RegulonDB (version 5.0): Escherichia coli K-12 transcriptional regulatory network, operon organization, and growth conditions

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RegulonDB (version 4.0): transcriptional regulation, operon organization and growth conditions in Escherichia coli K-12

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RegulonDB (version 3.2): transcriptional regulation and operon organization in Escherichia coli K-12

Salgado, H. (2001) · Nucleic Acids Research · doi:10.1093/nar/29.1.72 · Cited by 256

Sigma70 Promoters in Escherichia coli: Specific Transcription in Dense Regions of Overlapping Promoter-like Signals

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Dissecting the PhoP regulatory network of Escherichia coli and Salmonella enterica

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Prokaryotic Systems Biology

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Subspace Clustering of DNA Microarray Data

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Operon Prediction Using Neural Network Based on Multiple Information of Log-Likelihoods

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An Improved Position Weight Matrix Method Based on an Entropy Measure for the Recognition of Prokaryotic Promoters

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Reconstruction of Genome-Scale Metabolic Networks

Hefzi, H., Palsson, B. Ø., & Lewis, N. E. (2012) · Elsevier eBooks · doi:10.1016/b978-0-12-385944-0.00012-5 · Cited by 2

USING NEIGHBORHOOD GRAPHS FOR THE INVESTIGATION OF E. COLI GENE CLUSTERS

Scharl, T., & Leisch, F. (2008) · Research Online (University of Wollongong) · Cited by 2

Athena: Modular CAM/CAD Software for Synthetic BiologyPreprint

Chandran, D., Bergmann, F., & Sauro, H. M. (2009) · arXiv (Cornell University) · doi:10.48550/arxiv.0902.2598 · Cited by 2

Determining the Properties of Gene Regulatory Networks from Expression Data

Liebovitch, L. S., Shehadeh, L. A., Jirsa, V., Hütt, M. ‐., & Marr, C. (2010) · IGI Global eBooks · doi:10.4018/978-1-60566-685-3.ch017 · Cited by 2

Signed Network Structural Analysis and Applications with a Focus on Balance Theory

Arefkashfi, S. (2019) · ResearchSpace (University of Auckland) · Cited by 2

Trace metals availability controls terminal electron acceptor utilization in Escherichia coliPreprint

Ricciardelli, A., de Pins, B., Brusca, J., Correggia, M., Iorio, L. D., Cascone, M., Giardina, M., Castaldi, S., Isticato, R., Iacono, R., et al. (2025) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2025.01.08.631794 · Cited by 4

Advances in bacterial glycoprotein engineering: A critical review of current technologies, emerging challenges, and future directions

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Understanding the Model and the Menace: a Postgenomic View ofEscherichia Coli

Chaudhuri, R. R., & Thomas, G. H. (2014) · ASM Press eBooks · doi:10.1128/9781555815530.ch2 · Cited by 1

A PCA-Based approach for gene target selection to improve industrial strains

Jonnalagadda, S., & Srinivasan, R. (2007) · Computer-aided chemical engineering/Computer aided chemical engineering · doi:10.1016/s1570-7946(07)80193-3 · Cited by 1

Automated design of bacterial genome sequences

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Annotating bacterial genomes

Médigue, C., & Danchin, A. (2008) · Springer eBooks · doi:10.1007/978-3-211-75123-7_9 · Cited by 1

Reconstructing transcriptional Regulatory Networks using data integration and Text Mining

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Quantitative analysis of translational coupling in Escherichia coli

Zhang, S. (2012) · Illinois Digital Environment for Access to Learning and Scholarship (University of Illinois at Urbana-Champaign) · Cited by 1

Operon Prediction Based On an Iterative Self-learning Algorithm*

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Inferring Functional Relationships from Conservation of Gene Order

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Genome evolution and regulatory network structure in bacteria

Molina, N. (2010) · edoc (University of Basel) · doi:10.5451/unibas-005551395 · Cited by 1

Comparative Pathway Prediction Via Unified Graph Modeling of Genomic Structure Information

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The Application of Support Vector Machine to Operon Prediction

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A Revolutionary Paradigm of Bacterial Genome Regulation

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Decision Diagrams for Qualitative Biological Models

Borgne, M. L., & Veber, P. (2007) · HAL · Cited by 1

Quantitative RNA pseudouridine landscape reveals dynamic modification patterns and evolutionary conservation across bacterial speciesPreprint

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C. Elegans Metabolic Gene Regulatory Networks: A Dissertation

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Inferring E. coli SOS Response Pathway from Gene Expression Data Using IST-DBN with Time Lag Estimation

Chai, L. E., Mohamad, M. S., Deris, S., Chong, C. K., & Choon, Y. W. (2013) · Studies in computational intelligence · doi:10.1007/978-3-642-37137-0_3

Genome wide analyses of the Escherichia coli primary and secondary transcriptomes

Alvarez, D. R. (2014) · White Rose eTheses Online (University of Leeds, The University of Sheffield, University of York)

Operon Prediction with Bayesian Classifiers

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Integrative bioinformatics of metabolic networks.

Notebaart, R. A. (2009) · Radboud Repository (Radboud University)

Comparisons of statistical modeling for constructing gene regulatory networks

Chen, X. (2009) · cIRcle (University of British Columbia) · doi:10.14288/1.0066924

AUTOMATIC COMPUTATIONAL DESIGN OF SYNTHETIC GENOMES

Carrera, J. (2012) · RiuNet (Universitat Politècnica de València) · doi:10.4995/thesis/10251/35380

Gene Interactions Sub-networks and Soft Computing

Das, R., & Mitra, S. (2009) · Studies in computational intelligence · doi:10.1007/978-3-540-92916-1_13

Qualitative response of interaction networks: application to the validation of biological models

Siegel, A., Guziołowski, C., Veber, P., Radulescu, O., & Borgne, M. L. (2007) · PAMM · doi:10.1002/pamm.200700379

Scalable learning of large networks

Roy, S., Plis, S., Werner‐Washburne, M., & Lane, T. D. R. (2009) · IET Systems Biology · doi:10.1049/iet-syb.2008.0161

Condensing Biochemistry into Gene Regulatory Networks

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SEARCHPATTOOL: a new method for mining the most specific frequent patterns for binding sites with application to prokaryotic DNA sequences

Elloumi, F., & Nason, M. (2007) · BMC Bioinformatics · doi:10.1186/1471-2105-8-354

An MM-Based Optimization Algorithm for Sparse Linear Modeling on Microarray Data Analysis

Chen, X., & Gottardo, R. (2009) · International Conference on Bioinformatics and Biomedical Engineering · doi:10.1109/icbbe.2009.5162334

Transcription Factor Discovery using Support Vector Machines and Heterogeneous Data

Barbe, J. F., Tewfik, A. H., & Khodursky, A. B. (2007) · IEEE International Workshop on Genomic Signal Processing and Statistics · doi:10.1109/gensips.2007.4365812

Reconstruction of Regulator Activity in E. coli Post-Transcription Processes

Wang, R., Jin, G., Zhang, X.-S., & Chen, L. (2008) · IEEE International Conference on Bioinformatics and Biomedicine (BIBM) · doi:10.1109/bibm.2008.18

A comparative analysis on computational methods for fitting an ERGM to biological network data

Saha, S., & Begum, M. (2013) · Cardinal Scholar (Ball State University)

Network-based mixture models for genomic data

Wei, P. (2009) · University of Minnesota Digital Conservancy (University of Minnesota)

INFERRING MECHANISM-BASED GENE REGULATORY NETWORK MODELS FROM EXPRESSION AND SEQUENCE DATA

Pan, Y. (2009)

Trace: Tennessee Research and Creative Exchange

Shah, P., & Gilchrist, M. A. (2010)

SURVEY AND SUMMARY On the power and limits of evolutionary conservation—unraveling bacterial gene regulatory networks

Baumbach, J. (2010)

Genomic Data Mining for the Computational Prediction of Small Non-coding RNA Genes

Tran, T. (2009) · SMARTech Repository (Georgia Institute of Technology)

Building and validating gene regulatory networks (GRN) with delays from multiple data sources

Liu, W. (2015) · doi:10.32657/10356/65383

Sequence Analysis of the Bacterial Protein Elongation Factor P

Lau, L. Y. S. (2008) · UWSpace (University of Waterloo)

Genome-comparative computational approach for investigating prokaryotic ORF expression potentialities, in relation with potentially high transcriptionPreprint

Sinoquet, C., Demey, S., & Braun, F. (2007) · HAL

Bayesian Modeling for High Throughput Genomic Data.

Hu, M. (2010) · Deep Blue (University of Michigan)

A modelling and computational study of the frustration index in signed networksPreprint

Aref, S., Mason, A., & Wilson, M. C. (2016) · arXiv (Cornell University) · doi:10.48550/arxiv.1611.09030

A Semi-Supervised Approach to GRN Inference Using Learning and Optimization

Daoudi, M., Meshoul, S., & Boucherkha, S. (2021) · International Journal of Applied Metaheuristic Computing · doi:10.4018/ijamc.2021100109

Comparative Functional Analysis and Identification of Regulatory Control in Gene Networks Using the Leucine-Responsive Regulatory protein and its Regulon as a Model System

Lintner, R. E. (2007) · OhioLink ETD Center (Ohio Library and Information Network)

Subspace Clustering of DNA Microarray Data

Tchagang, A., Famili, F. A., & Pan, Y. (2019) · IGI Global eBooks · doi:10.4018/978-1-5225-8903-7.ch009

Introduction

Gong, M., Cai, Q., Ma, L., Wang, S., & Lei, Y. (2017) · Springer eBooks · doi:10.1007/978-981-10-4558-5_1

Prokaryotic Systems Biology

Kacmarczyk, T. J., Waltman, P., & Bonneau, R. (2017) · Wiley eBooks · doi:10.1002/9781119312994.apr0374

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RegulonDB (version 5.0): Escherichia coli K-12 transcriptional regulatory network, operon

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RegulonDB (version 4.0): transcriptional regulation, operon organization and growth conditions in Escherichia coli K-12

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RegulonDB (version 3.0): transcriptional regulation and operon organization in Escherichia coli K-12

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