Profil

MULLER Emilie

Main Referenced Co-authors
WILMES, Paul  (46)
ROUME, Hugo  (20)
LEBRUN, Laura  (18)
MAY, Patrick  (17)
LACZNY, Cedric Christian  (13)
Main Referenced Keywords
Integrated omics (3); Biomolecular isolation (2); Eco-Systems Biology (2); Microbial communities (2); activated sludge (1);
Main Referenced Unit & Research Centers
Luxembourg Centre for Systems Biomedicine (LCSB): Eco-Systems Biology (Wilmes Group) (18)
Luxembourg Centre for Systems Biomedicine (LCSB): Bioinformatics Core (R. Schneider Group) (5)
Luxembourg Centre for Systems Biomedicine (LCSB): Machine Learning (Vlassis Group) (2)
ULHPC - University of Luxembourg: High Performance Computing (2)
Centre Hospitalier de Luxembourg (1)
Main Referenced Disciplines
Microbiology (43)
Environmental sciences & ecology (32)
Biotechnology (9)
Genetics & genetic processes (7)
Biochemistry, biophysics & molecular biology (4)

Publications (total 47)

The most downloaded
684 downloads
Kaysen, A., Heintz, A., Muller, E., Narayanasamy, S., Wampach, L., Laczny, C. C., Graf, N., Simon, A., Franke, K., Bittenbring, J., Wilmes, P., & Schneider, J. (2017). Integrated meta-omic analyses of the gastrointestinal tract microbiome in patients undergoing allogeneic hematopoietic stem cell transplantation. Translational Research: the Journal of Laboratory and Clinical Medicine. doi:10.1016/j.trsl.2017.06.008 https://hdl.handle.net/10993/32068

The most cited

185 citations (Scopus®)

Wampach, L., Heintz, A., Hogan, A., Muller, E., Narayanasamy, S., Laczny, C. C., Hugerth, L., Bindl, L., Bottu, J., Andersson, A., de Beaufort, C., & Wilmes, P. (2017). Colonization and Succession within the Human Gut Microbiome by Archaea, Bacteria, and Microeukaryotes during the First Year of Life. Frontiers in Microbiology. doi:10.3389/fmicb.2017.00738 https://hdl.handle.net/10993/31318

DELOGU, F., Kunath, B. J., Queirós, P. M., HALDER, R., LEBRUN, L., Pope, P. B., MAY, P., Widder, S., MULLER, E., & WILMES, P. (2023). Forecasting the dynamics of a complex microbial community using integrated meta-omics. Nature Ecology and Evolution. doi:10.1038/s41559-023-02241-3
Peer Reviewed verified by ORBi

Martinez Arbas, S., Busi, S. B., Teixeira Queirós, P., de Nies, L., Herold, M., May, P., Wilmes, P., Muller, E., & Narayanasamy, S. (2021). Challenges, Strategies, and Perspectives for Reference-Independent Longitudinal Multi-Omic Microbiome Studies. Frontiers in Genetics. doi:10.3389/fgene.2021.666244
Peer Reviewed verified by ORBi

Hayoun, K., Geersens, E., Laczny, C. C., Halder, R., Lázaro Sánchez, C., Manna, A., Bringel, F., Ryckelynck, M., Wilmes, P., Muller, E., Alpha-Bazin, A., & Vuilleumier, S. (2020). Dichloromethane Degradation Pathway from Unsequenced Hyphomicrobium sp. MC8b Rapidly Explored by Pan-Proteomics. Microorganisms. doi:10.3390/microorganisms8121876
Peer reviewed

Herold, M., Narayanasamy, S., Martinez Arbas, S., Muller, E., Kleine-Borgmann, A. L., Lebrun, L., Roume, H., Sheik, A., Bessarab, I., Williams, R., Gillece, J., Schupp, J., Keim, P., Jäger, C., Hoopmann, M., Li, S., Tang, H., Heintz, A., May, P., ... Wilmes, P. (August 2018). Integrated time-resolved multi-omics for understanding microbial niche ecology [Poster presentation]. 17th International Symposium on Microbial Ecology, Leipzig, Germany.

Trezzi, J.-P., Heintz, A., Muller, E., Narayanasamy, S., Jarosz, Y., Herold, M., Kaysen, A., Laczny, C. C., May, P., & Wilmes, P. (August 2018). Microbiome-derived Multi-omicBiomarkers for Early-stage Detection and Stratification of Parkinson's Disease [Poster presentation]. 17th International Symposium on Microbial Ecology.

Shah, P., Muller, E., Lebrun, L., Wampach, L., & Wilmes, P. (2018). Sequential Isolation of DNA, RNA, Protein, and Metabolite Fractions from Murine Organs and Intestinal Contents for Integrated Omics of Host-Microbiota Interactions. In Microbial Proteomics. United States: Springer. doi:10.1007/978-1-4939-8695-8_19

Calusinska, M., Goux, X., Fossepre, M., Muller, E., Wilmes, P., & Delfosse, P. (2018). A 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. Biotechnology for Biofuels, 11, 196. doi:10.1186/s13068-018-1195-8
Peer Reviewed verified by ORBi

Chaib De Mares, M., Jimenez, D. J., Palladino, G., Gutleben, J., Lebrun, L., Muller, E., Wilmes, P., Sipkema, D., & van Elsas, J. D. (2018). Expressed protein profile of a Tectomicrobium and other microbial symbionts in the marine sponge Aplysina aerophoba as evidenced by metaproteomics. Scientific Reports, 8 (1), 11795. doi:10.1038/s41598-018-30134-0
Peer Reviewed verified by ORBi

Muller, E., Faust, K., Widder, S., Herold, M., Martinez Arbas, S., & Wilmes, P. (2018). Using metabolic networks to resolve ecological properties of microbiomes. Current Opinion in Systems Biology. doi:10.1016/j.coisb.2017.12.004
Peer reviewed

Muller, E.* , Narayanasamy, S.* , Zeimes, M., Laczny, C. C., Lebrun, L., Herold, M., Hicks, N. D., Gillice, J. D., Schupp, J. M., Keim, P., & Wilmes, P. (18 October 2017). First draft genome sequence of a strain belonging to the Zoogloea genus and its gene expression in situ. Standards in Genomic Sciences, 12 (64). doi:10.1186/s40793-017-0274-y
Peer Reviewed verified by ORBi
* These authors have contributed equally to this work.

Wampach, L., Heintz, A., Hogan, A., Muller, E., Narayanasamy, S., Laczny, C. C., Hugerth, L., Bindl, L., Bottu, J., Andersson, A., de Beaufort, C., & Wilmes, P. (2017). Colonization and Succession within the Human Gut Microbiome by Archaea, Bacteria, and Microeukaryotes during the First Year of Life. Frontiers in Microbiology. doi:10.3389/fmicb.2017.00738
Peer Reviewed verified by ORBi

Kaysen, A., Heintz, A., Muller, E., Narayanasamy, S., Wampach, L., Laczny, C. C., Graf, N., Simon, A., Franke, K., Bittenbring, J., Wilmes, P., & Schneider, J. (2017). Integrated meta-omic analyses of the gastrointestinal tract microbiome in patients undergoing allogeneic hematopoietic stem cell transplantation. Translational Research: the Journal of Laboratory and Clinical Medicine. doi:10.1016/j.trsl.2017.06.008
Peer Reviewed verified by ORBi

Narayanasamy, S., Jarosz, Y., Muller, E., Buschart, A., Herold, M., Kaysen, A., Laczny, C. C., Pinel, N., May, P., & Wilmes, P. (December 2016). IMP: a pipeline for reproducible referenceindependent integrated metagenomic and metatranscriptomic analyses. Genome Biology, 17, 260. doi:10.1186/s13059-016-1116-8
Peer Reviewed verified by ORBi

Laczny, C. C., Muller, E., Heintz, A., Herold, M., Lebrun, L., Hogan, A., May, P., de Beaufort, C., & Wilmes, P. (2016). Identification, recovery, and refinement of hitherto undescribed population-level genomes from the human gastrointestinal tract. Frontiers in Microbiology, 7 (884). doi:10.3389/fmicb.2016.00884
Peer Reviewed verified by ORBi

Narayanasamy, S., Muller, E., Sheik, A., & Wilmes, P. (2015). Integrated omics for the identification of key functionalities in biological wastewater treatment microbial communities. Microbial Biotechnology. doi:10.1111/1751-7915.12255
Peer Reviewed verified by ORBi

Roume, H., Buschart, A., Muller, E., May, P., Satagopam, V., Laczny, C. C., Narayanasamy, S., Lebrun, L., Hoopmann, M., Schupp, J., Gillece, J., Hicks, N., Engelthaler, D., Sauter, T., Keim, P., Moritz, R., & Wilmes, P. (2015). Comparative integrated omics: identification of key functionalities in microbial community-wide metabolic networks. Biofilms and Microbiomes, 1 (15007). doi:10.1038/npjbiofilms.2015.7
Peer Reviewed verified by ORBi

Sheik, A., Muller, E., Audinot, J.-N., Lebrun, L., Grysan, P., Guignard, C., & Wilmes, P. (2015). In situ phenotypic heterogeneity among single cells of the filamentous bacterium Candidatus Microthrix parvicella. ISME Journal. doi:10.1038/ismej.2015.181
Peer Reviewed verified by ORBi

Muller, E., Pinel, N., Laczny, C. C., Hoopmann, M., Narayanasamy, S., Lebrun, L., Roume, H., Lin, J., May, P., Hicks, N., Buschart, A., Wampach, L., Liu, C., Price, L., Gillece, J., Guignard, C., Schupp, J., Vlassis, N., Baliga, ... Wilmes, P. (2014). Community-integrated omics links dominance of a microbial generalist to fine-tuned resource usage. Nature Communications. doi:10.1038/ncomms6603
Peer Reviewed verified by ORBi

Sheik, A., Muller, E., Audinot, J.-N., Lebrun, L., Grysan, P., & Wilmes, P. (16 October 2014). In situ single-cell investigations of substrate utilisation by Candidatus Microthrix parvicella [Poster presentation]. Phenotypic heterogeneity and sociobiology of bacterial populations, Irsee, Germany.

Heintz, A., Muller, E., Lange, B., Mollenhauer, B., Oertel, W., & Wilmes, P. (October 2014). Characterization of the gastrointestinal microbiome in patients with REM-sleep behaviour disorder and newly diagnosed Parkinson’s disease [Paper presentation]. 2nd International PD symposium.

Sheik, A., Muller, E., Audinot, J.-N., Lebrun, L., Grysan, P., & Wilmes, P. (29 September 2014). Bet-hedging strategy for substrate usage among single cells of Candidatus Microthrix parvicella? [Paper presentation]. International Society for Microbial Ecology (ISME15), Seoul, South Korea.

Gruffaz, Muller, E., Yousra, L.-J., Yella, N., Gilles, G., & Bringel, F. (March 2014). Genes of the N-methylglutamate pathway are essential for growth of Methylobacterium extorquens DM4 with monomethylamine. Applied and Environmental Microbiology, 80 (11). doi:10.1128/AEM.04160-13
Peer Reviewed verified by ORBi

Sheik, A., Muller, E., & Wilmes, P. (22 January 2014). A hundred years of activated sludge: time for a rethink. Frontiers in Microbiology, 5 (47), 1-7. doi:10.3389/fmicb.2014.00047
Peer Reviewed verified by ORBi

Calusinska, M., Goux, X., Muller, E., Wilmes, P., & Delfosse, P. (2014). A 16S rRNA gene Illumina–based barcoded assay design for high throughput characterisation of microbial communities from anaerobic digesters [Poster presentation]. 2nd International Conference on Biogas Microbiology.

Muller, E., Pinel, N., Laczny, C. C., Hoopmann, M., Lebrun, L., Roume, H., May, P., Hicks, N., Liu, C., Price, L., Gillece, J., Guignard, C., Schupp, J., Vlassis, N., Moritz, R., Baliga, N., Keim, P., & Wilmes, P. (2014). Community integrated omics links the dominance of a microbial generalist to fine-tuned resource usage [Paper presentation]. 15th International Symposium on Microbial Ecology.

Muller, E., Pinel, N., Laczny, C. C., Hoopmann, M., Lebrun, L., Roume, H., May, P., Hicks, N., Liu, C., Price, L., Gillece, J., Guignard, C., Schupp, J., Vlassis, N., Moritz, R., Baliga, N., Keim, P., & Wilmes, P. (2014). Community integrated omics links the dominance of a microbial generalist to fine-tuned resource usage [Poster presentation]. Phenotypic heterogeneity and sociobiology of bacterial populations.

Hugerth, L., Muller, E., Hu, Y., Lebrun, L., Roume, H., Lundin, D., Wilmes, P., & Andersson, A. (2014). Systematic Design of 18S rRNA Gene Primers for Determining Eukaryotic Diversity in Microbial Consortia. PLoS ONE. doi:10.1371/journal.pone.0095567
Peer Reviewed verified by ORBi

Muller, E., Sheik, A., & Wilmes, P. (2014). Lipid-based biofuel production from wastewater. Current Opinion in Biotechnology, 30, 9-16. doi:10.1016/j.copbio.2014.03.007
Peer Reviewed verified by ORBi

Muller, E., Buschart, A., Roume, H., Lebrun, L., & Wilmes, P. (2014). The sequential isolation of metabolites, RNA, DNA, and proteins from a single, undivided mixed microbial community sample. Methods in Enzymology.

Dilimulati, Y., Heintz, A., Ghosal, A., Upadhyaya, B. B., Fritz, J., Laczny, C. C., May, P., Muller, E., Shah, P., Desai, M., Roume, H., Huang, D., Wang, K., Galas, D. J., & Wilmes, P. (October 2013). The exogenous RNA spectrum in human plasma and the gastrointestinal tract [Poster presentation]. 2nd International Systems Biomedicine Symposium, Belval, Luxembourg.

Muller, E., Pinel, N., May, P., Hussong, R., Roume, H., Lebrun, L., liu, C., Aziz, M., Price, L., Moritz, R., Schupp, J., Keim, P., & Wilmes, P. (2013). Systematic molecular measurements reveal key microbial populations driving community-wide phenotype [Poster presentation]. 12th Symposium on Bacterial Genetics and Ecology (BAGECO).

Muller, E., Roume, H., & Wilmes, P. (2013). Eco-systems biology of microbial communities: integration of biomolecular information from unique samples [Poster presentation]. New Approaches and Concepts in Microbiology.

Roume, H., Satagopam, V., Muller, E., May, P., Hussong, R., & Wilmes, P. (2013). Integrated omics highlights keystone genes in community-wide metabolic networks [Poster presentation]. 2013 International Conference on Genomics in Europe.

Roume, H., Satagopam, V., Muller, E., May, P., Hussong, R., & Wilmes, P. (2013). Integrated omics highlights keystone genes in community-wide metabolic networks [Poster presentation]. 5th congress of European Microbiologists (FEMS).

Muller, E., & Wilmes, P. (2013). Ecological success of a microbial generalist is defined by the fine tuning of gene expressions [Paper presentation]. COST WG3: Linking microbial ecology & evolution.

Muller, E., Pinel, N., May, P., Roume, H., & Wilmes, P. (2013). Linking mixed microbial community phenotype to individual genotypes [Poster presentation]. 14th International Symposium on Microbial Ecology.

Muller, E., Glaab, E., May, P., Vlassis, N., & Wilmes, P. (2013). Condensing the omics fog of microbial communities. Trends in Microbiology, 21 (7), 325–333. doi:10.1016/j.tim.2013.04.009
Peer reviewed

Muller, E., Roume, H., Buschart, A., Pinel, N., Laczny, C. C., Satagopam, V., May, P., Lebrun, L., & Wilmes, P. (2013). A model microbial community for Eco-Systems Biology [Poster presentation]. 2nd International Systems Biomedicine Symposium.

Roume, H., Heintz-Buschart, A., Muller, E., & Wilmes, P. (2013). Sequential isolation of metabolites, RNA, DNA, and proteins from the same unique sample. Methods in Enzymology, 531, 219-236. doi:10.1016/B978-0-12-407863-5.00011-3
Peer Reviewed verified by ORBi

Roume, H., Muller, E., Cordes, T., Renaut, J., Hiller, K., & Wilmes, P. (2013). A biomolecular isolation framework for eco-systems biology. ISME Journal, 7 (1), 110-121. doi:10.1038/ismej.2012.72
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Muller, E., Roume, H., Shah, P., & Wilmes, P. (2012). A Biomolecular Isolation Framework for Molecular Eco-Systems Biology [Poster presentation]. 112th General Meeting of the American Society for Microbiology.

Roume, H., Muller, E., Shah, P., & Wilmes, P. (2012). A biomolecular isolation protocol for Eco-Systems Biology: How to isolate DNA, RNA, proteins and metabolites from a single unique sample [Poster presentation]. 11th Annual International Symposium Addresses Systems Biology and the Microbiome.

Roume, H., Muller, E., Cordes, T., Hiller, K., & Wilmes, P. (2012). A biomolecular isolation framework for eco-systems biology [Poster presentation]. 14th International Symposium on Microbial Ecology.

Muller, E., & Wilmes, P. (2012). From gut to sludge: Molecular Eco-Systems Biology of Microbial Consortia [Paper presentation]. Conference on Systems Biology applied to Plants and Environment.

Muller, E., Pinel, N., Gillece, J. D., Schupp, J. M., Price, L. B., Engelthaler, D. M., Levantesi, C., Tandoi, V., Luong, K., Baliga, N. S., Korlach, J., Keim, P. S., & Wilmes, P. (2012). Genome Sequence of "Candidatus Microthrix parvicella" Bio17-1, a Long-Chain-Fatty-Acid-Accumulating Filamentous Actinobacterium from a Biological Wastewater Treatment Plant. Journal of Bacteriology, 194 (23), 6670-6671. doi:10.1128/JB.01765-12
Peer Reviewed verified by ORBi

Muller, E., Roume, H., Lebrun, L., & Wilmes, P. (27 September 2011). Eco-Systems Biology of Natural Lipid-Accumulating Microbial Communities [Poster presentation]. 1st International Systems Biomedicine Symposium.

Roume, H., Muller, E., Cordes, T., Hiller, K., & Wilmes, P. (2011). Isolation of biomolecules from a single sample: the first step towards integrated omic analyses [Poster presentation]. 1st International Systems Biomedicine Symposium.

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