Publications

Choi, J.; Lysakovskai, K.; Lysakovskaia, K.; Stik, G.; Demel, C.; Söding, J.; Tian, T. V.; Graf, T.; Cramer, P.: Evidence for additive and synergistic action of mammalian enhancers during cell fate determination. eLife 10, e65381 (2021)

Zhao, B.; Katuwawala, A.; Oldfield, C. J.; Dunker, A. K.; Faraggi, E.; Gsponer, J.; Kloczkowski, A.; Malhis, N.; Mirdita, M.; Obradovic, Z. et al.; Soding, J.; Steinegger, M.; Zhou, Y.; Kurgan, L.: DescribePROT: database of amino acid-level protein structure and function predictions. Nucleic Acids Research 49 (D1), pp. D298 - D308 (2021)

Gabler, F.; Nam, S.-Z.; Till, S.; Mirdita, M.; Steinegger, M.; Söding, J.; Lupas, A. N.; Alva, V.: Protein sequence analysis using the MPI Bioinformatics Toolkit. Current Protocols in Bioinformatics 72, e108 (2020)

Erijman, A.; Kozlowski, L.; Sohrabi-Jahromi, S.; Fishburn, J.; Warfield, L.; Schreiber, J.; Noble, W. S.; Söding, J.; Hahn, S.: A high-throughput screen for transcription activation domains reveals their sequence features and permits prediction by deep learning (Correction). Molecular Cell 79 (6), p. 1066 (2020)

Erijman, A.; Kozlowski, L. P.; Sohrabi-Jahromi, S.; Fishburn, J.; Warfield, L.; Schreiber, J.; Noble, W. S.; Söding, J.; Hahn, S.: A high-throughput screen for transcription activation domains reveals their sequence features and permits prediction by deep learning. Molecular Cell 78 (5), pp. 890 - 902.e6 (2020)

Levy Karin, E.; Mirdita, M.; Söding, J.: MetaEuk—sensitive, high-throughput gene discovery, and annotation for large-scale eukaryotic metagenomics. Microbiome 8, 48 (2020)

Söding, J.; Zwicker, D.; Sohrabi-Jahromi, S.; Böhning, M.; Kirschbaum, J.: Mechanisms for active regulation of biomolecular condensates. Trends in Cell Biology 30 (1), pp. 4 - 14 (2020)

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), pp. 8961 - 8974 (2019)

Papadopoulos, N.; Parra, R. G.; Söding, J.: PROSSTT: Probabilistic simulation of single-cell RNA-seq data for complex differentiation processes. Bioinformatics 35 (18), pp. 3517 - 3519 (2019)

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), 473 (2019)

Mirdita, M.; Steinegger, M.; Söding, J.: MMseqs2 desktop and local web server app for fast, interactive sequence searches. Bioinformatics 35 (16), pp. 2856 - 2858 (2019)

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), 2909 (2019)

Steinegger, M.; Mirdita, M.; Söding, J.: Protein-level assembly increases protein sequence recovery from metagenomic samples manyfold. Nature Methods 16, pp. 603 - 606 (2019)

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, e47040 (2019)

Banerjee, S.; Zeng, L.; Schunkert, H.; Söding, J.: Bayesian multiple logistic regression for case-control GWAS. PLoS Genetics 14 (12), e1007856. (2018)

Vorberg, S.; Seemayer, S.; Söding, J.: Synthetic protein alignments by CCMgen quantify noise in residue-residue contact prediction. PLoS Computational Biology 14 (11), e1006526 (2018)

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)

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)

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)

Steinegger, M.; Söding, J.: Clustering huge protein sequence sets in linear time. Nature Communications 9, 2542 (2018)