Gemma C. Atkinson
@gemmaatkinson.bsky.social
Lecturer & group leader in Lund University. Computational microbiologist, mostly working on toxin-antitoxin systems, ribosomes and bacterial defence against phages. Director of the LU-Fold protein structure prediction infrastructure of LU. Atkinson-lab.com
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...
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…
sciencedirect.com
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.
science.org
Looking forward to this!
Jason Nomburg@jnoms.bsky.social · last yr.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!
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 · last yr.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
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
Research Associate Genetic and functional analysis of Gram positive secretion systems and substrates
jobs.ncl.ac.uk
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
last day to apply for a post-doc position in my group #phagesky #microsky
Gemma C. Atkinson@gemmaatkinson.bsky.social · last yr.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
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 · last yr.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 -
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
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
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
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 ...
scilifelab.se
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
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
Big day for the family. Today one of these two became a full professor. Nice job @hauryliuk.bsky.social !
Such a good VH-GCA lab symposium day to round off the year!
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!
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 ...
biorxiv.org
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
Jason Wilson@jasonwils.bsky.social · 2y agoReally missed the sense of daily discovery of new papers and tools you used to get on the other place. Moved over a few days ago and already finding so much, and exactly what I've been looking for!
Anyone looking for an assistant professor position in biodiversity research? Not one but three positions available at Stockholm U: www.su.se/department-o...
Faculty of Science is recruiting Assistant Professors in Biodiversity - Department of Ecology, Environment and Plant Sciences
Faculty of Science is recruiting Assistant Professors in Biodiversity - Department of Ecology, Environment and Plant Sciences
su.se
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...
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...
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/...
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
Ville Friman@frimanscience.bsky.social · 3y agoThree-year postdoc available on anti-phage defense systems and phage biocontrol of phytopathogenic Ralstonia solanacearum at Helsinki (FIN) in collaboration with @hauryliuk.bsky.social and gemmaatkinson.bsky.social. Application deadline 29.2.2024. #phagesky #microsky jobs.helsinki.fi/job/Helsinki...
Join the fun! And stay tuned for a bioinformatics PhD position to work on the same project!
Ville Friman@frimanscience.bsky.social · 3y agoThree-year postdoc available on anti-phage defense systems and phage biocontrol of phytopathogenic Ralstonia solanacearum at Helsinki (FIN) in collaboration with @hauryliuk.bsky.social and gemmaatkinson.bsky.social. Application deadline 29.2.2024. #phagesky #microsky jobs.helsinki.fi/job/Helsinki...
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
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...
atkinson-lab.com
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...
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
