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

Network motifs in the transcriptional regulation network of Escherichia coli

Shen-Orr, S. S., Milo, R., Mangan, S., & Alon, U. S. (2002) · Nature Genetics · doi:10.1038/ng881 · Cited by 2,970

EcoCyc: a comprehensive database resource for Escherichia coli

Keseler, I. M. (2004) · Nucleic Acids Research · doi:10.1093/nar/gki108 · Cited by 737

Identifying global regulators in transcriptional regulatory networks in bacteria

Martínez‐Antonio, A., & Collado‐Vides, J. (2003) · Current Opinion in Microbiology · doi:10.1016/j.mib.2003.09.002 · Cited by 547

Parallel changes in gene expression after 20,000 generations of evolution in Escherichia coli

Cooper, T. F., Rozen, D. E., & Lenski, R. E. (2003) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0334340100 · Cited by 440

Operons in Escherichia coli: genomic analyses and predictions.

Salgado, H., Moreno-Hagelsieb, G., Smith, T., & Collado-Vides, J. (2000) · Proceedings of the National Academy of Sciences of the United States of America · doi:10.1073/pnas.110147297 · Cited by 411

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

Salgado, H. (2003) · Nucleic Acids Research · doi:10.1093/nar/gkh140 · Cited by 262

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

Huerta, A. M., & Collado‐Vides, J. (2003) · Journal of Molecular Biology · doi:10.1016/j.jmb.2003.07.017 · Cited by 233

Dissecting the PhoP regulatory network of Escherichia coli and Salmonella enterica

Zwir, I. J. S., Shin, D., Kato, A., Nishino, K., Latifi, T. N., Solomon, F., Hare, J. M., Huang, H. V., & Groisman, E. A. (2005) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0408238102 · Cited by 210

An extended transcriptional regulatory network of Escherichia coli and analysis of its hierarchical structure and network motifs

Ma, H.-W. (2004) · Nucleic Acids Research · doi:10.1093/nar/gkh1009 · Cited by 208

Large-scale mapping and validation of Escherichia coli transcriptional regulation from a compendium of expression profiles

Faith, J. J., Hayete, B., Thaden, J. T., Mogno, I., Wierzbowski, J., Cottarel, G., Kasif, S., Collins, J. J., & Gardner, T. S. (2007) · PLoS Biology · doi:10.1371/journal.pbio.0050008 · Cited by 1,563

Gene co-expression analysis for functional classification and gene–disease predictions

van Dam, S., Võsa, U., van der Graaf, A., Franke, L., & de Magalhães, J. P. (2017) · Briefings in Bioinformatics · doi:10.1093/bib/bbw139 · Cited by 995

Reconstruction of biochemical networks in microorganisms

Feist, A. M., Herrgård, M. J., Thiele, I., Reed, J. L., & Palsson, B. Ø. (2008) · Nature Reviews Microbiology · doi:10.1038/nrmicro1949 · Cited by 874

Using graph theory to analyze biological networks

Pavlopoulos, G. A., Secrier, M., Moschopoulos, C. N., Soldatos, T. G., Κοσσίδα, Σ., Aerts, J. A., Schneider, R., & Bagos, P. G. (2011) · BioData Mining · doi:10.1186/1756-0381-4-10 · Cited by 821

Mistranslation of Membrane Proteins and Two-Component System Activation Trigger Antibiotic-Mediated Cell Death

Kohanski, M. A., Dwyer, D. J., Wierzbowski, J., Cottarel, G., & Collins, J. J. (2008) · Cell · doi:10.1016/j.cell.2008.09.038 · Cited by 576

RegulonDB (version 6.0): gene regulation model of Escherichia coli K-12 beyond transcription, active (experimental) annotated promoters and Textpresso navigation

Gama‐Castro, S., Jacinto, V. J., Peralta-Gil, M., Santos-Zavaleta, A., Penaloza-Spinola, M. I., Contreras‐Moreira, B., Segura-Salazar, J., Muñiz-Rascado, L., Martínez‐Flores, I., Salgado, H., et al. (2007) · Nucleic Acids Research · doi:10.1093/nar/gkm994 · Cited by 491

Gyrase inhibitors induce an oxidative damage cellular death pathway in Escherichia coli

Dwyer, D. J., Kohanski, M. A., Hayete, B., & Collins, J. J. (2007) · Molecular Systems Biology · doi:10.1038/msb4100135 · Cited by 470

Graph theory and networks in Biology

Mason, O., & Verwoerd, M. (2007) · IET Systems Biology · doi:10.1049/iet-syb:20060038 · Cited by 410

Programming gene expression with combinatorial promoters

Cox, R. S., Surette, M. G., & Elowitz, M. B. (2007) · Molecular Systems Biology · doi:10.1038/msb4100187 · Cited by 359

Centrality Analysis Methods for Biological Networks and Their Application to Gene Regulatory Networks

Koschützki, D., & Schreiber, F. (2008) · Gene Regulation and Systems Biology · doi:10.4137/grsb.s702 · Cited by 352

What are DNA sequence motifs?

D’haeseleer, P. (2006) · Nature Biotechnology · doi:10.1038/nbt0406-423 · Cited by 339

A bagging SVM to learn from positive and unlabeled examples

Mordelet, F., & Vert, J. (2013) · Pattern Recognition Letters · doi:10.1016/j.patrec.2013.06.010 · Cited by 358

Regulation of gene expression by small non‐coding RNAs: a quantitative view

Shimoni, Y., Friedlander, G., Hetzroni, G., Niv, G., Altuvia, S., Biham, O., & Margalit, H. (2007) · Molecular Systems Biology · doi:10.1038/msb4100181 · Cited by 323

Evolvability and hierarchy in rewired bacterial gene networks

Isalan, M., Lemerle, C., Michalodimitrakis, K., Horn, C., Beltrao, P., Raineri, E., Garriga-Canut, M., & Serrano, L. (2008) · Nature · doi:10.1038/nature06847 · Cited by 307

Escherichia coli Histone-Like Protein H-NS Preferentially Binds to Horizontally Acquired DNA in Association with RNA Polymerase

Oshima, T., Ishikawa, S., Kurokawa, K., Hirofumi, A. I. B. A., & Ogasawara, N. (2006) · DNA Research · doi:10.1093/dnares/dsl009 · Cited by 297

High-affinity DNA binding sites for H-NS provide a molecular basis for selective silencing within proteobacterial genomes

Lang, B., Blot, N., Bouffartigues, E., Buckle, M., Geertz, M., Gualerzi, C. O., Mavathur, R. N., Muskhelishvili, G., Pon, C. L., Rimsky, S., et al. (2007) · Nucleic Acids Research · doi:10.1093/nar/gkm712 · Cited by 269

Genome-Wide Identification of Transcription Start Sites, Promoters and Transcription Factor Binding Sites in E. coli

Mendoza-Vargas, A., Olvera, L., Olvera, M., Grande, R., Vega‐Alvarado, L., Taboada, B., Jacinto, V. J., Salgado, H., Juárez, K., Contreras‐Moreira, B., et al. (2009) · PLoS ONE · doi:10.1371/journal.pone.0007526 · Cited by 264

Diversity of Human Vaginal Bacterial Communities and Associations with Clinically Defined Bacterial Vaginosis

Oakley, B. B., Fiedler, T. L., Marrazzo, J. M., & Fredricks, D. N. (2008) · Applied and Environmental Microbiology · doi:10.1128/aem.02884-07 · Cited by 264

Many Microbe Microarrays Database: uniformly normalized Affymetrix compendia with structured experimental metadata

Faith, J. J., Driscoll, M. E., Fusaro, V. A., Cosgrove, E. J., Hayete, B., Juhn, F., Schneider, S. J., & Gardner, T. S. (2007) · Nucleic Acids Research · doi:10.1093/nar/gkm815 · Cited by 259

Integrated biclustering of heterogeneous genome-wide datasets for the inference of global regulatory networks

Reiss, D. J., Baliga, N. S., & Bonneau, R. (2006) · BMC Bioinformatics · doi:10.1186/1471-2105-7-280 · Cited by 253

Prokaryotic genome regulation: multifactor promoters, multitarget regulators and hierarchic networks

Ishihama, A. (2010) · FEMS Microbiology Reviews · doi:10.1111/j.1574-6976.2010.00227.x · Cited by 248

High-Throughput, Kingdom-Wide Prediction and Annotation of Bacterial Non-Coding RNAs

Livny, J., Teonadi, H., Livny, M., & Waldor, M. K. (2008) · PLoS ONE · doi:10.1371/journal.pone.0003197 · Cited by 225

Transcription factor-based biosensors in biotechnology: current state and future prospects

Mahr, R., & Frunzke, J. (2015) · Applied Microbiology and Biotechnology · doi:10.1007/s00253-015-7090-3 · Cited by 220

Small RNAs encoded within genetic islands of Salmonella typhimurium show host-induced expression and role in virulence

Padalon‐Brauch, G., Hershberg, R., Elgrably‐Weiss, M., Baruch, K., Rosenshine, I., Margalit, H., & Altuvia, S. (2008) · Nucleic Acids Research · doi:10.1093/nar/gkn050 · Cited by 220

Comparative Genomic Reconstruction of Transcriptional Regulatory Networks in Bacteria

Rodionov, D. A. (2007) · Chemical Reviews · doi:10.1021/cr068309+ · Cited by 218

Novelty and Uniqueness Patterns of Rare Members of the Soil Biosphere

Elshahed, M. S., Youssef, N. H., Spain, A. M., Sheik, C. S., Najar, F. Z., Sukharnikov, L. O., Roe, B. A., Davis, J. P., Schloss, P. D., Bailey, V., et al. (2008) · Applied and Environmental Microbiology · doi:10.1128/aem.00410-08 · Cited by 217

Critical Dynamics in Genetic Regulatory Networks: Examples from Four Kingdoms

Balleza, E., Alvarez-Buylla, E. R., Chaos, Á., Kauffman, S. A., Shmulevich, I., & Aldana, M. (2008) · PLoS ONE · doi:10.1371/journal.pone.0002456 · Cited by 205

Tracking, tuning, and terminating microbial physiology using synthetic riboregulators

Callura, J. M., Dwyer, D. J., Isaacs, F. J., Cantor, C. R., & Collins, J. J. (2010) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1009747107 · Cited by 198

SIRENE: supervised inference of regulatory networks

Mordelet, F., & Vert, J. (2008) · Bioinformatics · doi:10.1093/bioinformatics/btn273 · Cited by 191

Comparing Statistical Methods for Constructing Large Scale Gene Networks

Allen, J. D., Xie, Y., Chen, M., Girard, L., & Xiao, G. (2012) · PLoS ONE · doi:10.1371/journal.pone.0029348 · Cited by 186

Ten years of bacterial genome sequencing: comparative-genomics-based discoveries

Binnewies, T. T., Motro, Y., Hallin, P. F., Lund, O., Dunn, D., La, T., Hampson, D. J., Bellgard, M., Wassenaar, T. M., & Ussery, D. W. (2006) · Functional & Integrative Genomics · doi:10.1007/s10142-006-0027-2 · Cited by 184

Multidimensional annotation of the Escherichia coli K-12 genome

Karp, P. D., Keseler, I. M., Shearer, A. G., Latendresse, M., Krummenacker, M., Paley, S., Paulsen, I. T., Collado‐Vides, J., Gama‐Castro, S., Peralta-Gil, M., et al. (2007) · Nucleic Acids Research · doi:10.1093/nar/gkm740 · Cited by 186

The HU Regulon Is Composed of Genes Responding to Anaerobiosis, Acid Stress, High Osmolarity and SOS Induction

Oberto, J., Nabti, S., Jooste, V., Mignot, H., & Rouvière‐Yaniv, J. (2009) · PLoS ONE · doi:10.1371/journal.pone.0004367 · Cited by 170

Small Stress Response Proteins in Escherichia coli : Proteins Missed by Classical Proteomic Studies

Hemm, M. R., Paul, B. J., Miranda‐Ríos, J., Zhang, A., Soltanzad, N., & Storz, G. (2009) · Journal of Bacteriology · doi:10.1128/jb.00872-09 · Cited by 163

Integration of Horizontally Transferred Genes into Regulatory Interaction Networks Takes Many Million Years

Lercher, M. J., & Pál, C. (2007) · Molecular Biology and Evolution · doi:10.1093/molbev/msm283 · Cited by 172

Large‐scale 13C‐flux analysis reveals distinct transcriptional control of respiratory and fermentative metabolism in Escherichia coli

van Rijsewijk, B. R. B. H., Nanchen, A., Nallet, S., Kleijn, R. J., & Sauer, U. (2011) · Molecular Systems Biology · doi:10.1038/msb.2011.9 · Cited by 160

An innovative approach for testing bioinformatics programs using metamorphic testing

Chen, T. Y., Ho, J. W. K., Liu, H., & Xie, X. (2009) · BMC Bioinformatics · doi:10.1186/1471-2105-10-24 · Cited by 159

Regulatory and metabolic rewiring during laboratory evolution of ethanol tolerance in E. coli

Goodarzi, H., Bennett, B. D., Amini, S., Reaves, M. L., Hottes, A. K., Rabinowitz, J. D., & Tavazoie, S. (2010) · Molecular Systems Biology · doi:10.1038/msb.2010.33 · Cited by 156

Introduction to Network Analysis in Systems Biology

Ma’ayan, A. (2011) · Science Signaling · doi:10.1126/scisignal.2001965 · Cited by 151

Universality of Rank-Ordering Distributions in the Arts and Sciences

Martínez‐Mekler, G., Martínez, R. A., del Río, M. B., Mansilla, R., Miramóntes, P., & Cocho, G. (2009) · PLoS ONE · doi:10.1371/journal.pone.0004791 · Cited by 151

SwissRegulon: a database of genome-wide annotations of regulatory sites

Pachkov, M. V., Erb, I., Molina, N., & van Nimwegen, E. (2006) · Nucleic Acids Research · doi:10.1093/nar/gkl857 · Cited by 150

Functional organisation of Escherichia coli transcriptional regulatory network

Martínez‐Antonio, A., Janga, S. C., & Thieffry, D. (2008) · Journal of Molecular Biology · doi:10.1016/j.jmb.2008.05.054 · Cited by 146

Multiple sequence alignment for phylogenetic purposes

Morrison, D. A. (2006) · Australian Systematic Botany · doi:10.1071/sb06020 · Cited by 146

Transcriptional regulatory networks in bacteria: from input signals to output responses

Seshasayee, A. S., Bertone, P., Fraser, G. M., & Luscombe, N. M. (2006) · Current Opinion in Microbiology · doi:10.1016/j.mib.2006.08.007 · Cited by 140

Learning biological networks: from modules to dynamics

Bonneau, R. (2008) · Nature Chemical Biology · doi:10.1038/nchembio.122 · Cited by 139

Optimal Signal Processing in Small Stochastic Biochemical Networks

Ziv, E., Nemenman, I. M., & Wiggins, C. H. (2007) · PLoS ONE · doi:10.1371/journal.pone.0001077 · Cited by 128

Rapid Changes in Gene Expression Dynamics in Response to Superoxide Reveal SoxRS-Dependent and Independent Transcriptional Networks

Blanchard, J. L., Wholey, W.-Y., Conlon, E. M., & Pomposiello, P. J. (2007) · PLoS ONE · doi:10.1371/journal.pone.0001186 · Cited by 135

Ecology of the Microbial Community Removing Phosphate from Wastewater under Continuously Aerobic Conditions in a Sequencing Batch Reactor

Ahn, J., Schroeder, S., Beer, M., McIlroy, S. J., Bayly, R. C., May, J. W., Vasiliadis, G., & Seviour, R. J. (2007) · Applied and Environmental Microbiology · doi:10.1128/aem.02080-06 · Cited by 121

Metabolic Regulation of a Bacterial Cell System with Emphasis onEscherichia coliMetabolism

Shimizu, K. (2013) · ISRN Biochemistry · doi:10.1155/2013/645983 · Cited by 117

Learning gene regulatory networks from only positive and unlabeled data

Cerulo, L., Elkan, C., & Ceccarelli, M. (2010) · BMC Bioinformatics · doi:10.1186/1471-2105-11-228 · Cited by 117

Comparing association network algorithms for reverse engineering of large-scale gene regulatory networks: synthetic versus real data

Soranzo, N., Ginestra Bianconi, A., & Altafini, C. (2007) · Bioinformatics · doi:10.1093/bioinformatics/btm163 · Cited by 115

Persistence drives gene clustering in bacterial genomes

Fang, G., Rocha, E. P., & Danchin, A. (2008) · BMC Genomics · doi:10.1186/1471-2164-9-4 · Cited by 112

Orthologous Transcription Factors in Bacteria Have Different Functions and Regulate Different Genes

Price, M. N., Dehal, P., & Arkin, A. P. (2007) · PLoS Computational Biology · doi:10.1371/journal.pcbi.0030175 · Cited by 105

Prokaryotic genome regulation: A revolutionary paradigm

Ishihama, A. (2012) · Proceedings of the Japan Academy Series B · doi:10.2183/pjab.88.485 · Cited by 108

RegTransBase - A Database Of Regulatory Sequences and Interactions in a Wide Range of \nProkaryotic Genomes

Kazakov, A. E., Cipriano, M. J., Novichkov, P. S., Minovitsky, S., Vinogradov, D. V., Arkin, A. P., Mironov, A. A., Gelfand, M. S., & Dubchak, I. L. (2006) · eScholarship (California Digital Library) · Cited by 105

The regulatory network of E. coli metabolism as a Boolean dynamical system exhibits both homeostasis and flexibility of response

Samal, A., & Jain, S. (2008) · BMC Systems Biology · doi:10.1186/1752-0509-2-21 · Cited by 103

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

Ernst, J., Beg, Q. K., Kay, K. A., Balázsi, G., Oltvai, Z. N., & Bar‐Joseph, Z. (2008) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1000044 · Cited by 103

The relative value of operon predictions

Brouwer, R. W. W., Kuipers, O. P., & van Hijum, S. A. F. T. (2008) · Briefings in Bioinformatics · doi:10.1093/bib/bbn019 · Cited by 101

Global gene expression analysis of glucose overflow metabolism in Escherichia coli and reduction of aerobic acetate formation

Veit, A., Polen, T., & Wendisch, V. F. (2006) · Applied Microbiology and Biotechnology · doi:10.1007/s00253-006-0680-3 · Cited by 97

A metabolic network in the evolutionary context: Multiscale structure and modularity

Spirin, V., Gelfand, M. S., Mironov, A. A., & Mirny, L. A. (2006) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0510258103 · Cited by 97

Co-Regulation of Metabolic Genes Is Better Explained by Flux Coupling Than by Network Distance

Notebaart, R. A., Teusink, B., Siezen, R. J., & Papp, B. (2008) · PLoS Computational Biology · doi:10.1371/journal.pcbi.0040026 · Cited by 96

Motifs emerge from function in model gene regulatory networks

Burda, Z., Krzywicki, A., Martin, O., & Zagórski, M. (2011) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1109435108 · Cited by 93

Network analyses in microbiome based on high-throughput multi-omics data

Liu, Z., Ma, A., Mathé, E. A., Merling, M. R., Ma, Q., & Liu, B. (2020) · Briefings in Bioinformatics · doi:10.1093/bib/bbaa005 · Cited by 93

Dissecting the logical types of network control in gene expression profiles

Marr, C., Geertz, M., Hütt, M. ‐., & Muskhelishvili, G. (2008) · BMC Systems Biology · doi:10.1186/1752-0509-2-18 · Cited by 95

Inference of Regulatory Gene Interactions from Expression Data Using Three‐Way Mutual Information

Watkinson, J., Liang, K., Wang, X., Zheng, T., & Anastassiou, D. (2009) · Annals of the New York Academy of Sciences · doi:10.1111/j.1749-6632.2008.03757.x · Cited by 85

Origins of Flagellar Gene Operons and Secondary Flagellar Systems

Liu, R., & Ochman, H. (2007) · Journal of Bacteriology · doi:10.1128/jb.00643-07 · Cited by 83

Identification of regulatory network topological units coordinating the genome-wide transcriptional response to glucose in Escherichia coli

Gutiérrez-Ríos, R.-M., Freyre-González, J. A., Reséndis-Antonio, O., Collado‐Vides, J., Saier, M. H., & Gosset, G. (2007) · BMC Microbiology · doi:10.1186/1471-2180-7-53 · Cited by 75

Theoretical and empirical quality assessment of transcription factor-binding motifs

Medina-Rivera, A., Abreu‐Goodger, C., Thomas‐Chollier, M., Salgado, H., Collado‐Vides, J., & van Helden, J. (2010) · Nucleic Acids Research · doi:10.1093/nar/gkq710 · Cited by 73

A linguistic rule-based approach to extract drug-drug interactions from pharmacological documents

Segura-Bédmar, I., Martı́nez, P., & de Pablo-Sánchez, C. (2011) · BMC Bioinformatics · doi:10.1186/1471-2105-12-s2-s1 · Cited by 79

Recombineering with tolC as a Selectable/Counter-selectable Marker: remodeling the rRNA Operons of Escherichia coli

DeVito, J. A. (2007) · Nucleic Acids Research · doi:10.1093/nar/gkm1084 · Cited by 72

Topology of the global regulatory network of carbon limitation in Escherichia coli

Hardiman, T., Lemuth, K., Keller, M. A., Reuß, M., & Siemann‐Herzberg, M. (2007) · Journal of Biotechnology · doi:10.1016/j.jbiotec.2007.08.029 · Cited by 70

Dynamics of the chili pepper transcriptome during fruit development

Martínez-López, L. A., Ochoa‐Alejo, N., & Martínez, O. (2014) · BMC Genomics · doi:10.1186/1471-2164-15-143 · Cited by 75

A predicted operon map for Mycobacterium tuberculosis

Roback, P., Beard, J. J., Baumann, D., Gille, C., Henry, K., Krohn, S., Wiste, H., Voskuil, M. I., Rainville, C., & Rutherford, R. S. (2007) · Nucleic Acids Research · doi:10.1093/nar/gkm518 · Cited by 70

Gene finding in metatranscriptomic sequences

Ismail, W. M., Ye, Y., & Tang, H. (2014) · BMC Bioinformatics · doi:10.1186/1471-2105-15-s9-s8 · Cited by 68

CoryneRegNet 4.0 – A reference database for corynebacterial gene regulatory networks

Baumbach, J. (2007) · BMC Bioinformatics · doi:10.1186/1471-2105-8-429 · Cited by 64

Resources, standards and tools for systems biology

Wierling, C., Herwig, R., & Lehrach, H. (2007) · Briefings in Functional Genomics and Proteomics · doi:10.1093/bfgp/elm027 · Cited by 69

Evolution of Penicillin-Binding Protein 2 Concentration and Cell Shape during a Long-Term Experiment withEscherichia coli

Philippe, N., Pélosi, L., Lenski, R. E., & Schneider, D. (2008) · Journal of Bacteriology · doi:10.1128/jb.01419-08 · Cited by 68

Introduction to systems biology

Bruggeman, F. J., Hornberg, J. J., Boogerd, F. C., & Westerhoff, H. V. (2007) · Birkhäuser Basel eBooks · doi:10.1007/978-3-7643-7439-6_1 · Cited by 65

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

Pauling, J., Röttger, R., Tauch, A., Azevedo, V., & Baumbach, J. (2011) · Nucleic Acids Research · doi:10.1093/nar/gkr883 · Cited by 65

Transcriptional regulation shapes the organization of genes on bacterial chromosomes

Janga, S. C., Salgado, H., & Martínez‐Antonio, A. (2009) · Nucleic Acids Research · doi:10.1093/nar/gkp231 · Cited by 65

Principles of transcriptional regulation and evolution of the metabolic system inE. coliPreprint

Seshasayee, A. S. N., Fraser, G. M., Babu, M. M., & Luscombe, N. M. (2008) · Genome Research · doi:10.1101/gr.079715.108 · Cited by 66

SutA is a bacterial transcription factor expressed during slow growth in Pseudomonas aeruginosa

Babin, B. M., Bergkessel, M., Sweredoski, M. J., Moradian, A., Hess, S. Y., Newman, D. K., & Tirrell, D. A. (2016) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1514412113 · Cited by 60

Gains and unexpected lessons from genome-scale promoter mapping

Shavkunov, K. S., Masulis, I. S., Tutukina, M. N., Деев, А. Д., & Ozoline, O. N. (2009) · Nucleic Acids Research · doi:10.1093/nar/gkp490 · Cited by 61

TRFBA: an algorithm to integrate genome-scale metabolic and transcriptional regulatory networks with incorporation of expression data

Motamedian, E., Mohammadi, M., Shojaosadati, S. A., & Heydari, M. (2016) · Bioinformatics · doi:10.1093/bioinformatics/btw772 · Cited by 64

Using RSAT oligo-analysis and dyad-analysis tools to discover regulatory signals in nucleic sequences

Defrance, M., Janky, R., Sand, O., & van Helden, J. (2008) · Nature Protocols · doi:10.1038/nprot.2008.98 · Cited by 63

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

Michoel, T., Smet, R. D., Joshi, A., de Peer, Y. V., & Kathleen Marchal, D. (2009) · BMC Systems Biology · doi:10.1186/1752-0509-3-49 · Cited by 60

Genetic Networks and Soft Computing

Mitra, S., Das, R., & Hayashi, Y. (2009) · IEEE Transactions on Computational Biology and Bioinformatics · doi:10.1109/tcbb.2009.39 · Cited by 60

CompareSVM: supervised, Support Vector Machine (SVM) inference of gene regularity networks

Gillani, Z., Akash, M. S. H., Rahaman, M. M., & Chen, M. (2014) · BMC Bioinformatics · doi:10.1186/s12859-014-0395-x · Cited by 60

Measuring partial balance in signed networks

Aref, S., & Wilson, M. C. (2017) · Journal of Complex Networks · doi:10.1093/comnet/cnx044 · Cited by 60

Genomic arrangement of bacterial operons is constrained by biological pathways encoded in the genome

Yin, Y.-B., Zhang, H., Olman, V., & Xu, Y. (2010) · Proceedings of the National Academy of Sciences of the United States of America · doi:10.1073/pnas.0911237107 · Cited by 47

Decomposing complex reaction networks using random sampling, principal component analysis and basis rotation

Barrett, C. L., Herrgård, M. J., & Palsson, B. Ø. (2009) · BMC Systems Biology · doi:10.1186/1752-0509-3-30 · Cited by 57

The impact of horizontal gene transfer in shaping operons and protein interaction networks – direct evidence of preferential attachment

Davids, W., & Zhang, Z. (2008) · BMC Evolutionary Biology · doi:10.1186/1471-2148-8-23 · Cited by 62

SYSTOMONAS -- an integrated database for systems biology analysis of Pseudomonas

Choi, C., Münch, R., Leupold, S., Klein, J., Siegel, I., Thielen, B., Benkert, B., Kucklick, M., Schobert, M., Barthelmes, J., et al. (2007) · Nucleic Acids Research · doi:10.1093/nar/gkl823 · Cited by 57

Global analysis of gene transcription regulation in prokaryotes

Zhou, D., & Yang, R. (2006) · Cellular and Molecular Life Sciences · doi:10.1007/s00018-006-6184-6 · Cited by 63

Universal patterns of purifying selection at noncoding positions in bacteriaPreprint

Molina, N., & van Nimwegen, E. (2007) · Genome Research · doi:10.1101/gr.6759507 · Cited by 57

Balance and frustration in signed networks

Aref, S., & Wilson, M. (2019) · MPG.PuRe (Max Planck Society) · Cited by 56

Automatic reconstruction of a bacterial regulatory network using Natural Language Processing

Rodriguez-Penagos, C. G., Salgado, H., Martínez‐Flores, I., & Collado‐Vides, J. (2007) · BMC Bioinformatics · doi:10.1186/1471-2105-8-293 · Cited by 55

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

Lemmens, K., Bie, T. D., Dhollander, T., Keersmaecker, S. C. J. D., Thijs, I. M. V., Schoofs, G., Weerdt, A. D., Moor, B. D., Vanderleyden, J., Collado‐Vides, J., et al. (2009) · Genome biology · doi:10.1186/gb-2009-10-3-r27 · Cited by 55

Determining the distance to monotonicity of a biological network: a graph-theoretical approach

Iacono, G., Ramezani, F., Soranzo, N., & Altafini, C. (2010) · IET Systems Biology · doi:10.1049/iet-syb.2009.0040 · Cited by 55

Compressed Adjacency Matrices: Untangling Gene Regulatory Networks

Dinkla, K., Westenberg, M. A., & van Wijk, J. J. (2012) · IEEE Transactions on Visualization and Computer Graphics · doi:10.1109/tvcg.2012.208 · Cited by 53

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

Conditions, G., Segura-salazar, J., & Collado‐Vides, J. (2005)

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

Salgado, H. (2003) · Nucleic Acids Research · doi:10.1093/nar/gkh140 · Cited by 262

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

Salgado, H. (2000) · Nucleic Acids Research · doi:10.1093/nar/28.1.65 · Cited by 68

RegulonDB (version 2.0): a database on transcriptional regulation in Escherichia coli

Salgado, H., Santos, A. D., Garza–Ramos, U., van Helden, J., Diaz, E., & Collado‐Vides, J. (1999) · Nucleic Acids Research · doi:10.1093/nar/27.1.59 · Cited by 46

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