Juan （胡安）
@angiopteris.bsky.social
Juan Carlos Lopez-Agudelo
PhD student at Academia Sinica, Taiwan
Agrobacteria | Plant-pathogen interactions | Bacterial evolution
Never stop exploring 🌱
PhD student at Academia Sinica, Taiwan
Agrobacteria | Plant-pathogen interactions | Bacterial evolution
Never stop exploring 🌱
Pinned
Juan （胡安）
@angiopteris.bsky.social
· Apr 23
www.biorxiv.org
Finally out! A follow-up to our Rhizobium rhizogenes story with @tolgaboz.bsky.social and Lida. We hope this work will make it easier to study many other plant species.
www.biorxiv.org/content/10.6...
www.biorxiv.org/content/10.6...
Reposted by Juan （胡安）
‼️Job altert🚨📢 please spread the word: We're looking for a postdoctoral researcher to join our new department "Phytopathology and Plant Protection" at @unihalle.bsky.social.
www.verwaltung.uni-halle.de/DEZERN3/AUSS...
www.verwaltung.uni-halle.de/DEZERN3/AUSS...
July 1, 2026 at 1:25 PM
‼️Job altert🚨📢 please spread the word: We're looking for a postdoctoral researcher to join our new department "Phytopathology and Plant Protection" at @unihalle.bsky.social.
www.verwaltung.uni-halle.de/DEZERN3/AUSS...
www.verwaltung.uni-halle.de/DEZERN3/AUSS...
Reposted by Juan （胡安）
We’re happy to introduce phageFACTor (Functional Annotation and Curation Tool)
👩💻Developed by Tanaïs Moreau, our most recent PhD candidate, and building on Phold, we were able to improve annotation of prophage genes by as much as 50% 🧬
You should check it out github.com/TMs-code/pha...
👩💻Developed by Tanaïs Moreau, our most recent PhD candidate, and building on Phold, we were able to improve annotation of prophage genes by as much as 50% 🧬
You should check it out github.com/TMs-code/pha...
July 1, 2026 at 5:24 PM
We’re happy to introduce phageFACTor (Functional Annotation and Curation Tool)
👩💻Developed by Tanaïs Moreau, our most recent PhD candidate, and building on Phold, we were able to improve annotation of prophage genes by as much as 50% 🧬
You should check it out github.com/TMs-code/pha...
👩💻Developed by Tanaïs Moreau, our most recent PhD candidate, and building on Phold, we were able to improve annotation of prophage genes by as much as 50% 🧬
You should check it out github.com/TMs-code/pha...
Reposted by Juan （胡安）
📢 PDRA Position - Plant Immune Receptor Bioengineering at Imperial College London
🌱 Start: Aug 2026 (flexible)
🧪 Wet lab + bioinformatics
📅 Up to 3 years (ERC-funded)
📍 South Kensington, on site
ℹ️ shorturl.at/VIITk
🔗 kourelislab.com
#PlantImmunity #PlantPathology
🙏 Share with interested candidates!
🌱 Start: Aug 2026 (flexible)
🧪 Wet lab + bioinformatics
📅 Up to 3 years (ERC-funded)
📍 South Kensington, on site
ℹ️ shorturl.at/VIITk
🔗 kourelislab.com
#PlantImmunity #PlantPathology
🙏 Share with interested candidates!
Description
Please note that job descriptions are not exhaustive, and you may be asked to take on additional duties that align with the key responsibilities ment...
shorturl.at
June 4, 2026 at 11:04 AM
📢 PDRA Position - Plant Immune Receptor Bioengineering at Imperial College London
🌱 Start: Aug 2026 (flexible)
🧪 Wet lab + bioinformatics
📅 Up to 3 years (ERC-funded)
📍 South Kensington, on site
ℹ️ shorturl.at/VIITk
🔗 kourelislab.com
#PlantImmunity #PlantPathology
🙏 Share with interested candidates!
🌱 Start: Aug 2026 (flexible)
🧪 Wet lab + bioinformatics
📅 Up to 3 years (ERC-funded)
📍 South Kensington, on site
ℹ️ shorturl.at/VIITk
🔗 kourelislab.com
#PlantImmunity #PlantPathology
🙏 Share with interested candidates!
Reposted by Juan （胡安）
Our paper on the YprA family of helicases and their roles in bacterial defence is now out!
We describe ARMADA, a defence system synergise with Druantia and show that both systems spread horizontally on a novel type of mobile genetic element that we call SPIDERs
www.sciencedirect.com/science/arti...
We describe ARMADA, a defence system synergise with Druantia and show that both systems spread horizontally on a novel type of mobile genetic element that we call SPIDERs
www.sciencedirect.com/science/arti...
YprA-family helicases provide the missing link between diverse prokaryotic immune systems
Bacteria and archaea possess an enormous variety of antiviral immune systems that often share homologous proteins and domains. YprA-family helicases a…
www.sciencedirect.com
June 12, 2026 at 2:34 PM
Our paper on the YprA family of helicases and their roles in bacterial defence is now out!
We describe ARMADA, a defence system synergise with Druantia and show that both systems spread horizontally on a novel type of mobile genetic element that we call SPIDERs
www.sciencedirect.com/science/arti...
We describe ARMADA, a defence system synergise with Druantia and show that both systems spread horizontally on a novel type of mobile genetic element that we call SPIDERs
www.sciencedirect.com/science/arti...
Reposted by Juan （胡安）
So proud to see this story finally out!🎉 We added new data since our previous preprint—transgenic barley plants with an engineered immune receptor that fights off two fungal pathogens at once. Short 🧵 and link to the original preprint thread on X👇
www.science.org/doi/10.1126/...
www.science.org/doi/10.1126/...
Molecular mimicry of a pathogen virulence target by a plant immune receptor
Plants and animals respond to pathogen attack by mounting innate immune responses that require intracellular nucleotide-binding leucine-rich repeat (NLR) proteins. These immune receptors detect pathog...
www.science.org
June 5, 2026 at 9:07 AM
So proud to see this story finally out!🎉 We added new data since our previous preprint—transgenic barley plants with an engineered immune receptor that fights off two fungal pathogens at once. Short 🧵 and link to the original preprint thread on X👇
www.science.org/doi/10.1126/...
www.science.org/doi/10.1126/...
Very exciting news, congratulations! :)
Excited to share that I will start my lab this summer as an ECL Unit Leader at RIKEN CSRS!
We will study perception by cell-surface receptors across diverse plant species.
I’ll be recruiting soon, so please reach out if you’re interested!
We will study perception by cell-surface receptors across diverse plant species.
I’ll be recruiting soon, so please reach out if you’re interested!
June 4, 2026 at 2:47 AM
Very exciting news, congratulations! :)
Reposted by Juan （胡安）
🌿🧬Bryophytes have a larger gene family space than vascular plants. New super pangenome analysis of 123 genomes reveals new immune receptors & microbial genes acquired through horizontal transfer
Small in size. Big in genetic toolkit #plantscience @natgenet.nature.com
www.nature.com/articles/s41...
Small in size. Big in genetic toolkit #plantscience @natgenet.nature.com
www.nature.com/articles/s41...
Bryophytes hold a larger gene family space than vascular plants - Nature Genetics
A super-pangenome analysis incorporating 123 newly sequenced bryophyte genomes reveals that bryophytes exhibit a larger number of unique and lineage-specific gene families than vascular plants.
www.nature.com
May 30, 2026 at 9:14 AM
🌿🧬Bryophytes have a larger gene family space than vascular plants. New super pangenome analysis of 123 genomes reveals new immune receptors & microbial genes acquired through horizontal transfer
Small in size. Big in genetic toolkit #plantscience @natgenet.nature.com
www.nature.com/articles/s41...
Small in size. Big in genetic toolkit #plantscience @natgenet.nature.com
www.nature.com/articles/s41...
Reposted by Juan （胡安）
A new preprint is OUT! 🚨
Thrilled to finally share our work on how decoy diversification underpins the regulation of an NLR-mediated autoimmunity.
Check out the full story on @bioRxiv: www.biorxiv.org/content/10.6...
(1/6)
Thrilled to finally share our work on how decoy diversification underpins the regulation of an NLR-mediated autoimmunity.
Check out the full story on @bioRxiv: www.biorxiv.org/content/10.6...
(1/6)
May 22, 2026 at 6:28 AM
A new preprint is OUT! 🚨
Thrilled to finally share our work on how decoy diversification underpins the regulation of an NLR-mediated autoimmunity.
Check out the full story on @bioRxiv: www.biorxiv.org/content/10.6...
(1/6)
Thrilled to finally share our work on how decoy diversification underpins the regulation of an NLR-mediated autoimmunity.
Check out the full story on @bioRxiv: www.biorxiv.org/content/10.6...
(1/6)
Reposted by Juan （胡安）
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 Juan （胡安）
See a brief review summarizing the use of synthetic microbial communities (SynComs) for revealing the ecology of specialized metabolites
[my holiday break writing exercise]
portlandpress.com/essaysbioche...
#MicrobiomeEcology at Institute of Biology Leiden (IBL)
[my holiday break writing exercise]
portlandpress.com/essaysbioche...
#MicrobiomeEcology at Institute of Biology Leiden (IBL)
May 11, 2026 at 7:10 AM
See a brief review summarizing the use of synthetic microbial communities (SynComs) for revealing the ecology of specialized metabolites
[my holiday break writing exercise]
portlandpress.com/essaysbioche...
#MicrobiomeEcology at Institute of Biology Leiden (IBL)
[my holiday break writing exercise]
portlandpress.com/essaysbioche...
#MicrobiomeEcology at Institute of Biology Leiden (IBL)
Reposted by Juan （胡安）
IQ-TREE 3: Phylogenomic Inference Software using Complex Evolutionary Models academic.oup.com/mbe/article/...
IQ-TREE 3: Phylogenomic Inference Software using Complex Evolutionary Models
Abstract. IQ-TREE (https://iqtree.github.io/) is a widely used open-source software tool for efficiently inferring phylogenetic trees under maximum likelih
academic.oup.com
May 6, 2026 at 5:00 PM
IQ-TREE 3: Phylogenomic Inference Software using Complex Evolutionary Models academic.oup.com/mbe/article/...
Reposted by Juan （胡安）
📢 EffectorGeneP is finally here! Stop missing small, single-exon or orphan genes from your favourite pathogen genome. Current tools only annotate 15%-78% of effector genes, EffectorGeneP finds 95% - including the large AvrSr26 family in stem rust. #Bioinformatics 📖 www.biorxiv.org/content/10.6...
www.biorxiv.org
May 7, 2026 at 5:09 AM
📢 EffectorGeneP is finally here! Stop missing small, single-exon or orphan genes from your favourite pathogen genome. Current tools only annotate 15%-78% of effector genes, EffectorGeneP finds 95% - including the large AvrSr26 family in stem rust. #Bioinformatics 📖 www.biorxiv.org/content/10.6...
Reposted by Juan （胡安）
Very excited to see our recent work on NRG1 organellar targeting now published!
It has been a pleasure working with Tarhan on this, combining synthetic biology/genetics with some incredible microscopy 🤝
www.science.org/doi/10.1126/...
It has been a pleasure working with Tarhan on this, combining synthetic biology/genetics with some incredible microscopy 🤝
www.science.org/doi/10.1126/...
A helper NLR channels organellar calcium to trigger plant immunity
Upon activation, plant nucleotide-binding leucine-rich repeat (NLR) immune receptors are known to assemble into oligomeric resistosomes that insert into the plasma membrane, forming calcium (Ca2+)–per...
www.science.org
May 1, 2026 at 4:22 PM
Very excited to see our recent work on NRG1 organellar targeting now published!
It has been a pleasure working with Tarhan on this, combining synthetic biology/genetics with some incredible microscopy 🤝
www.science.org/doi/10.1126/...
It has been a pleasure working with Tarhan on this, combining synthetic biology/genetics with some incredible microscopy 🤝
www.science.org/doi/10.1126/...
Reposted by Juan （胡安）
Big opportunities for researchers 🌍
We are investing nearly €400 million to help researchers share their work and collaborate with the best scientific teams across the EU.
The 2026 Marie Skłodowska-Curie Actions Postdoctoral Fellowships are now open.
More: link.europa.eu/PNxpxw
We are investing nearly €400 million to help researchers share their work and collaborate with the best scientific teams across the EU.
The 2026 Marie Skłodowska-Curie Actions Postdoctoral Fellowships are now open.
More: link.europa.eu/PNxpxw
April 9, 2026 at 9:58 AM
Big opportunities for researchers 🌍
We are investing nearly €400 million to help researchers share their work and collaborate with the best scientific teams across the EU.
The 2026 Marie Skłodowska-Curie Actions Postdoctoral Fellowships are now open.
More: link.europa.eu/PNxpxw
We are investing nearly €400 million to help researchers share their work and collaborate with the best scientific teams across the EU.
The 2026 Marie Skłodowska-Curie Actions Postdoctoral Fellowships are now open.
More: link.europa.eu/PNxpxw
Reposted by Juan （胡安）
Excited to share our preprint using Rhizobium rhizogenes AS109 for agroinfiltration, facilitating strong transient expression across non-model plants including sweet potato, mustard, Medicago and faba bean!
doi.org/10.64898/202...
1/7
doi.org/10.64898/202...
1/7
doi.org
April 23, 2026 at 8:59 AM
Excited to share our preprint using Rhizobium rhizogenes AS109 for agroinfiltration, facilitating strong transient expression across non-model plants including sweet potato, mustard, Medicago and faba bean!
doi.org/10.64898/202...
1/7
doi.org/10.64898/202...
1/7
Finally out! A follow-up to our Rhizobium rhizogenes story with @tolgaboz.bsky.social and Lida. We hope this work will make it easier to study many other plant species.
www.biorxiv.org/content/10.6...
www.biorxiv.org/content/10.6...
www.biorxiv.org
April 23, 2026 at 4:01 AM
Finally out! A follow-up to our Rhizobium rhizogenes story with @tolgaboz.bsky.social and Lida. We hope this work will make it easier to study many other plant species.
www.biorxiv.org/content/10.6...
www.biorxiv.org/content/10.6...
Reposted by Juan （胡安）
We are hiring! We’re excited to recruit a postdoc to our lab at UC Davis to work on plant immune engineering and single-cell analyses of plant pathogen interactions. Apply by June 1. Please repost. www.coakerlab.org/postdoctoral...
April 17, 2026 at 11:06 PM
We are hiring! We’re excited to recruit a postdoc to our lab at UC Davis to work on plant immune engineering and single-cell analyses of plant pathogen interactions. Apply by June 1. Please repost. www.coakerlab.org/postdoctoral...
Congratulations Mauricio! You and your work truly deserve it :)
As an emerging leader in plant innate immunity, we're thrilled to present Mauricio Contreras with a 2027 Early Career Research Award! Alongside advocating for Open Science and preprint review, Mauricio's "activation-and-release" and "NLR resurrection" models are already referenced worldwide.
April 15, 2026 at 1:38 PM
Congratulations Mauricio! You and your work truly deserve it :)
Reposted by Juan （胡安）
As an emerging leader in plant innate immunity, we're thrilled to present Mauricio Contreras with a 2027 Early Career Research Award! Alongside advocating for Open Science and preprint review, Mauricio's "activation-and-release" and "NLR resurrection" models are already referenced worldwide.
April 14, 2026 at 11:00 AM
As an emerging leader in plant innate immunity, we're thrilled to present Mauricio Contreras with a 2027 Early Career Research Award! Alongside advocating for Open Science and preprint review, Mauricio's "activation-and-release" and "NLR resurrection" models are already referenced worldwide.
Reposted by Juan （胡安）
Thrilled to share our paper now out in Nature Plants 🎉
We developed a genome-host association (GHA) approach to study pathogen adaptation directly from field metadata by using the originating host cultivar as phenotype.
www.nature.com/articles/s41...
We developed a genome-host association (GHA) approach to study pathogen adaptation directly from field metadata by using the originating host cultivar as phenotype.
www.nature.com/articles/s41...
Genome–host association mapping reveals wheat pathogen genes involved in host specialization - Nature Plants
This study introduces genome–host association (GHA), leveraging natural epidemics to map the genetic landscape of host adaptation in the pathogen Zymoseptoria tritici. Applied to 832 wheat fungal stra...
www.nature.com
April 15, 2026 at 9:31 AM
Thrilled to share our paper now out in Nature Plants 🎉
We developed a genome-host association (GHA) approach to study pathogen adaptation directly from field metadata by using the originating host cultivar as phenotype.
www.nature.com/articles/s41...
We developed a genome-host association (GHA) approach to study pathogen adaptation directly from field metadata by using the originating host cultivar as phenotype.
www.nature.com/articles/s41...
Reposted by Juan （胡安）
"Research is often described as ‘basic’, but there is nothing basic about it. The links between discovery-based research and downstream applications aren’t always clear at the outset. Although a translational output may require years to achieve"
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Advancing microbiology through foundational science - Nature Microbiology
Microorganisms have tremendous potential to impact humanity, but such revelations are only possible in the light of foundational, discovery-based microbiology research.
www.nature.com
April 9, 2026 at 7:47 AM
"Research is often described as ‘basic’, but there is nothing basic about it. The links between discovery-based research and downstream applications aren’t always clear at the outset. Although a translational output may require years to achieve"
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Reposted by Juan （胡安）
Reconstructing plant beneficial bacterial consortia by integrating dilution-to-extinction microbiome perturbation with genome-resolved synthetic ecology https://www.biorxiv.org/content/10.64898/2026.04.09.717421v1
April 11, 2026 at 4:19 AM
Reconstructing plant beneficial bacterial consortia by integrating dilution-to-extinction microbiome perturbation with genome-resolved synthetic ecology https://www.biorxiv.org/content/10.64898/2026.04.09.717421v1
Reposted by Juan （胡安）
Dear Conference Organizers,
Please for the love of all things, provide an easily printable agenda. These weird web interfaces to build your own and apps are just not it. I'm sure you could find better ways to spend our conference fees. Maybe on more coffee? #AcademicSky
Please for the love of all things, provide an easily printable agenda. These weird web interfaces to build your own and apps are just not it. I'm sure you could find better ways to spend our conference fees. Maybe on more coffee? #AcademicSky
a furry animal with yellow eyes is laying on a rock
ALT: a furry animal with yellow eyes is laying on a rock
media.tenor.com
April 9, 2026 at 1:27 PM
Dear Conference Organizers,
Please for the love of all things, provide an easily printable agenda. These weird web interfaces to build your own and apps are just not it. I'm sure you could find better ways to spend our conference fees. Maybe on more coffee? #AcademicSky
Please for the love of all things, provide an easily printable agenda. These weird web interfaces to build your own and apps are just not it. I'm sure you could find better ways to spend our conference fees. Maybe on more coffee? #AcademicSky
Reposted by Juan （胡安）
There is a lot of undescribed prokaryotic diversity in existing whole-genome metagenomic data!
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Unbinned contigs expand known diversity in the global microbiome - Nature Microbiology
Re-analysis of over 92,000 metagenomes reveals hundreds of thousands of previously undescribed Bacterial and Archaeal clades hidden in plain sight.
www.nature.com
April 6, 2026 at 3:36 PM
There is a lot of undescribed prokaryotic diversity in existing whole-genome metagenomic data!
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Reposted by Juan （胡安）
Super happy to share our new review about how bacteria adapt to plant environment over the years. It was a collaborative effort between the network #redplantmicro of researchers interested in molecular biology and plant microbe interactions.
How do evolutionary forces shape bacterial adaptation to the plant environment? 🌱🦠
Curious? Read our new review in @femsjournals.bsky.social Microbiology Reviews.
#PlantMicrobiome #MicrobialEvolution #HostMicrobeInteractions #Rhizosphere #Microbiome
🔗 doi.org/10.1093/fems...
Curious? Read our new review in @femsjournals.bsky.social Microbiology Reviews.
#PlantMicrobiome #MicrobialEvolution #HostMicrobeInteractions #Rhizosphere #Microbiome
🔗 doi.org/10.1093/fems...
March 2, 2026 at 6:50 PM
Super happy to share our new review about how bacteria adapt to plant environment over the years. It was a collaborative effort between the network #redplantmicro of researchers interested in molecular biology and plant microbe interactions.