Publications

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Østergaard, S. D. & Foldager, L. (2011). The association between physical illness and major depressive episode in general practice. Acta Psychiatrica Scandinavica, 123(4), 290-296. https://doi.org/10.1111/j.1600-0447.2010.01668.x

Østergaard, S. D. & Foldager, L. (2011). Reply. Acta Psychiatrica Scandinavica, 124(1), 75-6. https://doi.org/10.1111/j.1600-0447.2011.01694.x

Østergaard, S. D., Dinesen, P. T. & Foldager, L. (2011). Sensitivity x PPV is a recognized test called the clinical utility index (CUI+). The Authors Reply. European Journal of Epidemiology, 26, 252-252. https://doi.org/10.1007/s10654-011-9561-x

Østergaard, S. D., Foldager, L., Mors, O., Bech, P. & Correll, C. U. (2018). The validity and sensitivity of PANSS-6 in treatment-resistant schizophrenia. Acta Psychiatrica Scandinavica, 138(5), 420-431. https://doi.org/10.1111/acps.12952

Østergaard, S. D., Foldager, L., Mors, O., Beck, P. & Correll, C. U. (2018). The validity and sensitivity of PANSS-6 in treatment-resistant schizophrenia. Schizophrenia Bulletin, 44(Suppl_1), S341-S342.

Østergaard, S., Andersen, S., Sládecek, T. & Villesen, P. (2019). Hvornår får vi børn? – En historie om fødselsmønstre i et moderne samfund. Aktuel Naturvidenskab, 2019(5), 8-11. https://aktuelnaturvidenskab.dk/find-artikel/nyeste-numre/5-2019/

Østergaard, S., Krogh, M. A., Oliveira, V. H. S. D., Larsen, T., GplusE Consortium & Otten, N. D. (2020). Only few benefits from propylene glycol drench in early lactation for cows identified as physiologically imbalanced based on milk spectra analyses. Journal of Dairy Science, 103(2), 1831-1842. https://doi.org/10.3168/jds.2019-17205

Østergaard, S. D., Speed, M. S., Kellner, C. H., Mueller, M., McClintock, S. M., Husain, M. M., Petrides, G., McCall, W. V., Lisanby, S. H. & for the CORE/PRIDE workgroup (2020). Electroconvulsive therapy (ECT) for moderate-severity major depression among the elderly: Data from the pride study. Journal of Affective Disorders, 274, 1134-1141. https://doi.org/10.1016/j.jad.2020.05.039

Ostenfeld, M. S., Jeppesen, D. K., Laurberg, J. R., Boysen, A. T., Bramsen, J. B., Primdal-Bengtson, B., Hendrix, A., Lamy, P., Dagnaes-Hansen, F., Rasmussen, M. H., Bui, K. H., Fristrup, N., Christensen, E. I., Nordentoft, I., Morth, J. P., Jensen, J. B., Pedersen, J. S., Beck, M., Theodorescu, D. ... Orntoft, T. F. (2014). Cellular Disposal of miR23b by RAB27-Dependent Exosome Release Is Linked to Acquisition of Metastatic Properties. Cancer Research, 74(20), 5758-5771. https://doi.org/10.1158/0008-5472.CAN-13-3512

Ørnbjerg, L. M., Brahe, C. H., Linde, L., Jacobsson, L., Nissen, M. J., Kristianslund, E. K., Santos, M. J., Nordström, D., Rotar, Z., Gudbjornsson, B., Onen, F., Codreanu, C., Lindström, U., Möller, B., Kvien, T. K., Barcelos, A., Eklund, K. K., Tomšič, M., Love, T. J. ... Hetland, M. L. (2024). Drug effectiveness of 2nd and 3rd TNF inhibitors in psoriatic arthritis – relationship with the reason for withdrawal from the previous treatment. Joint Bone Spine, 91(4), Article 105729. https://doi.org/10.1016/j.jbspin.2024.105729

Ørbæk, M., Thorsteinsson, K., Moseholm Larsen, E., Katzenstein, T. L., Storgaard, M., Johansen, I. S., Pedersen, G., Bach, D., Helleberg, M., Weis, N. & Lebech, A. M. (2020). Risk factors during pregnancy and birth-related complications in HIV-positive versus HIV-negative women in Denmark, 2002–2014. HIV Medicine, 21(2), 84-95. https://doi.org/10.1111/hiv.12798

Omland, L. H., Holm-Hansen, C., Lebech, A. M., Dessau, R. B., Bodilsen, J., Andersen, N. S., Roed, C., Christiansen, C. B., Ellermann-Eriksen, S., Midgley, S., Nielsen, L., Benfield, T., Hansen, A. B. E., Andersen, C., Rothman, K. J., Sørensen, H. T., Fischer, T. K. & Obel, N. (2020). Long-Term Survival, Health, Social Functioning, and Education in Patients With an Enterovirus Central Nervous System Infection, Denmark, 1997-2016. The Journal of Infectious Diseases, 222(4), 619-627. https://doi.org/10.1093/infdis/jiaa151

Okholm, T. L. H., Nielsen, M. M., Hamilton, M., Christensen, L.-L., Vang, S., Hedegaard, J., Hansen, T. B., Kjems, J., Dyrskjøt, L. & Pedersen, J. S. (2017). Circular RNA expression is abundant and correlated to aggressiveness in early-stage bladder cancer. npj Genomic Medicine, 2(1), Article 36. https://doi.org/10.1038/s41525-017-0038-z

Okholm, T. L. H., Sathe, S., Park, S. S., Kamstrup, A. B., Rasmussen, A. M., Shankar, A., Chua, Z. M., Fristrup, N., Nielsen, M. M., Vang, S., Dyrskjøt, L., Aigner, S., Damgaard, C. K., Yeo, G. W. & Pedersen, J. S. (2020). Transcriptome-wide profiles of circular RNA and RNA-binding protein interactions reveal effects on circular RNA biogenesis and cancer pathway expression. Genome Medicine, 12(112), Article 112. https://doi.org/10.1186/s13073-020-00812-8

Okholm, K. R., Nooteboom, S. W., Vinther, J. N., Lamberti, V., Dey, S., Andersen, E. S., Zijlstra, P. & Sutherland, D. S. (2024). Single-Molecule Multivalent Interactions Revealed by Plasmon-Enhanced Fluorescence. ACS Nano, 18(52), 35429-35442. https://doi.org/10.1021/acsnano.4c12600

Nyegaard, M., Demontis, D., Foldager, L., Hedemand, A., Flint, T. J., Sørensen, K. M., Andersen, P. S., Nordentoft, M., Werge, T., Pedersen, C. B., Hougaard, D. M., Mortensen, P. B., Mors, O. & Børglum, A. D. (2010). CACNA1C (rs1006737) is associated with schizophrenia. Molecular Psychiatry, 15(2), 119-21. https://doi.org/10.1038/mp.2009.69

Nyborg, J., Nissen, P., Kjeldgaard, M., Thirup, S., Polekhina, G., Clark, B. F. & Reshetnikova, L. (1997). Macromolecular mimicry in protein biosynthesis. Structure, 2(3), S7-11.

Nyborg, J., Nissen, P., Kjeldgaard, M., Thirup, S., Polekhina, G. & Clark, B. F. (1996). Structure of the ternary complex of EF-Tu: macromolecular mimicry in translation. Trends in Biochemical Sciences, 21(3), 81-2.

Nordentoft, I. K., Lamy, P., Birkenkamp-Demtröder, K., Vang, S., Reinert, T., Hedegaard, J., Thorsen, K., Fristrup, N., Borre, M., Andersen, L. D., Pedersen, J. S. & Ørntoft, T. F. (2013). Whole genome and transcriptome analysis reveals novel genomic alterations in bladder cancer. Poster session presented at American Association for Cancer Research, Washington, DC, United States.

Nordentoft, I. K., Birkenkamp-Demtröder, K., Lamy, P., Reinert, T., Vang, S., Hedegaard, J., Thorsen, K., Dyrskjøt, L., Pedersen, J. S. & Ørntoft, T. F. (2014). Genome and RNA sequencing identifies fusion transcripts in bladder cancer. Abstract from AACR Annual Meeting 2014, San Diego, California, United States.

Nordentoft, I. K., Lamy, P., Birkenkamp-Demtröder, K., Shumansky, K., Vang, S., Hornshøj, H., Juul, M., Villesen, P., Hedegaard, J., Roth, A., Thorsen, K., Høyer, S., Borre, M., Reinert, T., Fristrup, N., Dyrskjøt, L., Shah, S., Pedersen, J. S. & Ørntoft, T. F. (2014). Mutational context and diverse clonal development in early and late bladder cancer: Genomic changes in bladder cancer. Cell Reports, 7(5), 1649–1663. https://doi.org/10.1016/j.celrep.2014.04.038

Norager, N. H., Olsen, M. H., Pedersen, S. H., Riedel, C. S., Czosnyka, M. & Juhler, M. (2021). Reference values for intracranial pressure and lumbar cerebrospinal fluid pressure: a systematic review. Fluids and Barriers of the CNS, 18(1), Article 19. https://doi.org/10.1186/s12987-021-00253-4

Noor, B. (2023). Optimization and Application of Convolution Neural Networks to Genomics. Århus Universitet.

Nissen, P., Kjeldgaard, M., Thirup, S., Clark, B. F. & Nyborg, J. (1996). The ternary complex of aminoacylated tRNA and EF-Tu-GTP. Recognition of a bond and a fold. Biochimie, 78(11-12), 921-33.

Nissen, P., Kjeldgaard, M., Thirup, S., Polekhina, G., Reshetnikova, L., Clark, B. F. & Nyborg, J. (1995). Crystal structure of the ternary complex of Phe-tRNAPhe, EF-Tu, and a GTP analog. Science, 270(5241), 1464-72.

Nissen, P., Reshetnikova, L., Siboska, G., Polekhina, G., Thirup, S., Kjeldgaard, M., Clark, B. F. & Nyborg, J. (1994). Purification and crystallization of the ternary complex of elongation factor Tu:GTP and Phe-tRNA(Phe). FEBS Letters, 356(2-3), 165-8.

Nissen, K. K., Laska, M. J., Hansen, B., Terkelsen, T., Villesen, P., Bahrami, S., Petersen, T., Pedersen, F. S. & Nexø, B. A. (2013). Endogenous retroviruses and multiple sclerosis-new pieces to the puzzle. B M C Neurology, 13(111), 1-5. https://doi.org/10.1186/1471-2377-13-111

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.

Nielsen, R. & Wiuf, C. (2005). Composite likelihood estimation applied to Single Nucleotide Polymorphism (SNP) data. ISI Conference Proceedings 2005.. Paper presented at Composite likelihood estimation applied to Single Nucleotide Polymorphism (SNP) data. ISI Conference Proceedings 2005..

Nielsen, J. & Mailund, T. (2008). SNPFile - A software library and file format for large scale association mapping and population genetics studies. B M C Bioinformatics, 9(526), 1-11. https://doi.org/10.1186/1471-2105-9-526

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.

Nielsen, J., le Quach, P., Emborg, C., Foldager, L. & Correll, C. U. (2010). 10-Year trends in the treatment and outcomes of patients with first-episode schizophrenia. Acta Psychiatrica Scandinavica, 122(5), 356-66. https://doi.org/10.1111/j.1600-0447.2010.01576.x

Nielsen, J. & Sand, A. (2011). Algorithms for a parallel implementation of Hidden Markov Models with a small state space. In 2011 IEEE IPDPS Workshops & PhD Forum (pp. 447-454). IEEE Computer Society Press. https://doi.org/10.1109/IPDPS.2011.181

Nielsen, J., Kristensen, A. K., Mailund, T. & Pedersen, C. N. S. (2011). A sub-cubic time algorithm for computing the quartet distance between two general trees. Algorithms for Molecular Biology, 6(15). https://doi.org/10.1186/1748-7188-6-15

Nielsen, J. (2011). Engineering Algorithms for Finding Patterns in Biological Data.

Nielsen, J. (2011). A Coarse-to-Fine Approach to Computing the k-best Viterbi Paths. Lecture Notes in Computer Science, 6661, 376-387. https://doi.org/10.1007/978-3-642-21458-5_32

Nielsen, M. M., Tataru, P., Madsen, T., Hobolth, A. & Pedersen, J. S. (2016). Motif discovery in ranked lists of sequences. (pp. 1-4). http://biorxiv.org/content/biorxiv/suppl/2016/01/11/035956.DC2/035956-1.pdf

Nielsen, S. M., de Gier, C., Dimopoulou, C., Gupta, V., Hansen, L. H. & Nørskov-Lauritsen, N. (2015). The capsule biosynthesis locus of Haemophilus influenzae show conspicuous similarity to the corresponding locus in Haemophilus sputorum and may have been recruited from this species by horizontal gene transfer. Microbiology, 161(6), 1182-1188. https://doi.org/10.1099/mic.0.000081

Nielsen, L. S., Villesen, P. & Lindholst, C. (2015). Stability of cocaine alkaloids and residual solvents applied in drug profiling.

Nielsen, L. S., Villesen, P. & Lindholst, C. (2016). Stability of cocaine impurity profiles during 12 months of storage. Forensic Science International, 264, 56-62. https://doi.org/10.1016/j.forsciint.2016.03.012

Nielsen, A. L.-L., Olsen, L. C., Saetrom, P., Drabløs, F., Besenbacher, S., Steenberg, L. R., Johansen, C. & Iversen, L. (2016). Pathway Analysis of Skin from Psoriasis Patients after Adalimumab Treatment Reveals New Early Events in the Anti-Inflammatory Mechanism of Anti-TNF-α. P L o S One, 11(12), e0167437. Article e0167437. https://doi.org/10.1371/journal.pone.0167437

Nielsen, L. S., Lindholst, C. & Villesen, P. (2016). Illegal drugs and bioinformatics - Classification and stability of amphetamine impurities applied in criminal investigations.

Nielsen, S., Simonsen, S. & Hobolth, A. (2016). Inferring Population Genetic Parameters: Particle Filtering, HMM, Ripley’s K-Function or Runs of Homozygosity? In M. Frith & C. Nørgaard Storm Pedersen (Eds.), Algorithms in Bioinformatics - 16th International Workshop, WABI 2016, Proceedings (Vol. 9838, pp. 234-245). Springer. http://link.springer.com/chapter/10.1007/978-3-319-43681-4_19/fulltext.html