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Department of Biology

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The most recently published scientific articles from the Department of Biology. The overview shows the Department's publications with the latest at the top:

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Larsen, S. A., Meldgaard, T. E. M., Mandrup, O. A., Olesen, C., Fridriksdottir, A., Holst, B. & Kristensen, P. (2012). Identification and analysis of cell-specific biomarkers of breast cancer subpopulations by recombinant antibody selection.

Hansen, J. P. (2012, Mar 23). Matematik. Hvad enhver bør vide om naturvidenskab - næsten.

Slotsbo, S., Hansen, L. M., Jordaens, K., Backeljau, T., Malmendal, A., Nielsen, N. C. & Holmstrup, M. (2012). Cold tolerance and freeze-induced glucose accumulation in three terrestrial slugs. Comparative Biochemistry and Physiology - Part A: Molecular & Integrative Physiology, 161(4), 443-449. https://doi.org/10.1016/j.cbpa.2012.01.002

Bretschneider, C., Karabanov, A., Nielsen, N. C. & Köckenberger, W. (2012). Conversion of parahydrogen induced longitudinal two-spin order to evenly distributed single spin polarisation by optimal control pulse sequences. Journal of Chemical Physics, 136(9), 094201. https://doi.org/10.1063/1.3691193

Jain, S. K., Bjerring, M. & Nielsen, N. C. (2012). Efficient and Robust Heteronuclear Cross-Polarization for High-Speed-Spinning Biological Solid-State NMR Spectroscopy. The Journal of Physical Chemistry Letters, 3, 703-708.

Eickmeyer, K., Hansen, K. A. & Verbin, E. (2012). Approximating the minmax value of 3-player games within a constant is as hard as detecting planted cliques. Electronic Colloquium on Computational Complexity, (TR12-25). http://eccc.hpi-web.de/report/2012/025/

Grönvall, E. & Kramp, G. (2011). LinkLights: a modular, user adaptable system to support rehabilitation practices. In Proceedings of the 4th International Conference on PErvasive Technologies Related to Assistive Environments Association for Computing Machinery. https://doi.org/10.1145/2141622.2141626

Demers-Carpentier, V., Goubert, G., Masini, F., Dong, Y., Rasmussen, A. M. H., Hammer, B. & McBreen, P. H. (2012). Scanning Tunneling Microscopy Measurements of the Full Cycle of a Heterogeneous Asymmetric Hydrogenation Reaction on Chirally Modified Pt(111). The Journal of Physical Chemistry Letters, 3(92), 92–96. https://doi.org/10.1021/jz2013853

Nilsson, L., Andersen, M., Bjerre, J., Balog, R., Hammer, B., Hornekær, L. & Stensgaard, I. (2012). Preservation of the Pt(100) surface reconstruction after growth of a continuous layer of graphene. Surface Science, 606(3-4), 464–469. https://doi.org/10.1016/j.susc.2011.11.007

Nilsson, L., Sljivancanin, Z., Balog, R., Xu, W., Linderoth, T. R., Lægsgaard, E., Stensgaard, I., Hammer, B., Besenbacher, F. & Hornekær, L. (2012). Linear hydrogen adsorbate structures on graphite induced by self-assembled molecular monolayers. Carbon, 50(5), 2052–2056. https://doi.org/10.1016/j.carbon.2011.12.050,

Huo, P., Hansen, J. Ø., Martinez, U., Salazar, E. L., Streber, R., Wei, Y., Lægsgaard, E., Hammer, B., Wendt, S. & Besenbacher, F. (2012). Ethanol Diffusion on Rutile TiO₂(110) Mediated by H Adatoms. The Journal of Physical Chemistry Letters, 3(3), 283–288. https://doi.org/10.1021/jz201616z

Jensen, C. S., Wyer, J. A., Houmøller, J., Hvelplund, P. & Nielsen, S. B. (2011). Electron-capture induced dissociation of doubly charged dipeptides: on the neutral losses and N-Cα bond cleavages. Physical Chemistry Chemical Physics, 13(41), 18373-8. https://doi.org/10.1039/c1cp21549c

Andersson, K. O. D., Hansen, K. A., Miltersen, P. B. & Sørensen, T. B. (2012). Deterministic Graphical Games Revisited. Journal of Logic and Computation, 22(2), 165-178. https://doi.org/10.1093/logcom/exq001

Handrup, M. M., Fuursted, K., Funch, P., Møller, J. K. & Schrøder, H. (2012). Biofilm formation in long-term central venous catheters in children with cancer: a randomized controlled open-labelled trial of taurolidine versus heparin. Acta Pathologica et Microbiologica Scandinavica APMIS, 120(10), 794-801. https://doi.org/10.1111/j.1600-0463.2012.02910.x

Hansen, J. P. (2012, Mar 30). Matematikken bag satellitnavigation. GPS - GLONASS - GALILEO.

Laumann, A., Bremholm, M., Hald, P., Holzapfel, M., Fehr, T. & Iversen, B. B. (2012). Rapid green continuous flow supercritical synthesis of high performance Li4Ti5O12 nanocrystals for Li ion battery applications. Journal of The Electrochemical Society, 159(2), 166-171. https://doi.org/10.1149/2.084202jes

Novotny, G. W., Belling, K. C., Bramsen, J. B., Nielsen, J. E., Bork-Jensen, J., Almstrup, K., Sonne, S. B., Kjems, J., Rajpert-De Meyts, E. & Leffers, H. (2012). MicroRNA expression profiling of carcinoma in situ (CIS) cells of the testis. Endocrine - Related Cancer, 365-379. https://doi.org/10.1530/ERC-11-0271

Bellemer, C., Bortolin-Cavaillé, M.-L., Schmidt, U., Jensen, S. M. R., Kjems, J., Bertrand, E. & Cavaillé, J. (2012). Microprocessor dynamics and interactions at endogenous imprinted C19MC microRNA genes. Journal of Cell Science, 125, 2709-2720 . https://doi.org/10.1242/jcs.100354

Schyth, B. D., Bramsen, J. B., Pakula, M. M., Larashati, S., Kjems, J., Wengel, J. & Lorenzen, N. (2012). In vivo screening of modified siRNAs for non-specific antiviral effect in a small fish model: number and localization in the strands are important. Nucleic Acids Research, 40(10), 4653-4665. https://doi.org/10.1093/nar/gks033

Bramsen, J. B., Laursen, M. B., Nielsen, A. F., Hansen, T. B., Bus, C., Langkjær, N., Babu, B. R., Højland, T., Abramov, M., Van Aerschot, A., Odadzic, D., Smicius, R., Haas, J., Andree, C., Barman, J., Wenska, M., Srivastava, P., Zhou, C., Honcharenko, D. ... Kjems, J. (2009). A large-scale chemical modification screen identifies design rules to generate siRNAs with high activity, high stability and low toxicity. Nucleic Acids Research, 37(9), 2867-81. https://doi.org/10.1093/nar/gkp106

Howard, K. A., Paludan, S. R., Behlke, M. A., Besenbacher, F., Deleuran, B. W. & Kjems, J. (2008). Chitosan/siRNA nanoparticle-mediated TNF-alpha knockdown in peritoneal macrophages for anti-inflammatory treatment in a murine arthritis model. Molecular Therapy, 17(1), 162-168. https://doi.org/10.1038/mt.2008.220

Otero Martin, R., Xu, W., Lukas, M., Kelly, R. E. A., Laegsgaard, E., Stensgaard, I., Kjems, J., Kantorovich, L. N. & Besenbacher, F. (2008). Specificity of Watson-Crick Base Pairing on a Solid Surface Studied at the Atomic Scale. Angewandte Chemie, 47(50), 9673-9676. https://doi.org/10.1002/anie.200803333

Astakhova, I., Korshun, V. A., Jahn, K., Kjems, J. & Wengel, J. (2008). Perylene attached to 2'-amino-LNA: synthesis, incorporation into oligonucleotides, and remarkable fluorescence properties in vitro and in cell culture. Bioconjugate Chemistry, 19(10), 1995-2007. https://doi.org/10.1021/bc800202v

Torarinsson, E., Yao, Z., Wiklund, E. D., Bramsen, J. B., Hansen, C. A., Kjems, J., Tommerup, N., Ruzzo, W. L. & Gorodkin, J. (2008). Comparative genomics beyond sequence-based alignments: RNA structures in the ENCODE regions. Genome Research, 18(2), 242-251. https://doi.org/10.1101/gr.6887408

Andersen, M. Ø., Howard, K. A., Paludan, S. R., Besenbacher, F. & Kjems, J. (2008). Delivery of siRNA from lyophilized polymeric surfaces. Biomaterials, 29(4), 506-512. https://doi.org/10.1016/j.biomaterials.2007.10.003

Odadzic, D., Bramsen, J. B., Smicius, R., Bus, C., Kjems, J. & Engels, J. W. (2008). Synthesis of 2'-O-modified adenosine building blocks and application for RNA interference. Bioorganic & Medicinal Chemistry, 16(1), 518-529. https://doi.org/10.1016/j.bmc.2007.09.019

Howard, K. A. & Kjems, J. (2007). Polycation-based nanoparticle delivery for improved RNA interference therapeutics. Expert opinion on biological therapy, 7(12), 1811-1822. https://doi.org/10.1517/14712598.7.12.1811

Bramsen, J. B., Laursen, M. B., Damgaard, C. K., Lena, S. W., Babu, B. R., Wengel, J. & Kjems, J. (2007). Improved silencing properties using small internally segmented interfering RNAs. Nucleic Acids Research, 35(17), 5886-5897. https://doi.org/10.1093/nar/gkm548

Lykke-Andersen, S., Piñol-Roma, S. & Kjems, J. (2007). Alternative splicing of the ADAR1 transcript in a region that functions either as a 5'-UTR or an ORF. RNA, 13(10), 1732-1744. https://doi.org/10.1261/rna.567807

Jakobsen, M. R., Haasnoot, J., Wengel, J., Berkhout, B. & Kjems, J. (2007). Efficient inhibition of HIV-1 expression by LNA modified antisense oligonucleotides and DNAzymes targeted to functionally selected binding sites. Retrovirology, 4(29), 1-13. https://doi.org/10.1186/1742-4690-4-29

Nielsen, K. B., Sørensen, S., Cartegni, L., Corydon, T. J., Doktor, T. K., Schroeder, L. D., Reinert, L. S., Elpeleg, O., Krainer, A. R., Gregersen, N., Kjems, J. & Andresen, B. S. (2007). Seemingly neutral polymorphic variants may confer immunity to splicing-inactivating mutations: a synonymous SNP in exon 5 of MCAD protects from deleterious mutations in a flanking exonic splicing enhancer. American Journal of Human Genetics, 80(3), 416-432. https://doi.org/10.1086/511992

Novotny, G. W., Sonne, S., Nielsen, J. E., Jonstrup, S. P., Hansen, M. A., Skakkebaek, N. E., Rajpert-De Meyts, E., Kjems, J. & Leffers, H. (2007). Translational repression of E2F1 mRNA in carcinoma in situ and normal testis correlates with expression of the miR-17-92 cluster. Cell Death and Differentiation, 14(4), 879-882. https://doi.org/10.1038/sj.cdd.4402090

Kammler, S., Otte, M., Hauber, I., Kjems, J., Hauber, J. & Schaal, H. (2006). The strength of the HIV-1 3' splice sites affects Rev function. Retrovirology, 3(89), 1-20. https://doi.org/10.1186/1742-4690-3-89

Jonstrup, S. P., Koch, J. & Kjems, J. (2006). A microRNA detection system based on padlock probes and rolling circle amplification. RNA, 12(9), 1747-1752. https://doi.org/10.1261/rna.110706

Howard, K. A., Rahbek, U. L., Liu, X., Damgaard, C. K., Glud, S. Z., Andersen, M. Ø., Hovgaard, M. B., Schmitz, A., Nyengaard, J. R., Besenbacher, F. & Kjems, J. (2006). RNA interference in Vitro and in Vivo using a novel chitosan/siRNA nanoparticle system. Molecular Therapy, 14(4), 476-484. https://doi.org/10.1016/j.ymthe.2006.04.010

Lützelberger, M., Reinert, L. S., Das, A. T., Berkhout, B. & Kjems, J. (2006). A novel splice donor site in the gag-pol gene is required for HIV-1 RNA stability. Journal of Biological Chemistry, 281(27), 18644-18651. https://doi.org/10.1074/jbc.M513698200

Mohey, R., Katzenstein, T. L., Black, F. T., Kjems, J. & Obel, N. (2006). Dynamics of proviral HIV-1 184M/V in circulating CD4+ T-cells: a 90 days follow-up study after initiation/switch of HAART. Scandinavian Journal of Infectious Diseases, 38(2), 119-123. https://doi.org/10.1080/00365540500348937

Paca-Uccaralertkun, S., Damgaard, C. K., Auewarakul, P., Thitithanyanont, A., Suphaphiphat, P., Essex, M., Kjems, J. & Lee, T.-H. (2006). The Effect of a Single Nucleotide Substitution in the Splicing Silencer in the tat/rev Intron on HIV Type 1 Envelope Expression. AIDS Research and Human Retroviruses, 22(1), 76-82. https://doi.org/10.1089/aid.2006.22.76

Mohey, R., Tolstrup, M., Jørgensen, L. B., Møller, B. K., Black, F. T., Kjems, J. & Obel, N. (2006). HIV-1 reverse Transcriptase Gene 103K/N and 184M/V Combinations in Tandem: Detection and Quantification of HIV-1 Populations in the CD45RO+ T-cell Compartment by a Double-ARMS Real-Time PCR assay. J A I D S, 41(2), 160-167. https://doi.org/10.1097/01.qai.0000191998.70034.64

Mukhopadhyay, R., Sumbayev, V. V., Lorentzen, M., Kjems, J., Andreasen, P. A. & Besenbacher, F. (2005). Cantilever sensor for nanomechanical detection of specific protein conformations. Nano Letters, 5(12), 2385-8. https://doi.org/10.1021/nl051449z

Mohey, R., Jørgensen, A. L., Møller, B. K., Black, F. T., Kjems, J. & Obel, N. (2005). Detection and quantification of proviral HIV-1 184 M/V in circulating CD4(+) T cells of patients on HAART with a viremia less than 1000 copies/ml. Journal of Clinical Virology, 34(4), 257-267. https://doi.org/10.1016/j.jcv.2005.02.015

Mukhopadhyay, R., Lorentzen, M., Kjems, J. & Besenbacher, F. (2005). Nanomechanical sensing of DNA sequences using piezoresistive cantilevers. Langmuir, 21(18), 8400-8408. https://doi.org/10.1021/la0511687

Furnes, C., Arnesen, T., Askjaer, P., Kjems, J. & Szilvay, A. M. (2005). HIV-1 Rev oligomerization is not obligatory in the presence of an extra basic domain. Retrovirology, 2, 39. https://doi.org/10.1186/1742-4690-2-39

Nielsen, M. H., Pedersen, F. S. & Kjems, J. (2005). Molecular strategies to inhibit HIV-1 replication. Retrovirology, 2, 10. https://doi.org/10.1186/1742-4690-2-10

Knudsen, B., Andersen, E. S., Damgaard, C. K., Kjems, J. & Gorodkin, J. (2004). Evolutionary rate variation and RNA secondary structure prediction. Computational Biology and Chemistry, 28(3), 219-26. https://doi.org/10.1016/j.compbiolchem.2004.04.001

Jakobsen, M. R., Damgaard, C. K., Andersen, E. S., Podhajska, A. & Kjems, J. (2004). A genomic selection strategy to identify accessible and dimerization blocking targets in the 5'-UTR of HIV-1 RNA. Nucleic Acids Research, 32(7), e67. https://doi.org/10.1093/nar/gnh064

Andersen, E. S., Contera, S. A., Knudsen, B., Damgaard, C. K., Besenbacher, F. & Kjems, J. (2004). Role of the trans-activation response element in dimerization of HIV-1 RNA. Journal of Biological Chemistry, 279(21), 22243-22249. https://doi.org/10.1074/jbc.M314326200

Damgaard, C. K., Andersen, E. S., Knudsen, B., Gorodkin, J. & Kjems, J. (2004). RNA interactions in the 5' region of the HIV-1 genome. Journal of Molecular Biology, 336(2), 369-79. https://doi.org/10.1016/j.jmb.2003.12.010

Zahler, A. M., Damgaard, C. K., Kjems, J. & Caputi, M. (2004). SC35 and heterogeneous nuclear ribonucleoprotein A/B proteins bind to a juxtaposed exonic splicing enhancer/exonic splicing silencer element to regulate HIV-1 tat exon 2 splicing. Journal of Biological Chemistry, 279(11), 10077-10084. https://doi.org/10.1074/jbc.M312743200

Freund, M., Asang, C., Kammler, S., Konermann, C., Krummheuer, J., Hipp, M., Meyer, I., Gierling, W., Theiss, S., Preuss, T., Schindler, D., Kjems, J. & Schaal, H. (2003). A novel approach to describe a U1 snRNA binding site. Nucleic Acids Research, 31(23), 6963-6975. https://doi.org/10.1093/nar/gkg901

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