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

Publikacje

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

Autorzy: 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
Opublikowane w: iScience, Numer 24/12, 2021, Strona(/y) 103444, ISSN 2589-0042
Wydawca: Cell Press
DOI: 10.1016/j.isci.2021.103444

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

Autorzy: 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
Opublikowane w: The EMBO Journal, Numer 39/18, 2020, ISSN 0261-4189
Wydawca: Nature Publishing Group
DOI: 10.15252/embj.2019103932

Off-the-shelf proximity biotinylation for interaction proteomics

Autorzy: Irene Santos-Barriopedro, Guido van Mierlo, Michiel Vermeulen
Opublikowane w: Nature Communications, Numer 12/1, 2021, ISSN 2041-1723
Wydawca: Nature Publishing Group
DOI: 10.1038/s41467-021-25338-4

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

Autorzy: 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
Opublikowane w: Cell Stem Cell, Numer 24/6, 2019, Strona(/y) 927-943.e6, ISSN 1934-5909
Wydawca: 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

Autorzy: 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
Opublikowane w: Nucleic Acids Research, Numer 51 (3), 2023, Strona(/y) 1277–1296, ISSN 0305-1048
Wydawca: Oxford University Press
DOI: 10.1093/nar/gkac1236

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

Autorzy: Jelmer J. Dijkstra; Hannah K. Neikes; Somayeh Rezaeifard; Xuhui Ma; Emile E. Voest; Daniele V. F. Tauriello; Michiel Vermeulen
Opublikowane w: J. Proteome Res., Numer 22, 2022, Strona(/y) 138–151, ISSN 1535-3893
Wydawca: American Chemical Society
DOI: 10.1021/acs.jproteome.2c00551

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

Autorzy: Cristina Furlan, René A. M. Dirks, Peter C. Thomas, Robert C. Jones, Jing Wang, Mark Lynch, Hendrik Marks, Michiel Vermeulen
Opublikowane w: Nature Communications, Numer 10/1, 2019, Strona(/y) 1525, ISSN 2041-1723
Wydawca: 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

Autorzy: Cathrin Gräwe; Miguel Hernandez-Quiles; Pascal W. T. C. Jansen; Annika Brimmers; Michiel Vermeulen
Opublikowane w: J. Proteome Res, Numer 22 (8), 2023, Strona(/y) 2683-2693, ISSN 1535-3893
Wydawca: American Chemical Society
DOI: 10.1021/acs.jproteome.3c00248

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

Autorzy: Dick W. Zijlmans; Miguel Hernández-Quiles; Pascal W.T.C. Jansen; Isabelle Becher; Frank Stein; Mikhail M. Savitski; Michiel Vermeulen
Opublikowane w: J Biol Chem, Numer 299 (11), 2023, Strona(/y) 105279, ISSN 0021-9258
Wydawca: 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

Autorzy: 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
Opublikowane w: Nature Biotechnology, 2023, ISSN 1087-0156
Wydawca: Nature Publishing Group
DOI: 10.1038/s41587-023-01715-w

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