Rafael Peña Miller

Systems Biology Researcher

Associate Professor

Academic history

Rafael Peña Miller was born in Mexico City where he obtained a degree in Mathematics from the Faculty of Sciences of the UNAM. He completed his doctoral studies in the Mathematics Department of Imperial College London funded by a CONACYT scholarship. One of the publications that emanated from her doctoral research was chosen as the winner of the Lee Segel Prize, a biannual prize awarded by the Society for Mathematical Biology to the best article published in the area of mathematical biology. Subsequently, he made postdoctoral stays at the University of Exeter and the University of Oxford, where he participated in various projects in the interface between mathematical modeling and experimental microbiology. He has been invited to do research stays in Switzerland, Spain, USA and Germany.

He is currently an Assistant Professor at the Systems Biology Program of the Center for Genomic Sciences, UNAM, studying the genetic and metabolic mechanisms that enable bacterial communities to implement collective strategies to survive – and thrive – in hostile and rapidly-changing environments. Specific projects in the Peña-Miller Lab can be grouped into the following general areas: 1) using mathematical modeling and experimental evolution to study how environments with complex spatio-temporal structure modulate antibiotic-resistance fitness landscapes. 2) using single-cell microfluidics and image analysis to study gene regulatory mechanisms that produce phenotypic heterogeneity in a population of genetically identical cells. 3) modeling the interaction between mobile genetic elements, their bacterial hosts, and the environment.



Selected publications

Multicopy plasmids allow bacteria to escape from fitness trade-offs during evolutionary innovation
J Rodriguez-Beltran, JCR Hernandez-Beltran, J DelaFuente, JAEscudero, A Fuentes-Hernandez, RC MacLean, R Peña-Miller and Alvaro San Millan
Nature Ecology and Evolution, Vol 2, 873–881 (2018).

Antibiotic cycling and antibiotic mixing: which one best mitigates antibiotic resistance?
R. Beardmore, R. Peña-Miller, F. Gori and J. Iridell.
Molecular Biology and Evolution, msw292 (2017).

Using a sequential regimen to eliminate bacteria at sub-lethal antibiotic dosages
A. Fuentes-Hernandez, J. Plucain, F. Gori, R. Peña-Miller, C. Reding, G. Jansen, H. Schulenburg, I. Gudelj and R. Beardmore
PLoS Biology, Vol. 12, No. 8 (2015).

Positive selection and compensatory adaptation interact to stabilize non-transmissible plasmids
A. San Millan, R. Peña-Miller, M. Toll-Riera, Z. Halbert, A. McLean, B. Cooper and C. MacLean
Nature Communications, Vol. 5, No. 5208 (2014).

Bistable expression of virulence genes in Salmonella leads to the formation of an antibiotic-tolerant subpopulation
M. Arnoldini, I. Avalos Vizcarra, R. Peña-Miller, N. Stocker, M. Diard, V. Vogel, R. Beardmore, W.-D. Hardt and M. Ackermann
PLoS Biology, Vol 12, No. 8 (2014).

When the most potent combination of antibiotics selects for the greatest bacterial load: the smile frown transition.
R. Peña-Miller, Lähnemann, Jansen, Fuentes-Hernandez, Rosenthiel, Schulenburg and Beardmore.
PLoS Biology, Vol. 11, No.4 (2013).

Selecting against antibiotic-resistant pathogens: optimal treatments in the presence of commensal bacteria *
R. Peña-Miller, D. Lähnemann, H. Schulenburg, M. Ackermann and R. Beardmore
Bulletin of Mathematical Biology, Vol 74, No. 4 pp. 908-943 (2011). (*Winner of the Lee Segel Prize)

Telephone: (777) 3291686
Email: rpm@ccg.unam.mx


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
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
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
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
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
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
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
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
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