Ma. del Socorro Gama Castro

Computational Genomics Laboratory Technician

Laboratory Technician

Academic history

Links

Scopus

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

Publications

YearPublicationPMID
2019Santos-Zavaleta, A, Salgado, H, Gama-Castro, S, Sánchez-Pérez, M, Gómez-Romero, L, Ledezma-Tejeida, D, García-Sotelo, J, Alquicira-Hernández, K, Muñiz-Rascado, L, Peña-Loredo, P, Ishida-Gutiérrez, C, Velázquez-Ramírez, D, Del Moral-Chávez, V, Bonavides-Martínez, C, Méndez-Cruz, C, Galagan, J, Collado-Vides, J. (2019). "RegulonDB v 10.5: tackling challenges to unify classic and high throughput knowledge of gene regulation in E. coli K-12". Nucleic Acids Research. 47(D1):212-220. [doi:10.1093/nar/gky1077]30395280
2019Tierrafría, 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
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():bax070-. [doi:10.1093/database/bax070]29220462
2017Keseler, I, Mackie, A, Santos-Zavaleta, A, Billington, R, Bonavides-Martínez, C, Caspi, R, Fulcher, C, Gama-Castro, S, Kothari, A, Krummenacker, M, Latendresse, M, Muñiz-Rascado, L, Ong, Q, Paley, S, Peralta-Gil, M, Subhraveti, P, Velázquez-Ramírez, D, Weaver, D, Collado-Vides, J, Paulsen, I, Karp, P. (2017). "The EcoCyc database: reflecting new knowledge about Escherichia coli K-12.". Nucleic Acids Research. 45(D1):543-550. [doi:10.1093/nar/gkw1003]27899573
2016Moretto, M, Sonego, P, Dierckxsens, N, Brilli, M, Bianco, L, Ledezma-Tejeida, D, Gama-Castro, S, Galardini, M, Romualdi, C, Laukens, K, Collado-Vides, J, Meysman, P, Engelen, K. (2016). "COLOMBOS v3.0: Leveraging gene expression compendia for cross-species analyses". Nucleic Acids Research. 44(D1):620-623. [doi:10.1093/nar/gkv1251]26586805
2016Gama-Castro, S, Salgado, H, Santos-Zavaleta, A, Ledezma-Tejeida, D, Muñiz-Rascado, L, García-Sotelo, J, Alquicira-Hernández, K, Martínez-Flores, I, Pannier, L, Castro-Mondragón, J, Medina-Rivera, A, Solano-Lira, H, Bonavides-Martínez, C, Pérez-Rueda, E, Alquicira-Hernández, S, Porrón-Sotelo, L, López-Fuentes, A, Hernández-Koutoucheva, A, Del Moral-Chavez, V, Rinaldi, F, Collado-Vides, J. (2016). "RegulonDB version 9.0: High-level integration of gene regulation, coexpression, motif clustering and beyond". Nucleic Acids Research. 44(D1):133-143. [doi:10.1093/nar/gkv1156]26527724
2016Wang, Q, Abdul, S, Almeida, L, Ananiadou, S, Balderas-Martinez, Y, Batista-Navarro, R, Campos, D, Chilton, L, Chou, H, Contreras, G, Cooper, L, Dai, H, Ferrell, B, Fluck, J, Gama-Castro, S, George, N, Gkoutos, G, Irin, A, Jensen, L, Jimenez, S, Jue, T, Keseler, I, Madan, S, Matos, S, McQuilton, P, Milacic, M, Mort, M, Natarajan, J, Pafilis, E, Pereira, E, Rao, S, Rinaldi, F, Rothfels, K, Salgado, D, Silva, R, Singh, O, Stefancsik, R, Su, C, Subramani, S, Tadepally, H, Tsaprouni, L, Vasilevsky, N, Wang, X, Chatr-Aryamontri, A, Laulederkind, S, Matis-Mitchell, S, McEntyre, J, Orchard, S, Pundir, S, Rodriguez-Esteban, R, Van Auken, K, Lu, Z, Schaeffer, M, Wu, C, Hirschman, L, Arighi, C. (2016). "Overview of the interactive task in BioCreative V". DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION. 2016():baw119-. [doi:10.1093/database/baw119]27589961
2014Gama Castro, M, Rinaldi, F, López Fuentes, A, Balderas MartÍnez, Y, Clematide, S, Ellendorff, T, Santos Zavaleta, A, Marques-Madeira, H, Collado Vides, P. (2014). "Assisted curation of regulatory interactions and growth conditions of OxyR in E. Colik-12". DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION. 2014():bau049-. [doi:10.1093/database/bau049]24903516
2014Meysman, P, 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
2013Salgado Osorio, H, Peralta Gil, M, Gama Castro, M, Santos Zavaleta, A, Muñíz Rascado, L, Garcia Sotelo, J, Weiss, V, Solano Lira, H, Martínez Flores, I, Medina Rivera, A, Salgado Osorio, G, Alquicira Hernández, S, Alquicira Hernández, K, López Fuentes, A, Porrón Sotelo, L, Huerta Moreno, A, Bonavides Martínez, C, Balderas MartÍnez, Y, Pannier, L, Olvera, M, Labastida, A, Jiménez-Jacinto, V, Vega-Alvarado, L, del Moral Chávez, V, Hernández Álvarez, A, Morett, E, Collado Vides, P. (2013). "RegulonDB v8.0: Omics data sets, evolutionary conservation, regulatory phrases, cross-validated gold standards and more". Nucleic Acids Research. 41(D1):203-213. [doi:10.1093/nar/gks1201]23203884
2013Keseler, I, Mackie, A, Peralta Gil, M, Santos Zavaleta, A, Gama Castro, M, Bonavides Martínez, C, Fulcher, C, Huerta Moreno, A, Kothari, A, Krummenacker, M, Latendresse, M, Muñíz Rascado, L, Ong, Q, Paley, S, Schroder, I, Shearer, A, Subhraveti, P, Travers, M, Weerasinghe, D, Weiss, V, Collado Vides, P, Gunsalus, R, Paulsen, I, Karp, P. (2013). "EcoCyc: Fusing model organism databases with systems biology". Nucleic Acids Research. 41(D1):605-612. [doi:10.1093/nar/gks1027]23143106
2011Santos Zavaleta, A, Gama Castro, M, Pérez Rueda, E. (2011). "A comparative genome analysis of the RpoS sigmulon shows a high diversity of responses and origins". MICROBIOLOGY-UK. 157(5):1393-1401. [doi:10.1099/mic.0.042937-0]21310789
2011Keseler, I, Collado Vides, P, Santos Zavaleta, A, Peralta Gil, M, Gama Castro, M, Muñíz Rascado, L, Bonavides Martínez, C, Paley, S, Krummenacker, M, Altman, T, Spaulding, A, Spaulding, A, Pacheco, J, Latendresse, M, Fulcher, C, Sarker, M, Shearer, A, Mackie, A, Paulsen, I, Gunsalus, R, Karp, P. (2011). "EcoCyc: A comprehensive database of Escherichia coli biology". Nucleic Acids Research. 39(SUPPL. 1):583-590. [doi:10.1093/nar/gkq1143]21097882
2011Gama Castro, M, Salgado Osorio, H, Peralta Gil, M, Santos Zavaleta, A, Muñíz Rascado, L, Solano Lira, H, Jimenez-Jacinto, V, Weiss, V, Garcia Sotelo, J, López Fuentes, A, Porrón Sotelo, L, Alquicira Hernández, S, Medina Rivera, A, Martínez Flores, I, Alquicira Hernández, K, Martínez Adame, R, Bonavides Martínez, C, Miranda-Ríos, J, Huerta Moreno, A, Mendoza-Vargas, A, Collado Torres, L, Taboada, B, Vega-Alvarado, L, Olvera, M, Olvera, L, Grande, R, Morett, E, Collado Vides, P. (2011). "RegulonDB version 7.0: Transcriptional regulation of Escherichia coli K-12 integrated within genetic sensory response units (Gensor Units)". Nucleic Acids Research. 39(SUPPL. 1):98-105. [doi:10.1093/nar/gkq1110]21051347
2009Collado-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
2008Gama 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
2007Karp, P, Keseler, I, Shearer, A, Latendresse, M, Krummenacker, M, Paley, S, Paulsen, I, Collado Vides, P, Gama Castro, M, Peralta Gil, M, Santos Zavaleta, A, Peñaloza Spinola, M, Bonavides Martínez, C, Ingraham, J. (2007). "Multidimensional annotation of the Escherichia coli K-12 genome". Nucleic Acids Research. 35(22):7577-7590. [doi:10.1093/nar/gkm740]17940092
2006Salgado 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
2006Salgado 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
2006Santos-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.
2005Keseler, I, Collado Vides, P, Gama Castro, M, Ingraham, J, Paley, S, Paulsen, I, Peralta Gil, M, Karp, P. (2005). "EcoCyc: A comprehensive database resource for Escherichia coli". Nucleic Acids Research. 33(DATABASE ISS.):334-337. [doi:10.1093/nar/gki108]15608210
2004Salgado Osorio, H, Gama Castro, M, Martínez Antonio, A, Díaz Peredo, E, Sánchez Solano, E, Peralta Gil, M, García Alonso, D, Jiménez Jacinto, V, Santos Zavaleta, A, Bonavides Martínez, C, Collado Vides, P. (2004). "RegulonDB (version 4.0): Transcriptional regulation, operon organization and growth conditions in Escherichia coli K-12". Nucleic Acids Research. 32(DATABASE ISS.):303-306. [doi:10.1093/nar/gkh140]14681419
2002Collado Vides, P, Moreno Hagelsieb, G, Pérez Rueda, E, Salgado Osorio, H, Huerta Moreno, A, Gutiérrez Ríos, R, Rosenblueth, D, Christen, A, Benítez Bellón, E, Medrano Soto, L, Gama Castro, M, Santos Zavaleta, A, Bonavides Martínez, C, DíPeredo, E, Sánchez Solano, E, Millá, D. (2002). "Genomics of Gene Regulation: The view from Escherichia coli". Gene Regulation and Metabolism, Post-Genomic Computational Approaches. ():103-128.
2002Karp, P, Riley, M, Saier, M, Paulsen, I, Collado-Vides, J, Paley, S, Pellegrini-Toole, A, Bonavides, C, Gama-Castro, S. (2002). "The EcoCyc database". Nucleic Acids Research. 30(1):56-58. [doi:10.1093/nar/30.1.56]11752253
2001Salgado, H, Santos-Zavaleta, A, Gama-Castro, S, Millen-Zarate, D, Diaz-Peredo, E, Sanchez-Solano, F, Pérez-Rueda, E, Bonavides-Martinez, C, Collado-Vides, J. (2001). "RegulonDB (version 3.2): Transcriptional regulation and operon organization in Escherichia coli K-12". Nucleic Acids Research. 29(1):72-74. [doi:10.1093/nar/29.1.72]11125053
2000Salgado, 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
2003Martínez Antonio, A, Salgado Osorio, H, Gama Castro, M, Gutiérrez Ríos, R, Jiménez Jacinto, V, Collado Vides, P. (2003). "Environmental Conditions and Transcriptional Regulation in Escherichia coli: A Physiological Integrative Approach". BIOTECHNOLOGY AND BIOENGINEERING. 84(7):743-749. [doi:10.1002/bit.10846]14708114
2006Peñaloza 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.
2017Rinaldi F, Lithgow O, Gama-Castro S, Solano H, Lopez A, Muñiz Rascado LJ, Ishida-Gutiérrez C, Méndez-Cruz CF, Collado-Vides J. (2017). "Strategies towards digital and semi-automated curation in RegulonDB". DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION. 2017(1):bax012-. [doi:10.1093/database/bax012]28365731
2018Santos-Zavaleta, A, Sanchez-Perez, M, Salgado, H, Velazquez-Ramirez, D, Gama-Castro, S, Tierrafria, V, Busby, S, Aquino, P, Fang, X, Palsson, B, Galagan, J, Collado-Vides, J. (2018). "A unified resource for transcriptional regulation in Escherichia coli K-12 incorporating high-throughput-generated binding data into RegulonDB version 10.0". BMC BIOLOGY. 16(1):91-91. [doi:10.1186/s12915-018-0555-y]30115066
2019Lithgow-Serrano, O, Gama-Castro, S, Ishida-Gutiérrez, C, Mejía-Almonte, C, Tierrafría, V, Martínez-Luna, S, Santos-Zavaleta, A, Velázquez-Ramírez, D, Collado-Vides, J. (2019). "Similarity corpus on microbial transcriptional regulation.". JOURNAL OF BIOMEDICAL SEMANTICS. 10(1):8-. [doi:10.1186/s13326-019-0200-x]31118102