🌱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

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! 🌊

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...

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

academic.oup.com

Anthony Mathelier@amathelier.bsky.social · last yr.

🚨 New preprint from group is now out on arXiv. inMOTIFin: A lightweight, flexible simulation toolkit for regulatory genomics. Simulate, implant, and modify transcription factor binding motifs with ease. 🔗 arxiv.org/abs/2506.20769 🧵👇

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

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.

IHSM La Mayora UMA-CSIC@ihsmumacsic.bsky.social · 7mo ago

🌱 Decoding Plant Transcription Factors: Tools, Protocols, and Practical Insights More information in our new article ⬇️ link.springer.com/book/10.1007...

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 🔬

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...

nature.com

More info: www.biomedcentral.com/collections/...

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...

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

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!

Plant Cell Atlas@plantcellatlas.bsky.social · last yr.

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

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.

Vandepoele lab@vandepoelelab.bsky.social · last yr.

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...

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

The Arabidopsis Information Resource (TAIR)@tairnews.bsky.social · last yr.

Arabidopsis Informatics Session… Dajo Smet next shows how deep learning ML can be used to predict ABA responses that they then validate experimentally #arabidopsis #icar2025

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...

Vandepoele lab@vandepoelelab.bsky.social · last yr.

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 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!

#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

Molecular Plant & Plant Communications@mplantpcom.bsky.social · last yr.

A map of integrated cis-regulatory elements enhances gene regulatory analysis in maize #resource #PlantCommunications cell.com/plant-commun...

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...

Molecular Life of Diatoms 8

22-26 June 2025, Ghent, Belgium

vibconferences.be

Vandepoele lab@vandepoelelab.bsky.social · last yr.

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

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

Vandepoele lab@vandepoelelab.bsky.social · last yr.

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...

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...

#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

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...

onlinelibrary.wiley.com

🌊🔬 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: Cell Reports www.cell.com/cell-reports...

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...

cell.com

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