Connecting quantitative regulatory-network models to the genome (original) (raw)

Inferring quantitative models of regulatory networks from expression data

Iftach Nachman

Bioinformatics, 2004

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Learning global models of transcriptional regulatory networks from data

Aviv Madar

Methods in molecular biology (Clifton, N.J.), 2009

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Inferring latent gene regulatory network kinetics

Ivan Vujacic

Statistical Applications in Genetics and Molecular Biology, 2013

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Reconstruction of Escherichia coli transcriptional regulatory networks via regulon-based associations

HOSSEIN ZARE

BMC Systems Biology, 2009

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Inferring transcriptional regulatory networks from high-throughput data

Ming Zhan

Bioinformatics, 2007

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Inferring gene regulatory networks by integrating static and dynamic data

Lucia Sacchi

International journal of …, 2007

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Reconstructing genome-wide regulatory network of E. coli using transcriptome data and predicted transcription factor activities

Julie Dickerson

BMC Bioinformatics, 2011

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Assigning numbers to the arrows: Parameterizing a gene regulation network by using accurate expression kinetics

Michal Ronen

Proceedings of the National Academy of Sciences, 2002

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Modelling in molecular biology: describing transcription regulatory networks at different scales

Alvis Chen

Philosophical Transactions of The Royal Society B: Biological Sciences, 2006

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An Integrated Approach to Reconstructing Genome-Scale Transcriptional Regulatory Networks

Daniel Noguera

PLOS Computational Biology, 2015

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Integrative inference of gene-regulatory networks in Escherichia coli using information theoretic concepts and sequence analysis

Reinhard Guthke

BMC Systems Biology, 2010

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Gene regulatory network inference: Data integration in dynamic models—A review

Reinhard Guthke

Biosystems, 2009

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A computational framework for gene regulatory network inference that combines multiple methods and datasets

Philipp Antczak

BMC Systems Biology, 2011

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Curating a Large-Scale Regulatory Network by Evaluating Its Consistency with Expression Datasets

Centre Atlantique

Lecture Notes in Computer Science, 2009

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Transcriptional regulatory network refinement and quantification through kinetic modeling, gene expression microarray data and information theory

Kagan Tuncay

BMC bioinformatics, 2007

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Inferring the conservative causal core of gene regulatory networks

Frank Emmert-Streib

BMC Systems Biology, 2010

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A model-based optimization framework for the inference of regulatory interactions using time-course DNA microarray expression data

Carlos mascagnini paredes

BMC …, 2007

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A guide to gene regulatory network inference for obtaining predictive solutions: Underlying assumptions and fundamental biological and data constraints

Ralf Takors

Biosystems, 2018

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Identifying gene regulatory networks from experimental data

Ting Chen

2001

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

José Faria

2013

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Inference of gene regulatory networks and compound mode of action from time course gene expression profiles

Giusy della gatta

Bioinformatics, 2006

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Learning transcriptional regulation on a genome scale: a theoretical analysis based on gene expression data

Ming Lok Wu

Briefings in bioinformatics, 2012

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Large-Scale Mapping and Validation of Escherichia coli Transcriptional Regulation from a Compendium of Expression Profiles

Jeremiah Faith, James E Collins

PLoS Biology, 2007

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Estimating dynamic models for gene regulation networks

Jiguo Cao

Bioinformatics, 2008

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The Inferelator 2.0: a scalable framework for reconstruction of dynamic regulatory network models

Aviv Madar

Conference proceedings : ... Annual International Conference of the IEEE Engineering in Medicine and Biology Society. IEEE Engineering in Medicine and Biology Society. Annual Conference, 2009

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Probabilistic integrative modeling of genome-scale metabolic and regulatory networks in Escherichia coli and Mycobacterium tuberculosis

Nathan Price

Proceedings of the National Academy of Sciences, 2010

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Faculty of 1000 evaluation for The global transcriptional regulatory network for metabolism in Escherichia coli exhibits few dominant functional states

John McKinney

F1000 - Post-publication peer review of the biomedical literature

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The Inferelator: an algorithm for learning parsimonious regulatory networks from systems-biology data sets de novo

Paul Shannon

Genome Biology, 2006

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A causal inference approach for constructing transcriptional regulatory networks

Mark Van Der Laan

Bioinformatics, 2005

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Functional States of the Genome-Scale Escherichia Coli Transcriptional Regulatory System

Andrew Joyce

PLoS Computational Biology, 2009

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Gene networks as a tool to understand transcriptional regulation

Fábio Vicente

Genetics and molecular research : GMR, 2006

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Modelling the Regulation of Gene Expression in Genetic Regulatory Networks

Maria Schilstra

2001

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Inference of gene regulatory networks using S-system: a unified approach

Lijun Qian

IET Systems Biology, 2010

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