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Divergent PCB organohalide-respiring consortia enriched from the efflux channel of a former Delor manufacturer in Eastern Europe

Christof Holliger, Pierre Rossi, Luiz Felippe De Alencastro, Martina Praveckova

Polychlorinated biphenyl (PCB) organohalide-respiring communities from the efflux channel of a former Delor manufacturer in Eastern Slovakia were assessed using metagenomic, statistical and cultivation-adapted approaches. Multivariate analysis of environme ...

Elsevier2015

Inferring the Evolutionary History of Primate microRNA Binding Sites: Overcoming Motif Counting Biases

Jeffrey David Jensen, Feng Gao

The first microRNAs (miRNAs) were identified as essential, conserved regulators of gene expression, targeting the same genes across nearly all bilaterians. However, there are also prominent examples of conserved miRNAs whose functions appear to have shifte ...

Oxford Univ Press2014

Study of cell differentiation by phylogenetic analysis using histone modification data

Bernard Moret, Philipp Bucher, Yu Lin, Nishanth Ulhas Nair, Paulina Grnarova, Jelena Antic, Ana Manasovska

Background: In cell differentiation, a cell of a less specialized type becomes one of a more specialized type, even though all cells have the same genome. Transcription factors and epigenetic marks like histone modifications can play a significant role in ...

BioMed Central2014

Mycobacterium leprae genomes from a British medieval leprosy hospital: towards understanding an ancient epidemic

Stewart Cole, Pushpendra Singh

Background: Leprosy has afflicted humankind throughout history leaving evidence in both early texts and the archaeological record. In Britain, leprosy was widespread throughout the Middle Ages until its gradual and unexplained decline between the 14th and ...

Biomed Central Ltd2014

Superinfection with drug-resistant HIV is rare and does not contribute substantially to therapy failure in a large European cohort

Istvan Bartha

Background: Superinfection with drug resistant HIV strains could potentially contribute to compromised therapy in patients initially infected with drug-sensitive virus and receiving antiretroviral therapy. To investigate the importance of this potential ro ...

Biomed Central Ltd2013

TIBA: a tool for phylogeny inference from rearrangement data with bootstrap analysis

Bernard Moret, Yu Lin, Vaibhav Rajan

TIBA is a tool to reconstruct phylogenetic trees from rearrangement data that consist of ordered lists of synteny blocks (or genes), where each synteny block is shared with all of its homologues in the input genomes. The evolution of these synteny blocks, ...

Oxford University Press2012

Taxonomic characterisation of Pseudomonas strain L48 and formal proposal of Pseudomonas entomophila sp nov

Bruno Lemaitre

An entomopathogenic, Gram-negative bacterium isolated from a female specimen of the fruit fly Drosophila melanogaster was taxonomically characterised. Strain L48(T) was strictly aerobic, non-fermentative, oxidase and catalase positive, rod-shaped, and moti ...

Elsevier2012

Reconstruction of Large-Scale Phylogenies : Advances in Algorithms and Statistical Methods

Vaibhav Rajan

The evolutionary relationships between organisms or phylogenies are fundamental to biology. They are invaluable as guiding tools to mine, organize and exploit the enormous amounts of biological data in the post-genomic era. The advent of high-throughput se ...

EPFL2012

Models and Algorithms for Whole-Genome Evolution and their Use in Phylogenetic Inference

Yu Lin

The rapid accumulation of sequenced genomes offers the chance to resolve longstanding questions about the evolutionary histories, or phylogenies, of groups of organisms. The relatively rare occurrence of large-scale evolutionary events in a whole genome, e ...

EPFL2012

Bootstrapping phylogenies inferred from rearrangement data

Bernard Moret, Yu Lin, Vaibhav Rajan

Background: Large-scale sequencing of genomes has enabled the inference of phylogenies based on the evolution of genomic architecture, under such events as rearrangements, duplications, and losses. Many evolutionary models and associated algorithms have be ...

BioMed Central2012

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Superinfection with drug-resistant HIV is rare and does not contribute substantially to therapy failure in a large European cohort

Istvan Bartha

Biomed Central Ltd2013

TIBA: a tool for phylogeny inference from rearrangement data with bootstrap analysis

Bernard Moret, Yu Lin, Vaibhav Rajan

Oxford University Press2012

Reconstruction of Large-Scale Phylogenies : Advances in Algorithms and Statistical Methods

Vaibhav Rajan

EPFL2012

Divergent PCB organohalide-respiring consortia enriched from the efflux channel of a former Delor manufacturer in Eastern Europe

Christof Holliger, Pierre Rossi, Luiz Felippe De Alencastro, Martina Praveckova

Elsevier2015