Publications

ZORA Publication List

Publications

• 2026

  • Journal Article

    • Gaio, D., Tackmann, J., Perez-Molphe-Montoya, E., Näpflin, N., Patsch, D., Malfertheiner, L., Peluso, M. E., & von Mering, C. (2026). Enhanced semantic classification of microbiome sample origins using Large Language Models (LLMs) GigaScience, Epub ahead of print. https://doi.org/10.1093/gigascience/giag015

• 2025

  • Journal Article

    • Hernández-Plaza, A., Deng, Z., Robledo-Yagüe, F., Szklarczyk, D., von Mering, C., Bork, P., & Huerta-Cepas, J. (2025). eggNOG v7: phylogeny-based orthology predictions and functional annotations Nucleic Acids Research, gkaf1249, 1–7. https://doi.org/10.1093/nar/gkaf1249
    • Huang, Q., Szklarczyk, D., Oehninger, J. R. R., & von Mering, C. (2025). PaxDb v6.0: reprocessed, LLM-selected, curated protein abundance data across organisms Nucleic Acids Research, gkaf1066. https://doi.org/10.1093/nar/gkaf1066
    • Hu, D., Szklarczyk, D., von Mering, C., & Jensen, L. J. (2025). SPACE: STRING proteins as complementary embeddings Bioinformatics, 41, btaf496. https://doi.org/10.1093/bioinformatics/btaf496
    • Näpflin, N., Schubert, C., Malfertheiner, L., Hardt, W.-D., & von Mering, C. (2025). Gene-level analysis of core carbohydrate metabolism across the Enterobacteriaceae pan-genome Communications Biology, 8, 1241. https://doi.org/10.1038/s42003-025-08640-5
    • Causevic, S., Tackmann, J., Sentchilo, V., Malfertheiner, L., von Mering, C., & van der Meer, J. R. (2025). Habitat filtering more than microbiota origin controls microbiome transplant outcomes in soil The ISME Journal, 19, wraf162. https://doi.org/10.1093/ismejo/wraf162
    • Karakulak, T., Zajac, N., Bolck, H. A., Bratus-Neuenschwander, A., Zhang, Q., Qi, W., Basu, D., Oltra, T. C., Rehrauer, H., von Mering, C., Moch, H., & Kahraman, A. (2025). Heterogeneous and novel transcript expression in single cells of patient-derived clear cell renal cell carcinoma organoids Genome Research, 35, 698–711. https://doi.org/10.1101/gr.279345.124
    • Bağcı, C., Nuhamunada, M., Goyat, H., Ladanyi, C., Sehnal, L., Blin, K., Kautsar, S. A., Tagirdzhanov, A., Gurevich, A., Mantri, S., von Mering, C., Udwary, D., Medema, M. H., Weber, T., & Ziemert, N. (2025). BGC Atlas: a web resource for exploring the global chemical diversity encoded in bacterial genomes Nucleic Acids Research, 53, D618–D624. https://doi.org/10.1093/nar/gkae953
    • Szklarczyk, D., Nastou, K., Koutrouli, M., Kirsch, R., Mehryary, F., Hachilif, R., Hu, D., Peluso, M. E., Huang, Q., Fang, T., Doncheva, N. T., Pyysalo, S., Bork, P., Jensen, L. J., & von Mering, C. (2025). The STRING database in 2025: protein networks with directionality of regulation Nucleic Acids Research, 53, D730–D737. https://doi.org/10.1093/nar/gkae1113

• 2024

  • Journal Article

    • Kienbeck, K., Malfertheiner, L., Zelger-Paulus, S., Johannsen, S., von Mering, C., & Sigel, R. K. O. (2024). From Enigma to Revelation: Unravelling Biological Functions of Ubiquitous Small Ribozymes Chimia, 78, 200–204. https://doi.org/10.2533/chimia.2024.200
    • Fang, T., Szklarczyk, D., Hachilif, R., & von Mering, C. (2024). Enhancing coevolutionary signals in protein-protein interaction prediction through clade-wise alignment integration Scientific Reports, 14, 6009. https://doi.org/10.1038/s41598-024-55655-9
    • Cherrak, Y., Salazar, M. A., Näpflin, N., Malfertheiner, L., Herzog, M. K.-M., Schubert, C., von Mering, C., & Hardt, W.-D. (2024). Non-canonical start codons confer context-dependent advantages in carbohydrate utilization for commensal E. coli in the murine gut Nature Microbiology, 9, 2696–2709. https://doi.org/10.1038/s41564-024-01775-x
    • Dmitrijeva, M., Tackmann, J., Matias Rodrigues, J. F., Huerta-Cepas, J., Coelho, L. P., & von Mering, C. (2024). A global survey of prokaryotic genomes reveals the eco-evolutionary pressures driving horizontal gene transfer Nature Ecology and Evolution, 8, 986–998. https://doi.org/10.1038/s41559-024-02357-0

• 2023

  • Journal Article

    • Huang, Q., Szklarczyk, D., Wang, M., Simonovic, M., & von Mering, C. (2023). PaxDb 5.0: Curated Protein Quantification Data Suggests Adaptive Proteome Changes in Yeasts Molecular & Cellular Proteomics, 22, 100640. https://doi.org/10.1016/j.mcpro.2023.100640
    • Doncheva, N. T., Morris, J. H., Holze, H., Kirsch, R., Nastou, K. C., Cuesta-Astroz, Y., Rattei, T., Szklarczyk, D., von Mering, C., & Jensen, L. J. (2023). Cytoscape stringApp 2.0: Analysis and Visualization of Heterogeneous Biological Networks Journal of Proteome Research, 22, 637–646. https://doi.org/10.1021/acs.jproteome.2c00651
    • Laganenka, L., Lee, J.-W., Malfertheiner, L., Dieterich, C. L., Fuchs, L., Piel, J., von Mering, C., Sourjik, V., & Hardt, W.-D. (2023). Chemotaxis and autoinducer-2 signalling mediate colonization and contribute to co-existence of Escherichia coli strains in the murine gut Nature Microbiology, 8, 204–217. https://doi.org/10.1038/s41564-022-01286-7
    • Szklarczyk, D., Kirsch, R., Koutrouli, M., Nastou, K., Mehryary, F., Hachilif, R., Gable, A. L., Fang, T., Doncheva, N. T., Pyysalo, S., Bork, P., Jensen, L. J., & von Mering, C. (2023). The STRING database in 2023: protein-protein association networks and functional enrichment analyses for any sequenced genome of interest Nucleic Acids Research, 51, D638–D646. https://doi.org/10.1093/nar/gkac1000
    • Hernández-Plaza, A., Szklarczyk, D., Botas, J., Cantalapiedra, C. P., Giner-Lamia, J., Mende, D. R., Kirsch, R., Rattei, T., Letunic, I., Jensen, L. J., Bork, P., von Mering, C., & Huerta-Cepas, J. (2023). eggNOG 6.0: enabling comparative genomics across 12 535 organisms Nucleic Acids Research, 51, D389–D394. https://doi.org/10.1093/nar/gkac1022
    • Fullam, A., Letunic, I., Schmidt, T. S. B., Ducarmon, Q. R., Karcher, N., Khedkar, S., Kuhn, M., Larralde, M., Maistrenko, O. M., Malfertheiner, L., Milanese, A., Rodrigues, J. F. M., Sanchis-López, C., Schudoma, C., Szklarczyk, D., Sunagawa, S., Zeller, G., Huerta-Cepas, J., von Mering, C., … Mende, D. R. (2023). proGenomes3: approaching one million accurately and consistently annotated high-quality prokaryotic genomes Nucleic Acids Research, 51, D760–D766. https://doi.org/10.1093/nar/gkac1078
    • Karakulak, T., Szklarczyk, D., Saylan, C. C., Moch, H., von Mering, C., & Kahraman, A. (2023). CanIsoNet: a database to study the functional impact of isoform switching events in diseases Bioinformatics Advances, 3, vbad050. https://doi.org/10.1093/bioadv/vbad050

• 2022

  • Journal Article

    • Gable, A. L., Szklarczyk, D., Lyon, D., Matias Rodrigues, J. F., & von Mering, C. (2022). Systematic assessment of pathway databases, based on a diverse collection of user-submitted experiments Briefings in Bioinformatics, 23, bbac355. https://doi.org/10.1093/bib/bbac355
    • Kannan, A., Suomalainen, M., Volle, R., Bauer, M., Amsler, M., Trinh, H. V., Vavassori, S., Pachlopnik Schmid, J., Vilhena, G., Marin-Gonzalez, A., Pérez, R., Franceschini, A., von Mering, C., Hemmi, S., & Greber, U. F. (2022). Sequence-Specific Features of Short Double-Strand, Blunt-End RNAs Have RIG-I- and Type 1 Interferon-Dependent or -Independent Anti-Viral Effects Viruses, 14, 1407. https://doi.org/10.3390/v14071407
    • Čaušević, S., Tackmann, J., Sentchilo, V., von Mering, C., & van der Meer, J. R. (2022). Reproducible Propagation of Species-Rich Soil Bacterial Communities Suggests Robust Underlying Deterministic Principles of Community Formation MSystems, 7, e0016022. https://doi.org/10.1128/msystems.00160-22
    • Sikorski, J., Baumgartner, V., Birkhofer, K., Boeddinghaus, R. S., Bunk, B., Fischer, M., Fösel, B. U., Friedrich, M. W., Göker, M., Hölzel, N., Huang, S., Huber, K. J., Kandeler, E., Klaus, V. H., Kleinebecker, T., Marhan, S., von Mering, C., Oelmann, Y., Prati, D., … Overmann, J. (2022). The Evolution of Ecological Diversity in Acidobacteria Frontiers in Microbiology, 13, 715637. https://doi.org/10.3389/fmicb.2022.715637

• 2021

  • Journal Article

    • Huang, R., Soneson, C., Germain, P.-L., Schmidt, T. S. B., von Mering, C., & Robinson, M. D. (2021). treeclimbR pinpoints the data-dependent resolution of hierarchical hypotheses Genome Biology, 22, 157. https://doi.org/10.1186/s13059-021-02368-1
    • Dmitrijeva, M., Kahlert, C. R., Feigelman, R., Kleiner, R. L., Nolte, O., Albrich, W. C., Baty, F., & von Mering, C. (2021). Strain-Resolved Dynamics of the Lung Microbiome in Patients with Cystic Fibrosis MBio, 12, e02863-20. https://doi.org/10.1128/mBio.02863-20
    • Szklarczyk, D., Gable, A. L., Nastou, K. C., Lyon, D., Kirsch, R., Pyysalo, S., Doncheva, N. T., Legeay, M., Fang, T., Bork, P., Jensen, L. J., & von Mering, C. (2021). The STRING database in 2021: customizable protein-protein networks, and functional characterization of user-uploaded gene/measurement sets. Nucleic Acids Research, 49, D605–D612. https://doi.org/10.1093/nar/gkaa1074

• 2020

  • Journal Article

    • Kahraman, A., Karakulak, T., Szklarczyk, D., & von Mering, C. (2020). Pathogenic impact of transcript isoform switching in 1,209 cancer samples covering 27 cancer types using an isoform-specific interaction network Scientific Reports, 10, 14453. https://doi.org/10.1038/s41598-020-71221-5
    • Villaseñor, R., Pfaendler, R., Ambrosi, C., Butz, S., Giuliani, S., Bryan, E., Sheahan, T. W., Gable, A. L., Schmolka, N., Manzo, M., Wirz, J., Feller, C., von Mering, C., Aebersold, R., Voigt, P., & Baubec, T. (2020). Publisher Correction: ChromID identifies the protein interactome at chromatin marks Nature Biotechnology, 38, 757. https://doi.org/10.1038/s41587-020-0484-5
    • Villaseñor, R., Pfaendler, R., Ambrosi, C., Butz, S., Giuliani, S., Bryan, E., Sheahan, T. W., Gable, A. L., Schmolka, N., Manzo, M., Wirz, J., Feller, C., von Mering, C., Aebersold, R., Voigt, P., & Baubec, T. (2020). ChromID identifies the protein interactome at chromatin marks Nature Biotechnology, 38, 728–736. https://doi.org/10.1038/s41587-020-0434-2

• 2019

  • Journal Article

    • Heller, D., Szklarczyk, D., & von Mering, C. (2019). Tree reconciliation combined with subsampling improves large scale inference of orthologous group hierarchies BMC Bioinformatics, 20, 228. https://doi.org/10.1186/s12859-019-2828-z
    • Tackmann, J., Matias Rodrigues, J. F., & von Mering, C. (2019). Rapid Inference of Direct Interactions in Large-Scale Ecological Networks from Heterogeneous Microbial Sequencing Data Cell Systems, 9, 286-296.e8. https://doi.org/10.1016/j.cels.2019.08.002
    • Modic, M., Grosch, M., Rot, G., Schirge, S., Lepko, T., Yamazaki, T., Lee, F. C. Y., Rusha, E., Shaposhnikov, D., Palo, M., Merl-Pham, J., Cacchiarelli, D., Rogelj, B., Hauck, S. M., von Mering, C., Meissner, A., Lickert, H., Hirose, T., Ule, J., & Drukker, M. (2019). Cross-Regulation between TDP-43 and Paraspeckles Promotes Pluripotency-Differentiation Transition Molecular Cell, 74, 951-965.e13. https://doi.org/10.1016/j.molcel.2019.03.041
    • Lun, X.-K., Szklarczyk, D., Gábor, A., Dobberstein, N., Zanotelli, V. R. T., Saez-Rodriguez, J., von Mering, C., & Bodenmiller, B. (2019). Analysis of the Human Kinome and Phosphatome by Mass Cytometry Reveals Overexpression-Induced Effects on Cancer-Related Signaling Molecular Cell, 74, 1086-1102.e5. https://doi.org/10.1016/j.molcel.2019.04.021
    • Szklarczyk, D., Gable, A. L., Lyon, D., Junge, A., Wyder, S., Huerta-Cepas, J., Simonovic, M., Doncheva, N. T., Morris, J. H., Bork, P., Jensen, L. J., & von Mering, C. (2019). STRING v11: protein-protein association networks with increased coverage, supporting functional discovery in genome-wide experimental datasets Nucleic Acids Research, 47, D607–D613. https://doi.org/10.1093/nar/gky1131
    • Huerta-Cepas, J., Szklarczyk, D., Heller, D., Hernández-Plaza, A., Forslund, S. K., Cook, H., Mende, D. R., Letunic, I., Rattei, T., Jensen, L. J., von Mering, C., & Bork, P. (2019). eggNOG 5.0: a hierarchical, functionally and phylogenetically annotated orthology resource based on 5090 organisms and 2502 viruses Nucleic Acids Research, 47, D309–D314. https://doi.org/10.1093/nar/gky1085

• 2018

  • Journal Article

    • Tackmann, J., Arora, N., Schmidt, T. S. B., Rodrigues, J. F. M., & von Mering, C. (2018). Ecologically informed microbial biomarkers and accurate classification of mixed and unmixed samples in an extensive cross-study of human body sites Microbiome, 6, 192. https://doi.org/10.1186/s40168-018-0565-6
    • Daga, N., Eicher, S., Kannan, A., Casanova, A., Low, S. H., Kreibich, S., Andritschke, D., Emmenlauer, M., Jenkins, J. L., Hardt, W.-D., Greber, U. F., Dehio, C., & von Mering, C. (2018). Growth-restricting effects of siRNA transfections: a largely deterministic combination of off-target binding and hybridization-independent competition Nucleic Acids Research, 46, 9309–9320. https://doi.org/10.1093/nar/gky798
    • Cook, H. V., Doncheva, N. T., Szklarczyk, D., von Mering, C., & Jensen, L. J. (2018). Viruses.STRING: A Virus-Host Protein-Protein Interaction Database Viruses, 10, 519. https://doi.org/10.3390/v10100519
    • Oprea, T. I., Bologa, C. G., Brunak, S., et al, & von Mering, C. (2018). Unexplored therapeutic opportunities in the human genome Nature Reviews : Drug Discovery, 17, 317–332. https://doi.org/10.1038/nrd.2018.14

• 2017

  • Journal Article

    • Leonardi, I., Gerstgrasser, A., Schmidt, T. S. B., Nicholls, F., Tewes, B., Greinwald, R., von Mering, C., Rogler, G., & Frey-Wagner, I. (2017). Preventive Trichuris suis ova (TSO) treatment protects immunocompetent rabbits from DSS colitis but may be detrimental under conditions of immunosuppression Scientific Reports, 7, 16500. https://doi.org/10.1038/s41598-017-16287-4
    • Matias Rodrigues, J. F., Schmidt, T. S. B., Tackmann, J., & von Mering, C. (2017). MAPseq: highly efficient k-mer search with confidence estimates, for rRNA sequence analysis Bioinformatics, 33, 3808–3810. https://doi.org/10.1093/bioinformatics/btx517
    • Huerta-Cepas, J., Forslund, K., Coelho, L. P., Szklarczyk, D., Jensen, L. J., von Mering, C., & Bork, P. (2017). Fast Genome-Wide Functional Annotation through Orthology Assignment by eggNOG-Mapper Molecular Biology and Evolution, 34, 2115–2122. https://doi.org/10.1093/molbev/msx148
    • Rot, G., Wang, Z., Huppertz, I., Modic, M., Lenče, T., Hallegger, M., Haberman, N., Curk, T., von Mering, C., & Ule, J. (2017). High-Resolution RNA Maps Suggest Common Principles of Splicing and Polyadenylation Regulation by TDP-43 Cell Reports, 19, 1056–1067. https://doi.org/10.1016/j.celrep.2017.04.028
    • Leuenberger, P., Ganscha, S., Kahraman, A., Cappelletti, V., Boersema, P. J., von Mering, C., Claassen, M., & Picotti, P. (2017). Cell-wide analysis of protein thermal unfolding reveals determinants of thermostability Science, 355, 1–13. https://doi.org/10.1126/science.aai7825
    • Feigelman, R., Kahlert, C. R., Baty, F., Rassouli, F., Kleiner, R. L., Kohler, P., Brutsche, M. H., & von Mering, C. (2017). Sputum DNA sequencing in cystic fibrosis: non-invasive access to the lung microbiome and to pathogen details Microbiome, 5, 20. https://doi.org/10.1186/s40168-017-0234-1
    • Junge, A., Refsgaard, J. C., Garde, C., Pan, X., Santos, A., Alkan, F., Anthon, C., von Mering, C., Workman, C. T., Jensen, L. J., & Gorodkin, J. (2017). RAIN: RNA-protein Association and Interaction Networks Database, 2017, 1–9. https://doi.org/10.1093/database/baw167
    • Schmidt, T. S. B., Matias Rodrigues, J. F., & von Mering, C. (2017). A family of interaction-adjusted indices of community similarity The ISME Journal, 11, 791–807. https://doi.org/10.1038/ismej.2016.139

• 2016

  • Journal Article

    • Dolowschiak, T., Mueller, A. A., Pisan, L. J., Feigelman, R., Felmy, B., Sellin, M. E., Namineni, S., Nguyen, B. D., Wotzka, S. Y., Heikenwalder, M., von Mering, C., Mueller, C., & Hardt, W.-D. (2016). IFN-γ Hinders Recovery from Mucosal Inflammation during Antibiotic Therapy for Salmonella Gut Infection Cell Host & Microbe, 20, 238–249. https://doi.org/10.1016/j.chom.2016.06.008
    • Huerta-Cepas, J., Szklarczyk, D., Forslund, K., Cook, H., Heller, D., Walter, M. C., Rattei, T., Mende, D. R., Sunagawa, S., Kuhn, M., Jensen, L. J., von Mering, C., & Bork, P. (2016). eggNOG 4.5: a hierarchical orthology framework with improved functional annotations for eukaryotic, prokaryotic and viral sequences Nucleic Acids Research, 44, D286–D293. https://doi.org/10.1093/nar/gkv1248

Pagination