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 🐈 & 🛫
@[email protected]
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 🐈 & 🛫
@[email protected]
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
Reposted by Dr Emma Hodcroft
Thanks to all the speakers of the great Bioinformatics in Infectious Diseases session at #bc2basel, chaired by EmmaHodcroft @firefoxx66.bsky.social and #JacquesFellay:
Aurelie Cobat, Charlyne Bürki, Andrea Di Gioacchino, KenoStrotjohann, Hesham ElAbd, Lisa Pagani, and Valeriia Timonina
Aurelie Cobat, Charlyne Bürki, Andrea Di Gioacchino, KenoStrotjohann, Hesham ElAbd, Lisa Pagani, and Valeriia Timonina
September 9, 2025 at 9:50 AM
Thanks to all the speakers of the great Bioinformatics in Infectious Diseases session at #bc2basel, chaired by EmmaHodcroft @firefoxx66.bsky.social and #JacquesFellay:
Aurelie Cobat, Charlyne Bürki, Andrea Di Gioacchino, KenoStrotjohann, Hesham ElAbd, Lisa Pagani, and Valeriia Timonina
Aurelie Cobat, Charlyne Bürki, Andrea Di Gioacchino, KenoStrotjohann, Hesham ElAbd, Lisa Pagani, and Valeriia Timonina
Reposted by Dr Emma Hodcroft
Ain't no way RFKJ wrote this when he literally called us "troubled" only a few hours ago. Sorry, anon comms person/maybe the AI forced to write this drivel...
We just added a few notes. Anything to be helpful! ✨😊😇
We just added a few notes. Anything to be helpful! ✨😊😇
August 29, 2025 at 2:00 AM
Ain't no way RFKJ wrote this when he literally called us "troubled" only a few hours ago. Sorry, anon comms person/maybe the AI forced to write this drivel...
We just added a few notes. Anything to be helpful! ✨😊😇
We just added a few notes. Anything to be helpful! ✨😊😇
Reposted by Dr Emma Hodcroft
AP live feed of the CDC walkout in Atlanta. www.youtube.com/watch?v=KZ7Q...
LIVE: CDC staff plan walkout at Atlanta HQ after Trump firings
YouTube video by Associated Press
www.youtube.com
August 28, 2025 at 7:02 PM
AP live feed of the CDC walkout in Atlanta. www.youtube.com/watch?v=KZ7Q...
🚀 More good news: website lift-off!
The Epidemiology & Virus Evolution (EVE) group at @swisstph.ch has a brand new home on the web:
eve-lab.org
🦠🌍
Check out our research, people, collaborations, & projects all in one place! 👇
1/4
The Epidemiology & Virus Evolution (EVE) group at @swisstph.ch has a brand new home on the web:
eve-lab.org
🦠🌍
Check out our research, people, collaborations, & projects all in one place! 👇
1/4
EVE – Epidemiology & Virus Evolution
EVE - Epidemiology and Virus Evolution - the Hodcroft lab
eve-lab.org
August 29, 2025 at 9:33 AM
🚀 More good news: website lift-off!
The Epidemiology & Virus Evolution (EVE) group at @swisstph.ch has a brand new home on the web:
eve-lab.org
🦠🌍
Check out our research, people, collaborations, & projects all in one place! 👇
1/4
The Epidemiology & Virus Evolution (EVE) group at @swisstph.ch has a brand new home on the web:
eve-lab.org
🦠🌍
Check out our research, people, collaborations, & projects all in one place! 👇
1/4
A very special day today, as I look back and remember our trepidation on how this crazy idea of a new pathogen database would go down. Would our work be for naught?
But no! I'm so grateful that we've been able to make a big impact on sequence sharing! Here's to year 2! 🥂
But no! I'm so grateful that we've been able to make a big impact on sequence sharing! Here's to year 2! 🥂
🗓 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
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
August 27, 2025 at 4:18 PM
A very special day today, as I look back and remember our trepidation on how this crazy idea of a new pathogen database would go down. Would our work be for naught?
But no! I'm so grateful that we've been able to make a big impact on sequence sharing! Here's to year 2! 🥂
But no! I'm so grateful that we've been able to make a big impact on sequence sharing! Here's to year 2! 🥂
Reposted by Dr Emma Hodcroft
🗓 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
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
August 27, 2025 at 3:57 PM
🗓 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
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
One thing I find endlessly endearing in Switzerland is that the Unis have little nicknames:
UniBas (University of Basel) @unibas.ch
UniBe (University of Bern) @unibe.ch
UNIL (University of Lausanne) @unil.bsky.social
Do the other Unis have little nicknames too?
UniBas (University of Basel) @unibas.ch
UniBe (University of Bern) @unibe.ch
UNIL (University of Lausanne) @unil.bsky.social
Do the other Unis have little nicknames too?
August 26, 2025 at 8:38 AM
One thing I find endlessly endearing in Switzerland is that the Unis have little nicknames:
UniBas (University of Basel) @unibas.ch
UniBe (University of Bern) @unibe.ch
UNIL (University of Lausanne) @unil.bsky.social
Do the other Unis have little nicknames too?
UniBas (University of Basel) @unibas.ch
UniBe (University of Bern) @unibe.ch
UNIL (University of Lausanne) @unil.bsky.social
Do the other Unis have little nicknames too?
Keep and eye 👁️ (and an ear! 👂) out for a new Binfie podcast all about Pathoplexus 1 year in!
@happykhan.mstdn.science.ap.brid.gy and I had a great time recording last week with @firefoxx66.bsky.social @theo.io and Arthur Shem, with the help of Clint. Episodes set to be released starting September 11.
#microbinfie
#microbinfie
August 26, 2025 at 8:37 AM
Keep and eye 👁️ (and an ear! 👂) out for a new Binfie podcast all about Pathoplexus 1 year in!
Reposted by Dr Emma Hodcroft
It was a great pleasure to contribute to this work by Jemma Fendley, @mmolari.bsky.social, and Boris Shraiman on pan-genomes, linkage, and recombination in phage genomes.
We analyzed data collected by the fantastic SEA-PHAGES program in phagesdb.org.
[1/6]
www.biorxiv.org/content/10.1...
We analyzed data collected by the fantastic SEA-PHAGES program in phagesdb.org.
[1/6]
www.biorxiv.org/content/10.1...
The Actinobacteriophage Database | Home
phagesdb.org
August 23, 2025 at 4:21 PM
It was a great pleasure to contribute to this work by Jemma Fendley, @mmolari.bsky.social, and Boris Shraiman on pan-genomes, linkage, and recombination in phage genomes.
We analyzed data collected by the fantastic SEA-PHAGES program in phagesdb.org.
[1/6]
www.biorxiv.org/content/10.1...
We analyzed data collected by the fantastic SEA-PHAGES program in phagesdb.org.
[1/6]
www.biorxiv.org/content/10.1...
Reposted by Dr Emma Hodcroft
Insisting on expertise over ideology is not “politicizing” science. The ideologues installing scientific and governmental policy that is contradicted by evidence and data are.
By emphasizing ideology over expertise, THEY have made arguing for expertise and evidence-based decision making partisan.
By emphasizing ideology over expertise, THEY have made arguing for expertise and evidence-based decision making partisan.
Scientists Are Caught in a Political Trap
Fighting back against the Trump administration means they start to look more like activists.
www.theatlantic.com
August 23, 2025 at 4:45 PM
Insisting on expertise over ideology is not “politicizing” science. The ideologues installing scientific and governmental policy that is contradicted by evidence and data are.
By emphasizing ideology over expertise, THEY have made arguing for expertise and evidence-based decision making partisan.
By emphasizing ideology over expertise, THEY have made arguing for expertise and evidence-based decision making partisan.