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Spörri, Livia; Uldry, Anne-Christine; Kreuzer, Marco; Herzog, Elio L; Zinkernagel, Martin S; Unterlauft, Jan D; Zysset, Denise C (2024). Exploring the Ocular Surface Microbiome and Tear Proteome in Glaucoma. International journal of molecular sciences, 25(11) MDPI 10.3390/ijms25116257

Gioutsos, Konstantinos; Ehrenreich, Lasse; Azenha, Luis Filipe; Quapp, Christopher Siegbert; Kocher, Gregor Jan; Lutz, Jon Andri; Peischl, Stephan; Dorn, Patrick (2024). Randomized Controlled Trial of Thresholds for Drain Removal After Anatomic Lung Resection. The annals of thoracic surgery, 117(6), pp. 1103-1109. Elsevier 10.1016/j.athoracsur.2023.09.011

Ory, Florine; Dietemann, Vincent; Guisolan, Anne; Ah, Ueli von; Fleuti, Charlotte; Michellod, Emilie; Schumpp, Olivier; Oberhaensli, Simone; Charrière, Jean-Daniel; Dainat, Benjamin (2024). Corrigendum: Paenibacillus melissococcoides sp. nov., isolated from a honey bee colony affected by European foulbrood disease. International journal of systematic and evolutionary microbiology, 74(6) Microbiology Society 10.1099/ijsem.0.006408

Morandi, Sophia C; Herzog, Elio L; Munk, Marion; Kreuzer, Marco; Largiadèr, Carlo R; Wolf, Sebastian; Zinkernagel, Martin; Zysset-Burri, Denise C (2024). The gut microbiome and HLA-B27-associated anterior uveitis: a case-control study. Journal of neuroinflammation, 21(120) BioMed Central 10.1186/s12974-024-03109-4

Roder, Thomas; Pimentel, Grégory; Fuchsmann, Pascal; Stern, Mireille Tena; von Ah, Ueli; Vergères, Guy; Peischl, Stephan; Brynildsrud, Ola; Bruggmann, Rémy; Bär, Cornelia (2024). Scoary2: rapid association of phenotypic multi-omics data with microbial pan-genomes. Genome biology, 25(1) BioMed Central 10.1186/s13059-024-03233-7

Thormann, Kathrin; Lüthi, Anne-Sophie; Deniau, Felix; Heider, Anja; Cazzaniga, Simone; Radonjic-Hoesli, Susanne; Lehmann, Mathias; Schlapbach, Christoph; Herzog, Elio L; Kreuzer, Marco; Zinkernagel, Martin S; Akdis, Cezmi A; Zysset, Denise C; Simon, Hans-Uwe; Simon, Dagmar (2024). Dupilumab-associated ocular surface disease is characterized by a shift from Th2/Th17 toward Th1/Th17 inflammation. Allergy, 79(4), pp. 937-948. Wiley-Blackwell 10.1111/all.16045

Anderegg, Manuel A; Olinger, Eric G; Bargagli, Matteo; Geraghty, Rob; Taylor, Lea; Nater, Alexander; Bruggmann, Rémy; Sayer, John A; Vogt, Bruno; Schaller, André; Fuster, Daniel G (2024). Prevalence and characteristics of genetic disease in adult kidney stone formers. (In Press). Nephrology, dialysis, transplantation Oxford University Press 10.1093/ndt/gfae074

Wu, Fei Hugo; Marquez Neila, Pablo; Zheng, Mingyi; Rafii-Tari, Hedyeh; Sznitman, Raphael (January 2024). Correlation-aware active learning for surgery video segmentation. In: WACV. IEEE/CVF

Schütz, Sara Doina; Brackmann, Maximilian; Liechti, Nicole; Moser, Michel; Wittwer, Matthias; Bruggmann, Rémy (2024). Functional characterization of Francisella tularensis subspecies holarctica genotypes during tick cell and macrophage infections using a proteogenomic approach. Frontiers in cellular and infection microbiology, 14 Frontiers 10.3389/fcimb.2024.1355113


Thoenen, Lisa; Giroud, Caitlin; Kreuzer, Marco; Waelchli, Jan; Gfeller, Valentin; Deslandes-Hérold, Gabriel; Mateo, Pierre; Robert, Christelle A M; Ahrens, Christian H; Rubio-Somoza, Ignacio; Bruggmann, Rémy; Erb, Matthias; Schlaeppi, Klaus (2023). Bacterial tolerance to host-exuded specialized metabolites structures the maize root microbiome. Proceedings of the National Academy of Sciences of the United States of America - PNAS, 120(44), e2310134120. National Academy of Sciences 10.1073/pnas.2310134120

Pitton, Melissa; Valente, Luca G; Oberhaensli, Simone; Casanova, Carlo; Sendi, Parham; Schnegg, Bruno; Jakob, Stephan M; Cameron, David R; Que, Yok-Ai; Fürholz, Monika (2023). Dynamics of bacterial pathogens at the driveline exit site in patients with ventricular assist devices: a prospective, observational, single-centre cohort study. The Journal of heart and lung transplantation, 42(10), pp. 1445-1454. Elsevier 10.1016/j.healun.2023.05.016

Meier, Joana; McGee, Matthew D; Marques, David A; Mwaiko, Salome; Kishe, Mary; Wandera, Sylvester; Neumann, Dirk; Mrosso, Hilary; Chapman, Lauren J; Chapman, Colin A; Kaufman, Les; Taabu-Munyaho, Anthony; Wagner, Catherine E; Bruggmann, Rémy; Excoffier, Laurent; Seehausen, Ole (2023). Cycles of fusion and fission enabled rapid parallel adaptive radiations in African cichlids. Science, 381(6665), eade2833. American Association for the Advancement of Science 10.1126/science.ade2833

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

Schlegel, Irina; De Goüyon Matignon de Pontourade, Claire M F; Lincke, Joel-Benjamin; Keller, Irene; Zinkernagel, Martin S; Zysset-Burri, Denise C (2023). The Human Ocular Surface Microbiome and Its Associations with the Tear Proteome in Dry Eye Disease. International journal of molecular sciences, 24(18) MDPI 10.3390/ijms241814091

Vannetti, Stefania M; Wynne, James W; English, Chloe; Huynh, Christine; Knüsel, Ralph; de Sales-Ribeiro, Carolina; Widmer, Maro; Delalay, Gary; Schmidt-Posthaus, Heike (2023). Amoeba species colonizing the gills of rainbow trout (Oncorhynchus mykiss) in Swiss aquaculture. Journal of fish diseases, 46(9), pp. 987-999. Wiley 10.1111/jfd.13819

Gander, Thi Thuy Hang; Schläfli, Joëlle; Baumgartner, Johanna; Walthert, Sabrina; Genitsch, Vera; van Geest, Geert; Galván, José A; Cardozo, Carmen; Graham Martinez, Cristina; Grans, Mona; Muth, Sabine; Bruggmann, Rémy; Probst, Hans Christian; Gabay, Cem; Freigang, Stefan (2023). Targeted removal of macrophage-secreted interleukin-1 receptor antagonist protects against lethal Candida albicans sepsis. Immunity, 56(8), 1743-1760.e9. Cell Press 10.1016/j.immuni.2023.06.023

Anderegg, Manuel A.; Olinger, Eric G.; Bargagli, Matteo; Geraghty, Rob; Pohlmeier, Lea; Nater, Alexander; Bruggmann, Rémy; Sayer, John A.; Vogt, Bruno; Schaller, André; Fuster, Daniel G. (27 July 2023). Prevalence and characteristics of monogenic disease in adult kidney stone formers (medRxiv). Cold Spring Harbor Laboratory 10.1101/2023.07.23.23292924

Pfefferli, Catherine; Bonvin, Marylène; Grepper, Dogan; Robatel, Steve; König, Désirée; Lischer, Heidi E L; Bruggmann, Rémy; Jaźwińska, Anna (2023). Parallels between oncogene-driven cardiac hyperplasia and heart regeneration in zebrafish. Development, 150(12) The Company of Biologists 10.1242/dev.201412

Sgammeglia, Noemi; Widmer, Yves F; Kaldun, Jenifer C; Fritsch, Cornelia; Bruggmann, Rémy; Sprecher, Simon G (2023). Memory phase-specific genes in the Mushroom Bodies identified using CrebB-target DamID. PLoS genetics, 19(6), e1010802. Public Library of Science 10.1371/journal.pgen.1010802

Wang, Xuejing; Peischl, Stephan; Heckel, Gerald (2023). Demographic history and genomic consequences of 10,000 generations of isolation in a wild mammal. Current biology, 33(10), 2051-2062.e4. Cell Press 10.1016/j.cub.2023.04.042

Bertschi, Nicole L; Steck, Oliver; Luther, Fabian; Bazzini, Cecilia; von Meyenn, Leonhard; Schärli, Stefanie; Vallone, Angela; Felser, Andrea; Keller, Irene; Friedli, Olivier; Freigang, Stefan; Begré, Nadja; Radonjic-Hoesli, Susanne; Lamos, Cristina; Gabutti, Max Philip; Benzaquen, Michael; Laimer, Markus; Simon, Dagmar; Nuoffer, Jean-Marc and Schlapbach, Christoph (2023). PPAR-γ regulates the effector function of human T helper 9 cells by promoting glycolysis. Nature Communications, 14(1), p. 2471. Springer Nature 10.1038/s41467-023-38233-x

Ory, Florine; Dietemann, Vincent; Guisolan, Anne; von Ah, Ueli; Fleuti, Charlotte; Oberhaensli, Simone; Charrière, Jean-Daniel; Dainat, Benjamin (2023). Paenibacillus melissococcoides sp. nov., isolated from a honey bee colony affected by European foulbrood disease. International journal of systematic and evolutionary microbiology, 73(4) Microbiology Society 10.1099/ijsem.0.005829

Sianta, Shelley A; Peischl, Stephan; Moeller, David A; Brandvain, Yaniv (2023). The efficacy of selection may increase or decrease with selfing depending upon the recombination environment. Evolution, 77(2), pp. 394-408. Oxford University Press 10.1093/evolut/qpac013

Hennink, Imke; Peters, Laureen; van Geest, Gerrit; Adamik, Katja-Nicole (2023). Evaluation of a Viscoelastic Coagulation Monitoring System (VCM Vet®) and Its Correlation with Thromboelastometry (ROTEM®) in Diseased and Healthy Dogs. Animals, 13(3), p. 405. MDPI 10.3390/ani13030405

Duruz, Jules; Sprecher, Marta; Kaldun, Jenifer C; Al-Soudy, Al-Sayed; Tschanz, Heidi E L; van Geest, Geert; Nicholson, Pamela; Bruggmann, Rémy; Sprecher, Simon G (2023). Molecular characterization of cell types in the squid Loligo vulgaris. eLife, 12 eLife Sciences Publications 10.7554/eLife.80670

Schütz, Sara Doina; Liechti, Nicole; Altpeter, Ekkehardt; Labutin, Anton; Wütrich, Tsering; Schmidt, Kristina Maria; Buettcher, Michael; Moser, Michel; Bruggmann, Rémy; Wittwer, Matthias (2023). Phylogeography of Francisella tularensis subspecies holarctica and epidemiology of tularemia in Switzerland. Frontiers in Microbiology, 14(1151049), p. 1151049. Frontiers 10.3389/fmicb.2023.1151049

Bise, Thomas; Pfefferli, Catherine; Bonvin, Marylène; Taylor, Lea; Lischer, Heidi E L; Bruggmann, Rémy; Jaźwińska, Anna (2023). The regeneration-responsive element careg monitors activation of Müller glia after MNU-induced damage of photoreceptors in the zebrafish retina. Frontiers in molecular neuroscience, 16, p. 1160707. Frontiers Research Foundation 10.3389/fnmol.2023.1160707

Herzog, Elio L; Kreuzer, Marco; Zinkernagel, Martin S; Zysset-Burri, Denise C (2023). Challenges and insights in the exploration of the low abundance human ocular surface microbiome. Frontiers in cellular and infection microbiology, 13(1232147), p. 1232147. Frontiers 10.3389/fcimb.2023.1232147

Giesen, Athene; Blanckenhorn, Wolf U; Schäfer, Martin A; Shimizu, Kentaro K; Shimizu-Inatsugi, Rie; Misof, Bernhard; Podsiadlowski, Lars; Niehuis, Oliver; Lischer, Heidi E L; Aeschbacher, Simon; Kapun, Martin (2023). Geographic Variation in Genomic Signals of Admixture Between Two Closely Related European Sepsid Fly Species. Evolutionary biology, 50(4), pp. 395-412. Springer 10.1007/s11692-023-09612-5


Roder, Thomas; Oberhänsli, Simone; Shani, Noam; Bruggmann, Rémy (2022). OpenGenomeBrowser: a versatile, dataset-independent and scalable web platform for genome data management and comparative genomics. BMC Genomics, 23(1), p. 855. BioMed Central 10.1186/s12864-022-09086-3

Cameron, David R; Pitton, Melissa; Oberhaensli, Simone; Schlegel, Katja; Prod'hom, Guy; Blanc, Dominique S; Jakob, Stephan M; Que, Yok-Ai (2022). Parallel Evolution of Pseudomonas aeruginosa during a Prolonged ICU-Infection Outbreak. Microbiology spectrum, 10(6), e0274322. American Society for Microbiology 10.1128/spectrum.02743-22

Kuhn, Jens H; Adkins, Scott; Alkhovsky, Sergey V; Avšič-Županc, Tatjana; Ayllón, María A; Bahl, Justin; Balkema-Buschmann, Anne; Ballinger, Matthew J; Bandte, Martina; Beer, Martin; Bejerman, Nicolas; Bergeron, Éric; Biedenkopf, Nadine; Bigarré, Laurent; Blair, Carol D; Blasdell, Kim R; Bradfute, Steven B; Briese, Thomas; Brown, Paul A; Bruggmann, Rémy; ... (2022). 2022 taxonomic update of phylum Negarnaviricota (Riboviria: Orthornavirae), including the large orders Bunyavirales and Mononegavirales. Archives of virology, 167(12), pp. 2857-2906. Springer 10.1007/s00705-022-05546-z

Spinelli, Marialuigia; Zdanowicz, Jarmila A; Keller, Irene; Nicholson, Pamela; Raio, Luigi; Amylidi-Mohr, Sofia; Mosimann, Beatrice; Surbek, Daniel; Mueller, Martin (2022). Hypertensive disorders of pregnancy share common cfDNA methylation profiles. Scientific Reports, 12(1), p. 19837. Nature Publishing Group 10.1038/s41598-022-24348-6

Schlichta, Flávia; Peischl, Stephan; Excoffier, Laurent (2022). The impact of genetic surfing on neutral genomic diversity. Molecular Biology and Evolution, 39(11) Oxford University Press 10.1093/molbev/msac249

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

Bertschi, Nicole L; Steck, Oliver; Luther, Fabian; Bazzini, Cecilia; von Meyenn, Leonhard; Felser, Andrea; Keller, Irene; Friedli, Olivier; Freigang, Stefan; Begré, Nadja; Lamos, Cristina; Gabutti, Max Philip; Benzaquen, Michael; Laimer, Markus; Simon, Dagmar; Nuoffer, Jean-Marc; Schlapbach, Christoph (16 August 2022). PPAR-γ regulates the effector function of human TH9 cells by promoting glycolysis (bioRxiv). Cold Spring Harbor Laboratory 10.1101/2022.08.16.503972

Deng, Haibin; Gao, Yanyun; Trappetti, Verdiana; Hertig, Damian; Karatkevich, Darya; Losmanová, Tereza; Urzì, Christian; Ge, Huixiang; Geest, Gerrit Adriaan; Bruggmann, Remy; Djonov, Valentin; Nuoffer, Jean-Marc; Vermathen, Peter; Zamboni, Nicola; Riether, Carsten; Ochsenbein, Adrian; Peng, Ren-Wang; Kocher, Gregor Jan; Schmid, Ralph; Dorn, Patrick; ... (2022). Targeting lactate dehydrogenase B-dependent mitochondrial metabolism affects tumor initiating cells and inhibits tumorigenesis of non-small cell lung cancer by inducing mtDNA damage. Cellular and molecular life sciences, 79(8), p. 445. SP Birkhäuser Verlag Basel 10.1007/s00018-022-04453-5

Barreto de Albuquerque, Juliana; Altenburger, Lukas M; Abe, Jun; von Werdt, Diego; Wissmann, Stefanie; Martínez Magdaleno, Jose; Francisco, David; van Geest, Geert; Ficht, Xenia; Iannacone, Matteo; Bruggmann, Remy; Mueller, Christoph; Stein, Jens V (2022). Microbial uptake in oral mucosa-draining lymph nodes leads to rapid release of cytotoxic CD8+ T cells lacking a gut-homing phenotype. Science immunology, 7(72), eabf1861. American Association for the Advancement of Science 10.1126/sciimmunol.abf1861

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

Dorn, Patrick; Pfister, Selina; Oberhaensli, Simone; Gioutsos, Konstantinos; Haenggi, Matthias; Kocher, Gregor J (2022). Operative versus non-operative management of rib fractures in flail chest after cardiopulmonary resuscitation manoeuvres. Interactive cardiovascular and thoracic surgery, 34(5), pp. 768-774. Oxford University Press 10.1093/icvts/ivac023

Walter, Justin D; Scherer, Melanie; Hutter, Cedric A J; Garaeva, Alisa A; Zimmermann, Iwan; Wyss, Marianne; Rheinberger, Jan; Ruedin, Yelena; Earp, Jennifer C; Egloff, Pascal; Sorgenfrei, Michèle; Hürlimann, Lea M; Gonda, Imre; Meier, Gianmarco; Remm, Sille; Thavarasah, Sujani; van Geest, Geert; Bruggmann, Rémy; Zimmer, Gert; Slotboom, Dirk J; ... (2022). Biparatopic sybodies neutralize SARS-CoV-2 variants of concern and mitigate drug resistance. EMBO reports, 23(4), e54199. EMBO press 10.15252/embr.202154199

Moinet, Antoine; Schlichta, Flavia; Peischl, Stephan; Excoffier, Laurent (2022). Strong neutral sweeps occurring during a population contraction. Genetics, 220(4) Oxford University Press 10.1093/genetics/iyac021

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

Barut, Güliz Tuba; Kreuzer, Marco; Bruggmann, Rémy; Summerfield, Artur; Talker, Stephanie C (2022). Single-cell transcriptomics reveals striking heterogeneity and functional organization of dendritic and monocytic cells in the bovine mesenteric lymph node. Frontiers in immunology, 13(1099357), p. 1099357. Frontiers Research Foundation 10.3389/fimmu.2022.1099357

Marchetti, Luca; Francisco, David; Soldati, Sasha; Haghayegh Jahromi, Neda; Barcos, Sara; Gruber, Isabelle; Pareja R., Javier; Thiriot, Aude; von Andrian, Ulrich; Deutsch, Urban; Lyck, Ruth; Bruggmann, Rémy; Engelhardt, Britta (2022). ACKR1 favors transcellular over paracellular T-cell diapedesis across the blood-brain barrier in neuroinflammation in vitro. European journal of immunology, 52(1), pp. 161-177. Wiley 10.1002/eji.202149238

García-Martín, Ana Bélen; Roder, Thomas; Schmitt, Sarah; Zeeh, Friederike; Bruggmann, Rémy; Perreten, Vincent (2022). Whole-genome analyses reveal a novel prophage and cgSNPs-derived sublineages of Brachyspira hyodysenteriae ST196. BMC Genomics, 23(1), p. 131. BioMed Central 10.1186/s12864-022-08347-5

Cvitas, Iva; Oberhaensli, Simone; Leeb, Tosso; Marti, Eliane (2022). Equine keratinocytes in the pathogenesis of insect bite hypersensitivity: Just another brick in the wall? PLoS ONE, 17(8), e0266263. Public Library of Science 10.1371/journal.pone.0266263

Talker, Stephanie C; Barut, G Tuba; Lischer, Heidi E L; Rufener, Reto; von Münchow, Lilly; Bruggmann, Rémy; Summerfield, Artur (2022). Monocyte biology conserved across species: Functional insights from cattle. Frontiers in immunology, 13, p. 889175. Frontiers Research Foundation 10.3389/fimmu.2022.889175


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

Trueb, Beat; Zhuang, Lei; Keller, Irene; von Köckritz, Leona; Kuchen, Stefan; Dufour, Jean-François; Villiger, Peter (2021). Coincidence of NOD2-Associated Autoinflammatory Disease (Yao Syndrome) and HCV Infection With Fatal Consequences: Interaction Between Genes and Environment. Journal of clinical rheumatology, 27(8S), S592-S594. Wolters Kluwer Health 10.1097/RHU.0000000000000963

Borcard, Loïc Vivien; Kick, Andrew Robert; Hug, Corinne; Lischer, Heidi Erika Lisa; Käser, Tobias; Summerfield, Artur (2021). Systems Immunology Analyses Following Porcine Respiratory and Reproductive Syndrome Virus Infection and Vaccination. Frontiers in immunology, 12, p. 779747. Frontiers Research Foundation 10.3389/fimmu.2021.779747

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

Brkic, Sime; Stivala, Simona; Santopolo, Alice; Szybinski, Jakub; Jungius, Sarah; Passweg, Jakob R; Tsakiris, Dimitrios; Dirnhofer, Stefan; Hutter, Gregor; Leonards, Katharina; Lischer, Heidi E L; Dettmer, Matthias S; Neel, Benjamin G; Levine, Ross L; Meyer, Sara C (2021). Dual targeting of JAK2 and ERK interferes with the myeloproliferative neoplasm clone and enhances therapeutic efficacy. Leukemia, 35(10), pp. 2875-2884. Springer Nature 10.1038/s41375-021-01391-2

Zysset-Burri, Denise C.; Schlegel, Irina; Lincke, Joel-Benjamin; Jaggi, Damian; Keller, Irene; Heller, Manfred; Braga Lagache, Sophie; Wolf, Sebastian; Zinkernagel, Martin S. (2021). Understanding the Interactions Between the Ocular Surface Microbiome and the Tear Proteome. Investigative ophthalmology & visual science, 62(10), p. 8. Association for Research in Vision and Ophthalmology 10.1167/iovs.62.10.8

Tavares-Gomes, Leticia; Monney, Camille; Neuhaus, Géraldine; Francisco, David; Solis, Diana; Summerfield, Artur; Erny, Daniel; Jagannathan, Vidhya; Oevermann, Anna (2021). Transcriptome of microglia reveals a species-specific expression profile in bovines with conserved and new signature genes. GLIA, 69(8), pp. 1932-1949. Wiley-Blackwell 10.1002/glia.24002

Hallal, Mahmoud; Braga-Lagache, Sophie; Jankovic, Jovana; Simillion, Cedric; Bruggmann, Rémy; Uldry, Anne-Christine; Allam, Ramanjaneyulu; Heller, Manfred; Bonadies, Nicolas (2021). Inference of kinase-signaling networks in human myeloid cell line models by Phosphoproteomics using kinase activity enrichment analysis (KAEA). BMC cancer, 21(1), p. 789. BioMed Central 10.1186/s12885-021-08479-z

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

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

Yang, Zhang; Liang, Shun-Qing; Yang, Haitang; Xu, Duo; Bruggmann, Rémy; Gao, Yanyun; Deng, Haibin; Berezowska, Sabina; Hall, Sean R R; Marti, Thomas M; Kocher, Gregor J; Zhou, Qinghua; Schmid, Ralph A; Peng, Ren-Wang (2021). CRISPR-Mediated Kinome Editing Prioritizes a Synergistic Combination Therapy for FGFR1-Amplified Lung Cancer. Cancer research, 81(11), pp. 3121-3133. American Association for Cancer Research AACR 10.1158/0008-5472.CAN-20-2276

Xu, Duo; Liang, Shun-Qing; Yang, Zhang; Yang, Haitang; Bruggmann, Rémy; Oberhaensli, Simone; Berezowska, Sabina; Marti, Thomas M; Hall, Sean R R; Dorn, Patrick; Kocher, Gregor J; Schmid, Ralph A; Peng, Ren-Wang (2021). Malignant pleural mesothelioma co-opts BCL-XL and autophagy to escape apoptosis. Cell death & disease, 12(4), p. 406. Nature Publishing Group 10.1038/s41419-021-03668-x

Yilmaz, Bahtiyar; Mooser, Catherine; Keller, Irene; Li, Hai; Zimmermann, Jakob; Bosshard, Lars; Fuhrer, Tobias; Gomez de Agüero, Mercedes; Fernandez Trigo, Nerea; Tschanz-Lischer, Heidi; Limenitakis, Julien P.; Hardt, Wolf-Dietrich; McCoy, Kathleen; Stecher, Bärbel; Excoffier, Laurent; Sauer, Uwe; Ganal-Vonarburg, Stephanie C.; Macpherson, Andrew J. (2021). Long-term evolution and short-term adaptation of microbiota strains and sub-strains in mice. Cell host & microbe, 29(4), 650-663.e9. Cell Press 10.1016/j.chom.2021.02.001

Juanola, Oriol; Hassan, Mohsin; Kumar, Pavitra; Yilmaz, Bahtiyar; Keller, Irene; Simillion, Cedric; Engelmann, Cornelius; Tacke, Frank; Dufour, Jean-François; De Gottardi, Andrea; Moghadamrad, Sheida (2021). Intestinal microbiota drives cholestasis-induced specific hepatic gene expression patterns. Gut microbes, 13(1), pp. 1-20. Taylor & Francis Group 10.1080/19490976.2021.1911534

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

Joerger-Messerli, Marianne S.; Thomi, Gierin; Haesler, Valérie; Keller, Irene; Renz, Patricia; Surbek, Daniel V.; Schoeberlein, Andreina (2021). Human Wharton’s jelly mesenchymal stromal cell-derived small extracellular vesicles drive oligodendroglial maturation by restraining MAPK/ERK and Notch signaling pathways. Frontiers in cell and developmental biology, 9, p. 622539. Frontiers 10.3389/fcell.2021.622539

Kiener, Sarah; Ribi, Camillo; Keller, Irene; Chizzolini, Carlo; Trendelenburg, Marten; Huynh-Do, Uyen; von Kempis, Johannes; Leeb, Tosso (2021). Variants Affecting the C-Terminal Tail of UNC93B1 Are Not a Common Risk Factor for Systemic Lupus Erythematosus. Genes, 12(8), p. 1268. MDPI, Molecular Diversity Preservation International 10.3390/genes12081268

Valente, Luca G.; Pitton, Melissa; Fürholz, Monika; Oberhaensli, Simone; Bruggmann, Rémy; Leib, Stephen L.; Jakob, Stephan M.; Resch, Grégory; Que, Yok-Ai; Cameron, David R. (2021). Isolation and characterization of bacteriophages from the human skin microbiome that infect Staphylococcus epidermidis. FEMS Microbes, 2 Oxford University Press 10.1093/femsmc/xtab003


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

Muri, Lukas; Oberhänsli, Simone; Buri, Michelle; Le, Ngoc Dung; Grandgirard, Denis; Bruggmann, Rémy; Müri, René M.; Leib, Stephen L. (2020). Repetitive transcranial magnetic stimulation activates glial cells and inhibits neurogenesis after pneumococcal meningitis. PLoS ONE, 15(9), e0232863. Public Library of Science 10.1371/journal.pone.0232863

Mohsin Hassan, Mohsin Hassan; Moghadamrad, Sheida; Sorribas, Marcel; G. Muntet, Sergi; Kellmann, Philipp; Trentesaux, Coralie; Fraudeau, Marie; Nanni, Paolo; Wolski, Witold; Keller, Irene; Hapfelmeier, Siegfried; Shroyer, Noah F; Wiest, Reiner; Romagnolo, Beatrice; De Gottardi, Andrea (2020). Paneth cells promote angiogenesis and regulate portal hypertension in response to microbial signals. Journal of hepatology, 73(3), pp. 628-639. Elsevier 10.1016/j.jhep.2020.03.019

Francisco, David M F; Marchetti, Luca; Rodríguez-Lorenzo, Sabela; Frías-Anaya, Eduardo; Figueiredo, Ricardo M; Winter, Peter; Romero, Ignacio Andres; de Vries, Helga E; Engelhardt, Britta; Bruggmann, Rémy (2020). Advancing brain barriers RNA sequencing: guidelines from experimental design to publication. Fluids and barriers of the CNS, 17(1), p. 51. BioMed Central 10.1186/s12987-020-00207-2

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

Roder, Thomas; Wüthrich, Daniel; Bär, Cornelia; Sattari, Zahra; Ah, Ueli von; Ronchi, Francesca; Macpherson, Andrew; Ganal-Vonarburg, Stephanie C.; Bruggmann, Rémy; Vergères, Guy (2020). In Silico Comparison Shows that the Pan-Genome of a Dairy-Related Bacterial Culture Collection Covers Most Reactions Annotated to Human Microbiomes. Microorganisms, 8(7) MDPI 10.3390/microorganisms8070966

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

Bosshard, Lars; Peischl, Stephan; Ackermann, Martin; Excoffier, Laurent (2020). Dissection of the mutation accumulation process during bacterial range expansions. BMC Genomics, 21(1) BioMed Central 10.1186/s12864-020-6676-z

Dąbrowska, Joanna; Keller, Irene; Karamon, Jacek; Kochanowski, Maciej; Gottstein, Bruno; Cencek, Tomasz; Frey, Caroline F.; Müller, Norbert (2020). Whole genome sequencing of a feline strain of Tritrichomonas foetus reveals massive genetic differences to bovine and porcine isolates. International journal for parasitology, 50(3), pp. 227-233. Elsevier 10.1016/j.ijpara.2019.12.007

Xu, Duo; Shun-Qing, Liang; Yang, Haitang; Bruggmann, Rémy; Berezowska, Sabina; Zhang, Yang; Marti, Thomas; Hall, Sean Ralph Robert; Gao, Yanyun; Kocher, Gregor J.; Schmid, Ralph A.; Peng, Ren-Wang (2020). CRISPR screening identifies WEE1 as a combination target for standard chemotherapy in malignant pleural mesothelioma. Molecular cancer therapeutics, 19(2), pp. 661-672. American Association for Cancer Research AACR 10.1158/1535-7163.MCT-19-0724

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

Gilbert, Kimberly J.; Pouyet, Fanny; Excoffier, Laurent; Peischl, Stephan (2020). Transition from Background Selection to Associative Overdominance Promotes Diversity in Regions of Low Recombination. Current Biology, 30(1), pp. 101-107. Cell Press 10.1016/j.cub.2019.11.063

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

Auray, Gael; Talker, Stephanie; Keller, Irene; Python, Sylvie; Gerber, Markus; Liniger, Matthias; Ganges, Llilianne; Bruggmann, Rémy; Ruggli, Nicolas; Summerfield, Artur (2020). High-Resolution Profiling of Innate Immune Responses by Porcine Dendritic Cell Subsets in vitro and in vivo. Frontiers in immunology, 11, p. 1429. Frontiers Research Foundation 10.3389/fimmu.2020.01429

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

Troxler, Lukas J.; Werren, Joel P.; Schaffner, Thierry O.; Mostacci, Nadezda; Vermathen, Peter; Vermathen, Martina; Wüthrich, Daniel; Simillion, Cedric; Brugger, Silvio D.; Bruggmann, Rémy; Hathaway, Lucy J.; Furrer, Julien; Hilty, Markus (2019). Carbon source regulates polysaccharide capsule biosynthesis in Streptococcus pneumoniae. Journal of biological chemistry, 294(46), pp. 17224-17238. American Society for Biochemistry and Molecular Biology 10.1074/jbc.RA119.010764

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

Radpour, Ramin; Riether, Carsten; Simillion, Cedric; Höpner, Sabine; Bruggmann, Rémy; Ochsenbein, Adrian (2019). CD8+ T cells expand stem and progenitor cells in favorable but not adverse risk acute myeloid leukemia. Leukemia, 33(10), pp. 2379-2392. Nature Publishing Group 10.1038/s41375-019-0441-9

Bosshard, Lars; Peischl, Stephan; Ackermann, Martin; Excoffier, Laurent (2019). Mutational and Selective Processes Involved in Evolution during Bacterial Range Expansions. Molecular Biology and Evolution, 36(10), pp. 2313-2327. Oxford University Press 10.1093/molbev/msz148

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

Frazão, Josias B; Colombo, Martino; Simillion, Cedric; Bilican, Adem; Keller, Irene; Wüthrich, Daniel; Zhu, Zhiqing; Okoniewski, Michal J; Bruggmann, Rémy; Condino-Neto, Antonio; Newburger, Peter E (2019). Gene expression in chronic granulomatous disease and interferon-γ receptor-deficient cells treated in vitro with interferon-γ. Journal of cellular biochemistry, 120(3), pp. 4321-4332. Wiley-Blackwell 10.1002/jcb.27718

Tièche, Colin; Gao, Yanyun; Bührer, Elias; Hobi, Nina; Berezowska, Sabina Anna; Wyler, Kurt; Froment, Laurène; Weis, Stefan; Peng, Ren-Wang; Bruggmann, Rémy; Schär, Primo; Amrein, Michael Alex; Hall, Sean; Dorn, Patrick; Kocher, Gregor; Riether, Carsten; Ochsenbein, Adrian; Schmid, Ralph; Marti, Thomas (2019). Tumor Initiation Capacity and Therapy Resistance Are Differential Features of EMT-Related Subpopulations in the NSCLC Cell Line A549. Neoplasia, 21(2), pp. 185-196. Elsevier 10.1016/j.neo.2018.09.008

Mota Castro Dias, Mariana; Coisne, Caroline Marie; Lazarevic, Ivana; Baden, Pascale; Hata, Masaki; Iwamoto, Noriko; Francisco, David Miguel Ferreira; Vanlandewijck, Michael; He, Liqun; Baier, Felix Alexander; Keogh-Stroka, Deborah M.; Bruggmann, Rémy; Lyck, Ruth; Enzmann, Gaby; Deutsch, Urban; Betsholtz, Christer; Furuse, Mikio; Tsukita, Shoichiro; Engelhardt, Britta (2019). Claudin-3-deficient C57BL/6J mice display intact brain barriers. Scientific Reports, 9(1), p. 203. Nature Publishing Group 10.1038/s41598-018-36731-3

V'kovski, Philip; Gerber, Markus; Kelly, Jenna Nicole; Pfänder, Stephanie; Ebert, Nadine; Braga Lagache, Sophie; Simillion, Cedric; Portmann, Jasmine; Stalder, Hanspeter; Gaschen, Véronique; Bruggmann, Rémy; Stoffel, Michael Hubert; Heller, Manfred; Dijkman, Ronald; Thiel, Volker Earl (2019). Determination of host proteins composing the microenvironment of coronavirus replicase complexes by proximity-labeling. eLife, 8 eLife Sciences Publications 10.7554/eLife.42037

Burkhard, Regula; Keller, Irene; Arambasic, Miroslav; Juskevicius, Darius; Tzankov, Alexandar; Lundberg, Pontus; Bruggmann, Rémy; Dirnhofer, Stephan; Radpour, Ramin; Novak, Urban (2019). TIRAP p.R81C is a novel lymphoma risk variant which enhances cell proliferation via NF-κB mediated signaling in B-cells. Haematologica - the hematology journal, 104(4), pp. 766-777. Ferrata-Storti Foundation 10.3324/haematol.2018.201590

Sande-Melón, Marcos; Marques, Inês J.; Galardi-Castilla, María; Langa, Xavier; Pérez-López, María; Botos, Marius-Alexandru; Sánchez-Iranzo, Héctor; Guzmán-Martínez, Gabriela; Ferreira Francisco, David Miguel; Pavlinic, Dinko; Benes, Vladimir; Bruggmann, Rémy; Mercader Huber, Nadia Isabel (2019). Adult sox10+ Cardiomyocytes Contribute to Myocardial Regeneration in the Zebrafish. Cell reports, 29(4), pp. 1041-1054. Cell Press 10.1016/j.celrep.2019.09.041

Braun, Roman Othmar; Brunner, Livia; Wyler, Kurt; Auray, Gael; Garcia Nicolas, Obdulio; Python, Sylvie; Zumkehr, Beatrice; Gaschen, Veronique; Stoffel, Michael Hubert; Collin, Nicolas; Barnier-Quer, Christophe; Bruggmann, Rémy; Summerfield, Artur (2019). Erratum: Author Correction: System immunology-based identification of blood transcriptional modules correlating to antibody responses in sheep. npj vaccines, 4(10), p. 10. Nature Publishing Group 10.1038/s41541-019-0100-1


Talker, Stephanie; Baumann, Arnaud; Barut, Güliz Tuba; Keller, Irene; Bruggmann, Rémy; Summerfield, Artur (2018). Precise Delineation and Transcriptional Characterization of Bovine Blood Dendritic-Cell and Monocyte Subsets. Frontiers in immunology, 9(2505), p. 2505. Frontiers Research Foundation 10.3389/fimmu.2018.02505

Braun, Roman Othmar; Brunner, Livia; Wyler, Kurt; Auray, Gael; Garcia Nicolas, Obdulio; Python, Sylvie; Zumkehr, Beatrice; Gaschen, Véronique; Stoffel, Michael Hubert; Collin, Nicolas; Barnier-Quer, Christophe; Bruggmann, Rémy; Summerfield, Artur (2018). System immunology-based identification of blood transcriptional modules correlating to antibody responses in sheep. npj vaccines, 3(41), p. 41. Nature Publishing Group 10.1038/s41541-018-0078-0

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

Brauchle, Michael Anton; Bilican, Adem; Eyer, Claudia; Bailly, X; Martinez, P; Ladurner, P; Bruggmann, Rémy; Sprecher, SG (2018). Xenacoelomorpha Survey Reveals That All 11 Animal Homeobox Gene Classes Were Present in the First Bilaterians. Genome biology and evolution, 10(9), pp. 2205-2217. Oxford University Press 10.1093/gbe/evy170

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

Koeck, Ivonne; Hashemi Gheinani, Ali; Baumgartner, Ulrich; Vassella, Erik; Bruggmann, Rémy; Burkhard, Fiona C.; Monastyrskaya, Katia (2018). Tumor Necrosis Factor-α Initiates miRNA-mRNA Signaling Cascades in Obstruction-Induced Bladder Dysfunction. The American journal of pathology, 188(8), pp. 1847-1864. Elsevier 10.1016/j.ajpath.2018.05.008

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

Xu, Duo; Shun-Qing, Liang; Yang, Haitang; Lüthi, Ursina; Riether, Carsten; Berezowska, Sabina Anna; Marti, Thomas; Hall, Sean; Bruggmann, Rémy; Kocher, Gregor; Schmid, Ralph; Peng, Ren-Wang (2018). Increased sensitivity to apoptosis upon endoplasmic reticulum stress-induced activation of the unfolded protein response in chemotherapy-resistant malignant pleural mesothelioma. British journal of cancer, 119(1), pp. 65-75. Nature Publishing Group 10.1038/s41416-018-0145-3

Hauser, Michel; Siegrist, Mark; Keller, Irene; Hofstetter, Wilhelm (2018). Healing of fractures in osteoporotic bones in mice treated with bisphosphonates - A transcriptome analysis. Bone, 112, pp. 107-119. Elsevier 10.1016/j.bone.2018.04.017

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

García-Martín, Ana B; Zwicky, Pascale; Gruber, Thomas; Matti, Christoph; Moalli, Federica; Stein, Jens Volker; Francisco, David; Enzmann, Gaby; Levesque, Mitchell P; Hewer, Ekkehard; Lyck, Ruth (2018). VLA-4 mediated adhesion of melanoma cells on the blood-brain barrier is the critical cue for melanoma cell intercalation and barrier disruption. Journal of cerebral blood flow and metabolism, 39(10), pp. 1995-2010. Sage 10.1177/0271678X18775887

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

Popadin, Konstantin; Peischl, Stephan; Garieri, Marco; Sailani, M. Reza; Letourneau, Audrey; Santoni, Federico; Lukowski, Samuel W.; Bazykin, Georgii A.; Nikolaev, Sergey; Meyer, Diogo; Excoffier, Laurent; Reymond, Alexandre; Antonarakis, Stylianos E. (2018). Slightly deleterious genomic variants and transcriptome perturbations in Down syndrome embryonic selection. Genome research, 28(1), pp. 1-10. Cold Spring Harbor, N.Y 10.1101/gr.228411.117

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

Chevalier, Morgan; Vermij, Sarah H.; Wyler, Kurt; Gillet, Ludovic; Keller, Irene; Abriel, Hugues (2018). Transcriptomic analyses of murine ventricular cardiomyocytes. Scientific data, 5(180170), p. 180170. Nature Publishing Group 10.1038/sdata.2018.170

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


Mager, Lukas Franz; Kölzer, Viktor Hendrik; Stuber Roos, Regula; Thoo Sin Lang, Lester; Keller, Irene; Köck, Ivonne; Langenegger, Maya; Simillion, Cedric; Pfister, Simona P; Faderl, Martin Richard; Genitsch Gratwohl, Vera; Tcymbarevich, Irina; Juillerat, Pascal; Li, Xiaohong; Xia, Yu; Karamitopoulou, Evanthia; Lyck, Ruth; Zlobec, Inti; Hapfelmeier, Siegfried Hektor; Bruggmann, Rémy; ... (2017). The ESRP1-GPR137 axis contributes to intestinal pathogenesis. eLife, 6 eLife Sciences Publications 10.7554/eLife.28366

Plüss, Michel; Kopps, Anna M; Keller, Irene; Meienberg, Janine; Caspar, Sylvan M; Dubacher, Nicolo; Bruggmann, Rémy; Vogel, Manfred; Matyas, Gabor (2017). Need for speed in accurate whole-genome data analysis: GENALICE MAP challenges BWA/GATK more than PEMapper/PECaller and Isaac. Proceedings of the National Academy of Sciences of the United States of America - PNAS, 114(40), E8320-E8322. National Academy of Sciences NAS 10.1073/pnas.1713830114

Bosshard, Lars; Dupanloup, Isabelle; Tenaillon, Olivier; Bruggmann, Rémy; Ackermann, Martin; Peischl, Stephan; Excoffier, Laurent (2017). Accumulation of Deleterious Mutations During Bacterial Range Expansions. Genetics, 207(2), pp. 669-684. Genetics Society of America 10.1534/genetics.117.300144

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

Truchet, Laura Rosyne Hedwig; Walland, Julia Gianna Marlene; Wüthrich, Daniel; Boujon, Céline; Posthaus, Horst; Bruggmann, Rémy; Schüpbach, Gertraud; Oevermann, Anna; Seuberlich, Torsten (2017). Neuropathological survey reveals underestimation of the prevalence of neuroinfectious diseases in cattle in Switzerland. Veterinary microbiology, 208, pp. 137-145. Elsevier 10.1016/j.vetmic.2017.07.027

Hashemi Gheinani, Ali; Kiss, Bernhard; Moltzahn, Felix Roman; Keller, Irene; Bruggmann, Rémy; Rehrauer, Hubert; Fournier, Catharine Aquino; Burkhard, Fiona C.; Monastyrskaya-Stäuber, Katia (2017). Characterization of miRNA-regulated networks, hubs of signaling, and biomarkers in obstruction-induced bladder dysfunction. JCI insight, 2(2), e89560. JCI Insight 10.1172/jci.insight.89560

Vazquez Pianzola, Maria Paula; Schaller, Bogdan; Colombo, Martino; Beuchle, Dirk; Neuenschwander, Samuel; Marcil, Anne; Bruggmann, Rémy; Suter, Beat (2017). The mRNA transportome of the BicD / Egl transport machinery. RNA biology, 14(1), pp. 73-89. Taylor and Francis 10.1080/15476286.2016.1251542

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

Simillion, Cedric André Marie; Liechti, Robin; Lischer, Heidi E.L.; Ioannidis, Vassilios; Bruggmann, Rémy (2017). Avoiding the pitfalls of gene set enrichment analysis with SetRank. BMC bioinformatics, 18(1), p. 151. BioMed Central 10.1186/s12859-017-1571-6

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

Anikster, Yair; Haack, Tobias B.; Vilboux, Thierry; Pode-Shakked, Ben; Thöny, Beat; Shen, Nan; Guarani, Virginia; Meissner, Thomas; Mayatepek, Ertan; Trefz, Friedrich K.; Marek-Yagel, Dina; Martinez, Aurora; Huttlin, Edward L.; Paulo, Joao A.; Berutti, Riccardo; Benoist, Jean-François; Imbard, Apolline; Dorboz, Imen; Heimer, Gali; Landau, Yuval; ... (2017). Biallelic Mutations in DNAJC12 Cause Hyperphenylalaninemia, Dystonia, and Intellectual Disability. American journal of human genetics, 100(2), pp. 257-266. Cell Press 10.1016/j.ajhg.2017.01.002

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

Henn, Brenna M.; Botigué, Laura R.; Peischl, Stephan; Duperret, Isabelle; Lipatov, Mikhail; Maples, Brian K.; Martin, Alicia R.; Musharoff, Shaila; Cann, Howard; Snyder, Michael P.; Excoffier, Laurent; Kidd, Jeffrey M.; Bustamante, Carlos D. (2016). Distance from Sub-Saharan Africa Predicts Mutational Load in Diverse Human Genomes. Proceedings of the National Academy of Sciences of the United States of America - PNAS, 113(4), E440-E449. National Academy of Sciences NAS 10.1073/pnas.1510805112

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

Duart Garcia, Carolina; Plattet, Philippe; Bruggmann, Rémy; Simillion, Cedric André Marie; Irene, Keller; Göran, Andersson; Braunschweig, Martin (2016). Evidence for two protein coding transcripts at the Igf2as locus. Gene Reports, 4, pp. 60-66. Elsevier 10.1016/j.genrep.2016.04.003

Menzi, Fiona; Keller, Irene; Reber, Irene; Beck, Julia; Brenig, Bertram; Schütz, Ekkehard; Leeb, Tosso; Drögemüller, Cord (2016). Genomic amplification of the caprine EDNRA locus might lead to a dose dependent loss of pigmentation. Scientific Reports, 6, p. 28438. Nature Publishing Group 10.1038/srep28438

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

Miclaus, Mihai; Balacescu, Ovidiu; Has, Ioan; Balacescu, Loredana; Has, Voichita; Suteu, Dana; Neuenschwander, Samuel; Keller, Irene; Bruggmann, Rémy (2016). Maize Cytolines Unmask Key Nuclear Genes That Are under the Control of Retrograde Signaling Pathways in Plants. Genome biology and evolution, 8(11), pp. 3256-3270. Oxford University Press 10.1093/gbe/evw245

Peischl, Stephan; Dupanloup, Isabelle; Bosshard, Lars; Excoffier, Laurent (2016). Genetic surfing in human populations: from genes to genomes. Current opinion in genetics & development, 41, pp. 53-61. Elsevier 10.1016/j.gde.2016.08.003

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

Wüthrich, Daniel; Boujon, Céline; Truchet, Laura Rosyne Hedwig; Selimovic-Hamza, Senija; Oevermann, Anna; Bouzalas, Ilias; Bruggmann, Rémy; Seuberlich, Torsten (2016). Exploring the virome of cattle with non-suppurative encephalitis of unknown etiology by metagenomics. Virology, 493, pp. 22-30. Academic Press 10.1016/j.virol.2016.03.009

Bouzalas, Ilias; Wüthrich, Daniel; Selimovic-Hamza, Senija; Drögemüller, Cord; Bruggmann, Rémy; Seuberlich, Torsten (2016). Full-genome based molecular characterization of encephalitis-associated bovine astroviruses. Infection, genetics and evolution, 44, pp. 162-168. Elsevier 10.1016/j.meegid.2016.06.052


Peischl, Stephan; Excoffier, Laurent (2015). Expansion load: recessive mutations and the role of standing genetic variation. Molecular Ecology, 24(9), pp. 2084-2094. Wiley-Blackwell 10.1111/mec.13154

Peischl, Stephan; Kirkpatrick, Mark; Excoffier, Laurent (2015). Expansion Load and the Evolutionary Dynamics of a Species Range. The American naturalist, 185(4), E81-E93. University of Chicago Press 10.1086/680220

Reber, Irene; Keller, Irene; Becker, Doreen; Flury, C; Welle, Monika Maria; Drögemüller, Cord (2015). Wattles in goats are associated with the FMN1/GREM1 region on chromosome 10. Animal genetics, 46(3), pp. 316-320. Blackwell 10.1111/age.12279

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

Piguet, Anne Christine; Saran, Uttara; Simillion, Cedric André Marie; Keller, Irene; Terracciano, Luigi; Reeves, Helen L; Dufour, Jean-François (2015). Regular exercise decreases liver tumors development in hepatocyte-specific PTEN-deficient mice independently of steatosis. Journal of hepatology, 62(6), pp. 1296-1303. Elsevier 10.1016/j.jhep.2015.01.017

Meienberg, Janine; Zerjavic, Katja; Keller, Irene; Okoniewski, Michal; Patrignani, Andrea; Ludin, Katja; Xu, Zhenyu; Steinmann, Beat; Carrel, Thierry; Röthlisberger, Benno; Schlapbach, Ralph; Bruggmann, Rémy; Matyas, Gabor (2015). New insights into the performance of human whole-exome capture platforms. Nucleic acids research, 43(11), e76. Oxford University Press 10.1093/nar/gkv216

Lu, Jiongming; Marygold, Steven J; Gharib, Walid H; Suter, Beat (2015). The aminoacyl-tRNA synthetases of Drosophila melanogaster. Fly, 9(2), pp. 53-61. Taylor & Francis 10.1080/19336934.2015.1101196

Li, Hai; Limenitakis, Julien Periclis Jean; Fuhrer, Tobias; Geuking, Markus; Lawson, Melissa A; Wyss, Madeleine; Brugiroux, Sandrine; Keller, Irene; Macpherson, Jamie A; Rupp, Sandra; Stolp, Bettina; Stein, Jens Volker; Stecher, Bärbel; Sauer, Uwe; McCoy, Kathleen; Macpherson, Andrew (2015). The outer mucus layer hosts a distinct intestinal microbial niche. Nature communications, 6, p. 8292. Nature Publishing Group 10.1038/ncomms9292

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


Hilty, Markus; Wüthrich, Daniel; Salter, Susannah J; Engel, Hans Jürg; Campbell, Samuel; Sá-Leão, Raquel; de Lencastre, Hermínia; Hermans, Peter; Sadowy, Ewa; Turner, Paul; Chewapreecha, Claire; Diggle, Mathew; Pluschke, Gerd; McGee, Lesley; Eser, Ozgen Köseoğlu; Low, Donald E; Smith-Vaughan, Heidi; Endimiani, Andrea; Küffer, Marianne; Dupasquier, Mélanie; ... (2014). Global phylogenomic analysis of nonencapsulated Streptococcus pneumoniae reveals a deep-branching classic lineage that is distinct from multiple sporadic lineages. Genome biology and evolution, 6(12), pp. 3281-3294. Oxford University Press 10.1093/gbe/evu263

Martins Conde e Sousa, Vitor; Peischl, Stephan; Excoffier, Laurent (2014). Impact of range expansions on current human genomic diversity. Current opinion in genetics & development, 29, pp. 22-30. Elsevier 10.1016/j.gde.2014.07.007

Rezaei, Mina; Andrieu, Thomas; Neuenschwander, Samuel; Bruggmann, Rémy; Mordasini, David; Frey, Felix J; Vogt, Bruno; Frey, Brigitte M. (2014). Regulation of 11β-hydroxysteroid dehydrogenase type 2 by microRNA. Hypertension, 64(4), pp. 860-866. American Heart Association 10.1161/HYPERTENSIONAHA.114.00002

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

Schaffner, Thierry Oliver; Hinds, Jason; Gould, Katherine A; Wüthrich, Daniel; Bruggmann, Rémy; Küffer, Marianne; Mühlemann, Kathrin; Hilty, Markus; Hathaway, Lucy Jane (2014). A point mutation in cpsE renders Streptococcus pneumoniae nonencapsulated and enhances its growth, adherence and competence. BMC microbiology, 14(210), p. 210. BioMed Central 10.1186/s12866-014-0210-x

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

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). Genomics and the origin of species. Nature Reviews. Genetics, 15(3), pp. 176-192. Natue Publishing Group 10.1038/nrg3644

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

Drögemüller, Michaela; Jagannathan, Vidhya; Howard, J.; Bruggmann, Rémy; Drögemüller, Cord; Ruetten, Maja; Leeb, Tosso; Kook, Peter H. (2014). A frameshift mutation in the cubilin gene (CUBN) in Beagles with Imerslund-Gräsbeck syndrome (selective cobalamin malabsorption). Animal genetics, 45(1), pp. 148-150. Blackwell 10.1111/age.12094

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

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). The genomic substrate for adaptive radiation in African cichlid fish. Nature, 513(7518), pp. 375-381. Macmillan Journals Ltd. 10.1038/nature13726

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


Bruggmann, Rémy; Jagannathan, Vidhya; Braunschweig, Martin (2013). In search of epigenetic marks in testes and sperm cells of differentially fed boars. PLoS ONE, 8(11), e78691. Public Library of Science 10.1371/journal.pone.0078691

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

Koch, Caroline Tina; Bruggmann, Rémy; Tetens, Jens; Drögemüller, Cord (2013). A non-coding genomic duplication at the HMX1 locus is associated with crop ears in highland cattle. PLoS ONE, 8(10), e77841. Public Library of Science 10.1371/journal.pone.0077841

Peischl, Stephan; Duperret, Isabelle; Kirkpatrick, Mark; Excoffier, Laurent (2013). On the accumulation of deleterious mutations during range expansions. Molecular Ecology, 22(24), pp. 5972-5982. Wiley-Blackwell 10.1111/mec.12524

Peischl, Stephan; Koch, E.; Guerrero, R. F.; Kirkpatrick, Mark (2013). A sequential coalescent algorithm for chromosomal inversions. Heredity, 111(3), pp. 200-209. Oliver and Boyd 10.1038/hdy.2013.38


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

Peischl, Stephan; Kirkpatrick, Mark (2012). Establishment of new mutations in changing environments. Genetics, 191(3), pp. 895-906. Genetics Society of America 10.1534/genetics.112.140756

Kirkpatrick, Mark; Peischl, Stephan (2012). Evolutionary rescue by beneficial mutations in environments that change in space and time. Proceedings of the Royal Society. Series B - biological sciences, 368(1610), p. 20120082. Royal Society of London 10.1098/rstb.2012.0082


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

Schneider, Kristan A.; Peischl, Stephan (2011). Evolution of assortative mating in a population expressing dominance. PLoS ONE, 6(4), e16821. Public Library of Science 10.1371/journal.pone.0016821


Peischl, Stephan; Schneider, Kristan A (2010). EVOLUTION OF DOMINANCE UNDER FREQUENCY-DEPENDENT INTRASPECIFIC COMPETITION IN AN ASSORTATIVELY MATING POPULATION. Evolution, 64(2), pp. 561-582. Wiley 10.1111/j.1558-5646.2009.00839.x

Peischl, Stephan (2010). Dominance and the maintenance of polymorphism in multiallelic migration-selection models with two demes. Theoretical population biology, 78(1), pp. 12-25. Elsevier 10.1016/j.tpb.2010.03.006


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; Bruggmann, Rémy; Lei, Xue; Georgiev, O; Schaffner, W; Rungger, D; Spaniol, P; Gerster, T (1998). Homologous recombination and DNA-end joining reactions in zygotes and early embryos of zebrafish (Danio rerio) and Drosophila melanogaster. Biological chemistry, 379(6), pp. 673-681. De Gruyter 10.1515/bchm.1998.379.6.673


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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