Sebastian Soyk
@sebastiansoyk.bsky.social
Developmental geneticist working on stem cells and plant architecture at the University of Lausanne
Pinned
New preprint from the lab on @biorxivpreprint.bsky.social! We show how SEPALLATA MADS-box genes in tomato functionally diverged to regulate inflorescence and floral organ development while maintaining redundant functions in conferring floral meristem identity.
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
Reposted by Sebastian Soyk
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...
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...
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...
www.nature.com
November 26, 2025 at 6:00 AM
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...
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...
Reposted by Sebastian Soyk
Es stehen erscheinende Tage für eine moderne, wissenschaftsbasierte Regulierung von Neuen Genomischen Techniken wie #CRISPR & Co. in der EU an.
Worum es geht und was damit zu erreichen ist, haben wir 👇 nochmal zusammengefasst.
#GiveGenesAChance
Worum es geht und was damit zu erreichen ist, haben wir 👇 nochmal zusammengefasst.
#GiveGenesAChance
🇪🇺 Warum sich eine moderne, sachgerechte Regulierung von NGT lohnt 🌱🧬
Die Neuen Genomischen Techniken (NGT) bieten ein echtes Potenzial für eine nachhaltige, klimaresiliente & effiziente Landwirtschaft. Wissenschaftliche Studien liefern keine belastbaren Hinweise auf Gefahren, während gleichzeitig/
Die Neuen Genomischen Techniken (NGT) bieten ein echtes Potenzial für eine nachhaltige, klimaresiliente & effiziente Landwirtschaft. Wissenschaftliche Studien liefern keine belastbaren Hinweise auf Gefahren, während gleichzeitig/
November 26, 2025 at 8:47 AM
Es stehen erscheinende Tage für eine moderne, wissenschaftsbasierte Regulierung von Neuen Genomischen Techniken wie #CRISPR & Co. in der EU an.
Worum es geht und was damit zu erreichen ist, haben wir 👇 nochmal zusammengefasst.
#GiveGenesAChance
Worum es geht und was damit zu erreichen ist, haben wir 👇 nochmal zusammengefasst.
#GiveGenesAChance
Reposted by Sebastian Soyk
Thanks @somssich.bsky.social for a truly fantastic lecture!
Six months after leaving Academia, I am back giving a lecture on #PlantScience History as Guest Speaker of the @snp2prot.bsky.social Program @unihalle.bsky.social.
Thank you @carolindelker.bsky.social for inviting & hosting me.
It was a pleasure to talk about Arabidopsis History to the students. 🙂
Thank you @carolindelker.bsky.social for inviting & hosting me.
It was a pleasure to talk about Arabidopsis History to the students. 🙂
November 26, 2025 at 11:15 AM
Thanks @somssich.bsky.social for a truly fantastic lecture!
Reposted by Sebastian Soyk
Very happy to share that this paper is now online on @currentbiology.bsky.social !! 🥳🧪 Check out the final published verion here: www.cell.com/current-biol...
#mimuluspropaganda
#mimuluspropaganda
November 24, 2025 at 4:25 PM
Very happy to share that this paper is now online on @currentbiology.bsky.social !! 🥳🧪 Check out the final published verion here: www.cell.com/current-biol...
#mimuluspropaganda
#mimuluspropaganda
Reposted by Sebastian Soyk
Thrilled to be among the recipients of the SNSF Starting Grants! Congrats to all the incredible researchers funded this year. Can’t wait to keep exploring how plants grow, sense, and respond to mechanical forces. Plants and biophysics rock!🌱⚛️
✨ Searching for extraterrestrial life or combating speech disorders: The SNSF is awarding #SNSFStartingGrants to 41 outstanding researchers. They will receive a maximum of CHF 1 million to lead a project with their own #research team at a Swiss university. 🚀
ℹ️ sohub.io/aq26
ℹ️ sohub.io/aq26
October 31, 2025 at 10:57 PM
Thrilled to be among the recipients of the SNSF Starting Grants! Congrats to all the incredible researchers funded this year. Can’t wait to keep exploring how plants grow, sense, and respond to mechanical forces. Plants and biophysics rock!🌱⚛️
New preprint from the lab on @biorxivpreprint.bsky.social! We show how SEPALLATA MADS-box genes in tomato functionally diverged to regulate inflorescence and floral organ development while maintaining redundant functions in conferring floral meristem identity.
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
November 21, 2025 at 8:30 AM
New preprint from the lab on @biorxivpreprint.bsky.social! We show how SEPALLATA MADS-box genes in tomato functionally diverged to regulate inflorescence and floral organ development while maintaining redundant functions in conferring floral meristem identity.
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
Reposted by Sebastian Soyk
CRISPR-Cas–mediated heritable chromosome fusions in Arabidopsis | Science www.science.org/doi/10.1126/...
Very nice work from Holger Puchta & colleagues
Very nice work from Holger Puchta & colleagues
CRISPR-Cas–mediated heritable chromosome fusions in Arabidopsis
The genome of Arabidopsis thaliana consists of 10 chromosomes. By inducing CRISPR-Cas–mediated breaks at subcentromeric and subtelomeric sequences, we fused entire chromosome arms, obtaining two eight...
www.science.org
November 20, 2025 at 8:47 PM
CRISPR-Cas–mediated heritable chromosome fusions in Arabidopsis | Science www.science.org/doi/10.1126/...
Very nice work from Holger Puchta & colleagues
Very nice work from Holger Puchta & colleagues
Reposted by Sebastian Soyk
🧪 Last chance! Registration for the #RigiWorkshop 2026 closes next week! Our guest speakers include @dudinlab.bsky.social, @michaelraissig.bsky.social, @annikaguse.bsky.social, @gautamdey.bsky.social & @jandevries.bsky.social. More details here 👉 biol.scnat.ch/rigiworkshop26
Only 1️⃣ month left to apply for the #RigiWorkshop 2026! Are you a #PhD student or postdoc in #biology? Come join us for a 3-days interdisciplinary #workshop in the Swiss Alps 👉 biol.scnat.ch/rigiworkshop26
October 8, 2025 at 7:00 AM
🧪 Last chance! Registration for the #RigiWorkshop 2026 closes next week! Our guest speakers include @dudinlab.bsky.social, @michaelraissig.bsky.social, @annikaguse.bsky.social, @gautamdey.bsky.social & @jandevries.bsky.social. More details here 👉 biol.scnat.ch/rigiworkshop26
Reposted by Sebastian Soyk
Our paper comparing stomata of the three annual Brachypodium species is out 🌾
bmcplantbiol.biomedcentral.com/articles/10....
A great collaborative effort between @lbmountain.bsky.social, & our friends at University of Silesia (Alexander Betekhtin and Anna Milewska-Hendel). Funded by @dfg.de and NAWA
bmcplantbiol.biomedcentral.com/articles/10....
A great collaborative effort between @lbmountain.bsky.social, & our friends at University of Silesia (Alexander Betekhtin and Anna Milewska-Hendel). Funded by @dfg.de and NAWA
October 10, 2025 at 2:53 PM
Our paper comparing stomata of the three annual Brachypodium species is out 🌾
bmcplantbiol.biomedcentral.com/articles/10....
A great collaborative effort between @lbmountain.bsky.social, & our friends at University of Silesia (Alexander Betekhtin and Anna Milewska-Hendel). Funded by @dfg.de and NAWA
bmcplantbiol.biomedcentral.com/articles/10....
A great collaborative effort between @lbmountain.bsky.social, & our friends at University of Silesia (Alexander Betekhtin and Anna Milewska-Hendel). Funded by @dfg.de and NAWA
Reposted by Sebastian Soyk
Our article "Guns in Rosettes: The Arabidopsis chemical weapons arsenal" is finally published @plantphys.bsky.social!
You can download the #OpenAccess PDF here:
doi.org/10.1093/plph...
But real connoisseurs of #AntimicrobialCompounds will want to get the vinyl boxset: #PlantScience #PlantImmunity
You can download the #OpenAccess PDF here:
doi.org/10.1093/plph...
But real connoisseurs of #AntimicrobialCompounds will want to get the vinyl boxset: #PlantScience #PlantImmunity
October 9, 2025 at 7:58 AM
Our article "Guns in Rosettes: The Arabidopsis chemical weapons arsenal" is finally published @plantphys.bsky.social!
You can download the #OpenAccess PDF here:
doi.org/10.1093/plph...
But real connoisseurs of #AntimicrobialCompounds will want to get the vinyl boxset: #PlantScience #PlantImmunity
You can download the #OpenAccess PDF here:
doi.org/10.1093/plph...
But real connoisseurs of #AntimicrobialCompounds will want to get the vinyl boxset: #PlantScience #PlantImmunity
Reposted by Sebastian Soyk
Congrats, Joe Ecker @salkinstitute.bsky.social, to receiving the McClintock Prize! Joe has been a visionary leader of the field of genetics and genomics – not only for plants – for decades
www.salk.edu/news-release...
www.salk.edu/news-release...
October 10, 2025 at 5:34 PM
Congrats, Joe Ecker @salkinstitute.bsky.social, to receiving the McClintock Prize! Joe has been a visionary leader of the field of genetics and genomics – not only for plants – for decades
www.salk.edu/news-release...
www.salk.edu/news-release...
Reposted by Sebastian Soyk
This discovery traces back to the spring of 2018, when I was a postdoc in nikogeldner.bsky.social 's lab. After shifting Arabidopsis seedlings from solid to liquid culture, I observed that the root commensal bacterium CHA0 rapidly colonized Casparian strip–defective mutants.
Using precise spatial and temporal analysis, researchers in Science provide insight into how bacteria around the root interact both with the plant and with each other.
Learn more in this week's issue: https://scim.ag/3WgNajk
Learn more in this week's issue: https://scim.ag/3WgNajk
October 8, 2025 at 12:26 PM
This discovery traces back to the spring of 2018, when I was a postdoc in nikogeldner.bsky.social 's lab. After shifting Arabidopsis seedlings from solid to liquid culture, I observed that the root commensal bacterium CHA0 rapidly colonized Casparian strip–defective mutants.
Reposted by Sebastian Soyk
Game changer for cell-based plant genetics: the labs of Caixia Gao & Jin-Long Qiu have developed very efficient self-replicating vectors and they just published a very nice proof-of-concept paper.
#plantscience
www.science.org/doi/10.1126/...
#plantscience
www.science.org/doi/10.1126/...
October 7, 2025 at 9:54 AM
Game changer for cell-based plant genetics: the labs of Caixia Gao & Jin-Long Qiu have developed very efficient self-replicating vectors and they just published a very nice proof-of-concept paper.
#plantscience
www.science.org/doi/10.1126/...
#plantscience
www.science.org/doi/10.1126/...
Reposted by Sebastian Soyk
We are looking for a new colleague to work as a postdoctoral researcher on crop genomics and machine learning! The position is within our GenomeDesigner project (www.ru.nl/en/research/...). Feel free to be in touch or directly apply here: www.ru.nl/en/working-a... Please share!!!
October 3, 2025 at 4:10 PM
We are looking for a new colleague to work as a postdoctoral researcher on crop genomics and machine learning! The position is within our GenomeDesigner project (www.ru.nl/en/research/...). Feel free to be in touch or directly apply here: www.ru.nl/en/working-a... Please share!!!
Reposted by Sebastian Soyk
Independent research fellowships leading to tenured positions at the John Innes Centre.
Repost = nice. Thank you very much!!!
Repost = nice. Thank you very much!!!
Shortlisted candidates will be invited to give a seminar at the Fellows Conference, which will be held on 10 March 2026.
Candidates who win Fellowships will be offered a Tenure Track Group Leader position from the outset, initially for 5 years.
Find out more: www.jic.ac.uk/training-car...
Candidates who win Fellowships will be offered a Tenure Track Group Leader position from the outset, initially for 5 years.
Find out more: www.jic.ac.uk/training-car...
Independent Research Fellowships Leading to Tenured Faculty Positions | John Innes Centre
The John Innes Centre (JIC), is a world leading centre of excellence in plant and microbial sciences based on the Norwich Research Park, UK. We are inviting applications from outstanding researchers…
www.jic.ac.uk
October 3, 2025 at 4:06 PM
Independent research fellowships leading to tenured positions at the John Innes Centre.
Repost = nice. Thank you very much!!!
Repost = nice. Thank you very much!!!
Reposted by Sebastian Soyk
Amazing work by the Santiago lab @unil.bsky.social. The malectin-LRR receptor kinase IGP1 senses cello-oligomers to alert the plant immune system & enhance disease resistance. Very nice discovery & mechanism.
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
September 30, 2025 at 2:18 PM
Amazing work by the Santiago lab @unil.bsky.social. The malectin-LRR receptor kinase IGP1 senses cello-oligomers to alert the plant immune system & enhance disease resistance. Very nice discovery & mechanism.
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
Reposted by Sebastian Soyk
Explore gene-regulatory mechanisms that drive developmental reprogramming at EMBO Workshop "Awakening the Genome During Developmental Reprogramming: From Embryos to Organoids" in Seville, Spain, 4–7 May 2026.
Deadline: 2 February
meetings.embo.org/event/26-awa...
#EMBOGenomeAwakening #EMBOevents 🧪
Deadline: 2 February
meetings.embo.org/event/26-awa...
#EMBOGenomeAwakening #EMBOevents 🧪
Awakening the Genome During Developmental Reprogramming: From Embryos to Organoids
This EMBO Workshop explores the gene-regulatory mechanisms that drive developmental reprogramming upon fertilization. It focuses on the interplay of transcriptional, post-transcriptional, and develop…
meetings.embo.org
September 30, 2025 at 4:55 PM
Explore gene-regulatory mechanisms that drive developmental reprogramming at EMBO Workshop "Awakening the Genome During Developmental Reprogramming: From Embryos to Organoids" in Seville, Spain, 4–7 May 2026.
Deadline: 2 February
meetings.embo.org/event/26-awa...
#EMBOGenomeAwakening #EMBOevents 🧪
Deadline: 2 February
meetings.embo.org/event/26-awa...
#EMBOGenomeAwakening #EMBOevents 🧪
Reposted by Sebastian Soyk
Dear @dfg.de & @erc.europa.eu Why don't you do the same? What's stopping us from adopting this model to all tax-payer funded research in Europe? journals.plos.org/plosbiology/...
September 25, 2025 at 5:40 AM
Dear @dfg.de & @erc.europa.eu Why don't you do the same? What's stopping us from adopting this model to all tax-payer funded research in Europe? journals.plos.org/plosbiology/...
Reposted by Sebastian Soyk
HHMI adopts Plan U journals.plos.org/plosbiology/...
September 24, 2025 at 6:08 PM
HHMI adopts Plan U journals.plos.org/plosbiology/...
Reposted by Sebastian Soyk
It’s official. Today I was appointed as full professor for Plant Physiology at the University of Würzburg. Looking forward to the challenge and many interactions.
September 23, 2025 at 2:42 PM
It’s official. Today I was appointed as full professor for Plant Physiology at the University of Würzburg. Looking forward to the challenge and many interactions.
Reposted by Sebastian Soyk
My department at UC Davis is hiring a mycologist, broadly interpreted. Please repost, share, and consider applying. recruit.ucdavis.edu/JPF07339
Assistant Professor of Plant Pathology
University of California, Davis is hiring. Apply now!
recruit.ucdavis.edu
September 22, 2025 at 5:36 PM
My department at UC Davis is hiring a mycologist, broadly interpreted. Please repost, share, and consider applying. recruit.ucdavis.edu/JPF07339
Reposted by Sebastian Soyk
We have an open Assistant Professor position in Evolutionary Cell and Molecular Biology in the @weillinstitute.bsky.social at Cornell University. academicjobsonline.org/ajo/jobs/30607
Cornell University, Molecular Biology & Genetics
Job #AJO30607, WDR-00055221 Assistant Professor, Molecular Biology & Genetics, Cornell University, Ithaca, New York, US
academicjobsonline.org
September 22, 2025 at 3:25 PM
We have an open Assistant Professor position in Evolutionary Cell and Molecular Biology in the @weillinstitute.bsky.social at Cornell University. academicjobsonline.org/ajo/jobs/30607
Reposted by Sebastian Soyk
Delighted to present our Tansley Insight on what we know about the potential of different root cortex layers to do develop into different things!
👩🔬 @dorotakawa.bsky.social @hannahschneider.bsky.social
📗 @newphyt.bsky.social
nph.onlinelibrary.wiley.com/doi/10.1111/...
👩🔬 @dorotakawa.bsky.social @hannahschneider.bsky.social
📗 @newphyt.bsky.social
nph.onlinelibrary.wiley.com/doi/10.1111/...
Coordination of cortex modifications in time, space, and under stress
In roots, cell-type-specific differentiation enables specialized responses to environmental stress. The cortex, located between the vasculature and epidermis, is a key site for stress-responsive modi....
nph.onlinelibrary.wiley.com
September 19, 2025 at 3:32 PM
Delighted to present our Tansley Insight on what we know about the potential of different root cortex layers to do develop into different things!
👩🔬 @dorotakawa.bsky.social @hannahschneider.bsky.social
📗 @newphyt.bsky.social
nph.onlinelibrary.wiley.com/doi/10.1111/...
👩🔬 @dorotakawa.bsky.social @hannahschneider.bsky.social
📗 @newphyt.bsky.social
nph.onlinelibrary.wiley.com/doi/10.1111/...
Reposted by Sebastian Soyk
Time-resolved reprogramming of single somatic cells into totipotent states during plant regeneration,
https://www.cell.com/cell/fulltext/S0092-8674(25)01020-7
https://www.cell.com/cell/fulltext/S0092-8674(25)01020-7
Time-resolved reprogramming of single somatic cells into totipotent states during plant regeneration, https://www.cell.com/cell/fulltext/S0092-8674(25)01020-7
• LEC2 reprograms somatic epidermal cells into totipotent somatic embryo founder cells
• LEC2 and SPCH co-activate local auxin biosynthesis by targeting TAA1 and YUC4
• GMC-auxin state marks stomatal cells shifting from differentiation to totipotency
• Transcriptional rewiring and auxin signaling drive reprogramming of stomatal cells
www.scoop.it
September 20, 2025 at 8:36 AM
Time-resolved reprogramming of single somatic cells into totipotent states during plant regeneration,
https://www.cell.com/cell/fulltext/S0092-8674(25)01020-7
https://www.cell.com/cell/fulltext/S0092-8674(25)01020-7
Reposted by Sebastian Soyk
Honoured to be sworn in as President of the 80th Session of the UN General Assembly.
Guided by our motto #BetterTogether, I will work with all 193 Member States to embrace unity in challenging times & strengthen the UN - for today, for tomorrow & for the next 80 years.
Guided by our motto #BetterTogether, I will work with all 193 Member States to embrace unity in challenging times & strengthen the UN - for today, for tomorrow & for the next 80 years.
September 14, 2025 at 8:43 PM
Honoured to be sworn in as President of the 80th Session of the UN General Assembly.
Guided by our motto #BetterTogether, I will work with all 193 Member States to embrace unity in challenging times & strengthen the UN - for today, for tomorrow & for the next 80 years.
Guided by our motto #BetterTogether, I will work with all 193 Member States to embrace unity in challenging times & strengthen the UN - for today, for tomorrow & for the next 80 years.