Soham Mukhopadhyay

Very excited to see this work out today!

Discovering viral immune antagonists directly from predicted protein structures. 🤩 www.science.org/doi/10.1126/...

Huge thanks to the amazing collaborators! 🤗

@ismpmi.bsky.social

Close up of a Kalanchoe stem where white roots emerging from needle holes

Emerged roots are green fluorescent as the agro strain injected carries a green fluorescent marker.

Close up of the green fluorescent roots emerging from the stem.

Plant weirdness. After injecting agro rhizogenes into the stem of Kalanchoe, they start sprouting roots from stem after few weeks later.

I recently reviewed a manuscript where the reviewer 3 submitted 5 pages of LLM nonsense 😅

True, it's a nightmare to juggle all those 'like', 'isoform x1' , 'like protein‘, etc. 😅 For non-model plants, I always keep two annotations— one against the broad NR database and one just with Arabidopsis, and then cross-check.

Is the lesson from this that, if ones reasoning is freed from the pull of gravity, one can still publish with MDPI?

@thaisdalsasso.bsky.social is applying new tools to address the evolution and functional diversification of secreted proteins of fungal plant pathogen. Preprint here: www.biorxiv.org/content/10.6...

GitHub - Gaius-Augustus/Tiberius: Tiberius is a deep learning gene finder. Tiberius is a deep learning gene finder. Contribute to Gaius-Augustus/Tiberius development by creating an account on GitHub.

What we more recently learnt about Tiberius: the models trained on softmasked genomes are very sensitive to how the genome was masked for inference. It seems safer to use models trained on unmasked genomes. #genomeannotation #geneprediction github.com/Gaius-August...

Out in @NaturePlants. We discover that the fungal pathogen Fusarium graminearum secretes an apoplastic effector that disrupts the N-glycosylation of a maize immune receptor, thereby inducing its degradation via selective autophagy. Very proud of the team~ doi.org/10.1038/s414...

The annotated blueprint: integrated functional genomic resources for a model tetraploid wheat Triticum turgidum cv Kronos Triticum turgidum cv Kronos is a tetraploid wheat cultivar that underpins one of the most widely used community platforms for functional genomics. Over the past decade, researchers have generated c. ...

Out in New Phytologist!

The annotated blueprint: integrated functional genomic resources for a model tetraploid wheat cv. Kronos 🌾
chromosome-scale genome, high-conf annotations, manually curated 1000+ NLRs, ~3000 remapped datasets

🔗 doi.org/10.1111/nph....
#Plants #Genomics #FunctionalGenomics

the estimated 1 billion biochemical reactions that occur every second in every cell of our bodies 🤯

Announcing the publication of TAIR12: Consult the fully reannotated genome on the European Nucleotide Archive - Phoenix Bioinformatics TAIR (The Arabidopsis Information Resource), together with our nonprofit host Phoenix Bioinformatics, is pleased to announce the public release of TAIR12

🎉📣 #TAIR12, the latest reannotation of the Arabidopsis thaliana genome, is now available under accession number PRJEB100887 on ENA and NCBI!

Thank you all the volunteer researchers whose hard work has made this possible!

#plantscience #plantbiology 🧪

bit.ly/3ZHtneT

Fitness effects of mutation: testing genetic redundancy in Arabidopsis thaliana Screens of organisms with disruptive mutations in a single gene often fail to detect phenotypic consequences for the majority of mutants. One explanation for this phenomenon is that the presence of p...

are you referring to the Rutter 2017 paper? onlinelibrary.wiley.com/doi/full/10....

Dihydroxyhexanoic acid biosynthesis controls turgor in pathogenic fungi Many plant pathogenic fungi penetrate host surfaces mechanically, using turgor pressure generated by specialized infection cells called appressoria. These appressoria develop semipermeable cell walls ...

Out in @science.org this week, two fungal enzymes synthesise DHHA, which controls cell wall porosity and turgor in plant pathogenic fungi www.science.org/doi/10.1126/...

#mycology
#plantscience

📣 Our latest story just dropped on bioRxiv:: A structurally unique effector shared between Verticillium dahliae and Fusarium oxysporum is involved in cotton defoliation and virulence on other hosts www.biorxiv.org/content/10.6... 🧵

MPMI Editorial Board

Thrilled to announce that I am joining the Editorial Board of Molecular Plant–Microbe Interactions as a Senior Editor! 🌱🦠 Grateful for the opportunity to serve this vibrant research community and help amplify impactful science 👏

🔗 apsjournals.apsnet.org/page/mpmi/ed...

Excited to join the team as Associate Editor!

😮😮

This article is now published! academic.oup.com/nargab/artic...
We’ve added a few new analyses. First off, we show that, while gene presence absence variation (PAV) scales with evolutionary distance in both plants and animals, the base level and rate of accrual are both twice as high in plants.

📣 Our lab is seeking a postdoc to study mutation mechanisms in fungi using cutting-edge sequencing + computational biology. No active posting/grant right now, but we’re excited to host postdoc fellowship applicants in our comparative immunology team.
Interested? Reach out DM email. krasilevalab.org

He is strictly vegetarian, thus avoidance of excessive branched chain amino acids might explain this!

A multi-plant transcriptomic atlas reveals conserved and lineage specific defense architectures in response to Botrytis cinerea Generalist pathogens pose a challenge to plant immunity by infecting diverse hosts while harboring extensive intraspecific genetic variation. Whether evolutionary distant plant lineages rely on a shar...

Ever wondered if diverse plant species respond similarly when infected by the same exact pathogen? Infect different asterids and rosids with the same Botrytis genotypes and teh short answer, quite differently.
www.biorxiv.org/content/10.6...

@annajomu.bsky.social @ccaseys.bsky.social

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Déjà vu in clubroot resistance: same genes, new names Despite decades of clubroot research, only three resistance (R) genes have been validated. However, many of the ‘new’ R genes are, in fact, identical to or allelic with these three. In this forum arti...

Although it went online in 2025, here is our second paper of 2026! 🎉

Bravo to @jiaxuwu.bsky.social for leading this (possibly) controversial, but much-needed, analysis. Enjoy! Now out in the January 2026 issue of Trends in Genetics.

🔗 www.cell.com/trends/genet...

Towards a quantitative view of NLR evolution in genome space -- check out where we think the field of #NLR #evolution research is heading in this review led by Luzie Wingen and Aurélien Tellier.
ecoevorxiv.org/repository/v...
#plantscience

Food will be more affordable — if we double funds for agriculture research now A global drop in public and private investment in agricultural science in the past four decades is partly to blame for high food prices, an analysis reveals.

Comment in @nature.com: "Food will be more affordable — if we double funds for agriculture research now" www.nature.com/articles/d41...

A global drop in public and private investment in agricultural science in the past four decades is partly to blame for high food prices, an analysis reveals.

We are thrilled to announce the first official release (v0.1.8) of #𝗯𝗲𝗱𝗱𝗲𝗿, the successor to one of our flagship tool, #𝗯𝗲𝗱𝘁𝗼𝗼𝗹𝘀! Based on ideas we conceived of long ago (!), this was achieved thanks to the dedication of Brent Pedersen.

1/n

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...

A Grammar of Graphics for Comparative Genomics An extension of ggplot2 for creating complex genomic maps. It builds on the power of ggplot2 and tidyverse adding new ggplot2-style geoms & positions and dplyr-style verbs to manipulate the…

gggenomes: A Grammar of Graphics for Comparative Genomics thackl.github.io/gggenomes/ #Rstats

Rewriting the code of plant immunity go.nature.com/475WgV7

Just when you thought plant galls couldn't be of any more shapes! Such cool findings!
"Dasineura asteriae Reprograms the Flower Gene Expressions of Vegetative Organs to Create Flower-Like Gall in Aster scaber"
onlinelibrary.wiley.com/doi/10.1111/...