Nucleic Acids Research, 1362-4962

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  1. 2020
  2. The human methyltransferase ZCCHC4 catalyses N6-methyladenosine modification of 28S ribosomal RNA

    Pinto, R., Vågbø, C. B., Magnus E Jakobsson, Kim, Y., Baltissen, M. P., O'Donohue, M-F., Guzmán, U. H., Małecki, J. M., Wu, J., Kirpekar, F., Olsen, J. V., Gleizes, P-E., Vermeulen, M., Leidel, S. A., Slupphaug, G. & Falnes, P. Ø., 2020 Jan 24, In : Nucleic Acids Research. 48, 2, p. 830-846 17 p.

    Research output: Contribution to journalArticle

  3. OGRDB: a reference database of inferred immune receptor genes

    Lees, W., Busse, C. E., Corcoran, M., Mats Ohlin, Scheepers, C., Matsen, F. A., Yaari, G., Watson, C. T., Collins, A., Shepherd, A. J. & AIRR Community, 2020, In : Nucleic Acids Research. 48, D1, p. D964-D970

    Research output: Contribution to journalArticle

  4. 2019
  5. Enzyme-free optical DNA mapping of the human genome using competitive binding

    Müller, V., Albertas Dvirnas, Andersson, J., Singh, V., Kk, S., Johansson, P., Ebenstein, Y., Tobias Ambjörnsson & Westerlund, F., 2019 Sep 5, In : Nucleic Acids Research. 47, 15, e89.

    Research output: Contribution to journalArticle

  6. 2018
  7. MutT homologue 1 (MTH1) catalyzes the hydrolysis of mutagenic O6-methyl-dGTP

    Jemth, A-S., Gustafsson, R., Bräutigam, L., Henriksson, L., Vallin, K. S. A., Sarno, A., Almlöf, I., Homan, E., Rasti, A., Warpman Berglund, U., Pål Stenmark & Helleday, T., 2018 Nov 16, In : Nucleic Acids Research. 46, 20, p. 10888-10904

    Research output: Contribution to journalArticle

  8. Mu transpososome activity-profiling yields hyperactive MuA variants for highly efficient genetic and genome engineering

    Rasila, T. S., Pulkkinen, E., Kiljunen, S., Haapa-Paananen, S., Pajunen, M. I., Salminen, A., Paulin, L., Mauno Vihinen, Rice, P. A. & Savilahti, H., 2018 May 18, In : Nucleic Acids Research. 46, 9, p. 4649-4661 13 p.

    Research output: Contribution to journalArticle

  9. The DNA damage response activates HPV16 late gene expression at the level of RNA processing

    Kersti Nilsson, Chengjun Wu, Naoko Kajitani, Yu, H., Tsimtsirakis, E., Gong, L., Winquist, E. B., Glahder, J., Lars Ekblad, Johan Wennerberg & Stefan Schwartz, 2018 Jan 1, In : Nucleic Acids Research. 46, 10, p. 5029-5049

    Research output: Contribution to journalArticle

  10. 2017
  11. hnRNP L controls HPV16 RNA polyadenylation and splicing in an Akt kinase-dependent manner

    Naoko Kajitani, Glahder, J., Wu, C., Yu, H., Kersti Nilsson & Stefan Schwartz, 2017 Sep 19, In : Nucleic Acids Research. 45, 16, p. 9654-9678 25 p.

    Research output: Contribution to journalArticle

  12. Methylation of human eukaryotic elongation factor alpha (eEF1A) by a member of a novel protein lysine methyltransferase family modulates mRNA translation

    Magnus E Jakobsson, Malecki, J., Nilges, B. S., Moen, A., Leidel, S. A. & Falnes, P. Ø., 2017 Aug 21, In : Nucleic Acids Research. 45, 14, p. 8239-8254 16 p.

    Research output: Contribution to journalArticle

  13. The novel lysine specific methyltransferase METTL21B affects mRNA translation through inducible and dynamic methylation of Lys-165 in human eukaryotic elongation factor 1 alpha (eEF1A)

    Malecki, J., Aileni, V. K., Ho, A. Y. Y., Schwarz, J., Moen, A., Sørensen, V., Nilges, B. S., Magnus E Jakobsson, Leidel, S. A. & Falnes, P. Ø., 2017 May 5, In : Nucleic Acids Research. 45, 8, p. 4370-4389 20 p.

    Research output: Contribution to journalArticle

  14. Expanded national database collection and data coverage in the FINDbase worldwide database for clinically relevant genomic variation allele frequencies

    Viennas, E., Komianou, A., Mizzi, C., Stojiljkovic, M., Mitropoulou, C., Muilu, J., Mauno Vihinen, Grypioti, P., Papadaki, S., Pavlidis, C., Zukic, B., Katsila, T., Van Der Spek, P. J., Pavlovic, S., Tzimas, G. & Patrinos, G. P., 2017 Jan 1, In : Nucleic Acids Research. 45, D1, p. D846-D853

    Research output: Contribution to journalArticle

  15. 2016
  16. A quantitative proteomics approach identifies ETV6 and IKZF1 as new regulators of an ERG-driven transcriptional network

    Unnikrishnan, A., Guan, Y. F., Huang, Y., Beck, D., Thoms, J. A. I., Peirs, S., Knezevic, K., Ma, S., de Walle, I. V., Ineke de Jong, Ali, Z., Zhong, L., Raftery, M. J., Taghon, T., Jonas Larsson, MacKenzie, K. L., Van Vlierberghe, P., Wong, J. W. H. & Pimanda, J. E., 2016 Dec 15, In : Nucleic Acids Research. 44, 22, p. 10644-10661

    Research output: Contribution to journalArticle

  17. 2015
  18. Bacteriophage strain typing by rapid single molecule analysis.

    Grunwald, A., Dahan, M., Giesbertz, A., Adam Nilsson, Nyberg, L. K., Weinhold, E., Tobias Ambjörnsson, Westerlund, F. & Ebenstein, Y., 2015, In : Nucleic Acids Research. 43, 18, p. e117

    Research output: Contribution to journalArticle

  19. Ionic switch controls the DNA state in phage λ.

    Li, D., Liu, T., Zuo, X., Li, T., Qiu, X. & Alex Evilevitch, 2015, In : Nucleic Acids Research. 43, 13, p. 6348-6358

    Research output: Contribution to journalArticle

  20. The Biobanking Analysis Resource Catalogue (BARCdb): a new research tool for the analysis of biobank samples.

    Galli, J., Oelrich, J., Taussig, M. J., Ulrika Andreasson, Eva Ortega-Paino & Landegren, U., 2015, In : Nucleic Acids Research. 43, D1, p. D1158-D1162

    Research output: Contribution to journalArticle

  21. 2014
  22. Quantification of DNA-associated proteins inside eukaryotic cells using single-molecule localization microscopy

    Etheridge, T. J., Boulineau, R. L., Herbert, A., Watson, A. T., Daigaku, Y., Tucker, J., George, S., Peter Jönsson, Palayret, M., Lando, D., Laue, E., Osborne, M. A., Klenerman, D., Lee, S. F. & Carr, A. M., 2014 Oct 29, In : Nucleic Acids Research. 42, 19, p. e146

    Research output: Contribution to journalArticle

  23. Competitive binding-based optical DNA mapping for fast identification of bacteria - multi-ligand transfer matrix theory and experimental applications on Escherichia coli.

    Adam Nilsson, Emilsson, G., Nyberg, L. K., Noble, C., Svensson Stadler, L., Fritzsche, J., Moore, E. R. B., Jonas Tegenfeldt, Tobias Ambjörnsson & Westerlund, F., 2014, In : Nucleic Acids Research. 42, 15, p. e118

    Research output: Contribution to journalArticle

  24. Major capsid reinforcement by a minor protein in herpesviruses and phage.

    Sae-Ueng, U., Liu, T., Catalano, C. E., Huffman, J. B., Homa, F. L. & Alex Evilevitch, 2014, In : Nucleic Acids Research. 42, 14, p. 9096-9107

    Research output: Contribution to journalArticle

  25. Nova1 is a master regulator of alternative splicing in pancreatic beta cells.

    Villate, O., Turatsinze, J-V., Mascali, L. G., Grieco, F. A., Nogueira, T. C., Cunha, D. A., Nardelli, T. R., Sammeth, M., Salunkhe, V. A., Jonathan Esguerra, Lena Eliasson, Marselli, L., Marchetti, P. & Eizirik, D. L., 2014, In : Nucleic Acids Research. 42, 18, p. 11818-11830

    Research output: Contribution to journalArticle

  26. REST mediates androgen receptor actions on gene repression and predicts early recurrence of prostate cancer.

    Svensson, C., Jens Ceder, Iglesias-Gato, D., Chuan, Y-C., Pang, S. T., Anders Bjartell, Martinez, R. M., Bott, L., Helczynski, L., David Ulmert, Wang, Y., Niu, Y., Collins, C. & Flores-Morales, A., 2014, In : Nucleic Acids Research. 42, 2, p. 999-1015

    Research output: Contribution to journalArticle

  27. 2013
  28. miR-23b regulates cytoskeletal remodeling, motility and metastasis by directly targeting multiple transcripts

    Pellegrino, L., Stebbing, J., Braga, V. M., Frampton, A. E., Jacob, J., Buluwela, L., Jiao, L. R., Periyasamy, M., Chris D Madsen, Caley, M. P., Ottaviani, S., Roca-Alonso, L., El-Bahrawy, M., Coombes, R. C., Krell, J. & Castellano, L., 2013 May 1, In : Nucleic Acids Research. 41, 10, p. 5400-12 13 p.

    Research output: Contribution to journalArticle

  29. DNA bending-induced phase transition of encapsidated genome in phage λ

    Lander, G. C., Johnson, J. E., Rau, D. C., Potter, C. S., Carragher, B. & Alex Evilevitch, 2013, In : Nucleic Acids Research. 41, 8, p. 4518

    Research output: Contribution to journalArticle

  30. HemaExplorer: a database of mRNA expression profiles in normal and malignant haematopoiesis.

    Bagger, F. O., Rapin, N., Theilgaard-Moench, K., Kaczkowski, B., Thorén, L., Jendholm, J., Winther, O. & Porse, B. T., 2013, In : Nucleic Acids Research. 41, D1, p. D1034-D1039

    Research output: Contribution to journalArticle

  31. PlantLoc: an accurate web server for predicting plant protein subcellular localization by substantiality motif.

    Tang, S., Li, T., Cong, P., Xiong, W., Wang, Z. & Jiangming Sun, 2013, In : Nucleic Acids Research. 41, W1, p. W441-W447

    Research output: Contribution to journalArticle

  32. Suppression of HPV-16 late L1 5'-splice site SD3632 by binding of hnRNP D proteins and hnRNP A2/B1 to upstream AUAGUA RNA motifs.

    Li, X., Johansson, C., Glahder, J., Mossberg, A. & Stefan Schwartz, 2013, In : Nucleic Acids Research. 41, 22, p. 10488-10508

    Research output: Contribution to journalArticle

  33. 2012
  34. HapZipper: sharing HapMap populations just got easier

    Chanda, P., Eran Elhaik & Bader, J. S., 2012 Nov 1, In : Nucleic Acids Research. 40, 20, 7 p., e159.

    Research output: Contribution to journalArticle

  35. Structure of the bifunctional methyltransferase YcbY (RlmKL) that adds the m7G2069 and m2G2445 modifications in Escherichia coli 23S rRNA

    Wang, K-T., Desmolaize, B., Jie Nan, Zhang, X-W., Li, L-F., Douthwaite, S. & Su, X-D., 2012 Jun, In : Nucleic Acids Research. 40, 11, p. 5138-48 11 p.

    Research output: Contribution to journalArticle

  36. Telomerase-dependent generation of 70-nt-long telomeric single-stranded 3' overhangs in yeast

    Fridholm, H., Astromskas, E. & Marita Cohn, 2012, In : Nucleic Acids Research.

    Research output: Contribution to journalArticle

  37. 2010
  38. Identifying compositionally homogeneous and nonhomogeneous domains within the human genome using a novel segmentation algorithm

    Eran Elhaik, Graur, D., Josić, K. & Landan, G., 2010 Aug, In : Nucleic Acids Research. 38, 15, 9 p., e158.

    Research output: Contribution to journalArticle

  39. 2009
  40. Kinetic and thermodynamic characterization of single-mismatch discrimination using single-molecule imaging

    Gunnarsson, A., Peter Jönsson, Zhdanov, V. P. & Höök, F., 2009 Aug, In : Nucleic Acids Research. 37, 14, p. e99

    Research output: Contribution to journalArticle

  41. SuperScent--a database of flavors and scents

    Dunkel, M., Schmidt, U., Struck, S., Berger, L., Gruening, B., Hossbach, J., Jaeger, I. S., Effmert, U., Piechulla, B., Eriksson, R., Knudsen, J. & Preissner, R., 2009, In : Nucleic Acids Research. 37, p. D291-D294

    Research output: Contribution to journalArticle

  42. Tissue-specific regulatory network extractor (TS-REX): a database and software resource for the tissue and cell type-specific investigation of transcription factor-gene networks.

    Colecchia, F., Kottwitz, D., Wagner, M., Pfenninger, C., Thiel, G., Tamm, I., Peterson, C. & Nuber, U., 2009, In : Nucleic Acids Research. 37, 11, p. e82

    Research output: Contribution to journalArticle

  43. 2007
  44. Conserved nucleotides in an RNA essential for hepatitis B virus replication show distinct mobility patterns.

    Petzold, K., Duchardt, E., Flodell, S., Larsson, G., Kidd-Ljunggren, K., Wijmenga, S. & Schleucher, J., 2007, In : Nucleic Acids Research. 35, 20, p. 6854-6861

    Research output: Contribution to journalArticle

  45. DNA binding mechanism revealed by high resolution crystal structure of Arabidopsis thaliana WRKY1 protein

    Duan, M-R., Jie Nan, Liang, Y-H., Mao, P., Lu, L., Li, L., Wei, C., Lai, L., Li, Y. & Su, X-D., 2007, In : Nucleic Acids Research. 35, 4, p. 1145-54 10 p.

    Research output: Contribution to journalArticle

  46. High-precision mapping of protein protein interfaces: an integrated genetic strategy combining en masse mutagenesis and DNA-level parallel analysis on a yeast two-hybrid platform.

    Pajunen, M., Turakainen, H., Poussu, E., Peränen, J., Mauno Vihinen & Savilahti, H., 2007, In : Nucleic Acids Research. 35, 16, p. e103

    Research output: Contribution to journalArticle

  47. 2006
  48. Solution structure of the apical stem-loop of the human hepatitis B virus encapsidation signal

    Flodell, S., Petersen, M., Girard, F., Zdunek, J., Kidd-Ljunggren, K., Schleucher, J. & Wijmenga, S., 2006, In : Nucleic Acids Research. 34, 16, p. 4449-4457

    Research output: Contribution to journalArticle

  49. 2005
  50. Expansion of the BioCyc collection of pathway/genome databases to 160 genomes

    Karp, P., Ouzounis, C., Moore-Kochlacs, C., Goldovsky, L., Kaipa, P., Dag Ahrén, Tsoka, S., Darzentas, N., Kunin, V. & López-Bigas, N., 2005, In : Nucleic Acids Research. 33, 19, p. 6083-6089

    Research output: Contribution to journalArticle

  51. Genome-wide selection of unique and valid oligonucleotides.

    Hyyrö, H., Juhola, M. & Mauno Vihinen, 2005, In : Nucleic Acids Research. 33, 13, p. e115

    Research output: Contribution to journalArticle

  52. Measuring genome conservation across taxa: divided strains and united kingdoms

    Kunin, V., Dag Ahrén, Goldovsky, L., Janssen, P. & Ouzounis, C. A., 2005, In : Nucleic Acids Research. 33, 2, p. 616-621

    Research output: Contribution to journalArticle

  53. 2004
  54. Human protein reference database as a discovery resource for proteomics

    Peri, S., Navarro, J. D., Kristiansen, T. Z., Amanchy, R., Surendranath, V., Muthusamy, B., Gandhi, T. K. B., Chandrika, K. N., Deshpande, N., Suresh, S., Rashmi, B. P., Shanker, K., Padma, N., Niranjan, V., Harsha, H. C., Talreja, N., Vrushabendra, B. M., Ramya, M. A., Yatish, A. J., Joy, M. & 13 others, Shivashankar, H. N., Kavitha, M. P., Menezes, M., Choudhury, D. R., Ghosh, N., Saravana, R., Chandran, S., Mohan, S. S., Jonnalagadda, C. K., Prasad, C. K., Kumar-Sinha, C., Deshpande, K. S. & Pandey, A., 2004 Jan 1, In : Nucleic Acids Research. 32, Database issue, p. D497-501

    Research output: Contribution to journalArticle

  55. ARAGORN, a program to detect tRNA genes and tmRNA genes in nucleotide sequences

    Laslett, D. & Björn Canbäck, 2004, In : Nucleic Acids Research. 32, 1, p. 11-16

    Research output: Contribution to journalArticle

  56. Two-dimensional conformation-dependent electrophoresis (2D-CDE) to separate DNA fragments containing unmatched bulge from complex DNA samples

    Gunnarsson, G. H., Thormar, H. G., Gudmundsson, B., Åkesson, L. & Jonsson, J. J., 2004, In : Nucleic Acids Research. 32, 2, p. 23

    Research output: Contribution to journalArticle

  57. 2002
  58. 23S rRNA assisted folding of cytoplasmic malate dehydrogenase is distinctly different from its self-folding

    Sanyal, S., Pal, S., Chaudhuri, S. & DasGupta, C., 2002, In : Nucleic Acids Research. 30, 11, p. 2390-2397

    Research output: Contribution to journalArticle

  59. IDR: the ImmunoDeficiency Resource.

    Väliaho, J., Pusa, M., Ylinen, T. & Mauno Vihinen, 2002, In : Nucleic Acids Research. 30, 1, p. 232-234

    Research output: Contribution to journalArticle

  60. The apical stem-loop of the hepatitis B virus encapsidation signal folds into a stable tri-loop with two underlying pyrimidine bulges

    Flodell, S., Schleucher, J., Cromsigt, J., Ippel, H., Kidd-Ljunggren, K. & Wijmenga, S., 2002, In : Nucleic Acids Research. 30, 21, p. 4803-4811

    Research output: Contribution to journalArticle

  61. 2001
  62. Detection of mitochondrial single nucleotide polymorphisms using a primer elongation reaction on oligonucleotide microarrays

    Erdogan, F., Kirchner, R., Mann, W., Ropers, H-H. & Nuber, U., 2001, In : Nucleic Acids Research. 29, 7, p. 36

    Research output: Contribution to journalArticle

  63. 2000
  64. KinMutBase, a database of human disease-causing protein kinase mutations

    Stenberg, KAE., Riikonen, PT. & Mauno Vihinen, 2000, In : Nucleic Acids Research. 28, 1, p. 369-371

    Research output: Contribution to journalArticle

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