Eberhard O. Voit
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View article: Analysis of systemic effects of dioxin on human health through template-and-anchor modeling
Analysis of systemic effects of dioxin on human health through template-and-anchor modeling Open
Dioxins are persistent environmental pollutants known for their multiple health effects, from skin rashes to liver dysfunction, reproductive toxicity and cancer. While the hazards of dioxins have been well documented, the challenge of deve…
View article: Hepatic cholesterol biosynthesis and dioxin-induced dysregulation: A multiscale computational approach
Hepatic cholesterol biosynthesis and dioxin-induced dysregulation: A multiscale computational approach Open
View article: What’s next for computational systems biology?
What’s next for computational systems biology? Open
Largely unknown just a few decades ago, computational systems biology is now a central methodology for biological and medical research. This amazing ascent raises the question of what the community should do next. The article outlines our …
View article: Mathematical models of cystic fibrosis as a systemic disease
Mathematical models of cystic fibrosis as a systemic disease Open
Cystic fibrosis (CF) is widely known as a disease of the lung, even though it is in truth a systemic disease, whose symptoms typically manifest in gastrointestinal dysfunction first. CF ultimately impairs not only the pancreas and intestin…
View article: A dynamic compartment model for xylem loading and long-distance transport of iron explains the effect of kanamycin on metal uptake in Arabidopsis
A dynamic compartment model for xylem loading and long-distance transport of iron explains the effect of kanamycin on metal uptake in Arabidopsis Open
Arabidopsis plants exposed to the antibiotic kanamycin (Kan) display altered metal homeostasis. Further, mutation of the WBC19 gene leads to increased sensitivity to kanamycin and changes in iron (Fe) and zinc (Zn) uptake. Here we propose …
View article: Polycraft World AI Lab (PAL): An Extensible Platform for Evaluating Artificial Intelligence Agents
Polycraft World AI Lab (PAL): An Extensible Platform for Evaluating Artificial Intelligence Agents Open
As artificial intelligence research advances, the platforms used to evaluate AI agents need to adapt and grow to continue to challenge them. We present the Polycraft World AI Lab (PAL), a task simulator with an API based on the Minecraft m…
View article: Inference of dynamic interaction networks: A comparison between Lotka-Volterra and multivariate autoregressive models
Inference of dynamic interaction networks: A comparison between Lotka-Volterra and multivariate autoregressive models Open
Networks are ubiquitous throughout biology, spanning the entire range from molecules to food webs and global environmental systems. Yet, despite substantial efforts by the scientific community, the inference of these networks from data sti…
View article: MaHPIC malaria systems biology data from Plasmodium cynomolgi sporozoite longitudinal infections in macaques
MaHPIC malaria systems biology data from Plasmodium cynomolgi sporozoite longitudinal infections in macaques Open
Plasmodium cynomolgi causes zoonotic malarial infections in Southeast Asia and this parasite species is important as a model for Plasmodium vivax and Plasmodium ovale . Each of these species produces hypnozoites in the liver, which can cau…
View article: Methods of quantifying interactions among populations using Lotka-Volterra models
Methods of quantifying interactions among populations using Lotka-Volterra models Open
The Lotka-Volterra (LV) model was introduced in the early 20th Century to describe predator-prey systems. Since then, the model has been expanded to capture the dynamics of numerous types of interacting populations and to include the effec…
View article: Perspective: Systems biology beyond biology
Perspective: Systems biology beyond biology Open
The past decades have witnessed an astounding rise of the nascent field of systems biology. By and large unknown or ignored for a long time, the field rapidly moved into the limelight and is now in the process of becoming a widely recogniz…
View article: Perspectives of (/memorandum for) systems thinking on COVID‐19 pandemic and pathology
Perspectives of (/memorandum for) systems thinking on COVID‐19 pandemic and pathology Open
Is data‐driven analysis sufficient for understanding the COVID‐19 pandemic and for justifying public health regulations? In this paper, we argue that such analysis is insufficient. Rather what is needed is the identification and implementa…
View article: A Passaged 3-species Synthetic Microbial Community
A Passaged 3-species Synthetic Microbial Community Open
We constructed de novo a community of three model bacterial species, Vibrio cholerae, Staphylococcus aureus, and Escherichia coli, which all constitutively produce a distinct fluorescent protein. This fluorescenc…
View article: A Passaged 3-species Synthetic Microbial Community
A Passaged 3-species Synthetic Microbial Community Open
We constructed de novo a community of three model bacterial species, Vibrio cholerae, Staphylococcus aureus, and Escherichia coli, which all constitutively produce a distinct fluorescent protein. This fluorescenc…
View article: Antibiotics Drive Expansion of Rare Pathogens in a Chronic Infection Microbiome Model
Antibiotics Drive Expansion of Rare Pathogens in a Chronic Infection Microbiome Model Open
We develop and clinically benchmark an experimental model of the cystic fibrosis (CF) lung infection microbiome to investigate the impacts of antibiotic exposures on chronic, polymicrobial infections. We show that a single experimental mod…
View article: Plasmodium knowlesi Cytoadhesion Involves SICA Variant Proteins
Plasmodium knowlesi Cytoadhesion Involves SICA Variant Proteins Open
Plasmodium knowlesi poses a health threat throughout Southeast Asian communities and currently causes most cases of malaria in Malaysia. This zoonotic parasite species has been studied in Macaca mulatta (rhesus monkeys) as a model for seve…
View article: Discrete Biochemical Systems Theory
Discrete Biochemical Systems Theory Open
Almost every biomedical systems analysis requires early decisions regarding the choice of the most suitable representations to be used. De facto the most prevalent choice is a system of ordinary differential equations (ODEs). This framewor…
View article: Dynamic Control Balancing Cell Proliferation and Inflammation is Crucial for an Effective Immune Response to Malaria
Dynamic Control Balancing Cell Proliferation and Inflammation is Crucial for an Effective Immune Response to Malaria Open
Malaria has a complex pathology with varying manifestations and symptoms, effects on host tissues, and different degrees of severity and ultimate outcome, depending on the causative Plasmodium pathogen and host species. Previously, we comp…
View article: Clinical recovery of Macaca fascicularis infected with Plasmodium knowlesi
Clinical recovery of Macaca fascicularis infected with Plasmodium knowlesi Open
View article: Emergence and Enhancement of Ultrasensitivity through Posttranslational Modulation of Protein Stability
Emergence and Enhancement of Ultrasensitivity through Posttranslational Modulation of Protein Stability Open
Signal amplification in biomolecular networks converts a linear input to a steeply sigmoid output and is central to a number of cellular functions including proliferation, differentiation, homeostasis, adaptation, and biological rhythms. O…
View article: Comparison Between Lotka-Volterra and Multivariate Autoregressive Models of Ecological Interaction Systems
Comparison Between Lotka-Volterra and Multivariate Autoregressive Models of Ecological Interaction Systems Open
Lotka-Volterra (LV) and Multivariate Autoregressive (MAR) models are computational frameworks with different mathematical structures that have both been proposed for the same purpose of extracting governing features of dynamic interactions…
View article: Dramatic transcriptomic differences in Macaca mulatta and Macaca fascicularis with Plasmodium knowlesi infections
Dramatic transcriptomic differences in Macaca mulatta and Macaca fascicularis with Plasmodium knowlesi infections Open
Plasmodium knowlesi, a model malaria parasite, is responsible for a significant portion of zoonotic malaria cases in Southeast Asia and must be controlled to avoid disease severity and fatalities. However, little is known about the host-pa…
View article: Inference and Validation of The Structure of Lotka-Volterra Models
Inference and Validation of The Structure of Lotka-Volterra Models Open
For close to a century, Lotka-Volterra (LV) models have been used to investigate interactions among populations of different species. For a few species, these investigations are straightforward. However, with the arrival of large and compl…
View article: Emergence and Enhancement of Ultrasensitivity through Posttranslational Modulation of Protein Stability
Emergence and Enhancement of Ultrasensitivity through Posttranslational Modulation of Protein Stability Open
Signal amplification converts a linear input to a steeply sigmoid output and is central to cellular functions. One canonical signal amplifying motif is zero-order ultrasensitivity through the posttranslational modification (PTM) cycle sign…
View article: Inference and Validation of the Structure of Lotka-Volterra Models
Inference and Validation of the Structure of Lotka-Volterra Models Open
For close to a century, Lotka-Volterra (LV) models have been used to investigate interactions among populations of different species. For a few species, these investigations are straightforward. However, with the arrival of large and compl…
View article: Toward Personalized Medicine for HIV/AIDS
Toward Personalized Medicine for HIV/AIDS Open
In 2019, approximately 38 million people were infected with HIV worldwide. Although there is still no cure that successfully eradicates the disease, combination antiretroviral therapy (cART) has improved to a point where undetectable viral…
View article: Clinical recovery of <i>Macaca fascicularis</i> infected with <i>Plasmodium knowlesi</i>
Clinical recovery of <i>Macaca fascicularis</i> infected with <i>Plasmodium knowlesi</i> Open
Background Kra monkeys ( Macaca fascicularis ), a natural host of Plasmodium knowlesi, control parasitaemia caused by this parasite species and escape death without treatment. Knowledge of the disease progression and resilience in kra monk…
View article: Antibiotics drive expansion of rare pathogens in a chronic infection microbiome model
Antibiotics drive expansion of rare pathogens in a chronic infection microbiome model Open
Chronic (long-lasting) infections are globally a major and rising cause of morbidity and mortality. Unlike typical acute infections, chronic infections are ecologically diverse, characterized by the presence of a polymicrobial mix of oppor…
View article: A model of dopamine and serotonin-kynurenine metabolism in cortisolemia: Implications for depression
A model of dopamine and serotonin-kynurenine metabolism in cortisolemia: Implications for depression Open
A major factor contributing to the etiology of depression is a neurochemical imbalance of the dopaminergic and serotonergic systems, which is caused by persistently high levels of circulating stress hormones. Here, a computational model is…
View article: Integration of Biology, Mathematics and Computing in the Classroom Through the Creation and Repeated Use of Transdisciplinary Modules
Integration of Biology, Mathematics and Computing in the Classroom Through the Creation and Repeated Use of Transdisciplinary Modules Open
The integration of biology with mathematics and computer science mandates the training of students capable of comfortably navigating among these fields. We address this formidable pedagogical challenge with the creation of transdisciplinar…
View article: Mechanistic Model of Signaling Dynamics Across an Epithelial Mesenchymal Transition
Mechanistic Model of Signaling Dynamics Across an Epithelial Mesenchymal Transition Open
Intracellular signaling pathways are at the core of cellular information processing. The states of these pathways and their inputs determine signaling dynamics and drive cell function. Within a cancerous tumor, many combinations of cell st…