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Number of items at this level: 88.


Dainat, Benjamin; Oberhaensli, Simone; Ory, Florine; Dietemann, Vincent (2023). New reference genomes of honey bee-associated bacteria Paenibacillus melissococcoides, Paenibacillus dendritiformis, and Paenibacillus thiaminolyticus. Microbiology resource announcements, 12(9), e0020923. American Society for Microbiology 10.1128/MRA.00209-23


Turgay, Meral; Falentin, Hélène; Irmler, Stefan; Fröhlich-Wyder, Marie-Therese; Meola, Marco; Oberhaensli, Simone; Berthoud-Dit-Gallon Marchand, Hélène (2022). Genomic rearrangements in the aspA-dcuA locus of Propionibacterium freudenreichii are associated with aspartase activity. Food microbiology, 106, p. 104030. Elsevier 10.1016/j.fm.2022.104030

Somerville, Vincent; Schowing, Thibault; Chabas, Hélène; Schmidt, Remo S; von Ah, Ueli; Bruggmann, Rémy; Engel, Philipp (2022). Extensive diversity and rapid turnover of phage defense repertoires in cheese-associated bacterial communities. Microbiome, 10(1), p. 137. BioMed Central 10.1186/s40168-022-01328-6

Tomasini, Matteo; Peischl, Stephan (2022). The role of spatial structure in multi-deme models of evolutionary rescue. Journal of evolutionary biology, 35(7), pp. 986-1001. Wiley 10.1111/jeb.14018

Ryser, Lorenz Timo; Arias-Roth, Emmanuelle; Berthoud, Hélène; Delbès-Paus, Céline; Chassard, Christophe; Bruggmann, Rémy; Imler, Stefan (2022). Cadaverine, putrescine, and histamine formation of Morganella morganii in raclette-type cheese. International dairy journal, 129, p. 105362. Elsevier 10.1016/j.idairyj.2022.105362

Gilbert, Kimberly J.; Moinet, Antoine; Peischl, Stephan (2022). Gene surfing of underdominant alleles promotes formation of hybrid zones. Philosophical transactions of the Royal Society. Series B - biological sciences, 377(1846), p. 20210006. Royal Society of London 10.1098/rstb.2021.0006

Hobi, Gabriel; Cline, J Mark; Ethun, Kelly F; Simillion, Cedric; Keller, Irene; Stute, Petra (2022). Impact of 6 month conjugated equine estrogen versus estradiol-treatment on biomarkers and enriched gene sets in healthy mammary tissue of non-human primates. PLoS ONE, 17(3), e0264057. Public Library of Science 10.1371/journal.pone.0264057

Silva, Sandro Valerio; Andermann, Tobias; Zizka, Alexander; Kozlowski, Gregor; Silvestro, Daniele (2022). Global Estimation and Mapping of the Conservation Status of Tree Species Using Artificial Intelligence. Frontiers in Plant Science, 13, p. 839792. Frontiers 10.3389/fpls.2022.839792


Duruz, Jules; Kaltenrieder, Cyrielle; Ladruner, Peter; Bruggmann, Rémy; Martinez, Pedro; Sprecher, Simon (2021). Acoel Single-Cell Transcriptomics: Cell Type Analysis of a Deep Branching Bilaterian. Molecular biology and evolution, 38(5), pp. 1888-1904. Oxford University Press 10.1093/molbev/msaa333

Shani, Noam; Oberhaensli, Simone; Berthoud, Hélène; Schmidt, Remo S.; Bachmann, Hans-Peter (2021). Antimicrobial Susceptibility of Lactobacillus delbrueckii subsp. lactis from Milk Products and Other Habitats. Foods, 10(12) MDPI 10.3390/foods10123145

Ryser, Lorenz Timo; Arias-Roth, Emmanuelle; Perreten, Vincent; Irmler, Stefan; Bruggmann, Rémy (2021). Genetic and Phenotypic Diversity of Morganella morganii Isolated From Cheese. Frontiers in Microbiology, 12(738492), p. 738492. Frontiers 10.3389/fmicb.2021.738492

Kuhn-Nentwig, Lucia; Lischer, Heidi E. L.; Pekár, Stano; Langenegger, Nicolas; Albo, Maria J.; Isaia, Marco; Nentwig, Wolfgang (2021). Linear Peptides-A Combinatorial Innovation in the Venom of Some Modern Spiders. Frontiers in Molecular Biosciences, 8, p. 705141. Frontiers 10.3389/fmolb.2021.705141

Shani, Noam; Oberhaensli, Simone; Arias-Roth, Emmanuelle (2021). Antibiotic susceptibility profiles of Pediococcus pentosaceus from various origins and their implications for the safety assessment of strains with food-technology applications. Journal of food protection, 84(7), pp. 1160-1168. International Association for Food Protection 10.4315/JFP-20-363

Zheng, Jia; Bratulic, Sinisa; Lischer, Heidi E. L.; Wagner, Andreas (2021). Mistranslation can promote the exploration of alternative evolutionary trajectories in enzyme evolution. Journal of evolutionary biology, 34(8), pp. 1302-1315. Wiley 10.1111/jeb.13892

Reuther, Julia; Schneider, Lukas; Iacovache, Ioan; Pircher, Andreas; Gharib, Walid H.; Zuber, Benoît; Polacek, Norbert (2021). A small ribosome-associated ncRNA globally inhibits translation by restricting ribosome dynamics. RNA biology, 18(12), pp. 2617-2632. Taylor and Francis 10.1080/15476286.2021.1935573

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), pp. 2350-2363. Wiley 10.1111/1755-0998.13442

Akiyama, Reiko; Janqiang, Sun; Hatakeyam, 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), pp. 3587-3601. Wiley-Blackwell 10.1111/nph.17101

Herzog, Elio L; Wäfler, Melania; Keller, Irene; Wolf, Sebastian; Zinkernagel, Martin S; Zysset-Burri, Denise C (2021). The importance of age in compositional and functional profiling of the human intestinal microbiome. PLoS ONE, 16(10), e0258505. Public Library of Science 10.1371/journal.pone.0258505


Dylus, David; Pillonel, Trestan; Opota, Onya; Wüthrich, Daniel; Seth-Smith, Helena M. B.; Egli, Adrian; Leo, Stefano; Lazarevic, Vladimir; Schrenzel, Jacques; Laurent, Sacha; Bertelli, Claire; Blanc, Dominique S.; Neuenschwander, Stefan; Ramette, Alban; Falquet, Laurent; Imkamp, Frank; Keller, Peter M.; Kahles, Andre; Oberhaensli, Simone; Barbié, Valérie; ... (2020). NGS-Based S. aureus Typing and Outbreak Analysis in Clinical Microbiology Laboratories: Lessons Learned From a Swiss-Wide Proficiency Test. Frontiers in Microbiology, 11, p. 591093. Frontiers 10.3389/fmicb.2020.591093

Tomasini, Matteo; Peischl, Stephan (2020). When does gene flow facilitate evolutionary rescue? Evolution, 74(8), pp. 1640-1653. Wiley 10.1111/evo.14038

Simon, R; Lischer, H. E. L.; Pieńkowska-Schelling, A.; Keller, I.; Häfliger, I. M.; Letko, A.; Schelling, C; Lühken, G; Drögemüller, C. (2020). New genomic features of the polled intersex syndrome variant in goats unraveled by long-read whole-genome sequencing. Animal genetics, 51(3), pp. 439-448. Wiley 10.1111/age.12918

Peischl, Stephan; Gilbert, Kimberly J. (2020). Evolution of dispersal can rescue populations from expansion load. The American naturalist, 195(2), pp. 349-360. University of Chicago Press 10.1086/705993

Cvitas, Iva; Oberhänsli, Simone; Leeb, Tosso; Dettwiler, Martina; Müller, Eliane Jasmine; Bruggmann, Rémy; Marti, Eliane Isabelle (2020). Investigating the epithelial barrier and immune signatures in the pathogenesis of equine insect bite hypersensitivity. PLoS ONE, 15(4), e0232189. Public Library of Science 10.1371/journal.pone.0232189

Zysset-Burri, Denise C.; Keller, Irene; Berger, Lieselotte E.; Largiadèr, Carlo R.; Wittwer, Matthias; Wolf, Sebastian; Zinkernagel, Martin S. (2020). Associations of the intestinal microbiome with the complement system in neovascular age-related macular degeneration. NPJ genomic medicine, 5(34), p. 34. Springer Nature 10.1038/s41525-020-00141-0

Barut, G. Tuba; Lischer, Heidi E. L.; Bruggmann, Rémy; Summerfield, Artur; Talker, Stephanie C. (2020). Transcriptomic profiling of bovine blood dendritic cells and monocytes following TLR stimulation. European journal of immunology, 50(11), pp. 1691-1711. Wiley-VCH 10.1002/eji.202048643

Rodriguez-Lorenzo, Sabela; Ferreira Francisco, David Miguel; Vos, Ricardo; van het Hof, Bert; Rijnsburger, Merel; Schroten, Horst; Ishikawa, Hiroshi; Beaino, Wissam; Bruggmann, Rémy; Kooji, Gjis; de Vries, Helga (2020). Altered secretory and neuroprotective function of the choroid plexus in progressive multiple sclerosis. Acta neuropathologica communications, 8(1), p. 35. BioMed Central 10.1186/s40478-020-00903-y


Brunet Avalos, Clarisse; Maier, G Larisa; Bruggmann, Rémy; Sprecher, Simon G (2019). Single cell transcriptome atlas of the Drosophila larval brain. eLife, 8 eLife Sciences Publications 10.7554/eLife.50354

Liechti, Nicole; Schürch, Nadia; Bruggmann, Rémy; Wittwer, Matthias (2019). Nanopore sequencing improves the draft genome of the human pathogenic amoeba Naegleria fowleri. Scientific reports, 9(16040), pp. 1-10. Springer Nature 10.1038/s41598-019-52572-0

Peischl, Stephan; Gidoin, Cindy (2019). Range Expansion Theories Could Shed Light on the Spatial Structure of Intra-tumour Heterogeneity. Bulletin of mathematical biology, 81(11), pp. 4761-4777. Springer 10.1007/s11538-018-00540-6

Machado, Ricardo A. R.; Bruno, Pamela; Arce, Carla C. M.; Liechti, Nicole; Köhler, Angela; Bernal, Julio; Bruggmann, Rémy; Turlings, Ted C. J. (2019). Photorhabdus khanii subsp. guanajuatensis subsp. nov., isolated from Heterorhabditis atacamensis, and Photorhabdus luminescens subsp. mexicana subsp. nov., isolated from Heterorhabditis mexicana entomopathogenic nematodes. International journal of systematic and evolutionary microbiology, 69(3), pp. 652-661. Society for General Microbiology SGM 10.1099/ijsem.0.003154

Luedin, Samuel M.; Liechti, Nicole; Cox, Raymond P.; Danza, Francesco; Frigaard, Niels-Ulrik; Posth, Nicole R.; Pothier, Joël F.; Roman, Samuele; Storelli, Nicola; Wittwer, Matthias; Tonolla, Mauro (2019). Draft Genome Sequence of Chromatium okenii Isolated from the Stratified Alpine Lake Cadagno. Scientific Reports, 9(1) Nature Publishing Group 10.1038/s41598-018-38202-1


Schmid, Marc W.; Heichinger, Christian; Coman Schmid, Diana; Guthörl, Daniela; Gagliardini, Valeria; Bruggmann, Rémy; Aluri, Sirisha; Aquino, Catharine; Schmid, Bernhard; Turnbull, Lindsay A.; Grossniklaus, Ueli (2018). Contribution of epigenetic variation to adaptation in Arabidopsis. Nature communications, 9(1), p. 4446. Nature Publishing Group 10.1038/s41467-018-06932-5

Lüdin, Petra; Roetschi, Alexandra; Wüthrich, Daniel; Bruggmann, Rémy; Berthoud, Hélène; Shani, Noam (2018). Update on Tetracycline Susceptibility of Pediococcus acidilactici Based on Strains Isolated from Swiss Cheese and Whey. Journal of food protection, 81(10), pp. 1582-1589. International Association for Food Protection 10.4315/0362-028X.JFP-18-160

Gilbert, Kimberly J.; Peischl, Stephan; Excoffier, Laurent (2018). Mutation load dynamics during environmentally-driven range shifts. PLoS genetics, 14(9), pp. 1-18. Public Library of Science 10.1371/journal.pgen.1007450

Liechti, Nicole; Schürch, Nadia; Bruggmann, Rémy; Wittwer, Matthias (2018). The genome of Naegleria lovaniensis, the basis for a comparative approach to unravel pathogenicity factors of the human pathogenic amoeba N. fowleri. BMC Genomics, 19(1), p. 654. BioMed Central 10.1186/s12864-018-4994-1

Machado, Ricardo A. R.; Wüthrich, Daniel; Kuhnert, Peter; Arce, Carla C. M.; Thönen, Lisa; Ruiz, Celia; Zhang, Xi; Robert, Christelle A. M.; Karimi, Javad; Kamali, Shokoofeh; Ma, Juan; Bruggmann, Rémy; Erb, Matthias (2018). Whole-genome-based revisit of Photorhabdus phylogeny: proposal for the elevation of most Photorhabdus subspecies to the species level and description of one novel species Photorhabdus bodei sp. nov., and one novel subspecies Photorhabdus laumondii subsp. clarkei subsp. nov. International journal of systematic and evolutionary microbiology, 68(8), pp. 2664-2681. Society for General Microbiology SGM 10.1099/ijsem.0.002820

Widmer, Yves F.; Bilican, Adem; Bruggmann, Rémy; Sprecher, Simon G. (2018). Regulators of Long-Term Memory Revealed by Mushroom Body-Specific Gene Expression Profiling in Drosophila melanogaster. Genetics, 209(4), pp. 1167-1181. Genetics Society of America 10.1534/genetics.118.301106

Tomasini, Matteo; Peischl, Stephan (2018). Establishment of Locally Adapted Mutations Under Divergent Selection. Genetics, 209(3), pp. 885-895. Oxford University Press 10.1534/genetics.118.301104

Hensel, Janine; Wetterwald, Antoinette; Temanni, Ramzi; Keller, Irene; Riether, Carsten; van der Pluijm, Gabri; Cecchini, Marco G; Thalmann, George N. (2018). Osteolytic cancer cells induce vascular/axon guidance processes in the bone/bone marrow stroma. OncoTarget, 9(48), pp. 28877-28896. Impact Journals LLC 10.18632/oncotarget.25608

Halbritter, Aud H.; Fior, Simone; Keller, Irene; Billeter, Regula; Edwards, Peter J.; Holderegger, Rolf; Karrenberg, Sophie; Pluess, Andrea R.; Widmer, Alex; Alexander, Jake M. (2018). Trait differentiation and adaptation of plants along elevation gradients. Journal of evolutionary biology, 31(6), pp. 784-800. Wiley 10.1111/jeb.13262

Peischl, Stephan; Dupanloup, I.; Foucal, A.; Jomphe, M.; Bruat, V.; Grenier, J.-C.; Gouy, A.; Gilbert, K. J.; Gbeha, E.; Bosshard, L.; Hip-Ki, E.; Agbessi, M.; Hodgkinson, A.; Vézina, H.; Awadalla, P.; Excoffier, Laurent (2018). Relaxed Selection During a Recent Human Expansion. Genetics, 208(2), pp. 763-777. Genetics Society of America 10.1534/genetics.117.300551

Oechslin, Corinne Pia; Lenz, Nicole; Liechti, Nicole; Ryter, Sarah; Agyeman, Philipp; Bruggmann, Rémy; Leib, Stephen; Beuret, Christian M (2018). Limited Correlation of Shotgun Metagenomics Following Host Depletion and Routine Diagnostics for Viruses and Bacteria in Low Concentrated Surrogate and Clinical Samples. Frontiers in cellular and infection microbiology, 8(375), p. 375. Frontiers 10.3389/fcimb.2018.00375

Wüthrich, Daniel; Irmler, Stefan; Berthoud, Hélène; Guggenbuhl, Barbara; Eugster, Elisabeth; Bruggmann, Rémy (2018). Conversion of Methionine to Cysteine in Lactobacillus paracasei Depends on the Highly Mobile cysK-ctl-cysE Gene Cluster. Frontiers in Microbiology, 9(2415) Frontiers 10.3389/fmicb.2018.02415

Wüthrich, Daniel; Wenzel, Claudia; Bavan, Tharmatha; Bruggmann, Rémy; Berthoud, Hélène; Irmler, Stefan (2018). Transcriptional Regulation of Cysteine and Methionine Metabolism in Lactobacillus paracasei FAM18149. Frontiers in Microbiology, 9(1261) Frontiers 10.3389/fmicb.2018.01261


Mele, Valentina; Sokol, Lena; Kölzer, Viktor; Pfaff, Dennis; Muraro, Manuele Giuseppe; Keller, Irene; Zahnd, Stefan Patrick; Centeno Ramos, Irene; Terracciano, Luigi Maria; Dawson, Heather; Zlobec, Inti; Iezzi, Giandomenica; Lugli, Alessandro (2017). The hyaluronan-mediated motility receptor RHAMM promotes growth, invasiveness and dissemination of colorectal cancer. OncoTarget, 8(41), pp. 70617-70629. Impact Journals LLC 10.18632/oncotarget.19904

Boujon, Céline; Koch, Michel Christoph; Wüthrich, Daniel; Werder, Simea; Jakupovic, Dennis; Bruggmann, Rémy; Seuberlich, Torsten (2017). Indication of Cross-Species Transmission of Astrovirus Associated with Encephalitis in Sheep and Cattle. Emerging infectious diseases, 23(9), pp. 1604-1608. U.S. National Center for Infectious Diseases 10.3201/eid2309.170168

Colombo, Martino; Karousis, Evangelos D.; Bourquin, Joëll; Bruggmann, Rémy; Mühlemann, Oliver (2017). Transcriptome-wide identification of NMD-targeted human mRNAs reveals extensive redundancy between SMG6- and SMG7-mediated degradation pathways. RNA - a publication of the RNA Society, 23(2), pp. 189-201. Cold Spring Harbor Laboratory Press 10.1261/rna.059055.116

Wüthrich, Daniel; Berthoud, Hélène; Wechsler, Daniel; Eugster, Elisabeth; Irmler, Stefan; Bruggmann, Rémy (2017). The Histidine Decarboxylase Gene Cluster of Lactobacillus parabuchneri Was Gained by Horizontal Gene Transfer and Is Mobile within the Species. Frontiers in Microbiology, 8(218) Frontiers 10.3389/fmicb.2017.00218

Awasthi, Nivedita; Drögemüller, Cord; Jagannathan, Vidhya; Keller, Irene; Wüthrich, Daniel; Bruggmann, Rémy; Beck, Julia; Schütz, Ekkehard; Brenig, Bertram; Demmel, Steffi; Moser, Simon; Signer-Hasler, Heidi; Pieńkowska-Schelling, Aldona; Schelling, Claude; Sande Melon, Marcos; Rongen, Ronald; Rieder, Stefan; Kelsh, Robert N.; Mercader Huber, Nadia and Leeb, Tosso (2017). A structural variant in the 5’-flanking region of the TWIST2 gene affects melanocyte development in belted cattle. PLoS ONE, 12(6), e0180170. Public Library of Science 10.1371/journal.pone.0180170

Rashpa, Ravish; Vazquez Pianzola, Maria Paula; Colombo, Martino; Hernandez, Greco; Beuchle, Dirk; Berger, Fabienne Chantal; Peischl, Stephan; Bruggmann, Rémy; Suter, Beat (2017). Cbp80 is needed for the expression of piRNA components and piRNAs. PLoS ONE, 12(7), e0181743. Public Library of Science 10.1371/journal.pone.0181743

Moser, Aline; Wüthrich, Daniel; Bruggmann, Rémy; Eugster-Meier, Elisabeth; Meile, Leo; Irmler, Stefan (2017). Amplicon Sequencing of the slpH Locus Permits Culture-Independent Strain Typing of Lactobacillus helveticus in Dairy Products. Frontiers in Microbiology, 8(1380) Frontiers 10.3389/fmicb.2017.01380


Auray, Gael; Keller, Irene; Python, Sylvie; Gerber, Markus Daniel; Bruggmann, Rémy; Ruggli, Nicolas; Summerfield, Artur (2016). Characterization and Transcriptomic Analysis of Porcine Blood Conventional and Plasmacytoid Dendritic Cells Reveals Striking Species-Specific Differences. Journal of immunology, 197(12), pp. 4791-4806. American Association of Immunologists 10.4049/jimmunol.1600672

Storari, Michelangelo; Kulli, Sandra; Wüthrich, Daniel; Bruggmann, Rémy; Berthoud, Hélène; Arias-Roth, Emmanuelle (2016). Genomic approach to studying nutritional requirements of Clostridium tyrobutyricum and other Clostridia causing late blowing defects. Food microbiology, 59, pp. 213-223. Elsevier 10.1016/j.fm.2016.05.013

Reber, Stefan; Stettler, Jolanda; Filosa, G.; Colombo, Martino; Jutzi, D.; Lenzken, S. C.; Schweingruber, Christoph; Bruggmann, Rémy; Bachi, A.; Barabino, S. M.; Mühlemann, Oliver; Ruepp, Marc-David (2016). Minor intron splicing is regulated by FUS and affected by ALS-associated FUS mutants. EMBO journal, 35(14), pp. 1504-1521. Nature Publishing Group 10.15252/embj.201593791

Bombarely, Aureliano; Moser, Michel; Amrad, Avichai Moshe; Bao, Manzhu; Bapaume, Laure; Barry, Cornelius S.; Bliek, Mattijs; Boersma, Maaike R.; Borghi, Lorenzo; Bruggmann, Rémy; Bucher, Marcel; D'Agostino, Nunzio; Davies, Kevin; Druege, Uwe; Dudareva, Natalia; Egea-Cortines, Marcos; Delledonne, Massimo; Fernandez-Pozo, Noe; Franken, Philipp; Grandont, Laurie; ... (2016). Insight into the evolution of the Solanaceae from the parental genomes of Petunia hybrida. Nature Plants, 2(6), p. 16074. Nature Publishing Group 10.1038/nplants.2016.74

Gaigher, A.; Burri, R.; Gharib, W. H.; Taberlet, P.; Roulin, A.; Fumagalli, L. (2016). Family-assisted inference of the genetic architecture of major histocompatibility complex variation. Molecular ecology resources, 16(6), pp. 1353-1364. Wiley 10.1111/1755-0998.12537

Leys, Marie; Keller, Irene; Räsänen, Katja; Gattolliat, Jean-Luc; Robinson, Christopher T. (2016). Distribution and population genetic variation of cryptic species of the Alpine mayfly Baetis alpinus (Ephemeroptera: Baetidae) in the Central Alps. BMC ecology and evolution, 16, p. 77. BioMed Central 10.1186/s12862-016-0643-y

Scheel, Troels K H; Luna, Joseph M; Liniger, Matthias; Nishiuchi, Eiko; Rozen-Gagnon, Kathryn; Shlomai, Amir; Auray, Gaël; Gerber, Markus; Fak, John; Keller, Irene; Bruggmann, Rémy; Darnell, Robert B; Ruggli, Nicolas; Rice, Charles M (2016). A Broad RNA Virus Survey Reveals Both miRNA Dependence and Functional Sequestration. Cell host & microbe, 19(3), pp. 409-423. Cell Press 10.1016/j.chom.2016.02.007

Meienberg, Janine; Bruggmann, Rémy; Oexle, Konrad; Matyas, Gabor (2016). Clinical sequencing: is WGS the better WES? Human genetics, 135(3), pp. 359-362. Springer 10.1007/s00439-015-1631-9

Swiss Institute of Bioinformatics Members, SIB (2016). The SIB Swiss Institute of Bioinformatics’ resources: focus on curated databases. Nucleic acids research, 44(D1), D27-37. Oxford University Press 10.1093/nar/gkv1310

Seuberlich, Torsten; Wüthrich, Daniel; Selimovic-Hamza, Senija; Drögemüller, Cord; Oevermann, Anna; Bruggmann, Rémy; Bouzalas, Ilias (2016). Identification of a second encephalitis-associated astrovirus in cattle. Emerging Microbes & Infections, 5(8), e71. Nature Publishing Group 10.1038/emi.2016.5

van Giesen, Lena; Hernandez-Nunez, Luis; Delasoie-Baranek, Sophie; Colombo, Martino; Renaud, Philippe; Bruggmann, Rémy; Benton, Richard; Samuel, Aravinthan D T; Sprecher, Simon G (2016). Multimodal stimulus coding by a gustatory sensory neuron in Drosophila larvae. Nature communications, 7(10687), p. 10687. Nature Publishing Group 10.1038/ncomms10687

Schlegel, Markus; Münsterkötter, Martin; Güldener, Ulrich; Bruggmann, Rémy; Duò, Angelo; Hainaut, Matthieu; Henrissat, Bernard; Sieber, Christian M. K.; Hoffmeister, Dirk; Grünig, Christoph R. (2016). Globally distributed root endophyte Phialocephala subalpina links pathogenic and saprophytic lifestyles. BMC Genomics, 17(1), p. 1015. BioMed Central 10.1186/s12864-016-3369-8

Malaspinas, Anna-Sapfo; Westaway, Michael C.; Muller, Craig; Sousa, Vitor C.; Lao, Oscar; Alves, Isabel; Bergström, Anders; Athanasiadis, Georgios; Cheng, Jade Y.; Crawford, Jacob E.; Heupink, Tim H.; Macholdt, Enrico; Peischl, Stephan; Rasmussen, Simon; Schiffels, Stephan; Subramanian, Sankar; Wright, Joanne L.; Albrechtsen, Anders; Barbieri, Chiara; Dupanloup, Isabelle; ... (2016). A genomic history of Aboriginal Australia. Nature, 538(7624), pp. 207-214. Macmillan Journals Ltd. 10.1038/nature18299


Becker, Doreen; Otto, Mandy; Ammann, P; Keller, Irene; Drögemüller, Cord; Leeb, Tosso (2015). The brown coat colour of Coppernecked goats is associated with a non-synonymous variant at the TYRP1 locus on chromosome 8. Animal genetics, 46(1), pp. 50-54. Blackwell 10.1111/age.12240

Storari, Michelangelo; Wüthrich, Daniel; Bruggmann, Rémy; Berthoud, Hélène; Arias-Roth, Emmanuelle (2015). Draft Genome Sequences of Clostridium tyrobutyricum Strains FAM22552 and FAM22553, Isolated from Swiss Semihard Red-Smear Cheese. Genome Announcements, 3(2) American Society for Microbiology 10.1128/genomeA.00078-15


Bouzalas, Ilias G; Wüthrich, Daniel; Walland, Julia Gianna Marlene; Drögemüller, Cord; Zurbriggen, Andreas; Vandevelde, Marc; Oevermann, Anna; Bruggmann, Rémy; Seuberlich, Torsten (2014). Neurotropic astrovirus in cattle with nonsuppurative encephalitis in Europe. Journal of clinical microbiology, 52(9), pp. 3318-3324. American Society for Microbiology 10.1128/JCM.01195-14

Simen, Birgitte B; Braverman, Michael S; Abbate, Isabella; Aerssens, Jeroen; Bidet, Yannick; Bouchez, Olivier; Gabriel, Christian; Izopet, Jacques; Kessler, Harald H; Stelzl, Evelyn; Di Giallonardo, Francesca; Schlapbach, Ralph; Radonic, Aleksander; Paredes, Roger; Recordon-Pinson, Patricia; Sakwa, James; St John, Elizabeth P; Schmitz-Agheguian, Gudrun G; Metzner, Karin J and Däumer, Martin P (2014). An international multicenter study on HIV-1 drug resistance testing by 454 ultra-deep pyrosequencing. Journal of virological methods, 204, pp. 31-37. Elsevier 10.1016/j.jviromet.2014.04.007

Greminger, Maja P; Stölting, Kai N; Nater, Alexander; Goossens, Benoit; Arora, Natasha; Bruggmann, Rémy; Patrignani, Andrea; Nussberger, Beatrice; Sharma, Reeta; Kraus, Robert H S; Ambu, Laurentius N; Singleton, Ian; Chikhi, Lounes; van Schaik, Carel P; Krützen, Michael (2014). Generation of SNP datasets for orangutan population genomics using improved reduced-representation sequencing and direct comparisons of SNP calling algorithms. BMC Genomics, 15(16), p. 16. BioMed Central 10.1186/1471-2164-15-16

Wiedemar, Natalie; Tetens, Jens; Jagannathan, Vidhya; Menoud, Annie; Neuenschwander, Samuel; Bruggmann, Rémy; Thaller, Georg; Drögemüller, Cord (2014). Independent polled mutations leading to complex gene expression differences in cattle. PLoS ONE, 9(3), e93435. Public Library of Science 10.1371/journal.pone.0093435

Adamsen, Dea; Ramaekers, Vincent; Ho, Horace Tb; Britschgi, Corinne; Rüfenacht, Véronique; Meili, David; Bobrowski, Elise; Philippe, Paule; Nava, Caroline; Van Maldergem, Lionel; Bruggmann, Rémy; Walitza, Susanne; Wang, Joanne; Grünblatt, Edna; Thöny, Beat (2014). Autism spectrum disorder associated with low serotonin in CSF and mutations in the SLC29A4 plasma membrane monoamine transporter (PMAT) gene. Molecular autism, 5(43), p. 43. BioMed Central 10.1186/2040-2392-5-43


Di Giallonardo, Francesca; Zagordi, Osvaldo; Duport, Yannick; Leemann, Christine; Joos, Beda; Künzli-Gontarczyk, Marzanna; Bruggmann, Rémy; Beerenwinkel, Niko; Günthard, Huldrych F.; Metzner, Karin J. (2013). Next-generation sequencing of HIV-1 RNA genomes: determination of error rates and minimizing artificial recombination. PLoS ONE, 8(9), e74249. Public Library of Science 10.1371/journal.pone.0074249

Wicker, Thomas; Oberhaensli, Simone; Parlange, Francis; Buchmann, Jan P; Shatalina, Margarita; Roffler, Stefan; Ben-David, Roi; Doležel, Jaroslav; Šimková, Hana; Schulze-Lefert, Paul; Spanu, Pietro D; Bruggmann, Rémy; Amselem, Joelle; Quesneville, Hadi; Ver Loren van Themaat, Emiel; Paape, Timothy; Shimizu, Kentaro K; Keller, Beat (2013). The wheat powdery mildew genome shows the unique evolution of an obligate biotroph. Nature genetics, 45(9), pp. 1092-1096. Nature America 10.1038/ng.2704

Issa, Shadi A.; Kienzler, Romeo; El-Kalioby, Mohamed; Tonellato, Peter J.; Wall, Dennis; Bruggmann, Rémy; Abouelhoda, Mohamed (2013). Streaming Support for Data Intensive Cloud-Based Sequence Analysis. BioMed research international, 2013(8), pp. 1-16. Hindawi Publishing Corporation 10.1155/2013/791051

Biason-Lauber, Anna; Böni-Schnetzler, Marianne; Hubbard, Basil P.; Bouzakri, Karim; Brunner, Andrea; Cavelti-Weder, Claudia; Keller, Cornelia; Meyer-Böni, Monika; Meier, Daniel T.; Brorsson, Caroline; Timper, Katharina; Leibowitz, Gil; Patrignani, Andrea; Bruggmann, Rémy; Boily, Gino; Zulewski, Henryk; Geier, Andreas; Cermak, Jennifer M; Elliott, Peter; Ellis, James L.; ... (2013). Identification of a SIRT1 mutation in a family with type 1 diabetes. Cell metabolism, 17(3), pp. 448-455. Cell Press 10.1016/j.cmet.2013.02.001


Kienzler, Romeo; Bruggmann, Rémy; Ranganathan, Anand; Tatbul, Nesime (2012). Incremental DNA Sequence Analysis in the Cloud. In: Ailamaki, Anastasia; Bowers, Shawn (eds.) Scientific and Statistical Database Management. Lecture Notes in Computer Science: Vol. 7338 (pp. 640-645). Heidelberg: Springer Verlag 10.1007/978-3-642-31235-9_50

Kienzler, R.; Bruggmann, Rémy; Ranganathan, A.; Tatbul, N. (2012). Stream as You Go: The Case for Incremental Data Access and Processing in the Cloud. In: Proceedings of the 2012 IEEE 28th International Conference on Data Engineering Workshops, 1.-5.4.2012 (pp. 159-166). Washington, DC: IEEE Computer Society 10.1109/ICDEW.2012.69

Testoni, Stefania; Bartolone, Elena; Rossi, Marco; Patrignani, Andrea; Bruggmann, Rémy; Lichtner, Peter; Tetens, Jens; Gentile, Arcangelo; Drögemüller, Cord (2012). KDM2B is implicated in bovine lethal multi-organic developmental dysplasia. PLoS ONE, 7(9), e45634. Lawrence, Kans.: Public Library of Science 10.1371/journal.pone.0045634

Duò, Angelo; Bruggmann, Rémy; Zoller, Stefan; Bernt, Matthias; Grünig, Christoph (2012). Mitochondrial genome evolution in species belonging to the Phialocephala fortinii s.l. - Acephala applanata species complex. BMC Genomics, 13(166), p. 166. London: BioMed Central 10.1186/1471-2164-13-166

Lindner, Heike; Raissig, Michael T.; Sailer, Christian; Shimosato-Asano, Hiroko; Bruggmann, Rémy; Grossniklaus, Ueli (2012). SNP-Ratio Mapping (SRM): Identifying Lethal Alleles and Mutations in Complex Genetic Backgrounds by Next-Generation Sequencing. Genetics, 191(4), pp. 1381-1386. Bethesda, Md.: Genetics Society of America 10.1534/genetics.112.141341

Bruggmann, Rémy; Tomato Genome Consortium, the (2012). The tomato genome sequence provides insights into fleshy fruit evolution. Nature, 485(7400), pp. 635-641. London: Macmillan Journals Ltd. 10.1038/nature11119


Asp, Torben; Byrne, Stephen; Gundlach, Heidrun; Bruggmann, Rémy; Mayer, Klaus F X; Andersen, Jeppe R; Xu, Mingliang; Greve, Morten; Lenk, Ingo; Lübberstedt, Thomas (2011). Comparative sequence analysis of VRN1 alleles of Lolium perenne with the co-linear regions in barley, wheat, and rice. Molecular genetics and genomics : MGG, 286(5-6), pp. 433-447. Springer 10.1007/s00438-011-0654-8

Calviño, Martín; Bruggmann, Rémy; Messing, Joachim (2011). Characterization of the small RNA component of the transcriptome from grain and sweet sorghum stems. BMC Genomics, 12(356), p. 356. BioMed Central 10.1186/1471-2164-12-356


Paterson, Andrew H; Bowers, John E; Bruggmann, Rémy; Dubchak, Inna; Grimwood, Jane; Gundlach, Heidrun; Haberer, Georg; Hellsten, Uffe; Mitros, Therese; Poliakov, Alexander; Schmutz, Jeremy; Spannagl, Manuel; Tang, Haibao; Wang, Xiyin; Wicker, Thomas; Bharti, Arvind K; Chapman, Jarrod; Feltus, F Alex; Gowik, Udo; Grigoriev, Igor V; ... (2009). The Sorghum bicolor genome and the diversification of grasses. Nature, 457(7229), pp. 551-556. Springer Nature 10.1038/nature07723


Ballvora, Agim; Jöcker, Anika; Viehöver, Prisca; Ishihara, Hirofumi; Paal, Jürgen; Meksem, Khalid; Bruggmann, Rémy; Schoof, Heiko; Weisshaar, Bernd; Gebhardt, Christiane (2007). Comparative sequence analysis of Solanum and Arabidopsis in a hot spot for pathogen resistance on potato chromosome V reveals a patchwork of conserved and rapidly evolving genome segments. BMC Genomics, 8(112), p. 112. BioMed Central 10.1186/1471-2164-8-112


Michel, Kathrin; Abderhalden, Olaf; Bruggmann, Rémy; Dudler, Robert (2006). Transcriptional changes in powdery mildew infected wheat and Arabidopsis leaves undergoing syringolin-triggered hypersensitive cell death at infection sites. Plant molecular biology, 62(4-5), pp. 561-578. Springer 10.1007/s11103-006-9045-7

Bruggmann, Rémy; Bharti, Arvind K; Gundlach, Heidrun; Lai, Jinsheng; Young, Sarah; Pontaroli, Ana C; Wei, Fusheng; Haberer, Georg; Fuks, Galina; Du, Chunguang; Raymond, Christina; Estep, Matt C; Liu, Renyi; Bennetzen, Jeffrey L; Chan, Agnes P; Rabinowicz, Pablo D; Quackenbush, John; Barbazuk, W Brad; Wing, Rod A; Birren, Bruce; ... (2006). Uneven chromosome contraction and expansion in the maize genome. Genome research, 16(10), pp. 1241-1251. Cold Spring Harbor, N.Y 10.1101/gr.5338906


Hagmann, M; Adlkofer, K; Pfeiffer, P; Bruggmann, Rémy; Georgiev, O; Rungger, D; Schaffner, W (1996). Dramatic changes in the ratio of homologous recombination to nonhomologous DNA-end joining in oocytes and early embryos of Xenopus laevis. Biological chemistry Hoppe-Seyler, 377(4), pp. 239-250. De Gruyter 10.1515/bchm3.1996.377.4.239

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