A5060869126- Genomics and Phylogenetic Studies
- Mycobacterium research and diagnosis
- Tuberculosis Research and Epidemiology
- Cell Image Analysis Techniques
- Nanopore and Nanochannel Transport Studies
- Machine Learning in Bioinformatics
- Big Data and Business Intelligence
- RNA and protein synthesis mechanisms
- Plant Pathogenic Bacteria Studies
- Molecular Biology Techniques and Applications
- Environmental DNA in Biodiversity Studies
- Data Analysis with R
- Antibiotic Resistance in Bacteria
- Cancer Genomics and Diagnostics
- Genetic factors in colorectal cancer
- Facial Rejuvenation and Surgery Techniques
- Microbial Community Ecology and Physiology
- Gene expression and cancer classification
- vaccines and immunoinformatics approaches
- Patient Safety and Medication Errors
- Lung Cancer Treatments and Mutations
- Nutrition, Genetics, and Disease
- Digital Innovation in Industries
- Bacteriophages and microbial interactions
- Pneumonia and Respiratory Infections
Peter Doherty Institute
2022-2024
The University of Melbourne
2022-2024
European Bioinformatics Institute
2019-2024
University of Cape Town
2022
Wellcome Centre for Infectious Diseases Research in Africa
2022
Stellenbosch University
2022
The University of Queensland
2017-2022
Centre Hospitalier Universitaire de Saint-Pierre
2021
University of San Diego
2021
University of Utah
2021
<ns4:p>Data analysis often entails a multitude of heterogeneous steps, from the application various command line tools to usage scripting languages like R or Python for generation plots and tables. It is widely recognized that data analyses should ideally be conducted in reproducible way. Reproducibility enables technical validation regeneration results on original even new data. However, reproducibility alone by no means sufficient deliver an lasting impact (i.e., sustainable) field, just...
Data analysis often entails a multitude of heterogeneous steps, from the application various command line tools to usage scripting languages like R or Python for generation plots and tables. It is widely recognized that data analyses should ideally be conducted in reproducible way. Reproducibility enables technical validation regeneration results on original even new data. However, reproducibility alone by no means sufficient deliver an lasting impact (i.e., sustainable) field, just one...
Sequencing by translocating DNA fragments through an array of nanopores is a rapidly maturing technology that offers faster and cheaper sequencing than other approaches. However, accurately deciphering the sequence from noisy complex electrical signal challenging. Here, we report Chiron, first deep learning model to achieve end-to-end basecalling directly translate raw without error-prone segmentation step. Trained with only small set 4,000 reads, show our provides state-of-the-art accuracy,...
<ns5:p>Two billion people are infected with <ns5:italic>Mycobacterium tuberculosis</ns5:italic>, leading to 10 million new cases of active tuberculosis and 1.5 deaths annually. Universal access drug susceptibility testing (DST) has become a World Health Organization priority. We previously developed software tool, <ns5:italic>Mykrobe predictor</ns5:italic>, which provided offline species identification resistance predictions for <ns5:italic>M. </ns5:italic>from whole genome sequencing (WGS)...
A fundamental requirement for many applications in genomics is the sequencing of genetic material (DNA/RNA).Different technologies exist, but all aim to accurately reproduce sequence nucleotides (the individual units DNA and RNA) under investigation.The result such efforts a text file containing fragments -termed "reads" -represented as strings letters (A, C, G, T/U).
While traditional microbiological freshwater tests focus on the detection of specific bacterial indicator species, including pathogens, direct tracing all aquatic DNA through metagenomics poses a profound alternative. Yet, in situ metagenomic water surveys face substantial challenges cost and logistics. Here, we present simple, fast, cost-effective remotely accessible diagnostics workflow centred around portable nanopore sequencing technology. Using defined compositions spatiotemporal...
We present pandora, a novel pan-genome graph structure and algorithms for identifying variants across the full bacterial pan-genome. As much adaptability hinges on accessory genome, methods which analyze SNPs in just core genome have unsatisfactory limitations. Pandora approximates sequenced as recombinant of references, detects variation pan-genotypes multiple samples. Using reference 578 Escherichia coli genomes, we compare 20 diverse isolates. recovers more rare than...
Universal access to drug susceptibility testing for newly diagnosed tuberculosis patients is recommended. Access culture-based diagnostics remains limited, and targeted molecular assays are vulnerable emerging resistance mutations. Improved protocols direct-from-sputum Mycobacterium sequencing would accelerate comprehensive typing. We assessed a thermo-protection buffer-based direct-from-sample M. whole-genome protocol. prospectively analyzed 60 acid-fast bacilli smear-positive clinical...
Variant calling is fundamental in bacterial genomics, underpinning the identification of disease transmission clusters, construction phylogenetic trees, and antimicrobial resistance detection. This study presents a comprehensive benchmarking variant accuracy genomes using Oxford Nanopore Technologies (ONT) sequencing data. We evaluated three ONT basecalling models both simplex (single-strand) duplex (dual-strand) read types across 14 diverse species. Our findings reveal that deep...
There are many short-read variant-calling tools, with different strengths and weaknesses. We present a tool, Minos, which combines outputs from arbitrary variant callers, increasing recall without loss of precision. benchmark on 62 samples three bacterial species an outbreak 385 Mycobacterium tuberculosis samples. Minos also enables joint genotyping; we demonstrate large (N=13k) M. cohort, building map non-synonymous SNPs indels in region where all such variants assumed to cause rifampicin...
Abstract Variant calling is fundamental in bacterial genomics, underpinning the identification of disease transmission clusters, construction phylogenetic trees, and antimicrobial resistance prediction. This study presents a comprehensive benchmarking SNP indel variant accuracy across 14 diverse species using Oxford Nanopore Technologies (ONT) Illumina sequencing. We generate gold standard reference genomes project variations from closely-related strains onto them, creating biologically...
Variant calling is fundamental in bacterial genomics, underpinning the identification of disease transmission clusters, construction phylogenetic trees, and antimicrobial resistance detection. This study presents a comprehensive benchmarking variant accuracy genomes using Oxford Nanopore Technologies (ONT) sequencing data. We evaluated three ONT basecalling models both simplex (single-strand) duplex (dual-strand) read types across 14 diverse species. Our findings reveal that deep...
Circulating cell-free DNA (cfDNA) in the plasma of cancer patients contains tumour (ctDNA) derived from cells and it has been widely recognized as a non-invasive source for diagnosis prognosis cancer. Molecular profiling ctDNA is often performed using targeted sequencing or low-coverage whole genome (WGS) to identify specific somatic mutations copy number aberrations (sCNAs). However, these approaches cannot efficiently detect all tumour-derived genomic changes ctDNA.We WGS analysis cfDNA 4...
Targeted Next Generation Sequencing (tNGS) and Whole Genome (WGS) are increasingly used for genotypic drug susceptibility testing (gDST) of Mycobacterium tuberculosis. Thirty-two multi-drugs resistant 40 susceptible isolates from Madagascar were tested with Deeplex® Myc-TB WGS using the Mykrobe analysis pipeline. Sixty-four 72 (89%) yielded concordant categorical gDST results drugs by both assays. didn't detect pncA K96T, Q141P, H51P, H82R, rrs C517T rpsL K43R mutations, which identified as...
Variant calling is fundamental in bacterial genomics, underpinning the identification of disease transmission clusters, construction phylogenetic trees, and antimicrobial resistance prediction. This study presents a comprehensive benchmarking SNP indel variant accuracy across 14 diverse species using Oxford Nanopore Technologies (ONT) Illumina sequencing. We generate gold standard reference genomes project variations from closelyrelated strains onto them, creating biologically realistic...
Hyaluronic acid filler can be safely used as a soft-tissue for correction of infraorbital hollowing. It has high overall patient satisfaction profile among patients.
Structural variants (SVs) are increasingly recognized as key drivers of bacterial evolution, yet their role has not been explored thoroughly. This is due to limitations in traditional short-read sequencing and linear reference-based analyses, which can miss complex structural changes. Tuberculosis (TB), a disease caused by Mycobacterium tuberculosis ( Mtb ), remains major global health concern. In this study, we harness long-read technologies genome graph tools construct pangenome reference...
Variant calling is fundamental in bacterial genomics, underpinning the identification of disease transmission clusters, construction phylogenetic trees, and antimicrobial resistance prediction. This study presents a comprehensive benchmarking SNP indel variant accuracy across 14 diverse species using Oxford Nanopore Technologies (ONT) Illumina sequencing. We generate gold standard reference genomes project variations from closely-related strains onto them, creating biologically realistic...
<b>Background:</b> As patients directly experience harm from adverse events, investigators have proposed patient-report to complement professional reporting of events. <b>Objective:</b> To investigate how an automated health assessment system can be used identify <b>Design and setting:</b> Internet survey responses April 2003 2005 involving communities clinical practices across the USA. <b>Patients:</b> 44 860 adults aged 19–69 years. <b>Outcome:</b> Patient perceptions events experienced...
Culture-free real-time sequencing of clinical metagenomic samples promises both rapid pathogen detection and antimicrobial resistance profiling. However, this approach introduces the risk patient DNA leakage. To mitigate risk, we need near-comprehensive removal human sequences at point sequencing, typically involving use resource-constrained devices. Existing benchmarks have largely focused on standardized databases ignored computational requirements depletion pipelines as well impact genome...
ABSTRACT Sequencing by translocating DNA fragments through an array of nanopores is a rapidly maturing technology which offers faster and cheaper sequencing than other approaches. However, accurately deciphering the sequence from noisy complex electrical signal challenging. Here, we report Chiron, first deep learning model to achieve end-to-end basecalling: directly translating raw without error-prone segmentation step. Trained with only small set 4000 reads, show that our provides...
ABSTRACT While traditional microbiological freshwater tests focus on the detection of specific bacterial indicator species, including pathogens, direct tracing all aquatic DNA through metagenomics poses a profound alternative. Yet, in situ metagenomic water surveys face substantial challenges cost and logistics. Here we present simple, fast, cost-effective remotely accessible diagnostics workflow centred around portable nanopore sequencing technology. Using defined compositions...