Search Results - "Flores, Kevin B"

Biologically-informed neural networks guide mechanistic modeling from sparse experimental data by Lagergren, John H, Nardini, John T, Baker, Ruth E, Simpson, Matthew J, Flores, Kevin B

“…Biologically-informed neural networks (BINNs), an extension of physics-informed neural networks [1], are introduced and used to discover the underlying…”
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Hybrid modeling and prediction of dynamical systems by Hamilton, Franz, Lloyd, Alun L, Flores, Kevin B

“…Scientific analysis often relies on the ability to make accurate predictions of a system's dynamics. Mechanistic models, parameterized by a number of unknown…”
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Topological data analysis distinguishes parameter regimes in the Anderson-Chaplain model of angiogenesis by Nardini, John T, Stolz, Bernadette J, Flores, Kevin B, Harrington, Heather A, Byrne, Helen M

“…Angiogenesis is the process by which blood vessels form from pre-existing vessels. It plays a key role in many biological processes, including embryonic…”
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Deep learning-enabled analysis reveals distinct neuronal phenotypes induced by aging and cold-shock by Saberi-Bosari, Sahand, Flores, Kevin B, San-Miguel, Adriana

“…Abstract Background Access to quantitative information is crucial to obtain a deeper understanding of biological systems. In addition to being low-throughput,…”
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A tutorial review of mathematical techniques for quantifying tumor heterogeneity by Everett, Rebecca, B. Flores, Kevin, Henscheid, Nick, Lagergren, John, Larripa, Kamila, Li, Ding, T. Nardini, John, T. T. Nguyen, Phuong, Bruce Pitman, E., M. Rutter, Erica

“…Intra-tumor and inter-patient heterogeneity are two challenges in developing mathematical models for precision medicine diagnostics. Here we review several…”
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Learning differential equation models from stochastic agent-based model simulations by Nardini, John T, Baker, Ruth E, Simpson, Matthew J, Flores, Kevin B

“…Agent-based models provide a flexible framework that is frequently used for modelling many biological systems, including cell migration, molecular dynamics,…”
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Learning partial differential equations for biological transport models from noisy spatio-temporal data by Lagergren, John H, Nardini, John T, Michael Lavigne, G, Rutter, Erica M, Flores, Kevin B

“…We investigate methods for learning partial differential equation (PDE) models from spatio-temporal data under biologically realistic levels and forms of…”
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Estimation of Parameter Distributions for Reaction-Diffusion Equations with Competition using Aggregate Spatiotemporal Data by Nguyen, Kyle, Rutter, Erica M., Flores, Kevin B.

“…Reaction-diffusion equations have been used to model a wide range of biological phenomenon related to population spread and proliferation from ecology to…”
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Role of Methylation of DNA in Environmental Adaptation by Flores, Kevin B, Wolschin, Florian, Amdam, Gro V

“…Methylation of DNA is an epigenetic mechanism that influences patterns of gene expression. DNA methylation marks contribute to adaptive phenotypic variation…”
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Learning Equations from Biological Data with Limited Time Samples by Nardini, John T., Lagergren, John H., Hawkins-Daarud, Andrea, Curtin, Lee, Morris, Bethan, Rutter, Erica M., Swanson, Kristin R., Flores, Kevin B.

“…Equation learning methods present a promising tool to aid scientists in the modeling process for biological data. Previous equation learning studies have…”
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Predicting Inter-individual Variability During Lipid Resuscitation of Bupivacaine Cardiotoxicity in Rats: A Virtual Population Modeling Study by McDaniel, Matthew, Flores, Kevin B., Akpa, Belinda S.

“…Introduction Intravenous lipid emulsions (ILE) have been credited for successful resuscitation in drug intoxication cases where other cardiac life-support…”
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Quantifying collective motion patterns in mesenchymal cell populations using topological data analysis and agent-based modeling by Nguyen, Kyle C., Jameson, Carter D., Baldwin, Scott A., Nardini, John T., Smith, Ralph C., Haugh, Jason M., Flores, Kevin B.

“…Fibroblasts in a confluent monolayer are known to adopt elongated morphologies in which cells are oriented parallel to their neighbors. We collected and…”
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Forecasting and Uncertainty Quantification Using a Hybrid of Mechanistic and Non-mechanistic Models for an Age-Structured Population Model by Lagergren, John, Reeder, Amanda, Hamilton, Franz, Smith, Ralph C., Flores, Kevin B.

“…In this paper, we present a new method for the prediction and uncertainty quantification of data-driven multivariate systems. Traditionally, either mechanistic…”
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Stoichiometric Ecotoxicology for a Multisubstance World by Peace, Angela, Frost, Paul C, Wagner, Nicole D, Danger, Michael, Accolla, Chiara, Antczak, Philipp, Brooks, Bryan W, Costello, David M, Everett, Rebecca A, Flores, Kevin B, Heggerud, Christopher M, Karimi, Roxanne, Kang, Yun, Kuang, Yang, Larson, James H, Mathews, Teresa, Mayer, Gregory D, Murdock, Justin N, Murphy, Cheryl A, Nisbet, Roger M, Pecquerie, Laure, Pollesch, Nathan, Rutter, Erica M, Schulz, Kimberly L, Scott, J Thad, Stevenson, Louise, Wang, Hao

“…Abstract Nutritional and contaminant stressors influence organismal physiology, trophic interactions, community structure, and ecosystem-level processes;…”
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Detection of Bladder Contractions From the Activity of the External Urethral Sphincter in Rats Using Sparse Regression by Rutter, Erica M., Langdale, Christopher L., Hokanson, James A., Hamilton, Franz, Tran, Hien, Grill, Warren M., Flores, Kevin B.

“…Bladder overactivity and incontinence and dysfunction can be mitigated by electrical stimulation of the pudendal nerve applied at the onset of a bladder…”
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Deciphering a methylome: what can we read into patterns of DNA methylation? by Flores, Kevin B, Amdam, Gro V

“…The methylation of cytosines within cytosine-guanine (CG) dinucleotides is an epigenetic mark that can modify gene transcription. With the advent of…”
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Optimal design of non-equilibrium experiments for genetic network interrogation by Adoteye, Kaska, Banks, H.T., Flores, Kevin B.

“…Many experimental systems in biology, especially synthetic gene networks, are amenable to perturbations that are controlled by the experimenter. We developed…”
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Continuous Structured Population Models for Daphnia magna by Rutter, Erica M., Banks, H. T., LeBlanc, Gerald A., Flores, Kevin B.

“…We continue our efforts in modeling Daphnia magna , a species of water flea, by proposing a continuously structured population model incorporating…”
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Immuno-modulatory strategies for reduction of HIV reservoir cells by Banks, H.T., Flores, Kevin B., Hu, Shuhua, Rosenberg, Eric, Buzon, Maria, Yu, Xu, Lichterfeld, Matthias

“…Antiretroviral therapy is able to suppress the viral load to below the detection limit, but it is not able to eradicate HIV reservoirs. Thus, there is a…”
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A structured population modeling framework for quantifying and predicting gene expression noise in flow cytometry data by Flores, Kevin B.

“…We formulated a structured population model with distributed parameters to identify mechanisms that contribute to gene expression noise in time-dependent flow…”
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