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Pangenomic analysis identifies structural variation associated with heat tolerance in pearl millet
Pearl millet is an important cereal crop worldwide and shows superior heat tolerance. Here, we developed a graph-based pan-genome by assembling ten...
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A de novo germline pathogenic BRCA1 variant identified following an osteosarcoma pangenomic molecular analysis
De novo germline pathogenic variants (gPV) of the BReast CAncer 1 ( BRCA1 ) gene are very rare. Only a few have been described up to date, usually in...
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Insights for precision oncology from the integration of genomic and clinical data of 13,880 tumors from the 100,000 Genomes Cancer Programme
The Cancer Programme of the 100,000 Genomes Project was an initiative to provide whole-genome sequencing (WGS) for patients with cancer, evaluating...
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Copy number signatures and CCNE1 amplification reveal the involvement of replication stress in high-grade endometrial tumors oncogenesis
PurposeManaging high-grade endometrial cancer in Martinique poses significant challenges. The diversity of copy number alterations in high-grade...
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Exome sequencing allows detection of relevant pharmacogenetic variants in epileptic patients
Beyond the identification of causal genetic variants in the diagnosis of Mendelian disorders, exome sequencing can detect numerous variants with...
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Sequencing-based analysis of microbiomes
Microbiomes occupy a range of niches and, in addition to having diverse compositions, they have varied functional roles that have an impact on...
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Metapangenomics reveals depth-dependent shifts in metabolic potential for the ubiquitous marine bacterial SAR324 lineage
BackgroundOceanic microbiomes play a pivotal role in the global carbon cycle and are central to the transformation and recycling of carbon and energy...
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Exposure to Trypanosoma parasites induces changes in the microbiome of the Chagas disease vector Rhodnius prolixus
BackgroundThe causative agent of Chagas disease, Trypanosoma cruzi , and its nonpathogenic relative, Trypanosoma rangeli , are transmitted by...
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Characterization of two keystone taxa, sulfur-oxidizing, and nitrate-reducing bacteria, by tracking their role transitions in the benzo[a]pyrene degradative microbiome
BackgroundKeystone taxa are drivers of microbiome structure and functioning, which may play critical roles in microbiome-level responses to...
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Genomic characterization of emerging invasive Streptococcus agalactiae serotype VIII in Alberta, Canada
Invasive Group B Streptococcus (GBS) can infect pregnant women, neonates, and older adults. Invasive GBS serotype VIII is infrequent in Alberta;...
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A consortia of clinical E. coli strains with distinct in vitro adherent/invasive properties establish their own co-colonization niche and shape the intestinal microbiota in inflammation-susceptible mice
BackgroundInflammatory bowel disease (IBD) patients experience recurrent episodes of intestinal inflammation and often follow an unpredictable...
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Genomic profiling of Nitrospira species reveals ecological success of comammox Nitrospira
BackgroundThe discovery of microorganisms capable of complete ammonia oxidation to nitrate (comammox) has prompted a paradigm shift in our...
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Genome-centric metagenomics reveals the host-driven dynamics and ecological role of CPR bacteria in an activated sludge system
BackgroundCandidate phyla radiation (CPR) constitutes highly diverse bacteria with small cell sizes and are likely obligate intracellular symbionts....
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Metagenomic analysis of nepoviruses: diversity, evolution and identification of a genome region in members of subgroup A that appears to be important for host range
Data mining and metagenomic analysis of 277 open reading frame sequences of bipartite RNA viruses of the genus Nepovirus , family Secoviridae , were...
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New insights into bioaugmented removal of sulfamethoxazole in sediment microcosms: degradation efficiency, ecological risk and microbial mechanisms
BackgroundBioaugmentation has the potential to enhance the ability of ecological technology to treat sulfonamide-containing wastewater, but the low...
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Multi-site tumor sampling highlights molecular intra-tumor heterogeneity in malignant pleural mesothelioma
BackgroundMalignant pleural mesothelioma (MPM) is a heterogeneous cancer. Better knowledge of molecular and cellular intra-tumor heterogeneity...
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A second look at exome sequencing data: detecting mobile elements insertion in a rare disease cohort
About 0.3% of all variants are due to de novo mobile element insertions (MEIs). The massive development of next-generation sequencing has made it...
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Leave no stone unturned: individually adapted xerotolerant Thaumarchaeota sheltered below the boulders of the Atacama Desert hyperarid core
BackgroundThe hyperarid core of the Atacama Desert is an extremely harsh environment thought to be colonized by only a few heterotrophic bacterial...
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Plant pangenomes for crop improvement, biodiversity and evolution
Plant genome sequences catalogue genes and the genetic elements that regulate their expression. Such inventories further research aims as diverse as...
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The potential impact of a probiotic: Akkermansia muciniphila in the regulation of blood pressure—the current facts and evidence
Akkermansia muciniphila ( A. muciniphila ) is present in the human gut microbiota from infancy and gradually increases in adulthood. The potential...
