Dr Emma Hodcroft
@firefoxx66.bsky.social
Die Virenjägerin! 🏹🧬!
Using programming & phylogenetics, I study & track viruses. Co-developer of Nextstrain, based at Swiss TPH & Uni Basel.
Founder of the orig SC2 variant-tracking website, CoVariants.org
I like 🐈 & 🛫
@firefoxx66@mstdn.science
Using programming & phylogenetics, I study & track viruses. Co-developer of Nextstrain, based at Swiss TPH & Uni Basel.
Founder of the orig SC2 variant-tracking website, CoVariants.org
I like 🐈 & 🛫
@firefoxx66@mstdn.science
Just a reminder - if you're in Zurich tonight and interested in open data sharing, come hear me speak at 18.00! (Only 20 minutes, in English!)
In Zurich on Monday evening? Want to hear about #opendata & data sharing, and how critical it is for preparing for and responding to infectious diseases? 🔓🧬
Come hear me speak at Karl de Grosse Debattierhaus Winterreden! 🪟💬
👉🏻 19 Jan, 18.00, 20 mins, English
www.karldergrosse.ch/programm/ver...
Come hear me speak at Karl de Grosse Debattierhaus Winterreden! 🪟💬
👉🏻 19 Jan, 18.00, 20 mins, English
www.karldergrosse.ch/programm/ver...
January 19, 2026 at 4:35 PM
Just a reminder - if you're in Zurich tonight and interested in open data sharing, come hear me speak at 18.00! (Only 20 minutes, in English!)
Reposted by Dr Emma Hodcroft
In Zurich on Monday evening? Want to hear about #opendata & data sharing, and how critical it is for preparing for and responding to infectious diseases? 🔓🧬
Come hear me speak at Karl de Grosse Debattierhaus Winterreden! 🪟💬
👉🏻 19 Jan, 18.00, 20 mins, English
www.karldergrosse.ch/programm/ver...
Come hear me speak at Karl de Grosse Debattierhaus Winterreden! 🪟💬
👉🏻 19 Jan, 18.00, 20 mins, English
www.karldergrosse.ch/programm/ver...
January 13, 2026 at 1:14 PM
In Zurich on Monday evening? Want to hear about #opendata & data sharing, and how critical it is for preparing for and responding to infectious diseases? 🔓🧬
Come hear me speak at Karl de Grosse Debattierhaus Winterreden! 🪟💬
👉🏻 19 Jan, 18.00, 20 mins, English
www.karldergrosse.ch/programm/ver...
Come hear me speak at Karl de Grosse Debattierhaus Winterreden! 🪟💬
👉🏻 19 Jan, 18.00, 20 mins, English
www.karldergrosse.ch/programm/ver...
In Zurich on Monday evening? Want to hear about #opendata & data sharing, and how critical it is for preparing for and responding to infectious diseases? 🔓🧬
Come hear me speak at Karl de Grosse Debattierhaus Winterreden! 🪟💬
👉🏻 19 Jan, 18.00, 20 mins, English
www.karldergrosse.ch/programm/ver...
Come hear me speak at Karl de Grosse Debattierhaus Winterreden! 🪟💬
👉🏻 19 Jan, 18.00, 20 mins, English
www.karldergrosse.ch/programm/ver...
January 13, 2026 at 1:14 PM
In Zurich on Monday evening? Want to hear about #opendata & data sharing, and how critical it is for preparing for and responding to infectious diseases? 🔓🧬
Come hear me speak at Karl de Grosse Debattierhaus Winterreden! 🪟💬
👉🏻 19 Jan, 18.00, 20 mins, English
www.karldergrosse.ch/programm/ver...
Come hear me speak at Karl de Grosse Debattierhaus Winterreden! 🪟💬
👉🏻 19 Jan, 18.00, 20 mins, English
www.karldergrosse.ch/programm/ver...
Reposted by Dr Emma Hodcroft
Sigh. For the hundredth time, we are not judging his character, we are judging his actions. The RS position would be fine if it was a gentlemen's club, who can have who it damn well pleases. But it positions itself as represnting British science and scientists. Now an embarrassment, to be frank.
Musk should remain member of UK Royal Society, says president ft.trib.al/tC0vaAa
Musk should remain member of UK Royal Society, says president
Paul Nurse tells FT that national science academy should avoid ‘making judgments’ about ‘character’ of fellows
ft.trib.al
January 9, 2026 at 9:24 PM
Sigh. For the hundredth time, we are not judging his character, we are judging his actions. The RS position would be fine if it was a gentlemen's club, who can have who it damn well pleases. But it positions itself as represnting British science and scientists. Now an embarrassment, to be frank.
This needs boosting.
How we share data now, determines how prepared we are for tomorrow. That includes having access to *all* who need it (inccitizen scientists like @ryanhisner.bsky.social) & being able to use it in dashboards & apps.
Having one place control it all - is dangerous.
#OpenScience
How we share data now, determines how prepared we are for tomorrow. That includes having access to *all* who need it (inccitizen scientists like @ryanhisner.bsky.social) & being able to use it in dashboards & apps.
Having one place control it all - is dangerous.
#OpenScience
“[P]utting data into GISAID is like dropping it in a mail slot in an unmarked building,” says @colincarlson.bsky.social. “It’s wonderful that there’s so much cool stuff in that building. It would be great if we knew who owned it, or who paid for it, or what they plan to do with it.”
#IDsky 🧪
#IDsky 🧪
Fresh conflicts erupt around giant database for flu and COVID-19 sequences
Critics say “autocratic” behavior by GISAID could hamper response to a future pandemic
www.science.org
January 8, 2026 at 3:05 PM
This needs boosting.
How we share data now, determines how prepared we are for tomorrow. That includes having access to *all* who need it (inccitizen scientists like @ryanhisner.bsky.social) & being able to use it in dashboards & apps.
Having one place control it all - is dangerous.
#OpenScience
How we share data now, determines how prepared we are for tomorrow. That includes having access to *all* who need it (inccitizen scientists like @ryanhisner.bsky.social) & being able to use it in dashboards & apps.
Having one place control it all - is dangerous.
#OpenScience
POV, you need to be out of the rental house by 11am tomorrow, so all hands on deck to finish the Christmas Puzzle!
Wishing you all a joyful and merry Christmas, full of puzzles and loved ones! 🎁🎄☃️
Wishing you all a joyful and merry Christmas, full of puzzles and loved ones! 🎁🎄☃️
December 26, 2025 at 3:11 AM
POV, you need to be out of the rental house by 11am tomorrow, so all hands on deck to finish the Christmas Puzzle!
Wishing you all a joyful and merry Christmas, full of puzzles and loved ones! 🎁🎄☃️
Wishing you all a joyful and merry Christmas, full of puzzles and loved ones! 🎁🎄☃️
Best Christmas Card of 2025 award goes out to the @biozentrum.unibas.ch for this incredible building-themed-advent-calendar! Opening a window each day has been fantastic! ❄️☃️😁
December 11, 2025 at 8:30 AM
Best Christmas Card of 2025 award goes out to the @biozentrum.unibas.ch for this incredible building-themed-advent-calendar! Opening a window each day has been fantastic! ❄️☃️😁
One of my neighbors has been putting up these fish facts posters. All kinds of different fish, marine, freshwater, deep, shallow, all kinds. This is a good one. “Stg this real fish” took me out. Good work, neighbor.
December 7, 2025 at 7:47 PM
Reposted by Dr Emma Hodcroft
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: pathoplexus.org/news/2025-11...
You can read more detail about adding Marburg here: pathoplexus.org/news/2025-11...
November 28, 2025 at 12:37 PM
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: pathoplexus.org/news/2025-11...
You can read more detail about adding Marburg here: pathoplexus.org/news/2025-11...
The change to the CDC website to reflect unscientific, agenda-driven mindsets is deeply upsetting.
But let's not forget there are a lot of excellent scientists still working there. Persisting. Trying to minimise damage.
Let's not stop supporting them - while condemning those in charge!
But let's not forget there are a lot of excellent scientists still working there. Persisting. Trying to minimise damage.
Let's not stop supporting them - while condemning those in charge!
November 23, 2025 at 12:42 PM
The change to the CDC website to reflect unscientific, agenda-driven mindsets is deeply upsetting.
But let's not forget there are a lot of excellent scientists still working there. Persisting. Trying to minimise damage.
Let's not stop supporting them - while condemning those in charge!
But let's not forget there are a lot of excellent scientists still working there. Persisting. Trying to minimise damage.
Let's not stop supporting them - while condemning those in charge!
1/ 🚀 Exciting news: we’ve just released the first Nextclade dataset for Enterovirus D68 (EV-D68), developed in collaboration with the European Non-Polio Enterovirus Network (ENPEN).
👉🏻 Check out the dataset on Nextclade! clades.nextstrain.org?dataset-name...
#EVD68 #Enterovirus #OpenData
👉🏻 Check out the dataset on Nextclade! clades.nextstrain.org?dataset-name...
#EVD68 #Enterovirus #OpenData
November 20, 2025 at 12:49 PM
1/ 🚀 Exciting news: we’ve just released the first Nextclade dataset for Enterovirus D68 (EV-D68), developed in collaboration with the European Non-Polio Enterovirus Network (ENPEN).
👉🏻 Check out the dataset on Nextclade! clades.nextstrain.org?dataset-name...
#EVD68 #Enterovirus #OpenData
👉🏻 Check out the dataset on Nextclade! clades.nextstrain.org?dataset-name...
#EVD68 #Enterovirus #OpenData
Reposted by Dr Emma Hodcroft
1/ 🚀 Big thanks to our community - since August we’ve added thousands of new sequences, rolled out major new features, and welcomed fresh faces into the #Pathoplexus world. Let’s dive into what’s new.👇🏻
Read the full update: pathoplexus.org/news/2025-11...
Read the full update: pathoplexus.org/news/2025-11...
November 18, 2025 at 7:01 PM
1/ 🚀 Big thanks to our community - since August we’ve added thousands of new sequences, rolled out major new features, and welcomed fresh faces into the #Pathoplexus world. Let’s dive into what’s new.👇🏻
Read the full update: pathoplexus.org/news/2025-11...
Read the full update: pathoplexus.org/news/2025-11...
Looking forward to sharing @pathoplexus.org next week at the @evbc.bsky.social Viruses in Silico lecture! Tune in if you'd like to hear about open but protected data sharing, simple uploads, & transparent governance - all to help with easier, faster viral genome sharing!
#opendata #openscience
#opendata #openscience
📢 Next Viruses in silico lecture:
🎙️ Pathoplexus: A Community-Driven Solution for Transparent and Equitable Viral Genomic Data Sharing
👩🔬 Emma Hodcroft @firefoxx66.bsky.social (@swisstph.ch @sib.swiss)
🗓️ 27 Nov 2025 🕑 4 PM CET
📍 Zoom - Register to receive login details
👉 tinyurl.com/VirInSilico
🎙️ Pathoplexus: A Community-Driven Solution for Transparent and Equitable Viral Genomic Data Sharing
👩🔬 Emma Hodcroft @firefoxx66.bsky.social (@swisstph.ch @sib.swiss)
🗓️ 27 Nov 2025 🕑 4 PM CET
📍 Zoom - Register to receive login details
👉 tinyurl.com/VirInSilico
November 18, 2025 at 7:53 AM
Looking forward to sharing @pathoplexus.org next week at the @evbc.bsky.social Viruses in Silico lecture! Tune in if you'd like to hear about open but protected data sharing, simple uploads, & transparent governance - all to help with easier, faster viral genome sharing!
#opendata #openscience
#opendata #openscience
Reposted by Dr Emma Hodcroft
📢 Next Viruses in silico lecture:
🎙️ Pathoplexus: A Community-Driven Solution for Transparent and Equitable Viral Genomic Data Sharing
👩🔬 Emma Hodcroft @firefoxx66.bsky.social (@swisstph.ch @sib.swiss)
🗓️ 27 Nov 2025 🕑 4 PM CET
📍 Zoom - Register to receive login details
👉 tinyurl.com/VirInSilico
🎙️ Pathoplexus: A Community-Driven Solution for Transparent and Equitable Viral Genomic Data Sharing
👩🔬 Emma Hodcroft @firefoxx66.bsky.social (@swisstph.ch @sib.swiss)
🗓️ 27 Nov 2025 🕑 4 PM CET
📍 Zoom - Register to receive login details
👉 tinyurl.com/VirInSilico
November 17, 2025 at 10:27 PM
📢 Next Viruses in silico lecture:
🎙️ Pathoplexus: A Community-Driven Solution for Transparent and Equitable Viral Genomic Data Sharing
👩🔬 Emma Hodcroft @firefoxx66.bsky.social (@swisstph.ch @sib.swiss)
🗓️ 27 Nov 2025 🕑 4 PM CET
📍 Zoom - Register to receive login details
👉 tinyurl.com/VirInSilico
🎙️ Pathoplexus: A Community-Driven Solution for Transparent and Equitable Viral Genomic Data Sharing
👩🔬 Emma Hodcroft @firefoxx66.bsky.social (@swisstph.ch @sib.swiss)
🗓️ 27 Nov 2025 🕑 4 PM CET
📍 Zoom - Register to receive login details
👉 tinyurl.com/VirInSilico
Reposted by Dr Emma Hodcroft
Open position at the Swiss Institute of Bioinformatics:
We are looking for a Director of the Center of Pathogen Bioinformatics
apply.refline.ch/499599/0346/...
I am in the Center's steering board together with fantastic colleagues (Emma Hodcroft @firefoxx66.bsky.social, Richard Neher @neher.io, and
We are looking for a Director of the Center of Pathogen Bioinformatics
apply.refline.ch/499599/0346/...
I am in the Center's steering board together with fantastic colleagues (Emma Hodcroft @firefoxx66.bsky.social, Richard Neher @neher.io, and
Director, Center for Pathogen Bioinformatics
The Centre for Pathogen Bioinformatics (CPB) is a unit of SIB which offers expertise and services in pathogen bioinformatics, computational molecular epidemiology and related multi-site project manage...
apply.refline.ch
October 25, 2025 at 1:03 PM
Open position at the Swiss Institute of Bioinformatics:
We are looking for a Director of the Center of Pathogen Bioinformatics
apply.refline.ch/499599/0346/...
I am in the Center's steering board together with fantastic colleagues (Emma Hodcroft @firefoxx66.bsky.social, Richard Neher @neher.io, and
We are looking for a Director of the Center of Pathogen Bioinformatics
apply.refline.ch/499599/0346/...
I am in the Center's steering board together with fantastic colleagues (Emma Hodcroft @firefoxx66.bsky.social, Richard Neher @neher.io, and
I want to spell this out in case the implications aren't clear:
This means all public tools/webapps of GISAID data (all the ones you've been used to seeing thru the pandemic, as far as we can tell) are prohibited.
The file allowed this. Cut that - cut off all tools the public & others were using.
This means all public tools/webapps of GISAID data (all the ones you've been used to seeing thru the pandemic, as far as we can tell) are prohibited.
The file allowed this. Cut that - cut off all tools the public & others were using.
On Oct 1, 2025, GISAID informed us that they had ended updates to the flat file of SARS-CoV-2 genomic sequences and associated metadata that we had used to update Nextstrain analyses since Feb 2020. GISAID's stated rationale was that their "resources are limited". 1/5
November 7, 2025 at 2:41 PM
I want to spell this out in case the implications aren't clear:
This means all public tools/webapps of GISAID data (all the ones you've been used to seeing thru the pandemic, as far as we can tell) are prohibited.
The file allowed this. Cut that - cut off all tools the public & others were using.
This means all public tools/webapps of GISAID data (all the ones you've been used to seeing thru the pandemic, as far as we can tell) are prohibited.
The file allowed this. Cut that - cut off all tools the public & others were using.
Reposted by Dr Emma Hodcroft
On Oct 1, 2025, GISAID informed us that they had ended updates to the flat file of SARS-CoV-2 genomic sequences and associated metadata that we had used to update Nextstrain analyses since Feb 2020. GISAID's stated rationale was that their "resources are limited". 1/5
November 6, 2025 at 9:46 PM
On Oct 1, 2025, GISAID informed us that they had ended updates to the flat file of SARS-CoV-2 genomic sequences and associated metadata that we had used to update Nextstrain analyses since Feb 2020. GISAID's stated rationale was that their "resources are limited". 1/5
From @torstenseemann.bsky.social at @pha4ge.bsky.social Conference; "We are stealing from research money to support public health."
We need dedicated funding for maintaining & supporting public health infrastructure & pipelines. Not just startup, not just in pandemics.
We need dedicated funding for maintaining & supporting public health infrastructure & pipelines. Not just startup, not just in pandemics.
October 28, 2025 at 8:52 AM
From @torstenseemann.bsky.social at @pha4ge.bsky.social Conference; "We are stealing from research money to support public health."
We need dedicated funding for maintaining & supporting public health infrastructure & pipelines. Not just startup, not just in pandemics.
We need dedicated funding for maintaining & supporting public health infrastructure & pipelines. Not just startup, not just in pandemics.
Thrilled & honoured to have run the first @pathoplexus.org workshop with @chaoranchen.de @pagasi.bsky.social @kanyerezi30.bsky.social & Arthur Shem Kasambula at @pha4ge.bsky.social on Saturday! 🎉🤝
A fantastic turnout & wonderful time spent with curious users!
A fantastic turnout & wonderful time spent with curious users!
October 27, 2025 at 7:58 AM
Thrilled & honoured to have run the first @pathoplexus.org workshop with @chaoranchen.de @pagasi.bsky.social @kanyerezi30.bsky.social & Arthur Shem Kasambula at @pha4ge.bsky.social on Saturday! 🎉🤝
A fantastic turnout & wonderful time spent with curious users!
A fantastic turnout & wonderful time spent with curious users!
Reposted by Dr Emma Hodcroft
BREAKING: Friday night massacre underway at CDC. Doznes of "disease detectives," high-level scientists, entire Washington staff and editors of the MMWR (Morbidity and Mortality Weekly Report) have all been RIFed and received the following notice:
October 11, 2025 at 2:10 AM
BREAKING: Friday night massacre underway at CDC. Doznes of "disease detectives," high-level scientists, entire Washington staff and editors of the MMWR (Morbidity and Mortality Weekly Report) have all been RIFed and received the following notice:
The cruelty is the point.
They are using this as an excuse to fire even more of our best, most dedicated scientists, researchers, and civil servants.
They do this because they do not believe in science, and they do not genuinely care about the health of America.
They are using this as an excuse to fire even more of our best, most dedicated scientists, researchers, and civil servants.
They do this because they do not believe in science, and they do not genuinely care about the health of America.
We have breaking news in Inside Medicine.
We had heard rumors of RIFs to CDC.
But this is the first visual confirmation that it has occurred tonight, and at high levels in the agency.
Here is what we know...and then some well-sourced rumors (but rumors, nonetheless, not confirmed) 🧵...
We had heard rumors of RIFs to CDC.
But this is the first visual confirmation that it has occurred tonight, and at high levels in the agency.
Here is what we know...and then some well-sourced rumors (but rumors, nonetheless, not confirmed) 🧵...
October 11, 2025 at 7:03 AM
The cruelty is the point.
They are using this as an excuse to fire even more of our best, most dedicated scientists, researchers, and civil servants.
They do this because they do not believe in science, and they do not genuinely care about the health of America.
They are using this as an excuse to fire even more of our best, most dedicated scientists, researchers, and civil servants.
They do this because they do not believe in science, and they do not genuinely care about the health of America.
Reposted by Dr Emma Hodcroft
We have breaking news in Inside Medicine.
We had heard rumors of RIFs to CDC.
But this is the first visual confirmation that it has occurred tonight, and at high levels in the agency.
Here is what we know...and then some well-sourced rumors (but rumors, nonetheless, not confirmed) 🧵...
We had heard rumors of RIFs to CDC.
But this is the first visual confirmation that it has occurred tonight, and at high levels in the agency.
Here is what we know...and then some well-sourced rumors (but rumors, nonetheless, not confirmed) 🧵...
October 11, 2025 at 3:17 AM
We have breaking news in Inside Medicine.
We had heard rumors of RIFs to CDC.
But this is the first visual confirmation that it has occurred tonight, and at high levels in the agency.
Here is what we know...and then some well-sourced rumors (but rumors, nonetheless, not confirmed) 🧵...
We had heard rumors of RIFs to CDC.
But this is the first visual confirmation that it has occurred tonight, and at high levels in the agency.
Here is what we know...and then some well-sourced rumors (but rumors, nonetheless, not confirmed) 🧵...
Reposted by Dr Emma Hodcroft
“Goebbels Ends Careers of Five ‘Aryan’ Actors Who Made Witticisms About the Nazi Regime”
September 18, 2025 at 4:38 PM
“Goebbels Ends Careers of Five ‘Aryan’ Actors Who Made Witticisms About the Nazi Regime”
Reposted by Dr Emma Hodcroft
🎙️ Just dropped: #MicroBinfie Pathoplexus Part 1!
Join @happykhan.mstdn.science.ap.brid.gy, Lee & guest Clint as they deep-dive with @firefoxx66.bsky.social, Theo Sanderson & Arthur Shem Kasambula into Pathoplexus.
Ready for a journey? 🚀 Listen now: pca.st/episode/c1f8...
Join @happykhan.mstdn.science.ap.brid.gy, Lee & guest Clint as they deep-dive with @firefoxx66.bsky.social, Theo Sanderson & Arthur Shem Kasambula into Pathoplexus.
Ready for a journey? 🚀 Listen now: pca.st/episode/c1f8...
144 - micro binfie Pathoplexus part 1
pca.st
September 11, 2025 at 12:05 PM
🎙️ Just dropped: #MicroBinfie Pathoplexus Part 1!
Join @happykhan.mstdn.science.ap.brid.gy, Lee & guest Clint as they deep-dive with @firefoxx66.bsky.social, Theo Sanderson & Arthur Shem Kasambula into Pathoplexus.
Ready for a journey? 🚀 Listen now: pca.st/episode/c1f8...
Join @happykhan.mstdn.science.ap.brid.gy, Lee & guest Clint as they deep-dive with @firefoxx66.bsky.social, Theo Sanderson & Arthur Shem Kasambula into Pathoplexus.
Ready for a journey? 🚀 Listen now: pca.st/episode/c1f8...
Reposted by Dr Emma Hodcroft
Amid the concerning news of a new Ebola Zaire outbreak in DRC, teams on the ground have already managed to sample, sequence, and share data. This rapid turnaround is a testament to their commitment and capacity to respond.
Read more: virological.org/t/the-16th-e...
1/7
Read more: virological.org/t/the-16th-e...
1/7
The 16th Ebola Virus Disease Outbreak in Bulape Health Zone, Kasai, Democratic Republic of the Congo: A new spillover event from an unknown reservoir host
Background The Democratic Republic of the Congo (DRC) is currently facing concurrent outbreaks including mpox, cholera and malaria (1-4). The Ministry of Public Health, DRC has declared the 16th Ebola...
virological.org
September 10, 2025 at 10:00 AM
Amid the concerning news of a new Ebola Zaire outbreak in DRC, teams on the ground have already managed to sample, sequence, and share data. This rapid turnaround is a testament to their commitment and capacity to respond.
Read more: virological.org/t/the-16th-e...
1/7
Read more: virological.org/t/the-16th-e...
1/7