Juan （胡安）
@angiopteris.bsky.social
Juan Carlos Lopez-Agudelo
PhD student at Academia Sinica, Taiwan
Agrobacteria | Plant-pathogen interactions | Bacterial genetics
Never stop exploring 🌱
PhD student at Academia Sinica, Taiwan
Agrobacteria | Plant-pathogen interactions | Bacterial genetics
Never stop exploring 🌱
Pinned
Juan （胡安）
@angiopteris.bsky.social
· Apr 14
Last Friday we celebrated at Chih-Hang’s lab the publication of my first paper. He even baked two RUBY cakes! (The 火龍果 color just did the trick).
Thanks to everyone who supported me during this journey! Feels great to finally become a scientific author. Finally up at PBJ:
doi.org/10.1111/pbi....
Thanks to everyone who supported me during this journey! Feels great to finally become a scientific author. Finally up at PBJ:
doi.org/10.1111/pbi....
Reposted by Juan （胡安）
This is first paper from a new line of research in my lab, with more to come soon. If interested in PDPs I highly recommend this @baym.lol paper www.nature.com/articles/s41... and this classic from Matti Jalasvuori royalsocietypublishing.org/doi/10.1098/...
Diverse and abundant phages exploit conjugative plasmids - Nature Communications
Some phages use plasmid-encoded conjugation proteins as receptors to infect their bacterial hosts, making their host range dependent on horizontal transfer of the plasmid. Here, the authors present a method for identification of new plasmid-dependent phages, and find that they are common and abundant in wastewater and their genetic diversity is largely unexplored.
www.nature.com
October 9, 2025 at 10:07 AM
This is first paper from a new line of research in my lab, with more to come soon. If interested in PDPs I highly recommend this @baym.lol paper www.nature.com/articles/s41... and this classic from Matti Jalasvuori royalsocietypublishing.org/doi/10.1098/...
Reposted by Juan （胡安）
A first dive in fern x pathogen interaction! More to come!
Congratulations @baptistebio.bsky.social @jacquet-chris.bsky.social et al.!
Congratulations @baptistebio.bsky.social @jacquet-chris.bsky.social et al.!
Want to see ferns under attack and how they respond to pathogens? Check out our latest paper!
doi.org/10.1186/s129...
Congrats on this huge team effort to @baptistebio.bsky.social @madeleinebaker.bsky.social @kellerjeanphd.bsky.social @maximebonhomme.bsky.social @pierremarcdelaux.bsky.social
doi.org/10.1186/s129...
Congrats on this huge team effort to @baptistebio.bsky.social @madeleinebaker.bsky.social @kellerjeanphd.bsky.social @maximebonhomme.bsky.social @pierremarcdelaux.bsky.social
October 9, 2025 at 3:47 PM
A first dive in fern x pathogen interaction! More to come!
Congratulations @baptistebio.bsky.social @jacquet-chris.bsky.social et al.!
Congratulations @baptistebio.bsky.social @jacquet-chris.bsky.social et al.!
Reposted by Juan （胡安）
Thrilled to share that our TEtrimmer paper has just been published in Nature Communications! A big thank you to all collaborators — the article is now online ;)
www.nature.com/articles/s41...
www.nature.com/articles/s41...
TEtrimmer: a tool to automate the manual curation of transposable elements - Nature Communications
Transposons are repetitive DNA sequences that are hard to identify and map accurately. TEtrimmer automates key manual steps, enabling faster and more reliable annotation of transposable elements in any genome.
www.nature.com
September 25, 2025 at 12:32 PM
Thrilled to share that our TEtrimmer paper has just been published in Nature Communications! A big thank you to all collaborators — the article is now online ;)
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Reposted by Juan （胡安）
Very important paper and resource. Bryophyte genomes expanded by one order of magnitude. 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
September 22, 2025 at 11:23 AM
Very important paper and resource. Bryophyte genomes expanded by one order of magnitude. www.nature.com/articles/s41...
Reposted by Juan （胡安）
For those recalling the awesome session on ecology and evolution of zoonoses at GRC MPB 2023, or those who wish they were there, these authors and topic were on Rosie's and my wish list.
Ancient pathogen genomes have much to say.
www.cell.com/cell/fulltex...
Ancient pathogen genomes have much to say.
www.cell.com/cell/fulltex...
Bronze Age Yersinia pestis genome from sheep sheds light on hosts and evolution of a prehistoric plague lineage
A Yersinia pestis genome from a Bronze Age domesticated sheep provides insight into
the host range, evolution, and possible transmission scenarios of an ancient lineage
of the plague-causing bacteria,...
www.cell.com
August 13, 2025 at 7:42 PM
For those recalling the awesome session on ecology and evolution of zoonoses at GRC MPB 2023, or those who wish they were there, these authors and topic were on Rosie's and my wish list.
Ancient pathogen genomes have much to say.
www.cell.com/cell/fulltex...
Ancient pathogen genomes have much to say.
www.cell.com/cell/fulltex...
Reposted by Juan （胡安）
This looks like an amazing tool
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
Phyling: phylogenetic inference from annotated genomes
Phyling is a fast, scalable, and user-friendly tool supporting phylogenomic reconstruction of species phylogenies directly from protein-encoded genomic data. It identifies orthologous genes by searchi...
www.biorxiv.org
August 6, 2025 at 8:50 PM
This looks like an amazing tool
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
Reposted by Juan （胡安）
A root-specific NLR network mediates immune signaling of resistance genes against plant parasitic nematodes (Daniel Lüdke , Toshiyuki Sakai , Jiorgos Kourelis , et al) doi.org/10.1093/plce... #PlantScience
August 1, 2025 at 4:45 PM
A root-specific NLR network mediates immune signaling of resistance genes against plant parasitic nematodes (Daniel Lüdke , Toshiyuki Sakai , Jiorgos Kourelis , et al) doi.org/10.1093/plce... #PlantScience
Reposted by Juan （胡安）
I’m very grateful and excited to start our ARIA-funded project on redesigning plant immunity!
NEWS - Radical approach to improve plant immunity secures funding for Programmable Plants initiative
@philcarella.bsky.social’s group has been awarded ARIA funding for an ambitious research programme which seeks to protect major crops from disease.
www.jic.ac.uk/news/radical...
@philcarella.bsky.social’s group has been awarded ARIA funding for an ambitious research programme which seeks to protect major crops from disease.
www.jic.ac.uk/news/radical...
July 23, 2025 at 1:38 PM
I’m very grateful and excited to start our ARIA-funded project on redesigning plant immunity!
Reposted by Juan （胡安）
Conserved Phytophthora effector protease cleaves BAK1 to suppress defense. www.nature.com/articles/s41...
A conserved Phytophthora apoplastic trypsin-like serine protease targets the receptor-like kinase BAK1 to dampen plant immunity - Nature Plants
Phytophthora secretes a conserved trypsin-like serine protease, PsTry1, that suppresses apoplastic immunity by cleaving the extracellular domain of the co-receptor BAK1, revealing a novel mechanism by...
www.nature.com
July 23, 2025 at 4:25 PM
Conserved Phytophthora effector protease cleaves BAK1 to suppress defense. www.nature.com/articles/s41...
It fills me with pride listening to Yi-Feng Chen talking about his research at #2025ISMPMI. I am happy to see the fruits of his effort. Congratulations!
July 17, 2025 at 3:48 PM
It fills me with pride listening to Yi-Feng Chen talking about his research at #2025ISMPMI. I am happy to see the fruits of his effort. Congratulations!
Reposted by Juan （胡安）
Plz RT. We are looking for a postdoc to join our collborative project on AI-guided bioengineering of plant immune receptors @tolgaboz.bsky.social and @jiorgoskourelis.bsky.social labs: www.jobs.ac.uk/job/DNV032/r...
Research Associate in Programmable Plant Immunity at Imperial College London
Apply for the Research Associate in Programmable Plant Immunity role on jobs.ac.uk, the top job board for academic positions in higher education. View details and apply now.
www.jobs.ac.uk
July 7, 2025 at 3:01 PM
Plz RT. We are looking for a postdoc to join our collborative project on AI-guided bioengineering of plant immune receptors @tolgaboz.bsky.social and @jiorgoskourelis.bsky.social labs: www.jobs.ac.uk/job/DNV032/r...
Very happy to finally present my poster to a very interested audience! It’s always a pleasure to discuss about agro, commonly seen as a tool, but still a (cool) plant pathogen. Still at #2025ISMPMI, so if you are interested in my work, don’t be shy to say hi!
July 17, 2025 at 7:28 AM
Very happy to finally present my poster to a very interested audience! It’s always a pleasure to discuss about agro, commonly seen as a tool, but still a (cool) plant pathogen. Still at #2025ISMPMI, so if you are interested in my work, don’t be shy to say hi!
It was an amazing sciences day at #2025ISMPMI!
Right after the “Population, biology, ecology and genomics” session, I had the opportunity to have lunch and discuss about this topic with the co-chair @honour.bsky.social
Right after the “Population, biology, ecology and genomics” session, I had the opportunity to have lunch and discuss about this topic with the co-chair @honour.bsky.social
July 14, 2025 at 9:19 PM
It was an amazing sciences day at #2025ISMPMI!
Right after the “Population, biology, ecology and genomics” session, I had the opportunity to have lunch and discuss about this topic with the co-chair @honour.bsky.social
Right after the “Population, biology, ecology and genomics” session, I had the opportunity to have lunch and discuss about this topic with the co-chair @honour.bsky.social
Reposted by Juan （胡安）
String manipulation is a critical daily task for bioinformaticians.
Here is a cheatsheet using stringr: rstudio.github.io/cheatsheets...
I probably use stringr::str_replace() once every other day...
to clean up metadata (of course!) #rstats
Here is a cheatsheet using stringr: rstudio.github.io/cheatsheets...
I probably use stringr::str_replace() once every other day...
to clean up metadata (of course!) #rstats
July 14, 2025 at 1:45 PM
String manipulation is a critical daily task for bioinformaticians.
Here is a cheatsheet using stringr: rstudio.github.io/cheatsheets...
I probably use stringr::str_replace() once every other day...
to clean up metadata (of course!) #rstats
Here is a cheatsheet using stringr: rstudio.github.io/cheatsheets...
I probably use stringr::str_replace() once every other day...
to clean up metadata (of course!) #rstats
Just arrived to #2025ISMPMI!
I am very excited to learn a lot about plant-pathogen interactions from all of you!
If you want to learn more about A4 and our current progress, feel free to visit me at P-211 on Wednesday!
I am very excited to learn a lot about plant-pathogen interactions from all of you!
If you want to learn more about A4 and our current progress, feel free to visit me at P-211 on Wednesday!
July 13, 2025 at 2:04 PM
Just arrived to #2025ISMPMI!
I am very excited to learn a lot about plant-pathogen interactions from all of you!
If you want to learn more about A4 and our current progress, feel free to visit me at P-211 on Wednesday!
I am very excited to learn a lot about plant-pathogen interactions from all of you!
If you want to learn more about A4 and our current progress, feel free to visit me at P-211 on Wednesday!
Reposted by Juan （胡安）
Thrilled to share our latest preprint! This work started during my PhD and was finished together with @jmadhuprakash.bsky.social. We found a Phytophthora infestans L-shaped effector that bridges a host TOL protein to activated NLRs to suppress immunity!
www.biorxiv.org/content/10.1...
1/15
www.biorxiv.org/content/10.1...
1/15
July 9, 2025 at 1:03 PM
Thrilled to share our latest preprint! This work started during my PhD and was finished together with @jmadhuprakash.bsky.social. We found a Phytophthora infestans L-shaped effector that bridges a host TOL protein to activated NLRs to suppress immunity!
www.biorxiv.org/content/10.1...
1/15
www.biorxiv.org/content/10.1...
1/15
Reposted by Juan （胡安）
Cell-type-specific execution of effector-triggered immunity
Our new preprint is online, 1 July⬇️
With @himanshuchhillar.bsky.social @leonardojo.bsky.social Amey Redkar @kaisakajala.bsky.social @jonathandgjones.bsky.social
For early readers & community feedback🙏🏼
#openscience @erc.europa.eu
Our new preprint is online, 1 July⬇️
With @himanshuchhillar.bsky.social @leonardojo.bsky.social Amey Redkar @kaisakajala.bsky.social @jonathandgjones.bsky.social
For early readers & community feedback🙏🏼
#openscience @erc.europa.eu
Cell-type-specific execution of effector-triggered immunity https://www.biorxiv.org/content/10.1101/2025.06.28.662111v1
July 1, 2025 at 8:26 PM
Cell-type-specific execution of effector-triggered immunity
Our new preprint is online, 1 July⬇️
With @himanshuchhillar.bsky.social @leonardojo.bsky.social Amey Redkar @kaisakajala.bsky.social @jonathandgjones.bsky.social
For early readers & community feedback🙏🏼
#openscience @erc.europa.eu
Our new preprint is online, 1 July⬇️
With @himanshuchhillar.bsky.social @leonardojo.bsky.social Amey Redkar @kaisakajala.bsky.social @jonathandgjones.bsky.social
For early readers & community feedback🙏🏼
#openscience @erc.europa.eu
Reposted by Juan （胡安）
So, has this reached us yet? Yes, it did. I did a quick #rstats analysis of the literature in ecology. 📊
🔗 See my new blog post: www.pieceofk.fr/the-rise-of-...
🔗 See my new blog post: www.pieceofk.fr/the-rise-of-...
July 8, 2025 at 9:37 AM
So, has this reached us yet? Yes, it did. I did a quick #rstats analysis of the literature in ecology. 📊
🔗 See my new blog post: www.pieceofk.fr/the-rise-of-...
🔗 See my new blog post: www.pieceofk.fr/the-rise-of-...
Reposted by Juan （胡安）
This is textbook cell biology material by chin-hang Wu and colleagues . Check it out 👇 #plantsci #plantpath #immunology #NLRbiology www.biorxiv.org/content/10.1...
July 5, 2025 at 8:51 AM
This is textbook cell biology material by chin-hang Wu and colleagues . Check it out 👇 #plantsci #plantpath #immunology #NLRbiology www.biorxiv.org/content/10.1...
Reposted by Juan （胡安）
Massive #NLRbiology paper drop by Yi-Feng @YiFeng_eYFP Chih-Hang @AdamWu9527 and colleagues 👏
"Single-cell-resolved calcium and organelle dynamics in resistosome-mediated cell death."
doi.org/10.1101/2025...
"Single-cell-resolved calcium and organelle dynamics in resistosome-mediated cell death."
doi.org/10.1101/2025...
July 1, 2025 at 5:05 PM
Massive #NLRbiology paper drop by Yi-Feng @YiFeng_eYFP Chih-Hang @AdamWu9527 and colleagues 👏
"Single-cell-resolved calcium and organelle dynamics in resistosome-mediated cell death."
doi.org/10.1101/2025...
"Single-cell-resolved calcium and organelle dynamics in resistosome-mediated cell death."
doi.org/10.1101/2025...
Reposted by Juan （胡安）
📜 Exploring the formation and permeability of plasmodesmata in the liverwort, Marchantia polymorpha
🧑🔬 Chia-Yun Hsu, Chia-Hsuan Hsu, Hui-Yu Chang, Kuan-Ju Lu
📔 @plantcellphysiol.bsky.social
🔗 academic.oup.com/pcp/article/...
#️⃣ #PlantScience #PlantEvoDevo #Marchantia #Plasmodesmata
🧑🔬 Chia-Yun Hsu, Chia-Hsuan Hsu, Hui-Yu Chang, Kuan-Ju Lu
📔 @plantcellphysiol.bsky.social
🔗 academic.oup.com/pcp/article/...
#️⃣ #PlantScience #PlantEvoDevo #Marchantia #Plasmodesmata
Exploring the formation and permeability of plasmodesmata in the liverwort, Marchantia polymorpha
Abstract. Plasmodesmata are cell-wall-embedded channels that evolved in the common ancestor of land plants to increase cell-to-cell communication. Whether
academic.oup.com
April 28, 2025 at 7:25 AM
📜 Exploring the formation and permeability of plasmodesmata in the liverwort, Marchantia polymorpha
🧑🔬 Chia-Yun Hsu, Chia-Hsuan Hsu, Hui-Yu Chang, Kuan-Ju Lu
📔 @plantcellphysiol.bsky.social
🔗 academic.oup.com/pcp/article/...
#️⃣ #PlantScience #PlantEvoDevo #Marchantia #Plasmodesmata
🧑🔬 Chia-Yun Hsu, Chia-Hsuan Hsu, Hui-Yu Chang, Kuan-Ju Lu
📔 @plantcellphysiol.bsky.social
🔗 academic.oup.com/pcp/article/...
#️⃣ #PlantScience #PlantEvoDevo #Marchantia #Plasmodesmata
Last Friday we celebrated at Chih-Hang’s lab the publication of my first paper. He even baked two RUBY cakes! (The 火龍果 color just did the trick).
Thanks to everyone who supported me during this journey! Feels great to finally become a scientific author. Finally up at PBJ:
doi.org/10.1111/pbi....
Thanks to everyone who supported me during this journey! Feels great to finally become a scientific author. Finally up at PBJ:
doi.org/10.1111/pbi....
April 14, 2025 at 12:50 PM
Last Friday we celebrated at Chih-Hang’s lab the publication of my first paper. He even baked two RUBY cakes! (The 火龍果 color just did the trick).
Thanks to everyone who supported me during this journey! Feels great to finally become a scientific author. Finally up at PBJ:
doi.org/10.1111/pbi....
Thanks to everyone who supported me during this journey! Feels great to finally become a scientific author. Finally up at PBJ:
doi.org/10.1111/pbi....
Very nice work in identifying a natural Pseudomonas pathogen in Marchantia. Excited to know more about the diversity of Marchantia pathogens!
Conserved effectors underpin the virulence of liverwort-isolated Pseudomonas in divergent plants
Very happy to share the published version of our work on natural Marchantia-Pseudomonas interactions.
Out now in Current Biology: www.cell.com/current-biol...
Very happy to share the published version of our work on natural Marchantia-Pseudomonas interactions.
Out now in Current Biology: www.cell.com/current-biol...
Conserved effectors underpin the virulence of liverwort-isolated Pseudomonas in divergent plants
Robinson et al. identify pathogenic Pseudomonas viridiflava in wild Marchantia polymorpha
liverworts and interrogate the mechanisms enabling virulence in non-flowering and
flowering plants. Their resu...
www.cell.com
April 2, 2025 at 3:13 AM
Very nice work in identifying a natural Pseudomonas pathogen in Marchantia. Excited to know more about the diversity of Marchantia pathogens!
Reposted by Juan （胡安）
OUT NOW: Inducible transposon mutagenesis identifies bacterial fitness determinants during infection in mice
#microsky 🧪
www.nature.com/articles/s41...
#microsky 🧪
www.nature.com/articles/s41...
Inducible transposon mutagenesis identifies bacterial fitness determinants during infection in mice - Nature Microbiology
InducTn-seq, a method for inducible mutagenesis followed by transposon insertion site sequencing, enables temporal control of transposition to bypass population bottlenecks and enable the quantificati...
www.nature.com
March 27, 2025 at 4:35 PM
OUT NOW: Inducible transposon mutagenesis identifies bacterial fitness determinants during infection in mice
#microsky 🧪
www.nature.com/articles/s41...
#microsky 🧪
www.nature.com/articles/s41...
Reposted by Juan （胡安）
Functional genomic perspectives on plant terrestrialization
@cp-trendsgenetics.bsky.social from Jan de Vries
www.cell.com/trends/genet...
@cp-trendsgenetics.bsky.social from Jan de Vries
www.cell.com/trends/genet...
March 28, 2025 at 8:51 AM
Functional genomic perspectives on plant terrestrialization
@cp-trendsgenetics.bsky.social from Jan de Vries
www.cell.com/trends/genet...
@cp-trendsgenetics.bsky.social from Jan de Vries
www.cell.com/trends/genet...