Seminars and Colloquia by Series

Organizational meeting

Series
Mathematical Biology Seminar
Time
Wednesday, August 21, 2019 - 11:00 for 30 minutes
Location
Skiles 006
Speaker
Christine HeitschGeorgia Tech

A brief meeting to discuss the plan for the semester, followed by an informal discussion over lunch (most likely at Ferst Place).

Stochastic models for the transmission and establishment of HIV infection

Series
Mathematical Biology Seminar
Time
Wednesday, March 27, 2019 - 10:00 for 1 hour (actually 50 minutes)
Location
Skiles 005
Speaker
Dan CoombsUBC (visiting Emory)
The likelihood of HIV infection following risky contact is believed to be low. This suggests that the infection process is stochastic and governed by rare events. I will present mathematical branching process models of early infection and show how we have used them to gain insights into the duration of the undetectable phase of HIV infection, the likelihood of success of pre- and post-exposure prophylaxis, and the effects of prior infection with HSV-2. Although I will describe quite a bit of theory, I will try to keep giant and incomprehensible formulae to a minimum.

Inference of evolutionary dynamics of heterogeneous cancer and viral populations

Series
Mathematical Biology Seminar
Time
Wednesday, February 27, 2019 - 11:01 for 1 hour (actually 50 minutes)
Location
Skiles 005
Speaker
Pavel SkumsGSU/CDC

Inference of evolutionary dynamics of heterogeneous cancer and viral populations Abstract: Genetic diversity of cancer cell populations and intra-host viral populations is one of the major factors influencing disease progression and treatment outcome. However, evolutionary dynamics of such populations remain poorly understood. Quantification of selection is a key step to understanding evolutionary mechanisms driving cancer and viral diseases. We will introduce a mathematical model and an algorithmic framework for inference of fitness landscapes of heterogeneous populations from genomic data. It is based on a maximal likelihood approach, whose objective is to estimate a vector of clone/strain fitnesses which better fits the observed tumor phylogeny, observed population structure and the dynamical system describing evolution of the population as a branching process. We will discuss our approach to solve the problem by transforming the original continuous maximum likelihood problem into a discrete optimization problem, which could be considered as a variant of scheduling problem with precedent constraints and with non-linear cumulative cost function.

Exploring the impact of inoculum dose on host immunity and morbidity to inform model-based vaccine design

Series
Mathematical Biology Seminar
Time
Wednesday, January 30, 2019 - 11:00 for 1 hour (actually 50 minutes)
Location
Skiles 005
Speaker
Andreas HandelUGA
Vaccination is an effective method to protect against infectious diseases. An important consideration in any vaccine formulation is the inoculum dose, i.e., amount of antigen or live attenuated pathogen that is used. Higher levels generally lead to better stimulation of the immune response but might cause more severe side effects and allow for less population coverage in the presence of vaccine shortages. Determining the optimal amount of inoculum dose is an important component of rational vaccine design. A combination of mathematical models with experimental data can help determine the impact of the inoculum dose. We designed mathematical models and fit them to data from influenza A virus (IAV) infection of mice and human parainfluenza virus (HPIV) of cotton rats at different inoculum doses. We used the model to predict the level of immune protection and morbidity for different inoculum doses and to explore what an optimal inoculum dose might be. We show how a framework that combines mathematical models with experimental data can be used to study the impact of inoculum dose on important outcomes such as immune protection and morbidity. We find that the impact of inoculum dose on immune protection and morbidity depends on the pathogen and both protection and morbidity do not always increase with increasing inoculum dose. An intermediate inoculum dose can provide the best balance between immune protection and morbidity, though this depends on the specific weighting of protection and morbidity. Once vaccine design goals are specified with required levels of protection and acceptable levels of morbidity, our proposed framework which combines data and models can help in the rational design of vaccines and determination of the optimal amount of inoculum.

Mathematical models for matrix regeneration and remodeling in biological soft tissues

Series
Mathematical Biology Seminar
Time
Wednesday, January 31, 2018 - 11:00 for 1 hour (actually 50 minutes)
Location
Skiles 006
Speaker
Prof. Mansoor HaiderNorth Carolina State University, Department of Mathematics & Biomathematics
Many biological soft tissues exhibit complex interactions between passive biophysical or biomechanical mechanisms, and active physiological responses. These interactions affect the ability of the tissue to remodel in order to maintain homeostasis, or govern alterations in tissue properties with aging or disease. In tissue engineering applications, such interactions also influence the relationship between design parameters and functional outcomes. In this talk, I will discuss two mathematical modeling problems in this general area. The first problem addresses biosynthesis and linking of articular cartilage extracellular matrix in cell-seeded scaffolds. A mixture approach is employed to, inherently, capture effects of evolving porosity in the tissue-engineered construct. We develop a hybrid model in which cells are represented, individually, as inclusions within a continuum reaction-diffusion model formulated on a representative domain. The second problem addresses structural remodeling of cardiovascular vessel walls in the presence of pulmonary hypertension (PH). As PH advances, the relative composition of collagen, elastin and smooth muscle cells in the cardiovascular network becomes altered. The ensuing wall stiffening increases blood pressure which, in turn, can induce further vessel wall remodeling. Yet, the manner in which these alterations occur is not well understood. I will discuss structural continuum mechanics models that incorporate PH-induced remodeling of the vessel wall into 1D fluid-structure models of pulmonary cardiovascular networks. A Holzapfel-Gasser-Ogden (HGO)-type hyperelastic constitutive law for combined bending, inflation, extension and torsion of a nonlinear elastic tube is employed. Specifically, we are interested in formulating new, nonlinear relations between blood pressure and vessel wall cross-sectional area that reflect structural alterations with advancing PH.

Comparative genomics meets topology: a novel view on genome median and halving problems

Series
Mathematical Biology Seminar
Time
Wednesday, March 15, 2017 - 11:05 for 1 hour (actually 50 minutes)
Location
Skiles 006
Speaker
Max AlekseyevGeorge Washington University
Genome median and genome halving are combinatorial optimization problems that aim at reconstruction of ancestral genomes by minimizing the number of possible evolutionary events between the reconstructed genomes and the genomes of extant species. While these problems have been widely studied in past decades, their known algorithmic solutions are either not efficient or produce biologically inadequate results. These shortcomings have been recently addressed by restricting the problems solution space. We show that the restricted variants of genome median and halving problems are, in fact, closely related and have a neat topological interpretation in terms of embedded graphs and polygon gluings. Hence we establish a somewhat unexpected link between comparative genomics and topology, and further demonstrate its advantages for solving genome median and halving problems in some particular cases. As a by-product, we also determine the cardinality of the genome halving solution space.

Constrained exact optimization in Phylogenetics

Series
Mathematical Biology Seminar
Time
Tuesday, October 18, 2016 - 11:05 for 1 hour (actually 50 minutes)
Location
Skiles 005
Speaker
Tandy WarnowThe University of Illinois at Urbana-Champaign
The estimation of phylogenetic trees from molecular sequences (e.g., DNA, RNA, or amino acid sequences) is a major step in many biological research studies, and is typically approached using heuristics for NP-hard optimization problems. In this talk, I will describe a new approach for computing large trees: constrained exact optimization. In a constrained exact optimization, we implicitly constrain the search space by providing a set X of allowed bipartitions on the species set, and then use dynamic programming to find a globally optimal solution within that constrained space. For many optimization problems, the dynamic programming algorithms can complete in polynomial time in the input size. Simulation studies show that constrained exact optimization also provides highly accurate estimates of the true species tree, and analyses of both biological and simulated datasets shows that constrained exact optimization provides improved solutions to the optimization criteria efficiently. We end with some discussion of future research in this topic. (Refreshments will be served before the talk at 10:30.)

Limits to estimating the severity of emerging epidemics due to inherent noise

Series
Mathematical Biology Seminar
Time
Wednesday, July 6, 2016 - 11:00 for 1 hour (actually 50 minutes)
Location
Skiles 005
Speaker
Bradford TaylorSchool of Biology, Georgia Tech

Please Note: When a disease outbreak occurs, mathematical models are used to estimate the potential severity of the epidemic. The average number of secondary infections resulting from the initial infection or reproduction number, R_0, quantifies this severity. R_0 is estimated from the models by leveraging observed case data and understanding of disease epidemiology. However, the leveraged data is not perfect. How confident should we be about measurements of R_0 given noisy data? I begin my talk by introducing techniques used to model epidemics. I show how to adapt standard models to specific diseases by using the 2014-2015 Ebola outbreak in West Africa as an example throughout the talk. Nest, I introduce the inverse problem: given real data tracking the infected population how does one estimate the severity of the outbreak. Through a novel method I show how to account for both inherent noise arising from discrete interactions between individuals (demographic stochasticity) and from uncertainty in epidemiological parameters. By applying this, I argue that the first estimates of R_0 during the Ebola outbreak were overconfident because demographic stochasticity was ignored. This talk will be accessible to undergraduates.

Algebraic models of gene regulatory networks

Series
Mathematical Biology Seminar
Time
Wednesday, June 29, 2016 - 11:00 for 1 hour (actually 50 minutes)
Location
Skiles 005
Speaker
Elena DimitrovaClemson University
Progress in systems biology relies on the use of mathematical and statistical models for system level studies of biological processes. This talk will focus on discrete models of gene regulatory networks and the challenges they present, in particular data selection and model stability. Careful data selection is important for model identification since the process is sensitive to the amount and type of data used as input. We will discuss a criterion for deciding when a set of data points identifies an algebraic model with special minimality properties. Stability is another important requirement for models of gene regulatory networks. Canalizing functions, a particular class of Boolean functions, show stable dynamic behavior and are thus suitable for expressing gene regulatory relationships. However, in practice, relaxing the canalizing requirement on some variables is appropriate. We will present the class of partially nested canalizing functions and some of their properties and applications.

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