Collado-Vides J - Search Results

1

Redefining fundamental concepts of transcription initiation in bacteria.

Mejía-Almonte C, Busby SJW, Wade JT, van Helden J, Arkin AP, Stormo GD, Eilbeck K, Palsson BO, Galagan JE, Collado-Vides J. Mejía-Almonte C, et al. Nat Rev Genet. 2020 Nov;21(11):699-714. doi: 10.1038/s41576-020-0254-8. Epub 2020 Jul 14. Nat Rev Genet. 2020. PMID: 32665585 Free PMC article. Review.

2

Extracting regulatory sites from the upstream region of yeast genes by computational analysis of oligonucleotide frequencies.

van Helden J, André B, Collado-Vides J. van Helden J, et al. J Mol Biol. 1998 Sep 4;281(5):827-42. doi: 10.1006/jmbi.1998.1947. J Mol Biol. 1998. PMID: 9719638

3

RegulonDB (version 2.0): a database on transcriptional regulation in Escherichia coli.

Salgado H, Santos A, Garza-Ramos U, van Helden J, Díaz E, Collado-Vides J. Salgado H, et al. Nucleic Acids Res. 1999 Jan 1;27(1):59-60. doi: 10.1093/nar/27.1.59. Nucleic Acids Res. 1999. PMID: 9847141 Free PMC article.

4

A web site for the computational analysis of yeast regulatory sequences.

van Helden J, André B, Collado-Vides J. van Helden J, et al. Yeast. 2000 Jan 30;16(2):177-87. doi: 10.1002/(SICI)1097-0061(20000130)16:2<177::AID-YEA516>3.0.CO;2-9. Yeast. 2000. PMID: 10641039

5

Discovering regulatory elements in non-coding sequences by analysis of spaced dyads.

van Helden J, Rios AF, Collado-Vides J. van Helden J, et al. Nucleic Acids Res. 2000 Apr 15;28(8):1808-18. doi: 10.1093/nar/28.8.1808. Nucleic Acids Res. 2000. PMID: 10734201 Free PMC article.

6

A comparative genomics approach to prediction of new members of regulons.

Tan K, Moreno-Hagelsieb G, Collado-Vides J, Stormo GD. Tan K, et al. Genome Res. 2001 Apr;11(4):566-84. doi: 10.1101/gr.149301. Genome Res. 2001. PMID: 11282972 Free PMC article.

7

MCO: towards an ontology and unified vocabulary for a framework-based annotation of microbial growth conditions.

Tierrafría VH, Mejía-Almonte C, Camacho-Zaragoza JM, Salgado H, Alquicira K, Ishida C, Gama-Castro S, Collado-Vides J. Tierrafría VH, et al. Bioinformatics. 2019 Mar 1;35(5):856-864. doi: 10.1093/bioinformatics/bty689. Bioinformatics. 2019. PMID: 30137210 Free PMC article.

8

Regulatory promoter architectures in the hands of thermodynamic modelling.

Collado-Vides J. Collado-Vides J. Nat Rev Genet. 2023 Jun;24(6):349. doi: 10.1038/s41576-023-00578-w. Nat Rev Genet. 2023. PMID: 36747003 No abstract available.

9

RegulonDB v12.0: a comprehensive resource of transcriptional regulation in E. coli K-12.

Salgado H, Gama-Castro S, Lara P, Mejia-Almonte C, Alarcón-Carranza G, López-Almazo AG, Betancourt-Figueroa F, Peña-Loredo P, Alquicira-Hernández S, Ledezma-Tejeida D, Arizmendi-Zagal L, Mendez-Hernandez F, Diaz-Gomez AK, Ochoa-Praxedis E, Muñiz-Rascado LJ, García-Sotelo JS, Flores-Gallegos FA, Gómez L, Bonavides-Martínez C, Del Moral-Chávez VM, Hernández-Alvarez AJ, Santos-Zavaleta A, Capella-Gutierrez S, Gelpi JL, Collado-Vides J. Salgado H, et al. Among authors: collado vides j. Nucleic Acids Res. 2024 Jan 5;52(D1):D255-D264. doi: 10.1093/nar/gkad1072. Nucleic Acids Res. 2024. PMID: 37971353 Free PMC article.

10

Flexible gold standards 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: collado vides j. Front Genet. 2024 Mar 5;15:1353553. doi: 10.3389/fgene.2024.1353553. eCollection 2024. Front Genet. 2024. PMID: 38505828 Free PMC article.

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