Systems Biology

Group Staff

Rafael Peña MillerResearcherAssociate 3291686
Diego Cortez QuezadaResearcherAssociate 3291686
Deyanira Pérez MoralesSupport 3291686
Julio Augusto Freyre GonzálezResearcherAssociate 3291777 Ext. 38483

Group Publications

2022Hernandez-Beltran, J.C.R., Miró Pina, V., Siri-Jégousse, A., Palau, S., Peña-Miller, R., González Casanova, A.. (2022). "Segregational instability of multicopy plasmids: A population genetics approach.". ECOLOGY AND EVOLUTION. 12(12):-. [doi:10.1002/ece3.9469]36479025
2022Taboada-Castro, H., Gil, J., Gómez-Caudillo, L., Escorcia-Rodríguez, J.M., Freyre-González, J.A., Encarnación-Guevara, S.. (2022). "Rhizobium etli CFN42 proteomes showed isoenzymes in free-living and symbiosis with a different transcriptional regulation inferred from a transcriptional regulatory network.". Frontiers in Microbiology. 13():-. [doi:10.3389/fmicb.2022.947678]36312930
2022Cisneros-Mayoral, S., Graña-Miraglia, L., Pérez-Morales, D., Peña-Miller, R., Fuentes-Hernández, A.. (2022). "Evolutionary History and Strength of Selection Determine the Rate of Antibiotic Resistance Adaptation.". MOLECULAR BIOLOGY AND EVOLUTION. 39(9):-. [doi:10.1093/molbev/msac185]36062982
2022Escorcia-Rodríguez, J.M., Esposito, M., Freyre-González, J.A., Moreno-Hagelsieb, G.. (2022). "Non-synonymous to synonymous substitutions suggest that orthologs tend to keep their functions, while paralogs are a source of functional novelty.". Peerj. 10():-. [doi:10.7717/peerj.13843]36065404
2022Suárez-Varón, G., Mendoza-Cruz, E., Acosta, A., Cruz, M.V.S., Cortez, D., Hernández-Gallegos, O.. (2022). "Genetic determination and JARID2 over-expression in a thermal incubation experiment in Casque-Headed Lizard.". Plos One. 17(7):-. [doi:10.1371/journal.pone.0263804]35797377
2022Freyre-Gonzalez, Julio A., Escorcia-Rodriguez, Juan M., Gutierrez-Mondragon, Luis F., Marti-Vertiz, Jeronimo, Torres-Franco, Camila N., Zorro-Aranda, Andrea. (2022). "System Principles Governing the Organization, Architecture, Dynamics, and Evolution of Gene Regulatory Networks.". Frontiers in bioengineering and biotechnology. 10():-. [doi:10.3389/fbioe.2022.888732]35646858
2022Reyes-González D, De Luna-Valenciano H, Utrilla J, Sieber M, Peña-Miller R, Fuentes-Hernández A. (2022). "Dynamic proteome allocation regulates the profile of interaction of auxotrophic bacterial consortia.". Royal Society open science. 9(5):212008-212008. [doi:10.1098/rsos.212008]35592760
2022Zorro-Aranda, A., Escorcia-Rodríguez, J.M., González-Kise, J.K., Freyre-González, J.A.. (2022). "Curation, inference, and assessment of a globally reconstructed gene regulatory network for Streptomyces coelicolor.". SCIENTIFIC REPORTS. 12(1):2840-2840. [doi:10.1038/s41598-022-06658-x]35181703
2022Suárez-Varón, G., Mendoza-Cruz, E., Acosta, A., Villagrán-Santa Cruz, M., Cortez D, Hernández-Gallegos, O.. (2022). "A study of thermally-induced sex reversal in casque-headed lizards". bioRxiv. ():-. [doi:]
2022Trujillo, N., Pacheco, M.M., Soldatini, C., Ancona, S., Young, R.C., Barajas, Y.V.A., Orta, A.H., Rodriguez, C., Szekely, T., Drummond, H., Urrutia, A.O., Cortez, D.. (2022). "Lack of age-related mosaic loss of W chromosome in long-lived birds.". BIOLOGY LETTERS. 18(2):-. [doi:10.1098/rsbl.2021.0553]35193370
2022Tardío Pi, C., Reyez-González, D., Fernandez-Duque, A., Fuentes-Hernández, A., Santos-Escobar, F., Peña Miller, Rafael. (2022). "A 3D Printable Device for Macroscopic Quantification of Fluorescent Bacteria in Space and Time". Journal Of Open Source Software. 6():1-. [doi:10.5334/joh.44]
2021Escorcia-Rodríguez, J.M., Tauch, A., Freyre-González, J.A.. (2021). "Corynebacterium glutamicum Regulation beyond Transcription: Organizing Principles and Reconstruction of an Extended Regulatory Network Incorporating Regulations Mediated by Small RNA and Protein-Protein Interactions.". Microorganisms. 9(7):-. [doi:10.3390/microorganisms9071395]34203422
2021Hernandez-Beltran, J.C.R., Rodríguez-Beltrán, J., Millán, A.S., Peña-Miller, R., Fuentes-Hernández, A.. (2021). "Quantifying plasmid dynamics using single-cell microfluidics and image bioinformatics.". Plasmid. 113():-. [doi:10.1016/j.plasmid.2020.102517]32535165
2021Suárez-Varón, G, Cortez D, Villagrán-Santa Cruz, M, Rojas-Hernández, U, Hernández-Gallegos, O. (2021). "Variación del estadio embrionario de Basiliscus vittatus (Squamata: Corytophanidae) en la oviposición". REVISTA MEXICANA DE BIODIVERSIDAD. 92():923795-. [doi:]
2021Alvear, V.M.H., Mateos, M., Cortez, D., Tamborindeguy, C., Martinez-Romero, E.. (2021). "Differential gene expression in a tripartite interaction: Drosophila , spiroplasma and parasitic wasps.". Peerj. 9():-. [doi:10.7717/peerj.11020]33717711
2021Vences-Guzmán, M.Á., Peña-Miller, R., Hidalgo-Aguilar, N.A., Vences-Guzmán, M.L., Guan, Z., Sohlenkamp, C.. (2021). "Identification of the Flavobacterium johnsoniae cysteate-fatty acyl transferase required for capnine synthesis and for efficient gliding motility.". Environmental Microbiology. 23(5):2448-2460. [doi:10.1111/1462-2920.15445]33626217
2021León-Buitimea, A., Morones-Ramírez, J.R., Yang, J.H., Peña-Miller, R.. (2021). "Editorial: Facing the Upcoming of Multidrug-Resistant and Extensively Drug-Resistant Bacteria: Novel Antimicrobial Therapies (NATs).". Frontiers in bioengineering and biotechnology. 9():-. [doi:10.3389/fbioe.2021.636278]33732690
2021Camacho-Hernández, D.A., Nieto-Caballero, V.E., León-Burguete, J.E., Freyre-González, J.A.. (2021). "Partition Quantitative Assessment (PQA): A Quantitative Methodology to Assess the Embedded Noise in Clustered Omics and Systems Biology Data". APPLIED SCIENCES-BASEL. 11(13):-. [doi:10.3390/app11135999]
2021Merchant-Larios, H., Diáz-Hernández, V., Cortez, D.. (2021). "Molecular and Cellular Mechanisms Underlying Temperature-Dependent Sex Determination in Turtles.". SEXUAL DEVELOPMENT. 15(1-3):38-46. [doi:10.1159/000515296]34167126
2021Hernández-Beltrán, J.C.R., San Millán, A., Fuentes-Hernández, A., Peña-Miller, R.. (2021). "Mathematical Models of Plasmid Population Dynamics.". Frontiers in Microbiology. 12():-. [doi:10.3389/fmicb.2021.606396]34803935
2021Suárez-Varón, G., Cortez, D., Cruz, M.V.S., Rojas-Hernández, U., Hernández-Gallegos, O.. (2021). "Variation of the embryonic stage of Basiliscus vittatus (Squamata: Corytophanidae) at oviposition". REVISTA MEXICANA DE BIODIVERSIDAD. 92():-. [doi:10.22201/IB.20078706E.2021.92.3795]
2021Orta, A.H., Bush, S.J., Gutiérrez-Mariscal, M., Castro-Obregón, S., Jaimes-Hoy, L., Grande, R., Vázquez, G., Gorostieta-Salas, E., Martínez-Pacheco, M., Díaz-Barba, K., Cornejo-Páramo, P., Sanchez-Flores, A., Székely, T., Urrutia, A.O., Cortez, D.. (2021). "Rats exhibit age-related mosaic loss of chromosome Y.". Communications Biology. 4(1):-. [doi:10.1038/s42003-021-02936-y]34934158
2021Alonso-del Valle, A., León-Sampedro, R., Rodríguez-Beltrán, J., DelaFuente, J., Hernández-García, M., Ruiz-Garbajosa, P., Cantón, R., Peña-Miller, R., San Millán, A.. (2021). "Variability of plasmid fitness effects contributes to plasmid persistence in bacterial communities.". Nature Communications. 12(1):-. [doi:10.1038/s41467-021-22849-y]33976161
2020Martínez-Pacheco, M., Tenorio, M., Almonte, L., Fajardo, V., Godínez, A., Fernández, D., Cornejo-Páramo, P., Díaz-Barba, K., Halbert, J., Liechti, A., Székely, T., Urrutia, A.O., Cortez, D.. (2020). "Expression Evolution of Ancestral XY Gametologs across All Major Groups of Placental Mammals.". Genome Biology And Evolution. 12(11):2015-2028. [doi:10.1093/gbe/evaa173]32790864
2020Cornejo-Páramo, P., Lira-Noriega, A., Ramírez-Suástegui, C., Méndez-De-La-Cruz, F.R., Székely, T., Urrutia, A.O., Cortez, D.. (2020). "Sex determination systems in reptiles are related to ambient temperature but not to the level of climatic fluctuation.". Bmc Evolutionary Biology. 20(1):-. [doi:10.1186/s12862-020-01671-y]32807071
2020Rodríguez-Beltrán, J., Sørum, V., Toll-Riera, M., de la Vega, C., Peña-Miller, R., Millán, Á.S.. (2020). "Genetic dominance governs the evolution and spread of mobile genetic elements in bacteria.". PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA. 117(27):15755-15762. [doi:10.1073/pnas.2001240117]32571917
2020Cornejo-Páramo, P., Dissanayake, D.S.B., Lira-Noriega, A., Martínez-Pacheco, M.L., Acosta, A., Ramírez-Suástegui, C., Méndez-de-la-Cruz, F.R., Székely, T., Urrutia, A.O., Georges, A., Cortez, D.. (2020). "Viviparous Reptile Regarded to Have Temperature-Dependent Sex Determination Has Old XY Chromosomes.". Genome Biology And Evolution. 12(6):924-930. [doi:10.1093/gbe/evaa104]32433751
2020Escorcia-Rodríguez, J.M., Tauch, A., Freyre-González, J.A.. (2020). "Abasy Atlas v2.2: The most comprehensive and up-to-date inventory of meta-curated, historical, bacterial regulatory networks, their completeness and system-level characterization.". Computational and Structural Biotechnology Journal. 18():1228-1237. [doi:10.1016/j.csbj.2020.05.015]32542109
2019Acosta, A., Suárez-Varón, G., Rodríguez-Miranda, L.A., Lira-Noriega, A., Aguilar-Gómez, D., Gutiérrez-Mariscal, M., Hernández-Gallegos, O., Méndez-de-la-Cruz, F., Cortez, D.. (2019). "Corytophanids Replaced the Pleurodont XY System with a New Pair of XY Chromosomes.". Genome Biology And Evolution. 11(9):2666-2677. [doi:10.1093/gbe/evz196]31557287
2019Gabriel Suárez-Varón, Orlando Suárez-Rodríguez, Gisela Granados-González, Maricela Villagrán-Santa Cruz, Kevin M. Gribbins, Diego Cortez-Quezada, Oswaldo Hernández-Gallegos. (2019). "Relative clutch mass of Basiliscus vittatus Wiegmann, 1828 (Squamata, Corytophanidae): female morphological constraints". Herpetozoa. 32(3):211-219. [doi:10.3897/herpetozoa.32.e35910]
2019Acosta, A., Martínez-Pacheco, M.L., Díaz-Barba, K., Porras, N., Gutiérrez-Mariscal, M., Cortez, D.. (2019). "Deciphering Ancestral Sex Chromosome Turnovers Based on Analysis of Male Mutation Bias.". Genome Biology And Evolution. 11(11):3054-3067. [doi:10.1093/gbe/evz221]31605487
2019Campos, A.I., Freyre-González, J.A.. (2019). "Evolutionary constraints on the complexity of genetic regulatory networks allow predictions of the total number of genetic interactions.". SCIENTIFIC REPORTS. 9(1):-. [doi:10.1038/s41598-019-39866-z]30842463
2018Rodriguez-Beltran, J., Hernandez-Beltran, J.C.R., Delafuente, J., Escudero, J.A., Fuentes-Hernandez, A., MacLean, R.C., Peña-Miller, R., San Millan, A.. (2018). "Multicopy plasmids allow bacteria to escape from fitness trade-offs during evolutionary innovation". Nature Ecology & Evolution. 2(5):873-881. [doi:10.1038/s41559-018-0529-z]29632354
2017Marin, R., Cortez, D., Lamanna, F., Pradeepa, M.M., Leushkin, E., Julien, P., Liechti, A., Halbert, J., Brüning, T., Mössinger, K., Trefzer, T., Conrad, C., Kerver, H.N., Wade, J., Tschopp, P., Kaessmann, H.. (2017). "Convergent origination of a Drosophila-like dosage compensation mechanism in a reptile lineage". GENOME RESEARCH. 27(12):1974-1987. [doi:10.1101/gr.223727.117]29133310
2017Freyre-González, J.A., Tauch, A.. (2017). "Functional architecture and global properties of the Corynebacterium glutamicum regulatory network: Novel insights from a dataset with a high genomic coverage". JOURNAL OF BIOTECHNOLOGY. 257():199-210. [doi:10.1016/j.jbiotec.2016.10.025]27829123
2017Link V, Aguilar-Gómez D, Ramírez-Suástegui C, Hurst LD, Cortez D. (2017). "Male mutation bias is the main force shaping chromosomal substitution rates in monotreme mammals". Genome Biology And Evolution. 9(9):2198-2210. [doi:10.1093/gbe/evx155]28922870
2017Beardmore, Robert Eric, Pena-Miller, Rafael, Gori, Fabio, Iredell, Jonathan. (2017). "Antibiotic cycling and antibiotic mixing: Which one best mitigates antibiotic resistance?". MOLECULAR BIOLOGY AND EVOLUTION. 34(4):802-817. [doi:10.1093/molbev/msw292]28096304
2017Vicens, Alberto, Andrade-Lopez, Karla, Cortez, Diego, Maria Gutierrez, Rosa, Trevino, Claudia L.. (2017). "Premammalian origin of the sperm-specific Slo3 channel". FEBS OPEN BIO. 7(3):382-390. [doi:10.1002/2211-5463.12186]28286733
2016Degli Esposti M, Cortez D, Lozano L, Rasmussen S, Nielsen HB, Martinez Romero E. (2016). "Alpha proteobacterial ancestry of the [Fe-Fe]-hydrogenases in anaerobic eukaryotes". Biology Direct. 11(1):34-34. [doi:10.1186/s13062-016-0136-3]27473689
2015Fuentes-Hernandez, Ayari, Plucain, Jessica, Gori, Fabio, Pena-Miller, Rafael, Reding, Carlos, Jansen, Gunther, Schulenburg, Hinrich, Gudelj, Ivana, Beardmore, Robert. (2015). "Using a Sequential Regimen to Eliminate Bacteria at Sublethal Antibiotic Dosages". Plos Biology. 13(4):-. [doi:10.1371/journal.pbio.1002104]25853342
2014San Millan, A., Pena-Miller, R., Toll-Riera, M., Halbert, Z. V., McLean, A. R., Cooper, B. S., MacLean, R. C.. (2014). "Positive selection and compensatory adaptation interact to stabilize non-transmissible plasmids". Nature Communications. 5():5208-5208. [doi:10.1038/ncomms6208]25302567
2014Arnoldini, Markus, Vizcarra, Ima Avalos, Pena-Miller, Rafael, Stocker, Nicolas, Diard, Mederic, Vogel, Viola, Beardmore, Robert E., Hardt, Wolf-Dietrich, Ackermann, Martin. (2014). "Bistable expression of virulence genes in Salmonella leads to the formation of an antibiotic-tolerant subpopulation". Plos Biology. 12(8):-. [doi:10.1371/journal.pbio.1001928]25136970
2014Peña-Miller, R., Fuentes-Hernandez, A., Reding, C., Gudelj, I., Beardmore, R.. (2014). "Testing the optimality properties of a dual antibiotic treatment in a two-locus, two-allele model". JOURNAL OF THE ROYAL SOCIETY INTERFACE. 11(96):20131035-20131035. [doi:10.1098/rsif.2013.1035]24812050