Chaoran Chen

134 Followers
47 Following
52 Posts
PhD student at ETH Zurich and developer of GenSpectrum (https://genspectrum.org, https://cov-spectrum.org)
GitHubhttps://github.com/chaoran-chen

1/ 🚀 Pathoplexus now supports Marburg virus (MARV) and Ravn virus (RAVN) (sister viruses in the same genus). MARV has two main clades and causes severe disease with reported fatality rates of 24–88%.

You can read more detail about adding Marburg here: https://pathoplexus.org/news/2025-11-28-expanding-pathoplexus-marburg

🗓 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: https://pathoplexus.org/news/2025-08-27-happy-birthday-world

1/10

In the wake of the “GitHub CEO stepped down, no longer independent” news, I’m reminded that not enough people know about @Codeberg — free Git hosting run by a non-profit organization.

No tracking, no ads, no corporate buyout risk. Just open-source, community-driven software hosting.

Give it a try → https://codeberg.org

#opensource #freesoftware #git #devcommunity #indieweb #decentralization

Codeberg.org

Codeberg is a non-profit community-led organization that aims to help free and open source projects prosper by giving them a safe and friendly home.

Codeberg.org

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

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

Register: https://www.bc2.ch/registration-info

#bioinformatics #openScience

📢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 Swiss TPH has an opening working with ARTIC2, @pathoplexus , & Loculus - read on!

1/5

🗓️ 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

Thanks to sterling work from Uganda's Central Public Health Laboratory and partners (including us at SANBI, UWC), the sequence from the "index case" of the new Ebola outbreak in Uganda is up on @pathoplexus (PP_0011CQ4) with a post describing it on virological: https://virological.org/t/near-real-time-genomic-characterization-of-the-2025-sudan-ebolavirus-outbreak-in-uganda-s-index-case-insights-into-evolutionary-origins/990 - TLDR; this is a new spillover, not related to the 2022 outbreak. And it took less than 4 days to go from the case detection to genome publication - quite incredible.
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 Mulago National Referral Hospital. The index case, a 32-year-old male nurse, presented with fever and other symptoms on 19th January 2025 and sought care at three healthcare facilities, one in Kampala one in Wakiso and another in Mbale district, before succumbing to the illness 10 days later (29th Janua...

Virological
We have just received an updated dataset from GISAID for https://cov-spectrum.org. Many thanks to the GISAID team for fixing the data feed!
covSPECTRUM

covSPECTRUM is an interactive platform aiming to help scientists investigate and identify variants of SARS-CoV-2.

Information for CoV-Spectrum users: The GISAID data on CoV-Spectrum has not been updated since 23 December due to an interruption in the data feed. We have contacted GISAID regarding this issue and are hopeful for a resolution soon.
GenSpectrum just added a mpox dashboard using data from @pathoplexus – see https://genspectrum.org
GenSpectrum Dashboards

GenSpectrum is an interactive dashboard to query and analyze pathogen sequences, currently available for Influenza H5N1, RSV, SARS-CoV-2 and the West Nile virus.