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Reposted by Gemma C. Atkinson

Roni Odai @rodai.bsky.social · 11d

Viral AlphaFold Database (VAD) is live in Science Advances

~27,000 predicted viral protein monomers & homodimers

Conserved folds across bacteria, archaea & eukaryotic viruses

New toxin–antitoxin system KreTA uncovered

Vast “functional darkness” remains uncharted

www.science.org/doi/10.1126/...

The Viral AlphaFold Database of monomers and homodimers reveals conserved protein folds in viruses of bacteria, archaea, and eukaryotes

VAD is a Viral AlphaFold Database of protein monomers and homodimers from viruses infecting hosts across the tree of life.

www.science.org

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Gemma C. Atkinson @gemmaatkinson.bsky.social · 20d

Great! Enjoy! Sending my best wishes

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Gemma C. Atkinson @gemmaatkinson.bsky.social · Jun 17

Looking forward to this!

Jason Nomburg @jnoms.bsky.social · Jun 12

Hello everyone! I am pleased to share information on the first ever Computational Structural Virology Symposium, conducted August 4th on zoom and highlighting work in this emerging field. You can register for this event here: forms.gle/CNiqskMwQEuV.... Please re-post!

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Gemma C. Atkinson @gemmaatkinson.bsky.social · May 19

I do, if I can squeeze it in 😁

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Gemma C. Atkinson @gemmaatkinson.bsky.social · May 19

ooo this looks fun, and in ❤️York❤️

Daniela Barillà @danielabarilla.bsky.social · Mar 20

Fancy a journey back in time to Roman Eboracum by walking on the city walls?And a visit to the Norman Clifford Tower? A stroll down the Middle Age Shambles? All this whilst enjoying a full immersion into chromosome biology? 🧬 Join us at The Biology & Physics of Prokaryotic Chromosomes!
🦠🧪🧬

A tower of the Roman walls on top of a green hill with some daffodils 🌼 and a blue sky in the background.

Merchant Gate Hall and surrounding gardens.

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Gemma C. Atkinson @gemmaatkinson.bsky.social · May 19

Really excited to share our resource and analysis of AlphaFold-predicted monomers and homodimers across viruses and phages. Project driven by fab PhD student @rodai.bsky.social and with our great collaborators Joana Pereira @joanampereira.bsky.social and @ninjani.bsky.social

bioRxiv Molecular Biology @biorxiv-molbio.bsky.social · May 17

The Viral AlphaFold Database of monomers and homodimers reveals conserved protein folds in viruses of bacteria, archaea, and eukaryotes https://www.biorxiv.org/content/10.1101/2025.05.14.653371v1

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Reposted by Gemma C. Atkinson

Tracy Palmer @proftracypalmer.bsky.social · Apr 9

Two ERC-funded postdoc positions available in the team - one here and second to follow - please repost! jobs.ncl.ac.uk/job/Newcastl...

Research Associate Genetic and functional analysis of Gram positive secretion systems and substrates

jobs.ncl.ac.uk

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Reposted by Gemma C. Atkinson

PLOS Biology @plosbiology.org · Apr 8

The BASEL collection of E. coli #phages is limited by its host strain. @humollidorentina.bsky.social @damienpiel.bsky.social @aharms485.bsky.social &co use a modified host to add 36 new phages, revealing roles of O-antigen in recognition & R-M systems in immunity @plosbiology.org 🧪 plos.io/4jirGvX

A fanciful depiction of BASEL phages on a roadmap. Credit: Fabienne Estermann

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Gemma C. Atkinson @gemmaatkinson.bsky.social · Apr 8

last day to apply for a post-doc position in my group #phagesky #microsky

Gemma C. Atkinson @gemmaatkinson.bsky.social · Mar 19

Please spread the word! We have an opening in the Atkinson lab for a post-doc with a focus on the molecular mechanisms of microbial immune systems. Can be a fully computational or experimental or hybrid project.

Read more and apply here:
lu.varbi.com/en/what:job/...
#phage #bioinformatics

Postdoctoral research fellow with a focus on the molecular mechanisms of bacteriophage-host interactions

Description of the Workplace In the Atkinson lab we are interested in making discoveries about protein function and structure, with a focus on bacterial immune system components that protect against b

lu.varbi.com

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Reposted by Gemma C. Atkinson

João Botelho @joaoftsbotelho.bsky.social · Mar 29

Looking forward to attending this conference for the 1st time and co-chairing this session with amazing speakers!

Join us on 2 and 3 April and listen to @gemmaatkinson.bsky.social, @epcrocha.bsky.social , @tatianadimitriu.bsky.social and Tim Blower!

#Microbio25

Microbiology Society @microbiologysociety.org · Mar 21

Microbes in Combat! Join us at #Microbio25 for Microbial Warfare: Conflicts Between Species, Strains, and Mobile Genetic Elements. Delve into microbial defence mechanisms and the implications for microbial evolution. Registration is still open -

Annual Conference 2025

31 March - 03 April 2025

microb.io

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Gemma C. Atkinson @gemmaatkinson.bsky.social · Mar 25

Reminder about two open positions:
1) tenure track group leader position on data driven infection research lu.varbi.com/en/what:job/...
2) post-doc in mine/Vasili's join team lu.varbi.com/en/what:job/...
#phagesky #microsky

Postdoctoral research fellow with a focus on the molecular mechanisms of bacteriophage-host interactions

Description of the Workplace In the Atkinson lab we are interested in making discoveries about protein function and structure, with a focus on bacterial immune system components that protect against b

lu.varbi.com

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Gemma C. Atkinson @gemmaatkinson.bsky.social · Mar 19

Please spread the word! We have an opening in the Atkinson lab for a post-doc with a focus on the molecular mechanisms of microbial immune systems. Can be a fully computational or experimental or hybrid project.

Read more and apply here:
lu.varbi.com/en/what:job/...
#phage #bioinformatics

Postdoctoral research fellow with a focus on the molecular mechanisms of bacteriophage-host interactions

Description of the Workplace In the Atkinson lab we are interested in making discoveries about protein function and structure, with a focus on bacterial immune system components that protect against b

lu.varbi.com

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Gemma C. Atkinson @gemmaatkinson.bsky.social · Mar 7

Bioinformatics junior group leader position in Lund, specialising in infection and/or epidemiology. These are really nice positions with generous support. Please spread the word to anyone who might be interested in becoming our colleague! lu.varbi.com/en/what:job/...

Associate Senior Lecturer (DDLS fellow) in data driven epidemiology and biology of infection

Lund is strategically positioned close to the continent, hosting major national and European research infrastructures, such as MAX.IV Laboratory and the European Spallation Source (ESS). In the field

lu.varbi.com

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Gemma C. Atkinson @gemmaatkinson.bsky.social · Feb 28

Does this also apply to research on viruses of bacteria?

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Gemma C. Atkinson @gemmaatkinson.bsky.social · Feb 26

Post-doc opportunities! Wet/dry/hybrid projects available in my group. Drop me an email with CV if interested.
www.scilifelab.se/research/pul...

Pulse - Application

Application PULSE postdoc applicants have the opportunity to choose between an academic or an entrepreneurial track. Both fellowship tracks will include advanced training in research and transferable ...

www.scilifelab.se

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Gemma C. Atkinson @gemmaatkinson.bsky.social · Feb 25

Excited to share that our paper on locus visualisation tool LoVis4u is out! Entirely driven by fantastic PhD student Artyom Egorov @egorov.bsky.social academic.oup.com/nargab/artic...

LoVis4u: a locus visualization tool for comparative genomics and coverage profiles

Abstract. Comparative genomic analysis often involves visualization of alignments of genomic loci. While several software tools are available for this task

academic.oup.com

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Gemma C. Atkinson @gemmaatkinson.bsky.social · Jan 23

Some exciting news about our structure prediction infrastructure LU-Fold: we have joined forces with SciLifeLab to improve accessibility to technologies and expertise. Read more here nbis.se/news/LUfold

NBIS - LU-Fold and NBIS join forces to Enhance Protein Structure Prediction Services at SciLifeLab

nbis.se

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Gemma C. Atkinson @gemmaatkinson.bsky.social · Jan 16

Big day for the family. Today one of these two became a full professor. Nice job @hauryliuk.bsky.social !

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Gemma C. Atkinson @gemmaatkinson.bsky.social · Dec 19

Such a good VH-GCA lab symposium day to round off the year!

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Gemma C. Atkinson @gemmaatkinson.bsky.social · Dec 4

Sorry I missed you! Hope to catch up sometime here or in Umeå or somewhere else :)

Gemma C. Atkinson @gemmaatkinson.bsky.social · Dec 3

Thanks, and a belated congrats to you Lars-Anders for your big grant and big prize!

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Gemma C. Atkinson @gemmaatkinson.bsky.social · Dec 3

Grateful to the Swedish Research Council (Vetenskapsrådet) for funding a 3 year project on antibiotic resistance & phages in my group. If you're looking for a post-doc position in 2025, have a phagey background, & are interested in combining wet and dry research then keep a look out for an ad soon!

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Gemma C. Atkinson @gemmaatkinson.bsky.social · Dec 1

Any tips?

Sara Marti @saramarti2.bsky.social · Nov 29

Gemma, we are interested in visualizing the alignment between two plasmids in a circular format. Could you recommend us a tool?

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Gemma C. Atkinson @gemmaatkinson.bsky.social · Dec 1

Hi Sara, hm good question. I don’t think I’ve come across such a tool, but I’ll share your question

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Reposted by Gemma C. Atkinson

Melanie Blokesch @mblokesch.bsky.social · Nov 25

Exciting times! Our latest preprint is now live 🤩!
After nearly 16 yrs of running my lab, I truly believe this is one of the most significant contributions we've made. It offers fresh hypotheses about how pandemic Vibrio cholerae spreads globally. Let’s dive in!🧵..1/n
www.biorxiv.org/content/10.1...

Diverse phage defence systems define West African South American pandemic Vibrio cholerae

Our understanding of the factors underlying the evolutionary success of different lineages of pandemic Vibrio cholerae remains incomplete. Interestingly, two unique genetic signatures define the West ...

www.biorxiv.org

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