A systems biology approach to investigate cell fate switches in intestinal organoids

Pubblicazioni

Retinoic acid signaling drives differentiation toward the absorptive lineage in colorectal cancer

Autori: Roelof A. Wester, Lisa van Voorthuijsen, Hannah K. Neikes, Jelmer J. Dijkstra, Lieke A. Lamers, Siebren Frölich, Maarten van der Sande, Colin Logie, Rik G.H. Lindeboom, Michiel Vermeulen
Pubblicato in: iScience, Numero 24/12, 2021, Pagina/e 103444, ISSN 2589-0042
Editore: Cell Press
DOI: 10.1016/j.isci.2021.103444

RNF 43 truncations trap CK 1 to drive niche‐independent self‐renewal in cancer

Autori: Maureen Spit, Nicola Fenderico, Ingrid Jordens, Tomasz Radaszkiewicz, Rik GH Lindeboom, Jeroen M Bugter, Alba Cristobal, Lars Ootes, Max van Osch, Eline Janssen, Kim E Boonekamp, Katerina Hanakova, David Potesil, Zbynek Zdrahal, Sylvia F Boj, Jan Paul Medema, Vitezslav Bryja, Bon‐Kyoung Koo, Michiel Vermeulen, Madelon M Maurice
Pubblicato in: The EMBO Journal, Numero 39/18, 2020, ISSN 0261-4189
Editore: Nature Publishing Group
DOI: 10.15252/embj.2019103932

Off-the-shelf proximity biotinylation for interaction proteomics

Autori: Irene Santos-Barriopedro, Guido van Mierlo, Michiel Vermeulen
Pubblicato in: Nature Communications, Numero 12/1, 2021, ISSN 2041-1723
Editore: Nature Publishing Group
DOI: 10.1038/s41467-021-25338-4

Probing the Tumor Suppressor Function of BAP1 in CRISPR-Engineered Human Liver Organoids

Autori: Benedetta Artegiani, Lisa van Voorthuijsen, Rik G.H. Lindeboom, Daniëlle Seinstra, Inha Heo, Pablo Tapia, Carmen López-Iglesias, Daniel Postrach, Talya Dayton, Rurika Oka, Huili Hu, Ruben van Boxtel, Johan H. van Es, Johan Offerhaus, Peter J. Peters, Jacco van Rheenen, Michiel Vermeulen, Hans Clevers
Pubblicato in: Cell Stem Cell, Numero 24/6, 2019, Pagina/e 927-943.e6, ISSN 1934-5909
Editore: Cell Press
DOI: 10.1016/j.stem.2019.04.017

ONECUT2 regulates RANKL-dependent enterocyte and microfold cell differentiation in the small intestine; a multi-omics study

Autori: Maria V Luna Velez; Hannah K Neikes; Rebecca R Snabel; Yarah Quint; Chen Qian; Aniek Martens; Gert Jan C Veenstra; Michael R Freeman; Simon J van Heeringen; Michiel Vermeulen
Pubblicato in: Nucleic Acids Research, Numero 51 (3), 2023, Pagina/e 1277–1296, ISSN 0305-1048
Editore: Oxford University Press
DOI: 10.1093/nar/gkac1236

Multiomics of Colorectal Cancer Organoids Reveals Putative Mediators of Cancer Progression Resulting from SMAD4 Inactivation.

Autori: Jelmer J. Dijkstra; Hannah K. Neikes; Somayeh Rezaeifard; Xuhui Ma; Emile E. Voest; Daniele V. F. Tauriello; Michiel Vermeulen
Pubblicato in: J. Proteome Res., Numero 22, 2022, Pagina/e 138–151, ISSN 1535-3893
Editore: American Chemical Society
DOI: 10.1021/acs.jproteome.2c00551

Miniaturised interaction proteomics on a microfluidic platform with ultra-low input requirements

Autori: Cristina Furlan, René A. M. Dirks, Peter C. Thomas, Robert C. Jones, Jing Wang, Mark Lynch, Hendrik Marks, Michiel Vermeulen
Pubblicato in: Nature Communications, Numero 10/1, 2019, Pagina/e 1525, ISSN 2041-1723
Editore: Nature Publishing Group
DOI: 10.1038/s41467-019-09533-y

Determining DNA–Protein Binding Affinities and Specificities from Crude Lysates Using a Combined SILAC/TMT Labeling Strategy

Autori: Cathrin Gräwe; Miguel Hernandez-Quiles; Pascal W. T. C. Jansen; Annika Brimmers; Michiel Vermeulen
Pubblicato in: J. Proteome Res, Numero 22 (8), 2023, Pagina/e 2683-2693, ISSN 1535-3893
Editore: American Chemical Society
DOI: 10.1021/acs.jproteome.3c00248

STPP-UP: An alternative method for drug target identification using protein thermal stability

Autori: Dick W. Zijlmans; Miguel Hernández-Quiles; Pascal W.T.C. Jansen; Isabelle Becher; Frank Stein; Mikhail M. Savitski; Michiel Vermeulen
Pubblicato in: J Biol Chem, Numero 299 (11), 2023, Pagina/e 105279, ISSN 0021-9258
Editore: American Society for Biochemistry and Molecular Biology Inc.
DOI: 10.1016/j.jbc.2023.105279

Quantification of absolute transcription factor binding affinities in the native chromatin context using BANC-seq

Autori: Hannah K. Neikes, Katarzyna W. Kliza, Cathrin Gräwe, Roelof A. Wester, Pascal W. T. C. Jansen, Lieke A. Lamers, Marijke P. Baltissen, Simon J. van Heeringen, Colin Logie, Sarah A. Teichmann, Rik G. H. Lindeboom & Michiel Vermeulen
Pubblicato in: Nature Biotechnology, 2023, ISSN 1087-0156
Editore: Nature Publishing Group
DOI: 10.1038/s41587-023-01715-w

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