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Page 1
Predictive Biophysical Neural Network Modeling of a Compendium of in vivo Transcription Factor DNA Binding Profiles for Escherichia coli.
Lally P, Gómez-Romero L, Tierrafría VH, Aquino P, Rioualen C, Zhang X, Kim S, Baniulyte G, Plitnick J, Smith C, Babu M, Collado-Vides J, Wade JT, Galagan JE. Lally P, et al. Among authors: tierrafria vh. bioRxiv [Preprint]. 2024 May 24:2024.05.23.594371. doi: 10.1101/2024.05.23.594371. bioRxiv. 2024. PMID: 38826350 Free PMC article. Preprint.
The EcoCyc Database (2023).
Karp PD, Paley S, Caspi R, Kothari A, Krummenacker M, Midford PE, Moore LR, Subhraveti P, Gama-Castro S, Tierrafria VH, Lara P, Muñiz-Rascado L, Bonavides-Martinez C, Santos-Zavaleta A, Mackie A, Sun G, Ahn-Horst TA, Choi H, Covert MW, Collado-Vides J, Paulsen I. Karp PD, et al. Among authors: tierrafria vh. EcoSal Plus. 2023 Dec 12;11(1):eesp00022023. doi: 10.1128/ecosalplus.esp-0002-2023. Epub 2023 May 11. EcoSal Plus. 2023. PMID: 37220074 Free PMC article. Review.
A Gold Standard for Transcription Factor Regulatory Interactions in Escherichia coli K-12: Architecture of Evidence Types.
Lara P, Gama-Castro S, Salgado H, Rioualen C, Tierrafría VH, Muñiz-Rascado LJ, Bonavides-Martínez C, Collado-Vides J. Lara P, et al. Among authors: tierrafria vh. bioRxiv [Preprint]. 2023 Dec 11:2023.02.25.530038. doi: 10.1101/2023.02.25.530038. bioRxiv. 2023. Update in: Front Genet. 2024 Mar 05;15:1353553. doi: 10.3389/fgene.2024.1353553. PMID: 37163020 Free PMC article. Updated. Preprint.
RegulonDB 11.0: Comprehensive high-throughput datasets on transcriptional regulation in Escherichia coli K-12.
Tierrafría VH, Rioualen C, Salgado H, Lara P, Gama-Castro S, Lally P, Gómez-Romero L, Peña-Loredo P, López-Almazo AG, Alarcón-Carranza G, Betancourt-Figueroa F, Alquicira-Hernández S, Polanco-Morelos JE, García-Sotelo J, Gaytan-Nuñez E, Méndez-Cruz CF, Muñiz LJ, Bonavides-Martínez C, Moreno-Hagelsieb G, Galagan JE, Wade JT, Collado-Vides J. Tierrafría VH, et al. Microb Genom. 2022 May;8(5):mgen000833. doi: 10.1099/mgen.0.000833. Microb Genom. 2022. PMID: 35584008 Free PMC article.
Sensory Systems and Transcriptional Regulation in Escherichia coli.
Femerling G, Gama-Castro S, Lara P, Ledezma-Tejeida D, Tierrafría VH, Muñiz-Rascado L, Bonavides-Martínez C, Collado-Vides J. Femerling G, et al. Among authors: tierrafria vh. Front Bioeng Biotechnol. 2022 Feb 14;10:823240. doi: 10.3389/fbioe.2022.823240. eCollection 2022. Front Bioeng Biotechnol. 2022. PMID: 35237580 Free PMC article. Review.
Lisen&Curate: A platform to facilitate gathering textual evidence for curation of regulation of transcription initiation in bacteria.
Díaz-Rodríguez M, Lithgow-Serrano O, Guadarrama-García F, Tierrafría VH, Gama-Castro S, Solano-Lira H, Salgado H, Rinaldi F, Méndez-Cruz CF, Collado-Vides J. Díaz-Rodríguez M, et al. Among authors: tierrafria vh. Biochim Biophys Acta Gene Regul Mech. 2021 Nov-Dec;1864(11-12):194753. doi: 10.1016/j.bbagrm.2021.194753. Epub 2021 Aug 28. Biochim Biophys Acta Gene Regul Mech. 2021. PMID: 34461312 Free PMC article.
The EcoCyc Database in 2021.
Keseler IM, Gama-Castro S, Mackie A, Billington R, Bonavides-Martínez C, Caspi R, Kothari A, Krummenacker M, Midford PE, Muñiz-Rascado L, Ong WK, Paley S, Santos-Zavaleta A, Subhraveti P, Tierrafría VH, Wolfe AJ, Collado-Vides J, Paulsen IT, Karp PD. Keseler IM, et al. Among authors: tierrafria vh. Front Microbiol. 2021 Jul 28;12:711077. doi: 10.3389/fmicb.2021.711077. eCollection 2021. Front Microbiol. 2021. PMID: 34394059 Free PMC article.
Correction to: Deletion of the hypothetical protein SCO2127 of Streptomyces coelicolor allowed identification of a new regulator of actinorhodin production.
Tierrafría VH, Licona-Cassani C, Maldonado-Carmona N, Romero-Rodríguez A, Centeno-Leija S, Marcellin E, Rodríguez-Sanoja R, Ruiz-Villafán B, Nielsen LK, Sánchez S. Tierrafría VH, et al. Appl Microbiol Biotechnol. 2020 Apr;104(8):3687. doi: 10.1007/s00253-020-10499-x. Appl Microbiol Biotechnol. 2020. PMID: 32152688
Similarity corpus on microbial transcriptional regulation.
Lithgow-Serrano O, Gama-Castro S, Ishida-Gutiérrez C, Mejía-Almonte C, Tierrafría VH, Martínez-Luna S, Santos-Zavaleta A, Velázquez-Ramírez D, Collado-Vides J. Lithgow-Serrano O, et al. Among authors: tierrafria vh. J Biomed Semantics. 2019 May 22;10(1):8. doi: 10.1186/s13326-019-0200-x. J Biomed Semantics. 2019. PMID: 31118102 Free PMC article.
16 results