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Title: Evolutionary dynamics of conserved non-coding DNA elements: Big bang or gradual accretion?

Abstract:
Background Previous studies have found that DNA elements are highly conserved
in species from the same lineage, even though they do not code for proteins or RNA.
One proposed function of such conserved non-coding elements (CNEs) is that they
are cis-regulatory sequences for developmental genes which act as an abstraction of
genetic regulatory networks, thus allowing new animal body plans to be specified in
a modular way. This thesis tests the specific proposal by a previous study that CNEs
arose in a big bang in the Precambrian, approximately 600 million years ago.

Results The evolutionary dynamics of CNEs were studied by first identifying the
elements, and then examining their levels of identity over time. Pairwise comparative
sequence analysis of five contemporary nematode species provided a window into
the past because these species diverged at different points of time over the last ap-
proximately 700 million years. The number of CNEs and their basic properties for the
three most recently diverged species match the results obtained by other researchers,
although no clear trend is visible in the change in identity of CNEs with respect to
time since divergence. On adding two more species to the analysis, it was found that
no such elements could be identified for species pairs with deep divergences.

Conclusions The absence of CNEs for pairwise comparisons of species that diverged
earliest indicates that CNEs did not arise in a big bang. CNEs that were found for the
three Caenorhabditis species that diverged relatively recently (approximately 100 mil-
lion years ago) seem to be specific only to that clade. However, the big bang hypothe-
sis cannot be conclusively discarded because it is possible that the elements exist, but
are short, or have multiple components spread across the genome, and are therefore
difficult to detect. Missing CNEs could therefore be a limitation of computational ap-
proaches to discovering CNEs, and this study also suggests some ways to overcome
those limitations.

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I work as the bio-informatician for the Edinburgh Sequencing Facility of the Natural Environment Research Council (NERC), and the School of Biological Sciences Sequencing Service (SBSSS) of the University of Edinburgh.

Degree awarded with Distinction (Equivalent GPA 4.0 on a scale of 4.0). Also awarded the Informatics Prize for the highest overall mark in the MSc course.

My goal was to learn more about how complexity emerges in biological systems and in computational (or robotic) systems.
Semester 1
Genetic Algorithms and Genetic Programming
Learning from Data
Bioinformatics I
Applied Databases
Informatics Research Review - DNA Computation

Semester 2
Computational Systems Biology
Computational Neuroscience of Vision
Intelligent Autonomous Robotics
Bioinformatics 2
Informatics Research Proposal - Evolutionary Genomics

MSc Dissertation
Evolutionary dynamics of conserved non-coding DNA elements: Big bang or gradual accretion? [PDF]

Abstract

Traffic signals and traffic flow models have been studied extensively in the past and have provided valuable insights on the design of signalling systems, congestion control, and punitive policies. This paper takes a slightly different tack and describes what happens at an intersection where the traffic signals are malfunctioning and stuck in some configuration. By modelling individual vehicles as agents, we were able to replicate the surprisingly organized traffic flow that we observed at a real malfunctioning intersection in urban India. Counter-intuitively, the very lawlessness that normally causes jams was causing traffic to flow smoothly at this intersection. We situate this research in the context of other research on emergent complex phenomena in traffic, and suggest further lines of research that could benefit from the analysis and modelling of rule-breaking behaviour.

Index Terms—Self-organizing systems, complex systems, traffic, emergent behaviour, agent-based modelling, rule-breaking

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