Phagocytosis in cellular defense and nutrition: a food-centered approach to the evolution of macrophages

V Hartenstein, P Martinez - Cell and tissue research, 2019 - Springer
The uptake of macromolecules and larger energy-rich particles into the cell is known as
phagocytosis. Phagocytosed material is enzymatically degraded in membrane-bound …

Implementing computational modeling in tissue engineering: where disciplines meet

JN Post, S Loerakker, RMH Merks… - Tissue Engineering Part …, 2022 - liebertpub.com
In recent years, the mathematical and computational sciences have developed novel
methodologies and insights that can aid in designing advanced bioreactors, microfluidic …

Reconciling qualitative, abstract, and scalable modeling of biological networks

L Paulevé, J Kolčák, T Chatain, S Haar - Nature communications, 2020 - nature.com
Predicting biological systems' behaviors requires taking into account many molecular and
genetic elements for which limited information is available past a global knowledge of their …

Reprogramming cancer into antigen-presenting cells as a novel immunotherapy

MH Linde, AC Fan, T Köhnke, AC Trotman-Grant… - Cancer …, 2023 - aacrjournals.org
Therapeutic cancer vaccination seeks to elicit activation of tumor-reactive T cells capable of
recognizing tumor-associated antigens (TAA) and eradicating malignant cells. Here, we …

The CoLoMoTo interactive notebook: accessible and reproducible computational analyses for qualitative biological networks

A Naldi, C Hernandez, N Levy, G Stoll… - Frontiers in …, 2018 - frontiersin.org
Analysing models of biological networks typically relies on workflows in which different
software tools with sensitive parameters are chained together, many times with additional …

Models of cell processes are far from the edge of chaos

KH Park, FX Costa, LM Rocha, R Albert, JC Rozum - PRX life, 2023 - APS
Complex living systems are thought to exist at the “edge of chaos” separating the ordered
dynamics of robust function from the disordered dynamics of rapid environmental …

Logical modeling and analysis of cellular regulatory networks with GINsim 3.0

A Naldi, C Hernandez, W Abou-Jaoudé… - Frontiers in …, 2018 - frontiersin.org
The logical formalism is well adapted to model large cellular networks, in particular when
detailed kinetic data are scarce. This tutorial focuses on this well-established qualitative …

DUX4r, ZNF384r and PAX5-P80R mutated B-cell precursor acute lymphoblastic leukemia frequently undergo monocytic switch

M Novakova, M Zaliova, K Fiser… - …, 2020 - pmc.ncbi.nlm.nih.gov
Recently, we described B-cell precursor acute lymphoblastic leukemia (BCP-ALL) subtype
with an early switch to the monocytic lineage and the loss of the B-cell immunophenotype …

A logic-incorporated gene regulatory network deciphers principles in cell fate decisions

G Xue, X Zhang, W Li, L Zhang, Z Zhang, X Zhou… - Elife, 2024 - elifesciences.org
Organisms utilize gene regulatory networks (GRN) to make fate decisions, but the regulatory
mechanisms of transcription factors (TF) in GRNs are exceedingly intricate. A longstanding …

A novel Boolean network inference strategy to model early hematopoiesis aging

L Hérault, M Poplineau, E Duprez, É Remy - Computational and Structural …, 2023 - Elsevier
Hematopoietic stem cell (HSC) aging is a multifactorial event leading to changes in HSC
properties and functions, which are intrinsically coordinated and affect the early …