Prolonged Ezh2 Depletion in Glioblastoma Causes a Robust Switch in Cell Fate Resulting in Tumor Progression

Nienke A. de Vries , Danielle Hulsman , Waseem Akhtar , Johann de Jong
Cell Reports 10 ( 3) 383 -397

52
2015
Chromatin Position Effects Assayed by Thousands of Reporters Integrated in Parallel

Waseem Akhtar , Johann de Jong , Alexey V. Pindyurin , Ludo Pagie
Cell 154 ( 4) 914 -927

224
2013
Deep learning for clustering of multivariate clinical patient trajectories with missing values.

Johann de Jong , Mohammad Asif Emon , Ping Wu , Reagon Karki
GigaScience 8 ( 11)

31
2019
An Explainable Multimodal Neural Network Architecture for Predicting Epilepsy Comorbidities Based on Administrative Claims Data

Johann De Jong , Victor Kiri , Chao Lu , Kathrin Haeffs
Frontiers in Artificial Intelligence 4

2021
Correction: Corrigendum: Using TRIP for genome-wide position effect analysis in cultured cells

Waseem Akhtar , Alexey V Pindyurin , Johann De Jong , Ludo Pagie
Nature Protocols 10 ( 4) 644 -644

2015
Analysis of a spatial gene expression database for sea anemone Nematostella vectensis during early development

Daniel Botman , Fredrik Jansson , Eric Röttinger , Mark Q Martindale
BMC Systems Biology 9 ( 1) 63 -63

5
2015
Towards realizing the vision of precision medicine: AI based prediction of clinical drug response.

Johann de Jong , Matthew Page , Ioana Cutcutache , Martin Armstrong
Brain

20
2021
Computational identification of insertional mutagenesis targets for cancer gene discovery

Johann de Jong , Jeroen de Ridder , Louise van der Weyden , Ning Sun
Nucleic Acids Research 39 ( 15)

24
2011
Dosage-dependent tumor suppression by histone deacetylases 1 and 2 through regulation of c-Myc collaborating genes and p53 function.

Marinus R. Heideman , Roel H. Wilting , Eva Yanover , Arno Velds
Blood 121 ( 11) 2038 -2050

64
2013
10
2017
Applications of DNA integrating elements: Facing the bias bully

Johann de Jong , Lodewyk F A Wessels , Maarten van Lohuizen , Jeroen de Ridder
Mobile genetic elements 4 ( 6) 1 -6

3
2014
A cell-based model of Nematostella vectensis gastrulation including bottle cell formation, invagination and zippering

Carlos Tamulonis , Marten Postma , Heather Q. Marlow , Craig R. Magie
Developmental Biology 351 ( 1) 217 -228

50
2011
3D hotspots of recurrent retroviral insertions reveal long-range interactions with cancer genes

Sepideh Babaei , Waseem Akhtar , Johann de Jong , Marcel Reinders
Nature Communications 6 ( 1) 6381 -6381

27
2015
Mutational genomics for cancer pathway discovery

Jeroen de Ridder , Jaap Kool , Anthony G. Uren , Jan Bot
pattern recognition in bioinformatics 35 -46

2013
Analysis of a spatial gene expression database for sea anemone Nematostella vectensis during early development

Daniel Botman , Fredrik Jansson , Eric Röttinger , Mark Q Martindale
BMC Systems Biology 9 ( 1) 63 -63

5
2015
A Computational Approach towards a Gene Regulatory Network for the Developing Nematostella vectensis Gut

Daniel Botman , Eric Röttinger , Mark Q Martindale , Johann de Jong
PLOS ONE 9 ( 7)

13
2014
Multiplexed Cas9 targeting reveals genomic location effects and gRNA-based staggered breaks influencing mutation efficiency.

Santiago Gisler , Joana P. Gonçalves , Waseem Akhtar , Johann de Jong
Nature Communications 10 ( 1) 1598

47
2019
TRIP through the chromatin: a high throughput exploration of enhancer regulatory landscapes.

Alexey V. Pindyurin , Johann de Jong , Waseem Akhtar
Genomics 106 ( 3) 171 -177

2015
Chromatin Landscapes of Retroviral and Transposon Integration Profiles

Johann de Jong , Waseem Akhtar , Jitendra Badhai , Alistair G. Rust
PLoS Genetics 10 ( 4) e1004250

62
2014
Chemical Profiling of the Genome With Anti-Cancer Drugs Defines Target Specificities

Baoxu Pang , Johann de Jong , Xiaohang Qiao , Lodewyk F A Wessels
Nature Chemical Biology 11 ( 7) 472 -480

32
2015