  | 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. |
 | 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 |
 | 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 |
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 |
 | 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. |
 | 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., 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. |
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., 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., & 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., 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). |
 | 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 |
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., 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 Peer Reviewed verified by ORBi |
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. |