Genome-scale bacterial transcriptional regulatory networks: reconstruction and integrated analysis with metabolic models

A Whole-Cell Computational Model Predicts Phenotype from Genotype

(2012) Jonathan R. Karr et al.   CELL

Implications of functional similarity for gene regulatory interactions

(2012) K. Glass et al.   Journal of the Royal Society Interface

GeneNetWeaver: in silico benchmark generation and performance profiling of network inference methods

(2011) Thomas Schaffter et al.   BIOINFORMATICS

Systems analysis of multiple regulator perturbations allows discovery of virulence factors in Salmonella

(2011) Hyunjin Yoon et al.   BMC Systems Biology

Network-based functional modeling of genomics, transcriptomics and metabolism in bacteria

(2011) Lore Cloots et al.   CURRENT OPINION IN MICROBIOLOGY

Evidence-Based Annotation of Transcripts and Proteins in the Sulfate-Reducing Bacterium Desulfovibrio vulgaris Hildenborough

(2011) M. N. Price et al.   JOURNAL OF BACTERIOLOGY

Comparative Genomic Analysis of the Hexuronate Metabolism Genes and Their Regulation in Gammaproteobacteria

(2011) I. A. Suvorova et al.   JOURNAL OF BACTERIOLOGY

Control of Proteobacterial Central Carbon Metabolism by the HexR Transcriptional Regulator

(2011) Semen A. Leyn et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

CoryneRegNet 6.0--Updated database content, new analysis methods and novel features focusing on community demands

(2011) J. Pauling et al.   NUCLEIC ACIDS RESEARCH

Interactive Tree Of Life v2: online annotation and display of phylogenetic trees made easy

(2011) I. Letunic et al.   NUCLEIC ACIDS RESEARCH

COLOMBOS: Access Port for Cross-Platform Bacterial Expression Compendia

(2011) Kristof Engelen et al.   PLoS One

Modeling formalisms in Systems Biology

(2011) Daniel Machado et al.   AMB Express

A Decade of Systems Biology

(2010) Han-Yu Chuang et al.   Annual Review of Cell and Developmental Biology

Integrating quantitative proteomics and metabolomics with a genome-scale metabolic network model

(2010) K. Yizhak et al.   BIOINFORMATICS

A computational tool for the simulation and optimization of microbial strains accounting integrated metabolic/regulatory information

(2010) Paulo Vilaça et al.   BIOSYSTEMS

Learning gene regulatory networks from only positive and unlabeled data

(2010) Luigi Cerulo et al.   BMC BIOINFORMATICS

FITBAR: a web tool for the robust prediction of prokaryotic regulons

(2010) Jacques Oberto   BMC BIOINFORMATICS

A semi-supervised learning approach to predict synthetic genetic interactions by combining functional and topological properties of functional gene network

(2010) Zhu-Hong You et al.   BMC BIOINFORMATICS

Genome-wide inference of regulatory networks in Streptomyces coelicolor

(2010) Marlene Castro-Melchor et al.   BMC GENOMICS

OptORF: Optimal metabolic and regulatory perturbations for metabolic engineering of microbial strains

(2010) Joonhoon Kim et al.   BMC Systems Biology

Metabolic reconstruction, constraint-based analysis and game theory to probe genome-scale metabolic networks

(2010) Eytan Ruppin et al.   CURRENT OPINION IN BIOTECHNOLOGY

Studying bacterial transcriptomes using RNA-seq

(2010) Nicholas J Croucher et al.   CURRENT OPINION IN MICROBIOLOGY

A comprehensive assessment of methods for de-novo reverse-engineering of genome-scale regulatory networks

(2010) Varun Narendra et al.   GENOMICS

A Survey on Methods for Modeling and Analyzing Integrated Biological Networks

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

High-throughput generation, optimization and analysis of genome-scale metabolic models

(2010) Christopher S Henry et al.   NATURE BIOTECHNOLOGY

Tackling the widespread and critical impact of batch effects in high-throughput data

(2010) Jeffrey T. Leek et al.   NATURE REVIEWS GENETICS

Advantages and limitations of current network inference methods

(2010) Riet De Smet et al.   NATURE REVIEWS MICROBIOLOGY

ODB: a database for operon organizations, 2011 update

(2010) S. Okuda et al.   NUCLEIC ACIDS RESEARCH

RegulonDB version 7.0: transcriptional regulation of Escherichia coli K-12 integrated within genetic sensory response units (Gensor Units)

(2010) S. Gama-Castro et al.   NUCLEIC ACIDS RESEARCH

RegPredict: an integrated system for regulon inference in prokaryotes by comparative genomics approach

(2010) P. S. Novichkov et al.   NUCLEIC ACIDS RESEARCH

EcoCyc: a comprehensive database of Escherichia coli biology

(2010) I. M. Keseler et al.   NUCLEIC ACIDS RESEARCH

NCBI GEO: archive for functional genomics data sets--10 years on

(2010) T. Barrett et al.   NUCLEIC ACIDS RESEARCH

Improved Reconstruction of In Silico Gene Regulatory Networks by Integrating Knockout and Perturbation Data

(2010) Kevin Y. Yip et al.   PLoS One

DREAM3: Network Inference Using Dynamic Context Likelihood of Relatedness and the Inferelator

(2010) Aviv Madar et al.   PLoS One

Towards a Rigorous Assessment of Systems Biology Models: The DREAM3 Challenges

(2010) Robert J. Prill et al.   PLoS One

Inferring Regulatory Networks from Expression Data Using Tree-Based Methods

(2010) Vân Anh Huynh-Thu et al.   PLoS One

DREAM4: Combining Genetic and Dynamic Information to Identify Biological Networks and Dynamical Models

(2010) Alex Greenfield et al.   PLoS One

Probabilistic integrative modeling of genome-scale metabolic and regulatory networks inEscherichia coliandMycobacterium tuberculosis

(2010) Sriram Chandrasekaran et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Revealing strengths and weaknesses of methods for gene network inference

(2010) D. Marbach et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Reverse Engineering of Gene Networks with LASSO and Nonlinear Basis Functions

(2009) Mika Gustafsson et al.   Annals of the New York Academy of Sciences

Lessons from the DREAM2 Challenges

(2009) Gustavo Stolovitzky et al.   Annals of the New York Academy of Sciences

Module networks revisited: computational assessment and prioritization of model predictions

(2009) A. Joshi et al.   BIOINFORMATICS

Comparative analysis of module-based versus direct methods for reverse-engineering transcriptional regulatory networks

(2009) Tom Michoel et al.   BMC Systems Biology

A Yeast Synthetic Network for In Vivo Assessment of Reverse-Engineering and Modeling Approaches

(2009) Irene Cantone et al.   CELL

Predicting Metabolic Fluxes Using Gene Expression Differences As Constraints

(2009) Rogier J P van Berlo et al.   IEEE-ACM Transactions on Computational Biology and Bioinformatics

Generating Realistic In Silico Gene Networks for Performance Assessment of Reverse Engineering Methods

(2009) Daniel Marbach et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

Supervised learning with decision tree-based methods in computational and systems biology

(2009) Pierre Geurts et al.   Molecular BioSystems

From Corynebacterium glutamicum to Mycobacterium tuberculosis--towards transfers of gene regulatory networks and integrated data analyses with MycoRegNet

(2009) J. Krawczyk et al.   NUCLEIC ACIDS RESEARCH

RegPrecise: a database of curated genomic inferences of transcriptional regulatory interactions in prokaryotes

(2009) Pavel S. Novichkov et al.   NUCLEIC ACIDS RESEARCH

Genome-scale metabolic networks

(2009) Marco Terzer et al.   Wiley Interdisciplinary Reviews-Systems Biology and Medicine

A Strand-Specific RNA–Seq Analysis of the Transcriptome of the Typhoid Bacillus Salmonella Typhi

(2009) Timothy T. Perkins et al.   PLoS Genetics

Coordinated Regulation of Virulence during Systemic Infection of Salmonella enterica Serovar Typhimurium

(2009) Hyunjin Yoon et al.   PLoS Pathogens

DISTILLER: a data integration framework to reveal condition dependency of complex regulons in Escherichia coli

(2009) Karen Lemmens et al.   GENOME BIOLOGY

SIRENE: supervised inference of regulatory networks

(2008) F. Mordelet et al.   BIOINFORMATICS

W-AlignACE: an improved Gibbs sampling algorithm based on more accurate position weight matrices learned from sequence and gene expression/ChIP-chip data

(2008) Xin Chen et al.   BIOINFORMATICS

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

(2008) Markus W. Covert et al.   BIOINFORMATICS

On the Potential for Integrating Gene Expression and Metabolic Flux Data

(2008) Meric Ovacik et al.   Current Bioinformatics

Stoichiometric modelling of cell metabolism

(2008) Francisco Llaneras et al.   JOURNAL OF BIOSCIENCE AND BIOENGINEERING

Boolean network models of cellular regulation: prospects and limitations

(2008) S. Bornholdt   Journal of the Royal Society Interface

Network-based prediction of human tissue-specific metabolism

(2008) Tomer Shlomi et al.   NATURE BIOTECHNOLOGY

Learning biological networks: from modules to dynamics

(2008) Richard Bonneau   Nature Chemical Biology

Mapping and quantifying mammalian transcriptomes by RNA-Seq

(2008) Ali Mortazavi et al.   NATURE METHODS

RNA-Seq: a revolutionary tool for transcriptomics

(2008) Zhong Wang et al.   NATURE REVIEWS GENETICS

Reconstruction of biochemical networks in microorganisms

(2008) Adam M. Feist et al.   NATURE REVIEWS MICROBIOLOGY

Modelling and analysis of gene regulatory networks

(2008) Guy Karlebach et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

sRNAMap: genomic maps for small non-coding RNAs, their regulators and their targets in microbial genomes

(2008) Hsi-Yuan Huang et al.   NUCLEIC ACIDS RESEARCH

PRODORIC (release 2009): a database and tool platform for the analysis of gene regulation in prokaryotes

(2008) A. Grote et al.   NUCLEIC ACIDS RESEARCH

NCBI GEO: archive for high-throughput functional genomic data

(2008) T. Barrett et al.   NUCLEIC ACIDS RESEARCH

The Transcriptional Landscape of the Yeast Genome Defined by RNA Sequencing

(2008) U. Nagalakshmi et al.   SCIENCE

Dynamic Analysis of Integrated Signaling, Metabolic, and Regulatory Networks

(2008) Jong Min Lee et al.   PLoS Computational Biology

A Semi-Supervised Method for Predicting Transcription Factor–Gene Interactions in Escherichia coli

(2008) Jason Ernst et al.   PLoS Computational Biology

Horizontal gene transfer and the evolution of transcriptional regulation in Escherichia coli

(2008) Morgan N Price et al.   GENOME BIOLOGY