Carsten Wiuf

Summary

Affiliation: University of Aarhus
Country: Denmark

Publications

  1. pmc Genotyping and annotation of Affymetrix SNP arrays
    Philippe Lamy
    Bioinformatics Research Center, University of Aarhus, Høegh Guldbergsgade 10, Bldg 1090, 8000 Aarhus C, Denmark
    Nucleic Acids Res 34:e100. 2006
  2. pmc The CATH database
    Michael Knudsen
    Bioinformatics Research Centre, Aarhus University, DK 8000 Aarhus C, Denmark
    Hum Genomics 4:207-12. 2010
  3. pmc An Algebro-topological description of protein domain structure
    Robert Clark Penner
    Center for the Topology and Quantization of Moduli Spaces, Department of Mathematical Sciences, Aarhus University, Aarhus, Denmark
    PLoS ONE 6:e19670. 2011
  4. pmc Are microRNAs located in genomic regions associated with cancer?
    P Lamy
    Bioinformatics Research Center BiRC, University of Aarhus, Hoegh Guldbergs Gade 10, Bldg 1090, Aarhus C, Denmark
    Br J Cancer 95:1415-8. 2006
  5. pmc A review of software for microarray genotyping
    Philippe Lamy
    Bioinformatics Research Centre, Aarhus C, Denmark
    Hum Genomics 5:304-9. 2011
  6. pmc The association between genetic variants in hMLH1 and hMSH2 and the development of sporadic colorectal cancer in the Danish population
    Lise Lotte Christensen
    Molecular Diagnostic Laboratory, Department of Clinical Biochemistry, Aarhus University Hospital, Skejby, Denmark
    BMC Med Genet 9:52. 2008
  7. pmc Tumor-specific usage of alternative transcription start sites in colorectal cancer identified by genome-wide exon array analysis
    Kasper Thorsen
    Department of Molecular Medicine, Aarhus University Hospital, Skejby, 8200 Aarhus N, Denmark
    BMC Genomics 12:505. 2011
  8. pmc Genome-wide scans using archived neonatal dried blood spot samples
    Mads V Hollegaard
    Section of Neonatal Screening and Hormones, Statens Serum Institut, Copenhagen, Denmark
    BMC Genomics 10:297. 2009
  9. pmc Chromosomal imbalance in the progression of high-risk non-muscle invasive bladder cancer
    Karsten Zieger
    Department of Molecular Medicine, Aarhus University Hospital Skejby, Aarhus N, Denmark
    BMC Cancer 9:149. 2009
  10. pmc Tumor heterogeneity in neoplasms of breast, colon, and skin
    Jian Li
    BiRC Bioinformatics Research Centre, Aarhus University, DK 8000 Aarhus, Denmark
    BMC Res Notes 3:321. 2010

Collaborators

Detail Information

Publications56

  1. pmc Genotyping and annotation of Affymetrix SNP arrays
    Philippe Lamy
    Bioinformatics Research Center, University of Aarhus, Høegh Guldbergsgade 10, Bldg 1090, 8000 Aarhus C, Denmark
    Nucleic Acids Res 34:e100. 2006
    ..Finally, we have validated our method on HapMap data and shown that the performance of our method is comparable to other methods...
  2. pmc The CATH database
    Michael Knudsen
    Bioinformatics Research Centre, Aarhus University, DK 8000 Aarhus C, Denmark
    Hum Genomics 4:207-12. 2010
    ..cathdb.info) provides an easy-to-use entry to the classification, allowing for both browsing and downloading of data. Here, we give a brief review of the database, its corresponding website and some related tools...
  3. pmc An Algebro-topological description of protein domain structure
    Robert Clark Penner
    Center for the Topology and Quantization of Moduli Spaces, Department of Mathematical Sciences, Aarhus University, Aarhus, Denmark
    PLoS ONE 6:e19670. 2011
    ..In addition, we combine our method with two other methods thereby using primary, secondary, and tertiary structure information, and show that we can identify a large percentage of new and unclassified structures in CATH...
  4. pmc Are microRNAs located in genomic regions associated with cancer?
    P Lamy
    Bioinformatics Research Center BiRC, University of Aarhus, Hoegh Guldbergs Gade 10, Bldg 1090, Aarhus C, Denmark
    Br J Cancer 95:1415-8. 2006
    ..This suggests that miRNA expression is regulated through different mechanisms than mRNA expression...
  5. pmc A review of software for microarray genotyping
    Philippe Lamy
    Bioinformatics Research Centre, Aarhus C, Denmark
    Hum Genomics 5:304-9. 2011
    ..The release of new arrays is generally followed by new, or updated, algorithms...
  6. pmc The association between genetic variants in hMLH1 and hMSH2 and the development of sporadic colorectal cancer in the Danish population
    Lise Lotte Christensen
    Molecular Diagnostic Laboratory, Department of Clinical Biochemistry, Aarhus University Hospital, Skejby, Denmark
    BMC Med Genet 9:52. 2008
    ..The purpose was to reveal if any of the common variants lead to increased susceptibility to colorectal cancer...
  7. pmc Tumor-specific usage of alternative transcription start sites in colorectal cancer identified by genome-wide exon array analysis
    Kasper Thorsen
    Department of Molecular Medicine, Aarhus University Hospital, Skejby, 8200 Aarhus N, Denmark
    BMC Genomics 12:505. 2011
    ..Aberrant expression patterns promoting carcinogenesis, however, may arise from alternative promoter usage...
  8. pmc Genome-wide scans using archived neonatal dried blood spot samples
    Mads V Hollegaard
    Section of Neonatal Screening and Hormones, Statens Serum Institut, Copenhagen, Denmark
    BMC Genomics 10:297. 2009
    ..Whole-genome amplified DNA from 24 neonatal dried blood spot samples stored between 15 to 25 years was tested, and high-quality genomic DNA from 8 of the same individuals was used as reference...
  9. pmc Chromosomal imbalance in the progression of high-risk non-muscle invasive bladder cancer
    Karsten Zieger
    Department of Molecular Medicine, Aarhus University Hospital Skejby, Aarhus N, Denmark
    BMC Cancer 9:149. 2009
    ..However, the individual course is difficult to predict. Chromosomal instability (CI) is associated with high tumor stage and grade, and possibly with the risk of progression...
  10. pmc Tumor heterogeneity in neoplasms of breast, colon, and skin
    Jian Li
    BiRC Bioinformatics Research Centre, Aarhus University, DK 8000 Aarhus, Denmark
    BMC Res Notes 3:321. 2010
    ..Thus, heterogeneity is an important feature of tumors. However, due to limitations in experimental and analytical techniques, tumor heterogeneity has rarely been studied in detail...
  11. pmc A likelihood approach to analysis of network data
    Carsten Wiuf
    Bioinformatics Research Center, University of Aarhus, Høegh Guldbergsgade 10, Building 1090, 8000 Aarhus C, Denmark
    Proc Natl Acad Sci U S A 103:7566-70. 2006
    ..We illustrate the power of this approach by estimating growth parameters for the Caenorhabditis elegans protein interaction network...
  12. ncbi Consistency of estimators of population scaled parameters using composite likelihood
    Carsten Wiuf
    Bioinformatics Research Center, University of Aarhus, Høegh Guldbergsgade 10, Building 1090, 8000 Aarhus C, Denmark
    J Math Biol 53:821-41. 2006
    ..g. mutation rates, demographic parameters and the recombination rate) is a consistent estimator as the number of regions tends to infinity...
  13. pmc A Hidden Markov Model to estimate population mixture and allelic copy-numbers in cancers using Affymetrix SNP arrays
    Philippe Lamy
    Bioinformatics Research Center, University of Aarhus, Hoegh Guldbergsgade 10, Bldg 1090, 8000 Aarhus C, Denmark
    BMC Bioinformatics 8:434. 2007
    ..Further with this approach we are able to estimate the proportion of normal cells in the tumour (mixture proportion)...
  14. ncbi SNPTools: a software tool for visualization and analysis of microarray data
    Frank J Sørensen
    Bioinformatics Research Center, University of Aarhus, Høegh Guldbergs Gade 10, Aarhus C, Denmark
    Bioinformatics 23:1550-2. 2007
    ..For explorative use, SNPTools allows various genome information to be loaded onto the graphs. AVAILABILITY: The software, example data sets and tutorials are freely available from http://www.birc.au.dk/snptools..
  15. doi DNA copy number aberrations in breast cancer by array comparative genomic hybridization
    Jian Li
    Institute of Human Genetics, University of Aarhus, Denmark
    Genomics Proteomics Bioinformatics 7:13-24. 2009
    ..Our study provides clues for further investigations of the underlying mechanisms of breast carcinogenesis...
  16. pmc Short tandem repeats in human exons: a target for disease mutations
    Bo Eskerod Madsen
    Bioinformatics Research Center, University of Aarhus, DK 8000 Aarhus C, Denmark
    BMC Genomics 9:410. 2008
    ..In particular, we test whether they share the hypermutability of the longer tandem repeats and whether disease-related genes have a higher STR content than non-disease-related genes...
  17. pmc Estimation of tumor heterogeneity using CGH array data
    Kai Wang
    Institute of Human Genetics, University of Aarhus, Aarhus, Denmark
    BMC Bioinformatics 10:12. 2009
    ..However, most tumors are heterogeneous and show variation in DNA copy numbers across tumor cells. The challenge is to reveal the copy number profiles of the subpopulations in a tumor and to estimate the percentage of each subpopulation...
  18. doi High-resolution melting analysis for mutation screening of RGSL1, RGS16, and RGS8 in breast cancer
    Emilia Wiechec
    Institute of Human Genetics, University of Aarhus, Aarhus C, Denmark
    Cancer Epidemiol Biomarkers Prev 20:397-407. 2011
    ..We evaluated the use of high-resolution melting (HRM) to screen for mutations in the genes of interest and assess their clinical significance...
  19. doi Omics-based profiling of carcinoma of the breast and matched regional lymph node metastasis
    Jian Li
    Institute of Human Genetics, University of Aarhus, Aarhus C, Denmark
    Proteomics 8:5038-52. 2008
    ..Besides confirming the omics-derived data, the IHC analysis revealed that in two cases the ALN metastases may have been derived from a distinct minor cell subpopulation present in the primary tumor rather than from the bulk of it...
  20. ncbi Role of activating fibroblast growth factor receptor 3 mutations in the development of bladder tumors
    Karsten Zieger
    Molecular Diagnostic Laboratory, Department of Clinical Biochemistry, Aarhus University, Denmark
    Clin Cancer Res 11:7709-19. 2005
    ..The aim of this clinical follow-up study was to investigate the role of FGFR3 mutations in bladder cancer development in a longitudinal study...
  21. pmc A beta-mixture model for dimensionality reduction, sample classification and analysis
    Kirsti Laurila
    Bioinformatics Research Centre, Aarhus University, C F Møllers Allé 8, DK 8000 Arhus C, Denmark
    BMC Bioinformatics 12:215. 2011
    ..The model is described by 37 parameters, which reduces the dimensionality of a typical methylation microarray significantly. We used methylation microarray data from 42 colon cancer samples to assess the model...
  22. pmc Ab initio identification of human microRNAs based on structure motifs
    Markus Brameier
    Bioinformatics Research Center BiRC, University of Aarhus, 8000 Aarhus C, Denmark
    BMC Bioinformatics 8:478. 2007
    ..Unlike comparative genomics approaches, ab initio approaches are able to discover species-specific miRNAs without known sequence homology...
  23. pmc A periodic pattern of SNPs in the human genome
    Bo Eskerod Madsen
    Bioinformatics Research Center, University of Aarhus, Hoegh Guldbergs Gade 10, DK 8000 Aarhus C, Denmark
    Genome Res 17:1414-9. 2007
    ..The latter may have important consequences for SNP and association studies...
  24. ncbi Co-clustering and visualization of gene expression data and gene ontology terms for Saccharomyces cerevisiae using self-organizing maps
    Markus Brameier
    Bioinformatics Research Center BiRC, University of Arhus, Arhus C, Denmark
    J Biomed Inform 40:160-73. 2007
    ..To cope with the high variety and specificity of GO terms, gene and cluster annotations are mapped to a reduced vocabulary of more general GO terms. In particular, this advances the ability of SOMs to act as gene function predictors...
  25. doi A bimodular mechanism of calcium control in eukaryotes
    Henning Tidow
    Centre for Membrane Pumps in Cells and Disease PUMPKIN, Aarhus University, Gustav Wieds Vej 10C, DK 8000 Aarhus C, Denmark
    Nature 491:468-72. 2012
    ....
  26. doi A computational method to preclude multistationarity in networks of interacting species
    Elisenda Feliu
    Department of Mathematical Sciences, University of Copenhagen, 2100 Copenhagen, Denmark
    Bioinformatics 29:2327-34. 2013
    ..A class is defined by imposing mild assumptions on the interaction rates. In this framework, we investigate whether there can be multiple positive steady states in some ODE models in a given class...
  27. ncbi Conflicting results in SNP genotype assessment
    Lise Lotte Hansen
    Danish Centre for Molecular Gerontology, Institute of Human Genetics, University of Aarhus, Denmark
    Biotechniques 43:756, 758, 760 passim. 2007
    ..The problem we have encountered may originate from specific structures in the genomic DNA sequence, rather than being a methodological problem...
  28. pmc Quality assessment of DNA derived from up to 30 years old formalin fixed paraffin embedded (FFPE) tissue for PCR-based methylation analysis using SMART-MSP and MS-HRM
    Lasse S Kristensen
    Institute of Human Genetics, University of Aarhus, The Bartholin Building, Aarhus C, Denmark
    BMC Cancer 9:453. 2009
    ..Sensitive Melting Analysis after Real Time - Methylation Specific PCR (SMART-MSP) and Methylation Sensitive - High Resolution Melting (MS-HRM) are two methods for single locus DNA methylation detection based on HRM...
  29. ncbi High-density single nucleotide polymorphism array defines novel stage and location-dependent allelic imbalances in human bladder tumors
    Karen Koed
    Molecular Diagnostic Laboratory, Department of Clinical Biochemistry, Aarhus University Hospital, Aarhus, Denmark
    Cancer Res 65:34-45. 2005
    ..05). These data show the power of high-resolution SNP arrays for defining clinically relevant AIs...
  30. doi Exact analysis of intrinsic qualitative features of phosphorelays using mathematical models
    Michael Knudsen
    Bioinformatics Research Centre, Aarhus University, Aarhus, Denmark
    J Theor Biol 300:7-18. 2012
    ..Aside from providing biological insight, the formulas may also be used to replace the time-consuming simulations in numerical analyses...
  31. pmc Germline mutation in RNASEL predicts increased risk of head and neck, uterine cervix and breast cancer
    Bo Eskerod Madsen
    Bioinformatics Research Center, University of Aarhus, Aarhus, Denmark
    PLoS ONE 3:e2492. 2008
    ..A genetic predisposition could explain why some viral infections persist and induce cancer, while others disappear spontaneously. This points at RNASEL as a strong susceptibility gene...
  32. doi Development of a hypoxia gene expression classifier with predictive impact for hypoxic modification of radiotherapy in head and neck cancer
    Kasper Toustrup
    Department of Experimental Clinical Oncology, Aarhus University Hospital and Bioinformatics Research Centre, Aarhus University, Aarhus C, Denmark
    Cancer Res 71:5923-31. 2011
    ..Thus, findings show that the classifier attained both prognostic and predictive impact, and its pretherapeutic use may provide a method to identify those patients who will benefit from hypoxic modification of radiotherapy...
  33. doi Signaling cascades: consequences of varying substrate and phosphatase levels
    Elisenda Feliu
    Bioinformatics Research Centre, Aarhus University, Aarhus, Denmark
    Adv Exp Med Biol 736:81-94. 2012
    ..Our results provide insight into how the cascade response is affected by crosstalk and external regulation...
  34. pmc Inference on recombination and block structure using unphased data
    Carsten Wiuf
    Bioinformatics Research Center, University of Aarhus, 8000 Aarhus C, Denmark
    Genetics 166:537-45. 2004
    ..The new statistics are applied to real data from human genes. The results from this application are discussed with reference to recent suggestions that recombination in the human genome is highly heterogeneous...
  35. pmc Simplifying biochemical models with intermediate species
    Elisenda Feliu
    Department of Mathematical Sciences, University of Copenhagen, Universitetsparken 5, 2100 Copenhagen, Denmark
    J R Soc Interface 10:20130484. 2013
    ..Importantly, our results provide guidelines to the modeller in choosing between models and in distinguishing their properties. Further, our work provides a formal way of comparing models that share a common skeleton. ..
  36. pmc Large scale identification and categorization of protein sequences using structured logistic regression
    Bjørn P Pedersen
    Centre for Membrane Pumps in Cells and Disease PUMPKIN, Danish National Research Foundation, Aarhus C, Denmark Department of Molecular Biology, Aarhus University, Aarhus C, Denmark
    PLoS ONE 9:e85139. 2014
    ....
  37. doi Modelling the contribution of family history and variation in single nucleotide polymorphisms to risk of schizophrenia: a Danish national birth cohort-based study
    Esben Agerbo
    National Centre for Register Based Research, Aarhus University, Denmark
    Schizophr Res 134:246-52. 2012
    ....
  38. pmc Enzyme-sharing as a cause of multi-stationarity in signalling systems
    Elisenda Feliu
    Bioinformatics Research Centre, Aarhus University, C F Møllers Allé 8, 8000 Aarhus, Denmark
    J R Soc Interface 9:1224-32. 2012
    ..Our approach relies on mass-action kinetics, and the conclusions are drawn in full generality without resorting to simulations or random generation of parameters. The approach is extensible to other systems...
  39. doi The genealogy, site frequency spectrum and ages of two nested mutant alleles
    Asger Hobolth
    Bioinformatics Research Center, Aarhus University, Aarhus, Denmark
    Theor Popul Biol 75:260-5. 2009
    ..We show that the age of the youngest mutation does not depend on the frequency of the single mutant allele and that the frequency spectra for the single mutant allele and the zero mutant allele are the same...
  40. pmc Identification of endogenous retroviral reading frames in the human genome
    Palle Villesen
    Bioinformatics Research Center, University of Aarhus, Høegh Guldbergs Gade 10, Bldg 090, DK 8000 Aarhus, Denmark
    Retrovirology 1:32. 2004
    ..Additional intact HERV genes may exist, since retroviral reading frames have not been systematically annotated on a genome-wide scale...
  41. pmc Temporal development and collapse of an Arctic plant-pollinator network
    Clementine Pradal
    Bioinformatics Research Centre, Aarhus University, C, F, Mollers Alle 8, Building 1110, DK 8000 Aarhus C, Denmark
    BMC Ecol 9:24. 2009
    ..Here we study an Arctic plant-pollinator network in two consecutive years using a simple mathematical model and describe the temporal dynamics (daily assembly and disassembly of links) by random mechanisms...
  42. ncbi Convergence properties of the degree distribution of some growing network models
    Oskar Hagberg
    Bioinformatics Research Center, University of Aarhus, Høegh Guldbergsgade 10, Building 90, 8000 Aarhus C, Denmark
    Bull Math Biol 68:1275-91. 2006
    ....
  43. doi Diagnostic and prognostic microRNAs in stage II colon cancer
    Troels Schepeler
    Department of Clinical Biochemistry, Molecular Diagnostic Laboratory, Aarhus University Hospital, Aarhus N, Denmark
    Cancer Res 68:6416-24. 2008
    ....
  44. ncbi Frequent occurrence of uniparental disomy in colorectal cancer
    Claus Lindbjerg Andersen
    Molecular Diagnostic Laboratory, Department of Clinical Biochemistry, Aarhus University Hospital, Skejby DK 8200, Aarhus N, Denmark
    Carcinogenesis 28:38-48. 2007
    ..In conclusion, we demonstrate that uniparental disomy is frequent in CRC, and identify genomic alterations associated with TP53 inactivation and lymph node status...
  45. pmc Estimating the size of the human interactome
    Michael P H Stumpf
    Division of Molecular Biosciences, Imperial College London, Wolfson Building, London SW7 2AZ, United Kingdom
    Proc Natl Acad Sci U S A 105:6959-64. 2008
    ..We find that the human interaction network is one order of magnitude bigger than the Drosophila melanogaster interactome and approximately 3 times bigger than in Caenorhabditis elegans...
  46. ncbi Simulating haplotype blocks in the human genome
    David Posada
    Variagenics Inc, 60 Hampshire St, Cambridge, MA 02139 1548, USA
    Bioinformatics 19:289-90. 2003
    ..The samples generated can be very useful to better understand the architecture of the human genome and to investigate its impact in association studies searching for disease genes...
  47. pmc The effects of incomplete protein interaction data on structural and evolutionary inferences
    Eric de Silva
    Theoretical Genomics Group, Centre for Bioinformatics, Division of Molecular Biosciences, Imperial College London, London, UK
    BMC Biol 4:39. 2006
    ..Here we demonstrate the need to consider network sampling properties explicitly and from the outset in any analysis...
  48. pmc Using likelihood-free inference to compare evolutionary dynamics of the protein networks of H. pylori and P. falciparum
    Oliver Ratmann
    Department of Public Health and Epidemiology, Imperial College London, London, United Kingdom
    PLoS Comput Biol 3:e230. 2007
    ....
  49. pmc Bioinformatic identification of FGF, p38-MAPK, and calcium signalling pathways associated with carcinoma in situ in the urinary bladder
    Malene Herbsleb
    Molecular Diagnostic Laboratory, Aarhus University Hospital Skejby, Brendstrupgaardsvej 100, DK 8200 Aarhus N, Denmark
    BMC Cancer 8:37. 2008
    ..Carcinoma in situ (CIS) is believed to be a precursor of invasive bladder cancer. Identification of CIS is a valuable prognostic factor since radical treatment strategies can be offered these patients before the disease becomes invasive...
  50. ncbi Some notes on the combinatorial properties of haplotype tagging
    Carsten Wiuf
    Variagenics, 60 Hampshire Street, Cambridge, MA 02139, USA
    Math Biosci 185:205-16. 2003
    ..We derive a number of results that relate the number of markers required to tag a set of haplotypes to the set of markers themselves...
  51. ncbi Inferring population history from genealogical trees
    Carsten Wiuf
    Department of Statistics, University of Oxford, Oxford, OX1 3TG, UK
    J Math Biol 46:241-64. 2003
    ..g., the mutation rate typically converges at rate under the assumption that all historical mutations can be observed in the sample. In addition, various results for the distribution of maximum likelihood estimators are presented...
  52. pmc A coalescent model of recombination hotspots
    Carsten Wiuf
    Variagenics, Cambridge, Massachusetts 02139, USA
    Genetics 164:407-17. 2003
    ..A number of new analytical results about the model are derived...
  53. pmc The probability and chromosomal extent of trans-specific polymorphism
    Carsten Wiuf
    Department of Statistics, University of Oxford, Oxford, OX1 3TG, United Kingdom
    Genetics 168:2363-72. 2004
    ..When trans-specific polymorphism is obvious, on the other hand, it may be reasonable to argue that selection must be acting on multiple sites or that recombination is suppressed in the surrounding region...
  54. ncbi SOX4 expression in bladder carcinoma: clinical aspects and in vitro functional characterization
    Mads Aaboe
    Molecular Diagnostic Laboratory, Department of Clinical Biochemistry, Aarhus University Hospital Skejby Sygehus, 8200 Aarhus N, Denmark
    Cancer Res 66:3434-42. 2006
    ..The gene set identified in vitro was analyzed in the clinical bladder material and a small subset of the genes showed a high correlation to SOX4 expression. The present data suggest a role of SOX4 in the bladder cancer disease...
  55. pmc Recharacterization of ancient DNA miscoding lesions: insights in the era of sequencing-by-synthesis
    M Thomas P Gilbert
    Center for Ancient Genetics, Niels Bohr Institute and Biological Institutes, The University of Copenhagen, Juliane Maries Vej 30, DK 2100 Copenhagen Ø, Denmark
    Nucleic Acids Res 35:1-10. 2007
    ..How widespread these implications are for aDNA will become apparent as future studies analyse data recovered from a wider range of substrates...
  56. ncbi On the minimum number of topologies explaining a sample of DNA sequences
    Carsten Wiuf
    Variagenics, 60 Hampshire Street, Cambridge, Massachusetts 02139 1548, USA
    Theor Popul Biol 62:357-63. 2002
    ..Further, a number of theorems relating general lists of topologies to the number T(M) is presented. The results are discussed in relation to the true minimum number of recombination events required to explain an alignment...