iiinova — where your digital self keeps evolving

Sebastian Gregoricchio, Ph.D. @sgregoricchio.bsky.social · 11/02/2026

💻 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...

001

Sebastian Gregoricchio, Ph.D. @sgregoricchio.bsky.social · 11/02/2026

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

111

Sebastian Gregoricchio, Ph.D. @sgregoricchio.bsky.social · 11/02/2026

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

101

Sebastian Gregoricchio, Ph.D. @sgregoricchio.bsky.social · 11/02/2026

🔍 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

101

Sebastian Gregoricchio, Ph.D. @sgregoricchio.bsky.social · 11/02/2026

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.

111

Reposted by Sebastian Gregoricchio, Ph.D.

Netherlands Cancer Institute @nkinl.bsky.social · 09/12/2025

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/...

192

Reposted by Sebastian Gregoricchio, Ph.D.

Elzo de Wit lab @ NKI @dewitlab.bsky.social · 18/08/2025

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...

cell.com

A 3D genome compendium of breast cancer progression

Genomics; Chromosome organization; Molecular Genetics; Cancer

1145

Sebastian Gregoricchio, Ph.D. @sgregoricchio.bsky.social · 05/07/2025

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!

040

Reposted by Sebastian Gregoricchio, Ph.D.

Elizabeth McKenna @elizsmckenna.bsky.social · 16/06/2025

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...

053

Sebastian Gregoricchio, Ph.D. @sgregoricchio.bsky.social · 07/05/2025

📢 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:

oncodeinstitute.nl

Masterclass: ATAC-seq data analysis and applications | Oncode Institute

By Sebastian Gregoricchio (lab Wilbert Zwart, Netherlands Cancer Institute)

041

Reposted by Sebastian Gregoricchio, Ph.D.

bioRxivpreprint @biorxivpreprint.bsky.social · 17/02/2025

TRIM33 loss reduces Androgen Receptor transcriptional output and H2BK120 ubiquitination www.biorxiv.org/content/10.1101/202…

011