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Items: 1 to 50 of 112

1.

General theory for stochastic admixture graphs and F-statistics.

Soraggi S, Wiuf C.

Theor Popul Biol. 2019 Feb;125:56-66. doi: 10.1016/j.tpb.2018.12.002. Epub 2018 Dec 15.

PMID:
30562538
2.

Node balanced steady states: Unifying and generalizing complex and detailed balanced steady states.

Feliu E, Cappelletti D, Wiuf C.

Math Biosci. 2018 Jul;301:68-82. doi: 10.1016/j.mbs.2018.03.002. Epub 2018 Mar 28.

PMID:
29601834
3.

Some properties of the conditioned reconstructed process with Bernoulli sampling.

Wiuf C.

Theor Popul Biol. 2018 Jul;122:36-45. doi: 10.1016/j.tpb.2018.02.003. Epub 2018 Feb 13.

PMID:
29452133
4.

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

Soraggi S, Wiuf C, Albrechtsen A.

G3 (Bethesda). 2018 Feb 2;8(2):551-566. doi: 10.1534/g3.117.300192.

5.

Identifying parameter regions for multistationarity.

Conradi C, Feliu E, Mincheva M, Wiuf C.

PLoS Comput Biol. 2017 Oct 3;13(10):e1005751. doi: 10.1371/journal.pcbi.1005751. eCollection 2017 Oct.

6.

Intermediates and Generic Convergence to Equilibria.

de Freitas MM, Wiuf C, Feliu E.

Bull Math Biol. 2017 Jul;79(7):1662-1686. doi: 10.1007/s11538-017-0303-4. Epub 2017 Jun 15.

PMID:
28620882
7.

epiG: statistical inference and profiling of DNA methylation from whole-genome bisulfite sequencing data.

Vincent M, Mundbjerg K, Skou Pedersen J, Liang G, Jones PA, Ørntoft TF, Dalsgaard Sørensen K, Wiuf C.

Genome Biol. 2017 Feb 21;18(1):38. doi: 10.1186/s13059-017-1168-4.

8.

Challenges in microbial ecology: building predictive understanding of community function and dynamics.

Widder S, Allen RJ, 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 JU, Rainey PB, Freilich S, Schuster S, Milferstedt K, van der Meer JR, Groβkopf T, Huisman J, Free A, Picioreanu C, Quince C, Klapper I, Labarthe S, Smets BF, Wang H; Isaac Newton Institute Fellows, Soyer OS.

ISME J. 2016 Nov;10(11):2557-2568. doi: 10.1038/ismej.2016.45. Epub 2016 Mar 29. Review.

9.

Core signalling motif displaying multistability through multi-state enzymes.

Feng S, Sáez M, Wiuf C, Feliu E, Soyer OS.

J R Soc Interface. 2016 Oct;13(123). pii: 20160524.

10.

Intermediates, catalysts, persistence, and boundary steady states.

Marcondes de Freitas M, Feliu E, Wiuf C.

J Math Biol. 2017 Mar;74(4):887-932. doi: 10.1007/s00285-016-1046-9. Epub 2016 Aug 1.

PMID:
27480320
11.

LandScape: a simple method to aggregate p-values and other stochastic variables without a priori grouping.

Wiuf C, Schaumburg-Müller Pallesen J, Foldager L, Grove J.

Stat Appl Genet Mol Biol. 2016 Aug 1;15(4):349-61. doi: 10.1515/sagmb-2015-0085.

PMID:
27269897
12.

Graphical reduction of reaction networks by linear elimination of species.

Sáez M, Wiuf C, Feliu E.

J Math Biol. 2017 Jan;74(1-2):195-237. doi: 10.1007/s00285-016-1028-y. Epub 2016 May 24.

PMID:
27221101
13.

Lyapunov Functions, Stationary Distributions, and Non-equilibrium Potential for Reaction Networks.

Anderson DF, Craciun G, Gopalkrishnan M, Wiuf C.

Bull Math Biol. 2015 Sep;77(9):1744-67. doi: 10.1007/s11538-015-0102-8. Epub 2015 Sep 16.

PMID:
26376889
14.

Finding the positive feedback loops underlying multi-stationarity.

Feliu E, Wiuf C.

BMC Syst Biol. 2015 May 28;9:22. doi: 10.1186/s12918-015-0164-0.

15.

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 E, Harrington HA, Kirk P, Wiuf C, Buck M, Stumpf MP.

Mol Biosyst. 2015 May;11(5):1348-59. doi: 10.1039/c4mb00720d.

PMID:
25797699
16.

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

Pedersen BP, Ifrim G, Liboriussen P, Axelsen KB, Palmgren MG, Nissen P, Wiuf C, Pedersen CN.

PLoS One. 2014 Jan 20;9(1):e85139. doi: 10.1371/journal.pone.0085139. eCollection 2014.

17.

Phosphorelays provide tunable signal processing capabilities for the cell.

Kothamachu VB, Feliu E, Wiuf C, Cardelli L, Soyer OS.

PLoS Comput Biol. 2013;9(11):e1003322. doi: 10.1371/journal.pcbi.1003322. Epub 2013 Nov 7.

18.

Simplifying biochemical models with intermediate species.

Feliu E, Wiuf C.

J R Soc Interface. 2013 Jul 24;10(87):20130484. doi: 10.1098/rsif.2013.0484. Print 2013 Oct 6.

19.

A computational method to preclude multistationarity in networks of interacting species.

Feliu E, Wiuf C.

Bioinformatics. 2013 Sep 15;29(18):2327-34. doi: 10.1093/bioinformatics/btt400. Epub 2013 Jul 9.

PMID:
23842805
20.

Cellular compartments cause multistability and allow cells to process more information.

Harrington HA, Feliu E, Wiuf C, Stumpf MP.

Biophys J. 2013 Apr 16;104(8):1824-31. doi: 10.1016/j.bpj.2013.02.028.

21.

Genome-wide study of association and interaction with maternal cytomegalovirus infection suggests new schizophrenia loci.

Børglum AD, Demontis D, Grove J, Pallesen J, Hollegaard MV, Pedersen CB, Hedemand A, Mattheisen M; GROUP investigators10, Uitterlinden A, Nyegaard M, Ørntoft T, Wiuf C, Didriksen M, Nordentoft M, Nöthen MM, Rietschel M, Ophoff RA, Cichon S, Yolken RH, Hougaard DM, Mortensen PB, Mors O.

Mol Psychiatry. 2014 Mar;19(3):325-33. doi: 10.1038/mp.2013.2. Epub 2013 Jan 29.

22.

A bimodular mechanism of calcium control in eukaryotes.

Tidow H, Poulsen LR, Andreeva A, Knudsen M, Hein KL, Wiuf C, Palmgren MG, Nissen P.

Nature. 2012 Nov 15;491(7424):468-72. doi: 10.1038/nature11539. Epub 2012 Oct 21.

PMID:
23086147
23.

Variable elimination in post-translational modification reaction networks with mass-action kinetics.

Feliu E, Wiuf C.

J Math Biol. 2013 Jan;66(1-2):281-310. doi: 10.1007/s00285-012-0510-4. Epub 2012 Feb 5.

PMID:
22311196
24.

Exact analysis of intrinsic qualitative features of phosphorelays using mathematical models.

Knudsen M, Feliu E, Wiuf C.

J Theor Biol. 2012 May 7;300:7-18. doi: 10.1016/j.jtbi.2012.01.007. Epub 2012 Jan 13.

PMID:
22266661
25.

Signaling cascades: consequences of varying substrate and phosphatase levels.

Feliu E, Knudsen M, Wiuf C.

Adv Exp Med Biol. 2012;736:81-94. doi: 10.1007/978-1-4419-7210-1_4.

PMID:
22161323
26.

Monitoring endangered freshwater biodiversity using environmental DNA.

Thomsen PF, Kielgast J, Iversen LL, Wiuf C, Rasmussen M, Gilbert MT, Orlando L, Willerslev E.

Mol Ecol. 2012 Jun;21(11):2565-73. doi: 10.1111/j.1365-294X.2011.05418.x. Epub 2011 Dec 13.

PMID:
22151771
27.

Modelling the contribution of family history and variation in single nucleotide polymorphisms to risk of schizophrenia: a Danish national birth cohort-based study.

Agerbo E, Mortensen PB, Wiuf C, Pedersen MS, McGrath J, Hollegaard MV, Nørgaard-Pedersen B, Hougaard DM, Mors O, Pedersen CB.

Schizophr Res. 2012 Feb;134(2-3):246-52. doi: 10.1016/j.schres.2011.10.025. Epub 2011 Nov 22.

PMID:
22108675
28.

Enzyme-sharing as a cause of multi-stationarity in signalling systems.

Feliu E, Wiuf C.

J R Soc Interface. 2012 Jun 7;9(71):1224-32. doi: 10.1098/rsif.2011.0664. Epub 2011 Nov 2.

29.

Tumor-specific usage of alternative transcription start sites in colorectal cancer identified by genome-wide exon array analysis.

Thorsen K, Schepeler T, Øster B, Rasmussen MH, Vang S, Wang K, Hansen KQ, Lamy P, Pedersen JS, Eller A, Mansilla F, Laurila K, Wiuf C, Laurberg S, Dyrskjøt L, Ørntoft TF, Andersen CL.

BMC Genomics. 2011 Oct 14;12:505. doi: 10.1186/1471-2164-12-505.

30.

Gene expression classifier predicts for hypoxic modification of radiotherapy with nimorazole in squamous cell carcinomas of the head and neck.

Toustrup K, Sørensen BS, Lassen P, Wiuf C, Alsner J, Overgaard J; Danish Head and Neck Cancer Group (DAHANCA).

Radiother Oncol. 2012 Jan;102(1):122-9. doi: 10.1016/j.radonc.2011.09.010. Epub 2011 Oct 11.

PMID:
21996521
31.

Development of a hypoxia gene expression classifier with predictive impact for hypoxic modification of radiotherapy in head and neck cancer.

Toustrup K, Sørensen BS, Nordsmark M, Busk M, Wiuf C, Alsner J, Overgaard J.

Cancer Res. 2011 Sep 1;71(17):5923-31. doi: 10.1158/0008-5472.CAN-11-1182. Epub 2011 Aug 16.

32.

Common variants at VRK2 and TCF4 conferring risk of schizophrenia.

Steinberg S, de Jong S; Irish Schizophrenia Genomics Consortium, Andreassen OA, Werge T, Børglum AD, Mors O, Mortensen PB, Gustafsson O, Costas J, Pietiläinen OP, Demontis D, Papiol S, Huttenlocher J, Mattheisen M, Breuer R, Vassos E, Giegling I, Fraser G, Walker N, Tuulio-Henriksson A, Suvisaari J, Lönnqvist J, Paunio T, Agartz I, Melle I, Djurovic S, Strengman E; GROUP, Jürgens G, Glenthøj B, Terenius L, Hougaard DM, Ørntoft T, Wiuf C, Didriksen M, Hollegaard MV, Nordentoft M, van Winkel R, Kenis G, Abramova L, Kaleda V, Arrojo M, Sanjuán J, Arango C, Sperling S, Rossner M, Ribolsi M, Magni V, Siracusano A, Christiansen C, Kiemeney LA, Veldink J, van den Berg L, Ingason A, Muglia P, Murray R, Nöthen MM, Sigurdsson E, Petursson H, Thorsteinsdottir U, Kong A, Rubino IA, De Hert M, Réthelyi JM, Bitter I, Jönsson EG, Golimbet V, Carracedo A, Ehrenreich H, Craddock N, Owen MJ, O'Donovan MC; Wellcome Trust Case Control Consortium 2, Ruggeri M, Tosato S, Peltonen L, Ophoff RA, Collier DA, St Clair D, Rietschel M, Cichon S, Stefansson H, Rujescu D, Stefansson K.

Hum Mol Genet. 2011 Oct 15;20(20):4076-81. doi: 10.1093/hmg/ddr325. Epub 2011 Jul 26.

33.

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 FM, Lamy P, Wojdacz TK, Hansen LL, Wiuf C, Borre M, Dyrskjøt L, Orntoft TF.

Clin Cancer Res. 2011 Sep 1;17(17):5582-92. doi: 10.1158/1078-0432.CCR-10-2659. Epub 2011 Jul 25.

34.

A review of software for microarray genotyping.

Lamy P, Grove J, Wiuf C.

Hum Genomics. 2011 May;5(4):304-9. Review.

35.

An Algebro-topological description of protein domain structure.

Penner RC, Knudsen M, Wiuf C, Andersen JE.

PLoS One. 2011;6(5):e19670. doi: 10.1371/journal.pone.0019670. Epub 2011 May 24.

36.

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

Laurila K, Oster B, Andersen CL, Lamy P, Orntoft T, Yli-Harja O, Wiuf C.

BMC Bioinformatics. 2011 May 27;12:215. doi: 10.1186/1471-2105-12-215.

37.

An algebraic approach to signaling cascades with N layers.

Feliu E, Knudsen M, Andersen LN, Wiuf C.

Bull Math Biol. 2012 Jan;74(1):45-72. doi: 10.1007/s11538-011-9658-0. Epub 2011 Apr 27.

PMID:
21523510
38.

High-resolution melting analysis for mutation screening of RGSL1, RGS16, and RGS8 in breast cancer.

Wiechec E, Wiuf C, Overgaard J, Hansen LL.

Cancer Epidemiol Biomarkers Prev. 2011 Feb;20(2):397-407. doi: 10.1158/1055-9965.EPI-10-0514. Epub 2010 Dec 6.

39.

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

Lamy P, Wiuf C, Ørntoft TF, Andersen CL.

Bioinformatics. 2011 Feb 1;27(3):419-20. doi: 10.1093/bioinformatics/btq668. Epub 2010 Dec 5.

PMID:
21134892
40.

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

Li J, Wang K, Jensen TD, Li S, Bolund L, Wiuf C.

BMC Res Notes. 2010 Nov 25;3:321. doi: 10.1186/1756-0500-3-321.

41.

Incomplete and noisy network data as a percolation process.

Stumpf MP, Wiuf C.

J R Soc Interface. 2010 Oct 6;7(51):1411-9. doi: 10.1098/rsif.2010.0044. Epub 2010 Apr 8.

42.

The CATH database.

Knudsen M, Wiuf C.

Hum Genomics. 2010 Feb;4(3):207-12.

43.

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

Ratmann O, Wiuf C, Pinney JW.

HFSP J. 2009 Oct;3(5):290-306. doi: 10.2976/1.3167215. Epub 2009 Oct 19.

44.

Short tandem repeats and genetic variation.

Madsen BE, Villesen P, Wiuf C.

Methods Mol Biol. 2010;628:297-306. doi: 10.1007/978-1-60327-367-1_16.

PMID:
20238088
45.

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 LS, Wojdacz TK, Thestrup BB, Wiuf C, Hager H, Hansen LL.

BMC Cancer. 2009 Dec 21;9:453. doi: 10.1186/1471-2407-9-453.

46.

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

Pradal C, Olesen JM, Wiuf C.

BMC Ecol. 2009 Dec 4;9:24. doi: 10.1186/1472-6785-9-24.

47.

DNA copy number aberrations in breast cancer by array comparative genomic hybridization.

Li J, Wang K, Li S, Timmermans-Wielenga V, Rank F, Wiuf C, Zhang X, Yang H, Bolund L.

Genomics Proteomics Bioinformatics. 2009 Jun;7(1-2):13-24. doi: 10.1016/S1672-0229(08)60029-7.

48.

Genome-wide scans using archived neonatal dried blood spot samples.

Hollegaard MV, Grauholm J, Børglum A, Nyegaard M, Nørgaard-Pedersen B, Ørntoft T, Mortensen PB, Wiuf C, Mors O, Didriksen M, Thorsen P, Hougaard DM.

BMC Genomics. 2009 Jul 4;10:297. doi: 10.1186/1471-2164-10-297.

49.

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

Ratmann O, Andrieu C, Wiuf C, Richardson S.

Proc Natl Acad Sci U S A. 2009 Jun 30;106(26):10576-81. doi: 10.1073/pnas.0807882106. Epub 2009 Jun 12.

50.

Chromosomal imbalance in the progression of high-risk non-muscle invasive bladder cancer.

Zieger K, Wiuf C, Jensen KM, Ørntoft TF, Dyrskjøt L.

BMC Cancer. 2009 May 16;9:149. doi: 10.1186/1471-2407-9-149.

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