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Vandepoele lab

@vandepoelelab.bsky.social
1.1K followers 169 following 21 posts

Vandepoele lab @ VIB-UGent Center for Plant Systems Biology | www.vandepoelelab.be | ERC Adv multiCODE

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VIB Training & Conferences @vibtrainconf.bsky.social · 03/03/2026
🌱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
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Gust Bilcke @gustbilcke.bsky.social · 27/03/2026
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! 🌊
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Anthony Mathelier @amathelier.bsky.social · 20/01/2026
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...
academic.oup.com
inMOTIFin: a lightweight end-to-end simulation software for regulatory sequences
AbstractSummary. The accurate development, assessment, interpretation, and benchmarking of bioinformatics frameworks for analyzing transcriptional regulato
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The Plant Cell @theplantcell.bsky.social · 22/01/2026
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
doi.org
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
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Vandepoele lab @vandepoelelab.bsky.social · 16/01/2026
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.
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Vandepoele lab @vandepoelelab.bsky.social · 23/12/2025
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
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Vandepoele lab @vandepoelelab.bsky.social · 11/12/2025
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...
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Gust Bilcke @gustbilcke.bsky.social · 18/11/2025
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 🔬
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Gust Bilcke @gustbilcke.bsky.social · 18/11/2025
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:
nature.com
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...
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Vandepoele lab @vandepoelelab.bsky.social · 13/08/2025
More info: www.biomedcentral.com/collections/...
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Pingtao Ding (he/him) @dinglab.bsky.social · 02/07/2025
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...
rdcu.be
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...
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Vandepoele lab @vandepoelelab.bsky.social · 01/08/2025
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!
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Vandepoele lab @vandepoelelab.bsky.social · 16/07/2025
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
vandepoelelab.be
Jobs | Vandepoele Lab
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Vandepoele lab @vandepoelelab.bsky.social · 16/07/2025
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
vandepoelelab.be
Jobs | Vandepoele Lab
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Vandepoele lab @vandepoelelab.bsky.social · 23/06/2025
#MLD8 Early Career Researcher event
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Vandepoele lab @vandepoelelab.bsky.social · 23/06/2025
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.
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Vandepoele lab @vandepoelelab.bsky.social · 21/06/2025
All set for a week of diatom biology. Expect fascinating talks from diverse research disciplines, as well as sun and high temperatures.
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Vandepoele lab @vandepoelelab.bsky.social · 19/06/2025
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
vandepoelelab.be
Front page | Vandepoele Lab
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Vandepoele lab @vandepoelelab.bsky.social · 16/06/2025
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
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Vandepoele lab @vandepoelelab.bsky.social · 29/05/2025
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...
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Peter Koo @pkoo562.bsky.social · 16/05/2025
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!
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Vandepoele lab @vandepoelelab.bsky.social · 15/05/2025
#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
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Vandepoele lab @vandepoelelab.bsky.social · 05/05/2025
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...
vibconferences.be
Molecular Life of Diatoms 8
22-26 June 2025, Ghent, Belgium
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Vandepoele lab @vandepoelelab.bsky.social · 22/04/2025
@mldiatoms.bsky.social @gustbilcke.bsky.social @evelinepinseel.bsky.social
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Vandepoele lab @vandepoelelab.bsky.social · 22/04/2025
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...
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Vandepoele lab @vandepoelelab.bsky.social · 17/03/2025
#diatoms #genomics #resources DiatOmicBase: a versatile gene-centered platform for mining functional omics data in diatom research @theplantjournal.bsky.social onlinelibrary.wiley.com/doi/10.1111/... joint work with @afalciat.bsky.social
onlinelibrary.wiley.com
DiatOmicBase: a versatile gene‐centered platform for mining functional omics data in diatom research
In recent years, diatoms have become the subject of increasing interest because of their ecological importance and their biotechnological potential for natural products such as pigments and polyunsat...
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VIB Training & Conferences @vibtrainconf.bsky.social · 03/02/2025
🌊🔬 The 8th International Diatom Meeting is coming to Ghent! Join top researchers & young scientists at #MLD8 to explore diatom biology, ecology & biotech potential. Network, share ideas & enjoy Belgium’s rich gastronomy. Don’t miss it! Find out more: vibbio.tech/40Gz1Of #Microalgae #DiatomResearch
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Bert De Rybel @bertderybel.bsky.social · 02/02/2025
A single-cell and spatial wheat root atlas with cross-species annotations delineates conserved tissue-specific marker genes and regulators: Cell Reports www.cell.com/cell-reports...
cell.com
A single-cell and spatial wheat root atlas with cross-species annotations delineates conserved tissue-specific marker genes and regulators
Accurate scRNA-sequencing cluster annotation in less-studied plant species remains a major challenge due to the lack of validated marker genes. Ke et al. provide an orthology-based annotation pipeline...
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Anthony Mathelier @amathelier.bsky.social · 04/12/2024
We want to make JASPAR even better for our users! Please share your experience and ideas to help us enhance the database by taking a quick survey at nettskjema.no/a/467839. Your insights make a difference! Thank you so much for your participation.
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Vandepoele lab @vandepoelelab.bsky.social · 03/12/2024
Genome Biology is calling for submissions to our Collection on Regulatory elements in plants. Guest Editors: - Pil Joon Seo, PhD, Seoul National University, South Korea - Klaas Vandepoele, PhD, Ghent University, Belgium More info: www.biomedcentral.com/collections/... please RT
biomedcentral.com
Call for papers - Regulatory elements in plants
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SPS Saclay Plant Sciences @spsplantsciences.bsky.social · 07/11/2024
The workshop "PLant science in the ANThropocene" (March 24th to April 4th 2025 at University Paris-Saclay) will address key challenges from basic sciences to socio-economic and environmental aspects. Applications are open eng-saclay-plant-sciences.hub.inrae.fr/events/works...
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Vandepoele lab @vandepoelelab.bsky.social · 20/11/2024
#ourlatest Application of orthology and network biology to infer gene functions in non-model plants. Vandepoele K, Thierens S, Van Bel M. Physiol Plant. 2024 Jul-Aug;176(4):e14441. doi.org/10.1111/ppl.... #Review
doi.org
Northern light reviews – Application of orthology and network biology to infer gene functions in non‐model plants
Approximately 60% of the genes and gene products in the model species Arabidopsis thaliana have been functionally characterized. In non-model plant species, the functional annotation of the gene spac...
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Vandepoele lab @vandepoelelab.bsky.social · 20/11/2024
Great start of the new VIB.AI center at the #VIBAIsymposium Looking forward to collaborate on exciting new research projects #AI #synthetic
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