Metabolomics meets systems immunology

J Fu, F Zhu, CJ Xu, Y Li - EMBO reports, 2023 - embopress.org
Metabolic processes play a critical role in immune regulation. Metabolomics is the
systematic analysis of small molecules (metabolites) in organisms or biological samples …

Tuneable resolution as a systems biology approach for multi‐scale, multi‐compartment computational models

DE Kirschner, CA Hunt, S Marino… - … Systems Biology and …, 2014 - Wiley Online Library
The use of multi‐scale mathematical and computational models to study complex biological
processes is becoming increasingly productive. Multi‐scale models span a range of spatial …

Circulating tumor cells: when a solid tumor meets a fluid microenvironment

KA Rejniak - … of Tumor Microenvironment: Quantitative Modeling and …, 2016 - Springer
Solid tumor dissemination from the primary site to the sites of metastasis involves tumor cell
transport through the blood or lymph circulation systems. Once the tumor cells enter the …

In silico, in vitro, and in vivo studies indicate the potential use of bolaamphiphiles for therapeutic siRNAs delivery

T Kim, KA Afonin, M Viard, AY Koyfman… - … Therapy-Nucleic Acids, 2013 - cell.com
Specific small interfering RNAs (siRNAs) designed to silence different oncogenic pathways
can be used for cancer therapy. However, non-modified naked siRNAs have short half-lives …

Contrasting model mechanisms of alanine aminotransferase (ALT) release from damaged and necrotic hepatocytes as an example of general biomarker mechanisms

AK Smith, GEP Ropella, MR McGill… - PLoS computational …, 2020 - journals.plos.org
Interpretations of elevated blood levels of alanine aminotransferase (ALT) for drug-induced
liver injury often assume that the biomarker is released passively from dying cells. However …

Systems immunology: a survey of modeling formalisms, applications and simulation tools

V Narang, J Decraene, SY Wong, BS Aiswarya… - Immunologic …, 2012 - Springer
Immunological studies frequently analyze individual components (eg, signaling pathways) of
immune systems in a reductionist manner. In contrast, systems immunology aims to give a …

Agent‐based modeling: a systematic assessment of use cases and requirements for enhancing pharmaceutical research and development productivity

CA Hunt, RC Kennedy, SHJ Kim… - … : Systems Biology and …, 2013 - Wiley Online Library
A crisis continues to brew within the pharmaceutical research and development (R&D)
enterprise: productivity continues declining as costs rise, despite ongoing, often dramatic …

Phenotypic transition maps of 3D breast acini obtained by imaging-guided agent-based modeling

J Tang, H Enderling, S Becker-Weimann… - Integrative …, 2011 - academic.oup.com
We introduce an agent-based model of epithelial cell morphogenesis to explore the complex
interplay between apoptosis, proliferation, and polarization. By varying the activity levels of …

Adhesion between P. falciparum infected erythrocytes and human endothelial receptors follows alternative binding dynamics under flow and febrile conditions

P Lubiana, P Bouws, LK Roth, M Dörpinghaus… - Scientific reports, 2020 - nature.com
Characterizing the adhesive dynamics of Plasmodium falciparum infected erythrocytes (IEs)
to different endothelial cell receptors (ECRs) in flow is a big challenge considering available …

MDCK cystogenesis driven by cell stabilization within computational analogues

JA Engelberg, A Datta, KE Mostov… - PLoS Computational …, 2011 - journals.plos.org
The study of epithelial morphogenesis is fundamental to increasing our understanding of
organ function and disease. Great progress has been made through study of culture systems …