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Choice of assembly software has a critical impact on virome characterisation
BackgroundThe viral component of microbial communities plays a vital role in driving bacterial diversity, facilitating nutrient turnover and sha**...
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Sequencing-based methods and resources to study antimicrobial resistance
Antimicrobial resistance extracts high morbidity, mortality and economic costs yearly by rendering bacteria immune to antibiotics. Identifying and...
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Metagenomic analysis of basal ice from an Alaskan glacier
BackgroundGlaciers cover ~ 10% of land but are among the least explored environments on Earth. The basal portion of glaciers often harbors unique...
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An expanded global inventory of allelic variation in the most extremely polymorphic region of Plasmodium falciparum merozoite surface protein 1 provided by short read sequence data
BackgroundWithin Plasmodium falciparum merozoite surface protein 1 (MSP1), the N-terminal block 2 region is a highly polymorphic target of naturally...
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Targeted genomic landscape of metastases compared to primary tumours in clear cell metastatic renal cell carcinoma
BackgroundThe genomic landscape of primary clear cell renal cell carcinoma (ccRCC) has been well described. However, little is known about cohort...
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Bioinformatics Assembling and Assessment of Novel Coxsackievirus B1 Genome
The human microbiome project via application of metagenomic next-generation sequencing techniques has found surprising large and diverse amounts of...
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Whole-genome sequencing of eukaryotes: From sequencing of DNA fragments to a genome assembly
Rapid advances in sequencing technologies of second- and even third-generation made the whole genome sequencing a routine procedure. However, the...
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Pan-Genome Storage and Analysis Techniques
Computational pan-genome analysis has emerged from the rapid increase of available genome sequencing data. Starting from a microbial pan-genome, the...
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De novo assembly and characterization of breast cancer transcriptomes identifies large numbers of novel fusion-gene transcripts of potential functional significance
BackgroundGene-fusion or chimeric transcripts have been implicated in the onset and progression of a variety of cancers. Massively parallel RNA...
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Host-hijacking and planktonic piracy: how phages command the microbial high seas
Microbial communities living in the oceans are major drivers of global biogeochemical cycles. With nutrients limited across vast swathes of the...
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Next Generation Sequencing for the Detection of Foodborne Microbial Pathogens
Next generation sequencing (NGS) has become a central tool for pathogen detection since the introduction of the first NGS platform over a decade ago....
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The occurrence of potato common scab correlates with the community composition and function of the geocaulosphere soil microbiome
BackgroundSoil microorganisms can mediate the occurrence of plant diseases. Potato common scab (CS) is a refractory disease caused by pathogenic Streptomyces...
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High Throughput Sequencing-Based Approaches for Gene Expression Analysis
Next-generation sequencing has emerged as the method of choice to answer fundamental questions in biology. The massively parallel sequencing...
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Bioinformatics for Analysis of Poxvirus Genomes
In recent years, there have been numerous technological advances in the field of molecular biology; these include next- and third-generation...
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Comparative Methods for Reconstructing Ancient Genome Organization
Comparative genomics considers the detection of similarities and differences between extant genomes, and, based on more or less formalized hypotheses...
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Hybrid de novo tandem repeat detection using short and long reads
BackgroundAs one of the most studied genome rearrangements, tandem repeats have a considerable impact on genetic backgrounds of inherited diseases....
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Sera of Peruvians with fever of unknown origins include viral nucleic acids from non-vertebrate hosts
Serum samples collected from 88 Peruvians with unexplained fever were analyzed for viral sequences using metagenomics. Nucleic acids of...
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The sea lamprey germline genome provides insights into programmed genome rearrangement and vertebrate evolution
The sea lamprey ( Petromyzon marinus ) serves as a comparative model for reconstructing vertebrate evolution. To enable more informed analyses, we...
