NEMo: An Evolutionary Model with Modularity for PPI Networks

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An Interactive Gameplay to Crowdsource Multiple Sequence Alignment of Genome Sequences: Genenigma

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Comparative genomics is a field of research that compares genomes of different organisms to identify common patterns. It is a powerful method used to identify the genetic diseases that cause mutations. Multiple Sequence Alignment (MSA) is an intermediate s ...

ASSOC COMPUTING MACHINERY2019

Beyond silence : a functional and evolutionary study of KRAB zinc finger proteins

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Transposable elements (TEs) are genetic units capable of spreading within the genomes of their host. TEs contribute a readily recognizable 45% of the human DNA, reflecting in part their co-option for some as source of protein-coding sequences, for others a ...

EPFL2019

The Least Cost Path From Landscape Genetics to Landscape Genomics: Challenges and Opportunities to Explore NGS Data in a Spatially Explicit Context

Stéphane Joost

Ecosystems are the stage on which the play of evolution is acted. Inferring evolutionary processes from the spatial and temporal genetic patterns they produce in populations is challenging because ecosystems are highly complex, spatially structured, and te ...

2018

Slow dynamics in structured neural network models

Samuel Pavio Muscinelli

Humans and some other animals are able to perform tasks that require coordination of movements across multiple temporal scales, ranging from hundreds of milliseconds to several seconds. The fast timescale at which neurons naturally operate, on the order of ...

EPFL2018

Learning Neural Connectivity from Firing Activity: Scalable Algorithms with Provable Guarantees

Martin Vetterli, Amin Karbasi, Amir Hesam Salavati

The connectivity of a neuronal network has a major effect on its functionality and role. It is generally believed that the complex network structure of the brain provides a physiological basis for information processing. Therefore, identifying the network’ ...

Springer New York LLC2018

Computational and Statistical analyses of Molecular Evolution and Demography using Large-scale Sequencing Data

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Evolution can be described as the change of allele frequencies over time. Four forces - mutation, migration, genetic drift, and selection, drive this change. The aim of my thesis was to accurately estimate and differentiate the parameters governing each of ...

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Highly Reduced Genome of the New Species Mycobacterium uberis, the Causative Agent of Nodular Thelitis and Tuberculoid Scrotitis in Livestock and a Close Relative of the Leprosy Bacilli

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Nodular thelitis is a chronic enzootic infection affecting dairy cows and goats. The causative agent was recently shown to be related to the leprosy-causing bacilli Mycobacterium leprae and Mycobacterium lepromatosis. In this study, the genome of this path ...

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Exploring the diversity of social preferences: Is a heterogeneous population evolutionarily stable under assortative matching?

Boris Thurm, Charles Chadi Ayoubi

Why do individuals make different decisions when confronted with similar choices? This paper investigates whether the answer lies in an evolutionary process. Our analysis builds on recent work in evolutionary game theory showing the superiority of a given ...

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NEMo: An Evolutionary Model With Modularity for PPI Networks

Bernard Moret, Xiuwei Zhang, Min Ye, Qijia Jiang, Gabriela Clara Racz

Modeling the evolution of biological networks is a major challenge. Biological networks are usually represented as graphs; evolutionary events not only include addition and removal of vertices and edges but also duplication of vertices and their associated ...

IEEE Press2017

Models and Algorithms in Biological Network Evolution with Modularity

Min Ye

Networks are commonly used to represent key processes in biology; examples include transcriptional regulatory networks, protein-protein interaction (PPI) networks, metabolic networks, etc. Databases store many such networks, as graphs, observed or inferred ...

EPFL2017

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