P. Molenaar publications

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Publications P. Molenaar

Position
Other Academic Staff
Main activities
Research, Other
Specialisation
Bioinformatics, Networks, High-throughput data analysis
Focus of research

Overall goal
The development of a dedicated bio-informatics platform to structure results of high-throughput experiments directed to pathway identification. This includes the testing of such a platform and providing a user-friendly solution to research groups identifying cellular pathways.
Reaching this goal
R2 is our in house developed web-based bioinformatics platform that enables graph-based 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). Through integration with Cytoscape, the resulting gene lists of this data analysis can be visualized directly as a network.
This provides access to a wealth of plugins to further functionally the network and derive new biologically testable hypotheses. Specifically the causal nature of time-series gene manipulation experiments can be explored in this way.
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 in a pathway context.
 

Amsterdam UMC Research Institutes
AMC departments
All publications

2020

  • Narayan Ravi S., Molenaar Piet, Teng Jian, Cornelissen Fleur M. G., Roelofs Irene, Menezes Renee, Dik Rogier, Lagerweij Tonny, Broersma Yoran, Petersen Naomi, Marin Soto Jhon Alexander, Brands Eelke, van Kuiken Philip, Lecca Maria C., Lenos Kristiaan J., in ‘t Veld Sjors G. J. G., van Wieringen Wessel, Lang Frederick F., Sulman Erik, Verhaak Roel, Baumert Brigitta G., Stalpers Lucas J. A., Vermeulen Louis, Watts Colin, Bailey David, Slotman Ben J., Versteeg Rogier, Noske David, Sminia Peter, Tannous Bakhos A., Wurdinger Tom, Koster Jan, Westerman Bart A. A cancer drug atlas enables synergistic targeting of independent drug vulnerabilities Nature communications 2020;11 (1) [PubMed]

2019

  • Hira V.V.V. No more hide and seek for glioma stem cells in their protective niches 2019. 183p. ISBN 9789463755757. [UvA Dissertations Online] University of Amsterdam. (Supervisor: Reits E.A.J.; Co-supervisor: Molenaar R.J.)

2018

  • Demchak Barry, Otasek David, Pico Alexander R., Bader Gary D., Ono Keiichiro, Settle Brett, Sage Eric, Morris John H., Longabaugh William, Lopes Christian, Kucera Michael, Treister Adam, Schwikowski Benno, Molenaar Piet, Ideker Trey The Cytoscape Automation app article collection [version 1; referees: Not peer reviewed] F1000Research 2018;7 [PubMed]

2017

  • 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]

2014

  • Pico Alexander R., Bader Gary D., Demchak Barry, Guitart Pla Oriol, Hull Timothy, Longabaugh William, Lopes Christian, Lotia Samad, Molenaar Piet, Montojo Jason, Morris John H., Ono Keiichiro, Schwikowski Benno, Welker David, Ideker Trey The Cytoscape app article collection F1000Research 2014;3:138 [PubMed]

2012

  • 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]

2008

  • van den Hoek A., van de Weerd J., Baayen D., Molenaar P., Sonder G. J., van Ouwerkerk I., de Vries Henry J. C. A persistent problem with scabies in and outside a nursing home in Amsterdam: indications for resistance to Lindane and Ivermectin Infectieziekten-bulletin 2008;6:204-206
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