Positions

  • (2023-Present) Monfort Professor, Colorado State University, Fort Collins CO
  • (2020-Present) Associate Professor; Chemical and Biological Engineering; Colorado State University, Fort Collins CO
  • (2014-2020) Assistant Professor; Chemical and Biological Engineering; Colorado State University, Fort Collins CO
  • (2014-Present) Affiliate Professor; School of Biomedical Engineering; Colorado State University, Fort Collins CO
  • (2016-Present) Keck Scholar; Colorado State University, Fort Collins CO
  • (2010-Present) Director of the q-bio Summer School
  • (2010-2016) Research Scientist; New Mexico Consortium; Los Alamos NM
  • (2013); Scientist II, Los Alamos National Laboratory; Los Alamos, NM
  • (2010-2013); Richard P Feynman Distinguished Postdoctoral Fellow in Theory and Computing; Los Alamos National Laboratory; Los Alamos, NM
  • (2008-2010); Director’s Postdoctoral Fellow; Los Alamos National Laboratory; Los Alamos, NM

Education

Funding

  • Monfort Professor, “The Cyborg Scientist to Observe, Model, and Predict Cellular Dynamics”, 2023-2025.
  • NSF CAREER Award, “Stochastic Analyses to Optimize Designs for Single-Cell Optical Microscopy Experiments,” 2020-2025.
  • NIGMS Maximizing investigator Research Award (MIRA, R35): “Using Cellular Fluctuations and Computational Analyses to Probe Biological Mechanisms,” Sponsored by HHS-NIH-National Institutes of Health (September 15, 2017 – August 31, 2027). PI.
  • DTRA “Bet-hedging in Pathogens: Targeting Bacterial Persistence to Combat Infectious Disease,” Sponsored by DOE-NNSA-Los Alamos National Laboratory. (January 17, 2017 – December 31, 2017), co-I.
  • W. M. Keck Foundation Medical Research Area Grant, “Quantifying Multiplexed Real-Time RNA to Protein Translation in Live Cells”, (July 1, 2016 – June 30, 2020), co-PI.
  • NIH R25, “The q-bio Summer School”, (Jan. 01 2012 – Dec. 31, 2016), co-PI.
  • NSF/I2CAM Workshop Support Award ($25,000 in support), 2011, PI.

Awards

  • Monfort Professorship, 2023
  • NSF CAREER Award, 2020
  • George T. Abell Outstanding Early Career Faculty Award, 2019
  • WM Keck Foundation, 2016
  • Los Alamos National Laboratory Postdoctoral Distinguished Performance award, 2012
  • SIAM Conference in the Life Sciences (LS10) Poster Award, 2010
  • Leon Heller Postdoctoral Publication Prize in Theoretical Physics, 2010
  • Richard P. Feynman Distinguished Postdoctoral Fellowship, 2010
  • UCSB Department of Mechanical Engineering Best Ph.D. Dissertation for the 2007-2008 Academic Year, 2009
  • Los Alamos National Laboratory Directors Postdoctoral Fellowship, 2008
  • Best Presentation in Session, 27th American Controls Conference, 2008
  • UCSB Student Travel Grant, 2007
  • UCSB Department of Mechanical Engineering Graduate Research Fellowship, 2003
  • UCSB Chancellor’s Graduate Research Fellowship, 2003
  • National Defense Science and Engineering Graduate Fellowship, 2001
  • American Helicopter Society Vertical Flight Foundation Award, 1999 and 2000
  • Penn State University Schreyer Ambassador Travel Grant, 1999
  • Mary Ilgen Memorial Scholarship, 1999
  • Schreyer Honors College Academic Excellence Award, 1996

Luis Aguilera

I am a postdoc in the group of Dr. Brian Munsky at CSU. The focus of my work is to develop high-throughput computational techniques to understand complex biological systems, such as viral infections and innate immune responses. I obtained my Ph.D. in Biomedical Engineering and Physics from the National Polytechnic Institute in Mexico.

 

Email: Luis.aguilera at colostate.edu

CV/Resume

 

Publications:

  • Aguilera LU, Galindo BE, Sánchez D & Santillán M (2012) What is the core oscillator in the speract- activated pathway of the Strongylocentrotus purpuratus sperm flagellum? Biophysical Journal 102: 2481– 2488.
  • Aguilera LU & Rodríguez-González J (2014) Studying HIV latency by modeling the interaction between HIV proteins and the innate immune response. Journal of Theoretical Biology 360: 67–77.
  • Aguilera LU, Zimmer C, Kummer U (2017). A New Efficient Approach to Fit Stochastic Models on the Basis of High-throughput Experimental Data Using a Model of IRF7 Gene Expression as Case Study. BMC Systems Biology. 11:26.
  • Aguilera, LU, Rodríguez-González, J. (2019). Modeling the effect of tat inhibitors on HIV latency. Journal of theoretical biology, 473, 20-27.
  • Lyon, K., Aguilera, LU, Morisaki, T., Munsky, B., Stasevich, T. J. (2019). Live-cell single RNA imaging reveals bursts of translational frameshifting. Molecular cell.
  • Aguilera, LU, Bergmann, F. T., Dalmasso, G., Elmas, S., Elsässer, T., Großeholz, R., …, Veith, N. (2019). Robustness of frequency vs. amplitude coding of calcium oscillations during changing temperatures. Biophysical chemistry, 245, 17-24.
  • Aguilera, L., Raymond, W., Fox, Z. R., May, M. P., Djokic, E., Morisaki, T., Stasevich T.J., Munsky, B. (2019). Computational design and interpretation of live-cell, single-RNA translation experiments. PLoS Computational Biology 15 (10).
  • Koch A., Aguilera L., Morisaki T., Munsky B., Stasevich T.J. (2020). Quantifying the dynamics of IRES and cap translation with single-molecule resolution in live cells. Nature Structural and Molecular Biology.
  • Castaño-Arcila, Mauricio, Aguilera L., and Jesús Rodríguez-González. (2021). Modeling the intracellular dynamics of the dengue viral infection and the innate immune response. Journal of Theoretical Biology. 509:110529.

Lisa Weber

I received an MS in Mechanical Engineering with a biological emphasis from the University of Denver in 2012, and have engineering experience in multiple industries (Oil and Gas, Pharmaceuticals, and Aerospace). I am currently an Instructor and a PhD Candidate in Chemical Engineering at Colorado State University. My research involves performing computational modeling of various biological processes, including aspects of gene expression and DNA/Oligonucleotide binding interactions in relation to multiple experimental variables, integrating computational methods with experimental data. I also perform research on implementing and teaching implicit bias, inclusion, and diversity-related topics to undergraduate engineering students. In addition, I was a Graduate Teaching Fellow from 2017-2019, and I am currently the Instructor for CBE 160: Introduction to MATLAB for Chemical and Biological Engineers (from 2018-Present). 

Email: llweber@rams.colostate.edu

CV/Resume

Publications:

  • L. Weber, W. Raymond, and B. Munsky. (2018) Identification of gene regulation models from single-cell data. Physical Biology, 15 (5), 055001. https://doi.org/10.1088/1478-3975/aabc31
  • L. Weber, W. Raymond, and B. Munsky, “Tutorial on the Identification of Gene Regulation Models from Single-Cell Data,” in Quantitative Biology: Theory, Computational Methods, and Models, B. Munsky, W. S. Hlavacek, and L. S. Tsimring, Ed. Cambridge, MA: The MIT Press, 2018, pp. 599-616.
  • M.S. Thesis: “Pulmonary particle deposition in relation to age, body weight, and species”
    • Deposition based on therapeutic volume delivered and determined by static probabilistic mathematical model.  Evaluation of deposition based on variable breathing rates. Sensitivity analysis performed to determine sensitivity of particle deposition to changes in particle size and breathing rate.
  • Worden RN, Weber LM, and Lengsfeld CS. September 2012. Optimal Parameters for Pulmonary Particle Deposition as a Function of Age.ICLASS 2012, 12th  International Conference on Liquid Atomization and Spray Systems. Heidelberg, Germany.
  • Weber LM and Lengsfeld CS. May 2011. Spray Nebulizer Deposition Efficiency as a Function of Age. ILASS Americas, 23rd Annual Conference on Liquid Atomization and Spray Systems, Ventura, CA (Best Conference Paper Finalist).
  • Weber LM and Lengsfeld CS. May 2011. Spray Nebulizer Deposition Efficiency Impact of Species. ILASS Americas, 23rd Annual Conference on Liquid Atomization and Spray Systems, Ventura, CA.

Michael May

My work focuses on branching the gap between theoretical quantitative biology and traditional microbiology wet-labs. Currently, I am working on using the variability predicted in stochastic models as a tool to help identify genes imaged though new techniques developed by a collaborator at CSU. My background is in biomedical and chemical engineering and my interests are in modeling and simulation.

Email: michael.may at rams.colostate.edu

CV/Resume

Will Raymond

I graduated in May 2017 from Colorado State University with a Bachelors in Biomedical Engineering and a Bachelors in Chemical and Biological Engineering. 

I have been a PhD student in Dr. Munsky’s lab since 2019 working on a myriad of projects. I am currently the lead developer on the rSNAPsim, an open source Python TASEP mRNA simulation package. In addition to that, I also work on implementing machine learning for nascent chain tracking fluorescent spot identification.

My primary area of interest is the intersection of machine learning, bioinformatics, and RNA biology. I am most excited about novel ncRNA discovery and advancements in structural identification and disease classification.

 

Email: wsraymon@rams.colostate.edu / williamscottraymond@gmail.com

CV/Resume

Publications:

  • L. Forero, W. Raymond, T. Handa, M. Saxton, T. Morisaki, B. Munsky, T. Stasevich. (2021) Live-cell imaging reveals the spatiotemporal organization of endogenous RNA polymerase II phosphorylation at a single gene. Nature Communications – Accepted for publication
  • L. Aguilera, W. Raymond, Z. Fox, M. May, E. Djokic, T. Morisaki, T. Stasevich, B. Munsky. (2019) Computational design and interpretation of single-RNA translation experiments. PLOS Computational Biology. 15(10): e1007425. https://doi.org/10.1371/journal.pcbi.1007425
  • L. Weber, W. Raymond, and B. Munsky. (2018) Identification of gene regulation models from single-cell data. Physical Biology, 15 (5), 055001. https://doi.org/10.1088/1478-3975/aabc31
  • L. Weber, W. Raymond, and B. Munsky, “Tutorial on the Identification of Gene Regulation Models from Single-Cell Data,” in Quantitative Biology: Theory, Computational Methods, and Models, B. Munsky, W. S. Hlavacek, and L. S. Tsimring, Ed. Cambridge, MA: The MIT Press, 2018, pp. 599-616.

Eric Ron

I received my undergraduate degree in biochemistry from Colorado State University in 2013. I then worked as an analytical chemist for two years in industry before working as product development lead and cofounder of a start-up company until 2018. Currently, I am working on my Master’s Degree and am interested in single-cell microscopy and the integration of stochastic models with transcription and translation dynamics. In my current work I am helping with the optimization of smFISH experiments and assisting with the automation of image processing.

Email: Eric.Ron@colostate.edu

Toggle Content

I received my undergraduate degree in chemistry and philosophy, with a certificate in computer sciences, from UW-Madison in 2014. After graduate coursework and a brief professional research appointment in chemistry, I worked for five years as a software developer at De Novo Software, makers of leading products for the analysis and visualization of flow cytometry data. Throughout this period, I continued my involvement in scientific research, occasionally at the bench but more frequently in hypothesis development and technical communication.


In the Munsky group, my work has two major aims:

  1. Improving our stochastic system modelling tools and applying them to new scientific problems, e.g. probing the dynamics of catalyzed nanoparticle assembly and optimal design of field experiments to better understand disease spread.
  2. Developing our automated microscope as a cyber-physical system, validating it using formal methods, and extending its capabilities through additional hardware, e.g. FPGAs, and hardware/software co-design.

Email: Dmitri.Svetlov@colostate.edu

GitHub: dmitrisvetlov  

Former Undergraduate Team Members

  • Joshua Cook (B.S. in Chemical & Biological Engineering and Biomedical Engineering, May 2021). Now a Research Associate at CSU. 
  • Sawyer Halingstad, (B.S. in Chemical & Biological Engineering and Biomedical Engineering, May 2023). Now a Renewable Energy Researcher at the National Renewable Energy Laboratory.
  • Alison Shad, (B.S. in Chemical & Biological Engineering and Biomedical Engineering, May 2023). Now a Ph.D. Student at Stanford University.
  • Katie Davis, (B.S. in Chemical & Biological Engineering and Biomedical Engineering, May 2021).  Now a Process Development Engineer at Tolmar Inc.
  • Rachel Keating, (B.S. in Chemical & Biological Engineering and Biomedical Engineering, May 2021).  Now a Systems Engineer II at Abbott.
  • Stuart McKnight (B.S. in Chemical & Biological Engineering and Biomedical Engineering, May 2021). Now a Systems Engineer Terumo Blood and Cell Technologies.
  • Elliot Djokic, Undergraduate, Chemical and Biological Engineering and Biomedical Engineering (Dual B.S. Degrees, 2020). Now a Systems Engineer at Epic.
  • Charis Ellis, Undergraduate, Chemical and Biological Engineering (B.S., 2019). Now a CVD Shift Process Engineer at Micron Technology, Inc.
  • Zach Haigh, Undergraduate, Chemical and Biological Engineering and Biomedical Engineering (Dual B.S. Degrees, 2020). Now a Ph.D. student at University of Minnesota.
  • Chase Hunter, Undergraduate, Chemical and Biological Engineering (B.S., 2017). Now a RDA Engineering Manager at 3D DRAM.
  • Torin Moore, Undergraduate, Chemical and Biological Engineering and Biomedical Engineering (Dual B.S. Degrees, 2020). 
  • Charlotte Mitchell, Undergraduate, Chemical and Biological Engineering and Biomedical Engineering (Dual B.S. Degrees, 2017). Now a Global Strategist at Raytheon.
  • Lucas Suazo, Undergraduate, Chemical and Biological Engineering and Biomedical Engineering (Dual B.S. Degrees, 2016). Now at Stanford Medical School.

Former Graduate Team Members

  • Joshua Cook, (M.S., 2023), Now a Research Associate at Colorado State University
  • Zachary Fox (Ph.D., 2019), Now a Research Scientist at Oak Ridge National Laboratory.
  • Mohammad Tanhaemami (M.S., 2020), Now a Bioinformatics Analyst at Dana Farber Cancer Institute.
  • Jaron Thompson (M.S., 2020), Now a Ph.D. Student in Chemical and Biological Engineering at University of Wisconsin, Madison.

Former Postdocs

  • Douglas Shepherd, Postdoc, Now Assistant Professor of Physics at Arizona State University
  • Huy Vo, Postdoc, Now a Research Investigator at Bristol Meyer Squibb.
  • Linda Forero Quintero, Postdoc, Now a Research Scientist II at Mosaic Biosciences