Paul Daly

Construction of a randomly barcoded insertional mutant library in the filamentous fungus Trichoderma atroviride https://www.biorxiv.org/content/10.1101/2025.11.30.691285v1

Calling all OrthoFinder users!

We’ve just released GLADE, a tool to infer gene gains, losses, duplications, and ancestral genomes across a phylogeny.

GLADE runs directly on OrthoFinder results.
www.biorxiv.org/content/10.6...
github.com/lauriebelch/...

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Warfare among rice sheath pathogens: Rhizoctonia solani AG 1-IA neutralizes Pseudomonas fuscovaginae cyclic lipopeptides | Applied and Environmental Microbiology Rice is a global staple crop that is susceptible to various pathogens, including Pseudomonas fuscovaginae, causing sheath brown rot, and Rhizoctonia solani AG 1-IA, which causes sheath blight. Notably...

Warfare among rice sheath pathogens: Rhizoctonia solani AG 1-IA neutralizes Pseudomonas fuscovaginae cyclic lipopeptides

#ApplEnvironMicrobiol by Jasmine De Rop from Monica Höfte at @fbwugent.bsky.social

journals.asm.org/doi/10.1128/...

Please take a look our recent method paper (please DM me for full text)

Rapid detection of Pythium soft rot in ginger (Zingiber officinale) caused by Pythium myriotylum using LAMP | Plant Disease apsjournals.apsnet.org/doi/10.1094/...

The changing roles of Escherichia coli Nature Microbiology - Richard Lenski traces the legacy of Escherichia coli and how science is evolving to use this model organism in new ways.

"The changing roles of Escherichia coli" -- a short essay by yours truly.

rdcu.be/eVtXT

Illustration of a clinical therapy setting in which a clinician sits at a desk holding playing cards while a computer screen displays a LLM prompt reading, ‘How does that make you feel?’ A patient lies on a couch in the background, conveying a conceptual commentary on the use of artificial intelligence in therapy. Image credit: Dave Cutler (artist).

Opinion: The “machinal bypass” examines how #AI can replace—not augment—our own presence. From #researchers to #clinicians, what happens when we let machines stand in for ourselves? In PNAS Front Matter: https://ow.ly/Tro450XLB5q

#AI #psychology #psychiatry #MentalHealth #LLM

Mapping the Earth’s Hidden Fungal Kingdom | Joint Genome Institute Leveraging massive comparative genomics to decode millions of mystery genes and lay a future-ready foundation

“The enormous diversity of fungal genomes...offers catalogs of enzymes, secondary metabolites & other parts lists for biotechnology, bioenergy & biomaterials."—Igor Grigoriev, Fungal & Algal Program Head.
🖥️🧬🍄🍄‍🟫

https://jgi.doe.gov/user-science/science-stories/mapping-earths-hidden-fungal-kingdom

How #fungi sense and respond to light.

Primer in our current issue👇

www.cell.com/current-biol...

Cell wall patterning regulates plant stem cell dynamics The plant cell wall regulates development through spatiotemporal modulation of its chemical and mechanical properties. Pectin methylesterification is recognized as a rheological switch controlling wal...

Out in @science.org this week:
PME5 is sequestered in the nucleus and released during cytokinesis allowing its activity to be timed with cell division.

www.science.org/doi/10.1126/...

#PlantScience
#PlantSci

Helixer: ab initio prediction of primary eukaryotic gene models combining deep learning and a hidden Markov model - Nature Methods By leveraging both deep learning and hidden Markov models, Helixer achieves broad taxonomic coverage for ab initio gene annotation of eukaryotic genomes from fungi, plants, vertebrates and invertebrat...

AI model Helixer predicts eukaryotic genes ab initio, directly from a plain text FASTA file.

No RNA-seq.
No protein homology.
No repeats, hints, or curated evidence.

Raw genome → accurate gene models.
Deep learning + HMM, published in @natmethods.nature.com

www.nature.com/articles/s41...

Congrats to the prize winners at Asian Mycological Congress #AMC2025 #mycology #fungi

Keynote talk from Zhensheng Kang at #AMC2025 on wheat stripe rust. Very interesting pathogen life cycle.

Great to present at #AMC2025 in session with @sunilmundra.bsky.social @qurban38.bsky.social Sakae Horisawa and Feng Cai

Starship transposons, HGT on ToxA from Fei Liu from CAS at #AMC2025

Interesting talk from Marta @mf-s.bsky.social at AMC 2025 #AMC2025 on astromycology

Lots of tools & resources for Cordyceps militaris for gene editing from Caihong Dong at #AMC2025

Interesting talk at AMC 2025 #AMC2025 from Arend van Peer on incompatibility in mushrooms

Interesting keynote talk from Chengshu Wang at AMC 2025 #AMC2025

Interesting opening talk of AMC 2025 from Marc Stadler @ms-fungi.bsky.social

AMC 2025 starting today in Guangzhou, China with next-gen mycologists symposium. lots of details of the schedule on website www.amc2025.cn

#AMC2025

Big life-size schedule

Check it out!

Demystifying fungal systematics: A gateway to fungal literacy and societal/ecological relevance through familiar species Fungal systematics can feel overwhelming given the vast species diversity within this kingdom, with numerous subgroups at every taxonomic rank. This often creates a disconnect between the undertsnidn...

We are delighted to let you know that your Plants, People, Planet article 'Demystifying Fungal Systematics: A Gateway to Fungal Literacy and Societal/Ecological Relevance Through Familiar Species' has been published on Early View.

nph.onlinelibrary.wiley.com/doi/10.1002/...

Please take a look at our latest work on regulation in Trichoderma harzianum in response to oomycete cell walls

Share link (free access until end Dec 2025): authors.elsevier.com/a/1m55I3MmJP...
See also from here: doi.org/10.1016/j.mi...

Beware giving this site your unpublished data Users noticed the website had fake testimonials and a domain name registered seemingly overnight.

PSA: Many of you may have noticed a website floating around called formatmypaper(dot)com. People rightly noted something was fishy. I dig into what happened here:
open.substack.com/pub/ubadah/p...

Assistant Professor of Plant Pathology University of California, Davis is hiring. Apply now!

My department at UC Davis is hiring a mycologist, broadly interpreted. Please repost, share, and consider applying. recruit.ucdavis.edu/JPF07339

The registration link and program for the 5th Virtual ChemBioTalks are finally available! If you are interested in the field of Chemical Biology, make sure to register for this free, virtual event on September 30th, 2025!
cvent.me/G1geWW (1/4)
#Chemsky #ChemBio

How fungi see the world: fungal photoreceptors and their role in the regulation of fungal biology | Microbiology and Molecular Biology Reviews SUMMARYFungi use light as a signal for the regulation of development, to guide the growth of reproductive structures, and to protect the fungal cell from DNA damage produced by light and UV radiation....

"Fungi can see and react to a wide range of colors." journals.asm.org/doi/abs/10.1...

Myco-Ed: Mycological curriculum for education and discovery Fungi are important and hyperdiverse organisms, yet chronically understudied. Most fungal clades have no reference genomes, impeding our understanding of their ecosystem functions and use as solutions...

Have you heard about MycoEd yet? A model educational program offering training for students on fungal genome sequencing and analysis. how powerful!! #mycofam #thefutureisfungal

journals.plos.org/plospathogen...

The History of Enzyme Evolution Embedded in Metabolism Phylogenetic reconstructions are a primary record of protein evolution. But what other records can attest to the deep history of enzymes, and what tools are needed to decode their meaning? Here, we de...

The History of Enzyme Evolution Embedded in Metabolism
doi.org/10.1101/2025...

KIPEs3: Automatic annotation of biosynthesis pathways
doi.org/10.1101/2022...

AlphaFold - A practical guide AlphaFold - A practical guide

Recently I learnt that EMBL-EBI has a free online course about AlphaFold — how it works, strengths and limitations, how to use it — and it's very good!

There are also little quizzes and interactives.
www.ebi.ac.uk/training/onl...