Search Results - "Nardini, John T"

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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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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Modeling keratinocyte wound healing dynamics: Cell–cell adhesion promotes sustained collective migration by Nardini, John T., Chapnick, Douglas A., Liu, Xuedong, Bortz, David M.

“…The in vitro migration of keratinocyte cell sheets displays behavioral and biochemical similarities to the in vivo wound healing response of keratinocytes in…”
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Forecasting and Predicting Stochastic Agent-Based Model Data with Biologically-Informed Neural Networks by Nardini, John T.

“…Collective migration is an important component of many biological processes, including wound healing, tumorigenesis, and embryo development. Spatial…”
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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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Statistical and topological summaries aid disease detection for segmented retinal vascular images by Nardini, John T., Pugh, Charles W. J., Byrne, Helen M.

“…Objective Disease complications can alter vascular network morphology and disrupt tissue functioning. Microvascular diseases of the retina are assessed by…”
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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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INVESTIGATION OF A STRUCTURED FISHER'S EQUATION WITH APPLICATIONS IN BIOCHEMISTRY by NARDINI, JOHN T., BORTZ, D. M.

“…Recent biological research has sought to understand how biochemical signaling pathways, such as the mitogen-activated protein kinase (MAPK) family, influence…”
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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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Learning partial differential equations for biological transport models from noisy spatio-temporal data by Lagergren, John H., Nardini, John T., Lavigne, G. Michael, 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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Forecasting and predicting stochastic agent-based model data with biologically-informed neural networks by Nardini, John T

“…Collective migration is an important component of many biological processes, including wound healing, tumorigenesis, and embryo development. Spatial…”
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Statistical and Topological Summaries Aid Disease Detection for Segmented Retinal Vascular Images by Nardini, John T, Pugh, Charles W. J, Byrne, Helen M

“…Disease complications can alter vascular network morphology and disrupt tissue functioning. Diabetic retinopathy, for example, is a complication of types 1 and…”
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The Influence of Numerical Error on an Inverse Problem Methodology in PDE Models by Nardini, John T, Bortz, D. M

“…The inverse problem methodology is a commonly-used framework in the sciences for parameter estimation and inference. It is typically performed by fitting a…”
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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

“…Journal of the Royal Society Interface 18 (176) 2021 Agent-based models provide a flexible framework that is frequently used for modelling many biological…”
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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…”
Get full text

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…”
Get full text

Investigation of a Structured Fisher's Equation with Applications in Biochemistry by Nardini, John T, Bortz, D. M

“…Recent biological research has sought to understand how biochemical signaling pathways, such as the mitogen-activated protein kinase (MAPK) family, influence…”
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Analyzing Collective Motion with Machine Learning and Topology by Bhaskar, Dhananjay, Manhart, Angelika, Milzman, Jesse, Nardini, John T, Storey, Kathleen, Topaz, Chad M, Ziegelmeier, Lori

“…Chaos 29, 123125 (2019) We use topological data analysis and machine learning to study a seminal model of collective motion in biology [D'Orsogna et al., Phys…”
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