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von Mering group
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ZORA Publication List
Publications
2024
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
Kannan, Abhilash; Suomalainen, Maarit; Volle, Romain; Bauer, Michael; Amsler, Marco; Trinh, Hung V; Vavassori, Stefano; Pachlopnik Schmid, Jana; 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.
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
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
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
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.
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
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.
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.
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.
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.
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; 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.
2015
Journal Article
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.
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.
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