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Unique publications

  1. Mills RH, Vázquez-Baeza Y, Zhu Q, Jiang L, Gaffney J, Humphrey G, et al. Evaluating Metagenomic Prediction of the Metaproteome in a 4.5-Year Study of a Patient with Crohn’s Disease. mSystems. 2019;4. pmid:30801026
  2. 5.Moya A, Ferrer M. Functional edundancy-nduced stability of gut microbiota subjected to disturbance. Trends Microbiol. 2016:402–13. pmid:26996765
  3. 6.Heintz-Buschart A, Wilmes P. Human gut microbiome: function matters. Trends Microbiol. 2018;26:563–74. pmid:29173869
  4. 7.Kleiner M. Metaproteomics: much more than measuring gene expression in microbial communities. mSystems. 2019;4. pmid:31117019
  5. 8.Wilmes P, Bond PL. The application of two-dimensional polyacrylamide gel electrophoresis and downstream analyses to a mixed community of prokaryotic microorganisms. Environ Microbiol. 2004;6:911–20. pmid:15305916
  6. 9.Lassek C, Burghartz M, Chaves-Moreno D, Otto A, Hentschker C, Fuchs S, et al. A metaproteomics approach to elucidate host and pathogen protein expression during catheter-associated urinary tract infections (CAUTIs). Mol Cell Proteomics. 2015;14:989–1008. pmid:25673765
  7. 10.Patnode ML, Beller ZW, Han ND, Cheng J, Peters SL, Terrapon N, et al. Interspecies competition impacts targeted manipulation of human gut bacteria by fiber-derived glycans. Cell. 2019;179:59–73.e13. 10.1016/j.cell.2019.08.011 pmid:31539500
  8. 11.Pathak KV, McGilvrey MI, Hu CK, Garcia-Mansfield K, Lewandoski K, Eftekhari Z, et al. Molecular profiling of innate immune response mechanisms in ventilator-associated Pneumonia. Mol Cell Proteomics. 2020;19:1688–705.
  9. 12.Belda-Ferre P, Williamson J, Simón-Soro Á, Artacho A, Jensen ON, Mira A. The human oral metaproteome reveals potential biomarkers for caries disease. Proteomics. 2015;15:3497–507. pmid:26272225
  10. 13.Gavin PG, Mullaney JA, Loo D, Cao KAL, Gottlieb PA, Hill MM, et al. Intestinal metaproteomics reveals host-microbiota interactions in subjects at risk for type 1 diabetes. Diabetes Care. 2018;41:2178–86. pmid:30100563
  11. 14.Tanca A, Palomba A, Fraumene C, Manghina V, Silverman M, Uzzau S. Clostridial Butyrate Biosynthesis enzymes are significantly depleted in the gut microbiota of nonobese diabetic mice. mSphere. 2018;3. pmid:30355671
  12. 15.Zhang X, Deeke SA, Ning Z, Starr AE, Butcher J, Li J, et al. Metaproteomics reveals associations between microbiome and intestinal extracellular vesicle proteins in pediatric inflammatory bowel disease. Nat Commun. 2018;9. pmid:29339724
  13. 16.Kleiner M, Thorson E, Sharp CE, Dong X, Liu D, Li C, et al. Assessing species biomass contributions in microbial communities via metaproteomics. Nat Commun. 2017;8:1–38. pmid:28232747
  14. 17.Kleiner M, Dong X, Hinzke T, Wippler J, Thorson E, Mayer B, et al. A metaproteomics method to determine carbon sources and assimilation pathways of species in microbial communities. Proc Natl Acad Sci U S A. 2018;115:E5576–84. pmid:29844191
  15. 18.Jehmlich N, Vogt C, Lünsmann V, Richnow HH, von Bergen M. Protein-SIP in environmental studies. Curr Opin Biotechnol. 2016:26–33. pmid:27116035
  16. 19.Smyth P, Zhang X, Ning Z, Mayne J, Moore JI, Walker K, et al. Studying the dynamics of the gut microbiota using metabolically stable isotopic labeling and metaproteomics. bioRxiv. 2020.
  17. 20.Hinzke T, Kouris A, Hughes R-A, Strous M, Kleiner M. More Is Not Always Better: Evaluation of 1D and 2D-LC-MS/MS Methods for Metaproteomics. Front Microbiol. 2019;10:238. pmid:30837968
  18. 21.Meier F, Brunner AD, Koch S, Koch H, Lubeck M, Krause M, et al. Online parallel accumulation–serial fragmentation (PASEF) with a novel trapped ion mobility mass spectrometer. Mol Cell Proteomics. 2018;17:2534–45. pmid:30385480
  19. 22.Aakko J, Pietilä S, Suomi T, Mahmoudian M, Toivonen R, Kouvonen P, et al. Data-Independent Acquisition mass spectrometry in metaproteomics of gut microbiota—implementation and computational analysis. J Proteome Res. 2020;19:432–6. pmid:31755272
  20. 23.Long S, Yang Y, Shen C, Wang Y, Deng A, Qin Q, et al. Metaproteomics characterizes human gut microbiome function in colorectal cancer. NPJ Biofilms Microbiomes. 2020;6:1–10. pmid:32210237
  21. 24.Tanca A, Palomba A, Fraumene C, Pagnozzi D, Manghina V, Deligios M, et al. The impact of sequence database choice on metaproteomic results in gut microbiota studies. Microbiome. 2016:51. pmid:27671352
  22. 25.Rechenberger J, Samaras P, Jarzab A, Behr J, Frejno M, Djukovic A, et al. Challenges in clinical metaproteomics highlighted by the analysis of acute leukemia patients with gut colonization by multidrug-resistant enterobacteriaceae. Proteomes. 2019;7:2. pmid:30626002
  23. 26.Kumar P, Johnson JE, Easterly C, Mehta S, Sajulga R, Nunn B, et al. A sectioning and database enrichment approach for improved peptide spectrum matching in large, genome-guided protein sequence databases. bioRxiv. 2019:843078.

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Omics Publications

  1. Tanca A, Palomba A, Deligios M, Cubeddu T, Fraumene C, Biosa G, et al. Evaluating the Impact of Different Sequence Databases on Metaproteome Analysis: Insights from a Lab-Assembled Microbial Mixture. PLoS ONE. 2013;8:e82981. pmid:24349410
  2. 28.McNulty NP, Wu M, Erickson AR, Pan C, Erickson BK, Martens EC, et al. Effects of diet on resource Utilization by a model human gut microbiota containing Bacteroides cellulosilyticus WH2, a symbiont with an extensive glycobiome. PLoS Biol. 2013;11:e1001637. pmid:23976882
  3. 29.Hettich RL, Pan C, Chourey K, Giannone RJ. Metaproteomics: harnessing the power of high performance mass spectrometry to identify the suite of proteins that control metabolic activities in microbial communities. Anal Chem. 2013;85:4203–14. pmid:23469896
  4. 30.Saito MA, Bulygin VV, Moran DM, Taylor C, Scholin C. Examination of microbial proteome preservation techniques applicable to autonomous environmental sample collection. Front Microbiol. 2011;2. pmid:21687401
  5. 31.Zhang X, Li L, Mayne J, Ning Z, Stintzi A, Figeys D. Assessing the impact of protein extraction methods for human gut metaproteomics. J Proteome. 2018;180:120–7. pmid:28705725
  6. 32.Taylor P, Nielsen PA, Trelle MB, Horning OB, Andersen MB, Vorm O, et al. Automated 2D peptide separation on a 1D nano-LC-MS system. J Proteome Res. 2009;8:1610–6. pmid:19178303
  7. 33.Wiśniewski JR, Zougman A, Nagaraj N, Mann M. Universal sample preparation method for proteome analysis. Nat Methods. 2009;6:359–62. pmid:19377485
  8. 34.Gonzalez CG, Wastyk HC, Topf M, Gardner CD, Sonnenburg JL, Elias JE. High-throughput stool metaproteomics: method and application to human specimens. bioRxiv. 2020. pmid:32606025
  9. 35.Tyanova S, Temu T, Cox J. The MaxQuant computational platform for mass spectrometry-based shotgun proteomics. Nat Protoc. 2016;11:2301–19. pmid:27809316
  10. 36.Citing R packages in your Thesis/Paper/Assignments | Oxford Protein Informatics Group [Internet]. [cited 2020 Jun 12]. Available from: https://www.blopig.com/blog/2013/07/citing-r-packages-in-your-thesispaperassignments/
    • 37.Tyanova S, Temu T, Sinitcyn P, Carlson A, Hein MY, Geiger T, et al. The Perseus computational platform for comprehensive analysis of (prote)omics data. Nat Methods. 2016:731–40. pmid:27348712
    • 38.Heyer R, Schallert K, Büdel A, Zoun R, Dorl S, Behne A, et al. A robust and universal metaproteomics workflow for research studies and routine diagnostics within 24 h using phenol extraction, FASP digest, and the MetaProteomeAnalyzer. Front Microbiol. 2019;101883. pmid:31474963
    • 39.Easterly CW, Sajulga R, Mehta S, Johnson J, Kumar P, Hubler S, et al. MetaQuantome: An integrated, quantitative metaproteomics approach reveals connections between taxonomy and protein function in complex microbiomes. Mol Cell Proteomics. 2019;18:S82–91. pmid:31235611

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    Lieven Gevaert, CEO

    Founder and chief visionary, Lieven is the driving force behind the company. He loves to keep his hands full by participating in the development of the software, marketing, and customer experience strategies.

    Djoumana Ounassis, COO

    Mich loves taking on challenges. With his multi-year experience as Commercial Director in the software industry, Mich has helped the company to get where it is today. Mich is among the best minds.

    Aline Turner, CTO

    Aline is one of the iconic people in life who can say they love what they do. She mentors 100+ in-house developers and looks after the community of thousands of developers.

    Iris Joe, CFO

    Iris, with her international experience, helps us easily understand the numbers and improves them. She is determined to drive success and delivers her professional acumen to bring the company to the next level.