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The metagenome of the marine anammox bacterium ‘Candidatus Scalindua profunda’ illustrates the versatility of this globally important nitrogen cycle bacterium

Van de Vossenberg, J. (author), Woebken, D. (author), Maalcke, W.J. (author), Wessels, H.J.C.T. (author), Dutllh, B.E. (author), Kartal, B. (author), Janssen-Megens, E.M. (author), Roeselers, G. (author), Yan, J. (author), Speth, D. (author), Gloerich, J. (author), Geerts, W. (author), Van der Blezen, E. (author), Pluk, W. (author), Francoijs, K.J. (author), Russ, L. (author), Lam, P. (author), Malfatti, S.A. (author), Green Tringe, S. (author), Haaijer, S.C.M. (author), Op den Camp, H.J.M. (author), Stunnenberg, H.G. (author), Amann, R. (author), Kuypers, M.M.M. (author), Jetten, M.S.M. (author)

Anaerobic ammonium-oxidizing (anammox) bacteria are responsible for a significant portion of the loss of fixed nitrogen from the oceans, making them important players in the global nitrogen cycle. To date, marine anammox bacteria found in marine water columns and sediments worldwide belong almost exclusively to the ‘Candidatus Scalindua’ species...

journal article 2012

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Effects of Nitrogen Dioxide and Anoxia on Global Gene and Protein Expression in Long-Term Continuous Cultures of Nitrosomonas eutropha C91

Kartal, B. (author), Wessels, H.J. C. T. (author), Van der Biezen, E. (author), Francoijs, K.J. (author), Jetten, M.S.M. (author), Klotz, M.G. (author), Stein, L.Y. (author)

Nitrosomonas eutropha is an ammonia-oxidizing betaproteobacterium found in environments with high ammonium levels, such as wastewater treatment plants. The effects of NO2 on gene and protein expression under oxic and anoxic conditions were determined by maintaining N. eutropha strain C91 in a chemostat fed with ammonium under oxic, oxic-plus-NO2...

journal article 2012

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Computational identification of insertional mutagenesis targets for cancer gene discovery

De Jong, J. (author), De Ridder, J. (author), Van der Weyden, L. (author), Sun, N. (author), Van Uitert, M. (author), Berns, A. (author), Van Lohuizen, M. (author), Jonkers, J. (author), Adams, D.J. (author), Wessels, L.F.A. (author)

Insertional mutagenesis is a potent forward genetic screening technique used to identify candidate cancer genes in mouse model systems. An important, yet unresolved issue in the analysis of these screens, is the identification of the genes affected by the insertions. To address this, we developed Kernel Convolved Rule Based Mapping (KC-RBM). KC...

journal article 2011

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Specific genomic aberrations in primary colorectal cancer are associated with liver metastases

Bruin, S.C. (author), Klijn, C.N. (author), Liefers, G.J. (author), Braaf, L.M. (author), Joosse, S.A. (author), Van Beers, E.H. (author), Verwaal, V.J. (author), Morreau, H. (author), Wessels, L.F. (author), Van Velthuysen, M.L.F. (author), Tollenaar, R.A.E.M. (author), Van 't Veer, L.J. (author)

Background: Accurate staging of colorectal cancer (CRC) with clinicopathological parameters is important for predicting prognosis and guiding treatment but provides no information about organ site of metastases. Patterns of genomic aberrations in primary colorectal tumors may reveal a chromosomal signature for organ specific metastases. Methods:...

journal article 2010

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Specific genomic aberrations in primary colorectal cancer are associated with liver metastases

Bruin, Sjoerd C. (author), Klijn, C.N. (author), Liefers, Gerrit Jan (author), Braaf, Linde M. (author), Joosse, Simon A. (author), Van Beers, Eric H. (author), Verwaal, Victor J. (author), Morreau, Hans (author), Wessels, L.F.A. (author), Van Velthuysen, Marie Louise F. (author), Tollenaar, Rob A.E.M. (author), Van't Veer, Laura J. (author)

Background: Accurate staging of colorectal cancer (CRC) with clinicopathological parameters is important for predicting prognosis and guiding treatment but provides no information about organ site of metastases. Patterns of genomic aberrations in primary colorectal tumors may reveal a chromosomal signature for organ specific metastases...

journal article 2010

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KC-SMARTR: An R package for detection of statistically significant aberrations in multi-experiment aCGH data

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

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Somatic structural rearrangements in genetically engineered mouse mammary tumors

Varela, I. (author), Klijn, C.N. (author), Stephens, P.J. (author), Mudie, L.J. (author), Stebbings, L. (author), Galappaththige, D. (author), Van der Gulden, H. (author), Schut, E. (author), Klarenbeek, S. (author), Campbell, P.J. (author), Wessels, L.F.A. (author), Stratton, M.R. (author), Jonkers, J. (author), Futreal, P.A. (author), Adams, D.J. (author)

Background: Here we present the first paired-end sequencing of tumors from genetically engineered mouse models of cancer to determine how faithfully these models recapitulate the landscape of somatic rearrangements found in human tumors. These were models of Trp53-mutated breast cancer, Brca1- and Brca2-associated hereditary breast cancer, and E...

journal article 2010

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Cross-species comparison of aCGH data from mouse and human BRCA1- and BRCA2-mutated breast cancers

Holstege, H. (author), Van Beers, E. (author), Velds, A. (author), Liu, X. (author), Joosse, S.A. (author), Klarenbeek, S. (author), Schut, E. (author), Kerkhoven, R. (author), Klijn, C.N. (author), Wessels, L.F.A. (author), Nederlof, P.M. (author), Jonkers, J. (author)

Background: Genomic gains and losses are a result of genomic instability in many types of cancers. BRCA1- and BRCA2-mutated breast cancers are associated with increased amounts of chromosomal aberrations, presumably due their functions in genome repair. Some of these genomic aberrations may harbor genes whose absence or overexpression may give...

journal article 2010

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Inferring combinatorial association logic networks in multimodal genome-wide screens

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

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Identification of Networks of Co-Occurring, Tumor-Related DNA Copy Number Changes Using a Genome-Wide Scoring Approach

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

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Analysis of mass spectrometry data using sub-spectra

Meuleman, W. (author), Engwegen, J.Y.M.N. (author), Gast, M.C.W. (author), Wessels, L.F.A. (author), Reinders, M.J.T. (author)

journal article 2009

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Knowledge driven decomposition of tumor expression profiles

Van Vliet, M.H. (author), Wessels, L.F.A. (author), Reinders, M.J.T. (author)

journal article 2009

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Combinatorial effects of environmental parameters on transcriptional regulation in Saccharomyces cerevisiae: A quantitative analysis of a compendium of chemostat-based transcriptome data

Knijnenburg, T.A. (author), Daran, J.M.G. (author), Van den Broek, M.A. (author), Daran-Lapujade, P.A.S. (author), De Winde, J.H. (author), Pronk, J.T. (author), Reinders, M.J.T. (author), Wessels, L.F.A. (author)

OA Fund TU delft Background: Microorganisms adapt their transcriptome by integrating multiple chemical and physical signals from their environment. Shake-flask cultivation does not allow precise manipulation of individual culture parameters and therefore precludes a quantitative analysis of the (combinatorial) influence of these parameters on...

journal article 2009

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Biclustering Sparse Binary Genomic Data

Van Uitert, M. (author), Meuleman, W. (author), Wessels, L.F.A. (author)

Genomic datasets often consist of large, binary, sparse data matrices. In such a dataset, one is often interested in finding contiguous blocks that (mostly) contain ones. This is a biclustering problem, and while many algorithms have been proposed to deal with gene expression data, only two algorithms have been proposed that specifically deal...

journal article 2008

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Combinatorial influence of environmental parameters on transcription factor activity

Knijnenburg, T.A. (author), Wessels, L.F.A. (author), Reinders, M.J.T. (author)

Motivation: Cells receive a wide variety of environmental signals, which are often processed combinatorially to generate specific genetic responses. Changes in transcript levels, as observed across different environmental conditions, can, to a large extent, be attributed to changes in the activity of transcription factors (TFs). However, in...

journal article 2008

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Identification of cancer genes using a statistical framework for multiexperiment analysis of nondiscretized array CGH data

Klijn, C.N. (author), Holstege, H. (author), De Ridder, J. (author), Liu, X. (author), Reinders, M. (author), Jonkers, J. (author), Wessels, L. (author)

Tumor formation is in part driven by DNA copy number alterations (CNAs), which can be measured using microarray-based Comparative Genomic Hybridization (aCGH). Multiexperiment analysis of aCGH data from tumors allows discovery of recurrent CNAs that are potentially causal to cancer development. Until now, multiexperiment aCGH data analysis has...

journal article 2008

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Comparison of normalisation methods for surface-enhanced laser desorption and ionisation (SELDI) time-of-flight (TOF) mass spectrometry data

Meuleman, W. (author), Engwegen, J.Y.M.N. (author), Gast, M.C.W. (author), Beijnen, J.H. (author), Reinders, M.J.T. (author), Wessels, L.F.A. (author)

OA Fund TU Delft

journal article 2008

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A comprehensive analysis of prognostic signatures reveals the high predictive capacity of the Proliferation, Immune response and RNA splicing modules in breast cancer

Reyal, F. (author), Van Vliet, M.H. (author), Armstrong, N.J. (author), Horlings, H.M. (author), De Visser, K.E. (author), Kok, M. (author), Teschendorff, A.E. (author), Mook, S. (author), Van 't Veer, L. (author), Caldas, C. (author), Salmon, R.J. (author), Vijver, M.J. (author), Wessels, L.F.A. (author)

journal article 2008

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Pooling breast cancer datasets has a synergetic effect on classification performance and improves signature stability

Van Vliet, M.H. (author), Reyal, F. (author), Horlings, H.M. (author), Van De Vijver, M.J. (author), Reinders, M.J.T. (author), Wessels, L.F.A. (author)

OA fund TU Delft

journal article 2008

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Module-Based Outcome Prediction Using Breast Cancer Compendia

Van Vliet, M.H. (author), Klijn, C.N. (author), Wessels, L.F. (author), Reinders, M.J.T. (author)

Background. The availability of large collections of microarray datasets (compendia), or knowledge about grouping of genes into pathways (gene sets), is typically not exploited when training predictors of disease outcome. These can be useful since a compendium increases the number of samples, while gene sets reduce the size of the feature space....

journal article 2007