Linking Transcription Factor Binding Dynamics to Promoter Output

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

Autores: 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
Publicado en: Nature Communications, Edición 11/1, 2020, ISSN 2041-1723
Editor: Nature Publishing Group
DOI: 10.1038/s41467-020-15155-6

LGR6 marks nephron progenitor cells

Autores: 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
Publicado en: Developmental Dynamics, Edición 13 April 2021, 2021, ISSN 1058-8388
Editor: John Wiley & Sons Inc.
DOI: 10.1002/dvdy.346

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

Autores: Wim J de Jonge, Mariël Brok, Philip Lijnzaad, Patrick Kemmeren, Frank CP Holstege
Publicado en: Molecular Systems Biology, Edición 16/10, 2020, ISSN 1744-4292
Editor: Nature Publishing Group
DOI: 10.15252/msb.20209885

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

Autores: Wim J. de Jonge, Mariël Brok, Patrick Kemmeren, Frank C.P. Holstege
Publicado en: STAR Protocols, Edición 1/1, 2020, Página(s) 100020, ISSN 2666-1667
Editor: Elsevier
DOI: 10.1016/j.xpro.2020.100020

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

Autores: 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
Publicado en: Science Advances, Edición 7/6, 2021, Página(s) eabd3311, ISSN 2375-2548
Editor: AAAS
DOI: 10.1126/sciadv.abd3311

Molecular mechanisms that distinguish TFIID housekeeping from regulatable SAGA promoters

Autores: Wim J de Jonge, Eoghan O'Duibhir, Philip Lijnzaad, Dik van Leenen, Marian JA Groot Koerkamp, Patrick Kemmeren, Frank CP Holstege
Publicado en: The EMBO Journal, Edición 36/3, 2017, Página(s) 274-290, ISSN 0261-4189
Editor: Nature Publishing Group
DOI: 10.15252/embj.201695621

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

Autores: Jurrian K de Kanter, Philip Lijnzaad, Tito Candelli, Thanasis Margaritis, Frank C P Holstege
Publicado en: Nucleic Acids Research, 2019, ISSN 0305-1048
Editor: 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

Autores: 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
Publicado en: Proceedings of the National Academy of Sciences, Edición 118/5, 2021, Página(s) e2022350118, ISSN 0027-8424
Editor: 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

Autores: 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
Publicado en: Leukemia, Edición July 24 2021, 2021, ISSN 0887-6924
Editor: Nature Publishing Group
DOI: 10.1038/s41375-021-01341-y

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

Autores: Tito Candelli, Philip Lijnzaad, Mauro J Muraro, Hindrik Kerstens, Patrick Kemmeren, Alexander van Oudenaarden, Thanasis Margaritis, Frank Holstege
Publicado en: BioRxiv (preprint server), Edición 7 February 2018, 2018
Editor: CSHL
DOI: 10.1101/250811

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