Systems & Synthetic Biology
Center for Genomic Sciences
UNAM — Mexico

Peña-Miller Lab

Research Interests

A standard household disinfectant claims it can kill 99.99% of bacteria. We study the remaining 0.01%. In particular, our research focuses on 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 our lab can be grouped into four general areas: 1) We study how environments with complex spatio-temporal structure modulate antibiotic-resistance fitness landscapes. 2) We study the gene regulatory mechanisms that produce phenotypic heterogeneity in a population of genetically-identical cells. 3) We study the interaction between mobile genetic elements, their bacterial hosts, and the environment.
+52 (777) 313 4152

Centro de Ciencias Genómicas
Av. Universidad s/n.
Chamilpa, CP 62261.
Cuernavaca, Mexico.

Current funding:

Selected publications

  • Genetic dominance governs the evolution and spread of mobile genetic elements in bacteria

    PNAS (2020).

    J Rodríguez-Beltrán, V Sørum, M Toll-Riera, C Vega, R Peña-Miller and A San Millan

  • Quantifying plasmid dynamics using single-cell microfluidics and image bioinformatics

    Plasmid (2020).

    JCR Hernandez-Beltran, J Rodriguez-Beltran, A San Millan, R Peña-Miller* & A Fuentes-Hernandez*

  • Diffusion-driven enhancement of the antibiotic resistance selection window

    Journal of the Royal Society Interface, 16 (158), 20190363 (2019).

    A. Fuentes-Hernández, A. Hernández-Koutoucheva, A.F. Muñoz, R. Domínguez Palestino, R. Peña-Miller

  • Multicopy plasmids allow bacteria to escape from fitness trade-offs during evolutionary innovation

    Nature Ecology and Evolution (2018).

    J Rodriguez-Beltran, JCR Hernandez-Beltran, J DelaFuente, JA Escudero, A Fuentes-Hernandez, RC MacLean, R Peña-Miller & A San Millan

    Behind the paper (Nature Ecology & Evolution Community):
    What do pill-bugs and Escherichia coli have in common? »

    Agustín B. Ávila wrote about this paper:
    La diversidad es la mejor estrategia para sobrevivir »

  • Antibiotic Cycling and Antibiotic Mixing: which one best mitigates antibiotic resistance?

    Molecular Biology and Evolution, msw292 (2017).

    R. E. Beardmore, R. Pena-Miller, F. Gori and J. Iredell

    We wrote a blog for The Conversation:
    Why hospitals have got it wrong when it comes to resistance »

  • Positive selection and compensatory adaptation interact to stabilize non-transmissible plasmids

    Nature Communications, Vol. 5, No. 5208 (2014).

    A San Millan, R Peña-Miller, M Toll-Riera, Z Halbert, A McLean, B Cooper and C MacLean

    Highlighted in Nature Reviews Microbiology:
    How to keep your plasmids. »


Rafael Peña-Miller
Fernando Santos
JCR Hernández (Charly)
Carles Tardío Pi
Eric Isay Espinosa
Bruno Aguilar Luviano
Haydee de Luna
Andrea Fernández Duque
Jesús Vélez
Lab Alumni
  • Marian Domínguez (now PhD student, Georgia Tech)
  • Afra Salazar (now PhD student, Erasmus Mundus)
  • Alán Muñoz (now PhD student, University of Edinburgh)
  • Sandra Mayoral (now PhD student, UNAM)
  • Rogelio Rodríguez (now PhD student, Georgia Tech)
  • Raúl Domínguez (now Molecular Genomic Pharma)



    As part of a collaborative effort at UNAM, we participated in the design, manufacture and development of a decontamination protocol for an adjustable Venturi valve to be used in respirators of Mexican public hospitals.

    Ficha pública Reporte bioseguridad

    A 3D printable device for spatio-temporal quantification of fluorescently-tagged bacteria in spatially-explicit environments

    Fab Lab

    Galileo allegedly said, "Measure what is measurable, and make measurable what is not so". Following his advice, every once in a while, we turn our lab into a FabLab where we collectively design and build wet lab instrumentation using free and open-source software and open-source hardware.

    We've built incubators, laminar hoods, chemostats, syringe pumps, image acquisition systems and hacked pipetting robots and 3D printers to extrude cells.


    2o Taller de Probablidad y Biología

    2nd interdisciplinary meeting focusing on the application and development of probability models in biology.  

    More info

    Are you interested in using quantitative methodologies to study complex biological processes? This school consists of a series of courses, workshops and plenary talks to introduce quantitative tools used in Genomics, Synthetic Biology and Systems Biology.

    qBio18:Summer School in Quantitative Biology will be held at the Genomic Sciences Center of the UNAM in Cuernavaca, Morelos, from July 23 to August 3, 2018. Scholarships for lodging and food will be offered to all attendees.

    More info
    Systems Biology of Drug Resistance

    An international conference assembling a cross-disciplinary panel of internationally leading speakers presenting current research that uses a wide range of quantitative methodological approaches to understand the evolutionary processes by which living systems acquire resistance to chemotherapy.

    More info


We welcome students and postdoctoral applicants with a biomedical or a quantitative background, interested in developing interdisciplinary research projects somewhere in the interface between experimental microbiology, mathematical modelling and computational biology.

If you are interested in joining our lab as a postdoctoral fellow, graduate student, or undergraduate researcher, please send an email to rpm (at) with a CV and a brief description of your research interests.