ORCID Profile
0000-0002-4045-4571
Current Organisation
Garvan Institute of Medical Research
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Publisher: Springer Science and Business Media LLC
Date: 03-01-2022
DOI: 10.1038/S41587-021-01147-4
Abstract: Nanopore sequencing depends on the FAST5 file format, which does not allow efficient parallel analysis. Here we introduce SLOW5, an alternative format engineered for efficient parallelization and acceleration of nanopore data analysis. Using the ex le of DNA methylation profiling of a human genome, analysis runtime is reduced from more than two weeks to approximately 10.5 h on a typical high-performance computer. SLOW5 is approximately 25% smaller than FAST5 and delivers consistent improvements on different computer architectures.
Publisher: American Society for Clinical Investigation
Date: 15-04-2022
DOI: 10.1172/JCI120901
Publisher: Springer Science and Business Media LLC
Date: 27-01-2022
DOI: 10.1007/S41781-021-00062-2
Abstract: The accurate simulation of additional interactions at the ATLAS experiment for the analysis of proton–proton collisions delivered by the Large Hadron Collider presents a significant challenge to the computing resources. During the LHC Run 2 (2015–2018), there were up to 70 inelastic interactions per bunch crossing, which need to be accounted for in Monte Carlo (MC) production. In this document, a new method to account for these additional interactions in the simulation chain is described. Instead of s ling the inelastic interactions and adding their energy deposits to a hard-scatter interaction one-by-one, the inelastic interactions are pres led, independent of the hard scatter, and stored as combined events. Consequently, for each hard-scatter interaction, only one such pres led event needs to be added as part of the simulation chain. For the Run 2 simulation chain, with an average of 35 interactions per bunch crossing, this new method provides a substantial reduction in MC production CPU needs of around 20%, while reproducing the properties of the reconstructed quantities relevant for physics analyses with good accuracy.
Publisher: Springer Science and Business Media LLC
Date: 22-12-2017
Publisher: Cold Spring Harbor Laboratory
Date: 25-05-2023
DOI: 10.1101/2023.05.25.542242
Abstract: DNA methylation (5-methylcytosine, 5mC) is a repressive gene regulatory mark widespread in vertebrate genomes, yet the developmental dynamics in which 5mC patterns are established vary across species. While mammals undergo two rounds of global 5mC erasure, the zebrafish genome exhibits localized maternal-to-paternal 5mC remodeling, in which the sperm epigenome is inherited in the early embryo. To date, it is unclear how evolutionarily conserved such 5mC remodeling strategies are, and what their biological function is. Here, we studied 5mC dynamics during the embryonic development of sea l rey ( Petromyzon marinus ), a jawless vertebrate which occupies a critical phylogenetic position as the sister group of the jawed vertebrates. We employed base-resolution 5mC quantification in the l rey germline, embryonic and somatic tissues, and discovered large-scale maternal-to-paternal epigenome remodeling that affects % of the embryonic genome and is predominantly associated with partially methylated domains (PMDs). We further demonstrate that sequences eliminated during programmed genome rearrangement (PGR), a hallmark of l rey embryogenesis, are hypermethylated in sperm prior to the onset of PGR. Our study thus unveils important insights into the evolutionary origins of vertebrate 5mC reprogramming, and how this process might participate in erse developmental strategies.
Publisher: Research Square Platform LLC
Date: 18-11-2020
DOI: 10.21203/RS.3.RS-105996/V1
Abstract: Accumulating evidence supports the high prevalence of co-infections among Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) patients, and their potential to worsen the clinical outcome of COVID-19. However, there are few data on Southern Hemisphere populations, and most studies to date have investigated a narrow spectrum of viruses using targeted qRT-PCR. Here we assessed respiratory viral co-infections among SARS-CoV-2 patients in Australia, through respiratory virome characterization. Nasopharyngeal swabs of 92 SARS-CoV-2-positive cases were sequenced using pan-viral hybrid-capture and the Twist Respiratory Virus Panel. In total, 8% of cases were co-infected, with rhinovirus (6%) or influenzavirus (2%). Twist capture also achieved near-complete sequencing ( % coverage, -fold depth) of the SARS-CoV-2 genome in 95% of specimens with Ct . Our results highlight the importance of assessing all pathogens in symptomatic patients, and the dual-functionality of Twist hybrid-capture, for SARS-CoV-2 whole-genome sequencing without licon generation and the simultaneous identification of viral co-infections with ease.
Publisher: Research Square Platform LLC
Date: 28-12-2020
DOI: 10.21203/RS.3.RS-135125/V1
Abstract: Background Basenjis are considered an ancient dog breed of central African origins that still live and hunt with tribesmen in the African Congo. Nicknamed the barkless dog, Basenjis possess unique phylogeny, geographical origins and traits, making their genome structure of great interest. The increasing number of available canid reference genomes allows us to examine the impact the choice of reference genome makes with regard to reference genome quality and breed relatedness. Results Here, we report two high quality de novo Basenji genome assemblies: a female, China (CanFam_Bas), and a male, Wags. We conduct pairwise comparisons and report structural variations between assembled genomes of three dog breeds: Basenji (CanFam_Bas), Boxer (CanFam3.1) and German Shepherd Dog (GSD) (CanFam_GSD). CanFam_Bas is superior to CanFam3.1 in terms of genome contiguity and comparable overall to the high quality CanFam_GSD assembly. By aligning short read data from 58 representative dog breeds to three reference genomes, we demonstrate how the choice of reference genome significantly impacts both read mapping and variant detection. Conclusions The growing number of high-quality canid reference genomes means the choice of reference genome is an increasingly critical decision in subsequent canid variant analyses. The basal position of the Basenji makes it suitable for variant analysis for targeted applications of specific dog breeds. However, we believe more comprehensive analyses across the entire family of canids is more suited to a pangenome approach. Collectively this work highlights the importance the choice of reference genome makes in all variation studies.
Publisher: Cold Spring Harbor Laboratory
Date: 11-11-2020
DOI: 10.1101/2020.11.11.379073
Abstract: Basenjis are considered an ancient dog breed of central African origins that still live and hunt with tribesmen in the African Congo. Nicknamed the barkless dog, Basenjis possess unique phylogeny, geographical origins and traits, making their genome structure of great interest. The increasing number of available canid reference genomes allows us to examine the impact the choice of reference genome makes with regard to reference genome quality and breed relatedness. Here, we report two high quality de novo Basenji genome assemblies: a female, China (CanFam_Bas), and a male, Wags. We conduct pairwise comparisons and report structural variations between assembled genomes of three dog breeds: Basenji (CanFam_Bas), Boxer (CanFam3.1) and German Shepherd Dog (GSD) (CanFam_GSD). CanFam_Bas is superior to CanFam3.1 in terms of genome contiguity and comparable overall to the high quality CanFam_GSD assembly. By aligning short read data from 58 representative dog breeds to three reference genomes, we demonstrate how the choice of reference genome significantly impacts both read mapping and variant detection. The growing number of high-quality canid reference genomes means the choice of reference genome is an increasingly critical decision in subsequent canid variant analyses. The basal position of the Basenji makes it suitable for variant analysis for targeted applications of specific dog breeds. However, we believe more comprehensive analyses across the entire family of canids is more suited to a pangenome approach. Collectively this work highlights the importance the choice of reference genome makes in all variation studies.
Publisher: Springer Science and Business Media LLC
Date: 2022
Abstract: A search for the exotic decay of the Higgs boson ( H ) into a b $$ \\overline{b} $$ b ¯ resonance plus missing transverse momentum is described. The search is performed with the ATLAS detector at the Large Hadron Collider using 139 fb − 1 of pp collisions at $$ \\sqrt{s} $$ s = 13 TeV. The search targets events from ZH production in an NMSSM scenario where H → $$ {\\overset{\\sim }{\\chi}}_2^0{\\overset{\\sim }{\\chi}}_1^0 $$ χ ~ 2 0 χ ~ 1 0 , with $$ {\\overset{\\sim }{\\chi}}_2^0 $$ χ ~ 2 0 → $$ a{\\overset{\\sim }{\\chi}}_1^0 $$ a χ ~ 1 0 , where a is a light pseudoscalar Higgs boson and $$ {\\overset{\\sim }{\\chi}}_{1,2}^0 $$ χ ~ 1 , 2 0 are the two lightest neutralinos. The decay of the a boson into a pair of b -quarks results in a peak in the dijet invariant mass distribution. The final-state signature consists of two leptons, two or more jets, at least one of which is identified as originating from a b -quark, and missing transverse momentum. Observations are consistent with Standard Model expectations and upper limits are set on the product of cross section times branching ratio for a three-dimensional scan of the masses of the $$ {\\overset{\\sim }{\\chi}}_2^0 $$ χ ~ 2 0 , $$ {\\overset{\\sim }{\\chi}}_1^0 $$ χ ~ 1 0 and a boson.
Publisher: Springer Science and Business Media LLC
Date: 29-09-2020
DOI: 10.1038/S42003-020-01270-Z
Abstract: The advent of portable nanopore sequencing devices has enabled DNA and RNA sequencing to be performed in the field or the clinic. However, advances in in situ genomics require parallel development of portable, offline solutions for the computational analysis of sequencing data. Here we introduce Genopo , a mobile toolkit for nanopore sequencing analysis. Genopo compacts popular bioinformatics tools to an Android application, enabling fully portable computation. To demonstrate its utility for in situ genome analysis, we use Genopo to determine the complete genome sequence of the human coronavirus SARS-CoV-2 in nine patient isolates sequenced on a nanopore device, with Genopo executing this workflow in less than 30 min per s le on a range of popular smartphones. We further show how Genopo can be used to profile DNA methylation in a human genome s le, illustrating a flexible, efficient architecture that is suitable to run many popular bioinformatics tools and accommodate small or large genomes. As the first ever smartphone application for nanopore sequencing analysis, Genopo enables the genomics community to harness this cheap, ubiquitous computational resource.
Publisher: American Association for the Advancement of Science (AAAS)
Date: 28-08-2019
DOI: 10.1126/SCITRANSLMED.AAV3879
Abstract: Inhaled corticosteroids promote bacterial infection in chronic obstructive pulmonary disease by suppressing the antimicrobial peptide cathelicidin.
Publisher: Springer Science and Business Media LLC
Date: 2022
DOI: 10.1140/EPJC/S10052-021-09843-W
Abstract: A technique is presented to measure the efficiency with which c -jets are mistagged as b -jets (mistagging efficiency) using $$t\\bar{t}$$ t t ¯ events, where one of the W bosons decays into an electron or muon and a neutrino and the other decays into a quark–antiquark pair. The measurement utilises the relatively large and known $$W\\rightarrow cs$$ W → c s branching ratio, which allows a measurement to be made in an inclusive c -jet s le. The data s le used was collected by the ATLAS detector at $$\\sqrt{s} = 13$$ s = 13 $$\\text {TeV}$$ TeV and corresponds to an integrated luminosity of 139 fb $$^{-1}$$ - 1 . Events are reconstructed using a kinematic likelihood technique which selects the mapping between jets and $$t\\bar{t}$$ t t ¯ decay products that yields the highest likelihood value. The distribution of the b -tagging discriminant for jets from the hadronic W decays in data is compared with that in simulation to extract the mistagging efficiency as a function of jet transverse momentum. The total uncertainties are in the range 3–17%. The measurements generally agree with those in simulation but there are some differences in the region corresponding to the most stringent b -jet tagging requirement.
Publisher: Springer Science and Business Media LLC
Date: 09-12-2020
DOI: 10.1038/S41467-020-20075-6
Abstract: Viral whole-genome sequencing (WGS) provides critical insight into the transmission and evolution of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2). Long-read sequencing devices from Oxford Nanopore Technologies (ONT) promise significant improvements in turnaround time, portability and cost, compared to established short-read sequencing platforms for viral WGS (e.g., Illumina). However, adoption of ONT sequencing for SARS-CoV-2 surveillance has been limited due to common concerns around sequencing accuracy. To address this, here we perform viral WGS with ONT and Illumina platforms on 157 matched SARS-CoV-2-positive patient specimens and synthetic RNA controls, enabling rigorous evaluation of analytical performance. We report that, despite the elevated error rates observed in ONT sequencing reads, highly accurate consensus-level sequence determination was achieved, with single nucleotide variants (SNVs) detected at % sensitivity and % precision above a minimum ~60-fold coverage depth, thereby ensuring suitability for SARS-CoV-2 genome analysis. ONT sequencing also identified a surprising ersity of structural variation within SARS-CoV-2 specimens that were supported by evidence from short-read sequencing on matched s les. However, ONT sequencing failed to accurately detect short indels and variants at low read-count frequencies. This systematic evaluation of analytical performance for SARS-CoV-2 WGS will facilitate widespread adoption of ONT sequencing within local, national and international COVID-19 public health initiatives.
Publisher: IOP Publishing
Date: 2022
DOI: 10.1088/1748-0221/17/01/P01013
Abstract: The semiconductor tracker (SCT) is one of the tracking systems for charged particles in the ATLAS detector. It consists of 4088 silicon strip sensor modules. During Run 2 (2015–2018) the Large Hadron Collider delivered an integrated luminosity of 156 fb -1 to the ATLAS experiment at a centre-of-mass proton-proton collision energy of 13 TeV. The instantaneous luminosity and pile-up conditions were far in excess of those assumed in the original design of the SCT detector. Due to improvements to the data acquisition system, the SCT operated stably throughout Run 2. It was available for 99.9% of the integrated luminosity and achieved a data-quality efficiency of 99.85%. Detailed studies have been made of the leakage current in SCT modules and the evolution of the full depletion voltage, which are used to study the impact of radiation damage to the modules.
Publisher: Elsevier BV
Date: 2022
Publisher: Springer Science and Business Media LLC
Date: 08-06-2018
DOI: 10.1038/S41467-018-04574-1
Abstract: Inhaled corticosteroids (ICS) have limited efficacy in reducing chronic obstructive pulmonary disease (COPD) exacerbations and increase pneumonia risk, through unknown mechanisms. Rhinoviruses precipitate most exacerbations and increase susceptibility to secondary bacterial infections. Here, we show that the ICS fluticasone propionate (FP) impairs innate and acquired antiviral immune responses leading to delayed virus clearance and previously unrecognised adverse effects of enhanced mucus, impaired antimicrobial peptide secretion and increased pulmonary bacterial load during virus-induced exacerbations. Exogenous interferon-β reverses these effects. FP suppression of interferon may occur through inhibition of TLR3- and RIG-I virus-sensing pathways. Mice deficient in the type I interferon-α/β receptor ( IFNAR1 −/− ) have suppressed antimicrobial peptide and enhanced mucin responses to rhinovirus infection. This study identifies type I interferon as a central regulator of antibacterial immunity and mucus production. Suppression of interferon by ICS during virus-induced COPD exacerbations likely mediates pneumonia risk and raises suggestion that inhaled interferon-β therapy may protect.
Publisher: American Society for Microbiology
Date: 16-10-2023
DOI: 10.1128/JVI.00705-23
Publisher: Elsevier BV
Date: 06-2022
Publisher: Springer International Publishing
Date: 2021
Publisher: Cold Spring Harbor Laboratory
Date: 30-06-2021
DOI: 10.1101/2021.06.29.450255
Abstract: Nanopore sequencing is an emerging genomic technology with great potential. However, the storage and analysis of nanopore sequencing data have become major bottlenecks preventing more widespread adoption in research and clinical genomics. Here, we elucidate an inherent limitation in the file format used to store raw nanopore data – known as FAST5 – that prevents efficient analysis on high-performance computing (HPC) systems. To overcome this, we have developed SLOW5, an alternative file format that permits efficient parallelisation and, thereby, acceleration of nanopore data analysis. For ex le, we show that using SLOW5 format, instead of FAST5, reduces the time and cost of genome-wide DNA methylation profiling by an order of magnitude on common HPC systems, and delivers consistent improvements on a wide range of different architectures. With a simple, accessible file structure and a ~ 25% reduction in size compared to FAST5, SLOW5 format will deliver substantial benefits to all areas of the nanopore community.
Publisher: Springer Science and Business Media LLC
Date: 03-2022
Abstract: Searches are conducted for new spin-0 or spin-1 bosons using events where a Higgs boson with mass 125 GeV decays into four leptons ( ℓ = e , μ ). This decay is presumed to occur via an intermediate state which contains two on-shell, promptly decaying bosons: H → XX/ZX → 4 ℓ , where the new boson X has a mass between 1 and 60 GeV. The search uses pp collision data collected with the ATLAS detector at the LHC with an integrated luminosity of 139 fb − 1 at a centre-of-mass energy $$ \\sqrt{s} $$ s = 13 TeV. The data are found to be consistent with Standard Model expectations. Limits are set on fiducial cross sections and on the branching ratio of the Higgs boson to decay into XX/ZX , improving those from previous publications by a factor between two and four. Limits are also set on mixing parameters relevant in extensions of the Standard Model containing a dark sector where X is interpreted to be a dark boson.
Publisher: Research Square Platform LLC
Date: 13-07-2021
DOI: 10.21203/RS.3.RS-668517/V1
Abstract: Nanopore sequencing is an emerging genomic technology with great potential. However, the storage and analysis of nanopore sequencing data have become major bottlenecks preventing more widespread adoption in research and clinical genomics. Here, we elucidate an inherent limitation in the file format used to store raw nanopore data – known as FAST5 – that prevents efficient analysis on high-performance computing (HPC) systems. To overcome this we have developed SLOW5, an alternative file format that permits efficient parallelisation and, thereby, acceleration of nanopore data analysis. For ex le, we show that using SLOW5 format, instead of FAST5, reduces the time and cost of genome-wide DNA methylation profiling by an order of magnitude on common HPC systems, and delivers consistent improvements on a wide range of different architectures. With a simple, accessible file structure and a ~25% reduction in size compared to FAST5, SLOW5 format will deliver substantial benefits to all areas of the nanopore community.
Publisher: Springer Science and Business Media LLC
Date: 10-08-2022
DOI: 10.1038/S41586-022-05054-9
Abstract: The notion that mobile units of nucleic acid known as transposable elements can operate as genomic controlling elements was put forward over six decades ago
No related grants have been discovered for Jillian Hammond.