Publikationen

2.

Zeitschriftenartikel

Arangasamy, Y.; Morice, É.; Jochheim, A.; Lieser, B.; Söding, J.: Evaluation of metagenome binning: advances and challenges. Bioinformatics 26 (6), bbaf617 (2025)

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3.

Zeitschriftenartikel

Kraft, L.; Söding, J.; Steinegger, M.; Jochheim, A.; Wad Sackett, P.; Fernandez-Guerra, A.; Renaud, G.: CarpeDeam: a de novo metagenome assembler for heavily damaged ancient datasets. Genome Biology 26, 372 (2025)

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4.

Zeitschriftenartikel

Parvathy, J.; Yazhini, A.; Srinivasan, N.; Sowdhamini, R.: Understanding the Roles of Secondary Shell Hotspots in Protein–Protein Complexes. Proteins: Structure, Function, and Bioinformatics (2025)

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5.

Zeitschriftenartikel

Yazhini, A.; Söding, J.: Enhancing genome recovery across metagenomic samples using MAGmax. Bioinformatics 41 (10), btaf538 (2025)

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6.

Zeitschriftenartikel

Zhang, R.; Mirdita, M.; Söding, J.: De novo discovery of conserved gene clusters in microbial genomes with Spacedust. Nature Methods 22, S. 2065 - 2073 (2025)

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7.

Zeitschriftenartikel

Maddah, R.; Aghili, Z. S.; Ghanbari, F.; Hajialiasgary Najafabadi, A.; Asgary, S.: Integrative bioinformatics and deep learning to identify common genetic pathways in Crohn’s disease and ischemic cardiomyopathy. Journal of Genetic Engineering and Biotechnology 23 (3), 100529 (2025)

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8.

Zeitschriftenartikel

Riahi, T.; Shateri-Amiri, B.; Hajialiasgary Najafabadi, A.; Garazhian, S.; Radkhah, H.; Zooravar, D.; Mansouri, S.; Aghazadeh, R.; Bordbar, M.; Raiszadeh, S.: Lung Cancer Management: Revolutionizing Patient Outcomes Through Machine Learning and Artificial Intelligence. Cancer Reports 8 (7), e70240 (2025)

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9.

Zeitschriftenartikel

Zelenskaia, M.; Arangasamy, Y.; Mirdita, M.; Söding, J.; Raghavan, V.: TransAnnot—a fast transcriptome annotation pipeline. Bioinformatics Advances 4 (1), vbae152 (2024)

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10.

Zeitschriftenartikel

Jochheim, A.; Jochheim, F. A.; Kolodyazhnaya, A.; Morice, É.; Steinegger, M.; Söding, J.: Strain-resolved de-novo metagenomic assembly of viral genomes and microbial 16S rRNAs. Microbiome 12, 187 (2024)

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11.

Zeitschriftenartikel

Soheilifar, M.H.; Masoudi-Khoram, N.; Hassani, M.; Hajialiasgary Najafabadi, A.; Khojasteh, M.; Keshmiri Neghab, H.; Jalili, Z.: Angio-microRNAs in diabetic foot ulcer-: Mechanistic insights and clinical perspectives. Progress in Biophysics and Molecular Biology 192, S. 1 - 10 (2024)

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12.

Zeitschriftenartikel

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 42, S. 243 - 246 (2024)

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13.

Zeitschriftenartikel

Hajialiasgary Najafabadi, A.; Soheilifar, M. H.; Masoudi-Khoram, N.: Exosomes in skin photoaging: biological functions and therapeutic opportunity. Cell Communication and Signaling 22, 32 (2024)

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14.

Zeitschriftenartikel

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 52 (D1), S. D426 - D433 (2024)

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15.

Zeitschriftenartikel

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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16.

Zeitschriftenartikel

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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17.

Zeitschriftenartikel

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

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18.

Zeitschriftenartikel

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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19.

Zeitschriftenartikel

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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20.

Zeitschriftenartikel

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), S. 3364 - 3366 (2021)

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21.

Zeitschriftenartikel

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

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22.

Zeitschriftenartikel

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

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23.

Zeitschriftenartikel

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

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24.

Zeitschriftenartikel

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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25.

Zeitschriftenartikel

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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26.

Zeitschriftenartikel

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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27.

Zeitschriftenartikel

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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28.

Zeitschriftenartikel

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), S. D298 - D308 (2021)

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29.

Zeitschriftenartikel

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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30.

Zeitschriftenartikel

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), S. 1066 (2020)

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31.

Zeitschriftenartikel

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), S. 890 - 902.e6 (2020)

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32.

Zeitschriftenartikel

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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33.

Zeitschriftenartikel

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

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34.

Zeitschriftenartikel

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)

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35.

Zeitschriftenartikel

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)

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36.

Zeitschriftenartikel

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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37.

Zeitschriftenartikel

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)

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38.

Zeitschriftenartikel

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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39.

Zeitschriftenartikel

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

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40.

Zeitschriftenartikel

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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41.

Zeitschriftenartikel

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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42.

Zeitschriftenartikel

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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43.

Zeitschriftenartikel

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)

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44.

Zeitschriftenartikel

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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45.

Zeitschriftenartikel

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)

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46.

Zeitschriftenartikel

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

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47.

Zeitschriftenartikel

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)

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ZIP

48.

Zeitschriftenartikel

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)

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49.

Zeitschriftenartikel

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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50.

Zeitschriftenartikel

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)

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