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Items: 1 to 50 of 107

1.

The Empusa code generator and its application to GBOL, an extendable ontology for genome annotation.

van Dam JCJ, Koehorst JJ, Vik JO, Martins Dos Santos VAP, Schaap PJ, Suarez-Diez M.

Sci Data. 2019 Nov 4;6(1):254. doi: 10.1038/s41597-019-0263-7.

2.

In silico-guided engineering of Pseudomonas putida towards growth under micro-oxic conditions.

Kampers LFC, van Heck RGA, Donati S, Saccenti E, Volkers RJM, Schaap PJ, Suarez-Diez M, Nikel PI, Martins Dos Santos VAP.

Microb Cell Fact. 2019 Oct 22;18(1):179. doi: 10.1186/s12934-019-1227-5.

3.

Designing Eukaryotic Gene Expression Regulation Using Machine Learning.

de Jongh RPH, van Dijk ADJ, Julsing MK, Schaap PJ, de Ridder D.

Trends Biotechnol. 2019 Aug 17. pii: S0167-7799(19)30176-3. doi: 10.1016/j.tibtech.2019.07.007. [Epub ahead of print] Review.

PMID:
31431299
4.

Distant Non-Obvious Mutations Influence the Activity of a Hyperthermophilic Pyrococcus furiosus Phosphoglucose Isomerase.

Subramanian K, Mitusińska K, Raedts J, Almourfi F, Joosten HJ, Hendriks S, Sedelnikova SE, Kengen SWM, Hagen WR, Góra A, Martins Dos Santos VAP, Baker PJ, van der Oost J, Schaap PJ.

Biomolecules. 2019 May 31;9(6). pii: E212. doi: 10.3390/biom9060212.

5.

Modeling Host-Pathogen Interaction to Elucidate the Metabolic Drug Response of Intracellular Mycobacterium tuberculosis.

Rienksma RA, Schaap PJ, Martins Dos Santos VAP, Suarez-Diez M.

Front Cell Infect Microbiol. 2019 May 8;9:144. doi: 10.3389/fcimb.2019.00144. eCollection 2019.

6.

Aspergillus niger citrate exporter revealed by comparison of two alternative citrate producing conditions.

Odoni DI, Vazquez-Vilar M, van Gaal MP, Schonewille T, Martins Dos Santos VAP, Tamayo-Ramos JA, Suarez-Diez M, Schaap PJ.

FEMS Microbiol Lett. 2019 Apr 1;366(7). pii: fnz071. doi: 10.1093/femsle/fnz071.

7.

Risk-Based Bioengineering Strategies for Reliable Bacterial Vaccine Production.

Kamminga T, Slagman SJ, Martins Dos Santos VAP, Bijlsma JJE, Schaap PJ.

Trends Biotechnol. 2019 Aug;37(8):805-816. doi: 10.1016/j.tibtech.2019.03.005. Epub 2019 Apr 5. Review.

8.

Consistency, Inconsistency, and Ambiguity of Metabolite Names in Biochemical Databases Used for Genome-Scale Metabolic Modelling.

Pham N, van Heck RGA, van Dam JCJ, Schaap PJ, Saccenti E, Suarez-Diez M.

Metabolites. 2019 Feb 6;9(2). pii: E28. doi: 10.3390/metabo9020028.

9.

Forward Genetics by Genome Sequencing Uncovers the Central Role of the Aspergillus niger goxB Locus in Hydrogen Peroxide Induced Glucose Oxidase Expression.

Laothanachareon T, Tamayo-Ramos JA, Nijsse B, Schaap PJ.

Front Microbiol. 2018 Sep 24;9:2269. doi: 10.3389/fmicb.2018.02269. eCollection 2018.

10.

Modeling the Metabolic State of Mycobacterium tuberculosis Upon Infection.

Rienksma RA, Schaap PJ, Martins Dos Santos VAP, Suarez-Diez M.

Front Cell Infect Microbiol. 2018 Aug 3;8:264. doi: 10.3389/fcimb.2018.00264. eCollection 2018.

11.

Modulating D-amino acid oxidase (DAAO) substrate specificity through facilitated solvent access.

Subramanian K, Góra A, Spruijt R, Mitusińska K, Suarez-Diez M, Martins Dos Santos V, Schaap PJ.

PLoS One. 2018 Jun 15;13(6):e0198990. doi: 10.1371/journal.pone.0198990. eCollection 2018.

12.

Neochloris oleoabundans is worth its salt: Transcriptomic analysis under salt and nitrogen stress.

de Jaeger L, Carreres BM, Springer J, Schaap PJ, Eggink G, Martins Dos Santos VAP, Wijffels RH, Martens DE.

PLoS One. 2018 Apr 13;13(4):e0194834. doi: 10.1371/journal.pone.0194834. eCollection 2018.

13.

Studying microbial functionality within the gut ecosystem by systems biology.

Hornung B, Martins Dos Santos VAP, Smidt H, Schaap PJ.

Genes Nutr. 2018 Mar 6;13:5. doi: 10.1186/s12263-018-0594-6. eCollection 2018. Review.

14.

Deciphering the trophic interaction between Akkermansia muciniphila and the butyrogenic gut commensal Anaerostipes caccae using a metatranscriptomic approach.

Chia LW, Hornung BVH, Aalvink S, Schaap PJ, de Vos WM, Knol J, Belzer C.

Antonie Van Leeuwenhoek. 2018 Jun;111(6):859-873. doi: 10.1007/s10482-018-1040-x. Epub 2018 Feb 19.

15.

Model-driven design of a minimal medium for Akkermansia muciniphila confirms mucus adaptation.

van der Ark KCH, Aalvink S, Suarez-Diez M, Schaap PJ, de Vos WM, Belzer C.

Microb Biotechnol. 2018 May;11(3):476-485. doi: 10.1111/1751-7915.13033. Epub 2018 Jan 26.

16.

Regulation of Three Virulence Strategies of Mycobacterium tuberculosis: A Success Story.

Zondervan NA, van Dam JCJ, Schaap PJ, Martins Dos Santos VAP, Suarez-Diez M.

Int J Mol Sci. 2018 Jan 24;19(2). pii: E347. doi: 10.3390/ijms19020347. Review.

17.

Comparative Genomics Highlights Symbiotic Capacities and High Metabolic Flexibility of the Marine Genus Pseudovibrio.

Versluis D, Nijsse B, Naim MA, Koehorst JJ, Wiese J, Imhoff JF, Schaap PJ, van Passel MWJ, Smidt H, Sipkema D.

Genome Biol Evol. 2018 Jan 1;10(1):125-142. doi: 10.1093/gbe/evx271.

18.

SAPP: functional genome annotation and analysis through a semantic framework using FAIR principles.

Koehorst JJ, van Dam JCJ, Saccenti E, Martins Dos Santos VAP, Suarez-Diez M, Schaap PJ.

Bioinformatics. 2018 Apr 15;34(8):1401-1403. doi: 10.1093/bioinformatics/btx767.

19.

Genomic and functional analysis of Romboutsia ilealis CRIBT reveals adaptation to the small intestine.

Gerritsen J, Hornung B, Renckens B, van Hijum SAFT, Martins Dos Santos VAP, Rijkers GT, Schaap PJ, de Vos WM, Smidt H.

PeerJ. 2017 Sep 11;5:e3698. doi: 10.7717/peerj.3698. eCollection 2017.

20.

Improving heterologous membrane protein production in Escherichia coli by combining transcriptional tuning and codon usage algorithms.

Claassens NJ, Siliakus MF, Spaans SK, Creutzburg SCA, Nijsse B, Schaap PJ, Quax TEF, van der Oost J.

PLoS One. 2017 Sep 13;12(9):e0184355. doi: 10.1371/journal.pone.0184355. eCollection 2017.

21.

Aspergillus niger Secretes Citrate to Increase Iron Bioavailability.

Odoni DI, van Gaal MP, Schonewille T, Tamayo-Ramos JA, Martins Dos Santos VAP, Suarez-Diez M, Schaap PJ.

Front Microbiol. 2017 Aug 2;8:1424. doi: 10.3389/fmicb.2017.01424. eCollection 2017.

22.

Identification of methylated GnTI-dependent N-glycans in Botryococcus brauni.

Schulze S, Urzica E, Reijnders MJMF, van de Geest H, Warris S, Bakker LV, Fufezan C, Martins Dos Santos VAP, Schaap PJ, Peters SA, Hippler M.

New Phytol. 2017 Sep;215(4):1361-1369. doi: 10.1111/nph.14713. Epub 2017 Jul 24.

23.

Protein domain architectures provide a fast, efficient and scalable alternative to sequence-based methods for comparative functional genomics.

Koehorst JJ, Saccenti E, Schaap PJ, Martins Dos Santos VAP, Suarez-Diez M.

Version 3. F1000Res. 2016 Aug 15 [revised 2017 Jan 1];5:1987. doi: 10.12688/f1000research.9416.3. eCollection 2016.

24.

Genome-Scale Model and Omics Analysis of Metabolic Capacities of Akkermansia muciniphila Reveal a Preferential Mucin-Degrading Lifestyle.

Ottman N, Davids M, Suarez-Diez M, Boeren S, Schaap PJ, Martins Dos Santos VAP, Smidt H, Belzer C, de Vos WM.

Appl Environ Microbiol. 2017 Aug 31;83(18). pii: e01014-17. doi: 10.1128/AEM.01014-17. Print 2017 Sep 15.

25.

Metabolic modeling of energy balances in Mycoplasma hyopneumoniae shows that pyruvate addition increases growth rate.

Kamminga T, Slagman SJ, Bijlsma JJE, Martins Dos Santos VAP, Suarez-Diez M, Schaap PJ.

Biotechnol Bioeng. 2017 Oct;114(10):2339-2347. doi: 10.1002/bit.26347. Epub 2017 Jul 27.

26.

Monascus ruber as cell factory for lactic acid production at low pH.

Weusthuis RA, Mars AE, Springer J, Wolbert EJ, van der Wal H, de Vrije TG, Levisson M, Leprince A, Houweling-Tan GB, Pha Moers A, Hendriks SN, Mendes O, Griekspoor Y, Werten MW, Schaap PJ, van der Oost J, Eggink G.

Metab Eng. 2017 Jul;42:66-73. doi: 10.1016/j.ymben.2017.05.005. Epub 2017 Jun 3.

PMID:
28583672
27.

CorNet: Assigning function to networks of co-evolving residues by automated literature mining.

van den Bergh T, Tamo G, Nobili A, Tao Y, Tan T, Bornscheuer UT, Kuipers RKP, Vroling B, de Jong RM, Subramanian K, Schaap PJ, Desmet T, Nidetzky B, Vriend G, Joosten HJ.

PLoS One. 2017 May 18;12(5):e0176427. doi: 10.1371/journal.pone.0176427. eCollection 2017.

28.

Concurrent Haloalkanoate Degradation and Chlorate Reduction by Pseudomonas chloritidismutans AW-1T.

Peng P, Zheng Y, Koehorst JJ, Schaap PJ, Stams AJM, Smidt H, Atashgahi S.

Appl Environ Microbiol. 2017 May 31;83(12). pii: e00325-17. doi: 10.1128/AEM.00325-17. Print 2017 Jun 15.

29.

Comparative proteomics of Rhizopus delemar ATCC 20344 unravels the role of amino acid catabolism in fumarate accumulation.

Odoni DI, Tamayo-Ramos JA, Sloothaak J, van Heck RGA, Martins Dos Santos VAP, de Graaff LH, Suarez-Diez M, Schaap PJ.

PeerJ. 2017 Mar 30;5:e3133. doi: 10.7717/peerj.3133. eCollection 2017.

30.

Persistence of Functional Protein Domains in Mycoplasma Species and their Role in Host Specificity and Synthetic Minimal Life.

Kamminga T, Koehorst JJ, Vermeij P, Slagman SJ, Martins Dos Santos VA, Bijlsma JJ, Schaap PJ.

Front Cell Infect Microbiol. 2017 Feb 7;7:31. doi: 10.3389/fcimb.2017.00031. eCollection 2017.

31.

Draft Genome Sequence of the Oleaginous Green Alga Tetradesmus obliquus UTEX 393.

Carreres BM, de Jaeger L, Springer J, Barbosa MJ, Breuer G, van den End EJ, Kleinegris DM, Schäffers I, Wolbert EJ, Zhang H, Lamers PP, Draaisma RB, Martins Dos Santos VA, Wijffels RH, Eggink G, Schaap PJ, Martens DE.

Genome Announc. 2017 Jan 19;5(3). pii: e01449-16. doi: 10.1128/genomeA.01449-16.

32.

Complete Genome Sequence of Akkermansia glycaniphila Strain PytT, a Mucin-Degrading Specialist of the Reticulated Python Gut.

Ouwerkerk JP, Koehorst JJ, Schaap PJ, Ritari J, Paulin L, Belzer C, de Vos WM.

Genome Announc. 2017 Jan 5;5(1). pii: e01098-16. doi: 10.1128/genomeA.01098-16.

33.

Identification of a Novel L-rhamnose Uptake Transporter in the Filamentous Fungus Aspergillus niger.

Sloothaak J, Odoni DI, Martins Dos Santos VA, Schaap PJ, Tamayo-Ramos JA.

PLoS Genet. 2016 Dec 16;12(12):e1006468. doi: 10.1371/journal.pgen.1006468. eCollection 2016 Dec.

34.

Comparison of 432 Pseudomonas strains through integration of genomic, functional, metabolic and expression data.

Koehorst JJ, van Dam JC, van Heck RG, Saccenti E, Dos Santos VA, Suarez-Diez M, Schaap PJ.

Sci Rep. 2016 Dec 6;6:38699. doi: 10.1038/srep38699.

35.

Complete genome sequence of thermophilic Bacillus smithii type strain DSM 4216(T).

Bosma EF, Koehorst JJ, van Hijum SA, Renckens B, Vriesendorp B, van de Weijer AH, Schaap PJ, de Vos WM, van der Oost J, van Kranenburg R.

Stand Genomic Sci. 2016 Aug 24;11(1):52. doi: 10.1186/s40793-016-0172-8. eCollection 2016.

36.

Identification and functional characterization of novel xylose transporters from the cell factories Aspergillus niger and Trichoderma reesei.

Sloothaak J, Tamayo-Ramos JA, Odoni DI, Laothanachareon T, Derntl C, Mach-Aigner AR, Martins Dos Santos VAP, Schaap PJ.

Biotechnol Biofuels. 2016 Jul 20;9:148. doi: 10.1186/s13068-016-0564-4. eCollection 2016.

37.

NG-Tax, a highly accurate and validated pipeline for analysis of 16S rRNA amplicons from complex biomes.

Ramiro-Garcia J, Hermes GDA, Giatsis C, Sipkema D, Zoetendal EG, Schaap PJ, Smidt H.

Version 2. F1000Res. 2016 Jul 22 [revised 2018 Jan 1];5:1791. doi: 10.12688/f1000research.9227.2. eCollection 2016.

38.

Functional Profiling of Unfamiliar Microbial Communities Using a Validated De Novo Assembly Metatranscriptome Pipeline.

Davids M, Hugenholtz F, Martins dos Santos V, Smidt H, Kleerebezem M, Schaap PJ.

PLoS One. 2016 Jan 12;11(1):e0146423. doi: 10.1371/journal.pone.0146423. eCollection 2016.

39.

RDF2Graph a tool to recover, understand and validate the ontology of an RDF resource.

van Dam JC, Koehorst JJ, Schaap PJ, Martins Dos Santos VA, Suarez-Diez M.

J Biomed Semantics. 2015 Oct 23;6:39. doi: 10.1186/s13326-015-0038-9. eCollection 2015.

40.

Aspergillus niger membrane-associated proteome analysis for the identification of glucose transporters.

Sloothaak J, Odoni DI, de Graaff LH, Martins Dos Santos VAP, Schaap PJ, Tamayo-Ramos JA.

Biotechnol Biofuels. 2015 Sep 17;8:150. doi: 10.1186/s13068-015-0317-9. eCollection 2015.

41.

Assessing the Metabolic Diversity of Streptococcus from a Protein Domain Point of View.

Saccenti E, Nieuwenhuijse D, Koehorst JJ, Martins dos Santos VA, Schaap PJ.

PLoS One. 2015 Sep 14;10(9):e0137908. doi: 10.1371/journal.pone.0137908. eCollection 2015.

42.

Draft genome sequence and characterization of Desulfitobacterium hafniense PCE-S.

Goris T, Hornung B, Kruse T, Reinhold A, Westermann M, Schaap PJ, Smidt H, Diekert G.

Stand Genomic Sci. 2015 Feb 24;10:15. doi: 10.1186/1944-3277-10-15. eCollection 2015.

43.

Unravelling the one-carbon metabolism of the acetogen Sporomusa strain An4 by genome and proteome analysis.

Visser M, Pieterse MM, Pinkse MW, Nijsse B, Verhaert PD, de Vos WM, Schaap PJ, Stams AJ.

Environ Microbiol. 2016 Sep;18(9):2843-55. doi: 10.1111/1462-2920.12973. Epub 2015 Aug 11.

PMID:
26147498
44.

Comparative genomics of Streptococcus pyogenes M1 isolates differing in virulence and propensity to cause systemic infection in mice.

Fiebig A, Loof TG, Babbar A, Itzek A, Koehorst JJ, Schaap PJ, Nitsche-Schmitz DP.

Int J Med Microbiol. 2015 Sep;305(6):532-43. doi: 10.1016/j.ijmm.2015.06.002. Epub 2015 Jun 23.

PMID:
26129624
45.

Proteomic analysis of nitrate-dependent acetone degradation by Alicycliphilus denitrificans strain BC.

Oosterkamp MJ, Boeren S, Atashgahi S, Plugge CM, Schaap PJ, Stams AJ.

FEMS Microbiol Lett. 2015 Jun;362(11). pii: fnv080. doi: 10.1093/femsle/fnv080. Epub 2015 May 14.

PMID:
25977262
46.

Effects of Argonaute on Gene Expression in Thermus thermophilus.

Swarts DC, Koehorst JJ, Westra ER, Schaap PJ, van der Oost J.

PLoS One. 2015 Apr 22;10(4):e0124880. doi: 10.1371/journal.pone.0124880. eCollection 2015.

47.

Genome and proteome analysis of Pseudomonas chloritidismutans AW-1T that grows on n-decane with chlorate or oxygen as electron acceptor.

Mehboob F, Oosterkamp MJ, Koehorst JJ, Farrakh S, Veuskens T, Plugge CM, Boeren S, de Vos WM, Schraa G, Stams AJ, Schaap PJ.

Environ Microbiol. 2016 Oct;18(10):3247-3257. doi: 10.1111/1462-2920.12880. Epub 2015 Jun 5.

PMID:
25900248
48.

Comprehensive insights into transcriptional adaptation of intracellular mycobacteria by microbe-enriched dual RNA sequencing.

Rienksma RA, Suarez-Diez M, Mollenkopf HJ, Dolganov GM, Dorhoi A, Schoolnik GK, Martins Dos Santos VA, Kaufmann SH, Schaap PJ, Gengenbacher M.

BMC Genomics. 2015 Feb 5;16:34. doi: 10.1186/s12864-014-1197-2.

49.

Green genes: bioinformatics and systems-biology innovations drive algal biotechnology.

Reijnders MJ, van Heck RG, Lam CM, Scaife MA, dos Santos VA, Smith AG, Schaap PJ.

Trends Biotechnol. 2014 Dec;32(12):617-26. doi: 10.1016/j.tibtech.2014.10.003. Epub 2014 Oct 21. Review. Erratum in: Trends Biotechnol. 2015 May;33(5):315.

PMID:
25457388
50.

RNA targeting by the type III-A CRISPR-Cas Csm complex of Thermus thermophilus.

Staals RH, Zhu Y, Taylor DW, Kornfeld JE, Sharma K, Barendregt A, Koehorst JJ, Vlot M, Neupane N, Varossieau K, Sakamoto K, Suzuki T, Dohmae N, Yokoyama S, Schaap PJ, Urlaub H, Heck AJ, Nogales E, Doudna JA, Shinkai A, van der Oost J.

Mol Cell. 2014 Nov 20;56(4):518-30. doi: 10.1016/j.molcel.2014.10.005. Epub 2014 Nov 6.

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