| 1 | Fine-tuned GPT-based foundation models effectively reconstruct bacterial transcriptional regulatory networks from literature | Coautor: Collado-Vides, J, Romero-Vilchis, J, Barajas-Sánchez, M, Azpeitia-García, KI, et al. | 2026 | Frontiers In Artificial Intelligence | WoS-id: 001750440100001
Scopus-id: 2-s2.0-105040573098
| 0 | 0 |
| 2 | The allostery principle supports the symbolic character of signaling circuits: gene regulation provides a form of intelligence to living systems | 1ᵉʳ autor y autor de correspondencia: Collado-Vides J. | 2026 | THEORY IN BIOSCIENCES | WoS-id: 001816391200001
Scopus-id: 2-s2.0-105044081275
| 0 | 0 |
| 3 | Predictive biophysical neural network modeling of a compendium of in vivo transcription factor DNA binding profiles for Escherichia coli | Coautor: Collado-Vides J., Lally P., Gómez-Romero L., Tierrafría V.H., et al. | 2025 | NATURE COMMUNICATIONS | WoS-id: 001484461600007
Scopus-id: 2-s2.0-105004438689
| 7 | 8 |
| 4 | The EcoCyc database (2025) | Coautor: Collado-Vides J., Karp P.D., Paley S., Caspi R., et al. | 2025 | EcoSal Plus | Scopus-id: 2-s2.0-105025018823
| 0 | 18 |
| 5 | RegulonDB v12.0:ã comprehensive resource of transcriptional regulation in E. coli K-12 | Coautor: Collado-Vides J., Salgado H., Gama-Castro S., Lara P., et al. | 2024 | NUCLEIC ACIDS RESEARCH | WoS-id: 001102810900001
Scopus-id: 2-s2.0-85181777832
| 85 | 83 |
| 6 | Flexible gold standards for transcription factor regulatory interactions in Escherichia coli K-12: architecture of evidence types | Coautor: Collado-Vides J., Lara P., Gama-Castro S., Salgado H., et al. | 2024 | Frontiers in Genetics | WoS-id: 001186999100001
Scopus-id: 2-s2.0-85188101282
| 1 | 1 |
| 7 | Regulatory promoter architectures in the hands of thermodynamic modelling | 1ᵉʳ autor y autor de correspondencia: Collado-Vides, Julio | 2023 | NATURE REVIEWS GENETICS | WoS-id: 000926340700001
Scopus-id: 2-s2.0-85159659631
| 0 | 0 |
| 8 | The EcoCyc Database (2023) | Coautor: Collado-Vides J., Karp P.D., Paley S., Caspi R., et al. | 2023 | EcoSal Plus | Scopus-id: 2-s2.0-85176768413
| 0 | 77 |
| 9 | Sensory Systems and Transcriptional Regulation in Escherichia coli | Coautor: Collado-Vides, Julio, Femerling, Georgette, Gama-Castro, Socorro, Lara, Paloma, et al. | 2022 | Frontiers in Bioengineering and Biotechnology | WoS-id: 000761661300001
Scopus-id: 2-s2.0-85125402152
| 8 | 9 |
| 10 | RegulonDB 11.0: Comprehensive high-throughput datasets on transcriptional regulation in Escherichia coli K-12 | Coautor: Collado-Vides J., Tierrafría V.H., Rioualen C., Salgado H., et al. | 2022 | Microbial Genomics | WoS-id: 000812938700011
Scopus-id: 2-s2.0-85130765382
| 84 | 87 |
| 11 | Missing Links Between Gene Function and Physiology in Genomics | 1ᵉʳ autor: Collado-Vides, Julio, Gaudet, Pascale, de Lorenzo, Victor | 2022 | FRONTIERS IN PHYSIOLOGY | WoS-id: 001027066100001
Scopus-id: 2-s2.0-105033332996
| 2 | 3 |
| 12 | The EcoCyc Database in 2021 | Coautor: Collado-Vides, Julio, Keseler, Ingrid M., Gama-Castro, Socorro, Mackie, Amanda, et al. | 2021 | FRONTIERS IN MICROBIOLOGY | WoS-id: 000683854200001
Scopus-id: 2-s2.0-85112326830
| 179 | 185 |
| 13 | Lisen&Curate: A platform to facilitate gathering textual evidence for curation of regulation of transcription initiation in bacteria | Coautor: Collado-Vides J., Díaz-Rodríguez M., Lithgow-Serrano O., Guadarrama-García F., et al. | 2021 | BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS | WoS-id: 000703308500001
Scopus-id: 2-s2.0-85115326527
| 3 | 3 |
| 14 | Redefining fundamental concepts of transcription initiation in bacteria | Coautor: Collado-Vides, Julio, Mejia-Almonte, Citlalli, Busby S.J.W., Wade, Joseph T., et al. | 2020 | NATURE REVIEWS GENETICS | WoS-id: 000548509000001
Scopus-id: 2-s2.0-85087861944
| 116 | 125 |
| 15 | PulmonDB: a curated lung disease gene expression database | Coautor: Collado-Vides, Julio, Villaseñor-Altamirano A.B., Moretto, Marco, Maldonado, Mariel, et al. | 2020 | SCIENTIFIC REPORTS | WoS-id: 000551462200030
Scopus-id: 2-s2.0-85077940854
| 13 | 17 |
| 16 | Knowledge extraction for assisted curation o f summaries of bacterial transcription factor prorerties | Coautor: Collado-Vides, Julio, Mendez-Cruz, Carlos-Francisco, Blanchet, Antonio, Godinez, Alan, et al. | 2020 | DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION | WoS-id: 000601278100001
Scopus-id: 2-s2.0-85098471761
| 2 | 2 |
| 17 | RegulonDB v 10.5: tackling challenges to unify classic and high throughput knowledge of gene regulation in E. coli K-12 | Coautor: Collado-Vides J., Santos-Zavaleta A., Salgado H., Gama-Castro S., et al. | 2019 | NUCLEIC ACIDS RESEARCH | WoS-id: 000462587400034
Scopus-id: 2-s2.0-85059797142
| 266 | 275 |
| 18 | Tracing the phylogenetic history of the Crl regulon through the Bacteria and Archaea genomes | Coautor: Collado-Vides, J., Santos-Zavaleta, A., Perez-Rueda, E., Sanchez-Perez, M., et al. | 2019 | Bmc Genomics | WoS-id: 000464872800001
Scopus-id: 2-s2.0-85064404456
| 6 | 6 |
| 19 | MCO: towards an ontology and unified vocabulary for a framework-based annotation of microbial growth conditions | Coautor: Collado-Vides, J., Tierrafria, V. H., Mejia-Almonte, C., Camacho-Zaragoza, J. M., et al. | 2019 | Bioinformatics | WoS-id: 000467227300017
Scopus-id: 2-s2.0-85062289226
| 4 | 4 |
| 20 | In the pursuit of semantic similarity for literature on microbial transcriptional regulation | 2ᵒ autor y autor de correspondencia: Collado-Vides, Julio, Lithgow-Serrano, Oscar | 2019 | JOURNAL OF INTELLIGENT & FUZZY SYSTEMS | WoS-id: 000467907000072
Scopus-id: 2-s2.0-85066442965
| 3 | 3 |
| 21 | Similarity corpus on microbial transcriptional regulation | Coautor: Collado-Vides J., Lithgow-Serrano O., Gama-Castro S., Ishida-Gutiérrez C., et al. | 2019 | JOURNAL OF BIOMEDICAL SEMANTICS | WoS-id: 000468929800001
Scopus-id: 2-s2.0-85066457982
| 8 | 9 |
| 22 | Limits to a classic paradigm: most transcription factors in E. coli regulate genes involved in multiple biological processes | Coautor: Collado-Vides, Julio, Ledezma-Tejeida, Daniela, Altamirano-Pacheco, Luis, Fajardo, Vicente | 2019 | NUCLEIC ACIDS RESEARCH | WoS-id: 000490556600014
Scopus-id: 2-s2.0-85070183436
| 9 | 9 |
| 23 | Integrating Bacterial ChIP-seq and RNA-seq Data With SnakeChunks | Coautor: Collado-Vides J., Rioualen C., Charbonnier-Khamvongsa L., van Helden J. | 2019 | Current Protocols In Bioinformatics | Scopus-id: 2-s2.0-85061926958
| 0 | 3 |
| 24 | A unified resource for transcriptional regulation in Escherichia coli K-12 incorporating high-throughput-generated binding data into RegulonDB version 10.0 | Coautor: Collado-Vides J., Santos-Zavaleta A., Sánchez-Pérez M., Salgado H., et al. | 2018 | BMC BIOLOGY | WoS-id: 000441842200001
Scopus-id: 2-s2.0-85051701959
| 37 | 37 |
| 25 | Proof of Concept of Eukaryotic Genetic Sensory Response Units in TGF-beta Signaling in Idiopathic Pulmonary Fibrosis | Coautor: Collado-Vides, J., Balderas-Martinez, Y. I., Moreno-Quiroga, B., Negreros, M., et al. | 2018 | AMERICAN JOURNAL OF RESPIRATORY AND CRITICAL CARE MEDICINE | WoS-id: 000449980302223
| 1 | 0 |
| 26 | PulmonDB: A Gene Expression Lung Diseases | Coautor: Collado-Vides, J., Villasenor-Altamirano, A. B., Balderas-Martinez, Y. I., Moretto, M., et al. | 2018 | AMERICAN JOURNAL OF RESPIRATORY AND CRITICAL CARE MEDICINE | WoS-id: 000449980305432
| 0 | 0 |
| 27 | Using RegulonDB, the Escherichia coli K-12 Gene Regulatory Transcriptional Network Database | Coautor: Collado-Vides J., Salgado H., Martínez-Flores I., Bustamante V.H., et al. | 2018 | Current Protocols In Bioinformatics | Scopus-id: 2-s2.0-85050792661
| 0 | 9 |
| 28 | The EcoCyc Database | Coautor: Collado-Vides J., Karp P.D., Ong W.K., Paley S., et al. | 2018 | EcoSal Plus | Scopus-id: 2-s2.0-85056491267
| 0 | 69 |
| 29 | A falsification approach to create and check ontology definitions | 2ᵒ autor y autor de correspondencia: Collado-Vides J., Mejía-Almonte C. | 2018 | CEUR Workshop Proceedings | Scopus-id: 2-s2.0-85059844005
| 0 | 0 |
| 30 | The EcoCyc database: reflecting new knowledge about Escherichia coli K-12 | Coautor: Collado-Vides, Julio, Keseler, Ingrid M., Mackie, Amanda, Santos-Zavaleta, Alberto, et al. | 2017 | NUCLEIC ACIDS RESEARCH | WoS-id: 000396575500076
Scopus-id: 2-s2.0-85015989839
| 412 | 426 |
| 31 | Effect of genomic distance on coexpression of coregulated genes in E. coli | Coautor: Collado-Vides J., Pannier L., Merino E., Marchal K. | 2017 | PLOS ONE | WoS-id: 000399875200005
Scopus-id: 2-s2.0-85017618528
| 17 | 17 |
| 32 | Improving biocuration of microRNAs in diseases: a case study in idiopathic pulmonary fibrosis | Coautor: Collado-Vides, Julio, Itzel Balderas-Martinez, Yalbi, Rinaldi, Fabio, Contreras, Gabriela, et al. | 2017 | DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION | WoS-id: 000402291100001
Scopus-id: 2-s2.0-85015939383
| 3 | 4 |
| 33 | Genome-Wide Mapping of Transcriptional Regulation and Metabolism Describes Information-Processing Units in Escherichia coli | Coautor y autor de correspondencia: Collado-Vides J., Ledezma-Tejeida D., Ishida C. | 2017 | FRONTIERS IN MICROBIOLOGY | WoS-id: 000406854400003
Scopus-id: 2-s2.0-85026825893
| 12 | 13 |
| 34 | First steps in automatic summarization of transcription factor properties for RegulonDB: classification of sentences about structural domains and regulated processes | Coautor: Collado-Vides, Julio, Mendez-Cruz, Carlos-Francisco, Gama-Castro, Socorro, Mejia-Almonte, Citlalli, et al. | 2017 | DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION | WoS-id: 000412308000001
Scopus-id: 2-s2.0-85050188913
| 6 | 6 |
| 35 | Strategies towards digital and semi-automated curation in RegulonDB (vol 2017, bax012, 2017) | Coautor: Collado-Vides, Julio, Rinaldi, Fabio, Lithgow, Oscar, Gama-Castro, Socorro, et al. | 2017 | DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION | WoS-id: 000427186500001
Scopus-id: 2-s2.0-85063712388
| 0 | 0 |
| 36 | RegulonDB version 9.0: high-level integration of gene regulation, coexpression, motif clustering and beyond | Coautor: Collado-Vides, Julio, Gama-Castro, Socorro, Salgado, Heladia, Santos-Zavaleta, Alberto, et al. | 2016 | NUCLEIC ACIDS RESEARCH | WoS-id: 000371261700018
Scopus-id: 2-s2.0-84976874666
| 369 | 388 |
| 37 | COLOMBOS v3.0: leveraging gene expression compendia for cross- species analyses | Coautor: Collado-Vides, Julio, Moretto, Marco, Sonego, Paolo, Dierckxsens, Nicolas, et al. | 2016 | NUCLEIC ACIDS RESEARCH | WoS-id: 000371261700087
Scopus-id: 2-s2.0-84976905759
| 52 | 51 |
| 38 | In silico clustering of Salmonella global gene expression data reveals novel genes co-regulated with the SPI-1 virulence genes through HilD | Coautor: Collado-Vides, Julio, Martinez-Flores, Irma, Perez-Morales, Deyanira, Sanchez-Perez, Mishael, et al. | 2016 | SCIENTIFIC REPORTS | WoS-id: 000388557100003
Scopus-id: 2-s2.0-84998610822
| 22 | 23 |
| 39 | Mathematical modeling of the apo and holo transcriptional regulation in Escherichia coli | Coautor: Collado-Vides J., Alvarez-Vasquez F.J., Freyre-González J.A., Balderas-Martínez Y.I., et al. | 2015 | MOLECULAR BIOSYSTEMS | WoS-id: 000351493300002
Scopus-id: 2-s2.0-84924953665
| 1 | 1 |
| 40 | Structural properties of prokaryotic promoter regions correlate with functional features | 2ᵒ autor: Collado-Vides J., Meysman P., Morett E., Viola R., et al. | 2014 | PLOS ONE | WoS-id: 000330834400078
Scopus-id: 2-s2.0-84895755061
| 22 | 24 |
| 41 | COLOMBOS v2.0: An ever expanding collection of bacterial expression compendia | Coautor: Collado-Vides J., Meysman P., Sonego P., Bianco L., et al. | 2014 | NUCLEIC ACIDS RESEARCH | WoS-id: 000331139800095
Scopus-id: 2-s2.0-84891750356
| 30 | 30 |
| 42 | In silico identification and experimental characterization of regulatory elements controlling the expression of the salmonella csrB and csrC genes | Coautor: Collado-Vides, J, Martinez, LC, Martinez-Flores, I, Salgado, H, et al. | 2014 | JOURNAL OF BACTERIOLOGY | WoS-id: 000332624300013
Scopus-id: 2-s2.0-84890942426
| 28 | 29 |
| 43 | Assisted curation of regulatory interactions and growth conditions of OxyR in E. Colik-12 | Coautor: Collado-Vides J., Gama-Castro S., Rinaldi F., López-Fuentes A., et al. | 2014 | DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION | WoS-id: 000338567900001
Scopus-id: 2-s2.0-84987638658
| 13 | 13 |
| 44 | The EcoCyc database | Coautor: Collado-Vides J., Karp P.D., Weaver D., Paley S., et al. | 2014 | EcoSal Plus | Scopus-id: 2-s2.0-84932633215
| 0 | 63 |
| 45 | RegulonDB v8.0: Omics data sets, evolutionary conservation, regulatory phrases, cross-validated gold standards and more | Coautor: Collado-Vides, J, Salgado, H, Peralta-Gil, M, Gama-Castro, S, et al. | 2013 | NUCLEIC ACIDS RESEARCH | WoS-id: 000312893300028
Scopus-id: 2-s2.0-84876543942
| 332 | 345 |
| 46 | EcoCyc: fusing model organism databases with systems biology | Coautor: Collado-Vides J., Keseler I.M., Mackie A., Peralta-Gil M., et al. | 2013 | NUCLEIC ACIDS RESEARCH | WoS-id: 000312893300086
Scopus-id: 2-s2.0-84876556918
| 442 | 452 |
| 47 | Evidence classification of high-throughput protocols and confidence integration in RegulonDB | Coautor: Collado-Vides, J, Weiss, V, Medina-Rivera, A, Huerta, AM, et al. | 2013 | DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION | WoS-id: 000316174600001
Scopus-id: 2-s2.0-84879348696
| 12 | 16 |
| 48 | Transcription Factors in Escherichia coli Prefer the Holo Conformation | Coautor: Collado-Vides J., Balderas-Martínez Y.I., Savageau M., Salgado H., et al. | 2013 | PLOS ONE | WoS-id: 000320322400048
Scopus-id: 2-s2.0-84878913760
| 20 | 23 |
| 49 | The BioPAX community standard for pathway data sharing (Nature Biotechnology (2010) 28, (935-942)) | Coautor: Collado-Vides J., Demir E., Cary M.P., Paley S., et al. | 2012 | Nature Biotechnology | WoS-id: 000302785000028
Scopus-id: 2-s2.0-84859638634
| 0 | 1 |
| 50 | On the trail of EHEC/EAEC-unraveling the gene regulatory networks of human pathogenic Escherichia coli bacteria | Coautor: Collado-Vides J., Pauling J., Rottger, R, Neuner A., et al. | 2012 | INTEGR BIOL-UK | WoS-id: 000305694800003
Scopus-id: 2-s2.0-84863701397
| 6 | 7 |
| 51 | RegulonDB version 7.0: Transcriptional regulation of Escherichia coli K-12 integrated within genetic sensory response units (Gensor Units) | Coautor: Collado-Vides J., Gama-Castro S., Salgado H., Peralta-Gil M., et al. | 2011 | NUCLEIC ACIDS RESEARCH | WoS-id: 000285831700018
Scopus-id: 2-s2.0-78651299341
| 283 | 301 |
| 52 | EcoCyc: a comprehensive database of Escherichia coli biology | 2ᵒ autor: Collado-Vides J., Keseler I.M., Santos-Zavaleta A., Peralta-Gil M., et al. | 2011 | NUCLEIC ACIDS RESEARCH | WoS-id: 000285831700092
Scopus-id: 2-s2.0-78651281217
| 363 | 396 |
| 53 | Theoretical and empirical quality assessment of transcription factor-binding motifs | Coautor: Collado-Vides J., Medina-Rivera A., Abreu-Goodger C., Thomas-Chollier M., et al. | 2011 | NUCLEIC ACIDS RESEARCH | WoS-id: 000287257500010
Scopus-id: 2-s2.0-79951570672
| 51 | 55 |
| 54 | The BioPAX community standard for pathway data sharing | Coautor: Collado-Vides J., Demir E., Cary M.P., Paley S., et al. | 2010 | Nature Biotechnology | WoS-id: 000281719100019
Scopus-id: 2-s2.0-77956664073
| 482 | 577 |
| 55 | Erratum: The BioPAX community standard for pathway data sharing (Nat. Biotechnol. (2010) 28 (935-942) | Coautor: Collado-Vides J., Demir E., Paley S., Fukuda K., et al. | 2010 | Nature Biotechnology | WoS-id: 000285088400029
Scopus-id: 2-s2.0-78650004198
| 5 | 4 |
| 56 | Regulation by transcription factors in bacteria: Beyond description | Coautor: Collado-Vides, J, Balleza, E, Lopez-Bojorquez, LN, Martinez-Antonio, A, et al. | 2009 | FEMS MICROBIOLOGY REVIEWS | WoS-id: 000261621600009
Scopus-id: 2-s2.0-57549107143
| 162 | 161 |
| 57 | Bioinformatics Resources for the Study of Gene Regulation in Bacteria | 1ᵉʳ autor: Collado-Vides, J, Salgado, H, Morett, E, Gama-Castro, S, et al. | 2009 | JOURNAL OF BACTERIOLOGY | WoS-id: 000261628100002
Scopus-id: 2-s2.0-58149495994
| 21 | 23 |
| 58 | EcoCyc: A comprehensive view of Escherichia coli biology | Coautor: Collado-Vides J., Keseler I.M., Bonavides-Martínez C., Gama-Castro S., et al. | 2009 | NUCLEIC ACIDS RESEARCH | WoS-id: 000261906200084
Scopus-id: 2-s2.0-58149179979
| 284 | 314 |
| 59 | The Condition-Dependent Transcriptional Network in Escherichia coli | Coautor: Collado-Vides J., Lemmens K., De Bie T., Dhollander T., et al. | 2009 | ANNALS OF THE NEW YORK ACADEMY OF SCIENCES | WoS-id: 000265650800003
Scopus-id: 2-s2.0-63849229020
| 3 | 4 |
| 60 | DISTILLER: a data integration framework to reveal condition dependency of complex regulons in Escherichia coli | Coautor: Collado-Vides J., Lemmens K., De Bie T., Dhollander T., et al. | 2009 | GENOME BIOLOGY | WoS-id: 000266544500007
Scopus-id: 2-s2.0-63449134229
| 45 | 48 |
| 61 | Evolution of Bacterial Regulatory Networks:"The Role of DNA-Binding Specificity" | Coautor y autor de correspondencia: Collado-Vides, J, Lozada-Chvez, I, Contreras-Moreira, B | 2009 | ORIGINS OF LIFE AND EVOLUTION OF BIOSPHERES | WoS-id: 000267033300104
| 0 | 0 |
| 62 | Genome-Wide Identification of Transcription Start Sites, Promoters and Transcription Factor Binding Sites in E. coli | Coautor: Collado-Vides, J, Mendoza-Vargas, A, Olvera, L, Olvera, M, et al. | 2009 | PLOS ONE | WoS-id: 000270880900016
Scopus-id: 2-s2.0-70449380939
| 204 | 221 |
| 63 | From sequence to dynamics: the effects of transcription factor and polymerase concentration changes on activated and repressed promoters | Coautor: Collado-Vides J., Perez, AG, Angarica, VE, Vasconcelos, ATR | 2009 | BMC MOL BIOL | WoS-id: 000271289700001
Scopus-id: 2-s2.0-70449429102
| 5 | 5 |
| 64 | Structural and functional map of a bacterial nucleoid | Coautor y autor de correspondencia: Collado-Vides J., Martínez-Antonio A., Medina-Rivera A. | 2009 | GENOME BIOLOGY | WoS-id: 000274289000002
Scopus-id: 2-s2.0-77951885904
| 14 | 8 |
| 65 | RegulonDB (version 6.0): gene regulation model of Escherichia coli K-12 beyond transcription, active (experimental) annotated promoters and Textpresso navigation | Coautor: Collado-Vides, J, Gama-Castro, S, Jimenez-Jacinto, V, Peralta-Gil, M, et al. | 2008 | NUCLEIC ACIDS RESEARCH | WoS-id: 000252545400022
Scopus-id: 2-s2.0-38549140094
| 379 | 409 |
| 66 | Impact of Transcription Units rearrangement on the evolution of the regulatory network of gamma-proteobacteria | Coautor: Collado-Vides J., Perez, ADG, González E.G., Angarica V.E., et al. | 2008 | Bmc Genomics | WoS-id: 000255706300001
Scopus-id: 2-s2.0-42549136538
| 10 | 10 |
| 67 | The Role of DNA-binding Specificity in the Evolution of Bacterial Regulatory Networks | Coautor: Collado-Vides J., Lozada-Chávez I., Angarica V.E., Contreras-Moreira B. | 2008 | JOURNAL OF MOLECULAR BIOLOGY | WoS-id: 000256586500021
Scopus-id: 2-s2.0-43649086589
| 42 | 39 |
| 68 | Transcriptional regulation constrains the organization of genes on eukaryotic chromosomes | 2ᵒ autor: Collado-Vides J., Janga S.C., Babu M.M. | 2008 | PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA | WoS-id: 000260240900024
Scopus-id: 2-s2.0-57349140010
| 54 | 59 |
| 69 | Functional architecture of Escherichia coli: new insights provided by a natural decomposition approach | Coautor: Collado-Vides, J, Freyre-Gonzalez, JA, Alonso-Pavon, JA, Trevino-Quintanilla, LG | 2008 | GENOME BIOLOGY | WoS-id: 000260587300016
Scopus-id: 2-s2.0-57049166435
| 39 | 43 |
| 70 | Prediction of TF target sites based on atomistic models of protein-DNA complexes | Coautor: Collado-Vides J., Angarica V.E., Pérez A.G., Vasconcelos A.T., et al. | 2008 | Bmc Bioinformatics | WoS-id: 000261533500001
Scopus-id: 2-s2.0-56749102973
| 41 | 45 |
| 71 | Tractor_DB (version 2.0): A database of regulatory interactions in gamma-proteobacterial genomes | Coautor: Collado-Vides J., Pérez A.G., Angarica V.E., Vasconcelos A.T.R. | 2007 | NUCLEIC ACIDS RESEARCH | WoS-id: 000243494600027
Scopus-id: 2-s2.0-33846073825
| 20 | 20 |
| 72 | Internal Versus External Effector and Transcription Factor Gene Pairs Differ in Their Relative Chromosomal Position in Escherichia coli | Coautor: Collado-Vides J., Janga S.C., Salgado H., Martínez-Antonio A. | 2007 | JOURNAL OF MOLECULAR BIOLOGY | WoS-id: 000245672500023
Scopus-id: 2-s2.0-33947420169
| 13 | 16 |
| 73 | Identification of regulatory network topological units coordinating the genome-wide transcriptional response to glucose in Escherichia coli | Coautor: Collado-Vides J., Gutierrez-Ríos R.M., Freyre-Gonzalez J.A., Resendis O., et al. | 2007 | BMC MICROBIOLOGY | WoS-id: 000247696500001
Scopus-id: 2-s2.0-34347396784
| 62 | 62 |
| 74 | TFmodeller: Comparative modelling of protein-DNA complexes | Coautor y autor de correspondencia: Collado-Vides J., Contreras-Moreira B., Branger P.-A. | 2007 | Bioinformatics | WoS-id: 000248620400018
Scopus-id: 2-s2.0-34547844091
| 22 | 28 |
| 75 | Automatic reconstruction of a bacterial regulatory network using Natural Language Processing | Coautor: Collado-Vides J., Rodríguez-Penagos C., Salgado H., Martínez-Flores I. | 2007 | Bmc Bioinformatics | WoS-id: 000249274300002
Scopus-id: 2-s2.0-34548499877
| 34 | 42 |
| 76 | Development of genomic sciences in Mexico: A good start and a long way to go | 2ᵒ autor y autor de correspondencia: Collado-Vides J., Palacios R. | 2007 | PLOS COMPUTATIONAL BIOLOGY | WoS-id: 000249767400002
Scopus-id: 2-s2.0-34848868151
| 9 | 11 |
| 77 | Metabolic reconstruction and modeling of nitrogen fixation in Rhizobium etli | Coautor: Collado-Vides J., Resendis-Antonio O., Reed J.L., Encarnación S., et al. | 2007 | PLOS COMPUTATIONAL BIOLOGY | WoS-id: 000251113500009
Scopus-id: 2-s2.0-35748961978
| 71 | 78 |
| 78 | Coordination logic of the sensing machinery in the transcriptional regulatory network of Escherichia coli | Coautor: Collado-Vides J., Janga S.C., Salgado H., Martínez-Antonio A. | 2007 | NUCLEIC ACIDS RESEARCH | WoS-id: 000251336000030
Scopus-id: 2-s2.0-36749095093
| 22 | 20 |
| 79 | Multidimensional annotation of the Escherichia coli K-12 genome | Coautor: Collado-Vides J., Karp P.D., Keseler I.M., Shearer A., et al. | 2007 | NUCLEIC ACIDS RESEARCH | WoS-id: 000252125900021
Scopus-id: 2-s2.0-38049007503
| 136 | 154 |
| 80 | Structure and evolution of gene regulatory networks in microbial genomes | 2ᵒ autor y autor de correspondencia: Collado-Vides J., Janga S.C. | 2007 | RESEARCH IN MICROBIOLOGY | WoS-id: 000252370300008
Scopus-id: 2-s2.0-36849063165
| 45 | 43 |
| 81 | NLP-based curation of bacterial regulatory networks | Coautor: Collado-Vides J., Rodríguez-Penagos C., Salgado H., Martínez-Flores I. | 2007 | Lecture Notes in Computer Science | Scopus-id: 2-s2.0-37149056907
| 0 | 1 |
| 82 | Internal-sensing machinery directs the activity of the regulatory network in Escherichia coli | Coautor: Collado-Vides J., Martínez-Antonio A., Janga S.C., Salgado H. | 2006 | TRENDS IN MICROBIOLOGY | WoS-id: 000235123200007
Scopus-id: 2-s2.0-30344484891
| 72 | 78 |
| 83 | The comprehensive updated regulatory network of Escherichia coli K-12 | Coautor: Collado-Vides J., Salgado H., Santos-Zavaleta A., Gama-Castro S., et al. | 2006 | Bmc Bioinformatics | WoS-id: 000235550300001
Scopus-id: 2-s2.0-30644465547
| 50 | 49 |
| 84 | The partitioned Rhizobium etli genome: Genetic and metabolic redundancy in seven interacting replicons | Coautor: Collado-Vides J., González V., Santamaría R.I., Bustos P., et al. | 2006 | PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA | WoS-id: 000236225300060
Scopus-id: 2-s2.0-33644861233
| 314 | 321 |
| 85 | Positional conservation of clusters of overlapping promoter-like sequences in enterobacterial genomes | 2ᵒ autor: Collado-Vides J., Huerta A.M., Francino M.P. | 2006 | MOLECULAR BIOLOGY AND EVOLUTION | WoS-id: 000237320800020
Scopus-id: 2-s2.0-33646540406
| 4 | 4 |
| 86 | RegulonDB (version 5.0): Escherichia coli K-12 transcriptional regulatory network, operon organization, and growth conditions. | Coautor: Collado-Vides J., Salgado H., Gama-Castro S., Peralta-Gil M., et al. | 2006 | NUCLEIC ACIDS RESEARCH | WoS-id: 000239307700086
Scopus-id: 2-s2.0-33644873438
| 276 | 307 |
| 87 | Bacterial regulatory networks are extremely flexible in evolution | Coautor y autor de correspondencia: Collado-Vides J., Lozada-Chávez I., Janga S.C. | 2006 | NUCLEIC ACIDS RESEARCH | WoS-id: 000239908000010
Scopus-id: 2-s2.0-33746207758
| 155 | 158 |
| 88 | Selection for unequal densities of s70 promoter-like signals in different regions of large bacterial genomes | Coautor: Collado-Vides J., Huerta A.M., Francino M.P., Morett E. | 2006 | PLOS GENETICS | WoS-id: 000242374600007
Scopus-id: 2-s2.0-33751369021
| 41 | 41 |
| 89 | Comparative footprinting of DNA-binding proteins | 2ᵒ autor y autor de correspondencia: Collado-Vides J., Contreras-Moreira B. | 2006 | Bioinformatics | WoS-id: 000250005000010
Scopus-id: 2-s2.0-33747892311
| 17 | 16 |
| 90 | Modular analysis of the transcriptional regulatory network of E. coli | Coautor: Collado-Vides J., Resendis-Antonio O., Freyre-González J.A., Menchaca-Méndez R., et al. | 2005 | TRENDS IN GENETICS | WoS-id: 000226485800005
Scopus-id: 2-s2.0-13144283679
| 80 | 83 |
| 91 | TRACTOR_DB: A database of regulatory networks in gamma-proteobacterial genomes | Coautor: Collado-Vides J., González A.D., Espinosa V., Vasconcelos A.T., et al. | 2005 | NUCLEIC ACIDS RESEARCH | WoS-id: 000226524300017
Scopus-id: 2-s2.0-13444270901
| 18 | 18 |
| 92 | EcoCyc: A comprehensive database resource for Escherichia coli | 2ᵒ autor: Collado-Vides J., Keseler I.M., Gama-Castro S., Ingraham J., et al. | 2005 | NUCLEIC ACIDS RESEARCH | WoS-id: 000226524300069
Scopus-id: 2-s2.0-13444262374
| 524 | 602 |
| 93 | Nebulon: A system for the inference of functional relationships of gene products from the rearrangement of predicted operons | 2ᵒ autor: Collado-Vides J., Janga S.C., Moreno-Hagelsieb G. | 2005 | NUCLEIC ACIDS RESEARCH | WoS-id: 000229113100027
Scopus-id: 2-s2.0-18244386245
| 37 | 35 |
| 94 | The network of transcriptional interactions imposes linear constrains in the genome | Coautor y autor de correspondencia: Collado-Vides J., Menchaca-Mendez R., Janga S.C. | 2005 | OMICS | WoS-id: 000230306800003
Scopus-id: 2-s2.0-22044453999
| 5 | 4 |
| 95 | Nonlinear software sensor for monitoring genetic regulation processes with noise and modeling errors | Coautor: Collado-Vides J., Ibarra-Junquera V., Torres L.A., Rosu H.C., et al. | 2005 | PHYSICAL REVIEW E | WoS-id: 000230886900090
Scopus-id: 2-s2.0-27244442717
| 6 | 5 |
| 96 | Diversification of DNA sequences in the symbiotic genome of Rhizobium etli | Coautor: Collado-Vides J., Flores M., Morales L., Avila A., et al. | 2005 | JOURNAL OF BACTERIOLOGY | WoS-id: 000232786100004
Scopus-id: 2-s2.0-27144444025
| 28 | 26 |
| 97 | Comparative studies of transcriptional regulation mechanisms in a group of eight gamma-proteobacterial genomes | Coautor: Collado-Vides J., Espinosa V., González A.D., Vasconcelos A.T., et al. | 2005 | JOURNAL OF MOLECULAR BIOLOGY | WoS-id: 000233310800014
Scopus-id: 2-s2.0-27344438594
| 15 | 14 |
| 98 | Minimum information requested in the annotation of biochemical models (MIRIAM) | Coautor: Collado-Vides J., Le Novère N., Finney A., Hucka M., et al. | 2005 | Nature Biotechnology | WoS-id: 000233866300027
Scopus-id: 2-s2.0-28644433993
| 433 | 489 |
| 99 | Complementing computationally predicted regulatory sites in Tractor_DB using a pattern matching approach | Coautor: Collado-Vides J., Guía M.H., Pérez A.G., Angarica V.E., et al. | 2005 | In Silico Biology | Scopus-id: 2-s2.0-22144437778
| 0 | 6 |
| 100 | BClass: A Bayesian approach based on mixture models for clustering and classification of heterogeneous biological data | Coautor y autor de correspondencia: Collado-Vides J., Medrano-Soto A., Christen J.A. | 2005 | JOURNAL OF STATISTICAL SOFTWARE | Scopus-id: 2-s2.0-15944412514
| 0 | 3 |
| 101 | RegulonDB (version 4.0): Transcriptional regulation, operon organization and growth conditions in Escherichia coli K-12 | Coautor: Collado-Vides J., Salgado H., Gama-Castro S., Martínez-Antonio A., et al. | 2004 | NUCLEIC ACIDS RESEARCH | WoS-id: 000188079000071
Scopus-id: 2-s2.0-9144270496
| 192 | 227 |
| 102 | Distribution of minigenes in the bacteriophage lambda chromosome | Coautor: Collado-Vides J., Oviedo N.-A., Salgado H., Guarneros G. | 2004 | Gene | WoS-id: 000220856300012
Scopus-id: 2-s2.0-1642412681
| 4 | 3 |
| 103 | Successful lateral transfer requires codon usage compatibility between foreign genes and recipient genomes | Coautor: Collado-Vides J., Medrano-Soto A., Moreno-Hagelsieb G., Vinuesa P., et al. | 2004 | MOLECULAR BIOLOGY AND EVOLUTION | WoS-id: 000224013100007
Scopus-id: 2-s2.0-4944262629
| 60 | 66 |
| 104 | The growth of random networks as a diffusion process | 2ᵒ autor y autor de correspondencia: Collado-Vides J., Resendis-Antonio O. | 2004 | PHYSICA A-STATISTICAL MECHANICS AND ITS APPLICATIONS | WoS-id: 000224311800011
Scopus-id: 2-s2.0-4544240259
| 1 | 1 |
| 105 | Phylogenetic distribution of DNA-binding transcription factors in bacteria and archaea | 2ᵒ autor: Collado-Vides J., Pérez-Rueda E., Segovia L. | 2004 | Computational Biology And Chemistry | WoS-id: 000226382900003
Scopus-id: 2-s2.0-9544237144
| 79 | 81 |
| 106 | The E. coli EcoCyc database: No longer just a metabolic pathway database | Coautor: Collado-Vides J., Karp P.D., Arnaud M., Ingraham J., et al. | 2004 | Asm News | Scopus-id: 2-s2.0-6944256505
| 0 | 44 |
| 107 | The mosaic structure of the symbiotic plasmid of Rhizobium etli CFN42 and its relation to other symbiotic genome compartments. | Coautor: Collado-Vides J., González V., Bustos P., Ramírez-Romero M.A., et al. | 2003 | Genome Biology | WoS-id: 000183720100006
Scopus-id: 2-s2.0-0037562601
| 127 | 124 |
| 108 | Sigma70 promoters in Escherichia coli: Specific transcription in dense regions of overlapping promoter-like signals | 2ᵒ autor y autor de correspondencia: Collado-Vides J., Huerta A.M. | 2003 | JOURNAL OF MOLECULAR BIOLOGY | WoS-id: 000185852000004
Scopus-id: 2-s2.0-0141758085
| 181 | 186 |
| 109 | Identifying global regulators in transcriptional regulatory networks in bacteria | 2ᵒ autor y autor de correspondencia: Collado-Vides J., Martínez-Antonio A. | 2003 | CURRENT OPINION IN MICROBIOLOGY | WoS-id: 000186155100011
Scopus-id: 2-s2.0-0242386460
| 407 | 438 |
| 110 | Regulatory network of Escherichia coli: Consistency between literature knowledge and microarray profiles | Coautor: Collado-Vides J., Gutiérrez-Ríos R.M., Rosenblueth D.A., Loza J.A., et al. | 2003 | GENOME RESEARCH | WoS-id: 000186357000009
Scopus-id: 2-s2.0-0242407438
| 95 | 97 |
| 111 | Conservation of DNA curvature signals in regulatory regions of prokaryotic genes | Coautor: Collado-Vides J., Jáuregui R., Abreu-Goodger C., Moreno-Hagelsieb G., et al. | 2003 | NUCLEIC ACIDS RESEARCH | WoS-id: 000186802500015
Scopus-id: 2-s2.0-17944395329
| 56 | 56 |
| 112 | Environmental Conditions and Transcriptional Regulation in Escherichia coli: A Physiological Integrative Approach | Coautor: Collado-Vides J., Martínez-Antonio A., Salgado H., Gama-Castro S., et al. | 2003 | BIOTECHNOLOGY AND BIOENGINEERING | WoS-id: 000187634500003
Scopus-id: 2-s2.0-0348062847
| 17 | 17 |
| 113 | With the finished human genome in hand, what next? | 1ᵉʳ autor: Collado-Vides J., Medrano-Soto A., Tusié-Luna M.T. | 2003 | GENOME BIOLOGY | Scopus-id: 2-s2.0-0042810681
| 0 | 1 |
| 114 | Regulation of expression of symbiotic genes in Rhizobium sp. NGR234 | Coautor y autor de correspondencia: Collado-Vides J., Perret X., Kobayashi H. | 2003 | INDIAN J EXP BIOL | Scopus-id: 2-s2.0-0141941138
| 0 | 12 |
| 115 | The EcoCyc database | Coautor: Collado-Vides J., Karp P.D., Riley M., Saier M., et al. | 2002 | NUCLEIC ACIDS RESEARCH | WoS-id: 000173077100013
Scopus-id: 2-s2.0-0036084127
| 309 | 357 |
| 116 | Erratum: Common pitfalls in bioinformatics based analyses: Look before you leap (Trends in Genetics (2001) 17 (541-545) PII S0168952502026628) | Coautor: Collado-Vides J., Huerta A.M., Glasner J.D., Gutiérrez-Ríos R.M., et al. | 2002 | TRENDS IN GENETICS | WoS-id: 000174770300015
Scopus-id: 2-s2.0-33846265712
| 1 | 0 |
| 117 | Analysis of the cellular functions of Escherichia coli operons and their conservation in Bacillus subtilis | 2ᵒ autor: Collado-Vides J., De Daruvar A., Valencia A. | 2002 | JOURNAL OF MOLECULAR EVOLUTION | WoS-id: 000176691400008
Scopus-id: 2-s2.0-0036306989
| 35 | 34 |
| 118 | Evaluation of thresholds for the detection of binding sites for regulatory proteins in Escherichia coli K12 DNA. | Coautor y autor de correspondencia: Collado-Vides J., Benítez-Bellón E., Moreno-Hagelsieb G. | 2002 | Genome Biology | Scopus-id: 2-s2.0-0036371372
| 0 | 23 |
| 119 | Operon conservation from the point of view of Escherichia coli, and inference of functional interdependence of gene products from genome context | 2ᵒ autor y autor de correspondencia: Collado-Vides J., Moreno-Hagelsieb G. | 2002 | In Silico Biology | Scopus-id: 2-s2.0-0036014557
| 0 | 20 |
| 120 | A powerful non-homology method for the prediction of operons in prokaryotes. | 2ᵒ autor y autor de correspondencia: Collado-Vides J., Moreno-Hagelsieb G. | 2002 | Bioinformatics | Scopus-id: 2-s2.0-0001291140
| 0 | 177 |
| 121 | Towards a bioinformatics network for Latin America and the Caribbean (LACBioNet). | Coautor: Collado-Vides J., Degrave W.M., Vargas R., Alvarez F., et al. | 2002 | Applied Bioinformatics | Scopus-id: 2-s2.0-2442665628
| 0 | 7 |
| 122 | Microbial computational genomics of gene regulation | 1ᵉʳ autor: Collado-Vides J., Moreno-Hagelsieb G., Medrano-Soto A. | 2002 | PURE AND APPLIED CHEMISTRY | Scopus-id: 2-s2.0-0036327036
| 0 | 2 |
| 123 | RegulonDB (version 3.2): Transcriptional regulation and operon organization in Escherichia coli K-12 | Coautor: Collado-Vides J., Salgado H., Santos-Zavaleta A., Gama-Castro S., et al. | 2001 | NUCLEIC ACIDS RESEARCH | WoS-id: 000166360300017
Scopus-id: 2-s2.0-0035162782
| 183 | 194 |
| 124 | Conserved regulatory elements of the promoter sequence of the gene rpoH of enteric bacteria | 2ᵒ autor: Collado-Vides J., Ramírez-Santos J., García-Varela M., Gómez-Eichelmann M.C. | 2001 | NUCLEIC ACIDS RESEARCH | WoS-id: 000166506500004
Scopus-id: 2-s2.0-0035863745
| 18 | 18 |
| 125 | A comparative genomics approach to prediction of new members of regulons | Coautor: Collado-Vides J., Tan K., Moreno-Hagelsieb G., Stormo G.D. | 2001 | GENOME RESEARCH | WoS-id: 000167885400008
Scopus-id: 2-s2.0-0035051602
| 106 | 112 |
| 126 | Transcription unit conservation in the three domains of life: A perspective from Escherichia coli | Coautor: Collado-Vides J., Moreno-Hagelsieb G., Trevio V., Pérez-Rueda E., et al. | 2001 | TRENDS IN GENETICS | WoS-id: 000168718300004
Scopus-id: 2-s2.0-0035313453
| 36 | 41 |
| 127 | Common history at the origin of the position - Function correlation in transcriptional regulators in archaea and bacteria | 2ᵒ autor y autor de correspondencia: Collado-Vides J., Pérez-Rueda E. | 2001 | JOURNAL OF MOLECULAR EVOLUTION | WoS-id: 000170659000002
Scopus-id: 2-s2.0-0034873196
| 68 | 67 |
| 128 | RegulonDB (version 3.0): Transcriptional regulation and operon organization in Escherichia coli K-12 | Coautor: Collado-Vides J., Salgado H., Santos-Zavaleta A., Gama-Castro S., et al. | 2000 | NUCLEIC ACIDS RESEARCH | WoS-id: 000084896300016
Scopus-id: 2-s2.0-0033971476
| 50 | 53 |
| 129 | A web site for the computational analysis of yeast regulatory sequences | Coautor y autor de correspondencia: Collado-Vides J., Van Helden J., André B. | 2000 | Yeast | WoS-id: 000085307200007
Scopus-id: 2-s2.0-0034731822
| 139 | 155 |
| 130 | Operons in Escherichia coli: Genomic analyses and predictions | Coautor: Collado-Vides J., Salgado H., Moreno-Hagelsieb G., Smith T.F. | 2000 | PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA | WoS-id: 000087526300076
Scopus-id: 2-s2.0-0034612277
| 286 | 305 |
| 131 | Discovering regulatory elements in non-coding sequences by analysis of spaced dyads | Coautor y autor de correspondencia: Collado-Vides J., Van Helden J., Rios A.F. | 2000 | NUCLEIC ACIDS RESEARCH | WoS-id: 000207916400028
Scopus-id: 2-s2.0-0034656326
| 207 | 249 |
| 132 | The repertoire of DNA-binding transcriptional regulators in Escherichia coli K-12 | 2ᵒ autor y autor de correspondencia: Collado-Vides J., Pérez-Rueda E. | 2000 | NUCLEIC ACIDS RESEARCH | WoS-id: 000207916400031
Scopus-id: 2-s2.0-0343963178
| 229 | 242 |
| 133 | Promoter interference in a bacteriophage lambda control region: Effects of a range of interpromoter distances | Coautor: Collado-Vides J., Strainic Jr. M.G., Sullivan J.J., DeHaseth P.L. | 2000 | JOURNAL OF BACTERIOLOGY | Scopus-id: 2-s2.0-0343066722
| 0 | 15 |
| 134 | RegulonDB (version 2.0): A database on transcriptional regulation in Escherichia coli | Coautor: Collado-Vides J., Salgado H., Santos A., Garza-Ramos U., et al. | 1999 | NUCLEIC ACIDS RESEARCH | WoS-id: 000077983000012
Scopus-id: 2-s2.0-0032947086
| 32 | 37 |
| 135 | Modeling and simulation of gene regulation and metabolic pathways | 1ᵉʳ autor: Collado-Vides J., Hofestadt R., Mavrovouniotis M., Michal G. | 1999 | Biosystems | Scopus-id: 2-s2.0-0032952652
| 0 | 4 |
| 136 | Genomic position analyses and the transcription machinery | Coautor y autor de correspondencia: Collado-Vides J., Pérez-Rueda E., Gralla J.D. | 1998 | JOURNAL OF MOLECULAR BIOLOGY | WoS-id: 000071635900001
Scopus-id: 2-s2.0-0342818061
| 29 | 28 |
| 137 | Networks of transcriptional regulation encoded in a grammatical model | 1ᵉʳ autor: Collado-Vides J., Gutièrrez-Ríos R.M., Bel-Enguix G. | 1998 | Biosystems | WoS-id: 000075066100008
Scopus-id: 2-s2.0-0345267173
| 13 | 13 |
| 138 | From specific gene regulation to genomic networks: A global analysis of transcriptional regulation in Escherichia coli | Coautor: Collado-Vides J., Thieffry D., Huerta A.M., Pérez-Rueda E. | 1998 | Bioessays | WoS-id: 000075208400010
Scopus-id: 2-s2.0-0032077377
| 385 | 421 |
| 139 | Extracting regulatory sites from the upstream region of yeast genes by computational analysis of oligonucleotide frequencies | Coautor y autor de correspondencia: Collado-Vides J., Van Helden J., André B. | 1998 | JOURNAL OF MOLECULAR BIOLOGY | WoS-id: 000075771200007
Scopus-id: 2-s2.0-0032483307
| 543 | 630 |
| 140 | RegulonDB: A database on transcriptional regulation in Escherichia coli | Coautor: Collado-Vides J., Huerta A.M., Salgado H., Thieffry D. | 1998 | NUCLEIC ACIDS RESEARCH | Scopus-id: 2-s2.0-0031811851
| 116 | 161 |
| 141 | Prediction of transcriptional regulatory sites in the complete genome sequence of Escherichia coli K-12 | Coautor: Collado-Vides J., Thieffry D., Salgado H., Huerta A.M. | 1998 | Bioinformatics | Scopus-id: 2-s2.0-0031827572
| 0 | 79 |
| 142 | Definite-clause grammars for the analysis of cis-regulatory regions in E. coli. | Coautor: Collado-Vides J., Thieffry D., Rosenblueth D.A., Huerta A.M., et al. | 1997 | Pacific Symposium On Biocomputing. Pacific Symposium On Biocomputing | Scopus-id: 2-s2.0-0031305541
| 0 | 3 |
| 143 | The complete genome sequence of Escherichia coli K-12 | Coautor: Collado-Vides J., Blattner F.R., Plunkett III G., Bloch C.A., et al. | 1997 | Science | WoS-id: A1997XV42900030
Scopus-id: 2-s2.0-15444350252
| 6170 | 6572 |
| 144 | Three models of gene regulation in E. coli | 1ᵉʳ autor: Collado-Vides J., Huerta A.M., Klose K. | 1997 | Lecture Notes in Computer Science | Scopus-id: 2-s2.0-2642604569
| 0 | 1 |
| 145 | Towards a unified grammatical model of s70 and s54 bacterial promoters | 1ᵉʳ autor y autor de correspondencia: Collado-Vides J. | 1996 | Biochimie | WoS-id: A1996VN34200008
Scopus-id: 2-s2.0-0029852417
| 5 | 6 |
| 146 | Modeling and simulation of metabolic pathways, gene regulation and cell differentiation. International Conference and Research Center for Computer Science, Schloss Dagstuhl, Saarland, Germany, 22-27 October, 1995 | Coautor: Collado-Vides J., Hofestadt R., Mavrovouniotis M., Loffler M. | 1996 | Bioessays | WoS-id: A1996UF91600011
Scopus-id: 2-s2.0-0030131148
| 1 | 4 |
| 147 | Syntactic recognition of regulatory regions in escherichia coli | Coautor: Collado-Vides J., Rosenblueth D.A., Thieffry D., Huerta A.M., et al. | 1996 | Bioinformatics | WoS-id: A1996WA43400009
Scopus-id: 2-s2.0-0030474940
| 29 | 29 |
| 148 | Some ideas towards a grammatical model of the s54 bacterial promoters | 1ᵉʳ autor y autor de correspondencia: Collado-Vides Julio | 1995 | American Society Of Mechanical Engineers (paper) | Scopus-id: 2-s2.0-0029210008
| 0 | 0 |
| 149 | A linguistic representation of the regulation of transcription initiation. I. An ordered array of complex symbols with distinctive features | 1ᵉʳ autor y autor de correspondencia: Collado-Vides J. | 1993 | Biosystems | WoS-id: A1993LM75400003
Scopus-id: 2-s2.0-0027254889
| 14 | 16 |
| 150 | A linguistic representation of the regulation of transcription initiation. II. Distinctive features of sigma 70 promoters and their regulatory binding sites | 1ᵉʳ autor y autor de correspondencia: Collado-Vides J. | 1993 | Biosystems | WoS-id: A1993LM75400004
Scopus-id: 2-s2.0-0027320283
| 8 | 9 |
| 151 | The elements for a classification of units of genetic information with a combinatorial component | 1ᵉʳ autor y autor de correspondencia: Collado-Vides J. | 1993 | JOURNAL OF THEORETICAL BIOLOGY | WoS-id: A1993MA53000009
Scopus-id: 2-s2.0-0027508315
| 5 | 8 |
| 152 | Grammatical model of the regulation of gene expression | 1ᵉʳ autor y autor de correspondencia: Collado-Vides J. | 1992 | PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA | WoS-id: A1992JT97700009
Scopus-id: 2-s2.0-0026756312
| 38 | 39 |
| 153 | The search for a grammatical theory of gene regulation is formally justified by showing the inadequacy of context-free grammars | 1ᵉʳ autor y autor de correspondencia: Collado-Vides J. | 1991 | Bioinformatics | WoS-id: A1991FY07100006
Scopus-id: 2-s2.0-0025908881
| 27 | 34 |
| 154 | Control site location and transcriptional regulation in Escherichia coli | 1ᵉʳ autor: Collado-Vides J., Magasanik B., Gralla J.D. | 1991 | MICROBIOL REV | WoS-id: A1991GE81200003
Scopus-id: 2-s2.0-0026003072
| 485 | 433 |
| 155 | A syntactic representation of units of genetic information-A syntax of units of genetic information | 1ᵉʳ autor y autor de correspondencia: Collado-Vides J. | 1991 | JOURNAL OF THEORETICAL BIOLOGY | WoS-id: A1991EX42300008
Scopus-id: 2-s2.0-0026081170
| 20 | 19 |
| 156 | A transformational-grammar approach to the study of the regulation of gene expression | 1ᵉʳ autor y autor de correspondencia: Collado-Vides J. | 1989 | JOURNAL OF THEORETICAL BIOLOGY | WoS-id: A1989T647100003
Scopus-id: 2-s2.0-0024554795
| 36 | 38 |
ID's SCOPUS 
ORCID's 