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Comparative genomics of the genus Desulfitobacterium

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The bacterium Vibrio cholerae exhibits two distinct lifestyles, one as an aquatic bacterium and the other as the etiological agent of the pandemic human disease cholera. Here, we report closed genome sequences of two seventh pandemic V. cholerae O1 El Tor ...

2018

New Genome Similarity Measures based on Conserved Gene Adjacencies

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

Persona: A High-Performance Bioinformatics Framework

James Richard Larus, Edouard Bugnion, Christos Kozyrakis, Stuart Anthony Byma, Sam David Whitlock

Next-generation genome sequencing technology has reached a point at which it is becoming cost-effective to sequence all patients. Biobanks and researchers are faced with an oncoming deluge of genomic data, whose processing requires new and scalable bioinfo ...

2017

Insights from the Genome Sequence of Mycobacterium lepraemurium: Massive Gene Decay and Reductive Evolution

Stewart Cole, Andrej Benjak, Charlotte Avanzi

Mycobacterium lepraemurium is the causative agent of murine leprosy, a chronic, granulomatous disease similar to human leprosy. Due to the similar clinical manifestations of human and murine leprosy and the difficulty of growing both bacilli axenically, My ...

Amer Soc Microbiology2017

Identification of the inactivating factors and mechanisms exerted on MS2 coliphage in concentrated synthetic urine

Tamar Kohn, Loïc Decrey

Volume reduction (condensation) is a key for the practical usage of human urine as a fertilizer because it enables the saving of storage space and the reduction of transportation cost. However, concentrated urine may carry infectious disease risks resultin ...

Elsevier2017

Phylogenetic comparison of Desulfotomaculum species of subgroup 1a and description of Desulfotomaculum reducens sp.nov.

Rizlan Bernier-Latmani, Manon Frutschi

A genome and physiological comparison was made of the type strains of Desulfotomaculum species belonging to subgroup 1a and of 'Desulfotomaculum reducens' strain MI-1. Phenotypically, 'Desulfotomaculum reducens' strain MI-1 can be distinguished from the ot ...

Society for General Microbiology2016

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

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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

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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

Understanding the metabolism of tetrachloroethene-respiring Dehalobacter restrictus

Aamani Rupakula Boyanapalli

Tetra- and trichloroethene (PCE, TCE) are organohalides polluting the environment as a result of inappropriate use, storage, and disposal by various industries. Anthropogenic pollution by organohalides is a major source of concern because of their undesira ...

EPFL2015