Computational Genomics
The Program of Computational Genomics is focused, in the field of bioinformatics, on the challenge of accelerating access to genomic knowledge, in particular on the regulation of microbial gene expression. The backbone of our work is the design and expansion of the RegulonDB database, with knowledge of the genetic regulation in Escherichia coli K-12 extracted by curators, both from classical experiments and from High-Throughput (HT) post-genomic methods. We work with algorithms for the identification of binding sites, promoters and transcription units, as well as co-regulation, and for the processing of data from HT methods, such as ChIP-seq, among others. We work in an ontology and a controlled vocabulary of microbial growth conditions, and in an ontology of microbial genetic regulation. An important aspect is the use of Natural language processing (NLP) to enrich knowledge extraction strategies that shall allow us to expand the biocuration to other bacteria such as Salmonella, and other few more bacteria. We have supported integrative concepts such as regulatory phrases and, more recently, the genetic-metabolic sensory-response units (GENSOR Units), which pose a lot of new questions. We are investigating the formalism of S-systems by Michael Savageau for the modeling, initially, of GENSOR Units; extending it to complete circuits and, if possible, to an integral modeling of the cell at the molecular level. This with a novel approach of computational algebraic geometry.
All this way of seeing and conceiving scientific knowledge has its application with similar strategies in a project that seeks to break the separation between texts for laymen and texts for experts with the Conogasi project (conogasi.org).
Tools and resources for COVID-19
Group Staff
| Name | Position | Category | Telephone | |
|---|---|---|---|---|
| Pedro Julio Collado Vides | Researcher | Emeritus Professor | colladojulio@gmail.com | (777) 3139877 |
| César Augusto Bonavides Martínez | Laboratory Technician | Laboratory Technician | cbona18@ccg.unam.mx | (777) 3132063 |
| Ma. del Socorro Gama Castro | Laboratory Technician | Laboratory Technician | sgama@ccg.unam.mx | (777) 3132063 |
| Heladia Salgado Osorio | Laboratory Technician | Laboratory Technician | heladia@ccg.unam.mx | (777) 3132063 |
| Carlos Francisco Méndez Cruz | Researcher | Assistant Professor | cmendezc@ccg.unam.mx | (777) 3132063 |
| Martin Jair Díaz Rodríguez | Support staff | Other | mjdiaz@ccg.unam.mx | (777) 3132063 |
| Francisco de Jesus Guadarrama García | Support staff | Other | franguad@ccg.unam.mx | (777) 3132063 |
| Jose Daniel Gutierrez Nieto | Support staff | Other | danezoj@gmail.com | (777) 3132063 |
| Luis José Muñíz Rascado | Support staff | UNAM | ljmuniz@ccg.unam.mx | (777) 3132063 |
| Pablo Emilio Peña Loredo | Support staff | Other | pablopl@ccg.unam.mx | (777) 3132063 |
| Victor Hugo Tierrafria Pulido | Support staff | UNAM | vhugotp@ccg.unam.mx | (777) 3132063 |
| Shirley Alquicira Hernández | Laboratory Technician | Laboratory Technician | alquicir@ccg.unam.mx | (777) 3132063 |
| Mashaal Sohail | Researcher | Associate Professor | mashaal@ccg.unam.mx | (777) 3132063 |
Group Publications
| Year | Publication | PMID |
|---|---|---|
| 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, Blanchet, A, Godínez, A, Arroyo-Fernández, I, Gama-Castro, S, Martínez-Luna, S, 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 |
| 2020 | Mejía-Almonte, C, Busby, S, Wade, J, van Helden, J, Arkin, A, Stormo, G, Eilbeck, K, Palsson, B, Galagan, J, 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][https://rdcu.be/cfeHw] | 32665585 |
| 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] | |
| 2019 | Santos-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 |
| 2019 | Arroyo Fernández, I, Méndez Cruz, C, Sierra, G, Sidorov, G, Torres-Moreno, J. (2019). "Unsupervised Sentence Representations as Word Information Series: Revisiting TF--IDF". COMPUTER SPEECH AND LANGUAGE. 56():107-129. [doi:10.1016/j.csl.2019.01.005] | |
| 2019 | Giner-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 |
| 2019 | Santos-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):299-. [doi:10.1186/s12864-019-5619-z] | 30991941 |
| 2019 | Arroyo Fernández, I, Curiel, A, Méndez, C. (2019). "Language features in extractive summarization: Humans Vs. Machines". KNOWLEDGE-BASED SYSTEMS. 180():1-11. [doi:10.1016/j.knosys.2019.05.014] | |
| 2019 | Lithgow-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.". JOURNAL OF BIOMEDICAL SEMANTICS. 10(1):8-. [doi:10.1186/s13326-019-0200-x] | 31118102 |
| 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):e72-. [doi:10.1002/cpbi.72] | 30786165 |
| 2019 | Centeno-Leija, S, Tapia-Cabrera, S, Guzman-Trampe, S, Esquivel, B, Esturau-Escofet, N, Tierrafria, V, Rodriguez-Sanoja, R, Zarate-Romero, A, Stojanoff, V, Rudino-Pinera, E, Sanchez, S, Serrano-Posada, H. (2019). "The structure of (E)-biformene synthase provides insights into the biosynthesis of bacterial bicyclic labdane-related diterpenoids". JOURNAL OF STRUCTURAL BIOLOGY. 207(1):29-39. [doi:10.1016/j.jsb.2019.04.010] | 30981884 |
| 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 | Tierrafría, V, Mejía-Almonte, C, Camacho-Zaragoza, J, 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 |
| 2018 | Balderas-Martinez, Y, 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, 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 |
| 2018 | Villasenor-Altamirano, A, Balderas-Martinez, Y, Moretto, M, Zayas-Del Moral, A, Maldonado, M, Munguia-Reyes, A, Garcia-Sotelo, J, Aguilar Bautista, L, 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 | Méndez Cruz, C, Arroyo Fernández, I. (2018). "Análisis automático de unidades morfológicas: segmentación y agrupamiento en español, maya y náhuatl". Ámbitos Morfológicos. Descripciones y métodos. ():-. | |
| 2018 | Gomez-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 |
| 2018 | Arroyo 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. ():-. | |
| 2018 | Santos-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 BIOLOGY. 16(1):91-91. [doi:10.1186/s12915-018-0555-y] | 30115066 |
| 2017 | Keseler, 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 |
| 2017 | Castillo-Villalba MP, Gomez-Romero, L, Collado-Vides, J. (2017). "Genetic-metabolic networks can be modeled as toric varities". arXiv. ():-. [doi:arXiv:1708.05384v1] | |
| 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():bax070-. [doi:10.1093/database/bax070] | 29220462 |
| 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):bax012-. [doi:10.1093/database/bax012] | 28365731 |
| 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):e0174887-. [doi:10.1371/journal.pone.0174887] | 28419102 |
| 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():bax030-. [doi:10.1093/database/bax030] | 28605770 |
| 2017 | De 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.". BRIEFINGS IN BIOINFORMATICS. 20(2):390-397. [doi:10.1093/bib/bbx064] | 28981567 |
| 2017 | Perez-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 |
| 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 |
| 2016 | Mendez-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] | |
| 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 | Wang, 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 |
| 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, 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 |
| 2015 | Alvarez-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 |
| 2014 | Meysman, 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 |
| 2014 | Gama 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 |
| 2014 | Martinez, 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 |
| 2014 | Meysman, 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 |
| 2013 | Keseler, 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 |
| 2013 | Salgado 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 |
| 2013 | Balderas 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 |
| 2013 | Weiss, 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 |
| 2012 | Salgado 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 |
| 2012 | Pauling, 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 |
| 2011 | Medina 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 |
| 2011 | Reyes 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 |
| 2011 | Keseler, 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 |
| 2011 | Santos 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 |
| 2011 | Salgado 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. ():-. | |
| 2011 | Gama 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 |
| 2010 | Zepeda-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 |
| 2010 | Salgado Osorio, H, López Fuentes, A, Martínez Flores, I, Garcia Sotelo, J, Porrón Sotelo, L, Solano Lira, H, Muñíz Rascado, L, Collado Vides, P. (2010). "Extracting regulatory networks of Escherichia coli from RegulonDB". Bacterial Molecular Networks: Methods and Protocols. ():-. | |
| 2010 | Martínez Flores, I, Jiménez-Jacinto, V, López Fuentes, A, Collado Vides, P. (2010). "Expanding BioPAX format by integrating Gene Regulation". EMBnet.journal. 16():39-43. | |
| 2010 | Demir, 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 |
| 2009 | Martinez-Antonio, A, Medina-Rivera, A, 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 |
| 2009 | Mendoza-Vargas, A, Olvera, L, Olvera, M, Grande, R, Vega-Alvarado, L, Taboada, B, Jimenez-Jacinto, V, Salgado, H, Juarez, K, Contreras-Moreira, B, Huerta, A, Collado-Vides, J, Morett, E. (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 |
| 2009 | Gonzalez Perez, A, Espinosa Angarica, V, Collado-Vides, J, Ribeiro Vasconcelos, A. (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, I, Contreras-Moreira, B, 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. | |
| 2009 | Janga, S, Salgado, H, Martinez-Antonio, A. (2009). "Transcriptional regulation shapes the organization of genes on bacterial chromosomes". Nucleic Acids Research. 37(11):3680-3688. [doi:10.1093/nar/gkp231] | 19372274 |
| 2009 | Lemmens, K, De Bie, T, Dhollander, T, De Keersmaecker, S, Thijs, I, Schoofs, G, De Weerdt, A, De Moor, B, Vanderleyden, J, Collado-Vides, J, Engelen, K, Marchal, K. (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 |
| 2009 | Collado-Vides, J, Salgado, H, Morett, E, Gama-Castro, S, Jimenez-Jacinto, V, Martinez-Flores, I, Medina-Rivera, A, Muniz-Rascado, L, Peralta-Gil, M, 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 |
| 2009 | Balleza, E, Lopez-Bojorquez, L, Martinez-Antonio, A, Resendis-Antonio, O, Lozada-Chavez, I, Balderas-Martinez, Y, Encarnacion, S, 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 |
| 2009 | Lemmens, K, De Bie, T, Dhollander, T, Monsieurs, P, De Moor, B, Collado Vides, P, 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 |
| 2008 | Martínez-Antonio, A, Collado Vides, P. (2008). "Comparative mechanisms for transcription and regulatory signals in archaea and bacteria". Computational Methods for Understanding Bacterial and Archaeal Genomes. (0):185-208. | |
| 2008 | Freyre González, J, Alonso Pavón, J, Treviño Quintanilla, L, Collado Vides, P. (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 | Espinosa Angarica, V, Gonzalez Perez, A, Vasconcelos, A, Collado-Vides, J, Contreras-Moreira, B. (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 | Janga, S, Collado-Vides, J, Babu, M. (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 | Hernandez-Romano, J, Carlos-Rivera, F, Salgado, H, Lamadrid-Figueroa, H, Valverde-Garduno, V, Rodriguez, M, Martinez-Barnetche, J. (2008). "Immunity related genes in dipterans share common enrichment of AT-rich motifs in their 5' regulatory regions that are potentially involved in nucleosome formation". Bmc Genomics. 9():326-326. [doi:10.1186/1471-2164-9-326] | 18613977 |
| 2008 | Lozada-Chavez, I, Angarica, V, Collado-Vides, J, Contreras-Moreira, B. (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 | Hernandez-Lucas, I, Gallego-Hernandez, A, Encarnacion, S, Fernandez-Mora, M, Martinez-Batallar, A, Salgado, H, Oropeza, R, Calva, E. (2008). "The LysR-type transcriptional regulator LeuO controls expression of several genes in Salmonella enterica serovar typhi". Journal Of Bacteriology. 190(5):1658-1670. [doi:10.1128/JB.01649-07] | 18156266 |
| 2008 | Perez, A, Gonzalez, E, Angarica, V, Vasconcelos, A, Collado Vides, P. (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, M, Jiménez Jacinto, V, Peralta Gil, M, Santos Zavaleta, A, Peñaloza Spinola, M, Contreras Moreira, B, Segura Salazar, J, Muñíz Rascado, L, Martínez Flores, I, Salgado Osorio, H, Bonavides Martínez, C, Abreu Goodger, C, Rodríguez Penagos, C, Miranda-Ríos, J, Morett Sánchez, J, Merino, E, Huerta Moreno, A, Treviño Quintanilla, L, Collado Vides, P. (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 |
| 2007 | Palacios, 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 |
| 2007 | Resendis 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 |
| 2007 | Rodríguez Penagos, C, Salgado Osorio, H, Martínez Flores, I, Collado Vides, P. (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, Freyre González, J, Resendis Antonio, O, Collado Vides, P, 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 | Salgado, H, Martinez-Antonio, A, Janga, S. (2007). "Conservation of transcriptional sensing systems in prokaryotes: A perspective from Escherichia coli". FEBS LETTERS. 581(18):3499-3506. [doi:10.1016/j.febslet.2007.06.059] | 17617412 |
| 2007 | Guo, X, Flores, M, Morales, L, Garcia, D, Bustos, P, Gonzalez, V, Palacios, R, Davila, G. (2007). "DNA diversification in two Sinorhizobium species". Journal Of Bacteriology. 189(17):6474-6476. [doi:10.1128/JB.00384-07] | 17601787 |
| 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] | |
| 2007 | Contreras Moreira, B, Fernández, P, Collado Vides, P. (2007). "TFmodeller: Comparative modelling of protein-DNA complexes". Bioinformatics. 23(13):1694-1696. [doi:10.1093/bioinformatics/btm148] | 17459960 |
| 2007 | Janga, S, 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, S, Salgado Osorio, H, Collado Vides, P, Martínez Antonio, A. (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 | Flores López, M, Morales Reyes, L, Gonzaga Jáuregui, C, Domínguez Vidaña, R, Zepeda Mendoza, C, Yáñez Cuna, J, Gutiérrez Arcelus, M, Lemus Vergara, T, Valle García, D, Ávila Arcos, M, Blanco Melo, D, Medina Ruiz, S, Meza Sosa, K, Ayala Ortega, E, García Alonso, D, Bustos Arcos, V, González Zúñiga, V, Girard Cuesy, M, Tusie-Luna, T, Dávila Ramos, J, Palacios de la Lama, R. (2007). "Recurrent DNA inversion rearrangements in the human genome". PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA. 104(15):6099-6106. [doi:10.1073/pnas.0701631104] | 17389356 |
| 2007 | Rodríguez Penagos, C, Martínez Flores, I, Salgado Osorio, H, Collado Vides, P. (2007). "NLP-based curation of bacterial regulatory networks". Computational Linguistics And Intelligent Text Processing. 4394():575-. | |
| 2007 | Rodríguez Penagos, C, Salgado Osorio, H, Martínez Flores, I, Collado Vides, P. (2007). "NLP-Based Curation of Bacterial Regulatory Networks". CICLing. ():575-586. | |
| 2007 | Perez, 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 |
| 2007 | Karp, 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 |
| 2007 | Janga, S, Salgado Osorio, H, Martínez Antonio, A, Collado Vides, P. (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 |
| 2006 | Martínez Antonio, A, Janga, S, Salgado Osorio, H, Collado Vides, P. (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 | Santos-Zavaleta, A, Salgado, H, Gama-Castro, S, Peralta-Gil, M, Contreras-Moreira, B, Penaloza-Spinola, M, 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, I, Janga, S, 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 |
| 2006 | Huerta 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 |
| 2006 | Peñaloza Spinola, M, Peralta Gil, M, Gama Castro, M, Contreras Moreira, B, Santos Zavaleta, A, Martínez Flores, I, Collado Vides, P. (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, B, Collado Vides, P. (2006). "Comparative footprinting of DNA-binding proteins". Bioinformatics. 22(14):74-80. [doi:10.1093/bioinformatics/btl215] | 16873524 |
| 2006 | Huerta 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 |
| 2006 | González Zúñiga, V, Santamaria Gutiérrez, R, Bustos Arcos, V, Hernández González, I, Medrano Soto, L, Moreno Hagelsieb, G, Janga, S, Ramírez Romero, M, Jiménez Jacinto, V, Collado Vides, P, Dávila Ramos, J. (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 | Salgado Osorio, H, Santos Zavaleta, A, Gama Castro, M, Peralta Gil, M, Peñaloza Spinola, M, Martínez Antonio, A, Karp, P, Collado Vides, P. (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 | Salgado Osorio, H, Gama Castro, M, Peralta Gil, M, Díaz Peredo, E, Sánchez Solano, E, Santos Zavaleta, A, Martínez Flores, I, Jiménez Jacinto, V, Bonavides Martínez, C, Segura Salazar, J, Martínez Antonio, A, Collado Vides, P. (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, 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 |
| 2005 | Le Novere, N, Finney, A, Hucka, M, Bhalla, U, Campagne, F, Collado Vides, P, Crampin, E, Halstead, M, Klipp, E, Mendes, P, Nielsen, P, Sauro, H, Shapiro, B, Snoep, J, Spence, H, Wanner, B. (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, Vasconcelos, A, Huerta Moreno, A, Collado Vides, P. (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, M, Morales Reyes, L, Ávila Casanueva, A, González Zúñiga, V, Bustos Arcos, V, García Alonso, D, Pérez-Tejada Domínguez, Y, Guo, X, Collado Vides, P, Pinero, D, Dávila Ramos, J, Mora Celis, J, Palacios de la Lama, R. (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, Perez, A, Angarica, V, Vasconcelos, A, Collado Vides, P. (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, R, Janga, S, Collado Vides, P. (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, 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 |
| 2005 | Medrano-Soto, A, Christen, J, 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, Espinosa, V, Vasconcelos, A, Perez-Rueda, E, Collado Vides, P. (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, 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 |
| 2005 | Resendis Antonio, O, Freyre González, J, Menchaca Mendez, R, Gutiérrez Ríos, R, Martínez Antonio, A, Ávila Sánchez, C, Collado Vides, P. (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 | Salgado 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 |
| 2004 | Perez-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 |
| 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, L, Moreno Hagelsieb, G, Vinuesa Fleischmann, P, Christen, J, Collado Vides, P. (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, 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 |
| 2004 | Karp, P, Arnaud, M, Collado-Vides, J, Ingraham, J, Paulsen, I, Saier, M. (2004). "The E. coli EcoCyc database: No longer just a metabolic pathway database". Asm News. 70(1):25-30. | |
| 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 | Martínez 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 |
| 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 | Gutiérrez Ríos, R, Rosenblueth, D, Loza, J, Huerta Moreno, A, Glasner, J, Blattner, F, Collado Vides, P. (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 | Huerta, A, 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 | Perret, 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 |
| 2003 | Collado 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 |
| 2003 | González Zúñiga, V, Bustos Arcos, V, Ramírez Romero, M, Medrano Soto, L, Salgado Osorio, H, Hernández González, I, Hernández Celis, J, Quintero Hernández, V, Moreno Hagelsieb, G, Girard Cuesy, M, Rodríguez Sánchez, O, Flores López, M, Cevallos Gaos, M, Collado Vides, P, Romero Camarena, D, Dávila Ramos, J. (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 |
| 2002 | Degrave, W, Vargas, R, Alvarez, F, Collado Vides, P, Nunez, L, Ramirez, J, Grau, O. (2002). "Towards a bioinformatics network for Latin America and the Caribbean (LACBioNet).". Applied Bioinformatics. 1(1):53-56. | 15130857 |
| 2002 | Karp, 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 |
| 2002 | Huerta, 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] | |
| 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 | Collado 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. | |
| 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 | 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 | Moreno Hagelsieb, G, Collado Vides, P. (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 | Benítez 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 |
| 2002 | Moreno 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 |
| 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, 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 |
| 2001 | Moreno-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 |
| 2001 | Tan, 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 |
| 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 |
| 2000 | van 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 |
| 2000 | Salgado 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 |
| 2000 | Salgado, 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 |
| 2000 | Strainic, 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 |
| 2000 | Perez-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 |
| 2000 | van 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 |
| 1999 | Collado 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 |
| 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 |
| 1998 | Pérez 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 |
| 1998 | Thieffry 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 |
| 1998 | van 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 |
| 1998 | Thieffry, 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 |
| 1998 | Collado-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 |
| 1998 | Huerta, 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 |
| 1997 | Thieffry 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 |
| 1997 | Blattner, 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 |
| 1997 | Collado-Vides, J, Huerta, A, Klose, K. (1997). "Three models of gene regulation in E. coli". LECT NOTES COMPUT SC. 1278():72-78. | |
| 1996 | Hofestadt, 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 |
| 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 | Rosenblueth, 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. [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, 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 |
| 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 |