Team:UIUC Illinois/Attributions
Attributions
Acknowledgement
Project Support & AdviceDr. Rao, Anna Fedders, Carl Schultz, Matthew Waugh, William Woodruff, Daniel Ryerson
CollaboratorHarvard iGEM for NEGEM conference, iGEM Ionis for Worldwide Meetup, and Technion iGEM
InterviewersDr. Brenda Wilson, Professor of Microbiology of University of Illinois Urbana-Champaign, provided idea of using software as a proof of concept using other data and introduced us GISAID database, which we used to build our database
Dr. Diwakar Shukla, Blue Waters Assistant Professor at University of Illinois Urbana-Champaign, 1)modified the antibody structure to build different antiviral agents that binds to as many mutated spike proteins as possible, 2)introduced point mutations of spike proteins and according changes in spike protein structures, and 3)utilized machine learning concepts like the genetic algorithm for point mutations
Dr. Erik Procko, Assistant Professor of Biochemistry and Professor of Biophysics and Quantitative Biology, suggested 1)End-user implementation: how current researchers of COVID-19 are already looking into the mutant diversity of the virus, and 2)the possibility of noise/sequencing errors in mutation research; look into how this could affect the construction of a sequence database for spike proteins
Dr. Huimin Zhao, Steven L. Miller Chair, Professor of chemical and biomolecular engineering and professor of biochemistry, biophysics, and bioengineering, suggested 1)End-user possibilities: discussed how the implementation of a new sequence database could help current COVID researchers design a new vaccine/treatment a lot faster, and 2)various parameters that could affect antibody design and vaccine development, such as specific mutations and multiple unknowns/assumptions that have to be made
Dr. Mohammed El-Kebir, Assistant professor of Computer Science, proposed 1)nonsynonymous mutation visualization can be performed using PyRosetta and a phylogenetic tree, and 2)generation of multiple sequence alignments using Nexstrain, since it’s important to index the sequence
Dr. Nicholas Wu, Assistant professor at the School of Molecular and Cellular Biology, discussed general research with antibody design and how effective a new antibody would be against a rapidly mutating pathogen (i.e. the coronavirus), and evaluated what parts of the spike protein should be targeted for an effective treatment to COVID-19
Palash Sashittal, Graduate Student of Dr. El-Kebir assisted with troubleshooting the Snakemake build setup as part of our phylogenetic tree development. Specifically, we ran into a “duplicate key” error which Palash helped us to fix. Through reformatting our metadata file we were able to move past this error and produce the phylogenetic tree successfully.
General SupportParents and friends of all team members
We thank all for the support from the professors and advisors for cooperation and valuable advice amid COVID-19 pandemic