Pedro Julio Collado Vides

Computational Genomics Researcher

Full 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 and the computational modeling of regulation of transcription initiation in Escherichia coli, contained in RegulonDB. 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 currently has more than 100 papers in international peer-reviewed (click on “Publications” –above–) journals, which have been cited more than 8000 times, as well as over 13 chapters in books. 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 invited member for program committees of international conferences in his area, and an organizer of various international conferences. The National Institutes of Health (NIH) of the United States have invited him to participate in three occasions to be part of grant evaluation panels in the areas of genomics, computational biology, technology and modeling. 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 is currently President of the recently founded Iberoamerican Society for Bioinformatics.

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.

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Links

Scopus

Telephone: (777) 3139877
Email: collado@ccg.unam.mx

Publications

YearPublicationPMID
2019Santos-Zavaleta, A, Salgado, H, Gama-Castro, S, Sánchez-Pérez, M., Gómez-Romero, L., Ledezma-Tejeida, D., García-Sotelo, J.S., Alquicira-Hernández, K, Muñíz-Rascado, L, Peña-Loredo, P., Ishida-Gutiérrez, C., Velázquez-Ramírez, D.A., Del Moral-Chávez, V, Bonavides-Martínez, C, Méndez-Cruz, CF, Galagan, J. and 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
2017Keseler IM, Mackie A, Santos-Zavaleta, A, Billington R, Bonavides-Martínez, C, Caspi R, Fulcher C, Gama-Castro, S, Kothari A, Krummenacker M, Latendresse M, Muñíz-Rascado, L, Ong Q, Paley S, Peralta-Gil M, Subhraveti P, Velázquez-Ramírez DA, Weaver D, Collado-Vides, J, Paulsen I and Karp PD. (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
2017Ledezma-Tejeida D, Ishida C and 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
2017Méndez-Cruz, CF, Gama-Castro, S, Mejía-Almonte C, Castillo-Villalba MP, Muñíz-Rascado, L and 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
2016Gama-Castro, S, Salgado, H, Santos-Zavaleta, A, Ledezma-Tejeida, D., Muñíz-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-Chávez, V, Rinaldi, F. and 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
2016Moretto, 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. and 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
2015Alvarez-Vasquez, Fernando J., Freyre-González, JA, Balderas-Martinez, Yalbi I., Delgado-Carrillo, Monica I. and Collado-Vides, J. (2015). "Mathematical modeling of the apo and holo transcriptional regulation in Escherichia coli". Molecular Biosystems. 11(4):994-1003. [doi:10.1039/c4mb00561a]25683745
2014Meysman, Pieter, Collado-Vides, J, Morett, Enrique, Viola, Roberto, Engelen, Kristof and Laukens, Kris. (2014). "Structural properties of prokaryotic promoter regions correlate with functional features". Plos One. 9(2):e88717-. [doi:10.1371/journal.pone.0088717]24516674
2014Gama-Castro, S, Rinaldi, F., López-Fuentes, A, Balderas MartÍnez, Yalbi Itzel, Clematide, S., Ellendorff, T.R., Santos-Zavaleta, A, Marques-Madeira, H. and Collado-Vides, J. (2014). "Assisted curation of regulatory interactions and growth conditions of OxyR in E. Colik-12". DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION. 2014():bau049-. [doi:10.1093/database/bau049]24903516
2014Martinez, L.C., Martínez-Flores, I, Salgado, H, Fernández-Mora, M., Medina Rivera, Alejandra Eugenia, Puente, J.L., Collado-Vides, J and 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
2014Meysman, P., Sonego, P., Bianco, L., Fu, Q., Ledezma Tejeida, Daniela Elizabeth, Gama-Castro, S, Liebens, V., Laukens, K., Marchal, K., Collado-Vides, J and 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
2013Balderas MartÍnez, Yalbi Itzel, Savageau, M., Salgado, H, Pérez-Rueda, E, Morett, E. and Collado-Vides, J. (2013). "Transcription Factors in Escherichia coli Prefer the holo Conformation". Plos One. 8(6):e65723-. [doi:10.1371/journal.pone.0065723]23776535
2013Weiss, V., Medina-Rivera, A, Huerta, AM, Santos-Zavaleta, A, Salgado, H, Morett, E. and Collado-Vides, J. (2013). "Evidence classification of high-throughput protocols and confidence integration in RegulonDB". DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION. 2013():bas059-. [doi:10.1093/database/bas059]23327937
2013Salgado, H, Peralta Gil, Martín, Gama-Castro, S, Santos-Zavaleta, A, Muñíz-Rascado, L, Garcia Sotelo, Jair Santiago, Weiss, V., Solano Lira, Hilda, Martínez-Flores, I, Medina Rivera, Alejandra Eugenia, Salgado Osorio, Gerardo, Alquicira-Hernández, S, Alquicira-Hernández, K, López-Fuentes, A, Porrón Sotelo, Liliana, Huerta Moreno, Araceli, Bonavides-Martínez, C, Balderas MartÍnez, Yalbi Itzel, Pannier, Lucia, Olvera, M., Labastida, A., Jiménez-Jacinto, V., Vega-Alvarado, L., Del Moral-Chávez, V, Hérnandez-Álvarez, A, Morett, E. and Collado-Vides, J. (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
2013Keseler, I.M., Mackie, A., Peralta Gil, Martín, Santos-Zavaleta, A, Gama-Castro, S, Bonavides-Martínez, C, Fulcher, C., Huerta Moreno, Araceli, Kothari, A., Krummenacker, M., Latendresse, M., Muñíz-Rascado, L, Ong, Q., Paley, S., Schroder, I., Shearer, A.G., Subhraveti, P., Travers, M., Weerasinghe, D., Weiss, V., Collado-Vides, J, Gunsalus, R.P., Paulsen, I. and 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
2012Pauling, J., Rottger, R., Neuner, A., Salgado, H, Collado-Vides, J, Kalaghatgi, P., Azevedo, V., Tauch, A., Puhlerg, A. and 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
2011Medina Rivera, Alejandra Eugenia, Abreu-Goodger, C., Thomas-Chollier, M., Salgado, H, Collado-Vides, J and 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
2011Gama-Castro, S, Salgado, H, Peralta Gil, Martín, Santos-Zavaleta, A, Muñíz-Rascado, L, Solano Lira, Hilda, Jimenez-Jacinto, V., Weiss, V., Garcia Sotelo, Jair Santiago, López-Fuentes, A, Porrón Sotelo, Liliana, Alquicira-Hernández, S, Medina Rivera, Alejandra Eugenia, Martínez-Flores, I, Alquicira-Hernández, K, Martínez Adame, Ruth, Bonavides-Martínez, C, 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. and Collado-Vides, J. (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
2011Keseler, I.M., Collado-Vides, J, Santos-Zavaleta, A, Peralta Gil, Martín, Gama-Castro, S, Muñíz-Rascado, L, Bonavides-Martínez, C, 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. and 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
2011Salgado, H, Martínez-Flores, I, López-Fuentes, A, Garcia Sotelo, Jair Santiago, Porrón Sotelo, Liliana, Muñíz-Rascado, L and Collado-Vides, J. (2011). "Extracting regulatory networks of/Escherichia coli/from RegulonDB". Bacterial Molecular Networks: Methods and Protocols. ():-.
2010Demir, 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, I, 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, J, Goto, S., Hucka, M., Le Novere, N., Maltsev, N., Pandey, A., Thomas, P., Wingender, E., Karp, P.D., Sander, C. and Bader, G.D.. (2010). "The BioPAX community standard for pathway data sharing". Nature Biotechnology. 28(9):935-942. [doi:10.1038/nbt.1666]20829833
2010Salgado, H, López-Fuentes, A, Martínez-Flores, I, Garcia Sotelo, Jair Santiago, Porrón Sotelo, Liliana, Solano Lira, Hilda, Muñíz-Rascado, L and Collado-Vides, J. (2010). "Extracting regulatory networks of Escherichia coli from RegulonDB". Bacterial Molecular Networks: Methods and Protocols. ():-.
2010Martínez-Flores, I, Jiménez-Jacinto, V., López-Fuentes, A and Collado-Vides, J. (2010). "Expanding BioPAX format by integrating Gene Regulation". EMBnet.journal. 16():39-43.
2009Martinez-Antonio, Agustino, Medina-Rivera, Alejandra and Collado-Vides, J. (2009). "Structural and functional map of a bacterial nucleoid". Genome Biology. 10(12):247-247. [doi:10.1186/gb-2009-10-12-247]19995411
2009Keseler, Ingrid M., Bonavides-Martinez, Cesar, Collado-Vides, J, Gama-Castro, S, Gunsalus, Robert P., Johnson, D. Aaron, Krummenacker, Markus, Nolan, Laura M., Paley, Suzanne, Paulsen, Ian T., Peralta-Gil, Martin, Santos-Zavaleta, A, Glennon Shearer, Alexander and Karp, Peter D.. (2009). "EcoCyc: A comprehensive view of Escherichia coli biology". Nucleic Acids Research. 37(SUPPL. 1):464-470. [doi:10.1093/nar/gkn751]18974181
2009Lemmens, 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, J, Engelen, Kristof and Marchal, Kathleen. (2009). "DISTILLER: A data integration framework to reveal condition dependency of complex regulons in Escherichia coli". Genome Biology. 10(3):R27-. [doi:10.1186/gb-2009-10-3-r27]19265557
2009Lozada-Chvez, Irma, Contreras-Moreira, Bruno and Collado-Vides, J. (2009). "Evolution of Bacterial Regulatory Networks:"The Role of DNA-Binding Specificity"". Origins Of Life And Evolution Of Biospheres. 39(3-4):280-281.
2009Lemmens, K., De Bie, T., Dhollander, T., Monsieurs, P., De Moor, B., Collado-Vides, J, Engelen, K. and 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
2009Collado-Vides, J, Salgado, H, Morett, Enrique, Gama-Castro, S, Jimenez-Jacinto, Veronica, Martínez-Flores, I, Medina-Rivera, Alejandra, Muñíz-Rascado, L, Peralta-Gil, Martin and Santos-Zavaleta, A. (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
2009Balleza, Enrique, Lopez-Bojorquez, Lucia N., Martinez-Antonio, Agustino, Resendis-Antonio, Osbaldo, Lozada-Chavez, Irma, Balderas-Martinez, Yalbi I., Encarnación, S and Collado-Vides, J. (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
2008Lozada-Chavez, Irma, Angarica, Vladimir Espinosa, Collado-Vides, J and 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
2008Gama-Castro, S, Jiménez Jacinto, Verónica, Peralta Gil, Martín, Santos-Zavaleta, A, Peñaloza Spinola, Mónica Ivonne, Contreras Moreira, Bruno, Segura Salazar, Juan, Muñíz-Rascado, L, Martínez-Flores, I, Salgado, H, Bonavides-Martínez, C, Abreu Goodger, Cei Leander Gastón, Rodríguez Penagos, Carlos, Miranda-Ríos, J., Morett Sánchez, Juan Enrique, Merino, E., Huerta Moreno, Araceli, Treviño Quintanilla, Luis Gerardo and Collado-Vides, J. (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
2008Martínez-Antonio, A. and Collado-Vides, J. (2008). "Comparative mechanisms for transcription and regulatory signals in archaea and bacteria". Computational Methods for Understanding Bacterial and Archaeal Genomes. (0):185-208.
2007Gutierrez-Rios, R.M., Freyre-González, JA, Resendis Antonio, Osbaldo, Collado-Vides, J, Saier, M. and 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
2007Rodríguez Penagos, Carlos, Salgado, H, Martínez-Flores, I and Collado-Vides, J. (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
2007Janga, Sarath Chandra and 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
2007Karp, P.D., Keseler, I.M., Shearer, A., Latendresse, M., Krummenacker, M., Paley, S.M., Paulsen, I., Collado-Vides, J, Gama-Castro, S, Peralta Gil, Martín, Santos-Zavaleta, A, Peñaloza Spinola, Mónica Ivonne, Bonavides-Martínez, C and 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
2007Janga, Sarath Chandra, Salgado, H, Martínez Antonio, Agustino and Collado-Vides, J. (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
2007Resendis Antonio, Osbaldo, Reed, J.L., Encarnación, S, Collado-Vides, J and 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
2007Palacios, Rafael and Collado-Vides, J. (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
2007Contreras Moreira, Bruno, Fernández, Pierre-Alain and Collado-Vides, J. (2007). "TFmodeller: Comparative modelling of protein-DNA complexes". Bioinformatics. 23(13):1694-1696. [doi:10.1093/bioinformatics/btm148]17459960
2007Rodríguez Penagos, Carlos, Martínez-Flores, I, Salgado, H and Collado-Vides, J. (2007). "NLP-based curation of bacterial regulatory networks". Computational Linguistics And Intelligent Text Processing. 4394():575-.
2007Rodríguez Penagos, Carlos, Salgado, H, Martínez-Flores, I and Collado-Vides, J. (2007). "NLP-Based Curation of Bacterial Regulatory Networks". CICLing. ():575-586.
2007Perez, A.G., Angarica, V.E., Vasconcelos, A.T.R. and Collado-Vides, J. (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
2006Huerta Moreno, Araceli, Francino, M.P., Morett Sánchez, Juan Enrique and Collado-Vides, J. (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
2006González, V, Santamaria, RI, Bustos, P, Hernández González, Ismael Luis, Medrano Soto, Luis Arturo, Moreno Hagelsieb, Gabriel, Janga, Sarath Chandra, Ramírez Romero, Miguel Ángel, Jiménez Jacinto, Verónica, Collado-Vides, J and 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
2006Salgado, H, Santos-Zavaleta, A, Gama-Castro, S, Peralta Gil, Martín, Peñaloza Spinola, Mónica Ivonne, Martínez Antonio, Agustino, Karp, P.D. and Collado-Vides, J. (2006). "The comprehensive updated regulatory network of Escherichia coli K-12". Bmc Bioinformatics. 7():5-5. [doi:10.1186/1471-2105-7-5]16398937
2006Lozada-Chavez, Irma, Janga, Sarath Chandra and Collado-Vides, J. (2006). "Bacterial regulatory networks are extremely flexible in evolution". Nucleic Acids Research. 34(12):3434-3445. [doi:10.1093/nar/gkl423]16840530
2006Huerta Moreno, Araceli, Collado-Vides, J and 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
2006Salgado, H, Gama-Castro, S, Peralta Gil, Martín, Díaz Peredo, Edgar Ulises, Sánchez Solano, Erika Fabiola, Santos-Zavaleta, A, Martínez-Flores, I, Jiménez Jacinto, Verónica, Bonavides-Martínez, C, Segura Salazar, Juan, Martínez Antonio, Agustino and Collado-Vides, J. (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
2006Martínez Antonio, Agustino, Janga, Sarath Chandra, Salgado, H and Collado-Vides, J. (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
2005Janga, SC, Collado-Vides, J and 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
2005Le Novere, N., Finney, A., Hucka, M., Bhalla, U.S., Campagne, F., Collado-Vides, J, Crampin, E.J., Halstead, M., Klipp, E., Mendes, P., Nielsen, P., Sauro, H., Shapiro, B., Snoep, J.L., Spence, H.D. and 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
2005Flores López, Margarita, Morales Reyes, Lucía Guadalupe, Ávila Casanueva, Agustin Bernardo, González, V, Bustos, P, García-Alonso, D, Pérez-Tejada Domínguez, Yolanda, Guo, Xianwu, Collado-Vides, J, Pinero, D., Dávila Ramos, José Guillermo, Mora, J and 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
2005Ibarra-Junquera, V, Torres, LA, Rosu, HC, Arguello, G and 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
2005Medrano-Soto, A, Christen, JA and 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.
2005Resendis Antonio, Osbaldo, Freyre-González, JA, Menchaca Mendez, Ricardo, Gutiérrez Ríos, Rosa María, Martínez Antonio, Agustino, Ávila Sánchez, Cristhian and Collado-Vides, J. (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
2005Gonzalez, A.D., Espinosa, V., Vasconcelos, A.T., Perez-Rueda, E. and Collado-Vides, J. (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
2005Collado-Vides, J. (2005). "De cuantas historias se hace nuestro cuerpo". Libro de Lecturas para Secundaria. ():-.
2005Collado-Vides, J. (2005). "De que Tamaño es Nuestro Cuerpo". Libro de Lecturas para Secundaria. ():-.
2005Keseler, I.M., Collado-Vides, J, Gama-Castro, S, Ingraham, J., Paley, S., Paulsen, I.T., Peralta Gil, Martín and 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
2004Perez-Rueda, E., Collado-Vides, J and 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
2004Resendis-Antonio, O and 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]
2004Medrano Soto, Luis Arturo, Moreno Hagelsieb, Gabriel, Vinuesa, P, Christen, J.A. and Collado-Vides, J. (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
2004Salgado, H, Gama-Castro, S, Martínez Antonio, Agustino, Díaz Peredo, Edgar Ulises, Sánchez Solano, Erika Fabiola, Peralta Gil, Martín, García-Alonso, D, Jiménez Jacinto, Verónica, Santos-Zavaleta, A, Bonavides-Martínez, C and Collado-Vides, J. (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
2004Karp, PD, Arnaud, M, Collado-Vides, J, Ingraham, J, Paulsen, IT and Saier, MH. (2004). "The E. coli EcoCyc database: No longer just a metabolic pathway database". Asm News. 70(1):25-30.
2003Collado-Vides, J, Medrano Soto, Luis Arturo and 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
2003González, V, Bustos, P, Ramírez Romero, Miguel Ángel, Medrano Soto, Luis Arturo, Salgado, H, Hernández González, Ismael Luis, Hernández Celis, Juan Carlos, Quintero Hernández, Verónica, Moreno Hagelsieb, Gabriel, Girard, L, Rodríguez, O, Flores López, Margarita, Cevallos, MA, Collado-Vides, J, Romero, D and 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):R36-. [doi:10.1186/gb-2003-4-6-r36]12801410
2003Jauregui, R, Abreu-Goodger, C, Moreno-Hagelsieb, G, Collado-Vides, J and 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
2003Gutiérrez Ríos, Rosa María, Rosenblueth, D.A., Loza, José Antonio, Huerta Moreno, Araceli, Glasner, J.D., Blattner, F.R. and Collado-Vides, J. (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
2003Perret, X., Kobayashi, H. and Collado-Vides, J. (2003). "Regulation of expression of symbiotic genes in Rhizobium sp. NGR234". INDIAN JOURNAL OF EXPERIMENTAL BIOLOGY. 41(10):1101-1113. 15242276
2003Martinez-Antonio, A and 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
2002Collado-Vides, J, Moreno-Hagelsieb, G. and Medrano-Soto, A.. (2002). "Microbial computational genomics of gene regulation". PURE AND APPLIED CHEMISTRY. 74(6):899-905.
2002Collado-Vides, J, Moreno Hagelsieb, Gabriel, Pérez Rueda, Ernesto, Salgado, H, Huerta Moreno, Araceli, Gutiérrez Ríos, Rosa María, Rosenblueth, David A., Christen, Andrés, Benítez Bellón, Esperanza, Medrano Soto, Luis Arturo, Gama-Castro, S, Santos Zavaleta, Alberto, Bonavides-Martínez, C, DíPeredo, Edgar, Sánchez Solano, Erika Fabiola and Millá, Dulce María. (2002). "Genomics of Gene Regulation: The view from Escherichia coli". Gene Regulation and Metabolism, Post-Genomic Computational Approaches. ():103-128.
2002Moreno Hagelsieb, Gabriel and Collado-Vides, J. (2002). "A powerful non-homology method for the prediction of operons in prokaryotes.". Bioinformatics. 18 Suppl 1():329-336. 12169563
2002Degrave, W.M., Vargas, R., Alvarez, F., Collado-Vides, J, Nunez, L., Ramirez, J.L. and Grau, O.. (2002). "Towards a bioinformatics network for Latin America and the Caribbean (LACBioNet).". Applied Bioinformatics. 1(1):53-56. 15130857
2002Collado-Vides, J, Moreno-Hagelsieb, G and Medrano-Soto, A. (2002). "Microbial computational genomics of gene regulation". PURE AND APPLIED CHEMISTRY. 74(6):899-905. [doi:10.1351/pac200274060899]
2002Huerta, AM, Glasner, JD, Gutierrez-Rios, RM, Blattner, FR and 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]
2002Moreno Hagelsieb, Gabriel and Collado-Vides, J. (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
2002Karp, PD, Riley, M, Saier, M, Paulsen, IT, Collado-Vides, J, Paley, SM, Pellegrini-Toole, A, Bonavides-Martínez, C and Gama-Castro, S. (2002). "The EcoCyc database". Nucleic Acids Research. 30(1):56-58. [doi:10.1093/nar/30.1.56]11752253
2001Tan, K., Moreno Hagelsieb, Gabriel, Collado-Vides, J and 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
2001Pérez-Rueda, E and 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
2001Moreno-Hagelsieb, G, Trevino, V, Pérez-Rueda, E, Smith, TF and 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
2001Salgado, H, Santos-Zavaleta, A, Gama-Castro, S, Millen-Zarate, D, Diaz-Peredo, E, Sanchez-Solano, F, Pérez-Rueda, E, Bonavides-Martínez, C and 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
2000Salgado, H, Moreno Hagelsieb, Gabriel, Smith, T.F. and Collado-Vides, J. (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
2000Strainic, MG, Sullivan, JJ, Collado-Vides, J and 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
2000Salgado, H, Santos-Zavaleta, A, Gama-Castro, S, Millan-Zarate, D, Blattner, FR and 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
1999Salgado, H, Santos, A, Garza-Ramos, U, van Helden, J, Diaz, E and 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
1998Thieffry, D, Salgado, H, Huerta, AM and 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
1998van Helden, J., Andre, B. and Collado-Vides, J. (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
1998Collado-Vides, J, Gutierrez-Rios, RM and 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
1998Thieffry Jacot-Descombes, Denis Louis, Huerta Moreno, Araceli, Pérez Rueda, Ernesto and Collado-Vides, J. (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
1998Huerta, AM, Salgado, H, Thieffry, D and 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
1997Blattner, FR, Plunkett, G, Bloch, CA, Perna, NT, Burland, V, Riley, M, Collado-Vides, J, Glasner, JD, Rode, CK, Mayhew, GF, Gregor, J, Davis, NW, Kirkpatrick, HA, Goeden, MA, Rose, DJ, Mau, B and 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
1997Collado-Vides, J, Huerta, AM and Klose, K. (1997). "Three models of gene regulation in E. coli". LECT NOTES COMPUT SC. 1278():72-78.
1997Thieffry Jacot-Descombes, Denis Louis, Rosenblueth, D.A., Huerta Moreno, Araceli, Salgado, H and Collado-Vides, J. (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
1996Collado-Vides, 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
1996Rosenblueth, DA, Thieffry, D, Huerta, AM, Salgado, H and Collado-Vides, J. (1996). "Syntactic recognition of regulatory regions in Escherichia coli". COMPUTER APPLICATIONS IN THE BIOSCIENCES. 12(5):415-422. 8996790
1996Hofestadt, R., Mavrovouniotis, M., Collado-Vides, J and 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
1993Collado-Vides, 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
1993Collado-Vides, 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
1991Collado-Vides, 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
1991Collado-Vides, J. (1991). "The search for a grammatical theory of gene regulation is formally justified by showing the inadequacy of context-free grammars". Bioinformatics. 7(3):321-326. [doi:10.1093/bioinformatics/7.3.321]1913213
2007Rodríguez-Penagos, C., Salgado, H, Martínez-Flores, I and Collado-Vides, J. (2007). "NLP-based curation of bacterial regulatory networks". LECT NOTES COMPUT SC. 4394 LNCS():575-586.
1991Collado-Vides, J, MAGASANIK, B and GRALLA, JD. (1991). "Control site location and transcriptional regulation in Escherichia coli". MICROBIOLOGICAL REVIEWS. 55(3):371-394. 1943993
2000Perez-Rueda, Ernesto and Collado-Vides, J. (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
2000van Heiden, Jacques, Rios, Alma. F. and Collado-Vides, J. (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
1992Collado-Vides, 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
2001Ramirez-Santos, J, Collado-Vides, J, Garcia-Varela, M and 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
2005Menchaca Mendez, Ricardo, Janga, Sarath Chandra and Collado-Vides, J. (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
2008Janga, Sarath Chandra, Collado-Vides, J and 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
2012Salgado, H, Martínez-Flores, I, López-Fuentes, A, Garcia Sotelo, Jair Santiago, Porrón Sotelo, Liliana, Muñíz-Rascado, L and Collado-Vides, J. (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
1999Collado-Vides, J, Hofestadt, R., Mavrovouniotis, M. and 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
2005Espinosa, V., Gonzalez, A.D., Vasconcelos, A.T., Huerta Moreno, Araceli and Collado-Vides, J. (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
2006Contreras Moreira, Bruno and Collado-Vides, J. (2006). "Comparative footprinting of DNA-binding proteins". Bioinformatics. 22(14):74-80. [doi:10.1093/bioinformatics/btl215]16873524
2006Peñaloza Spinola, Mónica Ivonne, Peralta Gil, Martín, Gama-Castro, S, Contreras Moreira, Bruno, Santos-Zavaleta, A, Martínez-Flores, I and Collado-Vides, J. (2006). "RegulonDB: Going beyond transcriptional regulation". Proceedings Of The Fifth International Conference On Bioinformatics Of Genome Regulation And Structure, Vol 3. ():322-322.
2007Janga, Sarath Chandra, Salgado, H, Collado-Vides, J and 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
2008Perez, A.D.G., Gonzalez, E.G., Angarica, V.E., Vasconcelos, A.T.R. and Collado-Vides, J. (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
2004Oviedo, N.A., Salgado, H, Collado-Vides, J and 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
2003Martínez Antonio, Agustino, Salgado, H, Gama-Castro, S, Gutiérrez Ríos, Rosa María, Jiménez Jacinto, Verónica and Collado-Vides, J. (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
2003Huerta, AM and 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
2002de Daruvar, A, Collado-Vides, J and 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
2002Benítez Bellón, Esperanza, Moreno Hagelsieb, Gabriel and Collado-Vides, J. (2002). "Evaluation of thresholds for the detection of binding sites for regulatory proteins in Escherichia coli K12 DNA.". Genome Biology. 3(3):RESEARCH0013-. 11897025
2000van Helden, J., Andre, B. and Collado-Vides, J. (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
1998Pérez Rueda, Ernesto, Gralla, J.D. and Collado-Vides, J. (1998). "Genomic position analyses and the transcription machinery". Journal Of Molecular Biology. 275(2):165-170. [doi:10.1006/jmbi.1997.1465]9466899
2009Mendoza-Vargas, Alfredo, Olvera, Leticia, Olvera, Maricela, Grande, Ricardo, Vega-Alvarado, Leticia, Taboada, Blanca, Jimenez-Jacinto, Veronica, Salgado, H, Juarez, Katy, Contreras-Moreira, Bruno, Huerta, Araceli M., Collado-Vides, J and Morett, Enrique. (2009). "Genome-wide identification of transcription start sites, promoters and transcription factor binding sites in E. coli". Plos One. 4(10):e7526-. [doi:10.1371/journal.pone.0007526]19838305
1993Collado-Vides, J. (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
2005Guia, M.H., Perez, A.G., Angarica, V.E., Vasconcelos, A.T. and Collado-Vides, J. (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
2018Tierrafría VH, Mejía-Almonte C, Camacho-Zaragoza JM, Salgado, H, Alquicira-Hernández, K, Gama-Castro, S, Ishida C and Collado-Vides, J. (2018). "MCO: towards an ontology and unified vocabulary for a framework-based annotation of microbial growth conditions.". Bioinformatics. ():-. [doi:10.1093/bioinformatics/bty689]30137210
2018Santos-Zavaleta, A, Sanchez-Perez, Mishael, Salgado, H, Velazquez-Ramirez, David A., Gama-Castro, S, Tierrafria, Victor H., Busby, Stephen J. W., Aquino, Patricia, Fang, Xin, Palsson, Bernhard O., Galagan, James E. and Collado-Vides, J. (2018). "A unified resource for transcriptional regulation in Escherichia coli K-12 incorporating high-throughput-generated binding data into RegulonDB version 10.0". BMC BIOL. 16(1):91-91. [doi:10.1186/s12915-018-0555-y]30115066
2008Espinosa Angarica, Vladimir, Gonzalez Perez, Abel, Vasconcelos, Ana T., Collado-Vides, J and 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
2017Balderas-Martínez YI, Rinaldi F, Contreras G, Solano-Lira H, Sánchez-Pérez M, Collado-Vides, J, Selman M and 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():bax030-. [doi:10.1093/database/bax030]28605770
2017Pannier L, Merino E, Marchal K and Collado-Vides, J. (2017). "Effect of genomic distance on coexpression of coregulated genes in E. coli". Plos One. 12(4):e0174887-. [doi:10.1371/journal.pone.0174887]28419102
2017Rinaldi F, Lithgow O, Gama-Castro, S, Solano H, López-Fuentes, A, Muñíz-Rascado, L, Ishida-Gutiérrez C, Méndez-Cruz, CF and Collado-Vides, J. (2017). "Strategies towards digital and semi-automated curation in RegulonDB". DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION. 2017(1):bax012-. [doi:10.1093/database/bax012]28365731
2008Freyre-González, JA, Alonso Pavón, José Antonio, Treviño Quintanilla, Luis Gerardo and Collado-Vides, J. (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
2009Gonzalez Perez, Abel, Espinosa Angarica, Vladimir, Collado-Vides, J and 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
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