Sofia Paraskevopoulou
@akifoss.bsky.social
Viruses - Evolution - Bioinformatics
Berlin // Robert Koch Institute
Berlin // Robert Koch Institute
Reposted by Sofia Paraskevopoulou
I'm excited to introduce our new workflow for detecting endogenous viral elements - HI-FEVER. 🖥️🧬
academic.oup.com/bioinformati...
🧵
Big thanks to @ariskatzourakis.bsky.social, @humanceae.bsky.social, José Gabriel and Cormac for bringing this from conception to fruition!
academic.oup.com/bioinformati...
🧵
Big thanks to @ariskatzourakis.bsky.social, @humanceae.bsky.social, José Gabriel and Cormac for bringing this from conception to fruition!
HI-FEVER: a Nextflow pipeline for the high-throughput discovery and annotation of endogenous viral elements
AbstractSummary. Endogenous viral elements (EVEs) offer valuable insights into virus and host evolution, but their detection remains computationally and bi
academic.oup.com
November 13, 2025 at 11:14 AM
I'm excited to introduce our new workflow for detecting endogenous viral elements - HI-FEVER. 🖥️🧬
academic.oup.com/bioinformati...
🧵
Big thanks to @ariskatzourakis.bsky.social, @humanceae.bsky.social, José Gabriel and Cormac for bringing this from conception to fruition!
academic.oup.com/bioinformati...
🧵
Big thanks to @ariskatzourakis.bsky.social, @humanceae.bsky.social, José Gabriel and Cormac for bringing this from conception to fruition!
Reposted by Sofia Paraskevopoulou
Monumental effort led by Peter Simmonds and Jens Kuhn to reorganize the Family Flaviviridae based on analysis of RNA-directed RNA polymerase (RdRP) hallmark gene sequences is finally out. Enjoy reading. #ICTV @utmbhealth.bsky.social @astmh.bsky.social @sbvirologia.bsky.social
October 31, 2025 at 12:44 PM
Monumental effort led by Peter Simmonds and Jens Kuhn to reorganize the Family Flaviviridae based on analysis of RNA-directed RNA polymerase (RdRP) hallmark gene sequences is finally out. Enjoy reading. #ICTV @utmbhealth.bsky.social @astmh.bsky.social @sbvirologia.bsky.social
Reposted by Sofia Paraskevopoulou
New publication alert!
Fertilization impacts microbiomes along the grassland trophic chain academic.oup.com/ismecommun/a...
#organicfertilizers #landusechange #microbiome #grasslands #onehealth
Fertilization impacts microbiomes along the grassland trophic chain academic.oup.com/ismecommun/a...
#organicfertilizers #landusechange #microbiome #grasslands #onehealth
Validate User
academic.oup.com
September 18, 2025 at 7:55 AM
New publication alert!
Fertilization impacts microbiomes along the grassland trophic chain academic.oup.com/ismecommun/a...
#organicfertilizers #landusechange #microbiome #grasslands #onehealth
Fertilization impacts microbiomes along the grassland trophic chain academic.oup.com/ismecommun/a...
#organicfertilizers #landusechange #microbiome #grasslands #onehealth
Reposted by Sofia Paraskevopoulou
New Element in the Philosophy of Biology series—free to download until Oct. 24! @djnicholson.bsky.social uncovers Schrödinger’s motivations for writing "What Is Life?", revisits its central arguments & examines the book’s lasting impact on cell & molecular biology👇 www.cambridge.org/core/element...
October 17, 2025 at 11:23 AM
New Element in the Philosophy of Biology series—free to download until Oct. 24! @djnicholson.bsky.social uncovers Schrödinger’s motivations for writing "What Is Life?", revisits its central arguments & examines the book’s lasting impact on cell & molecular biology👇 www.cambridge.org/core/element...
Reposted by Sofia Paraskevopoulou
And now NextStrain as well.
Next up, will GISAID start charging open-source community tools to have access?
That would completely shaft users who contributed to GISAID, where we never agreed to that and assumed GISAID would be good custodians of the data we contributed. They're not.
Next up, will GISAID start charging open-source community tools to have access?
That would completely shaft users who contributed to GISAID, where we never agreed to that and assumed GISAID would be good custodians of the data we contributed. They're not.
October 16, 2025 at 7:48 PM
And now NextStrain as well.
Next up, will GISAID start charging open-source community tools to have access?
That would completely shaft users who contributed to GISAID, where we never agreed to that and assumed GISAID would be good custodians of the data we contributed. They're not.
Next up, will GISAID start charging open-source community tools to have access?
That would completely shaft users who contributed to GISAID, where we never agreed to that and assumed GISAID would be good custodians of the data we contributed. They're not.
Reposted by Sofia Paraskevopoulou
Viro3D paper is out! We predicted 85,000 protein structures from human & animal viruses. 1/5 🧵
📑 Paper doi.org/10.1038/s443...
🔭 Explore virosphere viro3d.cvr.gla.ac.uk
📑 Paper doi.org/10.1038/s443...
🔭 Explore virosphere viro3d.cvr.gla.ac.uk
Viro3D: a comprehensive database of virus protein structure predictions | Molecular Systems Biology
imageimageViro3D provides proteome-level, high confidence AI-protein structure predictions for
>4,400 viruses, allowing mapping of form and function across the human and animal
virosphere. Viro3D i...
doi.org
September 26, 2025 at 2:06 PM
Viro3D paper is out! We predicted 85,000 protein structures from human & animal viruses. 1/5 🧵
📑 Paper doi.org/10.1038/s443...
🔭 Explore virosphere viro3d.cvr.gla.ac.uk
📑 Paper doi.org/10.1038/s443...
🔭 Explore virosphere viro3d.cvr.gla.ac.uk
Reposted by Sofia Paraskevopoulou
New paper alert 🎉
We explore the origins of deltaviruses and find they have infected and co-evolved with termites for 141 million years 🐜🕑🦴
This was a fascinating story to work on with @ariskatzourakis.bsky.social, Jose Gabriel and @anselmojiro.bsky.social
www.sciencedirect.com/science/arti...
We explore the origins of deltaviruses and find they have infected and co-evolved with termites for 141 million years 🐜🕑🦴
This was a fascinating story to work on with @ariskatzourakis.bsky.social, Jose Gabriel and @anselmojiro.bsky.social
www.sciencedirect.com/science/arti...
Endogenous viral elements in termite genomes reveal extensive diversity of deltaviruses and provide insights into their origins
Deltaviruses are subviral agents of animals, which, in humans, require a hepadnavirus helper for transmission. The absence of deltavirus-like endogeno…
www.sciencedirect.com
September 15, 2025 at 11:16 AM
New paper alert 🎉
We explore the origins of deltaviruses and find they have infected and co-evolved with termites for 141 million years 🐜🕑🦴
This was a fascinating story to work on with @ariskatzourakis.bsky.social, Jose Gabriel and @anselmojiro.bsky.social
www.sciencedirect.com/science/arti...
We explore the origins of deltaviruses and find they have infected and co-evolved with termites for 141 million years 🐜🕑🦴
This was a fascinating story to work on with @ariskatzourakis.bsky.social, Jose Gabriel and @anselmojiro.bsky.social
www.sciencedirect.com/science/arti...
Reposted by Sofia Paraskevopoulou
I'm excited to share with you all a conference I'm planning Oct. 10-12: Dialectical Biology Today: Legacies of Richard Lewontin.
It will be hybrid in Toronto and on zoom, so please join us however you can! Register for zoom link here: ihpst.utoronto.ca/events/diale...
It will be hybrid in Toronto and on zoom, so please join us however you can! Register for zoom link here: ihpst.utoronto.ca/events/diale...
September 15, 2025 at 5:35 PM
I'm excited to share with you all a conference I'm planning Oct. 10-12: Dialectical Biology Today: Legacies of Richard Lewontin.
It will be hybrid in Toronto and on zoom, so please join us however you can! Register for zoom link here: ihpst.utoronto.ca/events/diale...
It will be hybrid in Toronto and on zoom, so please join us however you can! Register for zoom link here: ihpst.utoronto.ca/events/diale...
Reposted by Sofia Paraskevopoulou
Endogenous Deltaviruses (EVEs) in termite genomes !
Endogenous viral elements in termite genomes reveal extensive diversity of deltaviruses and provide insights into their origins
Deltaviruses are subviral agents of animals, which, in humans, require a hepadnavirus helper for transmission. The absence of deltavirus-like endogeno…
www.sciencedirect.com
September 14, 2025 at 5:09 AM
Endogenous Deltaviruses (EVEs) in termite genomes !
Reposted by Sofia Paraskevopoulou
🚨 New Perspective in Nature Water 🚰💻
"Augmenting wastewater epidemiology with machine learning" 🧠🌍
A huge interdisciplinary collab w/ amazing colleagues @rki.de & beyond! 🙌
Special thx to lead author PhD student Eva & shared last Christopher for this effort!
🔗 www.nature.com/articles/s44...
"Augmenting wastewater epidemiology with machine learning" 🧠🌍
A huge interdisciplinary collab w/ amazing colleagues @rki.de & beyond! 🙌
Special thx to lead author PhD student Eva & shared last Christopher for this effort!
🔗 www.nature.com/articles/s44...
Augmentation of wastewater-based epidemiology with machine learning to support global health surveillance - Nature Water
Wastewater-based epidemiology has already proven to be a powerful tool to monitor the spread of a number of diseases. This Perspective discusses the integration with machine learning, highlighting its...
www.nature.com
June 24, 2025 at 5:18 PM
🚨 New Perspective in Nature Water 🚰💻
"Augmenting wastewater epidemiology with machine learning" 🧠🌍
A huge interdisciplinary collab w/ amazing colleagues @rki.de & beyond! 🙌
Special thx to lead author PhD student Eva & shared last Christopher for this effort!
🔗 www.nature.com/articles/s44...
"Augmenting wastewater epidemiology with machine learning" 🧠🌍
A huge interdisciplinary collab w/ amazing colleagues @rki.de & beyond! 🙌
Special thx to lead author PhD student Eva & shared last Christopher for this effort!
🔗 www.nature.com/articles/s44...
Reposted by Sofia Paraskevopoulou
🚀 Excited to share our NatComm paper on varVAMP – a open-source tool for degenerate primer design in viral genome seq & qPCR!
🔬 Supports diverse viruses SC2, HEV, Polio ...
🤝 Built in collaboration with amazing virus experts
🔗 github.com/jonas-fuchs/varVAMP
🧬 nature.com/articles/s41467-025-60175-9
🔬 Supports diverse viruses SC2, HEV, Polio ...
🤝 Built in collaboration with amazing virus experts
🔗 github.com/jonas-fuchs/varVAMP
🧬 nature.com/articles/s41467-025-60175-9
GitHub - jonas-fuchs/varVAMP: Design degenerated primers on highly variable alignments for full genome sequencing or qPCR. Specifically developed for viruses.
Design degenerated primers on highly variable alignments for full genome sequencing or qPCR. Specifically developed for viruses. - jonas-fuchs/varVAMP
github.com
June 9, 2025 at 12:31 PM
🚀 Excited to share our NatComm paper on varVAMP – a open-source tool for degenerate primer design in viral genome seq & qPCR!
🔬 Supports diverse viruses SC2, HEV, Polio ...
🤝 Built in collaboration with amazing virus experts
🔗 github.com/jonas-fuchs/varVAMP
🧬 nature.com/articles/s41467-025-60175-9
🔬 Supports diverse viruses SC2, HEV, Polio ...
🤝 Built in collaboration with amazing virus experts
🔗 github.com/jonas-fuchs/varVAMP
🧬 nature.com/articles/s41467-025-60175-9
Reposted by Sofia Paraskevopoulou
What can wastewater tell us about viruses? 💩🚽🧬📈
During the COVID-19 pandemic many labs turned to wastewater monitoring to detect viruses. However, Prof White's group @unswbabs.bsky.social has been using wastewater for over 10 years to monitor circulating norovirus 🤮. 🧵
doi.org/10.1080/2374...
During the COVID-19 pandemic many labs turned to wastewater monitoring to detect viruses. However, Prof White's group @unswbabs.bsky.social has been using wastewater for over 10 years to monitor circulating norovirus 🤮. 🧵
doi.org/10.1080/2374...
Molecular epidemiology and evolution of norovirus in Australia and New Zealand, 2018 to 2020
Norovirus causes an estimated 699 million cases of gastroenteritis and 219,000 deaths each year. Historically, novel strains with a genogroup II genotype 4 (GII.4) capsid have emerged every 3–5 yea...
doi.org
June 5, 2025 at 9:57 PM
What can wastewater tell us about viruses? 💩🚽🧬📈
During the COVID-19 pandemic many labs turned to wastewater monitoring to detect viruses. However, Prof White's group @unswbabs.bsky.social has been using wastewater for over 10 years to monitor circulating norovirus 🤮. 🧵
doi.org/10.1080/2374...
During the COVID-19 pandemic many labs turned to wastewater monitoring to detect viruses. However, Prof White's group @unswbabs.bsky.social has been using wastewater for over 10 years to monitor circulating norovirus 🤮. 🧵
doi.org/10.1080/2374...
Reposted by Sofia Paraskevopoulou
Reposted by Sofia Paraskevopoulou
This approach enabled us to infer a mechanistic model of behaviour change for the 2022 Mpox outbreak in Berlin. You can preprint here: www.researchsquare.com/article/rs-6... 5/5
Transient behavior changes and depletion of susceptibles in high contact groups led to case decline during 2022 mpox outbreak in MSM in Berlin
Mpox denotes a viral zoonosis caused by monkeypox virus (MPXV), which is endemic in West and Central Africa. In spring 2022, notable outbreaks of mpox clade IIb were recorded in several high-income co...
www.researchsquare.com
June 2, 2025 at 7:25 PM
This approach enabled us to infer a mechanistic model of behaviour change for the 2022 Mpox outbreak in Berlin. You can preprint here: www.researchsquare.com/article/rs-6... 5/5
Reposted by Sofia Paraskevopoulou
Very pleased to see our latest work on sampling of spreading processes on adaptive temporal network published at @plos.org Complex Systems!
Read more at doi.org/10.1371/jour... or find some information below
1/5🧵
Read more at doi.org/10.1371/jour... or find some information below
1/5🧵
Efficient and accurate simulation of infectious diseases on adaptive networks
Author summary Infectious disease spreading is often affected by the dynamics of human-human contacts. These contact dynamics may change over time, and in direct response to infection kinetics, throug...
doi.org
June 2, 2025 at 7:22 PM
Very pleased to see our latest work on sampling of spreading processes on adaptive temporal network published at @plos.org Complex Systems!
Read more at doi.org/10.1371/jour... or find some information below
1/5🧵
Read more at doi.org/10.1371/jour... or find some information below
1/5🧵
Reposted by Sofia Paraskevopoulou
"Roughly 1,500 babies have been born HIV-positive every day since January 21, because Musk cut off their mothers’ medication." prospect.org/power/2025-0...
Go, Elon, and Never Darken Our Doors Again
The worst ultra-billionaire on Earth says he’s leaving government. Let’s hope he actually does it.
prospect.org
May 30, 2025 at 1:15 PM
"Roughly 1,500 babies have been born HIV-positive every day since January 21, because Musk cut off their mothers’ medication." prospect.org/power/2025-0...
Reposted by Sofia Paraskevopoulou
Nature research paper: SARS-CoV-2 evolution on a dynamic immune landscape
https://go.nature.com/4aCPDem
https://go.nature.com/4aCPDem
SARS-CoV-2 evolution on a dynamic immune landscape - Nature
A modelling approach predicts SARS-CoV-2 variant dynamics on the basis of immunity and cross-neutralization, which was shaped by a region’s SARS-CoV-2 infection history.
go.nature.com
January 29, 2025 at 6:01 PM
Nature research paper: SARS-CoV-2 evolution on a dynamic immune landscape
https://go.nature.com/4aCPDem
https://go.nature.com/4aCPDem
Reposted by Sofia Paraskevopoulou
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.
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.
May 28, 2025 at 11:02 PM
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.
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.
Reposted by Sofia Paraskevopoulou
Happy to share this interview with Weijie Zhao from NSR at #OxfordUniversityPress. It covers questions I’m often asked—why I chose Korea, AlphaFold2, my unconventional journey into academia, and research insights. Thanks again for the fun conversation.
📄 academic.oup.com/nsr/article/...
📄 academic.oup.com/nsr/article/...
New methods are revolutionizing biology: an interview with Martin Steinegger
Martin Steinegger, who is the only non-DeepMind-affiliated author of the AlphaFold2 Nature paper, offers unique insights and personal reflections.
academic.oup.com
May 19, 2025 at 12:08 PM
Happy to share this interview with Weijie Zhao from NSR at #OxfordUniversityPress. It covers questions I’m often asked—why I chose Korea, AlphaFold2, my unconventional journey into academia, and research insights. Thanks again for the fun conversation.
📄 academic.oup.com/nsr/article/...
📄 academic.oup.com/nsr/article/...
Reposted by Sofia Paraskevopoulou
I'm thinking of organising a meeting on endogenous viral elements (RNA, DNA and retroviral) - if you'd potentially be interested, please fill out the form here - forms.gle/wrCiWMw4yXZe... - so I can gauge interest. Please RT or share with anyone maybe interested! 🧪🧬🖥️🦠 #virology #bioinformatics
EVE Meeting Expression of Interest
forms.gle
May 27, 2025 at 11:53 AM
I'm thinking of organising a meeting on endogenous viral elements (RNA, DNA and retroviral) - if you'd potentially be interested, please fill out the form here - forms.gle/wrCiWMw4yXZe... - so I can gauge interest. Please RT or share with anyone maybe interested! 🧪🧬🖥️🦠 #virology #bioinformatics
Very glad to have participated in #ViBioM2025 and an honor to be in this panel! An amazing week of talks, posters, and discussing with colleagues at IHMT NOVA in Lisbon. Huge thanks to the @evbc.bsky.social and everyone in the organizing committee ✨😊
#VirusBioinformatics #IHMT #EVBC
#VirusBioinformatics #IHMT #EVBC
May 26, 2025 at 12:31 PM
Very glad to have participated in #ViBioM2025 and an honor to be in this panel! An amazing week of talks, posters, and discussing with colleagues at IHMT NOVA in Lisbon. Huge thanks to the @evbc.bsky.social and everyone in the organizing committee ✨😊
#VirusBioinformatics #IHMT #EVBC
#VirusBioinformatics #IHMT #EVBC
Reposted by Sofia Paraskevopoulou
What a week in Lisbon! 🇵🇹 ViBioM 2025 brought 150+ virus bioinformaticians from 34 countries to explore viral evolution, ML tools, & taxonomy challenges. 🌱 All plant-based thanks to @desafiovegetariano! Huge thanks to organizers, speakers, and community! #ViBioM2025 #Viromics
May 19, 2025 at 8:06 AM
What a week in Lisbon! 🇵🇹 ViBioM 2025 brought 150+ virus bioinformaticians from 34 countries to explore viral evolution, ML tools, & taxonomy challenges. 🌱 All plant-based thanks to @desafiovegetariano! Huge thanks to organizers, speakers, and community! #ViBioM2025 #Viromics
Reposted by Sofia Paraskevopoulou
We just succeeded in formally linking a specific rodent species - the otherwise charming fire-footed rope squirrel - to the onset of a mpox outbreak in a primate species - sooty mangabeys. Here Kai’s report on the preprint we released yesterday 1/2
Researchers have been trying for a long time to nail down where in nature mpox lurks.
Now they appear to have caught the virus that causes mpox in the act of spilling over from squirrels to monkeys.
“It is the best clue so far for what the reservoir might be”, says @kgandersen.bsky.social
#IDsky 🧪
Now they appear to have caught the virus that causes mpox in the act of spilling over from squirrels to monkeys.
“It is the best clue so far for what the reservoir might be”, says @kgandersen.bsky.social
#IDsky 🧪
How do mpox outbreaks start? Dead baby monkey provides important clue
“Landmark” study fingers fire-footed rope squirrel as a reservoir of fatal disease
www.science.org
April 9, 2025 at 6:24 AM
We just succeeded in formally linking a specific rodent species - the otherwise charming fire-footed rope squirrel - to the onset of a mpox outbreak in a primate species - sooty mangabeys. Here Kai’s report on the preprint we released yesterday 1/2
Reposted by Sofia Paraskevopoulou
The Department of Health and Human Services (HHS) is being decimated right now. Mass layoffs happening across agencies (NIH, FDA, CDC etc).
Some employees found out by security badge being denied. Others got email.
Line outside Health Resources and Services Administration this AM shared with me:
Some employees found out by security badge being denied. Others got email.
Line outside Health Resources and Services Administration this AM shared with me:
April 1, 2025 at 1:48 PM
The Department of Health and Human Services (HHS) is being decimated right now. Mass layoffs happening across agencies (NIH, FDA, CDC etc).
Some employees found out by security badge being denied. Others got email.
Line outside Health Resources and Services Administration this AM shared with me:
Some employees found out by security badge being denied. Others got email.
Line outside Health Resources and Services Administration this AM shared with me:
Reposted by Sofia Paraskevopoulou
RFK, Jr. Laying Off the entire OIDP - Office Of Infectious Disease And HIV/AIDS Policy
Problem is: general public not aware of what OIDP stands for, let alone what it does - and why this vision, strategy and organization is crucial
Here's just a small segment of what OIDP:
🧵
Problem is: general public not aware of what OIDP stands for, let alone what it does - and why this vision, strategy and organization is crucial
Here's just a small segment of what OIDP:
🧵
RFK, Jr. Laying Off Entire Office Of Infectious Disease And HIV/AIDS Policy
Robert F. Kennedy, Jr., the Secretary of Health and Human Services is reportedly laying off the entire Office Of Infectious Disease And HIV/AIDS Policy. Here's the impact
www.forbes.com
March 30, 2025 at 11:58 AM
RFK, Jr. Laying Off the entire OIDP - Office Of Infectious Disease And HIV/AIDS Policy
Problem is: general public not aware of what OIDP stands for, let alone what it does - and why this vision, strategy and organization is crucial
Here's just a small segment of what OIDP:
🧵
Problem is: general public not aware of what OIDP stands for, let alone what it does - and why this vision, strategy and organization is crucial
Here's just a small segment of what OIDP:
🧵