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Rodrigues, João F Matias; 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.

Endo, Tomoyuki; Shimizu, Kentaro K. Examination of cutting-edge research institutes. In: Nikkei Sangyou Shimbun (Japan Economy Industry Newspaper), 30 January 2017, p.010.

Izuno, Ayako; Kitayama, Kanehiro; Onoda, Yusuke; Tsujii, Yuki; Hatakeyama, Masaomi; Nagano, Atsushi J; Honjo, Mie N; Shimizu-Inatsugi, Rie; Kudoh, Hiroshi; Shimizu, Kentaro K; Isagi, Yuji (2017). The population genomic signature of environmental association and gene flow in an ecologically divergent tree species Metrosideros polymorpha (Myrtaceae). Molecular Ecology, 26(6):1515-1532.

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.

Bui, Linh T; Pandzic, Dzevida; Youngstrom, Christopher E; Wallace, Simon; Irish, Erin E; Szövényi, Peter; Cheng, Chi-Lien (2017). A fern AINTEGUMENTA gene mirrors BABY BOOM in promoting apogamy in Ceratopteris richardii. The Plant Journal, 90(1):122-132.

Hirao, Akira S; Onda, Yoshihiko; Shimizu-Inatsugi, Rie; Sese, Jun; Shimizu, Kentaro K; Kenta, Tanaka (2017). Cost-Effective Discovery of Nucleotide Polymorphisms in Populations of an Allopolyploid Species Using Pool-Seq. American Journal of Molecular Biology, 07(04):1031-1046.

Yousefi, Narjes; Hassel, Kristian; Flatberg, Kjell Ivar; Kemppainen, Petri; Trucchi, Emiliano; Shaw, A. Jonathan; Kyrkjeeide, Magni Olsen; Szövényi, Peter; Stenøien, Hans K (2017). Divergent evolution and niche differentiation within the common peatmoss Sphagnum magellanicum. American Journal of Botany, 104(7):1060-1072.

Briskine, Roman V; Paape, Timothy; Shimizu-Inatsugi, Rie; Nishiyama, Tomoaki; Akama, Satoru; Sese, Jun; Shimizu, Kentaro K (2017). Genome assembly and annotation ofArabidopsis halleri, a model for heavy metal hyperaccumulation and evolutionary ecology. Molecular Ecology Notes, 17(5):1025-1036.

Li, Fay-Wei; Villarreal, Juan Carlos; Szövényi, Peter (2017). Hornworts: an overlooked window into carbon-concentrating mechanisms. Trends in Plant Science, 22(4):275-277.

Widmer, Manuel; Auderset, Sandra; Nichols, Johanna; Widmer, Paul; Bickel, Balthasar (2017). NP recursion over time: evidence from indo-european. Language. Journal of the Linguistic Society of America, 93(4):799-826.

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.

Lischer, Heidi E L; Shimizu, Kentaro K (2017). Reference-guided de novo assembly approach improves genome reconstruction for related species. BMC Bioinformatics, 18(1):474.

Szövényi, Peter; Ullrich, Kristian K; Rensing, Stefan A; Lang, Daniel; van Gessel, Nico; Stenøien, Hans K; Conti, Elena; Reski, Ralf (2017). Selfing in haploid plants and efficacy of selection: codon usage bias in the model moss Physcomitrella patens. Genome Biology and Evolution, 9(6):1528-1546.


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.

Altenhoff, Adrian M; et al (2016). Standardized benchmarking in the quest for orthologs. Nature Methods, 13(5):425-430.

Izuno, Ayako; Hatakeyama, Masaomi; Nishiyama, Tomoaki; Tamaki, Ichiro; Shimizu-Inatsugi, Rie; Sasaki, Ryuta; Shimizu, Kentaro K; Isagi, Yuji (2016). Genome sequencing of Metrosideros polymorpha (Myrtaceae), a dominant species in various habitats in the Hawaiian Islands with remarkable phenotypic variations. Journal of Plant Research, 129(4):727-736.

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.

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.

Paape, Timothy; Hatakeyama, Masaomi; Shimizu-Inatsugi, Rie; Cereghetti, Teo; Onda, Yoshihiko; Kenta, Tanaka; Sese, Jun; Shimizu, Kentaro K (2016). Conserved but attenuated parental gene expression in allopolyploids: constitutive zinc hyperaccumulation in the allotetraploidArabidopsis kamchatica. Molecular Biology and Evolution:1-44.

Kellenberger, Roman T; Schlüter, Philipp M; Schiestl, Florian P (2016). Herbivore-induced DNA demethylation changes floral signalling and attractiveness to pollinators in Brassica rapa. PLoS ONE, 11(11):online.

Menardo, Fabrizio; Praz, Coraline R; Wyder, Stefan; Ben-David, Roi; Bourras, Salim; Matsumae, Hiromi; McNally, Kaitlin E; Parlange, Francis; Riba, Andrea; Roffler, Stefan; Schaefer, Luisa K; Shimizu, Kentaro K; Valenti, Luca; Zbinden, Helen; Wicker, Thomas; Keller, Beat (2016). Hybridization of powdery mildew strains gives rise to pathogens on novel agricultural crop species. Nature Genetics, 48(2):201-205.

Shimizu-Inatsugi, Rie; Terada, Aika; Hirose, Kyosuke; Kudoh, Hiroshi; Sese, Jun; Shimizu, Kentaro K (2016). Plant adaptive radiation mediated by polyploid plasticity in transcriptomes. Molecular Ecology:1-35.

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.

Gan, Xiangchao; Hay, Angela; et al; Briskine, Roman V; Shimizu, Kentaro K; Shimizu-Inatsugi, Rie (2016). The Cardamine hirsuta genome offers insight into the evolution of morphological diversity. Nature Plants, 2(11):16167.


Shimizu, Kentaro K; Tsuchimatsu, Takashi (2015). Evolution of selfing: recurrent patterns in molecular adaptation. Annual Review of Ecology, Evolution and Systematics, 46:593-622.

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.

Kawabata, Hiroto; Shimizu, Kentaro K. Visiting a laboratory: Prof. Kentaro Shimizu at the Institute of Evolutionary Biology and Environmental Studies, University of Zurich, series 1 to 7. In: National Geographic Web Japan, 4 March 2015, p.online.

Tedder, Andrew; Helling, Matthias; Pannell, John R; Shimizu-Inatsugi, Rie; Kawagoe, Tetsuhiro; van Campen, Julia; Sese, Jun; Shimizu, Kentaro K (2015). Female sterility associated with increased clonal propagation suggests a unique combination of androdioecy and asexual reproduction in populations of Cardamine amara (Brassicaceae). Annals of Botany, 115(5):763-776.

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.

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.

Stockenhuber, Reinhold; Zoller, Stefan; Shimizu-Inatsugi, Rie; Gugerli, Felix; Shimizu, Kentaro K; Widmer, Alex; Fischer, Martin C (2015). Efficient detection of novel nuclear markers for brassicaceae by transcriptome sequencing. PLoS ONE, 10(6):e0128181.

Tedder, Andrew; Carleial, Samuel; Gołębiewska, Martyna; Kappel, Christian; Shimizu, Kentaro K; Stift, Marc (2015). Evolution of the Selfing Syndrome in Arabis alpina (Brassicaceae). PLoS ONE, 10(6):e0126618.

Kubo, Ken-ichi; Paape, Timothy; Hatakeyama, Masaomi; Entani, Tetsuyuki; Takara, Akie; Kajihara, Kie; Tsukahara, Mai; Shimizu-Inatsugi, Rie; Shimizu, Kentaro K; Takayama, Seiji (2015). Gene duplication and genetic exchange drive the evolution of S-RNase-based self-incompatibility in Petunia. Nature Plants, 1:14005.

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.

Shimizu, Kentaro K; Akiyama, Reiko; Hatakeyama, Masaomi (2015). Science channel: addressing evolutionary questions using whole genome sequencing. : Science Channel, Japan Science and Technology Agency.

Shimizu-Inatsugi, Rie; Shimizu, Kentaro K (2015). Speciation after the 20th century: adaptation to new environments by genome duplications. In: Hasebe, Mitsuyasu. Solving evolutionary mysteries using genomics. Tokyo: Shujunsha, 48-57.

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.


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.

Shimizu, Kentaro K (2014). A Japanese PI in Switzerland. HFSP Matters, 4:8-9.

Shimizu, Kentaro K (2014). Network merging analysis of duplicate genome function in recently hybridized species. In: Awardees of Human Frontier Science Program. Tokyo: s.n., 26-27.

Trachana, Kalliopi; Forslund, Kristoffer; Larsson, Tomas; Powell, Sean; Doerks, Tobias; von Mering, Christian; Bork, Peer (2014). A phylogeny-based benchmarking test for orthology inference reveals the limitations of function-based validation. PLoS ONE, 9(11):e111122.

Schmidt, Thomas S B; Matias Rodrigues, João F; von Mering, Christian (2014). Ecological consistency of SSU rRNA-based operational taxonomic units at a global scale. PLoS Computational Biology, 10(4):e1003594.

Stockinger, Heinz; Altenhoff, Adrian M; Arnold, Konstantin; Bairoch, Amos; Bastian, Frederic; Bergmann, Sven; Bougueleret, Lydie; Bucher, Philipp; Delorenzi, Mauro; Lane, Lydie; Le Mercier, Philippe; Lisacek, Frédérique; Michielin, Olivier; Palagi, Patricia M; Rougemont, Jacques; Schwede, Torsten; von Mering, Christian; van Nimwegen, Erik; Walther, Daniel; Xenarios, Ioannis; Zavolan, Mihaela; Zdobnov, Evgeny M; Zoete, Vincent; Appel, Ron D (2014). Fifteen years SIB Swiss Institute of Bioinformatics: life science databases, tools and support. Nucleic Acids Research, 42(Web Server):W436-W441.

Meier, Roger; Franceschini, Andrea; Horvath, Peter; Tetard, Marilou; Mancini, Roberta; von Mering, Christian; Helenius, Ari; Lozach, Pierre-Yves (2014). Genome-Wide Small Interfering RNA Screens Reveal VAMP3 as a Novel Host Factor Required for Uukuniemi Virus Late Penetration. Journal of Virology, 88(15):8565-8578.

Akama, Satoru; Shimizu-Inatsugi, Rie; Shimizu, Kentaro K; Sese, Jun (2014). Genome-wide quantification of homeolog expression ratio revealed nonstochastic gene regulation in synthetic allopolyploid Arabidopsis. Nucleic Acids Research, 42(6):e46.

Matias Rodrigues, João F; von Mering, Christian (2014). HPC-CLUST: distributed hierarchical clustering for large sets of nucleotide sequences. Bioinformatics, 30(2):287-288.

Zozomová-Lihova, Judita; Krak, Karol; Mandakova, Terezie; Shimizu, Kentaro K; Spaniel, Staniskav; Vit, Petr; Lysak, Martin A (2014). Multiple hybridization events in Cardamine (Brassicaceae) during the last 150 years: revisiting a textbook example of neoallopolyploidy. Annals of Botany, 113(5):817-830.

Shimizu-Inatsugi, Rie; Shimizu, Kentaro K (2014). Speciation after the 20th century: adaptation to new environments by genome duplications. Cell Technology, 33(8):878-883.

Franceschini, Andrea; Meier, Roger; Casanova, Alain; Kreibich, Saskia; Daga, Neha; Andritschke, Daniel; Dilling, Sabrina; Rämö, Pauli; Emmenlauer, Mario; Kaufmann, Andreas; Conde-Álvarez, Raquel; Low, Shyan Huey; Pelkmans, Lucas; Helenius, Ari; Hardt, Wolf-Dietrich; Dehio, Christoph; von Mering, Christian (2014). Specific inhibition of diverse pathogens in human cells by synthetic microRNA-like oligonucleotides inferred from RNAi screens. Proceedings of the National Academy of Sciences of the United States of America, 111(12):4548-4553.

Powell, Sean; Forslund, Kristoffer; Szklarczyk, Damian; Trachana, Kalliopi; Roth, Alexander; Huerta-Cepas, Jaime; Gabaldón, Toni; Rattei, Thomas; Creevey, Chris; Kuhn, Michael; Jensen, Lars J; von Mering, Christian; Bork, Peer (2014). eggNOG v4.0: nested orthology inference across 3686 organisms. Nucleic Acids Research, 42(1):D231-D239.


Ogura, Atsushi; Yoshida, Masa-aki; Moritaki, Takeya; Sese, Jun; Shimizu, Kentaro K; Sousounis, Konstantinos; Tsonis, Panagiotis A (2013). Loss of the six3/6 controlling pathways might have resulted in pinhole-eye evolution in Nautilus. Scientific Reports, 3:1432.

Shimizu, Kentaro K (2013). Pollen, Pollen tube, Selfing, Pistil, Ovule, Endosperm, Embryo sac, Sporangium, Stamen. In: Iwasa, Yoh; Kuratani, Shigeru; Saitou, Naruya; Tsukaya, Hirokazu. Iwanami Biology Dictionary, 5th Edition. Tokyo: Iwanami, nn-nn.

Tsuchimatsu, Takashi; Shimizu, Kentaro K (2013). Effects of pollen availability and the mutation bias on the fixation of mutations disabling the male specificity of self-incompatibility. Journal of Evolutionary Biology, 26(10):2221-2232.

Tsuchimatsu, Takashi; Shimizu, Kentaro K (2013). Evolutionary Ecology of self-incompatibility: studying natural selection on plant self-recognition systems. Iden : the Review of Biological Sciences, 67:244-251.

Franceschini, Andrea; Szklarczyk, Damian; Frankild, Sune; Kuhn, Michael; Simonovic, Milan; Roth, Alexander; Lin, Jianyi; Minguez, Pablo; Bork, Peer; von Mering, Christian; Jensen, Lars J (2013). STRING v9.1: protein-protein interaction networks, with increased coverage and integration. Nucleic Acids Research, 41(D 1):D808-D815.

Mandákova, Terezie; Kovarík, Ales; Zozomová-Lihova, Judita; Shimizu-Inatsugi, Rie; Shimizu, Kentaro K; Mummenhoff, Klaus; Marhold, Karol; Lysak, Martin A (2013). The more the merrier: Recent hybridization and polyploidy in Cardamine. Plant Cell, 25(9):3280-3295.

This list was generated on Sun Apr 22 00:58:04 2018 CEST.