The revolution in DNA sequencing

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Table of contents

I. INTRODUCTION
I.1 MODULARITY
I.2 NETWORKS AND BIG DATA
I.2.1 Data avalanche
I.2.2 Sequence Similarity Networks
I.2.3 Computational bottleneck of SSN
I.3 AIMS OF THE THESIS
II. NETWORK-THINKING IN EVOLUTION
II.1 NETWORKS: A COMPLEMENTARY METHOD TO PHYLOGENETIC ANALYSIS OF EVOLUTION
II.2 MULTI-LEVEL NETWORKS TO STUDY EVOLUTION
II.3 APPLICATION OF BIPARTITE GRAPHS FOR THE ANALYSIS OF INTERDOMAIN LGT BETWEEN ULTRASMALL AND LARGER PROKARYOTES
III. MODULARITY IN EVOLUTION
III.1 MOLECULAR EVOLUTION
III.1.1 CompositeSearch: A new tool for studying modularity in molecular evolution
III.1.2 Impact of genomic structure and mobility on gene remodeling in plasmids, allowing the evolution of new dependency systems.
III.1.3 Evolution of genes and rules of gene remodeling during the transition and stabilization of animal multicellularity
III.2 MORPHOLOGICAL EVOLUTION
III.3 LINGUISTIC EVOLUTION