| 2024 | Martínez-Pacheco, M., Díaz-Barba, K., Pérez-Molina, R., Marmolejo-Valencia, A., Collazo-Saldaña, P., Escobar-Rodríguez, M., Sánchez-Pérez, M., Meneses-Acosta, A., Martínez-Rizo, A.B., Sánchez-Pacheco, A.U., Furlan-Magaril, M., Merchant-Larios, H., Cortez, D.. (2024). "Gene expression dynamics during temperature-dependent sex determination in a sea turtle.". DEV BIOL. 514():99-108. [doi:10.1016/j.ydbio.2024.06.018] | 38914191 |
| 2024 | Hernandez-Beltran, J.C.R., Rodríguez-Beltrán, J., Aguilar-Luviano, O.B., Velez-Santiago, J., Mondragón-Palomino, O., MacLean, R.C., Fuentes-Hernández, A., San Millán, A., Peña-Miller, R.. (2024). "Plasmid-mediated phenotypic noise leads to transient antibiotic resistance in bacteria.". Nature Communications. 15(1):-. [doi:10.1038/s41467-024-45045-0] | 38521779 |
| 2023 | Tenorio, M., Serwatowska, J., Fernandez-Valverde, S.L., Oktaba, K., Cortez, D.. (2023). "Genome-wide analysis of RNA-chromatin interactions in lizards as a mean for functional lncRNA identification.". Bmc Genomics. 24(1):-. [doi:10.1186/s12864-023-09545-5] | 37550606 |
| 2023 | Davalos-Dehullu, E., Baty, S.M., Fisher, R.N., Scott, P.A., Dolby, G.A., Munguia-Vega, A., Cortez, D.. (2023). "Chromosome-Level Genome Assembly of the Blacktail Brush Lizard, Urosaurus nigricaudus, Reveals Dosage Compensation in an Endemic Lizard.". Genome Biology And Evolution. 15(12):-. [doi:10.1093/gbe/evad210] | 38056449 |
| 2023 | Cortez, D.. (2023). "Structural shifts in primate Y.". Nature Ecology & Evolution. 7(7):971-972. [doi:10.1038/s41559-023-01984-3] | 37268855 |
| 2023 | Ortega, S., Ramírez, J.P., Rodríguez, C., Pérez-Morales, D., Drummond, H.. (2023). "Extrapair offspring of the blue-footed booby show no sign of higher fitness in the first 10 years of life". ANIMAL BEHAVIOUR. 200():105-114. [doi:10.1016/j.anbehav.2023.03.015] | |
| 2023 | Beardmore, Robert, Hewlett, Mark, Pena-Miller, Rafael, Gudelj, Ivana, Meyer, Justin R.. (2023). "Canonical Host-Pathogen Trade-Offs Subverted by Mutations with Dual Benefits.". AMERICAN NATURALIST. 201(5):-. [doi:10.1086/723413] | 37130231 |
| 2023 | Escorcia-Rodríguez, J.M., Gaytan-Nuñez, E., Hernandez-Benitez, E.M., Zorro-Aranda, A., Tello-Palencia, M.A., Freyre-González, J.A.. (2023). "Improving gene regulatory network inference and assessment: The importance of using network structure.". Frontiers in Genetics. 14():-. [doi:10.3389/fgene.2023.1143382] | 36926589 |
| 2023 | Valle, A.A.D., Toribio-Celestino, L., Quirant, A., Pi, C.T., DelaFuente, J., Canton, R., Rocha, E.P.C., Ubeda, C., Peña-Miller, R., Millan, A.S.. (2023). "Antimicrobial resistance level and conjugation permissiveness shape plasmid distribution in clinical enterobacteria.". PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA. 120(51):-. [doi:10.1073/pnas.2314135120] | 38096417 |
| 2022 | Freyre-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 |
| 2022 | Trujillo, 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 |
| 2022 | Suárez-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:https://doi.org/10.1101/2022.01.28.478147] | |
| 2022 | Zorro-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 |
| 2022 | Reyes-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 |
| 2022 | Cisneros-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 |
| 2022 | Suárez-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 |
| 2022 | Escorcia-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 |
| 2022 | Taboada-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 |
| 2022 | Tardío 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] | |
| 2022 | Hernandez-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 |
| 2021 | Hernandez-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 |
| 2021 | León-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 |
| 2021 | Suárez-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:https://doi.org/10.22201/ib.20078706e.2021.92.3795] | |
| 2021 | Alvear, 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 |
| 2021 | Vences-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 |
| 2021 | Escorcia-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 |
| 2021 | Camacho-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] | |
| 2021 | Merchant-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 |
| 2021 | Hernández-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 |
| 2021 | Suárez-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] | |
| 2021 | Orta, 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 |
| 2021 | Alonso-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 |
| 2020 | Martínez-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 |
| 2020 | Cornejo-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 |
| 2020 | Rodríguez-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 |
| 2020 | Cornejo-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 |
| 2020 | Escorcia-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 |
| 2019 | Acosta, 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 |
| 2019 | Gabriel 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] | |
| 2019 | Acosta, 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 |
| 2019 | Campos, 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 |
| 2018 | Rodriguez-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 |
| 2017 | Marin, 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 |
| 2017 | Freyre-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 |
| 2017 | Link 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 |
| 2017 | Beardmore, 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 |
| 2017 | Vicens, 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 |
| 2016 | Degli 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 |
| 2015 | Fuentes-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 |
| 2014 | San 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 |
| 2014 | Arnoldini, 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 |
| 2014 | Peña-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 |
