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Section for Bioinformatics and Computational Biology

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McCauley, S., de Groot, S., Mailund, T. & Hein, J. (2007). Annotation of selection strengths in viral genomes. Bioinformatics, 23(22), 2978-2986. https://doi.org/10.1093/bioinformatics/btm472

Madsen, B. E., Villesen, P. & Wiuf, C. (2007). A periodic pattern of SNPs in the human genome. Poster session presented at High Throughput Biology: Genomics, Fluxomics, Proteomics, and Interactomics, Vejle, Denmark.

Madsen, B. E., Villesen, P. & Wiuf, C. (2007). A periodic pattern of SNPs in the human genome. Poster session presented at Genomics of Common Diseases, Cambridge.

Madsen, B. E., Villesen, P. & Wiuf, C. (2007). A periodic pattern of SNPs in the human genome. Genome Research, 17(10), 1414-1419.

Li, J., Wang, K., Wiuf, C. & Bolund, L. (2007). Array CGH Reveals High Similar Genetic Profiles between the Primary Tumor and Axillary Lymph Node Metastasis in Breast Cancer, presented at PhD Annual Day, Graduate School of Health, University of Aarhus.. Poster session presented at Array CGH Reveals High Similar Genetic Profiles between the Primary Tumor and Axillary Lymph Node Metastasis in Breast Cancer, presented at PhD Annual Day, Graduate School of Health, University of Aarhus., Denmark.

Dalevi, D., DeSantis, T. Z., Fredslund, J., Andersen, G. L., Markowitz, V. M. & Hugenholtz, P. (2007). Automated assignment of groups in large phylogenetic trees using GRUNT: Grouping, Ungrouping, Naming Tool. BMC Bioinformatics, 8, 402-407.

Frandsen, J., Hobolth, A., Østergaard, L., Vestergaard-Poulsen, P. & Jensen, E. B. V. (2007). Bayesian regularization of diffusion tensor images. Biostatistics, 8(4), 784-799. https://doi.org/10.1093/biostatistics/kxm005

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. https://doi.org/10.1016/j.jbi.2006.05.001

de Groot, S., Mailund, T. & Hein, J. (2007). Comparative Annotation of Viral Genomes with Non-Conserved Gene Structure. Bioinformatics, 23(9), 1080-1089. https://doi.org/10.1093/bioinformatics/btm078

Stissing, M., Mailund, T., Pedersen, C. N. S., Brodal, G. S. & Fagerberg, R. (2007). Computing the All-Pairs Quartet Distance on a Set of Evolutionary Trees. In Proceedings of the 5th Asia-Pacific Bioinformatics Conference (APBC) (pp. 91-100)

Stissing, M., Pedersen, C. N. S., Mailund, T. & Brodal, G. S. (2007). Computing the Quartet Distance between Evolutionary Trees of Bounded Degree. In Proceedings of the 5th Asia-Pacific Bioinformatics Conference (APBC) (pp. 101-110)

Hansen, L. L., Madsen, B. E., Pedersen, K. & Wiuf, C. (2007). Conflicting results in SNP genotype assessment. BioTechniques, (43), 756-762.

Wang, K., Wiuf, C. & Bolund, L. (2007). Development of Bioinformatics Tools for Diagnostic Procedures Involving Array Analyses of Degenerative Disease Processes, presented at PhD Annual Day, Graduate School of Health, University of Aarhus.. Poster session presented at Development of Bioinformatics Tools for Diagnostic Procedures Involving Array Analyses of Degenerative Disease Processes, presented at PhD Annual Day, Graduate School of Health, University of Aarhus..

Hougaard, B. K., Madsen, L. H., Fredslund, J., Schauser, L., Nielsen, A. M., Sandal, N. N., Rohde, T., Jacobsen, R. H. & Stougaard, J. (2007). Development of Legume Anchor Markers: a bioinformatic driven tool for genetic mapping and comparative genomics. Poster session presented at Plant Biotech Denmark Annual meeting 2007, København, Denmark.

Hebsgaard, MB., Wiuf, C., Gilbert, MTP., Glenner, H. & Willerslev, E. (2007). Evaluating Neandertal genetics and phylogeny. J. Mol. Evol., 64, 50-60. https://doi.org/10.1007/s00239-006-0017-y

Bataillon, T. & Ronfort, J. (2007). Evolutionary and Ecological Genetics of Medicago truncatula. In The Medicago Handbook [On line] http://www.noble.org/MedicagoHandbook/pdf/EvolutionaryEcologicalGenetics.pdf

Stumpf, M. P., Kelly, W. P., Thorne, T. & Wiuf, C. (2007). Evolution at the system level: The natural history of protein interaction networks. TREE, 22(7), 366-372.

Mailund, T., Pedersen, C. N. S., Bardino, J., Vinter, B. & Karlsen, H. (2007). Experiences with GeneRecon on MiG. Future Generation Computer Systems - The International Journal of eScience, 23, 580-586. https://doi.org/10.1016/j.future.2006.09.003

Villesen, P. (2007). FaBox: an online toolbox for FASTA sequences. Molecular Ecology Resources. https://doi.org/10.1111/j.1471-8286.2007.01821.x

Malmos, K., Dong, M., Besenbacher, F., Daasbjerg, K. & Pedersen, S. U. (2007). Formation with the use of Electrostatic Repulsion of Covalent Attached Thin Layer on Glassy Carbon Surface. Paper presented at Electrochemical Science and Technology, Aarhus, Denmark.

Andersen, C. L., Wiuf, C., Kruhøffer, M., Korsgaard, M., Laurberg, S. & Ørntoft, T. F. (2007). Frequent occurrence of uniparental disomy in colorectal cancer. Carcinogenesis, 28(1), 38-48. https://doi.org/10.1093/carcin/bgl086

Fredsted, T., Schierup, M. H., Groenevald, L. F. & Kappeler, P. M. (2007). Genetic structure, lack of sex-biased dispersal and behavioral flexibility in the pair-living fat-tailed dwarf lemur, Cheirogaleus medius. Behavioral Ecology and Sociobiology. https://doi.org/10.1007/s00265-006-0323-9

Christensen, L. L., Wikman, F., Wiuf, C., Madsen, B. E., Andersen, C. L. & Ørntoft, T. F. (2007). Genetic Variants in MLH1 and MSH2 are not Associated with the Development of Sporadic Colorectal Cancer in Denmark. Poster session presented at The 2nd Biennial Scientific Meeting of the International Society for Gastrointestinal Hereditary Tumours, Yokohama, Japan.

Tørring, N., Borre, M., Sørensen, K., Andersen, C. L., Wiuf, C. & Ørntoft, T. F. (2007). Genome-Wide analysis of allelic imbalance in laser microdissected prostate cancer tissue using the Affymetrix 50K Mapping array identifies genomic patterns associated with metastasis and differentiation. British Journal of Cancer, 96(3), 499-506. https://doi.org/10.1038/sj.bjc.6603476

Hobolth, A., Christensen, O. F., Mailund, T. & Schierup, M. H. (2007). Genomic relationships and speciation times of human, chimpanzee and gorilla inferred from a coalescent hidden Markov model. PLoS Genetics, 3(2). https://doi.org/10.1371/journal.pgen.0030007

Hobolth, A., Christensen, O. F., Mailund, T. & Schierup, M. H. (2007). Genomic Relationships and Speciation Times of Human, Chimpanzee and Gorilla inferred from a Coalescent Hidden Markov Model. Poster session presented at Beyond the HapMap, Boston, United States.

Lamy, P., Andersen, C. L. & Wiuf, C. (2007). Genotyping and Annotation of Affymetrix SNP Probe Sets, presented at PhD Annual Day, Graduate School of Health, University of Aarhus.. Poster session presented at Genotyping and Annotation of Affymetrix SNP Probe Sets, presented at PhD Annual Day, Graduate School of Health, University of Aarhus..

Haudry, A., Cenci, A., Ravel, C., Bataillon, T., Brunel, D., Poncet, C., Hochu, I., Poirier, S., Santoni, S., Glemin, S. & David, J. (2007). Grinding up Wheat: a Massive Loss of Nucleotide Diversity Since Domestication. Molecular Biology and Evolution, 24(7), 1506-1517. https://doi.org/10.1093/molbev/msm077

Jørgensen, F. G., Schierup, M. H. & Clark, A. G. (2007). Heterogeneity in Regional GC Content and Differential Usage of Codons and Amino Acids in GC-Poor and GC-Rich Regions of the Genome of Apis mellifera. Molecular Biology and Evolution, 24(2), 611-619. https://doi.org/10.1093/molbev/msl190

Ehlers, B. & Bataillon, T. (2007). ‘Inconstant males' and the maintenance of labilesex expression in subdioecious plants. New Phytologist. https://doi.org/10.1111/j.1469-8137.2007.01975.x

Ravn, P., Forsberg, R. & Christiansen, F. (2007). Influenza: - menneskets uforudsigelige følgesvend. Aktuel Naturvidenskab, 2007(2), 16-20.

De Mita, S., Ronfort, J., McKhann, H. I., Poncet, C., El Malki, R. & Bataillon, T. (2007). Investigation of the demographic and selective forces shaping the nucleotide diversity of genes involved in nod factor signaling in Medicago truncatula. Genetics, 177(4), 2123-33. https://doi.org/10.1534/genetics.107.076943

Brameier, M. & Banzhaf, W. (2007). Linear Genetic Programming. Springer.

Salek, P., Høst, S., Thøgersen, L., Jørgensen, P., Manninen, P., Olsen, J., Jansik, B., Reine, S., Pawlowski, F., Tellgren, E., Helgaker, T. & Coriani, S. (2007). Linear-scaling implementation of molecular electronic self-consistent field theory. Journal of Chemical Physics, 126, 114110-1 - 114110-16.

Coriani, S., Høst, S., Jansik, B., Thøgersen, L., Olsen, J., Jørgensen, P., Reine, S., Pawlowski, F., Helgaker, T. & Salek, P. (2007). Linear-scaling implementation of molecular response theory in self-consistent field electronic-structure theory. Journal of Chemical Physics, 126(15), 154108-1 - 154108-11.

Davies, J., Simancik, F., Lyngsø, R., Mailund, T. & Hein, J. (2007). On Recombination-Induced Multiple and Simultaneous Coalescent Events. Genetics, 177, 2151-2160.

Dinér, P., Laursen, A. K. K., Lie, M. A. & Jørgensen, K. A. (2007). On the Origin of the Stereoselectivity in Organocatalysed Reactions with Trimethylsilyl-Protected Diarylprolinol. Chemistry - A European Journal, 14(1), 122-127.

Fredslund, J. & Lange, M. (2007). primique: automatic design of specific PCR primers for each sequence in a family. BMC Bioinformatics, 8(369). https://doi.org/10.1186/1471-2105-8-369

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. Nucleic Acids Research, 35(1), 1-10. https://doi.org/10.1093/nar/gkl483

Li, S., Ma, L., Li, H., Vang, S., Hu, Y., Bolund, L. & Wang, J. (2007). Snap: An Integrated SNP Annotation Platform. Nucleic Acids Research, 35, D707-D710. https://doi.org/10.1093/nar/gkl969

Sørensen, F. J., Andersen, C. L. & Wiuf, C. (2007). SNPTools: A software tool for visualization and analysis of microarray data. Bioinformatics, 23(12), 1550-52. https://doi.org/10.1093/bioinformatics/btm122

Wiuf, C. & Ratmann, O. (2007). Statistical analysis of biological network data. In P. Linde (Ed.), Symposium i Anvendt Statistik 2007 (pp. 147-156)

Christensen, O. F., Frydenberg, M., Jensen, J. L. & Pedersen, J. G. (2007). Tests and confidence intervals for an extended variance component using the modified likelihood ratio statistic. Scandinavian Journal of Statistics, 34(2), 347-364. https://doi.org/10.1111/j.1467-9469.2006.00520.x

Leppälä, J., Bechsgaard, J. S., Schierup, M. H. & Savolainen, O. (2007). Transmission ratio distortion in Arabidopsis lyrata: effects of population divergence and the S-locus. Heredity, 100(1), 71-8. https://doi.org/10.1038/sj.hdy.6801066

Ewens, W. E., Choudhury, A. R., Lewontin, R. C. & Wiuf, C. (2007). Two variance results in population genetics theory. Math Popul Stud, 14, 93-110. https://doi.org/10.1080/08898480701298376

Ratmann, O., Jørgensen, 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). https://doi.org/10.1371/journal.pcbi.0030230.eor

Fredslund, J., Madsen, L. H., Hougaard, B. K., Nielsen, A. M., Nielsen, A. M., Bertioli, D., Sandal, N. N., Schauser, L. & Stougaard, J. (2006). A general pipeline for the development of anchor markers for comparative genomics in plants. BMC Genomics, 7, 207.

Wiuf, C., Brameier, M., Hagberg, O. & Stumpf, MPH. (2006). A likelihood approach to analysis of network data. Proceedings of the National Academy of Sciences (PNAS), 103(20), 7566-7570.

Mailund (2006). Analysing Infinite-State Systems by Combining Equivalence Reduction and the Sweep-Line Method. In Proceedings of International Conference on Application and Theory of Petri Nets (ICATPN 2002) (pp. 314-333)

Villesen, P. & Fredsted, T. (2006). A new sex identification tool: one primer pair can reliably sex ape and monkey DNA samples. Conservation Genetics, 1-5.

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Palle Villesen