Publications

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

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)

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)

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)

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)

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)

Callegher, G.; Kneib, T.; Söding, J.; Wiemann, P.: Stochastic Variational Inference for Structured Additive Distributional Regression. arXiv (2024)

Su, H.; Zhang, R.; Söding, J.: UniOP: a universal operon prediction for high-throughput prokaryotic (meta-)genomic data using intergenic distance. bioRxiv (2024)

Zhang, R.; Mirdita, M.; Söding, J.: De novo discovery of conserved gene clusters in microbial genomes with Spacedust. bioRxiv (2024)

Kraft, L.; Söding, J.; Steinegger, M.; Jochheim, A.; Sackett, P. W.; Fernandez-Guerra, A.; Renaud, G.: CarpeDeam: A De Novo Metagenome Assembler for Heavily Damaged Ancient Datasets. bioRxiv (2024)