Publikationen

Zeitschriftenartikel (97)

  1. 1.
    MPG.PuRe
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    Söding, J.; Zwicker, D.; Sohrabi-Jahromi, S.; Böhning, M.; Kirschbaum, J.: Mechanisms for active regulation of biomolecular condensates. Trends in Cell Biology 30 (1), S. 4 - 14 (2020)
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    Parra, R. G.; Papadopoulos, N.; Ahumada-Arranz, L.; El Kholtei, J.; Mottelson, N.; Horokhovsky, Y.; Treutlein, B.; Söding, J.: Reconstructing complex lineage trees from scRNA-seq data using MERLoT. Nucleic Acids Research 47 (17), S. 8961 - 8974 (2019)
  3. 3.
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    Papadopoulos, N.; Parra, R. G.; Söding, J.: PROSSTT: Probabilistic simulation of single-cell RNA-seq data for complex differentiation processes. Bioinformatics 35 (18), S. 3517 - 3519 (2019)
  4. 4.
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    Steinegger, M.; Meier, M.; Mirdita, M.; Vöhringer, H.; Haunsberger, S. J.; Söding, J.: HH-suite3 for fast remote homology detection and deep protein annotation. BMC Bioinformatics 20 (1) (2019)
  5. 5.
    MPG.PuRe
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    Mirdita, M.; Steinegger, M.; Söding, J.: MMseqs2 desktop and local web server app for fast, interactive sequence searches. Bioinformatics 35 (16), S. 2856 - 2858 (2019)
  6. 6.
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    Ukmar-Godec, T.; Hutten, S.; Grieshop, M. P.; Rezaei-Ghaleh, N.; Cima-Omori, M. O.; Biernat, J.; Mandelkow, E.; Söding, J.; Dormann, D.; Zweckstetter, M.: Lysine/RNA-interactions drive and regulate biomolecular condensation. Nature Communications 10 (1) (2019)
  7. 7.
    MPG.PuRe
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    Steinegger, M.; Mirdita, M.; Söding, J.: Protein-level assembly increases protein sequence recovery from metagenomic samples manyfold. Nature Methods 16, S. 603 - 606 (2019)
  8. 8.
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    Sohrabi-Jahromi, S.; Hofmann, K. B.; Boltendahl, A.; Roth, C.; Gressel, S.; Baejen, C.; Söding, J.; Cramer, P.: Transcriptome maps of general eukaryotic RNA degradation factors. eLife 8 (2019)
  9. 9.
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    Banerjee, S.; Zeng, L.; Schunkert, H.; Söding, J.: Bayesian multiple logistic regression for case-control GWAS. PLoS Genetics 14 (12), e1007856. (2018)
  10. 10.
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    Vorberg, S.; Seemayer, S.; Söding, J.: Synthetic protein alignments by CCMgen quantify noise in residue-residue contact prediction. PLoS Computational Biology 14 (11) (2018)
  11. 11.
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    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), S. 2237 - 2243 (2018)
  12. 12.
    MPG.PuRe
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    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 (2018)
  13. 13.
    MPG.PuRe
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    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), S. W215 - W220 (2018)
  14. 14.
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    Steinegger, M.; Söding, J.: Clustering huge protein sequence sets in linear time. Nature Communications 9 (2018)
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    MPG.PuRe
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    Steinegger, M.; Söding, J.: MMseqs2 enables sensitive protein sequence searching for the analysis of massive data sets. Nature Biotechnology 35 (11), S. 1026 - 1028 (2017)
  16. 16.
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    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), S. 3113 - 3114 (2017)
  17. 17.
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    Battaglia, S.; Lidschreiber, M.; Bäjen, C.; Torkler, P.; Vos, S. M.; Cramer, P.: RNA-dependent chromatin association of transcription elongation factors and Pol II CTD kinases. eLife 6 (2017)
  18. 18.
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    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), S. 38 - 49 (2017)
  19. 19.
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    Söding, J.: Big-data approaches to protein structure prediction. Science 355 (6322), S. 248 - 249 (2017)
  20. 20.
    MPG.PuRe
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    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), S. D170 - D176 (2017)
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