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2023

Menéndez, Lumila Paula; Barbieri, Chiara; López Cruz, Idalia Guadalupe; Schmelzle, Thomas; Breidenstein, Abagail M; Barquera, Rodrigo; Borzi, Guido; Schuenemann, Verena J; Sanchez-Villagra, Marcelo R (2023). On Roth’s “human fossil” from Baradero, Buenos Aires Province, Argentina: morphological and genetic analysis. Swiss Journal of Palaeontology, 142(1):26-45.

Akiyama, Reiko; Goto, Takao; Tameshige, Toshiaki; Sugisaka, Jiro; Kuroki, Ken; Sun, Jianqiang; Akita, Junichi; Hatakeyama, Masaomi; Kudoh, Hiroshi; Kenta, Tanaka; Tonouchi, Aya; Shimahara, Yuki; Sese, Jun; Kutsuna, Natsumaro; Shimizu-Inatsugi, Rie; Shimizu, Kentaro K (2023). Seasonal pigment fluctuation in diploid and polyploid Arabidopsis revealed by machine learning-based phenotyping method PlantServation. Nature Communications, 14(1):5792.

Sun, Jianqiang; Okada, Moeko; Tameshige, Toshiaki; Shimizu-Inatsugi, Rie; Akiyama, Reiko; Nagano, Atsushi J; Sese, Jun; Shimizu, Kentaro K (2023). A low-coverage 3′ RNA-seq to detect homeolog expression in polyploid wheat. NAR Genomics and Bioinformatics, 5(3):lqad067.

Arango-Isaza, Epifanía; Capodiferro, Marco Rosario; Aninao, María José; Babiker, Hiba; Aeschbacher, Simon; Achilli, Alessandro; Posth, Cosimo; Campbell, Robert; Martinez, Felipe I; Heggarty, Paul; Sadowsky, Scott; Shimizu, Kentaro K; Barbieri, Chiara (2023). The genetic history of the Southern Andes from present-day Mapuche ancestry. Current Biology, 33(13):2602-2615.e5.

Megremis, Spyridon; Constantinides, Bede; Xepapadaki, Paraskevi; Yap, Chuan Fu; Sotiropoulos, Alexandros G; Bachert, Claus; Finotto, Susetta; Jartti, Tuomas; Tapinos, Avraam; Vuorinen, Tytti; Andreakos, Evangelos; Robertson, David L; Papadopoulos, Nikolaos G (2023). Respiratory eukaryotic virome expansion and bacteriophage deficiency characterize childhood asthma. Scientific Reports, 13(1):8319.

Shimizu, Kentaro K; Nakamaru, Akio. Internationalization of research and challenges for Japan. In: The Nikkei, 16 May 2023, 32.

Waller, Manuel; Frangedakis, Eftychios; Marron, Alan O; Sauret-Gueto, Susanna; Rever, Jenna; Sabbagh, Cyrus Raja Rubenstein; Hibberd, Julian M; Haseloff, Jim; Renzaglia, Karen S; Szövényi, Péter (2023). An optimised transformation protocol for Anthoceros agrestis and three more hornwort species. The Plant Journal, 114(3):699-718.

Mueller, Kim-Kristine; Pfeifer, Lukas; Schuldt, Lina; Szövényi, Péter; de Vries, Sophie; de Vries, Jan; Johnson, Kim L; Classen, Birgit (2023). Fern cell walls and the evolution of arabinogalactan proteins in streptophytes. The Plant Journal, 114(4):875-894.

Capodiferro, Marco Rosario; Chero Osorio, Ana María; Rambaldi Migliore, Nicola; Tineo Tineo, Dean Herman; Raveane, Alessandro; Xavier, Catarina; Bodner, Martin; Simão, Filipa; Ongaro, Linda; Montinaro, Francesco; Lindo, John; Huerta-Sanchez, Emilia; Politis, Gustavo; Barbieri, Chiara; Parson, Walther; Gusmão, Leonor; Achilli, Alessandro (2023). The multifaceted genomic history of Ashaninka from Amazonian Peru. Current Biology, 33(8):1573-1581.e5.

Frangedakis, Eftychios; Marron, Alan O; Waller, Manuel; Neubauer, Anna; Tse, Sze Wai; Yue, Yuling; Ruaud, Stéphanie; Waser, Lucas; Sakakibara, Keiko; Szövényi, Péter (2023). What can hornworts teach us? Frontiers in Plant Science, 14:1108027.

Poretti, Manuel; Praz, Coraline R; Sotiropoulos, Alexandros G; Wicker, Thomas (2023). A survey of lineage-specific genes in Triticeae reveals de novo gene evolution from genomic raw material. Plant Direct, 7(3):e484.

Kunz, Lukas; Sotiropoulos, Alexandros G; Graf, Johannes; Razavi, Mohammad; Keller, Beat; Müller, Marion C (2023). The broad use of the Pm8 resistance gene in wheat resulted in hypermutation of the AvrPm8 gene in the powdery mildew pathogen. BMC Biology, 21(1):29.

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.

Shimizu-Inatsugi, Rie; Morishima, Aki; Mourato, Beatriz; Shimizu, Kentaro K; Sato, Yasuhiro (2023). Phenotypic variation of a new synthetic allotetraploid Arabidopsis. Frontiers in Plant Science, 13:1058522.

Frangedakis, Eftychios; Marron, Alan O; Waller, Manuel; Neubauer, Anna; Tse, Sze Wai; Yue, Yuling; Ruaud, Stephanie; Waser, Lucas; Sakakibara, Keiko; Szövényi, Péter (2023). What can hornworts teach us? Frontiers in Plant Science, 14:online.

2022

Sotiropoulos, Alexandros G; Sánchez-Martín, Javier; Widrig, Victoria; Isaksson, Jonatan; Bernasconi, Zoe; Koller, Teresa; Bearth, Giulia; Herren, Gerhard; Wicker, Thomas; Keller, Beat (2022). A fictional field case study to understand the genetic basis of host-fungal pathogen interactions using the wheat powdery mildew-wheat pathosystem. Journal of Biological Education:Epub ahead of print.

Sotiropoulos, Alexandros G; Arango-Isaza, Epifanía; Ban, Tomohiro; Barbieri, Chiara; Bourras, Salim; Cowger, Christina; Czembor, Paweł C; Ben-David, Roi; Dinoor, Amos; Ellwood, Simon R; Graf, Johannes; Hatta, Koichi; Helguera, Marcelo; Sánchez-Martín, Javier; McDonald, Bruce A; Morgounov, Alexey I; Müller, Marion C; Shamanin, Vladimir; Shimizu, Kentaro K; Yoshihira, Taiki; Zbinden, Helen; Keller, Beat; Wicker, Thomas (2022). Global genomic analyses of wheat powdery mildew reveal association of pathogen spread with historical human migration and trade. Nature Communications, 13(1):4315.

Prummel, Karin D; Crowell, Helena L; Nieuwenhuize, Susan; Brombacher, Eline C; Daetwyler, Stephan; Soneson, Charlotte; Kresoja-Rakic, Jelena; Kocere, Agnese; Ronner, Manuel; Ernst, Alexander; Labbaf, Zahra; Clouthier, David E; Firulli, Anthony B; Sánchez-Iranzo, Héctor; Naganathan, Sundar R; O’Rourke, Rebecca; Raz, Erez; Mercader, Nadia; Burger, Alexa; Felley-Bosco, Emanuela; Huisken, Jan; Robinson, Mark D; Mosimann, Christian (2022). Hand2 delineates mesothelium progenitors and is reactivated in mesothelioma. Nature Communications, 13(1):1677.

Barbieri, Chiara; Blasi, Damián E; Arango-Isaza, Epifanía; Sotiropoulos, Alexandros G; Hammarström, Harald; Wichmann, Søren; Greenhill, Simon J; Gray, Russell D; Forkel, Robert; Bickel, Balthasar; Shimizu, Kentaro K (2022). A global analysis of matches and mismatches between human genetic and linguistic histories. Proceedings of the National Academy of Sciences of the United States of America, 119:47.

Karve, Shraddha; Wagner, Andreas (2022). Environmental complexity is more important than mutation in driving the evolution of latent novel traits in E. coli. Nature Communications, 13(1):5904.

Thieme, Michael; Brêchet, Arthur; Bourgeois, Yann; Keller, Bettina; Bucher, Etienne; Roulin, Anne C (2022). Experimentally heat‐induced transposition increases drought tolerance in Arabidopsis thaliana. New Phytologist, 236(1):182-194.

Rayo, Enrique; Neukamm, Judith; Tomoum, Nadja; Eppenberger, Patrick; Breidenstein, Abagail; Bouwman, Abigail S; Schuenemann, Verena J; Rühli, Frank J (2022). Metagenomic analysis of Ancient Egyptian canopic jars. American journal of biological anthropology, 179(2):307-313.

Akagi, Takashi; Jung, Katharina; Masuda, Kanae; Shimizu, Kentaro K (2022). Polyploidy before and after domestication of crop species. Current Opinion in Plant Biology, 69:102255.

Hasterok, Robert; Catalan, Pilar; Hazen, Samuel P; Roulin, Anne C; Vogel, John P; Wang, Kai; Mur, Luis A J (2022). Brachypodium: 20 years as a grass biology model system; the way forward? Trends in Plant Science, 27(10):1002-1016.

Shimizu, Kentaro K (2022). Robustness and the generalist niche of polyploid species: Genome shock or gradual evolution? Current Opinion in Plant Biology, 69:102292.

COVID-19 Host Genetics Initiative (2022). A first update on mapping the human genetic architecture of COVID-19. Nature, 608(7921):E1-E10.

Müller, Marion C; Kunz, Lukas; Schudel, Seraina; Lawson, Aaron W; Kammerecker, Sandrine; Isaksson, Jonatan; Wyler, Michele; Graf, Johannes; Sotiropoulos, Alexandros G; Praz, Coraline R; Manser, Beatrice; Wicker, Thomas; Bourras, Salim; Keller, Beat (2022). Ancient variation of the AvrPm17 gene in powdery mildew limits the effectiveness of the introgressed rye Pm17 resistance gene in wheat. Proceedings of the National Academy of Sciences of the United States of America, 119(30):e2108808119.

Toll-Riera, Macarena; Olombrada, Miriam; Castro-Giner, Francesc; Wagner, Andreas (2022). A limit on the evolutionary rescue of an Antarctic bacterium from rising temperatures. Science Advances, 8(28):eabk3511.

Bergström, Anders; Stanton, David W G; Taron, Ulrike H; Pfrengle, Saskia; Schuenemann, Verena J; et al (2022). Grey wolf genomic history reveals a dual ancestry of dogs. Nature, 607(7918):313-320.

Moerman, Felix; Fronhofer, Emanuel A; Altermatt, Florian; Wagner, Andreas (2022). Selection on growth rate and local adaptation drive genomic adaptation during experimental range expansions in the protist Tetrahymena thermophila. Journal of Animal Ecology, 91(6):1088-1103.

Russo, Alessia; Mayjonade, Baptiste; Frei, Daniel; Potente, Giacomo; Kellenberger, Roman T; Frachon, Léa; Copetti, Dario; Studer, Bruno; Frey, Jürg E; Grossniklaus, Ueli; Schlüter, Philipp M (2022). Low-Input High-Molecular-Weight DNA Extraction for Long-Read Sequencing From Plants of Diverse Families. Frontiers in Plant Science, 13:883897.

Patrono, Livia V; Vrancken, Bram; Budt, Matthias; et al; Schuenemann, Verena J; Urban, Christian (2022). Archival influenza virus genomes from Europe reveal genomic variability during the 1918 pandemic. Nature Communications, 13(1):2314.

Jayakumar, Priyanikha; Figueiredo, Alexandre R T; Kümmerli, Rolf (2022). Evolution of the quorum sensing systems in Pseudomonas aeruginosa can involve both loss of regulon function and network modulation. bioRxiv 489656, Cold Spring Harbor Laboratory.

Rubinstein, Mark P; Williams, Cameron; Mart, Caroline; Beall, Jonathan; MacPherson, Linda; Azar, Joseph; Swiderska-Syn, Marzena; Manca, Paolo; Gibney, Barry C; Robinson, Mark D; Krieg, Carsten; Hill, Elizabeth G; Taha, Sharif A; Rock, Amy D; Lee, John H; Soon-Shiong, Patrick; Wrangle, John (2022). Phase I Trial Characterizing the Pharmacokinetic Profile of N-803, a Chimeric IL-15 Superagonist, in Healthy Volunteers. Journal of Immunology, 208(6):1362-1370.

Wicker, Thomas; Stritt, Christoph; Sotiropoulos, Alexandros G; Poretti, Manuel; Pozniak, Curtis J; Walkowiak, Sean; Gundlach, Heidrun; Stein, Nils (2022). Transposable Element Populations Shed Light on the Evolutionary History of Wheat and the Complex Co-Evolution of Autonomous and Non-Autonomous Retrotransposons. Advanced Genetics, 3(1):2100022.

Kakui, Hiroyuki; Yamazaki, Misako; Shimizu, Kentaro K (2022). 電気泳動でDNAの1塩基差を迅速・簡便に識別する遺伝子型判別法：PRIMA. Jikken Igaku, 40:601-608.

Neubauer, Anne; Ruaud, Stéphanie; Waller, Manuel; Frangedakis, Eftychios; Li, Fay‐Wei; Nötzold, Svenja I; Wicke, Susann; Bailly, Aurélien; Szövényi, Péter (2022). Step‐by‐step protocol for the isolation and transient transformation of hornwort protoplasts. Applications in Plant Sciences:online.

Potente, Giacomo; Léveillé-Bourret, Étienne; Yousefi, Narjes; Choudhury, Rimjhim Roy; Keller, Barbara; Diop, Seydina Issa; Duijsings, Daniël; Pirovano, Walter; Lenhard, Michael; Szövényi, Péter; Conti, Elena (2022). Comparative Genomics Elucidates the Origin of a Supergene Controlling Floral Heteromorphism. Molecular Biology and Evolution, 39(2):msac035.

Rayo, Enrique; Ferrari, Giada; Neukamm, Judith; Akgül, Gülfirde; Breidenstein, Abagail M; Cooke, Martyn; Phillips, Carina; Bouwman, Abigail S; Rühli, Frank J; Schuenemann, Verena J (2022). Non-destructive extraction of DNA from preserved tissues in medical collections. BioTechniques, 72(2):60-64.

Murer, Luca; Petkidis, Anthony; Vallet, Thomas; Vignuzzi, Marco; Greber, Urs F (2022). Chemical evolution of Rhinovirus identifies capsid-destabilizing mutations driving low pH-independent genome uncoating. Journal of Virology, 96(2):e0106021.

Izuno, Ayako; Onoda, Yusuke; Amada, Gaku; Kobayashi, Keito; Mukai, Mana; Isagi, Yuji; Shimizu, Kentaro K (2022). Demography and selection analysis of the incipient adaptive radiation of a Hawaiian woody species. PLoS Genetics, 18:e1009987.

Kakui, Hiroyuki; Tsuchimatsu, Takashi; Yamazaki, Misako; Hatakeyama, Masaomi; Shimizu, Kentaro K (2022). Pollen Number and Ribosome Gene Expression Altered in a Genome-Editing Mutant of REDUCED POLLEN NUMBER1 Gene. Frontiers in Plant Science, 12:768584.

Pla-Díaz, Marta; Sánchez-Busó, Leonor; Giacani, Lorenzo; Šmajs, David; Bosshard, Philipp P; Bagheri, Homayoun C; Schuenemann, Verena J; Nieselt, Kay; Arora, Natasha; González-Candelas, Fernando (2022). Evolutionary processes in the emergence and recent spread of the syphilis agent, Treponema pallidum. Molecular Biology and Evolution, 39(1):msab318.

Karve, Shraddha; Wagner, Andreas (2022). Multiple Novel Traits without Immediate Benefits Originate in Bacteria Evolving on Single Antibiotics. Molecular Biology and Evolution, 39(1):msab341.

Stritt, Christoph; Gimmi, Elena L; Wyler, Michele; Bakali, Abdelmonaim H; Skalska, Aleksandra; Hasterok, Robert; Mur, Luis A J; Pecchioni, Nicola; Roulin, Anne C (2022). Migration without interbreeding: Evolutionary history of a highly selfing Mediterranean grass inferred from whole genomes. Molecular Ecology, 31(1):70-85.

Figueiredo, Alexandre R T; Özkaya, Özhan; Kümmerli, Rolf; Kramer, Jos (2022). Siderophores drive invasion dynamics in bacterial communities through their dual role as public good versus public bad. Ecology Letters, 25(1):138-150.

Robin, Mathieu; Ferrari, Giada; Akgül, Gülfirde; Münger, Xenia; von Seth, Johanna; Schuenemann, Verena J; Dalén, Love; Grossen, Christine (2022). Ancient mitochondrial and modern whole genomes unravel massive genetic diversity loss during near extinction of Alpine ibex. Molecular Ecology, 31(13):3548-3565.

Mittelstrass, Jana. Biotic and abiotic factors that drive the assembly of microbiomes in two plant hosts. 2022, University of Zurich, Faculty of Science.

Sotiropoulos, Alexandros Georgios. Global population analyses of wheat powdery mildew using whole genome sequencing data. 2022, University of Zurich, Faculty of Science.

Kofler, Xeniya Valeriyivna. Pollinator-mediated mating system shifts in Brassica rapa. 2022, University of Zurich, Faculty of Science.

2021

Bai, Yu; Caussinus, Emmanuel; Leo, Stefano; Bosshardt, Fritz; Myachina, Faina; Rot, Gregor; Robinson, Mark D; Lehner, Christian F (2021). A cis-regulatory element promoting increased transcription at low temperature in cultured ectothermic Drosophila cells. BMC Genomics, 22:771.

Milosavljevic, Stefan; Kuo, Tony; Decarli, Samuele; Mohn, Lucas; Sese, Jun; Shimizu, Kentaro K; Shimizu-Inatsugi, Rie; Robinson, Mark D (2021). ARPEGGIO: Automated Reproducible Polyploid EpiGenetic GuIdance workflOw. BMC Genomics, 22:547.

Gerber, Reto; Robinson, Mark D (2021). Censcyt: censored covariates in differential abundance analysis in cytometry. BMC Bioinformatics, 22(1):235.

Aguirre-Fernández, Gabriel; Barbieri, Chiara; Graff, Anna; Pérez de Arce, José; Moreno, Hyram; Sánchez-Villagra, Marcelo R (2021). Cultural macroevolution of musical instruments in South America. Humanities & Social Sciences Communications, 8:208.

Müller, Marion C; Kunz, Lukas; Graf, Johannes; Schudel, Seraina; Keller, Beat (2021). Host Adaptation Through Hybridization: Genome Analysis of Triticale Powdery Mildew Reveals Unique Combination of Lineage-Specific Effectors. Molecular Plant-Microbe Interactions, 34(12):1350-1357.

Pfrengle, Saskia; Neukamm, Judith; et al; Schuenemann, Verena J (2021). Mycobacterium leprae diversity and population dynamics in medieval Europe from novel ancient genomes. BMC Biology, 19:220.

Abrouk, Michael; Athiyannan, Naveenkumar; Müller, Thomas; Pailles, Yveline; Stritt, Christoph; Roulin, Anne C; Chu, Chenggen; Liu, Shuyu; Morita, Takumi; Handa, Hirokazu; Poland, Jesse; Keller, Beat; Krattinger, Simon G (2021). Population genomics and haplotype analysis in spelt and bread wheat identifies a gene regulating glume color. Communications Biology, 4:375.

Schmeing, Stephan; Robinson, Mark D (2021). ReSeq simulates realistic Illumina high-throughput sequencing data. Genome Biology, 22:67.

Lankheet, Imke; Vicente, Mário; Barbieri, Chiara; Schlebusch, Carina (2021). The performance of common SNP arrays in assigning African mitochondrial haplogroups. BMC Genomics, 22:43.

Mittelstrass, Jana; Sperone, F Gianluca; Horton, Matthew W (2021). Using transects to disentangle the environmental drivers of plant‐microbiome assembly. Plant, Cell & Environment, 44(12):3515-3525.

Ng, Kevin Kit Siong; Kobayashi, Masaki J; Fawcett, Jeffrey A; Hatakeyama, Masaomi; Paape, Timothy; Ng, Chin Hong; Ang, Choon Cheng; Tnah, Lee Hong; Lee, Chai Ting; Nishiyama, Tomoaki; Sese, Jun; O'Brien, Michael J; Copetti, Dario; Isa, Mohd Noor Mat; Ong, Robert Cyril; Putra, Mahardika; Siregar, Iskandar Z; Indrioko, Sapto; Kosugi, Yoshiko; Izuno, Ayako; Isagi, Yuji; Lee, Soon Leong; Shimizu, Kentaro K (2021). The genome of Shorea leprosula (Dipterocarpaceae) highlights the ecological relevance of drought in aseasonal tropical rainforests. Communications Biology, 4:1166.

Leigh, Deborah M; Lischer, Heidi E L; Guillaume, Frédéric; Grossen, Christine; Günther, Torsten (2021). Disentangling adaptation from drift in bottlenecked and reintroduced populations of Alpine ibex. Molecular Ecology Resources, 21(7):2350-2363.

Figueiredo, Alexandre R T; Wagner, Andreas; Kümmerli, Rolf (2021). Ecology drives the evolution of diverse social strategies in Pseudomonas aeruginosa. Molecular Ecology, 30(20):5214-5228.

Halstead-Nussloch, Gwyneth; Tanaka, Tsuyoshi; Copetti, Dario; Paape, Timothy; Kobayashi, Fuminori; Hatakeyama, Masaomi; Kanamori, Hiroyuki; Wu, Jianzhong; Mascher, Martin; Kawaura, Kanako; Shimizu, Kentaro K; Handa, Hirokazu (2021). Multiple Wheat Genomes Reveal Novel Gli-2 Sublocus Location and Variation of Celiac Disease Epitopes in Duplicated α-Gliadin Genes. Frontiers in Plant Science, 12:715985.

Florez-Rueda, Ana Marcela; Fiscalini, Flurin; Roth, Morgane; Grossniklaus, Ueli; Städler, Thomas (2021). Endosperm and Seed Transcriptomes Reveal Possible Roles for Small RNA Pathways in Wild Tomato Hybrid Seed Failure. Genome Biology and Evolution, 13(8):evab107.

Frei, Daniel; Veekman, Elisabeth; Grogg, Daniel; Stoffel-Studer, Ingrid; Morishima, Aki; Shimizu-Inatsugi, Rie; Yates, Steven; Shimizu, Kentaro K; Frey, Jürg E; Studer, Bruno; Copetti, Dario (2021). Ultralong Oxford Nanopore reads enable the development of a reference-grade perennial ryegrass genome assembly. Genome Biology and Evolution, 13(8):evab159.

Matsumae, Hiromi; Ranacher, Peter; Savage, Patrick E; Blasi, Damián E; Currie, Thomas E; Koganebuchi, Kae; Nishida, Nao; Sato, Takehiro; Tanabe, Hideyuki; Tajima, Atsushi; Brown, Steven; Stoneking, Mark; Shimizu, Kentaro K; Oota, Hiroki; Bickel, Balthasar (2021). Exploring correlations in genetic and cultural variation across language families in northeast Asia. Science Advances, 7(34):eabd9223.

Stritt, Christoph; Thieme, Michael; Roulin, Anne C (2021). Rare transposable elements challenge the prevailing view of transposition dynamics in plants. American Journal of Botany, 108(8):1310-1314.

Toda, Yosuke; Tameshige, Toshiaki; Tomiyama, Masakazu; Kinoshita, Toshinori; Shimizu, Kentaro K (2021). An Affordable Image-Analysis Platform to Accelerate Stomatal Phenotyping During Microscopic Observation. Frontiers in Plant Science, 12:715309.

Meleshko, Olena; Martin, Michael D; Korneliussen, Thorfinn Sand; Schröck, Christian; Lamkowski, Paul; Schmutz, Jeremy; Healey, Adam; Piatkowski, Bryan T; Shaw, A Jonathan; Weston, David J; Flatberg, Kjell Ivar; Szövényi, Péter; Hassel, Kristian; Stenøien, Hans K (2021). Extensive Genome-Wide Phylogenetic Discordance Is Due to Incomplete Lineage Sorting and Not Ongoing Introgression in a Rapidly Radiated Bryophyte Genus. Molecular Biology and Evolution, 38(7):2750-2766.

Lütge, Almut; Zyprych-Walczak, Joanna; Brykczynska Kunzmann, Urszula; Crowell, Helena L; Calini, Daniela; Malhotra, Dheeraj; Soneson, Charlotte; Robinson, Mark D (2021). CellMixS: quantifying and visualizing batch effects in single-cell RNA-seq data. Life science alliance, 4(6):e202001004.

Nguyen, Huyen; Thorball, Christian Wandell; Fellay, Jacques; Böni, Jürg; Yerly, Sabine; Perreau, Matthieu; Hirsch, Hans H; Kusejko, Katharina; Thurnheer, Maria Christine; Battegay, Manuel; Cavassini, Matthias; Kahlert, Christian R; Bernasconi, Enos; Günthard, Huldrych F; Kouyos, Roger D; Swiss HIV Cohort Study (2021). Systematic screening of viral and human genetic variation identifies antiretroviral resistance and immune escape link. eLife, 10:e67388.

Rich, Mélanie K; Vigneron, Nicolas; Libourel, Cyril; Keller, Jean; Xue, Li; Hajheidari, Mohsen; Radhakrishnan, Guru V; Le Ru, Aurélie; Diop, Seydina Issa; Potente, Giacomo; Conti, Elena; Duijsings, Danny; Batut, Aurélie; Le Faouder, Pauline; Kodama, Kyoichi; Kyozuka, Junko; Sallet, Erika; Bécard, Guillaume; Rodriguez-Franco, Marta; Ott, Thomas; Bertrand-Michel, Justine; Oldroyd, Giles E D; Szövényi, Péter; Bucher, Marcel; Delaux, Pierre-Marc (2021). Lipid exchanges drove the evolution of mutualism during plant terrestrialization. Science, 372(6544):864-868.

Szövényi, Péter; Gunadi, Andika; Li, Fay-Wei (2021). Charting the genomic landscape of seed-free plants. Nature Plants, 7(5):554-565.

Manser, Beatrice; Koller, Teresa; Praz, Coraline Rosalie; Roulin, Anne C; Zbinden, Helen; Arora, Sanu; Steuernagel, Burkhard; Wulff, Brande B H; Keller, Beat; Sánchez‐Martín, Javier (2021). Identification of specificity‐defining amino acids of the wheat immune receptor Pm2 and powdery mildew effector AvrPm2. The Plant Journal, 106(4):993-1007.

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.

Shimizu-Inatsugi, Rie; Milosavljevic, Silvija; Shimizu, Kentaro K; Schaepman‐Strub, Gabriela; Tanoi, Keitaro; Sato, Yasuhiro (2021). Metal accumulation and its effect on leaf herbivory in an allopolyploid species Arabidopsis kamchatica inherited from a diploid hyperaccumulator A. halleri. Plant Species Biology, 36(2):208-217.

Shimizu, Kentaro K; Copetti, Dario; Okada, Moeko; Wicker, Thomas; Tameshige, Toshiaki; Hatakeyama, Masaomi; Shimizu-Inatsugi, Rie; Aquino, Catharine; et al (2021). De Novo Genome Assembly of the Japanese Wheat Cultivar Norin 61 Highlights Functional Variation in Flowering Time and Fusarium Resistance Genes in East Asian Genotypes. Plant & Cell Physiology, 62(1):8-27.

Hewitt, Tim; Müller, Marion C; Molnár, István; Mascher, Martin; Holušová, Kateřina; Šimková, Hana; Kunz, Lukas; Zhang, Jianping; Li, Jianbo; Bhatt, Dhara; Sharma, Raghvendra; Schudel, Seraina; Yu, Guotai; Steuernagel, Burkhard; Periyannan, Sambasivam; Wulff, Brande; Ayliffe, Mick; McIntosh, Robert; Keller, Beat; Lagudah, Evans; Zhang, Peng (2021). A highly differentiated region of wheat chromosome 7AL encodes a Pm1a immune receptor that recognizes its corresponding AvrPm1a effector from Blumeria graminis. New Phytologist, 229(5):2812-2826.

Akiyama, Reiko; Sun, Jianqiang; Hatakeyama, Masaomi; Lischer, Heidi E L; Briskine, Roman V; Hay, Angela; Gan, Xiangchao; Tsiantis, Miltos; Kudoh, Hiroshi; Kanaoka, Masahiro M; Sese, Jun; Shimizu, Kentaro K; Shimizu-Inatsugi, Rie (2021). Fine‐scale empirical data on niche divergence and homeolog expression patterns in an allopolyploid and its diploid progenitor species. New Phytologist, 229(6):3587-3601.

Brown, Jennifer A; Mbunkah, Herbert A; Lejone, Thabo I; Ringera, Isaac; Cheleboi, Molisana; Klimkait, Thomas; Metzner, Karin J; Günthard, Huldrych F; Labhardt, Niklaus D; Kouyos, Roger D; Tschumi, Nadine (2021). Emergence of Human Immunodeficiency Virus-1 Drug Resistance During the 3-Month World Health Organization-Recommended Enhanced Adherence Counseling Period in the CART-1 Cohort Study. Open Forum Infectious Diseases, 8(5):ofab046.

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.

Thieme, Michael; Roulin, Anne C (2021). Identification of Active Transposable Elements in Plants: The Mobilome-Seq Approach. In: Cho, Jungnam. Plant Transposable Elements. New York: Springer, 95-102.

Paro, Renato; Grossniklaus, Ueli; Santoro, Raffaella; Wutz, Anton Introduction to Epigenetics. Edited by: Paro, Renato; Santoro, Raffaella; Grossniklaus, Ueli; Wutz, Anton (2021). Cham, Schweiz: Springer Verlag.

Frangedakis, Eftychios; Shimamura, Masaki; Villarreal, Juan Carlos; Li, Fay‐Wei; Tomaselli, Marta; Waller, Manuel; Sakakibara, Keiko; Renzaglia, Karen S; Szövényi, Péter (2021). The hornworts: morphology, evolution and development. New Phytologist, 229(2):735-754.

Stritt, Christoph; Roulin, Anne C (2021). Detecting Signatures of TE Polymorphisms in Short-Read Sequencing Data. In: Cho, Jungnam. Plant transposable elements. New York: Springer, 177-187.

Germain, Pierre-Luc; Lun, Aaron; Garcia Meixide, Carlos; Macnair, Will; Robinson, Mark D (2021). Doublet identification in single-cell sequencing data using scDblFinder. F1000Research, 10:979.

Müller, Marion Claudia. Genomic and genetic analysis of host and cultivar adaption in the cereal powdery mildew pathosystem. 2021, University of Zurich, Faculty of Science.

Urban, Christian; Blom, Alette A; Pfrengle, Saskia; Walker-Meikle, Kathleen; Stone, Anne C; Inskip, Sarah A; Schuenemann, Verena J (2021). One Health Approaches to Trace Mycobacterium leprae's Zoonotic Potential Through Time. Frontiers in Microbiology, 12:762263.

Figueiredo, Alexandre R T. The Ecology and Evolution of Bacterial Social Interactions and How They Shape Microbial Communities and Interactions with Hosts. 2021, University of Zurich, Faculty of Science.

Gerber, Reto; Robinson, Mark D (2021). pubassistant.ch: consolidating publication profiles of researchers. F1000Research, 10:989.

2020

Walkowiak, Sean; Gao, Liangliang; Monat, Cecile; et al; Kolodziej, Markus C; Copetti, Dario; Krattinger, Simon G; Keller, Beat; Wicker, Thomas; Halstead-Nussloch, Gwyneth; Paape, Timothy; Shimizu-Inatsugi, Rie; Shimizu, Kentaro K (2020). Multiple wheat genomes reveal global variation in modern breeding. Nature, 588(7837):277-283.

Neukamm, Judith; Pfrengle, Saskia; Molak, Martyna; Seitz, Alexander; Francken, Michael; Eppenberger, Partick; Avanzi, Charlotte; Reiter, Ella; Urban, Christian; Welte, Beatrix; Stockhammer, Philipp W; Teßmann, Barbara; Herbig, Alexander; Harvati, Katerina; Nieselt, Kay; Krause, Johannes; Schuenemann, Verena J (2020). 2000-year-old pathogen genomes reconstructed from metagenomic analysis of Egyptian mummified individuals. BMC Biology, 18:108.

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

Furtwängler, Anja; Neukamm, Judith; Böhme, Lisa; Reiter, Ella; Vollstedt, Melanie; Arora, Natasha; Singh, Pushpendra; Cole, Stewart T; Knauf, Sascha; Calvignac-Spencer, Sébastien; Krause-Kyora, Ben; Krause, Johannes; Schuenemann, Verena J; Herbig, Alexander (2020). Comparison of target enrichment strategies for ancient pathogen DNA. BioTechniques, 69(6):455-459.

Urban, Matthias; Barbieri, Chiara (2020). North and South in the ancient Central Andes: Contextualizing the archaeological record with evidence from linguistics and molecular anthropology. Journal of Anthropological Archaeology, 60:101233.

Primo, Pasquale; Meccariello, Angela; Inghilterra, Maria Grazia; Gravina, Andrea; Del Corsano, Giuseppe; Volpe, Gennaro; Sollazzo, Germano; Aceto, Serena; Robinson, Mark D; Salvemini, Marco; Saccone, Giuseppe (2020). Targeting the autosomal Ceratitis capitata transformer gene using Cas9 or dCas9 to masculinize XX individuals without inducing mutations. BMC Genetics, 21(Suppl 2):150.

Crowell, Helena L; Soneson, Charlotte; Germain, Pierre-Luc; Calini, Daniela; Collin, Ludovic; Raposo, Catarina; Malhotra, Dheeraj; Robinson, Mark D (2020). muscat detects subpopulation-specific state transitions from multi-sample multi-condition single-cell transcriptomics data. Nature Communications, 11:6077.

Germain, Pierre-Luc; Sonrel, Anthony; Robinson, Mark D (2020). pipeComp, a general framework for the evaluation of computational pipelines, reveals performant single cell RNA-seq preprocessing tools. Genome Biology, 21(1):227.

Morozova, Irina; Kasianov, Artem; Bruskin, Sergey; Neukamm, Judith; Molak, Martyna; Batieva, Elena; Pudło, Aleksandra; Rühli, Frank J; Schuenemann, Verena J (2020). New ancient Eastern European Yersinia pestis genomes illuminate the dispersal of plague in Europe. Philosophical Transactions of the Royal Society of London. Series B: Biological Sciences, 375(1812):20190569.

Aubier, Thomas G; Galipaud, Matthias; Erten, E Yagmur; Kokko, Hanna (2020). Transmissible cancers and the evolution of sex under the Red Queen hypothesis. PLoS Biology, 18(11):e3000916.

Wyler, Michele; Stritt, Christoph; Walser, Jean-Claude; Baroux, Célia; Roulin, Anne C (2020). Impact of transposable elements on methylation and gene expression across natural accessions of Brachypodium distachyon. Genome Biology and Evolution, 12(11):1994-2001.

Huang, Ruizhu; Soneson, Charlotte; Ernst, Felix G M; Rue-Albrecht, Kevin C; Yu, Guangchuang; Hicks, Stephanie C; Robinson, Mark D (2020). TreeSummarizedExperiment: a S4 class for data with hierarchical structure. F1000Research, 9:1246.

Sun, Jianqiang; Shimizu-Inatsugi, Rie; Hofhuis, Hugo; Shimizu, Kentaro; Hay, Angela; Shimizu, Kentaro K; Sese, Jun (2020). A Recently Formed Triploid Cardamine insueta Inherits Leaf Vivipary and Submergence Tolerance Traits of Parents. Frontiers in Genetics, 11:567262.

Majander, Kerttu; Pfrengle, Saskia; Kocher, Arthur; Neukamm, Judith; du Plessis, Louis; Pla-Díaz, Marta; Arora, Natasha; Akgül, Gülfirde; Salo, Kati; Schats, Rachel; Inskip, Sarah; Oinonen, Markku; Valk, Heiki; Malve, Martin; Kriiska, Aivar; Onkamo, Päivi; González-Candelas, Fernando; Kühnert, Denise; Krause, Johannes; Schuenemann, Verena J (2020). Ancient Bacterial Genomes Reveal a High Diversity of Treponema pallidum Strains in Early Modern Europe. Current Biology, 30(19):3788-3803.e10.

Paape, Timothy; Akiyama, Reiko; Cereghetti, Teo; Onda, Yoshihiko; Hirao, Akira S; Kenta, Tanaka; Shimizu, Kentaro K (2020). Experimental and Field Data Support Range Expansion in an Allopolyploid Arabidopsis Owing to Parental Legacy of Heavy Metal Hyperaccumulation. Frontiers in Genetics, 11:1162.

Skalska, Aleksandra; Stritt, Christoph; Wyler, Michele; Williams, Hefin W; Vickers, Martin; Han, Jiwan; Tuna, Metin; Savas Tuna, Gulsemin; Susek, Karolina; Swain, Martin; Wóycicki, Rafał K; Chaudhary, Saurabh; Corke, Fiona; Doonan, John H; Roulin, Anne C; Hasterok, Robert; Mur, Luis A J (2020). Genetic and methylome variation in Turkish Brachypodium distachyon accessions differentiate two geographically distinct subpopulations. International Journal of Molecular Sciences, 21(18):6700.

Stritt, Christoph; Wyler, Michele; Gimmi, Elena L; Pippel, Martin; Roulin, Anne C (2020). Diversity, dynamics and effects of long terminal repeat retrotransposons in the model grass Brachypodium distachyon. New Phytologist, 227(6):1736-1748.

Lindner, Stefan; Keller, Bettina; Singh, Simrat P; Hasenkamp, Zsuzsanna; Jung, Esther; Müller, Marion C; Bourras, Salim; Keller, Beat (2020). Single residues in the LRR domain of the wheat PM3A immune receptor can control the strength and the spectrum of the immune response. The Plant Journal, 104(1):200-214.

Hanya, Goro; Tackmann, Janko; Sawada, Akiko; Lee, Wanyi; Pokharel, Sanjeeta Sharma; de Castro Maciel, Valdevino Gisele; Toge, Akito; Kuroki, Kota; Otsuka, Ryoma; Mabuchi, Ryoma; Liu, Jie; Hatakeyama, Masaomi; Yamasaki, Eri; von Mering, Christian; Shimizu-Inatsugi, Rie; Hayakawa, Takashi; Shimizu, Kentaro K; Ushida, Kazunari (2020). Fermentation Ability of Gut Microbiota of Wild Japanese Macaques in the Highland and Lowland Yakushima: In Vitro Fermentation Assay and Genetic Analyses. Microbial Ecology, 80(2):459-474.

Weber de Melo, Vanessa; Lowe, Robert; Hurd, Paul J; Petchey, Owen L (2020). Phenotypic responses to temperature in the ciliate Tetrahymena thermophila. Ecology and Evolution, 10(14):7616-7626.

Linde, Anna-Malin; Sawangproh, Weerachon; Cronberg, Nils; Szövényi, Péter; Lagercrantz, Ulf (2020). Evolutionary history of the Marchantia polymorpha complex. Frontiers in Plant Science, 11:829.

Kirbis, Alexander; Waller, Manuel; Ricca, Mariana; Bont, Zoe; Neubauer, Anna; Goffinet, Bernard; Szövényi, Péter (2020). Transcriptional landscapes of divergent sporophyte development in two mosses, Physcomitrium (Physcomitrella) patens and Funaria hygrometrica. Frontiers in Plant Science, 11:747.

Cairns, Johannes; Moerman, Felix; Fronhofer, Emanuel A; Altermatt, Florian; Hiltunen, Teppo (2020). Evolution in interacting species alters predator life-history traits, behaviour and morphology in experimental microbial communities. Proceedings of the Royal Society of London, Series B: Biological Sciences, 287(1928):20200652.

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.

Moerman, Felix; Fronhofer, Emanuel A; Wagner, Andreas; Altermatt, Florian (2020). Gene swamping alters evolution during range expansions in the protist Tetrahymena thermophila. Biology Letters, 16(6):20200244.

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.

Nakatsuka, Nathan; Lazaridis, Iosif; Barbieri, Chiara; Skoglund, Pontus; Rohland, Nadin; Mallick, Swapan; Posth, Cosimo; Harkins-Kinkaid, Kelly; Ferry, Matthew; Harney, Éadaoin; Michel, Megan; Stewardson, Kristin; Novak-Forst, Jannine; Capriles, José M; Durruty, Marta Alfonso; Álvarez, Karina Aranda; Beresford-Jones, David; Burger, Richard; Cadwallader, Lauren; Fujita, Ricardo; Isla, Johny; Lau, George; Aguirre, Carlos Lémuz; LeBlanc, Steven; Maldonado, Sergio Calla; Meddens, Frank; Messineo, Pablo G; Culleton, Brendan J; Harper, Thomas K; Quilter, Jeffrey; et al (2020). A Paleogenomic Reconstruction of the Deep Population History of the Andes. Cell, 181(5):1131-1145.e21.

Figueiredo, Alexandre R T; Kramer, Jos (2020). Cooperation and Conflict Within the Microbiota and Their Effects On Animal Hosts. Frontiers in Ecology and Evolution, 8:132.

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.

Wyder, Stefan; Rivera, Alejandro; Valdés, Ana E; Cañal, María Jesús; Gagliardini, Valeria; Fernández, Helena; Grossniklaus, Ueli (2020). Differential gene expression profiling of one- and two-dimensional apogamous gametophytes of the fern Dryopteris affinis ssp. affinis. Plant Physiology and Biochemistry, 148:302-311.

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.

Akiyama, Reiko; Milosavljevic, Stefan; Leutenegger, Matthias; Shimizu-Inatsugi, Rie (2020). Trait-dependent resemblance of the flowering phenology and floral morphology of the allopolyploid Cardamine flexuosa to those of the parental diploids in natural habitats. Journal of Plant Research, 133(2):147-155.

Tabrett, Alexandra; Horton, Matthew W (2020). The influence of host genetics on the microbiome. F1000Research, 9:84.

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.

Lähnemann, David; Köster, Johannes; Szczurek, Ewa; McCarthy, Davis J; Hicks, Stephanie C; Robinson, Mark D; et al (2020). Eleven grand challenges in single-cell data science. Genome Biology, 21:31.

Weber de Melo, Vanessa. Phenotype and Transcriptome Responses during Growth and Temperature Stress in the Ciliate Tetrahymena thermophila. 2020, University of Zurich, Faculty of Science.

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). From zygote to a multicellular soma: body size affects optimal growth strategies under cancer risk. bioRxiv 877118, Cold Spring Harbor Laboratory.

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.

Bergelson, Joy; Mittelstrass, Jana; Horton, Matthew W (2019). Characterizing both bacteria and fungi improves understanding of the Arabidopsis root microbiome. Scientific Reports, 9:24.

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.

Grize, Sofia A. Chromosomal Variation and Its Effects on Reproductive Isolation in the Western House Mouse Mus musculus domesticus. 2019, University of Zurich, Faculty of Science.

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.

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.

Perez-Shibayama, Christian; Gil-Cruz, Cristina; Cheng, Hung-Wei; Onder, Lucas; Printz, Andrea; Mörbe, Urs; Novkovic, Mario; Li, Conglei; Lopez-Macias, Constantino; Buechler, Matthew B; Turley, Shannon J; Mack, Matthias; Soneson, Charlotte; Robinson, Mark D; Scandella, Elke; Gommerman, Jennifer; Ludewig, Burkhard (2018). Fibroblastic reticular cells initiate immune responses in visceral adipose tissues and secure peritoneal immunity. Science Immunology, 3(26):eaar4539.

Kellenberger, Roman Tobias. Insect-mediated microevolution of flowering plants. 2018, University of Zurich, Faculty of Science.

Pinto Carbó, Marta Adriana. Leaf nodule symbiosis in the genomic era : new insights into bacterial symbiont evolution, function and transmission. 2018, University of Zurich, Faculty of Science.

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.

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.

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, 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.

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, 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; 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-Carbó, 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, 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.