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Olfactomedin 4 serves as a marker for disease severity in pediatric respiratory syncytial virus (RSV) infection

Brand, H.K. (author), Ahout, I.M.L. (author), De Ridder, D. (author), Diepen, A. (author), Li, Y. (author), Zaalberg, M. (author), Andeweg, A. (author), Roeleveld, N. (author), De Groot, R. (author), Warris, A. (author), Hermans, P.W.M. (author), Ferwerda, G. (author), Staal, F.J.T. (author)

Background Respiratory viral infections follow an unpredictable clinical course in young children ranging from a common cold to respiratory failure. The transition from mild to severe disease occurs rapidly and is difficult to predict. The pathophysiology underlying disease severity has remained elusive. There is an urgent need to better...

journal article 2015

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Single-molecule protein sequencing through fingerprinting: Computational assessment

Yao, Y. (author), Docter, M. (author), De Ridder, D. (author), Joo, C. (author)

Proteins are vital in all biological systems as they constitute the main structural and functional components of cells. Recent advances in mass spectrometry have brought the promise of complete proteomics by helping draft the human proteome. Yet, this commonly used protein sequencing technique has fundamental limitations in sensitivity. Here we...

journal article 2015

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FERAL: Network-based classifier with application to breast cancer outcome prediction

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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Unbiased Quantitative Models of Protein Translation Derived from Ribosome Profiling Data

Gritsenko, A.A. (author), Hulsman, M. (author), Reinders, M.J.T. (author), De Ridder, D. (author)

Translation of RNA to protein is a core process for any living organism. While for some steps of this process the effect on protein production is understood, a holistic understanding of translation still remains elusive. In silico modelling is a promising approach for elucidating the process of protein synthesis. Although a number of...

journal article 2015

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Hi-C Chromatin Interaction Networks Predict Co-expression in the Mouse Cortex

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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Genome wide DNA methylation profiles provide clues to the origin and pathogenesis of germ cell tumors

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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Insight into neutral and disease-associated human genetic variants through interpretable predictors

Van den Berg, B.A. (author), Reinders, M.J.T. (author), De Ridder, D. (author), De Beer, T.A.P. (author)

A variety of methods that predict human nonsynonymous single nucleotide polymorphisms (SNPs) to be neutral or disease-associated have been developed over the last decade. These methods are used for pinpointing disease-associated variants in the many variants obtained with next-generation sequencing technologies. The high performances of current...

journal article 2015

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

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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Integration of gene expression and DNA-methylation profiles improves molecular subtype classification in acute myeloid leukemia

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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Soft Skills: An Important Asset Acquired from Organizing Regional Student Group Activities

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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Scale-space measures for graph topology link protein network architecture to function

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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Chromatin Landscapes of Retroviral and Transposon Integration Profiles

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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SPiCE: A web-based tool for sequence-based protein classification and exploration

Van den Berg, B.A. (author), Reinders, M.J. (author), Roubos, J.A. (author), De Ridder, D. (author)

Background Amino acid sequences and features extracted from such sequences have been used to predict many protein properties, such as subcellular localization or solubility, using classifier algorithms. Although software tools are available for both feature extraction and classifier construction, their application is not straightforward,...

journal article 2014

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The young PI Buzz: Learning from the organizers of the junior principal investigator meeting at ISMB-ECCB 2013

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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The genetic heterogeneity and mutational burden of engineered melanomas in zebrafish model

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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Perception of length to width relations of city squares

Nefs, H.T. (author), Van Bilsen, A. (author), Pont, S.C. (author), De Ridder, H. (author), Wijntjes, M.W.A. (author), Van Doorn, A.J. (author)

In this paper, we focus on how people perceive the aspect ratio of city squares. Earlier research has focused on distance perception but not so much on the perceived aspect ratio of the surrounding space. Furthermore, those studies have focused on “open” spaces rather than urban areas enclosed by walls, houses and filled with people, cars, etc....

journal article 2013

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Don't Wear Your New Shoes (Yet): Taking the Right Steps to Become a Successful Principal Investigator

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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Detecting recurrent gene mutation in interaction network context using multi-scale graph diffusion

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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Understanding Regulation of Metabolism through Feasibility Analysis

Nikerel, I.E. (author), Berkhout, J. (author), Hu, F. (author), Teusink, B. (author), Reinders, M.J.T. (author), De Ridder, D. (author)

Understanding cellular regulation of metabolism is a major challenge in systems biology. Thus far, the main assumption was that enzyme levels are key regulators in metabolic networks. However, regulation analysis recently showed that metabolism is rarely controlled via enzyme levels only, but through non-obvious combinations of hierarchical ...

journal article 2012

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GRASS: A generic algorithm for scaffolding next-generation sequencing assemblies

Gritsenko, A.A. (author), Nijkamp, J.F. (author), Reinders, M.J.T. (author), De Ridder, D. (author)

Motivation: The increasing availability of second-generation highthroughput sequencing (HTS) technologies has sparked a growing interest in de novo genome sequencing. This in turn has fueled the need for reliable means of obtaining high-quality draft genomes from short-read sequencing data. The millions of reads usually involved in HTS...

journal article 2012