Publications

2020

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See detailIntegrative omics analysis of the termite gut system adaptation to Miscanthus diet identifies lignocellulose degradation enzymes.
Calusinska, Magdalena; Marynowska, Martyna; Bertucci, Marie; Untereiner, Boris; Klimek, Dominika; Goux, Xavier; Sillam-Dusses, David; Gawron, Piotr; Halder, Rashi; Wilmes, Paul; Ferrer, Pau; Gerin, Patrick; Roisin, Yves; Delfosse, Philippe

in Communications Biology (2020)

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See detailGlutathione Restricts Serine Metabolism to Preserve Regulatory T Cell Function
Kurniawan, Henry; Franchina, Davide G.; Guerra, Luana; Bonetti, Lynn; - Baguet, Leticia Soriano; Grusdat, Melanie; Schlicker, Lisa; Hunewald, Oliver; Dostert, Catherine; Merz, Myriam P.; Binsfeld, Carole; Duncan, Gordon S.; Farinelle, Sophie; Nonnenmacher, Yannic; Haight, Jillian; Das Gupta, Dennis; Ewen, Anouk; Taskesen, Rabia; Halder, Rashi; Chen, Ying; Jäger, Christian; Ollert, Markus; Wilmes, Paul; Vasiliou, Vasilis; Harris, Isaac S.; Knobbe-Thomsen, Christiane B.; Turner, Jonathan; Mak, Tak W.; Lohoff, Michael; Meiser, Johannes; Hiller, Karsten; Brenner, Dirk

in Cell Metabolism (2020), 31(5), 920--9367

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See detailCompositional and functional characterisation of biomass-degrading microbial communities in guts of plant fibre- and soil-feeding higher termites.
Marynowska, Martyna; Goux, Xavier; Sillam-Dusses, David; Rouland-Lefevre, Corinne; Halder, Rashi; Wilmes, Paul; Gawron, Piotr; Roisin, Yves; Delfosse, Philippe; Calusinska, Magdalena

in Microbiome (2020)

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See detailGenetic Architecture of Parkinson's Disease in the Indian Population: Harnessing Genetic Diversity to Address Critical Gaps in Parkinson's Disease Research.
Rajan, Roopa; Divya, K. P.; Kandadai, Rukmini Mridula; Yadav, Ravi; Satagopam, Venkata; Madhusoodanan, U. K.; Agarwal, Pankaj; Kumar, Niraj; Ferreira, Teresa; Kumar, Hrishikesh; Sreeram Prasad, A. V.; Shetty, Kuldeep; Mehta, Sahil; Desai, Soaham; Kumar, Suresh; Prashanth, L. K.; Bhatt, Mohit; Wadia, Pettarusp; Ramalingam, Sudha; Wali, G. M.; Pandey, Sanjay; Bartusch, Felix; Hannussek, Maximilian; Krüger, Jens; Kumar-Sreelatha, Ashwin; Grover, Sandeep; Lichtner, Peter; Sturm, Marc; Roeper, Jochen; Busskamp, Volker; Chandak, Giriraj R.; Schwamborn, Jens Christian; Seth, Pankaj; Gasser, Thomas; Riess, Olaf; Goyal, Vinay; Pal, Pramod Kumar; Borgohain, Rupam; Krüger, Rejko; Kishore, Asha; Sharma, Manu

in Frontiers in neurology (2020), 11

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See detailProgramme Démence Prévention (pdp ): A Nation-Wide Programme for Dementia Prevention in Luxembourg
Schröder, Valerie; Kaysen, Anne; Fritz, Joëlle; Kemp, Jennifer; Wagner, Sophie; Köhler, Sebastian; Hartmann, Tobias; Dodel, Richard; Kalbe, Elke; Leist, Anja; Krüger, Rejko

Poster (2020, April)

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See detailMicrobiome in Colorectal Cancer: How to Getfrom Meta-omics to Mechanism?
Ternes, Dominik; Karta, Jessica; Tsenkova, Mina; Wilmes, Paul; Haan, Serge; Letellier, Elisabeth

in Trends in Microbiology (2020)

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See detailBioKC: a platform for quality controlled curation and annotation of systems biology models
Vega Moreno, Carlos Gonzalo; Groues, Valentin; Ostaszewski, Marek; Satagopam, Venkata; Schneider, Reinhard

Scientific Conference (2020, September 04)

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See detailBioKC: a collaborative platform for systems biology model curation and annotation
Vega Moreno, Carlos Gonzalo; Groues, Valentin; Ostaszewski, Marek; Schneider, Reinhard; Satagopam, Venkata

in bioRxiv (2020)

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2019

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See detailDAISY: A Data Information System for accountability under the General Data Protection Regulation
Becker, Regina; Alper, Pinar; Groues, Valentin; Munoz, Sandrine; Jarosz, Yohan; Lebioda, Jacek; Rege, Kavita; Trefois, Christophe; Satagopam, Venkata; Schneider, Reinhard

in GigaScience (2019), 8(12),

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See detailDeep neural networks outperform human expert's capacity in characterizing bioleaching bacterial biofilm composition
Buetti-Dinh, Antoine; Galli, Vanni; Bellenberg, Sören; Ilie, Olga; Herold, Malte; Christel, Stephan; Boretska, Mariia; Pivkin, Igor V.; Wilmes, Paul; Sand, Wolfgang; Vera, Mario; Dopson, Mark

in Biotechnology Reports (2019)

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See detailInfluence of Macro-Substrate Composition in Wastewater on Micropollutant Removal
Christen, Anne; Gallé, Tom; Köhler, Christian; Wilmes, Paul; Frkova, Zuzana; Hansen, Joachim

in the mobile app "MICROPOL 2019" (2019)

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See detailIntegrated In Vitro and In Silico Modeling Delineates the Molecular Effects of a Synbiotic Regimen on Colorectal-Cancer-Derived Cells
Greenhalgh, Kacy; Ramiro Garcia, Javier; Heinken; Ullmann, Pit; Bintener, Tamara Jean Rita; Pacheco, Maria; Baginska, joanna; Shah, Pranjul; Frachet Bour, Audrey; Halder, Rashi; Fritz, Joëlle; Sauter, Thomas; Thiele, Ines; Haan, Serge; Letellier, Elisabeth; Wilmes, Paul

in Cell Reports (2019), 27

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See detailData and knowledge management in translational research: implementation of the eTRIKS platform for the IMI OncoTrack consortium
Gu, Wei; Yildirimman, Reha; Van der Stuyft, Emmanuel; Verbeeck, Denny; Herzinger, Sascha; Satagopam, Venkata; Barbosa-Silva, Adriano; Schneider, Reinhard; Lange, Bodo; Lehrach, Hans; Guo, Yike; Henderson, David; Rowe, Anthony; on behalf of the IMI OncoTrack and the IMI eTRIKS consortia

in BMC Bioinformatics (2019), 20(1), 164

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See detailExtensive transmission of microbes along the gastrointestinal tract
Schmidt, Thomas; Hayward, Matthew; Coelho, Luis; Li, Simone; Costea, Paul; Voigt, Anita; Wirbel, Jakob; Maistrenko, Oleksandr; Alves, Renato; Bergsten, Emma; de Beaufort, Carine; Sobhani, Irdaj; Heintz, Anna; Sunagawa, Shinichi; Zeller, Georg; Wilmes, Paul; Bork, Peer

in eLife (2019)

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See detailConnecting environmental exposure and neurodegeneration using cheminformatics and high resolution mass spectrometry: potential and challenges
Schymanski, Emma; Baker, Nancy C.; Williams, Antony J; Singh, Randolph; Trezzi, Jean-Pierre; Kolber, Pierre Luc; Wilmes, Paul; Krüger, Rejko; Paczia, Nicole; Linster, Carole; Balling, Rudi

in Environmental Science. Processes and Impacts (2019)

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2018

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See detailPresenting and Sharing Clinical Data using the eTRIKS Standards Master Tree for tranSMART
Barbosa-Silva, Adriano; Bratfalean, Dorina; Gu, Wei; Satagopam, Venkata; Houston, Paul; Becnel, Lauren B.; Eifes, Serge; Richard, Fabien; Tielmann, Andreas; Herzinger, Sascha; Rege, Kavita; Balling, Rudi; Peeters, Paul; Schneider, Reinhard

in Bioinformatics (2018)

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See detailAutomated Microscopic Analysis of Metal Sulfide Colonization by Acidophilic Microorganisms.
Bellenberg, Soren; Buetti-Dinh, Antoine; Galli, Vanni; Ilie, Olga; Herold, Malte; Christel, Stephan; Boretska, Mariia; Pivkin, Igor V.; Wilmes, Paul; Sand, Wolfgang; Vera, Mario; Dopson, Mark

in Applied and environmental microbiology (2018), 84(20),

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See detailA year of monitoring 20 mesophilic full-scale bioreactors reveals the existence of stable but different core microbiomes in bio-waste and wastewater anaerobic digestion systems.
Calusinska, Magdalena; Goux, Xavier; Fossepre, Marie; Muller, Emilie; Wilmes, Paul; Delfosse, Philippe

in Biotechnology for biofuels (2018), 11

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See detailExpressed protein profile of a Tectomicrobium and other microbial symbionts in the marine sponge Aplysina aerophoba as evidenced by metaproteomics.
Chaib De Mares, Maryam; Jimenez, Diego Javier; Palladino, Giorgia; Gutleben, Johanna; Lebrun, Laura; Muller, Emilie; Wilmes, Paul; Sipkema, Detmer; van Elsas, Jan Dirk

in Scientific reports (2018), 8(1), 11795

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See detailWeak Iron Oxidation by Sulfobacillus thermosulfidooxidans Maintains a Favorable Redox Potential for Chalcopyrite Bioleaching
Christel, Stephan; Herold, Malte; Bellenberg, Sören; Buetti-Dinh, Antoine; El Hajjami, Mohamed; Pivkin, Igor; Sand, Wolfgang; Wilmes, Paul; Poetsch, Ansgar; Dopson, Mark

in Frontiers in Microbiology (2018), 9(December), 1-12

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See detailExpanding the use of spectral libraries in proteomics.
Deutsch, Eric W.; Perez-Riverol, Yasset; Chalkley, Robert J.; Wilhelm, Mathias; Tate, Stephen; Sachsenberg, Timo; Walzer, Mathias; Kall, Lukas; Delanghe, Bernard; Bocker, Sebastian; Schymanski, Emma; Wilmes, Paul; Dorfer, Viktoria; Kuster, Bernhard; Volders, Pieter-Jan; Jehmlich, Nico; Vissers, Johannes P. C.; Wolan, Dennis W.; Wang, Ana Y.; Mendoza, Luis; Shofstahl, Jim; Dowsey, Andrew W.; Griss, Johannes; Salek, Reza M.; Neumann, Steffen; Binz, Pierre-Alain; Lam, Henry; Vizcaino, Juan Antonio; Bandeira, Nuno; Rost, Hannes

in Journal of proteome research (2018)

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See detailCominatorial effect of dietary fibre and Lactobacillus rhamnosus in the context of colorectal cancer therapy
Greenhalgh, Kacy; Ramiro Garcia, Javier; Heinken, Almut Katrin; Baginska, Joanna; Letellier, Elisabeth; Halder, Rashi; Frachet Bour, Audrey; Ullmann, Pit; Thiele, Ines; Haan, Serge; Wilmes, Paul

Poster (2018, February 16)

See detailExtraction and Analysis of RNA Isolated from Pure Bacteria-Derived Outer Membrane Vesicles
Habier, Janine; May, Patrick; Heintz-Buschart, Anna; Ghosal, Anubrata; Wienecke-Baldacchino, Anke; Nolte-'t Hoen, Esther N.M; Wilmes, Paul; Fritz, Joëlle

in Arluison, Véronique; Valverde, Claudio Valverde (Eds.) Bacterial Regulatory RNA (2018)

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See detailHuman Gut Microbiome: Function Matters.
Heintz-Buschart, Anna; Wilmes, Paul

in Trends in microbiology (2018), 26(7), 563-574

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See detailSmall RNA profiling of low biomass samples: identification and removal of contaminants
Heintz-Buschart, Anna; Yusuf, Dilmurat; Kaysen, Anne; Etheridge, Alton; Fritz, Joëlle; May, Patrick; de Beaufort, Carine; Upadhyaya, Bimal Babu; Ghosal, Anubrata; Galas, David J; Wilmes, Paul

in BMC Biology (2018), 16(52),

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See detailIntegrated time-resolved multi-omics for understanding microbial niche ecology
Herold, Malte; Narayanasamy, Shaman; Martinez Arbas, Susana; Muller, Emilie; Kleine-Borgmann, Anna Luise; Lebrun, Laura; Roume, Hugo; Sheik, Abdul; Bessarab, Irina; Williams, Rohan; Gillece, John; Schupp, Jim; Keim, Paul; Jäger, Christian; Hoopmann, Michael; Li, Sujun; Tang, Haixu; Heintz, Anna; May, Patrick; Laczny, Cedric Christian; Wilmes, Paul

Poster (2018, August)

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See detailFractalis: A scalable open-source service for platform-independent interactive visual analysis of biomedical data
Herzinger, Sascha; Groues, Valentin; Gu, Wei; Satagopam, Venkata; Banda, Peter; Trefois, Christophe; Schneider, Reinhard

in GigaScience (2018)

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See detailThe Luxembourg Parkinson’s Study: A Comprehensive Approach for Stratification and Early Diagnosis
Hipp Epouse D'amico, Géraldine; Vaillant, Michel; Diederich, Nico J.; Roomp, Kirsten; Satagopam, Venkata; Banda, Peter; Sandt, Estelle; Mommaerts, Kathleen; Schmitz, Sabine; Longhino, Laura; Schweicher, Alexandra; Hanff, Anne-Marie; Nicolai, Béatrice; Kolber, Pierre Luc; Reiter, Dorothea; Pavelka, Lukas; Binck, Sylvia; Pauly, Claire; Geffers, Lars; Betsou, Fay; Gantenbein, Manon; Klucken, Jochen; Gasser, Thomas; Hu, Michele; Balling, Rudi; Krüger, Rejko

in Frontiers in Aging Neuroscience (2018), 10

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See detailMechanisms of Persistence of the Ammonia-Oxidizing Bacteria Nitrosomonas to the Biocide Free Nitrous Acid.
Laloo, Andrew E.; Wei, Justin; Wang, Dongbo; Narayanasamy, Shaman; Vanwonterghem, Inka; Waite, David; Steen, Jason; Kaysen, Anne; Heintz-Buschart, Anna; Wang, Qilin; Schulz, Benjamin; Nouwens, Amanda; Wilmes, Paul; Hugenholtz, Philip; Yuan, Zhiguo; Bond, Philip L.

in Environmental science & technology (2018), 52(9), 5386-5397

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See detailMeasuring soil sustainability via soil resilience.
Ludwig, Marie; Wilmes, Paul; Schrader, Stefan

in The Science of the total environment (2018), 626

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See detailThe RNA Complement of Outer Membrane Vesicles From Salmonella enterica Serovar Typhimurium Under Distinct Culture Conditions
Malabirade, Antoine; Habier, Janine; Heintz-Buschart, Anna; May, Patrick; Godet, Julien; Halder, Rashi; Etheridge, Alton; Galas, David; Wilmes, Paul; Fritz, Joëlle

in Frontiers in Microbiology (2018), 9

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See detailA multi-omic view of invasive genetic elements and their linked prokaryotic population dynamics within a mixed microbial community
Martinez Arbas, Susana; Narayanasamy, Shaman; Herold, Malte; Lebrun, Laura; Hicks, Nathan D.; Price, Lance B.; Gillece, John D.; Schupp, James M.; Laczny, Cedric Christian; Keim, Paul S.; Muller, Emilie E.L.; May, Patrick; Wilmes, Paul

Poster (2018, September 11)

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See detailCritical transitions in microbial communities: mobile genetic elements as drivers of the microbial community dynamics within activated sludge of wastewater treatment
Martinez Arbas, Susana; Narayanasamy, Shaman; Herold, Malte; Lebrun, Laura; Hicks, Nathan D.; Price, Lance B.; Gillece, John D.; Schupp, James M.; Lam, Tony; Laczny, Cedric Christian; Ye, Yuzhen; Keim, Paul S.; Muller, Emilie E.L.; May, Patrick; Wilmes, Paul

Poster (2018, October 19)

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See detailUsing metabolic networks to resolve ecological properties of microbiomes
Muller, Emilie; Faust, Karoline; Widder, Stefanie; Herold, Malte; Martinez Arbas, Susana; Wilmes, Paul

in Current Opinion in Systems Biology (2018)

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See detailThe Gut Microbiota and Hematopoietic Stem Cell Transplantation: Challenges and Potentials.
Noor, Fozia; Kaysen, Anne; Wilmes, Paul; Schneider, Jochen

in Journal of innate immunity (2018)

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See detailMicrobiome-derived Multi-omicBiomarkers for Early-stage Detection and Stratification of Parkinson's Disease
Trezzi, Jean-Pierre; Heintz, Anna; Muller, Emilie; Narayanasamy, Shaman; Jarosz, Yohan; Herold, Malte; Kaysen, Anne; Laczny, Cedric Christian; May, Patrick; Wilmes, Paul

Poster (2018, August)

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See detailMicrobiome-derived Multi-omicBiomarkers for Early-stage Detection and Stratification of Parkinson's Disease
Trezzi, Jean-Pierre; Ramiro Garcia, Javier; Laczny, Cedric Christian; Daujeumont, Annegrät; Halder, Rashi; Lebrun, Laura; Heintz, Anna; Oertel, Wolfgang; Mollenhauer, Brit; Wilmes, Paul

Poster (2018, October)

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See detailBirth mode is associated with earliest strain-conferred gut microbiome functions and immunostimulatory potential
Wampach, Linda; Heintz, Anna; Fritz, Joëlle; Ramiro Garcia, Javier; Habier, Janine; Herold, Malte; Narayanasamy, Shaman; Kaysen, Anne; Hogan, Angela; Bindl, Lutz; Bottu, Jean; Halder, Rashi; Sjöqvist, Conny; May, Patrick; Andersson, Anders; de Beaufort, Carine; Wilmes, Paul

in Nature Communications (2018)

See detailThe ecology of the unseen
Wilmes, Paul

Scientific Conference (2018, October)

See detailThe human microbiome: a systems ecology perspective
Wilmes, Paul

Scientific Conference (2018, June)

See detailMicrobial Systems Ecology for unravelling key functions in situ
Wilmes, Paul

Scientific Conference (2018, April)

See detailMicrobiome: the environment within
Wilmes, Paul

Scientific Conference (2018, December)

See detailMicrobiomes in One Health
Wilmes, Paul

Scientific Conference (2018, May)

See detailLe microbiote et son rôle pour la santé de l’Homme
Wilmes, Paul

Presentation (2018, April)

See detailLe microbiote humain et son impacte sur la santé
Wilmes, Paul

Scientific Conference (2018, October)

See detailMulti-omics approach for microbial communities
Wilmes, Paul

Scientific Conference (2018, March)

See detailSystems ecology of microbiomes
Wilmes, Paul

Scientific Conference (2018, December)

See detailSystems ecology of microbiomes
Wilmes, Paul

Scientific Conference (2018, May)

See detailSystems Ecology of microbiomes: function is key
Wilmes, Paul

Scientific Conference (2018, April)

See detailSystems Ecology of microbiomes: identifying key functions
Wilmes, Paul

Scientific Conference (2018, August)

See detailSystems ecology of the human microbiome
Wilmes, Paul

Scientific Conference (2018)

See detailSystems ecology of the human microbiome
Wilmes, Paul

Scientific Conference (2018, November)

See detailUnderstanding the role of the microbiome in Parkinson’s disease
Wilmes, Paul

Scientific Conference (2018, October)

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See detailResolving host–microbe interactions in the gut: the promise of in vitro models to complement in vivo research
Wilmes, Paul; Calatayud, Marta; Van de Wiele, Tom

in Current Opinion in Microbiology (2018)

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2017

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See detailICoVeR - an interactive visualization tool for verification and refinement of metagenomic bins.
Broeksema, Bertjan; Calusinska, Magdalena; McGee, Fintan; Winter, Klaas; Bongiovanni, Francesco; Goux, Xavier; Wilmes, Paul; Delfosse, Philippe; Ghoniem, Mohammad

in BMC bioinformatics (2017), 18(1), 233

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See detailMulti-omics reveal the lifestyle of the acidophilic, mineral-oxidizing model species Leptospirillum ferriphilum(T).
Christel, Stephan; Herold, Malte; Bellenberg, Soren; El Hajjami, Mohamed; Buetti-Dinh, Antoine; Pivkin, Igor V.; Sand, Wolfgang; Wilmes, Paul; Poetsch, Ansgar; Dopson, Mark

in Applied and environmental microbiology (2017)

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See detailConfronting the catalytic dark matter encoded by sequenced genomes
Ellens, Kenneth W.; Christian, Nils; Satagopam, Venkata; May, Patrick; Linster, Carole

in Nucleic Acids Research (2017), 45(20), 11495-11514

See detailA study of the molecular mechanisms underlying teh response of human colorectal adenomacarcinoma enterocytes to prebiotics and probiotics
Greenhalgh, Kacy; Fritz, Joëlle; Letellier, Elisabeth; Ramiro Garcia, Javier; Halder, Rashi; Frachet Bour, Audrey; Baginska, Joanna; Ternes, Dominik; Jäger, Christian; Haan, Serge; Wilmes, Paul

Poster (2017)

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See detailThe nasal and gut microbiome in Parkinson's disease and idiopathic rapid eye movement sleep behavior disorder.
Heintz, Anna; Pandey, Urvashi; Wicke, Tamara; Sixel-Doring, Friederike; Janzen, Annette; Sittig-Wiegand, Elisabeth; Trenkwalder, Claudia; Oertel, Wolfgang H.; Mollenhauer, Brit; Wilmes, Paul

in Movement disorders : official journal of the Movement Disorder Society (2017)

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See detailIsolation of nucleic acids from low biomass samples: detection and removal of sRNA contaminants
Heintz-Buschart, Anna; Yusuf, Dilmurat; Kaysen, Anne; Etheridge, Alton; Fritz, Joëlle; May, Patrick; de Beaufort, Carine; Upadhyaya, Bimal Babu; Ghosal, Anubrata; Galas, David J.; Wilmes, Paul

E-print/Working paper (2017)

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See detailSmartR: An open-source platform for interactive visual analytics for translational research data.
Herzinger, Sascha; Gu, Wei; Satagopam, Venkata; Eifes, Serge; Rege, Kavita; Barbosa Da Silva, Adriano; Schneider, Reinhard

in Bioinformatics (Oxford, England) (2017)

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See detailIntegrated meta-omic analyses of the gastrointestinal tract microbiome in patients undergoing allogeneic hematopoietic stem cell transplantation.
Kaysen, Anne; Heintz, Anna; Muller, Emilie; Narayanasamy, Shaman; Wampach, Linda; Laczny, Cedric C.; Graf, Norbert; Simon, Arne; Franke, Katharina; Bittenbring, Jörg; Wilmes, Paul; Schneider, Jochen

in Translational Research: the Journal of Laboratory and Clinical Medicine (2017)

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See detailEngineering Solutions for Representative Models of the Gastrointestinal Human-Microbe Interface
Mac Giolla Eain, Marc; Baginska, Joanna; Greenhalgh, Kacy; Fritz, Joëlle; Zenhausern, Frederic; Wilmes, Paul

in Engineering (2017)

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See detailComparative integrated-omic analyses of phage-host interactions within natural and engineered microbial communities
Martinez Arbas, Susana; Narayanasamy, Shaman; Herold, Malte; May, Patrick; Wilmes, Paul

Poster (2017, July 21)

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See detailFirst draft genome sequence of a strain belonging to the Zoogloea genus and its gene expression in situ
Muller, Emilie; Narayanasamy, Shaman; Zeimes, Myriam; Laczny, Cedric Christian; Lebrun, Laura; Herold, Malte; Hicks, Nathan D.; Gillice, John D.; Schupp, James M.; Keim, Paul; Wilmes, Paul

in Standards in Genomic Sciences (2017), 12(64),

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See detailDark Matter in host-microbiome metabolomics: Tackling the unknowns-A review
Peisl, Beatrice Yasmin Loulou; Schymanski, Emma; Wilmes, Paul

in Analytica Chimica Acta (2017)

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See detailNinety-nine de novo assembled genomes from the moose (Alces alces) rumen microbiome provide new insights into microbial plant biomass degradation.
Svartstrom, Olov; Alneberg, Johannes; Terrapon, Nicolas; Lombard, Vincent; de Bruijn, Ino; Malmsten, Jonas; Dalin, Ann-Marie; El Muller, Emilie; Shah, Pranjul; Wilmes, Paul; Henrissat, Bernard; Aspeborg, Henrik; Andersson, Anders F.

in The ISME journal (2017), 11(11), 2538-2551

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See detailFrom meta-genomics to causality: Understanding the role of colon cancer-associated bacteria in colorectal cancer
Ternes, Dominik; Wilmes, Paul; Letellier, Elisabeth; Haan, Serge

Poster (2017, February 05)

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See detailColonization and Succession within the Human Gut Microbiome by Archaea, Bacteria, and Microeukaryotes during the First Year of Life
Wampach, Linda; Heintz, Anna; Hogan, Angela; Muller, Emilie; Narayanasamy, Shaman; Laczny, Cedric Christian; Hugerth, Luisa; Bindl, Lutz; Bottu, Jean; Andersson, Anders; de Beaufort, Carine; Wilmes, Paul

in Frontiers in Microbiology (2017)

See detailForm follows function: integrated multi-omics of the human gut microbiome
Wilmes, Paul

Scientific Conference (2017, September)

See detailFrom integrated multi-omics to microbial systems ecology: quo vadis?
Wilmes, Paul

Scientific Conference (2017, August)

See detailFunction First: Systems Ecology of the Human Gut Microbiome
Wilmes, Paul

Presentation (2017, November)

See detailIntegrated multi-omics for enhanced metaproteomics
Wilmes, Paul

Scientific Conference (2017, October)

See detailLe microbiome humain et son impact sur la santé
Wilmes, Paul

Scientific Conference (2017, October)

See detailSystems ecology of microbial pioneers in the gut
Wilmes, Paul

Presentation (2017, October)

See detailSystems ecology of microbiomes: a new frontier of discovery in microbiology
Wilmes, Paul

Scientific Conference (2017, September)

See detailTowards systems ecology of the human gut microbiome
Wilmes, Paul

Presentation (2017, March)

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2016

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See detailGene Regulatory Network Inference of Immunoresponsive Gene 1 (IRG1) Identifies Interferon Regulatory Factor 1 (IRF1) as Its Transcriptional Regulator in Mammalian Macrophages
Antony, Paul; Tallam, Aravind; Perumal, Thanneer Malai; Jäger, Christian; Fritz, Joëlle; Balling, Rudi; del Sol Mesa, Antonio; Michelucci, Alessandro; Vallar, Laurent

in PLoS ONE (2016)

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See detailA Dietary Fiber-Deprived Gut Microbiota Degrades the Colonic Mucus Barrier and Enhances Pathogen Susceptibility.
Desai, Mahesh S.; Seekatz, Anna M.; Koropatkin, Nicole M.; Kamada, Nobuhiko; Hickey, Christina A.; Wolter, Mathis; Pudlo, Nicholas A.; Kitamoto, Sho; Terrapon, Nicolas; Muller, Arnaud; Young, Vincent B.; Henrissat, Bernard; Wilmes, Paul; Stappenbeck, Thaddeus S.; Nunez, Gabriel; Martens, Eric C.

in Cell (2016), 167(5), 1339-135321

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See detailSources and Functions of Extracellular Small RNAs in Human Circulation.
Fritz, Joëlle; Heintz, Anna; Ghosal, Anubrata; Wampach, Linda; Etheridge, Alton; Galas, David; Wilmes, Paul

in Annual review of nutrition (2016)

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See detailMINERVA—a platform for visualization and curation of molecular interaction networks
Gawron, Piotr; Ostaszewski, Marek; Satagopam, Venkata; Gebel, Stephan; Mazein, Alexander; Kuzma, Michael; Zorzan, Simone; McGee, Fintan; Otjacques, Benoit; Balling, Rudi; Schneider, Reinhard

in NPJ Systems Biology and Applications (2016)

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See detailA study of the molecular mechanisms underlying the response of human colorectal adenomacarcinoma enterocytes to prebiotics and probiotics
Greenhalgh, Kacy; Fritz, Joëlle; Letellier, Elisabeth; Frachet Bour, Audrey; Baginska, Joanna; Shah, Pranjul; Desai, Mahesh; Glaab, Enrico; Jäger, Christian; Haan, Serge; Wilmes, Paul

Poster (2016, June)

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See detailThe human gut microbiome in health: establishment and resilience of microbiota over a lifetime
Greenhalgh, Kacy; Wilmes, Paul; Meyer, Kristen Michelle; Aagaard, Kjersti Michelle

in Environmental Microbiology (2016), 18(7), 21032116

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See detailErratum: Integrated multi-omics of the human gut microbiome in a case study of familial type 1 diabetes.
Heintz, Anna; May, Patrick; Laczny, Cedric C.; Lebrun, Laura; Bellora, Camille; Krishna, Abhimanyu; Wampach, Linda; Schneider, Jochen; Hogan, Angela; Beaufort, Carine De; Wilmes, Paul

in Nature microbiology (2016), 2

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See detailIntegrated multi-omics of the human gut microbiome in a case study of familial type 1 diabetes.
Heintz, Anna; May, Patrick; Laczny, Cedric C.; Lebrun, Laura; Bellora, Camille; Krishna, Abhimanyu; Wampach, Linda; Schneider, Jochen; Hogan, Angela; de Beaufort, Carine; Wilmes, Paul

in Nature microbiology (2016), 2

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See detailIdentification, recovery, and refinement of hitherto undescribed population-level genomes from the human gastrointestinal tract
Laczny, Cedric Christian; Muller, Emilie; Heintz, Anna; Herold, Malte; Lebrun, Laura; Hogan, Angela; May, Patrick; de Beaufort, Carine; Wilmes, Paul

in Frontiers in Microbiology (2016), 7(884),

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See detailGeneration of genome-scale metabolic reconstructions for 773 members of the human gut microbiota
Magnusdottir, Stefania; Heinken, Almut Katrin; Kutt, Laura; Ravcheev, Dmitry; Bauer, Eugen; Noronha, Alberto; Greenhalgh, Kacy; Jäger, Christian; Baginska, Joanna; Wilmes, Paul; Fleming, Ronan MT; Thiele, Ines

in Nature Biotechnology (2016)

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See detailIMP: a pipeline for reproducible referenceindependent integrated metagenomic and metatranscriptomic analyses
Narayanasamy, Shaman; Jarosz, Yohan; Muller, Emilie; Buschart, Anna; Herold, Malte; Kaysen, Anne; Laczny, Cedric Christian; Pinel, Nicolás; May, Patrick; Wilmes, Paul

in Genome Biology (2016), 17

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See detailIntegration and Visualization of Translational Medicine Data for Better Understanding of Human Diseases.
Satagopam, Venkata; Gu, Wei; Eifes, Serge; Gawron, Piotr; Ostaszewski, Marek; Gebel, Stephan; Barbosa-Silva, Adriano; Balling, Rudi; Schneider, Reinhard

in Big data (2016), 4(2), 97-108

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See detailA microfluidics-based in vitro model of the gastrointestinal human-microbe interface.
Shah, Pranjul; Fritz, Joëlle; Glaab, Enrico; Desai, Mahesh S.; Greenhalgh, Kacy; Frachet Bour, Audrey; Niegowska, Magdalena; Estes, Matthew; Jäger, Christian; Seguin-Devaux, Carole; Zenhausern, Frederic; Wilmes, Paul

in Nature communications (2016), 7

See detailFrom integrated omics to microbial systems ecology
Wilmes, Paul

Scientific Conference (2016, December)

See detailIntegration of meta-omics data: approaches and applications
Wilmes, Paul

Scientific Conference (2016, December)

See detailPiecing together the puzzle: integrated omics of microbial consortia
Wilmes, Paul

Scientific Conference (2016, February)

See detailSystems Biology of Microbiomes
Wilmes, Paul

Scientific Conference (2016, September)

See detailSystems ecology of human-microbe interactions
Wilmes, Paul

Scientific Conference (2016, June)

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2015

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See detailConstitutive activation of oncogenic PDGFRalpha-mutant proteins occurring in GIST patients induces receptor mislocalisation and alters PDGFRalpha signalling characteristics.
Bahlawane, Christelle; Eulenfeld, Rene; Wiesinger, Monique; Wang, Jiali; Muller, Arnaud; Girod, Andreas; Nazarov, Petr V.; Felsch, Kathrin; Vallar, Laurent; Sauter, Thomas; Satagopam, Venkata; Haan, Serge

in Cell Communication and Signaling (2015), 13

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See detailPhenotypic differentiation of gastrointestinal microbes is reflected in their encoded metabolic repertoires
Bauer, Eugen; Laczny, Cedric Christian; Magnusdottir, Stefania; Wilmes, Paul; Thiele, Ines

in Microbiome (2015), 3(55), 1-13

See detailIntegrated omics analyses of the human gut microbiome in a multiplex family study of type 1 diabetes mellitus.
Buschart, Anna; May, Patrick; Laczny, Cedric Christian; Lebrun, Laura; Wampach, Linda; Hogan, Angela; Schneider, Jochen; de Beaufort, Carine; Wilmes, Paul

Poster (2015, March)

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See detailSystems Biology of Acidophile Biofilms for Efficient Metal Extraction
Christel, Stephan; Dopson, Mark; Vera, Mario; Sand, Wolfgang; Herold, Malte; Wilmes, Paul; Buetti-Dinh, Antoine; Pivkin, Igor; Poetsch, Ansgar; Nygren, Jan; Kubista, Mikael

in Advanced Materials Research (2015), 1130

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See detailThe extracellular RNA complement of Escherichia coli
Ghosal, Anubrata; Upadhyaya, Bimal Babu; Fritz, Joëlle; Heintz, Anna; Desai, Mahesh; Dilimulati, Yusufujiangaili; Huang, David; Baumuratov, Aidos; Wang, Kai; Galas, David J.; Wilmes, Paul

in MicrobiologyOpen (2015)

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See detailThe oncogenic FIP1L1-PDGFRalpha fusion protein displays skewed signaling properties compared to its wild-type PDGFRalpha counterpart.
Haan, Serge; Bahlawane, Christelle; Wang, Jiali; Nazarov, Petr V.; Muller, Arnaud; Eulenfeld, Rene; Haan, Claude; Rolvering, Catherine; Vallar, Laurent; Satagopam, Venkata; Sauter, Thomas; Wiesinger, Monique

in JAK-STAT (2015), 4(1), 1062596

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See detailsiRNA screen identifies QPCT as a druggable target for Huntington's disease.
Jimenez-Sanchez, Maria; Lam, Wun; Hannus, Michael; Sonnichsen, Birte; Imarisio, Sara; Fleming, Angeleen; Tarditi, Alessia; Menzies, Fiona; Ed Dami, Teresa; Xu, Catherine; Gonzalez-Couto, Eduardo; Lazzeroni, Giulia; Heitz, Freddy; Diamanti, Daniela; Massai, Luisa; Satagopam, Venkata; Marconi, Guido; Caramelli, Chiara; Nencini, Arianna; Andreini, Matteo; Sardone, Gian Luca; Caradonna, Nicola P.; Porcari, Valentina; Scali, Carla; Schneider, Reinhard; Pollio, Giuseppe; O'Kane, Cahir J.; Caricasole, Andrea; Rubinsztein, David C.

in Nature chemical biology (2015), 11(5), 347354

See detailDynamic change of host gastrointestinal microbiome and immune status in relation to mucosal barrier effects during chemotherapy and immune ablative intervention in humans.
Kaysen, Anne; Buschart, Anna; May, Patrick; Laczny, Cedric Christian; Narayanasamy, Shaman; Graf, N; Simon, A; Bittenbring, J; Kreis, Stephanie; Schneider, Jochen; Wilmes, Paul

Poster (2015, June)

See detailChanges in the human gastrointestinal microbiome during cancer treatments
Kaysen, Anne; Heintz, Anna; Lebrun, Laura; Graf, N; Simon, A; Bittenbring, J; Kreis, Stephanie; Schneider, Jochen; Wilmes, Paul

Poster (2015, March)

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See detailVizBin - an application for reference-independent visualization and human-augmented binning of metagenomic data
Laczny, Cedric Christian; Sternal, Tomasz; Plugaru, Valentin; Gawron, Piotr; Atashpendar, Arash; Margossian, Houry Hera; Coronado, Sergio; van der Maaten, Laurens; Vlassis, Nikos; Wilmes, Paul

in Microbiome (2015)

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See detailMethod optimization for fecal sample collection and fecal DNA extraction.
Mathay, Conny; Hamot, Gael; Henry, Estelle; Georges, Laura; Bellora, Camille; Lebrun, Laura; de Witt, Brian; Ammerlaan, Wim; Buschart, Anna; Wilmes, Paul; Betsou, Fay

in Biopreservation and biobanking (2015), 13(2), 79-93

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See detailIntegrated omics for the identification of key functionalities in biological wastewater treatment microbial communities
Narayanasamy, Shaman; Muller, Emilie; Sheik, Abdul; Wilmes, Paul

in Microbial Biotechnology (2015)

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See detailA draft network of ligand–receptor-mediated multicellular signalling in human
Ramilowski, Jordan; Goldberg, Tatyana; Harshbarger, Jayson; Kloppman, Edda; Lizio, Marina; Satagopam, Venkata; Itoh, Masayoshi; Kawaji, Hideya; Carninci; Rost, Burkhard; Forrest, Alistair

in Nature Communications (2015), 6

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See detailComparative integrated omics: identification of key functionalities in microbial community-wide metabolic networks
Roume, Hugo; Buschart, Anna; Muller, Emilie; May, Patrick; Satagopam, Venkata; Laczny, Cedric Christian; Narayanasamy, Shaman; Lebrun, Laura; Hoopmann, Michael; Schupp, James; Gillece, John; Hicks, Nathan; Engelthaler, David; Sauter, Thomas; Keim, Paul; Moritz, Robert; Wilmes, Paul

in Biofilms and Microbiomes (2015), 1(15007),

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See detailIn situ phenotypic heterogeneity among single cells of the filamentous bacterium Candidatus Microthrix parvicella
Sheik, Abdul; Muller, Emilie; Audinot, Jean-Nicolas; Lebrun, Laura; Grysan, Patrick; Guignard, Cédric; Wilmes, Paul

in ISME Journal (The) (2015)

See detailEarly dynamics of the gastrointestinal microbiome in infants at risk of metabolic disease in adulthood
Wampach, Linda; Buschart, Anna; Hogan, Angela; Bindl, Lutz; Bottu, Jean; Schneider, Jochen; de Beaufort, Carine; Wilmes, Paul

Poster (2015, March)

See detailEarly dynamics of the gastrointestinal microbiome in infants at risk of metabolic disease in adulthood.
Wampach, Linda; Buschart, Anna; Hogan, Angela; Bindl, Lutz; Bottu, Jean; Schneider, Jochen; de Beaufort, Carine; Wilmes, Paul

Poster (2015, June)

See detailEco-Systems Biology of Natural Microbial Communities
Wilmes, Paul

Scientific Conference (2015, June)

See detailFrom integrated omics to causality: how to close the loop
Wilmes, Paul

Scientific Conference (2015, September)

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See detailA decade of metaproteomics: where we stand and what the future holds
Wilmes, Paul; Heintz, Anna; Bond, Philip

in Proteomics (2015)

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2014

See detailA 16S rRNA gene Illumina–based barcoded assay design for high throughput characterisation of microbial communities from anaerobic digesters
Calusinska, Magdalena; Goux, Xavier; Muller, Emilie; Wilmes, Paul; Delfosse, Philippe

Poster (2014)

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See detailThe HIV Mutation Browser: A Resource for Human Immunodeficiency Virus Mutagenesis and Polymorphism Data
Davey, Norman E.; Satagopam, Venkata; Santiago-Mozos, Salvador; Villacorta-Martin, Carlos; Bharat, Tanya A.M.; Schneider, Reinhard; Briggs, John A.G.

in PLoS Computational Biology (2014)

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See detailIntegrating Pathways of Parkinson's Disease in a Molecular Interaction Map
Fujita, Kazuhiro A.; Ostaszewski, Marek; Matsuoka, Yukiko; Ghosh, Samik; Glaab, Enrico; Trefois, Christophe; Crespo, Isaac; Perumal, Thanneer Malai; Jurkowski, Wiktor; Antony, Paul; Diederich, Nico; Buttini, Manuel; Kodama, Akihiko; Satagopam, Venkata; Eifes, Serge; del Sol Mesa, Antonio; Schneider, Reinhard; Kitano, Hiroaki; Balling, Rudi

in Molecular Neurobiology (2014)

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See detailRNA in circulation: sources and functions of extracellular exogenous RNA in blood
Galas, David J.; Wilmes, Paul; Wang, Kai

in Nelson, Karen (Ed.) Encyclopedia of Metagenomics (2014)

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See detailGenes of the N-methylglutamate pathway are essential for growth of Methylobacterium extorquens DM4 with monomethylamine
Gruffaz; Muller, Emilie; Yousra, Louhichi-Jelail; Yella, Nelli; Gilles, Guichard; Bringel, Françoise

in Applied and Environmental Microbiology (2014), 80(11),

See detailIntegrated Omic Analyses of the Human Gut Microbiome in a Multiplex Family Study of Type 1 Diabetes Mellitus
Heintz, Anna; May, Patrick; Laczny, Cedric Christian; Lebrun, Laura; Wampach, Linda; Hogan, Angela; Schneider, Jochen; Wilmes, Paul; De Beaufort, Carine

Poster (2014, April 30)

See detailCharacterization of the gastrointestinal microbiome in patients with REM-sleep behaviour disorder and newly diagnosed Parkinson’s disease
Heintz, Anna; Muller, Emilie; Lange, Bettina; Mollenhauer, Brit; Oertel, Wolfgang; Wilmes, Paul

Scientific Conference (2014, October)

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See detailSystematic Design of 18S rRNA Gene Primers for Determining Eukaryotic Diversity in Microbial Consortia
Hugerth, Luisa; Muller, Emilie; Hu, Yue; Lebrun, Laura; Roume, Hugo; Lundin, Daniel; Wilmes, Paul; Andersson, Anders

in PLoS ONE (2014)

See detailDynamic change of host gastrointestinal microbiome and immune status in relation to mucosal barrier effects during chemotherapy and immune ablative intervention in humans
Kaysen, Anne; Heintz, Anna; Lebrun, Laura; Graf, Norbert; Simon, Arne; Bittenbring, Jörg; Kreis, Stephanie; Schneider, Jochen; Wilmes, Paul

Poster (2014, April)

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See detailIdentification of condition-specific microbial populations from human metagenomic data
Laczny, Cedric Christian; May, Patrick; Vlassis, Nikos; Wilmes, Paul

Poster (2014, March)

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See detailAlignment-free Visualization of Metagenomic Data by Nonlinear Dimension Reduction
Laczny, Cedric Christian; Pinel, Nicolás; Vlassis, Nikos; Wilmes, Paul

in Scientific Reports (2014)

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See detailTowards the Identification of Condition-Specific Microbial Populations from Human Metagenomic Data
Laczny, Cedric Christian; Wilmes, Paul

in Keller, Andreas; Meese, Eckart (Eds.) Nucleic Acids as Molecular Diagnostics (2014)

See detailThe sequential isolation of metabolites, RNA, DNA, and proteins from a single, undivided mixed microbial community sample
Muller, Emilie; Buschart, Anna; Roume, Hugo; Lebrun, Laura; Wilmes, Paul

in Protocol Exchange (2014)

See detailCommunity integrated omics links the dominance of a microbial generalist to fine-tuned resource usage
Muller, Emilie; Pinel, Nicolás; Laczny, Cedric Christian; Hoopmann, Michael; Lebrun, Laura; Roume, Hugo; May, Patrick; Hicks, Nathan; Liu, Cindy; Price, Lance; Gillece, John; Guignard, Cédric; Schupp, James; Vlassis, Nikos; Moritz, Robert; Baliga, Nitin; Keim, Paul; Wilmes, Paul

Poster (2014)

See detailCommunity integrated omics links the dominance of a microbial generalist to fine-tuned resource usage
Muller, Emilie; Pinel, Nicolás; Laczny, Cedric Christian; Hoopmann, Michael; Lebrun, Laura; Roume, Hugo; May, Patrick; Hicks, Nathan; Liu, Cindy; Price, Lance; Gillece, John; Guignard, Cédric; Schupp, James; Vlassis, Nikos; Moritz, Robert; Baliga, Nitin; Keim, Paul; Wilmes, Paul

Scientific Conference (2014)

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See detailCommunity-integrated omics links dominance of a microbial generalist to fine-tuned resource usage
Muller, Emilie; Pinel, Nicolas; Laczny, Cedric Christian; Hoopmann, Michael; Narayanasamy, Shaman; Lebrun, Laura; Roume, Hugo; Lin, Jake; May, Patrick; Hicks, Nathan; Buschart, Anna; Wampach, Linda; Liu, Cindy; Price, Lance; Gillece, John; Guignard, Cédric; Schupp, James; Vlassis, Nikos; Baliga; Moritz, Robert; Keim, Paul; Wilmes, Paul

in Nature Communications (2014)

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See detailLipid-based biofuel production from wastewater
Muller, Emilie; Sheik, Abdul; Wilmes, Paul

in Current Opinion in Biotechnology (2014), 30

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See detailMEMBRANE ASSEMBLY
Shah, Pranjul; Wilmes, Paul

Patent (2014)

See detailBet-hedging strategy for substrate usage among single cells of Candidatus Microthrix parvicella?
Sheik, Abdul; Muller, Emilie; Audinot, Jean-Nicolas; Lebrun, Laura; Grysan, Patrick; Wilmes, Paul

Scientific Conference (2014, September 29)

See detailIn situ single-cell investigations of substrate utilisation by Candidatus Microthrix parvicella
Sheik, Abdul; Muller, Emilie; Audinot, Jean-Nicolas; Lebrun, Laura; Grysan, Patrick; Wilmes, Paul

Poster (2014, October 16)

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See detailA hundred years of activated sludge: time for a rethink
Sheik, Abdul; Muller, Emilie; Wilmes, Paul

in Frontiers in Microbiology (2014), 5(47), 1-7

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See detailReproducible Research Results R3
Trefois, Christophe; Jarosz, Yohan; Gu, Wei; Satagopam, Venkata; Coronado, Sergio; Schneider, Reinhard

Poster (2014, December)

See detailEco-Systems Biology of Natural Microbial Communities
Wilmes, Paul

Scientific Conference (2014, June)

See detailFrom integrated omics towards Eco-Systems Biology
Wilmes, Paul

Presentation (2014, November)

See detailIntegrated omics of microbial communities
Wilmes, Paul

Presentation (2014, May)

See detailMetaproteomics for a functional insight to activated sludge
Wilmes, Paul

Scientific Conference (2014, April)

See detailHuMiX: A MICROFLUIDICS-BASED IN VITRO CO-CULTURE DEVICE FOR INVESTIGATING HOST-MICROBE INTERACTIONS
Wilmes, Paul; estes, matt; zenhausern, frederic; Fritz, Joëlle; Shah, Pranjul

Scientific Conference (2014, October 30)

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2013

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See detailTreg induction by a rationally selected mixture of Clostridia strains from the human microbiota
Atarshi, Koji; Tanoue, Takeshi; Oshima, Kenshiro; Suda, Wataru; Nagano, Yuji; Nishikawa, Hiroyoshi; Fukuda, Shinji; Saito, Takuro; Narushima, Seiko; Hase, Koji; Kim, Sangwan; Fritz, Joëlle; Wilmes, Paul; Ueha, Satoshi; Matsushima, Kouji; Ohno, Hiroshi; Olle, Bernat; Sakaguchi, Shimon; Taniguchi, Tadtsugu; Morita, Hidetoshi; Hattori, Masahira; Honda, Kenya

in Nature (2013), 500

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See detailGenome-wide identification and functional analyses of microRNA signatures associated with cancer pain.
Bali, Kiran Kumar; Selvaraj, Deepitha; Satagopam, Venkata; Lu, Jianning; Schneider, Reinhard; Kuner, Rohini

in EMBO Molecular Medicine (2013), 5(11), 1740-58

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See detailTranscriptional mechanisms underlying sensitization of peripheral sensory neurons by Granulocyte-/Granulocyte-macrophage colony stimulating factors.
Bali, Kiran Kumar; Venkataramani, Varun; Satagopam, Venkata; Gupta, Pooja; Schneider, Reinhard; Kuner, Rohini

in Molecular pain (2013), 9(1), 48

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See detailSignaling in Insulin-Secreting MIN6 Pseudoislets and Monolayer Cells.
Chowdhury, Azazul; Satagopam, Venkata; Manukyan, Levon; Artemenko, Konstantin A.; Fung, Yi Man Eva; Schneider, Reinhard; Bergquist, Jonas; Bergsten, Peter

in Journal of proteome research (2013)

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See detailThe Young PI Buzz: Learning from the Organizers of the Junior Principal Investigator Meeting at ISMB-ECCB 2013.
de Ridder, Jeroen; Bromberg, Yana; Michaut, Magali; Satagopam, Venkata; Corpas, Manuel; Macintyre, Geoff; Alexandrov, Theodore

in PLoS computational biology (2013), 9(11), 1003350

See detailThe exogenous RNA spectrum in human plasma and the gastrointestinal tract
Dilimulati, Yusufujiangaili; Heintz, Anna; Ghosal, Anubrata; Upadhyaya, Bimal Babu; Fritz, Joëlle; Laczny, Cedric Christian; May, Patrick; Muller, Emilie; Shah, Pranjul; Desai, Mahesh; Roume, Hugo; Huang, D; Wang, K; Galas, David J.; Wilmes, Paul

Poster (2013, October)

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See detailFrom meta-omics to causality: experimental models for human microbiome research
Fritz, Joëlle; Desai, Mahesh; Shah, Pranjul; Schneider, Jochen; Wilmes, Paul

in Microbiome (2013), 1(14),

See detailMeta-omic Analyses of the Microbiome in a Family Study of Diabetes Mellitus
Heintz, Anna; May, Patrick; Lebrun, Laura; Ferrand, J; Trezzi, Jean-Pierre; Collignon, S; Wampach, Linda; Glaab, Enrico; Laczny, Cedric Christian; Martins Conde, Patricia; Kaysen, Anne; Schneider, Jochen; Hiller, Karsten; Hogan, Angela; Wilmes, Paul; de Beaufort, Carine

Poster (2013, October)

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See detailReproducibility: In praise of open research measures
Kolker, Eugene; Altintas, Ilkay; Bourne, Philip; Faris, Jack; Fox, Geoffrey; Fishman, Dmitrij; Geraci, Christy; Hancock, William; Lin, Biaoyang; Lancet, Doron; Lisitsa, Andrey; Knight, Rob; Martens, Lennart; Mesirov, Jill; Özdemir, Vural; Schultes, Eric; Smith, Todd; Snyder, Michael; Srivastava, Sanjeeva; Toppo, Stefano; Wilmes, Paul

in Nature (2013), 498

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See detailCondensing the omics fog of microbial communities
Muller, Emilie; Glaab, Enrico; May, Patrick; Vlassis, Nikos; Wilmes, Paul

in Trends in Microbiology (2013), 21(7), 325333

See detailSystematic molecular measurements reveal key microbial populations driving community-wide phenotype
Muller, Emilie; Pinel, Nicolás; May, Patrick; Hussong, René; Roume, Hugo; Lebrun, Laura; liu, Cindy; Aziz, Maliha; Price, Lance; Moritz, Robert; Schupp, James; Keim, Paul; Wilmes, Paul

Poster (2013)

See detailLinking mixed microbial community phenotype to individual genotypes
Muller, Emilie; Pinel, Nicolás; May, Patrick; Roume, Hugo; Wilmes, Paul

Poster (2013)

See detailA model microbial community for Eco-Systems Biology
Muller, Emilie; Roume, Hugo; Buschart, Anna; Pinel, Nicolas; Laczny, Cedric Christian; Satagopam, Venkata; May, Patrick; Lebrun, Laura; Wilmes, Paul

Poster (2013)

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See detailThe Parkinson's Disease Map: A Framework for Integration, Curation and Exploration of Disease-related Pathways
Ostaszewski, Marek; Fujita, Kazuhiro; Matsuoka, Yukiko; Ghosh, Samik; Glaab, Enrico; Trefois, Christophe; Crespo, Isaac; Perumal, Thanneer Malai; Jurkowski, Wiktor; Antony, Paul; Diederich, Nico; Buttini, Manuel; Kolodkin, Alexey; Kodama, Akihiko; Satagopam, Venkata; Biryukov, Maria; Eifes, Serge; del Sol Mesa, Antonio; Schneider, Reinhard; Kitano, Hiroaki; Balling, Rudi

Poster (2013, March 09)

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See detailOnTheFly 2.0: a tool for automatic annotation of files and biological information extraction.
Pafilis, Evangelos; Pavlopoulos, Georgios; Satagopam, Venkata; Papanikolaou, Nikolas; Horn, Heiko; Arvanitidis, Christos; Jensen, Lars Juhl; Schneider, Reinhard; Iliopoulos, Ioannis

Poster (2013)

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See detailSequential isolation of metabolites, RNA, DNA, and proteins from the same unique sample
Roume, Hugo; Heintz-Buschart, Anna; Muller, Emilie; Wilmes, Paul

in Methods in Enzymology (2013), 531

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See detailA biomolecular isolation framework for eco-systems biology
Roume, Hugo; Muller, Emilie; Cordes, Thekla; Renaut, Jenny; Hiller, Karsten; Wilmes, Paul

in ISME Journal (The) (2013), 7(1), 110-121

See detailIntegrated omics highlights keystone genes in community-wide metabolic networks
Roume, Hugo; Satagopam, Venkata; Muller, Emilie; May, Patrick; Hussong, René; Wilmes, Paul

Poster (2013)

See detailIntegrated omics highlights keystone genes in community-wide metabolic networks
Roume, Hugo; Satagopam, Venkata; Muller, Emilie; May, Patrick; Hussong, René; Wilmes, Paul

Poster (2013)

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See detailMEMBRANE ASSEMBLY
Shah, Pranjul; Wilmes, Paul

Patent (2013)

See detailFrom single-cell to global flux: NanoSIMS approach in microbial ecology
Sheik, Abdul

Scientific Conference (2013, October)

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See detailNuclear calcium signaling in spinal neurons drives a genomic program required for persistent inflammatory pain
Simonetti, Manuela; Hagenston, Anna; Vardeh, Daniel; Freitag, Eckehard; Mauceri, Daniela; Lu, Jianning; Satagopam, Venkata; Schneider, Reinhard; Costigan, Michael; Bading, Hilmar; Kuner, Rohini

in Neuron (2013), 77(1), 43-57

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See detailMicrobiome and type 1 diabetes
Wampach, Linda; Wilmes, Paul; De Beaufort, Carine

E-print/Working paper (2013)

See detailMicrobiome-derived small RNA in human circulation
Wilmes, Paul

Scientific Conference (2013, June)

See detailCell culture apparatus and culture methods using same
Wilmes, Paul; Zenhausern, Frederic; Estes, Matt; Shah, Pranjul

Patent (2013)

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2012

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See detailDeuterium-exchange metabolomics identifies N-methyl lyso phosphatidylethanolamines as abundant lipids in acidophilic mixed microbial communities
Fischer, C.R.; Wilmes, Paul; Bowen, B. P.; Northen, T. R.; Banfield, J. F.

in Metabolomics : Official journal of the Metabolomic Society (2012), 8(4), 566-578

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See detailGenome Sequence of "Candidatus Microthrix parvicella" Bio17-1, a Long-Chain-Fatty-Acid-Accumulating Filamentous Actinobacterium from a Biological Wastewater Treatment Plant
Muller, Emilie; Pinel, Nicolás; Gillece, John D.; Schupp, James M.; Price, Lance B.; Engelthaler, David M.; Levantesi, Caterina; Tandoi, Valter; Luong, Kkai; Baliga, Nitin S.; Korlach, Jonas; Keim, Paul S.; Wilmes, Paul

in Journal of Bacteriology (2012), 194(23), 6670-6671

See detailA Biomolecular Isolation Framework for Molecular Eco-Systems Biology
Muller, Emilie; Roume, Hugo; Shah, Pranjul; Wilmes, Paul

Poster (2012)

See detailFrom gut to sludge: Molecular Eco-Systems Biology of Microbial Consortia
Muller, Emilie; Wilmes, Paul

Scientific Conference (2012)

See detailA biomolecular isolation framework for eco-systems biology
Roume, Hugo; Muller, Emilie; Cordes, Thekla; Hiller, Karsten; Wilmes, Paul

Poster (2012)

See detailEffect of viruses on bacterial community structure and single-cell carbon and nitrogen assimilation
Sheik, Abdul; Corina; Phyllis, Lam; Gaute, Lavik; Kupyers, Marcel

Poster (2012)

See detailConstructing a comprehensive map of Parkinson’s disease to elucidate underlying mechanisms of its multifaceted molecular pathology
Trefois, Christophe; Fujita, A. K.; Ostaszewski, Marek; Matsuoka, Yukiko; Ghosh, Samic; Glaab, Enrico; Crespo, Isaac; Perumal, T. M.; Jurkowski, Wiktor; Antony, Paul; Diederich, Nico; Buttini, Manuel; Kodama, Akihiko; Satagopam, Venkata; Eifes, Serge; del Sol Mesa, Antonio; Schneider, Reinhard; Kitano, Hiroaki; Balling, Rudi

Poster (2012, August)

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See detailThe complex exogenous RNA spectra in human plasma: an interface with human gut biota?
Wang, K.; Li, H.; Yuan, Y.; Etheridge, A.; Zhou, Y.; Huang, D.; Wilmes, Paul; Galas, David J.

in PLoS ONE (2012), 7(12),

See detailEco-Systems Biology of natural microbial communities
Wilmes, Paul

Scientific Conference (2012, October)

See detailEco-Systems Biology of the Human Microbiome
Wilmes, Paul

Scientific Conference (2012, November)

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See detailGenome-based and functional differentiation: hallmarks of microbial adaptation, divergence and speciation?
Wilmes, Paul

in Ogilvie, L.A.; Hirsch, P.R (Eds.) Microbial Ecological Theory: Current Perspectives (2012)

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2011

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See detailCorrelative microscopy for phylogenetic and ultrastructural characterization of microbial communities
Knierim, B.; Luef, B.; Wilmes, Paul; Webb, R. I.; Auer, Manfred; Comolli, L. R.; Banfield, J. F.

in Environmental Microbiology Reports (2011)

See detailEco-Systems Biology of Natural Lipid-Accumulating Microbial Communities
Muller, Emilie; Roume, Hugo; Lebrun, Laura; Wilmes, Paul

Poster (2011, September 27)

See detailIsolation of biomolecules from a single sample: the first step towards integrated omic analyses
Roume, Hugo; Muller, Emilie; Cordes, Thekla; Hiller, Karsten; Wilmes, Paul

Poster (2011)

See detailViruses and the microbial loop: A single cell approach
Sheik, Abdul; Brussaard, Corina; Lam, Phyllis; Lavik, Gaute; Kuypers, Marcel

Scientific Conference (2011)

See detailCapturing the Structure and Dynamics of Complex Microbial Communities
Wilmes, Paul

Scientific Conference (2011, January)

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See detailMicrobial community proteomics
Wilmes, Paul

in de Bruijn, Frans (Ed.) Handbook of Molecular Microbial Ecology I: Metagenomics and Complementary Approaches (2011)

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See detailA Semi-Quantitative, Synteny-Based Method to Improve Functional Predictions for Hypothetical and Poorly Annotated Bacterial and Archaeal Genes
Yelton, Alexis P.; Thomas, Brian C.; Simmons, Sheri L.; Wilmes, Paul; Zemla, Adam; Thelen, Michael P.; Justice, Nicholas; Banfield, Jillian F.

in PLoS Computational Biology (2011), 7(10), 1002230

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2010

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See detailProteogenomic basis for ecological divergence of closely related bacteria in natural acidophilic microbial communities
Denef, Vincent J.; Kalnejais, Linda H.; Mueller, Ryan S.; Wilmes, Paul; Baker, Brett J.; Thomas, Brian C.; VerBerkmoes, Nathan C.; Hettich, Robert L.; Banfield, Jillian F.

in Proceedings of the National Academy of Sciences of the United States of America (2010), 107(6), 2383-2390

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See detailCharacterization of Extracellular Polymeric Substances from Acidophilic Microbial Biofilms
Jiao, Yongqin; Cody, George D.; Harding, Anna K.; Wilmes, Paul; Schrenk, Matthew; Wheeler, Korin E.; Banfield, Jillian F.; Thelen, Michael P.

in Applied and Environmental Microbiology (2010), 76(9), 2916-2922

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See detailDefective Lamin A-Rb Signaling in Hutchinson-Gilford Progeria Syndrome and Reversal by Farnesyltransferase Inhibition
Marji, Jackleen; O'Donoghue, Sean I.; McClintock, Dayle; Satagopam, Venkata; Schneider, Reinhard; Ratner, Desiree; Worman, Howard J.; Gordon, Leslie B.; Djabali, Karima

in PLoS ONE (2010), 5(6),

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See detailEcological distribution and population physiology defined by proteomics in a natural microbial community
Mueller, Ryan S.; Denef, Vincent J.; Kalnejais, Linda H.; Suttle, K. Blake; Thomas, Brian C.; Wilmes, Paul; Smith, Richard L.; Nordstrom, D. Kirk; McCleskey, R. Blaine; Shah, Manesh B.; VerBerkmoes, Nathan C.; Hettich, Robert L.; Banfield, Jillian F.

in Molecular Systems Biology (2010), 6

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See detailPhenotypic profiling of the human genome by time-lapse microscopy reveals cell division genes
Neumann, Beate; Walter, Thomas; Heriche, Jean-Karim; Bulkescher, Jutta; Erfle, Holger; Conrad, Christian; Rogers, Phill; Poser, Ina; Held, Michael; Liebel, Urban; Cetin, Cihan; Sieckmann, Frank; Pau, Gregoire; Kabbe, Rolf; Wuensche, Annelie; Satagopam, Venkata; Schmitz, Michael H. A.; Chapuis, Catherine; Gerlich, Daniel W.; Schneider, Reinhard; Eils, Roland; Huber, Wolfgang; Peters, Jan-Michael; Hyman, Anthony A.; Durbin, Richard; Pepperkok, Rainer; Ellenberg, Jan

in Nature (2010), 464(7289), 721-727

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See detailReflect: A practical approach to web semantics
O'Donoghue, Sean I.; Horn, Heiko; Pafilis, Evangelos; Haag, Sven; Kuhn, Michael; Satagopam, Venkata; Schneider, Reinhard; Jensen, Lars J.

in Journal of Web Semantics (2010), 8(2-3), 182-189

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See detailGPCRs, G-proteins, Effectors and their interactions: Human-gpDB, a database employing advanced visualization tools and data integration techniques
Satagopam, Venkata; Theodoropoulou, Margarita C.; Christos, Stampolakis K.; Pavlopoulos, Georgios A.; Papandreou, Nikolaos C.; Bagos, Pantelis G.; Schneider, Reinhard; Hamodrakas, Stavros J.

in Database: the Journal of Biological Databases and Curation (2010)

See detailThe effect of viruses on phytoplankton and prokaryotic nutrient assimilation: A single cell approach
Sheik, Abdul; Brussaard, Corina; Lavik, Gaute; Musat, Niculina; Kuypers, Marcel

Poster (2010)

See detailEco-systems biology: a new frontier in microbiology
Wilmes, Paul

Scientific Conference (2010, October)

See detailMetabolome-proteome differentiation reflects bacterial divergence
Wilmes, Paul

Scientific Conference (2010, March)

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See detailMetabolome-Proteome Differentiation Coupled to Microbial Divergence
Wilmes, Paul; Bowen, Benjamin P.; Thomas, Brian C.; Mueller, Ryan S.; Denef, Vincent J.; VerBerkmoes, Nathan C.; Hettich, Robert L.; Northen, Trent R.; Banfield, Jillian F.

in mBio (2010), 1(5), 00246-10

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2009

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See detailMicrobial community proteomics: elucidating the catalysts and metabolic mechanisms that drive the Earth's biogeochemical cycles
Wilmes, Paul; Bond, Philip L.

in Current Opinion in Microbiology (2009), 12(3), 310-317

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See detailNatural acidophilic biofilm communities reflect distinct organismal and functional organization
Wilmes, Paul; Remis, Jonathan P.; Hwang, Mona; Auer, Manfred; Thelen, Michael P.; Banfield, Jillian F.

in ISME Journal (The) (2009), 3(2), 266-270

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See detailThe dynamic genetic repertoire of microbial communities
Wilmes, Paul; Simmons, Sheri; Denef, Vincent J.; Banfield, Jillian F.

in FEMS Microbiology Reviews (2009), 33(1), 109-132

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