fluff: exploratory analysis and visualization of high-throughput sequencing data by Georgios Georgiou, Simon J. van Heeringen

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Investigating the effect of dependence between conditions with Bayesian Linear Mixed Models for motif activity analysis. by Simone Lederer, Tom Heskes, Simon J van Heeringen, Cornelis A Albers

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Role of p53 serine 46 in p53 target gene regulation. by Leonie Smeenk, Simon J van Heeringen, Max Koeppel, Bianca Gilbert, Eva Janssen-Megens, Hendrik G Stunnenberg, Marion Lohrum

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Seq2science: an end-to-end workflow for functional genomics analysis by Maarten van der Sande, Siebren Frölich, Tilman Schäfers, Jos G.A. Smits, Rebecca R. Snabel, Sybren Rinzema, Simon J. van Heeringen

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scANANSE gene regulatory network and motif analysis of single-cell clusters [version 2; peer review: 2 approved] by Julian A. Arts, Siebren Frölich, Jos G.A. Smits, Huiqing Zhou, Joost H.A. Martens, Simon J. van Heeringen, Rebecca R. Snabel, Branco M.H. Heuts

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Regulatory remodeling in the allo-tetraploid frog Xenopus laevis by Dei M. Elurbe, Sarita S. Paranjpe, Georgios Georgiou, Ila van Kruijsbergen, Ozren Bogdanovic, Romain Gibeaux, Rebecca Heald, Ryan Lister, Martijn A. Huynen, Simon J. van Heeringen, Gert Jan C. Veenstra

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Genetic identification of a network of factors that functionally interact with the nucleosome remodeling ATPase ISWI. by Giosalba Burgio, Gaspare La Rocca, Anna Sala, Walter Arancio, Dario Di Gesù, Marianna Collesano, Adam S Sperling, Jennifer A Armstrong, Simon J van Heeringen, Colin Logie, John W Tamkun, Davide F V Corona

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WDR5, BRCA1, and BARD1 Co-regulate the DNA Damage Response and Modulate the Mesenchymal-to-Epithelial Transition during Early Reprogramming by Georgina Peñalosa-Ruiz, Vicky Bousgouni, Jan P. Gerlach, Susan Waarlo, Joris V. van de Ven, Tim E. Veenstra, José C.R. Silva, Simon J. van Heeringen, Chris Bakal, Klaas W. Mulder, Gert Jan C. Veenstra

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Dendritic Cells Actively Limit Interleukin-10 Production Under Inflammatory Conditions via DC-SCRIPT and Dual-Specificity Phosphatase 4 by Jonas Nørskov Søndergaard, Simon J. van Heeringen, Maaike W. G. Looman, Chunling Tang, Vassilis Triantis, Pauline Louche, Eva M. Janssen-Megens, Anieta M. Sieuwerts, John W. M. Martens, Colin Logie, Hendrik G. Stunnenberg, Marleen Ansems, Gosse J. Adema

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Identification of the regulatory circuit governing corneal epithelial fate determination and disease. by Jos G A Smits, Dulce Lima Cunha, Maryam Amini, Marina Bertolin, Camille Laberthonnière, Jieqiong Qu, Nicholas Owen, Lorenz Latta, Berthold Seitz, Lauriane N Roux, Tanja Stachon, Stefano Ferrari, Mariya Moosajee, Daniel Aberdam, Nora Szentmary, Simon J van Heeringen, Huiqing Zhou

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p63 exerts spatio-temporal control of palatal epithelial cell fate to prevent cleft palate. by Rose Richardson, Karen Mitchell, Nigel L Hammond, Maria Rosaria Mollo, Evelyn N Kouwenhoven, Niki D Wyatt, Ian J Donaldson, Leo Zeef, Tim Burgis, Rognvald Blance, Simon J van Heeringen, Hendrik G Stunnenberg, Huiqing Zhou, Caterina Missero, Rose Anne Romano, Satrajit Sinha, Michael J Dixon, Jill Dixon

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Multi-omics analysis reveals distinct gene regulatory mechanisms between primary and organoid-derived human hepatocytes by Haoyu Wu, Annie S. P. Yang, Suzan Stelloo, Floris J. M. Roos, René H. M. te Morsche, Anne H. Verkerk, Maria V. Luna-Velez, Laura Wingens, Johannes H. W. de Wilt, Robert W. Sauerwein, Klaas W. Mulder, Simon J. van Heeringen, Monique M. A. Verstegen, Luc J. W. van der Laan, Hendrik Marks, Richárd Bártfai

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Genome-wide profiling of p63 DNA-binding sites identifies an element that regulates gene expression during limb development in the 7q21 SHFM1 locus. by Evelyn N Kouwenhoven, Simon J van Heeringen, Juan J Tena, Martin Oti, Bas E Dutilh, M Eva Alonso, Elisa de la Calle-Mustienes, Leonie Smeenk, Tuula Rinne, Lilian Parsaulian, Emine Bolat, Rasa Jurgelenaite, Martijn A Huynen, Alexander Hoischen, Joris A Veltman, Han G Brunner, Tony Roscioli, Emily Oates, Meredith Wilson, Miguel Manzanares, José Luis Gómez-Skarmeta, Hendrik G Stunnenberg, Marion Lohrum, Hans van Bokhoven, Huiqing Zhou

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