Publications

2.

Journal Article

Lieser, B.; Belousov, G.; Söding, J.: Phylograd: fast column-specific calculation of substitution model gradients. BMC Bioinformatics 27, 20 (2026)

MPG.PuRe

3.

Journal Article

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

MPG.PuRe

4.

Journal Article

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)

MPG.PuRe

5.

Journal Article

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

MPG.PuRe

6.

Journal Article

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

MPG.PuRe

7.

Journal Article

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)

MPG.PuRe

8.

Journal Article

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)

MPG.PuRe

9.

Journal Article

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

MPG.PuRe

10.

Journal Article

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)

MPG.PuRe

11.

Journal Article

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, pp. 1 - 10 (2024)

MPG.PuRe

12.

Journal Article

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, pp. 243 - 246 (2024)

MPG.PuRe

13.

Journal Article

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)

MPG.PuRe

14.

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

MPG.PuRe

15.

Journal Article

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)

MPG.PuRe

16.

Journal Article

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)

MPG.PuRe

17.

Journal Article

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)

MPG.PuRe

18.

Journal Article

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)

MPG.PuRe

19.

Journal Article

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)

MPG.PuRe

20.

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)

MPG.PuRe

21.

Journal Article

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)

MPG.PuRe

22.

Journal Article

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

MPG.PuRe

23.

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)

MPG.PuRe

24.

Journal Article

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)

MPG.PuRe

25.

Journal Article

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)

MPG.PuRe

26.

Journal Article

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)

MPG.PuRe

27.

Journal Article

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)

MPG.PuRe

28.

Journal Article

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)

MPG.PuRe

29.

Journal Article

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)

MPG.PuRe

30.

Journal Article

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)

MPG.PuRe

31.

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)

MPG.PuRe

32.

Journal Article

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

MPG.PuRe

33.

Journal Article

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)

MPG.PuRe

34.

Journal Article

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)

MPG.PuRe

35.

Journal Article

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)

MPG.PuRe

36.

Journal Article

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)

MPG.PuRe

37.

Journal Article

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)

MPG.PuRe

38.

Journal Article

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)

MPG.PuRe

39.

Journal Article

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

MPG.PuRe

40.

Journal Article

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)

MPG.PuRe

41.

Journal Article

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

MPG.PuRe

42.

Journal Article

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)

MPG.PuRe

43.

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)

MPG.PuRe

44.

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)

MPG.PuRe

45.

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)

MPG.PuRe

46.

Journal Article

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

MPG.PuRe

47.

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)

MPG.PuRe

ZIP

48.

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)

MPG.PuRe

49.

Journal Article

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)

MPG.PuRe

50.

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)

MPG.PuRe