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Linking Transcription Factor Binding Dynamics to Promoter Output

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Publications

An organoid biobank for childhood kidney cancers that captures disease and tissue heterogeneity

Author(s): Camilla Calandrini, Frans Schutgens, Rurika Oka, Thanasis Margaritis, Tito Candelli, Luka Mathijsen, Carola Ammerlaan, Ravian L. van Ineveld, Sepide Derakhshan, Sanne de Haan, Emmy Dolman, Philip Lijnzaad, Lars Custers, Harry Begthel, Hindrik H. D. Kerstens, Lindy L. Visser, Maarten Rookmaaker, Marianne Verhaar, Godelieve A. M. Tytgat, Patrick Kemmeren, Ronald R. de Krijger, Reem Al-Saadi, Kathy P
Published in: Nature Communications, Issue 11/1, 2020, ISSN 2041-1723
DOI: 10.1038/s41467-020-15155-6

LGR6 marks nephron progenitor cells

Author(s): Ravian L. Ineveld, Thanasis Margaritis, Berend A.P. Kooiman, Femke Groenveld, Hendrikus C.R. Ariese, Philip Lijnzaad, Hannah R. Johnson, Jeroen Korving, Ellen J. Wehrens, Frank Holstege, Jacco Rheenen, Jarno Drost, Anne C. Rios, Frank L. Bos
Published in: Developmental Dynamics, Issue 13 April 2021, 2021, ISSN 1058-8388
DOI: 10.1002/dvdy.346

Genome‐wide off‐rates reveal how DNA binding dynamics shape transcription factor function

Author(s): Wim J de Jonge, Mariël Brok, Philip Lijnzaad, Patrick Kemmeren, Frank CP Holstege
Published in: Molecular Systems Biology, Issue 16/10, 2020, ISSN 1744-4292
DOI: 10.15252/msb.20209885

An Optimized Chromatin Immunoprecipitation Protocol for Quantification of Protein-DNA Interactions

Author(s): Wim J. de Jonge, Mariël Brok, Patrick Kemmeren, Frank C.P. Holstege
Published in: STAR Protocols, Issue 1/1, 2020, Page(s) 100020, ISSN 2666-1667
DOI: 10.1016/j.xpro.2020.100020

Tumor to normal single-cell mRNA comparisons reveal a pan-neuroblastoma cancer cell

Author(s): Gerda Kildisiute, Waleed M. Kholosy, Matthew D. Young, Kenny Roberts, Rasa Elmentaite, Sander R. van Hooff, Clarissa N. Pacyna, Eleonora Khabirova, Alice Piapi, Christine Thevanesan, Eva Bugallo-Blanco, Christina Burke, Lira Mamanova, Kaylee M. Keller, Karin P.S. Langenberg-Ververgaert, Philip Lijnzaad, Thanasis Margaritis, Frank C.P. Holstege, Michelle L. Tas, Marc H.W.A. Wijnen, Max M. van Noese
Published in: Science Advances, Issue 7/6, 2021, Page(s) eabd3311, ISSN 2375-2548
DOI: 10.1126/sciadv.abd3311

Molecular mechanisms that distinguish TFIID housekeeping from regulatable SAGA promoters

Author(s): Wim J de Jonge, Eoghan O'Duibhir, Philip Lijnzaad, Dik van Leenen, Marian JA Groot Koerkamp, Patrick Kemmeren, Frank CP Holstege
Published in: The EMBO Journal, Issue 36/3, 2017, Page(s) 274-290, ISSN 0261-4189
DOI: 10.15252/embj.201695621

CHETAH: a selective, hierarchical cell type identification method for single-cell RNA sequencing

Author(s): Jurrian K de Kanter, Philip Lijnzaad, Tito Candelli, Thanasis Margaritis, Frank C P Holstege
Published in: Nucleic Acids Research, 2019, ISSN 0305-1048
DOI: 10.1093/nar/gkz543

Single-cell atlas of developing murine adrenal gland reveals relation of Schwann cell precursor signature to neuroblastoma phenotype

Author(s): Evelyn S. Hanemaaijer, Thanasis Margaritis, Karin Sanders, Frank L. Bos, Tito Candelli, Hanin Al-Saati, Max M. van Noesel, Friederike A. G. Meyer-Wentrup, Marc van de Wetering, Frank C. P. Holstege, Hans Clevers
Published in: Proceedings of the National Academy of Sciences, Issue 118/5, 2021, Page(s) e2022350118, ISSN 0027-8424
DOI: 10.1073/pnas.2022350118

Identification and characterization of relapse-initiating cells in MLL-rearranged infant ALL by single-cell transcriptomics

Author(s): Tito Candelli, Pauline Schneider, Patricia Garrido Castro, Luke A. Jones, Eduard Bodewes, Dedeke Rockx-Brouwer, Rob Pieters, Frank C. P. Holstege, Thanasis Margaritis, Ronald W. Stam
Published in: Leukemia, Issue July 24 2021, 2021, ISSN 0887-6924
DOI: 10.1038/s41375-021-01341-y