César Augusto Bonavides Martínez
Telephone: (777) 3132063
Email: cbona18@ccg.unam.mx
Publications
| Year | Publication | PMID |
|---|---|---|
| 2022 | Femerling, 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 |
| 2022 | Tierrafría, 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 |
| 2021 | Keseler, I.M., Gama-Castro, S., Mackie, A., Billington, R., Bonavides-Martínez, C., Caspi, R., Kothari, A., Krummenacker, M., Midford, P.E., Muñiz-Rascado, L., Ong, W.K., Paley, S., Santos-Zavaleta, A., Subhraveti, P., Tierrafría, V.H., Wolfe, A.J., Collado-Vides, J., Paulsen, I.T., Karp, P.D.. (2021). "The EcoCyc Database in 2021.". Frontiers in Microbiology. 12():-. [doi:10.3389/fmicb.2021.711077] | 34394059 |
| 2021 | D'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] | |
| 2019 | Santos-Zavaleta, A., Salgado, H., Gama-Castro, S., Sánchez-Pérez, M., Gómez-Romero, L., Ledezma-Tejeida, D., García-Sotelo, J.S., Alquicira-Hernández, K., Muñiz-Rascado, L.J., Peña-Loredo, P., Ishida-Gutiérrez, C., Velázquez-Ramírez, D.A., Del Moral-Chávez, V., Bonavides-Martínez, C., Méndez-Cruz, C.F., Galagan, J., Collado-Vides, J.. (2019). "RegulonDB v 10.5: tackling challenges to unify classic and high throughput knowledge of gene regulation in E. coli K-12". Nucleic Acids Research. 47(D1):212-220. [doi:10.1093/nar/gky1077] | 30395280 |
| 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 | Keseler, I.M., Mackie, A., Santos-Zavaleta, A., Billington, R., Bonavides-Martínez, C., Caspi, R., Fulcher, C., Gama-Castro, S., Kothari, A., Krummenacker, M., Latendresse, M., Muñiz-Rascado, L., Ong, Q., Paley, S., Peralta-Gil, M., Subhraveti, P., Velázquez-Ramírez, D.A., Weaver, D., Collado-Vides, J., Paulsen, I., Karp, P.D.. (2017). "The EcoCyc database: reflecting new knowledge about Escherichia coli K-12.". Nucleic Acids Research. 45(D1):543-550. [doi:10.1093/nar/gkw1003] | 27899573 |
| 2016 | Gama-Castro, S., Salgado, H., Santos-Zavaleta, A., Ledezma-Tejeida, D., Muñiz-Rascado, L., García-Sotelo, J.S., Alquicira-Hernández, K., Martínez-Flores, I., Pannier, L., Castro-Mondragón, J.A., Medina-Rivera, A., Solano-Lira, H., Bonavides-Martínez, C., Pérez-Rueda, E., Alquicira-Hernández, S., Porrón-Sotelo, L., López-Fuentes, A., Hernández-Koutoucheva, A., Del Moral-Chavez, V., Rinaldi, F., Collado-Vides, J.. (2016). "RegulonDB version 9.0: High-level integration of gene regulation, coexpression, motif clustering and beyond". Nucleic Acids Research. 44(D1):133-143. [doi:10.1093/nar/gkv1156] | 26527724 |
| 2013 | Salgado Osorio, Heladia, Peralta Gil, Martín, Gama Castro, Ma. del Socorro, Santos Zavaleta, Alberto, Muñíz Rascado, Luis José, Garcia Sotelo, Jair Santiago, Weiss, V., Solano Lira, Hilda, Martínez Flores, Irma, Medina Rivera, Alejandra Eugenia, Salgado Osorio, Gerardo, Alquicira Hernández, Shirley, Alquicira Hernández, Kevin, López Fuentes, Alejandra Cristina, Porrón Sotelo, Liliana, Huerta Moreno, Araceli, Bonavides Martínez, César Augusto, Balderas MartÍnez, Yalbi Itzel, Pannier, Lucia, Olvera, M., Labastida, A., Jiménez-Jacinto, V., Vega-Alvarado, L., del Moral Chávez, Victor Manuel, Hernández Álvarez, Alfredo José, Morett, E., Collado Vides, Pedro Julio. (2013). "RegulonDB v8.0: Omics data sets, evolutionary conservation, regulatory phrases, cross-validated gold standards and more". Nucleic Acids Research. 41(D1):203-213. [doi:10.1093/nar/gks1201] | 23203884 |
| 2013 | Keseler, I.M., Mackie, A., Peralta Gil, Martín, Santos Zavaleta, Alberto, Gama Castro, Ma. del Socorro, Bonavides Martínez, César Augusto, Fulcher, C., Huerta Moreno, Araceli, Kothari, A., Krummenacker, M., Latendresse, M., Muñíz Rascado, Luis José, Ong, Q., Paley, S., Schroder, I., Shearer, A.G., Subhraveti, P., Travers, M., Weerasinghe, D., Weiss, V., Collado Vides, Pedro Julio, Gunsalus, R.P., Paulsen, I., Karp, P.D.. (2013). "EcoCyc: Fusing model organism databases with systems biology". Nucleic Acids Research. 41(D1):605-612. [doi:10.1093/nar/gks1027] | 23143106 |
| 2011 | Gama Castro, Ma. del Socorro, Salgado Osorio, Heladia, Peralta Gil, Martín, Santos Zavaleta, Alberto, Muñíz Rascado, Luis José, Solano Lira, Hilda, Jimenez-Jacinto, V., Weiss, V., Garcia Sotelo, Jair Santiago, López Fuentes, Alejandra Cristina, Porrón Sotelo, Liliana, Alquicira Hernández, Shirley, Medina Rivera, Alejandra Eugenia, Martínez Flores, Irma, Alquicira Hernández, Kevin, Martínez Adame, Ruth, Bonavides Martínez, César Augusto, Miranda-Ríos, J., Huerta Moreno, Araceli, Mendoza-Vargas, A., Collado Torres, Leonardo, Taboada, B., Vega-Alvarado, L., Olvera, M., Olvera, L., Grande, R., Morett, E., Collado Vides, Pedro Julio. (2011). "RegulonDB version 7.0: Transcriptional regulation of Escherichia coli K-12 integrated within genetic sensory response units (Gensor Units)". Nucleic Acids Research. 39(SUPPL. 1):98-105. [doi:10.1093/nar/gkq1110] | 21051347 |
| 2011 | Keseler, I.M., Collado Vides, Pedro Julio, Santos Zavaleta, Alberto, Peralta Gil, Martín, Gama Castro, Ma. del Socorro, Muñíz Rascado, Luis José, Bonavides Martínez, César Augusto, Paley, S., Krummenacker, M., Altman, T., Spaulding, A., Spaulding, A., Pacheco, J., Latendresse, M., Fulcher, C., Sarker, M., Shearer, A.G., Mackie, A., Paulsen, I., Gunsalus, R.P., Karp, P.D.. (2011). "EcoCyc: A comprehensive database of Escherichia coli biology". Nucleic Acids Research. 39(SUPPL. 1):583-590. [doi:10.1093/nar/gkq1143] | 21097882 |
| 2009 | Aparicio, G., Blanco, F., Blanquer, I., Bonavides Martínez, César Augusto, Chaves, J.L., Embid, M., Hernández, Á., Hernández, V., Isea, R., Lagares, J.I., Aldama, D.L., Mayo, R., Montes, E., Mora Henry, R.. (2009). "Developing Biomedical Applications in the Framework of EELA". Handbook of Research on Grid Technologies and Utility Computing: Concepts for Managing Large-Scale Applications. ():206-218. | |
| 2008 | Gama Castro, Ma. del Socorro, Jiménez Jacinto, Verónica, Peralta Gil, Martín, Santos Zavaleta, Alberto, Peñaloza Spinola, Mónica Ivonne, Contreras Moreira, Bruno, Segura Salazar, Juan, Muñíz Rascado, Luis José, Martínez Flores, Irma, Salgado Osorio, Heladia, Bonavides Martínez, César Augusto, Abreu Goodger, Cei Leander Gastón, Rodríguez Penagos, Carlos, Miranda-Ríos, J., Morett Sánchez, Juan Enrique, Merino, E., Huerta Moreno, Araceli, Treviño Quintanilla, Luis Gerardo, Collado Vides, Pedro Julio. (2008). "RegulonDB (version 6.0): Gene regulation model of Escherichia coli K-12 beyond transcription, active (experimental) annotated promoters and Textpresso navigation". Nucleic Acids Research. 36(SUPPL. 1):120-124. [doi:10.1093/nar/gkm994] | 18158297 |
| 2007 | Karp, P.D., Keseler, I.M., Shearer, A., Latendresse, M., Krummenacker, M., Paley, S.M., Paulsen, I., Collado Vides, Pedro Julio, Gama Castro, Ma. del Socorro, Peralta Gil, Martín, Santos Zavaleta, Alberto, Peñaloza Spinola, Mónica Ivonne, Bonavides Martínez, César Augusto, Ingraham, J.. (2007). "Multidimensional annotation of the Escherichia coli K-12 genome". Nucleic Acids Research. 35(22):7577-7590. [doi:10.1093/nar/gkm740] | 17940092 |
| 2006 | Salgado Osorio, Heladia, Gama Castro, Ma. del Socorro, Peralta Gil, Martín, Díaz Peredo, Edgar Ulises, Sánchez Solano, Erika Fabiola, Santos Zavaleta, Alberto, Martínez Flores, Irma, Jiménez Jacinto, Verónica, Bonavides Martínez, César Augusto, Segura Salazar, Juan, Martínez Antonio, Agustino, Collado Vides, Pedro Julio. (2006). "RegulonDB (version 5.0): Escherichia coli K-12 transcriptional regulatory network, operon organization, and growth conditions.". Nucleic Acids Research. 34(Database issue):394-397. [doi:10.1093/nar/gkj156] | 16381895 |
| 2004 | Salgado Osorio, Heladia, Gama Castro, Ma. del Socorro, Martínez Antonio, Agustino, Díaz Peredo, Edgar Ulises, Sánchez Solano, Erika Fabiola, Peralta Gil, Martín, García Alonso, Delfino, Jiménez Jacinto, Verónica, Santos Zavaleta, Alberto, Bonavides Martínez, César Augusto, Collado Vides, Pedro Julio. (2004). "RegulonDB (version 4.0): Transcriptional regulation, operon organization and growth conditions in Escherichia coli K-12". Nucleic Acids Research. 32(DATABASE ISS.):303-306. [doi:10.1093/nar/gkh140] | 14681419 |
| 2002 | Collado Vides, Pedro Julio, Moreno Hagelsieb, Gabriel, Pérez Rueda, Ernesto, Salgado Osorio, Heladia, Huerta Moreno, Araceli, Gutiérrez Ríos, Rosa María, Rosenblueth, David A., Christen, Andrés, Benítez Bellón, Esperanza, Medrano Soto, Luis Arturo, Gama Castro, Ma. del Socorro, Santos Zavaleta, Alberto, Bonavides Martínez, César Augusto, DíPeredo, Edgar, Sánchez Solano, Erika Fabiola, Millá, Dulce María. (2002). "Genomics of Gene Regulation: The view from Escherichia coli". Gene Regulation and Metabolism, Post-Genomic Computational Approaches. ():103-128. | |
| 2002 | Karp, PD, Riley, M, Saier, M, Paulsen, IT, Collado-Vides, J, Paley, SM, Pellegrini-Toole, A, Bonavides, C, Gama-Castro, S. (2002). "The EcoCyc database". Nucleic Acids Research. 30(1):56-58. [doi:10.1093/nar/30.1.56] | 11752253 |
| 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 |