Format
Sort by
Items per page

Send to

Choose Destination

Search results

Items: 1 to 50 of 70

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.

Macrophage-Specific NF-κB Activation Dynamics Can Segregate Inflammatory Bowel Disease Patients.

Papoutsopoulou S, Burkitt MD, Bergey F, England H, Hough R, Schmidt L, Spiller DG, White MHR, Paszek P, Jackson DA, Martins Dos Santos VAP, Sellge G, Pritchard DM, Campbell BJ, Müller W, Probert CS.

Front Immunol. 2019 Sep 11;10:2168. doi: 10.3389/fimmu.2019.02168. eCollection 2019.

4.

Patient's characteristics and outcomes in necrotising soft-tissue infections: results from a Scandinavian, multicentre, prospective cohort study.

Madsen MB, Skrede S, Perner A, Arnell P, Nekludov M, Bruun T, Karlsson Y, Hansen MB, Polzik P, Hedetoft M, Rosén A, Saccenti E, Bergey F, Martins Dos Santos VAP; INFECT study group, Norrby-Teglund A, Hyldegaard O.

Intensive Care Med. 2019 Sep;45(9):1241-1251. doi: 10.1007/s00134-019-05730-x. Epub 2019 Aug 22.

PMID:
31440795
5.

Pseudomonas putida KT2440 is HV1 certified, not GRAS.

Kampers LFC, Volkers RJM, Martins Dos Santos VAP.

Microb Biotechnol. 2019 Sep;12(5):845-848. doi: 10.1111/1751-7915.13443. Epub 2019 Jun 14.

6.

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.

7.

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.

8.

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.

9.

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.

10.

SyNDI: synchronous network data integration framework.

Lindfors E, van Dam JCJ, Lam CMC, Zondervan NA, Martins Dos Santos VAP, Suarez-Diez M.

BMC Bioinformatics. 2018 Nov 6;19(1):403. doi: 10.1186/s12859-018-2426-5.

11.

Cofactors revisited - Predicting the impact of flavoprotein-related diseases on a genome scale.

Wegrzyn AB, Stolle S, Rienksma RA, Martins Dos Santos VAP, Bakker BM, Suarez-Diez M.

Biochim Biophys Acta Mol Basis Dis. 2019 Feb 1;1865(2):360-370. doi: 10.1016/j.bbadis.2018.10.021. Epub 2018 Oct 29.

12.

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.

13.

DMPy: a Python package for automated mathematical model construction of large-scale metabolic systems.

Smith RW, van Rosmalen RP, Martins Dos Santos VAP, Fleck C.

BMC Syst Biol. 2018 Jun 19;12(1):72. doi: 10.1186/s12918-018-0584-8.

14.

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.

15.

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.

16.

From correlation to causation: analysis of metabolomics data using systems biology approaches.

Rosato A, Tenori L, Cascante M, De Atauri Carulla PR, Martins Dos Santos VAP, Saccenti E.

Metabolomics. 2018;14(4):37. doi: 10.1007/s11306-018-1335-y. Epub 2018 Feb 27. Review.

17.

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.

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.

Necrotizing soft tissue infections - a multicentre, prospective observational study (INFECT): protocol and statistical analysis plan.

Madsen MB, Skrede S, Bruun T, Arnell P, Rosén A, Nekludov M, Karlsson Y, Bergey F, Saccenti E, Martins Dos Santos VAP, Perner A, Norrby-Teglund A, Hyldegaard O.

Acta Anaesthesiol Scand. 2018 Feb;62(2):272-279. doi: 10.1111/aas.13024. Epub 2017 Oct 29.

PMID:
29082520
20.

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.

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.

Predicting the murine enterocyte metabolic response to diets that differ in lipid and carbohydrate composition.

Sinha N, Suarez-Diez M, van Schothorst EM, Keijer J, Martins Dos Santos VAP, Hooiveld GJEJ.

Sci Rep. 2017 Aug 18;7(1):8784. doi: 10.1038/s41598-017-07350-1.

23.

Use of Microarray Datasets to generate Caco-2-dedicated Networks and to identify Reporter Genes of Specific Pathway Activity.

Venkatasubramanian PB, Toydemir G, de Wit N, Saccenti E, Martins Dos Santos VAP, van Baarlen P, Wells JM, Suarez-Diez M, Mes JJ.

Sci Rep. 2017 Jul 28;7(1):6778. doi: 10.1038/s41598-017-06355-0.

24.

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.

25.

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.

26.

More than just a gut feeling: constraint-based genome-scale metabolic models for predicting functions of human intestinal microbes.

van der Ark KCH, van Heck RGA, Martins Dos Santos VAP, Belzer C, de Vos WM.

Microbiome. 2017 Jul 14;5(1):78. doi: 10.1186/s40168-017-0299-x. Review.

27.

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.

28.

Multi-Level Integration of Environmentally Perturbed Internal Phenotypes Reveals Key Points of Connectivity between Them.

Benis N, Kar SK, Martins Dos Santos VAP, Smits MA, Schokker D, Suarez-Diez M.

Front Physiol. 2017 Jun 12;8:388. doi: 10.3389/fphys.2017.00388. eCollection 2017.

29.

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.

30.

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.

31.

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.

32.

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.

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.

Efficient Reconstruction of Predictive Consensus Metabolic Network Models.

van Heck RG, Ganter M, Martins Dos Santos VA, Stelling J.

PLoS Comput Biol. 2016 Aug 26;12(8):e1005085. doi: 10.1371/journal.pcbi.1005085. eCollection 2016 Aug.

35.

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.

36.

Integrated In Silico Analysis of Pathway Designs for Synthetic Photo-Electro-Autotrophy.

Volpers M, Claassens NJ, Noor E, van der Oost J, de Vos WM, Kengen SW, Martins Dos Santos VA.

PLoS One. 2016 Jun 23;11(6):e0157851. doi: 10.1371/journal.pone.0157851. eCollection 2016.

37.

The revisited genome of Pseudomonas putida KT2440 enlightens its value as a robust metabolic chassis.

Belda E, van Heck RG, José Lopez-Sanchez M, Cruveiller S, Barbe V, Fraser C, Klenk HP, Petersen J, Morgat A, Nikel PI, Vallenet D, Rouy Z, Sekowska A, Martins Dos Santos VA, de Lorenzo V, Danchin A, Médigue C.

Environ Microbiol. 2016 Oct;18(10):3403-3424. doi: 10.1111/1462-2920.13230. Epub 2016 Apr 28.

PMID:
26913973
38.

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.

39.

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.

40.

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.

41.

Network analysis of temporal functionalities of the gut induced by perturbations in new-born piglets.

Benis N, Schokker D, Suarez-Diez M, Martins Dos Santos VA, Smidt H, Smits MA.

BMC Genomics. 2015 Jul 29;16:556. doi: 10.1186/s12864-015-1733-8.

42.

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.

43.

Systems-level modeling of mycobacterial metabolism for the identification of new (multi-)drug targets.

Rienksma RA, Suarez-Diez M, Spina L, Schaap PJ, Martins dos Santos VA.

Semin Immunol. 2014 Dec;26(6):610-22. doi: 10.1016/j.smim.2014.09.013. Epub 2014 Oct 23. Review.

44.

Integration of heterogeneous molecular networks to unravel gene-regulation in Mycobacterium tuberculosis.

van Dam JC, Schaap PJ, Martins dos Santos VA, Suárez-Diez M.

BMC Syst Biol. 2014 Sep 26;8:111. doi: 10.1186/s12918-014-0111-5.

45.

Understanding the antimicrobial mechanism of TiO₂-based nanocomposite films in a pathogenic bacterium.

Kubacka A, Diez MS, Rojo D, Bargiela R, Ciordia S, Zapico I, Albar JP, Barbas C, Martins dos Santos VA, Fernández-García M, Ferrer M.

Sci Rep. 2014 Feb 19;4:4134. doi: 10.1038/srep04134.

46.

Microbial stratification in low pH oxic and suboxic macroscopic growths along an acid mine drainage.

Méndez-García C, Mesa V, Sprenger RR, Richter M, Diez MS, Solano J, Bargiela R, Golyshina OV, Manteca Á, Ramos JL, Gallego JR, Llorente I, Martins dos Santos VA, Jensen ON, Peláez AI, Sánchez J, Ferrer M.

ISME J. 2014 Jun;8(6):1259-74. doi: 10.1038/ismej.2013.242. Epub 2014 Jan 16.

47.

Gut microbiota disturbance during antibiotic therapy: a multi-omic approach.

Ferrer M, Martins dos Santos VA, Ott SJ, Moya A.

Gut Microbes. 2014 Jan-Feb;5(1):64-70. doi: 10.4161/gmic.27128. Epub 2013 Dec 13.

48.

Design and analysis of a tunable synchronized oscillator.

Ryback BM, Odoni DI, van Heck RG, van Nuland Y, Hesselman MC, Martins Dos Santos VA, van Passel MW, Hugenholtz F.

J Biol Eng. 2013 Nov 18;7(1):26. doi: 10.1186/1754-1611-7-26.

49.

Functional consequences of microbial shifts in the human gastrointestinal tract linked to antibiotic treatment and obesity.

Hernández E, Bargiela R, Diez MS, Friedrichs A, Pérez-Cobas AE, Gosalbes MJ, Knecht H, Martínez-Martínez M, Seifert J, von Bergen M, Artacho A, Ruiz A, Campoy C, Latorre A, Ott SJ, Moya A, Suárez A, Martins dos Santos VA, Ferrer M.

Gut Microbes. 2013 Jul-Aug;4(4):306-15. doi: 10.4161/gmic.25321. Epub 2013 Jun 12.

50.

Immunoglobulins drive terminal maturation of splenic dendritic cells.

Zietara N, Łyszkiewicz M, Puchałka J, Pei G, Gutierrez MG, Lienenklaus S, Hobeika E, Reth M, Martins dos Santos VA, Krueger A, Weiss S.

Proc Natl Acad Sci U S A. 2013 Feb 5;110(6):2282-7. doi: 10.1073/pnas.1210654110. Epub 2013 Jan 23.

Supplemental Content

Loading ...
Support Center