08 Faculty of Science > Department of Biology > Bioinformatics and Computational Biology > Computational Biology

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Number of items at this level: 45.


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


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

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

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

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


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

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

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


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

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

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

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

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


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

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

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


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

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


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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