Timofey Skvortsov

ProFlex Suite output screenshot

Finally, we provide a suite of tools that allow users users to convert PDB into ProFlex, search for proteins with similar flexibility patterns in structural databases, and compare ProFlex-encoded protein sequences with each other.

We hope that our approach will facilitate new insights into protein function and make a better use of the expanding structural atlas.

Manuscript: doi.org/10.1038/s414...
ProFlex Suite: github.com/DamianJM/pro...

#protein #dynamics #phage

Phylogenetic and similarity analysis of selected Tevenvirinae major capsid protein sequences and structures.

We analysed 15 major capsid protein sequences from Tevenvirinae phages using sequence, structutal and ProFlex comparisons and demonstrated that all tested approaches detect the underlying phylogenetic relationship and provide complementary information about the proteins.

Alignment of ProFlex-encoded protein sequences

Together with my very good friend and brilliant colleague Damian Magill we developed ProFlex, a protein “alphabet” that turns protein flexibility patterns into an easy-to-compare sequences.

Nature Communications paper: 𝗣𝗿𝗼𝗙𝗹𝗲𝘅 𝗮𝘀 𝗮 𝗹𝗶𝗻𝗴𝘂𝗶𝘀𝘁𝗶𝗰 𝗯𝗿𝗶𝗱𝗴𝗲 𝗳𝗼𝗿 𝗱𝗲𝗰𝗼𝗱𝗶𝗻𝗴 𝗽𝗿𝗼𝘁𝗲𝗶𝗻 𝗱𝘆𝗻𝗮𝗺𝗶𝗰𝘀 𝗶𝗻 𝗻𝗼𝗿𝗺𝗮𝗹 𝗺𝗼𝗱𝗲 𝗮𝗻𝗮𝗹𝘆𝘀𝗶𝘀

Superb news to kick off the week! 🎉 Our new paper is out today in
@natcomms.nature.com
𝗣𝗿𝗼𝗙𝗹𝗲𝘅 𝗮𝘀 𝗮 𝗹𝗶𝗻𝗴𝘂𝗶𝘀𝘁𝗶𝗰 𝗯𝗿𝗶𝗱𝗴𝗲 𝗳𝗼𝗿 𝗱𝗲𝗰𝗼𝗱𝗶𝗻𝗴 𝗽𝗿𝗼𝘁𝗲𝗶𝗻 𝗱𝘆𝗻𝗮𝗺𝗶𝗰𝘀 𝗶𝗻 𝗻𝗼𝗿𝗺𝗮𝗹 𝗺𝗼𝗱𝗲 𝗮𝗻𝗮𝗹𝘆𝘀𝗶𝘀

S3140 | SUSTAIN

Are you interested a fully funded PhD? We would like to understand the role phages play in well- and poorly-performing broiler flocks using AI!
Learn more here: sustain-cdt.ai/advertised-p...
Apply by Friday, 17 October @ 12:00:

This UKRI AI CDT SUSTAIN project and will be supervised by Dr Didier Devaurs and Dr Leighton Pritchard (Strathclyde), Dr Victoria Smyth (AFBI), and me.
You will learn a lot about #AI, machine learning, bioinformatics, microbiology, food production, animal health, and #phage!

S3140 | SUSTAIN

Are you interested a fully funded PhD? We would like to understand the role phages play in well- and poorly-performing broiler flocks using AI!
Learn more here: sustain-cdt.ai/advertised-p...
Apply by Friday, 17 October @ 12:00:

Very interesting - but I can't seem to find the upper size limit of the payload that can be delivered this way in the paper

🌟 Exciting news! We’re launching three fully-funded postdoc positions for "New Horizons for Synthetic Phages”

Join us in tackling antimicrobial resistance with cutting-edge synthetic biology + AI bioinformatics. Based at Flinders Uni in vibrant Adelaide.

👇 Read on for details!
#Phage

I really enjoyed working on this piece about #AI in #microbiology research with @thomacillin.bsky.social We are exploring how the data and the user affect the performance of AI, discuss reasoning, and outline 5 key principles of working with AI.

#MicroSky

Helping bring phage medicines to UK patients – guidance for industry Bacteriophages – viruses that selectively fight bacteria – may offer new hope in fighting infections and tackling antimicrobial resistance.

First official guidance on the development and use of #phage therapies in the UK has been published by MHRA!

www.gov.uk/government/n...

Massive congratulations to Darvel’s 2nd most famous microbiologist🦠🔬Ross Duncan 🏴󠁧󠁢󠁳󠁣󠁴󠁿 for passing his viva yesterday! Thanks to @tcoenye.bsky.social and Dr Deirdre Gilpin for conducting the viva, and @timskvortsov.bsky.social for chairing. Very proud supervisor #biofilms #coldplasma #pharmacyQUB

TEM of a phage with a top hat and a monocle. AI-generated

Thanks to #AI enhanced TEM, we can now see previously missed details of #phage morphology

Extremely proud of Akash Shambharkar, who successfully defended his PhD thesis investigating #phage based approaches against CAUTIs! It was a pleasure supervising Akash with Brendan Gilmore.
Many thanks to Brian Jones and Matthew Wylie for examining, and to Sheiliza Carmali for chairing the viva!

offers a world-leading research environment and abundant opportunities for personal and professional growth in a supportive and welcoming community. Further information about the scheme can be found on Queen's University website.
www.qub.ac.uk/Research/our...

#MCSA

I am looking for a post-doctoral researcher to develop a joint application for Marie Skłodowska-Curie Fellowship 2025, focusing on #phage biology and bioinformatics.
If interested, please send me your CV and a brief outline of your research project at your earliest opportunity.

Delighted to represent our lab together with our PhD student Shauna at the NI Science Festival 2025 (@niscifest.bsky.social) and to talk about the exciting bacteriophage research we are conducting at the QUB School of Pharmacy (@qubelfastofficial.bsky.social !

#NISF25 #phage

It's Phriday! Huge thanks to our student Maria for the #phage cake - it was as delicious as it was cool looking!

Finally, our work underscores the importance of integrating genomic data with public health measures to better prepare for future pandemics.

#SARSCoV2 #Ireland #NorthernIreland #COVID19 #SARS

Our study:
🔬 Demonstrates the critical role of whole genome sequencing (WGS) in identifying introduction events
🌍 Explores the influence of population density, deprivation, and policy on transmission
📊 Provides aa scalable framework for tracking infectious diseases globally

Key findings:
🔷 England accounted for 57% of introductions
🔷 Introduction rates for variants were comparable, except Delta, which was higher in NI
🔷 Over 60% of introductions resulted in detection of only a single descendant

SARS-CoV-2 introductions to the island of Ireland: a phylogenetic and geospatiotemporal study of infection dynamics - Genome Medicine Background Ireland’s COVID-19 response combined extensive SARS-CoV-2 testing to estimate incidence, with whole genome sequencing (WGS) for genome surveillance. As an island with two political jurisdic...

Happy to announce that our study on the introduction and spread of SARS-CoV-2 across the island of Ireland has now been published in Genome Medicine!

Using phylogenetics and geospatiotemporal analysis, we traced 4,439 #SARS-CoV-2 introductions to Ireland (2020–2022).

Prophage-DB: A comprehensive database to explore diversity, distribution, and ecology of prophages bioRxiv - the preprint server for biology, operated by Cold Spring Harbor Laboratory, a research and educational institution

If you are interested in prophages, we have a new database: Prophage-DB. Check it out and all feedback is welcome biorxiv.org/cgi/content/...