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James Zlosnik

@jameszlosnik.bsky.social
410 followers 357 following 163 posts

Public Health infectious disease microbiologist/bioinformatics, Avgeek, Cyclist, Friend of animals, Views my own. 🇨🇦🇬🇧🇪🇺 Slava Ukraine 🇺🇦

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Reposted by James Zlosnik
Vaughn Cooper @vscooper.micropopbio.org · 27/09/2026
How do Burkholderia multivorans bacteria adaptively evolve during infections of the cystic fibrosis airway? A longtime collab and intensive study of 8 patients links bacterial adaptations to disease progression. Our findings also unite prior studies. www.biorxiv.org/content/10.6...
biorxiv.org
Convergent genetic evolution within Burkholderia multivorans chronic infections correlates with lung function decline in cystic fibrosis patients
The patterns and pathways of pathogen adaptation during chronic infections can reveal the gateways microbes must unlock to colonize and persist. In chronic lung infections of cystic fibrosis (CF) pati...
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Richard McElreath 🐈‍⬛ @rmcelreath.bsky.social · 02/09/2026
Last year, I publicly complained multiple times (see e.g. elevanth.org/blog/2025/07...) that the open access movement had been captured by publishers, and we are now worse off than before open access. Well people got mad at me for saying it. But I think things are still getting worse.
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halfmarshall.bsky.social @halfmarshall.bsky.social · 16/07/2026
I support Wikipedia, where information is still human-created, fact-checked, and 100% free. Join me! donate.wikimedia.org
donate.wikimedia.org
Make your donation now - Wikimedia Foundation
Donate to the Wikimedia Foundation, the nonprofit that hosts Wikipedia and other crucial free knowledge projects. Each year, the generosity of the 2% of readers who donate allows us to expand the reac...
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ndweiss @11tulips.bsky.social · 17/07/2026
Truth has a value. As such, The Man will seek to control it. We must support @wikipedia.org. Let’s prevent information takeover.
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James Zlosnik @jameszlosnik.bsky.social · 28/05/2026
This is a very nice educational resource.
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Kristian G. Andersen @kgandersen.bsky.social · 21/05/2026
Just a shout-out to the folks over at @pathoplexus.org and, importantly, all the scientists sharing genomic data with such amazing speed. It's great to see the field having moved to a new platform, with non-transparent platforms being a thing of the past. Fantastic.
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Turvey Lab @turveylab.bsky.social · 08/05/2026
Really proud of this new review covering human primary atopic disorders. @jhumimmunity.org
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MAKS 26 👀🇺🇦 @maks23.bsky.social · 27/12/2025
🇺🇦🇨🇦 Zelensky arrived in Canada, — press secretary of the president Nikiforov. Here, Zelensky is scheduled to have a bilateral meeting with Canadian Prime Minister Carney, as well as a joint telephone conversation with European leaders.
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James Zlosnik @jameszlosnik.bsky.social · 29/09/2025
Braga, Portugal.🇵🇹
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James Zlosnik @jameszlosnik.bsky.social · 25/09/2025
747 forever incredible indeed. Great flight yesterday.
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James Zlosnik @jameszlosnik.bsky.social · 23/09/2025
Porto Pt3
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James Zlosnik @jameszlosnik.bsky.social · 23/09/2025
Porto Pt2
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James Zlosnik @jameszlosnik.bsky.social · 23/09/2025
Porto
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Reposted by James Zlosnik
Samuel Lampa @smllmp.bsky.social · 18/09/2025
Registered too late for a poster for @escmid.bsky.social #IMMEMXIV but happy to discuss SciCommander with anyone interested 😊 See: livesys.se/posts/rewrit... Captures provenance of ad-hoc commands while skipping already computed steps - "The benefits of a pipeline tool without the pipeline tool".
livesys.se
Rewrite of Scicommander in Go with much improved algorithm | Living Systems_
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James Zlosnik @jameszlosnik.bsky.social · 07/09/2025
Budapest today
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James Zlosnik @jameszlosnik.bsky.social · 07/09/2025
Seen in Budapest… “Scientists are human too”. Indeed we are!
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James Zlosnik @jameszlosnik.bsky.social · 07/09/2025
Yes. First time in Budapest was just there for a night. Much, much, better than I was expecting. Nice tree lined boulevards, lots of nice old buildings. Not lost on me that some of those buildings and squares might be in the news in the future!
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James Zlosnik @jameszlosnik.bsky.social · 06/09/2025
Budapest this evening
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James Zlosnik @jameszlosnik.bsky.social · 25/07/2025
👇💯
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Reposted by James Zlosnik
Dr Emma Hodcroft @firefoxx66.bsky.social · 25/07/2025
📢New job posting!📢 Are you excited by the idea of building global infrastructure to make pathogen sequencing more accessible, interpretable, and equitable? 🧑🏻‍💻🧬 My group at @swisstph.ch has an opening working with ARTIC2, @pathoplexus.org, & Loculus - read on! 1/5
An image showing the ARTIC and Pathoplexus logos connected by blue lines, with the text "Hiring: post-doc/software engineer" and "Global open-source pathogen tools" and "Join Swiss TPH, Work on ARTIC2 and Pathoplexus, Basel, Switzerland"
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Andrew Rambaut (🐏🎀) @arambaut.bsky.social · 15/07/2025
Some great new features and updates from the awesome Pathoplexus project. This is a new open pathogen genome database that can provide access to your sequences under a use-restricted license but also feed directly in to INSDC (EBI, Genbank etc) when you are ready. pathoplexus.org/news/2025-07...
pathoplexus.org
Pathoplexus | Pathoplexus July Update
Pathoplexus is a new, open-source database dedicated to the efficient sharing of human viral pathogen genomic data, fostering global collaboration and public health response.
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Pathoplexus @pathoplexus.org · 15/07/2025
In an awesome new feature, you can now use the ‘Tools’ button to send sequences from Pathoplexus to other analyses and visualizations - like maps or Nextclade! Have a tool that would be worth including? See our docs! pathoplexus.org/docs/how-to/... 5/9
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Pathoplexus @pathoplexus.org · 15/07/2025
🗓️As we close in on 11 months of Pathoplexus, we’re pleased to announce many new direct sequence uploads and some exciting new features that expand Pathoplexus’ utility! 📰 You can see our full News Item here: pathoplexus.org/news/2025-07-14-july-update 1/9
Screenshot of the July Update News article on the Pathoplexus website
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sylvain Brisse @sylvainbrisse.bsky.social · 12/06/2025
The BIGSdb-Pasteur project, running under my supervision since 20 years, is looking for a project manager - great opportunity to contribute to this high-profile international resource in the field of reference strain taxonomies, genomic epidemiology and antimicrobial resistance surveillance
research.pasteur.fr
Project manager: Genomic taxonomy of bacterial strains, epidemiological surveillance and antimicrobial resistance - Research
We are looking for a project manager to develop our activities around the genomic taxonomy of bacterial strains and the corresponding platform at https://bigsdb.pasteur.fr/. The project manager’s main...
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James Zlosnik @jameszlosnik.bsky.social · 12/06/2025
Yes that’s lovely 😊 . While if anyone deserved a longer healthy life he did, I am fortunate I recognized early on how special he was. Never took him for granted and loved every minute of the 14 years we were with him.
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James Zlosnik @jameszlosnik.bsky.social · 11/06/2025
Thank you Jaki, appreciate it. Seems odd to say, but those people are missing out. The pain is massive...but for good reason. They flood our life with joy and honest, uncomplicated, love in a way that, at least for me, other humans simply cannot.
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Hadley Wickham @hadley.nz · 11/06/2025
Happy 18th birthday ggplot2! #rstats
Balloon wall art inspired by the ggplot2 hex sticker. The display features a hexagonal frame made of black balloons, filled with white balloons inside and surrounded by a background of light and dark blue balloons. A line graph with black balloon segments and round coloured nodes runs across the centre, and the word “ggplot2” is spelled out in black balloon letters below the chart.
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James Zlosnik @jameszlosnik.bsky.social · 11/06/2025
💯
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James Zlosnik @jameszlosnik.bsky.social · 10/06/2025
Thank you, appreciate it! No, there's no real preparation, just that awful numb feeling looking at the world without them in it any more. Made harder by the timing having to be my decision. I had 14 very special years with him, that is indeed a great source of comfort.
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James Zlosnik @jameszlosnik.bsky.social · 10/06/2025
Thank you Dawn, appreciate it. They all never be forgotten by us.
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James Zlosnik @jameszlosnik.bsky.social · 10/06/2025
I lost one of my cats, my best friend, on Saturday 💔💔💔. I knew it was coming, knew what to expect, but still seemed sudden and has been far, far, harder than ever expected. He was the best, kindest man in the world. The definition of a gentle-man. It's just devastating to know he's not there.
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Nick Loman @pathogenomenick.bsky.social · 22/05/2025
Absolutely thrilled to announce the launch of ARTIC2 - a £5.5M 5 year project funded by @wellcometrust.bsky.social to build on the ARTIC approach of low-cost, globally accessible genome sequencing for surveillance of outbreaks, epidemics and endemic diseases: www.birmingham.ac.uk/news/2025/am...
birmingham.ac.uk
Ambitious project to develop low-cost genome sequencing for pathogens known and unknown - University of Birmingham
Project will build on research that helped diagnostic labs to adopt sequencing capacity for COVID-19 and permit characterisation of future infectious threats
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Reposted by James Zlosnik
Dr Emma Hodcroft @firefoxx66.bsky.social · 22/05/2025
Excited to announce the start of ARTIC2! 🎉 ARTIC2 builds on the success of ARTIC aiming to make sequencing more equitable and accessible. 🤝🧬 EVE Group at @swisstph.ch is a key team member - we'll be helping make sequences easier to store and share via Loculus & @pathoplexus.org ! 🌎 More below! 👀👇🏻
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Reposted by James Zlosnik
Zamin Iqbal @zaminiqbal.bsky.social · 19/05/2025
Delighted to see this paper from danderson123.bsky.social 's PhD out. We have been building tools for AMR gene detection for over a decade now, but multicopy genes remain challenging. Dan shows that with a gene-space de Bruijn graph and long reads, you can do well www.biorxiv.org/content/10.1...
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Mark Carney @mark-carney.bsky.social · 28/04/2025
This is Canada — and we decide what happens here.
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The Bulwark @thebulwark.com · 26/04/2025
"One thing that happens when you have that much lying is that people begin to ask, is anything true? How do we know whether anything is ever true?" Don't let Trump's lies fatigue you or turn you cynical. @anneapplebaum.bsky.social joins @sarahlongwell25.bsky.social on the The Focus Group pod:
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James Zlosnik @jameszlosnik.bsky.social · 26/04/2025
It’s been a while (quite a while!) but one of my favorite cycling routes used to be out to Horseshoe Bay on Marine drive and then along the upper levels before heading up Cypress…best of all going down Cypress. A tee line avenue with ocean and blue sky ahead. Bliss
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Dr. Jonathan N. Stea @jonathanstea.bsky.social · 25/04/2025
A person who views their health with a scientific lens is advantaged. Wellness grifters hold less power over those who can see through their charades.
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James Zlosnik @jameszlosnik.bsky.social · 25/04/2025
💯 agree. One of the best drives in the world. We’re so lucky to have it here on our door step. Love the bit on HWY 1 in West Van when you drive over the crest to be greeted by the Howe Sound. Also love the approaches to Whistler
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James Zlosnik @jameszlosnik.bsky.social · 20/04/2025
Excellent interview. For anyone in Canada, well worth a listen.
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Mark Carney @mark-carney.bsky.social · 19/04/2025
It’s time to protect our values as Canadians. That means more doctors and hospitals in our public health care system, protecting our lands and waters, and standing up for our Charter of Rights and Freedoms.
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James Zlosnik @jameszlosnik.bsky.social · 11/04/2025
Listened to it yesterday, very enjoyable.
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Matthias C. Rillig @mrillig.bsky.social · 05/04/2025
"We infer that the earliest aerobic bacteria emerged in the Archaean, predating the GOE by 900 million years." Oxygen tolerance may have been a prerequisite for, rather than a consequence of, the evolution of oxygenic photosynthesis www.science.org/doi/10.1126/...
science.org
A geological timescale for bacterial evolution and oxygen adaptation
Microbial life has dominated Earth’s history but left a sparse fossil record, greatly hindering our understanding of evolution in deep time. However, bacterial metabolism has left signatures in the ge...
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Jaki Chantler @jakichantler.bsky.social · 13/03/2025
The tragedy of young science trainees being driven out of research is incredibly upsetting. Doubtful they’ll ever find their way back and among them are the discoverers of future cures for cancers and other intractable diseases.
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Phil Ewels @ewels.bsky.social · 10/03/2025
Super happy to see the new @nextflow.io training videos up online 🎉 This is a brand new course for beginners, called #Hello #Nextflow - we've run it a few times and the feedback so far has been great! Material is at training.nextflow.io and videos are on YouTube: www.youtube.com/watch?v=G3CV...
youtube.com
Hello Nextflow: Intro and setup
YouTube video by Nextflow
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James Zlosnik @jameszlosnik.bsky.social · 08/03/2025
Glad to see The Atlantic reproduced it. Best watched in original French, with English subtitles (not dubbed). It is a superb speech. So unnecessarily, we are in such dark times. ☹️
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James Zlosnik @jameszlosnik.bsky.social · 08/03/2025
Fully agreed. My first vote as a Canadian was for Trudeau, we have been better for him.
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Krassensteins @krassenstein.bsky.social · 06/03/2025
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James Zlosnik @jameszlosnik.bsky.social · 06/03/2025
Unfortunately the current US situation and Brexit seem to have the same roots - Russia. Defeating them in Ukraine is crucial. Much can be salvaged if Europe, Canada and others can step up to do this
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