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Section for Bioinformatics and Computational Biology

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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.

Hobolth, A. & Stone, E. (2009). Simulation from endpoint-conditioned, continuous-time Markov chains on a finite state space, with applications to molecular evolution. Annals of Applied Statistics, 3(3), 1204-1231. https://doi.org/10.1214/09-AOAS247

Wiuf, C. H. & Andersen, C. L. (Eds.) (2009). Statistics and Informatics in Molecular Cancer Research. (1 ed.) Oxford University Press.

Wiuf, C. H. & Andersen, C. L. (Eds.) (2009). Statistics and Informatics in Molecular Cancer Research. Oxford University Press.

Andersen, L. N. & Mandjes, M. (2009). Structural properties of reflected Lévy processes. Queueing Systems, 63(1-4), 301-322. https://doi.org/10.1007/s11134-009-9116-y

Pradal, C., Olesen, J. M. & Wiuf, C. H. (2009). Temporal development and collapse of an Arctic plant-pollinator network. BMC Ecology, 9. https://doi.org/10.1186/1472-6785-9-24

Liljas, A., Liljas, L., Piskur, J., Lindblom, G., Nissen, P. & Kjeldgaard, M. (2009). Textbook on Structural Biology. (1 ed.) World Scientific.

Hobolth, A. & Wiuf, C. H. (2009). The genealogy, site frequency spectrum and ages of two nested mutant alleles. Theoretical Population Biology, 75(4), 260-265. https://doi.org/10.1016/j.tpb.2009.02.001

Schoustra, S. E., Bataillon, T., Gifford, D. R. & Kassen, R. (2009). The properties of adaptive walks in evolving populations of fungus. PLOS Biology, 7(11), e1000250. https://doi.org/10.1371/journal.pbio.1000250

Emily, M., Mailund, T., Hein, J., Schauser, L. & Schierup, M. H. (2009). Using biological networks to search for interacting loci in genomewide association studies. European Journal of Human Genetics. https://doi.org/10.1038/ejhg.2009.15

Djernes, J. K., Gulmann, N. C., Ibsen, M., Foldager, L., Olesen, F. & Munk-Jørgensen, P. (2008). A follow-up of elderly depressed patients. Nordic Journal of Psychiatry, 62(3), 233-41. https://doi.org/10.1080/08039480802088296

Kristensen, T. G. & Pedersen, C. S. (2008). All-to-all RF Distance Methods. Poster session presented at Bioinformatics 2008, Warszawa, Poland.

Knudsen, M. & Wiuf, C. (2008). A Markov chain approach to Randomly Grown Graphs. Journal of Applied Mathematics. https://doi.org/10.1155/2008/190836

Hobolth, A. (2008). A Markov chain Monte Carlo Expectation Maximization Algorithm for Statistical Analysis of DNA Sequence Evolution with Neighbor-Dependent Substitution Rates. Journal of Computational and Graphical Statistics, 17(1), 138-162.

Knudsen, M., Penner, R., Andersen, J. E. & Wiuf, C. H. (2008). An Algebraic Topology Approach to the Classification of Protein Domain Structures. Poster session presented at 6th Annual Rocky Mountain Bioinformatics Conference, Snowmass Village, Colorado, United States.

Wiuf, C., Ratmann, O. & Knudsen, M. (2008). Analysis of biological network data using likelihood-free inference techniques. In M. Ahdesmäki, K. Strimmer, N. Radde, J. Rahnenführer, K. Klemm, H. Lähdesmäki & O. Yli-Harja (Eds.), Ikke angivet (pp. 185-188)

Herbsleb, M., Christensen, O. F., Thykjaer, T., Wiuf, C., Borre, M., Ørntoft, T. F. & Dyrskjøt, L. (2008). Bioinformatic identification of FGF, p38-MAPK, and calcium signalling pathways associated with carcinoma in situ in the urinary bladder. B M C Cancer, 8, 37. https://doi.org/10.1186/1471-2407-8-37

Besenbacher, S. (2008). Challenges in whole-genome association mapping.

d'Amore, F., Chan, E., Iqbal, J., Geng, H., Young, K., Xiao, L., Hess, M. M., Sanger, W. G., Smith, L., Wiuf, C., Hagberg, O., Fu, K., Chan, W. C. & Dave, B. J. (2008). Clonal evolution in t(14;18)-positive follicular lymphoma, evidence for multiple common pathways, and frequent parallel clonal evolution. Clinical Cancer Research, 14(22), 7180-7. https://doi.org/10.1158/1078-0432.CCR-08-0752

Stissing, M., Mailund, T., Pedersen, C. S., Brodal, G. S. & Fagerberg, R. (2008). Computing the all-pairs quartet distance on a set of evolutionary trees. Journal of Bioinformatics and Computational Biology, 6(1), 37-50.

Johnson, S. S., Hebsgaard, M. B., Christensen, T. R., Mastepanov, M., Nielsen, R., Munch, K., Brand, T., Gilbert, M. T. P., Zuber, M. T., Bunce, M., Rønn, R., Gilichinsky, D., Froese, D. & Willerslev, E. (2008). Correction for Johnson et al., Ancient bacteria show evidence of DNA repair. Proceedings of the National Academy of Sciences (PNAS), 105(30). https://doi.org/10.1073/pnas.0804198105

Fredslund, J. (2008). DATFAP: A Database of Primers and Homology Alignments for Transcription Factors from 13 Plant Species. BMC Genomics.

Dutheil, J. (2008). Detecting site-specific biochemical constraints through substitution mapping. Journal of Molecular Evolution, 67(3), 257-65. https://doi.org/10.1007/s00239-008-9139-8

Schiøtt, B. & Lie, M. A. (2008). DFT Study of Solvation Effects on the Tautomeric Equlibrium and Catalytic Ylide Generation of Thiamin Models. Journal of Computational Chemistry, 29, 1037-1047.

Schepeler, T., Reinert, T., Ostenfeld, M. S., Christensen, L. L., Silahtaroglu, A. N., Dyrskjøt, L., Wiuf, C., Sørensen, F. J., Kruhøffer, M., Laurberg, S., Kauppinen, S., Ørntoft, T. F. & Andersen, C. L. (2008). Diagnostic and prognostic microRNAs in stage II colon cancer. Cancer Research, 68(15), 6416-24. https://doi.org/10.1158/0008-5472.CAN-07-6110

Ding, Z., Mailund, T. & Song, Y. (2008). Efficient Whole-Genome Association Mapping using Local Phylogenies for Unphased Genome Data. Bioinformatics, 2215-2221.

Stumpf, M. PH., Thorne, T., Silva, E., Stewart, R., An, HJ., Lappe, M. & Wiuf, C. H. (2008). Estimating the size of the human interactome. Proceedings of the National Academy of Sciences (PNAS), 105, 6059.

Christiansen, F. B. (2008). Evolutionær tilpasning. Matilde, (38), 16-19.

Penn, O., Stern, A., Rubinstein, N. D., Dutheil, J., Bacharach, E., Galtier, N. & Pupko, T. (2008). Evolutionary modeling of rate shifts reveals specificity determinants in HIV-1 subtypes. PLoS Computational Biology, 4(11), e1000214. https://doi.org/10.1371/journal.pcbi.1000214

Kjeldbjerg, A., Villesen, P., Aagaard, L. & Pedersen, F. S. (2008). Gene conversion and purifying selection of a placenta-specific ERV-V envelope gene during simian evolution. BMC Evolutionary Biology, 8(1), 266. https://doi.org/10.1186/1471-2148-8-266

Schierup, M. H. & Vekemans, X. (2008). Genomic consequences of selection on self-incompatibility genes. Current Opinion in Plant Biology, 116-122. https://doi.org/10.1016/j.pbi.2008.01.003

Madsen, B. E., Ramos, E. M., Boulard, M., Duda, K., Overgaard, J., Nordsmark, M., Wiuf, C. & Hansen, L. L. (2008). Germline mutation in RNASEL predicts increased risk of head and neck, uterine cervix and breast cancer. PLoS One, 3(6), e2492. https://doi.org/10.1371/journal.pone.0002492

Hobolth, A., Uyenoyama, M. K. & Wiuf, C. (2008). Importance sampling for the infinite sites model. Statistical Applications in Genetics and Molecular Biology, 7(1). https://doi.org/10.2202/1544-6115.1400

Herbsleb, M., Birkenkamp-Demtröder, K., Andersen, T. T., Wiuf, C., Hein, A.-M. K., Ørntoft, T. F. & Andersen, L. D. (2008). Increased cell motility and invasion upon knockdown of lipolysis stimulated lipoprotein receptor (LSR) in SW780 bladder cancer cells. BMC Medical Genomics, 1. https://doi.org/10.1186/1755-8794-1-31

Herbsleb, M., Birkenkamp-Demtroder, K., Thykjaer, T., Wiuf, C., Hein, A.-M. K., Orntoft, T. F. & Andersen, L. D. (2008). Increased cell motility and invasion upon knockdown of lipolysis stimulated lipoprotein receptor (LSR) in SW780 bladder cancer cells. BMC Medical Genomics, 1, 31. https://doi.org/10.1186/1755-8794-1-31

de Groot, S., Mailund, T., Lunter, G. & Hein, J. (2008). Investigating Selection on Viruses: A Statistical Alignment Approach. BMC Bioinformatics, 9(308).

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Palle Villesen