Publications

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2023
- Journal Article
  - Doncheva, Nadezhda T; Morris, John H; Holze, Henrietta; Kirsch, Rebecca; Nastou, Katerina C; Cuesta-Astroz, Yesid; Rattei, Thomas; Szklarczyk, Damian; von Mering, Christian; Jensen, Lars J (2023). Cytoscape stringApp 2.0: Analysis and Visualization of Heterogeneous Biological Networks. Journal of Proteome Research, 22(2):637-646.
  - Laganenka, Leanid; Lee, Jae-Woo; Malfertheiner, Lukas; Dieterich, Cora Lisbeth; Fuchs, Lea; Piel, Jörn; von Mering, Christian; Sourjik, Victor; Hardt, Wolf-Dietrich (2023). Chemotaxis and autoinducer-2 signalling mediate colonization and contribute to co-existence of Escherichia coli strains in the murine gut. Nature Microbiology, 8(2):204-217.
  - Szklarczyk, Damian; Kirsch, Rebecca; Koutrouli, Mikaela; Nastou, Katerina; Mehryary, Farrokh; Hachilif, Radja; Gable, Annika L; Fang, Tao; Doncheva, Nadezhda T; Pyysalo, Sampo; Bork, Peer; Jensen, Lars J; von Mering, Christian (2023). The STRING database in 2023: protein-protein association networks and functional enrichment analyses for any sequenced genome of interest. Nucleic Acids Research, 51(D1):D638-D646.
  - Hernández-Plaza, Ana; Szklarczyk, Damian; Botas, Jorge; Cantalapiedra, Carlos P; Giner-Lamia, Joaquín; Mende, Daniel R; Kirsch, Rebecca; Rattei, Thomas; Letunic, Ivica; Jensen, Lars J; Bork, Peer; von Mering, Christian; Huerta-Cepas, Jaime (2023). eggNOG 6.0: enabling comparative genomics across 12 535 organisms. Nucleic Acids Research, 51(D1):D389-D394.
  - Fullam, Anthony; Letunic, Ivica; Schmidt, Thomas S B; Ducarmon, Quinten R; Karcher, Nicolai; Khedkar, Supriya; Kuhn, Michael; Larralde, Martin; Maistrenko, Oleksandr M; Malfertheiner, Lukas; Milanese, Alessio; Rodrigues, Joao Frederico Matias; Sanchis-López, Claudia; Schudoma, Christian; Szklarczyk, Damian; Sunagawa, Shinichi; Zeller, Georg; Huerta-Cepas, Jaime; von Mering, Christian; Bork, Peer; Mende, Daniel R (2023). proGenomes3: approaching one million accurately and consistently annotated high-quality prokaryotic genomes. Nucleic Acids Research, 51(D1):D760-D766.
2022
- Journal Article
  - Gable, Annika L; Szklarczyk, Damian; Lyon, David; Matias Rodrigues, João F; von Mering, Christian (2022). Systematic assessment of pathway databases, based on a diverse collection of user-submitted experiments. Briefings in Bioinformatics, 23(5):1-13.
  - Kannan, Abhilash; Suomalainen, Maarit; Volle, Romain; Bauer, Michael; Amsler, Marco; Trinh, Hung V; Vavassori, Stefano; Schmid, Jana Pachlopnik; Vilhena, Guilherme; Marin-Gonzalez, Alberto; Pérez, Rubén; Franceschini, Andrea; von Mering, Christian; Hemmi, Silvio; Greber, Urs 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(7):1407.
  - Čaušević, Senka; Tackmann, Janko; Sentchilo, Vladimir; von Mering, Christian; van der Meer, Jan Roelof (2022). Reproducible Propagation of Species-Rich Soil Bacterial Communities Suggests Robust Underlying Deterministic Principles of Community Formation. mSystems, 7(2):e0016022.
  - Sikorski, Johannes; Baumgartner, Vanessa; Birkhofer, Klaus; Boeddinghaus, Runa S; Bunk, Boyke; Fischer, Markus; Fösel, Bärbel U; Friedrich, Michael W; Göker, Markus; Hölzel, Norbert; Huang, Sixing; Huber, Katharina J; Kandeler, Ellen; Klaus, Valentin H; Kleinebecker, Till; Marhan, Sven; von Mering, Christian; Oelmann, Yvonne; Prati, Daniel; Regan, Kathleen M; Richter-Heitmann, Tim; Rodrigues, João F Matias; Schmitt, Barbara; Schöning, Ingo; Schrumpf, Marion; Schurig, Elisabeth; Solly, Emily F; Wolters, Volkmar; Overmann, Jörg (2022). The Evolution of Ecological Diversity in Acidobacteria. Frontiers in Microbiology, 13:715637.
2021
- Journal Article
  - Huang, Ruizhu; Soneson, Charlotte; Germain, Pierre-Luc; Schmidt, Thomas S B; von Mering, Christian; Robinson, Mark D (2021). treeclimbR pinpoints the data-dependent resolution of hierarchical hypotheses. Genome Biology, 22:157.
  - Dmitrijeva, Marija; Kahlert, Christian R; Feigelman, Rounak; Kleiner, Rebekka L; Nolte, Oliver; Albrich, Werner C; Baty, Florent; von Mering, Christian (2021). Strain-Resolved Dynamics of the Lung Microbiome in Patients with Cystic Fibrosis. mBio, 12(2):e02863-20.
  - Szklarczyk, Damian; Gable, Annika L; Nastou, Katerina C; Lyon, David; Kirsch, Rebecca; Pyysalo, Sampo; Doncheva, Nadezhda T; Legeay, Marc; Fang, Tao; Bork, Peer; Jensen, Lars J; von Mering, Christian (2021). The STRING database in 2021: customizable protein-protein networks, and functional characterization of user-uploaded gene/measurement sets.. Nucleic Acids Research, 49(D1):D605-D612.
2020
- Journal Article
  - Kahraman, Abdullah; Karakulak, Tülay; Szklarczyk, Damian; von Mering, Christian (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.
  - Villaseñor, Rodrigo; Pfaendler, Ramon; Ambrosi, Christina; Butz, Stefan; Giuliani, Sara; Bryan, Elana; Sheahan, Thomas W; Gable, Annika L; Schmolka, Nina; Manzo, Massimiliano; Wirz, Joël; Feller, Christian; von Mering, Christian; Aebersold, Ruedi; Voigt, Philipp; Baubec, Tuncay (2020). Publisher Correction: ChromID identifies the protein interactome at chromatin marks. Nature Biotechnology, 38(6):757.
  - Villaseñor, Rodrigo; Pfaendler, Ramon; Ambrosi, Christina; Butz, Stefan; Giuliani, Sara; Bryan, Elana; Sheahan, Thomas W; Gable, Annika L; Schmolka, Nina; Manzo, Massimiliano; Wirz, Joël; Feller, Christian; von Mering, Christian; Aebersold, Ruedi; Voigt, Philipp; Baubec, Tuncay (2020). ChromID identifies the protein interactome at chromatin marks. Nature Biotechnology, 38(6):728-736.
2019
- Journal Article
  - Heller, Davide; Szklarczyk, Damian; von Mering, Christian (2019). Tree reconciliation combined with subsampling improves large scale inference of orthologous group hierarchies. BMC Bioinformatics, 20(1):228.
  - Tackmann, Janko; Matias Rodrigues, João Frederico; von Mering, Christian (2019). Rapid Inference of Direct Interactions in Large-Scale Ecological Networks from Heterogeneous Microbial Sequencing Data. Cell Systems, 9(3):286-296.e8.
  - Modic, Miha; Grosch, Markus; Rot, Gregor; Schirge, Silvia; Lepko, Tjasa; Yamazaki, Tomohiro; Lee, Flora C Y; Rusha, Ejona; Shaposhnikov, Dmitry; Palo, Michael; Merl-Pham, Juliane; Cacchiarelli, Davide; Rogelj, Boris; Hauck, Stefanie M; von Mering, Christian; Meissner, Alexander; Lickert, Heiko; Hirose, Tetsuro; Ule, Jernej; Drukker, Micha (2019). Cross-Regulation between TDP-43 and Paraspeckles Promotes Pluripotency-Differentiation Transition. Molecular Cell, 74(5):951-965.e13.
  - Lun, Xiao-Kang; Szklarczyk, Damian; Gábor, Attila; Dobberstein, Nadine; Zanotelli, Vito Riccardo Tomaso; Saez-Rodriguez, Julio; von Mering, Christian; Bodenmiller, Bernd (2019). Analysis of the Human Kinome and Phosphatome by Mass Cytometry Reveals Overexpression-Induced Effects on Cancer-Related Signaling. Molecular Cell, 74(5):1086-1102.e5.
  - Huerta-Cepas, Jaime; Szklarczyk, Damian; Heller, Davide; Hernández-Plaza, Ana; Forslund, Sofia K; Cook, Helen; Mende, Daniel R; Letunic, Ivica; Rattei, Thomas; Jensen, Lars J; von Mering, Christian; Bork, Peer (2019). eggNOG 5.0: a hierarchical, functionally and phylogenetically annotated orthology resource based on 5090 organisms and 2502 viruses. Nucleic Acids Research, 47(D1):D309-D314.
  - Szklarczyk, Damian; Gable, Annika L; Lyon, David; Junge, Alexander; Wyder, Stefan; Huerta-Cepas, Jaime; Simonovic, Milan; Doncheva, Nadezhda T; Morris, John H; Bork, Peer; Jensen, Lars J; von Mering, Christian (2019). STRING v11: protein-protein association networks with increased coverage, supporting functional discovery in genome-wide experimental datasets. Nucleic Acids Research, 47(D1):D607-D613.
2018
- Journal Article
  - Tackmann, Janko; Arora, Natasha; Schmidt, Thomas Sebastian Beedikt; Rodrigues, João Frederico Matias; von Mering, Christian (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.
  - Daga, Neha; Eicher, Simone; Kannan, Abhilash; Casanova, Alain; Low, Shyan H; Kreibich, Saskia; Andritschke, Daniel; Emmenlauer, Mario; Jenkins, Jeremy L; Hardt, Wolf-Dietrich; Greber, Urs F; Dehio, Christoph; von Mering, Christian (2018). Growth-restricting effects of siRNA transfections: a largely deterministic combination of off-target binding and hybridization-independent competition. Nucleic Acids Research, 46(18):9309-9320.
  - Cook, Helen Victoria; Doncheva, Nadezhda Tsankova; Szklarczyk, Damian; von Mering, Christian; Jensen, Lars Juhl (2018). Viruses.STRING: A Virus-Host Protein-Protein Interaction Database. Viruses, 10(10):519.
  - Oprea, Tudor I; Bologa, Cristian G; Brunak, Søren; et al; von Mering, Christian (2018). Unexplored therapeutic opportunities in the human genome. Nature Reviews. Drug Discovery, 17(5):317-332.
2017
- Journal Article
  - Leonardi, Irina; Gerstgrasser, Alexandra; Schmidt, Thomas S B; Nicholls, Flora; Tewes, Bernhard; Greinwald, Roland; von Mering, Christian; Rogler, Gerhard; Frey-Wagner, Isabelle (2017). Preventive Trichuris suis ova (TSO) treatment protects immunocompetent rabbits from DSS colitis but may be detrimental under conditions of immunosuppression. Scientific Reports, 7(1):16500.
  - Matias Rodrigues, João F; Schmidt, Thomas Sebastian Benedikt; Tackmann, Janko; von Mering, Christian (2017). MAPseq: highly efficient k-mer search with confidence estimates, for rRNA sequence analysis. Bioinformatics, 33(23):3808-3810.
  - Huerta-Cepas, Jaime; Forslund, Kristoffer; Coelho, Luis Pedro; Szklarczyk, Damian; Jensen, Lars Juhl; von Mering, Christian; Bork, Peer (2017). Fast Genome-Wide Functional Annotation through Orthology Assignment by eggNOG-Mapper. Molecular Biology and Evolution, 34(8):2115-2122.
  - Rot, Gregor; Wang, Zhen; Huppertz, Ina; Modic, Miha; Lenče, Tina; Hallegger, Martina; Haberman, Nejc; Curk, Tomaž; von Mering, Christian; Ule, Jernej (2017). High-Resolution RNA Maps Suggest Common Principles of Splicing and Polyadenylation Regulation by TDP-43. Cell Reports, 19(5):1056-1067.
  - Leuenberger, Pascal; Ganscha, Stefan; Kahraman, Abdullah; Cappelletti, Valentina; Boersema, Paul J; von Mering, Christian; Claassen, Manfred; Picotti, Paola (2017). Cell-wide analysis of protein thermal unfolding reveals determinants of thermostability. Science, 355(6327):1-13.
  - Feigelman, Rounak; Kahlert, Christian R; Baty, Florent; Rassouli, Frank; Kleiner, Rebekka L; Kohler, Philipp; Brutsche, Martin H; von Mering, Christian (2017). Sputum DNA sequencing in cystic fibrosis: non-invasive access to the lung microbiome and to pathogen details. Microbiome, 5(1):20.
  - Junge, Alexander; Refsgaard, Jan C; Garde, Christian; Pan, Xiaoyong; Santos, Alberto; Alkan, Ferhat; Anthon, Christian; von Mering, Christian; Workman, Christopher T; Jensen, Lars Juhl; Gorodkin, Jan (2017). RAIN: RNA-protein Association and Interaction Networks. Database, 2017:1-9.
  - Schmidt, Thomas Sebastian Benedikt; Matias Rodrigues, João Frederico; von Mering, Christian (2017). A family of interaction-adjusted indices of community similarity. The ISME journal, 11(3):791-807.
2016
- Journal Article
  - Dolowschiak, Tamas; Mueller, Anna Angelika; Pisan, Lynn Joanna; Feigelman, Rounak; Felmy, Boas; Sellin, Mikael Erik; Namineni, Sukumar; Nguyen, Bidong Dinh; Wotzka, Sandra Yvonne; Heikenwalder, Mathias; von Mering, Christian; Mueller, Christoph; Hardt, Wolf-Dietrich (2016). IFN-γ Hinders Recovery from Mucosal Inflammation during Antibiotic Therapy for Salmonella Gut Infection. Cell Host & Microbe, 20(2):238-249.
  - Huerta-Cepas, Jaime; Szklarczyk, Damian; Forslund, Kristoffer; Cook, Helen; Heller, Davide; Walter, Mathias C; Rattei, Thomas; Mende, Daniel R; Sunagawa, Shinichi; Kuhn, Michael; Jensen, Lars Juhl; von Mering, Christian; Bork, Peer (2016). eggNOG 4.5: a hierarchical orthology framework with improved functional annotations for eukaryotic, prokaryotic and viral sequences. Nucleic Acids Research, 44(D1):D286-D293.
  - Szklarczyk, Damian; Santos, Alberto; von Mering, Christian; Jensen, Lars Juhl; Bork, Peer; Kuhn, Michael (2016). STITCH 5: augmenting protein-chemical interaction networks with tissue and affinity data. Nucleic Acids Research, 44(D1):D380-D384.
  - Stockinger, Heinz; Palagi, Patricia M; Durinx, Christine; Baudis, Michael; von Mering, Christian; Szövenyi, Peter; et al (2016). The SIB Swiss Institute of Bioinformatics' resources: focus on curated databases. Nucleic Acids Research, 44(D1):D27-37.
  - Szklarczyk, Damian; Morris, John H; Cook, Helen; Kuhn, Michael; Wyder, Stefan; Simonovic, Milan; Santos, Alberto; Doncheva, Nadezhda T; Roth, Alexander; Bork, Peer; Jensen, Lars J; von Mering, Christian (2016). The STRING database in 2017: quality-controlled protein–protein association networks, made broadly accessible. Nucleic Acids Research, 45(D1):D362-D368.
  - Kamkina, Polina; Snoek, L Basten; Grossmann, Jonas; Volkers, Rita J M; Sterken, Mark G; Daube, Michael; Roschitzki, Bernd; Fortes, Claudia; Schlapbach, Ralph; Roth, Alexander; von Mering, Christian; Hengartner, Michael O; Schrimpf, Sabine P; Kammenga, Jan E (2016). Natural genetic variation differentially affects the proteome and transcriptome in Caenorhabditis elegans. Molecular & Cellular Proteomics, 15(5):1670-1680.
  - Franceschini, Andrea; Lin, Jianyi; von Mering, Christian; Jensen, Lars Juhl (2016). SVD-phy: improved prediction of protein functional associations through singular value decomposition of phylogenetic profiles. Bioinformatics, 32(7):1085-1087.
2015
- Journal Article
  - Wang, Mingcong; Herrmann, Christina J; Simonovic, Milan; Szklarczyk, Damian; von Mering, Christian (2015). Version 4.0 of PaxDb: Protein abundance data, integrated across model organisms, tissues, and cell-lines. Proteomics, 15(18):3163-3168.
  - Szklarczyk, Damian; Franceschini, Andrea; Wyder, Stefan; Forslund, Kristoffer; Heller, Davide; Huerta-Cepas, Jaime; Simonovic, Milan; Roth, Alexander; Santos, Alberto; Tsafou, Kalliopi P; Kuhn, Michael; Bork, Peer; Jensen, Lars J; von Mering, Christian (2015). STRING v10: protein-protein interaction networks, integrated over the tree of life. Nucleic Acids Research, 43(Database i):D447-52.
  - Schmich, Fabian; Szczurek, Ewa; Kreibich, Saskia; Dilling, Sabrina; Andritschke, Daniel; Casanova, Alain; Low, Shyan Huey; Eicher, Simone; Muntwiler, Simone; Emmenlauer, Mario; Rämö, Pauli; Conde-Alvarez, Raquel; von Mering, Christian; Hardt, Wolf-Dietrich; Dehio, Christoph; Beerenwinkel, Niko (2015). gespeR: a statistical model for deconvoluting off-target-confounded RNA interference screens. Genome Biology, 16:220.
  - Takeuchi, Yayoi; Chaffron, Samuel; Salcher, Michaela M; Shimizu-Inatsugi, Rie; Kobayashi, Masaki J; Diway, Bibian; von Mering, Christian; Pernthaler, Jakob; Shimizu, Kentaro K (2015). Bacterial diversity and composition in the fluid of pitcher plants of the genus Nepenthes. Systematic and Applied Microbiology, 38(5):330-339.
  - Schmidt, Thomas S B; Matias Rodrigues, João F; von Mering, Christian (2015). Limits to robustness and reproducibility in the demarcation of operational taxonomic units. Environmental Microbiology, 17(5):1689-1706.
2014
- Journal Article
  - Rämö, Pauli; Drewek, Anna; Arrieumerlou, Cécile; Beerenwinkel, Niko; Ben-Tekaya, Houchaima; Cardel, Bettina; Casanova, Alain; Conde-Alvarez, Raquel; Cossart, Pascale; Csúcs, Gábor; Eicher, Simone; Emmenlauer, Mario; Greber, Urs; Hardt, Wolf-Dietrich; Helenius, Ari; Kasper, Christoph; Kaufmann, Andreas; Kreibich, Saskia; Kühbacher, Andreas; Kunszt, Peter; Low, Shyan Huey; Mercer, Jason; Mudrak, Daria; Muntwiler, Simone; Pelkmans, Lucas; Pizarro-Cerdá, Javier; Podvinec, Michael; Pujadas, Eva; Rinn, Bernd; Rouilly, Vincent; Schmich, Fabian; Siebourg-Polster, Juliane; Snijder, Berend; Stebler, Michael; Studer, Gabriel; Szczurek, Ewa; Truttmann, Matthias; von Mering, Christian; Vonderheit, Andreas; Yakimovich, Artur; Bühlmann, Peter; Dehio, Christoph (2014). Simultaneous analysis of large-scale RNAi screens for pathogen entry. BMC Genomics, 15:1162.
  - Schulz, Juliane Caroline; Zampieri, Mattia; Wanka, Stefanie; von Mering, Christian; Sauer, Uwe (2014). Large-scale functional analysis of the roles of phosphorylation in yeast metabolic pathways. Science Signaling, 7(353):rs6.
  - Soste, Martin; Hrabakova, Rita; Wanka, Stefanie; Melnik, Andre; Boersema, Paul; Maiolica, Alessio; Wernas, Timon; Tognetti, Marco; von Mering, Christian; Picotti, Paola (2014). A sentinel protein assay for simultaneously quantifying cellular processes. Nature Methods, 11(10):1045-1048.
  - Warinner, Christina; Rodrigues, João F Matias; Vyas, Rounak; Trachsel, Christian; Shved, Natallia; Grossmann, Jonas; Radini, Anita; Hancock, Y; Tito, Raul Y; Fiddyment, Sarah; Speller, Camilla; Hendy, Jessica; Charlton, Sophy; Luder, Hans Ulrich; Salazar-García, Domingo C; Eppler, Elisabeth; Seiler, Roger; Hansen, Lars H; Castruita, José Alfredo Samaniego; Barkow-Oesterreicher, Simon; Teoh, Kai Yik; Kelstrup, Christian D; Olsen, Jesper V; Nanni, Paolo; Kawai, Toshihisa; Willerslev, Eske; von Mering, Christian; Lewis, Cecil M; Collins, Matthew J; Gilbert, M Thomas P; Rühli, Frank; Cappellini, Enrico (2014). Pathogens and host immunity in the ancient human oral cavity. Nature Genetics, 46(4):336-344.
  - Kuhn, Michael; Szklarczyk, Damian; Pletscher-Frankild, Sune; Blicher, Thomas H; von Mering, Christian; Jensen, Lars J; Bork, Peer (2014). STITCH 4: integration of protein–chemical interactions with user data. Nucleic Acids Research, 42(D1):D401-D407.

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