Section for Bioinformatics and Computational Biology

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 BiRC Research Publications

Publications

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de Groot, S., Mailund, T., Lunter, G. & Hein, J. (2008). Investigating Selection on Viruses: A Statistical Alignment Approach. BMC Bioinformatics, 9(308).
Christiansen, F. (2008). Leder. Matilde, (34), 2.
Hougaard, B. K., Madsen, L. H., Sandal, N., de Carvalho Moretzsohn, M., Fredslund, J., Schauser, L., Nielsen, A. M., Rohde, T., Sato, S., Tabata, S., Bertioli, D. J. & Stougaard, J. (2008). Legume anchor markers link syntenic regions between Phaseolus vulgaris, Lotus japonicus, Medicago truncatula and Arachis. Genetics, 179(4), 2299-312. https://doi.org/10.1534/genetics.108.090084
Besenbacher, S., Mailund, T. & Schierup, M. H. (2008). Local Phylogeny Mapping of Quantitative Traits: Higher Accuracy and Better Ranking Than Single Marker Association in Genomewide Scans. Genetics. https://doi.org/10.1534/genetics.108.092643
Musgaard, M., Thøgersen, L. & Schiøtt, H. B. (2008). Molecular Dynamics Simulations of the E2 Form of the Ca2+-ATPase: Preliminary Results. Poster session presented at 12th International ATPase Conference. Na,K-ATPase and Related Transport ATPases of P-type: Structures, Mechanisms, and Roles in Health and Disease, Aarhus, Denmark.
Dutheil, J. & Boussau, B. (2008). Non-homogeneous models of sequence evolution in the Bio++ suite of libraries and programs. BMC Evolutionary Biology, 8, 255. https://doi.org/10.1186/1471-2148-8-255
Li, J., Gromov, P., Gromova, I., Moreira, J. M., Timmermans-Wielenga, V., Rank, F., Wang, K., Li, S., Li, H., Wiuf, C., Yang, H., Zhang, X., Bolund, L. & Celis, J. E. (2008). Omics-based profiling of carcinoma of the breast and matched regional lymph node metastasis. Proteomics, 8(23-24), 5038-52. https://doi.org/10.1002/pmic.200800303
Andersen, L. N. & Asmussen, S. (2008). Parallel computing, failure recovery and extreme values. Journal of Statistical Theory and Practice, 2(2), 279-292.
Thøgersen, L., Schiøtt, B., Vosegaard, T., Nielsen, N. C. & Tajkhorshid, E. (2008). Peptide Aggregation and Pore Formation in a Lipid Bilayer: A Combined Coarse-Grained and All Atom Molecular Dynamics Study. Biophysical Journal, 95(9), 4337-4347. https://doi.org/10.1529/biophysj.108.133330
Simonsen, M., Mailund, T. & Pedersen, C. S. (2008). Rapid Neighbour-Joining. In Proceedings of the 8th International Workshop on Algorithms in Bioinformatics (WABI) (pp. 113-122)
Castric, V., Bechsgaard, J., Schierup, M. H. & Vekemans, X. (2008). Repeated adaptive introgression at a gene under multiallelic balancing selection. PLoS Genetics, 4(8), e1000168. https://doi.org/10.1371/journal.pgen.1000168
Vosegaard, T., Bertelsen, K., Pedersen, J. M., Thøgersen, L., Schiøtt, B., Tajkhorshid, E., Skrydstrup, T. & Nielsen, N. C. (2008). Resolution Enhancement in Solid-State NMR of Oriented Membrane Proteins by Anisotropic Differential Linebroadening. Journal of the American Chemical Society, 130, 5028-5029.
Preker, P., Nielsen, J., Kammler, S., Lykke-Andersen, S., Christensen, M. S., Mapendano, C. K., Schierup, M. H. & Jensen, T. H. (2008). RNA Exosome Depletion Reveals Transcription Upstream of Active Human Promoters. Science, 322(5909), 1851-1854. https://doi.org/10.1126/science.1164096
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. (2008). Schizophrenia and innate immune defense: association study of mannan-bindinglectin (MBL) and MBL-associated serine proteases-2 (MASP-2) deficiency. In WCPG 2008 Abstract Book (pp. 225)
Schierup, M. H., Bechsgaard, J. S. & Christiansen, F. B. (2008). Selection at work in self-incompatible Arabidopsis lyrata. II. Spatial distribution of S haplotypes in Iceland. Genetics, 180(2), 1051-9. https://doi.org/10.1534/genetics.108.088799
Jakobsen, H. J., Brorson, M., Bildsøe, H. K., Skibsted, J. & Hansen, M. R. (2008). Sensitivity Enhancement in Natural Abundance Solid-State 33S MAS NMR Spectroscopy Employing Adiabatic Inversion Pulses to the Satellite Transitions. Abstract from 49th Experimental NMR Conference, Asilomar, Pacific Grove, California, United States.
Jakobsen, H. J., Brorson, M., Bildsøe, H. K., Skibsted, J. & Hansen, M. R. (2008). Sensitivity Enhancement in Natural-Abundance Solid-State 33S MAS NMR Spectroscopy Employing Adiabatic Inversion Pulses to the Satellite Transitions. Poster session presented at 49th Experimental NMR Conference (ENC), Asilomar, California, United States.
Madsen, B. E., Villesen, P. & Wiuf, C. (2008). Short tandem repeats in human exons: a target for disease mutations. BMC Genomics, 9, 410. https://doi.org/10.1186/1471-2164-9-410
Villesen, P., Madsen, B. E. & Wiuf, C. H. (2008). Short Tandem Repeats in Human Exons: A Target for Disease Mutations. Poster session presented at Frontiers in genomics, Denmark.
Nielsen, J. & Mailund, T. (2008). SNPFile - A software library and file format for large scale association mapping and population genetics studies. BMC Bioinformatics, 9(526), 1-11. https://doi.org/10.1186/1471-2105-9-526
Penner, R., Andersen, J. E., Wiuf, C. H. & Knudsen, M. (2008). System and method for modelling a molecule with a graph. (Patent No. PA 2008 01009).
Christensen, L. L., Madsen, B. E., Wikman, F. P., Wiuf, C., Koed, K., Tjønneland, A., Olsen, A. V., Syvänen, A.-C., Andersen, C. L. & Orntoft, T. F. (2008). The association between genetic variants in hMLH1 and hMSH2 and the development of sporadic colorectal cancer in the Danish population. BMC Medical Genetics, 9, 52. https://doi.org/10.1186/1471-2350-9-52
Høst, S., Olsen, J., Jansik, B., Thøgersen, L., Jørgensen, P. & Helgaker, T. (2008). The augmented Roothaan-Hall method for optimizing Hartree-Fock and Kohn-Sham density matrices. Journal of Chemical Physics, 129, 124106.
Christiansen, F. (2008). Theories of Population Variation in Genes and Genomes. Princeton University Press.
Leppälä, J., Bechsgaard, J. S., Schierup, M. H. & Savolainen, O. (2008). Transmission ratio distortion in Arabidopsis lyrata: effects of population divergence and the S-locus. Heredity, 100, 71-78.
Villesen, P., Madsen, B. E. & Wiuf, C. H. (2008). Ultra short tandem repeats: A target for disease mutations. Poster session presented at 9th International Conference on Systems Biology, Gothenburg, Sweden.
Mansilla, F., Lamy, P., Ørntoft, T. F. & Birkenkamp-Demtröder, K. (2008). Upregulation of genes involved in rRNA processing in colon cancer. Poster session presented at EACR Annual Meeting of the European Association of Cancer Research, Lyon, France.
Nilsson, J., Sengupta, J., Gursky, R., Kjeldgaard, M., Nissen, P. & Frank, J. (2008). Visualization of the eEF2-80S ribosome transition-state complex by cryo-electron microscopy. Journal of Molecular Biology, 382(1), 179-187.
Ehlers, B. & Schierup, M. H. (2008). When gametophytic self-incompatibility meets gynodioecy. Genetics Research, 90(1), 27-35. https://doi.org/10.1017/S0016672307009007
Brameier, M. & Wiuf, C. (2007). Ab initio identification of human micoRNAs based on structure motifs.. Poster session presented at Bioinformatics Conference 2007, Umeå, Sweden.
Brameier, M. & Wiuf, C. (2007). Ab initio identification of human micoRNAs based on structure motifs.. Poster session presented at ISMB/ECCB 2007, Wien, Austria.
Brameier, M. & Wiuf, C. (2007). Ab initio identification of human miRNAs for genome scanning based on structure motifs. BMC. Bioinformatics, 8(478).
De Mita, S., Santoni, S., Ronfort, J. & Bataillon, T. (2007). Adaptive evolution of the symbiotic gene NORK is not correlated with shifts of rhizobial specificity in the genus Medicago. BMC Evolutionary Biology, 7. https://doi.org/10.1186/1471-2148-7-210
Lamy, P., Andersen, C. L., Andersen, L. D., Tørring, N. & Wiuf, C. (2007). A Hidden Markov Model to estimate population mixture and allelic copy-numbers in cancers using Affymetrix SNP arrays. BMC Bioinformatics, 8(434).
Kjeldbjerg, A. L., Villesen, P., Aagaard, L. & Pedersen, F. S. (2007). An active 70 million year old viral infection in humans. Poster session presented at High Throughput Biology: Genomics, Fluxomics, Proteomics, and Interactomics, Denmark.
Wang, K., Li, J., Wiuf, C. & Bolund, L. (2007). Analysis of Array CGH Data, presented at PhD Annual Day, Graduate School of Health, University of Aarhus.. Poster session presented at Analysis of Array CGH Data, presented at PhD Annual Day, Graduate School of Health, University of Aarhus., Denmark.
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.

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Palle Villesen