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Three models of gene regulation in E. coli
[chapter]
1996
Lecture Notes in Computer Science
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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
2014
EcoSal Plus
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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
2007
Nucleic Acids Research
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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
2008
Nucleic Acids Research
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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
2010
Nucleic Acids Research
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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
2020
Scientific Data
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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
2009
Nucleic Acids Research
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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
2006
Nucleic Acids Research
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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)
2018
PLoS ONE
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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
2007
Nucleic Acids Research
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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
2020
Computational and Structural Biotechnology Journal
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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]
2020
arXiv
pre-print
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Other Versions
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
2009
BMC Genomics
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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
2008
IET Systems Biology
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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
2016
Nucleic Acids Research
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The file type is application/pdf.
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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