Publications

 

2011

  1. Ferreira de Oliveira, JMP, van Passel MW, Schaap PJ, de Graaff LH. Proteomic analysis of the secretory response of Aspergillus niger to D-maltose and D-xylose. PlosOne, in press
  2. Andersen MR, Margarita P. Salazar MP, Schaap PJ et al., Comparative genomics of citric-acid-producing Aspergillus niger ATCC 1015 versus enzyme-producing CBS 513.88 Genome Res. 2011 Published in Advance May 4, 2011; doi:10.1101/gr.112169.110
  3. Kubicek CP, Tamayo-Ramos JA et al., Comparative genome sequence analysis underscores mycoparasitism as the ancestral life style of Trichoderma Genome Biology 2011, 12:R40 doi:10.1186/gb-2011-12-4-r40
  4. Omony J, de Graaff LH, van Straten G, van Boxtel AJB Modeling and analysis of the dynamic behavior of the XlnR regulaon in Aspergillus niger BMC Systems Biology 2011, 5:S14
  5. Mela F, Fritsche K, de Boer W, van Veen A, de Graaff LH, van den Berg M and Leveau JHJ Dual transcriptional profiling of a bacterial/fungal confrontation: Collimonas fungivorans versus Aspergillus niger, 2011 in press
  6. Ferreira de Oliveira, JMP and de Graaff LH Proteomics of industrial fungi: trends and insights for biotechnology, Applied Microbiology and Biotechnology, 2011 89:225-37
  7. Kant R, van Passel MW, Palva A, Lucas S, Lapidus A, Glavina Del Rio T, Dalin E, Tice H, Bruce D, Goodwin L, Pitluck S, Larimer FW, Land ML, Hauser L, Sangwan P, de Vos WM, Janssen PH, Smidt H. Genome sequence of Chthoniobacter flavus Ellin428, an aerobic heterotrophic soil bacterium. J Bacteriol. 2011 Apr 1. [Epub ahead of print] PubMed PMID: 21460085.
  8. Kant R, van Passel MW, Sangwan P, Palva A, Lucas S, Copeland A, Lapidus A, Glavina Del Rio T, Dalin E, Tice H, Bruce D, Goodwin L, Pitluck S, Chertkov O, Larimer FW, Land ML, Hauser L, Brettin TS, Detter JC, Han S, de Vos WM, Janssen PH, Smidt H. Genome sequence of Pedosphaera parvula Ellin514, an aerobic verrucomicrobial isolate from pasture soil. J Bacteriol. 2011 Apr 1. [Epub ahead of print] PubMed PMID: 21460084.
  9. van Passel MW, Kant R, Palva A, Copeland A, Lucas S, Lapidus A, Gavina Del Rio T, Pitluck S, Goltsman E, Clum A, Sun H, Schmutz J, Larimer FW, Land ML, Hauser L, Kyrpides N, Mikhailova N, Richardson PP, Janssen PH, de Vos WM, Smidt H. Genome sequence of the Verrucomicrobium Opitutus terrae PB90-1, an abundant inhabitant of rice paddy soil ecosystems. J Bacteriol. 2011 Mar 11. [Epub ahead of print] PubMed PMID: 21398538.
  10. van Passel MW, Kant R, Palva A, Lucas S, Copeland A, Lapidus A, Glavina Del Rio T, Dalin E, Tice H, Bruce D, Goodwin L, Pitluck S, Davenport KW, Sims D, Brettin TS, Detter JC, Han S, Larimer FW, Land ML, Hauser L, Kyrpides N, Ovchinnikova G, Richardson PP, de Vos WM, Smidt H, Zoetendal EG. Genome sequence of Victivallis vadensis ATCC BAA-548, an anaerobic bacterium from the phylum Lentisphaerae, isolated from the human gastro-intestinal tract. J Bacteriol. 2011 Mar 11. [Epub ahead of print] PubMed PMID: 21398537.
  11. van Passel MW, Kant R, Zoetendal EG, Plugge CM, Derrien M, Malfatti SA, Chain PS, Woyke T, Palva A, de Vos WM, Smidt H. The Genome of Akkermansia muciniphila, a Dedicated Intestinal Mucin Degrader, and Its Use in Exploring Intestinal Metagenomes. PLoS One. 2011 Mar 3;6(3):e16876. PubMed PMID: 21390229; PubMed Central PMCID: PMC3048395.
  12. Koutinas M, Kiparissides A, Silva-Rocha R, Lam MC, Martins Dos Santos VA, de Lorenzo V, Pistikopoulos EN, Mantalaris A. Improving the prediction of Pseudomonas putida mt-2 growth kinetics with the use of a gene expression regulation model of the TOL plasmid. 2011. Biochemical Engineering Journal, in press
  13. Leprince, A. de Lorenzo, V., Timmis K, Martins Dos Santos, VAP. Genome minimization through multi-transposon mutagenesis. In “Synthetic Gene Networks”, Methods in Molecular Biology, 2011, in Press
  14. Keurentjes JJ, Angenent GC, Dicke M, Santos VA, Molenaar J, van der Putten WH, de Ruiter PC, Struik PC, Thomma BP.Thomma. Redefining plant systems biology: from cell to community. Trends in Plant Sciences, 2011. 16:183-190
  15. Oberhardt M, Puchalka J, Martins dos Santos, VAP, Papin JA. Reconciliation of Genome-Scale Metabolic Reconstructions for Comparative Systems Analysis PLoS Comp Biol. 2011 Epub 2011 Mar 31
  16. Koutinas M, Kiparissides A, Silva-Rocha R, Lam MC, Martins Dos Santos VA, de Lorenzo V, Pistikopoulos EN, Mantalaris A. Linking genes to microbial growth kinetics-An integrated biochemical systems engineering approach. 2011, Metab Eng. Feb 16. [Epub ahead of print].
  17. Silva-Rocha R, Tamames J, Dos Santos VM, de Lorenzo V. The logicome of environmental bacteria: merging catabolic and regulatory events with Boolean formalisms. Environ Microbiol. 2011 Mar 16. doi: 10.1111/j.1462-2920.2011.02455.
  18. van Duuren JB, Brehmer B, Mars AE, Eggink G, Dos Santos VA, Sanders JP. A limited LCA of bio-adipic acid: Manufacturing the nylon-6,6 precursor adipic acid using the benzoic acid degradation pathway from different feedstocks. Biotechnol Bioeng. 2011 Feb 15. doi: 10.1002/bit.23074
  19. Rooijers K, Kolmeder C, Juste C, Dore J,de Been M, Boeren S, Galan P, Beauvallet C, de Vos WM, Schaap PJ An Iterative Workflow for Mining the Human Intestinal Metaproteome BMC Genomics 2011, 12:6

2010

  1. Braaksma M, Martens-Uzunova ES, Punt PJ, Schaap PJ An inventory of the Aspergillus niger secretome by combining in silico predictions with shotgun proteomics data BMC Genomics 2010, 11:584
  2. Ferreira de Oliveira, JMP and de Graaff LH Proteomics of industrial fungi: trends and insights for biotechnology, Applied Microbiology and Biotechnology, 2011 89:225-37
  3. Martins dos Santos, VAP, Damborski, J. Systems Biology at Work. Current Opinion in Biotechnology, 21(4):4981
  4. Derrien M, van Passel MW, van de Bovenkamp JH, Schipper RG, de Vos WM, Dekker J. Mucin-bacterial interactions in the human oral cavity and digestive tract. Gut Microbes. 2010 Jul;1(4):254-268. PubMed PMID: 21327032; PubMed Central PMCID: PMC3023607.
  5. Martins dos Santos, VAP, Muller, M, de Vos W. Systems Biology of the Gut: The Interplay of Food, Microbiota and Host at the Mucosal Interface Current Opinion in Biotechnology 21(4):539-550
  6. Oliveira JM and de Graaff, LH (2010) Proteomics of industrial fungi: trends and insights for biotechnology. Applied Microbiology and Biotechnology, 2010 76:4421-4429
  7. Koutinas M, Lam MC, Kiparissides A, Silva-Rocha R, Godinho M, Livingston AG, Pistikopoulos EN, de Lorenzo V, Martins Dos Santos VA, Mantalaris A. (2010) The regulatory logic of m-xylene biodegradation by Pseudomonas putida mt-2 exposed by dynamic modelling of the principal node Ps/Pr of the TOL plasmid. Environ Microbiol. 2010;12(6):1705-18.
  8. Fazzini RA, Preto MJ, Quintas AC, Bielecka A, Dos Santos VA. Consortia modulation of the stress response: proteomic analysis of single strain versus mixed culture. Environ Microbiol. 2010 12: 2436-2449
  9. Kuipers RK, Joosten HJ, van Berkel WJ, Leferink NG, Rooijen E, Ittmann E, van Zimmeren F, Jochens H, Bornscheuer U, Vriend G, dos Santos VA, Schaap PJ. 3DM: systematic analysis of heterogeneous superfamily data to discover protein functionalities. Proteins. 2010 Ju l;78(9):2101-13.
  10. Kuipers R, van den Bergh T, Joosten HJ, Lekanne Dit Deprez RH, Mannens MM, Schaap PJ. Novel tools for extraction and validation of disease-related mutations applied to fabry disease. Hum Mutat. 2010 Jul 13. [Epub ahead of print]
  11. Oliveira JM, van Passel MW, Schaap PJ, de Graaff LH. Shotgun proteomics of Aspergillus niger microsomes upon D-xylose induction. Appl Environ Microbiol. 2010
  12. Berg, R.A. van den; Braaksma, M.; Veen, D. van der; Werf, M.J. van der; Punt, P.J.; Oost, J. van der; Graaff, L.H. de (2010) Identification of modules in Aspergillus niger by gene co-expression network analysis. Fungal Genetics and Biology 47 (6). - p. 539 - 550.

2005 - 2009

  1. Martens-Uzunova ES, Schaap PJ. Assessment of the pectin degrading enzyme network of Aspergillus niger by functional genomics. Fungal Genet Biol. 2009 Mar;46 Suppl 1:S170-S179. PubMed PMID: 19618506.
  2. Kuipers RK, Joosten HJ, Verwiel E, Paans S, Akerboom J, van der Oost J, Leferink NG, van Berkel WJ, Vriend G, Schaap PJ. Correlated mutation analyses on super-family alignments reveal functionally important residues. Proteins. 2009 Aug 15;76(3):608-16. PubMed PMID: 19274741.
  3. van der Veen D, Oliveira JM, van den Berg WA, de Graaff LH. Analysis of variance components reveals the contribution of sample processing to transcript variation. Appl Environ Microbiol. 2009 Apr;75(8):2414-22. Epub 2009 Feb 20.
  4. Narayanan B, Niu W, Joosten HJ, Li Z, Kuipers RK, Schaap PJ, Dunaway-Mariano D, Herzberg O. Structure and function of 2,3-dimethylmalate lyase, a PEP mutase/isocitrate lyase superfamily member. J Mol Biol. 2009 Feb 20;386(2):486-503. Epub 2008 Dec 24. PubMed PMID: 19133276.
  5. Leferink NG, Fraaije MW, Joosten HJ, Schaap PJ, Mattevi A, van Berkel WJ. Identification of a gatekeeper residue that prevents dehydrogenases from acting as oxidases. J Biol Chem. 2009 Feb 13;284(7):4392-7. Epub 2008 Dec 16. PubMed PMID: 19088070.
  6. Martens-Uzunova ES, Schaap PJ. An evolutionary conserved d-galacturonic acid metabolic pathway operates across filamentous fungi capable of pectin degradation. Fungal Genet Biol. 2008 Nov;45(11):1449-57. Epub 2008 Aug 14. PubMed PMID: 18768163.
  7. van Passel MW, de Graaff LH. Mononucleotide repeats are asymmetrically distributed in fungal genes. BMC Genomics. 2008 Dec 11;9:596. PubMed PMID: 19077233; PubMed Central PMCID: PMC2621210.
  8. Oliveira JM, van der Veen D, de Graaff LH, Qin L. Efficient cloning system for construction of gene silencing vectors in Aspergillus niger. Appl Microbiol Biotechnol. 2008 Oct;80(5):917-24. Epub 2008 Aug 15. PubMed PMID: 18704394.
  9. Tamayo EN, Villanueva A, Hasper AA, de Graaff LH, Ramon D, Orejas M. CreA mediates repression of the regulatory gene xlnR which controls the production of xylanolytic enzymes in Aspergillus nidulans. Fungal Genet Biol. 2008 Jun;45(6):984-93. Epub 2008 Mar 10. PubMed PMID: 18420433.
  10. Stricker AR, Mach RL, de Graaff LH. Regulation of transcription of cellulases- and hemicellulases-encoding genes in Aspergillus niger and Hypocrea jecorina (Trichoderma reesei). Appl Microbiol Biotechnol. 2008 Feb;78(2):211-20. Epub 2008 Jan 16. Review. PubMed PMID: 18197406.
  11. Joosten HJ, Han Y, Niu W, Vervoort J, Dunaway-Mariano D, Schaap PJ. Identification of fungal oxaloacetate hydrolyase within the isocitrate lyase/PEP mutase enzyme superfamily using a sequence marker-based method. Proteins. 2008 Jan 1;70(1):157-66. PubMed PMID: 17654546.
  12. Pel HJ, de Winde JH, Archer DB, Dyer PS, Hofmann G, Schaap PJ, et al., Genome sequencing and analysis of the versatile cell factory Aspergillus niger CBS 513.88. Nat Biotechnol. 2007 Feb;25(2):221-31. PubMed PMID: 17259976.
  13. Han Y, Joosten HJ, Niu W, Zhao Z, Mariano PS, McCalman M, van Kan J, Schaap PJ, Dunaway-Mariano D. Oxaloacetate hydrolase, the C-C bond lyase of oxalate secreting fungi. J Biol Chem. 2007 Mar 30;282(13):9581-90. Epub 2007 Jan 23. PubMed PMID: 17244616.
  14. Martens-Uzunova ES, Zandleven JS, Benen JA, Awad H, Kools HJ, Beldman G, Voragen AG, Van den Berg JA, Schaap PJ. A new group of exo-acting family 28 glycoside hydrolases of Aspergillus niger that are involved in pectin degradation. Biochem J. 2006 Nov 15;400(1):43-52. PubMed PMID: 16822232; PubMed Central PMCID: PMC1635439.
  15. Jalving R, Godefrooij J, Veen WJ, van Ooyen AJ, Schaap PJ. Characterisation of the Aspergillus niger dapB gene, which encodes a novel fungal type IV dipeptidyl aminopeptidase. Mol Genet Genomics. 2005 Jun;273(4):319-25. Epub 2005 Apr 6. PubMed PMID: 15812650.
  16. Bourne Y, Hasper AA, Chahinian H, Renault L, Juin M, de Graaff LH, Marchot P. A. niger protein "EstA", perhaps a new electrotactin, defines a new class of fungal esterases within the alpha/beta hydrolase fold superfamily. Chem Biol Interact. 2005 Dec 15;157-158:395-6
  17. Basten DE, Moers AP, Ooyen AJ, Schaap PJ. Characterisation of Aspergillus niger prolyl aminopeptidase. Mol Genet Genomics. 2005 Feb;272(6):673-9. Epub 2005 Jan 15. PubMed PMID: 15654623.
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