Matt Bashton

Unicore identifies single-copy protein structures across genomes using Foldseek, bypassing slow structure predictions by utilizing 3Di predictions from ProstT5, enabling rapid phylogenetic inference at the tree-of-life scale. 1/n
📄 www.biorxiv.org/content/10.1...
💾 github.com/steineggerla...

Chromothripsis-associated chromosome 21 amplification orchestrates transformation to blast-phase MPN through targetable overexpression of DYRK1A - Nature Genetics Multiomic analysis of blast-phase myeloproliferative neoplasms identifies a chromosome 21 amplicon harboring DYRK1A as a clonal and therapeutically targetable event in around a quarter of cases.

This research with Oxford started during the pandemic when I spotted a familiar iAMP21 like copy number profile on chromosome 21 here termed chr. 21amp. It's lovely to see all the different omics techniques come together from all the collaborators! www.nature.com/articles/s41...

The age old "similar to putative function" annotation disease - only with AI, reinforcing suspect homology based matches in training data.

Congratulations, I guess you will be spending more time in Heidelberg!

This week at @northumbriauni.bsky.social we launched our new #HPC cluster Higgs, having been involved in shaping this project from the outset it's nice to see it finally come to fruition with our partners #Logicalis and #Lenovo. l'm looking forward to all the research our new cluster will enable.

The pigeon as a machine: Complex category structures can be acquired by a simple associative model Cognitive neuroscience; Machine learning

Can't afford an NVIDIA H100 just get a pigeon, readily available in all Northern towns too. cell.com/iscience/ful... #AI #Pigeon

I'm not sure why everyone is surprised by DeepSeek if you deny people access to the latest hardware then they will naturally develop more efficient algorithms. In this sense US "export" policy on AI hardware has been a massive own goal.

Extent of microfibre pollution from textiles to be explored at new research hub A newly established research hub in North East England will explore the extent and environmental impact of microfibre loss from textiles.

Designers and environmental scientists from Northumbria have teamed up with The Microfibre Consortium to establish the Fibre-fragmentation and Environment Research Hub (FibER Hub) to explore the extent and environmental impact of microfibre loss from textiles
www.northumbria.ac.uk/about-us/new...

Star Trek The Next Generation scene. Early series Picard is shown up close with a determined look of contentment. He's locked into eye contact with someone just off screen, and smouldering. Closed caption reads: (champagne fizzing)

Northern lights in Northumberland- beautiful and so counter intuitive that the camera is a far more faithful representation of the colours than your eyes (it’s a grey pink sky to the naked eye!)

Comprehensive Analysis of SARS-CoV-2 Spike Evolution: Epitope Classification and Immune Escape Prediction The evolution of SARS-CoV-2, the virus responsible for the COVID-19 pandemic, has produced unprecedented numbers of structures of the Spike protein. This study presents a comprehensive analysis of 1,560 published Spike protein structures, capturing most variants that emerged throughout the pandemic and covering diverse heteromerization and interacting complexes. We employ an interaction-energy informed geometric clustering to identify 14 epitopes characterized by their conformational specificity, shared interface with ACE2 binding, and glycosylation patterns. Our per-residue interaction evaluations accurately predict each residue's role in antibody recognition and as well as experimental measurements of immune escape, showing strong correlations with DMS data, thus making it possible to predict the behaviour of future variants. We integrate the structural analysis with a longitudinal analysis of nearly 3 million viral sequences. This broad-ranging structural and longitudinal analysis provides insight into the effect of specific mutations on the energetics of interactions and dynamics of the SARS-CoV-2 Spike protein during the course of the pandemic. Specifically, with the emergence of widespread immunity, we observe an enthalpic trade-off in which mutations in the receptor binding motif (RBM) that promote immune escape also weaken the interaction with ACE2. Additionally, we also observe a second mechanism, that we call entropic trade-off, in which mutations outside of the RBM contribute to decrease the occupancy of the open state of SARS-CoV-2 Spike, thus also contributing to immune escape at the expense of ACE2 binding but without changes on the ACE2 binding interface. This work not only highlights the role of mutations across SARS-CoV-2 Spike variants but also reveals the complex interplay of evolutionary forces shaping the evolution of the SARS-CoV-2 Spike protein over the course of the pandemic. ### Competing Interest Statement The authors have declared no competing interest.

and also our latest work, Natálias latest preprint, a collaboration with the groups of
@mattbashton.bsky.social and Ricardo Rajsbaum is out in BioRxiv. www.biorxiv.org/content/10.1...

I didn't have time to stop to play it, but it looks authentic, around the time it was current there were a lot of clone JAMA boards from Taiwan which had all sorts of unique enhancements like changing fighter mid match! Only they had 3x the PCB board count as reverse engineered all custom chips.

Been exploring some of the breathtaking John Portman architecture in Atlanta while at #SC24

Nice to see this CPS-1, duel CPU 68000/Z80 set-up at #SC24, it's all about those custom chips too! #retrogaming

Supercomputer investment will power world-leading research and innovation Northumbria University has announced a multi-million pound investment in its first university-wide high-performance computing facility which will give researchers access to state-of-the-art technology...

So #SC24 has been a lot of fun! We are also entering a new phase of HPC at @northumbriauni.bsky.social as we expand facilities for our researchers www.northumbria.ac.uk/about-us/new...

who knew it would be easier to get everyone to switch social media platforms than getting them to use hg38

Trashzymes: Mining Municipal solid waste and alkaliphilic species for brilliant cleaning at Procter & Gamble on FindAPhD.com PhD Project - Trashzymes: Mining Municipal solid waste and alkaliphilic species for brilliant cleaning at Procter & Gamble, listed on FindAPhD.com

If you find this work interesting I'm currently looking for a new PhD student, see the Add here www.findaphd.com/phds/project...

Interestingly if we look at promiscuous superfamilies' (those binding multiple ligands) we find they can fall into "generalised" - binding a wide range of chemically diverse ligands or "specialised" - binding some very chemically similar ligands, categories.

This the work of my PhD student Matt Crown, one of the nice things he did was this t-SNE plot of cognate ligand space within the PDB, in which we see some nice clusters of related compounds.

ProCogGraph: a graph-based mapping of cognate ligand domain interactions AbstractMotivation. Mappings of domain-cognate ligand interactions can enhance our understanding of the core concepts of evolution and be used to aid docki

Our latest work has been published in #Bioinformatics Advances ProCogGraph, the spiritual successor of PROCOGNATE. This graph database provides a linkage between proteins domains (SCOP/CATH/Pfam) and cognate ligands for #enzymes in the #PDB. academic.oup.com/bioinformati...

New graph algorithms for analysis of the genomes and pangenomes of bacteria and their mobile elements. at University of Bath on FindAPhD.com PhD Project - New graph algorithms for analysis of the genomes and pangenomes of bacteria and their mobile elements. at University of Bath, listed on FindAPhD.com

I'm advertising a PhD studentship (open to international students) working on long read pangenome / assembly algorithms in bacteria. Would suit someone with maths/compsci/coding background. Aptitude + interest more important than experience.
Details here:
www.findaphd.com/phds/project...

After editing, this very short letter to New Scientist is even shorter now. But I think it gets the point across! @faecalmatters.bsky.social

AI protein-prediction tool AlphaFold3 is now open source The code underlying the Nobel-prize-winning tool for modelling protein structures can now be downloaded by academics.

This is good news for science, although I'm not sure why it took so long, and also why the change of policy here from Google www.nature.com/articles/d41... #OpenScience #AlphaFold

Zoomed out we see a small, lone shuttlecraft flying through a cloudy sky. Closed caption reads, "(screaming)"

@suw.bsky.social @daivaughan.uk

This is perfection.

ProCogGraph: A Graph-Based Mapping of Cognate Ligand Domain Interactions AbstractMotivation. Mappings of domain-cognate ligand interactions can enhance our understanding of the core concepts of evolution and be used to aid docki

This work builds on our latest publication in Bioinformatics Advances doi.org/10.1093/bioa...

Trashzymes: Mining Municipal solid waste and alkaliphilic species for brilliant cleaning at Procter & Gamble on FindAPhD.com PhD Project - Trashzymes: Mining Municipal solid waste and alkaliphilic species for brilliant cleaning at Procter & Gamble, listed on FindAPhD.com

Please RT, come do a PhD with me as part of an industrial collaboration with P&G using metagenomes and AI to design new enzymes www.findaphd.com/phds/project... #pLMS #AI #enzymes #Bioinformatics

Michael Parkinson is back, with an AI voice that can fool even his own family The chatshow star’s son says digital replica will interview a new generation of stars

Deep Fusion Films Parkinson AI is spookily accurate, although it feels like an episode of Dark Mirror www.theguardian.com/media/2024/o...

I've had dengue. It was dintinctly unfun. If you needed another reason to do what you can to limit climate change, well this is a good excuse ...
www.npr.org/2024/10/22/n...

"LA is seeing cases of dengue, the range of which may be growing due to climate change"