Publications

 
 

* Indicates senior authorship.

78.            Wilmes P. (2019) The ecology of the unseen. Archives des Sciences Naturelles, Physiques et Mathématiques de l’Institut Grand-Ducal, in press.

77.            Wu, L., Ning, D., Zhang, B., … Wilmes P., … Jizhong Zhou (2019) Global diversity and biogeography of bacterial communities in wastewater treatment plants. Nature Microbiology, online early (doi: 10.1038/s41564-019-0426-5).

76.            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 in press (doi: 10.1016/j.btre.2019.e00321).

75.            Greenhalgh K., Ramiro-Garcia J., Heinken A., Ullmann P., Bintener T., Pacheco M.P., Baginska J., Frachet A., Halder R., Fritz J.V., Sauter T., Thiele I., Haan S., Letellier E., Wilmes P.* (2019) Integrated in vitro and in silico modelling delineates the molecular effects of a synbiotic regimen on colorectal cancer-derived cells. Cell Reports 27:1621-1632.e9 (doi: 10.1016/j.celrep.2019.04.001).

74.            Schmidt T.S.B., Hayward M.R., Coelho L.P., Li S.S., Costea P.I., Voigt A.Y., Maistrenko O.M., Alves R.J., Bergsten E., de Beaufort C., Sobhani I., Heintz-Buschart A., Sunagawa S., Zeller G., Wilmes P., Bork P. (2019) Extensive transmission of microbes along the gastrointestinal tract. eLife 8:e42693 (doi: 10.7554/eLife.42693).

73.            Wampach L., Heintz-Buschart A., Fritz J.V., Herold M., Narayanasamy S., Kaysen A., Hogan A., Bindl L., Bottu J., Sjöqvist C., Ramiro-Garcia J., May P., Andersson A.F., de Beaufort C., Wilmes P.* (2018) Birth mode is associated with earliest gut microbiome functions and immunostimulatory potential. Nature Communications 9:5091 (doi: 10.1038/s41467-018-07631-x).

72.            Christel S., Herold M., Bellenberg S., Buetti-Dinh A., El Hajjami M., Pivkin I.V., Sand W., Wilmes P., Poetsch A., Vera M., Dopson M. (2018) Weak iron oxidation by Sulfobacillus thermosulfidooxidans maintains a favorable redox potential for chalcopyrite bioleaching. Frontiers in Microbiology 9:3059 (doi: 10.3389/fmicb.2018.03059).

71.            Noor F., Kaysen A., Wilmes P., Schneider J. (2018) The gut microbiota and hematopoietic stem cell transplantation: challenges and potentials.  Journal of Innate Immunity, in press (doi: 10.1159/000492943).

70.            Wilmes P.*, Marta C., 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 44:28-33 (doi: 10.1016/j.mib.2018.07.001).

69.            Malabirade A., Habier J., Heintz-Buschart A., May P., Halder R., Etheridge A., Galas D.J., Wilmes P.*, Fritz J.V. (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).

68.            Calusinska M., Goux X., Fossépré M., Muller E.E.L., 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).

67.            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:e01835-18 (doi: 10.1128/AEM.01835-18).

66.            Deutsch E.W., Perez-Riverol Y., Chalkley R.J., Wilhelm M., Tate S., Sachsenberg T., Walzer M., Käll L., Delanghe B., Böcker S., Schymanski E.L., Wilmes P., Dorfer V., Kuster B., Volders P.J., Jehmlich N., Vissers J.P.C., Wolan D.W., Wang A.Y., Mendoza L., Shofstahl J., Dowsey A.W., Griss J., Salek R.M., Neumann S., Binz P.A., Lam H., Vizcaíno J.A., Bandeira N., Röst H. (2018) Expanding the use of spectral libraries in proteomics. Journal of Proteome Research 17: 4051-4060 (doi: 10.1021/acs.jproteome.8b00485).

65.            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 oxidising bacteria Nitrosomonas to the biocide Free Nitrous Acid. Environmental Science and Technology 52:5386-5397 (doi: 10.1021/acs.est.7b04273).

Heintz-Buschart_TiM.png

64.            Chaib De Mares M., Javier Jiménez D., Palladino G., Gutleben J., Lebrun L.A., Muller E.E.L., 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 8:11795 (doi: 10.1038/s41598-018-30134-0).

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

62.            Habier J., May P., Heintz-Buschart A., Ghosal A., Wienecke-Baldacchino A.K., Nolte-'t Hoen E.N.M., Wilmes P., Fritz J.V. (2018) Extraction and analysis of RNA isolated from pure bacteria-derived outer membrane vesicles. Methods in Molecular Biology, 1737:213-230 (doi: 10.1007/978-1-4939-7634-8).

61.            Shah P., Muller E.E.L., Lebrun L.A., 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. Methods in Molecular Biology, 1841:279-291 (doi: 10.1007/978-1-4939-8695-8_19).

60.            Heintz-Buschart A. and Wilmes P.* (2018) Human gut microbiome: function matters. Trends in Microbiology 26:563-574 (doi: 10.1016/j.tim.2017.11.002).

59.            Muller E.E.L., Widder S., Faust K., Herold M., Martinez Arbas S., Wilmes P.* (2018) Using metabolic networks to resolve ecological properties of microbiomes. Current Opinion in Systems Biology 8:73-80 (doi: 10.1016/j.coisb.2017.12.004).

58.            Peisl B.Y.L., Schymanski E., Wilmes P.* (2018) Dark matter in host-microbiome metabolomics: tackling the unknowns. Analytica Chimica Acta, 1037:13-27 (doi: 10.1016/j.aca.2017.12.034).

57.            Christel S., Herold M., Bellenberg S., El Hajjami M., Buetti-Dinh A., Pivkin I., Sand W., Wilmes P., Poetsch A., Dopson M. (2018) Multi-omics reveal the lifestyle of the acidophilic, mineral-oxidizing model species Leptospirillum ferriphilum T. Applied and Environmental Microbiology, 84:e02091-17 (doi: 10.1128/aem.02091-17).

56.            Ludwig M., Wilmes P., Schrader S. (2017) Measuring soil sustainability via soil resilience. Science of the Total Environment, 626:1484-1493 (doi: 10.1016/j.scitotenv.2017.10.043).

55.            Heintz-Buschart A., Pandey U., Wicke T., Sixel-Döring F., Janzen A., Sittig-Wiegand E., Trenkwalder C., Oertel W.H., Mollenhauer B., Wilmes P.* (2018) The nasal and gut microbiome in Parkinson’s disease and idiopathic rapid eye movement sleep behavior disorder. Movement Disorders 33:88-98 (doi: 10.1002/mds.27105). Article among the top 20 downloads in 2017-2018.

54.            Muller E.E.L., Narayanasamy S., Zeimes M., Laczny C.C., Lebrun L.A., Herold M., Hicks N.D., Gillece J.D., Schupp J.M., Keim P., Wilmes P.* (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).

53.            Svartström O., Alneberg J., Terrapon N., Lombard V., de Bruijn I., Malmsten J., Dalin A.M., Muller E.E.L., 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 11:2538-2551 (doi: 10.1038/ismej.2017.108).

52.            Kaysen A., Heintz-Buschart A., Muller E.E.L., Narayanasamy S., Wampach L., Laczny C.C., Graf N., Simon A., Franke K., Bittenbring J., Wilmes P.*, Schneider J.G. (2017) Integrated meta-omic analyses of the gastrointestinal tract microbiome in patients undergoing allogeneic hematopoietic stem cell transplantation. Translational Research 186:79-94 (doi: 10.1016/j.trsl.2017.06.008).

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

50.            Wampach L., Heintz-Buschart A., Hogan A., Muller E.E.L., Narayanasamy S., Laczny C.L., Hugerth L.W., Bindl L., Bottu J., Andersson A.F., 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 8:1-21 (doi: 10.3389/fmicb.2017.00738).

49.            Giolla Eain M.M., Baginska J., Greenhalgh K., Fritz J.V., Zenhausern F., Wilmes P.* (2017) Engineering solutions for representative models of the gastrointestinal human-microbe interface. Engineering 3:60-65 (doi: 10.1016/J.ENG.2017.01.011).

48.            Magnúsdóttir S., Heinken A., Kutt L., Ravcheev D.A., Bauer E., Noronha A., Greenhalgh K., Jäger C., Baginska J., Wilmes P., Fleming R.M.T., Thiele I. (2017) Generation of genome-scale metabolic reconstructions for 773 members of the human gut microbiota. Nature Biotechnology 35: 81-89 (doi: 10.1038/nbt.3703).

47.            Heintz-Buschart A., May P., Laczny C., Lebrun L., Bellora C., Krishna A., Wampach L., Schneider J., Hogan A., de Beaufort C., Wilmes P.* (2017) 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).

46.            Narayanasamy S., Jarosz Y., Muller E.E.L., Heintz-Buschart A., Herold M., Kaysen A., Laczny C.L., Pinel N., May P., Wilmes P.* (2016) IMP: a reproducible pipeline for reference-independent integrated metagenomic and metatranscriptomic analyses. Genome Biology 17:260 (doi: 10.1186/s13059-016-1116-8).

45.            Desai M.S., Seekatz A., Koropatkin N.M., Kamada N., Hickey C., Terrapon N., Muller A., Young V.B., Henrissat B., Wilmes P., Stappenbeck T., Núñez G., Martens E.C. (2016) A dietary fiber-deprived gut microbiota degrades the colonic mucus barrier and enhances pathogen susceptibility. Cell 167:1339–1353 (doi: 10.1016/j.cell.2016.10.043). Awarded Luxembourg National Research Fund (FNR) Award for Outstanding Scientific Publication in 2017.

44.            Shah P., Fritz J.V., Glaab E., Desai M., Greenhalgh K., Frachet 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). Awarded FNR Award for Outstanding Scientific Publication and Award for Outstanding Research-driven Innovation in 2017.

43.            Sheik A.R., Muller E.E.L., Audinot J.-N., Lebrun L.A., Grysan P., Guignard C., Wilmes P.* (2016) In situ phenotypic heterogeneity among single cells of the filamentous bacterium Candidatus Microthrix parvicella. The ISME Journal 10:1274-1279 (doi: 10.1038/ismej.2015.181).

42.            Widder S., Allen R.J., Pfeiffer T., … Wilmes P., Soyer O.S. (2016) Challenges in microbial ecology: building predictive understanding of community function and dynamics. The ISME Journal 10:2557–2568 (doi: 10.1038/ismej.2016.45). 

41.            Laczny C.C., Muller E.E.L., Heintz-Buschart A., Herold M., Lebrun L.A., Hogan A., May P., De Beaufort C., Wilmes P.* (2016) Recovery, refinement, and characterisation of hitherto undescribed population-level genomes from the human gastrointestinal tract. Frontiers in Microbiology 7:884 (doi: 10.3389/fmicb.2016.00884).

40.            Greenhalgh K., Meyer K.M., Aagaard K.M., Wilmes P.* (2016) The human gut microbiome in health: establishment and resilience of microbiota over a lifetime. Environmental Microbiology 18:2103-16 (doi: 10.1111/1462-2920.13318). 

39.            Fritz J.F., Heintz-Buschart 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 36:301-336 (doi: 10.1146/annurev-nutr-071715-050711).

38.            Wilmes P.*, Heintz-Buschart A., Bond P.L. (2015) A decade of metaproteomics: where we stand and what the future holds. Proteomics, 15:3409-3417 (doi: 10.1002/pmic.201500183).

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

36.            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 13:79-93 (doi: 10.1089/bio.2014.0031).

35.            Narayanasamy S., Muller E.E.L., Sheik A., Wilmes P.* (2015) Integrated omics for the identification of key functionalities in biological wastewater treatment microbial communities. Microbial Biotechnology 8:363-368 (doi: 10.1111/1751-7915.12255).

34.            Ghosal A., Upadhyaya B.B., Fritz J.V., Heintz-Buschart A., Desai M.S., Dilimulati Y., Huang D., Baumuratov A., Wang K., Galas D., Wilmes P.* (2015) The extracellular RNA complement of Escherichia coli. MicrobiologyOpen 4:252-266 (doi: 10.1002/mbo3.235).

33.            Laczny C.C., Sternal T., Plugaru V., Atashpendar A., Margossian H.H., Gawron P., Coronado S., van der Maaten L., Vlassis N., and Wilmes P.* (2015) VizBin - an application for reference-independent visualization and human-augmented binning of metagenomic data. Microbiome, 3:1 (doi: 10.1186/s40168-014-0066-1).

32.            Muller E.E.L., Pinel N., Laczny C., Hoopmann M.R., Lebrun L.A., Roume H., May P, Hicks N.D., Liu C.M., Price L.B., Gillece J., Guignard C., Schupp J.M., Vlassis N., Moritz R.L., Baliga N., Keim P.S., Wilmes P.* (2014) Community integrated omics links dominance of a microbial generalist to fine-tuned resource usage. Nature Communications 5:5603 (doi: 10.1038/ncomms6603).

31.            Galas D., Wilmes P. and Wang K. (2014) RNA in circulation: the presence and potential functions of extracellular RNA in the blood. Encyclopedia of Metagenomics. (Nelson K., ed.) Springer Publishing, New York, USA (doi: 10.1007/SpringerReference_303420 2014-02-03).

30.            Laczny C. and Wilmes P.* (2014) Identification of condition-specific microbial populations from human metagenomic data. Nucleic Acids as Molecular Diagnostics. (Keller A. & Meese E. eds.) Wiley-VCH, Weinheim, Germany (doi: 10.1002/9783527672165.ch11). 

29.            Muller E.E.L., Sheik A. R., Wilmes P.* (2014) Lipid-based biofuel production from wastewater. Current Opinion in Biotechnology 30:9–16 (doi: 10.1016/j.copbio.2014.03.007).

28.            Hugerth L.W., Muller E.E.L., Hu Y., Lebrun L.A.M., Roume H., Lundin D., Wilmes P.*, Andersson A.F. (2014) ­Systematic design of 18S rRNA gene primers for determining eukaryotic diversity in microbial consortia. PLoS one 9:e95567 (doi: 10.1371/journal.pone.0095567).

27.            Laczny C., Pinel N., Vlassis N. and Wilmes P.* (2014) Alignment-free visualization of metagenomic data by nonlinear dimension reduction. Scientific Reports 4:4516 (doi: 10.1038/srep04516).

26.            Sheik A. R., Muller E.E.L., Wilmes P.* (2014) A hundred years of activated sludge: time for a rethink. Frontiers in Microbiology 5:47 (doi: 10.3389/fmicb.2014.00047).

25.            Wampach L., Wilmes P., De Beaufort C. (2013) Microbiome and type 1 diabetes. Diapedia (doi:10.14496/dia.2104723411.14) Available from: http://www.diapedia.org/type-1-diabetes-mellitus/2104723411/microbiome-and-type-1-diabetes

24.            Roume H., Heintz-Buschart A., Muller E.E.L. and Wilmes P.* (2013) Sequential isolation of metabolites, RNA, DNA, and proteins from the same unique sample. Methods in Enzymology 513:219–236. Invited article for a special issue on “Microbial Metagenomics, Metatranscriptomics, and Metaproteomics” edited by Edward F. DeLong (doi: 10.1016/B978-0-12-407863-5.00011-3).

23.            Atarashi K., Tanoue T., Suda W., Oshima K., Nagano Y., Nishikawa H., Hase K., Narushima S., Kim S., Fukuda S., Ohno H., Fritz J.V., Wilmes P., Ueha S., Matsushima K., Olle B., Sakaguchi S., Taniguchi T., Morita H., Hattori M., Honda K. (2013) Treg induction by a rationally selected Clostridia cocktail from the human microbiota. Nature 500: 232–236 (doi: 10.1038/nature12331).

22.            Kolker E., Altintas I., Bourne P., Faris J., Fox G., Frishman 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., Toppo S., Wilmes P. (2013) Reproducibility: in praise of open research measures. Nature 498: 170 (doi: 10.1038/498170b).

21.            Muller E. E. L., Glaab E., May P., Vlassis N. and Wilmes P.* (2013) Condensing the omics fog of microbial communities. Trends in Microbiology 21:325-333 (doi: 10.1016/j.tim.2013.04.009). Article featured on the cover of the journal.

20.            Fritz J.V., Desai M.S., Shah P., Schneider J.G and Wilmes P.* (2013) From meta-omics to causality: experimental models for human microbiome research. Microbiome 1:14 (doi: 10.1186/2049-2618-1-14). Awarded “highly accessed” status 2 weeks after online publication.

19.            Roume H., Muller E.E.L., Cordes T., Renaut J., Hiller K., and Wilmes P.* (2013) A biomolecular isolation framework for Eco-Systems Biology. The ISME Journal 7:110–121 (doi: 10.1038/ismej.2012.72). Article among top 10 downloads in 2012. 

18.            Wang K., Li H., Yuan Y., Etheridge A., Huang D., Wilmes P.* and Galas D. (2012) The complex exogenous RNA spectra in human plasma: an interface with human gut biota? PLoS One 7: e51009 (doi: 10.1371/journal.pone.0051009).

17.            Muller E.E.L., 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).

16.            Fischer C.R.°, Wilmes P.°, Bowen B.P., Northen T.R., and Banfield J.F. (2012) Deuterium-exchange metabolomics identifies N-methyl lyso phosphatidylethanolamines as abundant lipids in acidophilic mixed microbial communities. Metabolomics 8:566-578 (°equal contribution; doi: 10.1007/s11306-011-0344-x).

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

14.            Knierim B., Luef B., Wilmes P., Webb R.I., Auer M., Comolli L.R., and Banfield J.F. (2011) Correlative microscopy for phylogenetic and ultrastructural characterization of microbial communities. Environmental Microbiology Reports 4:36-41 (doi: 10.1111/j.1758-2229.2011.00275.x).

13.            Wilmes P.* (2011) Microbial community proteomics. Handbook of Molecular Microbial Ecology I: Metagenomics and Complementary Approaches pp. 627-637. (de Bruijn, F.J., ed.). John Wiley & Sons, Inc., Hoboken, New Jersey, USA (doi: 10.1002/9781118010518.ch67).

12.            Wilmes P., Bowen B.P., Thomas B.C., Mueller R.S., Denef V.J., et al. (2010) Metabolome-proteome differentiation coupled to microbial divergence. mBio 1(5):e00246-10 (doi: 10.1128/mBio.00246-10).

11.            Mueller R.S., Denef V.J., Kalnejais L.H., Suttle K.B., Thomas B.C., Wilmes P., et al. (2010) Ecological distribution and population physiology defined by proteomics in a natural microbial community. Molecular Systems Biology 6:374 (doi: 10.1038/msb.2010.30).

10.            Jiao, Y., Cody, G. D., Harding, A. K., Wilmes P., Schrenk, M., et al. (2010) Characterization of extracellular polymeric substances from acidophilic microbial biofilms. Applied and Environmental Microbiology 76: 2916-2922 (doi: 10.1128/AEM.02289-09).

9.              Denef V.J., Kalnejais L.H., Mueller R.S., Wilmes P., Baker B.J., et al. (2010) Proteogenomic basis for ecological divergence of closely related bacteria in natural acidophilic microbial communities. Proceedings of the National Academy of Sciences 107: 2383-2390 (doi: 10.1073/pnas.0907041107).

8.              Wilmes P. and Bond P.L. (2009) Microbial community proteomics: elucidating the catalysts and metabolic mechanisms that drive the Earth’s biogeochemical cycles. Current Opinion in Microbiology (special issue on microbial proteomics) 3:310-317 (doi: 10.1016/j.mib.2009.03.004). Article featured on the cover of the journal.

7.              Wilmes P.*, Remis J.P., Hwang M., Auer M., Thelen M.P. and Banfield J.F. (2009) Natural acidophilic biofilm communities reflect distinct organismal and functional organization. The ISME Journal 3: 266-270 (doi: 10.1038/ismej.2008.90).

6.              Wilmes P., Simmons S.L., Denef V.J., Banfield J.F. (2009) The dynamic genetic repertoire of microbial communities. FEMS Microbiology Reviews (special issue on Systems Biology) 33: 109–132 (doi: 10.1111/j.1574-6976.2008.00144.x).

5.              Wilmes P., Andersson A.F., Lefsrud, M.G., Wexler M., Shah M., et al. (2008b) Community proteogenomics highlights microbial strain-variant protein expression within activated sludge performing enhanced biological phosphorus removal. The ISME Journal, 2: 853–864 (doi: 10.1038/ismej.2008.38).

4.              Wilmes P., Wexler M. and Bond P.L. (2008a) Metaproteomics provides functional insight into activated sludge wastewater treatment. PLoS ONE 3(3): e1778 (doi: 10.1371/journal.pone.0001778).

3.              Wilmes P.* and Bond P.L. (2006b) Metaproteomics: studying functional gene expression in microbial ecosystems. Trends in Microbiology 14:92-97 (doi: 10.1016/j.tim.2005.12.006).

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

1.                     Wilmes P.* and Bond P.L. (2004) The application of two-dimensional polyacrylamide gel electrophoresis and downstream analyses to a mixed community of prokaryotic microorganisms. Environmental Microbiology 6:911-920 (doi: 10.1111/j.1462-2920.2004.00687.x). Published in the special issue of the journal on Metagenomics.