Publications by authors named "Andre P Masella"

Article Synopsis
  • Prostate tumours show diverse responses to treatment, and current prognostic factors only account for some of this variation, prompting further investigation into their genetic profiles.* -
  • Analysis of 200 whole-genome and 277 whole-exome sequences revealed that localized, non-indolent tumours lack key mutations found in metastatic cases, instead featuring non-coding changes and large-scale rearrangements.* -
  • Many genetic abnormalities were linked to disease recurrence, and a new signature of these abnormalities was found to be more effective than established biomarkers, suggesting that targeted treatments could enhance cure rates for aggressive localized prostate cancer.*
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Background: It is extremely common to need to select a subset of reads from a BAM file based on their specific properties. Typically, a user unpacks the BAM file to a text stream using SAMtools, parses and filters the lines using AWK, then repacks them using SAMtools. This process is tedious and error-prone.

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Soil pH is an important determinant of microbial community composition and diversity, yet few studies have characterized the specific effects of pH on individual bacterial taxa within bacterial communities, both abundant and rare. We collected composite soil samples over 2 years from an experimentally maintained pH gradient ranging from 4.5 to 7.

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Background: Although high-throughput sequencing of small subunit rRNA genes has revolutionized our understanding of microbial ecosystems, these technologies generate data at depths that benefit from automated analysis. Here we present AXIOME (Automation, eXtension, and Integration Of Microbial Ecology), a highly flexible and extensible management tool for popular microbial ecology analysis packages that promotes reproducibility and customization in microbial research.

Findings: AXIOME streamlines and manages analysis of small subunit (SSU) rRNA marker data in QIIME and mothur.

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Background: Illumina paired-end reads are used to analyse microbial communities by targeting amplicons of the 16S rRNA gene. Publicly available tools are needed to assemble overlapping paired-end reads while correcting mismatches and uncalled bases; many errors could be corrected to obtain higher sequence yields using quality information.

Results: PANDAseq assembles paired-end reads rapidly and with the correction of most errors.

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Ammonia-oxidizing archaea (AOA) outnumber ammonia-oxidizing bacteria (AOB) in many terrestrial and aquatic environments. Although nitrification is the primary function of aquarium biofilters, very few studies have investigated the microorganisms responsible for this process in aquaria. This study used quantitative real-time PCR (qPCR) to quantify the ammonia monooxygenase (amoA) and 16S rRNA genes of Bacteria and Thaumarchaeota in freshwater aquarium biofilters, in addition to assessing the diversity of AOA amoA genes by denaturing gradient gel electrophoresis (DGGE) and clone libraries.

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