- document
-
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
- document
-
Van Geenhuizen, M.S. (author), Schoonman, J. (author), Reinders, A.H.M.E. (author)Places of large potentials of sustainable energy production and places of energy consumption are often very different and separated by large distances across the globe. This paper first discusses potentials of solar technology in terms of global availability using PV technology and actual energy production. Solar energy is widely under-used and...conference paper 2012
- document
- Winterbach, W. (author), De Ridder, D. (author), Wang, H.J. (author), Reinders, M. (author), Van Mieghem, P. (author) conference paper 2012
- document
-
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
- document
-
Nijkamp, J.F. (author), Van den Broek, M.A. (author), Datema, E. (author), De Kok, S. (author), Bosman, L. (author), Luttik, M.A.H. (author), Daran-Lapujade, P.A.S. (author), Vongsangnak, W. (author), Nielsen, J. (author), Heijne, W.H.M. (author), Klaassen, P. (author), Paddon, C.J. (author), Platt, D. (author), Kötter, P. (author), Van Ham, R.C. (author), Reinders, M.J.T. (author), Pronk, J.T. (author), De Ridder, D. (author), Daran, J.M. (author)Saccharomyces cerevisiae CEN.PK 113-7D is widely used for metabolic engineering and systems biology research in industry and academia. We sequenced, assembled, annotated and analyzed its genome. Single-nucleotide variations (SNV), insertions/deletions (indels) and differences in genome organization compared to the reference strain S. cerevisiae...journal article 2012
- document
-
Babaei, S. (author), Hulsman, M. (author), Reinders, M.J.T. (author), de Ridder, J. (author)We introduce a multi-scale kernel diffusion framework and apply it to a large collection of murine retroviral insertional mutagenesis data. The diffusion strength plays the role of scale parameter. As a result, in addition to detecting genes with frequent mutations in their genomic vicinity (red nodes in the interaction graph) we can also find...poster 2012
- document
- van den Berg, B.A. (author), Reinders, M.J.T. (author), Pel, HJ (author), Roubos, J.A. (author), de Ridder, D. (author) poster 2012
- document
- Reinders, A. (author) public lecture 2011
- document
-
van den Berg, B.A. (author), Reinders, M.J.T. (author), Pel, HJ (author), Wu, L (author), Roubos, J.A. (author), de Ridder, D. (author)Aspergillus niger is widely used for industrial enzyme production. Knowledge on high-level protein secretion could be useful to improve production rates. We used sequencebased classification methods to identify important properties<br/>for successful high-level secretion, which will be used to redesign proteins for improved secretion.poster 2011
- document
-
Sontrop, H.M.J. (author), Verhaegh, W.F.J. (author), Reinders, M.J.T. (author), Moerland, P.D. (author)In recent years increasing evidence appeared that breast cancer may not constitute a single disease at the molecular level, but comprises a heterogeneous set of subtypes. This suggests that instead of building a single monolithic predictor, better predictors might be constructed that solely target samples of a designated subtype, which are...journal article 2011
- document
-
Taskesen, E. (author), Havermans, Marije (author), van Lom, Kirsten (author), Sanders, Mathijs (author), van Norden, Yvette (author), Bindels, Eric (author), Hoogenboezem, Remco (author), Reinders, M.J.T. (author), Valk, P.J.M. (author)Acute Myeloid Leukemia is a highly diverse disease containing many cytogenetic and molecular abnormalities. We analyzed the DNA methylation<br/>(DMP) and gene expression profiles (GEP) of 344 AML patients using an unsupervised and supervised approach. We hypothesized to better<br/>characterize the disease phenotype by combing these features as...poster 2011
- document
- Hulsman, M. (author), Unadkat, HV (author), Cornelissen, Kamiel (author), de Boer, Jan (author), Reinders, M.J.T. (author) poster 2011
- document
- Winterbach, W. (author), Wang, H. (author), Reinders, M. (author), Van Mieghem, P. (author), De Ridder, D. (author) conference paper 2010
- document
-
Winterbach, W. (author), Wang, H. (author), Reinders, M. (author), Van Mieghem, P. (author), De Ridder, D. (author)Biological networks exhibit intriguing topological properties such as small-worldness. In this paper, we investigate whether the topology of a metabolic network is related to its robustness. We do so by perturbing a metabolic system in silico, one reaction at a time and studying the correlations between growth, as predicted by flux balance...conference paper 2010
- document
-
De Ronde, J.J. (author), Klijn, C. (author), Velds, A. (author), Holstege, H. (author), Reinders, M.J.T. (author), Jonkers, J. (author), Wessels, L.F.A. (author)Background: Most approaches used to find recurrent or differential DNA Copy Number Alterations (CNA) in array Comparative Genomic Hybridization (aCGH) data from groups of tumour samples depend on the discretization of the aCGH data to gain, loss or no-change states. This causes loss of valuable biological information in tumour samples, which are...journal article 2010
- document
-
Nijkamp, J.F. (author), Winterbach, W. (author), Van den Broek, M. (author), Daran, J.M. (author), Reinders, M.J.T. (author), De Ridder, D. (author)De novo assembly of a eukaryotic genome with next-generation sequencing data is still a challenging task. Over the past few years several assemblers have been developed, often suitable for one specific type of sequencing data. The number of known genomes is expanding rapidly, therefore it becomes possible to use multiple reference genomes for...journal article 2010
- document
-
De Ridder, J. (author), Gerrits, A. (author), Bot, J. (author), De Haan, G. (author), Reinders, M. (author), Wessels, L. (author)We propose an efficient method to infer combinatorial association logic networks from multiple genome-wide measurements from the same sample. We demonstrate our method on a genetical genomics dataset, in which we search for Boolean combinations of multiple genetic loci that associate with transcript levels. Our method provably finds the global...journal article 2010
- document
-
Taskesen, E. (author), Beekman, R. (author), De Ridder, J. (author), Wouters, B.J. (author), Peeters, J.K. (author), Touw, I.P. (author), Reinders, M.J.T. (author), Delwel, R. (author)Background: Tiling-arrays are applicable to multiple types of biological research questions. Due to its advantages (high sensitivity, resolution, unbiased), the technology is often employed in genome-wide investigations. A major challenge in the analysis of tiling-array data is to define regions-of-interest, i.e., contiguous probes with...journal article 2010
- document
-
Hulsman, M. (author), Mentink, A. (author), Van Someren, E.P. (author), Dechering, K.J. (author), De Boer, J. (author), Reinders, M.J.T. (author)Background: Oligonucleotide arrays have become one of the most widely used high-throughput tools in biology. Due to their sensitivity to experimental conditions, normalization is a crucial step when comparing measurements from these arrays. Normalization is, however, far from a solved problem. Frequently, we encounter datasets with significant...journal article 2010
- document
-
Klijn, C. (author), Bot, J. (author), Adams, D.J. (author), Reinders, M. (author), Wessels, L. (author), Jonkers, J. (author)Tumorigenesis is a multi-step process in which normal cells transform into malignant tumors following the accumulation of genetic mutations that enable them to evade the growth control checkpoints that would normally suppress their growth or result in apoptosis. It is therefore important to identify those combinations of mutations that...journal article 2010