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NUCLEIC ACIDS RES - Nucleic acids research

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Publications

  1. 2023

  2. Single-cell gene regulatory network prediction by explainable AI

    Keyl, P., Bischoff, P., Dernbach, G., Bockmayr, M., Fritz, R., Horst, D., Blüthgen, N., Montavon, G., Müller, K-R. & Klauschen, F., 28.02.2023, In: NUCLEIC ACIDS RES. 51, 4, p. e20

    Research output: SCORING: Contribution to journal › SCORING: Journal article › Research › peer-review

  3. 2020

  4. DNA binds to a specific site of the adhesive blood-protein von Willebrand factor guided by electrostatic interactions

    Sandoval-Pérez, A., Berger, R. M. L., Garaizar, A., Farr, S. E., Brehm, M. A., König, G., Schneider, S. W., Collepardo-Guevara, R., Huck, V., Rädler, J. O. & Aponte-Santamaría, C., 27.07.2020, In: NUCLEIC ACIDS RES. 48, 13, p. 7333-7344 12 p.

    Research output: SCORING: Contribution to journal › SCORING: Journal article › Research › peer-review

  5. Mechanism of conditional partner selectivity in MITF/TFE family transcription factors with a conserved coiled coil stammer motif

    Pogenberg, V., Ballesteros-Álvarez, J., Schober, R., Sigvaldadóttir, I., Obarska-Kosinska, A., Milewski, M., Schindl, R., Ögmundsdóttir, M. H., Steingrímsson, E. & Wilmanns, M., 24.01.2020, In: NUCLEIC ACIDS RES. 48, 2, p. 934-948 15 p.

    Research output: SCORING: Contribution to journal › SCORING: Journal article › Research › peer-review

  6. SEAweb: the small RNA Expression Atlas web application

    Rahman, R-U., Liebhoff, A-M., Bansal, V., Fiosins, M., Rajput, A., Sattar, A., Magruder, D. S., Madan, S., Sun, T., Gautam, A., Heins, S., Liwinski, T., Bethune, J., Trenkwalder, C., Fluck, J., Mollenhauer, B. & Bonn, S., 08.01.2020, In: NUCLEIC ACIDS RES. 48, D1, p. D204-D219

    Research output: SCORING: Contribution to journal › SCORING: Journal article › Research › peer-review

  7. 2019

  8. TDP-43 enhances translation of specific mRNAs linked to neurodegenerative disease

    Neelagandan, N., Gonnella, G., Dang, S., Janiesch, P. C., Miller, K. K., Küchler, K., Marques, R. F., Indenbirken, D., Alawi, M., Grundhoff, A., Kurtz, S. & Duncan, K. E., 10.01.2019, In: NUCLEIC ACIDS RES. 47, 1, p. 341-361 21 p.

    Research output: SCORING: Contribution to journal › SCORING: Journal article › Research › peer-review

  9. 2017

  10. Homeostatic nuclear RAGE-ATM interaction is essential for efficient DNA repair

    Kumar, V., Fleming, T., Terjung, S., Gorzelanny, C., Gebhardt, C., Agrawal, R., Mall, M. A., Ranzinger, J., Zeier, M., Madhusudhan, T., Ranjan, S., Isermann, B., Liesz, A., Deshpande, D., Häring, H-U., Biswas, S. K., Reynolds, P. R., Hammes, H-P., Peperkok, R., Angel, P., Herzig, S. & Nawroth, P. P., 13.10.2017, In: NUCLEIC ACIDS RES. 45, 18, p. 10595-10613 19 p.

    Research output: SCORING: Contribution to journal › SCORING: Journal article › Research › peer-review

  11. BRD4 promotes p63 and GRHL3 expression downstream of FOXO in mammary epithelial cells

    Nagarajan, S., Bedi, U., Budida, A., Hamdan, F. H., Mishra, V. K., Najafova, Z., Xie, W., Alawi, M., Indenbirken, D., Knapp, S., Chiang, C-M., Grundhoff, A., Kari, V., Scheel, C. H., Wegwitz, F. & Johnsen, S. A., 07.04.2017, In: NUCLEIC ACIDS RES. 45, 6, p. 3130-3145 16 p.

    Research output: SCORING: Contribution to journal › SCORING: Journal article › Research › peer-review

  12. BRD4 localization to lineage-specific enhancers is associated with a distinct transcription factor repertoire

    Najafova, Z., Tirado-Magallanes, R., Subramaniam, M., Hossan, T., Schmidt, G., Nagarajan, S., Baumgart, S. J., Mishra, V. K., Bedi, U., Hesse, E., Knapp, S., Hawse, J. R. & Johnsen, S. A., 09.01.2017, In: NUCLEIC ACIDS RES. 45, 1, p. 127-141 15 p.

    Research output: SCORING: Contribution to journal › SCORING: Journal article › Research › peer-review

  13. 2016

  14. The quorum-sensing regulator ComA from Bacillus subtilis activates transcription using topologically distinct DNA motifs

    Wolf, D., Rippa, V., Mobarec, J. C., Sauer, P., Adlung, L., Kolb, P. & Bischofs, I. B., 18.03.2016, In: NUCLEIC ACIDS RES. 44, 5, p. 2160-72 13 p.

    Research output: SCORING: Contribution to journal › SCORING: Journal article › Research › peer-review

  15. 2015

  16. NUCKS1 is a novel RAD51AP1 paralog important for homologous recombination and genome stability

    Parplys, A. C., Zhao, W., Sharma, N., Groesser, T., Liang, F., Maranon, D. G., Leung, S. G., Grundt, K., Dray, E., Idate, R., Østvold, A. C., Schild, D., Sung, P. & Wiese, C., 31.08.2015, In: NUCLEIC ACIDS RES. 43, 20, p. 9817-9834

    Research output: SCORING: Contribution to journal › SCORING: Journal article › Research › peer-review

  17. Destruction of a distal hypoxia response element abolishes trans-activation of the PAG1 gene mediated by HIF-independent chromatin looping

    Schörg, A., Santambrogio, S., Platt, J. L., Schödel, J., Lindenmeyer, M. T., Cohen, C. D., Schrödter, K., Mole, D. R., Wenger, R. H. & Hoogewijs, D., 13.07.2015, In: NUCLEIC ACIDS RES. 43, 12, p. 5810-23 14 p.

    Research output: SCORING: Contribution to journal › SCORING: Journal article › Research › peer-review

  18. mRNA transfection of a novel TAL effector nuclease (TALEN) facilitates efficient knockout of HIV co-receptor CCR5

    Mock, U., Machowicz, R., Hauber, I., Horn, S., Abramowski, P., Berdien, B., Hauber, J. & Fehse, B., 11.05.2015, In: NUCLEIC ACIDS RES. 43, 11, p. 5560-5571

    Research output: SCORING: Contribution to journal › SCORING: Journal article › Research › peer-review

  19. Involvement of ATM in homologous recombination after end resection and RAD51 nucleofilament formation

    Bakr, A., Oing, C., Köcher, S., Borgmann, K., Dornreiter, I., Petersen, C., Dikomey, E. & Mansour Khalfallah, W. Y., 31.03.2015, In: NUCLEIC ACIDS RES. 43, 6, p. 3154-66 13 p.

    Research output: SCORING: Contribution to journal › SCORING: Journal article › Research › peer-review

  20. 2014

  21. Lynx web services for annotations and systems analysis of multi-gene disorders

    Sulakhe, D., Taylor, A., Balasubramanian, S., Feng, B., Xie, B., Börnigen, D., Dave, U. J., Foster, I. T., Gilliam, T. C. & Maltsev, N., 07.2014, In: NUCLEIC ACIDS RES. 42, Web Server issue, p. W473-477

    Research output: SCORING: Contribution to journal › SCORING: Journal article › Research › peer-review

  22. Multiplexing clonality: combining RGB marking and genetic barcoding

    Cornils, K., Thielecke, L., Hüser, S., Forgber, M., Thomaschewski, M., Kleist, N., Hussein, K., Riecken, K., Volz, T., Gerdes, S., Glauche, I., Dahl, A., Dandri, M., Roeder, I. & Fehse, B., 01.04.2014, In: NUCLEIC ACIDS RES. 42, 7, p. e56

    Research output: SCORING: Contribution to journal › SCORING: Journal article › Research › peer-review

  23. Lynx: a database and knowledge extraction engine for integrative medicine

    Sulakhe, D., Balasubramanian, S., Xie, B., Feng, B., Taylor, A., Wang, S., Berrocal, E., Dave, U., Xu, J., Börnigen, D., Gilliam, T. C. & Maltsev, N., 01.2014, In: NUCLEIC ACIDS RES. 42, Database issue, p. D1007-12

    Research output: SCORING: Contribution to journal › SCORING: Journal article › Research › peer-review

  24. 2013

  25. Concordance of gene expression in human protein complexes reveals tissue specificity and pathology

    Börnigen, D., Pers, T. H., Thorrez, L., Huttenhower, C., Moreau, Y. & Brunak, S., 10.2013, In: NUCLEIC ACIDS RES. 41, 18, p. e171

    Research output: SCORING: Contribution to journal › SCORING: Journal article › Research › peer-review

  26. Genome-wide hydroxymethylation tested using the HELP-GT assay shows redistribution in cancer

    Bhattacharyya, S., Yu, Y., Suzuki, M., Campbell, N., Mazdo, J., Vasanthakumar, A., Bhagat, T. D., Nischal, S., Christopeit, M., Parekh, S., Steidl, U., Godley, L., Maitra, A., Greally, J. M. & Verma, A., 09.2013, In: NUCLEIC ACIDS RES. 41, 16, p. e157

    Research output: SCORING: Contribution to journal › SCORING: Journal article › Research › peer-review

  27. Dissection of cell cycle-dependent dynamics of Dnmt1 by FRAP and diffusion-coupled modeling

    Schneider, K., Fuchs, C., Dobay, A., Rottach, A., Qin, W., Wolf, P., Álvarez-Castro, J. M., Nalaskowski, M. M., Kremmer, E., Schmid, V., Leonhardt, H. & Schermelleh, L., 01.05.2013, In: NUCLEIC ACIDS RES. 41, 9, p. 4860-76 17 p.

    Research output: SCORING: Contribution to journal › SCORING: Journal article › Research › peer-review

  28. 2012

  29. Radiation-induced double-strand breaks require ATM but not Artemis for homologous recombination during S-phase.

    Köcher, S., Rieckmann, T., Rohaly, G., Mansour, W., Dikomey, E., Dornreiter, I. & Dahm-Daphi, J., 2012, In: NUCLEIC ACIDS RES. 40, 17, p. 8336-8347 17.

    Research output: SCORING: Contribution to journal › SCORING: Journal article › Research › peer-review

  30. SPOC1 modulates DNA repair by regulating key determinants of chromatin compaction and DNA damage response.

    Mund, A., Schubert, T., Staege, H., Kinkley, S., Reumann, K., Kriegs, M., Fritsch, L., Battisti, V., Ait-Si-Ali, S., Hoffbeck, A-S., Soutoglou, E. & Will, H., 2012, In: NUCLEIC ACIDS RES. 40, 22, p. 11363-11379 22.

    Research output: SCORING: Contribution to journal › SCORING: Journal article › Research › peer-review

  31. 2010

  32. Cohesin promotes the repair of ionizing radiation-induced DNA double-strand breaks in replicated chromatin

    Bauerschmidt, C., Arrichiello, C., Burdak-Rothkamm, S., Woodcock, M., Hill, M. A., Stevens, D. L. & Rothkamm, K., 01.2010, In: NUCLEIC ACIDS RES. 38, 2, p. 477-87 11 p.

    Research output: SCORING: Contribution to journal › SCORING: Journal article › Research › peer-review

  33. Functional cooperation between CREM and GCNF directs gene expression in haploid male germ cells.

    Rajkovic, M., Iwen, K. A. H., Hofmann, P. J., Harneit, A. & Weitzel, J. M., 2010, In: NUCLEIC ACIDS RES. 38, 7, p. 2268-2278 7.

    Research output: SCORING: Contribution to journal › SCORING: Journal article › Research › peer-review

  34. The alternative end-joining pathway for repair of DNA double-strand breaks requires PARP1 but is not dependent upon microhomologies.

    Mansour, W., Rhein, T. & Dahm-Daphi, J., 2010, In: NUCLEIC ACIDS RES. 38, 18, p. 6065-6077 18.

    Research output: SCORING: Contribution to journal › SCORING: Journal article › Research › peer-review

  35. 2009

  36. Modulation of gene expression in U251 glioblastoma cells by binding of mutant p53 R273H to intronic and intergenic sequences

    Brázdová, M., Quante, T., Tögel, L., Walter, K., Loscher, C., Tichý, V., Cincárová, L., Deppert, W. & Tolstonog, G. V., 04.2009, In: NUCLEIC ACIDS RES. 37, 5, p. 1486-500 15 p.

    Research output: SCORING: Contribution to journal › SCORING: Journal article › Research › peer-review

  37. 2008

  38. Assembly and structural analysis of a covalently closed nano-scale DNA cage.

    Andersen, F. F., Knudsen, B., Oliveira, C. L. P., Frøhlich, R. F., Krüger, D., Bungert, J., Agbandje-McKenna, M., McKenna, R., Juul, S., Veigaard, C., Koch, J., Rubinstein, J. L., Guldbrandtsen, B., Hede, M. S., Karlsson, G., Andersen, A. H., Pedersen, J. S. & Knudsen, B. R., 2008, In: NUCLEIC ACIDS RES. 36, 4, p. 1113-1119 4.

    Research output: SCORING: Contribution to journal › SCORING: Journal article › Research › peer-review

  39. Distinct roles of XRCC4 and Ku80 in non-homologous end-joining of endonuclease- and ionizing radiation-induced DNA double-strand breaks.

    Schulte-Uentrop, L., El-Awady, R. A., Schliecker, L., Willers, H. & Dahm-Daphi, J., 2008, In: NUCLEIC ACIDS RES. 36, 8, p. 2561-2569 8.

    Research output: SCORING: Contribution to journal › SCORING: Journal article › Research › peer-review

  40. Hierarchy of nonhomologous end-joining, single-strand annealing and gene conversion at site-directed DNA double-strand breaks.

    Mansour, W., Schumacher, S., Rosskopf, R., Rhein, T., Schmidt-Petersen, F., Gatzemeier, F., Haag, F., Borgmann, K., Willers, H. & Dahm-Daphi, J., 2008, In: NUCLEIC ACIDS RES. 36, 12, p. 4088-4098 12.

    Research output: SCORING: Contribution to journal › SCORING: Journal article › Research › peer-review

  41. Step-wise formation of eukaryotic double-row polyribosomes and circular translation of polysomal mRNA.

    Kopeina, G. S., Afonina, Z. A., Brune, K., Shirokov, V. A., Vasiliev, V. D. & Spirin, A. S., 2008, In: NUCLEIC ACIDS RES. 36, 8, p. 2476-2488 8.

    Research output: SCORING: Contribution to journal › SCORING: Journal article › Research › peer-review

  42. 2007

  43. Multiple conserved regulatory elements with overlapping functions determine Sox10 expression in mouse embryogenesis.

    Werner, T., Hammer, A., Wahlbuhl, M., Bösl, M. & Wegner, M., 2007, In: NUCLEIC ACIDS RES. 35, 19, p. 6526-6538 19.

    Research output: SCORING: Contribution to journal › SCORING: Journal article › Research › peer-review

  44. Quantitative analysis of the binding affinity of poly(ADP-ribose) to specific binding proteins as a function of chain length.

    Fahrer, J., Kranaster, R., Altmeyer, M., Marx, A. & Bürkle, A., 2007, In: NUCLEIC ACIDS RES. 35, 21, p. 143 21.

    Research output: SCORING: Contribution to journal › SCORING: Journal article › Research › peer-review

  45. 2004

  46. Enhanced fidelity for rejoining radiation-induced DNA double-strand breaks in the G2 phase of Chinese hamster ovary cells

    Krüger, I., Rothkamm, K. & Löbrich, M., 2004, In: NUCLEIC ACIDS RES. 32, 9, p. 2677-84 8 p.

    Research output: SCORING: Contribution to journal › SCORING: Journal article › Research › peer-review

  47. 2003

  48. SYBR Green real-time telomeric repeat amplification protocol for the rapid quantification of telomerase activity

    Wege, H., Chui, M. S., Le, H. T., Tran, J. M. & Zern, M. A., 15.01.2003, In: NUCLEIC ACIDS RES. 31, 2, p. E3-3

    Research output: SCORING: Contribution to journal › SCORING: Journal article › Research › peer-review

  49. 2001

  50. Heat effects on DNA repair after ionising radiation: hyperthermia commonly increases the number of non-repaired double-strand breaks and structural rearrangements.

    El-Awady, R. A., Dikomey, E. & Dahm-Daphi, J., 2001, In: NUCLEIC ACIDS RES. 29, 9, p. 1960-1966 9.

    Research output: SCORING: Contribution to journal › SCORING: Journal article › Research › peer-review

  51. 1999

  52. Rapid and efficient cloning of proviral flanking fragments by kanamycin resistance gene complementation

    Fehse, B., Kühlcke, K., Langer, A., Ostertag, W. & Lother, H., 15.01.1999, In: NUCLEIC ACIDS RES. 27, 2, p. 706-7 2 p.

    Research output: SCORING: Contribution to journal › SCORING: Journal article › Research › peer-review

  53. 1996

  54. Gene structure and characterization of the murine homologue of the B cell-specific transcriptional coactivator OBF-1

    Schubart, D. B., Sauter, P., Massa, S., Friedl, E. M., Schwarzenbach, H. & Matthias, P., 15.05.1996, In: NUCLEIC ACIDS RES. 24, 10, p. 1913-20 8 p.

    Research output: SCORING: Contribution to journal › SCORING: Journal article › Research › peer-review

  55. 1995

  56. Excision of specific DNA-sequences from integrated retroviral vectors via site-specific recombination

    Bergemann, J., Kühlcke, K., Fehse, B., Ratz, I., Ostertag, W. & Lother, H., 11.11.1995, In: NUCLEIC ACIDS RES. 23, 21, p. 4451-6 6 p.

    Research output: SCORING: Contribution to journal › SCORING: Journal article › Research › peer-review

  57. Molecular cloning of LSIRF, a lymphoid-specific member of the interferon regulatory factor family that binds the interferon-stimulated response element (ISRE)

    Matsuyama, T., Grossman, A., Mittrücker, H. W., Siderovski, D. P., Kiefer, F., Kawakami, T., Richardson, C. D., Taniguchi, T., Yoshinaga, S. K. & Mak, T. W., 25.06.1995, In: NUCLEIC ACIDS RES. 23, 12, p. 2127-36 10 p.

    Research output: SCORING: Contribution to journal › SCORING: Journal article › Research › peer-review

  58. 1989

  59. An EcoRI polymorphism in the human von Willebrand factor (vWF) gene

    Ewerhardt, B., Ludwig, M., Schwaab, R., Schneppenheim, R. & Olek, K., 11.07.1989, In: NUCLEIC ACIDS RES. 17, 13, p. 5416

    Research output: SCORING: Contribution to journal › SCORING: Journal article › Research › peer-review

  60. 1985

  61. The TGGCA protein binds to the MMTV-LTR, the adenovirus origin of replication, and the BK virus enhancer

    Nowock, J., Borgmeyer, U., Püschel, A. W., Rupp, R. A. & Sippel, A. E., 25.03.1985, In: NUCLEIC ACIDS RES. 13, 6, p. 2045-61 17 p.

    Research output: SCORING: Contribution to journal › SCORING: Journal article › Research › peer-review

  62. 1984

  63. The TGGCA-binding protein: a eukaryotic nuclear protein recognizing a symmetrical sequence on double-stranded linear DNA

    Borgmeyer, U., Nowock, J. & Sippel, A. E., 25.05.1984, In: NUCLEIC ACIDS RES. 12, 10, p. 4295-311 17 p.

    Research output: SCORING: Contribution to journal › SCORING: Journal article › Research › peer-review