Publications by authors named "Miguel A P Oliveira"

Article Synopsis
  • Constraint-based reconstruction and analysis (COBRA) is a framework for analyzing molecular biology data and predicting biological phenomena based on experimental data.
  • The COBRA Toolbox is a powerful software suite that allows users to customize protocols for various biochemical networks and has been updated to version 3.0, which includes new features for modeling and analyzing complex biological systems.
  • The latest version offers enhanced methods for data integration and visualization, as well as multi-lingual code capabilities to improve performance across different biological modeling scenarios.
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Parkinson's disease is a slowly progressive neurodegenerative disease characterised by dysfunction and death of selectively vulnerable midbrain dopaminergic neurons and the development of human in vitro cellular models of the disease is a major challenge in Parkinson's disease research. We constructed an automated cell culture platform optimised for long-term maintenance and monitoring of different cells in three dimensional microfluidic cell culture devices. The system can be flexibly adapted to various experimental protocols and features time-lapse imaging microscopy for quality control and electrophysiology monitoring to assess cellular activity.

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A specific set of brainstem nuclei are susceptible to degeneration in Parkinson's disease. We hypothesise that neuronal vulnerability reflects shared phenotypic characteristics that confer selective vulnerability to degeneration. Neuronal phenotypic specification is mainly the cumulative result of a transcriptional regulatory program that is active during the development.

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One of the hallmarks of sporadic Parkinson's disease is degeneration of dopaminergic neurons in the pars compacta of the substantia nigra. The aetiopathogenesis of this degeneration is still not fully understood, with dysfunction of many biochemical pathways in different subsystems suggested to be involved. Recent advances in constraint-based modelling approaches hold great potential to systematically examine the relative contribution of dysfunction in disparate pathways to dopaminergic neuronal degeneration, but few studies have employed these methods in Parkinson's disease research.

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