Lightnews — Scholar-powered news

Chaoran Chen @chaoranchen.de · Aug 28

Thank you very much to the UShER team (Jakob McBroome, @angieshinrichs.bsky.social, @russcd.bsky.social, Yatish Turakhia, and many more) for providing the daily-updated trees, @theo.io for developing Taxonium (and adding several features upon request!) and CDC AMD for funding. 4/4

4

Chaoran Chen @chaoranchen.de · Aug 28

The feature is only available on open.cov-spectrum.org which uses data from INSDC (GenBank/ENA/DDBJ), we unfortunately cannot provide it for data from GISAID.

If you have any questions or suggestions, please let us know! 3/4

1 4

Chaoran Chen @chaoranchen.de · Aug 28

You can choose to only display the sequences of the variant or the whole MRCA clade and color the tips by different metadata fields. You can also click on an inner node and search for a subtree. 2/4

1 1 4

Chaoran Chen @chaoranchen.de · Aug 28

Finally, CoV-Spectrum is meeting trees 🌳 – this week, we released a new feature to browse the SARS-CoV-2 UShER tree on CoV-Spectrum. With the new feature, you can see a subtree of your variant of interest. 1/4

1 8 22

Reposted by Chaoran Chen

Pathoplexus @pathoplexus.org · Aug 27

🗓 Pathoplexus turns ONE! 🎂🎉

In the past year we’ve grown from 4 pathogens to a truly global, community-driven platform for transparent, equitable & impactful pathogen sequence sharing.
📰 Read the full update: pathoplexus.org/news/2025-08...

1/10

1 20 38

Chaoran Chen @chaoranchen.de · Aug 11

If you would like to find out more about Loculus, you can still register for the Loculus tutorial at the [BC]2 Basel Computational Biology Conference 2025 on 8 September! Registration closes on 1 September.

www.bc2.ch/tutorials-wo...

SIB Swiss Institute of Bioinformatics @sib.swiss · Aug 11

“Loculus is remarkable for enabling efficient and secure sharing of pathogen genomic data, which is crucial for public health responses to infectious diseases."
🥁That’s what the committee said about this #SIBRemarkableOutputs 2024
👉Discover the output: tinyurl.com/53arz2rz

1 3

Reposted by Chaoran Chen

SIB Swiss Institute of Bioinformatics @sib.swiss · Aug 11

“Loculus is remarkable for enabling efficient and secure sharing of pathogen genomic data, which is crucial for public health responses to infectious diseases."
🥁That’s what the committee said about this #SIBRemarkableOutputs 2024
👉Discover the output: tinyurl.com/53arz2rz

1 3 5

Reposted by Chaoran Chen

Dr Emma Hodcroft @firefoxx66.bsky.social · Aug 8

Interested to learn about how to run your own Loculus (the database code behind @pathoplexus.org)? 🤔🖥️

Sign up for the Loculus Tutorial on Mon 8 Sept at BC2 Conference (@sib.swiss‬) in Basel, run by @chaoranchen.de & Anya Parker! 🧬

Register: www.bc2.ch/registration...

#bioinformatics #openScience

Image showing information on the BC2 (Basel Computational Biology Conference) from 8-10 Sept 2025. Says: "Tutorial: build a microbial genomic sequence database with Loculus - Register now. 8 Sept 2025 - Biozentrum, Basel. Early bird until 30 June 2025"

1 6 12

Reposted by Chaoran Chen

Biozentrum, University of Basel @biozentrum.unibas.ch · Aug 4

Loculus, an open-source software for building pathogen sequencing databases, is on the shortlist for #SIBRemarkableOutputs 2024. It’s a joint project by the teams of @neher.io, @tanjastadler.bsky.social and @firefoxx66.bsky.social xx66.bsky.social. Congratulations!

SIB Swiss Institute of Bioinformatics @sib.swiss · Jul 22

💡 The SIB Remarkable Outputs 2024 are out !
This shortlist of the most outstanding works produced by SIB members in 2024 showcase the latest advances in the Swiss bioinformatics field. Attend their presentations at [BC]2!

👉 Discover this shortlist of outstanding works
www.sib.swiss/remarkable-o...

6 11

Reposted by Chaoran Chen

Dr Emma Hodcroft @firefoxx66.bsky.social · Jul 25

📢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"

5 68 66

Reposted by Chaoran Chen

Pathoplexus @pathoplexus.org · Jul 15

🗓️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

1 7 19

Reposted by Chaoran Chen

Kristian G. Andersen @kgandersen.bsky.social · May 28

You might be wondering why we haven't updated outbreak.info for months.

Well, the reason is that GISAID cut our access in January - as they did others. Without telling us.

After a ♾️ back and forth, that is now permanent.

More on that soon - and why GISAID should not be trusted with critical data.

3 120 240

Reposted by Chaoran Chen

Pathoplexus @pathoplexus.org · May 22

📢Today Pathoplexus announces the inclusion of 2 new viral pathogens: RSV (A & B) and HMPV.

These respiratory viruses cause a serious health burden, particularly in infants & the vulnerable, & Pathoplexus aims to support sequence sharing to improve understanding & response.

1/4

Screenshot of the homepage of Pathoplexus, showing tiles to navigate to the supported pathogens CCHF, Ebola Sudan, Ebola Zaire, HMPV, Mpox, RSV-A, RSV-B, and West Nile virus.

2 27 43

Reposted by Chaoran Chen

SIB Swiss Institute of Bioinformatics @sib.swiss · May 13

🤔Interested in building and managing microbial genomic databases? Join the hands-on tutorial on #Loculus & learn how to set up, customize & deploy Loculus for your projects.
🔹 Tutorial organized by @chaoranchen.de & Anna Parker, from @ethz.ch
📆8 sept at #BC2Basel
👉 Register: tinyurl.com/5n8w3pwb

1 2 3

Reposted by Chaoran Chen

Lee Katz @lskatz.github.io · Apr 28

🚀 New proof-of-principle:
An interactive, searchable MLST hash database... all in your browser! 🔥
Live demo ➡️ lskatz.github.io/mlst-hash-te...
A natural extension of the hash database spec I developed last year: lskatz.github.io/mlst-hash-te...
🧵

Home

Using the MLST hash template as an example genomic epi database

lskatz.github.io

1 3 11

Reposted by Chaoran Chen

Sophie Seidel @seidels.bsky.social · Apr 17

Interested in #Bayesian #phylogenetics? 🧬
Join the Taming the BEAST workshop — theory + hands-on tutorials incl. #singleCell, #devBio & #lineageTracing!
📍Beijing, July 14–18, 2025
📅 Apply by April 25
I'll teach on TiDeTree & cell trees
🔗 taming-the-beast.org/news/Deadlin...

Application deadline extended for Taming the BEAST in Beijing!

taming-the-beast.org

5 9

Chaoran Chen @chaoranchen.de · Apr 16

The time is flying by.. Hard to believe that it has already been 7 months since we started Pathoplexus!

Pathoplexus @pathoplexus.org · Apr 16

🗓️ Pathoplexus has now been around for 7 months!

And both we and our users have been busy - so we wanted to share some updates & highlights!

📰 You can see our full News Item here: pathoplexus.org/news/2025-04-16-spring-update

1/9

Pathoplexus | Pathoplexus Spring 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

3

Reposted by Chaoran Chen

Pathoplexus @pathoplexus.org · Apr 16

🗓️ Pathoplexus has now been around for 7 months!

And both we and our users have been busy - so we wanted to share some updates & highlights!

📰 You can see our full News Item here: pathoplexus.org/news/2025-04-16-spring-update

1/9

Pathoplexus | Pathoplexus Spring 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

1 19 50

Reposted by Chaoran Chen

Duncan MacCannell @drm.bsky.social · Apr 6

I think I may buy a few dozen copies of this book and just hand them out to strangers.

bookshop.org/p/books/who-...

Who Is Government?: The Untold Story of Public Service

The Untold Story of Public Service

bookshop.org

3 8

Reposted by Chaoran Chen

SIB Swiss Institute of Bioinformatics @sib.swiss · Feb 4

The SIB Swiss Institute of #Bioinformatics is on Bluesky! We’re a non-profit organization dedicated to biological & biomedical #dataScience, supporting research & innovation. Follow us for updates on personalized health, biodiversity, pathogens, open science and more. Visit us at sib.swiss

SIB Swiss Institute of Bioinformatics | Data scientists for life

As a leading organization in biological and biomedical data science, SIB maximizes scientific impact through FAIR data, biodata resources, and innovation.

sib.swiss

14 27

Reposted by Chaoran Chen

Dr. Bethany Allen @bethanyjallen.bsky.social · Mar 7

Today I have resigned from my position as a Data Editor at Proceedings B. I believe the journal does great work, but it feels wrong to voluntarily spend my time holding authors to account on behalf of the Royal Society, while the Society refuses to hold its own Fellows to account.

4 34 170

Reposted by Chaoran Chen

Tanja Stadler @tanjastadler.bsky.social · Feb 10

Major cuts planned in SRF science journalism in Switzerland - the public service media. Scientists today launched a petition ‘Facts Instead of Misinformation: For Strong Science Journalism!’ Become one of over 1,800 signatories www.openpetition.eu/ch/petition/...

Facts Instead of Misinformation: For Strong Science Journalism! - Online-Petition

Open Letter from the Scientific Community to SRF Dear Management of SRG, Dear Executive Board of SRF, Dear Media and Science Policy Makers, We are deeply concerned about SRF’s plans to make significan...

www.openpetition.eu

1 4 7

Reposted by Chaoran Chen

Pathoplexus @pathoplexus.org · Feb 5

Thanks to huge efforts by Uganda’s Central Public Health Laboratory, Uganda Ministry of Health, UVRI, Africa CDC, & SANBI, UWC the sequence from the Ebola Sudan case in Kampala is now available on Pathoplexus pathoplexus.org/seq/PP_0011C... w full analysis here: virological.org/t/near-real-...

Screenshot of the virological post on the Ebolavirus sequence

Screenshot of the sequence on pathoplexus

11 33

Reposted by Chaoran Chen

Andrew Rambaut @arambaut.bsky.social · Feb 3

First genome sequence from the Ugandan Ebolavirus outbreak with analysis: virological.org/t/990 and first filovirus genome submitted to Pathoplexus database: pathoplexus.org/seq/PP_0011C.... Great (and rapid) work from the National Health Laboratory, UVRI and partners.

Near Real-Time Genomic Characterization of the 2025 Sudan Ebolavirus Outbreak in Uganda’s Index Case: Insights into Evolutionary Origins

Introduction Case History: On January 30, 2025, the Ministry of Health declared an outbreak of Sudan Ebola Virus (SUDV) Disease in Kampala, Uganda, following the death of a healthcare worker at Mula...

virological.org

3 65 100

Reposted by Chaoran Chen

Pathoplexus @pathoplexus.org · Jan 21

Interested in finding out more about @pathoplexus.org? We're running two Information/Q&A sessions!
22 Jan 15-17.00 CET
4 Feb 16-18.00 CET

Come join us & bring your questions, to find out more about using & sharing data with Pathoplexus! 😁

Sign up here: forms.gle/YRRZA1rRtgYy...

Pathoplexus Online Introduction and Q&A

Thank you for your interest in Pathoplexus! Are you interested in using Pathoplexus to upload your own sequences, either as Open or Restricted-Use? Do you have questions about how submission works, ...

forms.gle

7 12