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Abela, Irene A; Hauser, Anthony; Schwarzmüller, Magdalena; Pasin, Chloé; Kusejko, Katharina; Epp, Selina; Cavassini, Matthias; Battegay, Manuel; Rauch, Andri; Calmy, Alexandra; Notter, Julia; Bernasconi, Enos; Fux, Christoph A; Leuzinger, Karoline; Perreau, Matthieu; Ramette, Alban; Gottschalk, Jochen; Schindler, Eméry; Wepf, Alexander; Marconato, Maddalena; ... (2024). Deciphering factors linked with reduced SARS-CoV-2 susceptibility in the Swiss HIV Cohort Study. The journal of infectious diseases, 230(2), e292-e304. Oxford University Press 10.1093/infdis/jiae002
Lopez-Labrador, F Xavier; Huber, Michael; Sidorov, Igor A; Brown, Julianne R; Cuypers, Lize; Laenen, Lies; Vanmechelen, Bert; Maes, Piet; Fischer, Nicole; Pichler, Ian; Storey, Nathaniel; Atkinson, Laura; Schmutz, Stefan; Kufner, Verena; van Boheemen, Sander; Mulders, Claudia E; Grundhoff, Adam; Blümke, Patrick; Robitaille, Alexis; Cinek, Ondrej; ... (2024). Multicenter benchmarking of short and long read wet lab protocols for clinical viral metagenomics. Journal of clinical virology, 173(105695), p. 105695. Elsevier 10.1016/j.jcv.2024.105695
Wegner, Fanny; Cabrera-Gil, Blanca; Tanguy, Araud; Beckmann, Christiane; Beerenwinkel, Niko; Bertelli, Claire; Carrara, Matteo; Cerutti, Lorenzo; Chen, Chaoran; Cordey, Samuel; Dumoulin, Alexis; du Plessis, Louis; Friedli, Marc; Gerth, Yannick; Greub, Gilbert; Härri, Adrian; Hirsch, Hans; Howald, Cedric; Huber, Michael; Imhof, Alexander; ... (2024). How much should we sequence? An analysis of the Swiss SARS-CoV-2 surveillance effort. Microbiology spectrum, 12(5), e0362823. American Society for Microbiology 10.1128/spectrum.03628-23
Banholzer, Nicolas; Jent, Philipp; Bittel, Pascal; Zürcher, Kathrin; Furrer, Lavinia; Bertschinger, Simon; Weingartner, Ernest; Ramette, Alban; Egger, Matthias; Hascher, Tina; Fenner, Lukas (2024). Air Cleaners and Respiratory Infections in Schools: A Modeling Study Based on Epidemiologic, Environmental, and Molecular Data. Open Forum Infectious Diseases, 11(4), ofae169. Oxford University Press 10.1093/ofid/ofae169
Terrazos Miani, Miguel A; Borcard, Loïc; Gempeler, Sonja; Baumann, Christian; Bittel, Pascal; Leib, Stephen L; Neuenschwander, Stefan; Ramette, Alban Nicolas (2024). NASCarD (Nanopore Adaptive Sampling with Carrier DNA): A Rapid, PCR-Free Method for SARS-CoV-2 Whole-Genome Sequencing in Clinical Samples. Pathogens, 13(1) MDPI AG 10.3390/pathogens13010061
Zeeb, Marius; Pasin, Chloé; Cavassini, Matthias; Bieler-Aeschlimann, Mélanie; Frischknecht, Paul; Kusejko, Katharina; Fellay, Jacques; Blanquart, François; Metzner, Karin J; Neumann, Kathrin; Jörimann, Lisa; Tschumi, Jasmin; Bernasconi, Enos; Huber, Michael; Kovari, Helen; Leuzinger, Karoline; Notter, Julia; Perreau, Matthieu; Rauch, Andri; Ramette, Alban; ... (2024). Self-reported neurocognitive complaints in the Swiss HIV Cohort Study: a viral genome-wide association study. Brain Communications, 6(4) Oxford University Press 10.1093/braincomms/fcae188
Banholzer, Nicolas; Jent, Philipp; Bittel, Pascal; Zürcher, Kathrin; Furrer, Lavinia; Bertschinger, Simon; Weingartner, Ernest; Ramette, Alban; Egger, Matthias; Hascher, Tina; Fenner, Lukas (30 December 2023). Air cleaners and respiratory infections in schools: A modeling study using epidemiological, environmental, and molecular data. medRxiv 10.1101/2023.12.29.23300635
Scheier, T C; Franz, J; Boumasmoud, M; Andreoni, F; Chakrakodi, B; Duvnjak, B; Egli, A; Zingg, W; Ramette, A; Wolfensberger, A; Kouyos, R D; Brugger, S D (2023). Fourier-transform infrared spectroscopy for typing of vancomycin-resistant Enterococcus faecium: performance analysis and outbreak investigation. (In Press). Microbiology spectrum, 11(5), e0098423. American Society for Microbiology 10.1128/spectrum.00984-23
Anderegg, Nanina; Schwab, Tiana; Borcard, Loïc; Mugglin, Catrina; Keune-Dübi, Bettina; Ramette, Alban; Fenner, Lukas (2023). Population-based SARS-CoV-2 whole genome sequencing and contact tracing during the COVID-19 pandemic in Switzerland. Journal of infectious diseases, 228(3), pp. 251-260. Oxford University Press 10.1093/infdis/jiad074
Neves, Aitana; Walther, Daniel; Martin-Campos, Trinidad; Barbie, Valerie; Bertelli, Claire; Blanc, Dominique; Bouchet, Gérard; Erard, Frédéric; Greub, Gilbert; Hirsch, Hans H; Huber, Michael; Kaiser, Laurent; Leib, Stephen L; Leuzinger, Karoline; Lazarevic, Vladimir; Mäusezahl, Mirjam; Molina, Jorge; Neher, Richard A; Perreten, Vincent; Ramette, Alban; ... (2023). The Swiss Pathogen Surveillance Platform - towards a nation-wide One Health data exchange platform for bacterial, viral and fungal genomics and associated metadata. Microbial genomics, 9(5) Microbiology Society 10.1099/mgen.0.001001
Balakrishna, Suraj; Loosli, Tom; Zaheri, Maryam; Frischknecht, Paul; Huber, Michael; Kusejko, Katharina; Yerly, Sabine; Leuzinger, Karoline; Perreau, Matthieu; Ramette, Alban; Wymant, Chris; Fraser, Christophe; Kellam, Paul; Gall, Astrid; Hirsch, Hans H; Stoeckle, Marcel; Rauch, Andri; Cavassini, Matthias; Bernasconi, Enos; Notter, Julia; ... (2023). Frequency matters: comparison of drug resistance mutation detection by Sanger and next-generation sequencing in HIV-1. The journal of antimicrobial chemotherapy, 78(3), pp. 656-664. Oxford University Press 10.1093/jac/dkac430
Labarile, Marco; Loosli, Tom; Zeeb, Marius; Kusejko, Katharina; Huber, Michael; Hirsch, Hans H; Perreau, Matthieu; Ramette, Alban; Yerly, Sabine; Cavassini, Matthias; Battegay, Manuel; Rauch, Andri; Calmy, Alexandra; Notter, Julia; Bernasconi, Enos; Fux, Christoph; Günthard, Huldrych F; Pasin, Chloé; Kouyos, Roger D (2023). Quantifying and predicting ongoing Human Immunodeficiency Virus Type 1 (HIV-1) transmission dynamics in Switzerland using a distance-based clustering approach. The journal of infectious diseases, 227(4), pp. 554-564. Oxford University Press 10.1093/infdis/jiac457
Bigi, Sandra; Ramette, Alban; Barbani, Maria Teresa; Bieri, Andreas; Hoffmann, Angelika; Aebi, Christoph (2023). Acute flaccid myelitis in Switzerland - association with enterovirus D68. Swiss medical weekly, 153, p. 40045. EMH Schweizerischer Ärzteverlag 10.57187/smw.2023.40045
Terrazos Miani, Miguel A.; Borcard, Loïc; Gempeler, Sonja; Baumann, Christian; Bittel, Pascal; Leib, Stephen L.; Neuenschwander, Stefan; Ramette, Alban (2023). NASCarD (Nanopore Adaptive Sampling with Carrier DNA): A rapid, PCR-free method for whole genome sequencing of pathogens in clinical samples (Submitted) (medRxiv). Cold Spring Harbor Laboratory 10.1101/2023.03.10.23287094
Guan, Hang; Caggìa, Veronica; Gómez-Chamorro, Andrea; Fischer, Daniela; Coll-Crespí, Miquel; Liu, Xiaowen; Chávez-Capilla, Teresa; Schlaeppi, Klaus; Ramette, Alban; Mestrot, Adrien; Bigalke, Moritz (2023). The Effects of Soil Microbial Disturbance and Plants on Arsenic Concentrations and Speciation in Soil Water and Soils. Exposure and health, 16(3), pp. 805-820. Springer 10.1007/s12403-023-00593-6
Lux, Janine; Holivololona, Lalaina; San Millan Gutierrez, Raquel; Hilty, Markus; Ramette, Alban; Heller, Manfred; Hathaway, Lucy J (2022). AmiA and AliA peptide ligands are secreted by Klebsiella pneumoniae and inhibit growth of Streptococcus pneumoniae. Scientific reports, 12(1), p. 22268. Springer Nature 10.1038/s41598-022-26838-z
Kofler, Jacob; Ramette, Alban; Iseli, Patricia; Stauber, Lea; Fichtner, Jens; Droz, Sara; Zihler Berner, Annina; Meier, Anna Bettina; Begert, Michelle; Negri, Sabine; Jachmann, Anne; Keller, Peter Michael; Staehelin, Cornelia; Grützmacher, Barbara (2022). Ongoing toxin-positive diphtheria outbreaks in a federal asylum centre in Switzerland, analysis July to September 2022. Eurosurveillance, 27(44) European Centre for Disease Prevention and Control 10.2807/1560-7917.ES.2022.27.44.2200811
Chaudron, Sandra E; Leemann, Christine; Kusejko, Katharina; Nguyen, Huyen; Tschumi, Nadine; Marzel, Alex; Huber, Michael; Böni, Jürg; Perreau, Matthieu; Klimkait, Thomas; Yerly, Sabine; Ramette, Alban; Hirsch, Hans H; Rauch, Andri; Calmy, Alexandra; Vernazza, Pietro; Bernasconi, Enos; Cavassini, Matthias; Metzner, Karin J; Kouyos, Roger D; ... (2022). A systematic molecular epidemiology screen reveals numerous HIV-1 superinfections in the Swiss HIV Cohort Study. The journal of infectious diseases, 226(7), pp. 1256-1266. Oxford University Press 10.1093/infdis/jiac166
Grädel, C; Ireddy, N R; Koch, M C; Baumann, C; Terrazos Miani, M A; Barbani, M T; Steinlin-Schopfer, J; Suter-Riniker, F; Leib, S L; Ramette, A (2022). Genome Sequences of Rare Human Enterovirus Genotypes Recovered from Clinical Respiratory Samples in Bern, Switzerland. Microbiology resource announcements, 11(9), e0027622. American Society for Microbiology 10.1128/mra.00276-22
Kusejko, Katharina; Tschumi, Nadine; Chaudron, Sandra E; Nguyen, Huyen; Battegay, Manuel; Bernasconi, Enos; Böni, Jürg; Huber, Michael; Calmy, Alexandra; Cavassini, Matthias; Egle, Alexander; Grabmeier-Pfistershammer, Katharina; Haas, Bernhard; Hirsch, Hans; Klimkait, Thomas; Öllinger, Angela; Perreau, Matthieu; Ramette, Alban; Flury, Baharak Babouee; Sarcletti, Mario; ... (2022). Similar but different: Integrated phylogenetic analysis of Austrian and Swiss HIV-1 sequences reveal differences in transmission patterns of the local HIV-1 epidemics. Journal of acquired immune deficiency syndromes, 90(4), e4-e12. Wolters Kluwer Health 10.1097/QAI.0000000000002949
Nguyen, Huyen; Hampel, Benjamin; Nuñez, David Garcia; Battegay, Manuel; Hachfeld, Anna; Bernasconi, Enos; Calmy, Alexandra; Cavassini, Matthias; Vernazza, Pietro; Fellay, Jacques; Rudolph, Hannes; Huber, Michael; Leuzinger, Karoline; Perreau, Matthieu; Scherrer, Alexandra; Ramette, Alban Nicolas; Yerly, Sabine; Günthard, Huldrych F; Kouyos, Roger D and Kusejko, Katharina (2022). Identifying and Characterizing Trans women in the Swiss HIV Cohort Study as an Epidemiologically Distinct Risk Group. Clinical infectious diseases, 74(8), pp. 1468-1475. Oxford University Press 10.1093/cid/ciab628
Borcard, Loïc; Gempeler, Sonja; Terrazos Miani, Miguel A; Baumann, Christian; Grädel, Carole; Dijkman, Ronald; Suter-Riniker, Franziska; Leib, Stephen L; Bittel, Pascal; Neuenschwander, Stefan; Ramette, Alban (2022). Investigating the Extent of Primer Dropout in SARS-CoV-2 Genome Sequences During the Early Circulation of Delta Variants. Frontiers in Virology, 2 Frontiers 10.3389/fviro.2022.840952
Schenker, Carla; Hirzel, Cédric; Walti, Laura N.; Zeerleder, Sacha S.; Andres, Martin; Ramette, Alban; Barbani, Maria T.; Suter-Riniker, Franziska; Holbro, Andreas; Tritschler, Tobias (2022). Convalescent plasma and remdesivir for protracted COVID-19 in a patient with chronic lymphocytic leukaemia: a case report of late relapse after rapid initial response. British journal of haematology, 196(3), e27-e29. Wiley-Blackwell 10.1111/bjh.17806
Donà, Valentina; Ramette, Alban; Perreten, Vincent (2022). Comparative genomics of 26 complete circular genomes of 18 different serotypes of Actinobacillus pleuropneumoniae. Microbial genomics, 8(2), 000776. Microbiology Society 10.1099/mgen.0.000776
Wegner, Fanny; Roloff, Tim; Huber, Michael; Cordey, Samuel; Ramette, Alban; Gerth, Yannick; Bertelli, Claire; Stange, Madlen; Seth-Smith, Helena M B; Mari, Alfredo; Leuzinger, Karoline; Cerutti, Lorenzo; Harshman, Keith; Xenarios, Ioannis; Le Mercier, Philippe; Bittel, Pascal; Neuenschwander, Stefan; Opota, Onya; Fuchs, Jonas; Panning, Marcus; ... (2022). External quality assessment of SARS-CoV-2-sequencing: An ESGMD-SSM pilot trial across 15 European laboratories. Journal of clinical microbiology, 60(1), e0169821. American Society for Microbiology 10.1128/JCM.01698-21
Duran Ramirez, Jessy J; Ballouz, Tala; Nguyen, Huyen; Kusejko, Katharina; Chaudron, Sandra E; Huber, Michael; Hirsch, Hans H; Perreau, Matthieu; Ramette, Alban; Yerly, Sabine; Cavassini, Matthias; Stöckle, Marcel; Furrer, Hansjakob; Vernazza, Pietro; Bernasconi, Enos; Günthard, Huldrych F; Kouyos, Roger D (2022). Increasing Frequency and Transmission of HIV-1 Non-B Subtypes among Men Who Have Sex with Men in the Swiss HIV Cohort Study. The journal of infectious diseases, 225(2), pp. 306-316. Oxford University Press 10.1093/infdis/jiab360
Ramírez Mena, Adrià; Tine, Judicaël M; Fortes, Louise; Ndiaye, Ousseynou; Ka, Daye; Ngom, Ndeye Fatou; Ramette, Alban Nicolas; Bittel, Pascal; Seydi, Moussa; Wandeler, Gilles (2022). Hepatitis B screening practices and viral control among persons living with HIV in urban Senegal. Journal of viral hepatitis, 29(1), pp. 60-68. Blackwell Science 10.1111/jvh.13615
Akello, Joyce Odeke; Kamgang, Richard; Barbani, Maria Teresa; Suter-Riniker, Franziska; Aebi, Christoph; Beuret, Christian; Paris, Daniel H.; Leib, Stephen L.; Ramette, Alban (2021). Genomic analyses of human adenoviruses unravel novel recombinant genotypes associated with severe infections in pediatric patients. Scientific reports, 11(1), p. 24038. Springer Nature 10.1038/s41598-021-03445-y
Moser, Aline I.; Campos-Madueno, Edgar I.; Sendi, Parham; Perreten, Vincent; Keller, Peter M.; Ramette, Alban; Endimiani, Andrea (2021). Repatriation of a patient with COVID-19 contributed to the importation of an emerging carbapenemase producer. Journal of global antimicrobial resistance, 27, pp. 267-272. Elsevier 10.1016/j.jgar.2021.10.012
Peker, Nilay; Schuele, Leonard; Kok, Nienke; Terrazos, Miguel; Neuenschwander, Stefan M.; de Beer, Jessica; Akkerman, Onno; Peter, Silke; Ramette, Alban; Merker, Matthias; Niemann, Stefan; Couto, Natacha; Sinha, Bhanu; Rossen, John Wa (2021). Evaluation of whole-genome sequence data analysis approaches for short- and long-read sequencing of Mycobacterium tuberculosis. Microbial genomics, 7(11) Microbiology Society 10.1099/mgen.0.000695
Müller, Annelies; Schramm, Diana B; Kleynhans, Jackie; de Gouveia, Linda; Meiring, Susan; Ramette, Alban; von Gottberg, Anne; Hathaway, Lucy Jane (2021). Cytokine response in cerebrospinal fluid of meningitis patients and outcome associated with pneumococcal serotype. Scientific reports, 11(1), p. 19920. Springer Nature 10.1038/s41598-021-99190-3
Bachmann, Nadine; Kusejko, Katharina; Nguyen, Huyen; Chaudron, Sandra E; Kadelka, Claus; Turk, Teja; Böni, Jürg; Perreau, Matthieu; Klimkait, Thomas; Yerly, Sabine; Battegay, Manuel; Rauch, Andri; Ramette, Alban; Vernazza, Pietro; Bernasconi, Enos; Cavassini, Matthias; Günthard, Huldrych F; Kouyos, Roger D (2021). Phylogenetic Cluster Analysis Identifies Virological and Behavioral Drivers of HIV Transmission in MSM. Clinical infectious diseases, 72(12), pp. 2175-2183. Oxford University Press 10.1093/cid/ciaa411
Reichmuth, M L; Chaudron, S E; Bachmann, N; Nguyen, H; Böni, J; Metzner, K J; Perreau, M; Klimkait, T; Yerly, S; Hirsch, H H; Hauser, C; Ramette, A; Vernazza, P; Cavassini, M; Bernasconi, E; Günthard, H F; Kusejko, K; Kouyos, R D (2021). Using longitudinally sampled viral nucleotide sequences to characterize the drivers of HIV-1 transmission. HIV medicine, 22(5), pp. 346-359. Wiley 10.1111/hiv.13030
Ramette, Alban; Gasser, Michael; Nordmann, Patrice; Zbinden, Reinhard; Schrenzel, Jacques; Perisa, Damir; Kronenberg, Andreas (2021). Temporal and regional incidence of carbapenemase-producing Enterobacterales, Switzerland, 2013 to 2018. Eurosurveillance, 26(15) European Centre for Disease Prevention and Control 10.2807/1560-7917.ES.2021.26.15.1900760
Goncalves Cabecinhas, Ana Rita; Roloff, Tim; Stange, Madlen; Bertelli, Claire; Huber, Michael; Ramette, Alban; Chen, Chaoran; Nadeau, Sarah; Gerth, Yannick; Yerly, Sabine; Opota, Onya; Pillonel, Trestan; Schuster, Tobias; Metzger, Cesar M J A; Sieber, Jonas; Bel, Michael; Wohlwend, Nadia; Baumann, Christian; Koch, Michel C.; Bittel, Pascal; ... (2021). SARS-CoV-2 N501Y Introductions and Transmissions in Switzerland from Beginning of October 2020 to February 2021-Implementation of Swiss-Wide Diagnostic Screening and Whole Genome Sequencing. Microorganisms, 9(4), p. 677. MDPI 10.3390/microorganisms9040677
Werren, Joel P.; Troxler, Lukas J.; Oyewole, Oluwaseun Rume-Abiola; Ramette, Alban; Brugger, Silvio D.; Bruggmann, Rémy; van der Linden, Mark; Nahm, Moon H.; Gjuroski, Ilche; Casanova, Carlo; Furrer, Julien; Hilty, Markus (2021). Carbon Source-Dependent Changes of the Structure of Streptococcus pneumoniae Capsular Polysaccharide with Serotype 6F. International journal of molecular sciences, 22(9) MDPI 10.3390/ijms22094580
Borcard, Loïc; Gempeler, Sonja; Terrazos Miani, Miguel A.; Baumann, Christian; Grädel, Carole; Dijkman, Ronald; Suter-Riniker, Franziska; Leib, Stephen L; Bittel, Pascal; Neuenschwander, Stefan; Ramette, Alban (2021). Investigating the biological and technical origins of unknown bases in the S region of the SARS-CoV-2 Delta variant genome sequences (medRxiv). Cold Spring Harbor Laboratory 10.1101/2021.09.09.21262951
Akello, Joyce Odeke; Kamgang, Richard; Barbani, Maria Teresa; Suter-Riniker, Franziska; Aebi, Christoph; Beuret, Christian; Paris, Daniel H.; Leib, Stephen L.; Ramette, Alban (2021). Genomic analyses of human adenoviruses unravel novel recombinant genotypes associated with severe infections in pediatric patients (medRxiv). Cold Spring Harbor Laboratory 10.1101/2021.08.01.21261368
Hufsky, Franziska; Beerenwinkel, Niko; Meyer, Irmtraud M; Roux, Simon; Cook, Georgia May; Kinsella, Cormac M; Lamkiewicz, Kevin; Marquet, Mike; Nieuwenhuijse, David F; Olendraite, Ingrida; Paraskevopoulou, Sofia; Young, Francesca; Dijkman, Ronald; Ibrahim, Bashar; Kelly, Jenna; Le Mercier, Philippe; Marz, Manja; Ramette, Alban; Thiel, Volker (2020). The International Virus Bioinformatics Meeting 2020. Viruses, 12(12) MDPI 10.3390/v12121398
Endimiani, Andrea; Ramette, Alban; Rhoads, Daniel D.; Jacobs, Michael R. (2020). The Evolving Role of the Clinical Microbiology Laboratory in Identifying Resistance in Gram-Negative Bacteria: An Update. Infectious disease clinics of North America, 34(4), pp. 659-676. Elsevier 10.1016/j.idc.2020.08.001
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
Wasimuddin, Wasimuddin; Schlaeppi, Klaus; Ronchi, Francesca; Leib, Stephen L.; Erb, Matthias; Ramette, Alban (2020). Evaluation of primer pairs for microbiome profiling from soils to humans within the One Health framework. Molecular ecology resources, 20(6), pp. 1558-1571. Wiley 10.1111/1755-0998.13215
Flohr, Sarah; Ramette, Alban; Agyeman, Philipp K. A.; Duppenthaler, Andrea; Scherer, Cordula; Keller, Peter M.; Aebi, Christoph (2020). Recurrent Mycobacterium chelonae Skin Infection Unmasked as Factitious Disorder Using Bacterial Whole Genome Sequence Analysis. Open Forum Infectious Diseases, 7(11), ofaa506. Oxford University Press 10.1093/ofid/ofaa506
Grädel, Carole; Terrazos Miani, Miguel A.; Baumann, Christian; Barbani, Maria Teresa; Neuenschwander, Stefan; Leib, Stephen L.; Suter-Riniker, Franziska; Ramette, Alban (2020). Whole-Genome Sequencing of Human Enteroviruses from Clinical Samples by Nanopore Direct RNA Sequencing. Viruses, 12(8) MDPI 10.3390/v12080841
Akello, Joyce Odeke; Kamgang, Richard; Barbani, Maria Teresa; Suter-Riniker, Franziska; Leib, Stephen L; Ramette, Alban (2020). Epidemiology of Human Adenoviruses: A 20-Year Retrospective Observational Study in Hospitalized Patients in Bern, Switzerland. Clinical epidemiology, 12, pp. 353-366. Dove Medical Press 10.2147/CLEP.S246352
Neuenschwander, Stefan Moritz; Terrazos Miani, Miguel Angel; Amlang, Heiko; Perroulaz, Carmen; Bittel, Pascal; Casanova, Carlo; Droz, Sara; Flandrois, Jean-Pierre; Leib, Stephen L.; Suter-Riniker, Franziska; Ramette, Alban (2020). A Sample-to-Report Solution for Taxonomic Identification of Cultured Bacteria in the Clinical Setting Based on Nanopore Sequencing. Journal of clinical microbiology, 58(6) American Society for Microbiology 10.1128/JCM.00060-20
Wasimuddin, Wasimuddin; Schlaeppi, Klaus; Ronchi, Francesca; Leib, Stephen L.; Erb, Matthias; Ramette, Alban (15 November 2019). Evaluation of primer pairs for microbiome profiling across a food chain from soils to humans within the One Health framework (bioRxiv). Cold Spring Harbor Laboratory 10.1101/843144
Cameron, David R.; Ramette, Alban; Prazak, Josef; Entenza, José; Hänggi, Matthias; Que, Yok-Ai; Resch, Grégory (2019). Draft Genome Sequence of Methicillin-Resistant Staphylococcus aureus Strain AW7, Isolated from a Patient with Bacteremia. Microbiology resource announcements, 8(40) American Society for Microbiology 10.1128/MRA.00806-19
Grädel, Carole; Terrazos Miani, Miguel Angel; Barbani, Maria Teresa; Leib, Stephen L.; Suter-Riniker, Franziska; Ramette, Alban (2019). Rapid and Cost-Efficient Enterovirus Genotyping from Clinical Samples Using Flongle Flow Cells. Genes, 10(9) MDPI 10.3390/genes10090659
Junier, Thomas; Huber, Michael; Schmutz, Stefan; Kufner, Verena; Zagordi, Osvaldo; Neuenschwander, Stefan; Ramette, Alban; Kubacki, Jakub; Bachofen, Claudia; Qi, Weihong; Laubscher, Florian; Cordey, Samuel; Kaiser, Laurent; Beuret, Christian; Barbié, Valérie; Fellay, Jacques; Lebrand, Aitana (2019). Viral Metagenomics in the Clinical Realm: Lessons Learned from a Swiss-Wide Ring Trial. Genes, 10(9) MDPI 10.3390/genes10090655
Pedersen, Eva S L; Spycher, Ben D; de Jong, Carmen; Halbeisen, Florian; Ramette, Alban; Gaillard, Erol A; Granell, Raquel; Henderson, A John; Kuehni, Claudia E (2019). The simple 10-item PARC tool to predict childhood asthma - an external validation. The Journal of allergy and clinical immunology, 7(3), 943-953.e4. Elsevier 10.1016/j.jaip.2018.09.032
Ruff, S E; Felden, J; Gruber-Vodicka, H R; Marcon, Y; Knittel, K; Ramette, A.; Boetius, A (2019). In situ development of a methanotrophic microbiome in deep-sea sediments. The ISME journal, 13(1), pp. 197-213. Nature Publishing Group 10.1038/s41396-018-0263-1
Molari, Massimiliano; Guilini, Katja; Lins, Lidia; Ramette, Alban; Vanreusel, Ann (2019). CO2 leakage can cause loss of benthic biodiversity in submarine sands. Marine environmental research, 144, pp. 213-229. Elsevier 10.1016/j.marenvres.2019.01.006
Allemann, Aurélie; Krämer, Julia G.; Korten, Insa; Ramsey, Kathryn; Casaulta, Carmen; Wüthrich, Daniel; Ramette, Alban Nicolas; Endimiani, Andrea; Latzin, Philipp; Hilty, Markus (2019). Nasal Resistome Development in Infants With Cystic Fibrosis in the First Year of Life. Frontiers in Microbiology, 10(212), p. 212. Frontiers 10.3389/fmicb.2019.00212
Egli, Adrian; Blanc, Dominique S; Greub, Gilbert; Keller, Peter Michael; Lazarevic, Vladimir; Lebrand, Aitana; Leib, Stephen; Neher, Richard A; Perreten, Vincent; Ramette, Alban; Schrenzel, Jacques; Stephan, Roger; Wagner, Karolin; Wuethrich, Daniel; Xenarios, Ioannis (2018). Improving the quality and workflow of bacterial genome sequencing and analysis: paving the way for a Switzerland-wide molecular epidemiological surveillance platform. Swiss medical weekly, 148(w14693), w14693. EMH Media 10.4414/smw.2018.14693
van der Hoek, Lia; Verschoor, Ernst; Beer, Martin; Höper, Dirk; Wernike, Kerstin; Van Ranst, Marc; Matthijnssens, Jelle; Maes, Piet; Sastre, Patricia; Rueda, Paloma; Drexler, Jan Felix; Barr, John; Edwards, Thomas; Millner, Paul; Vermeij, Paul; de Groof, Ad; Thiel, Volker; Dijkman, Ronald; Suter, Franziska Marta; Leib, Stephen; ... (2018). Host switching pathogens, infectious outbreaks and zoonosis: A Marie Skłodowska-Curie innovative training network (HONOURs). Virus research, 257, pp. 120-124. Elsevier 10.1016/j.virusres.2018.09.002
Ramette, Alban; Spycher, Ben D; Wang, Jingying; Goutaki, Myrofora; Beardsmore, Caroline S; Kuehni, Claudia E (2018). Longitudinal Associations between Respiratory Infections and Asthma in Young Children. American journal of epidemiology, 187(8), pp. 1714-1720. Oxford University Press 10.1093/aje/kwy053
Ramette, Alban Nicolas; Kronenberg, Andreas Oskar (2018). Prevalence of carbapenem-resistant Acinetobacter baumannii from 2005 to 2016 in Switzerland. BMC infectious diseases, 18(159), pp. 1-6. BioMed Central 10.1186/s12879-018-3061-5
Kraemer, Julia G; Ramette, Alban; Aebi, Suzanne; Oppliger, Anne; Hilty, Markus (2018). Influence of pig farming on the human's nasal microbiota: The key role of the airborne microbial communities. Applied and environmental microbiology, 84(6) American Society for Microbiology 10.1128/AEM.02470-17
Molari, Massimiliano; Guilini, Katja; Lott, Christian; Weber, Miriam; de Beer, Dirk; Meyer, Stefanie; Ramette, Alban; Wegener, Gunter; Wenzhöfer, Frank; Martin, Daniel; Cibic, Tamara; De Vittor, Cinzia; Vanreusel, Ann; Boetius, Antje (2018). CO2 leakage alters biogeochemical and ecological functions of submarine sands. Science Advances, 4(2), eaao2040. American Association for the Advancement of Science 10.1126/sciadv.aao2040
Wang, Jingying; Ramette, Alban; Jurca, Maja; Goutaki, Myrofora; Beardsmore, Caroline S; Kuehni, Claudia E (2017). Association between breastfeeding and eczema during childhood and adolescence: A cohort study. PLoS ONE, 12(9), e0185066. Public Library of Science 10.1371/journal.pone.0185066
Donà, Valentina; Bernasconi, Odette Joëlle; Do Couto Pires, Joao Pedro; Collaud, Alexandra; Overesch, Gudrun; Ramette, Alban Nicolas; Perreten, Vincent; Endimiani, Andrea (2017). Heterogeneous Genetic Location of mcr-1 in Colistin-Resistant Escherichia coli Isolated from Humans and Retail Chicken Meat in Switzerland: Emergence of mcr-1-Carrying IncK2 Plasmids. Antimicrobial agents and chemotherapy, 61(11) American Society for Microbiology 10.1128/AAC.01245-17
Wang, Jingying; Ramette, Alban; Jurca, Maja; Goutaki, Myrofora; Beardsmore, Caroline S.; Kuehni, Claudia E (2017). Breastfeeding and respiratory tract infections during the first 2 years of life. ERJ Open Research, 3(2), 00143. European Respiratory Society 10.1183/23120541.00143-2016
Jurca, Maja; Ramette, Alban; Dogaru, Cristian M; Goutaki, Myrofora; Spycher, Ben D; Latzin, Philipp; Gaillard, Erol A; Kuehni, Claudia E (2017). Prevalence of cough throughout childhood: A cohort study. PLoS ONE, 12(5), e0177485. Public Library of Science 10.1371/journal.pone.0177485
Hassenrück, Christiane; Tegetmeyer, Halina E.; Ramette, Alban; Fabricius, Katharina E. (2017). Minor impacts of reduced pH on bacterial biofilms on settlement tiles along natural pH gradients at two CO2seeps in Papua New Guinea. ICES journal of marine science, 74(4), pp. 978-987. Oxford University Press 10.1093/icesjms/fsw204
Jessen, Gerdhard L.; Lichtschlag, Anna; Ramette, Alban; Pantoja, Silvio; Rossel, Pamela E.; Schubert, Carsten J.; Struck, Ulrich; Boetius, Antje (2017). Hypoxia causes preservation of labile organic matter and changes seafloor microbial community composition (Black Sea). Science Advances, 3(2), e1601897. American Association for the Advancement of Science 10.1126/sciadv.1601897
Ruff, S. Emil; Kuhfuss, Hanna; Wegener, Gunter; Lott, Christian; Ramette, Alban Nicolas; Wiedling, Johanna; Knittel, Katrin; Weber, Miriam (2016). Methane Seep in Shallow-Water Permeable Sediment Harbors High Diversity of Anaerobic Methanotrophic Communities, Elba, Italy. Frontiers in Microbiology, 7(374), p. 374. Frontiers 10.3389/fmicb.2016.00374
Hassenrück, Christiane; Fink, Artur; Lichtschlag, Anna; Tegetmeyer, Halina E.; de Beer, Dirk; Ramette, Alban (2016). Quantification of the effects of ocean acidification on sediment microbial communities in the environment: the importance of ecosystem approaches. FEMS microbiology ecology, 92(5), fiw027. Oxford University Press 10.1093/femsec/fiw027
Bienhold, Christina; Zinger, Lucie; Boetius, Antje; Ramette, Alban (2016). Diversity and Biogeography of Bathyal and Abyssal Seafloor Bacteria. PLoS ONE, 11(1), e0148016. Public Library of Science 10.1371/journal.pone.0148016
Ramette, Alban; Kuehni, Claudia Elisabeth (2015). Bed-sharing and childhood asthma: from associations to causal modelling. European respiratory journal, 45(3), pp. 596-600. European Respiratory Society 10.1183/09031936.00234814
Raulf, Felix F.; Fabricius, Katharina; Uthicke, Sven; de Beer, Dirk; Abed, Raeid M. M.; Ramette, Alban Nicolas (2015). Changes in microbial communities in coastal sediments along natural CO 2 gradients at a volcanic vent in Papua New Guinea. Environmental microbiology, 17(10), pp. 3678-3691. Wiley-Blackwell 10.1111/1462-2920.12729
Ramette, Alban Nicolas; Spycher, Ben; Beardsmore, Caroline; Kühni, Claudia (2015). Causal relationships between infections and asthma throughout childhood: A path analysis approach. European respiratory journal, 46(suppl 59), PA4512. European Respiratory Society 10.1183/13993003.congress-2015.pa4512
Wang, Jingying; Ramette, Alban Nicolas; Jurca, Maja; Halbeisen, Florian; Beardsmore, Caroline; Kühni, Claudia (2015). Does breastfeeding protect against childhood eczema? European respiratory journal, 46(suppl 59), OA1975. European Respiratory Society 10.1183/13993003.congress-2015.oa1975
Jurca, Maja; Ramette, Alban Nicolas; Spycher, Ben; Goutaki, Myrofora; Wang, Jingying; Latzin, Philipp; Gaillard, Erol; Kühni, Claudia (2015). Risk factors for chronic non-specific cough in 0-2 year olds: A cohort study. European respiratory journal, 46(suppl 59), OA4769. European Respiratory Society 10.1183/13993003.congress-2015.oa4769
Ruff, S. Emil; Biddle, Jennifer F.; Teske, Andreas P.; Knittel, Katrin; Boetius, Antje; Ramette, Alban Nicolas (2015). Global dispersion and local diversification of the methane seep microbiome. Proceedings of the National Academy of Sciences of the United States of America - PNAS, 112(13), pp. 4015-4020. National Academy of Sciences NAS 10.1073/pnas.1421865112
Ionescu, Danny; Heim, Christine; Polerecky, Lubos; Ramette, Alban Nicolas; Haeusler, Stefan; Bizic-Ionescu, Mina; Thiel, Volker; de Beer, Dirk (2015). Diversity of Iron Oxidizing and Reducing Bacteria in Flow Reactors in the Äspö Hard Rock Laboratory. Geomicrobiology Journal, 32(3-4), pp. 207-220. Taylor & Francis 10.1080/01490451.2014.884196
Buttigieg, Pier Luigi; Ramette, Alban Nicolas (2015). Biogeographic patterns of bacterial microdiversity in Arctic deep-sea sediments (HAUSGARTEN, Fram Strait). Frontiers in Microbiology, 5, p. 660. Frontiers 10.3389/fmicb.2014.00660
Hassenrück, Christiane; Hofmann, Laurie C.; Bischof, Kai; Ramette, Alban (2015). Seagrass biofilm communities at a naturally CO 2 -rich vent. Environmental Microbiology Reports, 7(3), pp. 516-525. Wiley 10.1111/1758-2229.12282
Pop Ristova, Petra; Wenzhöfer, Frank; Ramette, Alban; Felden, Janine; Boetius, Antje (2015). Spatial scales of bacterial community diversity at cold seeps (Eastern Mediterranean Sea). The ISME journal, 9(6), pp. 1306-1318. Nature Publishing Group 10.1038/ismej.2014.217
Zimmermann, Judith; Lott, Christian; Weber, Miriam; Ramette, Alban Nicolas; Bright, Monika; Dubilier, Nicole; Petersen, Jillian M. (2014). Dual symbiosis with co-occurring sulfur-oxidizing symbionts in vestimentiferan tubeworms from a Mediterranean hydrothermal vent. Environmental microbiology, 16(12), pp. 3638-3656. Wiley-Blackwell 10.1111/1462-2920.12427
Buttigieg, Pier Luigi; Ramette, Alban Nicolas (2014). A guide to statistical analysis in microbial ecology: a community-focused, living review of multivariate data analyses. FEMS Microbiology Ecology, 90(3), pp. 543-550. Wiley 10.1111/1574-6941.12437
Zinger, L.; Boetius, A.; Ramette, Alban Nicolas (2014). Bacterial taxa-area and distance-decay relationships in marine environments. Molecular Ecology, 23(4), pp. 954-964. Wiley-Blackwell 10.1111/mec.12640
Al-Najjar, Mohammad A. A.; Ramette, Alban Nicolas; Kühl, Michael; Hamza, Waleed; Klatt, Judith M.; Polerecky, Lubos (2014). Spatial patterns and links between microbial community composition and function in cyanobacterial mats. Frontiers in Microbiology, 5(406), p. 406. Frontiers 10.3389/fmicb.2014.00406
Ramette, Alban Nicolas; Buttigieg, Pier Luigi (2014). The R package otu2ot for implementing the entropy decomposition of nucleotide variation in sequence data. Frontiers in Microbiology, 5(601) Frontiers 10.3389/fmicb.2014.00601
Gobet, Angélique; Boetius, Antje; Ramette, Alban Nicolas (2013). Ecological coherence of diversity patterns derived from classical fingerprinting and Next Generation Sequencing techniques. Environmental microbiology, 16(9), pp. 2672-2681. Wiley-Blackwell 10.1111/1462-2920.12308
Meyer, Stefanie; Wegener, Gunter; Lloyd, Karen G.; Teske, Andreas; Boetius, Antje; Ramette, Alban Nicolas (2013). Microbial habitat connectivity across spatial scales and hydrothermal temperature gradients at Guaymas Basin. Frontiers in Microbiology, 4(207) Frontiers 10.3389/fmicb.2013.00207
Ruff, S. Emil; Arnds, Julia; Knittel, Katrin; Amann, Rudolf; Wegener, Gunter; Ramette, Alban Nicolas; Boetius, Antje (2013). Microbial Communities of Deep-Sea Methane Seeps at Hikurangi Continental Margin (New Zealand). PLoS ONE, 8(9), e72627. Public Library of Science 10.1371/journal.pone.0072627
Jacob, Marianne; Soltwedel, Thomas; Boetius, Antje; Ramette, Alban Nicolas (2013). Biogeography of Deep-Sea Benthic Bacteria at Regional Scale (LTER HAUSGARTEN, Fram Strait, Arctic). PLoS ONE, 8(9), e72779. Public Library of Science 10.1371/journal.pone.0072779
Schöttner, Sandra; Hoffmann, Friederike; Cárdenas, Paco; Rapp, Hans Tore; Boetius, Antje; Ramette, Alban Nicolas (2013). Relationships between Host Phylogeny, Host Type and Bacterial Community Diversity in Cold-Water Coral Reef Sponges. PLoS ONE, 8(2), e55505. Public Library of Science 10.1371/journal.pone.0055505
Pop Ristova, P.; Wenzhöfer, F.; Ramette, Alban Nicolas; Zabel, M.; Fischer, D.; Kasten, S.; Boetius, A. (2012). Bacterial diversity and biogeochemistry of different chemosynthetic habitats of the REGAB cold seep (West African margin, 3160 m water depth). Biogeosciences Discussions, 9(7), pp. 8337-8385. Copernicus 10.5194/bgd-9-8337-2012
Amend, Anthony S.; Oliver, Tom A.; Amaral-Zettler, Linda A.; Boetius, Antje; Fuhrman, Jed A.; Horner-Devine, M. Claire; Huse, Susan M.; Welch, David B. Mark; Martiny, Adam C.; Ramette, Alban Nicolas; Zinger, Lucie; Sogin, Mitchell L.; Martiny, Jennifer B. H.; Lambshead, John (2012). Macroecological patterns of marine bacteria on a global scale. Journal of Biogeography, 40(4), pp. 800-811. Blackwell Scientific Publications 10.1111/jbi.12034
Pop Ristova, P.; Wenzhöfer, F.; Ramette, Alban Nicolas; Zabel, M.; Fischer, D.; Kasten, S.; Boetius, A. (2012). Bacterial diversity and biogeochemistry of different chemosynthetic habitats of the REGAB cold seep (West African margin, 3160 m water depth). Biogeosciences, 9(12), pp. 5031-5048. Copernicus Publications 10.5194/bg-9-5031-2012
Sawall, Yvonne; Richter, Claudio; Ramette, Alban Nicolas (2012). Effects of Eutrophication, Seasonality and Macrofouling on the Diversity of Bacterial Biofilms in Equatorial Coral Reefs. PLoS ONE, 7(7), e39951. Public Library of Science 10.1371/journal.pone.0039951
Gobet, Angélique; Böer, Simone I; Huse, Susan M; van Beusekom, Justus E E; Quince, Christopher; Sogin, Mitchell L; Boetius, Antje; Ramette, Alban Nicolas (2012). Diversity and dynamics of rare and of resident bacterial populations in coastal sands. The ISME journal, 6(3), pp. 542-553. Nature Publishing Group 10.1038/ismej.2011.132
Kleindienst, Sara; Ramette, Alban Nicolas; Amann, Rudolf; Knittel, Katrin (2012). Distribution and in situ abundance of sulfate-reducing bacteria in diverse marine hydrocarbon seep sediments. Environmental microbiology, 14(10), pp. 2689-2710. Wiley-Blackwell 10.1111/j.1462-2920.2012.02832.x
Grünke, S.; Lichtschlag, A.; de Beer, D.; Felden, J.; Salman, V.; Ramette, Alban Nicolas; Schulz-Vogt, H. N.; Boetius, A. (2012). Mats of psychrophilic thiotrophic bacteria associated with cold seeps of the Barents Sea. Biogeosciences, 9(8), pp. 2947-2960. Copernicus Publications 10.5194/bg-9-2947-2012
Ionescu, Danny; Siebert, Christian; Polerecky, Lubos; Munwes, Yaniv Y.; Lott, Christian; Häusler, Stefan; Bižić-Ionescu, Mina; Quast, Christian; Peplies, Jörg; Glöckner, Frank Oliver; Ramette, Alban Nicolas; Rödiger, Tino; Dittmar, Thorsten; Oren, Aharon; Geyer, Stefan; Stärk, Hans-Joachim; Sauter, Martin; Licha, Tobias; Laronne, Jonathan B.; de Beer, Dirk; ... (2012). Microbial and Chemical Characterization of Underwater Fresh Water Springs in the Dead Sea. PLoS ONE, 7(6), e38319. Public Library of Science 10.1371/journal.pone.0038319
Abed, Raeid M.M.; Ramette, Alban Nicolas; Hübner, Vera; Deckker, Patrick; Beer, Dirk (2012). Microbial diversity of eolian dust sources from saline lake sediments and biological soil crusts in arid Southern Australia. FEMS Microbiology Ecology, 80(2), pp. 294-304. Wiley 10.1111/j.1574-6941.2011.01289.x
Bauermeister, Jan; Ramette, Alban Nicolas; Dattagupta, Sharmishtha (2012). Repeatedly Evolved Host-Specific Ectosymbioses between Sulfur-Oxidizing Bacteria and Amphipods Living in a Cave Ecosystem. PLoS ONE, 7(11), e50254. Public Library of Science 10.1371/journal.pone.0050254
Schöttner, Sandra; Wild, Christian; Hoffmann, Friederike; Boetius, Antje; Ramette, Alban Nicolas (2012). Spatial Scales of Bacterial Diversity in Cold-Water Coral Reef Ecosystems. PLoS ONE, 7(3), e32093. Public Library of Science 10.1371/journal.pone.0032093
Bienhold, Christina; Boetius, Antje; Ramette, Alban Nicolas (2012). The energy–diversity relationship of complex bacterial communities in Arctic deep-sea sediments. The ISME journal, 6(4), pp. 724-732. Nature Publishing Group 10.1038/ismej.2011.140
Kostadinov, Ivaylo; Kottmann, Renzo; Ramette, Alban Nicolas; Waldmann, Jost; Buttigieg, Pier Luigi; Glöckner, Frank (2011). Quantifying the effect of environment stability on the transcription factor repertoire of marine microbes. Microbial Informatics and Experimentation, 1(1), p. 9. BioMed Central 10.1186/2042-5783-1-9
Schöttner, Sandra; Pfitzner, Barbara; Grünke, Stefanie; Rasheed, Mohammed; Wild, Christian; Ramette, Alban Nicolas (2011). Drivers of bacterial diversity dynamics in permeable carbonate and silicate coral reef sands from the Red Sea. Environmental microbiology, 13(7), pp. 1815-1826. Wiley-Blackwell 10.1111/j.1462-2920.2011.02494.x
Rossel, Pamela E.; Elvert, Marcus; Ramette, Alban Nicolas; Boetius, Antje; Hinrichs, Kai-Uwe (2011). Factors controlling the distribution of anaerobic methanotrophic communities in marine environments: Evidence from intact polar membrane lipids. Geochimica et cosmochimica acta, 75(1), pp. 164-184. Elsevier Science 10.1016/j.gca.2010.09.031
Zinger, Lucie; Amaral-Zettler, Linda A.; Fuhrman, Jed A.; Horner-Devine, M. Claire; Huse, Susan M.; Welch, David B. Mark; Martiny, Jennifer B. H.; Sogin, Mitchell; Boetius, Antje; Ramette, Alban Nicolas (2011). Global Patterns of Bacterial Beta-Diversity in Seafloor and Seawater Ecosystems. PLoS ONE, 6(9), e24570. Public Library of Science 10.1371/journal.pone.0024570
Bru, D; Ramette, Alban Nicolas; Saby, N P A; Dequiedt, S; Ranjard, L; Jolivet, C; Arrouays, D; Philippot, L (2011). Determinants of the distribution of nitrogen-cycling microbial communities at the landscape scale. The ISME journal, 5(3), pp. 532-542. Nature Publishing Group 10.1038/ismej.2010.130
Ramette, Alban Nicolas; Frapolli, Michele; Saux, Marion Fischer-Le; Gruffaz, C.; Meyer, Jean-Marie; Défago, Geneviève; Sutra, Laurent; Moënne-Loccoz, Yvan (2011). Pseudomonas protegens sp. nov., widespread plant-protecting bacteria producing the biocontrol compounds 2,4-diacetylphloroglucinol and pyoluteorin. Systematic and applied microbiology, 34(3), pp. 180-188. Elsevier 10.1016/j.syapm.2010.10.005
Amaral-Zettler, Linda; Artigas, Luis Felipe; Baross, John; Bharathi P.A., Loka; Boetius, Antje; Chandramohan, Dorairajasingam; Herndl, Gerhard; Kogure, Kazuhiro; Neal, Phillip; Pedrós-Alió, Carlos; Ramette, Alban Nicolas; Schouten, Stefan; Stal, Lucas; Thessen, Anne; Leeuw, Jan de; Sogin, Mitchell (2010). A Global Census of Marine Microbes. In: McIntyre, Alasdair D. (ed.) Life in the World’s Oceans: Diversity, Distribution, and Abundance (pp. 221-245). Oxford: Blackwell Publishing Ltd 10.1002/9781444325508.ch12
Schauer, Regina; Bienhold, Christina; Ramette, Alban Nicolas; Harder, Jens (2010). Bacterial diversity and biogeography in deep-sea surface sediments of the South Atlantic Ocean. The ISME journal, 4(2), pp. 159-170. Nature Publishing Group 10.1038/ismej.2009.106
Petersen, Jillian M.; Ramette, Alban Nicolas; Lott, Christian; Cambon-Bonavita, Marie-Anne; Zbinden, Magali; Dubilier, Nicole (2010). Dual symbiosis of the vent shrimp Rimicaris exoculata with filamentous gamma- and epsilonproteobacteria at four Mid-Atlantic Ridge hydrothermal vent fields. Environmental microbiology, 12(8), pp. 2204-2218. Wiley-Blackwell 10.1111/j.1462-2920.2009.02129.x
Verna, Caroline; Ramette, Alban Nicolas; Wiklund, Helena; Dahlgren, Thomas G.; Glover, Adrian G.; Gaill, Françoise; Dubilier, Nicole (2010). High symbiont diversity in the bone-eating worm Osedax mucofloris from shallow whale-falls in the North Atlantic. Environmental microbiology, 12(8), pp. 2355-2370. Wiley-Blackwell 10.1111/j.1462-2920.2010.02299.x
Orcutt, Beth N.; Joye, Samantha B.; Kleindienst, Sara; Knittel, Katrin; Ramette, Alban Nicolas; Reitz, Anja; Samarkin, Vladimir; Treude, Tina; Boetius, Antje (2010). Impact of natural oil and higher hydrocarbons on microbial diversity, distribution, and activity in Gulf of Mexico cold-seep sediments. Deep-sea research. Part 2 - topical studies in oceanography, 57(21-23), pp. 2008-2021. Elsevier Science 10.1016/j.dsr2.2010.05.014
Alonso, C; Gómez-Pereira, P; Ramette, Alban Nicolas; Ortega, L; Fuchs, BM; Amann, R (2010). Multilevel analysis of the bacterial diversity along the environmental gradient Río de la Plata–South Atlantic Ocean. Aquatic Microbial Ecology, 61(1), pp. 57-72. Inter-Research 10.3354/ame01439
Gobet, A.; Quince, C.; Ramette, Alban Nicolas (2010). Multivariate Cutoff Level Analysis (MultiCoLA) of large community data sets. Nucleic acids research, 38(15), e155. Oxford University Press 10.1093/nar/gkq545
Grünke, Stefanie; Lichtschlag, Anna; Beer, Dirk de; Kuypers, Marcel; Lösekann-Behrens, Tina; Ramette, Alban Nicolas; Boetius, Antje (2010). Novel observations of Thiobacterium, a sulfur-storing Gammaproteobacterium producing gelatinous mats. The ISME journal, 4(8), pp. 1031-1043. Nature Publishing Group 10.1038/ismej.2010.23
Knief, Claudia; Ramette, Alban Nicolas; Frances, Lisa; Alonso-Blanco, Carlos; Vorholt, Julia A (2010). Site and plant species are important determinants of the Methylobacterium community composition in the plant phyllosphere. The ISME journal, 4(6), pp. 719-728. Nature Publishing Group 10.1038/ismej.2010.9
Meziti, Alexandra; Ramette, Alban Nicolas; Mente, Eleni; Kormas, Konstantinos Ar. (2010). Temporal shifts of the Norway lobster (Nephrops norvegicus) gut bacterial communities. FEMS Microbiology Ecology, 74(2), pp. 472-484. Wiley 10.1111/j.1574-6941.2010.00964.x
Santillano, D.; Boetius, A.; Ramette, Alban Nicolas (2010). Improved dsrA-Based Terminal Restriction Fragment Length Polymorphism Analysis of Sulfate-Reducing Bacteria. Applied and environmental microbiology, 76(15), pp. 5308-5311. American Society for Microbiology 10.1128/AEM.03004-09
Zhao, Shuo; Ramette, Alban Nicolas; Niu, Gui-Lan; Liu, Hong; Zhou, Ning-Yi (2009). Effects of nitrobenzene contamination and of bioaugmentation on nitrification and ammonia-oxidizing bacteria in soil. FEMS Microbiology Ecology, 70(2), pp. 315-323. Wiley 10.1111/j.1574-6941.2009.00773.x
Ramette, Alban Nicolas; Boetius, Antje (2009). Crystal ball - 2009. Environmental Microbiology Reports, 1(1), pp. 3-26. Wiley 10.1111/j.1758-2229.2008.00010.x
Ramette, Alban Nicolas; Tiedje, J.M.; Boetius, A. (2009). Impact of space, time and complex environments on microbial communities. Clinical microbiology and infection, 15(Suppl. 1), pp. 60-62. Blackwell Publishing 10.1111/j.1469-0691.2008.02692.x
Schöttner, Sandra; Hoffmann, Friederike; Wild, Christian; Rapp, Hans Tore; Boetius, Antje; Ramette, Alban Nicolas (2009). Inter- and intra-habitat bacterial diversity associated with cold-water corals. The ISME journal, 3(6), pp. 756-759. Nature Publishing Group 10.1038/ismej.2009.15
Ramette, Alban Nicolas (2009). Quantitative Community Fingerprinting Methods for Estimating the Abundance of Operational Taxonomic Units in Natural Microbial Communities. Applied and environmental microbiology, 75(8), pp. 2495-2505. American Society for Microbiology 10.1128/AEM.02409-08
Böer, Simone I; Hedtkamp, Stefanie I C; van Beusekom, Justus E E; Fuhrman, Jed A; Boetius, Antje; Ramette, Alban Nicolas (2009). Time- and sediment depth-related variations in bacterial diversity and community structure in subtidal sands. The ISME journal, 3(7), pp. 780-791. Nature Publishing Group 10.1038/ismej.2009.29
Kanzog, Corinna; Ramette, Alban Nicolas; Quéric, Nadia V.; Klages, Michael (2009). Response of benthic microbial communities to chitin enrichment: an in situ study in the deep Arctic Ocean. Polar Biology, 32(1), pp. 105-112. Springer 10.1007/s00300-008-0510-4
Kanzog, Corinna; Ramette, Alban Nicolas (2009). Microbial colonisation of artificial and deep-sea sediments in the Arctic Ocean. Marine ecology progress series, 30(4), pp. 391-404. Inter-Research 10.1111/j.1439-0485.2009.00290.x
Jacobs, J. L.; Fasi, A. C.; Ramette, Alban Nicolas; Smith, J. J.; Hammerschmidt, R.; Sundin, G. W. (2008). Identification and Onion Pathogenicity of Burkholderia cepacia Complex Isolates from the Onion Rhizosphere and Onion Field Soil. Applied and environmental microbiology, 74(10), pp. 3121-3129. American Society for Microbiology 10.1128/AEM.01941-07
Amaral-Zettler, Linda; Peplies, Jörg; Ramette, Alban Nicolas; Fuchs, Bernhard; Ludwig, Wolfgang; Glöckner, Frank Oliver (2008). Proceedings of the international workshop on Ribosomal RNA technology, April 7–9, 2008, Bremen, Germany. Systematic and applied microbiology, 31(4), pp. 258-268. Elsevier 10.1016/j.syapm.2008.08.004
Ramette, Alban Nicolas; Tiedje, James M. (2007). Biogeography: An Emerging Cornerstone for Understanding Prokaryotic Diversity, Ecology, and Evolution. Microbial ecology, 53(2), pp. 197-207. Springer 10.1007/s00248-005-5010-2
Ramette, Alban Nicolas; Tiedje, J. M. (2007). Multiscale responses of microbial life to spatial distance and environmental heterogeneity in a patchy ecosystem. Proceedings of the National Academy of Sciences of the United States of America - PNAS, 104(8), pp. 2761-2766. National Academy of Sciences NAS 10.1073/pnas.0610671104
Ramette, Alban Nicolas (2007). Multivariate analyses in microbial ecology. FEMS Microbiology Ecology, 62(2), pp. 142-160. Wiley 10.1111/j.1574-6941.2007.00375.x
Chain, P. S. G.; Denef, V. J.; Konstantinidis, K. T.; Vergez, L. M.; Agullo, L.; Reyes, V. L.; Hauser, L.; Cordova, M.; Gomez, L.; Gonzalez, M.; Land, M.; Lao, V.; Larimer, F.; LiPuma, J. J.; Mahenthiralingam, E.; Malfatti, S. A.; Marx, C. J.; Parnell, J. J.; Ramette, Alban Nicolas; Richardson, P.; ... (2006). Burkholderia xenovorans LB400 harbors a multi-replicon, 9.73-Mbp genome shaped for versatility. Proceedings of the National Academy of Sciences of the United States of America - PNAS, 103(42), pp. 15280-15287. National Academy of Sciences NAS 10.1073/pnas.0606924103
Konstantinidis, K. T.; Ramette, Alban Nicolas; Tiedje, J. M. (2006). The bacterial species definition in the genomic era. Philosophical transactions of the Royal Society. Series B - biological sciences, 361(1475), pp. 1929-1940. Royal Society of London 10.1098/rstb.2006.1920
Konstantinidis, K. T.; Ramette, Alban Nicolas; Tiedje, J. M. (2006). Toward a More Robust Assessment of Intraspecies Diversity, Using Fewer Genetic Markers. Applied and environmental microbiology, 72(11), pp. 7286-7293. American Society for Microbiology 10.1128/AEM.01398-06
Payne, George W.; Ramette, Alban Nicolas; Rose, Helen L.; Weightman, Andrew J.; Jones, T. Hefin; Tiedje, James M.; Mahenthiralingam, Eshwar (2006). Application of a recA gene-based identification approach to the maize rhizosphere reveals novel diversity in Burkholderia species. FEMS microbiology letters, 259(1), pp. 126-132. Wiley-Blackwell 10.1111/j.1574-6968.2006.00257.x
Ramette, Alban Nicolas; Möenne-Loccoz, Yvan; Défago, Geneviève (2006). Genetic diversity and biocontrol potential of fluorescent pseudomonads producing phloroglucinols and hydrogen cyanide from Swiss soils naturally suppressive or conducive to Thielaviopsis basicola-mediated black root rot of tobacco. FEMS Microbiology Ecology, 55(3), pp. 369-381. Blackwell Publishing Ltd 10.1111/j.1574-6941.2005.00052.x
Ramette, Alban Nicolas; LiPuma, J. J.; Tiedje, J. M. (2005). Species Abundance and Diversity of Burkholderia cepacia Complex in the Environment. Applied and environmental microbiology, 71(3), pp. 1193-1201. American Society for Microbiology 10.1128/AEM.71.3.1193-1201.2005
Ramette, Alban Nicolas; Frapolli, Michele; Défago, Geneviève; Moënne-Loccoz, Yvan (2003). Phylogeny of HCN Synthase-Encoding hcnBC Genes in Biocontrol Fluorescent Pseudomonads and Its Relationship with Host Plant Species and HCN Synthesis Ability. Molecular Plant-Microbe Interactions, 16(6), pp. 525-535. American Phytopathological Society 10.1094/MPMI.2003.16.6.525
Ramette, Alban Nicolas; Moenne-Loccoz, Yvan; Défago, Geneviève (2003). Prevalence of fluorescent pseudomonads producing antifungal phloroglucinols and/or hydrogen cyanide in soils naturally suppressive or conducive to tobacco black root rot. FEMS Microbiology Ecology, 44(1), pp. 35-43. Blackwell Publishing Ltd 10.1111/j.1574-6941.2003.tb01088.x
Wang, Chunxia; Ramette, Alban Nicolas; Punjasamarnwong, Patchara; Zala, Marcello; Natsch, Andreas; Moenne-Loccoz, Yvan; Défago, Geneviève (2001). Cosmopolitan distribution of phlD-containing dicotyledonous crop-associated biocontrol pseudomonads of worldwide origin. FEMS Microbiology Ecology, 37(2), pp. 105-116. Blackwell Publishing Ltd 10.1111/j.1574-6941.2001.tb00858.x
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