@DanRJKnight

Senior Bioinformatician and Genomic Epidemiologist at WA Health https://xitter.cf/t.co/uvEyPGOfKe

 Perth, Western Australia
research-repository.uwa.edu.au/en/persons/dan-knight
Joined October 2010
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  • Followers2K
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Grateful to have been awarded a @arc_gov_au #DECRA fellowship. Huge thanks to my mentors, colleagues, collaborators and friends who helped this finally get over the line. By far the toughest grant process I've encountered! uwa.edu.au/news/Article/2023…

Early career researchers awarded $2.15M federal funding

Five academics at The University of Western Australia have been awarded a total of $2.15 million in Federal Government funding for research projects ranging from pioneering biotechnology with liquid...

uwa.edu.au
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I’m excited to be hosting this community information evening. Please share with your networks and community groups.
WCVID@WCVID22 Sep 2023
Keen to learn more about preventing childhood #earinfections? The Wesfarmers Centre is hosting an information evening - hosted by four industry experts - about the latest research. The event is set for 19 October - More info below⬇️ tinyurl.com/bdzhez92
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New preprint with @DHelekal and Jere Koskela on inference of multiple mergers while dating a pathogen phylogeny biorxiv.org/content/10.1101/…
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Join us at Australia's leading public health laboratory MDU-PHL at @TheDohertyInst to continue our genomics implementation with a great team @KristyHoran14 @Jake_A_Lacey @norelle_sherry @BenjaminHowden #jobs #Bioinformatics #Melbourne jobs.staff.unimelb.edu.au/ci…
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A key step to designing better pneumonia trials is designing better patient/ parent reported outcomes and PROMs. Great first paper by Dan Oakes, part of his MPH and a sign of great work to come @WCVID @telethonkids @epid_oakes @_charliemcleod @emmanattabi err.ersjournals.com/content/…
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An insightful perspective on the state-of-the-art and future of pathogen genome surveillance.
guido werner@guwe3327 Apr 2023
Great collaborative effort of @ESGEM_ESCMID members @_natachacouto_ @EpicFeil_ @angelanovais16 @BenjaminHowden @SandraReuter9 et al: check out our new opinion paper 👇🏻👇🏻👇🏻microbiologyresearch.org/con…

Taking hospital pathogen surveillance to the next level

microbiologyresearch.org
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Feels a bit surreal tweeting this. I was awarded an FHRI Fellowship. bit.ly/3mXdIIb I said no thank you as I'm leaving academia for a role in WA Health within the public health genomics team at PathWest. The ECR ride has been wild but time for a new challenge!
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Our centre (#WCVID), program (#ENDRHD) and team (#StrepA pathogenesis and diagnostics) continue to grow 💪🏻. Come hunt microbes with me + others👇🏻🦠🧫👩🏼‍🔬🔬🧪@tim_barnett1
WCVID@WCVID7 Mar 2023
Join our team! We have some great roles available: *Lab/Research Assistants focusing on #StrepA & @ASAVI_StrepA *Program Manager for the #ID Epidemiology team *Aboriginal Development Manager If you have a passion for #ID research we want to hear you! 👇 telethonkids.csod.com/ux/ats…
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Happy to report that our In Focus article "𝑭𝒂𝒄𝒊𝒏𝒈 𝒐𝒖𝒓 𝒑𝒍𝒂𝒔𝒕𝒊𝒄 𝒘𝒂𝒔𝒕𝒆 𝒄𝒓𝒊𝒔𝒊𝒔: 𝒃𝒊𝒐𝒓𝒆𝒄𝒚𝒄𝒍𝒊𝒏𝒈 𝒂𝒔 𝒂 𝒑𝒓𝒐𝒎𝒊𝒔𝒊𝒏𝒈 𝒔𝒐𝒍𝒖𝒕𝒊𝒐𝒏" by Yi Peng, @aprabhu90, @ChristianRinke - all @ace_uq - is out Great teamwork! publish.csiro.au/ma/fulltext…
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SnakeMAGs: a simple, efficient, flexible and scalable workflow to reconstruct prokaryotic genomes from metagenomes ift.tt/QqgUJ50

SnakeMAGs: a simple, efficient, flexible and scalable workflow to reconstruct prokaryotic genomes...

Background: Over the last decade, we have observed in microbial ecology a transition from gene-centric to genome-centric analyses. Indeed, the advent of metagenomics combined with binning methods,...

pubmed.ncbi.nlm.nih.gov
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Dan Knight retweeted
Ryan Wick@rrwick7 Mar 2023
Our (me, @JuddLmj and @DrKatHolt) new paper was recently published in @PLOSCompBiol: doi.org/10.1371/journal.pcbi… I'm particularly fond of this one, as it takes my PhD thesis and distils it down to practical advice. (1/9)

Assembling the perfect bacterial genome using Oxford Nanopore and Illumina sequencing

A perfect bacterial genome assembly is one where the assembled sequence is an exact match for the organism’s genome—each replicon sequence is complete and contains no errors. While this has been...

journals.plos.org
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Dan Knight retweeted
𝕐@nomad4214 Mar 2023
This is pretty slick — query with an accession and directly download actual read files (with preference for SRA or ENA) directly in @rpetit3's fastq-dl github.com/rpetit3/fastq-dl; all wrapped up in a nice "rich" interface :).

GitHub - rpetit3/fastq-dl: Download FASTQ files from SRA or ENA repositories.

Download FASTQ files from SRA or ENA repositories. - rpetit3/fastq-dl

github.com
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We're proud to share that #AusTrakka recently surpassed the milestone of 200,000 genomes sequenced of SARS-CoV-2 #COVID19 🧬🎉 You can read more about this and how it all came together via the article here 👉 auspathogen.org.au/blog/aust…
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Dan Knight retweeted
ASM WA@ASM_WA_Branch13 Feb 2023
Thinking about your next conference? We are excited to welcome you to Perth for #ASM2023. A great range of speakers have already been lined up. Abstracts and discounted registrations open now! @AUSSOCMIC Register here 👉tinyurl.com/w7teexmt
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Now that Japanese Encephalitis Virus has emerged in Australia, if it sticks around, what are the highest risk locations? Based distributions of birds, pigs, mosquitos. 👉mdpi.com/1999-4915/15/2/450
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Dan Knight retweeted
ASM WA@ASM_WA_Branch5 Feb 2023
Registrations to #ASM2023 Perth are open now! Check out our plenary speakers below. Limited number of discounted student & #ECR registraions available! Get in quick to avoid price increases. Please RT🙏See you in Perth! 😊@AUSSOCMIC
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Tired of hairballs in your assembly graphs? We are excited to present stRainy - our new approach for metagenomic strain deconvolution using long reads! biorxiv.org/content/10.1101/…

stRainy: assembly-based metagenomic strain phasing using long reads

Bacterial species in microbial communities are often represented by mixtures of strains. Variation in strain genomes may have important phenotypic effects, however strain-level deconvolution of...

biorxiv.org
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Replying to @uwanews
@uwanews are investigating the transmission of a #superbug known as Clostridium difficile so better infectious disease interventions can be designed & implemented. If you have experience/interest in transmission of superbugs in the community, register now: bit.ly/3UX0w1j
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Big thanks to @ARC_Tracker for the public service announcement - to ask ARC for application assessment scores via a simple freedom-of-information request 👍 Just received the info (DP23), outside the FOI Act which seems fine, but unfortunately it's more depressing than useful 😰
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