Ideas about 'Systems Biology' | STIAS: The Stellenbosch Institute for Advanced Study

Project

What would it take to make a virtual microbiology lab?

Computational Biology offers a valuable complement to complex experimental approaches to study infectious diseases like HIV and tuberculosis.

Elsje Pienaar

Project

Complex microbial communities: application of supply-demand principles to advance the science from describing diversity to explaining diversity

This project will involve collaboration with Jannie Hofmeyr (SU) on, amongst others the principles of supply and demand as driving force of metabolic activity, and incorporating them: 1) into existing experimental data sets to explore adaptive behavior amongst bacteria as a basis for the maintenance of microbial community function in environmental processes, and 2) a state-of-science review related to microbiological considerations for repository engineering and long-term safety of deep geological repositories of nuclear waste, as well as formulating recommendations for the way forward to predict the potential impact of microbial activity on the stability of these repositories.

Project

The Pitfalls of Reductionism in Vaccine Research

Reductionism has been the predominant research strategy of molecular and structural biology in the 20th century.

Marc van Regenmortel

Project

Merging the layers of life

Developing a (mathematical) model suitable for the integration of the different levels of biological research (sub-molecular, molecular, organisms, populations) in one framework.

Project

Bringing Physics and Chemistry to Life: from random walks to robust organization

Hans V. Westerhoff will put together the theoretical foundations of today’s biology in a comprehensive new theory, by researching and establishing connections between the various theoretical approaches in use.

Hans Westerhoff

Project

Process Biology

Since around 500BCE, when Heraclitus declared that everything changes while Parmenides maintained that everything stays the same, the dichotomy of process and substance has been at the heart of Western philosophy.

John Dupré

Publication

Phenotypic Switching. Implications in Biology and Medicine

Levine, Herbert, Mohit Jolly, Prakash Kulkarni and Vidyanand Nanjundiah. 2020. Phenotypic Switching. Implications in Biology and Medicine. A...

Vidyanand Nanjundiah

Publication

An integrative network-driven pipeline for systematic identification of lncRNA-associated regulatory network motifs in metastatic melanoma

Singh, Nivedita, Martin Eberhardt, Olaf Wolkenhauer, Julio Vera and Shailendra K. Gupta. 2020. An integrative network-driven pipeline for sy...

Topic: Systems Biology

What would it take to make a virtual microbiology lab?

Complex microbial communities: application of supply-demand principles to advance the science from describing diversity to explaining diversity

The Pitfalls of Reductionism in Vaccine Research

Merging the layers of life

Bringing Physics and Chemistry to Life: from random walks to robust organization

Process Biology

Phenotypic Switching. Implications in Biology and Medicine

An integrative network-driven pipeline for systematic identification of lncRNA-associated regulatory network motifs in metastatic melanoma

Beyond Networks: an Organismic Systems Biology for the 21st Century

Homeostasis as a fundamental principle for a coherent theory of brains

Investigating the two-moment characterization of subcellular biochemical networks

Thresholds in transient dynamics of signal transduction pathways

The complexity of cell-biological systems

A stem cell niche dominance theorem

Analysis of cell adhesion during early stages of colon cancer based on an extended multi-valued logic approach

Quantitative modelling of amyloidogenic processing and its influence by SORLA in Alzheimer’s disease

Mathematical modelling unravels regulatory mechanisms of interferon-gamma-induced STAT1 serine-phosphorylation and MUC4 expression in pancreatic cancer cells

The role of theorem proving in systems biology

Diagrams as locality aids for explanation and model construction in cell biology

Analysing the impact of nucleo-cytoplasmic shuttling of beta-catenin and its antagonists APC, Axin and GSK3 on Wnt/beta-catenin signalling

Systems biology and pediatric research Introduction

The road from systems biology to systems medicine

Kinetic Modeling-Based Detection of Genetic Signatures That Provide Chemoresistance via the E2F1-p73/DNp73-miR-205 Network

Basic research in HIV vaccinology is hampered by reductionist thinking (Review)

Why model?

Enabling multiscale modeling in systems medicine

Tumors as chaotic attractors

Cooperative gene regulation by microRNA pairs and their identification using a computational workflow

Hybrid modeling of the crosstalk between signaling and transcriptional networks using ordinary differential equations and multi-valued logic

The balance between cell cycle arrest and cell proliferation: control by the extracellular matrix and by contact inhibition

Pushing Limits by Embracing Complexity

Anti-Inflammatory Effects of Reactive Oxygen Species – a Multi-Valued Logical Model Validated by Formal Concept Analysis

Systems Approach to the Study of Brain Damage in the Very Preterm Newborn

Coenzyme A-Transferase-Independent Butyrate Re-Assimilation in Clostridium Acetobutylicum—evidence from a Mathematical Model

Combining Computational Models, Semantic Annotations and Simulation Experiments in a Graph Database

Accounting for Randomness in Measurement and Sampling in Studying Cancer Cell Population Dynamics

Dissecting Long-Term Glucose Metabolism Identifies New Susceptibility Period for Metabolic Dysfunction in Aged Mice

Annotation-Based Feature Extraction from Sets of SBML Models

Explanation and Organizing Principles in Systems Biology

Autocrine TGF-β/ZEB/microRNA-200 Signal Transduction Drives Epithelial-Mesenchymal Transition: Kinetic Models Predict Minimal Drug Dose to Inhibit Metastasis

COMODI: An Ontology to Characterise Differences in Versions of Computational Models in Biology

An Algorithm to Detect and Communicate the Differences in Computational Models Describing Biological Systems

The RNA World in the 21st Century—a Systems Approach to Finding Non-Coding Keys to Clinical Questions

Understanding microRNA-Mediated Gene Regulatory Networks through Mathematical Modelling

Cell Fate Specification Based on Tristability in the Inner Cell Mass of Mouse Blastocysts

Dynamics of the Mammalian Cell Cycle in Physiological and Pathological Conditions

RNA Systems Biology for Cancer: From Diagnosis to Therapy

Systems Medicine

Network-Assisted Disease Classification and Biomarker Discovery

Systems biology studies on plant desiccation tolerance for food security

The Scientific Method in Biology and Biomedicine

Revised edition of the book ‘Biochemical Oscillations and Cellular Rhythms’

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