PI: James J. Collins

PhD Student

Bachelor of Science in Bioengineering – Biotechnology, University of California San Diego, 2018

Miguel is a Biological Engineering Ph.D. student in Prof. James J. Collins’ lab at MIT. Miguel’s research focuses on engineering synthetic probiotics for the treatment of gut dysbiosis-induced diseases and prevention of gut infection. He is also a National Science Foundation Graduate Research Fellow, an Alfred P. Sloan Scholar, and a Gates Millennium Scholar. Miguel received a Bachelor of Science in Bioengineering, Summa Cum Laude, from the from the much-warmer University of California San Diego. As a first-generation college- and graduate-student, Miguel is also passionate about engaging with and mentoring younger students from underrepresented groups in order to improve representation in STEM. To this end, he has participated in various outreach events such as serving as a career panelist at the John D. O’Bryant School of Science and Mathematics (a Boston public school) and judging / recruiting at the National ABRCMS conference. He is also actively involved with diversity and inclusion initiatives in his department via his role as Diversity co-Chair on the Biological Engineering Graduate Student Board. Miguel aspires to become a professor, where he hopes to make meaningful societal contributions through research and mentor future generations of scientists.


* Equal contribution

  • Jacqueline Valeri*, Katherine M. Collins*, Pradeep Ramesh*, Miguel A. Alcantar, Bianca A. Lepe, Timothy K. Lu, Diogo M. Camacho. “Sequence-to-function deep learning frameworks for engineered riboregulators”. In review
  • Michael M. Kaminski, Miguel A. Alcantar, Isadora Lape, Robert Greensmith, Allison C. Huske, Jacqueline A.
    Valeri, Francisco M. Marty, Verena Klämbt, Jamil Azzi, Enver Akalin, Leonardo V. Riella, and James J. Collins. “A CRISPR-based assay for the detection of opportunistic infections post-transplantation and for the monitoring of transplant rejection”. Nature Biomedical Engineering (2020).
  • Jason H. Yang, Sarah N. Wright, Meagan Hamblin, Douglas McCloskey, Miguel A. Alcantar, Lars Schrubbers, Allison J. Lopatkin, Sangeeta Satish, Amir Nili, Bernhard O. Palsson, Graham C. Walker, and James J. Collins. “A white-box machine learning approach for revealing antibiotic mechanisms of action”. Cell (2019).
  • Rajiv Ramasawmy, Toby Rodgers, Miguel A. Alcantar, Delaney R. McGuirt, Jaffar M. Khan, Peter Kellman, Anthony Z. Faranesh, Adrienne E. Campbell-Washburn, Robert J. Lederman, Daniel A. Herzka. “Blood volume measurement using MRI and ferumoxytol: preclinical validation”. Journal of Cardiovascular Magnetic Resonance (2018).
  • James T. Yurkovich*, Miguel A. Alcantar*, Zachary B. Haiman, and Bernhard O. Palsson. “Network-level allosteric effects are elucidated by detailing how ligand-binding events modulate utilization of catalytic potentials.” PLOS Computational Biology (2018).


  • National Science Foundation Graduate Research Fellowship – 2018
  • Lemelson Presidential Engineering Fellowship – 2018
  • GEM Associate Fellowship – 2018
  • Undergraduate Provost’s Honor Roll, every quarter at UC San Diego – 2014-2018
  • Genentech Scholar – 2017
  • Tau Beta Pi member – 2017
  • Gates Millennium Scholarship – 2014
  • CEDAR Southern California Scholarship – 2014