Genómica Computacional

El Programa de Genómica Computacional se dedica, en el ámbito de la bioinformática, al reto de acelerar el acceso al conocimiento genómico, en particular sobre la regulación de la expresión genética microbiana. La columna vertebral es el diseño y expansión de la base de datos RegulonDB, con conocimiento extraído por curadores de la regulación genética en Escherichia coli K-12, tanto de experimentos clásicos como con métodos masivos post-genómicos. Trabajamos algoritmos para la identificación de sitios de pegado, promotores y unidades de transcripción, así como de co-regulación, y para el procesamiento de datos de experimentos masivos tipo ChIP-seq, entre otros. Trabajamos en una ontología y vocabulario controlado de condiciones de crecimiento microbiano, y en una ontología de la regulación genética microbiana. Una vertiente importante es el uso de procesamiento de lenguaje natural (NLP) para enriquecer las estrategias de extracción del conocimiento lo que nos permite expandir la curación a otras bacterias como Salmonella, y otras cuantas bacterias. Hemos sustentado conceptos integrativos como el de frases de regulación y más recientemente el de unidades genético-metabólicas de sensado-respuesta (GENSOR Units), las cuales plantean una gran cantidad de preguntas nuevas. Estamos indagando el formalismo de S-systems de Michael Savageau para el modelaje, inicialmente, de GENSOR Units; ampliándolo a circuitos completos y, si es posible, a un modelaje integral de la célula a nivel molecular. Esto con un enfoque novedoso de geometría algebraica computacional.
Toda esta forma de ver y concebir el conocimiento científico tiene su aplicación con estrategias semejantes en un proyecto que busca romper la separación entre divulgación y comunicación entre expertos, en el proyecto Conogasi (conogasi.org).

Accede a nuestros proyectos si quieres conocer más detalle.

 

 

 

Académicos del Grupo

NombrePuestoCategoríaCorreoTeléfono
Pedro Julio Collado VidesInvestigadorInv. Tit. C T.C. Definitivocollado@ccg.unam.mx(777) 3139877
César Augusto Bonavides MartínezTécnico AcadémicoTec. Acad. Tit. C T.C. Definitivocbona18@ccg.unam.mx(777) 3132063
Ma. del Socorro Gama CastroTécnico AcadémicoTec. Acad. Tit. C T.C. Definitivosgama@ccg.unam.mx(777) 3132063
Heladia Salgado OsorioTécnico AcadémicoTec. Acad. Tit. C T.C. Definitivoheladia@ccg.unam.mx(777) 3132063
Victor Manuel del Moral ChávezTécnico AcadémicoTec. Acad. Tit. A T.C. Obra Det.victor@ccg.unam.mx(777) 3132063
Delfino García AlonsoTécnico AcadémicoTec. Acad. Tit. A T.C. Obra Det.delfinog@ccg.unam.mx(777) 3132063
Carlos Francisco Méndez CruzInvestigadorInv. Asoc. C T.C. Obra Det.cmendezc@ccg.unam.mx(777) 3132063
Kevin Alquicira HernándezTécnico por honorariosCONACYTkevin@ccg.unam.mx(777) 3132063
Shirley Alquicira HernándezTécnico por honorariosCONACYTalquicir@ccg.unam.mx(777) 3132063
Marco Polo Castillo VillalbaTécnico por honorariosOtromarcopol@ccg.unam.mx(777) 3132063
Martin Jair Díaz RodríguezTécnico por honorariosOtromjdiaz@ccg.unam.mx(777) 3132063
Francisco de Jesus Guadarrama GarcíaTécnico por honorariosOtrofranguad@ccg.unam.mx(777) 3132063
Jose Daniel Gutierrez NietoTécnico por honorariosOtrodanezoj@gmail.com(777) 3132063
Oscar William Lithgow SerranoTécnico por honorariosOtroolithgow@ccg.unam.mx(777) 3132063
Alejandra Cristina López FuentesTécnico por honorariosOtroaclopez@ccg.unam.mx(777) 3132063
Luis José Muñíz RascadoTécnico por honorariosUNAMljmuniz@ccg.unam.mx(777) 3132063
Pablo Emilio Peña LoredoTécnico por honorariosOtropablopl@ccg.unam.mx(777) 3132063
Mishael Sánchez PérezTécnico por honorariosOtromishael@ccg.unam.mx(777) 3132063
Victor Hugo Tierrafria PulidoTécnico por honorariosUNAMvhugotp@ccg.unam.mx(777) 3132063

Publicaciones del Grupo

AñoPublicaciónPMID
2019Rioualen, 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):e72-. [doi:10.1002/cpbi.72]30786165
2019Lithgow-Serrano, O, Gama-Castro, S, Ishida-Gutiérrez, C, Mejía-Almonte, C, Tierrafría, V, Martínez-Luna, S, Santos-Zavaleta, A, Velázquez-Ramírez, D, Collado-Vides, J. (2019). "Similarity corpus on microbial transcriptional regulation.". J BIOMED SEMANT. 10(1):-. [doi:10.1186/s13326-019-0200-x]31118102
2019Arroyo Fernández, I, Curiel, A, Méndez, C. (2019). "Language features in extractive summarization: Humans Vs. Machines". KNOWL-BASED SYST. 180():1-11. [doi:10.1016/j.knosys.2019.05.014]
2019Santos-Zavaleta, A, Pérez-Rueda, E, Sánchez-Pérez, M, Velázquez-Ramírez, D, 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
2019Giner-Lamia, J, Vinuesa, P, Betancor, L, Silva, C, Bisio, J, Soleto, L, Chabalgoity, J, Puente, J, Soncini, F, García-Vescovi, E, Flores, G, Pedraza, J, Yim, L, García, C, Astocondor, L, Ochoa, T, Hinostroza, N, Graciela Pucciarelli, M, Hernández-Alvarez, A, Del Moral, V, García-Del Portillo, F. (2019). "Genome analysis of Salmonella enterica subsp. diarizonae isolates from invasive human infections reveals enrichment of virulence-related functions in lineage ST1256". Bmc Genomics. 20(1):99-99. [doi:10.1186/s12864-018-5352-z]30704413
2019Arroyo Fernández, I, Méndez Cruz, C, Sierra, G, Sidorov, G, Torres-Moreno, J. (2019). "Unsupervised Sentence Representations as Word Information Series: Revisiting TF--IDF". COMPUT SPEECH LANG. 56():107-129. [doi:10.1016/j.csl.2019.01.005]
2019Santos-Zavaleta, A, Salgado, H, Gama-Castro, S, Sánchez-Pérez, M, Gómez-Romero, L, Ledezma-Tejeida, D, García-Sotelo, J, Alquicira-Hernández, K, Muñiz-Rascado, L, Peña-Loredo, P, Ishida-Gutiérrez, C, Velázquez-Ramírez, D, Del Moral-Chávez, V, Bonavides-Martínez, C, Méndez-Cruz, C, 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
2019Lithgow-Serrano, O, Collado-Vides, J. (2019). "In the pursuit of semantic similarity for literature on microbial transcriptional regulation". J INTELL FUZZY SYST. 36(5):4777-4786. [doi:10.3233/JIFS-179026]
2018Arroyo Fernández, I, Carrasco Ruiz, M, Méndez Cruz, C. (2018). "Procesamiento de lenguaje natural en la conservación de la herencia cultural: una red semántica del Popol Vuh". Latest Computational Approaches to Cultural Heritage. ():-.
2018Tierrafría VH, Mejía-Almonte C, Camacho-Zaragoza JM, Salgado H, Alquicira K, Gama-Castro S, Ishida C, 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, M, Salgado, H, Velazquez-Ramirez, D, Gama-Castro, S, Tierrafria, V, Busby, S, Aquino, P, Fang, X, Palsson, B, Galagan, J, 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
2018Méndez Cruz, C, Arroyo Fernández, I. (2018). "Análisis automático de unidades morfológicas: segmentación y agrupamiento en español, maya y náhuatl". Ámbitos Morfológicos. Descripciones y métodos. ():-.
2018Gomez-Romero, L, Palacios-Flores, K, Reyes, J, Garcia, D, Boege, M, Davila, G, Flores, M, Schatz, M, Palacios, R. (2018). "Precise detection of de novo single nucleotide variants in human genomes". PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA. 115(21):5516-5521. [doi:10.1073/pnas.1802244115]29735690
2018Salgado, H, Martínez-Flores, I, Bustamante, V, Alquicira-Hernández, K, García-Sotelo, J, 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
2017Ledezma-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
2017Perez-Morales, D, Banda, M, Elizabeth Chau, N, Salgado, H, Martinez-Flores, I, Antonio Ibarra, J, Ilyas, B, Coombes, B, Bustamante, V. (2017). "The transcriptional regulator SsrB is involved in a molecular switch controlling virulence lifestyles of Salmonella". PLOS PATHOGENS. 13(7):e1006497-. [doi:10.1371/journal.ppat.1006497]28704543
2017De Las Rivas J, Bonavides-Martínez C, Campos-Laborie FJ. (2017). "Bioinformatics in Latin America and SoIBio impact, a tale of spin-off and expansion around genomes and protein structures.". BRIEF BIOINFORM. ():-. [doi:10.1093/bib/bbx064]28981567
2017Balderas-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():bax030-. [doi:10.1093/database/bax030]28605770
2017Pannier 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):e0174887-. [doi:10.1371/journal.pone.0174887]28419102
2017Rinaldi 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):bax012-. [doi:10.1093/database/bax012]28365731
2017Méndez-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
2017Castillo-Villalba MP, Gomez-Romero, L, Collado-Vides, J. (2017). "Genetic-metabolic networks can be modeled as toric varities". arXiv. ():-. [doi:arXiv:1708.05384v1]
2017Keseler, I, 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, Weaver, D, Collado-Vides, J, Paulsen, I, Karp, P. (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
2016Mendez-Cruz, C, Medina-Urrea, A, Sierra, G. (2016). "Unsupervised morphological segmentation based on affixality measurements". PATTERN RECOGNITION LETTERS. 84():127-133. [doi:10.1016/j.patrec.2016.09.001]
2016Martínez-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
2016Wang, Q, Abdul, S, Almeida, L, Ananiadou, S, Balderas-Martinez, Y, Batista-Navarro, R, Campos, D, Chilton, L, Chou, H, Contreras, G, Cooper, L, Dai, H, Ferrell, B, Fluck, J, Gama-Castro, S, George, N, Gkoutos, G, Irin, A, Jensen, L, Jimenez, S, Jue, T, Keseler, I, Madan, S, Matos, S, McQuilton, P, Milacic, M, Mort, M, Natarajan, J, Pafilis, E, Pereira, E, Rao, S, Rinaldi, F, Rothfels, K, Salgado, D, Silva, R, Singh, O, Stefancsik, R, Su, C, Subramani, S, Tadepally, H, Tsaprouni, L, Vasilevsky, N, Wang, X, Chatr-Aryamontri, A, Laulederkind, S, Matis-Mitchell, S, McEntyre, J, Orchard, S, Pundir, S, Rodriguez-Esteban, R, Van Auken, K, Lu, Z, Schaeffer, M, Wu, C, Hirschman, L, Arighi, C. (2016). "Overview of the interactive task in BioCreative V". DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION. 2016():baw119-. [doi:10.1093/database/baw119]27589961
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, 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
2016Gama-Castro, S, Salgado, H, Santos-Zavaleta, A, Ledezma-Tejeida, D, Muñiz-Rascado, L, García-Sotelo, J, Alquicira-Hernández, K, Martínez-Flores, I, Pannier, L, Castro-Mondragón, J, 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
2015Alvarez-Vasquez, F, Freyre-Gonzalez, J, Balderas-Martinez, Y, Delgado-Carrillo, M, 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
2014Gama Castro, M, Rinaldi, F, López Fuentes, A, Balderas MartÍnez, Y, Clematide, S, Ellendorff, T, Santos Zavaleta, A, Marques-Madeira, H, Collado Vides, P. (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
2014Meysman, P, Collado-Vides, J, Morett, E, Viola, R, Engelen, K, Laukens, K. (2014). "Structural properties of prokaryotic promoter regions correlate with functional features". Plos One. 9(2):e88717-. [doi:10.1371/journal.pone.0088717]24516674
2014Martinez, L, Martínez Flores, I, Salgado Osorio, H, Fernández-Mora, M, Medina Rivera, A, Puente, J, Collado Vides, P, Bustamante, V. (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, D, Gama Castro, M, Liebens, V, Laukens, K, Marchal, K, Collado Vides, P, 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
2013Weiss, V, Medina-Rivera, A, Huerta, A, 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():bas059-. [doi:10.1093/database/bas059]23327937
2013Balderas MartÍnez, Y, Savageau, M, Salgado Osorio, H, Pérez-Rueda, E, Morett, E, Collado Vides, P. (2013). "Transcription Factors in Escherichia coli Prefer the holo Conformation". Plos One. 8(6):e65723-. [doi:10.1371/journal.pone.0065723]23776535
2013Salgado Osorio, H, Peralta Gil, M, Gama Castro, M, Santos Zavaleta, A, Muñíz Rascado, L, Garcia Sotelo, J, Weiss, V, Solano Lira, H, Martínez Flores, I, Medina Rivera, A, Salgado Osorio, G, Alquicira Hernández, S, Alquicira Hernández, K, López Fuentes, A, Porrón Sotelo, L, Huerta Moreno, A, Bonavides Martínez, C, Balderas MartÍnez, Y, Pannier, L, Olvera, M, Labastida, A, Jiménez-Jacinto, V, Vega-Alvarado, L, del Moral Chávez, V, Hernández Álvarez, A, Morett, E, Collado Vides, P. (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, Mackie, A, Peralta Gil, M, Santos Zavaleta, A, Gama Castro, M, Bonavides Martínez, C, Fulcher, C, Huerta Moreno, A, Kothari, A, Krummenacker, M, Latendresse, M, Muñíz Rascado, L, Ong, Q, Paley, S, Schroder, I, Shearer, A, Subhraveti, P, Travers, M, Weerasinghe, D, Weiss, V, Collado Vides, P, Gunsalus, R, Paulsen, I, Karp, P. (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 Osorio, H, Collado Vides, P, 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
2012Salgado Osorio, H, Martínez Flores, I, López Fuentes, A, Garcia Sotelo, J, Porrón Sotelo, L, Muñíz Rascado, L, Collado Vides, P. (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
2011Reyes López, J, Gómez-Romero, L, Ibarra-Soria, X, Palacios-Flores, K, Arriola, L, Wences, A, García, D, Boege, M, Davila, G, Flores, M, Palacios de la Lama, R. (2011). "Context-dependent individualization of nucleotides and virtual genomic hybridization allow the precise location of human SNPs". PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA. 108(37):15294-15299. [doi:10.1073/pnas.1112567108]21876154
2011Santos Zavaleta, A, Gama Castro, M, Pérez Rueda, E. (2011). "A comparative genome analysis of the RpoS sigmulon shows a high diversity of responses and origins". MICROBIOLOGY-SGM. 157(5):1393-1401. [doi:10.1099/mic.0.042937-0]21310789
2011Medina Rivera, A, Abreu-Goodger, C, Thomas-Chollier, M, Salgado Osorio, H, Collado Vides, P, 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, M, Salgado Osorio, H, Peralta Gil, M, Santos Zavaleta, A, Muñíz Rascado, L, Solano Lira, H, Jimenez-Jacinto, V, Weiss, V, Garcia Sotelo, J, López Fuentes, A, Porrón Sotelo, L, Alquicira Hernández, S, Medina Rivera, A, Martínez Flores, I, Alquicira Hernández, K, Martínez Adame, R, Bonavides Martínez, C, Miranda-Ríos, J, Huerta Moreno, A, Mendoza-Vargas, A, Collado Torres, L, Taboada, B, Vega-Alvarado, L, Olvera, M, Olvera, L, Grande, R, Morett, E, Collado Vides, P. (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, Collado Vides, P, Santos Zavaleta, A, Peralta Gil, M, Gama Castro, M, 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, Mackie, A, Paulsen, I, Gunsalus, R, Karp, P. (2011). "EcoCyc: A comprehensive database of Escherichia coli biology". Nucleic Acids Research. 39(SUPPL. 1):583-590. [doi:10.1093/nar/gkq1143]21097882
2011Salgado Osorio, H, Martínez Flores, I, López Fuentes, A, Garcia Sotelo, J, Porrón Sotelo, L, Muñíz Rascado, L, Collado Vides, P. (2011). "Extracting regulatory networks of/Escherichia coli/from RegulonDB". Bacterial Molecular Networks: Methods and Protocols. ():-.
2010Demir, E, Cary, M, Paley, S, Fukuda, K, Lemer, C, Vastrik, I, Wu, G, D Eustachio, P, Schaefer, C, Luciano, J, Schacherer, F, Martínez Flores, I, Hu, Z, Jiménez-Jacinto, V, Joshi-Tope, G, Kandasamy, K, López-Fuentes, A, Mi, H, 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, 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, Rzhetsky, A, Schachter, V, Sobral, B, Dogrusoz, U, McWeeney, S, Aladjem, M, Birney, E, Collado Vides, P, Goto, S, Hucka, M, Le Novere, N, Maltsev, N, Pandey, A, Thomas, P, Wingender, E, Karp, P, Sander, C, Bader, G. (2010). "The BioPAX community standard for pathway data sharing". Nature Biotechnology. 28(9):935-942. [doi:10.1038/nbt.1666]20829833
2010Zepeda-Mendoza, C, Lemus, T, Yanez, O, Garcia, D, Valle-Garcia, D, Meza-Sosa, K, Gutierrez-Arcelus, M, Marquez-Ortiz, Y, Dominguez-Vidana, R, Gonzaga-Jauregui, C, Flores, M, Palacios, R. (2010). "Identical repeated backbone of the human genome". Bmc Genomics. 11():60-60. [doi:10.1186/1471-2164-11-60]20096123
2010Martínez Flores, I, Jiménez-Jacinto, V, López Fuentes, A, Collado Vides, P. (2010). "Expanding BioPAX format by integrating Gene Regulation". EMBnet.journal. 16():39-43.
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2007Karp, P, Keseler, I, Shearer, A, Latendresse, M, Krummenacker, M, Paley, S, Paulsen, I, Collado Vides, P, Gama Castro, M, Peralta Gil, M, Santos Zavaleta, A, Peñaloza Spinola, M, Bonavides Martínez, C, 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
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2007Resendis Antonio, O, Reed, J, Encarnación Guevara, S, Collado Vides, P, Palsson, B. (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, R, 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
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2007Perez, A, Angarica, V, Vasconcelos, A, Collado Vides, P. (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
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2006Huerta Moreno, A, Francino, M, Morett Sánchez, J, Collado Vides, P. (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
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2006Contreras Moreira, B, Collado Vides, P. (2006). "Comparative footprinting of DNA-binding proteins". Bioinformatics. 22(14):74-80. [doi:10.1093/bioinformatics/btl215]16873524
2006Huerta Moreno, A, Collado Vides, P, Francino, M. (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
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2005Janga, S, 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
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2005Ibarra-Junquera, V, Torres, L, Rosu, H, 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
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2005Keseler, I, Collado Vides, P, Gama Castro, M, Ingraham, J, Paley, S, Paulsen, I, Peralta Gil, M, Karp, P. (2005). "EcoCyc: A comprehensive database resource for Escherichia coli". Nucleic Acids Research. 33(DATABASE ISS.):334-337. [doi:10.1093/nar/gki108]15608210
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2004Perez-Rueda, E, Collado Vides, P, 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, 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]
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2004Oviedo, N, Salgado Osorio, H, Collado Vides, P, 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
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2004Salgado Osorio, H, Gama Castro, M, Martínez Antonio, A, Díaz Peredo, E, Sánchez Solano, E, Peralta Gil, M, García Alonso, D, Jiménez Jacinto, V, Santos Zavaleta, A, Bonavides Martínez, C, Collado Vides, P. (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
2003Martínez Antonio, A, Salgado Osorio, H, Gama Castro, M, Gutiérrez Ríos, R, Jiménez Jacinto, V, Collado Vides, P. (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
2003Jauregui, 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
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2003Perret, X, Kobayashi, H, Collado Vides, P. (2003). "Regulation of expression of symbiotic genes in Rhizobium sp. NGR234". INDIAN JOURNAL OF EXPERIMENTAL BIOLOGY. 41(10):1101-1113. 15242276
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2003Collado Vides, P, Medrano Soto, L, Tusié-Luna, M. (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
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2002Collado-Vides, J, Moreno-Hagelsieb, G, Medrano-Soto, A. (2002). "Microbial computational genomics of gene regulation". PURE AND APPLIED CHEMISTRY. 74(6):899-905.
2002de 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
2002Collado Vides, P, Moreno Hagelsieb, G, Pérez Rueda, E, Salgado Osorio, H, Huerta Moreno, A, Gutiérrez Ríos, R, Rosenblueth, D, Christen, A, Benítez Bellón, E, Medrano Soto, L, Gama Castro, M, Santos Zavaleta, A, Bonavides Martínez, C, DíPeredo, E, Sánchez Solano, E, Millá, D. (2002). "Genomics of Gene Regulation: The view from Escherichia coli". Gene Regulation and Metabolism, Post-Genomic Computational Approaches. ():103-128.
2002Collado-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]
2002Huerta, A, Glasner, J, Gutierrez-Rios, R, Blattner, F, 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]
2002Benítez Bellón, E, Moreno Hagelsieb, G, Collado Vides, P. (2002). "Evaluation of thresholds for the detection of binding sites for regulatory proteins in Escherichia coli K12 DNA.". Genome Biology. 3(3):RESEARCH0013-. 11897025
2002Moreno Hagelsieb, G, Collado Vides, P. (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, P, Riley, M, Saier, M, Paulsen, I, Collado-Vides, J, Paley, S, 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
2001Pérez-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
2001Tan, K, Moreno Hagelsieb, G, Collado Vides, P, Stormo, G. (2001). "A comparative genomics approach to prediction of new members of regulons". GENOME RESEARCH. 11(4):566-584. [doi:10.1101/gr.149301]11282972
2001Moreno-Hagelsieb, G, Trevino, V, Pérez-Rueda, E, Smith, T, 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
2001Ramirez-Santos, J, Collado-Vides, J, Garcia-Varela, M, Gomez-Eichelmann, M. (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
2001Salgado, 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
2000Salgado Osorio, H, Moreno Hagelsieb, G, Smith, T, Collado Vides, P. (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
2000Perez-Rueda, E, 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, J, Rios, A, 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
2000van Helden, J, Andre, B, Collado Vides, P. (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
2000Salgado, H, Santos-Zavaleta, A, Gama-Castro, S, Millan-Zarate, D, Blattner, F, 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
2000Strainic, M, Sullivan, J, Collado-Vides, J, deHaseth, P. (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
1999Collado Vides, P, 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
1999Salgado, 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
1998Thieffry, D, Salgado, H, Huerta, A, 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, Collado Vides, P. (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, R, 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, D, Huerta Moreno, A, Pérez Rueda, E, Collado Vides, P. (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
1998Pérez Rueda, E, Gralla, J, Collado Vides, P. (1998). "Genomic position analyses and the transcription machinery". Journal Of Molecular Biology. 275(2):165-170. [doi:10.1006/jmbi.1997.1465]9466899
1998Huerta, A, 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
1997Blattner, F, Plunkett, G, Bloch, C, Perna, N, Burland, V, Riley, M, ColladoVides, J, Glasner, J, Rode, C, Mayhew, G, Gregor, J, Davis, N, Kirkpatrick, H, Goeden, M, Rose, D, 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
1997Thieffry Jacot-Descombes, D, Rosenblueth, D, Huerta Moreno, A, Salgado Osorio, H, Collado Vides, P. (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
1997Collado-Vides, J, Huerta, A, Klose, K. (1997). "Three models of gene regulation in E. coli". LECT NOTES COMPUT SC. 1278():72-78.
1996ColladoVides, 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, D, Thieffry, D, Huerta, A, Salgado, H, ColladoVides, 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, P, 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, P. (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
1993COLLADOVIDES, 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
1993COLLADOVIDES, 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
1992COLLADOVIDES, 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
1970Ledezma-Tejeida D, Altamirano-Pacheco L, Fajardo V, Collado-Vides J. (1970). "Limits to a classic paradigm: most transcription factors in E. coli regulate genes involved in multiple biological processes.". Nucleic Acids Research. ():-. [doi:10.1093/nar/gkz525]31194874