Home of Carsten Wiuf

    at the Department of Mathematical Sciences, University of Copenhagen

    "Every day, once a day, give yourself a present"


    Contact Details

    Phone:+45 513 19991
    Dept Fax:+45 353 20704
    Dept Web: http://www.math.ku.dk/

    Postal Address:Department of Mathematical Sciences
    University of Copenhagen
    Universitetsparken 5
    DK-2100 Copenhagen

    Research Interests

    I'm a professor at University of Copenhagen, Department of Mathematical Sciences. I'm generally interested in the application of mathematics, probability and statistics in the biosciences, and to develop mathematical and statistical theory for biological phenomena. Over the years I have worked on different issues, or themes, and applied modeling in many different contexts. Currently, my interests are in systems biology and population genetics.

    My publication list is divided into categories, organized in reverse chronological order starting from 2018 and going back to 1997; in addition to peer-reviewed publications it contains books, book contributions and various other science contributions. I also include a list of arXiv papers that have been submitted recently (if any). Many of my publications can be found on arXiv.

    Recent ArXiv Submissions (and other submissions)

  1. Hansen MS, Wiuf C. 2018 Existence of a unique quasi-stationary distribution for stochastic reaction networks. Submitted.
  2. Sáez M, Wiuf C, Feliu E. 2018 Nonnegative linear elimination for chemical reaction networks Submitted.
  3. Soraggi S, Wiuf C. 2018 General theory for stochastic admixture graphs and F-statistics. Submitted.

    Peer-Reviewed Publications


  1. Sáez M, Feliu E, Wiuf C. 2018 Graphical criteria for positive solutions to linear systems. Linear Algebra Appl 552: 166-193.
  2. Feliu E, Cappelletti D, Wiuf C. 2018 Node balanced steady states: Unifying and generalizing complex and detailed balanced steady states. Math Biosci 301: 68-82.
  3. Sáez M, Feliu E, Wiuf C. 2018 (Conference proceeding) Linear elimination in chemical reaction networks. SEMA SIMAI Springer Series 18: 169-186. Eds. JL García Guirao, JA Murillo Hernández, F Periago Esparza.
  4. Ferragut A, Valls C, Wiuf C. 2018 On the Liouville integrability of Edelstein's reaction system in R3. Chaos Soliton Fract 108: 129-135.
  5. Wiuf C. 2018 Some properties of the conditioned reconstructed process with Bernoulli sampling. Theor Pop Biol 122: 36-45.
  6. Soraggi S, Wiuf C, Albrechtsen, A. 2018 Powerful inference with the D-statistic on low-coverage whole-genome data. G3 8: 551-566.
  7. 2017

  8. Mahdia A, Ferragut A, Valls C, Wiuf C. 2017 Conservation laws in biochemical reaction networks. SIAM J Appl Dyn Syst 16(4): 2213-2232.
  9. Cappelletti D, Wiuf C. 2017 Uniform approximation of solutions by elimination of intermediate species in deterministic reaction networks. SIAM J Appl Dyn Syst 16(4): 2259-2286.
  10. Conradi C, Feliu E, Mincheva M, Wiuf C. 2017 Identifying parameter regions for multistationarity. PLOS Comp Biol 13(10): e1005751.
  11. Marcondes de Freitas, Wiuf C, Feliu E. 2017 Intermediates and generic convergence to equilibria. Bull Math Biol 79: 1662-1686.
  12. Vincent M, Mundbjerg K, Pedersen JS, Liang G, Jones PA, Orntoft TF, Sorensen KD, Wiuf C. 2017 EpiG: statistical inference and profiling of DNA methylation from whole-genome bisulphite sequencing data. Genome Biol 18: 38.
  13. Marcondes de Freitas M, Feliu E, Wiuf C. 2017 Intermediates, catalysts, persistence, and boundary steady states. J Math Biol 74: 887-932.
  14. Sáez M, Wiuf C, Feliu E. 2017 Graphical reduction of reaction networks by linear elimination of species. J Math Biol 74: 195-237.
  15. 2016

  16. Feng S, Sáez M, Wiuf C, Feliu E, Soyer OS. 2016 Core signalling motif displaying multistability through allosteric enzymes. J R Soc Interface 13: 20160524.
  17. Wiuf C, Pallesen JS-M, Foldager L, Grove J. 2016 LandScape: a simple method to aggregate p-values and other stochastic variables without a priori grouping. Stat Appl Genet Mol Biol 15: 349-361.
  18. Widder S, Allen R, Pfeiffer T, Curtis TP, Wiuf C, Sloan WT, Cordero OX, Brown SP, Momeni B, Shou W, Kettle H, Flint HJ, Haas AF, Laroche B, Kreft J-U, Rainey PB, Freilich S, Schuster S, Milferstedt K, van der Meer JR, Grosskopf T, Huisman J, Free A, Picioreanu C, Quince C, Klapper I, Labarthe S, Smets BF, Wang H, Isaac Newton Institute Fellows, Soyer OS. 2016 Challenges in microbial ecology: building predictive understanding of community function and dynamics. ISME Jl 10: 2557-2568.
  19. Cappelletti D, Wiuf C. 2016 Elimination of intermediate species in multiscale stochastic reaction networks. Ann Appl Probat 26: 2915-2958.
  20. Cappelletti D, Wiuf C. 2016 Product-form Poisson-like distributions and complex balanced reaction systems. SIAM J Appl Math 76: 411-432.
  21. 2015

  22. Anderson D, Craciun G, Gopalkrishnan M, Wiuf C. 2015 Lyapunov functions, stationary distributions, and non-equilibrium potential for chemical reaction networks. Bull Math Biol 77: 1744-1769. [journal]
  23. Jovanovic G, Sheng X, Ale A, Feliu E, Harrington H, Kirk P, Wiuf C, Buck M, Stumpf MPH. 2015 Phosphorelay in non-orthodox two component systems in vivo functions through a bi-molecular mechanism: the case of ArcB. Mol BioSysts 11: 1348. [pdf]
  24. Feliu E, Wiuf C. 2015 Finding the positive feedback loops underlying multi-stationarity. BMC Systems Biology 9: 22. [pdf]
  25. 2014

  26. Pedersen BP, Ifrim G, Liboriussen P, Axelsen KB, Palmgren MG, Nissen P, Wiuf C, Pedersen CNS. 2014 Large scale identification and categorization of protein sequences using Structured Logistic Regression. PLOS One 9: e85139. [pdf]
  27. Borglum AD, Demontis D, Grove J, Pallesen J, Hollegaard JV, Pedersen CB, Hedemand A, Mattheisen M, GROUP investigators, Uitterlinden A, Nyegaard M, Orntoft T, Wiuf C, Didriksen M, Nordentoft M, Nothen MM, Rietschel M, Roel A. Ophoff RA, Cichon S, Yolken RHY, Hougaard DM, Mortensen PB, Mors O. 2014 Genome-wide study of association and interaction with maternal cytomegalovirus infection suggests new schizophrenia loci. Mol Psychiatry 19: 325-333. [pdf]
  28. 2013

  29. Kothamachu VB, Feliu E, Wiuf C, Cardelli L, Soyer OS. 2013 Phosphorelays provide tunable signal processing capabilities for the cell. PLOS Comp Biol 9: e1003322. [pdf]
  30. Wiuf C, Feliu E. 2013 Power-law kinetics and determinant criteria for the preclusion of multistationarity in networks of interacting species. SIAM J Appl Dyn Syst 12: 1685-1721. [pdf]
  31. Feliu E, Wiuf C. 2013 A computational method to preclude multistationarity in networks of interacting species. Bioinformatics 29: 2327-2334. [pdf]
  32. Feliu E, Wiuf C. 2013 Simplifying biochemical models with intermediate species. J R Soc Interface 10: 20130484. [pdf]
  33. Harrington HA, Feliu E, Wiuf C, Stumpf MPH. 2013 Cellular compartments cause multistability in biochemical reaction networks and allow cells to process more information Biophys J 104: 1824-1831. [pdf]
  34. Feliu E, Wiuf C. 2013 Variable elimination in Post-Translational Modification Reaction Networks with mass-action kinetics. J Math Biol 66: 281-310. [pdf]
  35. 2012

  36. Feliu E, Wiuf C. 2012 Preclusion of switch behavior in networks with mass-action kinetics. Appl Math Comput 219: 1449-1467. [pdf]
  37. Feliu E, Wiuf C. 2012 Variable elimination in chemical reaction networks with mass action kinetics. SIAM J Appl Math 72: 959-981. [pdf]
  38. Knudsen M, Feliu E, Wiuf C. 2012 Exact analysis of intrinsic qualitative features of phosphorelays using mathematical models. J Theor Biol 300: 7-18. [pdf]
  39. Feliu E, Knudsen M, Andersen LN, Wiuf C. 2012 An algebraic approach to signaling cascades with n layers. Bull Math Biol 74: 45-72. [pdf]
  40. Feliu E, Knudsen M, Wiuf C. 2012 Signaling cascades: Consequences of varying substrate and phosphatase levels. Adv Exp Med Biol (Adv Syst Biol) 736: 81-94. [pdf]
  41. Feliu E, Wiuf C. 2012 Enzyme sharing as a cause of multistationarity in signaling systems. J R Soc Interface 9: 1224-1232. [pdf]
  42. Tidow H, Poulsen LR, Andreeva A, Knudsen M, Hein KL, Wiuf C, Palmgren MG, Nissen P. 2012 A biomodular mechanism of calcium control in eukaryotes. Nature 491: 468-472. [pdf]
  43. Agerbo E, Mortensen PB, Wiuf C, Pedersen MS, McGrath J, Hollegaard MV, Norgaard-Pedersen B, Hougaard DM, Mors O, Pedersen CB. 2012 Modelling the contribution of family history and variation in single nucleotide polymorphisms to risk of schizophrenia: A Danish national birth cohort-based study. Schizophr Res 134: 246-252. [pdf]
  44. Thomsen P, Kielgast J, Iversen L, Wiuf C, Rasmussen M, Orlando L, Gilbert MTP, Willerslev E. 2012 Monitoring endangered freshwater biodiversity by environmental DNA. Mol Ecol 21: 2565-2573. [pdf]
  45. Toustrup K, Sorensen BS, Lassen P, Wiuf C, Alsner J, Overgaard J. 2012 Gene expression classifier predicts for hypoxic modification of radiotherapy with nimorazole in squamous cell carcinomas of the head and neck. Radiother Oncol 102: 122-129. [pdf]
  46. 2011

  47. Penner RC, Knudsen M, Wiuf C, Andersen JE. 2011 An algebro-topological description of protein domain structure. PLOS One 6: e19670. [pdf]
  48. Laurila K, Oster B, Andersen CL, Lamy P, Orntoft T, Yli-Harja O, Wiuf C. 2011 A beta-mixture model reduces the dimensionality of methylation data. BMC Bioinformatics 12: 215. [pdf]
  49. Lamy P, Grove J, Wiuf C. 2011 (Review) A review of software for microarray genotyping. Hum Genomics 5: 304-309. [pdf]
  50. Lamy P, Wiuf C, Orntoft T, Andersen CL. 2011 Rseg - an R package to optimize segmentation of SNP array data. Bioinformatics 27: 419-420. [pdf]
  51. Ifrim G, Wiuf C. 2011 (Conference proceeding) Bounded coordinate-descent for biological sequence classification in high dimensional predictor space. Proceedings of the 17th ACM SIGKDD Conference 2011. [pdf]
  52. Toustrup K, Sorensen BS, Nordsmark M, Busk M, Wiuf C, Alsner J, Overgaard J. 2011 Development of a hypoxia gene expression classifier with predictive impact for hypoxic modification of radiotherapy in head and neck cancer. Cancer Res 71: 5923-5931. [pdf]
  53. Reinert T, Modin C, Lamy P, Wojdacz T, Hansen LL, Wiuf C, Borre M, Dyrskjot L, Orntoft T. 2011 Comprehensive genome methylation analysis in bladder cancer; identification and validation of novel methylated genes and application of these as urinary tumor markers. Clin Cancer Res 17: 5582-5592. [pdf]
  54. Thorsen K, Schepeler T, Oster B, Rasmussen MH, Vang S, Wang K, Hansen KQ, Lamy P, Pedersen JS, Eller AO, Mansilla F, Laurila K, Wiuf C, Laurberg S, Dyrskjot L, Orntoft TF, Andersen CL. 2011 Tumor-specific usage of alternative transcription start sites in colorectal cancer identified by genome-wide exon array analysis. BMC Genomics 12: 505. [pdf]
  55. Wiechec E, Wiuf C, Overgaard J, Hansen LL. 2011 High Resolution Melting (HRM) analysis for mutation screening of RGSL1, RGS16 and RGS8 in breast cancer. Cancer Epidem Biomar 20: 397-407. [pdf]
  56. 2010

  57. Stumpf MPH, Wiuf C. 2010 Incomplete and noisy network data as a percolation process. J R Soc Interface 7: 1411-1419. [pdf]
  58. Penner RC, Knudsen M, Wiuf C, Andersen JE. 2010 Fatgraph models of proteins. Commun Pur Appl Math 63: 1249-1297. [pdf]
  59. Knudsen M, Wiuf C. 2010 (Review) The CATH database. Hum Genomics 4: 207-212. [pdf]
  60. Madsen BE, Villesen P, Wiuf C. 2010 Short tandem repeats and genetic variation. Methods Mol Biol 628: 297-306. [pdf]
  61. 2009

  62. Pradal C, Olesen JM, Wiuf C. 2009 Temporal development and collapse of an Arctic plant-pollinator network. BMC Ecology 9: 24. [pdf]
  63. Ratmann O, Wiuf C, Pinney JW. 2009 (Review) From evidence to inference: probing the evolution of protein interaction networks. HFSP Journal 3: 290-306. [pdf]
  64. Ratmann O, Andrieu C, Wiuf C, Richardson S. 2009 Model criticism based on likelihood-free inference. PNAS 106: 10576-10581. [pdf]
  65. Hobolth A, Wiuf C. 2009 The genealogy, site frequency spectrum and ages of two nested mutant alleles. Theor Popul Biol 75: 260-265. [pdf]
  66. Wang K, Li J, Li S, Bolund L, Wiuf C. 2009 Estimation of tumor heterogeneity using CGH array data. BMC Bioinformatics 10: 12. [pdf]
  67. Kristensen LS, Wojdacz TK, Thestrup BB, Wiuf C, Hager H, Hansen LL. 2009 Quality assessment of DNA derived from up to 30 years old formalin fixed paraffin embedded tissue (FFPE) for PCR-based methylation analysis using SMART-MSP and MS-HRM. BMC Cancer 9: 453. [pdf]
  68. Li J, Wang K, Li S, Timmermans-Wielenga V, Rank F, Wiuf C, Zhang X, Yang H, Bolund L. 2009 DNA Copy number aberrations in breast cancer by array Comparative Genomic Hybridization. Genomics Proteomics and Bioinformatics 7: 13-24. [pdf]
  69. Hollegaard MV, Grauholm J, Borglum A, Nyegaard M, Norgaard-Pedersen B, Orntoft T, Mortensen PB, Wiuf C, Mors O, Didriksen M, Thorsen P, Hougaard DM. 2009 Genome-wide scans using archived neonatal dried blood spot samples. BMC Genomics 10: 297. [pdf]
  70. Zieger K, Wiuf C, Jensen KM-E, Orntoft TF, Dyrskjot L. 2009 Chromosomal imbalance in the progression of high-risk non-muscle invasive bladder cancer. BMC Cancer 9: 149. [pdf]
  71. 2008

  72. Hobolth A, Uyenoyama MK, Wiuf C. 2008 Importance sampling for the infinite sites model. Stat Appl Genet Mol Biol 7: 32 [pdf]
  73. Stumpf MPH, Thorne T, de Silva E, Stewart R, An HJ, Lappe M, Wiuf C. 2008 Estimating the size of the human interactome. PNAS 105: 6959-6964. [pdf] [comment]
  74. Knudsen M, Wiuf C. 2008 A Markov chain approach to Randomly Grown Graphs. J Applied Math 2008: 190836. [pdf]
  75. Madsen BE, Villesen P, Wiuf C. 2008 Short tandem repeats in human exons: A target for disease mutations. BMC Genomics 9: 410. [pdf]
  76. Herbsleb M, Christensen OF, Thykjaer T, Wiuf C, Borre M, Orntoft TF, Dyrskjot L. 2008 Bioinformatic identification of FGF, p38-MAPK, and calcium signalling pathways associated with carcinoma in situ in the urinary bladder. BMC Cancer 8: 37. [pdf]
  77. Li J, Gromov P, Gromova I, Moreira JM, Timmermans-Wielenga V, Rank F, Wang K, Li S, Li H, Wiuf C, Yang H, Zhang X, Bolund L, Celis JE. 2008 Omics-based profiling of carcinoma of the breast and matched regional lymph node metastasis. Proteomics 8: 5038-5052. [pdf]
  78. d'Amore F, Chan E, Iqbal J, Geng H, Young K, Xiao L, Hess MM, Sanger WG, Smith L, Wiuf C, Hagberg O, Fu K, Chan WC, Dave BJ. 2008 Clonal evolution in t(14;18)-positive follicular lymphoma, evidence for multiple common pathways, and frequent parallel clonal evolution. Clin Cancer Res 14: 7180-7187. [pdf]
  79. Schepeler T, Reinert JT, Christensen LL, Silahtaroglu AN, Dyrskjot L, Ostenfeld MS, Wiuf C, Sorensen FJ, Kruhoffer M, Laurberg S, Kauppinen S, Orntoft TF, Andersen CL. 2008 Diagnostic and prognostic microRNAs in stage II colon cancer. Cancer Res 68: 6416-6424. [pdf]
  80. Madsen BE, Ramos EM, Boulard M, Duda, Overgaard J, Nordsmark M, Wiuf C, Hansen LL. 2008 Germline mutation in RNASEL predicts increased risk of head and neck, uterine cervix and breast cancer. PLOS One 3: e2492. [pdf]
  81. Herbsleb M, Birkenkamp-Demtroder K, Thykjaer T, Wiuf C, Hein A-MK, Orntoft TF, Dyrskjot L. 2008 Increased cell motility and invasion upon knockdown of lipolysis stimulated lipoprotein receptor (LSR) in SW780 bladder cancer cells. BMC Med Genomics 1: 31. [pdf]
  82. Christensen LL, Madsen BE, Wikman FP, Wiuf C, Koed K, Tjonneland A, Olsen A, Syvanen A-C, Andersen CL, Orntoft TF. 2008 The association between genetic variants in hMLH1 and hMSH2 and the development of sporadic colorectal cancer in the Danish population. BMC Med Genet 9: 52. [pdf]
  83. 2007

  84. Ratmann O, Jorgensen O, Hinkley T, Stumpf M, Richardson S, Wiuf C. 2007 Using likelihood-free inference to compare evolutionary dynamics of the protein networks of H. pylori and P. falciparum. PLOS Comp Biol 3: e320. [pdf]
  85. Stumpf MPH, Kelly W, Thorne T, Wiuf C. 2007 (Review) Evolution at the system level: The natural history of protein interaction networks. Trends Ecol Evol 22: 366-372. [pdf]
  86. Ewens WJ, RoyChoudhury A, Lewontin RC, Wiuf C. 2007 Two variance results in population genetics theory. Math Popul Stud 14: 93-110. [pdf]
  87. Brameier M, Wiuf C. 2007 Ab initio identification of human miRNAs for genome scanning based on structure motifs. BMC Bioinformatics 8: 478. [pdf]
  88. Lamy P, Andersen CL, Dyrskjot L, Torring N, Wiuf C. 2007 A Hidden Markov Model to estimate population mixture and allelic copy-numbers in cancers using Affymetrix SNP arrays. BMC Bioinformatics 8: 434. [pdf]
  89. Sorensen FJ, Andersen CL, Wiuf C. 2007 SNPTools: A software tool for visualization and analysis of microarray data. Bioinformatics 23: 1550-1552. [pdf]
  90. Brameier M, Wiuf C. 2007 Co-clustering and visualization of gene expression data and gene ontology terms for Saccharomyces cerevisiae using self-organizing maps. J Biomed Inform 40: 160-173. [pdf]
  91. Madsen BE, Villesen P, Wiuf C. 2007 A periodic pattern of SNPs in the human genome. Genome Res 17: 1414-1419. [pdf]
  92. Gilbert MTP, Binladen J, Miller W, Wiuf C, Willerslev E, Poinar H, Carlson JE, Leebens-Mack JH, Schuster SC. 2007 Recharacterisation of ancient DNA miscoding lesions: Insights in the era of the sequencing-by-synthesis. Nuc Acids Res 35: 1-10. [pdf]
  93. Hebsgaard M, Wiuf C, Gilbert MTP, Glenner H, Willerslev E. 2007 Evaluating Neandertal genetics and phylogeny. J Mol Evol 64: 50-60. [pdf]
  94. Hansen LL, Madsen BE, Pedersen K, Wiuf C. 2007 Conflicting results in SNP genotype assessment. Biotechniques 43: 756-762. [pdf]
  95. Torring N, Borre M, Sorensen KD, Andersen CL, Wiuf C, Orntoft TF. 2007 Genome-wide analysis of allelic imbalance in prostate cancer using the Affymetrix 50K SNP mapping array. Br J Cancer 96: 499-506. [pdf]
  96. Andersen CL, Wiuf C, Kruhoffer M, Korsgaard M, Laurberg S, Orntoft TF. 2007 Frequent occurrence of uniparental disomy in colorectal cancer. Carcinogenesis 28: 38-48. [pdf]
  97. 2006

  98. Lamy P, Andersen CL, Wikman FP, Wiuf C. 2006 Genotyping and annotation of Affymetrix SNP arrays. Nuc Acids Res 34: e100. [pdf]
  99. de Silva E, Thorne T, Ingram P, Agrafioti I, Swire J, Wiuf C, Stumpf MPH. 2006 The effects of incomplete protein interaction data on structural and evolutionary inferences. BMC Biology 4: 39. [pdf]
  100. Wiuf C. 2006 Consistency of estimators of population scaled parameters using composite likelihood. J Math Biol 53: 821-841. [pdf]
  101. Hagberg O, Wiuf C. 2006 Convergence properties of the degree distribution of some growing network models. Bull Math Biol 68: 1275-1291. [pdf]
  102. Wiuf C, Brameier M, Hagberg O, Stumpf MPH. 2006 A likelihood approach to analysis of network data. PNAS 103: 7566-7570. [pdf]
  103. Wiuf C, Stumpf MPH. 2006 Binomial subsampling. Proc Roy Soc A 462: 1181-1195. [pdf]
  104. Hansen A, Mitchell D, Wiuf C, Paniker L, Brand T, Binladen J, Gilichinsky D, Ronn R, Willerslev E. 2006 Crosslinks rather than strand breaks determine access to ancient DNA sequences frozen sediments. Genetics 173: 1175-1179. [pdf]
  105. Binladen J, Wiuf C, Gilbert MTP, Bunce M, Barnett R, Larson G, Greenwood AD, Haile J, Ho SYW, Hansen AJ, Willerslev E. 2006 Assessing the fidelity of ancient DNA sequences amplified from nuclear genes. Genetics 172: 733-741. [pdf]
  106. Lamy P, Andersen CL, Dyrskjot L, Torring N, Orntoft T, Wiuf C. 2006 Are microRNAs located in cancer specific regions in the genome? Br J Cancer 95: 1415-1418. [pdf]
  107. Aaboe M, Birkenkamp-Demtroder K, Wiuf C, Sorensen FB, Thykjaer T, Sauter G, Jensen KM-E, Dyrskjot L, Orntoft T. 2006 SOX4 expression in bladder carcinoma: clinical aspects and in-vitro functional characterization. Cancer Res 66: 3434-3442. [pdf]
  108. 2005

  109. Stumpf MPH, Wiuf C. 2005 Sampling properties of random graphs: The degree distribution. Phys Rev E, 72: 036118. [pdf]
  110. Stumpf MPH, Ingram PJ, Nouvel I, Wiuf C. 2005 Statistical model selection methods applied to biological network data. Lect Notes Comput Sci 3737: 65-77. [pdf]
  111. Stumpf MPH, Wiuf C, May RM. 2005 Subnets of scale-free networks are not scale-free: Sampling properties of networks. PNAS 102: 4221-4224. [pdf]
  112. Zieger K, Dyrskjot L, Wiuf C, Jensen JL, Andersen CL, Jensen KM-E, Orntoft TF. 2005 Role of activating fibroblast growth factor receptor 3 mutations in the development of bladder tumors. Clin Cancer Res 11: 7709-7719. [pdf]
  113. Koed K, Wiuf C, Christensen LL, Wikman FP, Zieger K, Moller K, von der Maase H, Orntoft TF. 2005 High-density single nucleotide polymorphism array defines novel stage and location dependent allelic imbalances in human bladder tumors. Cancer Res 65: 34-45. [pdf]
  114. 2004

  115. Wiuf C, Zhao K, Innan H, Nordborg M. 2004 The probability and chromosomal extent of trans-specific polymorphisms. Genetics 168: 2363-2372. [pdf]
  116. Wiuf C. 2004 Inference on recombination and block structure using unphased data. Genetics 166: 537-545. [pdf]
  117. Villesen P, Aagaard L, Wiuf C, Pedersen FS. 2004 Identification of endogenous retroviral reading frames in the human genome. Retrovirology 1: 32. [pdf]
  118. Willerslev E, Hansen AJ, Ronn R, Brand TB, Barnes I, Wiuf C, Gilichinsky D, Mitchell D, Cooper A. 2004 Long-term persistence of bacterial DNA. Curr Biol 14: R9-R10. [pdf]
  119. 2003

  120. Wiuf C, Laidlaw Z, Stumpf MPH. 2003 Some notes on the combinatorial properties of haplotype tagging. Math Biosci 185: 205-216. [pdf]
  121. Wiuf C, Posada D. 2003 A coalescent model of hotspot recombination. Genetics 164: 407-417. [pdf]
  122. Wiuf C. 2003 Inferring population history from genealogical trees. J Math Biol 46: 241-264. [pdf]
  123. Posada D, Wiuf C. 2003 Simulating haplotype blocks in the human genome. Bioinformatics 19: 289-290. [pdf]
  124. Willerslev E, Hansen AJ, Binladen J, Brand TB, Gilbert MTP, Shapiro B, Bunce M, Wiuf C, Gilichinsky DA, Cooper A. 2003 Diverse plant and animal genetic records from holocene and pleistocene sediments. Science 300: 791-795. [pdf]
  125. 2002

  126. Wiuf C. 2002 On the minimum number of topologies explaining a sample of DNA sequences. Theor Popul Biol 62: 357-363. [pdf]
  127. 2001

  128. Wiuf C. 2001 Recombination in human mitochondrial DNA? Genetics 159: 749-756. [pdf]
  129. Wiuf C, Christensen T, Hein J. 2001 A simulation study of the reliability of recombination detection methods. Mol Biol Evol 18: 1929-1939. [pdf]
  130. Wiuf C. 2001 Rare alleles and selection. Theor Popul Biol 59: 287-296. [pdf]
  131. Wiuf C. 2001 Do ΔF508 heterozygotes have a selective advantage? Genet Res 78: 41-47. [pdf]
  132. Strimmer K, Wiuf C, Moulton V. 2001 Recombination analysis using directed graphical models. Mol Biol Evol 18: 97-99. [pdf]
  133. Hansen AJ, Willerslev E, Wiuf C, Mourier T, Arctander P. 2001 Statistical evidence for miscoding lesions in ancient DNA templates. Mol Biol Evol 18: 262-265. [pdf]
  134. 2000

  135. Hein J, Wiuf C, Moller MB, Knudsen B, Wibling G. 2000 Statistical alignment: computational properties, homology testing and goodness-of-fit. J Mol Biol 302: 265-279. [pdf]
  136. Wiuf C. 2000 On the genealogy of a sample of neutral rare alleles. Theor Popul Biol 58: 61-75. [pdf]
  137. Wiuf C. 2000 A coalescence approach to gene conversion. Theor Popul Biol 57: 357-367. [pdf]
  138. Wiuf C, Hein J. 2000 The coalescent with gene conversion. Genetics 155: 451-462. [pdf]
  139. 1999

  140. Wiuf C, Donnelly P. 1999 Conditional genealogies and the age of a neutral mutant. Theor Popul Biol 56: 183-201. [pdf]
  141. Wiuf C, Hein J. 1999 Recombination as a point process along sequences. Theor Popul Biol 55: 248-259. [pdf]
  142. Wiuf C, Hein J. 1999 The ancestry of a sample of sequences subject to recombination. Genetics 151: 1217-1228. [pdf]
  143. 1998

  144. Pedersen A-MK, Wiuf C, Christiansen FB. 1998 A codon-based model designed to describe lenti-viral evolution. Mol Biol Evol 15: 1069-1081. [pdf]
  145. 1997

  146. Wiuf C, Hein J. 1997 On the number of ancestors to a DNA sequence. Genetics 147: 1459-1468. [pdf]


  1. Stumpf MPH, Wiuf C (eds). 2010 Statistical and Evolutionary Analysis of Biological Networks. Imperial College Press. [ICP]
  2. Wiuf C, Andersen CL (eds). 2009 Statistics and Informatics in Molecular Cancer Research. Oxford University Press. [OUP]
  3. Hein J, Schierup MH, Wiuf C. 2005 Gene Genealogies, Variation, and Evolution. Oxford University Press. [OUP]

    Book Contributions

  1. Wiuf C. 2011 Algebraic statistics and methods in systems biology. In Handbook of Statistical Systems Biology, pp 114-132, eds MPH Stumpf, M Girolami and D Balding, John Wiley & Sons. [JW]
  2. Schierup MH, Wiuf C. 2010 The coalescent of bacterial populations. In Bacterial Population Genetics in Infectious Disease, pp 3-18, eds DA Robinson, EJ Feil and D Falush, John Wiley & Sons. [JW] [pdf]
  3. Wiuf C, Ratmann O. 2010 Evolutionary analysis of protein interaction networks. In Statistical and Evolutionary Analysis of Biological Networks, pp 17-43, eds MPH Stumpf and C Wiuf, Imperial College Press. [ICP]
  4. Stumpf MPH, Wiuf C. 2010 A network analysis primer. In Statistical and Evolutionary Analysis of Biological Networks, pp 1-15, eds MPH Stumpf and C Wiuf, Imperial College Press. [ICP]
  5. Wiuf C, Lamy P, Andersen CL. 2009 Methods for derivation of LOH and allelic copy numbers using SNP arrays. In Statistics and Informatics in Molecular Cancer Research, pp 62-77, eds C Wiuf and CL Andersen, Oxford University Press. [OUP]
  6. Wiuf C. 2003 The age of a rare mutation. In Highly Structured Stochastic Systems, pp 417-422, eds PJ Green, NL Hjort and S Richardson, Oxford University Press. [OUP] [pdf]

    Other Science Contributions

  1. Autio R, Shmulevich I, Strimmer K, Wiuf C (eds). 2013 Selected articles from the 10th International Workshop on Computational Systems Biology (WCSB) 2013: Systems Biology. BMC Systems Biology 7(Suppl 1). [pdf]
  2. (With many others). 2012 Association between genetic variation in a region on chromosome 11 and schizophrenia in large samples from Europe. Mol Psychiatry 17: 906-917. [pdf]
  3. (With many others). 2011 Common variants at VRK2 and TCF4 conferring risk of schizophrenia. Hum Mol Genet 20: 4076-4081. [pdf]
  4. Andersen FF, Villesen P, Knudsen B, Wiuf C, Desideri A, Knudsen BR. 2011 Utilization of computer science for construction and characterization of DNA nano-structures. In DNA Microarrays, Synthesis and Synthetic DNA, pp 317-330, ed MJ Campbell, Nova Science Publishers Inc. [NS] [pdf]
  5. Ratmann O, Andrieu C, Wiuf C, Richardson S. 2010 Reply to Robert et al: Model criticism informs model choice and model comparison. PNAS 107: E6-E7. [pdf]
  6. Li J, Wang K, Jensen TD, Li S, Bolund L, Wiuf C. 2010 Tumor heterogeneity in neoplasms of breast, colon, and skin. BMC Res Notes 3: 321. [pdf]
  7. Manninen T, Wiuf C, Lahdesmaki H, Grzegorczyk M, Rahnenfuhrer J, Ahdesmaki M, Linne M-J, Yli-Harja O (eds). 2009 Proceedings of the Sixth International Workshop on Computational Systems Biology (WCSB 2009), TICSP Series #48. [html]
  8. Ratmann O, Andrieu C, Wiuf C, Richardson S. 2009 Likelihood-free model criticism applied to stochastic models of protein network evolution. In Proceedings of the Sixth International Workshop on Computational Systems Biology (WCSB 2009), TICSP Series #48, pp 143-146, eds T Manninen, C Wiuf C, H Lahdesmaki, M Grzegorczyk, J Rahnenfuhrer, M Ahdesmaki, M-J Linne, O Yli-Harja. [pdf]
  9. Agerbo E, Madsen BE, Wiuf C. 2009 (Poster abstract) Schizophrenia genetics: Number of genes, environmental influences and disease penetrance under epistatic models. Schizophrenia Bull 35 (Suppl 1): 98. [pdf]
  10. Wiuf C. 2008 (in Danish) Simple matematiske modeller til beskrivelse af komplekse biologiske systemer. Mathilde 34: 12-15. [pdf]
  11. Wiuf C, Ratmann O, Knudsen M. 2008 Analysis of biological network data using likelihood-free inference techniques. In Proceedings of the Fifth International Workshop on Computational Systems Biology (WCSB 2008), TICSP Series #41, pp 185-188, eds M Ahdesmaki, K Strimmer, N Radde, J Rahnenfuhrer, K Klemm, H Lahdesmaki, O Yli-Harja. [pdf]
  12. Wiuf C, Ratmann O. 2007 Statistical analysis of biological network data. In Symposium i Anvendt Statistik 2007, pp 147-156, ed P Linde. [pdf]
  13. Nielsen R, Wiuf C. 2005 Composite likelihood estimation applied to Single Nucleotide Polymorphism (SNP) data. ISI Conference Proceedings 2005. [pdf]
  14. Hein J, Wiuf C. 2002 Review of GR Grant and WJ Ewens, "Statistical Methods in Bioinformatics: An Introduction". Brief Bioinf 3: 318-319. [pdf]
  15. Wiuf C, Hein J. 1999 Discussion of a paper by JT Chang, "Recent common ancestors of all present-day individuals". Adv Appl Prob 31: 1029-1030. [pdf]
  16. Donnelly P, Wiuf C. 1999 (Poster abstract) Shared chromosomal segments and genome-wide association mapping. Am J Hum Genet 65: A83. [html]
  17. Wiuf C. 1994 A generalization of a von Mises-Fisher conditional distribution result. Research Reports no 296, Department of Theoretical Statistics, University of Aarhus. [pdf]
  18. Wiuf C. 1994 Dual spaces and β-orthogeodesic models. Research Reports no 286, Department of Theoretical Statistics, University of Aarhus. [pdf]