Soham Mukhopadhyay
@sohambio.bsky.social
Plant Pathogen Interaction | Plant Galls | Postdoctoral Fellow & Adjunct Faculty @unm.edu | Associate Editor @MPMI | 🌐 soham.science | Try http://biosearch.chat
Reposted by Soham Mukhopadhyay
AlphaFold Database is expanding into pandemic preparedness. Together with NVIDIA, DeepMind, EBI et al. we exhaustively predicted ~1.7 million homo- & heterodimers across 2,812 viral proteomes, resulting in 8,028 high-confidence predictions.
📄 research.nvidia.com/labs/dbr/ass...
🌐 alphafold.ebi.ac.uk
📄 research.nvidia.com/labs/dbr/ass...
🌐 alphafold.ebi.ac.uk
September 24, 2026 at 2:24 PM
AlphaFold Database is expanding into pandemic preparedness. Together with NVIDIA, DeepMind, EBI et al. we exhaustively predicted ~1.7 million homo- & heterodimers across 2,812 viral proteomes, resulting in 8,028 high-confidence predictions.
📄 research.nvidia.com/labs/dbr/ass...
🌐 alphafold.ebi.ac.uk
📄 research.nvidia.com/labs/dbr/ass...
🌐 alphafold.ebi.ac.uk
Reposted by Soham Mukhopadhyay
Plants use the hormone salicylic acid (SA) to fight infection, but how it activates gene expression remained unclear. Two studies @nature show that the mechanism involves interaction between SA receptor NPR1 and a component of the transcriptional machinery.
shorturl.at/7PymL
&
shorturl.at/Iy4oY
shorturl.at/7PymL
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shorturl.at/Iy4oY
Mechanisms of Transcriptional Regulation by Salicylic Acid Receptors - Nature
Nature - Mechanisms of Transcriptional Regulation by Salicylic Acid Receptors
shorturl.at
September 16, 2026 at 6:44 PM
Plants use the hormone salicylic acid (SA) to fight infection, but how it activates gene expression remained unclear. Two studies @nature show that the mechanism involves interaction between SA receptor NPR1 and a component of the transcriptional machinery.
shorturl.at/7PymL
&
shorturl.at/Iy4oY
shorturl.at/7PymL
&
shorturl.at/Iy4oY
Reposted by Soham Mukhopadhyay
New paper! Amphibious plant, H. difformis, reprograms C3 to potential C4 photosynthesis underwater, highlighting its amazing plasticity of carbon assimilation machineries for aquatic environment. Congrats, Hongwei & the team🥳🌿🐸!
academic.oup.com/hr/advance-article/doi/10.1093/hr/uhag230/8708086
academic.oup.com/hr/advance-article/doi/10.1093/hr/uhag230/8708086
August 17, 2026 at 1:26 AM
New paper! Amphibious plant, H. difformis, reprograms C3 to potential C4 photosynthesis underwater, highlighting its amazing plasticity of carbon assimilation machineries for aquatic environment. Congrats, Hongwei & the team🥳🌿🐸!
academic.oup.com/hr/advance-article/doi/10.1093/hr/uhag230/8708086
academic.oup.com/hr/advance-article/doi/10.1093/hr/uhag230/8708086
Reposted by Soham Mukhopadhyay
Our latest views on deep ARF evolution are finally out in New Phytologist! nph.onlinelibrary.wiley.com/doi/10.1111/...
AUXIN RESPONSE FACTORs: from transcription factors to auxin effectors
Molecular evolution of AUXIN RESPONSE FACTOR (ARF) effector function.
nph.onlinelibrary.wiley.com
August 13, 2026 at 8:45 AM
Our latest views on deep ARF evolution are finally out in New Phytologist! nph.onlinelibrary.wiley.com/doi/10.1111/...
Reposted by Soham Mukhopadhyay
Plants can synthesize mimics of the insect molting hormone 20-hydroxyecdysone (20E) to defend against pests. In this preprint, we discover that two plant families independently evolved biosynthetic gene clusters to make 20E. Amazing team effort by my lab!
www.biorxiv.org/content/10.6...
www.biorxiv.org/content/10.6...
Convergent biosynthesis of insect molting hormones in plants
Insect herbivores have driven plants to evolve complex chemical defenses, including mimics of the arthropod molting hormone 20-hydroxyecdysone (20E). Many distantly related plants produce 20E, suggest...
www.biorxiv.org
August 10, 2026 at 1:35 PM
Plants can synthesize mimics of the insect molting hormone 20-hydroxyecdysone (20E) to defend against pests. In this preprint, we discover that two plant families independently evolved biosynthetic gene clusters to make 20E. Amazing team effort by my lab!
www.biorxiv.org/content/10.6...
www.biorxiv.org/content/10.6...
👏🏼👏🏼 this is how it should be done
In 2021, we published an article in eLife on the role of CLE40 in Arabidopsis shoot meristem development ( see here: elifesciences.org/articles/70934 ). We recently found that one of the Arabidopsis lines used in that publication.....
July 28, 2026 at 6:00 PM
👏🏼👏🏼 this is how it should be done
Reposted by Soham Mukhopadhyay
The demonstration of a single origin for nodule evolution, with nodule engineering in a non-nodulating species https://www.biorxiv.org/content/10.64898/2026.05.31.728964v1
June 3, 2026 at 8:02 PM
The demonstration of a single origin for nodule evolution, with nodule engineering in a non-nodulating species https://www.biorxiv.org/content/10.64898/2026.05.31.728964v1
Reposted by Soham Mukhopadhyay
Researchers have identified superparamagnetic macrophages in the livers of rock pigeons to be crucial for magnetic sensing. The finding uncovers an unexpected role for immune cells in sensory perception and may fundamentally change our understanding of animal navigation.
https://scim.ag/4nTQ3nq
https://scim.ag/4nTQ3nq
May 28, 2026 at 6:05 PM
Researchers have identified superparamagnetic macrophages in the livers of rock pigeons to be crucial for magnetic sensing. The finding uncovers an unexpected role for immune cells in sensory perception and may fundamentally change our understanding of animal navigation.
https://scim.ag/4nTQ3nq
https://scim.ag/4nTQ3nq
Excited to see the structurally conserved nucleoside hydrolase like fold that we found (elifesciences.org/articles/105...) to be conserved among biotrophs now being experimentally validated to target EDS1 !!
Link to the preprint - www.biorxiv.org/content/10.6...
Link to the preprint - www.biorxiv.org/content/10.6...
May 22, 2026 at 10:31 PM
Excited to see the structurally conserved nucleoside hydrolase like fold that we found (elifesciences.org/articles/105...) to be conserved among biotrophs now being experimentally validated to target EDS1 !!
Link to the preprint - www.biorxiv.org/content/10.6...
Link to the preprint - www.biorxiv.org/content/10.6...
Reposted by Soham Mukhopadhyay
Proud to share our new paper on how prion-like fungal effectors target plastids and modulate host metabolism during root symbiosis. Exciting collaborative work uncovering PEPSI effectors and the interaction of one of them with DXR in plants.
www.biorxiv.org/content/10.6...
bsky.app/profile/eell...
www.biorxiv.org/content/10.6...
bsky.app/profile/eell...
May 20, 2026 at 5:59 PM
Proud to share our new paper on how prion-like fungal effectors target plastids and modulate host metabolism during root symbiosis. Exciting collaborative work uncovering PEPSI effectors and the interaction of one of them with DXR in plants.
www.biorxiv.org/content/10.6...
bsky.app/profile/eell...
www.biorxiv.org/content/10.6...
bsky.app/profile/eell...
Reposted by Soham Mukhopadhyay
Check out our latest work! AlphaFold 3 revealed a transient immune receptor complex that eluded biochemical studies for almost a decade 🤯 We describe a conserved structural logic underlying sensor–helper communication in an NLR immune receptor network 🧵👇
May 20, 2026 at 11:42 AM
Check out our latest work! AlphaFold 3 revealed a transient immune receptor complex that eluded biochemical studies for almost a decade 🤯 We describe a conserved structural logic underlying sensor–helper communication in an NLR immune receptor network 🧵👇
Reposted by Soham Mukhopadhyay
We are excited to release the BAT!🦇🚨
We've used this phylogenetic analysis pipeline in our lab for years, and grad Ben Sheppard now presents a Github release and preprint.
I run BAT analyses almost daily. It makes exploring gene families routine, customizable, and fun🧵
We've used this phylogenetic analysis pipeline in our lab for years, and grad Ben Sheppard now presents a Github release and preprint.
I run BAT analyses almost daily. It makes exploring gene families routine, customizable, and fun🧵
May 13, 2026 at 12:22 AM
We are excited to release the BAT!🦇🚨
We've used this phylogenetic analysis pipeline in our lab for years, and grad Ben Sheppard now presents a Github release and preprint.
I run BAT analyses almost daily. It makes exploring gene families routine, customizable, and fun🧵
We've used this phylogenetic analysis pipeline in our lab for years, and grad Ben Sheppard now presents a Github release and preprint.
I run BAT analyses almost daily. It makes exploring gene families routine, customizable, and fun🧵
Reposted by Soham Mukhopadhyay
Hey #MPMI crowd, we are having trouble finding co-proteome papers looking into the host and pathogen proteome at the same time. I know they must exist but can’t find them. Any suggestions?
April 23, 2026 at 5:01 PM
Hey #MPMI crowd, we are having trouble finding co-proteome papers looking into the host and pathogen proteome at the same time. I know they must exist but can’t find them. Any suggestions?
Reposted by Soham Mukhopadhyay
Resequencing hundreds or thousands of individuals from the same species has become routine... but processing all those genomes efficiently? Still a headache!
Here's my solution that used to be lab-internal but that I am happy to share:
crolllab.github.io/genomepanel_...
Here's my solution that used to be lab-internal but that I am happy to share:
crolllab.github.io/genomepanel_...
Home – genomepanel_nf
Nextflow pipeline for reference genome mapping, SNP calling and quality checks on large genome panels
crolllab.github.io
April 3, 2026 at 8:38 PM
Resequencing hundreds or thousands of individuals from the same species has become routine... but processing all those genomes efficiently? Still a headache!
Here's my solution that used to be lab-internal but that I am happy to share:
crolllab.github.io/genomepanel_...
Here's my solution that used to be lab-internal but that I am happy to share:
crolllab.github.io/genomepanel_...
Reposted by 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! 🤗
Discovering viral immune antagonists directly from predicted protein structures. 🤩 www.science.org/doi/10.1126/...
Huge thanks to the amazing collaborators! 🤗
March 6, 2026 at 10:38 AM
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! 🤗
Discovering viral immune antagonists directly from predicted protein structures. 🤩 www.science.org/doi/10.1126/...
Huge thanks to the amazing collaborators! 🤗
Reposted by Soham Mukhopadhyay
#ISMPMI International Society for Molecular Plant Microbe Interactions members- read my letter about recent developments in the society- important changes to how we are managed. www.linkedin.com/feed/update/...
IS-MPMI News- From the President’s Desk
Dear IS-MPMI members
Since I became President in July 2025, I’ve been working hard to ensure that IS-MPMI has an enduring future and valuable programming for… |...
IS-MPMI News- From the President’s Desk
Dear IS-MPMI members
Since I became President in July 2025, I’ve been working hard to ensure that IS-MPMI has an enduring future and valuable programming for ou...
www.linkedin.com
March 5, 2026 at 10:42 PM
Reposted by Soham Mukhopadhyay
Plant weirdness. After injecting agro rhizogenes into the stem of Kalanchoe, they start sprouting roots from stem after few weeks later.
March 4, 2026 at 2:39 PM
Plant weirdness. After injecting agro rhizogenes into the stem of Kalanchoe, they start sprouting roots from stem after few weeks later.
Reposted by Soham Mukhopadhyay
Is the lesson from this that, if ones reasoning is freed from the pull of gravity, one can still publish with MDPI?
February 28, 2026 at 3:15 PM
Is the lesson from this that, if ones reasoning is freed from the pull of gravity, one can still publish with MDPI?
Reposted by Soham Mukhopadhyay
@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...
www.biorxiv.org
February 26, 2026 at 8:52 AM
@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...
Reposted by Soham Mukhopadhyay
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...
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.
github.com
February 16, 2026 at 8:48 AM
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...
Reposted by Soham Mukhopadhyay
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...
September 12, 2025 at 9:22 AM
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...
Reposted by Soham Mukhopadhyay
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 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 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. ...
doi.org
February 23, 2026 at 5:28 PM
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 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
Reposted by Soham Mukhopadhyay
the estimated 1 billion biochemical reactions that occur every second in every cell of our bodies 🤯
Density. Crowding. Tomato. Tomato 🍅
@gabepopkin.bsky.social kin.bsky.social @quantamagazine.bsky.social Thx for covering the debate! We promise we're all friends 🥰 @liamholt.bsky.social & @gwgl.bsky.social
Nothing would have been possible without @gucklab.bsky.social @vasilyzaburdaev.bsky.social
@gabepopkin.bsky.social kin.bsky.social @quantamagazine.bsky.social Thx for covering the debate! We promise we're all friends 🥰 @liamholt.bsky.social & @gwgl.bsky.social
Nothing would have been possible without @gucklab.bsky.social @vasilyzaburdaev.bsky.social
The Biophysical World Inside a Jam-Packed Cell | Quanta Magazine
Innovations in imaging and genetic engineering are coming together to probe the biophysics of cytoplasm inside living animals.
www.quantamagazine.org
February 23, 2026 at 10:31 AM
the estimated 1 billion biochemical reactions that occur every second in every cell of our bodies 🤯
Reposted by Soham Mukhopadhyay
🎉📣 #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
Thank you all the volunteer researchers whose hard work has made this possible!
#plantscience #plantbiology 🧪
bit.ly/3ZHtneT
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
bit.ly
February 19, 2026 at 6:40 PM
🎉📣 #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
Thank you all the volunteer researchers whose hard work has made this possible!
#plantscience #plantbiology 🧪
bit.ly/3ZHtneT