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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


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

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

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

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

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


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

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


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

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


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

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


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

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

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, e71. Nature Publishing Group 10.1038/emi.2016.5


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

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


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

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