César Augusto Bonavides Martínez

Computational Genomics Laboratory Technician

Laboratory Technician

Academic history

Links

Scopus

Telephone: (777) 3132063
Email: cbona18@ccg.unam.mx

Publications

YearPublicationPMID
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
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
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
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]
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
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
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
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
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
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
2009Aparicio, 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.
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
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
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
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
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.
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
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