Publications related to Inferring transcript phylogenies

Statistical learning quantifies transposable element-mediated cis-regulation

Didier Trono, Evaristo Jose Planet Letschert, Julien Léonard Duc, Alexandre Coudray, Julien Paul André Pontis, Delphine Yvette L Grun, Cyril David Son-Tuyên Pulver, Shaoline Sheppard

Background: Transposable elements (TEs) have colonized the genomes of most metazoans, and many TE-embedded sequences function as cis-regulatory elements (CREs) for genes involved in a wide range of biological processes from early embryo- genesis to innate ...

2023

Extracting phylogenetic dimensions of coevolution reveals hidden functional signals

Anne-Florence Raphaëlle Bitbol

Despite the structural and functional information contained in the statistical coupling between pairs of residues in a protein, coevolution associated with function is often obscured by artifactual signals such as genetic drift, which shapes a protein's ph ...

NATURE PORTFOLIO2022

Mild inborn errors of metabolism in commonly used inbred mouse strains

Johan Auwerx, Wei Zhang, Evan Graehl Williams

Inbred mouse strains are a cornerstone of translational research but paradoxically many strains carry mild inborn errors of metabolism. For example, alpha-aminoadipic acidemia and branched-chain ketoacid dehydrogenase deficiency are known in C57BL/6J mice. ...

ACADEMIC PRESS INC ELSEVIER SCIENCE2019

Bernard Moret, Shachi Shailesh Deshpande

Many important questions in molecular biology, evolution, and biomedicine can be addressed by comparative genomic approaches. One of the basic tasks when comparing genomes is the definition of measures of similarity (or dissimilarity) between two genomes, ...

Mary Ann Liebert2017

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

Identification of potential HIV restriction factors by combining evolutionary genomic signatures with functional analyses

Amalio Telenti, Danielle Thompson, Daniel Sauter, Jérémie Perreaud

Background: Known antiretroviral restriction factors are encoded by genes that are under positive selection pressure, induced during HIV-1 infection, up-regulated by interferons, and/or interact with viral proteins. To identify potential novel restriction ...

Biomed Central Ltd2015

Unraveling Patterns of Site-to-Site Synonymous Rates Variation and Associated Gene Properties of Protein Domains and Families

Slavica Dimitrieva Janeva

In protein-coding genes, synonymous mutations are often thought not to affect fitness and therefore are not subject to natural selection. Yet increasingly, cases of non-neutral evolution at certain synonymous sites were reported over the last decade. To ev ...

Public Library of Science2014

A transcript perspective on evolution

Bernard Moret, Yann Christinat

Alternative splicing is now recognized as a major mechanism for transcriptome and proteome diversity in higher eukaryotes, yet its evolution is poorly understood. Most studies focus on the evolution of exons and introns at the gene level, while only few co ...

Ieee Computer Soc2013

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Inferring transcript phylogenies

Statistical learning quantifies transposable element-mediated cis-regulation

Extracting phylogenetic dimensions of coevolution reveals hidden functional signals

Mild inborn errors of metabolism in commonly used inbred mouse strains

New Genome Similarity Measures based on Conserved Gene Adjacencies

Functional Characterization of Nucleoid Associated Proteins Acting as Global Transcription Factors in Mycobacterium tuberculosis

The Characteristics of Heterozygous Protein Truncating Variants in the Human Genome

Identification of potential HIV restriction factors by combining evolutionary genomic signatures with functional analyses

Computational studies in epigenomics using histone modification data

Unraveling Patterns of Site-to-Site Synonymous Rates Variation and Associated Gene Properties of Protein Domains and Families

A transcript perspective on evolution

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Chat with Graph Search

Extracting phylogenetic dimensions of coevolution reveals hidden functional signals

Statistical learning quantifies transposable element-mediated cis-regulation

New Genome Similarity Measures based on Conserved Gene Adjacencies

Mild inborn errors of metabolism in commonly used inbred mouse strains

Unraveling Patterns of Site-to-Site Synonymous Rates Variation and Associated Gene Properties of Protein Domains and Families

The Characteristics of Heterozygous Protein Truncating Variants in the Human Genome

Functional Characterization of Nucleoid Associated Proteins Acting as Global Transcription Factors in Mycobacterium tuberculosis

Identification of potential HIV restriction factors by combining evolutionary genomic signatures with functional analyses

Computational studies in epigenomics using histone modification data

A transcript perspective on evolution