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Feature Learning of Virus Genome Evolution With the Nucleotide Skip-Gram Neural Network

Related publications (41)

An Approximate Markov Model for the Wright-Fisher Diffusion and Its Application to Time Series Data

Jeffrey David Jensen, Anna Ferrer Admetlla

The joint and accurate inference of selection and demography from genetic data is considered a particularly challenging question in population genetics, since both process may lead to very similar patterns of genetic diversity. However, additional informat ...

Genetics Society America2016

Building Word Embeddings for Solving Natural Language Processing

Rémi Philippe Lebret

Word embedding is a feature learning technique which aims at mapping words from a vocabulary into vectors of real numbers in a low-dimensional space. By leveraging large corpora of unlabeled text, such continuous space representations can be computed for c ...

École Polytechnique Fédérale de Lausanne2016

Word Embeddings for Natural Language Processing

Rémi Philippe Lebret

EPFL2016

The Characteristics of Heterozygous Protein Truncating Variants in the Human Genome

Jacques Fellay, Amalio Telenti, Istvan Bartha, Nimisha Chaturvedi

Sequencing projects have identified large numbers of rare stop-gain and frameshift variants in the human genome. As most of these are observed in the heterozygous state, they test a gene's tolerance to haploinsufficiency and dominant loss of function. We a ...

Public Library Science2015

Characterizing neutral genomic diversity and selection signatures in indigenous populations of Moroccan goats (Capra hircus) using WGS data

Stéphane Joost, Sylvie Stucki, Kevin Leempoel, Pierre Taberlet

Since the time of their domestication, goats (Capra hircus) have evolved in a large variety of locally adapted populations in response to different human and environmental pressures. In the present era, many indigenous populations are threatened with extin ...

2015

Complete genome sequences of T5-related Escherichia coli bacteriophages DT57C and DT571/2 isolated from horse feces

Ricardo Cesar Guerrero Ferreira, Nikolai Prokhorov

We report the complete genome sequencing of two Escherichia coli T5-related bacteriophages, DT57C and DT571/2, isolated from the same specimen of horse feces. These two isolates share 96 % nucleotide sequence identity and can thus be considered representat ...

Springer Wien2015

Catch Me if You Can: Adaptation from Standing Genetic Variation to a Moving Phenotypic Optimum

Sebastian Matuszewski

Adaptation lies at the heart of Darwinian evolution. Accordingly, numerous studies have tried to provide a formal framework for the description of the adaptive process. Of these, two complementary modeling approaches have emerged: While so-called adaptive- ...

2015

Positive Selection Drives Preferred Segment Combinations during Influenza Virus Reassortment

Jeffrey David Jensen, Matthieu Foll

Influenza A virus (IAV) has a segmented genome that allows for the exchange of genome segments between different strains. This reassortment accelerates evolution by breaking linkage, helping IAV cross species barriers to potentially create highly virulent ...

Oxford University Press2015

Models and Algorithms for Comparative Genomics

Mingfu Shao

The deluge of sequenced whole-genome data has motivated the study of comparative genomics, which provides global views on genome evolution, and also offers practical solutions in deciphering the functional roles of components of genomes. A fundamental comp ...

EPFL2015

Insight into the evolution and origin of leprosy bacilli from the genome sequence of Mycobacterium lepromatosis

Stewart Cole, Andrej Benjak, Charlotte Avanzi, Philippe Busso, Pushpendra Singh

Mycobacterium lepromatosis is an uncultured human pathogen associated with diffuse lepromatous leprosy and a reactional state known as Lucio's phenomenon. By using deep sequencing with and without DNA enrichment, we obtained the near-complete genome sequen ...

National Academy of Sciences2015

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