An experimentally supported model of the Bacillus subtilis global transcriptional regulatory network
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journal
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November 2015 |
Gene Expression Profiling and the Use of Genome-Scale In Silico Models of Escherichia coli for Analysis: Providing Context for Content
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April 2009 |
An integrative, multi‐scale, genome‐wide model reveals the phenotypic landscape of E scherichia coli
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July 2014 |
A system‐level model for the microbial regulatory genome
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July 2014 |
The PurR regulon in Escherichia coli K-12 MG1655
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May 2011 |
The Mycobacterium tuberculosis regulatory network and hypoxia
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July 2013 |
Inferring Genetic Networks and Identifying Compound Mode of Action via Expression Profiling
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July 2003 |
Local and global regulation of transcription initiation in bacteria
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journal
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August 2016 |
Estimating mutual information
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June 2004 |
Shared control of gene expression in bacteria by transcription factors and global physiology of the cell
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journal
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January 2013 |
Detecting and Removing Inconsistencies between Experimental Data and Signaling Network Topologies Using Integer Linear Programming on Interaction Graphs
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September 2013 |
Determining the Control Circuitry of Redox Metabolism at the Genome-Scale
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April 2014 |
Model-based redesign of global transcription regulation
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February 2009 |
Functional determinants of transcription factors in Escherichia coli: protein families and binding sites
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journal
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February 2003 |
Nonsmooth nonnegative matrix factorization (nsNMF)
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journal
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March 2006 |
Deciphering Fur transcriptional regulatory network highlights its complex role beyond iron metabolism in Escherichia coli
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September 2014 |
Wisdom of crowds for robust gene network inference
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July 2012 |
Evidence classification of high-throughput protocols and confidence integration in RegulonDB
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January 2013 |
Metagenes and molecular pattern discovery using matrix factorization
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March 2004 |
Multi-omics integration accurately predicts cellular state in unexplored conditions for Escherichia coli
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October 2016 |
Decoding genome-wide GadEWX-transcriptional regulatory networks reveals multifaceted cellular responses to acid stress in Escherichia coli
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August 2015 |
Deciphering the transcriptional regulatory logic of amino acid metabolism
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journal
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November 2011 |
Capturing Heterogeneity in Gene Expression Studies by Surrogate Variable Analysis
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journal
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January 2007 |
COLOMBOS v3.0: leveraging gene expression compendia for cross-species analyses: Table 1.
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journal
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November 2015 |
Finding community structure in very large networks
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December 2004 |
The architecture of ArgR-DNA complexes at the genome-scale in Escherichia coli
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journal
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March 2015 |
DAVID: Database for Annotation, Visualization, and Integrated Discovery
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journal
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January 2003 |
limma powers differential expression analyses for RNA-sequencing and microarray studies
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journal
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January 2015 |
Mapping and manipulating the Mycobacterium tuberculosis transcriptome using a transcription factor overexpression-derived regulatory network
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November 2014 |
Prokaryotic genome regulation: A revolutionary paradigm
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journal
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January 2012 |
The Bacterial Response Regulator ArcA Uses a Diverse Binding Site Architecture to Regulate Carbon Oxidation Globally
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October 2013 |
Genome-scale reconstruction of the Lrp regulatory network in Escherichia coli
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journal
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December 2008 |
Systems biology definition of the core proteome of metabolism and expression is consistent with high-throughput data
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journal
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August 2015 |
Stability-driven nonnegative matrix factorization to interpret spatial gene expression and build local gene networks
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April 2016 |
Genome-scale reconstruction of the sigma factor network in Escherichia coli: topology and functional states
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journal
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January 2014 |
Gene Expression Prediction by Soft Integration and the Elastic Net—Best Performance of the DREAM3 Gene Expression Challenge
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February 2010 |
Genome-scale Analysis of Escherichia coli FNR Reveals Complex Features of Transcription Factor Binding
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June 2013 |
Functional organisation of Escherichia coli transcriptional regulatory network
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journal
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August 2008 |
Genome-wide Reconstruction of OxyR and SoxRS Transcriptional Regulatory Networks under Oxidative Stress in Escherichia coli K-12 MG1655
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journal
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August 2015 |
Large-Scale Mapping and Validation of Escherichia coli Transcriptional Regulation from a Compendium of Expression Profiles
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January 2007 |
Probabilistic integrative modeling of genome-scale metabolic and regulatory networks in Escherichia coli and Mycobacterium tuberculosis
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journal
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September 2010 |
Few regulatory metabolites coordinate expression of central metabolic genes in Escherichia coli
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journal
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January 2017 |
Integrating high-throughput and computational data elucidates bacterial networks
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journal
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May 2004 |
Subsystem Identification Through Dimensionality Reduction of Large-Scale Gene Expression Data
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July 2003 |
The DNA-binding network of Mycobacterium tuberculosi s
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journal
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January 2015 |
Comparing Clusterings by the Variation of Information
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book
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January 2003 |
Flexible structure alignment by chaining aligned fragment pairs allowing twists
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journal
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September 2003 |