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Sofia Paraskevopoulou

@akifoss.bsky.social
108 followers 150 following 2 posts

Viruses - Evolution - Bioinformatics Berlin // Robert Koch Institute opinions are my own

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Reposted by Sofia Paraskevopoulou
Ming Tommy Tang @tommytang.bsky.social · 23/01/2026
TSniffer: unbiased de novo identification of RNA editing sites and quantification of editing activity in RNA-seq data link.springer.com/article/10....
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Reposted by Sofia Paraskevopoulou
Robert Koch-Institut @rki.de · 17/12/2025
🦠 Wie hat sich #SARS-CoV-2 in 🇩🇪 von 2020-2023 entwickelt? In einem großen Review von RKI-Forschenden werden virologische Grundlagen, Variantenentwicklung, klinische Aspekte und die Rolle der Genomüberwachung beleuchtet. Fazit: Auf die Interdisziplinarität kommt es an! 🤝 ➡️ doi.org/10.1038/s438...
doi.org
A public health perspective of SARS-CoV-2 evolution and surveillance strategies in Germany from 2020 to 2023 - Communications Medicine
Oh, Hölzer et al., discuss the multidisciplinary approach used for monitoring the genomic and virological evolution of SARS-CoV-2 during the COVID-19 pandemic and its implications on public health in ...
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European Virus Bioinformatics Center @evbc.bsky.social · 01/12/2025
A #taxonomic revision of the human/animal RNA viruses #Flaviviridae identifies 4 divergent RdRP clades and restructures 12 genera across 3 families within Amarillovirales. #VirusEvolution 📄 doi.org/10.1038/s41564-025-02134-0 👤 EVBC: P. Simmonds, A. Butković, J. Mifsud, M. Beer, J.H. Kuhn
doi.org
Taxonomic expansion and reorganization of Flaviviridae - Nature Microbiology
Analysis of RNA polymerase hallmark gene phylogenies supported by protein structure relationships of flaviviruses and ‘flavi-like’ viruses underpins the taxonomic expansion and reorganization of Flaviviridae.
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Reposted by Sofia Paraskevopoulou
Emma Harding @emma-harding.bsky.social · 13/11/2025
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
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
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Reposted by Sofia Paraskevopoulou
Vasilakis Lab @vasilakislab.bsky.social · 31/10/2025
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
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Reposted by Sofia Paraskevopoulou
Kunal Jani @jaenomics.bsky.social · 18/09/2025
New publication alert! Fertilization impacts microbiomes along the grassland trophic chain academic.oup.com/ismecommun/a... #organicfertilizers #landusechange #microbiome #grasslands #onehealth
academic.oup.com
Validate User
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Reposted by Sofia Paraskevopoulou
The Ramsey Lab @theramseylab.bsky.social · 17/10/2025
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...
Book cover of “What Is Life? Revisted” by Daniel J. Nicholson, in the Cambridge Elements: The Philosophy of Biology series. Against a black background, the title is surrounded by Ernst Haeckel’s illustrations of marine organisms—radial, symmetrical forms in vivid blues, oranges, reds, and greens.
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Kristian G. Andersen @kgandersen.bsky.social · 16/10/2025
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.
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Ulad Litvin @ulad-litvin.bsky.social · 26/09/2025
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
doi.org
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...
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Reposted by Sofia Paraskevopoulou
Emma Harding @emma-harding.bsky.social · 15/09/2025
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...
sciencedirect.com
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…
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Reposted by Sofia Paraskevopoulou
Jonathan Basile @jonothingeb.bsky.social · 15/09/2025
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...
Conference title: Dialectical Biology Today: Legacies of Richard Lewontin, and image of Lewontin in Black and White with intense expression in front of a chalkboard holding up a fist, 
When and Where
Friday, October 10, 2025 11:30 am to Sunday, October 12, 2025 2:00 pm
Music Room (218)
Goldring Student Centre
150 Charles St W, Toronto, ON M5S 1K5 | and online via Zoom
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Reposted by Sofia Paraskevopoulou
Karim Majzoub @karimaj.bsky.social · 14/09/2025
Endogenous Deltaviruses (EVEs) in termite genomes !
sciencedirect.com
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…
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Reposted by Sofia Paraskevopoulou
Martin Hölzer @martinhoelzer.bsky.social · 24/06/2025
🚨 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...
nature.com
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...
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Reposted by Sofia Paraskevopoulou
Martin Hölzer @martinhoelzer.bsky.social · 09/06/2025
🚀 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
github.com
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
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Reposted by Sofia Paraskevopoulou
Emma Harding @emma-harding.bsky.social · 05/06/2025
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...
doi.org
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...
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Christian Drosten @cdrosten.bsky.social · 04/06/2025
zeitung.faz.net/faz/geistesw...
zeitung.faz.net
Freiheit und Pflicht der Wissenschaft
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Nils Gubela @nillegu.bsky.social · 02/06/2025
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
researchsquare.com
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...
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Reposted by Sofia Paraskevopoulou
Nils Gubela @nillegu.bsky.social · 02/06/2025
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🧵
doi.org
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...
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Reposted by Sofia Paraskevopoulou
ryan cooper @ryanlcooper.com · 30/05/2025
"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...
prospect.org
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.
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Reposted by Sofia Paraskevopoulou
Nature @nature.com · 29/01/2025
Nature research paper: SARS-CoV-2 evolution on a dynamic immune landscape go.nature.com/4aCPDem
go.nature.com
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.
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Reposted by Sofia Paraskevopoulou
Kristian G. Andersen @kgandersen.bsky.social · 29/05/2025
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.
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Reposted by Sofia Paraskevopoulou
Martin Steinegger 🇺🇦 @martinsteinegger.bsky.social · 19/05/2025
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
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.
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Reposted by Sofia Paraskevopoulou
Katy Brown @thekatybrown.bsky.social · 27/05/2025
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
forms.gle
EVE Meeting Expression of Interest
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Sofia Paraskevopoulou @akifoss.bsky.social · 26/05/2025
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
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European Virus Bioinformatics Center @evbc.bsky.social · 19/05/2025
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
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Sebastien Calvignac-Spencer @scs22.bsky.social · 09/04/2025
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
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Reposted by Sofia Paraskevopoulou
Marisa Kabas @marisakabas.bsky.social · 01/04/2025
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:
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Infectious Diseases @infectiousdz.bsky.social · 30/03/2025
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: 🧵
forbes.com
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
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Sofia Paraskevopoulou @akifoss.bsky.social · 30/01/2025
Very happy to share this work on #SARS-CoV-2 dynamics!✨ Model based on immunity & cross-neutralization, considering the variants' infection history of the population. @martinhoelzer.bsky.social and other colleagues at #RKI and #FUBerlin, congrats to all!
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