Pedro Julio Collado Vides
Computational Genomics Researcher
Emeritus Professor
Academic history
Julio Collado-Vides obtained a B.Sc. in Basic Biomedical Research (1983), a M.Sc. in Physical Chemistry (1985) and a Ph.D. in Biomedical Research (Biomathematics) (1989) at the National Autonomous University of Mexico (UNAM). Upon graduation he spent three years in the laboratory of Dr. Boris Magasanik in Department of Biology at the Massachusetts Institute of Technology (MIT) with a postdoctoral Fellowship awarded by the Fogarty International Center. In 1992 he was recognized as a Fellow of the John Simon Guggenheim Foundation and became part of the Center of Nitrogen Fixation (CIFN) at the Morelos Campus of UNAM, in Cuernavaca, in a tenure track position.
He is a Professor at UNAM in the area of bioinformatics of regulation of gene expression in bacteria. His work has been recognized in Mexico and abroad. His main contributions include a grammatical model of gene regulation, the computational modeling of regulation of transcription initiation in Escherichia coli, contained in RegulonDB and a review of the basic concepts of transcriptional regulation published in Nature Reviews Genetics (2020). His focus on gene regulation has contributed to generating algorithms to predict operons, applying bioinformatic methods to predict promoters and binding sites, as well as analyzing the regulatory network and its global properties.
He contributed to the annotation of regulation of the complete E.coli genome published in 1997 in Science. He has more than 130 papers in international peer-reviewed (click on “Publications” -above-) journals as well as over 13 chapters in books, which have accumulated more than 15,000 citations (H index 45). Additionally, he is editor of the books “Integrative Approaches to Molecular Biology” eds. Collado-Vides J., Smith T. and Magasanik B. (1996), and “Gene Regulation and Metabolism: Post-Genomic Computational Approaches” eds. Collado-Vides J. and Hofestadt R. (2002), both published by MIT Press.
He is a regular member of the Mexican Academy of Science; he has also been President Founder of the Mexican Society of Genomics (2000), and was recognized with the National University Award in Natural Science Research 2004 and the Scopus Elsevier recognition for his highly cited publications in 2007. His laboratory is responsible for the Bioinformatics Mexican National Node EMBNET and he was appointed Director of the Center for Genomic Sciences from 2005 to 2009.
He has been a member of the Board of Directors of the International Society for Computational Biology, an “ISCB Distinguished Fellow” Class 2015, and received the National Award in Sciences and Arts (2011) the highest recognition by the Mexican government. Since 2018 he is an Adjunct Professor at the Department of Bioengineering at Boston University.
He has been an invited member for program committees of international conferences in his area, and an organizer of various international conferences. He has been a member of the Genomics, Computation and Technology (GCAT) study section of the National Institutes of Health (NIH) of the United States. He has also evaluated grant applications from the National Science Foundation, Human Frontiers, the German Human Genome Project and book proposals to the MIT Press amongst others. He is a member of the International E.coli Alliance since 2002.
Dr. Collado-Vides has been awarded with grants from DOE as co-responsible investigator, and is one of the few researchers in our country with grants awarded by NIH as PI (Principal Investigator). He was awarded with the Robert F. Kennedy Visiting Professorship of the Americas from Harvard University in 2007, and was invited to contribute to the inaugural section on Computational Biology of the Journal of Bacteriology, 2009. He was President founder of the Iberoamerican Society for Bioinformatics in 2009.
Dr. Collado-Vides has mentored several undergraduate and graduate students. Some of his former students and posdocs are now investigators at UNAM, Cuba, Canada, the US, France, Spain and Belgium. He has collaborated in the creation of the Undergraduate Program of Genomics at UNAM, where he participates in overseeing and teaching courses in bioinformatics. He has also coordinated courses addressed to the teachers of the UNAM’s National High school in an attempt to bring genomics to upper middle education. The international workshop of bioinformatics has offered bioinformatics training for more than 700 academics and students in Mexico over the years.
Links
Telephone: (777) 3139877
Email: colladojulio@gmail.com
Publications
| Year | Publication | PMID |
|---|---|---|
| 2021 | Lithgow-Serrano, O., Gama-Castro, S., Ishida-Gutiérrez, Collado-Vides, J.. (2021). "L-Regulon: A novel “soft-curation” approach supported by a semantic enriched reading for RegulonDB literature". bioRxiv. ():-. [doi:https://doi.org/10.1101/2020.04.26.062745] | |
| 2021 | Keseler, I.M., Gama-Castro, S., Mackie, A., Billington, R., Bonavides-Martínez, C., Caspi, R., Kothari, A., Krummenacker, M., Midford, P.E., Muñiz-Rascado, L., Ong, W.K., Paley, S., Santos-Zavaleta, A., Subhraveti, P., Tierrafría, V.H., Wolfe, A.J., Collado-Vides, J., Paulsen, I.T., Karp, P.D.. (2021). "The EcoCyc Database in 2021.". Frontiers in Microbiology. 12():-. [doi:10.3389/fmicb.2021.711077] | 34394059 |
| 2021 | Díaz-Rodríguez, M., Lithgow-Serrano, O., Guadarrama-García, F., Tierrafría, V.H., Gama-Castro, S., Solano-Lira, H., Salgado, H., Rinaldi, F., Méndez-Cruz, C.F., Collado-Vides, J.. (2021). "Lisen&Curate: A platform to facilitate gathering textual evidence for curation of regulation of transcription initiation in bacteria.". BBA-GENE REGUL MECH. 1864(11-12):-. [doi:10.1016/j.bbagrm.2021.194753] | 34461312 |
| 2020 | Mejía-Almonte, C., Busby, S.J.W., Wade, J.T., van Helden, J., Arkin, A.P., Stormo, G.D., Eilbeck, K., Palsson, B.O., Galagan, J.E., Collado-Vides, J.. (2020). "Redefining fundamental concepts of transcription initiation in bacteria". NATURE REVIEWS GENETICS. 21(11):699-714. [doi:10.1038/s41576-020-0254-8] | 32665585 |
| 2020 | Villaseñor-Altamirano AB, Moretto M, Maldonado M, Zayas-Del Moral A, Munguía-Reyes A, Romero Y, García-Sotelo JS, Aguilar LA, Aldana-Assad O, Engelen K, Selman M, Collado-Vides J, Balderas-Martínez YI, Medina-Rivera A. (2020). "PulmonDB: a curated lung disease gene expression database.". SCIENTIFIC REPORTS. 10(1):514-514. [doi:10.1038/s41598-019-56339-5] | 31949184 |
| 2020 | Méndez-Cruz, C.F., Blanchet, A., Godínez, A., Arroyo-Fernández, I., Gama-Castro, S., Martínez-Luna, S.B., González-Colín, C., Collado-Vides, J.. (2020). "Knowledge extraction for assisted curation of summaries of bacterial transcription factor properties.". DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION. 2020():-. [doi:10.1093/database/baaa109] | 33306798 |
| 2019 | Ledezma-Tejeida D, Altamirano-Pacheco L, Fajardo V, Collado-Vides J. (2019). "Limits to a classic paradigm: most transcription factors in E. coli regulate genes involved in multiple biological processes.". Nucleic Acids Research. 47(13):6656-6667. [doi:10.1093/nar/gkz525] | 31194874 |
| 2019 | Rioualen, C., Charbonnier-Khamvongsa, L., Collado-Vides, J., van Helden, J.. (2019). "Integrating Bacterial ChIP-seq and RNA-seq Data With SnakeChunks.". Current Protocols in Bioinformatics. 66(1):-. [doi:10.1002/cpbi.72] | 30786165 |
| 2019 | Lithgow-Serrano, O., Gama-Castro, S., Ishida-Gutiérrez, C., Mejía-Almonte, C., Tierrafría, V.H., Martínez-Luna, S., Santos-Zavaleta, A., Velázquez-Ramírez, D., Collado-Vides, J.. (2019). "Similarity corpus on microbial transcriptional regulation.". JOURNAL OF BIOMEDICAL SEMANTICS. 10(1):-. [doi:10.1186/s13326-019-0200-x] | 31118102 |
| 2019 | Santos-Zavaleta, A., Pérez-Rueda, E., Sánchez-Pérez, M., Velázquez-Ramírez, D.A., Collado-Vides, J.. (2019). "Tracing the phylogenetic history of the Crl regulon through the Bacteria and Archaea genomes.". Bmc Genomics. 20(1):-. [doi:10.1186/s12864-019-5619-z] | 30991941 |
| 2019 | Tierrafría, V.H., Mejía-Almonte, C., Camacho-Zaragoza, J.M., Salgado, H., Alquicira, K., Ishida, C., Gama-Castro, S., Collado-Vides, J.. (2019). "MCO: towards an ontology and unified vocabulary for a framework-based annotation of microbial growth conditions.". Bioinformatics. 35(5):856-864. [doi:10.1093/bioinformatics/bty689] | 30137210 |
| 2019 | Santos-Zavaleta, A., Salgado, H., Gama-Castro, S., Sánchez-Pérez, M., Gómez-Romero, L., Ledezma-Tejeida, D., García-Sotelo, J.S., Alquicira-Hernández, K., Muñiz-Rascado, L.J., Peña-Loredo, P., Ishida-Gutiérrez, C., Velázquez-Ramírez, D.A., Del Moral-Chávez, V., Bonavides-Martínez, C., Méndez-Cruz, C.F., Galagan, J., Collado-Vides, J.. (2019). "RegulonDB v 10.5: tackling challenges to unify classic and high throughput knowledge of gene regulation in E. coli K-12". Nucleic Acids Research. 47(D1):212-220. [doi:10.1093/nar/gky1077] | 30395280 |
| 2019 | Lithgow-Serrano, O., Collado-Vides, J.. (2019). "In the pursuit of semantic similarity for literature on microbial transcriptional regulation". JOURNAL OF INTELLIGENT & FUZZY SYSTEMS. 36(5):4777-4786. [doi:10.3233/JIFS-179026] | |
| 2018 | Villasenor-Altamirano, A. B., Balderas-Martinez, Y. I., Moretto, M., Zayas-Del Moral, A., Maldonado, M., Munguia-Reyes, A., Garcia-Sotelo, J. S., Aguilar Bautista, L. A., Ramirez-Navarro, L., Santillan, O., Engelen, K., Selman, M., Medina-Rivera, A., Collado-Vides, J.. (2018). "PulmonDB: A Gene Expression Lung Diseases". AM J RESP CRIT CARE. 197():-. | |
| 2018 | Santos-Zavaleta, Alberto, Sanchez-Perez, Mishael, Salgado, Heladia, Velazquez-Ramirez, David A., Gama-Castro, Socorro, Tierrafria, Victor H., Busby, Stephen J. W., Aquino, Patricia, Fang, Xin, Palsson, Bernhard O., Galagan, James E., Collado-Vides, Julio. (2018). "A unified resource for transcriptional regulation in Escherichia coli K-12 incorporating high-throughput-generated binding data into RegulonDB version 10.0". BMC BIOLOGY. 16(1):91-91. [doi:10.1186/s12915-018-0555-y] | 30115066 |
| 2018 | Balderas-Martinez, Y. I., Moreno-Quiroga, B., Negreros, M., Ledezma-Tejeida, D., Pardo, A., Collado-Vides, J., Selman, M.. (2018). "Proof of Concept of Eukaryotic Genetic Sensory Response Units in TGF-beta Signaling in Idiopathic Pulmonary Fibrosis". AM J RESP CRIT CARE. 197():-. | |
| 2018 | Salgado, H., Martínez-Flores, I., Bustamante, V.H., Alquicira-Hernández, K., García-Sotelo, J.S., García-Alonso, D., Collado-Vides, J.. (2018). "Using RegulonDB, the Escherichia coli K-12 Gene Regulatory Transcriptional Network Database.". Current Protocols in Bioinformatics. 61(1):1321-13230. [doi:10.1002/cpbi.43] | 30040192 |
| 2017 | Ledezma-Tejeida D, Ishida C, Collado-Vides J. (2017). "Genome-wide mapping of transcriptional regulation and metabolism describes information-processing units in Escherichia coli". Frontiers in Microbiology. 8(AUG):1466-1466. [doi:10.3389/fmicb.2017.01466] | 28824593 |
| 2017 | Balderas-Martínez YI, Rinaldi F, Contreras G, Solano-Lira H, Sánchez-Pérez M, Collado-Vides J, Selman M, Pardo A. (2017). "Improving biocuration of microRNAs in diseases: a case study in idiopathic pulmonary fibrosis". DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION. 2017():-. [doi:10.1093/database/bax030] | 28605770 |
| 2017 | Pannier L, Merino E, Marchal K, Collado-Vides J. (2017). "Effect of genomic distance on coexpression of coregulated genes in E. coli". Plos One. 12(4):-. [doi:10.1371/journal.pone.0174887] | 28419102 |
| 2017 | Rinaldi F, Lithgow O, Gama-Castro S, Solano H, Lopez A, Muñiz Rascado LJ, Ishida-Gutiérrez C, Méndez-Cruz CF, Collado-Vides J. (2017). "Strategies towards digital and semi-automated curation in RegulonDB". DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION. 2017(1):-. [doi:10.1093/database/bax012] | 28365731 |
| 2017 | Méndez-Cruz CF, Gama-Castro S, Mejía-Almonte C, Castillo-Villalba MP, Muñiz-Rascado LJ, Collado-Vides J. (2017). "First steps in automatic summarization of transcription factor properties for RegulonDB: classification of sentences about structural domains and regulated processes". DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION. 2017():-. [doi:10.1093/database/bax070] | 29220462 |
| 2017 | Castillo-Villalba MP, Gomez-Romero, Laura, Collado-Vides, Julio. (2017). "Genetic-metabolic networks can be modeled as toric varities". arXiv. ():-. [doi:arXiv:1708.05384v1] | |
| 2017 | Keseler, I.M., Mackie, A., Santos-Zavaleta, A., Billington, R., Bonavides-Martínez, C., Caspi, R., Fulcher, C., Gama-Castro, S., Kothari, A., Krummenacker, M., Latendresse, M., Muñiz-Rascado, L., Ong, Q., Paley, S., Peralta-Gil, M., Subhraveti, P., Velázquez-Ramírez, D.A., Weaver, D., Collado-Vides, J., Paulsen, I., Karp, P.D.. (2017). "The EcoCyc database: reflecting new knowledge about Escherichia coli K-12.". Nucleic Acids Research. 45(D1):543-550. [doi:10.1093/nar/gkw1003] | 27899573 |
| 2016 | Martínez-Flores I, Pérez-Morales D, Sánchez-Pérez M, Paredes CC, Collado-Vides J, Salgado H, Bustamante VH. (2016). "In Silico clustering of Salmonella global gene expression data reveals novel genes co-regulated with the SPI-1 virulence genes through HilD". SCIENTIFIC REPORTS. 6():37858-37858. [doi:10.1038/srep37858] | 27886269 |
| 2016 | Moretto, M., Sonego, P., Dierckxsens, N., Brilli, M., Bianco, L., Ledezma-Tejeida, D., Gama-Castro, S., Galardini, M., Romualdi, C., Laukens, K., Collado-Vides, J., Meysman, P., Engelen, K.. (2016). "COLOMBOS v3.0: Leveraging gene expression compendia for cross-species analyses". Nucleic Acids Research. 44(D1):620-623. [doi:10.1093/nar/gkv1251] | 26586805 |
| 2016 | Gama-Castro, S., Salgado, H., Santos-Zavaleta, A., Ledezma-Tejeida, D., Muñiz-Rascado, L., García-Sotelo, J.S., Alquicira-Hernández, K., Martínez-Flores, I., Pannier, L., Castro-Mondragón, J.A., Medina-Rivera, A., Solano-Lira, H., Bonavides-Martínez, C., Pérez-Rueda, E., Alquicira-Hernández, S., Porrón-Sotelo, L., López-Fuentes, A., Hernández-Koutoucheva, A., Del Moral-Chavez, V., Rinaldi, F., Collado-Vides, J.. (2016). "RegulonDB version 9.0: High-level integration of gene regulation, coexpression, motif clustering and beyond". Nucleic Acids Research. 44(D1):133-143. [doi:10.1093/nar/gkv1156] | 26527724 |
| 2015 | Alvarez-Vasquez, Fernando J., Freyre-Gonzalez, Julio A., Balderas-Martinez, Yalbi I., Delgado-Carrillo, Monica I., Collado-Vides, Julio. (2015). "Mathematical modeling of the apo and holo transcriptional regulation in Escherichia coli". Molecular Biosystems. 11(4):994-1003. [doi:10.1039/c4mb00561a] | 25683745 |
| 2014 | Gama Castro, Ma. del Socorro, Rinaldi, F., López Fuentes, Alejandra Cristina, Balderas MartÍnez, Yalbi Itzel, Clematide, S., Ellendorff, T.R., Santos Zavaleta, Alberto, Marques-Madeira, H., Collado Vides, Pedro Julio. (2014). "Assisted curation of regulatory interactions and growth conditions of OxyR in E. Colik-12". DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION. 2014():-. [doi:10.1093/database/bau049] | 24903516 |
| 2014 | Martinez, L.C., Martínez Flores, Irma, Salgado Osorio, Heladia, Fernández-Mora, M., Medina Rivera, Alejandra Eugenia, Puente, J.L., Collado Vides, Pedro Julio, Bustamante, V.H.. (2014). "In Silico identification and experimental characterization of regulatory elements controlling the expression of the Salmonella csrB and csrC genes". Journal Of Bacteriology. 196(2):325-336. [doi:10.1128/JB.00806-13] | 24187088 |
| 2014 | Meysman, P., Sonego, P., Bianco, L., Fu, Q., Ledezma Tejeida, Daniela Elizabeth, Gama Castro, Ma. del Socorro, Liebens, V., Laukens, K., Marchal, K., Collado Vides, Pedro Julio, Engelen, K.. (2014). "COLOMBOS v2.0: An ever expanding collection of bacterial expression compendia". Nucleic Acids Research. 42(D1):649-653. [doi:10.1093/nar/gkt1086] | 24214998 |
| 2014 | Meysman, Pieter, Collado-Vides, Julio, Morett, Enrique, Viola, Roberto, Engelen, Kristof, Laukens, Kris. (2014). "Structural properties of prokaryotic promoter regions correlate with functional features". Plos One. 9(2):-. [doi:10.1371/journal.pone.0088717] | 24516674 |
| 2013 | Keseler, I.M., Mackie, A., Peralta Gil, Martín, Santos Zavaleta, Alberto, Gama Castro, Ma. del Socorro, Bonavides Martínez, César Augusto, Fulcher, C., Huerta Moreno, Araceli, Kothari, A., Krummenacker, M., Latendresse, M., Muñíz Rascado, Luis José, Ong, Q., Paley, S., Schroder, I., Shearer, A.G., Subhraveti, P., Travers, M., Weerasinghe, D., Weiss, V., Collado Vides, Pedro Julio, Gunsalus, R.P., Paulsen, I., Karp, P.D.. (2013). "EcoCyc: Fusing model organism databases with systems biology". Nucleic Acids Research. 41(D1):605-612. [doi:10.1093/nar/gks1027] | 23143106 |
| 2013 | Salgado Osorio, Heladia, Peralta Gil, Martín, Gama Castro, Ma. del Socorro, Santos Zavaleta, Alberto, Muñíz Rascado, Luis José, Garcia Sotelo, Jair Santiago, Weiss, V., Solano Lira, Hilda, Martínez Flores, Irma, Medina Rivera, Alejandra Eugenia, Salgado Osorio, Gerardo, Alquicira Hernández, Shirley, Alquicira Hernández, Kevin, López Fuentes, Alejandra Cristina, Porrón Sotelo, Liliana, Huerta Moreno, Araceli, Bonavides Martínez, César Augusto, Balderas MartÍnez, Yalbi Itzel, Pannier, Lucia, Olvera, M., Labastida, A., Jiménez-Jacinto, V., Vega-Alvarado, L., del Moral Chávez, Victor Manuel, Hernández Álvarez, Alfredo José, Morett, E., Collado Vides, Pedro Julio. (2013). "RegulonDB v8.0: Omics data sets, evolutionary conservation, regulatory phrases, cross-validated gold standards and more". Nucleic Acids Research. 41(D1):203-213. [doi:10.1093/nar/gks1201] | 23203884 |
| 2013 | Balderas MartÍnez, Yalbi Itzel, Savageau, M., Salgado Osorio, Heladia, Pérez-Rueda, E, Morett, E., Collado Vides, Pedro Julio. (2013). "Transcription Factors in Escherichia coli Prefer the holo Conformation". Plos One. 8(6):-. [doi:10.1371/journal.pone.0065723] | 23776535 |
| 2013 | Weiss, V., Medina-Rivera, A, Huerta, AM, Santos-Zavaleta, A, Salgado, H, Morett, E., Collado-Vides, J. (2013). "Evidence classification of high-throughput protocols and confidence integration in RegulonDB". DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION. 2013():-. [doi:10.1093/database/bas059] | 23327937 |
| 2012 | Salgado Osorio, Heladia, Martínez Flores, Irma, López Fuentes, Alejandra Cristina, Garcia Sotelo, Jair Santiago, Porrón Sotelo, Liliana, Muñíz Rascado, Luis José, Collado Vides, Pedro Julio. (2012). "Extracting regulatory networks of Escherichia coli from RegulonDB". Methods in Molecular Biology. 804():179-195. [doi:10.1007/978-1-61779-361-5_10] | 22144154 |
| 2012 | Pauling, J., Rottger, R., Neuner, A., Salgado Osorio, Heladia, Collado Vides, Pedro Julio, Kalaghatgi, P., Azevedo, V., Tauch, A., Puhlerg, A., Baumbach, J.. (2012). "On the trail of EHEC/EAEC - Unraveling the gene regulatory networks of human pathogenic Escherichia coli bacteria". Integrative Biology. 4(7):728-733. [doi:10.1039/c2ib00132b] | 22318347 |
| 2011 | Salgado Osorio, Heladia, Martínez Flores, Irma, López Fuentes, Alejandra Cristina, Garcia Sotelo, Jair Santiago, Porrón Sotelo, Liliana, Muñíz Rascado, Luis José, Collado Vides, Pedro Julio. (2011). "Extracting regulatory networks of/Escherichia coli/from RegulonDB". Bacterial Molecular Networks: Methods and Protocols. ():-. | |
| 2011 | Gama Castro, Ma. del Socorro, Salgado Osorio, Heladia, Peralta Gil, Martín, Santos Zavaleta, Alberto, Muñíz Rascado, Luis José, Solano Lira, Hilda, Jimenez-Jacinto, V., Weiss, V., Garcia Sotelo, Jair Santiago, López Fuentes, Alejandra Cristina, Porrón Sotelo, Liliana, Alquicira Hernández, Shirley, Medina Rivera, Alejandra Eugenia, Martínez Flores, Irma, Alquicira Hernández, Kevin, Martínez Adame, Ruth, Bonavides Martínez, César Augusto, Miranda-Ríos, J., Huerta Moreno, Araceli, Mendoza-Vargas, A., Collado Torres, Leonardo, Taboada, B., Vega-Alvarado, L., Olvera, M., Olvera, L., Grande, R., Morett, E., Collado Vides, Pedro Julio. (2011). "RegulonDB version 7.0: Transcriptional regulation of Escherichia coli K-12 integrated within genetic sensory response units (Gensor Units)". Nucleic Acids Research. 39(SUPPL. 1):98-105. [doi:10.1093/nar/gkq1110] | 21051347 |
| 2011 | Keseler, I.M., Collado Vides, Pedro Julio, Santos Zavaleta, Alberto, Peralta Gil, Martín, Gama Castro, Ma. del Socorro, Muñíz Rascado, Luis José, Bonavides Martínez, César Augusto, Paley, S., Krummenacker, M., Altman, T., Spaulding, A., Spaulding, A., Pacheco, J., Latendresse, M., Fulcher, C., Sarker, M., Shearer, A.G., Mackie, A., Paulsen, I., Gunsalus, R.P., Karp, P.D.. (2011). "EcoCyc: A comprehensive database of Escherichia coli biology". Nucleic Acids Research. 39(SUPPL. 1):583-590. [doi:10.1093/nar/gkq1143] | 21097882 |
| 2011 | Medina Rivera, Alejandra Eugenia, Abreu-Goodger, C., Thomas-Chollier, M., Salgado Osorio, Heladia, Collado Vides, Pedro Julio, Van Helden, J.. (2011). "Theoretical and empirical quality assessment of transcription factor-binding motifs". Nucleic Acids Research. 39(3):808-824. [doi:10.1093/nar/gkq710] | 20923783 |
| 2010 | Salgado Osorio, Heladia, López Fuentes, Alejandra Cristina, Martínez Flores, Irma, Garcia Sotelo, Jair Santiago, Porrón Sotelo, Liliana, Solano Lira, Hilda, Muñíz Rascado, Luis José, Collado Vides, Pedro Julio. (2010). "Extracting regulatory networks of Escherichia coli from RegulonDB". Bacterial Molecular Networks: Methods and Protocols. ():-. | |
| 2010 | Demir, E., Cary, M.P., Paley, S., Fukuda, K., Lemer, C., Vastrik, I., Wu, G.N., D Eustachio, P., Schaefer, C., Luciano, J., Schacherer, F., Martínez Flores, Irma, Hu, Z.J., Jiménez-Jacinto, V., Joshi-Tope, G., Kandasamy, K., López-Fuentes, A.C., Mi, H.Y., Pichler, E., Rodchenkov, I., Splendiani, A., Tkachev, S., Zucker, J., Gopinath, G., Rajasimha, H., Ramakrishnan, R., Shah, I., Syed, M., Anwar, N., Babur, O., Blinov, M., Brauner, E., Corwin, D., Donaldson, S., Gibbons, F., Goldberg, R., Hornbeck, P., Luna, A., Murray-Rust, P., Neumann, E., Reubenacker, O., Samwald, M., van Iersel, M., Wimalaratne, S., Allen, K., Braun, B., Whirl-Carrillo, M., Cheung, K.H., Dahlquist, K., Finney, A., Gillespie, M., Glass, E., Gong, L., Haw, R., Honig, M., Hubaut, O., Kane, D., Krupa, S., Kutmon, M., Leonard, J., Marks, D., Merberg, D., Petri, V., Pico, A., Ravenscroft, D., Ren L.Y., Shah, N., Sunshine, M., Tang, R., Whaley, R., Letovksy, S., Buetow, K.H., Rzhetsky, A., Schachter, V., Sobral, B., Dogrusoz, U., McWeeney, S., Aladjem, M., Birney, E., Collado Vides, Pedro Julio, Goto, S., Hucka, M., Le Novere, N., Maltsev, N., Pandey, A., Thomas, P., Wingender, E., Karp, P.D., Sander, C., Bader, G.D.. (2010). "The BioPAX community standard for pathway data sharing". Nature Biotechnology. 28(9):935-942. [doi:10.1038/nbt.1666] | 20829833 |
| 2010 | Martínez Flores, Irma, Jiménez-Jacinto, V., López Fuentes, Alejandra Cristina, Collado Vides, Pedro Julio. (2010). "Expanding BioPAX format by integrating Gene Regulation". EMBnet.journal. 16():39-43. | |
| 2009 | Martinez-Antonio, Agustino, Medina-Rivera, Alejandra, Collado-Vides, Julio. (2009). "Structural and functional map of a bacterial nucleoid". Genome Biology. 10(12):247-247. [doi:10.1186/gb-2009-10-12-247] | 19995411 |
| 2009 | Mendoza-Vargas, Alfredo, Olvera, Leticia, Olvera, Maricela, Grande, Ricardo, Vega-Alvarado, Leticia, Taboada, Blanca, Jimenez-Jacinto, Veronica, Salgado, Heladia, Juarez, Katy, Contreras-Moreira, Bruno, Huerta, Araceli M., Collado-Vides, Julio, Morett, Enrique. (2009). "Genome-wide identification of transcription start sites, promoters and transcription factor binding sites in E. coli". Plos One. 4(10):-. [doi:10.1371/journal.pone.0007526] | 19838305 |
| 2009 | Gonzalez Perez, Abel, Espinosa Angarica, Vladimir, Collado-Vides, Julio, Ribeiro Vasconcelos, Ana Tereza. (2009). "From sequence to dynamics: The effects of transcription factor and polymerase concentration changes on activated and repressed promoters". Bmc Molecular Biology. 10():92-92. [doi:10.1186/1471-2199-10-92] | 19772633 |
| 2009 | Lozada-Chvez, Irma, Contreras-Moreira, Bruno, Collado-Vides, Julio. (2009). "Evolution of Bacterial Regulatory Networks:"The Role of DNA-Binding Specificity"". Origins Of Life And Evolution Of Biospheres. 39(3-4):280-281. | |
| 2009 | Lemmens, Karen, De Bie, Tijl, Dhollander, Thomas, De Keersmaecker, Sigrid C., Thijs, Inge M., Schoofs, Geert, De Weerdt, Ami, De Moor, Bart, Vanderleyden, Jos, Collado-Vides, Julio, Engelen, Kristof, Marchal, Kathleen. (2009). "DISTILLER: A data integration framework to reveal condition dependency of complex regulons in Escherichia coli". Genome Biology. 10(3):-. [doi:10.1186/gb-2009-10-3-r27] | 19265557 |
| 2009 | Lemmens, K., De Bie, T., Dhollander, T., Monsieurs, P., De Moor, B., Collado Vides, Pedro Julio, Engelen, K., Marchal, K.. (2009). "The condition-dependent transcriptional network in Escherichia coli". Annals of the New York Academy of Sciences. 1158():29-35. [doi:10.1111/j.1749-6632.2008.03746.x] | 19348629 |
| 2009 | Balleza, Enrique, Lopez-Bojorquez, Lucia N., Martinez-Antonio, Agustino, Resendis-Antonio, Osbaldo, Lozada-Chavez, Irma, Balderas-Martinez, Yalbi I., Encarnacion, Sergio, Collado-Vides, Julio. (2009). "Regulation by transcription factors in bacteria: Beyond description". Fems Microbiology Reviews. 33(1):133-151. [doi:10.1111/j.1574-6976.2008.00145.x] | 19076632 |
| 2009 | Collado-Vides, Julio, Salgado, Heladia, Morett, Enrique, Gama-Castro, Socorro, Jimenez-Jacinto, Veronica, Martinez-Flores, Irma, Medina-Rivera, Alejandra, Muniz-Rascado, Luis, Peralta-Gil, Martin, Santos-Zavaleta, Alberto. (2009). "Bioinformatics resources for the study of gene regulation in bacteria". Journal Of Bacteriology. 91(1):23-31. [doi:10.1128/JB.01017-08] | 18978060 |
| 2008 | Lozada-Chavez, Irma, Angarica, Vladimir Espinosa, Collado-Vides, Julio, Contreras-Moreira, Bruno. (2008). "The Role of DNA-binding Specificity in the Evolution of Bacterial Regulatory Networks". Journal Of Molecular Biology. 379(3):627-643. [doi:10.1016/j.jmb.2008.04.008] | 18466918 |
| 2008 | Janga, Sarath Chandra, Collado-Vides, Julio, Babu, M. Madan. (2008). "Transcriptional regulation constrains the organization of genes on eukaryotic chromosomes". PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA. 105(41):15761-15766. [doi:10.1073/pnas.0806317105] | 18840678 |
| 2008 | Espinosa Angarica, Vladimir, Gonzalez Perez, Abel, Vasconcelos, Ana T., Collado-Vides, Julio, Contreras-Moreira, Bruno. (2008). "Prediction of TF target sites based on atomistic models of protein-DNA complexes". Bmc Bioinformatics. 9():436-436. [doi:10.1186/1471-2105-9-436] | 18922190 |
| 2008 | Freyre González, Julio Augusto, Alonso Pavón, José Antonio, Treviño Quintanilla, Luis Gerardo, Collado Vides, Pedro Julio. (2008). "Functional architecture of Escherichia coli: New insights provided by a natural decomposition approach". Genome Biology. 9(10):154-. [doi:10.1186/gb-2008-9-10-r154] | 18954463 |
| 2008 | Perez, A.D.G., Gonzalez, E.G., Angarica, V.E., Vasconcelos, A.T.R., Collado Vides, Pedro Julio. (2008). "Impact of Transcription Units rearrangement on the evolution of the regulatory network of gamma-proteobacteria". Bmc Genomics. 9():128-128. [doi:10.1186/1471-2164-9-128] | 18366643 |
| 2008 | Gama Castro, Ma. del Socorro, Jiménez Jacinto, Verónica, Peralta Gil, Martín, Santos Zavaleta, Alberto, Peñaloza Spinola, Mónica Ivonne, Contreras Moreira, Bruno, Segura Salazar, Juan, Muñíz Rascado, Luis José, Martínez Flores, Irma, Salgado Osorio, Heladia, Bonavides Martínez, César Augusto, Abreu Goodger, Cei Leander Gastón, Rodríguez Penagos, Carlos, Miranda-Ríos, J., Morett Sánchez, Juan Enrique, Merino, E., Huerta Moreno, Araceli, Treviño Quintanilla, Luis Gerardo, Collado Vides, Pedro Julio. (2008). "RegulonDB (version 6.0): Gene regulation model of Escherichia coli K-12 beyond transcription, active (experimental) annotated promoters and Textpresso navigation". Nucleic Acids Research. 36(SUPPL. 1):120-124. [doi:10.1093/nar/gkm994] | 18158297 |
| 2008 | Martínez-Antonio, A., Collado Vides, Pedro Julio. (2008). "Comparative mechanisms for transcription and regulatory signals in archaea and bacteria". Computational Methods for Understanding Bacterial and Archaeal Genomes. (0):185-208. | |
| 2007 | Resendis Antonio, Osbaldo, Reed, J.L., Encarnación Guevara, Sergio Manuel, Collado Vides, Pedro Julio, Palsson, B.O.. (2007). "Metabolic reconstruction and modeling of nitrogen fixation in Rhizobium etli". Plos Computational Biology. 3(10):1887-1895. [doi:10.1371/journal.pcbi.0030192] | 17922569 |
| 2007 | Karp, P.D., Keseler, I.M., Shearer, A., Latendresse, M., Krummenacker, M., Paley, S.M., Paulsen, I., Collado Vides, Pedro Julio, Gama Castro, Ma. del Socorro, Peralta Gil, Martín, Santos Zavaleta, Alberto, Peñaloza Spinola, Mónica Ivonne, Bonavides Martínez, César Augusto, Ingraham, J.. (2007). "Multidimensional annotation of the Escherichia coli K-12 genome". Nucleic Acids Research. 35(22):7577-7590. [doi:10.1093/nar/gkm740] | 17940092 |
| 2007 | Janga, Sarath Chandra, Collado-Vides, J.. (2007). "Structure and evolution of gene regulatory networks in microbial genomes". Research In Microbiology. 158(10):787-794. [doi:10.1016/j.resmic.2007.09.001] | 17996425 |
| 2007 | Janga, Sarath Chandra, Salgado Osorio, Heladia, Martínez Antonio, Agustino, Collado Vides, Pedro Julio. (2007). "Coordination logic of the sensing machinery in the transcriptional regulatory network of Escherichia coli". Nucleic Acids Research. 35(20):6963-6972. [doi:10.1093/nar/gkm743] | 17933780 |
| 2007 | Palacios, Rafael, Collado-Vides, Julio. (2007). "Development of genomic sciences in Mexico: A good start and a long way to go". Plos Computational Biology. 3(9):1670-1673. [doi:10.1371/journal.pcbi.0030143] | 17907791 |
| 2007 | Perez, A.G., Angarica, V.E., Vasconcelos, A.T.R., Collado Vides, Pedro Julio. (2007). "Tractor_DB (version 2.0): A database of regulatory interactions in gamma-proteobacterial genomes". Nucleic Acids Research. 35(SUPPL. 1):132-136. [doi:10.1093/nar/gkl800] | 17088283 |
| 2007 | Rodríguez Penagos, Carlos, Salgado Osorio, Heladia, Martínez Flores, Irma, Collado Vides, Pedro Julio. (2007). "Automatic reconstruction of a bacterial regulatory network using Natural Language Processing". Bmc Bioinformatics. 8():293-293. [doi:10.1186/1471-2105-8-293] | 17683642 |
| 2007 | Gutierrez-Rios, R.M., Freyre González, Julio Augusto, Resendis Antonio, Osbaldo, Collado Vides, Pedro Julio, Saier, M., Gosset, G.. (2007). "Identification of regulatory network topological units coordinating the genome-wide transcriptional response to glucose in Escherichia coli". Bmc Microbiology. 7():53-53. [doi:10.1186/1471-2180-7-53] | 17559662 |
| 2007 | Contreras Moreira, Bruno, Fernández, Pierre-Alain, Collado Vides, Pedro Julio. (2007). "TFmodeller: Comparative modelling of protein-DNA complexes". Bioinformatics. 23(13):1694-1696. [doi:10.1093/bioinformatics/btm148] | 17459960 |
| 2007 | Janga, Sarath Chandra, Salgado Osorio, Heladia, Collado Vides, Pedro Julio, Martínez Antonio, Agustino. (2007). "Internal Versus External Effector and Transcription Factor Gene Pairs Differ in Their Relative Chromosomal Position in Escherichia coli". Journal Of Molecular Biology. 368(1):263-272. [doi:10.1016/j.jmb.2007.01.019] | 17321548 |
| 2007 | Rodríguez Penagos, Carlos, Martínez Flores, Irma, Salgado Osorio, Heladia, Collado Vides, Pedro Julio. (2007). "NLP-based curation of bacterial regulatory networks". Computational Linguistics And Intelligent Text Processing. 4394():575-. | |
| 2007 | Rodríguez Penagos, Carlos, Salgado Osorio, Heladia, Martínez Flores, Irma, Collado Vides, Pedro Julio. (2007). "NLP-Based Curation of Bacterial Regulatory Networks". CICLing. ():575-586. | |
| 2007 | Rodríguez-Penagos, C., Salgado, H., Martínez-Flores, I., Collado-Vides, J.. (2007). "NLP-based curation of bacterial regulatory networks". LECT NOTES COMPUT SC. 4394 LNCS():575-586. [doi:10.1007/978-3-540-70939-8_51] | |
| 2006 | González Zúñiga, Víctor Manuel, Santamaria Gutiérrez, Rosa Isela, Bustos Arcos, Virginia Patricia, Hernández González, Ismael Luis, Medrano Soto, Luis Arturo, Moreno Hagelsieb, Gabriel, Janga, Sarath Chandra, Ramírez Romero, Miguel Ángel, Jiménez Jacinto, Verónica, Collado Vides, Pedro Julio, Dávila Ramos, José Guillermo. (2006). "The partitioned Rhizobium etli genome: Genetic and metabolic redundancy in seven interacting replicons". PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA. 103(10):3834-3839. [doi:10.1073/pnas.0508502103] | 16505379 |
| 2006 | Santos-Zavaleta, A., Salgado, H., Gama-Castro, S., Peralta-Gil, M., Contreras-Moreira, B., Penaloza-Spinola, M., I, Collado-Vides, J.. (2006). "RegulonDB. The most important database in transcriptional regulatory network, operon organization, and growth conditions of Escherichia coli K12". Proceedings Of The Fifth International Conference On Bioinformatics Of Genome Regulation And Structure, Vol 3. ():323-323. | |
| 2006 | Lozada-Chavez, Irma, Janga, Sarath Chandra, Collado-Vides, Julio. (2006). "Bacterial regulatory networks are extremely flexible in evolution". Nucleic Acids Research. 34(12):3434-3445. [doi:10.1093/nar/gkl423] | 16840530 |
| 2006 | Huerta Moreno, Araceli, Francino, M.P., Morett Sánchez, Juan Enrique, Collado Vides, Pedro Julio. (2006). "Selection for unequal densities of s70promoter-like signals in different regions of large bacterial genomes". Plos Genetics. 2(11):1740-1750. [doi:10.1371/journal.pgen.0020185] | 17096598 |
| 2006 | Peñaloza Spinola, Mónica Ivonne, Peralta Gil, Martín, Gama Castro, Ma. del Socorro, Contreras Moreira, Bruno, Santos Zavaleta, Alberto, Martínez Flores, Irma, Collado Vides, Pedro Julio. (2006). "RegulonDB: Going beyond transcriptional regulation". Proceedings Of The Fifth International Conference On Bioinformatics Of Genome Regulation And Structure, Vol 3. ():322-322. | |
| 2006 | Contreras Moreira, Bruno, Collado Vides, Pedro Julio. (2006). "Comparative footprinting of DNA-binding proteins". Bioinformatics. 22(14):74-80. [doi:10.1093/bioinformatics/btl215] | 16873524 |
| 2006 | Huerta Moreno, Araceli, Collado Vides, Pedro Julio, Francino, M.P.. (2006). "Positional conservation of clusters of overlapping promoter-like sequences in enterobacterial genomes". MOLECULAR BIOLOGY AND EVOLUTION. 23(5):997-1010. [doi:10.1093/molbev/msk004] | 16547149 |
| 2006 | Salgado Osorio, Heladia, Santos Zavaleta, Alberto, Gama Castro, Ma. del Socorro, Peralta Gil, Martín, Peñaloza Spinola, Mónica Ivonne, Martínez Antonio, Agustino, Karp, P.D., Collado Vides, Pedro Julio. (2006). "The comprehensive updated regulatory network of Escherichia coli K-12". Bmc Bioinformatics. 7():5-5. [doi:10.1186/1471-2105-7-5] | 16398937 |
| 2006 | Martínez Antonio, Agustino, Janga, Sarath Chandra, Salgado Osorio, Heladia, Collado Vides, Pedro Julio. (2006). "Internal-sensing machinery directs the activity of the regulatory network in Escherichia coli". TRENDS IN MICROBIOLOGY. 14(1):22-27. [doi:10.1016/j.tim.2005.11.002] | 16311037 |
| 2006 | Salgado Osorio, Heladia, Gama Castro, Ma. del Socorro, Peralta Gil, Martín, Díaz Peredo, Edgar Ulises, Sánchez Solano, Erika Fabiola, Santos Zavaleta, Alberto, Martínez Flores, Irma, Jiménez Jacinto, Verónica, Bonavides Martínez, César Augusto, Segura Salazar, Juan, Martínez Antonio, Agustino, Collado Vides, Pedro Julio. (2006). "RegulonDB (version 5.0): Escherichia coli K-12 transcriptional regulatory network, operon organization, and growth conditions.". Nucleic Acids Research. 34(Database issue):394-397. [doi:10.1093/nar/gkj156] | 16381895 |
| 2005 | Janga, SC, Collado-Vides, J, Moreno-Hagelsieb, G. (2005). "Nebulon: A system for the inference of functional relationships of gene products from the rearrangement of predicted operons". Nucleic Acids Research. 33(8):2521-2530. [doi:10.1093/nar/gki545] | 15867197 |
| 2005 | Le Novere, N., Finney, A., Hucka, M., Bhalla, U.S., Campagne, F., Collado Vides, Pedro Julio, Crampin, E.J., Halstead, M., Klipp, E., Mendes, P., Nielsen, P., Sauro, H., Shapiro, B., Snoep, J.L., Spence, H.D., Wanner, B.L.. (2005). "Minimum information requested in the annotation of biochemical models (MIRIAM)". Nature Biotechnology. 23(12):1509-1515. [doi:10.1038/nbt1156] | 16333295 |
| 2005 | Espinosa, V., Gonzalez, A.D., Vasconcelos, A.T., Huerta Moreno, Araceli, Collado Vides, Pedro Julio. (2005). "Comparative studies of transcriptional regulation mechanisms in a group of eight gamma-proteobacterial genomes". Journal Of Molecular Biology. 354(1):184-199. [doi:10.1016/j.jmb.2005.09.037] | 16236313 |
| 2005 | Flores López, Margarita, Morales Reyes, Lucía Guadalupe, Ávila Casanueva, Agustin Bernardo, González Zúñiga, Víctor Manuel, Bustos Arcos, Virginia Patricia, García Alonso, Delfino, Pérez-Tejada Domínguez, Yolanda, Guo, Xianwu, Collado Vides, Pedro Julio, Pinero, D., Dávila Ramos, José Guillermo, Mora Celis, Jaime, Palacios de la Lama, Rafael. (2005). "Diversification of DNA sequences in the symbiotic genome of Rhizobium etli". Journal Of Bacteriology. 187(21):7185-7192. [doi:10.1128/JB.187.21.7185-7192.2005] | 16237002 |
| 2005 | Guia, M.H., Perez, A.G., Angarica, V.E., Vasconcelos, A.T., Collado Vides, Pedro Julio. (2005). "Complementing computationally predicted regulatory sites in Tractor_DB using a pattern matching approach". In Silico Biology: Journal of Biological Systems Modeling and Multi-Scale Simulation. 5(2):209-219. | 15972018 |
| 2005 | Menchaca Mendez, Ricardo, Janga, Sarath Chandra, Collado Vides, Pedro Julio. (2005). "The network of transcriptional interactions imposes linear constrains in the genome". OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY. 9(2):139-145. [doi:10.1089/omi.2005.9.139] | 15969646 |
| 2005 | Ibarra-Junquera, V, Torres, LA, Rosu, HC, Arguello, G, Collado-Vides, J. (2005). "Nonlinear software sensor for monitoring genetic regulation processes with noise and modeling errors". PHYSICAL REVIEW E. 72(1):11919-11919. [doi:10.1103/PhysRevE.72.011919] | 16090013 |
| 2005 | Medrano-Soto, A, Christen, JA, Collado-Vides, J. (2005). "BClass: A Bayesian approach based on mixture models for clustering and classification of heterogeneous biological data". JOURNAL OF STATISTICAL SOFTWARE. 13(2):1-18. [doi:10.18637/jss.v013.i02] | |
| 2005 | Gonzalez, A.D., Espinosa, V., Vasconcelos, A.T., Perez-Rueda, E., Collado Vides, Pedro Julio. (2005). "TRACTOR_DB: A database of regulatory networks in gamma-proteobacterial genomes". Nucleic Acids Research. 33(DATABASE ISS.):98-102. [doi:10.1093/nar/gki054] | 15608293 |
| 2005 | Keseler, I.M., Collado Vides, Pedro Julio, Gama Castro, Ma. del Socorro, Ingraham, J., Paley, S., Paulsen, I.T., Peralta Gil, Martín, Karp, P.D.. (2005). "EcoCyc: A comprehensive database resource for Escherichia coli". Nucleic Acids Research. 33(DATABASE ISS.):334-337. [doi:10.1093/nar/gki108] | 15608210 |
| 2005 | Resendis Antonio, Osbaldo, Freyre González, Julio Augusto, Menchaca Mendez, Ricardo, Gutiérrez Ríos, Rosa María, Martínez Antonio, Agustino, Ávila Sánchez, Cristhian, Collado Vides, Pedro Julio. (2005). "Modular analysis of the transcriptional regulatory network of E. coli". TRENDS IN GENETICS. 21(1):16-20. [doi:10.1016/j.tig.2004.11.010] | 15680508 |
| 2004 | Karp, PD, Arnaud, M, Collado-Vides, J, Ingraham, J, Paulsen, IT, Saier, MH. (2004). "The E. coli EcoCyc database: No longer just a metabolic pathway database". Asm News. 70(1):25-30. | |
| 2004 | Perez-Rueda, E., Collado Vides, Pedro Julio, Segovia, L.. (2004). "Phylogenetic distribution of DNA-binding transcription factors in bacteria and archaea". COMPUTATIONAL BIOLOGY AND CHEMISTRY. 28(5-6):341-350. [doi:10.1016/j.compbiolchem.2004.09.004] | 15556475 |
| 2004 | Resendis-Antonio, O, Collado-Vides, J. (2004). "The growth of random networks as a diffusion process". PHYSICA A-STATISTICAL MECHANICS AND ITS APPLICATIONS. 342(3-4):551-560. [doi:10.1016/j.physa.2004.05.037] | |
| 2004 | Medrano Soto, Luis Arturo, Moreno Hagelsieb, Gabriel, Vinuesa Fleischmann, Pablo, Christen, J.A., Collado Vides, Pedro Julio. (2004). "Successful lateral transfer requires codon usage compatibility between foreign genes and recipient genomes". MOLECULAR BIOLOGY AND EVOLUTION. 21(10):1884-1894. [doi:10.1093/molbev/msh202] | 15240837 |
| 2004 | Oviedo, N.A., Salgado Osorio, Heladia, Collado Vides, Pedro Julio, Guarneros, G.. (2004). "Distribution of minigenes in the bacteriophage lambda chromosome". Gene. 329(1-2):115-124. [doi:10.1016/j.gene.2003.12.031] | 15033534 |
| 2004 | Salgado Osorio, Heladia, Gama Castro, Ma. del Socorro, Martínez Antonio, Agustino, Díaz Peredo, Edgar Ulises, Sánchez Solano, Erika Fabiola, Peralta Gil, Martín, García Alonso, Delfino, Jiménez Jacinto, Verónica, Santos Zavaleta, Alberto, Bonavides Martínez, César Augusto, Collado Vides, Pedro Julio. (2004). "RegulonDB (version 4.0): Transcriptional regulation, operon organization and growth conditions in Escherichia coli K-12". Nucleic Acids Research. 32(DATABASE ISS.):303-306. [doi:10.1093/nar/gkh140] | 14681419 |
| 2003 | Perret, X., Kobayashi, H., Collado Vides, Pedro Julio. (2003). "Regulation of expression of symbiotic genes in Rhizobium sp. NGR234". INDIAN JOURNAL OF EXPERIMENTAL BIOLOGY. 41(10):1101-1113. | 15242276 |
| 2003 | Gutiérrez Ríos, Rosa María, Rosenblueth, D.A., Loza, José Antonio, Huerta Moreno, Araceli, Glasner, J.D., Blattner, F.R., Collado Vides, Pedro Julio. (2003). "Regulatory network of Escherichia coli: Consistency between literature knowledge and microarray profiles". GENOME RESEARCH. 13(11):2435-2443. [doi:10.1101/gr.1387003] | 14597655 |
| 2003 | Collado Vides, Pedro Julio, Medrano Soto, Luis Arturo, Tusié-Luna, M.T.. (2003). "With the finished human genome in hand, what next?". Genome Biology. 4(7):328-328. [doi:10.1186/gb-2003-4-7-328] | 12844356 |
| 2003 | Martínez Antonio, Agustino, Salgado Osorio, Heladia, Gama Castro, Ma. del Socorro, Gutiérrez Ríos, Rosa María, Jiménez Jacinto, Verónica, Collado Vides, Pedro Julio. (2003). "Environmental Conditions and Transcriptional Regulation in Escherichia coli: A Physiological Integrative Approach". BIOTECHNOLOGY AND BIOENGINEERING. 84(7):743-749. [doi:10.1002/bit.10846] | 14708114 |
| 2003 | Jauregui, R, Abreu-Goodger, C, Moreno-Hagelsieb, G, Collado-Vides, J, Merino, E. (2003). "Conservation of DNA curvature signals in regulatory regions of prokaryotic genes". Nucleic Acids Research. 31(23):6770-6777. [doi:10.1093/nar/gkg882] | 14627810 |
| 2003 | Huerta, AM, Collado-Vides, J. (2003). "Sigma70 promoters in Escherichia coli: Specific transcription in dense regions of overlapping promoter-like signals". Journal Of Molecular Biology. 333(2):261-278. [doi:10.1016/j.jmb.2003.07.017] | 14529615 |
| 2003 | Martinez-Antonio, A, Collado-Vides, J. (2003). "Identifying global regulators in transcriptional regulatory networks in bacteria". Current Opinion In Microbiology. 6(5):482-489. [doi:10.1016/j.mib.2003.09.002] | 14572541 |
| 2003 | González Zúñiga, Víctor Manuel, Bustos Arcos, Virginia Patricia, Ramírez Romero, Miguel Ángel, Medrano Soto, Luis Arturo, Salgado Osorio, Heladia, Hernández González, Ismael Luis, Hernández Celis, Juan Carlos, Quintero Hernández, Verónica, Moreno Hagelsieb, Gabriel, Girard Cuesy, María de Lourdes, Rodríguez Sánchez, Oscar, Flores López, Margarita, Cevallos Gaos, Miguel Ángel Carlos, Collado Vides, Pedro Julio, Romero Camarena, David René, Dávila Ramos, José Guillermo. (2003). "The mosaic structure of the symbiotic plasmid of Rhizobium etli CFN42 and its relation to other symbiotic genome compartments.". Genome Biology. 4(6):-. [doi:10.1186/gb-2003-4-6-r36] | 12801410 |
| 2002 | Degrave, W.M., Vargas, R., Alvarez, F., Collado Vides, Pedro Julio, Nunez, L., Ramirez, J.L., Grau, O.. (2002). "Towards a bioinformatics network for Latin America and the Caribbean (LACBioNet).". Applied Bioinformatics. 1(1):53-56. | 15130857 |
| 2002 | Huerta, AM, Glasner, JD, Gutierrez-Rios, RM, Blattner, FR, Collado-Vides, J. (2002). "GETools: gene expression tool for analysis of transcriptome experiments in E. coli". TRENDS IN GENETICS. 18(4):217-218. [doi:10.1016/S0168-9525(01)02620-8] | |
| 2002 | Collado Vides, Pedro Julio, Moreno Hagelsieb, Gabriel, Pérez Rueda, Ernesto, Salgado Osorio, Heladia, Huerta Moreno, Araceli, Gutiérrez Ríos, Rosa María, Rosenblueth, David A., Christen, Andrés, Benítez Bellón, Esperanza, Medrano Soto, Luis Arturo, Gama Castro, Ma. del Socorro, Santos Zavaleta, Alberto, Bonavides Martínez, César Augusto, DíPeredo, Edgar, Sánchez Solano, Erika Fabiola, Millá, Dulce María. (2002). "Genomics of Gene Regulation: The view from Escherichia coli". Gene Regulation and Metabolism, Post-Genomic Computational Approaches. ():103-128. | |
| 2002 | Moreno Hagelsieb, Gabriel, Collado Vides, Pedro Julio. (2002). "A powerful non-homology method for the prediction of operons in prokaryotes.". Bioinformatics. 18 Suppl 1():329-336. [doi:10.1093/bioinformatics/18.suppl_1.s329] | 12169563 |
| 2002 | de Daruvar, A, Collado-Vides, J, Valencia, A. (2002). "Analysis of the cellular functions of Escherichia coli operons and their conservation in Bacillus Subtilis". Journal Of Molecular Evolution. 55(2):211-221. [doi:10.1007/s00239-002-2317-1] | 12107597 |
| 2002 | Collado-Vides, J, Moreno-Hagelsieb, G, Medrano-Soto, A. (2002). "Microbial computational genomics of gene regulation". PURE AND APPLIED CHEMISTRY. 74(6):899-905. [doi:10.1351/pac200274060899] | |
| 2002 | Benítez Bellón, Esperanza, Moreno Hagelsieb, Gabriel, Collado Vides, Pedro Julio. (2002). "Evaluation of thresholds for the detection of binding sites for regulatory proteins in Escherichia coli K12 DNA.". Genome Biology. 3(3):-. | 11897025 |
| 2002 | Moreno Hagelsieb, Gabriel, Collado Vides, Pedro Julio. (2002). "Operon conservation from the point of view of Escherichia coli, and inference of functional interdependence of gene products from genome context". In Silico Biology: Journal of Biological Systems Modeling and Multi-Scale Simulation. 2(2):87-95. | 12066843 |
| 2002 | Karp, PD, Riley, M, Saier, M, Paulsen, IT, Collado-Vides, J, Paley, SM, Pellegrini-Toole, A, Bonavides, C, Gama-Castro, S. (2002). "The EcoCyc database". Nucleic Acids Research. 30(1):56-58. [doi:10.1093/nar/30.1.56] | 11752253 |
| 2002 | Collado-Vides, J., Moreno-Hagelsieb, G., Medrano-Soto, A.. (2002). "Microbial computational genomics of gene regulation". PURE AND APPLIED CHEMISTRY. 74(6):899-905. [doi:10.1351/pac200274060899] | |
| 2001 | Pérez-Rueda, E, Collado-Vides, J. (2001). "Common history at the origin of the position - Function correlation in transcriptional regulators in archaea and bacteria". Journal Of Molecular Evolution. 53(3):172-179. [doi:10.1007/s002390010207] | 11523004 |
| 2001 | Tan, K., Moreno Hagelsieb, Gabriel, Collado Vides, Pedro Julio, Stormo, G.D.. (2001). "A comparative genomics approach to prediction of new members of regulons". GENOME RESEARCH. 11(4):566-584. [doi:10.1101/gr.149301] | 11282972 |
| 2001 | Moreno-Hagelsieb, G, Trevino, V, Pérez-Rueda, E, Smith, TF, Collado-Vides, J. (2001). "Transcription unit conservation in the three domains of life: A perspective from Escherichia coli". TRENDS IN GENETICS. 17(4):175-177. [doi:10.1016/S0168-9525(01)02241-7] | 11275307 |
| 2001 | Salgado, H, Santos-Zavaleta, A, Gama-Castro, S, Millen-Zarate, D, Diaz-Peredo, E, Sanchez-Solano, F, Pérez-Rueda, E, Bonavides-Martinez, C, Collado-Vides, J. (2001). "RegulonDB (version 3.2): Transcriptional regulation and operon organization in Escherichia coli K-12". Nucleic Acids Research. 29(1):72-74. [doi:10.1093/nar/29.1.72] | 11125053 |
| 2001 | Ramirez-Santos, J, Collado-Vides, J, Garcia-Varela, M, Gomez-Eichelmann, MC. (2001). "Conserved regulatory elements of the promoter sequence of the gene rpoH of enteric bacteria". Nucleic Acids Research. 29(2):380-386. [doi:10.1093/nar/29.2.380] | 11139607 |
| 2000 | Salgado, H, Santos-Zavaleta, A, Gama-Castro, S, Millan-Zarate, D, Blattner, FR, Collado-Vides, J. (2000). "RegulonDB (version 3.0): Transcriptional regulation and operon organization in Escherichia coli K-12". Nucleic Acids Research. 28(1):65-67. [doi:10.1093/nar/28.1.65] | 10592182 |
| 2000 | van Heiden, Jacques, Rios, Alma. F., Collado-Vides, Julio. (2000). "Discovering regulatory elements in non-coding sequences by analysis of spaced dyads". Nucleic Acids Research. 28(8):1808-1818. [doi:10.1093/nar/28.8.1808] | 10734201 |
| 2000 | van Helden, J., Andre, B., Collado Vides, Pedro Julio. (2000). "A web site for the computational analysis of yeast regulatory sequences". Yeast. 16(2):177-187. <a target="_blank" href="http://dx.doi.org/10.1002/(SICI)1097-0061(20000130)16:23.0.CO;2-9">[doi:10.1002/(SICI)1097-0061(20000130)16:23.0.CO;2-9] | 10641039 |
| 2000 | Strainic, MG, Sullivan, JJ, Collado-Vides, J, deHaseth, PL. (2000). "Promoter interference in a bacteriophage lambda control region: Effects of a range of interpromoter distances". Journal Of Bacteriology. 182(1):216-220. [doi:10.1128/JB.182.1.216-220.2000] | 10613884 |
| 2000 | Salgado Osorio, Heladia, Moreno Hagelsieb, Gabriel, Smith, T.F., Collado Vides, Pedro Julio. (2000). "Operons in Escherichia coli: Genomic analyses and predictions". PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA. 97(12):6652-6657. [doi:10.1073/pnas.110147297] | 10823905 |
| 2000 | Perez-Rueda, Ernesto, Collado-Vides, Julio. (2000). "The repertoire of DNA-binding transcriptional regulators in Escherichia coli K-12". Nucleic Acids Research. 28(8):1838-1847. [doi:10.1093/nar/28.8.1838] | 10734204 |
| 1999 | Salgado, H, Santos, A, Garza-Ramos, U, van Helden, J, Diaz, E, Collado-Vides, J. (1999). "RegulonDB (version 2.0): A database on transcriptional regulation in Escherichia coli". Nucleic Acids Research. 27(1):59-60. [doi:10.1093/nar/27.1.59] | 9847141 |
| 1999 | Collado Vides, Pedro Julio, Hofestadt, R., Mavrovouniotis, M., Michal, G.. (1999). "Modeling and simulation of gene regulation and metabolic pathways". Biosystems. 49(1):79-82. [doi:10.1016/S0303-2647(98)00081-1] | 10091975 |
| 1998 | Thieffry, D, Salgado, H, Huerta, AM, Collado-Vides, J. (1998). "Prediction of transcriptional regulatory sites in the complete genome sequence of Escherichia coli K-12". Bioinformatics. 14(5):391-400. [doi:10.1093/bioinformatics/14.5.391] | 9682052 |
| 1998 | Collado-Vides, J, Gutierrez-Rios, RM, Bel-Enguix, G. (1998). "Networks of transcriptional regulation encoded in a grammatical model". Biosystems. 47(1-2):103-118. [doi:10.1016/S0303-2647(98)00016-1] | 9715754 |
| 1998 | Huerta, AM, Salgado, H, Thieffry, D, Collado-Vides, J. (1998). "RegulonDB: A database on transcriptional regulation in Escherichia coli". Nucleic Acids Research. 26(1):55-59. [doi:10.1093/nar/26.1.55] | 9399800 |
| 1998 | van Helden, J., Andre, B., Collado Vides, Pedro Julio. (1998). "Extracting regulatory sites from the upstream region of yeast genes by computational analysis of oligonucleotide frequencies". Journal Of Molecular Biology. 281(5):827-842. [doi:10.1006/jmbi.1998.1947] | 9719638 |
| 1998 | Pérez Rueda, Ernesto, Gralla, J.D., Collado Vides, Pedro Julio. (1998). "Genomic position analyses and the transcription machinery". Journal Of Molecular Biology. 275(2):165-170. [doi:10.1006/jmbi.1997.1465] | 9466899 |
| 1998 | Thieffry Jacot-Descombes, Denis Louis, Huerta Moreno, Araceli, Pérez Rueda, Ernesto, Collado Vides, Pedro Julio. (1998). "From specific gene regulation to genomic networks: A global analysis of transcriptional regulation in Escherichia coli". Bioessays. 20(5):433-440. <a target="_blank" href="http://dx.doi.org/10.1002/(SICI)1521-1878(199805)20:53.0.CO;2-2">[doi:10.1002/(SICI)1521-1878(199805)20:53.0.CO;2-2] | 9670816 |
| 1997 | Thieffry Jacot-Descombes, Denis Louis, Rosenblueth, D.A., Huerta Moreno, Araceli, Salgado Osorio, Heladia, Collado Vides, Pedro Julio. (1997). "Definite-clause grammars for the analysis of CIS-regulatory regions in E. coli.". Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing. ():441-452. | 9390313 |
| 1997 | Collado-Vides, J, Huerta, AM, Klose, K. (1997). "Three models of gene regulation in E. coli". LECT NOTES COMPUT SC. 1278():72-78. | |
| 1997 | Blattner, FR, Plunkett, G, Bloch, CA, Perna, NT, Burland, V, Riley, M, ColladoVides, J, Glasner, JD, Rode, CK, Mayhew, GF, Gregor, J, Davis, NW, Kirkpatrick, HA, Goeden, MA, Rose, DJ, Mau, B, Shao, Y. (1997). "The complete genome sequence of Escherichia coli K-12". Science. 277(5331):1453-1462. [doi:10.1126/science.277.5331.1453] | 9278503 |
| 1996 | ColladoVides, J. (1996). "Towards a unified grammatical model of s70 and s54 bacterial promoters". Biochimie. 78(5):351-363. [doi:10.1016/0300-9084(96)84767-5] | 8905154 |
| 1996 | Hofestadt, R., Mavrovouniotis, M., Collado Vides, Pedro Julio, Loffler, M.. (1996). "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". Bioessays. 18(4):333-335. [doi:10.1002/bies.950180412] | 8967902 |
| 1996 | Rosenblueth, DA, Thieffry, D, Huerta, AM, Salgado, H, ColladoVides, J. (1996). "Syntactic recognition of regulatory regions in Escherichia coli". COMPUTER APPLICATIONS IN THE BIOSCIENCES. 12(5):415-422. [doi:10.1093/bioinformatics/12.5.415] | 8996790 |
| 1993 | COLLADOVIDES, J. (1993). "A linguistic representation of the regulation of transcription initiation. II. Distinctive features of sigma 70 promoters and their regulatory binding sites". Biosystems. 29(2-3):105-128. [doi:10.1016/0303-2647(93)90087-S] | 8374063 |
| 1993 | Collado Vides, Pedro Julio. (1993). "The elements for a classification of units of genetic information with a combinatorial component". JOURNAL OF THEORETICAL BIOLOGY. 163(4):527-548. [doi:10.1006/jtbi.1993.1136] | 8246512 |
| 1993 | COLLADOVIDES, J. (1993). "A linguistic representation of the regulation of transcription initiation. I. An ordered array of complex symbols with distinctive features". Biosystems. 29(2-3):87-104. [doi:10.1016/0303-2647(93)90086-R] | 8374070 |
| 1992 | COLLADOVIDES, J. (1992). "Grammatical model of the regulation of gene expression". PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA. 89(20):9405-9409. [doi:10.1073/pnas.89.20.9405] | 1409648 |
| 1991 | COLLADOVIDES, J, MAGASANIK, B, GRALLA, JD. (1991). "Control site location and transcriptional regulation in Escherichia coli". MICROBIOLOGICAL REVIEWS. 55(3):371-394. [doi:10.1128/MMBR.55.3.371-394.1991] | 1943993 |
| 1991 | COLLADOVIDES, J. (1991). "The search for a grammatical theory of gene regulation is formally justified by showing the inadequacy of context-free grammars". COMPUTER APPLICATIONS IN THE BIOSCIENCES. 7(3):321-326. [doi:10.1093/bioinformatics/7.3.321] | 1913213 |
| 1991 | COLLADOVIDES, J. (1991). "A syntactic representation of units of genetic information-A syntax of units of genetic information". JOURNAL OF THEORETICAL BIOLOGY. 148(3):401-429. [doi:10.1016/S0022-5193(05)80245-0] | 2016901 |
| 1989 | COLLADOVIDES, J. (1989). "A transformational-grammar approach to the study of the regulation of gene expression". JOURNAL OF THEORETICAL BIOLOGY. 136(4):403-425. [doi:10.1016/S0022-5193(89)80156-0] | 2811400 |