Publications of J. Söding

Hartmann, H.; Guthoehrlein, E. W.; Siebert, M.; Luehr, S.; Söding, J.: P-value-based regulatory motif discovery using positional weight matrices. Genome Research 23 (1), pp. 181 - 194 (2013)

Tischer, S.; Reineck, M.; Söding, J.; Münder, S.; Böttger, A.: Eph receptors and ephrin class B ligands are expressed at tissue boundaries in Hydra vulgaris. The International Journal of Develomental Biology 57, pp. 759 - 765 (2013)

Angermueller, C.; Biegert, A.; Söding, J.: Discriminative modelling of context-specific amino acid substitution probabilities. Bioinformatics 28 (24), pp. 3240 - 3247 (2012)

Close, P.; East, P.; Dirac-Svejstrup, A. B.; Hartmann, H.; Heron, M.; Maslen, S.; Chariot, A.; Söding, J.; Skehel, M.; Svejstrup, J. Q.: DBIRD complex integrates alternative mRNA splicing with RNA polymerase II transcript elongation. Nature 484 (7394), pp. 386 - 389 (2012)

Feller, C.; Prestel, M.; Hartmann, H.; Straub, T.; Söding, J.; Becker, P. B.: The MOF-containing NSL complex associates globally with housekeeping genes, but activates only a defined subset. Nucleic Acids Research 40 (4), pp. 1509 - 1522 (2012)

Luehr, S.; Hartmann, H.; Söding, J.: The XXmotif web server for eXhaustive, weight matriX-based motif discovery in nucleotide sequences. Nucleic Acids Research 40 (W1), pp. W104 - W109 (2012)

Remmert, M.; Biegert, A.; Hauser, A.; Söding, J.: HHblits: Lightning-fast iterative protein sequence searching by HMM-HMM alignment. Nature Methods 9 (2), pp. 173 - 175 (2012)

Seizl, M.; Hartmann, H.; Hoeg, F.; Kurth, F.; Martin, D. E.; Söding, J.; Cramer, P.: A conserved GA element in TATA-less RNA polymerase II promoters. PLoS One 6 (11), e27595 (2011)

Sievers, F.; Wilm, A.; Dineen, D.; Gibson, T. J.; Karplus, K.; Li, W.; Lopez, R.; McWilliam, H.; Remmert, M.; Söding, J. et al.; Thompson, J. D.; Higgins, D. G.: Fast, scalable generation of high-quality protein multiple sequence alignments using Clustal Omega. Molecular Systems Biology 7, 539 (2011)

Söding, J.; Remmert, M.: Protein sequence comparison and fold recognition: progress and good-practice benchmarking. Current Opinion in Structural Biology 21 (3), pp. 404 - 411 (2011)

Frauer, C.; Rottach, A.; Meilinger, D.; Bultmann, S.; Fellinger, K.; Hasenoeder, S.; Wang, M.; Qin, W.; Söding, J.; Spada, F. et al.; Leonhardt, H.: Different binding properties and function of CXXC zinc finger domains in Dnmt1 and Tet1. PLoS One 6 (2), e16627 (2011)

Lammens, K.; Bemeleit, D. J.; Moeckel, C.; Clausing, E.; Schele, A.; Hartung, S.; Schiller, C. B.; Lucas, M.; Angermueller, C.; Söding, J. et al.; Straesser, K.; Hopfner, K. P.: The Mre11:Rad50 structure shows an ATP-dependent molecular clamp in DNA double-strand break repair. Cell 145 (1), pp. 54 - 66 (2011)

Armache, J. P.; Jarasch, A.; Anger, A. M.; Villa, E.; Becker, T.; Bhushan, S.; Jossinet, F.; Habeck, M.; Dindar, G.; Franckenberg, S. et al.; Marquez, V.; Mielke, T.; Thomm, M.; Berninghausen, O.; Beatrix, B.; Söding, J.; Westhof, E.; Wilson, D. N.; Beckmann, R.: Cryo-EM structure and rRNA model of a translating eukaryotic 80S ribosome at 5.5-angstrom resolution. Proceedings of the National Academy of Sciences of the United States of America 107 (46), pp. 19748 - 19753 (2010)

Armache, J. P.; Jarasch, A.; Anger, A. M.; Villa, E.; Becker, T.; Bhushan, S.; Jossinet, F.; Habeck, M.; Dindar, G.; Franckenberg, S. et al.; Marquez, V.; Mielke, T.; Thomm, M.; Berninghausen, O.; Beatrix, B.; Söding, J.; Westhof, E.; Wilson, D. N.; Beckmann, R.: Localization of eukaryote-specific ribosomal proteins in a 5.5-angstrom cryo-EM map of the 80S eukaryotic ribosome. Proceedings of the National Academy of Sciences of the United States of America 107 (46), pp. 19754 - 19759 (2010)

Graebsch, A.; Roche, S.; Kostrewa, D.; Söding, J.; Niessing, D.: Of bits and bugs - On the use of bioinformatics and a bacterial crystal structure to solve a eukaryotic repeat-protein structure. PLoS One 5 (10), e13402 (2010)

Mayer, A.; Lidschreiber, M.; Siebert, M.; Leike, K.; Söding, J.; Cramer, P.: Uniform transitions of the general RNA polymerase II transcription complex. Nature Structural and Molecular Biology 17 (10), pp. 1272 - 1278 (2010)

Alva, V.; Remmert, M.; Biegert, A.; Lupas, A. N.; Söding, J.: A galaxy of folds. Protein Science 19 (1), pp. 124 - 130 (2010)

Lasi, M.; Pauly, B.; Schmidt, N.; Cikala, M.; Stiening, B.; Kaesbauer, T.; Zenner, G.; Popp, T.; Wagner, A.; Knapp, R. T. et al.; Huber, A. H.; Grunert, M.; Söding, J.; David, C. N.; Boettger, A.: The molecular cell death machinery in the simple cnidarian Hydra includes an expanded caspase family and pro- and anti-apoptotic Bcl-2 proteins. Cell Research 20 (7), pp. 812 - 825 (2010)

Remmert, M.; Biegert, A.; Linke, D.; Lupas, A. N.; Soeding, J.: Evolution of outer membrane beta-barrels from an ancestral beta beta hairpin. Molecular Biology and Evolution 27 (6), pp. 1348 - 1358 (2010)

Biegert, A.; Söding, J.: Sequence context-specific profiles for homology searching. Proceedings of the National Academy of Sciences of the United States of America 106 (10), pp. 3770 - 3775 (2009)