Zeynep Kalender-Atak, PhD

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14q32 rearrangements deregulating BCL11B mark a distinct subgroup of T-lymphoid and myeloid immature acute leukemia

D Di Giacomo, R La Starza, P Gorello, F Pellanera, Z Kalender Atak, ...

Blood 138 (9), 773-784

2021

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Interpretation of allele-specific chromatin accessibility using cell state–aware deep learning

ZK Atak, II Taskiran, J Demeulemeester, C Flerin, D Mauduit, L Minnoye, ...

Genome research 31 (6), 1082-1096

2021

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A multi-omics analysis of metastatic melanoma identifies a germinal center-like tumor microenvironment in HLA-DR-positive tumor areas

L Gadeyne, Y Van Herck, G Milli, ZK Atak, MM Bolognesi, J Wouters, ...

Frontiers in oncology 11, 636057

2021

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Robust gene expression programs underlie recurrent cell states and phenotype switching in melanoma

J Wouters, Z Kalender-Atak, L Minnoye, KI Spanier, M De Waegeneer, ...

Nature Cell Biology 22 (8), 986-998

2020

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Deep learning and cross-species analysis on single-cell ATAC-seq data to decipher melanoma enhancer logic

II Taskiran, L Minnoye, Z Kalender Atak, S Aerts

Systems Biology: Global Regulation of Gene Expression, Location: New York …

2020

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Yin Yang 1 sustains biosynthetic demands during brain development in a stage-specific manner

L Zurkirchen, S Varum, S Giger, A Klug, J Häusel, R Bossart, M Zemke, ...

Nature communications 10 (1), 1-16

2019

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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 Cantù, E Marzorati, ...

Cell Stem Cell 24 (4), 637-653. e9

2019

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Deep learning on single-cell genomics data to decipher regulatory code

II Taskiran, L Minnoye, Z Kalender Atak, S Makhzami, V Christiaens, ...

3rd International Summer School on Deep Learning, Location: Warsaw, Poland

2019

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Prioritization of enhancer mutations by combining allele-specific chromatin accessibility with deep learning

ZK Atak, II Taskiran, C Flerin, D Mauduit, L Minnoye, G Hulsemans, ...

bioRxiv

2019

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Single-cell gene regulatory network analysis reveals new melanoma cell states and transition trajectories during phenotype switching

J Wouters, Z Kalender-Atak, L Minnoye, KI Spanier, M De Waegeneer, ...

BiorXiv, 715995

2019

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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

2018

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Mapping gene regulatory networks from single-cell omics data

MWEJ Fiers, L Minnoye, S Aibar, C Bravo González-Blas, Z Kalender Atak, ...

Briefings in functional genomics 17 (4), 246-254

2018

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Single-cell ATAC-seq during time-series experiment maps the regulatory dynamics of transcriptional state transition in melanoma

L Minnoye, C Bravo Gonzalez-Blas, J Wouters, Z Kalender Atak, ...

Single Cell Biology, Date: 2018/03/06-2018/03/08, Location: Wellcome Genome …

2018

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Identification of cis-regulatory mutations generating de novo edges in personalized cancer gene regulatory networks

Z Kalender Atak, H Imrichova, D Svetlichnyy, G Hulselmans, V Christiaens, ...

Genome medicine 9 (1), 1-13

2017

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SCENIC: single-cell regulatory network inference and clustering

S Aibar, CB González-Blas, T Moerman, VA Huynh-Thu, H Imrichova, ...

Nature methods 14 (11), 1083-1086

2017

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Decoding transcriptional states in cancer

J Wouters, ZK Atak, S Aerts

Current Opinion in Genetics & Development 43, 82-92

2017

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Gene regulatory network analysis in single cells

S Aibar, C Bravo González-Blas, J Wouters, T Moerman, VA Huynh-Thu, ...

Conference on Intelligent Systems for Molecular Biology and European …

2017

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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

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Gene regulatory network inference from single-cell RNA-seq data reveals high-resolution cellular states

S Aibar, H Imrichova, G Hulselmans, Z Kalender Atak, S Aerts

Single Cell Genomics, Date: 2016/09/14-2016/09/16, Location: Hinxton, UK

2016

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Gene regulatory network inference from single-cell RNA-seq reveals high-resolution cellular states

S Aibar, H Imrichova, G Hulselmans, Z Kalender Atak, S Aerts

The Brain Mosaic: cellular heterogeneity in the CNS, Date: 2016/09/22-2016 …

2016