Mathematical Modeling and Computational Simulation for Error-Prone PCR

  2011cites this paper
• An Efficient Method of Computing Impact Degrees for Multiple Reactions in Metabolic Networks with Cycles

  2011cites this paper
• Integer programming-based method for completing signaling pathways and its application to analysis of colorectal cancer.

  2010cites this paper
• Hierarchical Density-Based Clustering of White Matter Tracts in the Human Brain

  2010cites this paper
• Exact Algorithms for Finding a Minimum Reaction Cut under a Boolean Model of Metabolic Networks

  2010cites this paper
• Efficient computation of impact degrees for multiple reactions in metabolic networks with cycles

  2009cites this paper