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WILMES Paul

University of Luxembourg > Luxembourg Centre for Systems Biomedicine (LCSB) > Systems Ecology

Main Referenced Co-authors
MAY, Patrick  (62)
MULLER, Emilie  (46)
LACZNY, Cedric Christian  (37)
LEBRUN, Laura  (35)
BUSCHART, Anna  (30)
Main Referenced Keywords
Microbiome (10); COVID-19 (9); Humans (9); Metagenomics (9); SARS-CoV-2 (8);
Main Referenced Unit & Research Centers
Luxembourg Centre for Systems Biomedicine (LCSB): Eco-Systems Biology (Wilmes Group) (65)
Luxembourg Centre for Systems Biomedicine (LCSB): Bioinformatics Core (R. Schneider Group) (28)
ULHPC - University of Luxembourg: High Performance Computing (19)
Luxembourg Centre for Systems Biomedicine (LCSB) (10)
Luxembourg Centre for Systems Biomedicine (LCSB): Medical Translational Research (J. Schneider Group) (7)
Main Referenced Disciplines
Microbiology (212)
Environmental sciences & ecology (63)
Life sciences: Multidisciplinary, general & others (25)
Biochemistry, biophysics & molecular biology (17)
Genetics & genetic processes (16)

Publications (total 303)

The most downloaded
1179 downloads
Heintz, A., May, P., Laczny, C. C., Lebrun, L., Bellora, C., Krishna, A., Wampach, L., Schneider, J., Hogan, A., de Beaufort, C., & Wilmes, P. (2016). Integrated multi-omics of the human gut microbiome in a case study of familial type 1 diabetes. Nature Microbiology, 2, 16180. doi:10.1038/NMICROBIOL.2016.180 https://hdl.handle.net/10993/28958

The most cited

2130 citations (Scopus®)

Atarshi, K.* , Tanoue, T.* , Oshima, K.* , Suda, W., Nagano, Y., Nishikawa, H., Fukuda, S., Saito, T., Narushima, S., Hase, K., Kim, S., Fritz, J., Wilmes, P., Ueha, S., Matsushima, K., Ohno, H., Olle, B., Sakaguchi, S., Taniguchi, T., ... Honda, K. (08 August 2013). Treg induction by a rationally selected mixture of Clostridia strains from the human microbiota. Nature, 500, 232-236. doi:10.1038/nature12331 https://hdl.handle.net/10993/15182

AHO, V., KLEE, M., LANDOULSI, Z., Heintz-Buschart, A., PAVELKA, L., LEIST, A., KRÜGER, R., MAY, P., WILMES, P., & NCER-PD Consortium. (06 April 2024). Gut microbiome is not associated with mild cognitive impairment in Parkinson's disease. NPJ Parkinson's Disease, 10 (1), 78. doi:10.1038/s41531-024-00687-1
Peer Reviewed verified by ORBi

KLEE, M., AHO, V., MAY, P., Heintz-Buschart, A., LANDOULSI, Z., JONSDOTTIR, S., PAULY, C., PAVELKA, L., DELACOUR, L., KAYSEN, A., Krüger, R., WILMES, P., LEIST, A., Acharya, G., Aguayo, G., Alexandre, M., ALI, M., Ammerlann, W., ARENA, G., ... ZELIMKHANOV, G. (2024). Education as Risk Factor of Mild Cognitive Impairment: The Link to the Gut Microbiome. Journal of Prevention of Alzheimer's Disease. doi:10.14283/jpad.2024.19
Peer reviewed

KLEE, M., AHO, V., MAY, P., KRÜGER, R., WILMES, P., & LEIST, A. (2023). EDUCATION AS A RISK FACTOR OF MILD COGNITIVE IMPAIRMENT—THE ROLE OF THE GUT MICROBIOME. Innovation in Aging. doi:10.1093/geroni/igad104.0228
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Marcos-Zambrano, L. J., López-Molina, V. M., Bakir-Gungor, B., Frohme, M., Karaduzovic-Hadziabdic, K., Klammsteiner, T., Ibrahimi, E., Lahti, L., Loncar-Turukalo, T., Dhamo, X., Simeon, A., Nechyporenko, A., Pio, G., Przymus, P., Sampri, A., Trajkovik, V., Lacruz-Pleguezuelos, B., Aasmets, O., Araujo, R., ... Carrillo de Santa Pau, E. (22 November 2023). A toolbox of machine learning software to support microbiome analysis. Frontiers in Microbiology, 14. doi:10.3389/fmicb.2023.1250806
Peer Reviewed verified by ORBi

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
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Klee, M., Aho, V., May, P., Heintz-Buschart, A., Landoulsi, Z., Jonsdottir, S., Pauly, C., Pavelka, L., Delacour, L., Kaysen, A., Krüger, R., Wilmes, P., Leist, A., & NCER-PD Consortium. (November 2023). Education as risk factor of Mild Cognitive Impairment - the role of the gut microbiome. Presentation in symposium: Social determinants of brain health: From the search for mechanisms to recommendations to increase equity [Paper presentation]. Annual Meeting of the Gerontological Society of America.

Santos da Silva, E., Servais, J.-Y., Kohnen, M., Arendt, V., Staub, T., The Con-Vince Consortium, The CoVaLux Consortium, Krüger, R., FAGHERAZZI, G., WILMES, P., Hübschen, J. M., OLLERT, M., Perez-Bercoff, D., & Seguin-Devaux, C. (06 October 2023). Validation of a SARS-CoV-2 Surrogate Neutralization Test Detecting Neutralizing Antibodies against the Major Variants of Concern. International Journal of Molecular Sciences, 24 (19), 14965. doi:10.3390/ijms241914965
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AHO, V., KLEE, M., LANDOULSI, Z., Heintz-Buschart, A., PAVELKA, L., LEIST, A.* , Krüger, R.* , MAY, P.* , & WILMES, P.*. (2023). Mild cognitive impairment is not associated with gut microbiota alterations in Parkinson’s disease. (v1). ORBilu-University of Luxembourg. https://orbilu.uni.lu/handle/10993/57437. doi:10.21203/rs.3.rs-3372525/v1
* These authors have contributed equally to this work.

SCHMIT, K.* , GARCIA, P.* , SCIORTINO, A., AHO, V., Pardo Rodriguez, B., THOMAS, M., GERARDY, J.-J., Bastero Acha, I., HALDER, R., CIALINI, C., HEURTAUX, T., Ostahi, I., BUSI, S. B., Grandmougin, L., LOWNDES, T., Singh, Y., Martens, E. C., MITTELBRONN, M., BUTTINI, M.* , & WILMES, P. (26 September 2023). Fiber deprivation and microbiome-borne curli shift gut bacterial populations and accelerate disease in a mouse model of Parkinson's disease. Cell Reports, 42 (9), 113071. doi:10.1016/j.celrep.2023.113071
Peer Reviewed verified by ORBi
* These authors have contributed equally to this work.

MUNIZ SACCO, F. C., VENDITTI, S. (Other coll.), WILMES, P. (Other coll.), & HANSEN, J. (Other coll.). (September 2023). PERSONAL CARE PRODUCTS REMOVAL FROM GREYWATER USING NATURE-BASED SOLUTIONS FOR WATER REUSE IN SUSTAINABLE BUILDINGS: THE “RECARE” PROJECT APPROACH [Poster presentation]. 10th International Symposium on Wetland Pollutant Dynamics and Control, Bruges, Belgium.
Peer reviewed

HANSEN, B., LACZNY, C. C., AHO, V., Frachet-Bour, A., Habier, J., OSTASZEWSKI, M., Michalsen, A., Hanslian, E., Koppold, D. A., Hartmann, A. M., Steckhan, N., Mollenhauer, B., Schade, S., RUMP, K., SCHNEIDER, J., & WILMES, P. (18 August 2023). Protocol for a multicentre cross-sectional, longitudinal ambulatory clinical trial in rheumatoid arthritis and Parkinson's disease patients analysing the relation between the gut microbiome, fasting and immune status in Germany (ExpoBiome). BMJ Open, 13 (8), 071380. doi:10.1136/bmjopen-2022-071380
Peer Reviewed verified by ORBi

Banas, I., Esser, S. P., Turzynski, V., Soares, A., Novikova, P., May, P., Moraru, C., Hasenberg, M., Rahlff, J., Wilmes, P., Klingl, A., & Probst, A. J. (2023). Spatio-functional organization in virocells of small uncultivated archaea from the deep biosphere. ISME Journal. doi:10.1038/s41396-023-01474-1
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Klee, M., Aho, V., May, P., Heintz-Buschart, A., Landoulsi, Z., Jonsdottir, S., Pauly, C., Pavelka, L., Delacour, L., Kaysen, A., Krüger, R., Wilmes, P., Leist, A., & NCER-PD Consortium, (Other coll.). (July 2023). Education as risk factor of Mild Cognitive Impairment - the role of the gut microbiome [Poster presentation]. Alzheimer’s Association (AAIC) Conference.

de Nies, L., Galata, V., Martin-Gallausiaux, C., Despotovic, M., Busi, S. B., Snoeck, C. J., Delacour, L., Budagavi, D. P., Laczny, C. C., Habier, J., Lupu, P.-C., Halder, R., Fritz, J. V., Marques, T., Sandt, E., O'Sullivan, M. P., Ghosh, S., Satagopam, V., Consortium, C.-V., ... Wilmes, P. (09 March 2023). Altered infective competence of the human gut microbiome in COVID-19. Microbiome, 11 (1), 46. doi:10.1186/s40168-023-01472-7
Peer Reviewed verified by ORBi

NOVIKOVA, P., BUSI, S. B., Probst, A. J., MAY, P., & WILMES, P. (2023). Functional prediction of proteins from the human gut archaeome. ORBilu-University of Luxembourg. https://orbilu.uni.lu/handle/10993/58071. doi:10.1101/2023.02.01.526569

BUSI, S. B., Peter, H., Brandani, J., Kohler, T. J., Fodelianakis, S., Pramateftaki, P., Bourquin, M., Ezzat, L., Michoud, G., Lane, S., WILMES, P., & Battin, T. J. (2023). Cross-domain interactions induce community stability to benthic biofilms in proglacial streams. ORBilu-University of Luxembourg. https://orbilu.uni.lu/handle/10993/58067. doi:10.1101/2023.01.31.526486

Despotovic, M., de Nies, L., Busi, S. B., & Wilmes, P. (2023). Reservoirs of antimicrobial resistance in the context of One Health. Current Opinion in Microbiology, 73, 102291. doi:10.1016/j.mib.2023.102291
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Klee, M., Aho, V., May, P., Krüger, R., Wilmes, P., Leist, A., & NCER-PD Consortium (Other coll.). (January 2023). Education as risk factor of Mild Cognitive Impairment - the role of the gut microbiome [Poster presentation]. Conference Precision Medicine in Parkinson’s: Past lessons and conquering new frontiers.

Schulz, A., Welsch, S.-K., Etringer, S., Hansen, G., Milbert, L., Schneider, J., Taddei, G., Gomez Bravo, R., Lygidakis, C., van Dyck, Z., Lutz, A., Wilmes, P., & Vögele, C. (2023). Lower gastric sensitivity in quiescent inflammatory bowel disease than in irritable bowel syndrome. Physiology and Behavior, 270 (1), 114293. doi:10.1016/j.physbeh.2023.114293
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Kunath, B., Hickl, O., Teixeira Queiros, P., Martin-Gallausiaux, C., Lebrun, L., Halder, R., Laczny, C. C., Schmidt, T. S., Hayward, M., Becher, D., Heintz-Buschart, A., de Beaufort, C., Bork, P., May, P., & Wilmes, P. (2022). Alterations of oral microbiota and impact on the gut microbiome in type 1 diabetes mellitus revealed by integrated multi-omic analyses. Microbiome. doi:10.1186/s40168-022-01435-4
Peer Reviewed verified by ORBi

Fischer, A., Badier, N., Zhang, L., Elbéji, A., WILMES, P., Oustric, P., Benoy, C., OLLERT, M., & FAGHERAZZI, G. (30 November 2022). Long COVID Classification: Findings from a Clustering Analysis in the Predi-COVID Cohort Study. International Journal of Environmental Research and Public Health, 19 (23), 16018. doi:10.3390/ijerph192316018
Peer Reviewed verified by ORBi

Delogu, F., Kunath, B., Queirós, P. M., Halder, R., Lebrun, L., Pope, P. B., May, P., Widder, S., Muller, E. E. L., & Wilmes, P. (2022). Forecasting of a complex microbial community using meta-omics. ORBilu-University of Luxembourg. https://orbilu.uni.lu/handle/10993/52862. doi:10.1101/2022.10.19.512887

Hickl, O., Queirós, P., Wilmes, P., May, P., & Heintz-Buschart, A. (2022). binny: an automated binning algorithm to recover high-quality genomes from complex metagenomic datasets. Briefings in Bioinformatics. doi:10.1093/bib/bbac431
Peer Reviewed verified by ORBi

de Nies, L., Busi, S. B., Kunath, B., May, P., & Wilmes, P. (16 September 2022). Mobilome-driven segregation of the resistome in biological wastewater treatment. eLife, 11, 81196. doi:10.7554/eLife.81196
Peer Reviewed verified by ORBi

Wilmes, P., Martin-Gallausiaux, C., Ostaszewski, M., Aho, V., Novikova, P., Laczny, C. C., & Schneider, J. (14 September 2022). The gut microbiome molecular complex in human health and disease. Cell Host and Microbe, 30 (9), 1201-1206. doi:10.1016/j.chom.2022.08.016
Peer Reviewed verified by ORBi

Aho, V., Ostaszewski, M., Martin-Gallausiaux, C., Laczny, C. C., Schneider, J., & Wilmes, P. (14 September 2022). SnapShot: The Expobiome Map. Cell Host and Microbe, 30 (9), 1340. doi:10.1016/j.chom.2022.08.015
Peer Reviewed verified by ORBi

McAdams, Z. L., BUSI, S. B., Gustafson, K. L., Bivens, N., Franklin, C. L., WILMES, P., & Ericsson, A. C. (2022). Multi-omics analysis of mouse fecal microbiome reveals supplier-dependent functional differences and novel metagenome-assembled genomes. ORBilu-University of Luxembourg. https://orbilu.uni.lu/handle/10993/58063. doi:10.1101/2022.09.12.507288

Fischer, A., Zhang, L., Elbéji, A., WILMES, P., Oustric, P., Staub, T., Nazarov, P. V., OLLERT, M., & FAGHERAZZI, G. (August 2022). Long COVID Symptomatology After 12 Months and Its Impact on Quality of Life According to Initial Coronavirus Disease 2019 Disease Severity. Open Forum Infectious Diseases, 9 (8), 397. doi:10.1093/ofid/ofac397
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SCHULZ, A., WELSCH, S.-K., ETRINGER, S. M., HANSEN, G., MILBERT, L., SCHNEIDER, J., Taddei, G., GOMEZ BRAVO, R., LYGIDAKIS, C., VAN DYCK, Z., LUTZ, A., WILMES, P., & VÖGELE, C. (August 2022). Gastric interoception and gastric myoelectrical activity in inflammatory bowel diseases and irritable bowel syndrome. Psychophysiology, 59 (S1), 70.
Peer Reviewed verified by ORBi

Talavera Andujar, B., Aurich, D., Aho, V., Singh, R. R., Cheng, T., Zaslavsky, L., Bolton, E. E., Mollenhauer, B., Wilmes, P., & Schymanski, E. (2022). Studying the Parkinson's disease metabolome and exposome in biological samples through different analytical and cheminformatics approaches: a pilot study. Analytical and Bioanalytical Chemistry. doi:10.1007/s00216-022-04207-z
Peer Reviewed verified by ORBi

Bourquin, M., BUSI, S. B., Fodelianakis, S., Peter, H., Washburne, A., Kohler, T. J., Ezzat, L., Michoud, G., WILMES, P., & Battin, T. J. (02 June 2022). The microbiome of cryospheric ecosystems. Nature Communications, 13 (1), 3087. doi:10.1038/s41467-022-30816-4
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Kohler, T. J., Fodelianakis, S., Michoud, G., Ezzat, L., Bourquin, M., Peter, H., BUSI, S. B., Pramateftaki, P., Deluigi, N., Styllas, M., Tolosano, M., de Staercke, V., Schön, M., Brandani, J., Marasco, R., Daffonchio, D., WILMES, P., & Battin, T. J. (June 2022). Glacier shrinkage will accelerate downstream decomposition of organic matter and alters microbiome structure and function. Global Change Biology, 28 (12), 3846 - 3859. doi:10.1111/gcb.16169
Peer Reviewed verified by ORBi

Ternes, D., Tsenkova, M., Pozdeev, V., Meyers, M., Koncina, E., Atatri, S., Schmitz, M., Karta, J., Schmoetten, M., Heinken, A., Rodriguez, F., Delbrouck, C., Gaigneaux, A., Ginolhac, A., Dan Nguyen, T. T., Grandmougin, L., Frachet-Bour, A., Martin-Gallausiaux, C., Pires Pacheco, M. I., ... Letellier, E. (2022). The gut microbial metabolite formate exacerbates colorectal cancer progression. Nature Metabolism. doi:10.1038/s42255-022-00558-0
Peer reviewed

Pauly, L., Klee, M., Paccoud, I., Satagopam, V., Ghosh, S., Fritz, J., O'Sullivan, M., Wilmes, P., Krüger, R., & Leist, A. (April 2022). Individual factors and beliefs determining COVID-19 vaccination willingness [Poster presentation]. ECCMID 2022.

Queirós, P., HICKL, O., MARTINEZ ARBAS, S., WILMES, P., & MAY, P. (2022). UniFuncNet: a flexible network annotation framework. ORBilu-University of Luxembourg. https://orbilu.uni.lu/handle/10993/58072. doi:10.1101/2022.03.15.484380

Wilmes, P. (February 2022). The ecology of the unseen. Archives des Sciences Naturelles, Physiques et Mathématiques, XLVIII, 45-50.
Peer reviewed

Sedrani, C. M., & Wilmes, P. (24 January 2022). Towards hypothesis-driven, personalized microbiome screening. Cell Reports Methods, 2 (1). doi:10.1016/j.crmeth.2021.100139

Capelle, C. M., Ciré, S., Domingues, O., Ernens, I., Hedin, F., Fischer, A., Snoeck, C. J., Ammerlaan, W., Konstantinou, M., Grzyb, K., Skupin, A., Carty, C. L., Hilger, C., Gilson, G., Celebic, A., Wilmes, P., Del Sol, A., Kaplan, I. M., Betsou, F., ... He, F. (2022). Combinatorial analysis reveals highly coordinated early-stage immune reactions that predict later antiviral immunity in mild COVID-19 patients. Cell Reports Medicine, 3 (4), 100600. doi:10.1016/j.xcrm.2022.100600
Peer reviewed

Schulz, A., Welsch, S., Etringer, S., Hansen, G., Milbert, L., Schneider, J., Taddei, G., Gomez Bravo, R., Lygidakis, C., van Dyck, Z., Lutz, A., Wilmes, P., & Vögele, C. (2022). Gastrische Interozeption und gastrische myoelektrische Aktivität bei chronisch-entzündlichen Darmerkrankungen und Reizdarmsyndrom. In M. Heinrichs & M. Schönauer, 47. Jahrestagung Psychologie und Gehirn (pp. 233).
Peer reviewed

Pauly, C., Glaab, E., Hansen, M., Martin-Gallausiaux, C., Ledda, M., Marques, T., Wilmes, P., Krüger, R., & Consortium, N.-P. (2022). Parkinson's Disease progression, resilience and inflammation markers during the COVID-19 pandemic. Movement Disorders, in press (doi: 10.1002/mds.29212) (in press). doi:10.1002/mds.29212
Peer Reviewed verified by ORBi

de Nies, L., Busi, S. B., Tsenkova, M., Halder, R., Letellier, E., & Wilmes, P. (2022). Evolution of the murine gut resistome following broad-spectrum antibiotic treatment. Nature Communications, 13 (1), 2296. doi:10.1038/s41467-022-29919-9
Peer Reviewed verified by ORBi

Trezzi, J.-P., Aho, V., Jäger, C., Schade, S., Janzen, A., Hickl, O., Kunath, B., Thomas, M., Schmit, K., Garcia, P., Sciortino, A., Martin-Gallausiaux, C., Halder, R., Huarte, O. U., Heurtaux, T., Heins-Marroquin, U., Gomez-Giro, G., Weidenbach, K., Delacour, L., ... Wilmes, P. (2022). An archaeal compound as a driver of Parkinson’s disease pathogenesis. (1). ORBilu-University of Luxembourg. https://orbilu.uni.lu/handle/10993/51987. doi:10.21203/rs.3.rs-1827631/v1

Hickl, O., Teixeira Queiros, P., Wilmes, P., May, P., & Heintz-Buschart, A. (2021). binny: an automated binning algorithm to recover high-quality genomes from complex metagenomic datasets 2021.12.22.473795. ORBilu-University of Luxembourg. https://orbilu.uni.lu/handle/10993/50004. doi:10.1101/2021.12.22.473795

de Saedeleer, B., Malabirade, A., Ramiro Garcia, J., Habier, J., Trezzi, J.-P., Peters, S., Daujeumont, A., Halder, R., Jäger, C., Busi, S. B., May, P., Oertel, W., Mollenhauer, B., Laczny, C. C., Hettich, R., & Wilmes, P. (2021). Systematic characterization of human gut microbiome-secreted molecules by integrated multi-omics. ISME Communications. doi:10.1038/s43705-021-00078-0
Peer Reviewed verified by ORBi

Van den Bossche, T., Arntzen, M., Becher, D., Benndorf, D., Eijsink, V., Henry, C., Jagtap, P., Jehmlich, N., Juste, C., Kunath, B., Mesuere, B., Muth, T., Pope, P., Seifert, J., Tanca, A., Uzzau, S., Wilmes, P., Hettich, R., & Armengaud, J. (December 2021). The Metaproteomics Initiative: a coordinated approach for propelling the functional characterization of microbiomes. Microbiome, 9 (1), 243. doi:10.1186/s40168-021-01176-w
Peer Reviewed verified by ORBi

Leist, A., Klee, M., Paccoud, I., Pauly, L., Ghosh, S., Fritz, J., O Sullivan, M. P., Rommes, B., Wilmes, P., Krüger, R., & CON-VINCE Consortium. (2021). Which demographic and socio-economic factors are associated with vaccination willingness and beliefs towards vaccination? Rapid report with first results.

Mirzayi, C., Renson, A., Genomic Standards Consortium, Massive Analysis and Quality Control Society, Zohra, F., Elsafoury, S., Geistlinger, L., Kasselman, L. J., Eckenrode, K., van de Wijgert, J., Loughman, A., Marques, F. Z., MacIntyre, D. A., Arumugam, M., Azhar, R., Beghini, F., Bergstrom, K., Bhatt, A., Bisanz, J. E., ... Waldron, L. (November 2021). Reporting guidelines for human microbiome research: the STORMS checklist. Nature Medicine, 27 (11), 1885 - 1892. doi:10.1038/s41591-021-01552-x
Peer Reviewed verified by ORBi

Herold, M., Fouquier d'herouël, A., May, P., Delogu, F., Wienecke-Baldacchino, A., Tapp, J., Walczak, C., Wilmes, P., Cauchie, H.-M., Fournier, G., & Ogorzaly, L. (27 October 2021). Genome Sequencing of SARS-CoV-2 Allows Monitoring of Variants of Concern through Wastewater. Water, 13 (21 3018). doi:10.3390/w13213018
Peer Reviewed verified by ORBi

Leist, A., Wilmes, P., Krüger, R., & NCER-PD Consortium. (2021). Zusammenhänge zwischen sozio-ökonomischem Status und Darmmikrobiom als Risiko für Demenz [Paper presentation]. Journée de Gérontologie, Dommeldange, Luxembourg.

Fodelianakis, S., Busi, S. B., Wilmes, P., Washburne, A., Bourquin, M., Pramateftaki, P., Kohler, T., Styllas, M., Tolosano, M., de Staercke, V., Schon, M., Brandani, J., Peter, H., & Battin, T. (2021). Microdiversity characterizes prevalent phylogenetic clades in the glacier-fed stream microbiome. ISME Journal. doi:10.1038/s41396-021-01106-6
Peer reviewed

Galata, V., Busi, S. B., Kunath, B., de Nies, L., Calusinska, M., Halder, R., May, P., Wilmes, P., & Laczny, C. C. (2021). Functional meta-omics provide critical insights into long- and short-read assemblies. Briefings in Bioinformatics. doi:10.1093/bib/bbab330
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

Lucchetti, M., Kaminska, M., Kehinde Oluwasegun, A., Mosig, A., & Wilmes, P. (2021). Emulating the gut–liver axis: Dissecting the microbiome's effect on drug metabolism using multiorgan-on-chip models. Current Opinion in Endocrine and Metabolic Research. doi:10.1016/j.coemr.2021.03.003
Peer reviewed

Teixeira Queiros, P., Delogu, F., Hickl, O., May, P., & Wilmes, P. (June 2021). Mantis: flexible and consensus-driven genome annotation. GigaScience, 10 (6). doi:10.1093/gigascience/giab042
Peer Reviewed verified by ORBi

WILMES, P., Mossong, J., & Dentzer, T. G. (June 2021). Generalisation of COVID-19 incidences provides a biased view of the actual epidemiological situation. The Lancet Regional Health. Europe, 5, 100116. doi:10.1016/j.lanepe.2021.100116
Peer Reviewed verified by ORBi

Teixeira Queiros, P., Novikova, P., Wilmes, P., & May, P. (2021). Unification of functional annotation descriptions using text mining. Biological Chemistry. doi:10.1515/hsz-2021-0125
Peer Reviewed verified by ORBi

Busi, S. B.* , de Nies, L.* , Habier, J., Wampach, L., Heintz-Buschart, A., Fritz, J., Halder, R., May, P., de Beaufort, C., & Wilmes, P. (2021). Persistence of birth mode-dependent effects on gut microbiome composition, immune system stimulation and antimicrobial resistance during the first year of life. ISME Communications. doi:10.1038/s43705-021-00003-5
Peer reviewed
* These authors have contributed equally to this work.

de Nies, L., Lopes, S., Busi, S. B., Galata, V., Heintz-Buschart, A., Laczny, C. C., May, P., & Wilmes, P. (2021). PathoFact: a pipeline for the prediction of virulence factors and antimicrobial resistance genes in metagenomic data. Microbiome. doi:10.1186/s40168-020-00993-9
Peer Reviewed verified by ORBi

Czypionka, T., Iftekhar, E., Prainsack, B., Priesemann, V., Bauer, S., Valdez, A. C., Cuschieri, S., Glaab, E., Grill, E., Krutzinna, J., Lionis, C., Machado, H., Martins, C., Pavlakis, G., Perc, M., Petelos, E., Pickersgill, M., Skupin, A., Schernhammer, E., ... Wilmes, P. (2021). The benefits, costs and feasibility of a low incidence COVID-19 strategy. The Lancet Regional Health - Europe, 12 (100193). doi:10.1016/j.lanepe.2021.100294
Peer reviewed

Busi, S. B., de Nies, L., Pramateftaki, P., Bourquin, M., Ezzat, L. I., Kohler, T. J., Fodelianakis, S., Michoud, G., Peter, H., Styllas, M., Tolosano, M., De Staercke, V., Schön, M., Galata, V., Wilmes, P., & Battin, T. (2021). Glacier-fed stream biofilms harbour diverse resistomes and biosynthetic gene clusters 2021.11.18.469141. ORBilu-University of Luxembourg. https://orbilu.uni.lu/handle/10993/48975. doi:10.1101/2021.11.18.469141

Busi, S. B., Bourquin, M., Fodelianakis, S., Michoud, G., Kohler, T. J., Peter, H., Pramateftaki, P., Styllas, M., Tolosano, M., De Staercke, V., Schön, M., de Nies, L., Marasco, R., Daffonchio, D., Ezzat, L. I., Wilmes, P., & Battin, T. J. (2021). Genomic and metabolic adaptations of biofilms to ecological windows of opportunities in glacier-fed streams 2021.10.07.463499. ORBilu-University of Luxembourg. https://orbilu.uni.lu/handle/10993/48976. doi:10.1101/2021.10.07.463499

de Nies, L., Busi, S. B., Kunath, B. J., May, P., & Wilmes, P. (2021). Mobilome-driven segregation of the resistome in biological wastewater treatment 2021.11.15.468621. ORBilu-University of Luxembourg. https://orbilu.uni.lu/handle/10993/48974. doi:10.1101/2021.11.15.468621

Van Den Bossche, T., Kunath, B., Schallert, K., Schäpe, S. S., Abraham, P. E., Armengaud, J., Arntzen, M. Ø., Bassignani, A., Benndorf, D., Fuchs, S., Giannone, R. J., Griffin, T. J., Hagen, L. H., Halder, R., Henry, C., Hettich, R. L., Heyer, R., Jagtap, P., Jehmlich, N., ... Muth, T. (2021). Critical Assessment of MetaProteome Investigation (CAMPI): a multi-laboratory comparison of established workflows. Nature Communications, 12 (1), 7305. doi:10.1038/s41467-021-27542-8
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Martinez Arbas, S., Narayanasamy, S., Herold, M., Lebrun, L., Hoopmann, M. R., Li, S., Lam, T. J., Kunath, B. J., Hicks, N. D., Liu, C. M., Price, L. B., Laczny, C. C., Gillece, J. D., Schupp, J. M., Keim, P. S., Moritz, R. L., Faust, K., Tang, H., Ye, Y., ... Wilmes, P. (2021). Roles of bacteriophages, plasmids and CRISPR immunity in microbial community dynamics revealed using time-series integrated meta-omics. Nature Microbiology, 6 (1), 123--135. doi:10.1038/s41564-020-00794-8
Peer Reviewed verified by ORBi

Wilmes, P., Zimmer, J., Schulz, J., Glod, F., Veiber, L., Mombaerts, L., Rodrigues, B., Aalto, A., Pastore, J., Snoeck, C. J., Ollert, M., Fagherazzi, G., Mossong, J., Goncalves, J., Skupin, A., & Nehrbass, U. (2021). SARS-CoV-2 transmission risk from asymptomatic carriers: Results from a mass screening programme in Luxembourg. The Lancet Regional Health. Europe, 4, 100056. doi:10.1016/j.lanepe.2021.100056
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Fodelianakis, S., Washburne, A. D., Bourquin, M., Pramateftaki, P., Kohler, T. J., Styllas, M., Tolosano, M., De Staercke, V., Schön, M., BUSI, S. B., Brandani, J., WILMES, P., Peter, H., & Battin, T. J. (2020). Homogeneous selection promotes microdiversity in the glacier-fed stream microbiome. ORBilu-University of Luxembourg. https://orbilu.uni.lu/handle/10993/58066. doi:10.1101/2020.12.03.409391

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

Kohler, T. J., Peter, H., Fodelianakis, S., Pramateftaki, P., Styllas, M., Tolosano, M., de Staercke, V., Schön, M., Busi, S. B., Wilmes, P., Washburne, A., & Battin, T. J. (19 November 2020). Patterns and Drivers of Extracellular Enzyme Activity in New Zealand Glacier-Fed Streams. Frontiers in Microbiology, 11, 2922. doi:10.3389/fmicb.2020.591465
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Martinez Arbas, S.* , Narayanasamy, S.* , Herold, M., Lebrun, L., Hoopmann, M. R., Li, S., Lam, T. J., Kunath, B., Hicks, N. D., Liu, C. M., Price, L. B., Laczny, C. C., Gillece, J. D., Schupp, J. M., Keim, P. S., Moritz, R. L., Faust, K., Tang, H., Ye, Y., ... Wilmes, P. (2020). Roles of bacteriophages, plasmids and CRISPR immunity in microbial community dynamics revealed using time-series integrated meta-omics. Nature Microbiology.
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* These authors have contributed equally to this work.

Busi, S. B.* , Pramateftaki, P.* , Brandani, J., Fodelianakis, S., Peter, H., Halder, R., Wilmes, P., & Battin, T. (2020). Optimised biomolecular extraction for metagenomic analysis of microbial biofilms from high-mountain streams. PeerJ. doi:10.7717/peerj.9973
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* These authors have contributed equally to this work.

Mossong, J., Mombaerts, L., Veiber, L., Pastore, J., LeCoroller, G., Schnell, M., Masi, S., Huiart, L., & Wilmes, P. (2020). SARS-CoV-2 Transmission in Educational Settings During an Early Summer Epidemic Wave in Luxembourg. ORBilu-University of Luxembourg. https://orbilu.uni.lu/handle/10993/44569. doi:10.2139

Herold, M., Martinez Arbas, S., Narayanasamy, S., Sheik, A. R., Kleine-Borgmann, L. A. K., Lebrun, L., Kunath, B., Roume, H., Bessarab, I., Williams, R. B. H., Gillece, J. D., Schupp, J. M., Keim, P. S., Jäger, C., Hoopman, M. R., Moritz, R. L., Ye, Y., Li, S., Tang, H., ... Wilmes, P. (2020). Integration of time-series meta-omics data reveals how microbial ecosystems respond to disturbance. Nature Communications. doi:10.1038/s41467-020-19006-2
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Marynowska, M., Goux, X., Sillam-Dusses, D., Rouland-Lefevre, C., Halder, R., Wilmes, P., Gawron, P., Roisin, Y., Delfosse, P., & Calusinska, M. (2020). Compositional and functional characterisation of biomass-degrading microbial communities in guts of plant fibre- and soil-feeding higher termites. Microbiome. doi:10.1186/s40168-020-00872-3
Peer Reviewed verified by ORBi

Calusinska, M., Marynowska, M., Bertucci, M., Untereiner, B., Klimek, D., Goux, X., Sillam-Dusses, D., Gawron, P., Halder, R., Wilmes, P., Ferrer, P., Gerin, P., Roisin, Y., & Delfosse, P. (2020). Integrative omics analysis of the termite gut system adaptation to Miscanthus diet identifies lignocellulose degradation enzymes. Communications Biology. doi:10.1038/s42003-020-1004-3
Peer Reviewed verified by ORBi

Kurniawan, H., Franchina, D. G., Guerra, L., Bonetti, L., - Baguet, L. S., Grusdat, M., Schlicker, L., Hunewald, O., Dostert, C., Merz, M. P., Binsfeld, C., Duncan, G. S., Farinelle, S., Nonnenmacher, Y., Haight, J., Das Gupta, D., Ewen, A., Taskesen, R., Halder, R., ... Brenner, D. (05 May 2020). Glutathione Restricts Serine Metabolism to Preserve Regulatory T Cell Function. Cell Metabolism, 31 (5), 920--936.e7. doi:10.1016/j.cmet.2020.03.004
Peer reviewed

Mao, J.-H., Kim, Y.-M., Zhou, Y.-X., Hu, D., Zhong, C., Chang, H., Brislawn, C. J., Fansler, S., Langley, S., Wang, Y., PEISL, B. Y. L., Celniker, S. E., Threadgill, D. W., WILMES, P., Orr, G., Metz, T. O., Jansson, J. K., & Snijders, A. M. (17 April 2020). Genetic and metabolic links between the murine microbiome and memory. Microbiome, 8 (1), 53. doi:10.1186/s40168-020-00817-w
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Ternes, D., Karta, J., Tsenkova, M., Koncina, E., Schmitz, M., Grandmougin, L., Ginolhac, A., Gaigneaux, A., Ramiro Garcia, J., Wilmes, P., Haan, S., & Letellier, E. (22 February 2020). Understanding the role of Fusobacterium nucleatum metabolism in colon cancer initiation and progression [Poster presentation]. The Microbiome, Viruses, and Cancer, Orlando, United States.

Ternes, D., Karta, J., Tsenkova, M., Wilmes, P., Haan, S., & Letellier, E. (2020). Microbiome in Colorectal Cancer: How to Getfrom Meta-omics to Mechanism? Trends in Microbiology. doi:10.1016/j.tim.2020.01.001
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MARTIN-GALLAUSIAUX, C., MALABIRADE, A., Habier, J., & WILMES, P. (2020). Fusobacterium nucleatum Extracellular Vesicles Modulate Gut Epithelial Cell Innate Immunity via FomA and TLR2. Frontiers in Immunology, 11, 583644. doi:10.3389/fimmu.2020.583644
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CZOLK, R. M., Klueber, J., Sørensen, M., WILMES, P., Codreanu-Morel, F., Skov, P. S., HILGER, C., Bindslev-Jensen, C., OLLERT, M., & KUEHN, A. (2020). IgE-Mediated Peanut Allergy: Current and Novel Predictive Biomarkers for Clinical Phenotypes Using Multi-Omics Approaches. Frontiers in Immunology, 11, 594350. doi:10.3389/fimmu.2020.594350
Peer Reviewed verified by ORBi

Schymanski, E., Baker, N. C., Williams, A. J., Singh, R., Trezzi, J.-P., Kolber, P. L., Wilmes, P., Krüger, R., Paczia, N., Linster, C., & Balling, R. (2019). Connecting environmental exposure and neurodegeneration using cheminformatics and high resolution mass spectrometry: potential and challenges. Environmental Science. Processes and Impacts. doi:10.1039/C9EM00068B
Peer Reviewed verified by ORBi

Greenhalgh, K., Ramiro Garcia, J., Heinken, Ullmann, P., Bintener, T. J. R., Pacheco, M., Baginska, J., Shah, P., Frachet Bour, A., Halder, R., Fritz, J., Sauter, T., Thiele, I., Haan, S., Letellier, E., & Wilmes, P. (30 April 2019). Integrated In Vitro and In Silico Modeling Delineates the Molecular Effects of a Synbiotic Regimen on Colorectal-Cancer-Derived Cells. Cell Reports, 27, 1621–1632. doi:10.1016/j.celrep.2019.04.001
Peer Reviewed verified by ORBi

Buetti-Dinh, A., Galli, V., Bellenberg, S., Ilie, O., Herold, M., Christel, S., Boretska, M., Pivkin, I. V., Wilmes, P., Sand, W., Vera, M., & Dopson, M. (2019). Deep neural networks outperform human expert's capacity in characterizing bioleaching bacterial biofilm composition. Biotechnology Reports. doi:10.1016/j.btre.2019.e00321
Peer Reviewed verified by ORBi

Schmidt, T., Hayward, M., Coelho, L., Li, S., Costea, P., Voigt, A., Wirbel, J., Maistrenko, O., Alves, R., Bergsten, E., de Beaufort, C., Sobhani, I., Heintz, A., Sunagawa, S., Zeller, G., Wilmes, P., & Bork, P. (2019). Extensive transmission of microbes along the gastrointestinal tract. eLife. doi:10.7554/eLife.42693
Peer Reviewed verified by ORBi

Christen, A., Gallé, T., Köhler, C., Wilmes, P., Frkova, Z., & Hansen, J. (2019). Influence of Macro-Substrate Composition in Wastewater on Micropollutant Removal. the mobile app "MICROPOL 2019".
Peer reviewed

Wilmes, P. (December 2018). Microbiome: the environment within [Paper presentation]. Personalised Medicine Consortium Annual Retreat, Esch-sur-Alzette, Luxembourg.

Wilmes, P. (December 2018). Systems ecology of microbiomes [Paper presentation]. Physics Meets Biology Meeting, Belvaux, Luxembourg.

Wilmes, P. (November 2018). L’écologie systémique du microbiote humain : Identification des fonctions essentielles au maintient de la physiologie humaine [Paper presentation]. Remise du Grand Prix en Sciences biologiques de l’Institut Grand-ducal, Chambre de Commerce, Luxembourg.

Wilmes, P. (November 2018). Systems ecology of the human microbiome [Paper presentation]. Fourth Annual European Microbiome Congress, London, United Kingdom.

Martinez Arbas, S., Narayanasamy, S., Herold, M., Lebrun, L., Hicks, N. D., Price, L. B., Gillece, J. D., Schupp, J. M., Lam, T., Laczny, C. C., Ye, Y., Keim, P. S., Muller, E. E. L., May, P., & Wilmes, P. (19 October 2018). Critical transitions in microbial communities: mobile genetic elements as drivers of the microbial community dynamics within activated sludge of wastewater treatment [Poster presentation]. PhD days 2018, Belval, Luxembourg.

Wilmes, P. (October 2018). The ecology of the unseen [Paper presentation]. TEDx UniversityofLuxembourg, Esch-sur-Alzette, Luxembourg.

Wilmes, P. (October 2018). Understanding the role of the microbiome in Parkinson’s disease [Paper presentation]. 4th International Parkinson’s Disease Symposium, Esch-sur-Alzette, Luxembourg.

Wilmes, P. (October 2018). Le microbiote humain et son impacte sur la santé [Paper presentation]. Journée de la Recherche Médicale, Luxembourg-City, Luxembourg.

Trezzi, J.-P., Ramiro Garcia, J., Laczny, C. C., Daujeumont, A., Halder, R., Lebrun, L., Heintz, A., Oertel, W., Mollenhauer, B., & Wilmes, P. (October 2018). Microbiome-derived Multi-omicBiomarkers for Early-stage Detection and Stratification of Parkinson's Disease [Poster presentation]. 4th International Parkinson's Disease Symposium.

Martinez Arbas, S., Narayanasamy, S., Herold, M., Lebrun, L., Hicks, N. D., Price, L. B., Gillece, J. D., Schupp, J. M., Laczny, C. C., Keim, P. S., Muller, E. E. L., May, P., & Wilmes, P. (11 September 2018). A multi-omic view of invasive genetic elements and their linked prokaryotic population dynamics within a mixed microbial community [Poster presentation]. ECCB Athens, Athens, Greece.

Wilmes, P. (September 2018). Microbial Systems Ecology for identifying key functions driving host-microbiome-diet interactions [Paper presentation]. 1st International Conference on Precision Nutrition and Metabolism in Public Health and Medicine, Crete, Greece.

Wilmes, P. (September 2018). Unraveling the combinatorial mechanisms linking the gut microbiome to Parkinson’s disease [Paper presentation]. 2nd Joint RIKEN-Luxembourg Symposium, Esch-sur-Alzette, Luxembourg.

Wilmes, P. (August 2018). The integration of quantitative big data from microbial consortia: what is there to gain? [Paper presentation]. 17th International Symposium on Microbial Ecology, Leipzig, Germany.

Wilmes, P. (August 2018). Systems Ecology of microbiomes: identifying key functions [Paper presentation]. Austrian Proteomics and Metabolomics Research Symposium, Vienna, Austria.

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.

Malabirade, A., Habier, J., Heintz-Buschart, A., May, P., Godet, J., Halder, R., Etheridge, A., Galas, D., Wilmes, P., & Fritz, J. (30 July 2018). The RNA Complement of Outer Membrane Vesicles From Salmonella enterica Serovar Typhimurium Under Distinct Culture Conditions. Frontiers in Microbiology, 9, 2015. doi:10.3389/fmicb.2018.02015
Peer Reviewed verified by ORBi

Wilmes, P. (June 2018). The human microbiome: a systems ecology perspective [Paper presentation]. Société Luxembourgeoise de Gynécologie et d’Obstétrique, Luxembourg-City, Luxembourg.

Wilmes, P. (June 2018). Systems ecology reveals key functions underpinning host-microbiome interactions in health and disease [Paper presentation]. 7th International Human Microbiome Congress, County Kerry, Ireland.

Heintz-Buschart, A., Yusuf, D., Kaysen, A., Etheridge, A., Fritz, J., May, P., de Beaufort, C., Upadhyaya, B. B., Ghosal, A., Galas, D. J., & Wilmes, P. (14 May 2018). Small RNA profiling of low biomass samples: identification and removal of contaminants. BMC Biology, 16 (52). doi:10.1186/s12915-018-0522-7
Peer Reviewed verified by ORBi

Wilmes, P. (May 2018). Microbiomes in One Health [Paper presentation]. 2nd Luxembourg Microbiology Day, Belvaux, Luxembourg.

Wilmes, P. (May 2018). Systems ecology of microbiomes [Paper presentation]. Annual Meeting of the Norwegian Society of Microbiology, Bergen, Norway.

Wilmes, P. (April 2018). Systems ecology of microbiome-human interactions: identifying which functions are key [Paper presentation]. International Yakult Symposium 2018, Ghent, Belgium.

Wilmes, P. (April 2018). Systems Ecology of microbiomes: function is key [Paper presentation]. Annual Conference 2018 of the Association for General and Applied Microbiology (VAAM), Wolfsburg, Germany.

Wilmes, P. (April 2018). Microbial Systems Ecology for unravelling key functions in situ [Paper presentation]. Microbiology Society Annual Conference, Birmingham, United Kingdom.

Wilmes, P. (April 2018). Le microbiote et son rôle pour la santé de l’Homme [Paper presentation]. Académie Lorraine des Sciences, Nancy, France.

Wilmes, P. (March 2018). Multi-omics approach for microbial communities [Paper presentation]. European Molecular Biology Laboratory (EMBL) Course: Analysis and Integration of Transcriptome and Proteome Data, Heidelberg, Germany.

Habier, J., May, P., Heintz-Buschart, A., Ghosal, A., Wienecke-Baldacchino, A., Nolte-'t Hoen, E. N. M., Wilmes, P., & Fritz, J. (2018). Extraction and Analysis of RNA Isolated from Pure Bacteria-Derived Outer Membrane Vesicles. In V. Arluison & C. V. Valverde, Bacterial Regulatory RNA (Methods in Molecular Biology, pp. 213-230). New York, United States: Humana Press. doi:10.1007/978-1-4939-7634-8_13
Peer reviewed

Greenhalgh, K., Ramiro Garcia, J., Heinken, A. K., Baginska, J., Letellier, E., Halder, R., Frachet Bour, A., Ullmann, P., Thiele, I., Haan, S., & Wilmes, P. (16 February 2018). Cominatorial effect of dietary fibre and Lactobacillus rhamnosus in the context of colorectal cancer therapy [Poster presentation]. Cell Immunology symposium.

Ludwig, M., Wilmes, P., & Schrader, S. (2018). Measuring soil sustainability via soil resilience. The Science of the total environment, 626, 1484-1493. doi:10.1016/j.scitotenv.2017.10.043
Peer reviewed

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

Wilmes, P. (2018). Systems ecology of the human microbiome [Paper presentation]. Innovative Medicines Initiative – 10 year anniversary: Medical data valorisation and sustainability, Dudelange, Luxembourg.

Deutsch, E. W., Perez-Riverol, Y., Chalkley, R. J., Wilhelm, M., Tate, S., Sachsenberg, T., Walzer, M., Kall, L., Delanghe, B., Bocker, S., Schymanski, E., Wilmes, P., Dorfer, V., Kuster, B., Volders, P.-J., Jehmlich, N., Vissers, J. P. C., Wolan, D. W., Wang, A. Y., ... Rost, H. (2018). Expanding the use of spectral libraries in proteomics. Journal of Proteome Research. doi:10.1021/acs.jproteome.8b00485
Peer Reviewed verified by ORBi

Bellenberg, S., Buetti-Dinh, A., Galli, V., Ilie, O., Herold, M., Christel, S., Boretska, M., Pivkin, I. V., Wilmes, P., Sand, W., Vera, M., & Dopson, M. (2018). Automated Microscopic Analysis of Metal Sulfide Colonization by Acidophilic Microorganisms. Applied and Environmental Microbiology, 84 (20). doi:10.1128/AEM.01835-18
Peer Reviewed verified by ORBi

Christel, S., Herold, M., Bellenberg, S., Buetti-Dinh, A., El Hajjami, M., Pivkin, I., Sand, W., Wilmes, P., Poetsch, A., & Dopson, M. (2018). Weak Iron Oxidation by Sulfobacillus thermosulfidooxidans Maintains a Favorable Redox Potential for Chalcopyrite Bioleaching. Frontiers in Microbiology, 9 (December), 1-12. doi:10.3389/fmicb.2018.03059
Peer Reviewed verified by ORBi

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

Wampach, L., Heintz, A., Fritz, J., Ramiro Garcia, J., Habier, J., Herold, M., Narayanasamy, S., Kaysen, A., Hogan, A., Bindl, L., Bottu, J., Halder, R., Sjöqvist, C., May, P., Andersson, A., de Beaufort, C., & Wilmes, P. (2018). Birth mode is associated with earliest strain-conferred gut microbiome functions and immunostimulatory potential. Nature Communications. doi:10.1038/s41467-018-07631-x
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

Noor, F., Kaysen, A., Wilmes, P., & Schneider, J. (2018). The Gut Microbiota and Hematopoietic Stem Cell Transplantation: Challenges and Potentials. Journal of Innate Immunity, 1-11. doi:10.1159/000492943
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

Heintz-Buschart, A., & Wilmes, P. (2018). Human Gut Microbiome: Function Matters. Trends in Microbiology, 26 (7), 563-574. doi:10.1016/j.tim.2017.11.002
Peer Reviewed verified by ORBi

Wilmes, P., Calatayud, M., & Van de Wiele, T. (2018). Resolving host–microbe interactions in the gut: the promise of in vitro models to complement in vivo research. Current Opinion in Microbiology. doi:10.1016/j.mib.2018.07.001
Peer Reviewed verified by ORBi

Laloo, A. E., Wei, J., Wang, D., Narayanasamy, S., Vanwonterghem, I., Waite, D., Steen, J., Kaysen, A., Heintz-Buschart, A., Wang, Q., Schulz, B., Nouwens, A., Wilmes, P., Hugenholtz, P., Yuan, Z., & Bond, P. L. (2018). Mechanisms of Persistence of the Ammonia-Oxidizing Bacteria Nitrosomonas to the Biocide Free Nitrous Acid. Environmental Science and Technology, 52 (9), 5386-5397. doi:10.1021/acs.est.7b04273
Peer Reviewed verified by ORBi

Peisl, B. Y. L., Schymanski, E., & Wilmes, P. (2017). Dark Matter in host-microbiome metabolomics: Tackling the unknowns-A review. Analytica Chimica Acta. doi:10.1016/j.aca.2017.12.034
Peer Reviewed verified by ORBi

Heintz-Buschart, A., Yusuf, D., Kaysen, A., Etheridge, A., Fritz, J., May, P., de Beaufort, C., Upadhyaya, B. B., Ghosal, A., Galas, D. J., & Wilmes, P. (2017). Isolation of nucleic acids from low biomass samples: detection and removal of sRNA contaminants. ORBilu-University of Luxembourg. https://orbilu.uni.lu/handle/10993/33905. doi:10.1101/232975

Wilmes, P. (November 2017). Function First: Systems Ecology of the Human Gut Microbiome [Paper presentation]. ARTORG Center for Biomedical Engineering Research, Bern, Switzerland.

Wilmes, P. (November 2017). Metaproteomics and integrated multi-omics: highlighting unknowns [Paper presentation]. Protein.DTU, University of Copenhagen, Denmark.

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.

Wilmes, P. (October 2017). Integrated multi-omics for enhanced metaproteomics [Paper presentation]. Dagstuhl Seminar on Computational Proteomics, Dagstuhl, Germany.

Wilmes, P. (October 2017). Le microbiome humain et son impact sur la santé [Paper presentation]. Série de conférences " Mieux comprendre la vie par les sciences, Luxembourg-City, Luxembourg.

Wilmes, P. (October 2017). Form follows function: systems ecology of the human gut microbiome [Paper presentation]. Keio University, Tokyo, Japan.

Wilmes, P. (October 2017). Systems ecology of microbial pioneers in the gut [Paper presentation]. Riken Institute for Integrative Medical Sciences, Yokohama, Japan.

Wilmes, P. (September 2017). Form follows function: integrated multi-omics of the human gut microbiome [Paper presentation]. EMBL-EBI Industry programme workshop on the human microbiome: challenges and opportunities for novel therapeutics, Hinxton, United Kingdom. doi:10.1038/nmicrobiol.2016.180

Wilmes, P. (September 2017). Systems ecology of microbiomes: a new frontier of discovery in microbiology [Paper presentation]. School of Environmental Sciences, Norwich, United Kingdom.

Wilmes, P. (August 2017). From integrated multi-omics to microbial systems ecology: quo vadis? [Paper presentation]. Multi-omics for Microbiomes, Washington, United States.

Wilmes, P. (August 2017). Systems ecology of microbiomes: a new frontier of discovery in microbiology [Paper presentation]. The Centre for Translational Medicine (TGen), Arizona, United States.

Wilmes, P. (August 2017). Systems ecology of microbiomes: a new frontier of discovery in microbiology [Paper presentation]. Northern Arizona University, Arizona, United States.

Martinez Arbas, S., Narayanasamy, S., Herold, M., May, P., & Wilmes, P. (21 July 2017). Comparative integrated-omic analyses of phage-host interactions within natural and engineered microbial communities [Poster presentation]. ISCB student council symposium, Prague, Czechia.

Wilmes, P. (June 2017). Integrated multi-omics for identifying discriminant features in the human microbiome [Paper presentation]. Second International Metaproteomics Symposium, Sardinia, Italy.

Wilmes, P. (May 2017). Untangling the microbial ecology of anaerobic digestion through integrated multi-omics [Paper presentation]. Third International Conference on Biogas Microbiology, Wageningen, Netherlands.

Wilmes, P. (May 2017). Systems Ecology of Microbiomes: A New Frontier of Discovery in Microbiology [Paper presentation]. First Luxembourg Microbiology Day, Dudelange, Luxembourg.

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

Wilmes, P. (April 2017). Metaproteomics and integrated multi-omics: What do they tell us about microbial community function? [Paper presentation]. Proteomic Forum 2017 Annual meeting of the German Society for Proteome Research, Potsdam, Germany.

Wilmes, P. (April 2017). From integrated multi-omics to causality: how to distil data, how to design experiments and how to conduct them [Paper presentation]. Fourth Microbiome R&D and Business Collaboration Forum, Amsterdam, Netherlands.

Wilmes, P. (March 2017). Towards systems ecology of the human gut microbiome [Paper presentation]. Nestlé Research Centre, Vers-chez-les-Blancs, Switzerland.

Wilmes, P. (March 2017). Systems Ecology of Microbiomes: A New Frontier of Discovery in Microbiology [Paper presentation]. Annual Meeting of the Strasbourg Society for Microbiology, Strasbourg, France.

Ternes, D., Wilmes, P., Letellier, E., & Haan, S. (05 February 2017). From meta-genomics to causality: Understanding the role of colon cancer-associated bacteria in colorectal cancer [Poster presentation]. Keystone symposia: Microbiome in Health and Disease (J8), Keystone, Colorado, United States.

Wilmes, P. (February 2017). From gut to sludge: how to sustainably manage microbial communities in future [Paper presentation]. Nature Conference on Environmental Microbial Biofilms and Human Microbiomes: Drivers of Future Sustainability, Singapore, Singapore.

Christel, S.* , Herold, M.* , Bellenberg, S., El Hajjami, M., Buetti-Dinh, A., Pivkin, I. V., Sand, W., Wilmes, P., Poetsch, A., & Dopson, M. (2017). Multi-omics reveal the lifestyle of the acidophilic, mineral-oxidizing model species Leptospirillum ferriphilum(T). Applied and Environmental Microbiology. doi:10.1128/AEM.02091-17
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* These authors have contributed equally to this work.

Svartstrom, O., Alneberg, J., Terrapon, N., Lombard, V., de Bruijn, I., Malmsten, J., Dalin, A.-M., El Muller, E., Shah, P., Wilmes, P., Henrissat, B., Aspeborg, H., & Andersson, A. F. (2017). Ninety-nine de novo assembled genomes from the moose (Alces alces) rumen microbiome provide new insights into microbial plant biomass degradation. The ISME journal, 11 (11), 2538-2551. doi:10.1038/ismej.2017.108
Peer reviewed

Broeksema, B., Calusinska, M., McGee, F., Winter, K., Bongiovanni, F., Goux, X., Wilmes, P., Delfosse, P., & Ghoniem, M. (2017). ICoVeR - an interactive visualization tool for verification and refinement of metagenomic bins. BMC Bioinformatics, 18 (1), 233. doi:10.1186/s12859-017-1653-5
Peer Reviewed verified by ORBi

Greenhalgh, K., Fritz, J., Letellier, E., Ramiro Garcia, J., Halder, R., Frachet Bour, A., Baginska, J., Ternes, D., Jäger, C., Haan, S., & Wilmes, P. (2017). A study of the molecular mechanisms underlying teh response of human colorectal adenomacarcinoma enterocytes to prebiotics and probiotics [Poster presentation]. ISAPP conference.

Mac Giolla Eain, M., Baginska, J., Greenhalgh, K., Fritz, J., Zenhausern, F., & Wilmes, P. (2017). Engineering Solutions for Representative Models of the Gastrointestinal Human-Microbe Interface. Engineering. doi:10.1016/J.ENG.2017.01.011
Peer reviewed

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

Heintz, A., Pandey, U., Wicke, T., Sixel-Doring, F., Janzen, A., Sittig-Wiegand, E., Trenkwalder, C., Oertel, W. H., Mollenhauer, B., & Wilmes, P. (2017). The nasal and gut microbiome in Parkinson's disease and idiopathic rapid eye movement sleep behavior disorder. Movement Disorders. doi:10.1002/mds.27105
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Wilmes, P. (December 2016). From integrated omics to microbial systems ecology [Paper presentation]. Thünen Symposium on Soil Metagenomics 2016, Braunschweig, Germany.

Wilmes, P. (December 2016). Integration of meta-omics data: approaches and applications [Paper presentation]. Thünen Symposium on Soil Metagenomics 2016, Braunschweig, Germany.

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
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Magnusdottir, S., Heinken, A. K., Kutt, L., Ravcheev, D., Bauer, E., Noronha, A., Greenhalgh, K., Jäger, C., Baginska, J., Wilmes, P., Fleming, R. M., & Thiele, I. (2016). Generation of genome-scale metabolic reconstructions for 773 members of the human gut microbiota. Nature Biotechnology. doi:10.1038/nbt.3703
Peer Reviewed verified by ORBi

Wilmes, P. (November 2016). HuMiX, an in vitro model to study the human gut microbiome and immune system [Paper presentation]. European Microbiome Congress, London, United Kingdom.

Wilmes, P. (September 2016). Beyond the shadow of Koch’s postulates: doesn’t expressed function ultimately count in microbiomes? [Paper presentation]. Cold Spring Harbor Asia Conference on Microbiology and the Environment, Suzhou, China.

Wilmes, P. (September 2016). Systems Biology of Microbiomes [Paper presentation]. 41st Federation of European Biochemical Societies Congress, Ephesus, Turkey.

Wilmes, P. (June 2016). Integrated multi-omics of oleaginous microbial consortia in biological wastewater treatment plants [Paper presentation]. Annual Meeting of the Society for Industrial and Microbial Biotechnology, New Orleans, United States.

Wilmes, P. (June 2016). Systems ecology of human-microbe interactions [Paper presentation]. International Kick-off Meeting of the Collaborative Research Centre 1182 "Origin and Function of Metaorganisms, Kiel, Germany.

Greenhalgh, K., Fritz, J., Letellier, E., Frachet Bour, A., Baginska, J., Shah, P., Desai, M., Glaab, E., Jäger, C., Haan, S., & Wilmes, P. (June 2016). A study of the molecular mechanisms underlying the response of human colorectal adenomacarcinoma enterocytes to prebiotics and probiotics [Poster presentation]. ISAPP conference.

Wilmes, P. (May 2016). From metaproteomics to integrated omics: how to figure out what microbes are doing and why this is important [Paper presentation]. University of Bochum, Bochum, Germany.

Greenhalgh, K., Wilmes, P., Meyer, K. M., & Aagaard, K. M. (April 2016). The human gut microbiome in health: establishment and resilience of microbiota over a lifetime. Environmental Microbiology, 18 (7), 2103–2116. doi:10.1111/1462-2920.13318
Peer Reviewed verified by ORBi

Wilmes, P. (March 2016). From meta-omics to microbial systems ecology: What to measure and what is there to learn? [Paper presentation]. European Space Agency workshop on "Short- and long-term research roadmap for the microbial characterization and process modeling of the MELiSSA C1 waste compartment, Leuven, Belgium.

Wilmes, P. (February 2016). Piecing together the puzzle: integrated omics of microbial consortia [Paper presentation]. Symposium on Advances and Application in Metaproteomics, Magdeburg, Germany.

Wilmes, P. (February 2016). From meta-omics to microbial systems ecology: What can we learn? [Paper presentation]. Helmholtz Centre for Infection Research, Braunschweig, Germany.

Desai, M. S., Seekatz, A. M., Koropatkin, N. M., Kamada, N., Hickey, C. A., Wolter, M., Pudlo, N. A., Kitamoto, S., Terrapon, N., Muller, A., Young, V. B., Henrissat, B., Wilmes, P., Stappenbeck, T. S., Nunez, G., & Martens, E. C. (2016). A Dietary Fiber-Deprived Gut Microbiota Degrades the Colonic Mucus Barrier and Enhances Pathogen Susceptibility. Cell, 167 (5), 1339-1353.e21. doi:10.1016/j.cell.2016.10.043
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Shah, P., Fritz, J., Glaab, E., Desai, M. S., Greenhalgh, K., Frachet Bour, A., Niegowska, M., Estes, M., Jäger, C., Seguin-Devaux, C., Zenhausern, F., & Wilmes, P. (2016). A microfluidics-based in vitro model of the gastrointestinal human-microbe interface. Nature Communications, 7, 11535. doi:10.1038/ncomms11535
Peer Reviewed verified by ORBi

Fritz, J., Heintz, A., Ghosal, A., Wampach, L., Etheridge, A., Galas, D., & Wilmes, P. (2016). Sources and Functions of Extracellular Small RNAs in Human Circulation. Annual Review of Nutrition. doi:10.1146/annurev-nutr-071715-050711
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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

Heintz, A., May, P., Laczny, C. C., Lebrun, L., Bellora, C., Krishna, A., Wampach, L., Schneider, J., Hogan, A., de Beaufort, C., & Wilmes, P. (2016). Integrated multi-omics of the human gut microbiome in a case study of familial type 1 diabetes. Nature Microbiology, 2, 16180. doi:10.1038/NMICROBIOL.2016.180
Peer Reviewed verified by ORBi

Heintz, A., May, P., Laczny, C. C., Lebrun, L., Bellora, C., Krishna, A., Wampach, L., Schneider, J., Hogan, A., Beaufort, C. D., & Wilmes, P. (2016). Erratum: Integrated multi-omics of the human gut microbiome in a case study of familial type 1 diabetes. Nature Microbiology, 2, 16227. doi:10.1038/nmicrobiol.2016.227
Peer Reviewed verified by ORBi

Wilmes, P. (November 2015). From integrated omic analyses of the human gastrointestinal microbiome to treatment strategies for improved patient care [Paper presentation]. European Microbiome Congress, London, United Kingdom.

Wilmes, P. (September 2015). From integrated omics to causality: how to close the loop [Paper presentation]. Unlocking the microbiome, London, United Kingdom.

Wilmes, P. (June 2015). Eco-Systems Biology of Natural Microbial Communities [Paper presentation]. Society for General Microbiology meeting on “Microbial Interfaces”, Galway, Ireland.

Kaysen, A., Buschart, A., May, P., Laczny, C. C., Narayanasamy, S., Graf, N., Simon, A., Bittenbring, J., Kreis, S., Schneider, J., & Wilmes, P. (June 2015). Dynamic change of host gastrointestinal microbiome and immune status in relation to mucosal barrier effects during chemotherapy and immune ablative intervention in humans [Poster presentation]. The Human Microbiome, Heidelberg, Germany.

Wampach, L., Buschart, A., Hogan, A., Bindl, L., Bottu, J., Schneider, J., de Beaufort, C., & Wilmes, P. (June 2015). Early dynamics of the gastrointestinal microbiome in infants at risk of metabolic disease in adulthood [Poster presentation]. The Human Microbiome, Heidelberg, Germany.

Wilmes, P. (April 2015). Microbial Systems Ecology: from defining niches to reconstructing matter flows through microbial consortia [Paper presentation]. International Human Microbiome Congress satellite workshop on Integrated Omics, Luxembourg-City, Luxembourg.

Buschart, A., May, P., Laczny, C. C., Lebrun, L., Wampach, L., Hogan, A., Schneider, J., de Beaufort, C., & Wilmes, P. (March 2015). Integrated omics analyses of the human gut microbiome in a multiplex family study of type 1 diabetes mellitus [Poster presentation]. 5th International Human Microbiome Congress, Luxembourg-City, Luxembourg.

Kaysen, A., Heintz, A., Lebrun, L., Graf, N., Simon, A., Bittenbring, J., Kreis, S., Schneider, J., & Wilmes, P. (March 2015). Changes in the human gastrointestinal microbiome during cancer treatments [Poster presentation]. 5th International Human Microbiome Congress, Luxembourg-City, Luxembourg.

Wampach, L., Buschart, A., Hogan, A., Bindl, L., Bottu, J., Schneider, J., de Beaufort, C., & Wilmes, P. (March 2015). Early dynamics of the gastrointestinal microbiome in infants at risk of metabolic disease in adulthood [Poster presentation]. 5th International Human Microbiome Congress, Luxembourg-City, Luxembourg.

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

Ghosal, A., Upadhyaya, B. B., Fritz, J., Heintz, A., Desai, M., Dilimulati, Y., Huang, D., Baumuratov, A., Wang, K., Galas, D. J., & Wilmes, P. (2015). The extracellular RNA complement of Escherichia coli. MicrobiologyOpen. doi:10.1002/mbo3.235
Peer Reviewed verified by ORBi

Laczny, C. C., Sternal, T., Plugaru, V., Gawron, P., Atashpendar, A., Margossian, H. H., Coronado, S., van der Maaten, L., Vlassis, N., & Wilmes, P. (2015). VizBin - an application for reference-independent visualization and human-augmented binning of metagenomic data. Microbiome. doi:10.1186/s40168-014-0066-1
Peer Reviewed verified by ORBi

Mathay, C., Hamot, G., Henry, E., Georges, L., Bellora, C., Lebrun, L., de Witt, B., Ammerlaan, W., Buschart, A., Wilmes, P., & Betsou, F. (2015). Method optimization for fecal sample collection and fecal DNA extraction. Biopreservation and Biobanking, 13 (2), 79-93. doi:10.1089/bio.2014.0031
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

Christel, S., Dopson, M., Vera, M., Sand, W., Herold, M., Wilmes, P., Buetti-Dinh, A., Pivkin, I., Poetsch, A., Nygren, J., & Kubista, M. (2015). Systems Biology of Acidophile Biofilms for Efficient Metal Extraction. Advanced Materials Research, 1130, 312-315. doi:10.4028/www.scientific.net/AMR.1130.312
Peer reviewed

Bauer, E., Laczny, C. C., Magnusdottir, S., Wilmes, P., & Thiele, I. (2015). Phenotypic differentiation of gastrointestinal microbes is reflected in their encoded metabolic repertoires. Microbiome, 3 (55), 1-13. doi:10.1186/s40168-015-0121-6
Peer Reviewed verified by ORBi

Wilmes, P., Heintz, A., & Bond, P. (2015). A decade of metaproteomics: where we stand and what the future holds. Proteomics. doi:10.1002/pmic.201500183
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

Wilmes, P. (November 2014). Ecosystems Biology: from data to control of microbial communities [Paper presentation]. Isaac Newton Institute for Mathematical Sciences, Cambridge, United Kingdom.

Wilmes, P. (November 2014). From integrated omics towards Eco-Systems Biology [Paper presentation]. Institute for Microbiology Seminar Series, Greifswald, Germany.

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

Wilmes, P., estes, M., zenhausern, F., Fritz, J., & Shah, P. (30 October 2014). HuMiX: A MICROFLUIDICS-BASED IN VITRO CO-CULTURE DEVICE FOR INVESTIGATING HOST-MICROBE INTERACTIONS [Paper presentation]. MICROTAS CONFERENCE 2014, SAN ANTONIO, TEXAS, United States.

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.

Wilmes, P. (October 2014). Eco-Systems Biology: from integrated omics to control strategies for mixed microbial communities [Paper presentation]. 4th Joint Conference of the German Society for Hygiene and Microbiology (DGHM) and the Association for General and Applied Microbiology (VAAM), Dresden, Germany.

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.

Wilmes, P. (June 2014). Eco-Systems Biology of human-microbe molecular interactions along the gastrointestinal tract [Paper presentation]. Annual Meeting of Intestinal Microbiology, Tokyo, Japan.

Wilmes, P. (June 2014). Eco-Systems Biology of Natural Microbial Communities [Paper presentation]. Second workshop of the Université de la Grande Région on "Systems Biology, Esch-sur-Alzette, Luxembourg.

Wilmes, P. (May 2014). Integrated omics to eluciate structure-function relationships in microbial biofilms [Paper presentation]. Biofilm6, Vienna, Austria.

Wilmes, P. (May 2014). Integrated omics of microbial communities [Paper presentation]. AllBio2014 workshop, Stockholm, Sweden.

Heintz, A., May, P., Laczny, C. C., Lebrun, L., Wampach, L., Hogan, A., Schneider, J., Wilmes, P., & De Beaufort, C. (30 April 2014). Integrated Omic Analyses of the Human Gut Microbiome in a Multiplex Family Study of Type 1 Diabetes Mellitus [Poster presentation]. EMBO|EMBL Symposium: Translating Diabetes.

Wilmes, P. (April 2014). Metaproteomics for a functional insight to activated sludge [Paper presentation]. Control of water-borne disease: A century of the activated sludge sewage treatment process, Manchester, United Kingdom.

Kaysen, A., Heintz, A., Lebrun, L., Graf, N., Simon, A., Bittenbring, J., Kreis, S., Schneider, J., & Wilmes, P. (April 2014). Dynamic change of host gastrointestinal microbiome and immune status in relation to mucosal barrier effects during chemotherapy and immune ablative intervention in humans [Poster presentation]. Exploring Human Host-Microbiome Interactions in Health and Disease.

Laczny, C. C., Pinel, N., Vlassis, N., & Wilmes, P. (2014). Alignment-free Visualization of Metagenomic Data by Nonlinear Dimension Reduction. Scientific Reports. doi:10.1038/srep04516
Peer Reviewed verified by ORBi

Wilmes, P. (07 March 2014). Method and kit for the isolation of genomic dna, rna, proteins and metabolites from a single biological sample.

Laczny, C. C., May, P., Vlassis, N., & Wilmes, P. (March 2014). Identification of condition-specific microbial populations from human metagenomic data [Poster presentation]. VizBi - Visualizing biological data 2014, Heidelberg, Germany.

Shah, P., & Wilmes, P. (30 January 2014). MEMBRANE ASSEMBLY.

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.

Galas, D. J., Wilmes, P., & Wang, K. (2014). RNA in circulation: sources and functions of extracellular exogenous RNA in blood. In K. Nelson (Ed.), Encyclopedia of Metagenomics. New York, United States: SpringerReference. doi:10.1007/978-1-4614-6418-1_105-2
Peer reviewed

Laczny, C. C., & Wilmes, P. (2014). Towards the Identification of Condition-Specific Microbial Populations from Human Metagenomic Data. In A. Keller & E. Meese (Eds.), Nucleic Acids as Molecular Diagnostics (pp. 241-269). Wiley. doi:10.1002/9783527672165.ch11

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.

Wampach, L., Wilmes, P., & De Beaufort, C. (2013). Microbiome and type 1 diabetes. ORBilu-University of Luxembourg. https://orbilu.uni.lu/handle/10993/15192. doi:10.14496/dia.2104723411.14

Wilmes, P. (October 2013). Eco-Systems Biology of activated sludge microbial communities [Paper presentation]. Department of Biotechnology Seminar Series, Delft, Netherlands.

Heintz, A., May, P., Lebrun, L., Ferrand, J., Trezzi, J.-P., Collignon, S., Wampach, L., Glaab, E., Laczny, C. C., Martins Conde, P., Kaysen, A., Schneider, J., Hiller, K., Hogan, A., Wilmes, P., & de Beaufort, C. (October 2013). Meta-omic Analyses of the Microbiome in a Family Study of Diabetes Mellitus [Poster presentation]. 2nd International Systems Biomedicine Symposium, Belval, Luxembourg.

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.

Shah, P., & Wilmes, P. (23 September 2013). MEMBRANE ASSEMBLY.

Atarshi, K.* , Tanoue, T.* , Oshima, K.* , Suda, W., Nagano, Y., Nishikawa, H., Fukuda, S., Saito, T., Narushima, S., Hase, K., Kim, S., Fritz, J., Wilmes, P., Ueha, S., Matsushima, K., Ohno, H., Olle, B., Sakaguchi, S., Taniguchi, T., ... Honda, K. (08 August 2013). Treg induction by a rationally selected mixture of Clostridia strains from the human microbiota. Nature, 500, 232-236. doi:10.1038/nature12331
Peer Reviewed verified by ORBi
* These authors have contributed equally to this work.

Wilmes, P. (July 2013). From integrated omics to Eco-Systems Biology of mixed microbial communities [Paper presentation]. University of Liège, Liège, Belgium.

Kolker, E., Altintas, I., Bourne, P., Faris, J., Fox, G., Fishman, D., Geraci, C., Hancock, W., Lin, B., Lancet, D., Lisitsa, A., Knight, R., Martens, L., Mesirov, J., Özdemir, V., Schultes, E., Smith, T., Snyder, M., Srivastava, S., ... Wilmes, P. (13 June 2013). Reproducibility: In praise of open research measures. Nature, 498, 170. doi:10.1038/498170b
Peer Reviewed verified by ORBi

Wilmes, P. (June 2013). Microbiome-derived small RNA in human circulation [Paper presentation]. Marabou Symposium on the Role of miRNA in Nutrition and Disease, Stockholm, Sweden.

Wilmes, P. (June 2013). From sludge to gut: towards eco-systems biology of the human microbiome [Paper presentation]. Joint LCSB-ISB Symposium, Luxembourg-City, Luxembourg.

Wilmes, P. (May 2013). From integrated omics to Eco-Systems Biology of microbial community-driven processes [Paper presentation]. EU MinoTaurus Workshop on Contaminated site remediation: application of advanced tools to control biological processes, Rome, Italy.

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.

Wilmes, P., Zenhausern, F., Estes, M., & Shah, P. (2013). Cell culture apparatus and culture methods using same.

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.

Fritz, J., Desai, M., Shah, P., Schneider, J., & Wilmes, P. (2013). From meta-omics to causality: experimental models for human microbiome research. Microbiome, 1 (14). doi:10.1186/2049-2618-1-14
Peer Reviewed verified by ORBi

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
Peer Reviewed verified by ORBi

Wilmes, P. (December 2012). Eco-Systems Biology of the human microbiome highlights the potential importance of small RNAs in human-microbe interactions [Paper presentation]. Research Center for Allergy and Immunology Seminar Series, Yokohama, Japan.

Wilmes, P. (November 2012). Eco-Systems Biology of the Human Microbiome [Paper presentation]. Personalised Medicine Consortium Retreat, Mondorf-les-Bains, Luxembourg.

Wilmes, P. (October 2012). Eco-Systems Biology of natural microbial communities [Paper presentation]. Annual Meeting of the French Society for Electrophoresis and Proteomic Analysis, Rouen, France.

Shah, P., & Wilmes, P. (25 August 2012). humix: a microfluidics-based in vitro co-culture device for investigating human-microbial molecular interactions [Paper presentation]. ISME Conference.

Wilmes, P. (June 2012). Inferring basic ecological and evolutionary processes in microbial communities from molecular network analysis [Paper presentation]. Tenth International Conference on Pathways, Rhodes, Greece.

Wilmes, P. (June 2012). Eco-Systems Biology: from wastewater plant to the human gastrointestinal tract [Paper presentation]. ISB-LCSB Symposium, Esch-sur-Alzette, Luxembourg.

Wilmes, P. (May 2012). Integrated “omics” for uncovering cryptic ecological and evolutionary processes in mixed microbial communities [Paper presentation]. Department of Limnology Seminar Series, Vienna, Austria.

Wilmes, P. (May 2012). Inferring synergism and antagonism in microbial communities from network dynamics [Paper presentation]. Molecular Microbial Ecology Seminar Series, Dübendorf, Switzerland.

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.

Wilmes, P. (2012). Genome-based and functional differentiation: hallmarks of microbial adaptation, divergence and speciation? In L. A. Ogilvie & P. R. Hirsch (Eds.), Microbial Ecological Theory: Current Perspectives (pp. 1-23). Norwich, United Kingdom: Horizon Scientific Press.
Peer reviewed

Fischer, C. R.* , Wilmes, P.* , Bowen, B. P., Northen, T. R., & Banfield, J. F. (2012). Deuterium-exchange metabolomics identifies N-methyl lyso phosphatidylethanolamines as abundant lipids in acidophilic mixed microbial communities. Metabolomics : Official journal of the Metabolomic Society, 8 (4), 566-578. doi:10.1007/s11306-011-0344-x
Peer reviewed
* These authors have contributed equally to this work.

Wang, K., Li, H., Yuan, Y., Etheridge, A., Zhou, Y., Huang, D., Wilmes, P., & Galas, D. J. (2012). The complex exogenous RNA spectra in human plasma: an interface with human gut biota? PLoS ONE, 7 (12). doi:10.1371/journal.pone.0051009
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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.

Wilmes, P. (August 2011). Architecture reflects function: high-resolution microscopic and molecular insights into acid mine drainage biofilms [Paper presentation]. Goldschmidt2011 conference, Prague, Czechia.

Wilmes, P. (2011). Microbial community proteomics. In F. de Bruijn (Ed.), Handbook of Molecular Microbial Ecology I: Metagenomics and Complementary Approaches. Wiley-Blackwell. doi:10.1002/9781118010518.ch67
Peer reviewed

Wilmes, P. (April 2011). Microbial Eco-Systems Biology: from molecules to ecosystems and back [Paper presentation]. SciLifeLab Seminar Series, Stockholm, Sweden.

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.

Yelton, A. P., Thomas, B. C., Simmons, S. L., Wilmes, P., Zemla, A., Thelen, M. P., Justice, N., & Banfield, J. F. (2011). A Semi-Quantitative, Synteny-Based Method to Improve Functional Predictions for Hypothetical and Poorly Annotated Bacterial and Archaeal Genes. PLoS Computational Biology, 7 (10), 1002230. doi:10.1371/journal.pcbi.1002230
Peer Reviewed verified by ORBi

Wilmes, P. (January 2011). Capturing the Structure and Dynamics of Complex Microbial Communities [Paper presentation]. Environmental Systems Biology Mini Symposium, Seattle, United States.

Wilmes, P. (January 2011). Microbial Eco-Systems Biology: from molecules to ecosystems and back [Paper presentation]. College of Medicine, Phoenix, United States.

Knierim, B., Luef, B., Wilmes, P., Webb, R. I., Auer, M., Comolli, L. R., & Banfield, J. F. (2011). Correlative microscopy for phylogenetic and ultrastructural characterization of microbial communities. Environmental Microbiology Reports. doi:10.1111/j.1758-2229.2011.00275.x
Peer Reviewed verified by ORBi

Wilmes, P. (November 2010). From molecules to ecosystems and back: bioinformatic approaches for Eco-Systems Biology [Paper presentation]. Lucilinx Annual Symposium, Luxembourg-City, Luxembourg.

Wilmes, P. (October 2010). Eco-systems biology: a new frontier in microbiology [Paper presentation]. Les Jeudis des Sciences, Kirchberg, Luxembourg.

Wilmes, P. (October 2010). Tandem proteomics and metabolomics for elucidating cryptic metabolic transformations within mixed microbial communities [Paper presentation]. Proteomlux 2010: International Conference on Proteomics in Plants, Kirchberg, Luxembourg.

Wilmes, P. (March 2010). Metabolome-proteome differentiation reflects bacterial divergence [Paper presentation]. Systems Biology of Microorganisms, Paris, France. doi:10.1128/mBio.00246-10

Denef, V. J., Kalnejais, L. H., Mueller, R. S., Wilmes, P., Baker, B. J., Thomas, B. C., VerBerkmoes, N. C., Hettich, R. L., & Banfield, J. F. (2010). Proteogenomic basis for ecological divergence of closely related bacteria in natural acidophilic microbial communities. Proceedings of the National Academy of Sciences of the United States of America, 107 (6), 2383-2390. doi:10.1073/pnas.0907041107
Peer Reviewed verified by ORBi

Mueller, R. S., Denef, V. J., Kalnejais, L. H., Suttle, K. B., Thomas, B. C., Wilmes, P., Smith, R. L., Nordstrom, D. K., McCleskey, R. B., Shah, M. B., VerBerkmoes, N. C., Hettich, R. L., & Banfield, J. F. (2010). Ecological distribution and population physiology defined by proteomics in a natural microbial community. Molecular Systems Biology, 6, 1-2. doi:10.1038/msb.2010.30
Peer Reviewed verified by ORBi

Jiao, Y., Cody, G. D., Harding, A. K., Wilmes, P., Schrenk, M., Wheeler, K. E., Banfield, J. F., & Thelen, M. P. (2010). Characterization of Extracellular Polymeric Substances from Acidophilic Microbial Biofilms. Applied and Environmental Microbiology, 76 (9), 2916-2922. doi:10.1128/AEM.02289-09
Peer Reviewed verified by ORBi

Wilmes, P., Bowen, B. P., Thomas, B. C., Mueller, R. S., Denef, V. J., VerBerkmoes, N. C., Hettich, R. L., Northen, T. R., & Banfield, J. F. (2010). Metabolome-Proteome Differentiation Coupled to Microbial Divergence. mBio, 1 (5), 00246-10. doi:10.1128/mBio.00246-10
Peer reviewed

Wilmes, P., & Bond, P. L. (2009). Microbial community proteomics: elucidating the catalysts and metabolic mechanisms that drive the Earth's biogeochemical cycles. Current Opinion in Microbiology, 12 (3), 310-317. doi:10.1016/j.mib.2009.03.004
Peer Reviewed verified by ORBi

Wilmes, P., Simmons, S., Denef, V. J., & Banfield, J. F. (2009). The dynamic genetic repertoire of microbial communities. FEMS Microbiology Reviews, 33 (1), 109-132. doi:10.1111/j.1574-6976.2008.00144.x
Peer Reviewed verified by ORBi

Wilmes, P., Remis, J. P., Hwang, M., Auer, M., Thelen, M. P., & Banfield, J. F. (2009). Natural acidophilic biofilm communities reflect distinct organismal and functional organization. ISME Journal, 3 (2), 266-270. doi:10.1038/ismej.2008.90
Peer Reviewed verified by ORBi

Wilmes, P. (October 2008). Community proteogenomics highlights microbial strain-variant protein expression within activated sludge performing enhanced biological phosphorus removal [Paper presentation]. Proteomlux 2008: International Conference on Proteomics in Plants, Kirchberg, Luxembourg. doi:10.1038/ismej.2008.38

Wilmes, P. (August 2008). Organismal and functional partitioning within natural microbial communities [Paper presentation]. 12th International Symposium on Microbial Ecology (ISME-12), Cairns, Australia.

Wilmes, P., Wexler, M., & Bond, P. L. (2008). Metaproteomics Provides Functional Insight into Activated Sludge Wastewater Treatment. PLoS ONE, 3 (3), 1-2. doi:10.1371/journal.pone.0001778
Peer Reviewed verified by ORBi

Wilmes, P., Andersson, A. F., Lefsrud, M. G., Wexler, M., Shah, M., Zhang, B., Hettich, R. L., Bond, P. L., VerBerkmoes, N. C., & Banfield, J. F. (2008). Community proteogenomics highlights microbial strain-variant protein expression within activated sludge performing enhanced biological phosphorus removal. ISME Journal, 2 (8), 853-864. doi:10.1038/ismej.2008.38
Peer Reviewed verified by ORBi

Wilmes, P. (December 2007). Natural microbial assemblages reflect distinct organismal and functional partitioning [Paper presentation]. American Geophysical Union Fall Meeting, California, United States.

Wilmes, P. (July 2006). Environmental proteomics, a new window on microbial community function [Paper presentation]. 11th International Symposium on Microbial Ecology (ISME-11), Vienna, Austria.

Wilmes, P. (June 2006). Metaproteomic investigations of enhanced biological phosphorus removal in activated sludge [Paper presentation]. Joint Genome Institute Microbial Ecology Program Seminar Series, California, United States.

Wilmes, P. (2006). Metaproteomics: studying functional gene expression in microbial ecosystems [Paper presentation]. Proteomlux 2006: Bridging the Gap Between Gene Expression and Biological Function, Kirchberg, Luxembourg.

Wilmes, P., & Bond, P. L. (2006). Towards exposure of elusive metabolic mixed-culture processes: the application of metaproteomic analyses to activated sludge. Water Science & Technology, 54 (1), 217-226. doi:10.2166/wst.2006.390
Peer reviewed

Wilmes, P., & Bond, P. L. (2006). Metaproteomics: studying functional gene expression in microbial ecosystems. Trends in Microbiology, 14 (2), 92-97. doi:10.1016/J.TIM.2005.12.006
Peer reviewed

Wilmes, P. (September 2005). Metaproteomics: studying functional gene expression in microbial ecosystems [Paper presentation]. Peptidomics: methods and applications, Surrey, United Kingdom.

Wilmes, P. (July 2005). Finding the proteomic keys to unlock the metabolic mysteries of enhanced biological phosphorus removal [Paper presentation]. UK Molecular Microbial Ecology Group meeting, Norwich, United Kingdom.

Wilmes, P. (July 2005). Towards exposure of elusive metabolic mixed-culture processes: the application of metaproteomic analyses to activated sludge [Paper presentation]. Fourth International Water Association Activated Sludge Population Dynamics Specialist Conference entitled Microbial Population Dynamics in Biological Wastewater Treatment, Gold Coast, Australia. doi:10.2166/wst.2006.390

Wilmes, P. (January 2005). The metaproteome: dynamic function of a complex microbial system [Paper presentation]. Microbes in Norwich, Norwich, United Kingdom.

Wilmes, P. (July 2004). Metaproteomic investigations of enhanced biological phosphorus removal in activated sludge [Paper presentation]. UK Molecular Microbial Ecology Group meeting, Colchester, United Kingdom.

Wilmes, P., & Bond, P. L. (2004). The application of two-dimensional polyacrylamide gel electrophoresis and downstream analyses to a mixed community of prokaryotic microorganisms. Environmental Microbiology, 6 (9), 911-920. doi:10.1111/j.1462-2920.2004.00687.x
Peer Reviewed verified by ORBi

Wilmes, P. (April 2003). Towards exposure of an elusive metabolic mixed culture process: microbial details of enhanced biological phosphate removal in activated sludge [Paper presentation]. UK Molecular Microbial Ecology Group meeting, Oxford, United Kingdom.

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