Sebastian Gregoricchio, Ph.D.

💻 If you want to know more about our package, I invite you to have a look at the following links: 👉 GitHub repository: github.com/sebastian-greg… 👉 Zenodo repository with both proteomics and RIME analysis tutorials: zenodo.org/records/174729…

4. Multiple types of differential protein discovery methods 5. Built-in GeneSetEnrichment and OverRepresentation Analyses 6. Many visualization methods: volcanos, MA-plots, PCA, correlations, expression/FoldChange hetamaps, gene netwroks and many more

💡“DEprot” is now out on NAR Genomics and Bioinformatics. With @nils_eickhoff (Zwart lab), we designed this “all-in-one” tool to facilitate the analyses of LFQ-based proteomics data. Check out the the paper at: academic.oup.com/nargab/article…

Nature research paper: Fasting boosts breast cancer therapy efficacy via glucocorticoid activation go.nature.com/4rPJxj5

Proud to be part of this story! Congrats @nuno_padrao !! 🎉🎉

Favorite study! Germline-somatic tandems dictate cancer subtypes, provide clinical insights, and fuel molecularly informed studies. Kudos: Blerta Stringa, @Paola_Gasperini, Alessandro Alaimo, and @LunardiLabCIBIO (co-last a!) @NimaSharifiMD doi.org/10.1158/2159-8… @UniTrento

🚨Our latest paper out on @GenomeBiology! We observed a high epigenetic reprogramming in endometrial tumor development, with highly interesting genome/epigenome interplay in endometrial tumorigenesis and disease progression. Many thanks to all coauthors!! genomebiology.biomedcentral.com/articles/10.11…

📢 Do you want to know more about ATAC-seq and it's applications? In this case join the @oncodeinstitute workshop that will take place the 19th of September at the @NKI_nl!! Places are limited to 35!! Subscribe at the following link: oncodeinstitute.nl/events/masterc…

On Thursday I had the opportunity to present my work on endometrial and breast cancer at the #EMBOnuclearReceptors meeting. It was an honor to be able to contribute to the vibrant scientific environment of this conference. @zwartlab @NKI_nl @oncodeinstitute

The first preprint of our PERICODE consortium: MPRA-trained deep learning provides insight into the regulatory logic of promoters and transcription factors. biorxiv.org/cgi/content/sh…

... and we used our platform of 19 chromatin-integrated pathway reporters to probe context-dependent effects of epigenetic drugs on Cas9 editing: academic.oup.com/nar/advance-ar…

@LucaBraccioli Really really happy for you! congratulations!! 🎉

I am thrilled to share that I will be starting my own research group in the Department of Developmental Biology at Utrecht University. My lab will explore the interplay between gene regulation and tissue-tissue interactions in embryo models. #BraccioliLab #UtrechtUniversity

Breast cancer risk SNPs converge on estrogen receptor binding sites commonly shared between breast tumors to locally alter estrogen signalling output biorxiv.org/cgi/content/sh… #bioRxiv

Loss of the FANCA pathway, known to control genetic instability, fosters the expansion of leukaemic cells carrying oncogenic mutations nature.com/articles/s4138… @GustaveRoussy #Leukaemia #OpenAccess

🎓We are looking for outstanding candidates who want to become the new generation of ambitious #PhDstudents in a lively international research community. Check our website to learn about our #PhDprogram in #ChromosomeBiology & #GeneRegulation ➡️bit.ly/44iOcOc

snHiC: a complete and simplified snakemake pipeline for grouped Hi-C data analysis by @s_gregoricchio & @WilbertZ in @BioinfoAdv doi.org/10.1093/bioadv… @zwartlab

3/3 𝘴𝘯𝘏𝘪𝘊 works in a conda environment in a snakemake system allowing for an efficient, reproducible and organized analysis of your Hi-C data! Check out the dedicated GitHub page: github.com/sebastian-greg…

2/3 𝘴𝘯𝘏𝘪𝘊 will help you in normalizing and correcting your data. It allows you to automatically run inter-groups analyses such as differential Hi-C contacts, differential compartments and, stripes, loops and TADs detection with the possibility to chose among different tools!

1/3 Are you struggling with different Hi-C data analysis and the handling of different input formats for different tools? Have a look at 𝘴𝘯𝘏𝘪𝘊: the new @zwartlab snakemake Hi-C pipeline, now published on @BioinfoAdv! DOI: doi.org/10.1093/bioadv… academic.oup.com/bioinformatics…