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Open AccessModeling the Role of Immune Cell Conversion in the Tumor-Immune Microenvironment
Tumors develop in a complex physical, biochemical, and cellular milieu, referred to as the tumor microenvironment. Of special interest is the set of immune cells that reciprocally interact with the tumor, the ...
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Chapter
Introduction to Evolutionary Dynamics
The theory of Darwinian evolution can be treated using the formalism of chemical systems where the reactions consist of birth, death and genomic changes. In this chapter we introduce this approach and focus on...
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Book
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Introduction to Models of Cell Motility
Biological cells are quintessentially active objects, using their stored energy to power motion. The field of cell motility is quite broad, ranging from bacteria to mammalian cells, from swimming to crawling t...
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Article
Open AccessAuthor Correction: Guidelines and definitions for research on epithelial–mesenchymal transition
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Article
Collective motility and mechanical waves in cell clusters
Epithelial cell clusters often move collectively on a substrate. Mechanical signals play a major role in organizing this behavior. There are a number of experimental observations in these systems which await a...
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Article
Decoding leader cells in collective cancer invasion
Collective cancer invasion with leader–follower organization is increasingly recognized as a predominant mechanism in the metastatic cascade. Leader cells support cancer invasion by creating invasion tracks, s...
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Open AccessAuthor Correction: Presynaptic endoplasmic reticulum regulates short-term plasticity in hippocampal synapses
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Open AccessSpatial distribution of B cells and lymphocyte clusters as a predictor of triple-negative breast cancer outcome
While tumor infiltration by CD8+ T cells is now widely accepted to predict outcomes, the clinical significance of intratumoral B cells is less clear. We hypothesized that spatial distribution rather than density ...
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Article
Towards decoding the coupled decision-making of metabolism and epithelial-to-mesenchymal transition in cancer
Cancer cells have the plasticity to adjust their metabolic phenotypes for survival and metastasis. A developmental programme known as epithelial-to-mesenchymal transition (EMT) plays a critical role during met...
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Article
Open AccessBreast cancer dormancy: need for clinically relevant models to address current gaps in knowledge
Breast cancer is the most commonly diagnosed cancer in the USA. Although advances in treatment over the past several decades have significantly improved the outlook for this disease, most women who are diagnos...
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Article
Rapid assessment of T-cell receptor specificity of the immune repertoire
Accurate assessment of T-cell-receptor (TCR)–antigen specificity across the whole immune repertoire lies at the heart of improved cancer immunotherapy, but predictive models capable of high-throughput assessme...
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Article
Open AccessPresynaptic endoplasmic reticulum regulates short-term plasticity in hippocampal synapses
Short-term plasticity preserves a brief history of synaptic activity that is communicated to the postsynaptic neuron. This is primarily regulated by a calcium signal initiated by voltage dependent calcium chan...
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Mathematical Modeling of Plasticity and Heterogeneity in EMT
The epithelial-mesenchymal transition (EMT) and the corresponding reverse process, mesenchymal-epithelial transition (MET), are dynamic and reversible cellular programs orchestrated by many changes at both bio...
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Article
Open AccessGuidelines and definitions for research on epithelial–mesenchymal transition
Epithelial–mesenchymal transition (EMT) encompasses dynamic changes in cellular organization from epithelial to mesenchymal phenotypes, which leads to functional changes in cell migration and invasion. EMT occ...
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Article
Histone deacetylases, Mbd3/NuRD, and Tet2 hydroxylase are crucial regulators of epithelial–mesenchymal plasticity and tumor metastasis
An epithelial–mesenchymal transition (EMT) represents a basic morphogenetic process of high cell plasticity underlying embryogenesis, wound healing, cancer metastasis and drug resistance. It involves a profoun...
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Article
Deciphering the Dynamics of Epithelial-Mesenchymal Transition and Cancer Stem Cells in Tumor Progression
The epithelial-mesenchymal transition (EMT) and the generation of cancer stem cells (CSCs) are two fundamental aspects contributing to tumor growth, acquisition of resistance to therapy, formation of metastase...
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Computational Modeling of Collective Cell Migration: Mechanical and Biochemical Aspects
Collective cell migration plays key roles in various physiological and pathological processes in multicellular organisms, including embryonic development, wound healing, and formation of cancer metastases. Suc...
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Protocol
Quantitative Characteristic of ncRNA Regulation in Gene Regulatory Networks
RNA is mostly known for its role in protein synthesis, where it encodes information for protein sequence in its messenger RNA (mRNA) form (translation). Yet, RNA molecules regulate several cellular processes o...
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Article
Open AccessRACIPE: a computational tool for modeling gene regulatory circuits using randomization
One of the major challenges in traditional mathematical modeling of gene regulatory circuits is the insufficient knowledge of kinetic parameters. These parameters are often inferred from existing experimental ...
