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Graff, Anna; Chousou-Polydouri, Natalia; Inman, David; Skirgård, Hedvig; Lischka, Marc; Zakharko, Taras; Barbieri, Chiara; Bickel, Balthasar (2025). Curating global datasets of structural linguistic features for independence. Scientific Data, 12(1):106.
Nomura, Yasuyuki; Okada, Moeko; Tameshige, Toshiaki; Takenaka, Shotaro; Shimizu, Kentaro K; Nasuda, Shuhei; Nagano, Atsushi J (2025). Subgenome-informed statistical modeling of transcriptomes in 25 common wheat accessions reveals $cis$- and $trans$-regulation architectures. Plant & Cell Physiology:Epub ahead of print.
Morris, Alan G; Salie, Tasneem; Mittnik, Alissa; Rebello, George; Barbieri, Chiara; Parkington, John; Krause, Johannes; Ramesar, Raj (2025). Reconstructing ancient Southern African mitochondrial genomes at Faraoskop. Archaeological and Anthropological Sciences, 17(1):11-26.
Sotiropoulos, Alexandros G; Sánchez-Martín, Javier; Widrig, Victoria; Isaksson, Jonatan; Bernasconi, Zoe; Koller, Teresa; Bearth, Giulia; Herren, Gerhard; Wicker, Thomas; Keller, Beat (2024). 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, 58(5):1022-1034.
Urban, Christian; Blom, Alette A; Avanzi, Charlotte; Walker-Meikle, Kathleen; Warren, Alaine K; White-Iribhogbe, Katie; Turle, Ross; Marter, Phil; Dawson-Hobbis, Heidi; Roffey, Simon; Inskip, Sarah A; Schuenemann, Verena J (2024). Ancient Mycobacterium leprae genome reveals medieval English red squirrels as animal leprosy host. Current Biology, 34(10):2221-2230.e8.
Wilkin, Shevan; Lanigan, Liam T; Montes, Nuria; Sharma, Mukul; Avanzi, Charlotte; Sejdiu, Donikë; Majander, Kerttu; Pfrengle, Saskia; Chiang, Yun; Kunz, Laura; Dittmann, Antje; Rühli, Frank; Singh, Pushpendra; Coll, Maria Fontanals; Collins, Matthew J; Taurozzi, Alberto J; Schuenemann, Verena J (2024). Sequential trypsin and ProAlanase digestions unearth immunological protein biomarkers shrouded by skeletal collagen. iScience, 27(5):109663.
Passmore, Sam; Wood, Anna L C; Barbieri, Chiara; Shilton, Dor; Daikoku, Hideo; Atkinson, Quentin D; Savage, Patrick E (2024). Global musical diversity is largely independent of linguistic and genetic histories. Nature Communications, 15(1):3964.
Dmitrijeva, Marija; Tackmann, Janko; Matias Rodrigues, João Frederico; Huerta-Cepas, Jaime; Coelho, Luis Pedro; von Mering, Christian (2024). A global survey of prokaryotic genomes reveals the eco-evolutionary pressures driving horizontal gene transfer. Nature Ecology and Evolution, 8(5):986-998.
Minadakis, Nikolaos; Kaderli, Lars; Horvath, Robert; Bourgeois, Yann; Xu, Wenbo; Thieme, Michael; Woods, Daniel P; Roulin, Anne C (2024). Polygenic architecture of flowering time and its relationship with local environments in the grass Brachypodium distachyon. Genetics, 227(1):iyae042.
Horvath, Robert; Minadakis, Nikolaos; Bourgeois, Yann; Roulin, Anne C (2024). The evolution of transposable elements in Brachypodium distachyon is governed by purifying selection, while neutral and adaptive processes play a minor role. eLife, 12:RP93284.
Thieme, Michael; Minadakis, Nikolaos; Himber, Christophe; Keller, Bettina; Xu, Wenbo; Rutowicz, Kinga; Matteoli, Calvin; Böhrer, Marcel; Rymen, Bart; Laudencia-Chingcuanco, Debbie; Vogel, John P; Sibout, Richard; Stritt, Christoph; Blevins, Todd; Roulin, Anne C (2024). Transposition of HOPPLA in siRNA-deficient plants suggests a limited effect of the environment on retrotransposon mobility in Brachypodium distachyon. PLoS Genetics, 20(3):e1011200.
Majander, Kerttu; Pla-Díaz, Marta; du Plessis, Louis; Arora, Natasha; Filippini, Jose; Pezo-Lanfranco, Luis; Eggers, Sabine; González-Candelas, Fernando; Schuenemann, Verena J (2024). Redefining the treponemal history through pre-Columbian genomes from Brazil. Nature, 627(8002):182-188.
Stockenhuber, Reinhold; Akiyama, Reiko; Tissot, Nicolas; Milosavljevic, Stefan; Yamazaki, Misako; Wyler, Michele; Arongaus, Adriana B; Podolec, Roman; Sato, Yasuhiro; Widmer, Alex; Ulm, Roman; Shimizu, Kentaro K (2024). The UV RESISTANCE LOCUS 8-Mediated UV-B Response Is Required Alongside CRYPTOCHROME 1 For Plant Survival Under Sunlight In Field Conditions. Plant & Cell Physiology, 65(1):35-48.
Okada, Moeko; Shimizu, Kentaro K (2024). Wheat: Recent Advances in Genomics to Explore the History of Domestication and Polyploidization. In: Osada, N; Kumagai, M; Suzuki, H; Endo, M. Phylogeographic History of Plants and Animals Coexisting with Humans in Asia. Singapore: Springer, 155-180.
Neubauer, Anna; Aros-Mualin, Daniela; Mariscal, Vicente; Szövényi, Péter (2024). Challenging the term symbiosis in plant-microbe associations to create an understanding across sciences. Journal of integrative plant biology, 66(1):7-11.
Giesen, Athene; Blanckenhorn, Wolf U; Schäfer, Martin A; Shimizu, Kentaro K; Shimizu-Inatsugi, Rie; Misof, Bernhard; Podsiadlowski, Lars; Niehuis, Oliver; Lischer, Heidi E L; Aeschbacher, Simon; Kapun, Martin (2023). Geographic Variation in Genomic Signals of Admixture Between Two Closely Related European Sepsid Fly Species. Evolutionary Biology, 50(4):395-412.
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.
Yew, Chow-Lih; Tsuchimatsu, Takashi; Shimizu-Inatsugi, Rie; Yasuda, Shinsuke; Hatakeyama, Masaomi; Kakui, Hiroyuki; Ohta, Takuma; Suwabe, Keita; Watanabe, Masao; Takayama, Seiji; Shimizu, Kentaro K (2023). Dominance in self-compatibility between subgenomes of allopolyploid Arabidopsis kamchatica shown by transgenic restoration of self-incompatibility. Nature Communications, 14(1):7618.
Arango-Isaza, Epifanía; Aninao, María José; Campbell, Roberto; Martinez, Felipe I; Shimizu, Kentaro K; Barbieri, Chiara (2023). Bridging the gap: returning genetic results to indigenous communities in Latin America. Frontiers in Genetics, 14:1304974.
Loponte, Daniel; Acosta, Alejandro; Gascue, Andrés; Pfrengle, Saskia; Schuenemann, Verena J; Bortolotto, Noelia; Carbonera, Mirian; García Esponda, César; Voglino, Damián; Milheira, Rafael; Ferrari, Alejandro; Borges, Caroline (2023). The Southernmost Pre-Columbian Dogs in the Americas: Phenotype, Chronology, Diet and Genetics. Environmental Archaeology, 28(6):443-474.
Loosli, Tom; Hossmann, Stefanie; Ingle, Suzanne M; Okhai, Hajra; Kusejko, Katharina; Mouton, Johannes; Bellecave, Pantxika; van Sighem, Ard; Stecher, Melanie; d'Arminio Monforte, Antonella; Gill, M John; Sabin, Caroline A; Maartens, Gary; Günthard, Huldrych F; Sterne, Jonathan A C; Lessells, Richard; Egger, Matthias; Kouyos, Roger D (2023). HIV-1 drug resistance in people on dolutegravir-based antiretroviral therapy: a collaborative cohort analysis. The Lancet : HIV, 10(11):e733-e741.
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.
Minadakis, Nikolaos; Williams, Hefin; Horvath, Robert; Caković, Danka; Stritt, Christoph; Thieme, Michael; Bourgeois, Yann; Roulin, Anne C (2023). The demographic history of the wild crop relative Brachypodium distachyon is shaped by distinct past and present ecological niches. Peer Community Journal, 3:e84.
Wilkin, Shevan; Hommel, Peter; Ventresca Miller, Alicia; Boivin, Nicole; Pedergnana, Antonella; Shishlina, Natalia; Trifonov, Viktor (2023). Curated cauldrons: Preserved proteins from early copper-alloy vessels illuminate feasting practices in the Caucasian steppe. iScience, 26(9):107482.
Wang, Ke; Prüfer, Kay; Krause-Kyora, Ben; Childebayeva, Ainash; Schuenemann, Verena J; Coia, Valentina; Maixner, Frank; Zink, Albert; Schiffels, Stephan; Krause, Johannes (2023). High-coverage genome of the Tyrolean Iceman reveals unusually high Anatolian farmer ancestry. Cell Genomics, 3(9):100377.
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.
Schmeing, Stephan; Robinson, Mark D (2023). Gapless provides combined scaffolding, gap filling, and assembly correction with long reads. Life Science Alliance, 6(7):e202201471.
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.
Sonrel, Anthony; Luetge, Almut; Soneson, Charlotte; Mallona, Izaskun; Germain, Pierre-Luc; Knyazev, Sergey; Gilis, Jeroen; Gerber, Reto; Seurinck, Ruth; Paul, Dominique; Sonder, Emanuel; Crowell, Helena L; Fanaswala, Imran; Al-Ajami, Ahmad; Heidari, Elyas; Schmeing, Stephan; Milosavljevic, Stefan; Saeys, Yvan; Mangul, Serghei; Robinson, Mark D (2023). Meta-analysis of (single-cell method) benchmarks reveals the need for extensibility and interoperability. Genome Biology, 24(1):119.
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.
Russo, Alessia. The genome assembly of Ophrys sphegodes to explore the genomic basis of rapid evolution in a mediterranean orchid. 2023, University of Zurich, Faculty of Science.
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.
Karve, Shraddha; Dasmeh, Pouria; Zheng, Jia; Wagner, Andreas (2022). Low protein expression enhances phenotypic evolvability by intensifying selection on folding stability. Nature Ecology and Evolution, 6(8):1155-1164.
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.
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.
Baumann, Chris; Pfrengle, Saskia; Münzel, Susanne C; Molak, Martyna; Feuerborn, Tatiana R; Breidenstein, Abagail; Reiter, Ella; Albrecht, Gerd; Kind, Claus-Joachim; Verjux, Christian; Leduc, Charlotte; Conard, Nicholas J; Drucker, Dorothée G; Giemsch, Liane; Thalmann, Olaf; Bocherens, Hervé; Schuenemann, Verena J (2021). A refined proposal for the origin of dogs: the case study of Gnirshöhle, a Magdalenian cave site. Scientific Reports, 11:5137.
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.
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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.
Novikova, Polina Yu; Hohmann, Nora; Nizhynska, Viktoria; Tsuchimatsu, Takashi; Ali, Jamshaid; Muir, Graham; Guggisberg, Alessia; Paape, Tim; Schmid, Karl; Fedorenko, Olga M; Holm, Svante; Säll, Torbjörn; Schlötterer, Christian; Marhold, Karol; Widmer, Alex; Sese, Jun; Shimizu, Kentaro K; Weigel, Detlef; Krämer, Ute; Koch, Marcus A; Nordborg, Magnus (2016). Sequencing of the genus Arabidopsis identifies a complex history of nonbifurcating speciation and abundant trans-specific polymorphism. Nature Genetics, 48(9):1077-1082.
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.
Shimizu, Kentaro K; Tsuchimatsu, Takashi (2015). Evolution of selfing: recurrent patterns in molecular adaptation. Annual Review of Ecology, Evolution and Systematics, 46:593-622.
Bratulic, Sinisa; Gerber, Florian; Wagner, Andreas (2015). Mistranslation drives the evolution of robustness in TEM-1 β-lactamase. Proceedings of the National Academy of Sciences of the United States of America, 112(41):12758-12763.
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.
Morger, Jennifer; Raberg, L; Hille, S M; Helsen, S; Štefka, J; Al-Sabi, M M; Kapel, C M O; Mappes, T; Essbauer, S; Ulrich, R G; Bartolommei, P; Mortelliti, A; Balčiauskas, L; van den Brink, N W; Rémy, A; Bajer, A; Cheprakov, M; Korva, M; García-Pérez, A L; Biek, R; Withenshaw, S; Tschirren, Barbara (2015). Distinct haplotype structure at the innate immune receptor Toll-like receptor 2 (TLR2) across bank vole populations and lineages in Europe. Biological Journal of the Linnean Society, 116(1):124-133.
Tschirren, Barbara (2015). Borrelia burgdorferi sensu lato infection pressure shapes innate immune gene evolution in natural rodent populations across Europe. Biology Letters, 11(5):20150263.
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.
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.
Morger, Jennifer; Bajnok, Jaroslav; Boyce, Kellyanne; Craig, Philip S; Rogan, Michel T; Lun, Zhao-Rong; Hide, Geoff; Tschirren, Barbara (2014). Naturally occurring Toll-like receptor 11 (TLR11) and Toll-like receptor 12 (TLR12) polymorphisms are not associated with Toxoplasma gondii infection in wild wood mice. Infection, Genetics and Evolution, 26:180-184.
Shimizu-Inatsugi, Rie; Shimizu, Kentaro K (2014). Speciation after the 20th century: adaptation to new environments by genome duplications. Cell Technology, 33(8):878-883.
Franceschini, Andrea; Meier, Roger; Casanova, Alain; Kreibich, Saskia; Daga, Neha; Andritschke, Daniel; Dilling, Sabrina; Rämö, Pauli; Emmenlauer, Mario; Kaufmann, Andreas; Conde-Álvarez, Raquel; Low, Shyan Huey; Pelkmans, Lucas; Helenius, Ari; Hardt, Wolf-Dietrich; Dehio, Christoph; von Mering, Christian (2014). Specific inhibition of diverse pathogens in human cells by synthetic microRNA-like oligonucleotides inferred from RNAi screens. Proceedings of the National Academy of Sciences of the United States of America, 111(12):4548-4553.
Powell, Sean; Forslund, Kristoffer; Szklarczyk, Damian; Trachana, Kalliopi; Roth, Alexander; Huerta-Cepas, Jaime; Gabaldón, Toni; Rattei, Thomas; Creevey, Chris; Kuhn, Michael; Jensen, Lars J; von Mering, Christian; Bork, Peer (2014). eggNOG v4.0: nested orthology inference across 3686 organisms. Nucleic Acids Research, 42(1):D231-D239.
Ogura, Atsushi; Yoshida, Masa-aki; Moritaki, Takeya; Sese, Jun; Shimizu, Kentaro K; Sousounis, Konstantinos; Tsonis, Panagiotis A (2013). Loss of the six3/6 controlling pathways might have resulted in pinhole-eye evolution in Nautilus. Scientific Reports, 3:1432.
Shimizu, Kentaro K (2013). Pollen, Pollen tube, Selfing, Pistil, Ovule, Endosperm, Embryo sac, Sporangium, Stamen. In: Iwasa, Yoh; Kuratani, Shigeru; Saitou, Naruya; Tsukaya, Hirokazu. Iwanami Biology Dictionary, 5th Edition. Tokyo: Iwanami, nn-nn.
Tsuchimatsu, Takashi; Shimizu, Kentaro K (2013). Effects of pollen availability and the mutation bias on the fixation of mutations disabling the male specificity of self-incompatibility. Journal of Evolutionary Biology, 26(10):2221-2232.
Tsuchimatsu, Takashi; Shimizu, Kentaro K (2013). Evolutionary Ecology of self-incompatibility: studying natural selection on plant self-recognition systems. Iden : the Review of Biological Sciences, 67:244-251.
Franceschini, Andrea; Szklarczyk, Damian; Frankild, Sune; Kuhn, Michael; Simonovic, Milan; Roth, Alexander; Lin, Jianyi; Minguez, Pablo; Bork, Peer; von Mering, Christian; Jensen, Lars J (2013). STRING v9.1: protein-protein interaction networks, with increased coverage and integration. Nucleic Acids Research, 41(D 1):D808-D815.
Mandákova, Terezie; Kovarík, Ales; Zozomová-Lihova, Judita; Shimizu-Inatsugi, Rie; Shimizu, Kentaro K; Mummenhoff, Klaus; Marhold, Karol; Lysak, Martin A (2013). The more the merrier: Recent hybridization and polyploidy in Cardamine. Plant Cell, 25(9):3280-3295.
