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Three models of gene regulation in E. coli [chapter]

Julio Collado-Vides, Araceli M. Huerta, Kathleen Klose
1996 Lecture Notes in Computer Science  
Multidimensional annotation of the Escherichia coli K-12 17 51. Laing, E., K. Sidhu, and S. J. Hubbard. Laubacher, M. E., and S. E. Ades. 2008.  ...  Prediction 15 of transcriptional regulatory sites in the complete genome sequence of Escherichia 16 coli K-12. Bioinformatics 14:391-400. 17 99. Thomas-Chollier, M., O. Sand, J. V. Turatsinze, R.  ...  A C C E P T E D A C C E P T E D A C C E P T E D A C C E P T E D A C C E P T E D C C E P T E D Large-scale validation of regulation from expression profiles. A C C E P T E D  ... 
doi:10.1007/bfb0033205 fatcat:rwaw2bjo7rg47bj26xv6d3kclq

The EcoCyc Database

Peter D. Karp, Daniel Weaver, Suzanne Paley, Carol Fulcher, Aya Kubo, Anamika Kothari, Markus Krummenacker, Pallavi Subhraveti, Deepika Weerasinghe, Socorro Gama-Castro, Araceli M. Huerta, Luis Muñiz-Rascado (+10 others)
2014 EcoSal Plus  
EcoCyc is a bioinformatics database available at EcoCyc.org that describes the genome and the biochemical machinery of Escherichia coli K-12 MG1655.  ...  of E. coli.  ...  Many contributors to EcoCyc are listed on the EcoCyc credits page. The development of EcoCyc is funded by NIH grants GM77678 and GM71962 from the NIH National Institute of General Medical Sciences.  ... 
doi:10.1128/ecosalplus.esp-0009-2013 pmid:26442933 pmcid:PMC4243172 fatcat:7pymd2qgnfaw3bauwad5hox5l4

Multidimensional annotation of the Escherichia coli K-12 genome

P. D. Karp, I. M. Keseler, A. Shearer, M. Latendresse, M. Krummenacker, S. M. Paley, I. Paulsen, J. Collado-Vides, S. Gama-Castro, M. Peralta-Gil, A. Santos-Zavaleta, M. I. Penaloza-Spinola (+2 others)
2007 Nucleic Acids Research  
The annotation of the Escherichia coli K-12 genome in the EcoCyc database is one of the most accurate, complete and multidimensional genome annotations.  ...  The database contains extensive descriptions of E. coli cellular networks, describing its metabolic, transport and transcriptional regulatory processes.  ...  The contents of this publication are solely the responsibility of the authors and do not necessarily represent the official views of the National Institutes of Health.  ... 
doi:10.1093/nar/gkm740 pmid:17940092 pmcid:PMC2190727 fatcat:nafpzty6i5hb5cocwmquj6gzka

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

Hsi-Yuan Huang, Heng-Yi Chang, Chih-Hung Chou, Ching-Ping Tseng, Shinn-Ying Ho, Chi-Dung Yang, Yih-Wei Ju, Hsien-Da Huang
2008 Nucleic Acids Research  
Recently, numerous sRNAs and their targets were identified in Escherichia coli and in other bacteria.  ...  It is crucial to have a comprehensive resource concerning the annotation of small non-coding RNAs in microbial genomes.  ...  ACKNOWLEDGEMENTS Special thanks for financial support go to the National Research Program for Genomic Medicine (NRPGM), Taiwan.  ... 
doi:10.1093/nar/gkn852 pmid:19015153 pmcid:PMC2686527 fatcat:sndgilmwvjavdjpplule5zemsu

EcoCyc: a comprehensive database of Escherichia coli biology

I. M. Keseler, J. Collado-Vides, A. Santos-Zavaleta, M. Peralta-Gil, S. Gama-Castro, L. Muniz-Rascado, C. Bonavides-Martinez, S. Paley, M. Krummenacker, T. Altman, P. Kaipa, A. Spaulding (+9 others)
2010 Nucleic Acids Research  
EcoCyc (http://EcoCyc.org) is a comprehensive model organism database for Escherichia coli K-12 MG1655.  ...  From the scientific literature, EcoCyc captures the functions of individual E. coli gene products; their regulation at the transcriptional, post-transcriptional and protein level; and their or-  ...  The content is solely the responsibility of the authors and does not necessarily represent the official views of the National Institute of General Medical Sciences of the National Institutes of Health.  ... 
doi:10.1093/nar/gkq1143 pmid:21097882 pmcid:PMC3013716 fatcat:7lmoity5x5hqlaxjpk5r7bmqeq

CoryneRegNet 7, the reference database and analysis platform for corynebacterial gene regulatory networks

Mariana Teixeira Dornelles Parise, Doglas Parise, Rodrigo Bentes Kato, Josch Konstantin Pauling, Andreas Tauch, Vasco Ariston de Carvalho Azevedo, Jan Baumbach
2020 Scientific Data  
Transcriptional regulation is one of the most important mechanisms for bacterial adaptation and survival. These mechanisms may be understood via an organism's network of regulatory interactions.  ...  We present the newest version of CoryneRegNet, the reference database for corynebacterial regulatory interactions, available at www.exbio.wzw.tum.de/coryneregnet/.  ...  It contains up-to-date regulatory information about the model organisms C. glutamicum ATCC 13032, E. coli K-12, M. tuberculosis H37Rv and B. subtilis 168, and predicted TRNs of 224 target organisms of  ... 
doi:10.1038/s41597-020-0484-9 pmid:32393779 fatcat:7sl5anbwxjasbnh52xol2z3se4

EcoCyc: A comprehensive view of Escherichia coli biology

I. M. Keseler, C. Bonavides-Martinez, J. Collado-Vides, S. Gama-Castro, R. P. Gunsalus, D. A. Johnson, M. Krummenacker, L. M. Nolan, S. Paley, I. T. Paulsen, M. Peralta-Gil, A. Santos-Zavaleta (+2 others)
2009 Nucleic Acids Research  
EcoCyc (http://EcoCyc.org) provides a comprehensive encyclopedia of Escherichia coli biology. EcoCyc integrates information about the genome, genes and gene products; the metabolic network;  ...  ACKNOWLEDGEMENTS We thank Dr Robert Landick for suggesting the graphtrack display.  ...  and the regulatory network of E. coli.  ... 
doi:10.1093/nar/gkn751 pmid:18974181 pmcid:PMC2686493 fatcat:tk5atoclqfbiza3tcyayuksfue

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

H. Salgado
2006 Nucleic Acids Research  
RegulonDB is the internationally recognized reference database of Escherichia coli K-12 offering curated knowledge of the regulatory network and operon organization.  ...  It is currently the largest electronically-encoded database of the regulatory network of any free-living organism.  ...  Funding to pay the Open Access publication charges for this article was provided by the same grants. Conflict of interest statement. None declared.  ... 
doi:10.1093/nar/gkj156 pmid:16381895 pmcid:PMC1347518 fatcat:cndjte444jfnbm6fsdnk3uck2q

Metabolic network reconstruction and phenome analysis of the industrial microbe, Escherichia coli BL21(DE3)

Hanseol Kim, Sinyeon Kim, Sung Ho Yoon
2018 PLoS ONE  
Here, we present the comprehensive metabolic network model of E. coli BL21(DE3), named iHK1487, based on the latest genome reannotation and phenome analysis.  ...  Escherichia coli BL21(DE3) is an industrial model microbe for the mass-production of bioproducts such as biofuels, biorefineries, and recombinant proteins.  ...  Table 1 . 1 Comparison of the metabolic network models of E. coli BL21(DE3).  ... 
doi:10.1371/journal.pone.0204375 pmid:30240424 pmcid:PMC6150544 fatcat:n3qiu2jpcvb4baqpcief5fzrb4

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

S. Gama-Castro, V. Jimenez-Jacinto, M. Peralta-Gil, A. Santos-Zavaleta, M. I. Penaloza-Spinola, B. Contreras-Moreira, J. Segura-Salazar, L. Muniz-Rascado, I. Martinez-Flores, H. Salgado, C. Bonavides-Martinez, C. Abreu-Goodger (+7 others)
2007 Nucleic Acids Research  
The integration and new way of understanding the biology of a single cell such as Escherichia coli K12 is a major challenge in genomics and should be a milestone for systems biology.  ...  RegulonDB is currently one of the largest database offering curated knowledge of the transcriptional regulatory network of any free-living organism (1) .  ...  Conflict of interest statement. None declared.  ... 
doi:10.1093/nar/gkm994 pmid:18158297 pmcid:PMC2238961 fatcat:urvakflembbkdajpzep5jxiph4

Abasy Atlas v2.2: The most comprehensive and up-to-date inventory of meta-curated, historical, bacterial regulatory networks, their completeness and system-level characterization

Juan M. Escorcia-Rodríguez, Andreas Tauch, Julio A. Freyre-González
2020 Computational and Structural Biotechnology Journal  
To tackle this problem, the updated version of Abasy Atlas presented in this work provides historical snapshots of regulatory networks.  ...  We leverage the recently found constraint in the complexity of regulatory networks to develop a novel model to quantify the total number of regulatory interactions as a function of the genome size.  ...  Acknowledgments 830 We thank all anonymous reviewers for their positive and 831 encouraging suggestions that helped to improve the manuscript.  ... 
doi:10.1016/j.csbj.2020.05.015 pmid:32542109 pmcid:PMC7283102 fatcat:lbvc3hiu4ngsxmid6dibu5zyge

Abasy Atlas v2.2: The most comprehensive and up-to-date inventory of meta-curated, historical, bacterial regulatory networks, their completeness and system-level characterization [article]

Juan M. Escorcia-Rodríguez
2020 arXiv   pre-print
To tackle this problem, the updated version of Abasy Atlas presented in this work provides historical snapshots of regulatory networks.  ...  We leverage the recently found constraint in the complexity of regulatory networks to develop a novel model to quantify the total number of regulatory interactions as a function of the genome size.  ...  Acknowledgments We thank all anonymous reviewers for their positive and encouraging suggestions that helped to improve the manuscript.  ... 
arXiv:2005.01914v2 fatcat:c2wdcwocyvefng6obhizlbwy5i

Genome reannotation of Escherichia coli CFT073 with new insights into virulence

Chengwei Luo, Gang-Qing Hu, Huaiqiu Zhu
2009 BMC Genomics  
As one of human pathogens, the genome of Uropathogenic Escherichia coli strain CFT073 was sequenced and published in 2002, which was significant in pathogenetic bacterial genomics research.  ...  In addition, 94 pseudogenes annotated in RefSeq were thoroughly inspected and updated. The number of miscellaneous genes (sRNAs) has been updated from 6 in RefSeq to 46 in the reannotation.  ...  This work received partial support from the National Natural Science Foundation (30970667, 30770499, 30300071 and 10721403) of China.  ... 
doi:10.1186/1471-2164-10-552 pmid:19930606 pmcid:PMC2785843 fatcat:7nyy5tdarjhw7foaofxm7l62za

Proximity of intracellular regulatory networks to monotone systems

A. Ma'ayan, A. Lipshtat, R. Iyengar, E.D. Sontag
2008 IET Systems Biology  
The authors assess whether the topology of biological regulatory networks is similar to the topology of monotone systems.  ...  For this, three intracellular regulatory networks are analysed where links are specified for the directionality and the effects of interactions.  ...  2] SALGADO H., GAMA-CASTRO S., PERALTA-GIL M., ET AL.: 'RegulonDB (version 5.0): Escherichia coli K-12 transcriptional regulatory network, operon organization, and growth conditions', Nucleic Acids Res  ... 
doi:10.1049/iet-syb:20070036 pmid:18537452 pmcid:PMC2453221 fatcat:acodhcum3bgw5hlomoja4n6seq

The EcoCyc database: reflecting new knowledge aboutEscherichia coliK-12

Ingrid M. Keseler, Amanda Mackie, Alberto Santos-Zavaleta, Richard Billington, César Bonavides-Martínez, Ron Caspi, Carol Fulcher, Socorro Gama-Castro, Anamika Kothari, Markus Krummenacker, Mario Latendresse, Luis Muñiz-Rascado (+9 others)
2016 Nucleic Acids Research  
EcoCyc (EcoCyc.org) is a freely accessible, comprehensive database that collects and summarizes experimental data for Escherichia coli K-12, the beststudied bacterial model organism.  ...  EcoCyc now supports running and modifying E. coli metabolic models directly on the EcoCyc website.  ...  INTRODUCTION Over the course of many decades, thousands of researchers have contributed to the experimental study of Escherichia coli.  ... 
doi:10.1093/nar/gkw1003 pmid:27899573 pmcid:PMC5210515 fatcat:27ttoout2zgfdgwa5rvtbc3xqu
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