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Farahpour, F.

Publications and source records attributed to Farahpour, F..

3 recordsLinked to original sources

Eco-Evolutionary Dynamics of Proliferation Heterogeneity: A Phenotype-Structured Model for Tumor Growth and Treatment Response

Intra-tumor heterogeneity in proliferation rates fundamentally influences cancer progression and treatment resistance. To investigate how continuous phenotypic variation shapes eco-evolutionary dynamics, we develop a phenotype-structured partial differential equation framework that explicitly models proliferation heterogeneity as a dynamic trait. Our model integrates three key biological principles: (1) phenotypic diffusion capturing heritable variation in proliferation rates, (2) global resource competition enforcing density-dependent growth constraints, and (3) an experimentally grounded life-history trade-off linking elevated proliferation to increased mortality. Using adaptive dynamics, we derive the optimum proliferation rate in a growing tumor, showing that the optimal phenotype dynamically shifts toward slower proliferation as tumors approach carrying capacity under control condition. We perform in silico treatment simulations for four different treatment regimes (pan-proliferation, low-, mid-, and high-proliferation targeting) to show how therapeutic selective pressures reshape fitness landscapes. While all treatments slow down tumor growth, they induce divergent evolutionary trajectories. We connect these dynamics with changes in mean proliferation rates during and after treatment. Our work establishes a predictive, evolutionarily grounded framework for understanding how therapy reshapes tumor proliferation landscapes, offering a mechanistic basis for designing strategies that anticipate and counteract adaptive resistance.

bioinformatics↗

scBubbletree: quantitative visualization of single cell RNA-seq data

MotivationVisualization approaches transform high-dimensional data from single cell RNA sequencing (scRNA-seq) experiments into two-dimensional plots that are used for analysis of cell relationships, and as a means of reporting biological insights. Yet, many standard approaches generate visuals that suffer from overplotting, lack of quantitative information, and distort global and local properties of biological patterns relative to the original high-dimensional space. ResultsWe present scBubbletree, a new, scalable method for visualization of scRNA-seq data. The method identifies clusters of cells of similar transcriptomes and visualizes such clusters as "bubbles" at the tips of dendrograms (bubble trees), corresponding to quantitative summaries of cluster properties and relationships. scBubbletree stacks bubble trees with further cluster-associated information in a visually easily accessible way, thus facilitating quantitative assessment and biological interpretation of scRNA-seq data. Availability and Implementationthe R package scBubbletree is freely available at: https://bioconductor.org/packages/scBubbletree/ Contactsimo.kitanovski@uni-due.de, daniel.hoffmann@uni-due.de

bioinformatics↗

Trade-off shapes diversity in eco-evolutionary dynamics

We introduce an Interaction and Trade-off based Eco-Evolutionary Model (ITEEM), in which species are competing for resources in a well-mixed system, and their evolution in interaction trait space is subject to a life-history trade-off between replication rate and competitive ability. We demonstrate that the strength of the trade-off has a fundamental impact on eco-evolutionary dynamics, as it imposes four phases of diversity, including a sharp phase transition. Despite its minimalism, ITEEM produces without further ad hoc features a remarkable range of observed patterns of eco-evolutionary dynamics. Most notably we find self-organization towards structured communities with high and sustainable diversity, in which competing species form interaction cycles similar to rock-paper-scissors games.

bioinformatics↗