Genómica Evolutiva

En el Programa de Genómica Evolutiva estamos interesados en estudiar los mecanismos de evolución de las bacterias desde los puntos de vista de la biología molecular, de la biología de sistemas, y de la genómica. Estamos especialmente interesados en bacterias que pueden establecer interacciones simbióticas y patogénicas con otros organismos. Nuestro Programa se compone de cuatro grupos de investigación dirigidos por el Dr. Santiago Castillo, el Dr. Julio Freyre, el Dr. Víctor González y el Dr. Miguel Ángel Cevallos. Una de las labores más importantes de nuestro Programa es la formación de recursos humanos especialmente de doctores, dentro del programa de Ciencias Biomédicas de la UNAM. Sin embargo, apoyamos a todos los estudiantes de licenciatura que deseen realizar su tesis bajo la dirección de alguno de nosotros.

Académicos del Grupo

NombrePuestoCategoríaCorreoTeléfono
Miguel Ángel Carlos Cevallos GaosInvestigadorInv. Tit. C T.C. Definitivomac@ccg.unam.mx(777) 3114663
Víctor Manuel González ZúñigaInvestigadorInv. Tit. B T.C. Definitivovgonzal@ccg.unam.mx(777) 3133881
Santiago Castillo RamírezInvestigadorInv. Tit. A T.C. Interinoiago@ccg.unam.mx(777) 3133881
Rosa Isela Santamaria GutiérrezTécnico AcadémicoTec. Acad. Tit. C T.C. Definitivorosa@ccg.unam.mx(777) 3133881
Virginia Patricia Bustos ArcosTécnico AcadémicoTec. Acad. Tit. C T.C. Definitivopaty@ccg.unam.mx(777) 3133881
María de los Angeles Pérez OsegueraTécnico AcadémicoTec. Acad. Tit. B T.C. Definitivoaperez@ccg.unam.mx(777) 3133881
Irma Martínez FloresTécnico AcadémicoTec. Acad. Tit. B T.C. Definitivoimartflo@ccg.unam.mx(777) 3291690
Ivana Daisy Blancas NavaTécnico por honorariosOtrobnio140371@upemor.edu.mx(777) 3133881
José Espíritu SalazarTécnico por honorariosUNAMspirit@ccg.unam.mx(777) 3291690
María Soledad Juárez RamírezTécnico por honorariosUNAMsjuarez@ccg.unam.mx(777) 3133881

Publicaciones del Grupo

AñoPublicaciónPMID
2018Graña-Miraglia, L., Arreguín-Pérez, C., López-Leal, G., Muñoz, A., Pérez-Oseguera, A., Miranda-Miranda, E., Cossío-Bayúgar, R. and Castillo-Ramirez, S. (2018). "Phylogenomics picks out the par excellence markers for species phylogeny in the genus Staphylococcus .". Peerj. 6(10):e5839-. [doi:10.7717/peerj.5839]30386709
2018Challagundla, Lavanya, Reyes, Jinnethe, Rafiqullah, Iftekhar, Sordelli, Daniel O., Echaniz-Aviles, Gabriela, Velazquez-Meza, Maria E., Castillo-Ramirez, S, Fittipaldi, Nahuel, Feldgarden, Michael, Chapman, Sinead B., Calderwood, Michael S., Carvajal, Lina P., Rincon, Sandra, Hanson, Blake, Planet, Paul J., Arias, Cesar A., Diaz, Lorena and Robinson, D. Ashley. (2018). "Phylogenomic Classification and the Evolution of Clonal Complex 5 Methicillin-Resistant Staphylococcus Aureus in the Western Hemisphere". Frontiers in Microbiology. 9():-. [doi:10.3389/fmicb.2018.01901]30186248
2018Frisch MB, Castillo-Ramirez, S, Petit RA 3rd, Farley MM, Ray SM, Albrecht VS, Limbago BM, Hernandez J, See I, Satola SW and Read TD. (2018). "Invasive Methicillin-Resistant Staphylococcus Aureus USA500 Strains from the U.S. Emerging Infections Program Constitute Three Geographically Distinct Lineages.". mSphere. 3(3):-. [doi:10.1128/mSphere.00571-17]29720528
2018Stefan, A., Van Cauwenberghe, J., Rosu, C.M., Stedel, C., Labrou, N.E., Flemetakis, E. and Efrose, R.C.. (2018). "Genetic diversity and structure of Rhizobium leguminosarum populations associated with clover plants are influenced by local environmental variables". Systematic And Applied Microbiology. 41(3):251-259. [doi:10.1016/j.syapm.2018.01.007]29452714
2018Mendoza-Hoffmann, F., Pérez-Oseguera, Á., Cevallos, M.Á., Zarco-Zavala, M., Ortega, R., Peña-Segura, C., Espinoza-Simón, E., Uribe-Carvajal, S. and García-Trejo, J.J.. (2018). "The Biological Role of the zeta Subunit as Unidirectional Inhibitor of the F1FO-ATPase of Paracoccus denitrificans". CELL REPORTS. 22(4):1067-1078. [doi:10.1016/j.celrep.2017.12.106]29386127
2018Julieta Solis-Gonzalez, Claudia, Dominguez-Malfavon, Lilianha, Vargas-Suarez, Martin, Gaytan, Itzel, Angel Cevallos, Miguel, Lozano, Luis, Javier Cruz-Gomez, M. and Loza-Tavera, Herminia. (2018). "Novel metabolic pathway for N-methylpyrrolidone degradation in Alicycliphilus sp. strain BQ1". Applied And Environmental Microbiology. 84(1):e02136-17-. [doi:10.1128/AEM.02136-17]29030443
2017Romero-Gutierrez, Teresa, Peguero-Sanchez, Esteban, Cevallos, Miguel A., Batista, Cesar V. F., Ortiz, Ernesto and Possani, Lourival D.. (2017). "A Deeper Examination of Thorellius Atrox Scorpion Venom Components with Omic Techonologies". Toxins. 9(12):399-. [doi:10.3390/toxins9120399]29231872
2017Olvera, C., Santamaría, R.I., Bustos, P., Vallejo, C., Montor, J.J., Wacher, C. and Munguia, A.L.. (2017). "Draft genome sequence of Leuconostoc citreum CW28 isolated from pozol, a pre-Hispanic fermented corn beverage". Genome Announcements. 5(48):e01283-17-. [doi:10.1128/genomeA.01283-17]
2017Graña-Miraglia L, Lozano LF, Velázquez C, Volkow-Fernández P, Pérez-Oseguera Á, Cevallos MA and Castillo-Ramirez, S. (2017). "Rapid gene turnover as a significant source of genetic variation in a recently seeded population of a healthcare-associated pathogen". Frontiers in Microbiology. 8(SEP):1817-1817. [doi:10.3389/fmicb.2017.01817]28979253
2017Pérez-Oseguera Á, Castro-Jaimes S, Salgado-Camargo AD, Silva-Sanchez J, Garza-González E, Castillo-Ramirez, S and Cevallos MÁ. (2017). "Complete genome sequence of a blaOXA-58-producing Acinetobacter Baumannii strain isolated from a Mexican hospital". Genome Announcements. 5(36):e00949-17-. [doi:10.1128/genomeA.00949-17]28883144
2017Santamaría RI, Bustos P, Pérez-Carrascal OM, Miranda-Sánchez F, Vinuesa P, Martínez-Flores I, Juárez S, Lozano L, Martínez-Romero E, Cevallos MÁ, Romero D, Dávila G, Ormeño-Orrillo E and González V. (2017). "Complete genome sequences of eight Rhizobium symbionts associated with common bean (Phaseolus vulgaris)". Genome Announcements. 5(30):e00645-17-. [doi:10.1128/genomeA.00645-17]28751391
2017Perez-Morales, Deyanira, Banda, Maria M., Elizabeth Chau, N. Y., Salgado, Heladia, Martinez-Flores, Irma, Antonio Ibarra, J., Ilyas, Bushra, Coombes, Brian K. and Bustamante, Victor H.. (2017). "The transcriptional regulator SsrB is involved in a molecular switch controlling virulence lifestyles of Salmonella". PLOS PATHOGENS. 13(7):e1006497-. [doi:10.1371/journal.ppat.1006497]28704543
2017Sigala, J.C., Suárez, B.P., Lara, A.R., Borgne, S.L., Bustos, P., Santamaría, R.I., González, V. and Martinez, A.. (2017). "Genomic and physiological characterization of a laboratory-isolated Acinetobacter Schindleri ACE strain that quickly and efficiently catabolizes acetate". MICROBIOLOGY-SGM. 163(7):1052-1064. [doi:10.1099/mic.0.000488]28671531
2017Osorio A, Camarena L, Cevallos MA and Poggio S. (2017). "A New Essential Cell Division Protein in Caulobacter Crescentus". Journal Of Bacteriology. 199(8):UNSP e00811-16-. [doi:10.1128/JB.00811-16]28167520
2017Bustos P, Santamaría RI, Pérez-Carrascal OM, Acosta JL, Lozano L, Juárez S, Martínez-Flores I, Martínez-Romero E, Cevallos MÁ, Romero D, Dávila G, Vinuesa P, Miranda F, Ormeño E and González V. (2017). "Complete genome sequences of three Rhizobium gallicum symbionts associated with common bean (Phaseolus vulgaris)". Genome Announcements. 5(11):e00030-17-. [doi:10.1128/genomeA.00030-17]28302777
2017Alatorre-Fernandez, Pamela, Mayoral-Teran, Claudia, Velazquez-Acosta, Consuelo, Franco-Rodriguez, Cecilia, Flores-Moreno, Karen, Angel Cevallos, Miguel, Lopez-Vidal, Yolanda and Volkow-Fernandez, Patricia. (2017). "A polyclonal outbreak of bloodstream infections by Enterococcus faecium in patients with hematologic malignancies". AMERICAN JOURNAL OF INFECTION CONTROL. 45(3):260-266. [doi:10.1016/j.ajic.2016.10.002]27852447
2017Vences-Guzman, M.A, Goetting-Minesky, M. Paula, Guan, Ziqiang, Castillo-Ramirez, S, America Cordoba-Castro, Luz, Lopez-Lara, I.M.,, Geiger, O., Sohlenkamp, C and Fenno, J. Christopher. (2017). "1,2-Diacylglycerol choline phosphotransferase catalyzes the final step in the unique Treponema denticola phosphatidylcholine biosynthesis pathway". Molecular Microbiology. 103(5):896-912. [doi:10.1111/mmi.13596]28009086
2017Saldaña-Ahuactzi Z., Cruz-Córdova A., Rodea G.E., Porta H., Navarro-Ocaña A., Eslava-Campos C., Cevallos M.A. and Xicohtencatl-Cortes J.. (2017). "Genome sequence of enterotoxigenic Escherichia coli strain FMU073332". Genome Announcements. 5(8):e01600-16-. [doi:10.1128/genomeA.01600-16]
2016Martínez-Flores I, Pérez-Morales D, Sánchez-Pérez M, Paredes CC, Collado-Vides J, Salgado H and Bustamante VH. (2016). "In Silico clustering of Salmonella global gene expression data reveals novel genes co-regulated with the SPI-1 virulence genes through HilD". SCIENTIFIC REPORTS. 6():37858-37858. [doi:10.1038/srep37858]27886269
2016Joseph, Sandeep J., Cox, Daniel, Wolff, Bernard, Morrison, Shatavia S., Kozak-Muiznieks, Natalia A., Frace, Michael, Didelot, Xavier, Castillo-Ramirez, S, Winchell, Jonas, Read, Timothy D. and Dean, Deborah. (2016). "Dynamics of genome change among Legionella species". SCIENTIFIC REPORTS. 6():33442-33442. [doi:10.1038/srep33442]27633769
2016Becker, Noemie S., Margos, Gabriele, Blum, Helmut, Krebs, Stefan, Graf, Alexander, Lane, Robert S., Castillo-Ramirez, S, Sing, Andreas and Fingerle, Volker. (2016). "Recurrent evolution of host and vector association in bacteria of the Borrelia burgdorferi sensu lato species complex". Bmc Genomics. 17(1):734-734. [doi:10.1186/s12864-016-3016-4]27632983
2016Perez Carrascal, Olga M., VanInsberghe, David, Juarez, Soledad, Polz, Martin F., Vinuesa, Pablo and Gonzalez, Victor. (2016). "Population genomics of the symbiotic plasmids of sympatric nitrogen-fixing Rhizobium species associated with Phaseolus vulgaris". Environmental Microbiology. 18(8):2660-2676. [doi:10.1111/1462-2920.13415]27312778
2016Garza-Ramos U, Silva-Sánchez J, Catalán-Nájera J, Barrios H, Rodríguez-Medina N, Garza-González E, Cevallos MA and Lozano L. (2016). "Draft genome sequence of a hypermucoviscous extended-spectrum-ß-lactamase-producing Klebsiella quasipneumoniae subsp. similipneumoniae clinical isolate". Genome Announcements. 4(4):e00475-16-. [doi:10.1128/genomeA.00475-16]27389261
2016Aanensen, David M., Feil, Edward J., Holden, Matthew T. G., Dordel, Janina, Yeats, Corin A., Fedosejev, Artemij, Goater, Richard, Castillo-Ramirez, S, Corander, Jukka, Colijn, Caroline, Chlebowicz, Monika A., Schouls, Leo, Heck, Max, Pluister, Gerlinde, Ruimy, Raymond, Kahlmeter, Gunnar, Ahman, Jenny, Matuschek, Erika, Friedrich, Alexander W., Parkhill, Julian, Bentley, Stephen D., Spratt, Brian G., Grundmann, Hajo, ESCMID Study Grp Mol Epidemiologic and European Staphylococcal Ref Lab Wo. (2016). "Whole-Genome Sequencing for Routine Pathogen Surveillance in Public Health: a Population Snapshot of Invasive Staphylococcus Aureus in Europe". Mbio. 7(3):e00444-16-. [doi:10.1128/mBio.00444-16]27150362
2016Bolanos, Luis M., Rosenblueth, Monica, Castillo-Ramirez, S, Figuier-Huttin, Gilles and Martinez-Romero, Esperanza. (2016). "Species-specific diversity of novel bacterial lineages and differential abundance of predicted pathways for toxic compound degradation in scorpion gut microbiota". Environmental Microbiology. 18(5):1364-1378. [doi:10.1111/1462-2920.12939]26058415
2016Gonzalez-Villoria, Ana M., Tamayo-Legorreta, Elsa, Garza-Ramos, Ulises, Barrios, Humberto, Sanchez-Perez, Alejandro, Rodriguez-Medina, Nadia, Uribe-Avina, Naville, Cevallos, Miguel A., Silva-Sanchez, Jesus and CRAB Study Grp. (2016). "A Multicenter Study in Mexico Finds Acinetobacter Baumannii Clinical Isolates Belonging to Clonal Complexes 636(B) (113(B)) and 92(B) Harboring OXA-72, OXA-239, and OXA-469". ANTIMICROBIAL AGENTS AND CHEMOTHERAPY. 60(4):2587-2588. [doi:10.1128/AAC.02042-15]26833167
2016Castillo-Ramirez, S, Fingerle, V., Jungnick, S., Straubinger, R. K., Krebs, S., Blum, H., Meinel, D. M., Hofmann, H., Guertler, P., Sing, A. and Margos, G.. (2016). "Trans-Atlantic exchanges have shaped the population structure of the Lyme disease agent Borrelia burgdorferi sensu stricto". SCIENTIFIC REPORTS. 6():22794-22794. [doi:10.1038/srep22794]26955886
2016Tamayo-Legorreta, Elsa, Turrubiartes-Martinez, Edgar, Garza-Ramos, Ulises, Nino-Moreno, Perla, Barrios, Humberto, Sanchez-Perez, Alejandro, Reyna-Flores, Fernando, Tovar-Oviedo, Juana, Magana-Aquino, Martin, Angel Cevallos, Miguel and Silva-Sanchez, Jesus. (2016). "Outbreak Caused by bla(OXA-72)-Producing Acinetobacter Baumannii ST417 Detected in Clinical and Environmental Isolates". MICROBIAL DRUG RESISTANCE. 22(2):129-133. [doi:10.1089/mdr.2015.0157]26954369
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. and 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
2016Castro-Jaimes S., Salgado-Camargo A.D., Gra�a-Miraglia L., Lozano L., Bocanegra-Ibarias P., Volkow-Fern�ndez P., Silva-Sanchez J., Castillo-Ramirez, S and Cevallos M.A.. (2016). "Complete genome sequence of a multidrug-resistant Acinetobacter Baumannii isolate obtained from a Mexican hospital (sequence type 422)". Genome Announcements. 4(3):e00583-16-. [doi:10.1128/genomeA.00583-16]
2016López-Leal G, Cevallos MA and Castillo-Ramirez, S. (2016). "Evolution of a sigma factor: An All-In-One of Gene Duplication, Horizontal Gene Transfer, Purifying Selection, and Promoter Differentiation". Frontiers in Microbiology. 7(APR):581-581. [doi:10.3389/fmicb.2016.00581]27199915
2016Mucito-Varela E., Castillo-Rojas G., Cevallos M.A., Lozano L., Merino E., L�pez-Leal G. and L�pez-Vidal Y.. (2016). "Complete genome sequence of Helicobacter Pylori strain 7C isolated from a Mexican patient with chronic gastritis". Genome Announcements. 4(1):e01503-15-. [doi:10.1128/genomeA.01503-15]
2016Graña-Miraglia L., Lozano L., Castro-Jaimes S., Cevallos M.A., Volkow P. and Castillo-Ramirez, S. (2016). "First genome sequence of a mexican multidrug-resistant Acinetobacter Baumannii isolate". Genome Announcements. 4(2):e00156-16-. [doi:10.1128/genomeA.00156-16]
2015Joseph, S.J., Marti, H., Didelot, X., Castillo-Ramirez, S, Read, T.D. and Dean, D.. (2015). "Chlamydiaceae Genomics Reveals Interspecies Admixture and the Recent Evolution of Chlamydia Abortus Infecting Lower Mammalian Species and Humans". Genome Biology And Evolution. 7(11):3070-3084. [doi:10.1093/gbe/evv201]26507799
2015Ormeño-Orrillo, E., Servín-Garcidueñas, L.E., Rogel, M.A., González, V., Peralta, H., Mora, J., Martínez-Romero, J. and Martínez-Romero, E.. (2015). "Taxonomy of Rhizobia and agrobacteria from the Rhizobiaceae family in light of genomics". Systematic And Applied Microbiology. 38(4):287-291. [doi:10.1016/j.syapm.2014.12.002]25660942
2015Lozano, Luis, Santamaria Gutiérrez, Rosa Isela and Bustos, P. (2015). "Genomic Tools for the Study of Azospirillum and Other Plant Growth-Promoting Rhizobacteria". Handbook for Azospirillum: Technical Issues and Protocols. ():83-97. [doi:10.1007/978-3-319-06542-7_5]
2015Ezewudo, Matthew N., Joseph, Sandeep J., Castillo-Ramirez, S, Dean, Deborah, del Rio, Carlos, Didelot, Xavier, Dillon, Jo-Anne, Selden, Richard F., Shafer, William M., Turingan, Rosemary S., Unemo, Magnus and Read, Timothy D.. (2015). "Population structure of Neisseria Gonorrhoeae based on whole genome data and its relationship with antibiotic resistance". Peerj. 3(3):e806-. [doi:10.7717/peerj.806]25780762
2015Rivera-Urbalejo, America, Perez-Oseguera, Angeles, Carreon-Rodriguez, Ofelia E. and Cevallos, Miguel A.. (2015). "Mutations in an antisense RNA, involved in the replication control of a repABC plasmid, that disrupt plasmid incompatibility and mediate plasmid speciation". Plasmid. 78(SI):48-58. [doi:10.1016/j.plasmid.2015.01.004]25644116
2015Padilla, J.C.A., Bustos, P., Castro-Escarpulli, G., Sánchez-Varela, A., Palma-Martinez, I., Arzate-Barbosa, P., García-Pérez, C.A., López-López, M.d.J., González, V. and Guo, X.. (2015). "Draft genome sequence of Aeromonas caviae strain 429865 INP, isolated from a Mexican patient". Genome Announcements. 3(5):e01240-15-. [doi:10.1128/genomeA.01240-15]26494682
2014Lopez-Leal, Gamaliel, Luisa Tabche, Maria, Castillo-Ramirez, S, Mendoza-Vargas, Alfredo, Ramirez-Romero, Miguel A. and Davila, Guillermo. (2014). "RNA-Seq analysis of the multipartite genome of Rhizobium etli CE3 shows different replicon contributions under heat and saline shock". Bmc Genomics. 15(1):770-770. [doi:10.1186/1471-2164-15-770]25201548
2014Alberto Batista-Garcia, Ramon, Sanchez-Reyes, Ayixon, Millan-Pacheco, Cesar, Manuel Gonzalez-Zuniga, Victor, Juarez, Soledad, Luis Folch-Mallol, Jorge and Pastor, Nina. (2014). "A novel TctA citrate transporter from an activated sludge metagenome: Structural and mechanistic predictions for the TTT family". Proteins-Structure Function And Bioinformatics. 82(9):1756-1764. [doi:10.1002/prot.24529]24493659
2014Rogel, M.A., Bustos, P., Santamaría, R.I., González, V., Romero, D., Cevallos, M.T., Lozano, L., Castro-Mondragón, J., Martínez-Romero, J., Ormeño-Orrillo, E. and Martínez-Romero, E.. (2014). "Genomic basis of symbiovar mimosae in Rhizobium etli". Bmc Genomics. 15(1):575-575. [doi:10.1186/1471-2164-15-575]25005495
2014Martinez, L.C., Martínez Flores, Irma, Salgado Osorio, Heladia, Fernández-Mora, M., Medina Rivera, Alejandra Eugenia, Puente, J.L., Collado Vides, Pedro Julio and 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
2014Santamaria Gutiérrez, Rosa Isela, Bustos Arcos, Virginia Patricia, Lozano Aguirre Beltrán, Luis Fernando, Rodríguez Sánchez, César, Fernandez Vázquez, José Luis, Juárez Ramírez, María Soledad, Kameyama, L., Guarneros, G., Dávila Ramos, José Guillermo and González Zúñiga, Víctor Manuel. (2014). "Narrow-Host-Range Bacteriophages That Infect Rhizobium etli Associate with Distinct Genomic Types". Applied And Environmental Microbiology. 80(2):446-454. [doi:10.1128/AEM.02256-13]24185856
2014Castillo-Ramirez, S and Feil, E.J.. (2014). "Towards a Synthesis of Population Genomics and Epidemiology: Next-Generation Sequencing of Bacterial Pathogens". Molecular Medical Microbiology: Second Edition. 1-3():337-345. [doi:10.1016/B978-0-12-397169-2.00018-4]
2013Wiesner, Magdalena, Fernandez-Mora, Marcos, Cevallos, Miguel A., Zavala-Alvarado, Crispin, Zaidi, Mussaret B., Calva, Edmundo and Silva, Claudia. (2013). "Conjugative transfer of an IncA/C plasmid-borne bla(CMY-2) gene through genetic re-arrangements with an IncX1 plasmid". Bmc Microbiology. 13():264-264. [doi:10.1186/1471-2180-13-264]24262067
2013Pérez Oseguera, María de los Angeles and Cevallos Gaos, Miguel Ángel Carlos. (2013). "RepA and RepB exert plasmid incompatibility repressing the transcription of the repABC operon". Plasmid. 70(3):362-376. [doi:10.1016/j.plasmid.2013.08.001]24016735
2013Gerardo Trevino-Quintanilla, Luis, Augusto Freyre-Gonzalez, Julio and Martinez-Flores, Irma. (2013). "Anti-Sigma Factors in E-coli: Common Regulatory Mechanisms Controlling Sigma Factors Availability". Current Genomics. 14(6):378-387. [doi:10.2174/1389202911314060007]24396271
2013Tsai, I.J., Zarowiecki, M., Holroyd, N., Garciarrubio, A., Sánchez-Flores, A., Brooks, K.L., Tracey, A., Bobes, R.J., Fragoso, G., Sciutto, E., Aslett, M., Beasley, H., Bennett, H.M., Cai, J., Camicia, F., Clark, R., Cucher, M., De Silva, N., Day, T.A., Deplazes, P., Estrada, K., Fernández, C., Holland, P.W., Hou, J., Hu, S., Huckvale, T., Hung, S.S., Kamenetzky, L., Keane, J.A., Kiss, F., Koziol, U., Lambert, O., Liu, K., Luo, X., Luo, Y., Macchiaroli, N., Nichol, S., Paps, J., Parkinson, J., Pouchkina-Stantcheva, N., Riddiford, N., Rosenzvit, M., Salinas, G., Wasmuth, J.D., Zamanian, M., Zheng, Y., Garciarrubio, A., Bobes, R.J., Fragoso, G., Sánchez-Flores, A., Estrada, K., Cevallos Gaos, Miguel Ángel Carlos, Morett, E., González Zúñiga, Víctor Manuel, Portillo, T., Ochoa-Leyva, A., José, M.V., Sciutto, E., Landa, A., Jiménez, L., Valdés, V., Carrero, J.C., Larralde, C., Morales-Montor, J., Limón-Lason, J., Soberón, X., Laclette, J.P., Cai, X., Soberón, X., Olson, P.D., Laclette, J.P., Brehm, K. and Berriman, M.. (2013). "The genomes of four tapeworm species reveal adaptations to parasitism". Nature. 496(7443):57-63. [doi:10.1038/nature12031]23485966
2013Pérez Segura, Gabriela, Pérez Oseguera, María de los Angeles and Cevallos Gaos, Miguel Ángel Carlos. (2013). "The repAC replication system of the Rhizobium leguminosarum pRL7 plasmid is functional: Implications regarding the origin and evolution of repABC plasmids". Plasmid. 69(1):49-57. [doi:10.1016/j.plasmid.2012.08.003]22975386
2013Salgado 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. and 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
2013Castillo-Ramirez, S and Feil, E.J.. (2013). "Population genetics". The Prokaryotes: Prokaryotic Biology And Symbiotic Associations. ():255-266. [doi:10.1007/978-3-642-30194-0_83]
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2012Althabegoiti, M.J., Lozano Aguirre Beltrán, Luis Fernando, Torres-Tejerizo, G., Ormeño Orrillo, Ernesto Aldo, Rogel Hernández, Marco Antonio, González Zúñiga, Víctor Manuel and Martínez Romero, María Esperanza. (2012). "Genome sequence of Rhizobium Grahamii CCGE502, a broad-host-range symbiont with low nodulation competitiveness in Phaseolus vulgaris". Journal Of Bacteriology. 194(23):6651-6652. [doi:10.1128/JB.01785-12]23144400
2012Wisniewski-Dye, Florence, Lozano, Luis, Acosta-Cruz, Erika, Borland, Stephanie, Drogue, Benoit, Prigent-Combaret, Claire, Rouy, Zoe, Barbe, Valerie, Mendoza Herrera, Alberto, Gonzalez, Victor and Mavingui, Patrick. (2012). "Genome sequence of Azospirillum brasilense CBG497 and comparative analyses of Azospirillum core and accessory genomes provide insight into niche adaptation". Genes. 3(4):576-602. [doi:10.3390/genes3040576]24705077
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2011Pappas, M. and Cevallos Gaos, Miguel Ángel Carlos. (2011). "Plasmids of the Rhizobiaceae and their role in interbacterial and transkingdom Interactions". Biocommunication in Soil Microorganisms. Series: Soil Biology. 23():474-.
2011Gama 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. and 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
2011Salgado Osorio, Heladia, Martínez Flores, Irma, López Fuentes, Alejandra Cristina, Garcia Sotelo, Jair Santiago, Porrón Sotelo, Liliana, Muñíz Rascado, Luis José and Collado Vides, Pedro Julio. (2011). "Extracting regulatory networks of/Escherichia coli/from RegulonDB". Bacterial Molecular Networks: Methods and Protocols. ():-.
2010Demir, E., Paley, S., Fukuda, K., Lemer, C., Vastrik, I., Wu, G., D'Eustachio, P., Schaefer, C., Luciano, J., Schacherer, F., Martinez-Flores, I., Hu, Z., Jimenez-Jacinto, V., Joshi-Tope, G., Kandasamy, K., Lopez-Fuentes, A.C., Mi, H., Pichler, E., Rodchenkov, I., Splendiani, A., Tkachev, S., Zucker, J., Gopinath, G., Rajasimha, H., Ramakrishnan, R., Shah, I., Syed, M., Anwar, N., Babur, O., Blinov, M., Brauner, E., Corwin, D., Donaldson, S., Gibbons, F., Goldberg, R., Hornbeck, P., Luna, A., Murray-Rust, P., Neumann, E., Reubenacker, O., Samwald, M., Van Iersel, M., Wimalaratne, S., Allen, K., Braun, B., Whirl-Carrillo, M., Cheung, K.H., Dahlquist, K., Finney, A., Gillespie, M., Glass, E., Gong, L., Haw, R., Honig, M., Hubaut, O., Kane, D., Krupa, S., Kutmon, M., Leonard, J., Marks, D., Merberg, D., Petri, V., Pico, A., Ravenscroft, D., Ren, L., Shah, N., Sunshine, M., Tang, R., Whaley, R., Letovksy, S., Buetow, K.H., Rzhetsky, A., Schachter, V., Sobral, B.S., Dogrusoz, U., McWeeney, S., Aladjem, M., Birney, E., Collado-Vides, J., Goto, S., Hucka, M., Novère, N.L., Maltsev, N., Pandey, A., Thomas, P., Wingender, E., Karp, P.D., Sander, C. and Bader, G.D.. (2010). "Erratum: The BioPAX community standard for pathway data sharing (Nat. Biotechnol. (2010) 28 (935-942)". Nature Biotechnology. 28(12):1308-1308. [doi:10.1038/nbt1210-1308c]
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2010Demir, E., Cary, M.P., Paley, S., Fukuda, K., Lemer, C., Vastrik, I., Wu, G.N., D Eustachio, P., Schaefer, C., Luciano, J., Schacherer, F., Martínez Flores, Irma, Hu, Z.J., Jiménez-Jacinto, V., Joshi-Tope, G., Kandasamy, K., López-Fuentes, A.C., Mi, H.Y., Pichler, E., Rodchenkov, I., Splendiani, A., Tkachev, S., Zucker, J., Gopinath, G., Rajasimha, H., Ramakrishnan, R., Shah, I., Syed, M., Anwar, N., Babur, O., Blinov, M., Brauner, E., Corwin, D., Donaldson, S., Gibbons, F., Goldberg, R., Hornbeck, P., Luna, A., Murray-Rust, P., Neumann, E., Reubenacker, O., Samwald, M., van Iersel, M., Wimalaratne, S., Allen, K., Braun, B., Whirl-Carrillo, M., Cheung, K.H., Dahlquist, K., Finney, A., Gillespie, M., Glass, E., Gong, L., Haw, R., Honig, M., Hubaut, O., Kane, D., Krupa, S., Kutmon, M., Leonard, J., Marks, D., Merberg, D., Petri, V., Pico, A., Ravenscroft, D., Ren L.Y., Shah, N., Sunshine, M., Tang, R., Whaley, R., Letovksy, S., Buetow, K.H., Rzhetsky, A., Schachter, V., Sobral, B., Dogrusoz, U., McWeeney, S., Aladjem, M., Birney, E., Collado Vides, Pedro Julio, Goto, S., Hucka, M., Le Novere, N., Maltsev, N., Pandey, A., Thomas, P., Wingender, E., Karp, P.D., Sander, C. and Bader, G.D.. (2010). "The BioPAX community standard for pathway data sharing". Nature Biotechnology. 28(9):935-942. [doi:10.1038/nbt.1666]20829833
2010Cervantes-Rivera, Ramon, Romero-Lopez, Cristina, Berzal-Herranz, Alfredo and Cevallos, Miguel A.. (2010). "Analysis of the Mechanism of Action of the Antisense RNA That Controls the Replication of the repABC Plasmid p42d". Journal Of Bacteriology. 192(13):3268-3278. [doi:10.1128/JB.00118-10]20435728
2010Gonzalez, Vctor, Acosta, Jose L., Santamaria, Rosa I., Bustos, Patricia, Fernandez, Jose L., Hernandez Gonzalez, Ismael L., Diaz, Rafael, Flores, Margarita, Palacios, Rafael, Mora, Jaime and Davila, Guillermo. (2010). "Conserved symbiotic plasmid DNA sequences in the multireplicon pangenomic structure of Rhizobium etli". Applied And Environmental Microbiology. 76(5):1604-1614. [doi:10.1128/AEM.02039-09]20048063
2010Martínez Flores, Irma, Jiménez-Jacinto, V., López Fuentes, Alejandra Cristina and 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 and Collado Vides, Pedro Julio. (2010). "Extracting regulatory networks of Escherichia coli from RegulonDB". Bacterial Molecular Networks: Methods and Protocols. ():-.
2009Castillo-Ramirez, S, Vazquez-Castellanos, Jorge F., Gonzalez, Victor and Cevallos, Miguel A.. (2009). "Horizontal gene transfer and diverse functional constrains within a common replication-partitioning system in Alphaproteobacteria: The repABC operon". Bmc Genomics. 10():536-536. [doi:10.1186/1471-2164-10-536]19919719
2009Garza-Ramos, U., Davila, G., Gonzalez, V., Alpuche-Aranda, C., Lopez-Collada, V. R., Alcantar-Curiel, D., Newton, O. and Silva-Sanchez, J.. (2009). "The blaSHV-5gene is encoded in a compound transposon duplicated in tandem in Enterobacter Cloacae". Clinical Microbiology And Infection. 15(9):878-880. [doi:10.1111/j.1469-0691.2009.02790.x]19519856
2009Morett, Enrique, Garciarubio, A., Bobes, R. J., Carrero, J. C., Cevallos, M. A., Fragoso, G., Gaytan, P., Gonzalez, V. M., Jose, M. V., Jimenez, L., Landa, A., Larralde, C., Morales-Montor, J., Sciutto, E., Soberon, X., de la Torre, P., Valdes, V., Yanez, J. and Laclette, J. P.. (2009). "The Genome Project of Taenia solium". Infection Genetics And Evolution. 9(3):368-369.
2009Martinez-Salazar, Jaime M., Sandoval-Calderon, Mario, Guo, Xianwu, Castillo-Ramirez, S, Reyes, Alma, Loza, Maria G., Rivera, Javier, Alvarado-Affantranger, Xochitl, Sanchez, Federico, Gonzalez, Victor, Davila, Guillermo and Ramirez-Romero, Miguel A.. (2009). "The Rhizobium etli RpoH1 and RpoH2 sigma factors are involved in different stress responses". MICROBIOLOGY-SGM. 155(2):386-397. [doi:10.1099/mic.0.021428-0]19202087
2009Pappas, K.M. and Cevallos Gaos, Miguel Ángel Carlos. (2009). "Plasmids of the Rhizobiaceae and their role in interbacterial and transkingdom interactions". Intracellular and Intercellular Biocommunication of Soil-Bacteria Guenther Witzany. ():-.
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 and 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
2008Garciarrubio, A., Bobes, R. J., Carrero, J. C., Cevallos, M. A., Fragoso, G., Gonzalez, V. M., Jose, M. V., Landa, A., Larralde, C., Mendoza, L., Morales-Montor, J., Morett, E., Sciutto, E., Soberon, X. and Laclette, J. P.. (2008). "The Genome Project of Taenia solium". International Journal Of Infectious Diseases. 12():395-395. [doi:10.1016/j.ijid.2008.05.1042]
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2008Cevallos, Miguel A., Cervantes-Rivera, Ramon and Gutierrez-Rios, Rosa Maria. (2008). "The repABC plasmid family". Plasmid. 60(1):19-37. [doi:10.1016/j.plasmid.2008.03.001]18433868
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2008Boyer, Mickael, Haurat, Jacqueline, Samain, Sylvie, Segurens, Beatrice, Gavory, Frederick, Gonzalez, Victor, Mavingui, Patrick, Rohr, Rene, Bally, Rene and Wisniewski-Dye, Florence. (2008). "Bacteriophage prevalence in the genus Azospirillum and analysis of the first genome sequence of an Azospirillum brasilense integrative phage". Applied And Environmental Microbiology. 74(3):861-874. [doi:10.1128/AEM.02099-07]18065619
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2008Gama 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 and 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
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2007Guo, Xianwu, Flores, Margarita, Morales, Lucia, Garcia, Delfino, Bustos, Patricia, Gonzalez, Victor, Palacios, Rafael and Davila, Guillermo. (2007). "DNA diversification in two Sinorhizobium species". Journal Of Bacteriology. 189(17):6474-6476. [doi:10.1128/JB.00384-07]17601787
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2007Guo, Xianwu, Castillo-Ramirez, S, Gonzalez, Victor, Bustos, Patricia, Fernandez-Vazquez, Jose Luis, Santamaria, Rosa Isela, Arellano, Jesus, Cevallos, Miguel A. and Davila, Guillermo. (2007). "Rapid evolutionary change of common bean (Phaseolus vulgaris L) plastome, and the genomic diversification of legume chloroplasts". Bmc Genomics. 8():228-228. [doi:10.1186/1471-2164-8-228]17623083
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2007Rodríguez Penagos, Carlos, Salgado Osorio, Heladia, Martínez Flores, Irma and Collado Vides, Pedro Julio. (2007). "NLP-Based Curation of Bacterial Regulatory Networks". CICLing. ():575-586.
2006Alvarez, R.G., de Mendoza, A.R., Escobedo, D.E., Felix, G.C., Sanchez, I.R., González Zúñiga, Víctor Manuel, Dávila Ramos, José Guillermo, Cao, Q., de Jong, P., Fu, Y.X. and Saldana, H.A.B.. (2006). "Growth hormone locus expands and diverges after the separation of New and Old World Monkeys". Gene. 380(1):38-45. [doi:10.1016/j.gene.2006.05.017]16872758
2006Peñaloza Spinola, Mónica Ivonne, Peralta Gil, Martín, Gama Castro, MA. DEL SOCORRO, Contreras Moreira, Bruno, Santos Zavaleta, Alberto, Martínez Flores, Irma and 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.
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