نتائج البحث

Flexible gold standards for transcription factor regulatory interactions in Escherichia coli K-12: architecture of evidence types

• Authors : Paloma Lara; Socorro Gama-Castro; Heladia Salgado

Subjects: regulatory interactions; E. coli; evidence codes

• Source: Frontiers in Genetics, Vol 15 (2024)

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Sensory Systems and Transcriptional Regulation in Escherichia coli

• Authors : Georgette Femerling; Socorro Gama-Castro; Paloma Lara

Subjects: signal; gene regulation; sensory-response genetic units

• Source: Frontiers in Bioengineering and Biotechnology, Vol 10 (2022)

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Missing Links Between Gene Function and Physiology in Genomics

• Authors : Julio Collado-Vides; Pascale Gaudet; Víctor de Lorenzo

Subjects: gene ontology; microbial annotations; gene function

• Source: Frontiers in Physiology, Vol 13 (2022)

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The EcoCyc Database in 2021

• Authors : Ingrid M. Keseler; Socorro Gama-Castro; Amanda Mackie

Subjects: Escherichia coli; EcoCyc; model-organism database

• Source: Frontiers in Microbiology, Vol 12 (2021)

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Similarity corpus on microbial transcriptional regulation

• Authors : Oscar Lithgow-Serrano; Socorro Gama-Castro; Cecilia Ishida-Gutiérrez

Subjects: Corpus; Similarity; Transcriptional-regulation

• Source: Journal of Biomedical Semantics, Vol 10, Iss 1, Pp 1-14 (2019)

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A unified resource for transcriptional regulation in Escherichia coli K-12 incorporating high-throughput-generated binding data into RegulonDB version 10.0

• Authors : Alberto Santos-Zavaleta; Mishael Sánchez-Pérez; Heladia Salgado

Subjects: Transcriptional regulation; Transcriptomics; Integrative analyses

• Source: BMC Biology, Vol 16, Iss 1, Pp 1-12 (2018)

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Genome-Wide Mapping of Transcriptional Regulation and Metabolism Describes Information-Processing Units in Escherichia coli

• Authors : Daniela Ledezma-Tejeida; Cecilia Ishida; Julio Collado-Vides

Subjects: data integration; networks; transcriptional regulation

• Source: Frontiers in Microbiology, Vol 8 (2017)

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Effect of genomic distance on coexpression of coregulated genes in E. coli.

• Authors : Lucia Pannier; Enrique Merino; Kathleen Marchal

Subjects: Medicine; Science

• Source: PLoS ONE, Vol 12, Iss 4, p e0174887 (2017)

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Metabolic reconstruction and modeling of nitrogen fixation in Rhizobium etli.

• Authors : Osbaldo Resendis-Antonio; Jennifer L Reed; Sergio Encarnación

Subjects: Biology (General); QH301-705.5

• Source: PLoS Computational Biology, Vol 3, Iss 10, Pp 1887-1895 (2007)

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Development of genomic sciences in Mexico: a good start and a long way to go.

• Authors : Rafael Palacios; Julio Collado-Vides

Subjects: Biology (General); QH301-705.5

• Source: PLoS Computational Biology, Vol 3, Iss 9, Pp 1670-1673 (2007)

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BClass: A Bayesian Approach Based on Mixture Models for Clustering and Classification of Heterogeneous Biological Data

• Authors : Arturo Medrano-Soto; J. Andres Christen; Julio Collado-vides

Subjects: Statistics; HA1-4737

• Source: Journal of Statistical Software, Vol 13, Iss 1, Pp 1-18 (2004)

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Structural properties of prokaryotic promoter regions correlate with functional features.

• Authors : Pieter Meysman; Julio Collado-Vides; Enrique Morett

Subjects: Medicine; Science

• Source: PLoS ONE, Vol 9, Iss 2, p e88717 (2014)

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Transcription factors in Escherichia coli prefer the holo conformation.

• Authors : Yalbi Itzel Balderas-Martínez; Michael Savageau; Heladia Salgado

Subjects: Medicine; Science

• Source: PLoS ONE, Vol 8, Iss 6, p e65723 (2013)

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Correction: Transcription Factors in Prefer the Conformation.

• Authors : Yalbi Itzel Balderas-Martínez; Michael Savageau; Heladia Salgado

Subjects: Medicine; Science

• Source: PLoS ONE, Vol 8, Iss 8 (2013)

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Genome-wide identification of transcription start sites, promoters and transcription factor binding sites in E. coli.

• Authors : Alfredo Mendoza-Vargas; Leticia Olvera; Maricela Olvera

Subjects: Medicine; Science

• Source: PLoS ONE, Vol 4, Iss 10, p e7526 (2009)

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Selection for unequal densities of sigma70 promoter-like signals in different regions of large bacterial genomes.

• Authors : Araceli M Huerta; M Pilar Francino; Enrique Morett

Subjects: Genetics; QH426-470

• Source: PLoS Genetics, Vol 2, Iss 11, p e185 (2006)

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BClass: A Bayesian Approach Based on Mixture Models for Clustering and Classification of Heterogeneous Biological Data

• Authors : Julio Collado-Vides; J. Andres Christen; Arturo Medrano-Soto

Subjects: Statistics; HA1-4737

• Source: Journal of Statistical Software, Vol 13, Iss 2 (2004)

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RegulonDB v12.0.0 ...

• Authors : Heladia Salgado; Socorro Gama-Castro; Citlalli Mejia-Almonte

Subjects: Escherichia coli K12; Genetic regulation; Database

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RegulonDB 11.0: Comprehensive high-throughput datasets on transcriptional regulation in

• Authors : Víctor H, Tierrafría; Claire, Rioualen; Heladia, Salgado

Subjects: Escherichia coli K12; Operon; Escherichia coli

• Source: Microbial genomics. 8(5)

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Regulatory promoter architectures in the hands of thermodynamic modelling

• Authors : Julio Collado-Vides

Subjects: Genetics; Molecular Biology; Genetics (clinical)

• Source: Nature Reviews Genetics. 24:349-349

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Gene Regulation and Metabolism : Post-Genomic Computational Approaches

• Authors : Julio Collado-Vides; Ralf Hofestädt

Subjects: Genetic regulation; Molecular biology--Mathematical models; Genetics--Mathematical modelsSCIENCE / Life Sciences / Molecular Biology

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RegulonDB 11.0: Comprehensive high-throughput datasets on transcriptional regulation in Escherichia coli K-12

• Authors : Julio Collado-Vides

Subjects: Escherichia coli K-12; Regulatory network; Regulation

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Sensory Systems and Transcriptional Regulation in

• Authors : Georgette, Femerling; Socorro, Gama-Castro; Paloma, Lara

• Source: Frontiers in bioengineering and biotechnology. 10

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Integrative Approaches to Molecular Biology

• Authors : Julio Collado-Vides; Boris Magasanik; Temple F. Smith

Subjects: Molecular biology--CongressesMEDICAL / Neuroscience

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Limits to a classic paradigm: most transcription factors in E. coli regulate genes involved in multiple biological processes

• Authors : Daniela Ledezma-Tejeida; Julio Collado-Vides; Luis Altamirano-Pacheco

Subjects: Metabolic network; Data Resources and Analyses; Computational biology

• Source: Nucleic Acids Research

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In the pursuit of semantic similarity for literature on microbial transcriptional regulation

• Authors : Oscar Lithgow-Serrano; Julio Collado-Vides

Subjects: Statistics and Probability; Semantic similarity; Artificial Intelligence

• Source: Journal of Intelligent & Fuzzy Systems. 36:4777-4786

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Similarity corpus on microbial transcriptional regulation

• Authors : David A. Velázquez-Ramírez; Cecilia Ishida-Gutiérrez; Socorro Gama-Castro

Subjects: Transcriptional-regulation; Transcription, Genetic; Computer Networks and Communications

• Source: Journal of Biomedical Semantics, Vol 10, Iss 1, Pp 1-14 (2019)Journal of Biomedical Semantics

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CONTENT ALERTS

• Authors : Martín Peralta-gil; Ra Medina-rivera; Socorro Gama-castro ...

• Source: http://jb.asm.org/content/191/1/23.full.pdf.

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Redefining fundamental concepts of transcription initiation in bacteria

• Authors : Stephen J. W. Busby; Gary D. Stormo; Joseph T. Wade ...

Subjects: Emerging technologies; [SDV]Life Sciences [q-bio]; Plant Biology

• Source: Nature Reviews GeneticsNature Reviews Genetics, Nature Publishing Group, 2020, 21 (11), pp.699-714. ⟨10.1038/s41576-020-0254-8⟩Nature reviews. Genetics, vol 21, iss 11Nat Rev

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PulmonDB: a curated lung disease gene expression database

• Authors : Marco Moretto; Adrián Munguía-Reyes; Alejandra Zayas-Del Moral

Subjects: 0301 basic medicine; Gene regulatory network; Pulmonary disease

• Source: Scientific Reports, Vol 10, Iss 1, Pp 1-9 (2020)Scientific Reports

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Knowledge extraction for assisted curation of summaries of bacterial transcription factor properties

• Authors : Carlos-Francisco Méndez-Cruz; Socorro Gama-Castro; Antonio Blanchet

Subjects: 0303 health sciences; Information retrieval; Escherichia coli K12

• Source: Database: The Journal of Biological Databases and Curation

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Bayesian Clustering and Prediction in Heterogeneous Data Bases Using Multivariate Mixtures

• Authors : J. Andrés Christen; Arturo Medrano-Soto; Julio Collado-Vides ...

Subjects: MCMC; AutoClass; Clustering

• Source: ftp://matmor.unam.mx/pub/inves/jac/bayclas_JC.ps.gz

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EcoCyc: a comprehensive database of Escherichia coli biology

• Authors : Ingrid M. Keseler; Julio Collado-vides; Alberto Santos-zavaleta ...

• Source: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3013716/pdf/gkq1143.pdf.

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RegulonDB version 7.0: transcriptional regulation of Escherichia coli K-12 integrated within genetic sensory response units (Gensor Units

• Authors : Socorro Gama-castro; Heladia Salgado; Martin Peralta-gil ...

• Source: ftp://ftp.ncbi.nlm.nih.gov/pub/pmc/4c/08/Nucleic_Acids_Res_2011_Jan_4_39(Database_issue)_D98-D105.tar.gz

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Theoretical and empirical quality assessment

• Authors : Heladia Salgado; Julio Collado-vides; Jacques Van Helden ...

• Source: ftp://ftp.ncbi.nlm.nih.gov/pub/pmc/b8/57/Nucleic_Acids_Res_2011_Feb_4_39(3)_808-824.tar.gz

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2009 Lemmens et Volume al. 10, Issue 3, Article R27 Open Access Method DISTILLER: a data integration framework to reveal condition dependency of complex regulons in Escherichia coli

• Authors : Karen Lemmens; Tijl De Bie; Thomas Dholl ...

• Source: http://www.biomedcentral.com/content/pdf/gb-2009-10-3-r27.pdf.

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EcoCyc: a comprehensive view of Escherichia coli biology. Nucleic Acids Res

• Authors : Ingrid M. Keseler; Julio Collado-vides; Socorro Gama-castro ...

• Source: http://nar.oxfordjournals.org/content/37/suppl_1/D464.full-text-lowres.pdf.

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Transcriptional regulation constrains the organization of genes on eukaryotic chromosomes

• Authors : Sarath Chandra Janga; Julio Collado-Vides; M Madan Babu ...

• Source: http://www.iupui.edu/%7Ejangalab/Janga-PNAS-2008.pdf.

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Bacillus subtilis Escherichia coli: Model with knowledge

• Authors : Campus Morelos; Julio Collado-vides; Autónoma México ...

Subjects: Sigma Factor No. of Promoters Promoters w- Strong Evidence

• Source: http://mlaa.com.au/giw2008/PDF/Julio_Collado_final.pdf.

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Correspondence: Julio Collado-Vides

• Authors : Enrique Balleza; Lucia N. López-bojorquez; Agustino Martínez-antonio ...

• Source: ftp://ftp.ncbi.nlm.nih.gov/pub/pmc/76/b7/FEMS_Microbiol_Rev_2009_Jan_33(1)_133-151.tar.gz

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BMC Bioinformatics BioMed Central

• Authors : Vladimir Espinosa Angarica; Abel González Pérez; Ana T Vasconcelos ...

• Source: ftp://ftp.ncbi.nlm.nih.gov/pub/pmc/48/6d/BMC_Bioinformatics_2008_Oct_16_9_436.tar.gz

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Coordination logic of the sensing machinery in the transcriptional regulatory network of

• Authors : Sarath Ch; Ra Janga; Heladia Salgado ...

• Source: http://nar.oxfordjournals.org/content/35/20/6963.full-text-lowres.pdf.

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transcriptional regulatory network of

• Authors : Sarath Ch; Ra Janga; Heladia Salgado ...

• Source: http://www.mrc-lmb.cam.ac.uk/genomes/sarath/Janga-NAR2007.pdf.

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doi:10.1093/nar/gkm740 Multidimensional annotation of the Escherichia coli K-12 genome

• Authors : Peter D. Karp; Ingrid M. Keseler; Er Shearer ...

• Source: http://nar.oxfordjournals.org/content/early/2007/10/16/nar.gkm740.full.pdf.

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RegulonDB (version 6.0): gene regulation model

• Authors : Juan Segura-salazar; Luis Muñiz-rascado; Irma Martínez-flores ...

• Source: http://www.eead.csic.es/compbio/papers/regulondb2008.pdf.

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Tractor_DB (version 2.0): a database of regulatory interactions in gammaproteobacterial genomes. Nucleic Acids Res

• Authors : Vladimir Espinosa Angarica; Ana Tereza; R. Vasconcelos ...

• Source: http://nar.oxfordjournals.org/content/early/2006/11/06/nar.gkl800.full.pdf.

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SURVEY AND SUMMARY Multidimensional annotation of the Escherichia coli K-12 genome

• Authors : Peter D. Karp; Ingrid M. Keseler; Er Shearer ...

• Source: ftp://ftp.ncbi.nlm.nih.gov/pub/pmc/31/28/Nucleic_Acids_Res_2007_Dec_35(22)_7577-7590.tar.gz

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Notes

• Authors : Rosa María Gutiérrez-ríos; David A. Rosenblueth; José Antonio Loza ...

• Source: http://bi.snu.ac.kr/SEMINAR/BioNetwork/Regulatory network of Escherichia coli consistency between literature knowledge and microarray profiles.pdf.

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interactions in

• Authors : Abel González Pérez; Vladimir Espinosa Angarica; Ana Tereza ...

• Source: http://arquivosweb.lncc.br/pdfs/Tractor_DB version 2.0 a database of regulatory interactions.pdf.

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Bacterial regulatory networks are extremely flexible in evolution. Nucleic Acids Res

• Authors : Sarath Ch; Ra Janga; Julio Collado-vides ...

• Source: http://nar.oxfordjournals.org/content/34/12/3434.full-text-lowres.pdf.

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