Publications

Selected Publications

    182.   Saunders, G., Baudis, M., Becker, R., Beltran, S., Béroud, C., Birney, E., Brooksbank, C., Brunak, S., Van den Bulcke, M., Drysdale, R., Capella-Gutierrez, S., Flicek, P., Florindi, F., Goodhand, P., Gut, I., Heringa, J., Holub, P., Hooyberghs, J., Juty, N., Keane, T. M., Korbel, J. O., Lappalainen, I., Leskosek, B., Matthijs, G., Mayrhofer, M. T., Metspalu, A., Navarro, A., Newhouse, S., Nyrönen, T., Page, A., Persson, B., Palotie, A., Parkinson, H., Rambla, J., Salgado, D., Steinfelder, E., Swertz, M. A., Valencia, A., Varma, S., Blomberg, N. & Scollen, S. (2019) Leveraging European infrastructures to access 1 million human genomes by 2022. Nature Reviews Genetics https://doi.org/10.1038/s41576-019-0156-9

    181.    Ison, J., Ienasescu, H., Chmura, P., Rydza, E., Ménager, H., Kalaš, M., Schwämmle, V., Grüning, B., Beard, N., Lopez, R., Duvaud, S., Stockinger, H., Persson, B., Vařeková, R.S., Raček, T., Vondrášek, J., Peterson, H., Salumets, A., Jonassen, I., Hooft, R., Nyrönen, T., Valencia, A., Capella, S., Gelpí, J., Zambelli, F., Savakis, B., Leskošek, B., Rapacki, K., Blanchet, C., Jimenez, R., Oliveira, A., Vriend, G., Collin, O., van Helden, J., Løngreen, P. & Brunak, S. (2019) The bio.tools registry of software tools and data resources for the life sciences. Genome Biol. 20, 164.

    180.    Das, S., Frisk, C., Eriksson, M.J., Walentinsson, A., Corbascio, M., Hage, C., Kumar, C., Asp, M., Lundeberg, J., Maret, E., Persson, H., Linde, C. & Persson, B. (2019) Transcriptomics of cardiac biopsies reveals differences in patients with or without diagnostic parameters for heart failure with preserved ejection fraction. Sci. Rep. 9, 3179.

    179.    Asp, M,, Salmén, F., Ståhl, P. L., Vickovic, S., Felldin, U., Löfling, M., Fernandez Navarro, J., Maskoola,  J., Eriksson, M. J., Persson, B., Corbascio, M., Persson, H., Linde, C. & Lundeberg, J. (2017) Spatial detection of fetal marker genes expressed at low level in adult human heart tissue. Sci. Rep. 7, 12941.

    177.    Östberg, L. J., Persson, B. & Höög, J.-O. (2016) Computational studies of human class V alcohol dehydrogenase – the odd sibling. BMC Biohemistry 17, 16.

    176.    Linde, C., Eriksson, M. J., Hage, C., Wallén, H., Persson, B., Corbascio, M., Lundeberg, J., Maret, E., Ugander, M. & Persson, H. (2016) Rationale and design of the PREFERS (Preserved and Reduced Ejection Fraction Epidemiological Regional Study) Stockholm Heart Failure study – an epidemiological Regional study in Stockholm county of 2.1 million inhabitants. Eur. J. Heart Fail. 18, 1287–1297.

    175.    Wilkinson, M., Dumontier, M., Aalbersberg, I. J., Appleton, G., Axton, M., Baak, A., Blomberg, N., Boiten, J.-W., Bonino da Silva Santos, L. O., Bourne, P., Bouwman, J., Brookes, A., Clark, T., Crosas, M., Dillo, I., Dumon, O., Edmunds, S., Evelo, C., Finkers, R., Gonzalez-Beltran, A., Gray, A., Groth, P., Goble, C., Grethe, J., Heringa, J., t Hoen, P., Hooft, R., Kuhn, T., Kok, R., Kok, J., Lusher, S., Martone, M., Mons, A., Packer, A., Persson, B., Rocca-Serra, P., Roos, M., van Schaik, R., Sansone, S., Schultes, E., Sengstag, T., Slater, T., Strawn, G., Swertz, M., Thompson, M., van der Lei, J., van Mulligen, E., Velterop, J., Waagmeester, A., Wittenburg, P., Wolstencroft, K., Zhao, J. & Mons, B. (2016) The FAIR Guiding Principles for scientific data management and stewardship. Nature Sci. Data 3, 160018.

    173.    Stödberg, T., McTague, A., Ruiz, A. J., Hirata, H., Zhen, J., Long, P., Farabella, I., Meyer, E., Kawahara, A., Vassallo, G., Stivaros, S. M., Bjursell, M. K., Stranneheim, H., Tigerschiöld, S., Persson, B., Bangash, I., Das, K., Hughes, D., Lesko, N., Lundeberg, J., Scott, R. C., Poduri, A., Scheffer, I. E., Smith, H., Gissen, P., Schorge, S., Reith, M. E., Topf, M., Kullmann, D. M., Harvey, R. J., Wedell, A. & Kurian, M. A. (2015) Mutations in SLC12A5 in epilepsy of infancy with migrating focal seizures. Nat. Commun. 6, 8038.

    171.    Östberg, L. J., Persson, B. & Höög, J.-O. (2015) The mammalian alcohol dehydrogenase genome shows several gene duplications and gene losses resulting in a large set of different enzymes including pseudoenzymes. Chem. Biol. Interact. 234, 80–84.

    165.    Östberg, L. J., Strömberg, P., Hedberg, J. J., Persson, B. & Höög, J.-O. (2013) Analysis of mammalian alcohol dehydrogenase 5 (ADH5): Characterisation of rat ADH5 with comparisons to the corresponding human variant. Chem. Biol. Interact. 202, 97–103.

    163.    Persson, B. & Kallberg, Y. (2013) Classification and nomenclature of the superfamily of short-chain dehydrogenases/reductases (SDRs). Chem. Biol. Interact. 202, 111–115.

    156.    Lysholm, F., Andersson, B. & Persson, B. (2011) An efficient simulator of 454 data using configurable statistical models. BMC Res. Notes 4, 449.    
    
    155.    Lysholm, F., Andersson, B. & Persson, B. (2011) FAAST: Flow-space Assisted Alignment Search Tool. BMC Bioinformatics 12, 293.

    149.    Hedlund, J., Jörnvall, H. & Persson, B. (2010) Subdivision of the MDR superfamily of medium-chain dehydrogenases/reductases through iterative hidden Markov model refinement. BMC Bioinformatics 11, 534.

    147.    Kallberg, Y., Oppermann, U. and Persson, B. (2010) Classification of the short-chain dehydrogenase/reductase (SDR) super-family using hidden Markov models. FEBS Journal 277, 2375–2386.

    142.    Hedlund, J., Johansson, J. & Persson, B. (2009) BRICHOS – A superfamily of multidomain proteins with diverse functions. BMC Res. Notes 2, 180.

    141.    Carlsson, J., Soussi, T. & Persson, B. (2009) Investigation and prediction of the severity of p53 mutants using parameters from structural calcuations. FEBS J. 276, 142–155.

    140.    Carlsson, B., Lindberg, A.M., Rodrigues-Díaz, J., Hedlund, K.-O., Persson, B. & Svensson, L. (2009) Quasispecies dynamics and molecular evolution of human novovirus capsid P region during chronic infection. J. Gen. Virol. 90, 432–441.
    
    139.    Persson, B., Kallberg, Y., Bray, J.E., Bruford, E., Dellaporta, S.L., Favia, A.D., Duarte, R.G., Jörnvall, H., Kavanagh, K.L., Kedishvili, N., Kisiela, M., Maser, E., Mindnich, R., Orchard, S., Penning, T.M., Thornton, J.M., Adamski, J. and Oppermann, U. (2009) The SDR (short-chain dehydrogenase/reductase and related enzymes) nomenclature initiative. Chem. Biol. Interact. 178, 94–98.

    130.    Bresell, A. & Persson, B. (2007) Characterization of oligopeptide patterns in large protein sets. BMC Genomics 8, 346.

    124.    Hedlund, J., Cantoni, R., Baltscheffsky, M., Baltscheffsky, H. & Persson, B. (2006) Analysis of ancient sequence motifs in the family of membrane-bound proton-pumping inorganic pyrophosphatases (H+-PPases). FEBS J. 273, 5183–5193.

    122.    Robins, T., Carlsson, J., Sunnerhagen, M., Wedell, A. & Persson, B. (2006) Structural model of human CYP21 based on mammalian CYP2C5 shows structural features to correlate with clinical severity of mutations causing congenital adrenal hyperplasia. Mol. Endocrin. 20, 2946–2964.

    121.    Kallberg, Y. & Persson, B. (2006) Prediction of coenzyme specificity in dehydrogenases/reductases. A hidden Markov model-based method and its application on complete genomes. FEBS J. 273, 1177–1184.