@phyTorres

Postdoctoral researcher at Wageningen University | Plant pathogens | (epi)Genomics | Evolution | he/him

 Wageningen, Nederland
Joined January 2011
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Im so happy to share this part of my PhD thesis just right now in ⁦@NatureComms⁩. Check it out! Implications of the 3D chromatin organization for genome evolution in a fungal plant pathogen Special thanks to ⁦@MFSeidl⁩ and ⁦@Team_Thomma⁩ nature.com/articles/s41467-0…
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David T retweeted
Yuan He@YuanHeJHUSep 22
A big week for the lab! Two new papers on how cells repair DNA double-strand breaks: one on getting NHEJ started in chromatin, one on processing the ends before ligation. Years of work by a fantastic team.
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Last talk today at #PPRM2026 by Moutassem Omary (Zipfel lab) illustrates the modularity and flexibility of PRR signalling: after redundant receptors, peptides and antipeptides, here come the secreted LRR domains that can basically replace BAK1 and interfere with various pathways.
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Landraces and wild species hold genetic diversity that could be key to developing new potato varieties, which are needed to help farmers adapt to climate change and other challenges. 🥔 Learn more on #NationalPotatoDay in this 2019 issue of Science: scim.ag/4xab4hA
For thousands of years, Andean farmers have cultivated colorful landraces of domesticated potatoes, such as lioness, tunica, and tarmeña shown in this arrangement. Landraces and wild species hold genetic diversity that could be key to developing new potato varieties, which are needed to help farmers adapt to climate change and other challenges. Photo: Gustavo Ramirez

ALT For thousands of years, Andean farmers have cultivated colorful landraces of domesticated potatoes, such as lioness, tunica, and tarmeña shown in this arrangement. Landraces and wild species hold genetic diversity that could be key to developing new potato varieties, which are needed to help farmers adapt to climate change and other challenges. Photo: Gustavo Ramirez

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New Publication: Tangerine: A new family of Starships from lichen-forming fungi (2026) tsl.ac.uk/publications/17348…

The Sainsbury Laboratory | Tangerine: A new family of Starships from…

tsl.ac.uk
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AF-Cluster recovers alternative protein conformations through MSA subsampling, but seq similarity isn't a good conformational signal. Introducing SF-Cluster, which instead guides MSA selection using energetic frustration to more reliably recover alternative conformations! 🔥 📜: arxiv.org/abs/2607.00180 🤗: huggingface.co/ChatterjeeLab… 🧵👇🏾
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AlphaFold 3.0.4 github.com/google-deepmind/a… - AlphaFold 3 now runs on CPU-only machines! - AlphaFold 3 now runs on Apple Silicon (mps backend, 3x faster than CPU-only)

Release AlphaFold v3.0.4 · google-deepmind/alphafold3

Version 3.0.4 makes AlphaFold 3 runnable on CPU-only machines and on Apple Silicon. Moreover, there are some performance improvements and small bug fixes. We thank everyone who reported issues, pro...

github.com
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Deyang Xu@DeyangXu_CNJun 8
Genomic analysis of 3,330 accessions provides insights into the evolutionary history and self-incompatibility locus of the Brassica A genome @NatureGenet nature.com/articles/s41588-0…

Genomic analysis of 3,330 accessions provides insights into the evolutionary history and self-inc...

Nature Genetics - Pan-genomic analyses shed light on the evolutionary history of the Brassica A subgenome and identify a unique barcode pattern of transposable elements that underpin the Brassica...

nature.com
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This is very awesome. Open source AlphaFold. From @ChanZuckerberg nature.com/articles/d41586-0…

Move over, AlphaFold: open-source model predicts shape of 1 billion proteins

Nature - An open-source atlas generated by an AI tool called ESMFold2 vastly increases the known protein universe.

nature.com
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Thrilled to see this finally out!! Our new work suggests #Starships helped #Colletotrichum acquire the genes needed to infect lupin. A glimpse into how fungal pathogens emerge through horizontal transfer and genome reshaping. biorxiv.org/content/10.64898… #Fungi #Genomics
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🚨 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. biorxiv.org/content/10.64898…
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Fantin Mesny@f_mesnyApr 30
🎉 📰 Very happy to share the journal publication of our manuscript "Plant-associated fungi co-opt ancient antimicrobials for host manipulation"! #ScienceAdvancesResearch @ScienceMagazine @Team_Thomma science.org/doi/10.1126/scia…

Plant-associated fungi co-opt ancient antimicrobials for host manipulation

Fungal effectors may have evolved from ancient antimicrobials, shaping plant microbiota and immunity during infection.

science.org
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nature
@NatureFeb 24
Nature research paper: Ancient co-option of LTR retrotransposons as yeast centromeres go.nature.com/404vd9X

Ancient co-option of LTR retrotransposons as yeast centromeres

Nature - Evolutionarily related ‘proto-point’ centromeres providing resolution to the evolutionary origins of point centromeres are identified in yeast, and comparison shows they...

nature.com
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Vorholt Lab re-created endosymbiosis in the lab: injected bacteria into a fungus and evolved a heritable partnership. Evolution, fast-forwarded. doi.org/10.1038/s41586-024-0…

Inducing novel endosymbioses by implanting bacteria in fungi

Nature - A study presents an approach to establish and track a new endosymbiotic partnership by implanting bacteria in a non-host fungus and shows that stable inheritance of the implanted bacteria...

nature.com
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Kobe Lab@Kobe_Lab_Feb 6
Check out our recent preprint on the structure of a non C-JID TNL resistosome from flax. We are very proud of the persistence of Natsumi who got this long running project over the line and a congratulations to all involved. Check it out... doi.org/10.64898/2026.02.03.…
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Genome contamination may lead to an overestimation of horizontal gene transfer inferences | Nature Communications nature.com/articles/s41467-0…

Genome contamination may lead to an overestimation of horizontal gene transfer inferences

Nature Communications - Genome contamination may lead to an overestimation of horizontal gene transfer inferences

nature.com
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📢 Three new #bioRxiv preprints from our team on holocentric chromosomes. Together, they connect centromere repeat evolution, karyotype dynamics, and meiotic recombination outcomes, revealing how holocentric genomes evolve and function. 🧬👇
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Big congrats to PhD @Ken_M_Mugambi for pulling together this amazing piece of work 🫡 This study details the genome biology of the largest #AMF genome (G. margarita) and its intricate links with its🦠 endosymbiont and 🌱hosts 😀 biorxiv.org/content/10.64898…

The 3D Genome of Gigaspora margarita Unveils Stable Chromatin and Nucleolar Organization and...

Arbuscular mycorrhizal fungi (AMF) are widespread plant symbionts that enhance nutrient acquisition and influence ecosystem productivity. Previous chromosome-level assemblies of a model species...

biorxiv.org
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Join us in Norwich this July for the TSL Summer Conference in Plant-Microbe Interactions! ☀️🌱🧬 Discuss the latest approaches & discoveries in plant health with international keynote and local speakers. APPLY by 30 March '26 ⬇️ Click link for more info tsl.ac.uk/tsl-summer-conf-20…

TSL Summer Conference in Plant-Microbe Interactions, 20th – 31st July…

* Applications have now closed* Inviting Early Career Researchers to join international experts in discussing the latest approaches and discoveries in…

tsl.ac.uk
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New online! Interplay between cohesin and RNA polymerase II in regulating chromatin interactions and gene transcription dlvr.it/TQKgsH
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David T retweeted
Alice Ting
@aliceytingJan 8
Can we design mutations that predictably bias proteins towards desired conformational states? Today in @ScienceMagazine, we introduce Conformational Biasing (CB), a simple and scalable computational method that uses contrastive scoring by inverse folding models to identify conformation-biasing mutations. science.org/doi/10.1126/scie…
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