How are mRNAs regulated during #zebrafish Maternal-to-Zygotic transition? Giraldez Lab identify combinatorial regulation using massively reporter assay and mass spec & propose model of #mRNA stability in vivo w/#MachineLearning genome.cshlp.org/cgi/content/lo…

Major new CRISPRscan release today! Check it out crisprscan.org #CRISPR #zebrafish Moreno-Mateos Lab Giraldez Lab

Very excited to release FONtools! JSON-based FON (Feature Object Notation) format and tools to simplify genomic annotations usage. Ensembl ZFIN Xenbase and others. github.com/vejnar/fontools Giraldez Lab #Bioinformatics

New preprint from the lab! Genome editing in animals with minimal PAM CRISPR-Cas9 enzymes. A pre-pandemic and fun collaboration with Ceron Lab led by @CarlosSnchzB2 and Jeremy Vicencio with the support of Ben Kleinstiver! Thread! 1/11 doi.org/10.1101/2021.0…

New CRISPRscan release. Our 10th release! Predictions for all species & genes including new SpG & SpRY. Limit off-target mismatch. New mouse GRCm39, zebrafish NHGRI-1 @SMBurgessLab and Ensembl 104. Check it out crisprscan.org #CRISPR #zebrafish Moreno-Mateos Lab Giraldez Lab

GeneAbacus is out! Finally released 😉 Count & profile reads in genes, chromosomes or constructs. Profile options adapted to Ribo-seq & CLIP-seq & mRNA-seq to MPRAs! github.com/vejnar/geneaba… #Bioinformatics Giraldez Lab BazziniLab Cifuentes Lab Miler Lee

Last minute Christmas gift🎄FONtools github.com/vejnar/fontools now imports Gene Ontology (GO) and zips using Zstandard. Ready-to-use FON1 files available here: data.giraldezlab.org/pub/annots/

Idea for your 2022 resolutions: better backup. Incremental, secure & simple. See how we do it doc.vejnar.org/doc/storage/ba…

GeneAbacus application github.com/vejnar/geneaba…. Visualize uORF/oORF/CDS translation plotting ribosome profiling on mRNA. Pre-computed genomic Ribo-seq profiles for zebrafish development provided BazziniLab See Jupyter Notebook github.com/vejnar/noteboo… #Bioinformatics Giraldez Lab

How does endogenous reprogramming take place in early development? We are excited to share what we have learned. authors.elsevier.com/c/1ecL03vVUPK7… Molecular Cell

ReadKnead is out: Knead your sequencing reads before baking! Clips, trims, demultiplexes & filters your reads. Simple state-of-the-art trimming mRNA-seq to complex library read prep. SourceHut sr.ht/~vejnar/ReadKn… & GitHub github.com/vejnar/ReadKne… #Bioinformatics Giraldez Lab

It’s a cornerstone! LabxPipe is out! Easy genomics pipelines: mapping, gene count & trackhubs. Integrated with LabxDB. Examples & code: SourceHut git.sr.ht/~vejnar/LabxPi… GitHub github.com/vejnar/LabxPipe #Bioinformatics Giraldez Lab

Want to save space & get genes annotation in script-friendly format (JSON-based)? FONtools 0.5.0 now compatible with Zstandard github.com/vejnar/FONtools or sr.ht/~vejnar/FONtoo…. Latest Ensembl 108 available as FON data.giraldezlab.org/pub/annots/

For anyone on Mastodon, found & follow me on @[email protected] genomic.social/@ceVejnar

Echinoderms are coming to CRISPRscan today! Bat star & Purple and green sea urchins. New genome assemblies for rat, marmoset, chicken & latest Xenopus laevis v10.1. Check out CRISPRscan at crisprscan.org #CRISPR Moreno-Mateos Lab Giraldez Lab Echinobase Xenbase

Our work describing Chromatin Expansion Microscopy is now out in Science Magazine science.org/doi/10.1126/sc… Check out how we were able to visualize transcription, chromatin, and TFs with molecular resolution in developing zebrafish embryos to understand gene regulation!

Plants (Arabidopsis, soybean, rice, sorghum, corn) for the first time in the latest CRISPRscan release! Also gRNAs for Sea lamprey. Check it out CRISPRscan.org #CRISPR Moreno-Mateos Lab Giraldez Lab

Apple snail (pomacea canaliculata) and Ensembl 112 in a small update to Moreno-Mateos Lab released today!