Meet the Team
Principal Investigator (PI) - Brian Munsky
- (2014-Present) Assistant Professor; Chemical and Biological Engineering; Colorado State University, Fort Collins CO
- (2014-Present) Assistant Professor; School of Biomedical Engineering; Colorado State University, Fort Collins CO
- (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
- Los Alamos National Laboratory Postdoctoral Distinguished Performance award, 2012
- NSF/I2CAM Workshop Support Award ($25,000 in support), 2011
- 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
Current Team Members
I obtained my Ph.D. in Biomedical Engineering and Physics at the Center for Research and Advanced Studies of the Mexican National Polytechnic Institute in collaboration with the University of Heidelberg, Germany. Currently, I am a WM Keck Postdoctoral Scholar at the Colorado State University in the group of Dr. Brian Munsky. During my postgraduate studies, I have developed high-performance computing technologies that are applied in the field of molecular virology and gene expression. As a result of my work, I have generated publications in international scientific journals with recognized impact factor, and international groups have cited those publications. My current research involves the design of efficient computational algorithms to integrate gene expression data with stochastic models.
Email: Luis.aguilera at colostate.edu
- 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, Zimmer C, Rodríguez-González J (2017). Modeling the Effect of Tat Inhibitors on HIV Latency. Submitted to Physical Biology.
Linda Forero Quintero
I obtained my PhD in natural sciences in 2016 from the university of Kaiserslautern, Germany. During my PhD research, I worked on Neurosciences and Brain Energy Metabolism. I particularly characterized the role of monocarboxylate transporters (MCTs) during epileptiform activity using pH and Ca2+ imaging. Currently, I am WM keck postdoctoral scholar at Colorado State University, working under the supervision of Dr. Brian Munsky and Dr. Tim Stasevich. In my present research, I will be developing new technology to enable multiplexed single molecule imaging of gene expression in living cells and in real time.
Email: Linda.Forero_Quintero at colostate.edu
- Francisco J. Sierra-Valdez, Linda S. Forero-Quintero, Patricio A. Zapata-Morin, Miguel Costas, Arturo Chavez-Reyes, Jesús C. Ruiz-Suárez. (2013). The influence of non-polar and polar molecules in mouse motile cell membranes and pure lipid bilayers. PloS-One. DOI: 10.1371/journal.pone.0059364.
- Valdebenito, R., Ruminot, I., Garrido-Gerter, P., Fernández-Moncada, I., Forero-Quintero, L., Alegría, K., Becker, H.M., Deitmer, J.W., Barros, L.F. (2015). Targeting of astrocytic glucose metabolism by beta-hydroxybutyrate. Journal of Cerebral Blood Flow & Metabolism. DOI: 10.1177/0271678X15613955.
- José, P. Torres-Rodríguez, L. S. Forero-Quintero, J. C. Chávez, J. L. de la Vega-Beltrán, F. Carta, C. T. Supuran, J. W. Deitmer, C. L. Treviño (2015). Carbonic anhydrases and their functional differences in human and mouse sperm physiology. Biochem. Biophys. Res. Commun. DOI: 10.1016/j.bbrc.2015.11.021.
- Forero-Quintero, L.S., Becker, H.M., Deitmer, J.W., (2017). Reduction of epileptiform activity in ketogenic mice: The role of monocarboxylate transporters. Scientific reports. DOI: 1038/s41598-017-05054-0
I obtained my Math Ph.D. in 2017 from the University of Alabama. I am interested in applying new methods in numerical linear algebra into solving high-dimensional problems in quantitative biology. I’m currently working on algorithms for simulating heterogeneous populations, and methods for parameter identification of stochastic gene expression models. My aim is to develop efficient codes in Fortran, C++ and MPI for the analysis of single-cell and single-molecule data sets.
Email: Huy.Vo at colostate.edu
- H. D. Vo and R. B. Sidje. Adaptive solution to the chemical master equation using tensors. Journal of Chemical Physics, Volume 147, Issue 4, July 2017.
- H. D. Vo and R. B. Sidje. Approximating the large sparse matrix exponential using incomplete orthogonalization and Krylov subspaces of variable dimensions. Numerical Linear Algebra with Applications, Volume 24, Issue 3, May 2017.
I started my PhD in Biomedical Engineering at Colorado State University in 2016. During my time here, I have worked on developing new tools to integrate modern single-cell, single-molecule biological data set with discrete stochastic models. These mathematical and computational tools allow for faster model identification and uncertainty quantification while still making use of the rich information provided by single cell data. I collaborate closely with groups that work on live-cell imaging of translation, and signal-activated gene expression in yeast.
Email: zrfox at engr.colostate.edu
- Predicting single-cell transcription dynamics even when the central limit theorem failsB Munsky, G Li, Z Fox, DP Shepherd, G NeuertbioRxiv, 154401
- Finite state projection based bounds to compare chemical master equation models using single-cell dataZ Fox, G Neuert, B MunskyJournal of Chemical Physics 145
- Integrating single-molecule experiments and discrete stochastic models to understand heterogeneous gene transcription dynamicsB Munsky, Z Fox, G NeuertMethods 85, 12-21
- Nonspecific transcription factor binding can reduce noise in the expression of downstream proteinsM Soltani, P Bokes, Z Fox, A SinghPhysical biology 12 (5), 055002
- Disorder, oscillatory dynamics and state switching: the role of c-MycN Rangarajan, Z Fox, A Singh, P Kulkarni, G RangarajanJournal of Theoretical Biology 386, 105-114
- Stochastic analysis of protein-mediated and microRNA-mediated feedback circuits in HIVZ Fox, A SinghIFAC Proceedings Volumes 47 (3), 1146-1151
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
I currently focus on data analysis of flow cytometry measurements to provide label-free quantification strategies to identify intrinsic properties of single cells. Based upon population statistics and machine learning, I integrate labeled and unlabeled training data and identify models for accurate label-free quantification.
Email: mtanha at colostate.edu
I received an MS in Mechanical Engineering with a biological emphasis from the University of Denver in 2012. I am currently a PhD student with an interest in computational modeling of various aspects of RNA translation, which can then be utilized in the analysis of single-cell data. I am also applying linear systems principles to these RNA translation models to obtain analytical solutions.
Email: llweber at rams.colostate.edu
- Co-authored Chapter 30, “Tutorial on the Identification of Gene Regulation Models from Single-Cell Data” in the textbook, Quantitative Biology: Theory, Computational Methods and Examples of Models
- 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.
Charlotte (Charlie) Mitchell - Website Developer
I am a fifth year undergraduate student obtaining two bachelors degrees from the Walter Scott Jr. College of Engineering at Colorado State University. I will be receiving my B.S. in Biomedical Engineering and my B.S. in Chemical & Biological Engineering with a minor in Mathematics upon graduation in May 2018. I plan to obtain my Engineering Intern Certification from the Colorado Department of Regulatory Agencies upon passing the Fundamentals of Engineering Exam in December 2017. After graduation, I hope to be employed with a company in the engineering industry.
Email: charlotte.r.mitchell at rams.colostate.edu