Linking Transcription Factor Binding Dynamics to Promoter Output

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

Autori: 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
Pubblicato in: Nature Communications, Numero 11/1, 2020, ISSN 2041-1723
Editore: Nature Publishing Group
DOI: 10.1038/s41467-020-15155-6

LGR6 marks nephron progenitor cells

Autori: 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
Pubblicato in: Developmental Dynamics, Numero 13 April 2021, 2021, ISSN 1058-8388
Editore: John Wiley & Sons Inc.
DOI: 10.1002/dvdy.346

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

Autori: Wim J de Jonge, Mariël Brok, Philip Lijnzaad, Patrick Kemmeren, Frank CP Holstege
Pubblicato in: Molecular Systems Biology, Numero 16/10, 2020, ISSN 1744-4292
Editore: Nature Publishing Group
DOI: 10.15252/msb.20209885

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

Autori: Wim J. de Jonge, Mariël Brok, Patrick Kemmeren, Frank C.P. Holstege
Pubblicato in: STAR Protocols, Numero 1/1, 2020, Pagina/e 100020, ISSN 2666-1667
Editore: Elsevier
DOI: 10.1016/j.xpro.2020.100020

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

Autori: 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
Pubblicato in: Science Advances, Numero 7/6, 2021, Pagina/e eabd3311, ISSN 2375-2548
Editore: AAAS
DOI: 10.1126/sciadv.abd3311

Molecular mechanisms that distinguish TFIID housekeeping from regulatable SAGA promoters

Autori: Wim J de Jonge, Eoghan O'Duibhir, Philip Lijnzaad, Dik van Leenen, Marian JA Groot Koerkamp, Patrick Kemmeren, Frank CP Holstege
Pubblicato in: The EMBO Journal, Numero 36/3, 2017, Pagina/e 274-290, ISSN 0261-4189
Editore: Nature Publishing Group
DOI: 10.15252/embj.201695621

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

Autori: Jurrian K de Kanter, Philip Lijnzaad, Tito Candelli, Thanasis Margaritis, Frank C P Holstege
Pubblicato in: Nucleic Acids Research, 2019, ISSN 0305-1048
Editore: Oxford University Press
DOI: 10.1093/nar/gkz543

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

Autori: 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
Pubblicato in: Proceedings of the National Academy of Sciences, Numero 118/5, 2021, Pagina/e e2022350118, ISSN 0027-8424
Editore: National Academy of Sciences
DOI: 10.1073/pnas.2022350118

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

Autori: 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
Pubblicato in: Leukemia, Numero July 24 2021, 2021, ISSN 0887-6924
Editore: Nature Publishing Group
DOI: 10.1038/s41375-021-01341-y

Sharq, A versatile preprocessing and QC pipeline for Single Cell RNA-seq

Autori: Tito Candelli, Philip Lijnzaad, Mauro J Muraro, Hindrik Kerstens, Patrick Kemmeren, Alexander van Oudenaarden, Thanasis Margaritis, Frank Holstege
Pubblicato in: BioRxiv (preprint server), Numero 7 February 2018, 2018
Editore: CSHL
DOI: 10.1101/250811

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