Systems Biology Program
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.

We use data-driven mathematical models to understand how bacteria evolve. We run these models through computer simulations, and then use what we learn to design microbiology experiments.We value diversity in both scientific approaches and disciplines. We work collaboratively, blending skills in mathematics, computer science, and microbiology to get a well-rounded understanding of bacterial survival in fluctuating environments.

Specific projects in our lab can be grouped into the following 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.

rpm@ccg.unam.mx
penamiller
+52 (777) 313 4152

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

Current funding:

Selected publications

  • Antibiotic heteroresistance generated by multi-copy plasmids

    bioRxiv (2022).

    JCR Hernandez-Beltran, J Rodriguez-Beltran, B Aguilar-Luviano, J Velez-Santiago, O Mondragon-Palomino, RC MacLean, A Fuentes-Hernandez, A San Millan and R Peña-Miller

  • Evolutionary history and strength of selection determine the rate of antibiotic resistance adaptation

    Molecular Biology and Evolution (2022).

    S Cisneros-Mayoral, L Graña-Miraglia, D Pérez-Morales, R Peña-Miller, A Fuentes-Hernáandez

  • Dynamic proteome allocation regulates the profile of interaction of auxotrophic bacterial consortia

    Royal Society Open Science, 9:5 (2022).

    D Reyes-González, H De Luna-Valenciano, J Utrilla, M Sieber, R Peña-Miller & A Fuentes-Hernandez

  • Variability of plasmid fitness effects contributes to plasmid persistence in bacterial communities

    Nature Communications (2021).

    A Alonso-del Valle, R León-Sampedro, J Rodríguez-Beltrán, J DelaFuente, M Hernández-García, P Ruiz-Garbajosa, R Cantón, R Peña-Miller & A San Millan

  • 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. »

People

Rafael Peña-Miller (PI)
Bruno Aguilar Luviano (PhD in Biochemistry)
María Isabel Malagón (Biology, UNAM)
Sandra Vázquez (Mathematics, UNAM)
Atziri Montiel Robles (Biology, UNAM)
Majo Pérez Montes (Bioengineering, UAEH)
Val Vergara (Bioengeering, UAEH)
Alison Jimenez (Biology, UNAM)
Lorena Martinez (Bioengineering, Upemor)
Past members
(last known coordinates)
  • Carles Tardío Pi (Postdoc, IIMAS-UNAM)
  • Fernando Santos (Research Associate, U Guanajuato)
  • JCR (Charly) Hernández-Beltrán (Postdoc, Max Planck Institute)
  • Eric Isay Espinosa
  • Hadee de Luna Valenciano (MSc student, CCG-UNAM)
  • Jesús Vélez Santiago
  • Andrea Fernández Duque (Scientific illustrator)
  • Yelitza Mendoza Sotelo
  • Marian Domínguez (PhD student, Georgia Tech)
  • Afra Salazar (PhD student, UNIL Lausanne)
  • Alán Muñoz (PhD student, University of Edinburgh)
  • Sandra Mayoral (PhD student, UNAM)
  • Rogelio Rodríguez (PhD student, Georgia Tech)
  • Raúl Domínguez (Molecular Genomic Pharma)

DIY

  •  
    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.


  •  
    BAFFLE

    A 3D printable device for spatio-temporal quantification of fluorescently-tagged bacteria in agar plates.




    GitHub Assembly instructions Metapaper

Events

  •  
    Red Mexicana de Matemáticas & Biología

    Inaugural event of the Mexican Network for Biology and Mathematics (RedMexBioMate), focused on fostering interdisciplinary collaboration and research at the intersection of biology and mathematics. The network aims to build an inclusive community that promotes scientific innovation and diversity.  



    More info Download poster
  •  
    2o Taller de Probablidad y Biología

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



    More info
  •  
    qBio18.mx

    This event gathered students from diverse backgrounds and institutions across Mexico and Latin America. The agenda featured courses, workshops, and talks focused on the integration of mathematical tools in the fields of Genomics, Synthetic Biology, and Systems Biology.

    qBio18:Summer School in Quantitative Biology was held at the Genomic Sciences Center of the UNAM in Cuernavaca, Morelos, from July 23 to August 3, 2018.


    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

Contact



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.

We are committed to creating a lab environment that is diverse, inclusive, and welcoming to all. We strongly believe that the amalgamation of diverse perspectives contributes to scientific excellence and innovation. We encourage individuals from all ethnic backgrounds, genders, ages, abilities, and orientations to apply.

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

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