Sebastian Gregoricchio, Ph.D.
@sgregoricchio.bsky.social
Postdoc in the Zwart lab at the Netherlands Cancer Institute (Amsterdam, Netherlands, @nkinl.bsky.social, @zwartlab.bsky.social). Studying gene regulation and 3D-genome organization in cancer.
X/Twitter: @s_gregoricchio
X/Twitter: @s_gregoricchio
Thank you very much!!
February 12, 2026 at 8:34 AM
Thank you very much!!
π» If you want to know more about our package, I invite you to have a look at the following links:
π GitHub repository: github.com/sebastian-gr...
π Zenodo repository with both proteomics and RIME analysis tutorials: zenodo.org/records/1747...
π GitHub repository: github.com/sebastian-gr...
π Zenodo repository with both proteomics and RIME analysis tutorials: zenodo.org/records/1747...
February 11, 2026 at 11:32 PM
π» If you want to know more about our package, I invite you to have a look at the following links:
π GitHub repository: github.com/sebastian-gr...
π Zenodo repository with both proteomics and RIME analysis tutorials: zenodo.org/records/1747...
π GitHub repository: github.com/sebastian-gr...
π 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
6. Many visualization methods: volcanos, MA-plots, PCA, correlations, expression/FoldChange hetamaps, gene netwroks and many more
February 11, 2026 at 11:32 PM
5. Built-in GeneSetEnrichment and OverRepresentation Analyses
6. Many visualization methods: volcanos, MA-plots, PCA, correlations, expression/FoldChange hetamaps, gene netwroks and many more
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
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
February 11, 2026 at 11:32 PM
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
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
π 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
1. In one tool we implemented normalization, batch correction, imputation, differential analyses, protein enrichment and a vast number of visualization methods
February 11, 2026 at 11:32 PM
π 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
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.
February 11, 2026 at 11:32 PM
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.
π‘βDEprotβ 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 βall-in-oneβ tool to facilitate the analyses of LFQ-based proteomics data.
academic.oup.com/nargab/artic...
With Nils Eickhoff ( @zwartlab.bsky.social, @nkinl.bsky.social & @oncodeinstitute.bsky.social), we designed this βall-in-oneβ tool to facilitate the analyses of LFQ-based proteomics data.
academic.oup.com/nargab/artic...
DEprot: a comprehensive R-package for the analysis of label-free quantitation mass spectrometry data
Abstract. In recent years, studies investigating proteinβprotein interactions on a proteome-wide scale have increased exponentially. These developments wer
academic.oup.com
February 11, 2026 at 11:32 PM
π‘βDEprotβ 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 βall-in-oneβ tool to facilitate the analyses of LFQ-based proteomics data.
academic.oup.com/nargab/artic...
With Nils Eickhoff ( @zwartlab.bsky.social, @nkinl.bsky.social & @oncodeinstitute.bsky.social), we designed this βall-in-oneβ 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 !!!
Nature research paper: Fasting boosts breast cancer therapy efficacy via glucocorticoid activation
go.nature.com/48yFe44
go.nature.com/48yFe44
Fasting boosts breast cancer therapy efficacy via glucocorticoid activation - Nature
Beneficial effects of fasting combined with endocrine therapy for oestrogen receptor-Ξ±-expressing breast cancers can be recapitulated using exogenous glucocorticoid receptor ligands instead of fasting to reduce harmful effects.
go.nature.com
December 10, 2025 at 10:32 PM
Proud to be part of this story! Congrats @nunopadrao.bsky.social !!!
Reposted by Sebastian Gregoricchio, Ph.D.
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. β‘οΈ www.nki.nl/news-events/...
December 10, 2025 at 4:30 PM
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. β‘οΈ www.nki.nl/news-events/...
Reposted by Sebastian Gregoricchio, Ph.D.
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: itβs complicated. www.cell.com/iscience/ful...
A 3D genome compendium of breast cancer progression
Genomics; Chromosome organization; Molecular Genetics; Cancer
www.cell.com
August 18, 2025 at 2:41 PM
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: itβs 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!
In todayβs publication in Science we introduce Zincore: a novel protein of QRICH1 and SEPHS1 and functions as a transcriptional coregulator dedicated to zinc finger transcription factors. Hereβs how we found it: 𧡠www.science.org/doi/10.1126/... 1/11
Zincore, an atypical coregulator, binds zinc finger transcription factors to control gene expression
Zinc finger proteins (ZNFs) are the largest family of transcription factors, yet how they activate gene expression remains unclear. In this study, we identified Zincore, a protein complex consisting o...
www.science.org
July 5, 2025 at 6:56 PM
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!
Reposted by Sebastian Gregoricchio, Ph.D.
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...
June 16, 2025 at 7:41 PM
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...
Reposted by Sebastian Gregoricchio, Ph.D.
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/
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 ERΞ±.
pubmed.ncbi.nlm.nih.gov
May 10, 2025 at 1:41 PM
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/
π’ 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:
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:
Masterclass: ATAC-seq data analysis and applications | Oncode Institute
By Sebastian Gregoricchio (lab Wilbert Zwart, Netherlands Cancer Institute)
oncodeinstitute.nl
May 7, 2025 at 9:03 AM
π’ 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:
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:
Reposted by Sebastian Gregoricchio, Ph.D.
TRIM33 loss reduces Androgen Receptor transcriptional output and H2BK120 ubiquitination https://www.biorxiv.org/content/10.1101/2025.02.14.638236v1
February 17, 2025 at 2:16 PM
TRIM33 loss reduces Androgen Receptor transcriptional output and H2BK120 ubiquitination https://www.biorxiv.org/content/10.1101/2025.02.14.638236v1
Reposted by Sebastian Gregoricchio, Ph.D.
Check out our latest preprint! Interested in Androgen Receptor, gene regulation and TRIM proteins? Well, in that case, I believe youβll like this story!
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
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...
www.biorxiv.org
February 17, 2025 at 3:21 PM
Check out our latest preprint! Interested in Androgen Receptor, gene regulation and TRIM proteins? Well, in that case, I believe youβll like this story!
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...