Publications of J. Söding

Journal Article (106)

21.
Journal Article
Zimmermann, L.; Stephens, A.; Nam, S. Z.; Rau, D.; Kübler , J.; Lozajic, M.; Gabler, F.; Söding, J.; Lupas, A. N.; Alva, V.: A completely reimplemented MPI Bioinformatics Toolkit with a new HHpred server at its core. Journal of Molecular Biology 430 (15), pp. 2237 - 2243 (2018)
22.
Journal Article
Keasar, C.; McGuffin, L. J.; Wallner, B.; Chopra, G.; Adhikari, B.; Bhattacharya, D.; Blake, L.; Bortot, L. O.; Cao, R.; Dhanasekaran, B. K. et al.; Dimas, I.; Faccioli, R. A.; Faraggi, E.; Ganzynkowicz, R.; Ghosh, S.; Ghosh, S.; Giełdoń, A.; Golon, L.; He, Y.; Heo, L.; Hou, J.; Khan, M.; Khatib, F.; Khoury, G. A.; Kieslich, C.; Kim, D. E.; Krupa, P.; Lee, G. R.; Li, H.; Li, J.; Lipska, A.; Liwo, A.; Maghrabi, A. H. A.; Mirdita, M.; Mirzaei, S.; Mozolewska, M. A.; Onel, M.; Ovchinnikov, S.; Shah, A.; Shah, U.; Sidi, T.; Sieradzan, A. K.; Ślusarz, M.; Ślusarz, R.; Smadbeck, J.; Tamamis, P.; Trieber, N.; Wirecki, T.; Yin, Y.; Zhang, Y.; Bacardit, J.; Baranowski, M.; Chapman, N.; Cooper, S.; Defelicibus, A.; Flatten, J.; Koepnick, B.; Popović, Z.; Zaborowski, B.; Baker, D.; Cheng, J.; Czaplewski, C.; Delbem, A. C. B.; Floudas, C.; Kloczkowski, A.; Ołdziej, S.; Levitt, M.; Scheraga, H.; Seok, C.; Söding, J.; Vishveshwara, S.; Xu, D.; Crivelli, S. N.: An analysis and evaluation of the WeFold collaborative for protein structure prediction and its pipelines in CASP11 and CASP12. Scientific Reports 8, 9938 (2018)
23.
Journal Article
Kiesel, A.; Roth, C.; Ge, W.; Weß, M.; Meier, M.; Söding, J.: The BaMM web server for de-novo motif discovery and regulatory sequence analysis. Nucleic Acids Research 46 (W1), pp. W215 - W220 (2018)
24.
Journal Article
Steinegger, M.; Söding, J.: Clustering huge protein sequence sets in linear time. Nature Communications 9, 2542 (2018)
25.
Journal Article
Steinegger, M.; Söding, J.: MMseqs2 enables sensitive protein sequence searching for the analysis of massive data sets. Nature Biotechnology 35 (11), pp. 1026 - 1028 (2017)
26.
Journal Article
Galiez, C.; Siebert, M.; Enault, F.; Vincent, J.; Söding, J.: WIsH: Who is the host? Predicting prokaryotic hosts from metagenomic phage contigs. Bioinformatics 33 (19), pp. 3113 - 3114 (2017)
27.
Journal Article
Bäjen, C.; Andreani, J.; Torkler, P.; Battaglia, S.; Schwalb, B.; Lidschreiber, M.; Maier, K. C.; Boltendahl, A.; Rus, P.; Esslinger, S. et al.; Söding, J.; Cramer, P.: Genome-wide analysis of RNA polymerase II termination at protein-coding genes. Molecular Cell 66 (1), pp. 38 - 49 (2017)
28.
Journal Article
Söding, J.: Big-data approaches to protein structure prediction. Science 355 (6322), pp. 248 - 249 (2017)
29.
Journal Article
Mirdita, M.; von den Driesch, L.; Galiez, C.; Martin, M. J.; Söding, J.; Steinegger, M.: Uniclust databases of clustered and deeply annotated protein sequences and alignments. Nucleic Acids Research 45 (D1), pp. D170 - D176 (2017)
30.
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)
31.
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)
32.
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)
33.
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)
34.
Journal Article
Alva, V.; Söding, J.; Lupas, A. N.: A vocabulary of ancient peptides at the origin of folded proteins. eLife 4, e09410 (2015)
35.
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)
36.
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)
37.
Journal Article
Meier, A.; Söding, J.: Context similarity scoring improves protein sequence alignments in the midnight zone. Bioinformatics 31 (5), pp. 674 - 681 (2015)
38.
Journal Article
Andreani, J.; Söding, J.: bbcontacts: Prediction of β-strand pairing from direct coupling patterns. Bioinformatics 31 (11), pp. 1729 - 1737 (2015)
39.
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)
40.
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)
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