Max Planck Institute for Multidisciplinary Sciences

Publications

Journal Article (118)

1.

Journal Article

Basu, S.; Zhao, B.; Biró, B.; Faraggi, E.; Gsponer, J.; Hu, G.; Kloczkowski, A.; Malhis, N.; Mirdita, M.; Söding, J. et al.; Steinegger, M.; Wang, D.; Wang, K.; Xu, D.; Zhang, J.; Kurgan, L.: DescribePROT in 2023: more, higher-quality and experimental annotations and improved data download options. Nucleic Acids Research, gkad985 (2023)

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2.

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Stitzinger, S. H.; Sohrabi-Jahromi, S.; Söding, J.: Cooperativity boosts affinity and specificity of proteins with multiple RNA-binding domains. NAR: genomics and bioinformatics 5 (2), lqad057 (2023)

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3.

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van Kempen, M.; Kim, S. S.; Tumescheit, C.; Mirdita, M.; Lee, J.; Gilchrist, C. L. M.; Söding, J.; Steinegger, M.: Fast and accurate protein structure search with Foldseek. Nature Biotechnology (2023)

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4.

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Soh, W. T.; Zhang, J.; Hollenberg, M. D.; Vliagoftis, H.; Rothenberg, M. E.; Sokol, C. L.; Robinson, C.; Jacquet, A.: Protease allergens as initiators–regulators of allergic inflammation. Allergy: European Journal of Allergy and Clinical Immunology 78 (5), pp. 1148 - 1168 (2023)

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Raghavan, V.; Eichele, G.; Larink, O.; Levy Karin, E.; Söding, J.: RNA sequencing indicates widespread conservation of circadian clocks in marine zooplankton. NAR: genomics and bioinformatics 5 (1), lqad007 (2023)

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Mirdita, M.; Schutze, K.; Moriwaki, Y.; Heo, L.; Ovchinnikov, S.; Steinegger, M.: ColabFold: making protein folding accessible to all. Nature Methods 19 (6), pp. 679 - 682 (2022)

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7.

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Luebben, A. V.; Bender, D.; Becker, S.; Crowther, L. M.; Erven, I.; Hofmann, K.; Söding, J.; Klemp, H.; Bellotti, C.; Stäuble, A. et al.; Qiu, T.; Kathayat, R. S.; Dickinson, B. C.; Gärtner, J.; Sheldrick, G. M.; Krätzner, R.; Steinfeld, R.: Cln5 represents a new type of cysteine-basedS-depalmitoylase linked to neurodegeneration. Science Advances 8 (15), eabj8633 (2022)

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8.

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Qi, Z.; Jung, C.; Bandilla, P.; Ludwig, C.; Heron, M.; Sophie Kiesel, A.; Museridze, M.; Philippou‐Massier, J.; Nikolov, M.; Renna Max Schnepf, A. et al.; Unnerstall, U.; Ceolin, S.; Mühlig, B.; Gompel, N.; Söding, J.; Gaul, U.: Large-scale analysis of Drosophila core promoter function using synthetic promoters. Molecular Systems Biology 18 (2), e9816 (2022)

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9.

Journal Article

Zhang, R.; Mirdita, M.; Levy Karin, E.; Norroy, C.; Galiez, C.; Söding, J.: SpacePHARER: sensitive identification of phages from CRISPR spacers in prokaryotic hosts. Bioinformatics 37 (19), pp. 3364 - 3366 (2021)

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10.

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Mirdita, M.; Steinegger, M.; Breitwieser, F.; Söding, J.; Levy Karin, E.: Fast and sensitive taxonomic assignment to metagenomic contigs. Bioinformatics 37 (18), pp. 3029 - 3031 (2021)

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11.

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Sohrabi-Jahromi, S.; Söding, J.: Thermodynamic modeling reveals widespread multivalent binding by RNA-binding proteins. Bioinformatics 37, pp. i308 - i316 (2021)

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12.

Journal Article

Sohrabi-Jahromi, S.; Söding, J.: Thermodynamic modeling reveals widespread multivalent binding by RNA-binding proteins. Bioinformatics 37 (Suppl. 1), pp. i308 - i316 (2021)

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13.

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Aevarsson, A.; Kaczorowska, A.-K.; Adalsteinsson, B. T.; Ahlqvist, J.; Al-Karadaghi, S.; Altenbuchner, J.; Arsin, H.; Átlasson, Ú. Á.; Brandt, D.; Cichowicz-Cieślak, M. et al.; Cornish, K. A. S.; Courtin, J.; Dabrowski, S.; Dahle, H.; Djeffane, S.; Dorawa, S.; Dusaucy, J.; Enault, F.; Fedøy, A.-E.; Freitag-Pohl, S.; Fridjonsson, O. H.; Galiez, C.; Glomsaker, E.; Guérin, M.; Gundesø, S. E.; Gudmundsdóttir, E. E.; Gudmundsson, H.; Håkansson, M.; Henke, C.; Helleux, A.; Henriksen, J. R.; Hjörleifdóttir, S.; Hreggvidsson, G. O.; Jasilionis, A.; Jochheim, A.; Jónsdóttir, I.; Jónsdóttir, L. B.; Jurczak-Kurek, A.; Kaczorowski, T.; Kalinowski, J.; Kozlowski, L. P.; Krupovic, M.; Kwiatkowska-Semrau, K.; Lanes, O.; Lange, J.; Lebrat, J.; Linares-Pastén, J.; Liu, Y.; Lorentsen, S. A.; Lutterman, T.; Mas, T.; Merré, W.; Mirdita, M.; Morzywołek, A.; Ndela, E. O.; Karlsson, E. N.; Olgudóttir, E.; Pedersen, C.; Perler, F.; Pétursdóttir, S. K.; Plotka, M.; Pohl, E.; Prangishvili, D.; Ray, J. L.; Reynisson, B.; Róbertsdóttir, T.; Sandaa, R.-A.; Sczyrba, A.; Skírnisdóttir, S.; Söding, J.; Solstad, T.; Steen, I. H.; Stefánsson, S. K.; Steinegger, M.; Overå, K. S.; Striberny, B.; Svensson, A.; Szadkowska, M.; Tarrant, J.; Terzian, P.; Tourigny, M.; van den Bergh, T.; Vanhalst, J.; Vincent, J.; Vroling, B.; Walse, B.; Wang, L.; Watzlawick, H.; Welin, M.; Werbowy, O.; Wons, E.; Zhang, R.: Going to extremes: A metagenomic journey into the dark matter of life. FEMS Microbiology Letters 368 (12), fnab067 (2021)

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14.

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Banerjee, S.; Simonetti, F.L.; Detrois, K. E.; Kaphle, A.; Mitra, R.; Nagial, R.; Söding, J.: Tejaas: reverse regression increases power for detecting trans-eQTLs. Genome Biology 22, 142 (2021)

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15.

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Ge, W.; Meier, M.; Roth, C.; Söding, J.: Bayesian Markov models improve the prediction of binding motifs beyond first order. NAR: Genomics and Bioinformatics 3 (2), lquab026 (2021)

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16.

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Choi, J.; 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)

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17.

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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)

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18.

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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 (1), e108 (2020)

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19.

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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)

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20.

Journal Article

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)

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21.

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

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22.

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

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23.

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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), pp. 8961 - 8974 (2019)

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24.

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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), pp. 3517 - 3519 (2019)

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25.

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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), 473 (2019)

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26.

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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), pp. 2856 - 2858 (2019)

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27.

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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), 2909 (2019)

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28.

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

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29.

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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, e47040 (2019)

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30.

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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)

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31.

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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), e1006526 (2018)

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32.

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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), pp. 2237 - 2243 (2018)

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33.

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)

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34.

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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), pp. W215 - W220 (2018)

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35.

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

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36.

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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), pp. 1026 - 1028 (2017)

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37.

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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), pp. 3113 - 3114 (2017)

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38.

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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, e25637 (2017)

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39.

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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), pp. 38 - 49 (2017)

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40.

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Söding, J.: Big-data approaches to protein structure prediction. Science 355 (6322), pp. 248 - 249 (2017)

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41.

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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), pp. D170 - D176 (2017)

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42.

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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)

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43.

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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)

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44.

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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)

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45.

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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)

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46.

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Alva, V.; Söding, J.; Lupas, A. N.: A vocabulary of ancient peptides at the origin of folded proteins. eLife 4, e09410 (2015)

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47.

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Meier, A.; Söding, J.: Automatic prediction of protein 3D Structures by probabilistic multi-template homology modeling. PLoS Computational Biology 11 (10), e1004343 (2015)

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48.

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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)

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49.

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Meier, A.; Söding, J.: Context similarity scoring improves protein sequence alignments in the midnight zone. Bioinformatics 31 (5), pp. 674 - 681 (2015)

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50.

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Andreani, J.; Söding, J.: bbcontacts: Prediction of β-strand pairing from direct coupling patterns. Bioinformatics 31 (11), pp. 1729 - 1737 (2015)

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