Searched for: author%3A%22De+Ridder%2C+J.%22
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De Ridder, J. (author), Ripepi, V. (author), Aerts, C. (author), Palaversa, L. (author), Eyer, L. (author), Holl, B. (author), Audard, M. (author), Rimoldini, L. (author), Hladczuk, N.A. (author)
Context. The Gaia DR3 catalogue contains, for the first time, about 800 000 solutions with either orbital elements or trend parameters for astrometric, spectroscopic, and eclipsing binaries, and combinations of these three.<br/><br/>Aims. With this paper, we aim to illustrate the huge potential of this large non-single-star catalogue.<br/><br/...
journal article 2023
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De Ridder, J. (author), Ripepi, V. (author), Aerts, C. (author), Palaversa, L. (author), Eyer, L. (author), Holl, B. (author), Audard, M. (author), Rimoldini, L. (author), Hladczuk, N.A. (author)
Context. The third Gaia data release provides photometric time series covering 34 months for about 10 million stars. For many of those stars, a characterisation in Fourier space and their variability classification are also provided. This paper focuses on intermediate- to high-mass (IHM) main sequence pulsators (M'a ¥''1.3'M') of spectral...
journal article 2023
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De Ridder, J. (author), Ripepi, V. (author), Aerts, C. (author), Palaversa, L. (author), Eyer, L. (author), Holl, B. (author), Audard, M. (author), Rimoldini, L. (author), Hladczuk, N.A. (author)
Context. The Gaia mission of the European Space Agency (ESA) has been routinely observing Solar System objects (SSOs) since the beginning of its operations in August 2014. The Gaia data release three (DR3) includes, for the first time, the mean reflectance spectra of a selected sample of 60 518 SSOs, primarily asteroids, observed between August...
journal article 2023
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Allahyar, A. (author), Ubels, J. (author), de Ridder, J. (author)
Robustly predicting outcome for cancer patients from gene expression is an important challenge on the road to better personalized treatment. Network-based outcome predictors (NOPs), which considers the cellular wiring diagram in the classification, hold much promise to improve performance, stability and interpretability of identified marker...
journal article 2019
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Taskesen, E. (author), Huisman, S.M.H. (author), Mahfouz, A.M.E.T.A. (author), Krijthe, J.H. (author), de Ridder, J. (author), van de Stolpe, A. (author), van den Akker, E.B. (author), Verhaegh, Wim (author), Reinders, M.J.T. (author)
The use of genome-wide data in cancer research, for the identification of groups of patients with similar molecular characteristics, has become a standard approach for applications in therapy-response, prognosis-prediction, and drug-development. To progress in these applications, the trend is to move from single genome-wide measurements in a...
journal article 2016
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Gilroy, Kathryn L. (author), Terry, Anne (author), Naseer, Asif (author), de Ridder, J. (author), Allahyar, A. (author), Wang, Weiwei (author), Carpenter, Eric (author), Mason, Andrew (author), Wong, Gane K.S. (author), Cameron, Ewan R. (author), Kilbey, Anna (author), Neil, James C. (author)
Retroviruses have been foundational in cancer research since early studies identified protooncogenes as targets for insertional mutagenesis. Integration of murine gamma-retroviruses into the host genome favours promoters and enhancers and entails interaction of viral integrase with host BET/bromodomain factors. We report that this integration...
journal article 2016
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Allahyar, A. (author), De Ridder, J. (author)
Motivation: Breast cancer outcome prediction based on gene expression profiles is an important strategy for personalize patient care. To improve performance and consistency of discovered markers of the initial molecular classifiers, network-based outcome prediction methods (NOPs) have been proposed. In spite of the initial claims, recent studies...
journal article 2015
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Babaei, S. (author), Mahfouz, A.M.E.T.A. (author), Hulsman, M. (author), Lelieveldt, B.P.F. (author), De Ridder, J. (author), Reinders, M.J.T. (author)
The three dimensional conformation of the genome in the cell nucleus influences important biological processes such as gene expression regulation. Recent studies have shown a strong correlation between chromatin interactions and gene co-expression. However, predicting gene co-expression from frequent long-range chromatin interactions remains...
journal article 2015
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Rijlaarsdam, M.A. (author), Tax, D.M.J. (author), Gillis, A.J.M. (author), Dorssers, L.C.J. (author), Koestler, D.C. (author), De Ridder, J. (author), Looijenga, L.H.J. (author)
The cell of origin of the five subtypes (I-V) of germ cell tumors (GCTs) are assumed to be germ cells from different maturation stages. This is (potentially) reflected in their methylation status as fetal maturing primordial germ cells are globally demethylated during migration from the yolk sac to the gonad. Imprinted regions are erased in the...
journal article 2015
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Babaei, S. (author), Akhtar, W. (author), De Jong, J. (author), Reinders, M.J.T. (author), De Ridder, J. (author)
Genomically distal mutations can contribute to the deregulation of cancer genes by engaging in chromatin interactions. To study this, we overlay viral cancer-causing insertions obtained in a murine retroviral insertional mutagenesis screen with genome-wide chromatin conformation capture data. Here we find that insertions tend to cluster in 3D...
journal article 2015
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Taskesen, E. (author), Babaei, S. (author), Reinders, M.J.M. (author), De Ridder, J. (author)
Background Acute Myeloid Leukemia (AML) is characterized by various cytogenetic and molecular abnormalities. Detection of these abnormalities is important in the risk-classification of patients but requires laborious experimentation. Various studies showed that gene expression profiles (GEP), and the gene signatures derived from GEP, can be used...
journal article 2015
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De Ridder, J. (author), Meysman, P. (author), Oluwagbemi, O. (author), Abeel, T. (author)
Contributing to a student organization, such as the International Society for Computational Biology Student Council (ISCB-SC) and its Regional Student Group (RSG) program, takes time and energy. Both are scarce commodities, especially when you are trying to find your place in the world of computational biology as a graduate student. It comes as...
journal article 2014
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Hulsman, M. (author), Dimitrakopoulos, C. (author), De Ridder, J. (author)
MOTIVATION: The network architecture of physical protein interactions is an important determinant for the molecular functions that are carried out within each cell. To study this relation, the network architecture can be characterized by graph topological characteristics such as shortest paths and network hubs. These characteristics have an...
journal article 2014
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De Jong, J. (author), Akhtar, W. (author), Badhai, J. (author), Rust, A.G. (author), Rad, R. (author), Hilkens, J. (author), Berns, A. (author), Van Lohuizen, M. (author), Wessels, L.F.A. (author), De Ridder, J. (author)
The ability of retroviruses and transposons to insert their genetic material into host DNA makes them widely used tools in molecular biology, cancer research and gene therapy. However, these systems have biases that may strongly affect research outcomes. To address this issue, we generated very large datasets consisting of to unselected...
journal article 2014
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Huser, C.A. (author), Gilroy, K.L. (author), De Ridder, J. (author), Kilbey, A. (author), Borland, G. (author), Mackay, N. (author), Jenkins, A. (author), Bell, M. (author), Herzyk, P. (author), Van der Weyden, L. (author)
Retroviral insertional mutagenesis (RIM) is a powerful tool for cancer genomics that was combined in this study with deep sequencing (RIM/DS) to facilitate a comprehensive analysis of lymphoma progression. Transgenic mice expressing two potent collaborating oncogenes in the germ line (CD2-MYC, -Runx2) develop rapid onset tumours that can be...
journal article 2014
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De Ridder, J. (author), Bromberg, Y. (author), Michaut, M. (author), Satagopam, V.P. (author), Corpas, M. (author), MacIntyre, G. (author), Alexandrov, T. (author)
journal article 2013
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Yen, J. (author), White, R.M. (author), Wedge, D.C. (author), Van Loo, P. (author), De Ridder, J. (author), Capper, A. (author), Richardson, J. (author), Jones, D. (author), Raine, K. (author), Watson, I.R. (author)
Melanoma is the most deadly form of skin cancer. Expression of oncogenic BRAF or NRAS, which are frequently mutated in human melanomas, promote the formation of nevi but are not sufficient for tumorigenesis. Even with germline mutated p53, these engineered melanomas present with variable onset and pathology, implicating additional somatic...
journal article 2013
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De Ridder, J. (author), Abeel, T. (author), Michaut, M. (author), Satagopam, V.P. (author), Gehlenborg, N. (author)
You finished your PhD, have been a postdoc for a while, and you start wondering, "What's next?" Suppose you come to the conclusion that you want to stay in academia, and move up the ladder to become a principal investigator (PI). How does one reach this goal given that academia is one of the most competitive environments out there? And suppose...
journal article 2013
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Babaei, S. (author), Hulsman, M. (author), Reinders, M.J.T. (author), De Ridder, J. (author)
Background Delineating the molecular drivers of cancer, i.e. determining cancer genes and the pathways which they deregulate, is an important challenge in cancer research. In this study, we aim to identify pathways of frequently mutated genes by exploiting their network neighborhood encoded in the protein-protein interaction network. To this end...
journal article 2013
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de Ridder, J. (author), Bromberg, Y (author), Michaut, M (author), Satagopam, VP (author), Corpas, M (author), Macintyre, G (author), Alexandrov, T (author)
journal article 2013
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