Sebastian Gregoricchio, Ph.D.

Thank you very much!!

💻 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-gr...
👉 Zenodo repository with both proteomics and RIME analysis tutorials: zenodo.org/records/1747...

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

2. We introduced a 2-step imputation approach specifically designed to better handle missing not-at-random (MNAR) values
3. Up to 9 different imputation methods are available, with the possibility to bechmark all of them on your own data
4. Multiple types of differential protein discovery methods

🔍 Some of the unique features of DEprot:
1. In one tool we implemented normalization, batch correction, imputation, differential analyses, protein enrichment and a vast number of visualization methods

Analyzing proteomics data can be quite challenging due to the large amount of missing data and the complexity of these datasets. This is even more complicated in the case of IP-MS/RIME data where the missingness of the data is not occuring always at random.

DEprot: a comprehensive R-package for the analysis of label-free quantitation mass spectrometry data Abstract. In recent years, studies investigating protein–protein interactions on a proteome-wide scale have increased exponentially. These developments wer

💡“DEprot” is now out on @narjournal.bsky.social Genomics and Bioinformatics.
With Nils Eickhoff ( @zwartlab.bsky.social, @nkinl.bsky.social & @oncodeinstitute.bsky.social), we designed this “all-in-one” tool to facilitate the analyses of LFQ-based proteomics data.

academic.oup.com/nargab/artic...

Proud to be part of this story! Congrats @nunopadrao.bsky.social !!!

Corticosteroids may re-sensitize metastatic HR+ breast cancer to endocrine therapy by mimicking cortisol-driven fasting responses. Our study, published in Nature, shows a potential new use for a cheap and widely used drug class. ➡️ www.nki.nl/news-events/...

A 3D genome compendium of breast cancer progression Genomics; Chromosome organization; Molecular Genetics; Cancer

We all know that cancers -even from the same subtype- are highly heterogeneous right? In a new study we asked whether this was also the case for the three-dimensional organization of the genome in breast cancer. The answer: it’s complicated. www.cell.com/iscience/ful...

Discover the role of #Zincore, a novel protein complex that acts as a co-regulator in activating DNA transcription by zinc finger transcription factors in this amazing work from @daaninthelab.bsky.social et al., now published in @science.org! Proud to have participated in this beautiful project!

Now online in Cancer Discovery: Germline-Somatic Liaison Dictates Cancer Subtype via de novo Steroid Biosynthesis - by Paola Gasperini, Alessandro Alaimo, Blerta Stringa, Andrea Lunardi, Francesca Demichelis, and colleagues doi.org/10.1158/2159...

Endometrial tumorigenesis involves epigenetic plasticity demarcating non-coding somatic mutations and 3D-genome alterations - PubMed In summary, we identify a complex genomic-epigenomic interplay in EC development and progression, altering 3D genome organization to enhance expression of the critical driver ERα.

Check out our latest paper! Out now in Genome Biology! Many thanks to all coauthors for their invaluable contributions on this lengthy journey pubmed.ncbi.nlm.nih.gov/40346709/

Masterclass: ATAC-seq data analysis and applications | Oncode Institute By Sebastian Gregoricchio (lab Wilbert Zwart, Netherlands Cancer Institute)

📢 Are you approaching the epigenetic world? Or you want to know more about ATAC-seq and it's applications?
In this case join the @oncodeinstitute.bsky.social workshop that will take place the 19th of September at the @nkinl.bsky.social !!
Places are limited to 35!! Subscribe at the following link:

TRIM33 loss reduces Androgen Receptor transcriptional output and H2BK120 ubiquitination https://www.biorxiv.org/content/10.1101/2025.02.14.638236v1

TRIM33 loss reduces Androgen Receptor transcriptional output and H2BK120 ubiquitination The Androgen Receptor (AR) is a ligand-dependent transcription factor that drives prostate cancer development and progression. Although, a detailed effect on AR biology has been described for a number...

Check out our latest preprint! Interested in Androgen Receptor, gene regulation and TRIM proteins? Well, in that case, I believe you’ll like this story!

www.biorxiv.org/content/10.1...