This is the official Twitter account of DANIO-CODE, an international collaborative effort that aims to annotate the functional elements of the zebrafish genome.
Joined July 2017
- Tweets56
- Following63
- Followers379
- Likes18
DANIO-CODE retweeted
Fantastic talk at @BCGB_UoB by @bogdanoviclab from @CABD_UPO_CSIC on DNA methylation during vertebrate development and evolution @daniocode #epigenetics #embryogenesis #daniocode
DANIO-CODE retweeted
One week ago we released zebrahub.org the @czbiohub #scRNAseq dataset of zebrafish development with a very intuitive explorer.
The data is open access here doi.org/10.6084/m9.figshare.…
In this #Thread I'm going to give you a tutorial on how to use #zebrahub 👇
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DANIO-CODE retweeted
📡 Big day today!
Our first #singlecell RNAseq dataset is now live on #Zebrahub: 10 #zebrafish developmental stages, 40 individual embryos, ~120'000 cells. Dataset spans end-of-gastrulation to 10-day larvae.
Portal: zebrahub.ds.czbiohub.org
Dataset: doi.org/10.6084/m9.figshare.…
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DANIO-CODE retweeted
The deep learning model integrated information about enhancer activity (like ChIP-seq data, histone modification data, known motif sequences and actual vertebrate data from zebrafish @daniocode. We found patterns of transcription factor binding site enrichment 8/n
DANIO-CODE retweeted
I’m proud to share my postdoctoral research in @SMBurgessLab identifying regeneration enhancers in zebrafish inner ears at single-cell resolution. 1/n
A regulatory network of Sox and Six transcription factors initiate a cell fate transformation during hearing regeneration in adult zebrafish dlvr.it/SX2xBS
DANIO-CODE retweeted
Congrats to @ferencemueller and the @daniocode team on their @NatureGenet paper! nature.com/articles/s41588-0…. Incredibly valuable resource. Underscores collaborative spirit in #zebrafish community. Maybe @NIH and @ERC_Research can step up for phase 2 support?
DANIO-CODE retweeted
Good to see this published and glad we could provide support.
The comprehensive atlas of developmental regulatory elements in zebrafish is published today in @NatureGenet nature.com/articles/s41588-0…. In addition to the BioRxiv submission xitter.cf/daniocode/status/14253… in this paper we added further resources and results. (1/n)
ALT black and white line genome browser track lines forming different developmental stages of zebrafish in the style of the album cover unknown pleasure by joy division.
ALT List of research highlights: Highlights • 1,802 samples, 38 stages, 38 labs, 19 assay types • precise TSS, alternative promoters, promoter architecture classes • developmental TF activity-qualified TFBS prediction • >140,000 cis-regulatory elements, single-cell based cell-type specificity • new visualisation of epigenetic profiles, new functional subclasses • H3K27ac-rich ensembles support early expression of developmental factors and long-range regulation • vertebrate epigenomic landscape conservation by anchored projection tool • vertebrate regulatory element equivalence without sequence conservation
DANIO-CODE retweeted
Excited to finally see this out. Thanks to the whole team, especially @McgarveyAlison @WolfgangKopp3 @Dusa_DV and @uwe_ohler. @BIMSB_MDC @helmholtz_en @StiftungCharite cell.com/cell-genomics/fullt…
DANIO-CODE retweeted
There’s a lot of interest right now for learning bioinformatics skills while lab research is suspended and everybody is working from home. I wanted to share *free* resources for learning coding basics and field-specific materials. Thread (1/n)
DANIO-CODE retweeted
This made my day 💚
EnhancerAtlas 2.0 (enhanceratlas.org/indexv2.ph…) an updated database covering 586 tissue/cell types that include a large number of normal tissues, cancer cell lines, and cells at different development stages across 9 species
in @NAR_Open
academic.oup.com/nar/article…
DANIO-CODE retweeted
Our ms on regulation of transcription in primordial germ cells is out in BioRxiv bit.ly/2tTXmoi led by @FabioDorazio @PiotrBalwierz with @vaquerizasjm @BorisLenhard B. Cairns lab #ZencodeITN #pgc #generegulation. See related study bit.ly/2sogBFX by @KettingLab
DANIO-CODE retweeted
Excited to announce that it is now published in PLOSGenetics journals.plos.org/plosgeneti…. Great experience to work with @PLOSGenetics. And congrats again to @mate_palfy @gunnar_schulze @eviledv.
Really happy to share our work with @gunnar_schulze @eviledv and @NVastenhouw on @biorxivpreprint about transcriptional priming in #zebrafish embryos! biorxiv.org/content/10.1101/… After dealing with preprints daily for the past year, I'm thrilled to finally post one 😀
DANIO-CODE retweeted
Looking forward to a great 3-day @ZencodeITN meeting: Developmental and medical genomics with animal models at Sounio, Greece..@ferencmueller @daublab @daniocode
DANIO-CODE retweeted
I'm proud to say that our latest work on the dynamics of chromatin organization through early development is out today in @CellReports. Teamwork by the labs of @ketting_rene and @deWitLab.
cell.com/cell-reports/fullte…
