Research
The Biomathematics Research Group (BRG) at UGA explores mathematical and computational models that connect genes to ecology. Our current direction of research includes: (i) integration of multiple omic technologies (transcriptomics, metabolomics, lipidomics, proteomics, etc) capturing the dynamics of host-pathogen interactions into mathematical, computational, and statistical models, and (ii) multi-scale epidemiology; particularly, our lab is building a continuous computational pipeline to integrate multi-omic data, within-host dynamics (i.e. pathogen vs. immune system), vector dispersal, and human movement. The BRG has expertise in mathematical modeling using a wide array of techniques, data management of very large and heterogeneous biological data sets, software development from micro-controllers to super-computers, and hardware design. The long-term research goal of the BRG is to build a computational facility capable of quantifying biological processes across multiple scales.
Our currently funded projects are:
- (PI Gutierrez) ALICE (Adaptive Learning for Interdisciplinary Learning Environments, 2016-2018, $299K), NSF award #1645325 : ALICE is a Web-based information system that generates individualized development plans, according to previous experiences and current challenges. Furthermore, ALICE is designed to connect lexias from multiple subject matters, thus bypassing disciplinary barriers that in many cases are artificial. The principles behind ALICE are generalizable, and hence it has the potential to be used in K-16, graduate, and continuing education.
- (Co-PI Gutierrez, PI Galinski) Technologies for Host Resilience (2016-2019, $1.9M UGA out of $6.5M) - Host Acute Models of Malaria to study Experimental Resilience (THoR's HAMMER), DARPA contract contract #W911NF-16-C-0008, 2016-2019. This project will explore the molecular mechanisms of resilience, susceptibility and resistance of non-human primate hosts when challenged with a malaria infection.
Our past funded projects are:
- (Co-I Gutierrez, PI Galinski) Malaria Host-Pathogen Interaction Center (2012-2017, $19M), MaHPIC, NIAID contract #HHSN272201200031C, 2012-2017. PI Mary Galinski. MaHPIC involves the multidisciplinary study of malaria infections, immunity and pathogenesis of P. falciparum, P. vivax and P. knowlesi in the context of host-pathogen interactions, in humans and nonhuman primates, using a systems biology approach. Three nonhuman primate malaria species will be studied: P. coatneyi to model P. falciparum, P. cynomolgi to model P. vivax, and P. knowlesi, a monkey malaria species that has been causing illness and cases of death in humans in Southeast Asia.
- (Co-I Gutierrez, PI Herrera) International Centers of Excellence in Malaria Research (2011-2017, $5.5M) - Center for non-Amazonian regions of Latin America - CLAIM, NIAID cooperative agreement #U19AI089702-01, 2010-2017. PI SÃ³crates Herrera. CLAIM is divided into three projects: Project 1 is evaluating the diversity of the ecology and parasite populations related to the epidemiology and clinical findings to establish a scientific framework that supports the development of new intervention strategies for malaria elimination in non-Amazonian areas of Latin America. Project 2 is addressing major gaps in understanding of the ecology, behavior, vector potential, and control of Anopheles malaria vectors to guide the development and implementation of more effective integrated vector management (IVM) strategies of National Malaria Control Programs (NMCPs). Project 3 aims to determine the clinical outcomes and their association with parasite and host features of malaria-infected individuals living in non-Amazon regions of LA with different intensities of malaria transmission.
We are currently interested in the following projects:
- Bioclassification: This research project involves the characterization of of biological objects (RNA, DNA, proteins, brains, time series, etc.) through a minimal set of data primitives. This system produces different types of data structures and feature vectors, e.g. higher order moments, knot invariants based on Gauss integrals, etc. and then applies a battery of pattern classification algorithms (e.g. Multiple Discriminant Analysis (MDA), Principal Component Analysis (PCA), clustering techniques, neural networks, etc.) for the purpose of automated object classification. We built a web front-end to a high-performance relational database for large data sets available at: www.bioclassification.org
Examples of past research projects are:
- Trojan chromosomes: The Trojan chromosome hypothesis states that it is possible to achieve local extinction of exotic species through the constant environmental introduction of sex-reversed organisms, which are produced via phenotypic and genotypic manipulations.
- Sonification: This project explores the possibility of hybridizing sound and visualization to represent complex data sets to harness the human ability to find patterns. For instance, a common problem in data visualization is the representation of higher dimensions. A surface plot could represent three dimensions. You can always add two additional dimensions via color and sound. First the deceivingly simple "color" option. If you use MATLAB, you know that you have several options for color maps that simply represent the Z axis... but what if your color is not related to the Z axis, but instead to other dimension. The second option is sonification of the image, that is to say, each point in your 3-D plot has a related sound that presents the 5th dimension of your data.
- Invasive Species Diffusion Model Prototype: Spatial spread of invasive species can be modeled with a system of advection-diffusion-reaction partial differential equations. Such a model was used to predict the advance of an invasive front of Channeled Apple Snails (CAS) and estimate population densities over time across the entire spatial domain. http://www.youtube.com/watch?v=joR4Rtzm12c&feature=PlayList&p=3A96AC32A930CE17&index=0&playnext=1
This list includes: (i) video demo of an invasion process of CAS in Lake Munson, Tallahassee, FL, (ii) video-manual to extract information from a map, (iii) video-manual to enter information into Scilab, (iv) video-manual to produce a invasion model video for a user-defined spatial domain.
- Analysis of Financial Time Series: In this project we studied a Terabyte-size database of quotes and trades for 38 symbol in a period of 4 months, and developed algorithms for data filtering that eliminate the delay associated with moving averages. The techniques used have to do with Fourier analysis, complex extensions of real functions, and use of fat-tail distributions to estimate variations. This project resulted in a proprietary trading algorithm used by Level 3 Data.
- Literatronica: An artificial intelligence engine that makes an approximation to a Hamiltonian cycle in a weighted graph with weights that vary in time according to a coupled set of ODEs, to achieve adaptivity in my own literary works. Adaptive digital narrative works reconfigure themselves for the reader, leading to a potentially unique read every time. Adaptive books cannot be reproduced on paper except, perhaps, as a reading path at a given moment. The solution of a multi-terminal network flow on such a graph solves the optimization problem of minimizing hypertextual attraction (a measure of narrative continuity) and hypertextual friction (a measure of the risk of loosing readers' attention). Available at: www.literatronica.net