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...

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

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.

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...

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 🔬

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...

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/...

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...

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...

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!

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

#MLD8 Early Career Researcher event

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.

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

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...

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!

GitHub - VIB-PSB/MINI-AC: Motif-Informed Network Inference based on Accessible Chromatin (MINI-AC) is a method that combines accessible chromatin data from bulk or single-cell experiments with transcr... Motif-Informed Network Inference based on Accessible Chromatin (MINI-AC) is a method that combines accessible chromatin data from bulk or single-cell experiments with transcription factor binding s...

MINI-AC is a method that combines accessible chromatin data from bulk or single-cell experiments with transcription factor binding site enrichment to learn gene regulatory networks (GRNs) in plants.
Git: github.com/VIB-PSB/MINI...
Ref: doi.org/10.1111/tpj....

#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...

@mldiatoms.bsky.social @gustbilcke.bsky.social @evelinepinseel.bsky.social

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...

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...

#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

🌊🔬 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

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...

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...

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.

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

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...