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2020

Tiberi, Simone; Robinson, Mark D (2020). BANDITS: Bayesian differential splicing accounting for sample-to-sample variability and mapping uncertainty. Genome Biology, 21:69.

Tsuchimatsu, Takashi; Kakui, Hiroyuki; Yamazaki, Misako; Marona, Cindy; Tsutsui, Hiroki; Hedhly, Afif; Meng, Dazhe; Sato, Yutaka; Städler, Thomas; Grossniklaus, Ueli; Kanaoka, Masahiro M; Lenhard, Michael; Nordborg, Magnus; Shimizu, Kentaro K (2020). Adaptive Reduction of Male Gamete Number in the Selfing Plant Arabidopsis Thaliana. Nature Communications, 11:2885.

Barquera, Rodrigo; Lamnidis, Thiseas C; Lankapalli, Aditya Kumar; Kocher, Arthur; Hernández-Zaragoza, Diana I; Nelson, Elizabeth A; Zamora-Herrera, Adriana C; Ramallo, Patxi; Bernal-Felipe, Natalia; Immel, Alexander; Bos, Kirsten; Acuña-Alonzo, Víctor; Barbieri, Chiara; Roberts, Patrick; Herbig, Alexander; Kühnert, Denise; Márquez-Morfín, Lourdes; Krause, Johannes (2020). Origin and Health Status of First-Generation Africans from Early Colonial Mexico. Current Biology, 30(11):2078-2091.e11.

Malan-Müller, Stefanie; de Souza, Vladimir B C; Daniels, Willie M U; Seedat, Soraya; Robinson, Mark D; Hemmings, Sîan M J (2020). Shedding Light on the Transcriptomic Dark Matter in Biological Psychiatry: Role of Long Noncoding RNAs in D-cycloserine-Induced Fear Extinction in Posttraumatic Stress Disorder. Omics : a journal of integrative biology, 24(6):352-369.

Diop, Seydina I; Subotic, Oliver; Giraldo‐Fonseca, Alejandro; Waller, Manuel; Kirbis, Alexander; Neubauer, Anna; Potente, Giacomo; Murray‐Watson, Rachel; Boskovic, Filip; Bont, Zoe; Hock, Zsofia; Payton, Adam C; Duijsings, Daniël; Pirovano, Walter; Conti, Elena; Grossniklaus, Ueli; McDaniel, Stuart F; Szövényi, Péter (2020). A pseudomolecule‐scale genome assembly of the liverwort Marchantia polymorpha. The Plant Journal, 101(6):1378-1396.

Li, Fay-Wei; Nishiyama, Tomoaki; Waller, Manuel; Frangedakis, Eftychios; Keller, Jean; Li, Zheng; Fernandez-Pozo, Noe; Barker, Michael S; Bennett, Tom; Blázquez, Miguel A; Cheng, Shifeng; Cuming, Andrew C; de Vries, Jan; de Vries, Sophie; Delaux, Pierre-Marc; Diop, Issa S.; Harrison, C Jill; Hauser, Duncan; Hernández-García, Jorge; Kirbis, Alexander; Meeks, John C; Monte, Isabel; Mutte, Sumanth K; Neubauer, Anna; Quandt, Dietmar; Robison, Tanner; Shimamura, Masaki; Rensing, Stefan A; Villarreal, Juan Carlos; Weijers, Dolf; Wicke, Susann; Wong, Gane K‐S; Sakakibara, Keiko; Szövényi, Péter (2020). Anthoceros genomes illuminate the origin of land plants and the unique biology of hornworts. Nature Plants, 6(3):259-272.

Kramer, Jos; Özkaya, Özhan; Kümmerli, Rolf (2020). Bacterial siderophores in community and host interactions. Nature Reviews. Microbiology, 18(3):152-163.

Poretti, Manuel; Praz, Coraline Rosalie; Meile, Lukas; Kälin, Carol; Schaefer, Luisa Katharina; Schläfli, Michael; Widrig, Victoria; Sanchez-Vallet, Andrea; Wicker, Thomas; Bourras, Salim (2020). Domestication of high-copy transposons underlays the wheat small RNA response to an obligate pathogen. Molecular Biology and Evolution, 37(3):839-848.

Moerman, Felix; Arquint, Angelina; Merkli, Stefanie; Wagner, Andreas; Altermatt, Florian; Fronhofer, Emanuel A (2020). Evolution under pH stress and high population densities leads to increased density‐dependent fitness in the protist Tetrahymena thermophila. Evolution, 74(3):573-586.

Gerke, Philipp; Szövényi, Péter; Neubauer, Anna; Lenz, Henning; Gutmann, Bernard; McDowell, Rose; Small, Ian; Schallenberg‐Rüdinger, Mareike; Knoop, Volker (2020). Towards a plant model for enigmatic U‐to‐C RNA editing: the organelle genomes, transcriptomes, editomes and candidate RNA editing factors in the hornwort Anthoceros agrestis. New Phytologist, 225(5):1974-1992.

Baur, Julian; Giesen, Athene; Rohner, Patrick T; Blanckenhorn, Wolf U; Schäfer, Martin A (2020). Exaggerated male forelegs are not more differentiated than wing morphology in two widespread sister species of black scavenger flies. Journal of Zoological Systematics and Evolutionary Research, 58(1):159-173.

Bell, David; Lin, Qianshi; Gerelle, Wesley K; Joya, Steve; Chang, Ying; Taylor, Z Nathan; Rothfels, Carl J; Larsson, Anders; Villarreal, Juan Carlos; Li, Fay‐Wei; Pokorny, Lisa; Szövényi, Péter; Crandall‐Stotler, Barbara; DeGironimo, Lisa; Floyd, Sandra K; Beerling, David J; Deyholos, Michael K; von Konrat, Matt; Ellis, Shona; Shaw, A Jonathan; Chen, Tao; Wong, Gane K‐S; Stevenson, Dennis W; Palmer, Jeffrey D; Graham, Sean W (2020). Organellomic data sets confirm a cryptic consensus on (unrooted) land‐plant relationships and provide new insights into bryophyte molecular evolution. American Journal of Botany, 107(1):91-115.

Kakui, Hiroyuki; Yamazaki, Misako; Hamaya, Naoto-Benjamin; Shimizu, Kentaro K (2020). Pollen Grain Counting Using a Cell Counter. In: Geitmann, Anja. Methods in Molecular Biology: Pollen and Pollen Tube Biology. Berlin: Springer, 1-11.

Grossen, Christine; Guillaume, Frédéric; Keller, Lukas F; Croll, Daniel (2020). Purging of highly deleterious mutations through severe bottlenecks in Alpine ibex. Nature Communications, 11:1001.

2019

Erten, E Yagmur; Kokko, Hanna (2019). Diverse ways to think about cancer: What can we learn about cancer by studying it across the tree of life? Mètode Science Studies Journal: Annual Review, (10):201-205.

Wyder, Stefan; Raissig, Michael T; Grossniklaus, Ueli (2019). Consistent Reanalysis of Genome-wide Imprinting Studies in Plants Using Generalized Linear Models Increases Concordance across Datasets. Scientific Reports, 9(1):1320-..

Översti, Sanni; Majander, Kerttu; Salmela, Elina; Salo, Kati; Arppe, Laura; Belskiy, Stanislav; Etu-Sihvola, Heli; Laakso, Ville; Mikkola, Esa; Pfrengle, Saskia; Putkonen, Mikko; Taavitsainen, Jussi-Pekka; Vuoristo, Katja; Wessman, Anna; Sajantila, Antti; Oinonen, Markku; Haak, Wolfgang; Schuenemann, Verena J; Krause, Johannes; Palo, Jukka U; Onkamo, Päivi (2019). Human mitochondrial DNA lineages in Iron-Age Fennoscandia suggest incipient admixture and eastern introduction of farming-related maternal ancestry. Scientific Reports, 9:16883.

Grize, Sofia A; Wilwert, Elodie; Searle, Jeremy B; Lindholm, Anna K (2019). Measurements of hybrid fertility and a test of mate preference for two house mouse races with massive chromosomal divergence. BMC Evolutionary Biology, 19(1):25.

Bourras, Salim; Kunz, Lukas; Xue, Minfeng; Praz, Coraline Rosalie; Müller, Marion Claudia; Kälin, Carol; Schläfli, Michael; Ackermann, Patrick; Flückiger, Simon; Parlange, Francis; Menardo, Fabrizio; Schaefer, Luisa Katharina; Ben-David, Roi; Roffler, Stefan; Oberhaensli, Simone; Widrig, Victoria; Lindner, Stefan; Isaksson, Jonatan; Wicker, Thomas; Yu, Dazhao; Keller, Beat (2019). The AvrPm3-Pm3 effector-NLR interactions control both race-specific resistance and host-specificity of cereal mildews on wheat. Nature Communications, 10(1):2292-2308.

Barbieri, Chiara; Barquera, Rodrigo; Arias, Leonardo; Sandoval, José R; Acosta, Oscar; Zurita, Camilo; Aguilar-Campos, Abraham; Tito-Álvarez, Ana M; Serrano-Osuna, Ricardo; Gray, Russell D; Heggarty, Paul; Shimizu, Kentaro K; Fujita, Ricardo; Stoneking, Mark; Pugach, Irina; Fehren-Schmitz, Lars (2019). The current genomic landscape of western South America: Andes, Amazonia and Pacific Coast. Molecular Biology and Evolution, 36(12):2698-2713.

Pineiro Fernandez, Laura; Byers, Kelsey J R P; Cai, Jing; Sedeek, Khalid E M; Kellenberger, Roman T; Russo, Alessia; Qi, Weihong; Aquino Fournier, Catharine; Schlüter, Philipp M (2019). A phylogenomic analysis of the floral transcriptomes of sexually deceptive and rewarding European orchids, Ophrys and Gymnadenia. Frontiers in Plant Science, 10:1553.

Izuno, Ayako; Wicker, Thomas; Hatakeyama, Masaomi; Copetti, Dario; Shimizu, Kentaro K (2019). Updated Genome Assembly and Annotation for Metrosideros polymorpha, an Emerging Model Tree Species of Ecological Divergence. G3 : Genes, Genomes, Genetics, 9(11):3513-3520.

Meccariello, Angela; Salvemini, Marco; Primo, Pasquale; Hall, Brantley; Koskinioti, Panagiota; Dalíková, Martina; Gravina, Andrea; Gucciardino, Michela Anna; Forlenza, Federica; Gregoriou, Maria-Eleni; Ippolito, Domenica; Monti, Simona Maria; Petrella, Valeria; Perrotta, Maryanna Martina; Schmeing, Stephan; Ruggiero, Alessia; Scolari, Francesca; Giordano, Ennio; Tsoumani, Konstantina T; Marec, František; Windbichler, Nikolai; Arunkumar, Kallare P; Bourtzis, Kostas; Mathiopoulos, Kostas D; Ragoussis, Jiannis; Vitagliano, Luigi; Tu, Zhijian; Papathanos, Philippos Aris; Robinson, Mark D; Saccone, Giuseppe (2019). Maleness-on-the-Y (MoY) orchestrates male sex determination in major agricultural fruit fly pests. Science, 365(6460):1457-1460.

Choobdar, Sarvenaz; Ahsen, Mehmet E; Crawford, Jake; Tomasoni, Mattia; Fang, Tao; Lamparter, David; Lin, Junyuan; Hescott, Benjamin; Hu, Xiaozhe; Mercer, Johnathan; Natoli, Ted; Narayan, Rajiv; von Mering, C; Subramanian, Aravind; Zhang, Jitao D; Stolovitzky, Gustavo; Kutalik, Zoltán; Lage, Kasper; Slonim, Donna K; Saez-Rodriguez, Julio; Cowen, Lenore J; Bergmann, Sven; Marbach, Daniel (2019). Assessment of network module identification across complex diseases. Nature Methods, 16(9):843-852.

Nguyen, Huyen; Thorball, Christian W; Fellay, Jacques; Böni, Jürg; Yerly, Sabine; Perreau, Matthieu; Klimkait, Thomas; Kusejko, Katharina; Bachmann, Nadine; Chaudron, Sandra E; Paioni, Paolo; Thurnheer, Maria C; Battegay, Manuel; Cavassini, Matthias; Vernazza, Pietro; Bernasconi, Enos; Günthard, Huldrych F; Kouyos, Roger; Swiss HIV Cohort Study (2019). HIV Transmission Chains Exhibit Greater HLA-B Homogeneity Than Randomly Expected. Journal of Acquired Immune Deficiency Syndromes, 81(5):508-515.

Gretzinger, Joscha; Molak, Martyna; Reiter, Ella; Pfrengle, Saskia; Urban, Christian; Neukamm, Judith; Blant, Michel; Conard, Nicholas J; Cupillard, Christophe; Dimitrijević, Vesna; Drucker, Dorothée G; Hofman-Kamińska, Emilia; Kowalczyk, Rafał; Krajcarz, Maciej T; Krajcarz, Magdalena; Münzel, Susanne C; Peresani, Marco; Romandini, Matteo; Rufí, Isaac; Soler, Joaquim; Terlato, Gabriele; Krause, Johannes; Bocherens, Hervé; Schuenemann, Verena J (2019). Large-scale mitogenomic analysis of the phylogeography of the Late Pleistocene cave bear. Scientific Reports, 9:10700.

van Gestel, Jordi; Ackermann, Martin; Wagner, Andreas (2019). Microbial life cycles link global modularity in regulation to mosaic evolution. Nature Ecology and Evolution, 3(8):1184-1196.

Soneson, Charlotte; Yao, Yao; Bratus-Neuenschwander, Anna; Patrignani, Andrea; Robinson, Mark D; Hussain, Shobbir (2019). A comprehensive examination of Nanopore native RNA sequencing for characterization of complex transcriptomes. Nature Communications, 10(1):3359.

Olearo, Flaminia; Nguyen, Huyen; Bonnet, Fabrice; Yerly, Sabine; Wandeler, Gilles; Stoeckle, Marcel; Cavassini, Matthias; Scherrer, Alexandra; Costagiola, Dominique; Schmid, Patrick; Günthard, Huldrych F; Bernasconi, Enos; Boeni, Jürg; D'arminio Monforte, Antonella; Zazzi, Maurizio; Rossetti, Barbara; Neau, Didier; Bellecave, Pantxika; Rijnders, Bart; Reiss, Peter; Wit, Ferdinand; Kouyos, Roger; Calmy, Alexandra (2019). Impact of the M184V/I Mutation on the Efficacy of Abacavir/Lamivudine/Dolutegravir Therapy in HIV Treatment-Experienced Patients. Open Forum Infectious Diseases, 6(10):ofz330.

Orjuela, Stephany; Huang, Ruizhu; Hembach, Katharina M; Robinson, Mark D; Soneson, Charlotte (2019). ARMOR: An Automated Reproducible MOdular Workflow for Preprocessing and Differential Analysis of RNA-seq Data. G3 : Genes, Genomes, Genetics, 9(7):2089-2096.

Weber, Lukas M; Saelens, Wouter; Cannoodt, Robrecht; Soneson, Charlotte; Hapfelmeier, Alexander; Gardner, Paul P; Boulesteix, Anne-Laure; Saeys, Yvan; Robinson, Mark D (2019). Essential guidelines for computational method benchmarking. Genome Biology, 20:125.

Müller, Marion C; Praz, Coraline R; Sotiropoulos, Alexandros G; Menardo, Fabrizio; Kunz, Lukas; Schudel, Seraina; Oberhänsli, Simone; Poretti, Manuel; Wehrli, Andreas; Bourras, Salim; Keller, Beat; Wicker, Thomas (2019). A chromosome-scale genome assembly reveals a highly dynamic effector repertoire of wheat powdery mildew. New Phytologist, 221(4):2176-2189.

Giesen, Athene; Schäfer, Martin A; Blanckenhorn, Wolf U (2019). Geographic patterns of postzygotic isolation between two closely related widespread dung fly species (Sepsis cynipsea and Sepsis neocynipsea; Diptera: Sepsidae). Journal of Zoological Systematics and Evolutionary Research, 57(1):80-90.

Soneson, Charlotte; Love, Michael I; Patro, Rob; Hussain, Shobbir; Malhotra, Dheeraj; Robinson, Mark D (2019). A junction coverage compatibility score to quantify the reliability of transcript abundance estimates and annotation catalogs. Life Science Alliance, 2(1):e201800175.

Nowicka, Malgorzata; Krieg, Carsten; Crowell, Helena L; Weber, Lukas M; Hartmann, Felix J; Guglietta, Silvia; Becher, Burkhard; Levesque, Mitchell P; Robinson, Mark D (2019). CyTOF workflow: differential discovery in high-throughput high-dimensional cytometry datasets. F1000Research, 6:748.

Stritt, Christoph; Wyler, Michele; Gimmi, Elena L; Pippel, Martin; Roulin, Anne C (2019). Diversity, dynamics and effects of long terminal repeat retrotransposons in the model grass Brachypodium distachyon. New Phytologist:Epub ahead of print.

Weber, Lukas M; Nowicka, Malgorzata; Soneson, Charlotte; Robinson, Mark D (2019). diffcyt: Differential discovery in high-dimensional cytometry via high-resolution clustering. Communications Biology, 2:183.

2018

Paape, Timothy; Briskine, Roman V; Halstead-Nussloch, Gwyneth; Lischer, Heidi E L; Shimizu-Inatsugi, Rie; Hatakeyama, Masaomi; Tanaka, Kenta; Nishiyama, Tomoaki; Sabirov, Renat; Sese, Jun; Shimizu, Kentaro K (2018). Patterns of polymorphism and selection in the subgenomes of the allopolyploid Arabidopsis kamchatica. Nature Communications, 9:3909.

Krieg, Carsten; Nowicka, Malgorzata; Guglietta, Silvia; Schindler, Sabrina; Hartmann, Felix J; Weber, Lukas M; Dummer, Reinhard; Robinson, Mark D; Levesque, Mitchell P; Becher, Burkhard (2018). Author Correction: High-dimensional single-cell analysis predicts response to anti-PD-1 immunotherapy. Nature Medicine, 24(11):1773-1775.

Butaitė, Elena; Kramer, Jos; Wyder, Stefan; Kümmerli, Rolf (2018). Environmental determinants of pyoverdine production, exploitation and competition in natural Pseudomonas communities. Environmental Microbiology, 20(10):3629-3642.

Roulin, Pascal S; Murer, Luca P; Greber, Urs F (2018). A single point mutation in the rhinovirus 2B protein reduces the requirement for phosphatidylinositol 4-kinase class 3beta in viral replication. Journal of Virology, 92(23):e01462-18.

Rezzoagli, Chiara; Wilson, David; Weigert, Michael; Wyder, Stefan; Kümmerli, Rolf (2018). Probing the evolutionary robustness of two repurposed drugs targeting iron uptake in Pseudomonas aeruginosa. Evolution, Medicine, and Public Health, 6:246-259.

Whitewoods, Chris D; Cammarata, Joseph; Nemec Venza, Zoe; Sang, Stephanie; Crook, Ashley D; et al; Waller, Manuel; Cuming, Andrew C; Szövényi, Peter (2018). CLAVATA was a genetic novelty for the morphological innovation of 3D growth in land plants. Current Biology, 28(15):2365-2376.

Leigh, D M; Lischer, H E L; Grossen, C; Keller, L F (2018). Batch effects in a multiyear sequencing study: false biological trends due to changes in read lengths. Molecular Ecology Resources, 18(4):778-788.

Perroud, Pierre-François; Haas, Fabian B; Hiss, Manuel; Ullrich, Kristian K; et al; Szövényi, Peter (2018). The Physcomitrella patens gene atlas project: large-scale RNA-seq based expression data. The Plant Journal, 95(1):168-182.

Praz, Coraline R; Menardo, Fabrizio; Robinson, Mark D; Müller, Marion C; Wicker, Thomas; Bourras, Salim; Keller, Beat (2018). Non-parent of Origin Expression of Numerous Effector Genes Indicates a Role of Gene Regulation in Host Adaption of the Hybrid Triticale Powdery Mildew Pathogen. Frontiers in Plant Science, 9:49.

Duò, Angelo; Robinson, Mark D; Soneson, Charlotte (2018). A systematic performance evaluation of clustering methods for single-cell RNA-seq data. F1000Research, 7:1141.

Ferrari, Giada; Lischer, Heidi; Neukamm, Judith; Rayo, Enrique; Borel, Nicole; Pospischil, Andreas; Rühli, Frank; Bouwman, Abigail; Campana, Michael (2018). Assessing Metagenomic Signals Recovered from Lyuba, a 42,000-Year-Old Permafrost-Preserved Woolly Mammoth Calf. Genes, 9(9):436.

Townsend, Simon W; Engesser, Sabrina; Stoll, Sabine; Zuberbühler, Klaus; Bickel, Balthasar (2018). Compositionality in animals and humans. PLoS Biology, 16(8):e2006425.

Pinto-Carbó, Marta; Gademann, Karl; Eberl, Leo; Carlier, Aurelien (2018). Leaf nodule symbiosis: function and transmission of obligate bacterial endophytes. Current Opinion in Plant Biology, 44:23-31.

Leigh, Deborah Marie. Population genomics in the Alpine ibex (Capra ibex). 2018, University of Zurich, Faculty of Science.

Kellenberger, Roman T; Desurmont, Gaylord A; Schlüter, Philipp M; Schiestl, Florian P (2018). Trans-generational inheritance of herbivory-induced phenotypic changes in Brassica rapa. Scientific Reports, 8:3536.

2017

Menardo, Fabrizio; Praz, Coraline R; Wicker, Thomas; Keller, Beat (2017). Rapid turnover of effectors in grass powdery mildew (Blumeria graminis). BMC Evolutionary Biology, 17(1):223.

Butaitė, Elena; Baumgartner, Michael; Wyder, Stefan; Kümmerli, Rolf (2017). Siderophore cheating and cheating resistance shape competition for iron in soil and freshwater Pseudomonas communities. Nature Communications, 8(1):414.

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.

Baumgartner, Michael; Roffler, Stefan; Wicker, Thomas; Pernthaler, Jakob (2017). Letting go: bacterial genome reduction solves the dilemma of adapting to predation mortality in a substrate-restricted environment. The ISME journal, 11(10):2258-2266.

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.

Menardo, Fabrizio; Wicker, Thomas; Keller, Beat (2017). Reconstructing the evolutionary history of powdery mildew lineages (Blumeria graminis) at different evolutionary time scales with NGS data. Genome Biology and Evolution, 9(2):446-456.

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.

Collier, Katie. Social Mongoose Vocal Communication: Insights into the Emergence of Linguistic Combinatoriality. 2017, University of Zurich, Faculty of Science.

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.

Giesen, Athene; Blanckenhorn, Wolf U; Schäfer, Martin A (2017). Behavioural mechanisms of reproductive isolation between two hybridizing dung fly species. Animal Behaviour, 132:155-166.

Collier, Katie; Townsend, Simon W; Manser, Marta B (2017). Call concatenation in wild meerkats. Animal Behaviour, 134:257-269.

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.

Ferrari, Giada. Detection of pathogens by metagenomic analysis in preserved historic and prehistoric soft tissues. 2017, University of Zurich, Faculty of Science.

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.

Giesen, Athene. Evolution of reproductive barriers between the two hybridizing sister species Sepsis cynipsea and S. neocynipsea (Diptera: Sepsidae). 2017, University of Zurich, Faculty of Science.

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.

Collier, Katie; Radford, Andrew N; Townsend, Simon W; Manser, Marta B (2017). Wild dwarf mongooses produce general alert and predator-specific alarm calls. Behavioral Ecology, 28(5):1293-1301.

2016

Menardo, Fabrizio. Evolutionary Genomics of Grass Powdery Mildew (Blumeria graminis). 2016, University of Zurich, Faculty of Science.

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.

Baumgartner, Michael. Experimental Evolution of a Freshwater Isolate with Inducible Aggregate Formation – Genome Streamlining and Variability of Phenotypic Plasticity. 2016, University of Zurich, Faculty of Science.

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.

Pinto-Carbó, Marta; Sieber, Simon; Dessein, Steven; Wicker, Thomas; Verstraete, Brecht; Gademann, Karl; Eberl, Leo; Carlier, Aurelien (2016). Evidence of horizontal gene transfer between obligate leaf nodule symbionts. The ISME journal, 10(9):2092-2105.

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.

Carlier, Aurelien; Fehr, Linda; Pinto, Marta; Schäberle, Till; Reher, Raphael; Dessein, Steven; König, Gabriele; Eberl, Leo (2016). The genome analysis of Candidatus Burkholderia crenata reveals that secondary metabolism may be a key function of the Ardisia crenata leaf nodule symbiosis. Environmental Microbiology, 18(8):2507-2522.

2015

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.

2014

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.

2013

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 Fri Aug 7 23:09:35 2020 CEST.