Vandepoele lab
@vandepoelelab.bsky.social
Vandepoele lab @ VIB-UGent Center for Plant Systems Biology | www.vandepoelelab.be | ERC Adv multiCODE
Reposted by Vandepoele lab
🌱Save the date! It’s time to plant the seeds of discovery at our 4th edition of #PlantResearch26. From roots to results, explore breakthroughs in genetics, sustainability, crop innovation, and future food systems.
Let’s grow ideas together, in Ghent, 17-18 September: vibbio.tech/4s31Pg5
#VIBConf
Let’s grow ideas together, in Ghent, 17-18 September: vibbio.tech/4s31Pg5
#VIBConf
March 3, 2026 at 5:25 PM
🌱Save the date! It’s time to plant the seeds of discovery at our 4th edition of #PlantResearch26. From roots to results, explore breakthroughs in genetics, sustainability, crop innovation, and future food systems.
Let’s grow ideas together, in Ghent, 17-18 September: vibbio.tech/4s31Pg5
#VIBConf
Let’s grow ideas together, in Ghent, 17-18 September: vibbio.tech/4s31Pg5
#VIBConf
Reposted by Vandepoele lab
In our new pre-print, we established massive single-cell RNA-sequencing for diatoms to investigate key cell fate transitions. Notably, we discovered that the diploid-to-haploid transition is regulated by Myb TFs, a process that is actively ongoing across the Global Ocean! 🌊
March 27, 2026 at 9:17 AM
In our new pre-print, we established massive single-cell RNA-sequencing for diatoms to investigate key cell fate transitions. Notably, we discovered that the diploid-to-haploid transition is regulated by Myb TFs, a process that is actively ongoing across the Global Ocean! 🌊
Reposted by Vandepoele lab
inMOTIFin is now published in Bioinformatics! 🎉
It lets you generate random sequences and TF motifs, and insert motif instances with custom spacing, co‑occurrence and orientation. Use cases for de novo motif discovery, cooperative TF binding, and DL explainability.
academic.oup.com/bioinformati...
It lets you generate random sequences and TF motifs, and insert motif instances with custom spacing, co‑occurrence and orientation. Use cases for de novo motif discovery, cooperative TF binding, and DL explainability.
academic.oup.com/bioinformati...
January 20, 2026 at 8:17 PM
inMOTIFin is now published in Bioinformatics! 🎉
It lets you generate random sequences and TF motifs, and insert motif instances with custom spacing, co‑occurrence and orientation. Use cases for de novo motif discovery, cooperative TF binding, and DL explainability.
academic.oup.com/bioinformati...
It lets you generate random sequences and TF motifs, and insert motif instances with custom spacing, co‑occurrence and orientation. Use cases for de novo motif discovery, cooperative TF binding, and DL explainability.
academic.oup.com/bioinformati...
Reposted by Vandepoele lab
From duplication to divergence: Single-cell insights into transcriptional and cis-regulatory landscapes in soybean (Xiang Li , Xuan Zhang , Robert J Schmitz) doi.org/10.1093/plce... #PlantScience @aspbofficial
From duplication to divergence: Single-cell insights into transcriptional and cis-regulatory landscapes in soybean
Differences in regulatory DNA shape gene expression diversity of duplicated genes in soybean, with patterns across cells within a tissue and across tissues
doi.org
January 22, 2026 at 9:08 PM
From duplication to divergence: Single-cell insights into transcriptional and cis-regulatory landscapes in soybean (Xiang Li , Xuan Zhang , Robert J Schmitz) doi.org/10.1093/plce... #PlantScience @aspbofficial
We contributed a chapter to the Plant Transcription Factors
book on Cell-Type-Specific Gene Regulatory Network Inference Using an Integrative Single-Cell Transcriptomics Approach (MINI-EX v2). link.springer.com/protocol/10.... Thanks José M. Franco-Zorrilla for the invitation.
book on Cell-Type-Specific Gene Regulatory Network Inference Using an Integrative Single-Cell Transcriptomics Approach (MINI-EX v2). link.springer.com/protocol/10.... Thanks José M. Franco-Zorrilla for the invitation.
🌱 Decoding Plant Transcription Factors: Tools, Protocols, and Practical Insights
More information in our new article ⬇️
link.springer.com/book/10.1007...
More information in our new article ⬇️
link.springer.com/book/10.1007...
January 16, 2026 at 1:44 PM
We contributed a chapter to the Plant Transcription Factors
book on Cell-Type-Specific Gene Regulatory Network Inference Using an Integrative Single-Cell Transcriptomics Approach (MINI-EX v2). link.springer.com/protocol/10.... Thanks José M. Franco-Zorrilla for the invitation.
book on Cell-Type-Specific Gene Regulatory Network Inference Using an Integrative Single-Cell Transcriptomics Approach (MINI-EX v2). link.springer.com/protocol/10.... Thanks José M. Franco-Zorrilla for the invitation.
We are pleased to announce the official release of PLAZA 5.1, our plant genomics platform, which comes with a major front-end redesign. This results in improved performance, enhanced visualization tools, and refined Toolboxes. Src: www.vandepoelelab.be/plaza/news#28
December 23, 2025 at 9:38 AM
We are pleased to announce the official release of PLAZA 5.1, our plant genomics platform, which comes with a major front-end redesign. This results in improved performance, enhanced visualization tools, and refined Toolboxes. Src: www.vandepoelelab.be/plaza/news#28
We just released a new version of MINI-EX, our tool to infer cell-type specific gene regulatory networks in plants starting from single-cell RNA-Seq data. MINI-EX v3.2 can now be run on large datasets of over 100,000 cells! More info here: github.com/VIB-PSB/MINI...
December 11, 2025 at 8:49 PM
We just released a new version of MINI-EX, our tool to infer cell-type specific gene regulatory networks in plants starting from single-cell RNA-Seq data. MINI-EX v3.2 can now be run on large datasets of over 100,000 cells! More info here: github.com/VIB-PSB/MINI...
Reposted by Vandepoele lab
This paper is the result of a fruitful collaboration between the Ferrante & Iudicone labs (Naples, Italy - @luciacampese.bsky.social) and the Vyverman and Vandepoele groups (Ghent, Belgium) @vandepoelelab.bsky.social . Shout-out to @fwovlaanderen.bsky.social for funding this research 🔬
November 18, 2025 at 6:31 AM
This paper is the result of a fruitful collaboration between the Ferrante & Iudicone labs (Naples, Italy - @luciacampese.bsky.social) and the Vyverman and Vandepoele groups (Ghent, Belgium) @vandepoelelab.bsky.social . Shout-out to @fwovlaanderen.bsky.social for funding this research 🔬
Reposted by Vandepoele lab
In our latest, we tackle a long-standing conundrum: when and where do diatoms reproduce sexually? Using a lab-to-field strategy, we designed conserved sex markers applied to microcosms & Tara Oceans metatranscriptomes, revealing widespread sex in the global ocean. Read all about it now in NatComm:
Conserved genetic markers reveal widespread diatom sexual reproduction in the global ocean - Nature Communications
Diatoms dominate the oceans, yet sexual reproduction - key to bloom dynamics and species evolvability - is rarely observed. Using a lab-to-field approach, this study presents conserved markers applica...
www.nature.com
November 18, 2025 at 6:31 AM
In our latest, we tackle a long-standing conundrum: when and where do diatoms reproduce sexually? Using a lab-to-field strategy, we designed conserved sex markers applied to microcosms & Tara Oceans metatranscriptomes, revealing widespread sex in the global ocean. Read all about it now in NatComm:
More info: www.biomedcentral.com/collections/...
August 13, 2025 at 7:06 AM
More info: www.biomedcentral.com/collections/...
Reposted by Vandepoele lab
Unlocking gene regulatory networks for crop resilience and sustainable agriculture
Our new review is now online @natbiotech.nature.com
w/ Richalynn, Xin, Bob, Toshi, & Jorge
A full-text view-only is accessible via rdcu.be/euscD
www.nature.com/articles/s41...
Our new review is now online @natbiotech.nature.com
w/ Richalynn, Xin, Bob, Toshi, & Jorge
A full-text view-only is accessible via rdcu.be/euscD
www.nature.com/articles/s41...
Unlocking gene regulatory networks for crop resilience and sustainable agriculture
Nature Biotechnology - Gene regulatory networks are crucial for understanding complex gene regulation in plants and could advance crop improvement for more sustainable and climate-resilient...
rdcu.be
July 2, 2025 at 12:23 PM
Unlocking gene regulatory networks for crop resilience and sustainable agriculture
Our new review is now online @natbiotech.nature.com
w/ Richalynn, Xin, Bob, Toshi, & Jorge
A full-text view-only is accessible via rdcu.be/euscD
www.nature.com/articles/s41...
Our new review is now online @natbiotech.nature.com
w/ Richalynn, Xin, Bob, Toshi, & Jorge
A full-text view-only is accessible via rdcu.be/euscD
www.nature.com/articles/s41...
Excited to share that two team members, Jasper Staut and @svitlanalukicheva.bsky.social , will present their research on single-cell regulatory networks and gene prioritization at the upcoming GRC conference on Single-Cell approaches in plant biology!
The last day for applications is July 13th!
To Apply to the GRC: lnkd.in/gvkMxuKR
Meet The Speakers of the Single-Cell Approaches in Plant Biology GRC Conference!
To Learn More About Dr. Dinneny's Research: dinnenylab.me
@josedinneny.bsky.social
To Apply to the GRC: lnkd.in/gvkMxuKR
Meet The Speakers of the Single-Cell Approaches in Plant Biology GRC Conference!
To Learn More About Dr. Dinneny's Research: dinnenylab.me
@josedinneny.bsky.social
August 1, 2025 at 8:17 AM
Excited to share that two team members, Jasper Staut and @svitlanalukicheva.bsky.social , will present their research on single-cell regulatory networks and gene prioritization at the upcoming GRC conference on Single-Cell approaches in plant biology!
Reposted by Vandepoele lab
We are hiring! If you have experience in plant genomics + AI, or promoter engineering + synthetic biology, check out our two open postdoc positions (computational + wetlab): www.vandepoelelab.be/Jobs please re-share RT #ERC
Jobs | Vandepoele Lab
www.vandepoelelab.be
July 16, 2025 at 8:45 PM
We are hiring! If you have experience in plant genomics + AI, or promoter engineering + synthetic biology, check out our two open postdoc positions (computational + wetlab): www.vandepoelelab.be/Jobs please re-share RT #ERC
We are hiring! If you have experience in plant genomics + AI, or promoter engineering + synthetic biology, check out our two open postdoc positions (computational + wetlab): www.vandepoelelab.be/Jobs please re-share RT #ERC
Jobs | Vandepoele Lab
www.vandepoelelab.be
July 16, 2025 at 8:45 PM
We are hiring! If you have experience in plant genomics + AI, or promoter engineering + synthetic biology, check out our two open postdoc positions (computational + wetlab): www.vandepoelelab.be/Jobs please re-share RT #ERC
The origin of the #MLD8 logo explained. We welcome >200 participants (from 26 countries) in the wonderful Bijloke concert hall for an update on diatom biology.
June 23, 2025 at 8:20 AM
The origin of the #MLD8 logo explained. We welcome >200 participants (from 26 countries) in the wonderful Bijloke concert hall for an update on diatom biology.
All set for a week of diatom biology. Expect fascinating talks from diverse research disciplines, as well as sun and high temperatures.
Don't miss "Molecular Life of Diatoms 8" - registration deadline is June 6th. We will have a diverse set of speakers (keynotes + 49! contributed talks) and >120 posters. Incl. the stunning scenery of Ghent www.vibconferences.be/events/molec...
June 21, 2025 at 9:34 AM
All set for a week of diatom biology. Expect fascinating talks from diverse research disciplines, as well as sun and high temperatures.
Interested in applying AI to study gene regulation in plants? Two postdoc positions will open soon (wetlab + computational), so keep an eye on www.vandepoelelab.be #ICAR2025 #ERC
June 19, 2025 at 1:27 PM
Interested in applying AI to study gene regulation in plants? Two postdoc positions will open soon (wetlab + computational), so keep an eye on www.vandepoelelab.be #ICAR2025 #ERC
Thu 19 June (Arabidopsis Informatics workshop), Dajo Smet will present our latest results on the application of explainable AI methods to unravel the regulatory code controlling gene expression #icar2025
June 16, 2025 at 7:12 PM
Thu 19 June (Arabidopsis Informatics workshop), Dajo Smet will present our latest results on the application of explainable AI methods to unravel the regulatory code controlling gene expression #icar2025
Don't miss "Molecular Life of Diatoms 8" - registration deadline is June 6th. We will have a diverse set of speakers (keynotes + 49! contributed talks) and >120 posters. Incl. the stunning scenery of Ghent www.vibconferences.be/events/molec...
May 29, 2025 at 5:54 PM
Don't miss "Molecular Life of Diatoms 8" - registration deadline is June 6th. We will have a diverse set of speakers (keynotes + 49! contributed talks) and >120 posters. Incl. the stunning scenery of Ghent www.vibconferences.be/events/molec...
Reposted by Vandepoele lab
The premier conference on Machine Learning for Computational Biology is Sep 9-10 at the NY Genome Center in NYC!
Submission deadline is June 1 for 2-page abstracts and 8-page papers (eligible for proceedings track).
Registration is now open! (Link below)
Please retweet!
Submission deadline is June 1 for 2-page abstracts and 8-page papers (eligible for proceedings track).
Registration is now open! (Link below)
Please retweet!
May 16, 2025 at 11:26 AM
The premier conference on Machine Learning for Computational Biology is Sep 9-10 at the NY Genome Center in NYC!
Submission deadline is June 1 for 2-page abstracts and 8-page papers (eligible for proceedings track).
Registration is now open! (Link below)
Please retweet!
Submission deadline is June 1 for 2-page abstracts and 8-page papers (eligible for proceedings track).
Registration is now open! (Link below)
Please retweet!
#ourlatest Mapping of functional cis-regulatory elements in the maize genome, incl. the role of specific TE families in controlling gene expression. Combining our iCREs with region-based TFBS enrichment (in MINI-AC) enhances GRN inference! 1/2
A map of integrated cis-regulatory elements enhances gene regulatory analysis in maize #resource #PlantCommunications cell.com/plant-commun...
May 15, 2025 at 12:40 PM
#ourlatest Mapping of functional cis-regulatory elements in the maize genome, incl. the role of specific TE families in controlling gene expression. Combining our iCREs with region-based TFBS enrichment (in MINI-AC) enhances GRN inference! 1/2
Early bird registration deadline for "Molecular Life of Diatoms 8" is May 9th. We will have an exciting mix of keynote speakers and 45+ contributed talks! More info: www.vibconferences.be/events/molec...
May 5, 2025 at 8:40 PM
Early bird registration deadline for "Molecular Life of Diatoms 8" is May 9th. We will have an exciting mix of keynote speakers and 45+ contributed talks! More info: www.vibconferences.be/events/molec...
The abstract submission deadline for the 8th edition of the Molecular Life of Diatoms conference has been extended: the new deadline is 27th of April 2025. Don’t miss a chance to present your breakthrough research! www.vibconferences.be/events/molec...
April 22, 2025 at 9:21 AM
The abstract submission deadline for the 8th edition of the Molecular Life of Diatoms conference has been extended: the new deadline is 27th of April 2025. Don’t miss a chance to present your breakthrough research! www.vibconferences.be/events/molec...
April 22, 2025 at 9:20 AM
The abstract submission deadline for the 8th edition of the Molecular Life of Diatoms conference has been extended: the new deadline is 27th of April 2025. Don’t miss a chance to present your breakthrough research! www.vibconferences.be/events/molec...