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LatentDAG: Representing core gene expression activity relationships using the latent structure implicit in bayesian networks academic.oup.com/bioinformatics…

In our new manuscript with Katharine Chen and Maria Toro-Moreno arxiv.org/abs/2408.09344, we show how wet-lab research groups can use GitHub to replace electronic lab notebooks, Slack-like collaboration tools, and software package managers. Here are the first three steps:

DIAMOND2GO for rapid GO assignment and enrichment testing twtr.to/7kwXU

Regional Active Transcription Associates with Homoeologous Exchange Breakpoints in Synthetic Brassica Tetraploids (Chengcheng Cai, Yinqing Yang, Lei Zhang, Yinan Cui, Jian Wu, Jianli Liang, Xing Li, Lingkui Zhang, Xin Zhang, et. al.) buff.ly/3XbnNAV ASPB #PlantSci

R2Dtool github.com/comprna/R2Dtool for handling, integrating, and viualising isoform-resolved RNA feature data - led by AJ Sethi #bioinformatics #RNA #isoforms academic.oup.com/bioinformatics…

Genetic–epigenetic interplay in the determination of plant 3D genome organization. #3Dgenome #Epigenetics Nucleic Acids Res academic.oup.com/nar/advance-ar…

New Article: "Chromosome-level scaffolding of haplotype-resolved assemblies using Hi-C data without reference genomes" rdcu.be/dR0zi With Research Briefing: "Achieving de novo scaffolding of chromosome-level haplotypes using Hi-C data" rdcu.be/dR0zn

Interested in an update on molecular concepts to explain heterosis in crops? Have a look at our latest review in TrendsPlantSci ⬇️Link to corrected proofs (open access): sciencedirect.com/science/articl…

#ASPBPlantCellTuesday #ICYMI

What’s remarkable about PlantCaduceus is its ability to be fine-tuned in Arabidopsis and still retain accuracy in distant species like major grass crops, such as corn. 🌱→ 🌽🌾 This class of models are a game changer for plant genomics! biorxiv.org/content/10.110…

For evolutionary biologists interested in tracing genomes back to their ancient ancestors, we’ve developed EdgeHOG—a tool that reconstructs ancestral gene orders at an unprecedented scale and speed. #Genomics #EvolutionaryBiology #EdgeHOG Thread!

Thrilled to share that my latest publication Nature Plants is now available! 🎉 This journey has been incredible. I am so proud to finally share it with you. nature.com/articles/s4147…

SVbyEye: A visual tool to characterize structural variation among whole genome assemblies biorxiv.org/content/10.110…

Check out SVbyEye: A new visualization tool to characterize structural variation among whole-genome assemblies (biorxiv.org/content/10.110…)

Transcriptomic balance and optimal growth are determined by cell size The transcriptome becomes widely perturbed in outsized cells cell.com/molecular-cell… Molecular Cell Aldea Lab Congrats Marti

Thrilled about Wolfram Höps Nature Communications paper on NAHRwhals to infer repeat-mediated series of SVs. These explain cryptic variation also in medically relevant regions e.g. TPSAB1 gene, 8p23.1, 22q11 & Sotos syndrome regions. nature.com/articles/s4146… Jan Korbel BCM HGSC EMBL

DNA copy number variation is strongly buffered at the protein level. The buffering is much stronger than at the RNA level.

Widespread Post-transcriptional Attenuation of Genomic Copy-Number Variation in Cancer

Varying recombination landscapes between individuals are driven by polymorphic transposable elements biorxiv.org/cgi/content/sh… #biorxiv_genomic

A broader view of the diversity of human gene expression. #GeneExpression #HumanPopulations #AncestryBiases nature nature.com/articles/d4158…