Zeynep Kalender Atak
Zeynep Kalender Atak
Research Associate at CRUK Cambridge Institute, Cambridge University
Verified email at cruk.cam.ac.uk
TitleCited byYear
iRegulon: from a gene list to a gene regulatory network using large motif and track collections
A Verfaillie, H ImrichovŠ, B Van de Sande, L Standaert, V Christiaens, ...
PLoS computational biology 10 (7), e1003731, 2014
3192014
Exome sequencing identifies mutation in CNOT3 and ribosomal genes RPL5 and RPL10 in T-cell acute lymphoblastic leukemia
K De Keersmaecker, ZK Atak, N Li, C Vicente, S Patchett, T Girardi, ...
Nature genetics 45 (2), 186, 2013
3072013
SCENIC: single-cell regulatory network inference and clustering
S Aibar, CB GonzŠlez-Blas, T Moerman, H Imrichova, G Hulselmans, ...
Nature methods 14 (11), 1083, 2017
2192017
Decoding the regulatory landscape of melanoma reveals TEADS as regulators of the invasive cell state
A Verfaillie, H Imrichova, ZK Atak, M Dewaele, F Rambow, G Hulselmans, ...
Nature communications 6, 6683, 2015
1532015
Comprehensive analysis of transcriptome variation uncovers known and novel driver events in T-cell acute lymphoblastic leukemia
ZK Atak, V Gianfelici, G Hulselmans, K De Keersmaecker, AG Devasia, ...
PLoS genetics 9 (12), e1003997, 2013
1112013
Mutation analysis of the tyrosine phosphatase PTPN2 in Hodgkin’s lymphoma and T-cell non-Hodgkin’s lymphoma
M Kleppe, T Tousseyn, E Geissinger, ZK Atak, S Aerts, A Rosenwald, ...
Haematologica 96 (11), 1723-1727, 2011
732011
High accuracy mutation detection in leukemia on a selected panel of cancer genes
ZK Atak, K De Keersmaecker, V Gianfelici, E Geerdens, R Vandepoel, ...
PloS one 7 (6), e38463, 2012
672012
Identification of a novel, recurrent MBTD1‐CXorf67 fusion in low‐grade endometrial stromal sarcoma
B Dewaele, J Przybyl, A Quattrone, J Finalet Ferreiro, V Vanspauwen, ...
International journal of cancer 134 (5), 1112-1122, 2014
632014
i-cisTarget 2015 update: generalized cis-regulatory enrichment analysis in human, mouse and fly
H ImrichovŠ, G Hulselmans, Z Kalender Atak, D Potier, S Aerts
Nucleic acids research 43 (W1), W57-W64, 2015
522015
The Drosophila homologue of the amyloid precursor protein is a conserved modulator of Wnt PCP signaling
A Soldano, Z Okray, P Janovska, K TmejovŠ, E Reynaud, A Claeys, J Yan, ...
PLoS biology 11 (5), e1001562, 2013
472013
Mapping gene regulatory networks from single-cell omics data
MWEJ Fiers, L Minnoye, S Aibar, C Bravo GonzŠlez-Blas, Z Kalender Atak, ...
Briefings in functional genomics 17 (4), 246-254, 2018
412018
Multiplex enhancer-reporter assays uncover unsophisticated TP53 enhancer logic
A Verfaillie, D Svetlichnyy, H Imrichova, K Davie, M Fiers, ZK Atak, ...
Genome research 26 (7), 882-895, 2016
352016
Variations in the exome of the LNCaP prostate cancer cell line
L Spans, ZK Atak, F Van Nieuwerburgh, D Deforce, E Lerut, S Aerts, ...
The Prostate 72 (12), 1317-1327, 2012
182012
Identification of high-impact cis-regulatory mutations using transcription factor specific random forest models
D Svetlichnyy, H Imrichova, M Fiers, ZK Atak, S Aerts
PLoS computational biology 11 (11), e1004590, 2015
162015
Using cisTargetX to Predict Transcriptional Targets and Networks in Drosophila
D Potier, ZK Atak, MN Sanchez, C Herrmann, S Aerts
Gene Regulatory Networks, 291-314, 2012
122012
Identification of cis-regulatory mutations generating de novo edges in personalized cancer gene regulatory networks
ZK Atak, H Imrichova, D Svetlichnyy, G Hulselmans, V Christiaens, ...
Genome medicine 9 (1), 80, 2017
62017
Decoding transcriptional states in cancer
J Wouters, ZK Atak, S Aerts
Current opinion in genetics & development 43, 82-92, 2017
42017
Yin Yang 1 Orchestrates a Metabolic Program Required for Both Neural Crest Development and Melanoma Formation
S Varum, A Baggiolini, L Zurkirchen, ZK Atak, C Cantý, E Marzorati, ...
Cell Stem Cell 24 (4), 637-653. e9, 2019
22019
A comprehensive inventory of TLX1 controlled long non-coding RNAs in T-cell acute lymphoblastic leukemia through polyA+ and total RNA sequencing
K Verboom, W Van Loocke, PJ Volders, B Decaesteker, FA Cobos, ...
haematologica 103 (12), e585-e589, 2018
22018
Discovery of regulators for co-expressed human genes using large sequence search spaces
B Van de Sande, ZK Atak, S Aerts
Bioinformatics for Regulatory Genomics (BioRegSIG) Special Interest Group†…, 2011
12011
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Articles 1–20