Ramette, Alban Nicolas

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Journal Article

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 : an official publication of the Infectious Diseases Society of America, 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

Goncalves Cabecinhas, Ana Rita; Roloff, Tim; , ; , ; , ; Ramette, Alban; , ; , ; , ; , ; , ; , ; , ; , ; , ; , ; , ; 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

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

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, Molecular Diversity Preservation International 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

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

Ramette, Alban Nicolas; Moënne-Loccoz, Yvan; Défago, Geneviève (2001). Polymorphism of the Polyketide Synthase Gene phlD in Biocontrol Fluorescent Pseudomonads Producing 2,4-Diacetylphloroglucinol and Comparison of PhlD with Plant Polyketide Synthases. Molecular Plant-Microbe Interactions, 14(5), pp. 639-652. American Phytopathological Society 10.1094/mpmi.2001.14.5.639

Book Section

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

Working Paper

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

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