iiinova — where your digital self keeps evolving

Gemma C. Atkinson @gemmaatkinson.bsky.social · 18/03/2026

Had a bit of a break from the socials and forgot my Bluesky password, but really happy to belatedly share some great work from PhD student Jose Nakamoto on the diversity of toxin-antitoxin-chaperone systems www.sciencedirect.com/science/arti...

sciencedirect.com

Structural and functional diversity of toxin-antitoxin-chaperone systems

Toxin-antitoxin-chaperone (TAC) systems are three-part gene clusters encoding a toxin, antitoxin, and specialized SecB-like chaperone (SecBTA) with em…

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Reposted by Gemma C. Atkinson

Roni Odai @rodai.bsky.social · 02/10/2025

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/...

science.org

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.

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Gemma C. Atkinson @gemmaatkinson.bsky.social · 19/05/2025

ooo this looks fun, and in ❤️York❤️

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Gemma C. Atkinson @gemmaatkinson.bsky.social · 19/05/2025

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

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PLOS Biology @plosbiology.org · 08/04/2025

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 · 08/04/2025

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

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Reposted by Gemma C. Atkinson

João Botelho @joaoftsbotelho.bsky.social · 29/03/2025

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

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Gemma C. Atkinson @gemmaatkinson.bsky.social · 19/03/2025

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

lu.varbi.com

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

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Gemma C. Atkinson @gemmaatkinson.bsky.social · 07/03/2025

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/...

lu.varbi.com

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

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Gemma C. Atkinson @gemmaatkinson.bsky.social · 23/01/2025

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.se

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

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Gemma C. Atkinson @gemmaatkinson.bsky.social · 16/01/2025

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 · 19/12/2024

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

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Gemma C. Atkinson @gemmaatkinson.bsky.social · 03/12/2024

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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Melanie Blokesch @mblokesch.bsky.social · 25/11/2024

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...

biorxiv.org

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 ...

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Gemma C. Atkinson @gemmaatkinson.bsky.social · 23/11/2024

So fab to hear when people find our lab tools useful. Now that he’s on Bluesky, I can tag Artyom @egorov.bsky.social , the amazing PhD student who made iLund4u and loVis4u

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Gemma C. Atkinson @gemmaatkinson.bsky.social · 24/10/2024

Sharing new tools made by Artyom Egorov in my group! 1) loVis4u sensitively compares & visualises #phage or #plasmid seqs with beautiful vector graphics www.biorxiv.org/content/10.1... 2) iLund4u finds diversity hotspots/islands encoding eg virulence/ defence systems www.biorxiv.org/content/10.1...

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Gemma C. Atkinson @gemmaatkinson.bsky.social · 01/03/2024

Very proud of my life and science other half Vasili Hauryliuk @hauryliuk.bsky.social being awarded the Göran Gustafsson prize in molecular biology from the Royal Swedish Academy of Sciences! www.kva.se/nyheter/33-m...

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Gemma C. Atkinson @gemmaatkinson.bsky.social · 23/02/2024

Senior lectureship available in Lund with specialisation in cryo-EM. Come and join us and have fun playing around with the brand new Glacios 2 #cryoem lu.varbi.com/en/what:job/...

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Gemma C. Atkinson @gemmaatkinson.bsky.social · 05/02/2024

Now we have a bioinformatics PhD position In my group in Lund to work on the same fun #phage defence project! Read more and apply here: lu.varbi.com/en/what:job/... deadline March 5th

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Gemma C. Atkinson @gemmaatkinson.bsky.social · 01/02/2024

Join the fun! And stay tuned for a bioinformatics PhD position to work on the same project!

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Gemma C. Atkinson @gemmaatkinson.bsky.social · 23/01/2024

In person/online LU-Fold drop-ins for researchers in Sweden! Interested in how AlphaFold2 can benefit your research? Planning a grant application? - Weds 24 Jan 10.30 Ecology, Café Le Mani - Mon 5th Feb 14.00-15.30 Zoom (link here atkinson-lab.com/lu-fold/) - Tues 6 Feb 10.00 Forum Medicum Cafe

atkinson-lab.com

LU-Fold: a protein structure prediction facility at Lund University

Welcome to LU-Fold! LU-Fold is a Lund University-based facility for helping researchers predict protein structures of interest using the cutting-edge method AlphaFold2 (Nature Methods method of the ye...

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Reposted by Gemma C. Atkinson

Ewan Birney @ewanbirney.bsky.social · 11/01/2024

Dear Swedish colleagues. I am giving a talk at KI at 3pm on Monday on genomics, imaging and AI. Do come along! news.ki.se/calendar/gen...

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Gemma C. Atkinson @gemmaatkinson.bsky.social · 10/01/2024

LU-Fold is now available to researchers across Sweden! Curious about how high-throughput #AlphaFold folding of monomers and co-folding of complexes can help your research? Get in touch for a chat! medicine.lu.se/lu-fold

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Reposted by Gemma C. Atkinson