Publications

2022

• Whole-genome analyses reveal a novel prophage and cgSNPs-derived sublineages of Brachyspira hyodysenteriae ST196. Ana Belén García-Martín, Thomas Roder, Sarah Schmitt, Friederike Zeeh, Rémy Bruggmann & Vincent Perreten. BMC Genomics 23, 131 (2022). https://doi.org/10.1186/s12864-022-08347-5
• Operative versus non-operative management of rib fractures in flail chest after cardiopulmonary resuscitation manoeuvres. Patrick Dorn, Selina Pfister, Simone Oberhaensli, Konstantinos Gioutsos, Matthias Haenggi, Gregor J Kocher. Interactive CardioVascular and Thoracic Surgery, 2022;, ivac023, https://doi.org/10.1093/icvts/ivac023
• Genomic rearrangements in the aspA-dcuA locus of Propionibacterium freudenreichii are associated with aspartase activity. Meral Turgay, Hélène Falentin, Stefan Irmler, Marie-Thérèse Fröhlich-Wyder, Marco Meola, Simone Oberhaensli, Hélène Berthoud-dit-Gallon Marchand. Food Microbiology, 2022, 104030, https://doi.org/10.1016/j.fm.2022.104030.
• Cadaverine, putrescine, and histamine formation of Morganella morganii in raclette-type cheese. 2022. Lorenz T. Ryser, Emmanuelle Arias-Roth, Hélène Berthoud, Céline Delbès-Paus, Christophe Chassard, Rémy Bruggmann, Stefan Irmler. International Dairy Journal. 129, 105362. https://doi.org/10.1016/j.idairyj.2022.105362
• Biparatopic sybodies neutralize SARS-CoV-2 variants of concern and mitigate drug resistance. Justin D Walter, Melanie Scherer, Cedric A J Hutter, Alisa A Garaeva, Iwan Zimmermann, Marianne Wyss, Jan Rheinberger, Yelena Ruedin, Jennifer C Earp, Pascal Egloff, Michèle Sorgenfrei, Lea M Hürlimann, Imre Gonda, Gianmarco Meier, Sille Remm, Sujani Thavarasah, Geert van Geest, Rémy Bruggmann, Gert Zimmer, Dirk J Slotboom, Cristina Paulino, Philippe Plattet, Markus A Seeger. EMBO reports, Volume 23
  Issue 4, 5 April 2022: http://dx.doi.org/10.15252/embr.202154199
• OpenGenomeBrowser: a versatile, dataset-independent and scalable web platform for genome data management and comparative genomics. Thomas Roder, Simone Oberhänsli, Noam Shani & Rémy Bruggmann; BMC Genomics, published December 27, 2022. https://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-022-09086-3

2021

• ACKR1 favors transcellular over paracellular T-cell diapedesis across the blood-brain barrier in neuroinflammation in vitro. Luca Marchetti, David Francisco, Sasha Soldati, Neda Haghayegh Jahromi, Sara Barcos, Isabelle Gruber, Javier R. Pareja, Aude Thiriot, Ulrich von Andrian, Urban Deutsch, Ruth Lyck, Rémy Bruggmann and Britta Engelhardt. EurJImmunol (2021) in press. doi: 10.1002/eji.202149238
• Inference of kinase-signaling networks in human myeloid cell line models by Phosphoproteomics using kinase activity enrichment analysis (KAEA). Mahmoud Hallal, Sophie Braga-Lagache, Jovana Jankovic, Cedric Simillion, Rémy Bruggmann, Anne-Christine Uldry, Ramanjaneyulu Allam, Manfred Heller, Nicolas Bonadies. BMC Cancer (2021) Jul 8;21(1):789. doi: 10.1186/s12885-021-08479-z.
• CRISPR-Mediated Kinome Editing Prioritizes a Synergistic Combination Therapy for FGFR1-Amplified Lung Cancer. Zhang Yang, Shun-Qing Liang, Haitang Yang, Duo Xu, Rémy Bruggmann, Yanyun Gao, Haibin Deng, Sabina Berezowska, Sean R R Hall, Thomas M Marti, Gregor J Kocher, Qinghua Zhou, Ralph A Schmid, Ren-Wang Peng. Cancer Res (2021) 81(11):3121-3133. doi: 10.1158/0008-5472.CAN-20-2276. Epub 2021 Mar 8.
• Acoel single-cell transcriptomics: cell type analysis of a deep branching bilaterian. Jules Duruz, Cyrielle Kaltenrieder, Peter Ladurner, Rémy Bruggmann, Pedro Martìnez, and Simon G. Sprecher. Mol Biol Evol (2021) 38(5):1888-1904. doi: 10.1093/molbev/msaa333
• Isolation and characterization of bacteriophages from the human skin microbiome that infect Staphylococcus epidermidis. Luca G Valente, Melissa Pitton, Monika Fürholz, Simone Oberhaensli, Rémy Bruggmann, Stephen L Leib, Stephan M Jakob, Grégory Resch, Yok-Ai Que, David R Cameron. FEMS Microbes, Volume 2, 2021, xtab003, https://doi.org/10.1093/femsmc/xtab003
• Malignant pleural mesothelioma co-opts BCL-XL and autophagy to escape apoptosis. Duo Xu, Shun-Qing Liang, Zhang Yang, Haitang Yang, Rémy Bruggmann, Simone Oberhaensli, Sabina Berezowska, Thomas M. Marti, Sean R. R. Hall, Patrick Dorn, Gregor J. Kocher, Ralph A. Schmid & Ren-Wang Peng. Cell Death Dis 12, 406 (2021)
• Variants affecting the C-terminal tail of UNC93B1 are not a common risk factor for systemic lupus erythematosus. Kiener, S., Ribi, C., Keller, I., Chizzolini, C., Trendelenburg, M., Huynh-Do, U., von Kempis, J., Leeb, T. 2021  Genes 12(8), 1268.
• Understanding the interactions between the ocular surface microbiome and the tear proteome. Zysset-Burri, D.C., Schlegel, I., Lincke J.-B., Jaggi, D., Keller, I., Heller, M., Braga Lagache, S., Wolf, S., Zinkernagel, M. S. 2021 Invest Ophthalmol Vis Sci 62(10):8
• Intestinal microbiota drives cholestasis-induced specific hepatic gene expression patterns and modulates liver injury. Juanola, O., Hassan, M., Kumar, P., Yilmaz, B., Keller. I., Simillion, C., Engelmann, C., Tacke, F., Dufour, J.-F., De Gottardi, A., Moghadamrad, S. 2021 Gut Microbes 13(1):1-20.
• Human Wharton’s jelly mesenchymal stromal cell-derived small extracellular vesicles drive oligodendroglial maturation by restraining MAPK/ERK and Notch signaling pathways. Joerger-Messerli, M.S, Thomi, G., Haesler, V., Keller, I., Surbek, D., Schoeberlein A. (2021) Frontiers in Cell and Developmental Biology 9: 622539.
• Dual targeting of JAK2 and ERK interferes with the myeloproliferative neoplasm clone and enhances therapeutic efficacy. Sime Brkic, Simona Stivala, Alice Santopolo, Jakub Szybinski, Sarah Jungius, Jakob R. Passweg, Dimitrios Tsakiris, Stefan Dirnhofer, Gregor Hutter, Katharina Leonards, Heidi E. L. Lischer, Matthias S. Dettmer, Benjamin G. Neel, Ross L. Levine & Sara C. Meyer (2021), Leukemia (https://doi.org/10.1038/s41375-021-01391-2)
• Linear Peptides -a Combinatorial Innovation in the Venom of Some Modern Spiders. Lucia Kuhn-Nentwig, Heidi E. L. Lischer, Stano Pekar, Nicolas Langenegger, Maria J. Albo, Marco Isaia, Wolfgang Nentwig (2021), Frontiers in Molecular Biosciences, Cellular Biochemistry (https://doi.org/10.3389/fmolb.2021.705141)
• Disentangling adaptation from drift in bottlenecked and reintroduced populations of Alpine ibex. Deborah M. Leigh, Heidi E. L. Lischer, Frédéric Guillaume, Christine Grossen, Torsten Günther (2021), Molecular Ecology Resources (https://doi.org/10.1111/1755-0998.13442)
• Mistranslation can promote the exploration of alternative evolutionary trajectories in enzyme evolution. Jia Zheng, Sinisa Bratulic, Heidi E. L. Lischer, Andreas Wagner (2021), Journal of Evolutionary Biology (34 (8): 1302-1315; https://doi.org/10.1111/jeb.13892)
• Long-term evolution and short-term adaptation of microbiota strains and sub-strains in mice. Bahtiyar Yilmaz, Catherine Mooser, Irene Keller, Hai Li, Jakob Zimmermann, Lars Bosshard, Tobias Fuhrer, Mercedes Gomez de Agüero, Nerea Fernandez Trigo, Heidi Tschanz-Lischer, Julien P Limenitakis, Wolf-Dietrich Hardt, Kathy D McCoy, Bärbel Stecher, Laurent Excoffier, Uwe Sauer, Stephanie C Ganal-Vonarburg, Andrew J Macpherson (2021), Cell Host Microbe (S1931-3128)
• Strong neutral sweeps occurring during a population contraction. A Moinet, S Peischl, L Excoffier. bioRxiv
• Genetic load may increase or decrease with selfing depending upon the recombination environment. SA Sianta, S Peischl, DA Moeller, Y Brandvain. bioRxiv
• Gene surfing of underdominant alleles promotes formation of hybrid zones. KJ Gilbert, AF Moinet, S Peischl (in press)

2020

• Advancing brain barriers RNA sequencing: guidelines from experimental design to publication. David M. F. Francisco, Luca Marchetti, Sabela Rodríguez-Lorenzo, Eduardo Frías-Anaya, Ricardo M. Figueiredo, BtRAIN Network, Peter Winter, Ignacio Andres Romero, Helga E. de Vries, Britta Engelhardt & Rémy Bruggmann. Fluids and Barriers of the CNS volume 17, Article number: 51 (2020) 
• In Silico Comparison Shows that the Pan-Genome of a Dairy-Related Bacterial Culture Collection Covers Most Reactions Annotated to Human Microbiomes. Thomas Roder, Daniel Wüthrich, Cornelia Bär, Zahra Sattari,Ueli von Ah, Francesca Ronchi, Andrew J. Macpherson, Stephanie C. Ganal-Vonarburg, Rémy Bruggmann and Guy Vergères
• Evolutionary rescue in one dimensional stepping stone models. M Tomasini, S Peischl. bioRxiv, 2020.10. 29.360842
• Transition from background selection to associative overdominance promotes diversity in regions of low recombination. KJ Gilbert, F Pouyet, L Excoffier, S Peischl. Current Biology 30 (1), 101-107. e3
• When does gene flow facilitate evolutionary rescue? Tomasini, M Peischl, S. Evolution (in press).  https://doi.org/10.1111/evo.14038    
• Dissection of the mutation accumulation process during bacterial range expansions. L Bosshard, S Peischl, M Ackermann, L Excoffier. BMC genomics 21, 1-11
• Evolution of dispersal can rescue populations from expansion load. Stephan Peischl, Kimberly J. Gilbert. The American Naturalist 195 (2) 349-360
• New genomic features of the polled intersex syndrome (PIS) variant in goats unraveled by long-read whole-genome sequencing. R. Simon, H.E.L. Lischer, A. Pienkowska-Schelling, I. Keller, I.M. Häfliger, A. Letko, C. Schelling, G. Lühken, C. Drögemüller (2020), Animal Genetics (51: 439-448)
• Transcriptomic profiling of bovine blood dendritic cells and monocytes following TLR stimulation. G. Tuba Barut, Heidi E. L. Lischer, Rémy Bruggmann, Artur Summerfield, Stephanie C. Talker (2020), European Journal of Immunology (50 (11): 1691-1711)
• Fibronectin Fragments and Inflammation during Canine Intervertebral Disc Disease. Manuel Roland Schmidli, Iva Cvitas, Benjamin Gantenbein, Heidi Erika Tschanz-Lischer, Simone Forterre, Franck Forterre, Karin Wuertz-Kozak (2020), Frontiers in Veterinary Science, section Comparative and Clinical Medicine
• Fine-scale empirical data on niche divergence and homeolog expression patterns in an allopolyploid and its diploid progenitor species. Reiko Akiyama, Sun Janqiang, Masaomi Hatakeyama, Heidi E.L. Lischer, Roman V. Briskine,  Angela Hay, Xiangchao Gan, Miltos Tsiantis, Hiroshi Kudoh, Masahiro M. Kanaoka, Jun Sese, Kentaro K. Shimizu, Rie Shimizu-Inatsugi (2020), New Phytologist
• Investigating the epithelial barrier and immune signatures in the pathogenesis of equine insect bite hypersensitivity. Iva Cvitas ,Simone Oberhänsli,Tosso Leeb,Martina Dettwiler,Eliane Müller,Remy Bruggman,Eliane Isabelle Marti, Plos one, April 28, 2020 https://doi.org/10.1371/journal.pone.0232189
• Repetitive transcranial magnetic stimulation activates glial cells and inhibits neurogenesis after pneumococcal meningitis. Lukas Muri, Simone Oberhänsli, Michelle Buri, Ngoc Dung Le, Denis Grandgirard, Rémy Bruggmann, René M. Müri, Stephen L. Leib. Plos one, September 11, 2020 https://doi.org/10.1371/journal.pone.0232863
• NGS-Based S. aureus Typing and Outbreak Analysis in Clinical Microbiology Laboratories: Lessons Learned From a Swiss-Wide Proficiency Test. David Dylus, Trestan Pillonel, Onya Opota, Daniel Wüthrich, Helena M. B. Seth-Smith, Adrian Egli, Stefano Leo, Vladimir Lazarevic, Jacques Schrenzel, Sacha Laurent, Claire Bertelli, Dominique S. Blanc, Stefan Neuenschwander, Alban Ramette, Laurent Falquet, Frank Imkamp, Peter M. Keller, Andre Kahles, Simone Oberhaensli, Valérie Barbié, Christophe Dessimoz, Gilbert Greub and Aitana Lebrand, Front. Microbiol., 24 November 2020 | https://doi.org/10.3389/fmicb.2020.591093
• Antibiotic susceptibility profiles of Pediococcus pentosaceus from various origins and their implications for the safety assessment of strains with food-technology applications. Noam Shani, Simone Oberhaensli, Emmanuelle Arias-Roth, J Food Prot. 2020 Dec 15. doi: 10.4315/JFP-20-363
• Associations of the intestinal microbiome with the complement system in age-related macular degeneration. Zysset-Burri, D.C., Keller, I., Berger, L.E., Largiadèr, C.R., Wittwer, M., Wolf, S., Zinkernagel, M.S., 2020, npj Genomic Medicine 5, Article number: 34.
• High-resolution profiling of innate immune responses by porcine dendritic- cell subsets in vitro and in vivo. Auray, G., Talker, S.C., Keller, I., Python, S., Gerber, M., Liniger, M., Ganges, L., Bruggmann, R., Ruggli, N., Summerfield, A., 2020, Frontiers in Immunology. https://doi.org/10.3389/fimmu.2020.01429.
• Paneth cells drive microbial induced signals to promote angiogenesis and regulate portal hypertension. Hassan, M. and 14 co-authors. 2020,  Journal of Hepatology 73(3): 628-639
• Whole genome sequencing of feline strain of Tritrichomonas foetus reveals massive genetic differences to bovine and porcine isolates. Dąbrowska, J., Keller, I., Karamon, J., Kochanowski, M., Gottstein, B., Cencek, T., Frey, C.F., Müller, N., 2020, International Journal for Parasitology 50(3): 227-233.

2019

• Single cell transcriptome atlas of the Drosophila larval brain. Brunet Avalos C, Bruggmann R, Sprecher SG., Elife. 2019 Nov 20;8. pii: e50354. doi: 10.7554/eLife.50354. [Epub ahead of print]
• CRISPR screening identifies WEE1 as a combination target for standard chemotherapy in malignant pleural mesothelioma. Xu D, Liang SQ, Yang H, Bruggmann R, Berezowska S, Yang Z, Marti TM, Hall SRR, Gao Y, Kocher GJ, Schmid RA, Peng RW., Mol Cancer Ther. 2019 Nov 6. pii: molcanther.0724.2019. doi: 10.1158/1535-7163.MCT-19-0724. [Epub ahead of print]
• Adult sox10+ Cardiomyocytes Contribute to Myocardial Regeneration in the Zebrafish. Sande-Melón M, Marques IJ, Galardi-Castilla M, Langa X, Pérez-López M, Botos MA, Sánchez-Iranzo H, Guzmán-Martínez G, Ferreira Francisco DM, Pavlinic D, Benes V, Bruggmann R, Mercader N., Cell Rep. 2019 Oct 22;29(4):1041-1054.e5. doi: 10.1016/j.celrep.2019.09.041.
• Carbon source regulates polysaccharide capsule biosynthesis in Streptococcus pneumoniae. Troxler LJ, Werren JP, Schaffner TO, Mostacci N, Vermathen P, Vermathen M, Wüthrich D, Simillion C, Brugger SD, Bruggmann R, Hathaway LJ, Furrer J, Hilty M., J Biol Chem. 2019 Nov 15;294(46):17224-17238. doi: 10.1074/jbc.RA119.010764. Epub 2019 Oct 8.
• Erratum: Author Correction: System immunology-based identification of blood transcriptional modules correlating to antibody responses in sheep. Braun RO, Brunner L, Wyler K, Auray G, García-Nicolás O, Python S, Zumkehr B, Gaschen V, Stoffel MH, Collin N, Barnier-Quer C, Bruggmann R, Summerfield A., NPJ Vaccines. 2019 Feb 19;4:10. doi: 10.1038/s41541-019-0100-1. eCollection 2019
• Evolution of dispersal can rescue populations from expansion load. S Peischl, KJ Gilbert. The American Naturalist (in press) (2019)
• Mutational and selective processes involved in evolution during bacterial range expansions. L Bosshard, S Peischl, M Ackermann, L Excoffier. Molecular biology and evolution (2019)
• TIRAP p.R81C is a novel lymphoma risk variant which enhances cell proliferation via NF-κB mediated signaling in B-cells. Burkhard, R., Keller, I., Arambasic, M., Juskevicius, D., Tzankov, A., Lundberg, P., Bruggmann, R., Dirnhofer, S., Radpour, R., Novak, U. (2019), Haematologica 104(4): 766-777.
• Gene expression in chronic granulomatous disease and interferon-gamma receptor deficient cells treated in vitro with interferon-gamma. Frazão, J. B., Colombo, M., Simillion, C., Bilican, A., Keller, I., Wüthrich, D., Zhu, Z., Okoniewski, M. J., Bruggmann, R., Condino-Neto, A., Newburger, P. E.  (2019)  Journal of Cellular Biochemistry 120(3): 4321-4332
• Claudin-3-deficient C57BL/6J mice display intact brain barriers. Mariana Castro Dias, Caroline Coisne, Ivana Lazarevic, Pascale Baden, Masaki Hata, Noriko Iwamoto, David Miguel Ferreira Francisco, Michael Vanlandewijck, Liqun He, Felix A. Baier, Deborah Stroka, Rémy Bruggmann, Ruth Lyck, Gaby Enzmann, Urban Deutsch, Christer Betsholtz, Mikio Furuse, Shoichiro Tsukita & Britta Engelhardt Sci Rep. (2019) 9:203; doi: 10.1038/s41598-018-36731-3
• CD8+ T cells expand stem and progenitor cells in favorable but not adverse risk acute myeloid leukemia. Ramin Radpour, Carsten Riether, Cedric Simillion, Sabine Höpner, Rémy Bruggmann, and Adrian F. Ochsenbein Leukemia. (2019) ; doi: 10.1038/s41375-019-0441-9
• Photorhabdus khanii subsp. guanajuatensis subsp. nov., isolated from Heterorhabditis atacamensis, and Photorhabdus luminescens subsp. mexicana subsp. nov., isolated from Heterorhabditis mexicana entomopathogenic nematodes. Ricardo AR Machado, Pamela Bruno,  Carla CM Arce, Nicole Liechti, Angela Köhler, Julio Bernal,  Rémy Bruggmann, Ted CJ Turlings Int J Syst Evol Microbiol. (2019) doi: 10.1099/ijsem.0.003154
• Determination of host proteins composing the microenvironment of coronavirus replicase complexes by proximity-labeling. Philip V'kovski, Markus Gerber, Jenna Kelly, Stephanie Pfaender, Nadine Ebert, Sophie Braga Lagache, Cedric Simillion, Jasmine Portmann, Hanspeter Stalder, Véronique Gaschen, Rémy Bruggmann, Michael H Stoffel, Manfred Heller, Ronald Dijkman Dijkman, Volker Thiel eLife. (2019) 11;8. pii: e42037. doi: 10.7554/eLife.42037
• Tumor Initiation Capacity and Therapy Resistance Are Differential Features of EMT-Related Subpopulations in the NSCLC Cell Line A5491. Colin Charles Tièche, Yanyun Gao, Elias Daniel Bührer, Nina Hobi, Sabina Anna Berezowska, Kurt Wyler, Laurène Froment, Stefan Weis, Ren-Wang Peng, Rémy Bruggmann, Primo Schär, Michael Alex Amrein, Sean Ralph Robert Hall, Patrick Dorn, Gregor Kocher, Carsten Riether, Adrian Ochsenbein, Ralph Alexander Schmid, and Thomas Michael Marti Neoplasia. (2019); 21(2):185–196. doi: 10.1016/j.neo.2018.09.008

2018

• Coincidence of NOD2-associated autoinflammatory disease (Yao syndrome) and HCV infection with fatal consequences: interaction between genes and environment. Trueb, B., Zhuan, L., Keller, I., von Köckritz, L., Kuchen, S., Dufour, F., Villiger, P.M. (2018)  Journal of Clinical Rheumatology DOI:10.1097/RHU.0000000000000963.
• Precise delineation and transcriptional characterization of bovine blood dendritic-cell and monocyte subsets. Talker, S.C., Baumann, A., Barut, G.T., Keller, I., Bruggmann, R., Summerfield, A. (2018) Frontiers in Immunology 9: 2505.
• Transcriptomic analyses of murine ventricular cardiomyocytes. Chevalier, M., Vermij, S., Wyler, K., Gillet, L., Keller, I., Abriel, H. (2018) Scientific Data 5: 180170.
• Healing of fractures in osteoporotic bones in mice treated with bisphosphonates - A transcriptome analysis. Hauser, M., Siegrist, M., Keller, I., Hofstetter, W. (2018)  Bone 112: 107-119.
• Trait differentiation and adaptation of plants along elevational gradients. Journal of Evolutionary Biology 31: 784-800. Halbritter, A.H., Fior, S., Keller, I., Billeter, R., Edwards, P., Holderegger, R., Karrenberg, S., Pluess, A.R., Widmer, A., Alexander J.M. (2018)
• VLA-4 Mediated Adhesion of Melanoma Cells on the Blood–Brain Barrier Is the Critical Cue for Melanoma Cell Intercalation and Barrier Disruption. García-Martín, Ana B, Pascale Zwicky, Thomas Gruber, Christoph Matti, Federica Moalli, Jens V Stein, David Francisco, et al.  Journal of Cerebral Blood Flow & Metabolism, (May 2018). doi:10.1177/0271678X18775887.
• Conversion of methionine to cysteine in Lactobacillus paracasei depends on the highly mobile cysK-ctl-cysE gene cluster. Daniel Wüthrich, Stefan Irmler, Hélène Berthoud, Barbara Guggenbühl, Elisabeth Eugster and Rémy Bruggmann Front Microbiol. (2018) 9:2415. doi: 10.3389/fmicb.2018.02415.
• Contribution of epigenetic variation to adaptation in Arabidopsis. Marc W. Schmid, Christian Heichinger, Diana Coman Schmid, Daniela Guthörl, Rémy Bruggmann, Sirisha Aluri, Catharine Aquino, Bernhard Schmid, Lindsay A. Turnbull, and Ueli Grossniklaus Nature Communications (2018) 25;9(1):4446. doi: 10.1038/s41467-018-06932-5.
• Limited Correlation of Shotgun Metagenomics Following Host Depletion and Routine Diagnostics for Viruses and Bacteria in Low Concentrated Surrogate and Clinical Samples. Corinne P. Oechslin, Nicole Lenz, Nicole Liechti, Sarah Ryter, Philipp Agyeman, Rémy Bruggmann, Stephen L. Leib, and Christian M. Beuret Front Cell Infect Microbiol. (2018) 8:375. doi: 10.3389/fcimb.2018.00375.
• System immunology-based identification of blood transcriptional modules correlating to antibody responses in sheep. Roman O. Braun, Livia Brunner, Kurt Wyler, Gaël Auray, Obdulio García-Nicolás, Sylvie Python, Beatrice Zumkehr, Véronique Gaschen, Michael H. Stoffel, Nicolas Collin, Christophe Barnier-Quer, Rémy Bruggmann, and Artur Summerfield NPJ Vaccines. (2018) 3:41. doi:  10.1038/s41541-018-0078-0
• Update on Tetracycline Susceptibility of Pediococcus acidilactici Based on Strains Isolated from Swiss Cheese and Whey. Petra Lüdin, Alexandra Roetschi, Daniel Wüthrich, Rémy Bruggmann, Hélène Berthoud, and Noam Shani J Food Prot. (2018) 81(10):1582-1589. doi: 10.4315/0362-028X.JFP-18-160
• The genome of Naegleria lovaniensis, the basis for a comparative approach to unravel pathogenicity factors of the human pathogenic amoeba N. fowleri. Nicole Liechti, Nadia Schürch, Rémy Bruggmann, and Matthias Wittwer BMC Genomics (2018) 5;19:654. doi: 10.1186/s12864-018-4994-1
• Xenacoelomorpha Survey Reveals That All 11 Animal Homeobox Gene Classes Were Present in the First Bilaterians. Michael Brauchle*, Adem Bilican, Claudia Eyer, Xavier Bailly, Pedro Martínez, Peter Ladurner, Rémy Bruggmann* and Simon G. Sprecher* Genome Biol Evol. (2018) 10: 2205–2217, doi: 10.1093/gbe/evy170 *corresponding authors
• Regulators of Long-Term Memory Revealed by Mushroom Body-Specific Gene Expression Profiling in Drosophila melanogaster.Yves F. Widmer, Adem Bilican, Rémy Bruggmann and Simon G. Sprecher Genetics (2018) vol. 209 no. 4 1167-1181;doi: 10.1534/genetics.118.301106
• Increased sensitivity to apoptosis upon endoplasmic reticulum stress-induced activation of the unfolded protein response in chemotherapy-resistant malignant pleural mesothelioma. Duo Xu, Shun-Qing Liang, Haitang Yang, Ursina Lüthi, Carsten Riether, Sabina Berezowska, Thomas M. Marti, Sean R. R. Hall, Rémy Bruggmann, Gregor J. Kocher, Ralph A. Schmid and Ren-Wang Peng British Journal of Cancer (2018) 119:65–75, doi: 10.1038/s41416-018-0145-3
• Transcriptional Regulation of Cysteine and Methionine Metabolism in Lactobacillus paracasei FAM18149. Daniel Wüthrich, Claudia Wenzel, Tharmatha Bavan, Rémy Bruggmann, Hélène Berthoud and Stefan Irmler Front Microbiol. (2018) 9:1261. doi:10.3389/fmicb.2018.01261.
• 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. Ricardo AR Machado, Daniel Wüthrich, Peter Kuhnert, Carla CM Arce, Lisa Thönen,  Celia Ruiz, Xi Zhang,  Christelle AM Robert, Javad Karimi,  Shokoofeh Kamali, Juan Ma, Rémy Bruggmann, Matthias Erb Int J Syst Evol Microbiol. (2018), doi:10.1099/ijsem.0.002820. ahead of print
• TNF-alpha initiates miRNA-mRNA signaling cascades in obstruction-induced bladder dysfunction. Ivonne Koeck, Ali Hashemi Gheinani, Ulrich Baumgartner, Erik Vassella, Rémy Bruggmann, Fiona C. Burkhard, and Katia Monastyrskaya Am J Pathol. (2018) 188(8):1847-1864, doi:10.1016/j.ajpath.2018.05.008

2017

• The ESRP1-GPR137 axis contributes to intestinal pathogenesis. Lukas Franz Mager, Viktor Hendrik Koelzer, Regula Stuber, Lester Thoo, Irene Keller, Ivonne Koeck, Maya Langenegger, Cedric Simillion, Simona P Pfister, Martin Faderl, Vera Genitsch, Irina Tcymbarevich, Pascal Juillerat, Xiaohong Li, Yu Xia, Eva Karamitopoulou, Ruth Lyck, Inti Zlobec, Siegfried Hapfelmeier, Rémy Bruggmann, Kathy D McCoy, Andrew J Macpherson, Christoph Müller, Bruce Beutler, Philippe Krebs. Elife. (2017) 4;6. pii: e28366, doi:10.7554/eLife.28366
• Need for speed in accurate whole-genome data analysis: GENALICE challenges BWA/GATK more than PEMapper/PECaller and Isaac. Michel Plüss, Anna M. Kopps, Irene Keller, Janine Meienberg, Sylvan M. Caspar, Nicolo Dubacher, Rémy Bruggmann, Manfred Vogel, Gabor Matyas. PNAS (2017), 3;114(40):E8320-E8322. doi: 10.1073/pnas.1713830114
• Accumulation of Deleterious Mutations During Bacterial Range Expansions. Lars Bosshard, Isabelle Dupanloup, Olivier Tenaillon, Rémy Bruggmann, Martin Ackermann, Stephan Peischl and Laurent Excoffier. Genetics (2017) vol. 207 no. 2 669-684
• Indication of Cross-Species Transmission of Astrovirus Associated with Encephalitis in Sheep and Cattle. Céline L. Boujon, Michel C. Koch, Daniel Wüthrich, Simea Werder, Dennis Jakupovic, Rémy Bruggmann, Torsten Seuberlich. Emerging Infectious Diseases (2017) 23:9, doi: 10.3201/eid2309.170168
• Neuropathological survey reveals underestimation of the prevalence of neuroinfectious diseases in cattle in Switzerland. Laura Truchet, Julia Walland, Daniel Wüthrich, Céline L. Boujona, Horst Posthausd, Rémy Bruggmann, Gertraud Schüpbach-Regula, Anna Oevermann, Torsten Seuberlich. Veterinary Microbiology (2017) 208:137–145, doi: 10.1016/j.vetmic.2017.07.027
• Cbp80 is needed for the expression of piRNA components and piRNAs. Ravish Rashpa, Paula Vazquez-Pianzola , Martino Colombo, Greco Hernandez, Dirk Beuchle, Fabienne Berger, Stephan Peischl, Rémy Bruggmann and Beat Suter. PLOS ONE (2017) July 26, doi: 10.1371/journal.pone.0181743
• Amplicon Sequencing of the slpH Locus Permits Culture-Independent Strain Typing of Lactobacillus helveticus in Dairy Products. Aline Moser, Daniel Wüthrich, Rémy Bruggmann, Elisabeth Eugster-Meier, Leo Meile and Stefan Irmler. Front. Microbiol.,(2017) 8:1380,  doi: 10.3389/fmicb.2017.01380
• A structural variant in the 5'-flanking region of the TWIST2 gene affects melanocyte development in belted cattle. Nivedita Awasthi Mishra, Cord Drögemüller, Vidhya Jagannathan, Irene Keller, Daniel Wüthrich, Rémy Bruggmann, Julia Beck, Ekkehard Schütz, Bertram Brenig, Steffi Demmel, Simon Moser, Heidi Signer-Hasler, Aldona Pieńkowska-Schelling, Claude Schelling, Marcos Sande, Ronald Rongen, Stefan Rieder, Robert N. Kelsh, Nadia Mercader, and Tosso Leeb. PLOS ONE 12(6): e0180170 doi: 10.1371/journal.pone.0180170.
• Avoiding the pitfalls of gene set enrichment analysis with SetRank. Cedric Simillion, Robin Liechti, Heidi EL Lischer, Vassilios Ioannidis, and Rémy Bruggmann. BMC Bioinformatics (2017) 18(1):151. doi: 10.1186/s12859-017-1571-6
• The histidine decarboxylase gene cluster of Lactobacillus parabuchneri was gained by horizontal gene transfer and is mobile within the species. Daniel Wüthrich, Hélène Berthoud, Daniel Wechsler, Elisabeth Eugster and Stefan Irmler, and Rémy Bruggmann. Front Microbiol. (2017) 8:218., doi:10.3389/fmicb.2017.00218
• Biallelic Mutations in DNAJC12 Cause Hyperphenylalaninemia, Dystonia, and Intellectual Disability. Yair Anikster, Tobias B. Haack, Thierry Vilboux, Ben Pode-Shakked, Beat Thöny, Nan Shen, Virginia Guarani, Thomas Meissner, Ertan Mayatepek, Friedrich K. Trefz, Dina Marek-Yagel, Aurora Martinez, Edward L. Huttlin, Joao A. Paulo, Riccardo Berutti, Jean-François Benoist, Apolline Imbard, Imen Dorboz, Gali Heimer, Yuval Landau, Limor Ziv-Strasser, May Christine V. Malicdan, Corinne Gemperle-Britschgi, Kirsten Cremer, Hartmut Engels, David Meili, Irene Keller, Rémy Bruggmann, Tim M. Strom, Thomas Meitinger, James C. Mullikin, Gerard Schwartz, Bruria Ben-Zeev, William A. Gahl, J. Wade Harper, Nenad Blau, Georg F. Hoffmann, Holger Prokisch, Thomas Opladen, Manuel Schiff. Am J Hum Genet. (2017) S0002-9297(17)30002-2, doi: 10.1016/j.ajhg.2017.01.002
• Characterization of miRNA-regulated networks, hubs of signaling, and biomarkers in obstruction-induced bladder dysfunction. Ali Hashemi Gheinani, Bernhard Kiss, Felix Moltzahn, Irene Keller, Rémy Bruggmann, Hubert Rehrauer, Catharine Aquino Fournier, Fiona C. Burkhard, and Katia Monastyrskaya. JCI Insight. (2017) 2(2): e89560, doi:10.1172/jci.insight.89560
• Association of the Intestinal Microbiome with the Development of Neovascular Age-Related Macular Degeneration. Zinkernagel, M.S., Zysset-Burry, D.C., Keller, I., Berger, L.E., Leichtle, A.B., Largiadèr, C.R., Fiedler, G.M., Wolf, S. 2017 Scientific Reports: 40826
• Spatio-temporal life history dynamics of cryptic lineages of the alpine mayfly Baetis alpinus (Ephemeroptera: Baetidae). Leys, M., Keller, I., Robinson, C.T. & Räsänen, K. Molecular Ecology (in press).
• The hyaluronan-mediated motility receptor RHAMM promotes growth, invasiveness and development of colorectal cancer. Mele, V., Sokol, L., Kölzer, V., Pfaff, D.; Muraro, M. G., Keller, I., Zahnd, S., Centeno, I., Terracciano, L.M., Dawson, H., Zlobec, I., Giandomenica, I., Lugli, A. 2017 Oncotarget 8(41): 70617–70629.
• Cbp80 is needed for the expression of piRNA components and piRNAs. Rashpa R, Vazquez-Pianzola P, Colombo M, Hernandez G, Beuchle D, Berger F, Peischl S, Bruggmann R, Suter B (2017). PloS one 12.7 (2017): e0181743.
• Relaxed selection during a recent human expansion. Peischl S*, Duperret I*, Foucal A, Jomphe, M, Bruat, V, Grenier J, Gbeha E, Hip-Ki E, Hodgkinson A, Vézina H, Awadalla P, and Excoffier L (2017). Genetics (in print: HTTP://DX.DOI.ORG/10.1534/GENETICS.117.300551)
• Slightly deleterious genomic variants and transcriptome perturbations in Down syndrome embryonic selection. Popadin, K, Peischl, S, Garieri, M, Sailani, M R, Letourneau, A, Santoni, F, ... , Stylianos E A (2017). Genome research (in print, HTTP://DX.DOI.ORG/10.1101/GR.228411.117 )

2016

• Globally distributed root endophyte Phialocephala subalpina links pathogenic and saprophytic lifestyles. Markus Schlegel, Martin Münsterkötter, Ulrich Güldener, Rémy Bruggmann, Angelo Duò, Matthieu Hainaut, Bernard Henrissat, Christian M. K. Sieber, Dirk Hoffmeister and Christoph R. Grünig. BMC Genomics (2016) 17(1):1015, doi:10.1186/s12864-016-3369-8
• Transcriptome-wide identification of NMD-targeted human mRNAs reveals extensive redundancy between SMG6- and SMG7-mediated degradation pathways. Martino Colombo, Evangelos D. Karousis, Joël Bourquin, Rémy Bruggmann and Oliver Mühlemann. RNA (2016); doi:10.1261/rna.059055.116
• Characterization and Transcriptomic Analysis of Porcine Blood Conventional and Plasmacytoid Dendritic Cells Reveals Striking Species-Specific Differences. Gael Auray, Irene Keller, Sylvie Python, Markus Gerber, Rémy Bruggmann, Nicolas Ruggli, and Artur Summerfield. J Immunol. (2016) 197(12):4791-4806, doi:10.4049/jimmunol.1600672
• The mRNA transportome of the BicD/Egl transport machinery. Paula Vazquez-Pianzola, Bogdan Schaller, Martino Colombo, Dirk Beuchle, Samuel Neuenschwander, Anne Marcil, Rémy Bruggmann and Beat Suter. RNA Biol. (2016); doi:10.1080/15476286.2016.1251542
• Maize cytolines unmask key nuclear genes that are under the control of retrograde signaling pathways in plants. Mihai Miclaus, Ovidiu Balacescu, Ioan Has, Loredana Balacescu, Voichita Has, Dana Suteu, Samuel Neuenschwander, Irene Keller, and Rémy Bruggmann. Genome Biol Evol. (2016)17;8(11):3256-3270, doi:10.1093/gbe/evw245
• Minor intron splicing is regulated by FUS and affected by ALS-associated FUS mutants. Stefan Reber, Jolanda Stettler, Giuseppe Filosa, Martino Colombo, Daniel Jutzi, Silvia C Lenzken, Christoph Schweingruber, Rémy Bruggmann, Angela Bachi, Silvia ML Barabino, Oliver Mühlemann, Marc‐David Ruepp. The EMBO Journal (2016) 35, 1504-152, doi: 10.15252/embj.201593791
• Full-genome based molecular characterization of encephalitis-associated bovine astroviruses. Ilias G. Bouzalas, Daniel Wüthrich, Senija Selimovic-Hamza, Cord Drögemüller, Rémy Bruggmann and Torsten Seuberlich. Infect Genet Evol (2016) 44,162-168, doi: 10.1016/j.meegid.2016.06.052
• Insight into the evolution of the Solanaceae from the parental genomes of Petunia hybrida. Aureliano Bombarely, Michel Moser, Avichai Amrad, Manzhu Bao, Laure Bapaume, Cornelius Barry, Mattijs Bliek, Maaike Boersma, Lorenzo Borghi, Rémy Bruggmann, et al.. Nature Plants (2016) 2,(6), 16074 doi: 10.1038/nplants.2016.74
• Multimodal stimulus coding by a gustatory sensory neuron in Drosophila larvae. Lena van Giesen, Luis Hernandez-Nunez, Sophie Delasoie-Baranek, Martino Colombo, Philippe Renaud, Rémy Bruggmann, Richard Benton, Aravinthan D.T. Samuel, and Simon G. Sprecher. Nature Communications (2016) 7, 10687 doi: 10.1038/ncomms10687
• Genomic approach to studying nutritional requirements of Clostridium tyrobutyricum and other Clostridia causing late blowing defects. Michelangelo Storari, Sandra Kulli, Daniel Wüthrich, Rémy Bruggmann, Hélène Berthoud, Emmanuelle Arias-Roth. Food Microbiology (2016) 59, 213-223, doi: 10.1016/j.fm.2016.05.013
• Evidence for two protein coding transcripts at the Igf2as locus. Carolina Duart-Garcia, Philippe Plattet, Rémy Bruggmann, Cedric Simillion, Irene Keller, Göran Andersson, Martin H. Braunschweig. Gene Reports (2016), 4, 60–66. http://doi.org/10.1016/j.genrep.2016.04.003
• Exploring the virome of cattle with non-suppurative encephalitis of unknown etiology by metagenomics. Daniel Wüthrich, Céline L. Boujonc, Laura Truchet, Senija Selimovic-Hamza, Anna Oevermann, Ilias G. Bouzalas, Rémy Bruggmann, Torsten Seuberlich. Virology (2016) 493, 22–30 doi: 10.1016/j.virol.2016.03.009
• A Broad RNA Virus Survey Reveals Both miRNA Dependence and Functional Sequestration. Troels K.H. Scheel, Joseph M. Luna, Matthias Liniger, Eiko Nishiuchi, Kathryn Rozen-Gagnon, Amir Shlomai, Gaël Auray, Markus Gerber, John Fak, Irene Keller, Rémy Bruggmann, Robert B. Darnell, Nicolas Ruggli, and Charles M. Rice. Cell Host Microbe (2016) 19, 409–423 doi:10.1016/j.chom.2016.02.007
• Identification of a second encephalitis-associated astrovirus in cattle. Torsten Seuberlich, Daniel Wüthrich, Senija Selimovic-Hamza, Cord Drögemüller, Anna Oevermann, Rémy Bruggmann and Ilias Bouzalas. Emerging Microbes and Infections (2016) 5, e5; doi:10.1038/emi.2016.5
• Clinical sequencing: is WGS the better WES? Janine Meienberg, Rémy Bruggmann, Konrad Oexle and Gabor Matyas. Hum Genet. (2016) 135(3), 359–362 doi:10.1007/s00439-015-1631-9
• Family-assisted inference of the genetic architecture of MHC variation. A. Gaigher, R. Burri, W. H. Gharib, P. Taberlet, A. Roulin & L. Fumagalli (2016). Molecular Ecology Resources, 1755-099810.1111/1755-0998.12537
• Distribution and population genetic variation of cryptic species of the Alpine mayfly Baetis alpinus (Ephemeroptera: Bae-tidae) in the Central Alps. Leys, M., Keller, I., Räsänen, K., Gattolliat, J.-L., Robinson, C.T. (2016) BMC Evolutionary Biology 16: 77.
• Genomic amplification of the caprine EDNRA locus leads to a dose dependent loss of pigmentation. Menzi, F., Keller, I., Reber, I., Beck, J., Brenig, B., Leeb, T., Drögemüller, C. (2016) Scientific Reports 28438.
• Distance from Sub-Saharan Africa Predicts Mutational Load in Diverse Human Genomes. Proceedings of the National Academy of Sciences. Henn B*, Botigué L*, Peischl S*, Dupanloup I, Maples B, Musharoff S, Martin A, Yee MC, Cann H, Synder M, Excoffier L, Kidd J, Bustamante CD (2016). E330 – E449
• A genomic history of Aboriginal Australia. Malaspinas AS, Westaway MC, Muller C, Sousa V, Lao O, Alves I, Bergström A, …, Peischl S, …, Nielsen R, Sandhu MS, Excoffier L, Lambert DM, Willerslev E (2016). Nature, 538, 207 – 214.
• Genetic surfing in human populations: from genes to genomes. Peischl S, Dupanloup I, Bosshard L, and Excoffier L (2016). Current Opinion in Genetics & Development 41, 53-61

2015

• The SIB Swiss Institute of Bioinformatics’ resources: focus on curated databases. SIB Swiss Institute of Bioinformatics Members. (2016). Nucleic Acids Research (2015) 44(D1), D27–D37, doi: 10.1093/nar/gkv1310
• New insights into the performance of human whole-exome capture platforms. Janine Meienberg, Katja Zerjavic, Irene Keller, Michal Okoniewski, Andrea Patrignani, Katja Ludin, Zhenyu Xu, Beat Steinmann, Thierry Carrel, Benno Röthlisberger, Ralph Schlapbach, Rémy Bruggmann and Gabor Matyas. Nucleic Acids Res. 43(11):e76. (2015) doi: 10.1093/nar/gkv216
• Draft Genome Sequences of Clostridium tyrobutyricum Strains FAM22552 and FAM22553, Isolated from Swiss Semihard Red-Smear Cheese. Michelangelo Storari, Daniel Wüthrich, Rémy Bruggmann, Hélène Berthoud, Emmanuelle Arias-Roth. Genome Announc. 12;3(2). pii: e00078-15 (2015). doi: 10.1128/genomeA.00078-15
• The aminoacyl-tRNA synthetases of Drosophila melanogaster. Lua, Jiongming; Marygoldb, Steven J; Gharib, Walid H;Suter, Beat (2015). Fly, 9:2, 53-61, 10.1080/19336934.2015.1101196
• Regular exercise decreases liver tumors development in hepatocyte-specific PTEN-deficient mice independently of steatosis. Piguet, Anne Christine; Saran, Uttara; Simillion, Cedric André Marie; Keller, Irene; Terracciano, Luigi; Reeves, Helen L; Dufour, Jean-François (2015). Journal of hepatology, 62(6), S. 1296-1303. Elsevier 10.1016/j.jhep.2015.01.017
• Wattles in goats are associated with the FMN1/GREM1 region on chromosome 10. Reber, Irene; Keller, Irene; Becker, Doreen; Flury, C; Welle, Monika Maria; Drögemüller, Cord (2015). Animal genetics, 46(3), S. 316-320. Blackwell 10.1111/age.12279
• The outer mucus layer hosts a distinct intestinal microbial niche. Li, H., Limenitakis, J., Fuhrer, T., Geuking, M., Lawson, M., Wyss, M., Brugiroux, S., Keller, I., Macpherson, J., Rupp, S., Stolp, B., Stein, J.V., Stecher, B., Sauer, U., McCoy, K.D. & Macpherson, A.J. (2015) Nature Communications, 6: 8292. 

2014

• Global phylogenomic analysis of nonencapsulated Streptococcus pneumoniae reveals a deep-branching classic lineage that is distinct from multiple sporadic lineages. Markus Hilty, Daniel Wüthrich, Susannah J. Salter, Hansjürg Engel, Samuel Campbell, Raquel Sá-Leão, Hermínia de Lencastre, Peter Hermans, Ewa Sadowy, Paul Turner, Claire Chewapreecha, Mathew Diggle, Gerd Pluschke, Lesley McGee, Özgen Köseoğlu Eser, Donald E. Low, Heidi Smith-Vaughan, Andrea Endimiani, Marianne Küffer, Mélanie Dupasquier, Emmanuel Beaudoing, Johann Weber, Rémy Bruggmann, William P. Hanage, Julian Parkhill, Lucy J. Hathaway, Kathrin Mühlemann and Stephen D. Bentley. Genome Biol Evol. 2014 Dec 4;6(12):3281-94. doi: 10.1093/gbe/evu263
• Autism spectrum disorder associated with low serotonin in CSF and mutations in the SLC29A4 plasma membrane monoamine transporter (PMAT) gene. Dea Adamsen, Vincent Ramaekers, Horace T. B. Ho, Corinne Britschgi, Véronique Wettstein, David Meili, Elise Bobrowski, Paule Philippe, Caroline Nava, Lionel Van Maldergem, Rémy Bruggmann, Susanne Walitza, Joanne Wang, Edna Grünblatt, and Beat Thöny. Molecular Autism, 5:43 (2014), doi:10.1186/2040-2392-5-43
• A point mutation in cpsE renders Streptococcus pneumoniae nonencapsulated and enhances its growth, adherence and competence. Thierry O. Schaffner, Jason Hinds, Katherine A. Gould, Daniel Wüthrich, Rémy Bruggmann, Marianne Küffer, Kathrin Mühlemann, Markus Hilty and Lucy J. Hathaway. BMC Microbiol. 2014 Aug 28;14(1):210. doi: 10.1186/s12866-014-0210-x
• An international multicenter study on HIV-1 drug resistance testing by 454 ultra-deep pyrosequencing. 454 HIV Alphastudy Group. J Virol Methods. 204:31-7 (2014). doi: 10.1016/j.jviromet.2014.04.007.
• Neurotropic Astrovirus in European Cattle with Non-suppurative Encephalitis. Ilias G. Bouzalas, Daniel Wüthrich, Julia Walland, Cord Drögemüller, Andreas Zurbriggen, Marc Vandevelde, Anna Oevermann, Rémy Bruggmann, and Torsten Seuberlich. J Clin Microbiol. 52(9):3318-24 (2014), doi:10.1128/JCM.01195-14
• Regulation of 11β-Hydroxysteroid Dehydrogenase Type 2 by MicroRNA. Mina Rezaei, Thomas Andrieu, Samuel Neuenschwander, Rémy Bruggmann, David Mordasini, Felix J. Frey, Bruno Vogt and Brigitte M. Frey. Hypertension, 64(4):860-6 (2014), doi:10.1161/HYPERTENSIONAHA.114.00002
• Generation of SNP datasets for orangutan population genomics using improved reduced-representation sequencing and direct comparisons of SNP calling algorithms. Maja P Greminger, Kai N Stölting, Alexander Nater, Benoit Goossens, Natasha Arora, Rémy Bruggmann, Andrea Patrignani, Beatrice Nussberger, Reeta Sharma, Robert H Kraus, Laurentius N Ambu, Ian Singleton, Lounes Chikhi, Carel P van Schaik and Michael Krützen. BMC Genomics, 15:16 (2014), doi:10.1186/1471-2164-15-16
• Independent polled mutations leading to complex gene expression differences in cattle. Natalie Wiedemar, Jens Tetens, Vidhya Jagannathan, Annie Menoud, Samuel Neuenschwander, Rémy Bruggmann, Georg Thaller, Cord Drögemüller. PLoS One. 26;9(3):e93435 (2014). doi: 10.1371/journal.pone.0093435. eCollection 2014.
• The brown coat colour of Coppernecked goats is associated with a non-synonymous variant at the TYRP1 locus on chromosome 8. Becker, Doreen; Otto, Mandy; Ammann, P; Keller, Irene; Drögemüller, Cord; Leeb, Tosso (2014). Animal genetics, 46(1), S. 50-54. Blackwell 10.1111/age.12240
• The genomic substrate for adaptive radiation in African cichlid fish. Brawand, David; Wagner, Catherine; Li, Yang I.; Malinsky, Milan; Keller, Irene; Fan, Shaohua; Simakov, Oleg; Ng, Alvin Y.; Lim, Zhi Wei; Bezault, Etienne; Turner-Maier, Jason; Johnson, Jeremy; Alcazar, Rosa; Noh, Hyun Ji; Russell, Pamela; Aken, Bronwen; Alföldi, Jessica; Amemiya, Chris; Azzouzi, Naoual; Baroiller, Jean-François; ... (2014). Nature, 513(7518), S. 375-381. Macmillan Journals Ltd. 10.1038/nature13726
• Genomics and the origin of species. Seehausen, Ole; Butlin, Roger K.; Keller, Irene; Wagner, Catherine; Boughman, Janette W.; Hohenlohe, Paul A.; Peichel, Catherine L.; Saetre, Glenn-Peter; Bank, Claudia; Brännström, Åke; Brelsford, Alan; Clarkson, Chris S.; Eroukhmanoff, Fabrice; Feder, Jeffrey L.; Fischer, Martin; Foote, Andrew D.; Franchini, Paolo; Jiggins, Chris D.; Jones, Felicity C.; Lindholm, Anna K.; ... (2014).  Nature Reviews Genetics, 15(3), S. 176-192. Natue Publishing Group 10.1038/nrg3644

2013

• In search of epigenetic marks in testes and sperm cells of differentially fed boars. Rémy Bruggmann, Vidhya Jagannathan, Martin Braunschweig. PlosOne, 8(11):e78691. (2013) doi: 10.1371/journal.pone.0078691
• The wheat powdery mildew genome shows the unique evolution of an obligate biotroph. Thomas Wicker, Simone Oberhaensli, Francis Parlange, Jan P Buchmann, Margarita Shatalina, Stefan Roffler, Roi Ben-David, Jaroslav Doležel, Hana Šimková, Paul Schulze-Lefert, Pietro D Spanu, Rémy Bruggmann, Joelle Amselem, Hadi Quesneville, Emiel Ver Loren van Themaat, Timothy Paape, Kentaro K Shimizu & Beat Keller. Nature Genetics, 45(9):1092-6, doi:10.1038/ng.2704 (2013)
• A frameshift mutation in the cubilin gene (CUBN) in Beagles with Imerslund–Gräsbeck syndrome (selective cobalamin malabsorption). Michaela Drögemüller, Vidhya Jagannathan, Judith Howard, Rémy Bruggmann, Cord Drögemüller, Maja Ruetten, Tosso Leeb, and Peter H. Kook. Animal Genetics, doi: 10.1111/age.12094 (2013)
• Streaming Support for Data Intensive Cloud Based Sequence Analysis. Shady Issa, Romeo Kienzler, Mohamed El-Kalioby, Peter Tonellato, Dennis Wall, Rémy Bruggmann*, Mohamed Abouelhoda*. BioMed Res Int., Article ID 791051 (2013) * corresponding authors
• A non-coding genomic duplication at the HMX1 locus is associated with crop ears in Highland cattle. Carolina T. Koch, Rémy Bruggmann, Jens Tetens, Cord Drögemüller. PlosOne, 8(10):e77841 (2013), doi: 10.1371/journal.pone.0077841
• Next-Generation Sequencing of HIV-1 RNA Genomes: Determination of Error Rates and Minimizing Artificial Recombination. Francesca Di Giallonardo, Osvaldo Zagordi, Yannick Duport, Christine Leemann, Beda Joos, Marzanna Künzli-Gontarczyk, Rémy Bruggmann, Niko Beerenwinkel, Huldrych F. Günthard, Karin J. Metzner. PlosOne, 8(9):e74249 (2013)
• Identification of a SIRT1 mutation in a family with type 1 diabetes. Biason-Lauber A, Böni-Schnetzler M, Hubbard BP, Bouzakri K, Brunner A, Cavelti-Weder C, Keller C, Meyer-Böni M, Meier DT, Brorsson C, Timper K, Leibowitz G, Patrignani A, Bruggmann R, Boily G, Zulewski H, Geier A, Cermak JM, Elliott P, Ellis JL, Westphal C, Knobel U, Eloranta JJ, Kerr-Conte J, Pattou F, Konrad D, Matter CM, Fontana A, Rogler G, Schlapbach R, Regairaz C, Carballido JM, Glaser B, McBurney MW, Pociot F, Sinclair DA, Donath MY. Cell Metab., 17(3):448-55 (2013)

2012

• KDM2B is implicated in bovine lethal multi-organic developmental dysplasia. Stefania Testoni, Elena Bartolone, Marco Rossi, Andrea Patrignani, Rémy Bruggmann, Peter Lichtner, Jens Tetens, Arcangelo Gentile, Cord Drögemüller. PLoS One, 7(9):e45634 (2012)
• The tomato genome sequence provides insights into fleshy fruit evolution. The Tomato Genome Consortium. Nature, 485: 635–641 (2012)
• SNP-Ratio Mapping (SRM): Identifying Lethal Alleles and Mutations in Complex Genetic Backgrounds by Next-Generation Sequencing. Heike Lindner, Michael T. Raissig, Christian Sailer, Hiroko Shimosato-Asano, Rémy Bruggmann and Ueli Grossniklaus. Genetics, (191), 1381-1386 (2012)
• Mitochondrial genome evolution in species belonging to the Phialocephala fortinii s.l. - Acephala applanata species complex. Angelo Duò, Rémy Bruggmann, Stefan Zoller, Matthias Bernt and Christoph R. Grünig. BMC Genomics, 13(1), 166 (2012)
• Incremental DNA Sequence Analysis in the Cloud. Romeo Kienzler, Rémy Bruggmann, Anand Ranganathan, Nesime Tatbul. 24th International Conference on Scientific and Statistical Database Management (SSDBM 2012), ISBM/ISSN: 978-3642312342
• Stream As You Go: The Case for Incremental Data Access and Processing in the Cloud. Romeo Kienzler, Rémy Bruggmann, Anand Ranganathan, Nesime Tatbul. IEEE ICDE International Workshop on Data Management in the Cloud (DMC'12), Washington, DC, USA, IEEE, 2012

2011

• Comparative sequence analysis of VRN1 alleles of Lolium perenne with the co-linear regions in barley, wheat, and rice. Torben Asp, Stephen Byrne, Heidrun Gundlach, Rémy Bruggmann, Klaus F. X. Mayer, Jeppe R. Andersen, Mingliang Xu, Morten Greve, Ingo Lenk, Thomas Lübberstedt. Mol Genet Genomics, 286:433-447 (2011)
• Characterization of the small RNA component of the transcriptome from grain and sweet sorghum stems. Martín Calviño, Rémy Bruggmann, and Joachim Messing. BMC Genomics, 12:356 (2011)
• Large-scale DNA Sequence Analysis in the Cloud: A Stream-based Approach. Romeo Kienzler, Rémy Bruggmann, Anand Ranganathan and Nesime Tatbul. Euro-Par 6th Workshop on Virtualization in High-Performance Cloud Computing (VHPC'11) ISBN/ISSN: 978-3642297397, (2011).

2010+

• The Genome sequencing and analysis of the model grass Brachypodium distachyon. The International Brachypodium Initiative et al. Nature, 463:763-768 (2010)
• The Sorghum bicolor genome and the diversification of grasses. Andrew Paterson, John Bowers , Rémy Bruggmann, Inna Dubchak, Jane Grimwood, Heidrun Gundlach, Georg Haberer, Uffe Hellsten, Therese Mitros, Alexander Poliakov, Jeremy Schmutz, Manuel Spannagl, Haibao Tang, Xiyin Wang, Thomas Wicker, Arvind Bharti, Brad Chapman, Frank Feltus, Udo Gowik, Igor Grigoriev, Eric Lyons, Christopher Maher, Mihaela Martis, Apurva Narechania, Robert Otillar, Bryan Penning, Asaf Salomov, Yu Wang, Lifang Zhang, Nicholas Carpita, Michael Freeling, Alan Gingle, Charles Hash, Beat Keller, Patricia Klein, Stephen Kresovich, Maureen Mccann, Ray Ming, Daniel Peterson, Mehboob ur-Rahman, Doreen Ware, Peter Westhoff, Klaus Mayer, Joachim Messing, Daniel Rohksar. Nature, 457:551-556 (2009)
• Molecular Markers for Sweet Sorghum Based on Microarray Expression Data. Martin Calviño, Mihai Miclaus, Rémy Bruggmann, Joachim Messing. Rice, 2:129-142. (2009)
• A snapshot of the emerging tomato genome sequence. Lukas Mueller, René Klein Lankhorst, Steven D. Tanksley, James J. Giovannoni, Ruth White, Julia Vrebalov, Zhangjun Fei, Joyes van Eck, et al. The Plant Genome, 2, 78-92 (2009)
• Screen of Genes Linked to High-Sugar Content in Stems by Comparative Genomics. Martin Calviño, Rémy Bruggmann, Joachim Messing. Rice, 1:166-176 (2008)
• 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. Agim Ballvora, Anika Jöcker, Prisca Viehöver, Hirofumi Ishihara, Jürgen Paal, Khalid Meksem, Rémy Bruggmann, Heiko Schoof, Bernd Weisshaar, Christiane Gebhardt. BMC Genomics 8, 112 (2007)
• Uneven Chromosome Contraction and Expansion in the Maize Genome. Rémy Bruggmann*, Arvind K. Bharti*, Heidrun Gundlach*, Jinsheng Lai, Sarah Young, Ana C. Pontaroli, Fusheng Wei, Georg Haberer, Galina Fuks, Chunguang Du, Christina Raymond, Matt C. Estep, Renyi Liu, Jeffrey L. Bennetzen, Agnes P. Chan, Pablo D. Rabinowicz, John Quackenbush, W. Brad Barbazuk, Rod A. Wing, Bruce Birren, Chad Nusbaum, Steve Rounsley, Klaus F.X. Mayer, and Joachim Messing. *equal contribution. Genome Research 16, 1241-1251 (2006)
• Transcriptional changes in powdery mildew infected wheat and Arabidopsis leaves undergoing syringolin-triggered hypersensitive cell death at infection sites. Kathrin Michel*, Olaf Abderhalden*, Rémy Bruggmann, and Robert Dudler *These authors contributed equally to the paper. Plant Molecular Biology 62, 561-578 (2006)
• Analysis of epidermis- and mesophyll-specific transcript accumulation in powdery mildew-inoculated wheat leaves. Rémy Bruggmann, Olaf Abderhalden, Philippe Reymond and Robert Dudler. Plant Molecular Biology 58, 247-267 (2005)
• Homologous Recombination and DNA-End Joining Reactions in Zygotes and Early Embryos of Zebrafish (Danio rerio) and Drosophila melanogaster. Michael Hagmann*, Rémy Bruggmann*, Lei Xue, Oleg Georgiev, Walter Schaffner, Duri Rungger, Philipp Spaniol and Thomas Gerster. *These authors contributed equally to the paper. Biological Chemistry 379, 673–681 (1998)
• Dramatic Changes in the Ratio of Homologous Recombination to Nonhomologous DMA-End-Joining in Oocytes and Early Embryos of Xenopus laevis. Michael Hagmann, Katrin Adlkofer, Petra Pfeiffer, Rémy Bruggmann, Oleg Georgiev, Duri Rungger and Walter Schaffner. Biological Chemistry Hoppe-Seyler 377, 239–250 (1996)