Paul Wilmes

Associate professor / Chief scientist 2 in Systems Ecology

Faculté ou Centre Luxembourg Centre for Systems Biomedicine
Unité de recherche LCSB
Adresse postale Campus Belval, Université du Luxembourg
7, Avenue des Hauts Fourneaux
L-4362 Esch-sur-Alzette
Bureau sur le campus BioTech I, 4.11
E-mail
Téléphone (+352) 46 66 44 6188
Video Dr. Paul Wilmes (LCSB)
Dr. Paul Wilmes (LCSB)
 
Dr. Paul Wilmes (LCSB)

Paul Wilmes is Associate Professor of Systems Ecology at the Luxembourg Centre for Systems Biomedicine (LCSB) of the University of Luxembourg, where he is Deputy Head of the Systems Biomedicine Department and Head of the Eco-Systems Biology research group (Wilmes Lab). Paul obtained his PhD in 2006 from the School of Environmental Sciences at the University of East Anglia in Norwich (UK), a part of his doctoral research having been conducted at the Max Planck Institute for Marine Microbiology in Bremen (Germany). After three years of postdoctoral research at the University of California, Berkeley (USA), he returned to his native Luxembourg in early 2010 through an ATTRACT Fellowship of the Luxembourg National Research Fund (FNR). He initially established his research group at the Centre de Recherche Public – Gabriel Lippmann but later joined the LCSB.

Paul’s main primary research focus is on using Systems Biology approaches to identify key functionalities of microbial communities including human associated microbiota. His group has pioneered appropriate methodologies for carrying out systematic molecular measurements of microbial consortia over space and time. This allows for example to define lifestyle strategies of distinct populations and link these to genetic and functional traits. The same approaches allow the study of microbiome-host molecular interactions. In this context, his group has pioneered the development of a microfluidics-based in vitro model of the human-microbial gastrointestinal interface called HuMiX.

Paul has authored more than 80 peer-review publications. He is a frequent invited speaker at international scientific symposia and academic institutions. Paul is a member of several national and international scientific organizations, and he has won several prizes for his scientific work.

FNR ATTRACT Fellows in Biomedicine (Video)

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Last updated on: jeudi 07 février 2019

 

2018 – present

 

 

 

 

 

 

 

 

 

 

 

 

Head of the Integrative Molecular Biomedicine Department, LCSB, University of Luxembourg, Luxembourg

May 2017 – present

 

 

 

 

 

 

 

 

 

 

 

 

Deputy Head of the Systems Biomedicine Department, University of Luxembourg, Luxembourg Centre for Systems Biomedicine, Esch-sur-Alzette, Luxembourg

December 2017 – May 2018

 

 

 

 

 

 

 

 

 

 

 

 

Career break, parental leave

February 2015 – present

 

 

 

 

 

 

 

 

 

 

 

 

Associate Professor; Head of the Eco-Systems Biology research group, University of Luxembourg, Luxembourg

October 2011 – January 2015

 

 

 

 

 

 

 

 

 

 

 

 

Principal investigator, ATTRACT Research Fellow; Head of the Eco-Systems Biology research group, 
University of Luxembourg, Luxembourg

February 2010 – September 2011

 

 

 

 

 

 

 

 

 

 

 

 

Project leader (Luxembourg National Research Fund ATTRACT fellow), Centre de Recherche Public – Gabriel Lippmann, Belvaux, Luxembourg

May 2006 – December 2009

 

 

 

 

 

 

 

 

 

 

 

 

Postdoctoral research scholar; Host: Prof. Dr. Jillian F. Banfield, University of California, Berkeley, USA



Last updated on: 07 fév 2019

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Articles publiés dans des périodiques scientifiques

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

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

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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 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 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)

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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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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 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 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)

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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 detailThe nasal and gut microbiome in Parkinson's disease and idiopathic rapid eye movement sleep behavior disorder.
Heintz-Buschart, 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 detailIntegrated meta-omic analyses of the gastrointestinal tract microbiome in patients undergoing allogeneic hematopoietic stem cell transplantation.
Kaysen, Anne; Heintz-Buschart, 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 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 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 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 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-Buschart, Anna; Ghosal, Anubrata; Wampach, Linda; Etheridge, Alton; Galas, David; Wilmes, Paul

in Annual review of nutrition (2016)

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See detailErratum: Integrated multi-omics of the human gut microbiome in a case study of familial type 1 diabetes.
Heintz-Buschart, 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-Buschart, 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 C.; Muller, Emilie; Heintz-Buschart, 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 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

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

in MicrobiologyOpen (2015)

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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 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

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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 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 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)

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

in Proteomics (2015)

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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 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 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 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)

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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 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 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 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),

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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

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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

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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

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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),

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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)

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See detailMicrobial community proteomics
Wilmes, Paul

in 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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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 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 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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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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See detailCommunity proteogenomics highlights microbial strain-variant protein expression within activated sludge performing enhanced biological phosphorus removal
Wilmes, Paul; Andersson, Anders F.; Lefsrud, Mark G.; Wexler, Margaret; Shah, Manesh; Zhang, Bing; Hettich, Robert L.; Bond, Philip L.; VerBerkmoes, Nathan C.; Banfield, Jillian F.

in ISME Journal (The) (2008), 2(8), 853-864

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See detailMetaproteomics Provides Functional Insight into Activated Sludge Wastewater Treatment
Wilmes, Paul; Wexler, Margaret; Bond, Philip L.

in PLoS ONE (2008), 3(3), 1-2

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See detailMetaproteomics: studying functional gene expression in microbial ecosystems
Wilmes, Paul; Bond, P. L.

in Trends in Microbiology (2006), 14(2), 92-97

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Périodiques Scientifiques – Autres

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)

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Contributions à des ouvrages collectifs

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 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)

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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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E-Prints/Working papers – diffusé en premier sur un site externe

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

E-print/Working paper (2013)

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Contributions à des encyclopédies, dictionnaires...

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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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Brevets

Full Text
See detailMEMBRANE ASSEMBLY
Shah, Pranjul; Wilmes, Paul

Patent (2014)

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See detailMEMBRANE ASSEMBLY
Shah, Pranjul; Wilmes, Paul

Patent (2013)

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

Patent (2013)

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Colloques et congrès scientifiques – Communication orale non publiée

See detailMicrobiome: the environment within
Wilmes, Paul

Scientific Conference (2018, December)

See detailSystems ecology of microbiomes
Wilmes, Paul

Scientific Conference (2018, December)

See detailSystems ecology of the human microbiome
Wilmes, Paul

Scientific Conference (2018, November)

See detailThe ecology of the unseen
Wilmes, Paul

Scientific Conference (2018, October)

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

Scientific Conference (2018, October)

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

Scientific Conference (2018, October)

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

Scientific Conference (2018, August)

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

Scientific Conference (2018, June)

See detailMicrobiomes in One Health
Wilmes, Paul

Scientific Conference (2018, May)

See detailSystems ecology of microbiomes
Wilmes, Paul

Scientific Conference (2018, May)

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

Scientific Conference (2018, April)

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

Scientific Conference (2018, April)

See detailMulti-omics approach for microbial communities
Wilmes, Paul

Scientific Conference (2018, March)

See detailSystems ecology of the human microbiome
Wilmes, Paul

Scientific Conference (2018)

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

Scientific Conference (2017, September)

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

Scientific Conference (2017, September)

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

Scientific Conference (2017, August)

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 detailSystems Biology of Microbiomes
Wilmes, Paul

Scientific Conference (2016, September)

See detailSystems ecology of human-microbe interactions
Wilmes, Paul

Scientific Conference (2016, June)

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

Scientific Conference (2016, February)

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

Scientific Conference (2015, September)

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

Scientific Conference (2015, June)

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)

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)

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 detailEco-Systems Biology of Natural Microbial Communities
Wilmes, Paul

Scientific Conference (2014, June)

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

Scientific Conference (2014, April)

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)

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

Scientific Conference (2013, June)

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

Scientific Conference (2012, November)

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

Scientific Conference (2012, October)

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

Scientific Conference (2012)

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

Scientific Conference (2011, January)

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)

See detailMetaproteomics: studying functional gene expression in microbial ecosystems
Wilmes, Paul

Scientific Conference (2005, September)

See detailThe metaproteome: dynamic function of a complex microbial system
Wilmes, Paul

Scientific Conference (2005, January)

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Colloques et congrès scientifiques – Communication poster

Full Text
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 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 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 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 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 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)

Full Text
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)

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 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 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)

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)

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 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)

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 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-Buschart, Anna; Lebrun, Laura; Graf, Norbert; Simon, Arne; Bittenbring, Jörg; Kreis, Stephanie; Schneider, Jochen; Wilmes, Paul

Poster (2014, April)

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

Poster (2014, March)

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)

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 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)

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)

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)

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)

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

Poster (2012)

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

Poster (2012)

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)

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Présentations scientifiques dans des Universités ou centres de recherche

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

Presentation (2018, April)

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

Presentation (2017, November)

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

Presentation (2017, October)

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

Presentation (2017, March)

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

Presentation (2014, November)

See detailIntegrated omics of microbial communities
Wilmes, Paul

Presentation (2014, May)

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