Systems Biology Commons^™

Msis-Kadelka: Modularizing The Control Search For Biological Systems, David Murrugarra

Annual Symposium on Biomathematics and Ecology Education and Research

No abstract provided.

Msis-Kadelka: Canalization Reduces The Nonlinearity Of Regulation In Biological Networks, Claus Kadelka, David Murrugarra

Annual Symposium on Biomathematics and Ecology Education and Research

No abstract provided.

Modeling Nonsegmented Negative-Strand Rna Virus (Nnsv) Transcription With Ejective Polymerase Collisions And Biased Diffusion, Felipe-Andres Piedra

Research Symposium

Background: The textbook model of NNSV transcription predicts a gene expression gradient. However, multiple studies show non-gradient gene expression patterns or data inconsistent with a simple gradient. Regarding the latter, several studies show a dramatic decrease in gene expression over the last two genes of the respiratory syncytial virus (RSV) genome (a highly studied NNSV). The textbook model cannot explain these phenomena.

Methods: Computational models of RSV and vesicular stomatitis virus (VSV – another highly studied NNSV) transcription were written in the Python programming language using the Scientific Python Development Environment. The model code is freely available on GitHub: …

Pathogen Emergence As Complex Biological Invasion: Lessons From Dynamical Systems Modeling, Sudam Surasinghe, Marisabel Rodriguez, Victor Meszaros, Jane Molofsky, Salvador Almagro-Moreno, Brandon Ogbunugafor

Northeast Journal of Complex Systems (NEJCS)

Infectious disease emergence has become the target of cross-disciplinary efforts
that aim to understand and predict the shape of outbreaks. The many challenges
involved with the prediction of disease emergence events is a characteristic that in-
fectious diseases share with biological invasions in many subfields of ecology (e.g.,
how certain plants are able to successfully invade a new niche). Like infectious
diseases, biological invasions by plants and animals involve interactions between
agents (pathogens and plants in their respective cases) and a recipient niche. In
this study, we examine the problem of pathogen emergence through the lens of a
framework first …

Modularity And Boolean Network Decomposition, Matthew Wheeler

Annual Symposium on Biomathematics and Ecology Education and Research

No abstract provided.

The Nonlinearity Of Regulation In Biological Networks, Santosh Manicka, Kathleen Johnson, Michael Levin, David Murrugarra

Annual Symposium on Biomathematics and Ecology Education and Research

No abstract provided.

Modularity In Gene Regulatory Networks, Mehak Kapoor, Claus Kadelka

Annual Symposium on Biomathematics and Ecology Education and Research

No abstract provided.

Symmetry-Inspired Analysis Of Biological Networks, Ian Leifer

Dissertations, Theses, and Capstone Projects

The description of a complex system like gene regulation of a cell or a brain of an animal in terms of the dynamics of each individual element is an insurmountable task due to the complexity of interactions and the scores of associated parameters. Recent decades brought about the description of these systems that employs network models. In such models the entire system is represented by a graph encapsulating a set of independently functioning objects and their interactions. This creates a level of abstraction that makes the analysis of such large scale system possible. Common practice is to draw conclusions about …

Inferring Dynamics Of Biological Systems, Tracey G. Oellerich

Biology and Medicine Through Mathematics Conference

No abstract provided.

Effective Dose Fractionation Schemes Of Radiotherapy For Prostate Cancer, Jose Alvarez, Kathleen M. Storey, Pavitra Kannan, Heyrim Cho

Spora: A Journal of Biomathematics

Radiation therapy remains as one of the main cancer treatment modalities. Typical regimens for radiotherapy comprise a constant dose administered on weekdays, and no radiation on weekends. In this paper, we examine adaptive dosages of radiation treatment strategies for heterogeneous tumors using a dynamical system model that consist of radiation-resistant and parental populations with unique interactive properties, namely, PC3 and DU145 prostate cancer cell lines. We show that stronger doses of radiation given in longer time intervals, while keeping the overall dosage the same, are effective in PC3 cell lines, but not in DU145 cell lines. In addition, we tested …

Convergence Properties Of Solutions Of A Length-Structured Density-Dependent Model For Fish, Geigh Zollicoffer

Rose-Hulman Undergraduate Mathematics Journal

We numerically study solutions to a length-structured matrix model for fish populations in which the probability that a fish grows into the next length class is a decreasing nonlinear function of the total biomass of the population. We make conjectures about the convergence properties of solutions to this equation, and give numerical simulations which support these conjectures. We also study the distribution of biomass in the different age classes as a function of the total biomass.

Identification Of Control Targets In Boolean Networks Via Computational Algebra, Alan Veliz-Cuba

Annual Symposium on Biomathematics and Ecology Education and Research

No abstract provided.

Building Model Prototypes From Time-Course Data, David Murrugarra, Alan Veliz-Cuba

Annual Symposium on Biomathematics and Ecology Education and Research

No abstract provided.

Mathematical Model Describing The Behavior Of Biomass, Acidity, And Viscosity As A Function Of Temperature In The Shelf Life Of Yogurt, Manuel Alvarado, Paul A. Valle, Yolocuauhtli Salazar

Annual Symposium on Biomathematics and Ecology Education and Research

No abstract provided.

Neural Network Controller Vs Pulse Control To Achieve Complete Eradication Of Cancer Cells In A Mathematical Model, Joel A. Quevedo, Sergio A. Puga, Paul A. Valle

Annual Symposium on Biomathematics and Ecology Education and Research

No abstract provided.

Chemoimmunotherapy Treatment Strategies On A Mathematical Model Of Cancer Evolution, Sandra M. Lopez, Yolocuauhtli Salazar, Paul A. Valle

Annual Symposium on Biomathematics and Ecology Education and Research

No abstract provided.

Reconstructing Mathematical Models With Chaotic Attractors Via Genetic Algorithms, Luis A. Ramirez Islas, Paul A. Valle

Annual Symposium on Biomathematics and Ecology Education and Research

No abstract provided.

A New Mathematical Theory For The Dynamics Of Large Tumor Populations, A Potential Mechanism For Cancer Dormancy & Recurrence And Experimental Observation Of Melanoma Progression In Zebrafish, Adeyinka A. Lesi

Dissertations and Theses

Cancer, a family of over a hundred disease varieties, results in 600,000 deaths in the U.S. alone. Yet, improvements in imaging technology to detect disease earlier, pharmaceutical developments to shrink or eliminate tumors, and modeling of biological interactions to guide treatment have prevented millions of deaths. Cancer patients with initially similar disease can experience vastly different outcomes, including sustained recovery, refractory disease or, remarkably, recurrence years after apparently successful treatment. The current understanding of such recurrences is that they depend on the random occurrence of critical mutations. Clearly, these biological changes appear to be sufficient for recurrence, but are they …

Mathematical Modeling Of Lung Inflammation: Macrophage Polarization And Ventilator-Induced Lung Injury With Methods For Predicting Outcome, Sarah B. Minucci

Theses and Dissertations

Lung insults, such as respiratory infections and lung injuries, can damage the pulmonary epithelium, with the most severe cases needing mechanical ventilation for effective breathing and survival. Furthermore, despite the benefits of mechanical ventilators, prolonged or misuse of ventilators may lead to ventilation-associated/ventilation-induced lung injury (VILI). Damaged epithelial cells within the alveoli trigger a local immune response. A key immune cell is the macrophage, which can differentiate into a spectrum of phenotypes ranging from pro- to anti-inflammatory. To gain a greater understanding of the mechanisms of the immune response in the lungs and possible outcomes, we developed several mathematical models …

Mathematical Modelling And In Silico Experimentation To Estimate The Quantity Of Covid-19 Infected Individuals In Tijuana, México, Karla A. Encinas, Luis N. Coria, Paul A. Valle

Annual Symposium on Biomathematics and Ecology Education and Research

No abstract provided.

Metabolic Modeling Of Multispecies Microbial Biofilms, Poonam Phalak

Doctoral Dissertations

Biofilms are ubiquitous in medical, environmental, and engineered microbial systems. The majority of naturally occurring microbes grow as mixed species biofilms. These complicated biofilm consortia are comprised of many cell phenotypes with complex interactions and self-organized into three-dimensional structures. Approximately 2% of the US population suffers from non-healing chronic wounds infected by a combination of commensal and pathogenic bacteria whereas about 500,000 cases of Clostridium difficile infections (CDI) are reported annually. These polymicrobial infections are often resilient to antibiotic treatment due to the nutrient-rich environments and species interactions that promote community stability and robustness. This thesis focusses on developing metabolic …

Mathematics Saves Lives: Models And Signals Enabling Medicine And Biology, Raina Robeva

Annual Symposium on Biomathematics and Ecology Education and Research

No abstract provided.

Network Reconstruction Using Computational Algebra And Gene Knockouts, Matthew Macauley

Annual Symposium on Biomathematics and Ecology Education and Research

No abstract provided.

Transient Dynamics Of Infection Transmission In An Intensive Care Unit, Christopher Short, Matthew S. Mietchen, Eric T. Lofgren

Annual Symposium on Biomathematics and Ecology Education and Research

No abstract provided.

Do Metabolic Networks Follow A Power Law? A Psamm Analysis, Ryan Geib, Lubos Thoma, Ying Zhang

Senior Honors Projects

Inspired by the landmark paper “Emergence of Scaling in Random Networks” by Barabási and Albert, the field of network science has focused heavily on the power law distribution in recent years. This distribution has been used to model everything from the popularity of sites on the World Wide Web to the number of citations received on a scientific paper. The feature of this distribution is highlighted by the fact that many nodes (websites or papers) have few connections (internet links or citations) while few “hubs” are connected to many nodes. These properties lead to two very important observed effects: the …

Determination Of Optimal Parameter Estimates For Medical Interventions In Human Metabolism And Inflammation, Marcella Torres

Theses and Dissertations

In this work we have developed three ordinary differential equation models of biological systems: body mass change in response to exercise, immune system response to a general inflammatory stimulus, and the immune system response in atherosclerosis. The purpose of developing such computational tools is to test hypotheses about the underlying biological processes that drive system outcomes as well as possible real medical interventions. Therefore, we focus our analysis on understanding key interactions between model parameters and outcomes to deepen our understanding of these complex processes as a means to developing effective treatments in obesity, sarcopenia, and inflammatory diseases.

We develop …

Using Canalization For The Control Of Discrete Networks, David Murrugarra

Annual Symposium on Biomathematics and Ecology Education and Research

No abstract provided.

Generation Of Nonlinear-Differential-Equations System From A Model Of Boolean Relationships In Arabidopsis Salt Stress Network, Renee Dale

Biology and Medicine Through Mathematics Conference

No abstract provided.

Mental Models And Neutrosophic Cognitive Maps (Modelos Mentales Y Mapas Cognitivos Neutrosóficos), Maykel Leyva-Vazquez, Rebeca Escobar-Jara, Florentin Smarandache

Branch Mathematics and Statistics Faculty and Staff Publications

In this work, elements related to mental models elicitation and analysis are addressed through causal models. Issues related to the need to include indeterminacy in causal relationships through neutrophic cognitive maps are discussed. A proposal for static analysis in neutrosophic cognitive maps is presented. The following activities are included in the proposal: Calculate, measures of centrality, Classify nodes, De-neutrosification, and Ranking nodes. As future works, the incorporation of new metrics of centrality in neutrosophic cognitive maps is proposed. The inclusion of scenario analysis to the proposal is another area of future work.

Comparison Of The Regulatory Dynamics Of Related Small Gene Regulatory Networks That Control The Response To Cold Shock In Saccharomyces Cerevisiae, Natalie Williams

Honors Thesis

The Dahlquist Lab investigates the global, transcriptional response of Sacchromyces cerevisiae, baker’s yeast, to the environmental stress of cold shock, using DNA microarrays for the wild type strain and strains deleted for a particular regulatory transcription factor. Gene regulatory networks (GRNs) consist of transcription factors (TF), genes, and the regulatory connections between them that control the resulting mRNA and protein expression levels. We use mathematical modeling to determine the dynamics of the GRN controlling the cold shock response to determine the relative influence of each transcription factor in the network. A family of GRNs has been derived from the …