User:Miroslav Gasparek

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Contact Info

Miro Gasparek (overly artistic interpretation)
  • Miroslav Gasparek
  • Visiting Undergraduate Intern at Endy Lab, Stanford University
  • Undergraduate student at Imperial College London

E-mail: miroslav.gasparek15@imperial.ac.uk
Email me through OpenWetWare
GitHub: MiroGasparek
Twitter: @MiroGasparek

I am an undergraduate student of biomedical engineering at Imperial College London and I currently work in the Endy Lab at Stanford University. My summer research focuses on the experimental and computational identification of the function of the essential unknown genes of the minimal genome.

Previous research experience

(February 2016 - August 2016) Tanaka Group, Imperial College London: Mathematical and computational modelling of the optimal treatment of atopic dermatitis (eczema).
(Jully 2017 - October 2017) Murray Lab, California Institute of Technology: Mathematical and computational modeling of simple artificial cell and development of general framework for rapid implementation of modularization of its subsystems.

Education

  • 2019 (expected), MEng Biomedical Engineering, Imperial College London
  • 2015, Maturita Final Exam, Sukromne Gymnazium Zilina, Slovakia

Research interests

1. Essential Unknowns:
Identification of the function of essential unknown genes in the minimal genome using protein-protein interaction network.
One of the factors determining the success of the effort to build an artificial cell is our ability to characterize and understand the function of the genes essential for the viability of life. The smallest viable living organism, JCVI-syn3.0 contains 473 genes, of which 149 is of unknown function. My specific research goal is to facilitate our understanding of the function of these essential (and quasi-essential) genes for life through the experimental development of the protein-protein interaction network of the JCVI-syn3.0 and computational investigation of the properties of the unknown essential genes.


2. PUREity of expression:
Investigation of the function of essential unknown genes of minimal genome using cell-free expression in PURE system.
The advances in the cell-free synthetic biology enabled us to quickly prototype various genetic circuits using cell free extracts, such as PURE system or TX-TL. In-vitro expression of the genome of JCVI-syn3.0 in a cell-free PURE system could give us the information about the interactions between the products of these genes and hence help us identify their functions. Alternatively, the individual expression of the genes of the minimal genome could provide us with knowledge about the reaction kinetics of the essential unknown genes and therefore assist us in determination of their function, for instance, by comparison of the reaction kinetics of unknown genes to the reaction kinetics of the other genes with known functions.


3. How do they click together?
Computational and mathematical investigation of the input/output behavior of the interconnected cell-free biomolecular subsystems.'
The complex biomolecular systems suffer from the problems arising due to mutual interactions of the species in different subsystems, such as retroactivity and resource competition. During my internship in the Murray Lab at Caltech, I have started developing BioSIMI, a MATLAB framework for the simple input/output modelling of interconnected biomolecular subsystems, particularly applicable to the TX-TL reactions. The framework still needs a lot of work - feel free to join me at GitHub!

Resources

(To be added soon)
Publications that I read and that allow me to do the research...
Additional relevant information...