Anna Nordin and I from Claudio Cantù lab are thrilled to have hosted Kim Boonekamp and Johannes Werner from Boutroslab to learn CUT&RUN LoV-U and start an exciting collaboration! For details 👇 doi.org/10.1242/dev.20… Wallenberg Centre For Molecular Medicine_Linköping Linköpings universitet

Last 'Cut&Run' team goodbyes with Anna Nordin Gianluca Zambanini. 💕

The #UNCOUPLING of #WNT target gene expression previously on bioRxiv is now with #PeerReview in Experimental Cell Research By Simon Söderholm Amaia Pierfrancesco Pagella Valeria Ghezzi Gianluca Zambanini Anna Nordin CantùLab is Wallenberg Centre For Molecular Medicine_Linköping sciencedirect.com/science/articl…

Deepest dive into the data I've ever taken and wow did we find some unexpected things! This was such an exciting project to be a part of, as always it was amazing to work with Pierfrancesco Pagella, Gianluca Zambanini, and Claudio Cantù at Linköpings universitet Wallenberg Centre For Molecular Medicine_Linköping

The Time-Resolved Genomic Impact of #WNT/β-catenin signaling Cell Systems Cell Press cell.com/cell-systems/f… We show -β-catenin repositions over TIME ⏰ -How this impacts global transcription⬆️⬇️ -Preceding and following chromatin dynamics🧬 Efforts driven by Pierfrancesco Pagella

Ever looked at your ATAC-seq signal and thought: there must be a better way to model this than peaks or windows? Happy to present ChromatinHD, a method that models scATAC+RNA data using the raw fragments. With @BartDeplancke Olga Pushkarev biorxiv.org/content/10.110…

Super happy that my first first-author paper of my PhD is now out in Genome Biology! Try filtering out the suspect list peaks to improve your CUT&RUN analysis - and we are always grateful for feedback! Thanks to the amazing Gianluca Zambanini, Pierfrancesco Pagella and Claudio Cantù.

We had previously shown that TBX3 and #WNT cooperate in limb #DevBio We now have a shocking finding 😲 TBX3 physically engages with β-catenin to drive metastasis genes in #ColorectalCancer (CRC) Look where TBX3 is expressed in hCRC > together with AXIN2 and in LGR5+ cells

A big part of my PhD work so far (and my favorite project 🩷) is now out on bioRxiv! Check out the tweetorial if you're interested in what Wnt does to CTCF/3D genome!

Had an incredible first conference experience at the Genome Organization & Nuclear Function meeting at Cold Spring Harbor! I'm grateful to have had a chance to present our work and listen to and learn from so many amazing scientists. Heading home to Sweden inspired! #cshlnucleus

The Deadline for registration approaches - register asap to the #PALSSummerSchool2024 💜⬇️

Such a great experience at #PALSschool2024! Super thankful to have been given the opportunity to try my hand at giving a workshop, especially with students (almost) as excited about peaks as I am ❤️🧬⛰️

RNAseq is commonly performed. We compared N=30 wild-type Bl6 mice to an N=30 heterozygotic knockout with a phenotype, and then downsized. We found you need at least an N= 8-12 to avoid a >50% false positive rate. A 2nd line confirmed the finding. biorxiv.org/content/10.110…

One of the most common bioinformatics questions when I analyze data is: what cutoff should I use? chatomics! Bioinformatics is not (just) statistics divingintogeneticsandgenomics.com/post/bioinform…

I'm so excited to have this out! Please use the data, and we love feedback! A huge team effort as always, especially thanks to Gianluca Zambanini (You can blame me for the ❤️🧡💛💚💙💜🩷 though 😅) Claudio Cantù Pierfrancesco Pagella

The Wild West of spike-in normalization go.nature.com/3XLUMw3

Excited to share our latest preprint on benchmarking peak-calling methods for CUT&RUN biorxiv.org/content/10.110… | Amin Noorani In this work, we compared four popular methods—MACS2, SEACR, GoPeaks, and LanceOtron, in a subset of 4DNucleome samples profiled for 3 histone marks.