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Paul Wilmes

Paul Wilmes

Associate professor

Faculty or Centre Luxembourg Centre for Systems Biomedicine
Postal Address Campus Belval, Université du Luxembourg
7, Avenue des Hauts Fourneaux
L-4362 Esch-sur-Alzette
Campus Office BioTech I, 4.11
Email
Telephone (+352) 46 66 44 6188
Video Dr. Paul Wilmes (LCSB)
Dr. Paul Wilmes (LCSB)
 
Dr. Paul Wilmes (LCSB)

Principal Investigator in the Eco-Systems Biology group (Wilmes Lab)

FNR ATTRACT Fellows in Biomedicine (Video)

Last updated on: Tuesday, 27 October 2015

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Articles published in scientific periodicals

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See detailA microfluidics-based in vitro model of the gastrointestinal human-microbe interface.
Shah, Pranjul; Fritz, Joelle V.; Glaab, Enrico; Desai, Mahesh S.; Greenhalgh, Kacy; Frachet, 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, Cédric; 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, Cédric; Magnusdottir, Stefania; Wilmes, Paul; Thiele, Ines

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

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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, Cédric; 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, Cédric; 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, Cédric; 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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Scientific Periodicals – Other

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 to collective works

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See detailTowards the Identification of Condition-Specific Microbial Populations from Human Metagenomic Data
Laczny, Cédric; 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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Contributions to encyclopaedias, dictionaries, …

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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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Scientific congresses, symposiums and conference proceedings – Unpublished conferences

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 detailCommunity integrated omics links the dominance of a microbial generalist to fine-tuned resource usage
Muller, Emilie; Pinel, Nicolás; Laczny, Cédric; 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 detailFrom gut to sludge: Molecular Eco-Systems Biology of Microbial Consortia
Muller, Emilie; Wilmes, Paul

Scientific Conference (2012)

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Scientific congresses, symposiums and conference proceedings – Posters

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, Cédric; 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)

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, Cédric; 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 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, Cédric; 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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Scientific presentations in Universities or research centres

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Patents

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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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E-Prints/Working papers – already available on another site

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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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