Arunapuram, P., Edvardsson, I., Golden, M., Anderson, J. W. J., Novák, A., Sükösd, Z. & Hein, J. (2013). StatAlign 2.0: Combining statistical alignment with RNA secondary structure prediction. Bioinformatics, 29(5), 654-655. https://doi.org/10.1093/bioinformatics/btt025

Sand, A. & Steel, M. (2013). The standard lateral gene transfer model is statistically consistent for pectinate four-taxon trees. Journal of Theoretical Biology, 335, 295-298. https://doi.org/10.1016/j.jtbi.2013.07.002

Roug, A. S., Nederby, L., Kjeldsen, E., Villesen, P. & Nyvold, C. G. (2013). Two Hematological Pre-Malignancies In a Pair Of Homozygous Twins Revealing Differences In Their Pre-and Postnatal Development. Blood, 122(21), 5262-5262.

Castagnini, A. & Foldager, L. (2013). Variations in incidence rates and age of onset of acute and transient psychotic disorders. Social Psychiatry and Psychiatric Epidemiology, 48(12), 1917-1922. https://doi.org/10.1007/s00127-013-0726-7

Sand, A., Kristiansen, M., Pedersen, C. N. S. & Mailund, T. (2013). zipHMMlib: a highly optimised HMM library exploiting repetitions in the input to speed up the forward algorithm. BMC Bioinformatics , 14(339), 339-348. https://doi.org/10.1186/1471-2105-14-339

Ehlers, B. K., Grøndahl, E., Ronfort, J. & Bataillon, T. (2012). "Ménage à trois": the presence/absence of thyme shapes the mutualistic interaction between the host plant Medicago truncatula (Fabaceae) and its symbiotic bacterium Sinorhizobium meliloti. Ecology and Evolution, 2(7), 1676-81. https://doi.org/10.1002/ece3.270

Gupta, V., Markmann, K., Pedersen, C. N. S., Stougaard, J. & Andersen, S. U. (2012). shortran: A pipeline for small RNA-seq data analysis. Bioinformatics, 28(20), 2698-2700. https://doi.org/10.1093/bioinformatics/bts496

Mailund, T., Halager, A. E., Westergaard, M., Dutheil, J. Y., Munch, K., Andersen, L. N., Lunter, G., Prüfer, K., Scally, A., Hobolth, A. & Schierup, M. H. (2012). A New Isolation with Migration Model along Complete Genomes Infers Very Different Divergence Processes among Closely Related Great Ape Species. P L o S Genetics, 8(12), e1003125. https://doi.org/10.1371/journal.pgen.1003125

Tidow, H., Poulsen, L. R., Andreeva, A., Knudsen, M., Hein, K. L., Wiuf, C., Palmgren, M. G. & Nissen, P. (2012). A bimodular mechanism of calcium control in eukaryotes. Nature, 491, 468-472. https://doi.org/10.1038/nature11539

Stukenbrock, E. H. & Bataillon, T. (2012). A population genomics perspective on the emergence and adaptation of new plant pathogens in agro-ecosystems. P L o S Pathogens, 8(9), e1002893. https://doi.org/10.1371/journal.ppat.1002893

Abdallah, M., Larsen, N., Grove, J., Nørgaard-Pedersen, B., Thorsen, P., Mortensen, E. L. & Hougaard, D. M. (2012). Amniotic Fluid Chemokines and Autism Spectrum Disorders: An Exploratory Study Utilizing a Danish Historic Birth Cohort. Brain, Behavior, and Immunity, 26(1), 170-176. https://doi.org/10.1016/j.bbi.2011.09.003

Abdallah, M., Pearce, B. D., Larsen, N., Greaves-Lord, K., Nørgaard-Pedersen, B., Hougaard, D. M., Mortensen, E. L. & Grove, J. (2012). Amniotic Fluid MMP-9 and Neurotrophins in Autism Spectrum Disorders: An Exploratory Study. Autism Research, 5(6), 428-33. https://doi.org/10.1002/aur.1254

Jin, X., He, M., Ferguson, B., Meng, Y., Ouyang, L., Ren, J., Mailund, T., Sun, F., Sun, L., Shen, J., Zhuo, M., Song, L., Wang, J., Ling, F., Zhu, Y., Hvilsom, C., Siegismund, H., Liu, X., Gong, Z. ... Wang, X. (2012). An effort to use human-based exome capture methods to analyze chimpanzee and macaque exomes. P L o S One, 7(7), e40637. https://doi.org/10.1371/journal.pone.0040637

Groenen, M. A. M., Archibald, A. L., Uenishi, H., Tuggle, C. K., Takeuchi, Y., Rothschild, M. F., Rogel-Gaillard, C., Park, C., Milan, D., Megens, H-J., Li, S., Larkin, D. M., Kim, H., Frantz, L. A. F., Caccamo, M., Ahn, H., Aken, B. L., Anselmo, A., Anthon, C. ... Schook, L. B. (2012). Analyses of pig genomes provide insight into porcine demography and evolution. Nature, 491(7424), 393-398. https://doi.org/10.1038/nature11622

Li, J., Wang, K., Gao, F., Jensen, T. D., Li, S. T., Deangelis, P. M., Kølvraa, S., Proby, C., Forslund, O., Bolund, L. & Clausen, O. P. F. (2012). Array comparative genomic hybridization of keratoacanthomas and squamous cell carcinomas: different patterns of genetic aberrations suggest two distinct entities. Journal of Investigative Dermatology, 132(8), 2060-6. https://doi.org/10.1038/jid.2012.104

Rietschel, M., Mattheisen, M., Degenhardt, F., Kahn, R. S., Linszen, D. H., Os, J. V., Wiersma, D., Bruggeman, R., Cahn, W., de Haan, L., Krabbendam, L., Myin-Germeys, I., Mühleisen, T. W., Kirsch, P., Esslinger, C., Herms, S., Demontis, D., Steffens, M., Strohmaier, J. ... Cichon, S. (2012). Association between genetic variation in a region on chromosome 11 and schizophrenia in large samples from Europe. Molecular Psychiatry, 17(9), 906–917. https://doi.org/10.1038/mp.2011.80

Besenbacher, S., Mailund, T. & Schierup, M. H. (2012). Association mapping and disease: evolutionary perspectives. Methods in Molecular Biology, 856, 275-91. https://doi.org/10.1007/978-1-61779-585-5_11

Simonsen, M., Maetschke, S. R. & Ragan, M. A. (2012). Automatic selection of reference taxa for protein-protein interaction prediction with phylogenetic profiling. Bioinformatics, 28(6), 851-857. https://doi.org/10.1093/bioinformatics/btr720

Simonsen, M., Maetschke, S. R. & Ragan, M. A. (2012). Automatic selection of reference taxa for protein–protein interaction prediction with phylogenetic profiling. Bioinformatics, 28(6), 851-857. https://doi.org/10.1093/bioinformatics/btr720

Ho-Huu, J., Ronfort, J., De Mita, S., Bataillon, T., Hochu, I., Weber, A. & Chantret, N. (2012). Contrasted patterns of selective pressure in three recent paralogous gene pairs in the Medicago genus (L.). B M C Evolutionary Biology, 12, 195. https://doi.org/10.1186/1471-2148-12-195

Walker, R. S., Wichmann, S., Mailund, T. & Atkisson, C. J. (2012). Cultural phylogenetics of the tupi language family in lowland South america. P L o S One, 7(4), e35025. https://doi.org/10.1371/journal.pone.0035025

Elfving, B., Buttenschøn, H. N., Foldager, L., Poulsen, P. H. P., Andersen, J. H., Grynderup, M. B., Hansen, A. M., Kolstad, H. A., Kaerlev, L., Mikkelsen, S., Thomsen, J. F., Børglum, A. D., Wegener, G. & Mors, O. (2012). Depression, the Val66Met polymorphism, age, and gender influence the serum BDNF level. Journal of Psychiatric Research, 46(9), 1118-1125. https://doi.org/10.1016/j.jpsychires.2012.05.003

Feliu, E. & Wiuf, C. H. (2012). Enzyme-sharing as a cause of multi-stationarity in signalling systems. Journal of the Royal Society. Interface, 9(71), 1224-1232. https://doi.org/10.1098/rsif.2011.0664

Pedersen, C. N. S., Axelsen, K. B., Harper, J. F. & Palmgren, M. G. (2012). Evolution of plant P-type ATPases. Frontiers in Plant Science, 21. https://doi.org/10.3389/fpls.2012.00031

Anderson, J. WJ., Tataru, P. C., Stains, J., Hein, J. & Lyngsø, R. (2012). Evolving stochastic context-free grammars for RNA secondary structure prediction. B M C Bioinformatics, 13(78). https://doi.org/10.1186/1471-2105-13-78

Knudsen, M., Feliu, E. & Wiuf, C. H. (2012). Exact Analysis of Intrinsic Qualitative Features of Phosphorelays using Mathematical Models. Journal of Theoretical Biology, 300, 7-18. https://doi.org/10.1016/j.jtbi.2012.01.007

Hvilsom, C., Qian, Y., Bataillon, T., Li, Y., Mailund, T., Sallé, B., Carlsen, F., Li, R., Zheng, H., Jiang, T., Jiang, H., Jin, X., Munch, K., Hobolth, A., Siegismund, H. R., Wang, J. & Schierup, M. H. (2012). Extensive X-linked adaptive evolution in central chimpanzees. Proceedings of the National Academy of Sciences of the United States of America. https://doi.org/10.1073/pnas.1106877109

Thøgersen, L. & Nissen, P. (2012). Flexible P-type ATPases interacting with the membrane. Current Opinion in Structural Biology, 22(4), 491-499. https://doi.org/10.1016/j.sbi.2012.05.009

Stukenbrock, E. H., Christiansen, F. B., Hansen, T. T., Dutheil, J. & Schierup, M. H. (2012). Fusion of two divergent fungal individuals led to the recent emergence of a unique widespread pathogen species. Proceedings of the National Academy of Sciences of the United States of America, 107(27). https://doi.org/10.1073/pnas.1201403109

Swenson, M. S., Anderson, J., Ash, A., Gaurav, P., Sükösd, Z., Bader, D. A., Harvey, S. C. & Heitsch, C. E. (2012). GTfold: Enabling parallel RNA secondary structure prediction on multi-core desktops. BMC Research Notes, 5(341). https://doi.org/10.1186/1756-0500-5-341

Holmstrup, M., Sørensen, J. G., Maraldo, K., Schmidt, I., Tietema, A., Smith, A., Schmelz, R., Bataillon, T. & Ehlers, B. (2012). Increased frequency of drought depletes species richness of enchytraeid communities in both wet and dry heathland soils. Soil Biology & Biochemistry, 53, 43-49. https://doi.org/10.1016/j.soilbio.2012.05.001

Holmstrup, M., Sørensen, J. G., Maraldo, K., Schmidt, I. K., Mason, S., Tietema, A., Smith, A. R., Emmett, B., Schmelz, R., Bataillon, T., Beier, C. & Ehlers, B. K. (2012). Increased frequency of drought reduces species richness of enchytraeid communities in both wet and dry heathland soils. Soil Biology & Biochemistry, 53, 43-49. https://doi.org/10.1016/j.soilbio.2012.05.001

W. Abdallah, M., M. Hougaard, D., Nørgaard-Pedersen, B., Grove, J., Bonefeld-Jørgensen, E. C. & L. Mortensen, E. (2012). Infections during Pregnancy and after birth and risk of autism spectrum disorders: a register-based study utilizing a Danish historic birth cohort. Turk Psikiyatri Dergisi, 23(4). https://doi.org/10.5080/u6847

Scally, A., Dutheil, J. Y., Hillier, L. W., Jordan, G. E., Goodhead, I., Herrero, J., Hobolth, A., Lappalainen, T., Mailund, T., Marques-Bonet, T., McCarthy, S., Montgomery, S. H., Schwalie, P. C., Tang, Y. A., Ward, M. C., Xue, Y., Yngvadottir, B., Alkan, C., Andersen, L. N. ... Durbin, R. (2012). Insights into hominid evolution from the gorilla genome sequence. Nature, 483(7388), 169-75. https://doi.org/10.1038/nature10842

Foldager, L., Steffensen, R. N., Thiel, S., Als, T. D., Nielsen, H. J., Nordentoft, M., Mortensen, P. B., Mors, O. & Jensenius, J. C. (2012). MBL and MASP-2 concentrations in serum and MBL2 promoter polymorphisms are associated to schizophrenia. Acta Neuropsychiatrica, 24(4), 199-207. https://doi.org/10.1111/j.1601-5215.2011.00618.x

Saetre, P., Grove, J., Børglum, A., Mors, O., Werge, T. M., Andreassen, O. A., Vares, M., Agartz, I., Terenius, L. & Jönsson, E. G. (2012). Methylenetetrahydrofolate reductase (MTHFR) C677T polymorphism and age at onset of schizophrenia: no consistent evidence for an association in the Nordic population. American Journal of Medical Genetics. Part B: Neuropsychiatric Genetics, 159B(8).

Kraft, J. F., Vestergaard, M., Schiøtt, B. & Thøgersen, L. (2012). Modeling the Self-assembly and Stability of DHPC Micelles using Atomic Resolution and Coarse Grained MD Simulations. Journal of Chemical Theory and Computation, 8(5), 1556–1569. https://doi.org/10.1021/ct200921u

Agerbo, E., Mortensen, P. B., Wiuf, C., Pedersen, M. S., McGrath, J., Hollegaard, M. V., Nørgaard-Pedersen, B., Hougaard, D. M., Mors, O. & Pedersen, C. B. (2012). Modelling the contribution of family history and variation in single nucleotide polymorphisms to risk of schizophrenia: A Danish national birth cohort-based study. Schizophrenia Research, 134(2-3), 246-52. https://doi.org/10.1016/j.schres.2011.10.025

Tuni, C., Goodacre, S., Bechsgaard, J. S. & Bilde, T. (2012). Moderate multiple parentage and low genetic variation reduces the potential for genetic incompatibility avoidance despite high risk of inbreeding. P L o S One, 7(1), e29636. https://doi.org/10.1371/journal.pone.0029636

Thomsen, P. F., Kielgast, J., Iversen, L. L., Wiuf, C. H., Rasmussen, M., Gilbert, M. T. P., Orlando, L. A. A. & Willerslev, E. (2012). Monitoring endangered freshwater biodiversity using environmental DNA. Molecular Ecology, 21(11), 2565-2573. https://doi.org/10.1111/j.1365-294X.2011.05418.x

Abdallah, M., Larsen, N., Mortensen, E. L., Atladóttir, H. Ó., Nørgaard-Pedersen, B., Bonefeld-Jørgensen, E. C., Grove, J. & Hougaard, D. M. (2012). Neonatal levels of cytokines and risk of autism spectrum disorders: An exploratory register-based historic birth cohort study utilizing the Danish Newborn Screening Biobank. Journal of Neuroimmunology, 252, 75-82. https://doi.org/10.1016/j.jneuroim.2012.07.013

Mattila, T., Bechsgaard, J. S., Hansen, T., Schierup, M. H. & Bilde, T. (2012). Ortholog genes identified by transcriptome sequencing in the spider genus Stegodyphus. B M C Genomics, 13(70). https://doi.org/10.1186/1471-2164-13-70