Carsten Wiuf

Carsten Wiuf

Professor

ORCID: 0000-0002-1302-4445

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  1. Published

    Phosphorelay of non-orthodox two component systems functions through a bi-molecular mechanism in vivo: the case of ArcB

    Jovanovic, G., Sheng, X., Ale, A., Feliu, Elisenda, Harrington, H. A., Kirk, P., Wiuf, Carsten, Buck, M. & Stumpf, M. P. H., 23 Mar 2015, In: Molecular BioSystems. 11, p. 1348-1359

    Research output: Contribution to journal › Journal article › Research › peer-review

  2. Published

    Exact analysis of intrinsic qualitative features of phosphorelays using mathematical models

    Knudsen, M., Feliu, Elisenda & Wiuf, Carsten, 2012, In: Journal of Theoretical Biology. 300, p. 7-18 12 p.

    Research output: Contribution to journal › Journal article › Research › peer-review

  3. A Markov chain approach to randomly grown graphs

    Knudsen, M. & Wiuf, Carsten, 9 Jul 2008, In: Journal of Applied Mathematics. 2008, 190836.

    Research output: Contribution to journal › Journal article › Research › peer-review

  4. The CATH database.

    Knudsen, M. & Wiuf, Carsten, 1 Jan 2010, In: Human Genomics. 4, 3, p. 207-212 6 p.

    Research output: Contribution to journal › Journal article › Research › peer-review

  5. High-density single nucleotide polymorphism array defines novel stage and location-dependent allelic imbalances in human bladder tumors

    Koed, K., Wiuf, Carsten, Christensen, L. L., Wikman, F. P., Zieger, K., Møller, K., Von Der Maase, H. & Ørntoft, T. F., 1 Jan 2005, In: Cancer Research. 65, 1, p. 34-45 12 p.

    Research output: Contribution to journal › Journal article › Research › peer-review

  6. Published

    Phosphorelays provide tunable signal processing capabilities for the cell

    Kothamachu, V. B., Feliu, Elisenda, Wiuf, Carsten, Cardelli, L. & Soyer, O. S., 2013, In: P L o S Computational Biology (Online). 9, 11, p. e1003322

    Research output: Contribution to journal › Journal article › Research › peer-review

  7. 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

    Kristensen, L. S., Wojdacz, T. K., Thestrup, B. B., Wiuf, Carsten, Hager, H. & Hansen, L. L., 21 Dec 2009, In: BMC Cancer. 9, 453.

    Research output: Contribution to journal › Journal article › Research › peer-review

  8. Are microRNAs located in genomic regions associated with cancer?

    Lamy, P., Andersen, C. L., Dyrskjøt, L., Tørring, N., Ørntoft, T. & Wiuf, Carsten, 20 Nov 2006, In: British Journal of Cancer. 95, 10, p. 1415-1418 4 p.

    Research output: Contribution to journal › Journal article › Research › peer-review

  9. Genotyping and annotation of Affymetrix SNP arrays

    Lamy, P., Andersen, C. L., Wikman, F. P. & Wiuf, Carsten, 21 Sep 2006, In: Nucleic Acids Research. 34, 14, e100.

    Research output: Contribution to journal › Journal article › Research › peer-review

  10. A Hidden Markov Model to estimate population mixture and allelic copy-numbers in cancers using Affymetrix SNP arrays

    Lamy, P., Andersen, C. L., Dyrskjot, L., Torring, N. & Wiuf, Carsten, 9 Nov 2007, In: BMC Bioinformatics. 8, 434.

    Research output: Contribution to journal › Journal article › Research › peer-review

  11. Rseg-an R package to optimize segmentation of SNP array data

    Lamy, P., Wiuf, Carsten, Ørntoft, T. F. & Andersen, C. L., 1 Feb 2011, In: Bioinformatics. 27, 3, p. 419-420 2 p., btq668.

    Research output: Contribution to journal › Journal article › Research › peer-review

  12. A review of software for microarray genotyping

    Lamy, P., Grove, J. & Wiuf, Carsten, 1 Jan 2011, In: Human Genomics. 5, 4, p. 304-309 6 p.

    Research output: Contribution to journal › Review › Research › peer-review

  13. A Beta-mixture model for dimensionality reduction, sample classification and analysis

    Laurila, K., Oster, B., Andersen, C. L., Lamy, P., Orntoft, T., Yli-Harja, O. & Wiuf, Carsten, 27 May 2011, In: BMC Bioinformatics. 12, 215.

    Research output: Contribution to journal › Journal article › Research › peer-review

  14. Tumor heterogeneity in neoplasms of breast, colon, and skin

    Li, J., Wang, K., Jensen, T. D., Li, S., Bolund, L. & Wiuf, Carsten, 29 Nov 2010, In: BMC Research Notes. 3, 321.

    Research output: Contribution to journal › Journal article › Research › peer-review

  15. Germline mutation in RNASEL predicts increased risk of head and neck, uterine cervix and breast cancer

    Madsen, B. E., Ramos, E. M., Boulard, M., Duda, K., Overgaard, J., Nordsmark, M., Wiuf, Carsten & Hansen, L. L., 25 Jun 2008, In: PLOS ONE. 3, 6, e2492.

    Research output: Contribution to journal › Journal article › Research › peer-review

  16. Short tandem repeats in human exons: A target for disease mutations

    Madsen, B. E., Villesen, P. & Wiuf, Carsten, 12 Sep 2008, In: BMC Genomics. 9, 410.

    Research output: Contribution to journal › Journal article › Research › peer-review

  17. A periodic pattern of SNPs in the human genome

    Madsen, B. E., Villesen, P. & Wiuf, Carsten, 1 Oct 2007, In: Genome Research. 17, 10, p. 1414-1419 6 p.

    Research output: Contribution to journal › Journal article › Research › peer-review

  18. Short tandem repeats and genetic variation

    Madsen, B. E., Villesen, P. & Wiuf, Carsten, 1 Jan 2010, Genetic Variation: Methods and Protocols. Humana Press, p. 297-306 10 p. (Methods in Molecular Biology, Vol. 628).

    Research output: Chapter in Book/Report/Conference proceeding › Book chapter › Research › peer-review

  19. Published

    Conservation Laws in Biochemical Reaction Networks

    Mahdi, A., Ferragut, A., Valls, C. & Wiuf, Carsten, 2017, In: S I A M Journal on Applied Dynamical Systems. 16, 4, p. 2213-2232

    Research output: Contribution to journal › Journal article › Research › peer-review

  20. Published

    Intermediates and Generic Convergence to Equilibria

    Marcondes de Freitas, M., Wiuf, Carsten & Feliu, Elisenda, 2017, In: Bulletin of Mathematical Biology. 79, 7, p. 1662–1686

    Research output: Contribution to journal › Journal article › Research › peer-review

  21. Published

    Intermediates, Catalysts, Persistence, and Boundary Steady States

    Marcondes de Freitas, M., Feliu, Elisenda & Wiuf, Carsten, 2017, In: Journal of Mathematical Biology. 74, 4, p. 887–932

    Research output: Contribution to journal › Journal article › Research › peer-review

  22. Published

    Parchment Glutamine Index (PQI): A novel method to estimate glutamine deamidation levels in parchment collagen obtained from low-quality MALDI-TOF data

    Anila Bhuvanendran Nair, Bharath, Palomo, I. R., Markussen, Bo, Wiuf, Carsten, Fiddyment, S. & Collins, Matthew James, 2023, In: Peer Community Journal. 3, 18 p., e10.

    Research output: Contribution to journal › Journal article › Research › peer-review

  23. A codon-based model designed to describe lentiviral evolution

    Pedersen, A. M. K., Wiuf, Carsten & Christiansen, F. B., 1 Jan 1998, In: MOLECULAR BIOLOGY AND EVOLUTION . 15, 8, p. 1069-1081 13 p.

    Research output: Contribution to journal › Journal article › Research › peer-review

  24. Published

    Large scale identification and categorization of protein sequences using structured logistic regression

    Pedersen, B. P., Ifrim, G., Liboriussen, P., Axelsen, K. B., Palmgren, Michael, Nissen, P., Wiuf, Carsten & Pedersen, C. N. S., 20 Jan 2014, In: PLOS ONE. 9, 1, 11 p., e85139.

    Research output: Contribution to journal › Journal article › Research › peer-review

  25. Fatgraph models of proteins

    Penner, R. C., Knudsen, M., Wiuf, Carsten & Andersen, J. E., 1 Oct 2010, In: Communications on Pure and Applied Mathematics. 63, 10, p. 1249-1297 49 p.

    Research output: Contribution to journal › Journal article › Research › peer-review

  26. An algebro-topological description of protein domain structure

    Penner, R. C., Knudsen, M., Wiuf, Carsten & Andersen, J. E., 27 May 2011, In: PLoS ONE. 6, 5, e19670.

    Research output: Contribution to journal › Journal article › Research › peer-review

  27. Simulating haplotype blocks in the human genome

    Posada, D. & Wiuf, Carsten, 1 Feb 2003, In: Bioinformatics. 19, 2, p. 289-290 2 p.

    Research output: Contribution to journal › Journal article › Research › peer-review

  28. Temporal development and collapse of an Arctic plant-pollinator network

    Pradal, C., Olesen, J. M. & Wiuf, Carsten, 1 Dec 2009, In: BMC Ecology. 9, 24.

    Research output: Contribution to journal › Journal article › Research › peer-review

  29. Published

    Estimation of site frequency spectra from low-coverage sequencing data using stochastic EM reduces overfitting, runtime, and memory usage

    Rasmussen, Malthe Sebro, Garcia Erill, Genís, Korneliussen, Thorfinn Sand, Wiuf, Carsten & Albrechtsen, Anders, 2022, In: Genetics. 222, 4, 15 p., iyac148.

    Research output: Contribution to journal › Journal article › Research › peer-review

  30. Model criticism based on likelihood-free inference, with an application to protein network evolution

    Ratmann, O., Andrieu, C., Wiuf, Carsten & Richardson, S., 30 Jun 2009, In: Proceedings of the National Academy of Sciences of the United States of America. 106, 26, p. 10576-10581 6 p.

    Research output: Contribution to journal › Journal article › Research › peer-review

  31. Using likelihood-free inference to compare evolutionary dynamics of the protein networks of H. pylori and P. falciparum

    Ratmann, O., Jørgensen, O., Hinkley, T., Stumpf, M., Richardson, S. & Wiuf, Carsten, 1 Nov 2007, In: PLOS Computational Biology. 3, 11, p. 2266-2278 13 p.

    Research output: Contribution to journal › Journal article › Research › peer-review

  32. From evidence to inference: Probing the evolution of protein interaction networks

    Ratmann, O., Wiuf, Carsten & Pinney, J. W., 1 Oct 2009, In: HFSP Journal. 3, 5, p. 290-306 17 p.

    Research output: Contribution to journal › Journal article › Research › peer-review

  33. Reply to Robert et al. Model criticism informs model choice and model comparison

    Ratmann, O., Andrieu, C., Wiuf, Carsten & Richardson, S., 19 Jan 2010, In: Proceedings of the National Academy of Sciences of the United States of America. 107, 3

    Research output: Contribution to journal › Letter › Research › peer-review

  34. Comprehensive genome methylation analysis in bladder cancer: Identification and validation of novel methylated genes and application of these as urinary tumor markers

    Reinert, T., Modin, C., Castano, F. M., Lamy, P., Wojdacz, T. K., Hansen, L. L., Wiuf, Carsten, Borre, M., Dyrskjøt, L. & Ørntoft, T. F., 1 Sep 2011, In: Clinical Cancer Research. 17, 17, p. 5582-5592 11 p.

    Research output: Contribution to journal › Journal article › Research › peer-review

  35. Association between genetic variation in a region on chromosome 11 and schizophrenia in large samples from Europe

    Rietschel, M., Mattheisen, M., Degenhardt, F., Kahn, R. S., Linszen, D. H., Os, J. V., Wiersma, D., Bruggeman, R., Cahn, W., de Haan, L., Krabbendam, L., Myin-Germeys, I., Mühleisen, T. W., Kirsch, P., Esslinger, C., Herms, S., Demontis, D., Steffens, M., Strohmaier, J., Haenisch, B. & 82 others, Breuer, R., Czerski, P. M., Giegling, I., Strengman, E., Schmael, C., Mors, O., Mortensen, P. B., Hougaard, D. M., Orntoft, T., Kapelski, P., Priebe, L., Basmanav, F. B., Forstner, A. J., Hoffmann, P. F. F., Meier, S., Nikitopoulos, J., Moebus, S., Alexander, M., Mössner, R., Wichmann, H., Schreiber, S., Rivandeneira, F., Hofman, A., Uitterlinden, A. G., Wienker, T. F., Schumacher, J., Hauser, J., Maier, W., Cantor, R., Erk, S., Schulze, T. G., Stefansson, H., Steinberg, S., Gustafsson, O., Sigurdsson, E., Petursson, H., Kong, A., Stefansson, K., Pietiläinen, O. P. H., Tuulio-Henriksson, A., Paunio, T., Lonnqvist, J., Suvisaari, J., Peltonen, L., Ruggeri, M., Tosato, S., Walshe, M., Murray, R., Collier, D. A., Clair, D. S., Hansen, T., Ingason, A., Jakobsen, K. D., Duong, L., Werge, T., Melle, I., Andreassen, O. A., Djurovic, S., Bitter, I., Réthelyi, J. M., Abramova, L., Kaleda, V., Golimbet, V., Jönsson, E. G., Terenius, L., Agartz, I., Winkel, R. V., Kenis, G., Hert, M. D., Veldink, J., Wiuf, Carsten, Didriksen, M., Craddock, N., Owen, M. J., O'Donovan, M. C., Børglum, A., Rujescu, D., Walter, H., Meyer-Lindenberg, A., Nöthen, M. M., Ophoff, R. A. & Cichon, S., 2012, In: Molecular Psychiatry. 17, 9, p. 906-917 12 p.

    Research output: Contribution to journal › Journal article › Research › peer-review

  36. Published

    Graphical criteria for positive solutions to linear systems

    Saez, M., Feliu, Elisenda & Wiuf, Carsten, 1 Sep 2018, In: Linear Algebra and Its Applications. 552, p. 166-193

    Research output: Contribution to journal › Journal article › Research › peer-review

  37. Published

    Graphical reduction of reaction networks by linear elimination of species

    Saez Cornellana, M., Wiuf, Carsten & Feliu, Elisenda, 2017, In: Journal of Mathematical Biology. 74, 1, p. 195–237

    Research output: Contribution to journal › Journal article › Research › peer-review

  38. The Coalescent of Bacterial Populations

    Schierup, M. H. & Wiuf, Carsten, 9 Apr 2010, Bacterial Population Genetics in Infectious Disease. Wiley, p. 1-18 18 p.

    Research output: Chapter in Book/Report/Conference proceeding › Book chapter › Research › peer-review

  39. Published

    A Reaction Network Scheme Which Implements Inference and Learning for Hidden Markov Models

    Singh, A., Wiuf, Carsten, Behera, A. & Gopalkrishnan, M., 2019, DNA Computing and Molecular Programming - 25th International Conference, DNA 25, Proceedings. Liu, Y. & Thachuk, C. (eds.). Springer, p. 54-79 26 p. (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), Vol. 11648 LNCS).

    Research output: Chapter in Book/Report/Conference proceeding › Article in proceedings › Research › peer-review

  40. Published

    General theory for stochastic admixture graphs and F-statistics

    Soraggi, S. & Wiuf, Carsten, 2019, In: Theoretical Population Biology. 125, p. 56-66 11 p.

    Research output: Contribution to journal › Journal article › Research › peer-review

  41. Published

    Powerful Inference With the D-Statistic on Low-Coverage Whole-Genome Data

    Soraggi, S., Wiuf, Carsten & Albrechtsen, Anders, 2018, In: G3: Genes, Genomes, Genetics (Bethesda). 8, 2, p. 551-566

    Research output: Contribution to journal › Journal article › Research › peer-review

  42. Recombination analysis using directed graphical models [4]

    Strimmer, K., Wiuf, Carsten & Moulton, V., 1 Jan 2001, In: MOLECULAR BIOLOGY AND EVOLUTION . 18, 1, p. 97-99 3 p.

    Research output: Contribution to journal › Letter › Research › peer-review

  43. Evolution at the system level: the natural history of protein interaction networks

    Stumpf, M. P. H., Kelly, W. P., Thorne, T. & Wiuf, Carsten, 1 Jul 2007, In: Trends in Ecology and Evolution. 22, 7, p. 366-373 8 p.

    Research output: Contribution to journal › Review › Research › peer-review

  44. Statistical and evolutionary analysis of biological networks

    Stumpf, M. P. H. & Wiuf, Carsten, 1 Jan 2009, Imperial College Press. 170 p.

    Research output: Book/Report › Book › Research › peer-review

  45. Statistical model selection methods applied to biological networks

    Stumpf, M. P. H., Ingram, P. J., Nouvel, I. & Wiuf, Carsten, 1 Dec 2005, Transactions on Computational systems Biology III. p. 65-77 13 p. (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), Vol. 3737 LNBI).

    Research output: Chapter in Book/Report/Conference proceeding › Article in proceedings › Research › peer-review

  46. Published

    Estimating the size of the human interactome

    Stumpf, M. P. H., Thorne, T., De Silva, E., Stewart, R., Hyeong, J. A., Lappe, M. & Wiuf, Carsten, 13 May 2008, In: Proceedings of the National Academy of Sciences of the United States of America. 105, 19, p. 6959-6964 6 p.

    Research output: Contribution to journal › Journal article › Research › peer-review

  47. Subnets of scale-free networks are not scale-free: Sampling properties of networks

    Stumpf, M. P. H., Wiuf, Carsten & May, R. M., 22 Mar 2005, In: Proceedings of the National Academy of Sciences of the United States of America. 102, 12, p. 4221-4224 4 p.

    Research output: Contribution to journal › Journal article › Research › peer-review

  48. Incomplete and noisy network data as a percolation process

    Stumpf, M. P. H. & Wiuf, Carsten, 6 Oct 2010, In: Journal of the Royal Society Interface. 7, 51, p. 1411-1419 9 p.

    Research output: Contribution to journal › Review › Research › peer-review

  49. Sampling properties of random graphs: The degree distribution

    Stumpf, M. P. H. & Wiuf, Carsten, 1 Sep 2005, In: Physical Review E - Statistical, Nonlinear, and Soft Matter Physics. 72, 3, 036118.

    Research output: Contribution to journal › Journal article › Research › peer-review

  50. Published

    Nonnegative linear elimination for chemical reaction networks

    Sáez, M., Wiuf, Carsten & Feliu, Elisenda, 2019, In: SIAM Journal on Applied Mathematics. 79, 6, p. 2434-2455

    Research output: Contribution to journal › Journal article › Research › peer-review

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