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Section for Bioinformatics and Computational Biology

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Knudsen, M., Feliu, E., Wiuf, C. H. & Andersen, L. N. (2010). Steady States of Phosphorelays and Two-Component Systems. Poster session presented at The 11th International Conference on Systems Biology, Edinburgh, United Kingdom.

Hobolth, A. & Jensen, J. L. (2010). Summary statistics for end-point conditioned continuous-time Markov chains. Thiele Centre, Institut for Matematiske Fag, Aarhus Universitet.

Knudsen, M. & Wiuf, C. H. (2010). The CATH Database. Human Genomics (Online).

Schierup, M. H. & Wiuf, C. H. (2010). The coalescent in bacterial populations. In D. A. Robinson, D. Falush & E. J. Feil (Eds.), Bacterial population genetics in infectious disease (pp. 3-19). Wiley-Blackwell.

Kristensen, T. G. (2010). Transforming Tanimoto queries on real valued vectors to range queries in Euclidian space. Journal of Mathematical Chemistry, 48(2), 287-289. https://doi.org/10.1007/s10910-010-9668-4

Li, J., Wang, K., Jensen, T. D., Li, S., Bolund, L. & Wiuf, C. (2010). Tumor heterogeneity in neoplasms of breast, colon, and skin. BMC Research Notes, 3, 321. https://doi.org/10.1186/1756-0500-3-321

Foldager, L. (2010). Using logic regression to identify SNP interactions based on individually time-matched case-control data. Abstract from PhD Day 2010, Århus, Denmark.

Simonsen, M., Sand, A., Mailund, T. & Pedersen, C. N. S. (2010). Using the Power of Modern Processors in Bioformatics. Poster session presented at Conference on IT research at AU, Århus, Denmark.

Stukenbrock, E., Jørgensen, F., Zala, M., Hansen, T. T., McDonald, B. A. & Schierup, M. H. (2010). Whole-genome and chromosome evolution associated with host adaptation and speciation of the wheat pathogen Mycosphaerella graminicola. PLoS Genetics, 23(6).

Glémin, S. & Bataillon, T. (2009). A comparative view of the evolution of grasses under domestication. New Phytologist, 183(2), 273-90. https://doi.org/10.1111/j.1469-8137.2009.02884.x

Besenbacher, S., Pedersen, C. S. & Mailund, T. (2009). A fast algorithm for genome wide haplotype pattern mining. BMC Bioinformatics, (suppl. 1), 772. https://doi.org/10.1186/1471-2105-10-S1-S74

Bertioli, D., Moretzsohn, M., Madsen, L., Sandal, N., Leal-Bertioli, S., Guimaraes, P., Hougaard, B., Fredslund, J., Schauser, L., Nielsen, A., Sato, S., Tabata, S., Cannon, S. & Stougaard, J. (2009). An analysis of synteny of Arachis with Lotus and Medicago sheds new light on the structure, stability and evolution of legume genomes. BMC Genomics, 10(1), 45. https://doi.org/10.1186/1471-2164-10-45

Dutheil, J., Ganapathy, G., Hobolth, A., Mailund, T., Uyenoyama, M. & Schierup, M. H. (2009). Ancestral population genomics: the coalescent hidden Markov model approach. Genetics, 183(1), 259–274. https://doi.org/10.1534/genetics.109.103010

Li, J., Gao, F., Li, N., Li, S., Yin, G., Tian, G., Jia, S., Wang, K., Zhang, X., Yang, H., Nielsen, A. L. & Bolund, L. (2009). An improved method for genome wide DNA methylation profiling correlated to transcription and genomic instability in two breast cancer cell lines. BMC Genomics, 10, 223. https://doi.org/10.1186/1471-2164-10-223

Mailund, T., Nielsen, J. & Pedersen, C. S. (2009). A Quadratic Time Algorithm for Computing the Quartet Distance between Two General Trees. In Proceedings of IJCBS 2009 (pp. 565-568). IEEE Computer Society Press. https://doi.org/10.1109/IJCBS.2009.42

Foldager, L., Steffensen, R. N., Thiel, S., Als, T. D., Kristensen, A. S., Straarup, S., Nielsen, H. J., Nordentoft, M., Mortensen, P. B., Rosenberg, R., Mors, O. & Jensenius, J. C. (2009). Are defects in the innate immune defense contributing factors for mental disorders? In PhD Day 2009 Abstract Book (pp. 107)

Kristensen, T. G., Nielsen, J. & Pedersen, C. N. S. (2009). A tree based method for the rapid screening of chemical fingerprints. Lecture Notes in Computer Science, 5724, 194-205. https://doi.org/10.1007/978-3-642-04241-6_17

Liboriussen, P., Pedersen, B. P., Ifrim, G., Nissen, P. & Pedersen, C. S. (2009). Automatic classification of P-Type ATPases using SLR. Poster session presented at 17th Annual International Conference on Intelligent Systems for Molecular Biology (ISMB) & 8th European Conference on Computational Biology (ECCB), Stockholm, Sweden.

Simonsen, M., Mailund, T. & Pedersen, C. S. (2009). Building very large neighbour-joining trees. Poster session presented at 17th Annual International Conference on Intelligent Systems for Molecular Biology (ISMB) & 8th European Conference on Computational Biology (ECCB), Stockholm, Sweden.

Zieger, K., Wiuf, C., Jensen, K. M.-E., Ørntoft, T. F. & Andersen, L. D. (2009). Chromosomal imbalance in the progression of high-risk non-muscle invasive bladder cancer. B M C Cancer, 9, 149. https://doi.org/10.1186/1471-2407-9-149

Zieger, K., Wiuf, C. H., Jensen, K. M.-E., Ørntoft, T. F. & Andersen, L. D. (2009). Chromosomal imbalance in the progression of high-risk non-muscle invasive bladder cancer. B M C Cancer, 9, 149.

Høgslund, N., Radutoiu, S., Krusell, L., Voroshilova, V., Hannah, M. A., Goffard, N., Sanchez, D. H., Lippold, F., Ott, T., Sato, S., Tabata, S., Liboriussen, P., Lohmann, G. V., Schauser, L., Weiller, G. F., Udvardi, M. K. & Stougaard, J. (2009). Dissection of symbiosis and organ development by integrated transcriptome analysis of lotus japonicus mutant and wild-type plants. PLoS One, 4(8), e6556. https://doi.org/10.1371/journal.pone.0006556

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 & Bioinformatics, 7(1-2), 13-24. https://doi.org/10.1016/S1672-0229(08)60029-7

Wang, K., Li, J., Li, S., Bolund, L. & Wiuf, C. (2009). Estimation of tumor heterogeneity using CGH array data. BMC Bioinformatics, 10(1), 12. https://doi.org/10.1186/1471-2105-10-12

Christiansen, F. & Fenchel, T. (2009). Evolution - Den forudsigelige vilkårlighed. Aarhus Universitetsforlag.

Boggs, N. A., Dwyer, K. G., Shah, P., McCulloch, A. A., Bechsgaard, J., Schierup, M. H., Nasrallah, M. E. & Nasrallah, J. B. (2009). Expression of distinct self-incompatibility specificities in Arabidopsis thaliana. Genetics, 182(4), 1313-21. https://doi.org/10.1534/genetics.109.102442

Ratmann, O., Wiuf, C. H. & Pinney, J. W. (2009). From evidence to inference: probing the evolution of protein interaction networks. HFSP Journal, 3(5), 290-306. https://doi.org/10.2976/1.3167215

Hollegaard, M., Grauholm, J., Børglum, A., Nyegaard, M., Nørgaard-Pedersen, B., Ørntoft, T., Mortensen, P. B., Wiuf, C., Mors, O., Didriksen, M., Thorsen, P. & Hougaard, D. M. (2009). Genome-wide scans using archived neonatal dried blood spot samples. BMC Genomics, 10, 297. https://doi.org/10.1186/1471-2164-10-297

Schierup, M. H., Mailund, T., Li, H., Wang, J., Tjønneland, A., Vogel, U., Bolund, L. & Nexø, B. A. (2009). Haplotype frequencies in a sub-region of chromosome 19q13.3, related to risk and prognosis of cancer, differ dramatically between ethnic groups. BMC Medical Genetics, 10, 20. https://doi.org/10.1186/1471-2350-10-20

Martins, H. & Villesen, P. (2009). Highly improved dating of primate ERV integrations. Poster session presented at Frontiers of Retrovirology: Complex retroviruses, retroelements and their hosts, Montpellier, France. https://doi.org/10.1186/1742-4690-6-S2-P54

Staunstrup, N. H., Moldt, B., Mátés, L., Villesen, P., Jakobsen, M., Ivics, Z., Izsvák, Z. & Mikkelsen, J. G. (2009). Hybrid Lentivirus-transposon Vectors With a Random Integration Profile in Human Cells. Molecular Therapy, 17(7), 1205-14. https://doi.org/10.1038/mt.2009.10

Dittmer, J., Thøgersen, L., Underhaug, J., Bertelsen, K., Vosegaard, T., Pedersen, J. M., Schiøtt, H. B., Tajkhorshid, E., Skrydstrup, T. & Nielsen, N. C. (2009). Incorporation of Antimicrobial Peptides into Membranes: A Combined Liquid-State NMR and Molecular Dynamics Study of Alamethicin in DMPC/DHPC Bicelles. Journal of Physical Chemistry Part B: Condensed Matter, Materials, Surfaces, Interfaces & Biophysical, 113(19), 6928-6937. https://doi.org/10.1021/jp811494p

Jørgensen, F. G. & Schierup, M. H. (2009). Increased rate of human mutations where DNA and RNA polymerases collide. Trends in Genetics, 25(12), 523-527. https://doi.org/10.1016/j.tig.2009.10.002

Nielsen, J., Foldager, L. & Meyer, J. M. (2009). Increased use of antibiotics in patients treated with clozapine. European Neuropsychopharmacology, 19(7), 483-486.

Nielsen, J., Pedersen, C. S. & Hein, J. (2009). Investigation of a simple heuristic improving the speed of statistical alignments. Poster session presented at 17th Annual International Conference on Intelligent Systems for Molecular Biology (ISMB) & 8th European Conference on Computational Biology (ECCB), Stockholm, Sweden.

Kristensen, T. G., Pedersen, C. S., Thomsen, R. & Christensen, M. H. (2009). Largest Common Chemical Feature Subtree as a Virtual Screening Method. Poster session presented at 17th Annual International Conference on Intelligent Systems for Molecular Bioligy (ISMB) & 8th European Conference on Computational Biology (ECCB), Stockholm, Sweden. http://www.iscb.org/ismbeccb2009/poster_list.php?cat=C

Besenbacher, S., Mailund, T. & Schierup, M. H. (2009). Local phylogeny mapping of quantitative traits: Higher accuracy and better ranking than single marker association in genomewide scans. Genetics, 181, 747-753.

Wiuf, C. H., Lamy, P. & Andersen, C. L. (2009). Methods for derivation of LOH and allelic copy numbers using SNP arrays. In C. H. Wiuf & C. L. Andersen (Eds.), Statistics and Informatics in Molecular Cancer Research (pp. 62-77). Oxford University Press.

Ratmann, O., Andrieu, C., Wiuf, C. H. & Richardson, S. (2009). Model criticism based on likelihood-free inference: with an application to protein network evolution. Proceedings of the National Academy of Sciences (PNAS), 106, 10576-10581. https://doi.org/10.1073/pnas.0807882106

Knudsen, M. & Nielsen, R. (2009). Modeling cis- and trans-regulation in Drosophila species. In Tampere International Center for Signal Processing, TICSP Series 48 Tampere International Center for Signal Processing.

Kraft, J. F., Lie, M. A. & Schiøtt, H. B. (2009). Molecular Docking Simulations: Improvement of methodologies for membrane proteins. Poster session presented at iNANO autumn school 2007.

Justesen, P. & Ursem, R. K. (2009). Multiobjective Distinct Candidates Optimization (MODCO): A Cluster-Forming Differential Evolution Algorithm. In M. Ehrgott, C. Fonseca, X. Gandibleux, J.-K. Hao & M. Sevaux (Eds.), Evolutionary Multi-Criterion Optimization: 5th International Conference, EMO 2009. Nantes, France, April 2009. Proceedings (Vol. 5, pp. 525-539). Springer. https://doi.org/10.1007/978-3-642-01020-0_41

Kristensen, T. G. & Pedersen, C. S. (2009). Optimal Overlay of Ligands with Flexible Bonds Using Differential Evolution. In J. Zhang, G.-Z. Li & J. Y. Yang (Eds.), Proceedings of the 2009 International Joint conferences on Bioinformatics, System biology and Intelligent Computing (IJCBS2009) (pp. 331-334). IEEE Computer Society Press. https://doi.org/10.1109/IJCBS.2009.36

Pedersen, C. S. & Kristensen, T. G. (2009). Optimal Overlay of Ligands with Flexible Bonds Using Differential Evolution. Poster session presented at 17th Annual International Conference on Intelligent Systems for Molecular Bioligy (ISMB) & 8th European Conference on Computational Biology (ECCB), Stockholm, Sweden. http://www.iscb.org/ismbeccb2009/poster_list.php?cat=C

Thøgersen, L. (2009). Protein Domain Model: A preliminary exploration. Poster session presented at Faraday Discussion: Multiscale Modelling of Soft Matter, Groningen, Netherlands.

Kristensen, L. S., Wojdacz, T. K., Thestrup, B. B., Wiuf, C. H., Hager, H. & Hansen, L. L. (2009). 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. B M C Cancer, 9(453), 453.

Guo, Y.-L., Bechsgaard, J. S., Slotte, T., Neuffer, B., Lascoux, M., Weigel, D. & Schierup, M. H. (2009). Recent speciation of Capsella rubella from Capsella grandiflora, associated with loss of self-incompatibility and an extreme bottleneck. Proceedings of the National Academy of Sciences (PNAS), 106(13), 5246-51. https://doi.org/10.1073/pnas.0808012106

Kristensen, T. G. (2009). Recombining Angles in Differential Evolution. In IEEE Congress on Evolutionary Computation, CEC 2009 (pp. 3353 - 3356). IEEE Press. https://doi.org/10.1109/CEC.2009.4983370

Bertelsen, K., Jensen, B. P., Thøgersen, L., Tajkhorshid, E., Schiøtt, H. B., Skrydstrup, T., Nielsen, N. C. & Vosegaard, T. (2009). Residue-Specific Information about the Dynamics of Antimicrobial Peptides from ¹H−¹⁵N and ²H Solid-State NMR Spectroscopy. Journal of the American Chemical Society, 131(51), 18335–18342. https://doi.org/10.1021/ja908604u

Preker, P., Nielsen, J., Schierup, M. H. & Jensen, T. H. (2009). RNA polymerase plays both sides: Vivid and bidirectional transcription around and upstream of active promoters. Cell Cycle, 8(8), 1106-1107.

Displaying results 951 to 1000 out of 1390

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Palle Villesen