Structural and dynamical analysis of biological networks

CentiLib: comprehensive analysis and exploration of network centralities

(2012) J. Grassler et al.   BIOINFORMATICS

Flux balance analysis of primary metabolism in Chlamydomonas reinhardtii

(2012) Nanette R Boyle et al.   BMC Systems Biology

Identifying co-targets to fight drug resistance based on a random walk model

(2012) Liang-Chun Chen et al.   BMC Systems Biology

A new essential protein discovery method based on the integration of protein-protein interaction and gene expression data

(2012) Min Li et al.   BMC Systems Biology

Metabolic network analysis predicts efficacy of FDA-approved drugs targeting the causative agent of a neglected tropical disease

(2012) Arvind K Chavali et al.   BMC Systems Biology

Differential network biology

(2012) Trey Ideker et al.   Molecular Systems Biology

BioNetSim: a Petri net-based modeling tool for simulations of biochemical processes

(2012) Junhui Gao et al.   Protein & Cell

Prioritizing disease candidate genes by a gene interconnectedness-based approach

(2011) Chia-Lang Hsu et al.   BMC GENOMICS

Steady-state global optimization of metabolic non-linear dynamic models through recasting into power-law canonical models

(2011) Carlos Pozo et al.   BMC Systems Biology

Elementary signaling modes predict the essentiality of signal transduction network components

(2011) Rui-Sheng Wang et al.   BMC Systems Biology

Rule-based multi-level modeling of cell biological systems

(2011) Carsten Maus et al.   BMC Systems Biology

Mathematical modeling of gene expression: a guide for the perplexed biologist

(2011) Ahmet Ay et al.   CRITICAL REVIEWS IN BIOCHEMISTRY AND MOLECULAR BIOLOGY

Importance of metabolic coupling for the dynamics of gene expression following a diauxic shift in Escherichia coli

(2011) Valentina Baldazzi et al.   JOURNAL OF THEORETICAL BIOLOGY

Regulation by Small RNAs in Bacteria: Expanding Frontiers

(2011) Gisela Storz et al.   MOLECULAR CELL

A Genome-Wide Approach to Discovery of Small RNAs Involved in Regulation of Virulence in Vibrio cholerae

(2011) Evan S. Bradley et al.   PLoS Pathogens

Using graph theory to analyze biological networks

(2011) Georgios A Pavlopoulos et al.   BioData Mining

Modular rate laws for enzymatic reactions: thermodynamics, elasticities and implementation

(2010) Wolfram Liebermeister et al.   BIOINFORMATICS

Mass Action Stoichiometric Simulation Models: Incorporating Kinetics and Regulation into Stoichiometric Models

(2010) Neema Jamshidi et al.   BIOPHYSICAL JOURNAL

A Survey on Methods for Modeling and Analyzing Integrated Biological Networks

(2010) N Tenazinha et al.   IEEE-ACM Transactions on Computational Biology and Bioinformatics

Mathematical Modeling: Bridging the Gap between Concept and Realization in Synthetic Biology

(2010) Yuting Zheng et al.   JOURNAL OF BIOMEDICINE AND BIOTECHNOLOGY

Targeting multiple targets inPseudomonas aeruginosaPAO1 using flux balance analysis of a reconstructed genome-scale metabolic network

(2010) Deepak Perumal et al.   JOURNAL OF DRUG TARGETING

Bacterial adaptation through distributed sensing of metabolic fluxes

(2010) Oliver Kotte et al.   Molecular Systems Biology

Multiple small RNAs identified in Mycobacterium bovis BCG are also expressed in Mycobacterium tuberculosis and Mycobacterium smegmatis

(2010) J. M. DiChiara et al.   NUCLEIC ACIDS RESEARCH

Graph methods for the investigation of metabolic networks in parasitology

(2010) LUDOVIC COTTRET et al.   PARASITOLOGY

Comparative genome-wide analysis of small RNAs of major Gram-positive pathogens: from identification to application

(2010) Mobarak A. Mraheil et al.   Microbial Biotechnology

The Carbon Assimilation Network in Escherichia coli Is Densely Connected and Largely Sign-Determined by Directions of Metabolic Fluxes

(2010) Valentina Baldazzi et al.   PLoS Computational Biology

Genome-scale comparison and constraint-based metabolic reconstruction of the facultative anaerobic Fe(III)-reducer Rhodoferax ferrireducens

(2009) Carla Risso et al.   BMC GENOMICS

Modeling metabolic networks in C. glutamicum: a comparison of rate laws in combination with various parameter optimization strategies

(2009) Andreas Dräger et al.   BMC Systems Biology

Genome-scale constraint-based modeling of Geobacter metallireducens

(2009) Jun Sun et al.   BMC Systems Biology

Flux balance analysis of biological systems: applications and challenges

(2009) K. Raman et al.   BRIEFINGS IN BIOINFORMATICS

Bottlenecks and Hubs in Inferred Networks Are Important for Virulence in Salmonella typhimurium

(2009) Jason E. McDermott et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

Dynamic network topology changes in functional modules predict responses to oxidative stress in yeast

(2009) Peddinti V. Gopalacharyulu et al.   Molecular BioSystems

The powerful law of the power law and other myths in network biology

(2009) Gipsi Lima-Mendez et al.   Molecular BioSystems

Genome-scale gene/reaction essentiality and synthetic lethality analysis

(2009) Patrick F Suthers et al.   Molecular Systems Biology

VisANT 3.5: multi-scale network visualization, analysis and inference based on the gene ontology

(2009) Zhenjun Hu et al.   NUCLEIC ACIDS RESEARCH

A Big World Inside Small-World Networks

(2009) Zhihua Zhang et al.   PLoS One

Identifying Hubs in Protein Interaction Networks

(2009) Ravishankar R. Vallabhajosyula et al.   PLoS One

Hypergraphs and Cellular Networks

(2009) Steffen Klamt et al.   PLoS Computational Biology

Minimal Escherichia coli Cell for the Most Efficient Production of Ethanol from Hexoses and Pentoses

(2008) C. T. Trinh et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Integrating metabolic, transcriptional regulatory and signal transduction models in Escherichia coli

(2008) Markus W. Covert et al.   BIOINFORMATICS

A hybrid model of anaerobicE. coliGJT001: Combination of elementary flux modes and cybernetic variables

(2008) Jin Il Kim et al.   BIOTECHNOLOGY PROGRESS

Modularity in the genetic disease-phenotype network

(2008) Xingpeng Jiang et al.   FEBS LETTERS

An Introduction to Metabolic Networks and Their Structural Analysis

(2008) V. Lacroix et al.   IEEE-ACM Transactions on Computational Biology and Bioinformatics

Spectral centrality measures in complex networks

(2008) Nicola Perra et al.   PHYSICAL REVIEW E

Single and multiple input modules in regulatory networks

(2008) Arun S. Konagurthu et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Genome-Scale Reconstruction and Analysis of the Pseudomonas putida KT2440 Metabolic Network Facilitates Applications in Biotechnology

(2008) Jacek Puchałka et al.   PLoS Computational Biology

Why Do Hubs in the Yeast Protein Interaction Network Tend To Be Essential: Reexamining the Connection between the Network Topology and Essentiality

(2008) Elena Zotenko et al.   PLoS Computational Biology