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).

Recientemente, la Dra. Sohail se incorporó al programa. Sus líneas de investigación se enfocan en genómica humana, mediante el uso de métodos computacionales y estadísticos para investigar la arquitectura genética y la evolución de enfermedades y rasgos complejos, y el impacto de la historia demográfica en la variación de rasgos y en la incidencia de enfermedades. Por ejemplo, un nuevo proyecto busca usar aprendizaje profundo y grandes conjuntos de datos de genómica para predecir enfermedades complejas como la diabetes tipo 2 en humanos.

Accede a nuestros proyectos aquí y aquí si quieres conocer más detalle.

Tools and resources for COVID-19

Académicos del Grupo

NombrePuestoCategoríaCorreoTeléfono
Pedro Julio Collado VidesInvestigadorInv. Eméritocolladojulio@gmail.com(777) 3139877
Mashaal Sohail InvestigadorInv. Tit. A T.C. Obra Det.mashaal@ccg.unam.mx(777) 3132063
Daniela Elizabeth Ledezma TejeidaInvestigadorInv. Tit. A T.C. Obra Det.dledezma@lcg.unam.mx(777) 3132063
Carlos Francisco Méndez CruzInvestigadorInv. Tit. A T.C. Interinocmendezc@ccg.unam.mx(777) 3132063
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
Shirley Alquicira HernándezTécnico AcadémicoTec. Acad. Tit. A T.C. Obra Det.alquicir@ccg.unam.mx(777) 3132063
Amara Shaukat PosdoctoralDGAPAashaukat@ccg.unam.mx(777) 3132063
Victor Hugo Tierrafria PulidoTécnico por honorariosUNAMvhugotp@ccg.unam.mx(777) 3132063
Paloma Lara FigueroaTécnico por honorariosOtropalomalf@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
Pablo Emilio Peña LoredoTécnico por honorariosOtropablopl@ccg.unam.mx(777) 3132063

Publicaciones del Grupo

AñoPublicaciónPMID
2024Lara, P., Gama-Castro, S., Salgado, H., Rioualen, C., Tierrafría, V.H., Muñiz-Rascado, L.J., Bonavides-Martínez, C., Collado-Vides, J.. (2024). "Flexible gold standards for transcription factor regulatory interactions in Escherichia coli K-12: architecture of evidence types.". Frontiers in Genetics. 15():-. [doi:10.3389/fgene.2024.1353553]38505828
2024Sohail M, Moreno-Estrada A. (2024). "The Mexican Biobank Project promotes genetic discovery, inclusive science and local capacity building.". DIS MODEL MECH. 17(1):-. [doi:10.1242/dmm.050522]38299665
2024Salgado, H., Gama-Castro, S., Lara, P., Mejia-Almonte, C., Alarcón-Carranza, G., López-Almazo, A.G., Betancourt-Figueroa, F., Peña-Loredo, P., Alquicira-Hernández, S., Ledezma-Tejeida, D., Arizmendi-Zagal, L., Mendez-Hernandez, F., Diaz-Gomez, A.K., Ochoa-Praxedis, E., Muñiz-Rascado, L.J., García-Sotelo, J.S., Flores-Gallegos, F.A., Gómez, L., Bonavides-Martínez, C., Del Moral-Chávez, V.M., Hernández-Alvarez, A.J., Santos-Zavaleta, A., Capella-Gutierrez, S., Gelpi, J.L., Collado-Vides, J.. (2024). "RegulonDB v12.0: a comprehensive resource of transcriptional regulation in E. coli K-12.". Nucleic Acids Research. 52(D1):255-264. [doi:10.1093/nar/gkad1072]37971353
2023Kun, E., Javan, E.M., Smith, O., Gulamali, F., de la Fuente, J., Flynn, B.I., Vajrala, K., Trutner, Z., Jayakumar, P., Tucker-Drob, E.M., Sohail, M., Singh, T., Narasimhan, V.M.. (2023). "The genetic architecture and evolution of the human skeletal form.". Science. 381(6655):8009-8009. [doi:10.1126/science.adf8009]37471560
2023Dauda, B., Molina, S.J., Allen, D.S., Fuentes, A., Ghosh, N., Mauro, M., Neale, B.M., Panofsky, A., Sohail, M., Zhang, S.R., Lewis, A.C.F.. (2023). "Ancestry: How researchers use it and what they mean by it.". Frontiers in Genetics. 14():-. [doi:10.3389/fgene.2023.1044555]36755575
2023Mendez-Cruz, Carlos-Francisco, Joel Rodríguez-Herrera, Alfredo Varela-Vega, Valeria Mateo-Estrada, Castillo Ramírez, Santiago. (2023). "Unsupervised Learning and Natural Language Processing Point Out Bias in Research Trends of a Superbug". Social Science Research Network. ():-. [doi:10.2139/ssrn.4503262]
2023Anna C. F. Lewis, Santiago J. Molina, Paul S. Appelbaum, Bege Dauda, Agustin Fuentes, Stephanie M. Fullerton, Nanibaa A. Garrison, NayanikaGhosh, Robert C. Green, Evelynn M. Hammonds, Janina M. Jeff, David S.Jones, Eimear E. Kenny, Peter Kraft, Madelyn Mauro, Anil P. S. Ori, Aaron Panofsky, Mashaal Sohail, Benjamin M. Neale, Danielle S. Allen. (2023). "An Ethical Framework for Research Using Genetic Ancestry". Johns Hopkins University Press. ():-. [doi:https://doi.org/10.1353/pbm.0.0176]
2023Collado-Vides, Julio. (2023). "Regulatory promoter architectures in the hands of thermodynamic modelling.". NATURE REVIEWS GENETICS. 24(6):349-349. [doi:10.1038/s41576-023-00578-w]36747003
2023Juárez, K., Reza, L., Bretón-Deval, L., Morales-Guzmán, D., Trejo-Hernández, M.R., García-Guevara, F., Lara, P.. (2023). "Microaerobic degradation of crude oil and long chain alkanes by a new Rhodococcus strain from Gulf of Mexico.". World Journal Of Microbiology & Biotechnology. 39(10):-. [doi:10.1007/s11274-023-03703-3]37515608
2023Mashaal Sohail, María J. Palma-Martínez, Amanda Y. Chon, Consuelo D. Quinto-Cortés, Carmina Barberena-Jonas, Santiago G. Medina-Muñoz, Aaron Ragsdale, Guadalupe Delgado-Sánchez, Luis Pablo Cruz-Hervert, Leticia Ferreyra-Reyes, Elizabeth Ferreira-Guerrero, Norma Mongua-Rodríguez, Sergio Canizales-Quintero, Andrés Jimenez-Kaufmann, Hortensia Moreno-Macías, Carlos A. Aguilar-Salinas, Kathryn Auckland, Adrián Cortés, Víctor Acuña-Alonzo, Christopher R. Gignoux, Genevieve L. Wojcik, Alexander G. Ioannidis, Selene L. Fernández-Valverde, Adrian V. S. Hill, María Teresa Tusié-Luna, Alexander J. Mentzer, John Novembre, Lourdes García-García, Andrés Moreno-Estrada. (2023). "Mexican Biobank advances population and medical genomics of diverse ancestries". Nature. ():-. [doi:https://doi.org/10.1038/s41586-023-06560-0]
2023Karp, P.D., Paley, S., Caspi, R., Kothari, A., Krummenacker, M., Midford, P.E., Moore, L.R., Subhraveti, P., Gama-Castro, S., Tierrafria, V.H., Lara, P., Muñizrascado, L., Bonavides-Martinez, C., Santos-Zavaleta, A., Mackie, A., Sun, G., Ahn-Horst, T.A., Choi, H., Covert, M.W., Collado-Vides, J., Paulsen, I.. (2023). "The EcoCyc Database (2023).". EcoSal Plus. 11(1):-. [doi:10.1128/ecosalplus.esp-0002-2023]37220074
2023Lara, P., Gama-Castro, S., Salgado, H., Claire Rioualen, Tierrafría, V.H., Muñiz-Rascado LJ, Bonavides-Martinez, C., Collado-Vides, J.. (2023). "A Gold Standard for Transcription Factor Regulatory Interactions in Escherichia coli K-12: Architecture of Evidence Types". bioRxiv. ():-. [doi:https://doi.org/10.1101/2023.02.25.530038]
2023Sohail, M.. (2023). "Swapping genes within and beyond our bodies.". NATURE REVIEWS GENETICS. 25(3):164-164. [doi:10.1038/s41576-023-00689-4]38123710
2022Méndez Cruz, Carlos Francisco, Arroyo Fernández, Ignacio. (2022). "Análisis automático de unidades morfológicas: segmentación y agrupamiento en español, maya y náhuatl". Ámbitos Morfológicos. Descripciones y métodos. México: UNAM. ISBN 978-607-30-5946-6. ():-.
2022Lewis ACF, Molina SJ, Appelbaum PS, Dauda B, Di Rienzo A, Fuentes A, Fullerton SM, Garrison NA, Ghosh N, Hammonds EM, Jones DS, Kenny EE, Kraft P, Lee SS, Mauro M, Novembre J, Panofsky A, Sohail M, Neale BM, Allen DS. (2022). "Getting genetic ancestry right for science and society.". Science. 376(6590):250-252. [doi:10.1126/science.abm7530]35420968
2022Sohail, M, Chong, AY, Palma, MJ, Quinto-Cortes, CD, Ragsdale, A, Medina, SG, Delgado-Sánchez, G, Cruz-Hervert, LP, Ferreyra-Reyes, L, Moreno-Macías, H, Aguilar-Salinas, CA, Cortes, A, Fernandez-Valverde, SL, Acuîa-Alonzo, V, Wojcik, G, Gignoux, CR, Bustamante, CD, Hill, A, Tusie, MT, Mentzer, AJ, Novembre, J, García-García, L, Moreno-Estrada, A. (2022). "Unraveling demographic history and complex trait architecture from 6,000 Mexican genomes". American Journal Of Biological Anthropology. 177():172-172.
2022Ortega-Del Vecchyo, D., Berg, J., Sohail, M.. (2022). "Editorial: Genetic Architecture and Evolution of Complex Traits and Diseases in Diverse Human Populations.". Frontiers in Genetics. 13():-. [doi:10.3389/fgene.2022.869056]35368673
2022Collado-Vides J, Gaudet P, de Lorenzo V. (2022). "Missing Links Between Gene Function and Physiology in Genomics.". FRONTIERS IN PHYSIOLOGY. 13():815874-815874. [doi:10.3389/fphys.2022.815874]35295568
2022Femerling, G., Gama-Castro, S., Lara, P., Ledezma-Tejeida, D., Tierrafría, V.H., Muñiz-Rascado, L., Bonavides-Martínez, C., Collado-Vides, J.. (2022). "Sensory Systems and Transcriptional Regulation in Escherichia coli .". Frontiers in bioengineering and biotechnology. 10():-. [doi:10.3389/fbioe.2022.823240]35237580
2022Jiménez-Kaufmann, A., Chong, A.Y., Cortés, A., Quinto-Cortés, C.D., Fernandez-Valverde, S.L., Ferreyra-Reyes, L., Cruz-Hervert, L.P., Medina-Muñoz, S.G., Sohail, M., Palma-Martinez, M.J., Delgado-Sánchez, G., Mongua-Rodríguez, N., Mentzer, A.J., Hill, A.V.S., Moreno-Macías, H., Huerta-Chagoya, A., Aguilar-Salinas, C.A., Torres, M., Kim, H.L., Kalsi, N., Schuster, S.C., Tusié-Luna, T., Del-Vecchyo, D.O., García-García, L., Moreno-Estrada, A.. (2022). "Imputation Performance in Latin American Populations: Improving Rare Variants Representation With the Inclusion of Native American Genomes.". Frontiers in Genetics. 12():-. [doi:10.3389/fgene.2021.719791]35046991
2022Tierrafría, V.H., Rioualen, C., Salgado, H., Lara, P., Gama-Castro, S., Lally, P., Gómez-Romero, L., Peña-Loredo, P., López-Almazo, A.G., Alarcón-Carranza, G., Betancourt-Figueroa, F., Alquicira-Hernández, S., Polanco-Morelos, J.E., García-Sotelo, J., Gaytan-Nuñez, E., Méndez-Cruz, C.F., Muñiz, L.J., Bonavides-Martínez, C., Moreno-Hagelsieb, G., Galagan, J.E., Wade, J.T., Collado-Vides, J.. (2022). "RegulonDB 11.0: Comprehensive high-throughput datasets on transcriptional regulation in Escherichia coli K-12.". Microbial genomics. 8(5):-. [doi:10.1099/mgen.0.000833]35584008
2021D'Elia, D., Bonavides-Martínez, C., Bongcam-Rudloff, E., Barreto-Hernandez, E., Efthimiadou, A., Papakonstantinou, E., Vlachakis, E., Klucar, L.. (2021). "The EMBnet International Conference 2020: Bioinformatics Approaches to Precision Research". EMBnet.journal. 26():1006-. [doi:10.14806/ej.26.A.1006]
2021Keseler, I.M., Gama-Castro, S., Mackie, A., Billington, R., Bonavides-Martínez, C., Caspi, R., Kothari, A., Krummenacker, M., Midford, P.E., Muñiz-Rascado, L., Ong, W.K., Paley, S., Santos-Zavaleta, A., Subhraveti, P., Tierrafría, V.H., Wolfe, A.J., Collado-Vides, J., Paulsen, I.T., Karp, P.D.. (2021). "The EcoCyc Database in 2021.". Frontiers in Microbiology. 12():-. [doi:10.3389/fmicb.2021.711077]34394059
2021Lithgow-Serrano O, Cornelius J, Kanjirangat V, Méndez-Cruz CF, Rinaldi F. (2021). "Improving classification of low-resource COVID-19 literature by using Named Entity Recognition.". Genomics & informatics. 19(3):-. [doi:10.5808/gi.21018]34638169
2021Lithgow-Serrano, O., Gama-Castro, S., Ishida-Gutiérrez, Collado-Vides, J.. (2021). "L-Regulon: A novel “soft-curation” approach supported by a semantic enriched reading for RegulonDB literature". bioRxiv. ():-. [doi:https://doi.org/10.1101/2020.04.26.062745]
2021Sohail, M., Izarraras-Gomez, A., Ortega-Del Vecchyo, D.. (2021). "Populations, Traits, and Their Spatial Structure in Humans.". Genome Biology And Evolution. 13(12):-. [doi:10.1093/gbe/evab272]34894236
2021Arroyo-Fernández, Ignacio, Carrasco-Ruiz, Mauricio, Méndez, C.. (2021). "Procesamiento de lenguaje natural en la conservación de la herencia cultural: una red semántica del Popol Vuh". Patrimonio digital. Métodos computacionales y medios interactivos para estudiar y divulgar el patrimonio cultural. ():25-34.
2021Díaz-Rodríguez, M., Lithgow-Serrano, O., Guadarrama-García, F., Tierrafría, V.H., Gama-Castro, S., Solano-Lira, H., Salgado, H., Rinaldi, F., Méndez-Cruz, C.F., Collado-Vides, J.. (2021). "Lisen&Curate: A platform to facilitate gathering textual evidence for curation of regulation of transcription initiation in bacteria.". BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS. 1864(11-12):-. [doi:10.1016/j.bbagrm.2021.194753]34461312
2020Chávez, J., Barberena-Jonas, C., Sotelo-Fonseca, J.E., Alquicira-Hernández, J., Salgado, H., Collado-Torres, L., Reyes, A.. (2020). "Programmatic access to bacterial regulatory networks with regutools.". Bioinformatics. 36(16):4532-4534. [doi:10.1093/bioinformatics/btaa575]32573705
2020Mejía-Almonte, C., Busby, S.J.W., Wade, J.T., van Helden, J., Arkin, A.P., Stormo, G.D., Eilbeck, K., Palsson, B.O., Galagan, J.E., Collado-Vides, J.. (2020). "Redefining fundamental concepts of transcription initiation in bacteria". NATURE REVIEWS GENETICS. 21(11):699-714. [doi:10.1038/s41576-020-0254-8][https://rdcu.be/cfeHw]32665585
2020Villaseñor-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
2020Méndez-Cruz, C.F., Blanchet, A., Godínez, A., Arroyo-Fernández, I., Gama-Castro, S., Martínez-Luna, S.B., González-Colín, C., Collado-Vides, J.. (2020). "Knowledge extraction for assisted curation of summaries of bacterial transcription factor properties.". DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION. 2020():-. [doi:10.1093/database/baaa109]33306798
2020Jiménez-Jacinto V., Gómez-Romero, L., Méndez-Cruz CF. (2020). "Pattern Recognition Applied to the Analysis of Genomic Data and Its Association to Diseases". Pattern Recognition Techniques Applied to Biomedical Problems. ():31-61.
2019Tierrafría, V.H., Mejía-Almonte, C., Camacho-Zaragoza, J.M., Salgado, H., Alquicira, K., Ishida, C., Gama-Castro, S., Collado-Vides, J.. (2019). "MCO: towards an ontology and unified vocabulary for a framework-based annotation of microbial growth conditions.". Bioinformatics. 35(5):856-864. [doi:10.1093/bioinformatics/bty689]30137210
2019Lithgow-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]
2019Santos-Zavaleta, A., Salgado, H., Gama-Castro, S., Sánchez-Pérez, M., Gómez-Romero, L., Ledezma-Tejeida, D., García-Sotelo, J.S., Alquicira-Hernández, K., Muñiz-Rascado, L.J., Peña-Loredo, P., Ishida-Gutiérrez, C., Velázquez-Ramírez, D.A., Del Moral-Chávez, V., Bonavides-Martínez, C., Méndez-Cruz, C.F., Galagan, J., Collado-Vides, J.. (2019). "RegulonDB v 10.5: tackling challenges to unify classic and high throughput knowledge of gene regulation in E. coli K-12". Nucleic Acids Research. 47(D1):212-220. [doi:10.1093/nar/gky1077]30395280
2019Arroyo Fernández, Ignacio, Méndez, C., Sierra, Gerardo, Sidorov, Grigori, Torres-Moreno, Juan-Manuel. (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]
2019Giner-Lamia, J., Vinuesa, P., Betancor, L., Silva, C., Bisio, J., Soleto, L., Chabalgoity, J.A., Puente, J.L., Soncini, F.C., 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, Ignacio, Curiel, Arturo, 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]
2019Santos-Zavaleta, A., Pérez-Rueda, E., Sánchez-Pérez, M., Velázquez-Ramírez, D.A., Collado-Vides, J.. (2019). "Tracing the phylogenetic history of the Crl regulon through the Bacteria and Archaea genomes.". Bmc Genomics. 20(1):-. [doi:10.1186/s12864-019-5619-z]30991941
2019Lithgow-Serrano, O., Gama-Castro, S., Ishida-Gutiérrez, C., Mejía-Almonte, C., Tierrafría, V.H., Martínez-Luna, S., Santos-Zavaleta, A., Velázquez-Ramírez, D., Collado-Vides, J.. (2019). "Similarity corpus on microbial transcriptional regulation.". JOURNAL OF BIOMEDICAL SEMANTICS. 10(1):-. [doi:10.1186/s13326-019-0200-x]31118102
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):-. [doi:10.1002/cpbi.72]30786165
2019Centeno-Leija, Sara, Tapia-Cabrera, Silvana, Guzman-Trampe, Silvia, Esquivel, Baldomero, Esturau-Escofet, Nuria, Tierrafria, Victor H., Rodriguez-Sanoja, Romina, Zarate-Romero, Andres, Stojanoff, Vivian, Rudino-Pinera, Enrique, Sanchez, Sergio, Serrano-Posada, Hugo. (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
2019Ledezma-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
2018Santos-Zavaleta, Alberto, Sanchez-Perez, Mishael, Salgado, Heladia, Velazquez-Ramirez, David A., Gama-Castro, Socorro, Tierrafria, Victor H., Busby, Stephen J. W., Aquino, Patricia, Fang, Xin, Palsson, Bernhard O., Galagan, James E., Collado-Vides, Julio. (2018). "A unified resource for transcriptional regulation in Escherichia coli K-12 incorporating high-throughput-generated binding data into RegulonDB version 10.0". BMC BIOLOGY. 16(1):91-91. [doi:10.1186/s12915-018-0555-y]30115066
2018Gomez-Romero, Laura, Palacios-Flores, Kim, Reyes, Jose, Garcia, Delfino, Boege, Margareta, Davila, Guillermo, Flores, Margarita, Schatz, Michael C., Palacios, Rafael. (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.H., Alquicira-Hernández, K., García-Sotelo, J.S., García-Alonso, D., Collado-Vides, J.. (2018). "Using RegulonDB, the Escherichia coli K-12 Gene Regulatory Transcriptional Network Database.". Current Protocols in Bioinformatics. 61(1):1321-13230. [doi:10.1002/cpbi.43]30040192
2018Balderas-Martinez, Y. I., Moreno-Quiroga, B., Negreros, M., Ledezma-Tejeida, D., Pardo, A., Collado-Vides, J., Selman, M.. (2018). "Proof of Concept of Eukaryotic Genetic Sensory Response Units in TGF-beta Signaling in Idiopathic Pulmonary Fibrosis". AMERICAN JOURNAL OF RESPIRATORY AND CRITICAL CARE MEDICINE. 197():-.
2018Villasenor-Altamirano, A. B., Balderas-Martinez, Y. I., Moretto, M., Zayas-Del Moral, A., Maldonado, M., Munguia-Reyes, A., Garcia-Sotelo, J. S., Aguilar Bautista, L. A., Ramirez-Navarro, L., Santillan, O., Engelen, K., Selman, M., Medina-Rivera, A., Collado-Vides, J.. (2018). "PulmonDB: A Gene Expression Lung Diseases". AMERICAN JOURNAL OF RESPIRATORY AND CRITICAL CARE MEDICINE. 197():-.
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, Deyanira, Banda, Maria M., Elizabeth Chau, N. Y., Salgado, Heladia, Martinez-Flores, Irma, Antonio Ibarra, J., Ilyas, Bushra, Coombes, Brian K., Bustamante, Victor H.. (2017). "The transcriptional regulator SsrB is involved in a molecular switch controlling virulence lifestyles of Salmonella". PLOS PATHOGENS. 13(7):-. [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.". BRIEFINGS IN BIOINFORMATICS. 20(2):390-397. [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():-. [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):-. [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):-. [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, Laura, Collado-Vides, Julio. (2017). "Genetic-metabolic networks can be modeled as toric varities". arXiv. ():-. [doi:arXiv:1708.05384v1]
2017Keseler, I.M., Mackie, A., Santos-Zavaleta, A., Billington, R., Bonavides-Martínez, C., Caspi, R., Fulcher, C., Gama-Castro, S., Kothari, A., Krummenacker, M., Latendresse, M., Muñiz-Rascado, L., Ong, Q., Paley, S., Peralta-Gil, M., Subhraveti, P., Velázquez-Ramírez, D.A., Weaver, D., Collado-Vides, J., Paulsen, I., Karp, P.D.. (2017). "The EcoCyc database: reflecting new knowledge about Escherichia coli K-12.". Nucleic Acids Research. 45(D1):543-550. [doi:10.1093/nar/gkw1003]27899573
2016Mendez-Cruz, Carlos-Francisco, Medina-Urrea, Alfonso, Sierra, Gerardo. (2016). "Unsupervised morphological segmentation based on affixality measurements". PATTERN RECOGNITION LETTERS. 84():127-133. [doi:10.1016/j.patrec.2016.09.001]
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2016Wang, Qinghua, Abdul, Shabbir S., Almeida, Lara, Ananiadou, Sophia, Balderas-Martinez, Yalbi I., Batista-Navarro, Riza, Campos, David, Chilton, Lucy, Chou, Hui-Jou, Contreras, Gabriela, Cooper, Laurel, Dai, Hong-Jie, Ferrell, Barbra, Fluck, Juliane, Gama-Castro, Socorro, George, Nancy, Gkoutos, Georgios, Irin, Afroza K., Jensen, Lars J., Jimenez, Silvia, Jue, Toni R., Keseler, Ingrid, Madan, Sumit, Matos, Sergio, McQuilton, Peter, Milacic, Marija, Mort, Matthew, Natarajan, Jeyakumar, Pafilis, Evangelos, Pereira, Emiliano, Rao, Shruti, Rinaldi, Fabio, Rothfels, Karen, Salgado, David, Silva, Raquel M., Singh, Onkar, Stefancsik, Raymund, Su, Chu-Hsien, Subramani, Suresh, Tadepally, Hamsa D., Tsaprouni, Loukia, Vasilevsky, Nicole, Wang, Xiaodong, Chatr-Aryamontri, Andrew, Laulederkind, Stanley J. F., Matis-Mitchell, Sherri, McEntyre, Johanna, Orchard, Sandra, Pundir, Sangya, Rodriguez-Esteban, Raul, Van Auken, Kimberly, Lu, Zhiyong, Schaeffer, Mary, Wu, Cathy H., Hirschman, Lynette, Arighi, Cecilia N.. (2016). "Overview of the interactive task in BioCreative V". DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION. 2016():-. [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.S., Alquicira-Hernández, K., Martínez-Flores, I., Pannier, L., Castro-Mondragón, J.A., Medina-Rivera, A., Solano-Lira, H., Bonavides-Martínez, C., Pérez-Rueda, E., Alquicira-Hernández, S., Porrón-Sotelo, L., López-Fuentes, A., Hernández-Koutoucheva, A., Del Moral-Chavez, V., Rinaldi, F., Collado-Vides, J.. (2016). "RegulonDB version 9.0: High-level integration of gene regulation, coexpression, motif clustering and beyond". Nucleic Acids Research. 44(D1):133-143. [doi:10.1093/nar/gkv1156]26527724
2015Alvarez-Vasquez, Fernando J., Freyre-Gonzalez, Julio A., Balderas-Martinez, Yalbi I., Delgado-Carrillo, Monica I., Collado-Vides, Julio. (2015). "Mathematical modeling of the apo and holo transcriptional regulation in Escherichia coli". Molecular Biosystems. 11(4):994-1003. [doi:10.1039/c4mb00561a]25683745
2014Meysman, Pieter, Collado-Vides, Julio, Morett, Enrique, Viola, Roberto, Engelen, Kristof, Laukens, Kris. (2014). "Structural properties of prokaryotic promoter regions correlate with functional features". Plos One. 9(2):-. [doi:10.1371/journal.pone.0088717]24516674
2014Meysman, P., Sonego, P., Bianco, L., Fu, Q., Ledezma, D., Gama, M., Liebens, V., Laukens, K., Marchal, K., Collado, 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
2014Martinez, L.C., Martínez, I., Salgado, H., Fernández-Mora, M., Medina, A., Puente, J.L., Collado, P., 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
2014Gama, M., Rinaldi, F., López, A., Balderas, Y., Clematide, S., Ellendorff, T.R., Santos, A., Marques-Madeira, H., Collado, 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():-. [doi:10.1093/database/bau049]24903516
2013Salgado, H., Peralta, M., Gama, M., Santos, A., Muñíz, L., Garcia, J., Weiss, V., Solano, H., Martínez, I., Medina, A., Salgado, G., Alquicira, S., Alquicira, K., López, A., Porrón, L., Huerta, A., Bonavides, C., Balderas, Y., Pannier, L., Olvera, M., Labastida, A., Jiménez-Jacinto, V., Vega-Alvarado, L., del Moral, V., Hernández, A., Morett, E., Collado, 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.M., Mackie, A., Peralta, M., Santos, A., Gama, M., Bonavides, C., Fulcher, C., Huerta, A., Kothari, A., Krummenacker, M., Latendresse, M., Muñíz, L., Ong, Q., Paley, S., Schroder, I., Shearer, A.G., Subhraveti, P., Travers, M., Weerasinghe, D., Weiss, V., Collado, P., Gunsalus, R.P., Paulsen, I., Karp, P.D.. (2013). "EcoCyc: Fusing model organism databases with systems biology". Nucleic Acids Research. 41(D1):605-612. [doi:10.1093/nar/gks1027]23143106
2013Weiss, V., Medina-Rivera, A, Huerta, AM, Santos-Zavaleta, A, Salgado, H, Morett, E., Collado-Vides, J. (2013). "Evidence classification of high-throughput protocols and confidence integration in RegulonDB". DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION. 2013():-. [doi:10.1093/database/bas059]23327937
2013Balderas, Y., Savageau, M., Salgado, H., Pérez-Rueda, E, Morett, E., Collado, P.. (2013). "Transcription Factors in Escherichia coli Prefer the holo Conformation". Plos One. 8(6):-. [doi:10.1371/journal.pone.0065723]23776535
2012Salgado, H., Martínez, I., López, A., Garcia, J., Porrón, L., Muñíz, L., Collado, 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
2012Pauling, J., Rottger, R., Neuner, A., Salgado, H., Collado, 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
2011Salgado Osorio, Heladia, Martínez Flores, Irma, López Fuentes, Alejandra Cristina, Garcia Sotelo, Jair Santiago, Porrón Sotelo, Liliana, Muñíz Rascado, Luis José, Collado Vides, Pedro Julio. (2011). "Extracting regulatory networks of/Escherichia coli/from RegulonDB". Bacterial Molecular Networks: Methods and Protocols. ():-.
2011Reyes, J., Gómez-Romero, L., Ibarra-Soria, X., Palacios-Flores, Kim, Arriola, L.R., Wences, A., García, D., Boege, M., Davila, G, Flores, M, Palacios, 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, A., Gama, M., Pérez, 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, A., Abreu-Goodger, C., Thomas-Chollier, M., Salgado, H., Collado, 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, M., Salgado, H., Peralta, M., Santos, A., Muñíz, L., Solano, H., Jimenez-Jacinto, V., Weiss, V., Garcia, J., López, A., Porrón, L., Alquicira, S., Medina, A., Martínez, I., Alquicira, K., Martínez, R., Bonavides, C., Miranda-Ríos, J., Huerta, A., Mendoza-Vargas, A., Collado, L., Taboada, B., Vega-Alvarado, L., Olvera, M., Olvera, L., Grande, R., Morett, E., Collado, 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.M., Collado, P., Santos, A., Peralta, M., Gama, M., Muñíz, L., Bonavides, 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., 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
2010Martínez Flores, Irma, Jiménez-Jacinto, V., López Fuentes, Alejandra Cristina, Collado Vides, Pedro Julio. (2010). "Expanding BioPAX format by integrating Gene Regulation". EMBnet.journal. 16():39-43.
2010Salgado Osorio, Heladia, López Fuentes, Alejandra Cristina, Martínez Flores, Irma, Garcia Sotelo, Jair Santiago, Porrón Sotelo, Liliana, Solano Lira, Hilda, Muñíz Rascado, Luis José, Collado Vides, Pedro Julio. (2010). "Extracting regulatory networks of Escherichia coli from RegulonDB". Bacterial Molecular Networks: Methods and Protocols. ():-.
2010Zepeda-Mendoza, Cinthya J., Lemus, Tzitziki, Yanez, Omar, Garcia, Delfino, Valle-Garcia, David, Meza-Sosa, Karla F., Gutierrez-Arcelus, Maria, Marquez-Ortiz, Yamile, Dominguez-Vidana, Rocio, Gonzaga-Jauregui, Claudia, Flores, Margarita, Palacios, Rafael. (2010). "Identical repeated backbone of the human genome". Bmc Genomics. 11(1):60-60. [doi:10.1186/1471-2164-11-60]20096123
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2009Janga, Sarath Chandra, Salgado, Heladia, Martinez-Antonio, Agustino. (2009). "Transcriptional regulation shapes the organization of genes on bacterial chromosomes". Nucleic Acids Research. 37(11):3680-3688. [doi:10.1093/nar/gkp231]19372274
2009Collado-Vides, Julio, Salgado, Heladia, Morett, Enrique, Gama-Castro, Socorro, Jimenez-Jacinto, Veronica, Martinez-Flores, Irma, Medina-Rivera, Alejandra, Muniz-Rascado, Luis, Peralta-Gil, Martin, Santos-Zavaleta, Alberto. (2009). "Bioinformatics resources for the study of gene regulation in bacteria". Journal Of Bacteriology. 91(1):23-31. [doi:10.1128/JB.01017-08]18978060
2009Mendoza-Vargas, Alfredo, Olvera, Leticia, Olvera, Maricela, Grande, Ricardo, Vega-Alvarado, Leticia, Taboada, Blanca, Jimenez-Jacinto, Veronica, Salgado, Heladia, Juarez, Katy, Contreras-Moreira, Bruno, Huerta, Araceli M., Collado-Vides, Julio, Morett, Enrique. (2009). "Genome-wide identification of transcription start sites, promoters and transcription factor binding sites in E. coli". Plos One. 4(10):-. [doi:10.1371/journal.pone.0007526]19838305
2009Gonzalez Perez, Abel, Espinosa Angarica, Vladimir, Collado-Vides, Julio, Ribeiro Vasconcelos, Ana Tereza. (2009). "From sequence to dynamics: The effects of transcription factor and polymerase concentration changes on activated and repressed promoters". Bmc Molecular Biology. 10():92-92. [doi:10.1186/1471-2199-10-92]19772633
2009Lozada-Chvez, Irma, Contreras-Moreira, Bruno, Collado-Vides, Julio. (2009). "Evolution of Bacterial Regulatory Networks:"The Role of DNA-Binding Specificity"". Origins Of Life And Evolution Of Biospheres. 39(3-4):280-281.
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, Julio, Engelen, Kristof, Marchal, Kathleen. (2009). "DISTILLER: A data integration framework to reveal condition dependency of complex regulons in Escherichia coli". Genome Biology. 10(3):-. [doi:10.1186/gb-2009-10-3-r27]19265557
2009Lemmens, K., De Bie, T., Dhollander, T., Monsieurs, P., De Moor, B., Collado, 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
2009Balleza, Enrique, Lopez-Bojorquez, Lucia N., Martinez-Antonio, Agustino, Resendis-Antonio, Osbaldo, Lozada-Chavez, Irma, Balderas-Martinez, Yalbi I., Encarnacion, Sergio, Collado-Vides, Julio. (2009). "Regulation by transcription factors in bacteria: Beyond description". Fems Microbiology Reviews. 33(1):133-151. [doi:10.1111/j.1574-6976.2008.00145.x]19076632
2009Martinez-Antonio, Agustino, Medina-Rivera, Alejandra, Collado-Vides, Julio. (2009). "Structural and functional map of a bacterial nucleoid". Genome Biology. 10(12):247-247. [doi:10.1186/gb-2009-10-12-247]19995411
2008Hernandez-Romano, Jesus, Carlos-Rivera, Francisco J., Salgado, Heladia, Lamadrid-Figueroa, Hector, Valverde-Garduno, Veronica, Rodriguez, Mario H., Martinez-Barnetche, Jesus. (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
2008Gama, M., Jiménez, V., Peralta, M., Santos, A., Peñaloza, M., Contreras, B., Segura, J., Muñíz, L., Martínez, I., Salgado, H., Bonavides, C., Abreu, C., Rodríguez, C., Miranda-Ríos, J., Morett, J., Merino, E., Huerta, A., Treviño, L., Collado, 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
2008Perez, A.D.G., Gonzalez, E.G., Angarica, V.E., Vasconcelos, A.T.R., Collado, 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
2008Lozada-Chavez, Irma, Angarica, Vladimir Espinosa, Collado-Vides, Julio, Contreras-Moreira, Bruno. (2008). "The Role of DNA-binding Specificity in the Evolution of Bacterial Regulatory Networks". Journal Of Molecular Biology. 379(3):627-643. [doi:10.1016/j.jmb.2008.04.008]18466918
2008Martínez-Antonio, A., Collado Vides, Pedro Julio. (2008). "Comparative mechanisms for transcription and regulatory signals in archaea and bacteria". Computational Methods for Understanding Bacterial and Archaeal Genomes. (0):185-208.
2008Janga, Sarath Chandra, Collado-Vides, Julio, Babu, M. Madan. (2008). "Transcriptional regulation constrains the organization of genes on eukaryotic chromosomes". PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA. 105(41):15761-15766. [doi:10.1073/pnas.0806317105]18840678
2008Espinosa Angarica, Vladimir, Gonzalez Perez, Abel, Vasconcelos, Ana T., Collado-Vides, Julio, Contreras-Moreira, Bruno. (2008). "Prediction of TF target sites based on atomistic models of protein-DNA complexes". Bmc Bioinformatics. 9():436-436. [doi:10.1186/1471-2105-9-436]18922190
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2008Hernandez-Lucas, I., Gallego-Hernandez, A. L., Encarnacion, S., Fernandez-Mora, M., Martinez-Batallar, A. G., 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
2007Rodríguez-Penagos, C., Salgado, H., Martínez-Flores, I., Collado-Vides, J.. (2007). "NLP-based curation of bacterial regulatory networks". LECTURE NOTES IN COMPUTER SCIENCE. 4394 LNCS():575-586. [doi:10.1007/978-3-540-70939-8_51]
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2007Gutierrez-Rios, R.M., Freyre, J., Resendis, O., Collado, 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
2007Perez, A.G., Angarica, V.E., Vasconcelos, A.T.R., Collado, 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
2007Rodríguez Penagos, Carlos, Salgado Osorio, Heladia, Martínez Flores, Irma, Collado Vides, Pedro Julio. (2007). "NLP-Based Curation of Bacterial Regulatory Networks". CICLing. ():575-586.
2007Rodríguez Penagos, Carlos, Martínez Flores, Irma, Salgado Osorio, Heladia, Collado Vides, Pedro Julio. (2007). "NLP-based curation of bacterial regulatory networks". Computational Linguistics And Intelligent Text Processing. 4394():575-.
2007Flores, M., Morales, L., Gonzaga, C., Domínguez, R., Zepeda, C., Yáñez, J., Gutiérrez, M., Lemus, T., Valle, D., Ávila, M., Blanco, D., Medina, S., Meza, K., Ayala, E., García, D., Bustos, V., González, V., Girard, M., Tusie-Luna, T., Dávila, J., Palacios, 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
2007Janga, S., Salgado, H., Collado, P., Martínez, 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
2007Contreras, B., Fernández, P., Collado, P.. (2007). "TFmodeller: Comparative modelling of protein-DNA complexes". Bioinformatics. 23(13):1694-1696. [doi:10.1093/bioinformatics/btm148]17459960
2007Rodríguez, C., Salgado, H., Martínez, I., Collado, 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
2007Palacios, Rafael, Collado-Vides, Julio. (2007). "Development of genomic sciences in Mexico: A good start and a long way to go". Plos Computational Biology. 3(9):1670-1673. [doi:10.1371/journal.pcbi.0030143]17907791
2007Resendis, O., Reed, J.L., Encarnación, S., Collado, P., 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
2007Janga, S., Salgado, H., Martínez, A., Collado, 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
2007Janga, Sarath Chandra, Collado-Vides, J.. (2007). "Structure and evolution of gene regulatory networks in microbial genomes". Research In Microbiology. 158(10):787-794. [doi:10.1016/j.resmic.2007.09.001]17996425
2007Karp, P.D., Keseler, I.M., Shearer, A., Latendresse, M., Krummenacker, M., Paley, S.M., Paulsen, I., Collado, P., Gama, M., Peralta, M., Santos, A., Peñaloza, M., Bonavides, 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
2006Huerta, A., Collado, P., 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, M., Peralta, M., Díaz, E., Sánchez, E., Santos, A., Martínez, I., Jiménez, V., Bonavides, C., Segura, J., Martínez, A., Collado, 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
2006Martínez, A., Janga, S., Salgado, H., Collado, 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
2006Salgado, H., Santos, A., Gama, M., Peralta, M., Peñaloza, M., Martínez, A., Karp, P.D., Collado, 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
2006González, V., Santamaria, R., Bustos, V., Hernández, I., Medrano, L., Moreno, G., Janga, S., Ramírez, M., Jiménez, V., Collado, P., Dávila, 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
2006Santos-Zavaleta, A., Salgado, H., Gama-Castro, S., Peralta-Gil, M., Contreras-Moreira, B., Penaloza-Spinola, M., I, Collado-Vides, J.. (2006). "RegulonDB. The most important database in transcriptional regulatory network, operon organization, and growth conditions of Escherichia coli K12". Proceedings Of The Fifth International Conference On Bioinformatics Of Genome Regulation And Structure, Vol 3. ():323-323.
2006Contreras, B., Collado, P.. (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, Ma. del Socorro, Contreras Moreira, Bruno, Santos Zavaleta, Alberto, Martínez Flores, Irma, Collado Vides, Pedro Julio. (2006). "RegulonDB: Going beyond transcriptional regulation". Proceedings Of The Fifth International Conference On Bioinformatics Of Genome Regulation And Structure, Vol 3. ():322-322.
2006Huerta, A., Francino, M.P., Morett, J., Collado, 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
2006Lozada-Chavez, Irma, Janga, Sarath Chandra, Collado-Vides, Julio. (2006). "Bacterial regulatory networks are extremely flexible in evolution". Nucleic Acids Research. 34(12):3434-3445. [doi:10.1093/nar/gkl423]16840530
2005Ibarra-Junquera, V, Torres, LA, Rosu, HC, Arguello, G, Collado-Vides, J. (2005). "Nonlinear software sensor for monitoring genetic regulation processes with noise and modeling errors". PHYSICAL REVIEW E. 72(1):11919-11919. [doi:10.1103/PhysRevE.72.011919]16090013
2005Le Novere, N., Finney, A., Hucka, M., Bhalla, U.S., Campagne, F., Collado, P., Crampin, E.J., Halstead, M., Klipp, E., Mendes, P., Nielsen, P., Sauro, H., Shapiro, B., Snoep, J.L., Spence, H.D., Wanner, B.L.. (2005). "Minimum information requested in the annotation of biochemical models (MIRIAM)". Nature Biotechnology. 23(12):1509-1515. [doi:10.1038/nbt1156]16333295
2005Espinosa, V., Gonzalez, A.D., Vasconcelos, A.T., Huerta, A., Collado, 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
2005Janga, SC, Collado-Vides, J, Moreno-Hagelsieb, G. (2005). "Nebulon: A system for the inference of functional relationships of gene products from the rearrangement of predicted operons". Nucleic Acids Research. 33(8):2521-2530. [doi:10.1093/nar/gki545]15867197
2005Flores, M., Morales, L., Ávila, A., González, V., Bustos, V., García, D., Pérez-Tejada, Y., Guo, X., Collado, P., Pinero, D., Dávila, J., Mora, J., Palacios, 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
2005Guia, M.H., Perez, A.G., Angarica, V.E., Vasconcelos, A.T., Collado Vides, Pedro Julio. (2005). "Complementing computationally predicted regulatory sites in Tractor_DB using a pattern matching approach". In Silico Biology: Journal of Biological Systems Modeling and Multi-Scale Simulation. 5(2):209-219. 15972018
2005Menchaca, R., Janga, S., Collado, 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
2005Medrano-Soto, A, Christen, JA, Collado-Vides, J. (2005). "BClass: A Bayesian approach based on mixture models for clustering and classification of heterogeneous biological data". JOURNAL OF STATISTICAL SOFTWARE. 13(2):1-18. [doi:10.18637/jss.v013.i02]
2005Keseler, I.M., Collado, P., Gama, M., Ingraham, J., Paley, S., Paulsen, I.T., Peralta, M., 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
2005Resendis, O., Freyre, J., Menchaca, R., Gutiérrez, R., Martínez, A., Ávila, C., Collado, 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
2005Gonzalez, A.D., Espinosa, V., Vasconcelos, A.T., Perez-Rueda, E., Collado, 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
2004Perez-Rueda, E., Collado, 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]
2004Medrano, L., Moreno, G., Vinuesa, P., Christen, J.A., Collado, 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
2004Oviedo, N.A., Salgado, H., Collado, 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
2004Salgado, H., Gama, M., Martínez, A., Díaz, E., Sánchez, E., Peralta, M., García, D., Jiménez, V., Santos, A., Bonavides, C., Collado, 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
2004Karp, PD, Arnaud, M, Collado-Vides, J, Ingraham, J, Paulsen, IT, Saier, MH. (2004). "The E. coli EcoCyc database: No longer just a metabolic pathway database". Asm News. 70(1):25-30.
2003Collado Vides, Pedro Julio, Medrano Soto, Luis Arturo, Tusié-Luna, M.T.. (2003). "With the finished human genome in hand, what next?". Genome Biology. 4(7):328-328. [doi:10.1186/gb-2003-4-7-328]12844356
2003Perret, X., Kobayashi, H., Collado Vides, Pedro Julio. (2003). "Regulation of expression of symbiotic genes in Rhizobium sp. NGR234". INDIAN JOURNAL OF EXPERIMENTAL BIOLOGY. 41(10):1101-1113. 15242276
2003González, V., Bustos, V., Ramírez, M., Medrano, L., Salgado, H., Hernández, I., Hernández, J., Quintero, V., Moreno, G., Girard, M., Rodríguez, O., Flores, M., Cevallos, M., Collado, P., Romero, D., Dávila, 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):-. [doi:10.1186/gb-2003-4-6-r36]12801410
2003Martinez-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
2003Huerta, AM, Collado-Vides, J. (2003). "Sigma70 promoters in Escherichia coli: Specific transcription in dense regions of overlapping promoter-like signals". Journal Of Molecular Biology. 333(2):261-278. [doi:10.1016/j.jmb.2003.07.017]14529615
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
2003Martínez, A., Salgado, H., Gama, M., Gutiérrez, R., Jiménez, V., Collado, 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
2003Gutiérrez, R., Rosenblueth, D.A., Loza, J., Huerta, A., Glasner, J.D., Blattner, F.R., Collado, 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
2002Karp, PD, Riley, M, Saier, M, Paulsen, IT, Collado-Vides, J, Paley, SM, Pellegrini-Toole, A, Bonavides, C, Gama-Castro, S. (2002). "The EcoCyc database". Nucleic Acids Research. 30(1):56-58. [doi:10.1093/nar/30.1.56]11752253
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, Pedro Julio, Moreno Hagelsieb, Gabriel, Pérez Rueda, Ernesto, Salgado Osorio, Heladia, Huerta Moreno, Araceli, Gutiérrez Ríos, Rosa María, Rosenblueth, David A., Christen, Andrés, Benítez Bellón, Esperanza, Medrano Soto, Luis Arturo, Gama Castro, Ma. del Socorro, Santos Zavaleta, Alberto, Bonavides Martínez, César Augusto, DíPeredo, Edgar, Sánchez Solano, Erika Fabiola, Millá, Dulce María. (2002). "Genomics of Gene Regulation: The view from Escherichia coli". Gene Regulation and Metabolism, Post-Genomic Computational Approaches. ():103-128.
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, AM, Glasner, JD, Gutierrez-Rios, RM, Blattner, FR, Collado-Vides, J. (2002). "GETools: gene expression tool for analysis of transcriptome experiments in E. coli". TRENDS IN GENETICS. 18(4):217-218. [doi:10.1016/S0168-9525(01)02620-8]
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]
2002Moreno Hagelsieb, Gabriel, Collado Vides, Pedro Julio. (2002). "Operon conservation from the point of view of Escherichia coli, and inference of functional interdependence of gene products from genome context". In Silico Biology: Journal of Biological Systems Modeling and Multi-Scale Simulation. 2(2):87-95. 12066843
2002Benítez Bellón, Esperanza, Moreno Hagelsieb, Gabriel, Collado Vides, Pedro Julio. (2002). "Evaluation of thresholds for the detection of binding sites for regulatory proteins in Escherichia coli K12 DNA.". Genome Biology. 3(3):-. [doi:10.1186/gb-2002-3-3-research0013]11897025
2002Moreno, G., Collado, 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
2002Degrave, W.M., Vargas, R., Alvarez, F., Collado Vides, Pedro Julio, Nunez, L., Ramirez, J.L., Grau, O.. (2002). "Towards a bioinformatics network for Latin America and the Caribbean (LACBioNet).". Applied Bioinformatics. 1(1):53-56. 15130857
2001Moreno-Hagelsieb, G, Trevino, V, Pérez-Rueda, E, Smith, TF, Collado-Vides, J. (2001). "Transcription unit conservation in the three domains of life: A perspective from Escherichia coli". TRENDS IN GENETICS. 17(4):175-177. [doi:10.1016/S0168-9525(01)02241-7]11275307
2001Ramirez-Santos, J, Collado-Vides, J, Garcia-Varela, M, Gomez-Eichelmann, MC. (2001). "Conserved regulatory elements of the promoter sequence of the gene rpoH of enteric bacteria". Nucleic Acids Research. 29(2):380-386. [doi:10.1093/nar/29.2.380]11139607
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
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, G., Collado, P., 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
2000van Helden, J., Andre, B., Collado, P.. (2000). "A web site for the computational analysis of yeast regulatory sequences". Yeast. 16(2):177-187. 3.0.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, FR, Collado-Vides, J. (2000). "RegulonDB (version 3.0): Transcriptional regulation and operon organization in Escherichia coli K-12". Nucleic Acids Research. 28(1):65-67. [doi:10.1093/nar/28.1.65]10592182
2000Salgado, H., Moreno, G., Smith, T.F., Collado, 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
2000Strainic, MG, Sullivan, JJ, Collado-Vides, J, deHaseth, PL. (2000). "Promoter interference in a bacteriophage lambda control region: Effects of a range of interpromoter distances". Journal Of Bacteriology. 182(1):216-220. [doi:10.1128/JB.182.1.216-220.2000]10613884
2000van Heiden, Jacques, Rios, Alma. F., Collado-Vides, Julio. (2000). "Discovering regulatory elements in non-coding sequences by analysis of spaced dyads". Nucleic Acids Research. 28(8):1808-1818. [doi:10.1093/nar/28.8.1808]10734201
2000Perez-Rueda, Ernesto, Collado-Vides, Julio. (2000). "The repertoire of DNA-binding transcriptional regulators in Escherichia coli K-12". Nucleic Acids Research. 28(8):1838-1847. [doi:10.1093/nar/28.8.1838]10734204
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
1999Collado, 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
1998Thieffry, D, Salgado, H, Huerta, AM, Collado-Vides, J. (1998). "Prediction of transcriptional regulatory sites in the complete genome sequence of Escherichia coli K-12". Bioinformatics. 14(5):391-400. [doi:10.1093/bioinformatics/14.5.391]9682052
1998Collado-Vides, J, Gutierrez-Rios, RM, Bel-Enguix, G. (1998). "Networks of transcriptional regulation encoded in a grammatical model". Biosystems. 47(1-2):103-118. [doi:10.1016/S0303-2647(98)00016-1]9715754
1998Huerta, AM, Salgado, H, Thieffry, D, Collado-Vides, J. (1998). "RegulonDB: A database on transcriptional regulation in Escherichia coli". Nucleic Acids Research. 26(1):55-59. [doi:10.1093/nar/26.1.55]9399800
1998Pérez, E., Gralla, J.D., Collado, P.. (1998). "Genomic position analyses and the transcription machinery". Journal Of Molecular Biology. 275(2):165-170. [doi:10.1006/jmbi.1997.1465]9466899
1998Thieffry, D., Huerta, A., Pérez, E., Collado, P.. (1998). "From specific gene regulation to genomic networks: A global analysis of transcriptional regulation in Escherichia coli". Bioessays. 20(5):433-440. 3.0.CO;2-2">[doi:10.1002/(SICI)1521-1878(199805)20:53.0.CO;2-2]9670816
1998van Helden, J., Andre, B., Collado, 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
1997Thieffry Jacot-Descombes, Denis Louis, Rosenblueth, D.A., Huerta Moreno, Araceli, Salgado Osorio, Heladia, Collado Vides, Pedro Julio. (1997). "Definite-clause grammars for the analysis of CIS-regulatory regions in E. coli.". Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing. ():441-452. 9390313
1997Blattner, FR, Plunkett, G, Bloch, CA, Perna, NT, Burland, V, Riley, M, ColladoVides, J, Glasner, JD, Rode, CK, Mayhew, GF, Gregor, J, Davis, NW, Kirkpatrick, HA, Goeden, MA, Rose, DJ, Mau, B, Shao, Y. (1997). "The complete genome sequence of Escherichia coli K-12". Science. 277(5331):1453-1462. [doi:10.1126/science.277.5331.1453]9278503
1997Collado-Vides, J, Huerta, AM, Klose, K. (1997). "Three models of gene regulation in E. coli". LECTURE NOTES IN COMPUTER SCIENCE. 1278():72-78.
1996Hofestadt, R., Mavrovouniotis, M., Collado, 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
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, DA, Thieffry, D, Huerta, AM, Salgado, H, ColladoVides, J. (1996). "Syntactic recognition of regulatory regions in Escherichia coli". COMPUTER APPLICATIONS IN THE BIOSCIENCES. 12(5):415-422. [doi:10.1093/bioinformatics/12.5.415]8996790
1993Collado, 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