Articles with public access mandates - Julio Collado-VidesLearn more
Not available anywhere: 2
Extracting Regulatory Networks of Escherichia coli from RegulonDB
H Salgado, I Martínez-Flores, A López-Fuentes, JS García-Sotelo, ...
Bacterial Molecular Networks: Methods and Protocols, 179-195, 2012
Mandates: US National Institutes of Health
In the pursuit of semantic similarity for literature on microbial transcriptional regulation
O Lithgow-Serrano, J Collado-Vides
Journal of Intelligent & Fuzzy Systems 36 (5), 4777-4786, 2019
Mandates: US National Institutes of Health
Available somewhere: 60
The BioPAX community standard for pathway data sharing
E Demir, MP Cary, S Paley, K Fukuda, C Lemer, I Vastrik, G Wu, ...
Nature biotechnology 28 (9), 935-942, 2010
Mandates: US National Institutes of Health, Genome Canada
EcoCyc: fusing model organism databases with systems biology
IM Keseler, A Mackie, M Peralta-Gil, A Santos-Zavaleta, S Gama-Castro, ...
Nucleic acids research 41 (D1), D605-D612, 2013
Mandates: US National Institutes of Health
The EcoCyc database: reflecting new knowledge about Escherichia coli K-12
IM Keseler, A Mackie, A Santos-Zavaleta, R Billington, ...
Nucleic acids research 45 (D1), D543-D550, 2017
Mandates: US National Institutes of Health
EcoCyc: a comprehensive database of Escherichia coli biology
IM Keseler, J Collado-Vides, A Santos-Zavaleta, M Peralta-Gil, ...
Nucleic acids research 39 (suppl_1), D583-D590, 2010
Mandates: US National Institutes of Health
RegulonDB version 9.0: high-level integration of gene regulation, coexpression, motif clustering and beyond
S Gama-Castro, H Salgado, A Santos-Zavaleta, D Ledezma-Tejeida, ...
Nucleic acids research 44 (D1), D133-D143, 2016
Mandates: US National Institutes of Health
RegulonDB v8. 0: omics data sets, evolutionary conservation, regulatory phrases, cross-validated gold standards and more
H Salgado, M Peralta-Gil, S Gama-Castro, A Santos-Zavaleta, ...
Nucleic acids research 41 (D1), D203-D213, 2013
Mandates: US National Institutes of Health
EcoCyc: A comprehensive view of Escherichia coli biology
IM Keseler, C Bonavides-Martínez, J Collado-Vides, S Gama-Castro, ...
Nucleic acids research 37 (suppl_1), D464-D470, 2009
Mandates: US National Institutes of Health
RegulonDB version 7.0: transcriptional regulation of Escherichia coli K-12 integrated within genetic sensory response units (Gensor Units)
S Gama-Castro, H Salgado, M Peralta-Gil, A Santos-Zavaleta, ...
Nucleic acids research 39 (suppl_1), D98-D105, 2010
Mandates: US National Institutes of Health
RegulonDB v 10.5: tackling challenges to unify classic and high throughput knowledge of gene regulation in E. coli K-12
A Santos-Zavaleta, H Salgado, S Gama-Castro, M Sánchez-Pérez, ...
Nucleic acids research 47 (D1), D212-D220, 2019
Mandates: US National Institutes of Health
Genome-wide identification of transcription start sites, promoters and transcription factor binding sites in E. coli
A Mendoza-Vargas, L Olvera, M Olvera, R Grande, L Vega-Alvarado, ...
PloS one 4 (10), e7526, 2009
Mandates: US National Institutes of Health
Regulation by transcription factors in bacteria: beyond description
E Balleza, LN Lopez-Bojorquez, A Martínez-Antonio, O Resendis-Antonio, ...
FEMS microbiology reviews 33 (1), 133-151, 2008
Mandates: US National Institutes of Health
The EcoCyc database in 2021
IM Keseler, S Gama-Castro, A Mackie, R Billington, C Bonavides-Martínez, ...
Frontiers in microbiology 12, 711077, 2021
Mandates: US National Institutes of Health
The ecocyc database
PD Karp, WK Ong, S Paley, R Billington, R Caspi, C Fulcher, A Kothari, ...
EcoSal Plus 8 (1), 10.1128/ecosalplus. ESP-0006-2018, 2018
Mandates: US National Institutes of Health
Redefining fundamental concepts of transcription initiation in bacteria
C Mejía-Almonte, SJW Busby, JT Wade, J van Helden, AP Arkin, ...
Nature Reviews Genetics 21 (11), 699-714, 2020
Mandates: US Department of Energy, US National Institutes of Health, UK Biotechnology …
RegulonDB 11.0: Comprehensive high-throughput datasets on transcriptional regulation in Escherichia coli K-12
VH Tierrafría, C Rioualen, H Salgado, P Lara, S Gama-Castro, P Lally, ...
Microbial Genomics 8 (5), 000833, 2022
Mandates: US National Institutes of Health, Natural Sciences and Engineering Research …
Theoretical and empirical quality assessment of transcription factor-binding motifs
A Medina-Rivera, C Abreu-Goodger, M Thomas-Chollier, H Salgado, ...
Nucleic acids research 39 (3), 808-824, 2011
Mandates: US National Institutes of Health
DISTILLER: a data integration framework to reveal condition dependency of complex regulons in Escherichia coli
K Lemmens, T De Bie, T Dhollander, SC De Keersmaecker, IM Thijs, ...
Genome biology 10, 1-13, 2009
Mandates: Research Foundation (Flanders)
COLOMBOS v3. 0: leveraging gene expression compendia for cross-species analyses
M Moretto, P Sonego, N Dierckxsens, M Brilli, L Bianco, ...
Nucleic acids research 44 (D1), D620-D623, 2016
Mandates: Research Foundation (Flanders)
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