Boris H. Aguilar

Estimating glioblastoma migration-to-proliferation ratio from single time-point MRI data via radial density distribution

A reaction-diffusion model fitted to shell-averaged tumor density from one pre-treatment MRI estimates glioblastoma migration/proliferation ratio (D/k); in BraTS 2017, higher D/k went with shorter overall survival.

KGBN: Augmenting and optimizing logical gene regulatory networks using knowledge graphs

KGBN enhances logical gene regulatory networks by integrating knowledge graphs and experimental data to create context-aware models for drug response prediction in AML.

LM-Merger: A workflow for merging logical models with an application to gene regulation

LM-Merger merges logical gene regulatory network models to improve coverage and predictive accuracy in disease contexts.

Uncovering potential interventions for pancreatic cancer patients via mathematical modeling

This paper uses a Boolean model to study the impact of mutations in pancreatic cancer and identifies potential drug targets based on simulation and clinical data.

Modeling the biomechanics of cells on microcarriers in a stirred-tank bioreactor An ABM-CFD coupling approach

This paper develops a computational model combining agent-based modeling and computational fluid dynamics to study how rotor speed affects cell growth on microcarriers in bioreactors.

Multicellular Reservoir Computing

This paper introduces diffusion-based multicellular reservoir computing as a framework for complex temporal signal processing, demonstrating its feasibility and computational advantages over single-cell systems.

SL-Cloud: A Computational Resource to Support Synthetic Lethal Interaction Discovery

SL-Cloud is a cloud-based resource that facilitates the prediction and comparison of context-specific synthetic lethal interactions using multi-omic datasets.

Patient-specific cell communication networks associate with disease progression in cancer

The paper develops a method to generate patient-specific cell communication networks from gene expression data and shows that specific communication edges are associated with disease progression in cancer.

Intricate genetic programs controlling dormancy in Mycobacterium tuberculosis

The paper identifies a six-state genetic program in Mycobacterium tuberculosis that enables entry into and exit from hypoxia-induced dormancy through high-resolution transcriptional time-course analysis.

An Integrated Multiscale, Multicellular Skin Model

This paper describes a computational multiscale multicellular skin model that integrates various modeling styles to simulate barrier formation and response to perturbations.