Publications associées à Inferring transcript phylogenies

Ancestral genome reconstruction enhances transposable element annotation by identifying degenerate integrants

Didier Trono, Evaristo Jose Planet Letschert, Wayo Matsushima

Growing evidence indicates that transposable elements (TEs) play important roles in evolution by providing genomes with coding and non-coding sequences. Identification of TE-derived functional elements, however, has relied on TE annotations in individual s ...

2024

Computational identification and experimental characterization of preferred downstream positions in human core promoters

Philipp Bucher, René Dreos

Author summary Transcription of genes by the RNA polymerase II enzyme initiates at a genomic region termed the core promoter. The core promoter is a regulatory region that may contain diverse short DNA sequence motifs/elements that confer specific properti ...

2021

KRAB zinc finger protein-mediated control of transposon-embedded regulatory sequences from human germline to early embryos

Alexandra Iouranova

Transposable elements (TEs), also called jumping genes, are genetic elements capable of changing their position within the genome of their host. They make up large fractions of genomes, including 45% of human DNA content, according to current estimates. S ...

EPFL2021

Mild inborn errors of metabolism in commonly used inbred mouse strains

Johan Auwerx, Evan Graehl Williams, Wei Zhang

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

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

Stewart Cole, Andrej Benjak, Charlotte Avanzi

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 ...

AMER SOC MICROBIOLOGY2018

The phenotypic impact of naturally occurring genetic and molecular mitochondrial variation in a Drosophila Genetic Reference Population

Roel Paulus Josephus Bevers

Genome-wide association (GWA) studies aim to dissect the relationship between genotype and phenotype. So far, the focus has been on nuclear genetic determinants as variation in the mitochondrial genome is often low in the study cohorts. Despite this observ ...

EPFL2018

Phase specific transcriptional regulation of circadian clock and metabolism in mouse liver

Jonathan Aryeh Sobel

The molecular clock has been conserved from cyanobacteria to mammals and is believed to align behavioral and biochemical processes with the diurnal cycle. This cellular mechanism has been an advantage to increase the fitness of organisms through the abilit ...

EPFL2016

The Characteristics of Heterozygous Protein Truncating Variants in the Human Genome

Amalio Telenti, Jacques Fellay, Istvan Bartha, Paul Jack Mc Laren, 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, Jérémie Perreaud, Danielle Thompson, Paul Jack Mc Laren, Daniel Sauter

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

An Exact Algorithm to Compute the Double-Cut-and-Join Distance for Genomes with Duplicate Genes

Bernard Moret, Yu Lin, Mingfu Shao

Computing the edit distance between two genomes is a basic problem in the study of genome evolution. The double-cut-and-join (DCJ) model has formed the basis for most algorithmic research on rearrangements over the last few years. The edit distance under t ...

Mary Ann Liebert2015

Assessing Recent Selection and Functionality at Long Noncoding RNA Loci in the Mouse Genome

Anamaria Necsulea

Long noncoding RNAs (lncRNAs) are one of the most intensively studied groups of noncoding elements. Debate continues over what proportion of lncRNAs are functional or merely represent transcriptional noise. Although characterization of individual lncRNAs h ...

Oxford Univ Press2015

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

Yann Christinat, Bernard Moret

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

The influence of genomic context on mutation patterns in the human genome inferred from rare variants

Jian Li

Understanding patterns of spontaneous mutations is of fundamental interest in studies of human genome evolution and genetic disease. Here, we used extremely rare variants in humans to model the molecular spectrum of single-nucleotide mutations. Compared to ...

Cold Spring Harbor Lab Press, Publications Dept2013

Personal receptor repertoires: olfaction as a model

Sebastian Martin Waszak

Background: Information on nucleotide diversity along completely sequenced human genomes has increased tremendously over the last few years. This makes it possible to reassess the diversity status of distinct receptor proteins in different human individual ...

BioMed Central2012

Human U6 promoter drives stronger shRNA activity than its schistosome orthologue in Schistosoma mansoni and human fibrosarcoma cells

Raphaël Duvoisin, Nicola Harris

Blood flukes or schistosomes are the causative agents of human schistosomiasis, one of the major neglected tropical diseases. Draft genome sequences have been reported for schistosomes, but functional genomics tools are needed to investigate the role and e ...

2011

Exploring the transcriptional landscape of plant circadian rhythms using genome tiling arrays

Felix Naef

BACKGROUND: Organisms are able to anticipate changes in the daily environment with an internal oscillator know as the circadian clock. Transcription is an important mechanism in maintaining these oscillations. Here we explore, using whole genome tiling arr ...

BioMed Central2009

Innate immunity against retroviral pathogens: from an ambiguous genetic self to novel therapeutic approaches

Didier Trono

Almost half of the human genome is derived from exogenous genetic invaders, most of them related to retroviruses. This is the consequence of longstanding interactions between retroelements and higher organisms, governed by a delicate equilibrium between vi ...

Swiss Medical Publishers Ltd / EMH Swiss Medical Publishers2009