Mark McMullan @mcmullan0.bsky.social

Our new preprint co-led with colleagues from #IOCAS and #BGI: The genetic repertoire of the deep sea: from sequence to structure and function biorxiv.org/content/10.648… @uniofeastanglia @micronorwich

NEW PAPER: UKCropDiversity-HPC: A collaborative high-performance computing resource approach for sustainable agriculture and biodiversity conservation. Read open access paper ➡️ nph.onlinelibrary.wiley.com/doi/full/10.10…

Exciting news! The latest hifiasm release from @ChengChhy and @lh3lh3 adds beta support for @nanopore simplex R10 reads. Initial results look very promising. 🚀 Check it out: github.com/chhylp123/hifi…"

We're happy to present a pre-print from the Hogenhout lab (@SaskiaHogenhout), describing how a family of proteases in aphid oral secretions suppress plant immunity

BLOG - How, and why, do plants and microbes interact? Microbes have evolved over the past 3.5 billion years to survive in diverse habitats, including in/on plants. But whilst some are beneficial, others can cause devastating diseases @micronorwich okt.to/943IhA

Pleased to be part of this analysis of the emerging threat of resistance to Fungal Anti-Microbial Resistance and its multi-faceted effects on human healthcare, animal/plant health and agriculture. nature.com/articles/s4425…

Very happy to see @annaliisalaine's & my article out in @ScienceMagazine today! We reveal that the more a plant species invests in defense, the less potential it has for growth. All made possible by lots of public data & amazing open science contributions! science.org/doi/10.1126/sc…

We can offer free conference attendance to one member of any couple who will be sharing childcare duties during the conference. To apply, please specify this in your booking. Additionally you can apply for a Carers Award from the genetics society (genetics.org.uk/grants/carers-…). (4/4)

BLOG - A pint of the living dead – making beer with zombie plants 🌱🍻 This #Halloween, @samtmugford reveals the strange science of #phytoplasmas, a group of plant-infecting bacteria, and how he made his own delicious zombie beer… Read (if you dare): okt.to/kwtZzX

Our latest preprint is online: “Population genomics and molecular epidemiology of wheat powdery mildew in Europe”. Thank to first author @jigi_sha and to the many collaborators that contributed to this study! 1/8 biorxiv.org/content/10.110…

Dominance reversal protects large-effect resistance polymorphisms in temporally varying environments biorxiv.org/cgi/content/sh… #biorxiv_evobio

AlphaBridge: tools for the analysis of predicted macromolecular complexes • AlphaBridge introduces tools to analyze and visualize the interfaces between predicted macromolecular complexes using data from AlphaFold3. It processes the predicted interactions into intuitive diagrams and 3D models for easy interpretation. • The tool uses a novel “Predicted Merged Confidence” (PMC) matrix, which combines the Predicted Local Distance Difference Test (pLDDT) and Predicted Aligned Error (PAE) metrics to identify multi-component structural modules and binary interfaces with high confidence. • AlphaBridge uses graph-based community clustering to detect interaction motifs in biomolecular complexes, then visualizes these interactions as chord diagrams (“AlphaBridge diagrams”) to provide a clear and intuitive summary of predicted binding interfaces. • The tool allows researchers to evaluate the reliability of interactions in predicted protein-protein, protein-DNA, and protein-RNA complexes, offering a scoring and ranking system for predicted interfaces before detailed analysis. • By varying the cut-off for contact predictions, AlphaBridge can help distinguish between reliable and unreliable predictions, providing insights into physiological relevance. It was particularly useful for evaluating interactions in DNA mismatch repair proteins and RNA binding proteins. • The AlphaBridge webserver (alpha-bridge.eu) offers an interactive platform where users can upload AlphaFold3 prediction files, visualize the predicted 3D structures, and analyze contact interfaces through an integrated web viewer. • AlphaBridge enhances accessibility for both expert and non-expert users by combining multiple layers of information—contact links, prediction confidence, and visual representations—into one interactive diagram, simplifying the evaluation of complex predictions. @TassosPerrakis @rborza_ 💻Code: github.com/PDB-REDO/Alpha… 📜Paper: biorxiv.org/content/10.110…

@aberdeenuni @neilhall_uk @SallyWarring Jess Peers, now in her fourth year of PhD, rejoined the Earlham Institute after her placement year investigating the genetic diversity and divergence of the ash dieback pathogen with Dr Mark McMullan. @jesspeers12

Santa Walker studied an MSci in Biotechnology from @aberdeenuni, spending her Year in Industry at the Earlham Institute exploring resistance genes in wild seabeet. This month Santa returned to EI to begin her PhD research with @neilhall_uk and @SallyWarring.

Tomorrow (10th October) we will have some great sessions on: JBrowse2 with Colin Diesh @usejbrowse at 8am UTC Intro to Manual Curation (Bird Microchromosomes) with @Thomas_Mathers at 1pm UTC We'll also stream live on YouTube, so no one misses out! @darwintreelife @EBPgenome

Trees are under increasing pressure from harmful pests and pathogens and the growth of global trade and travel increases the chances of introduction ✈️🚢🚛 We have launched a new biosecurity page online, which includes a useful Biosecurity action plan and links to report suspected tree pests or disease. Find out more ➡️ forestresearch.gov.uk/climate-change… @FR_CCRG #biosecurity

So, this afternoon I got home to find a lovely letter from @northernassist telling me about how they wanted to prosecute me for using the below ticket to travel on the specified route at a peak time. I paid £1.90 less than the fare they say I should have paid. A thread 🧵

Fantastic talk from @RowenaCHill sharing the wonder of fungi! @EarlhamInst

Check out the preliminary program for Popgroup58 on the website now --> populationgeneticsgroup.org.uk

A joint framework for studying population structure using principal component analysis and F-statistics biorxiv.org/cgi/content/sh… #biorxiv_evobio