J.J.B. Koster PhD

PhD J.J.B. Koster

Positions

Associate Professor, Research Associate

Main activities

Research

Specialisation

bioinformatics, genomics, high-throughput analyses

Focus of research

Overall goal

Development of a dedicated bioinformatics platform, loaded with tools and methods which allow wetlab biologists to interpret their own high-throughput experiments (mircoarray data,chip on chip, whole genome sequencing).

Reaching this goal

R2 is our in house developed web-based bioinformatics analysis and visualization platform that enables analysis of probable targets in the context of (tumor) microarray data (url: http://r2.amc.nl). Specifically focusing at biologists, R2 aids in the analysis and visualization of microarray data (tumor series, experiments) and their annotated features (such as clinical information). R2 contains an expanding set of analyses which are heavily inter-connected, allowing users to quickly hop from one view (representation of the data) to another. Currently R2 supports all major chip designs for human, mouse and rat and harbors nearly 30.000 microarray samples (divided over more than 250 datasets). R2 is also being employed in the integration, analysis and visualization of aCGH / ChIP on chip / Whole genome sequence information.

Public use of the project results

The main research-objective of our group is the fast translation of probable drug targets for childhood tumors from the wet-lab to the clinic. The tools developed are used to determine these targets.

Amsterdam UMC Research Institutes

AMC departments

Oncogenomics

Key publications

Molenaar Jan J., Koster Jan, Zwijnenburg Danny A., van Sluis Peter, Valentijn Linda J., van der Ploeg Ida, Hamdi Mohamed, van Nes Johan, Westerman Bart A., van Arkel Jennemiek, Ebus Marli E., Haneveld Franciska, Lakeman Arjan, Schild Linda, Molenaar Piet, Stroeken Peter, van Noesel Max M., Ora Ingrid, Santo Evan E., Caron Huib N., Westerhout Ellen M., Versteeg Rogier Sequencing of neuroblastoma identifies chromothripsis and defects in neuritogenesis genes Nature 2012;483 (7391):589-U107 [PubMed]
Valentijn Linda J., Koster Jan, Zwijnenburg Danny A., Hasselt Nancy E., van Sluis Peter, Volckmann Richard, van Noesel Max M., George Rani E., Tytgat Godelieve A. M., Molenaar Jan J., Versteeg Rogier TERT rearrangements are frequent in neuroblastoma and identify aggressive tumors Nature genetics 2015;47 (12):1411-+ [PubMed]
Eleveld Thomas F., Oldridge Derek A., Bernard Virginie, Koster Jan, Daage Leo Colmet, Diskin Sharon J., Schild Linda, Bentahar Nadia Bessoltane, Bellini Angela, Chicard Mathieu, Lapouble Eve, Combaret Valérie, Legoix-Né Patricia, Michon Jean, Pugh Trevor J., Hart Lori S., Rader JulieAnn, Attiyeh Edward F., Wei Jun S., Zhang Shile, Naranjo Arlene, Gastier-Foster Julie M., Hogarty Michael D., Asgharzadeh Shahab, Smith Malcolm A., Guidry Auvil Jaime M., Watkins Thomas B. K., Zwijnenburg Danny A., Ebus Marli E., van Sluis Peter, Hakkert Anne, van Wezel Esther, van der Schoot C. Ellen, Westerhout Ellen M., Schulte Johannes H., Tytgat Godelieve A., Dolman M. Emmy M., Janoueix-Lerosey Isabelle, Gerhard Daniela S., Caron Huib N., Delattre Olivier, Khan Javed, Versteeg Rogier, Schleiermacher Gudrun, Molenaar Jan J., Maris John M. Relapsed neuroblastomas show frequent RAS-MAPK pathway mutations Nature genetics 2015;47 (8):864-871 [PubMed]
van Groningen Tim, Koster Jan, Valentijn Linda J., Zwijnenburg Danny A., Akogul Nurdan, Hasselt Nancy E., Broekmans Marloes, Haneveld Franciska, Nowakowska Natalia E., Bras Johannes, van Noesel Carel J. M., Jongejan Aldo, van Kampen Antoine H., Koster Linda, Baas Frank, van Dijk-Kerkhoven Lianne, Huizer-Smit Margriet, Lecca Maria C., Chan Alvin, Lakeman Arjan, Molenaar Piet, Volckmann Richard, Westerhout Ellen M., Hamdi Mohamed, van Sluis Peter G., Ebus Marli E., Molenaar Jan J., Tytgat Godelieve A., Westerman Bart A., van Nes Johan, Versteeg Rogier Neuroblastoma is composed of two super-enhancer-associated differentiation states Nature genetics 2017;49 (8):1261-1266 [PubMed]
Valentijn Linda J., Koster Jan, Haneveld Franciska, Aissa Rachida Ait, van Sluis Peter, Broekmans Marloes E. C., Molenaar Jan J., van Nes Johan, Versteeg Rogier Functional MYCN signature predicts outcome of neuroblastoma irrespective of MYCN amplification Proceedings of the National Academy of Sciences of the United States of America 2012;109 (47):19190-19195 [PubMed]