Z
Zeynep Kalender Atak
Researcher at Katholieke Universiteit Leuven
Publications - 28
Citations - 5736
Zeynep Kalender Atak is an academic researcher from Katholieke Universiteit Leuven. The author has contributed to research in topics: Gene regulatory network & Enhancer. The author has an hindex of 16, co-authored 27 publications receiving 3022 citations. Previous affiliations of Zeynep Kalender Atak include University of Cambridge.
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SCENIC: single-cell regulatory network inference and clustering.
Sara Aibar,Carmen Bravo González-Blas,Thomas Moerman,Vân Anh Huynh-Thu,Hana Imrichova,Gert Hulselmans,Florian Rambow,Jean-Christophe Marine,Pierre Geurts,Jan Aerts,Joost van den Oord,Zeynep Kalender Atak,Jasper Wouters,Stein Aerts +13 more
TL;DR: On a compendium of single-cell data from tumors and brain, it is demonstrated that cis-regulatory analysis can be exploited to guide the identification of transcription factors and cell states.
Posted ContentDOI
SCENIC: Single-Cell Regulatory Network Inference And Clustering
Sara Aibar,Carmen Bravo González-Blas,Thomas Moerman,Jasper Wouters,Vân Anh Huynh-Thu,Hana Imrichova,Zeynep Kalender Atak,Gert Hulselmans,Michael Dewaele,Florian Rambow,Pierre Geurts,Jan Aerts,Jean-Christophe Marine,Joost van den Oord,Stein Aerts +14 more
TL;DR: SCENIC (Single Cell rEgulatory Network Inference and Clustering) is the first method to analyze scRNA-seq data using a network-centric, rather than cell-centric approach and allows for the simultaneous tracing of genomic regulatory programs and the mapping of cellular identities emerging from these programs.
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iRegulon: from a gene list to a gene regulatory network using large motif and track collections.
Rekin's Janky,Annelien Verfaillie,Hana Imrichova,Bram Van de Sande,Laura Standaert,Valerie Christiaens,Gert Hulselmans,Koen Herten,Marina Naval Sanchez,Delphine Potier,Dmitry Svetlichnyy,Zeynep Kalender Atak,Mark Fiers,Jean-Christophe Marine,Stein Aerts +14 more
TL;DR: Over-activate p53 in breast cancer cells, followed by RNA-seq and ChIP-seq, and could identify an extensive up-regulated network controlled directly by p53 and a repressive network with no indication of direct p53 regulation but rather an indirect effect via E2F and NFY are mapped.
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Exome sequencing identifies mutation in CNOT3 and ribosomal genes RPL5 and RPL10 in T-cell acute lymphoblastic leukemia
Kim De Keersmaecker,Zeynep Kalender Atak,Ning Li,Carmen Vicente,Stephanie Patchett,Tiziana Girardi,Valentina Gianfelici,Ellen Geerdens,Emmanuelle Clappier,Michaël Porcu,Idoya Lahortiga,Rossella Luca,Jiekun Yan,Gert Hulselmans,Hilde Vranckx,Roel Vandepoel,Bram Sweron,Kris Jacobs,Nicole Mentens,Iwona Wlodarska,Barbara Cauwelier,Jacqueline Cloos,Jean Soulier,Anne Uyttebroeck,Claudia Bagni,Bassem A. Hassan,Peter Vandenberghe,Arlen W. Johnson,Stein Aerts,Jan Cools +29 more
TL;DR: Exome sequencing on 67 T-ALLs is used to gain insight into the mutational spectrum in these leukemias and identify the ribosome as a potential oncogenic factor.
Journal ArticleDOI
Decoding the regulatory landscape of melanoma reveals TEADS as regulators of the invasive cell state
Annelien Verfaillie,Hana Imrichova,Zeynep Kalender Atak,Michael Dewaele,Florian Rambow,Gert Hulselmans,Valerie Christiaens,Dmitry Svetlichnyy,Flavie Luciani,Laura Van den Mooter,Sofie Claerhout,Mark Fiers,Fabrice Journe,Ghanem Elias Ghanem,Carl Herrmann,Georg Halder,Jean-Christophe Marine,Stein Aerts +17 more
TL;DR: Using regulatory landscapes and in silico analysis, it is shown that transcriptional reprogramming underlies the distinct cellular states present in melanoma and reveals an essential role for the TEADs, linking it to clinically relevant mechanisms such as invasion and resistance.