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Journal Article (97)

21.
Journal Article
Siebert, M.; Söding, J.: Bayesian Markov models consistently outperform PWMs at predicting motifs in nucleotide sequences. Nucleic Acids Research 44 (13), pp. 6055 - 6069 (2016)
22.
Journal Article
Alva, V.; Nam, S. Z.; Söding, J.; Lupas, A. N.: The MPI bioinformatics Toolkit as an integrative platform for advanced protein sequence and structure analysis. Nucleic Acids Research 44 (W1), pp. W410 - W415 (2016)
23.
Journal Article
Hauser, M.; Steinegger, M.; Söding, J.: MMseqs software suite for fast and deep clustering and searching of large protein sequence sets. Bioinformatics 32 (9), pp. 1323 - 1330 (2016)
24.
Journal Article
Stützer, A.; Liokatis, S.; Kiesel, A.; Schwarzer, D.; Sprangers, R.; Söding, J.; Selenko, P.; Fischle, W.: Modulations of DNA contacts by linker histones and post-translational modifications determine the mobility and modifiability of nucleosomal H3 tails. Molecular Cell 61 (2), pp. 247 - 259 (2016)
25.
Journal Article
Alva, V.; Söding, J.; Lupas, A. N.: A vocabulary of ancient peptides at the origin of folded proteins. eLife 4, e09410 (2015)
26.
Journal Article
Meier, A.; Söding, J.: Automatic prediction of protein 3D Structures by probabilistic multi-template homology modeling. PLoS Computational Biology 11 (10), e1004343 (2015)
27.
Journal Article
Mühlbacher, W.; Mayer, A.; Sun, M.; Remmert, M.; Cheung, A. C. M.; Niesser, J.; Söding, J.; Cramer, P.: Structure of Ctk3, a subunit of the RNA polymerase II CTD kinase complex, reveals a non-canonical CTD-interacting domain fold. Proteins: Structure, Function, and Bioinformatics 83 (10), pp. 1849 - 1858 (2015)
28.
Journal Article
Meier, A.; Söding, J.: Context similarity scoring improves protein sequence alignments in the midnight zone. Bioinformatics 31 (5), pp. 674 - 681 (2015)
29.
Journal Article
Andreani, J.; Söding, J.: bbcontacts: Prediction of β-strand pairing from direct coupling patterns. Bioinformatics 31 (11), pp. 1729 - 1737 (2015)
30.
Journal Article
Seemayer, S.; Gruber, M.; Söding, J.: CCMpred-fast and precise prediction of protein residue-residue contacts from correlated mutations. Bioinformatics 30 (21), pp. 3128 - 3130 (2014)
31.
Journal Article
Bäjen, C.; Torkler, P.; Gressel, S.; Essig, K.; Söding, J.; Cramer, P.: Transcriptome maps of mRNP biogenesis factors define pre-mRNA recognition. Molecular Cell 55 (5), pp. 745 - 757 (2014)
32.
Journal Article
Siebert, M.; Söding, J.: Universality of core promoter elements? Nature 511 (7510), pp. E11 - E12 (2014)
33.
Journal Article
Wickles, S.; Singharoy, A.; Andreani, J.; Seemayer, S.; Bischoff, L.; Berninghausen, O.; Söding, J.; Schulten, K.; van der Sluis, E. O.; Beckmann, R.: A structural model of the active ribosome-bound membrane protein insertase YidC. eLife 3, e03035 (2014)
34.
Journal Article
Saponaro, M.; Mitter, R.; Kantidakis, T.; Kelly, G. P.; Heron, M.; Williams, H.; Söding, J.; Stewart, A.; Svejstrup, J. Q.: RECQL5 controls transcript elongation and suppresses genome instability associated with transcription stress. Cell 157 (5), pp. 1037 - 1049 (2014)
35.
Journal Article
Runge, S.; Sparrer, K. M. J.; Lässig, C.; Hembach, K.; Baum, A.; Garcia-Sastre, A.; Söding, J.; Conzelmann, K. K.; Hopfner, K. P.: In vivo ligands of MDA5 and RIG-I in measles virus-infected cells. PLoS Pathogens 10 (4), e1004081 (2014)
36.
Journal Article
Söding, J.: In silico-Funktions- und Strukturvorhersagen bei Proteinen. BIOspektrum 20 (2), pp. 158 - 160 (2014)
37.
Journal Article
Meinel, D. M.; Burkert-Kautzsch, C.; Kieser, A.; O'Duibhir, E.; Siebert, M.; Mayer, A.; Cramer, P.; Söding, J.; Holstege, F. C.; Sträßer, K.: Recruitment of TREX to the transcription machinery by its direct binding to the phospho-CTD of RNA polymerase II. PLoS Genetics 9 (11), e1003914 (2013)
38.
Journal Article
Schulz, D.; Schwalb, B.; Kiesel, A.; Baejen, C.; Torkler, P.; Gagneur, J.; Söding, J.; Cramer, P.: Transcriptome surveillance by selective termination of noncoding RNA synthesis. Cell 155 (5), pp. 1075 - 1087 (2013)
39.
Journal Article
Hauser, M.; Mayer, C. E.; Söding, J.: kClust: Fast and sensitive clustering of large protein sequence databases. BMC Bioinformatics 14, 248 (2013)
40.
Journal Article
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)
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