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We've engineered new tools for developing + hosting Nextflow workflows x.com/kenbwork/statu…

The International Rice Research Institute IRRI 🌾 has launched data for 130+ rice varieties on the Genesys PGR platform. Supported by the Crop Trust, this ensures global accessibility to their vital 🌾collections for research and breeding innovations. irri.org/news-and-event…

What is the most common type of mutations, causing cancer and genetic diseases? C to T mutations in CpGs: Signature 1. What is the best understood mutational signature? Signature 1. Or is it? Results of over 8 years of our work is finally out! 🧵1/ nature.com/articles/s4158…

#InTheMedia: Scientists are developing protein-rich rice varieties that cause minimal spikes in blood sugar levels. 🌾 Learn more about this breakthrough here: bit.ly/3BA8xVO

I've recently discovered a really useful R package by Jan Broder Engler called tidyheatmaps. It's designed to make creating heatmaps from tidy data easy, especially for publication-quality visuals. The package uses pheatmap for detailed heatmaps with less coding. If you work

Today we report in Nature Genetics the genetic landscape of cancer drug resistance mechanisms from CRISPR base editing screens nature.com/articles/s4158…

PhenoMultiOmics for biomarker & drug target discovery An online platform for integrated multi-omic (transcriptome-proteome-metabolome) analysis phenomultiomics.shinyapps.io/cancer/ 5540 enzyme reactions 45 cancer types 759558 gene-protein-metabolite-phenotype/disease associations data from

Excited to share CpGPT, a new foundation model for DNA methylation, crafted to understand the 'language' of epigenetics! 🧬🤖 What’s CpGPT? CpGPT is a transformer model pre-trained on CpGCorpus, a huge dataset of public DNA methylation info. By integrating sequence, positional,

Out in Nature Communications ! ChromaFold predicts 3D contact maps using single-cell ATAC-seq alone. nature.com/articles/s4146…

Extensive binding of uncharacterized human transcription factors to genomic dark matter (Razavi et al., 2024) biorxiv.org/content/10.110… ▶️166 uncharacterized human TFs ▶️"Dark TFs", mainly bind closed chromatin enriched for transposable elements ▶️Some Dark TFs contain KRAB domain

How to write a grant? 1. Write it for the reviewer, not you, the applicant. 2. Communicate in stories. 3. Make your story cohesive—leave no puzzling gaps. 4. Make your story resonate to keep the reviewer reading. 5. Accept chance and noise in peer-review. pnas.org/doi/epub/10.10…

Our research in Al Jazeera!

PhD Unlocked, Level Up Achieved! 🚀🎓 Congrats to Dr. Rhowell Tiozon from Alisdair Fernie's group at the MPIMP Potsdam Golm 🌱🧪, wishing you all the best! Rhowell Jr. Tiozon

I promised to write an end-to-end tutorial to replicate this genomics figure during the holidays. Now it is ready 👇

To add a statistical test in #tidyplots , just do `add_test_pvalue()` 🚀 Then you can decide, whether you want to compare every group to every group, or one control group to all other groups. jbengler.github.io/tidyplots/refe… #rstats #dataviz #phd

A wheat phytohormone atlas spanning major tissues across the entire life cycle provides novel insights into cytokinin and jasmonic acid interplay #research #MolecularPlant cell.com/molecular-plan…

There are three main verbs in #tidyplots - add 👉 to add elements to the plots - adjust 👉 to modify elements in the plot - remove 👉 to remove elements from the plot #rstats #dataviz #phd

🌾 Rice feeds over half the world but must adapt to climate change while reducing its environmental impact. IRRI 🌾 DG Dr. Yvonne Pinto shares insights on balancing rice's cultural significance with sustainability on BBC World Service’s The Food Chain: buff.ly/3EbHG3y

DeepSeek-R1 is great, but it still does not handle genomics yet :) 🚀 We’re thrilled to announce that IntegrAO (pronounced "integral") 🧬🔬—our new multi-omics integration framework—has been published in Nature Machine Intelligence! 📑 Paper: nature.com/articles/s4225… 💻 Code:

Beginner Mistakes in Genomics Data Analysis (And How to Avoid Them) 1/ When I started with genomics, I made mistakes. Here are key lessons I learned the hard way. Don't repeat them. (I wrote it 10 years ago)