James Zlosnik
@jameszlosnik.bsky.social
Public Health infectious disease microbiologist/bioinformatics, Avgeek, Cyclist, Friend of animals, Views my own. 🇨🇦🇬🇧🇪🇺 Slava Ukraine 🇺🇦
Braga, Portugal.🇵🇹
September 28, 2025 at 11:10 PM
Braga, Portugal.🇵🇹
747 forever incredible indeed. Great flight yesterday.
September 25, 2025 at 6:40 PM
747 forever incredible indeed. Great flight yesterday.
Reposted by James Zlosnik
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".
Captures provenance of ad-hoc commands while skipping already computed steps - "The benefits of a pipeline tool without the pipeline tool".
Rewrite of Scicommander in Go with much improved algorithm | Living Systems_
livesys.se
September 18, 2025 at 10:11 AM
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".
Captures provenance of ad-hoc commands while skipping already computed steps - "The benefits of a pipeline tool without the pipeline tool".
Seen in Budapest… “Scientists are human too”. Indeed we are!
September 7, 2025 at 6:27 PM
Seen in Budapest… “Scientists are human too”. Indeed we are!
Budapest this evening
September 6, 2025 at 8:46 PM
Budapest this evening
👇💯
My biggest, loudest job application advice:
WHY do you want this job? This SPECIFIC job? What about it interests you? What do you think of it? What can you bring to it?
I know this sounds obvious but a generic cover letter isn't doing you favours - really. *Show me you know the job!*
1/7
WHY do you want this job? This SPECIFIC job? What about it interests you? What do you think of it? What can you bring to it?
I know this sounds obvious but a generic cover letter isn't doing you favours - really. *Show me you know the job!*
1/7
July 25, 2025 at 12:32 PM
👇💯
Reposted by James Zlosnik
📢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
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
July 25, 2025 at 10:44 AM
📢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
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
Reposted by James Zlosnik
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 | 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.
pathoplexus.org
July 15, 2025 at 2:05 PM
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...
Reposted by James Zlosnik
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
Have a tool that would be worth including? See our docs!
pathoplexus.org/docs/how-to/...
5/9
July 15, 2025 at 10:13 AM
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
Have a tool that would be worth including? See our docs!
pathoplexus.org/docs/how-to/...
5/9
Reposted by James Zlosnik
🗓️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
📰 You can see our full News Item here: pathoplexus.org/news/2025-07-14-july-update
1/9
July 15, 2025 at 10:13 AM
🗓️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
📰 You can see our full News Item here: pathoplexus.org/news/2025-07-14-july-update
1/9
Reposted by James Zlosnik
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
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...
research.pasteur.fr
June 12, 2025 at 2:46 PM
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
Reposted by James Zlosnik
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...
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
www.birmingham.ac.uk
May 22, 2025 at 10:57 AM
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...
Reposted by James Zlosnik
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! 👀👇🏻
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! 👀👇🏻
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...
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
www.birmingham.ac.uk
May 22, 2025 at 11:56 AM
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! 👀👇🏻
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! 👀👇🏻
Reposted by James Zlosnik
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...
www.biorxiv.org/content/10.1...
May 19, 2025 at 9:28 AM
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...
www.biorxiv.org/content/10.1...
Reposted by James Zlosnik
This is Canada — and we decide what happens here.
April 28, 2025 at 2:17 PM
This is Canada — and we decide what happens here.
Reposted by James Zlosnik
"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:
@anneapplebaum.bsky.social joins @sarahlongwell25.bsky.social on the The Focus Group pod:
April 26, 2025 at 1:30 PM
"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:
@anneapplebaum.bsky.social joins @sarahlongwell25.bsky.social on the The Focus Group pod:
Reposted by James Zlosnik
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.
Wellness grifters hold less power over those who can see through their charades.
April 25, 2025 at 7:58 PM
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.
Wellness grifters hold less power over those who can see through their charades.
Excellent interview. For anyone in Canada, well worth a listen.
Great to talk with Canadian Prime Minister @mark-carney.bsky.social on the podcast. link.chtbl.com/ProfGPod?sid...
April 20, 2025 at 12:40 AM
Excellent interview. For anyone in Canada, well worth a listen.
Reposted by James Zlosnik
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.
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.
April 19, 2025 at 9:12 PM
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.
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.
Reposted by James Zlosnik
"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/...
Oxygen tolerance may have been a prerequisite for, rather than a consequence of, the evolution of oxygenic photosynthesis
www.science.org/doi/10.1126/...
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...
www.science.org
April 5, 2025 at 11:11 AM
"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/...
Oxygen tolerance may have been a prerequisite for, rather than a consequence of, the evolution of oxygenic photosynthesis
www.science.org/doi/10.1126/...