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Items: 37

1.

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.

2.

Simulation and Reconstruction of Metabolite-Metabolite Association Networks Using a Metabolic Dynamic Model and Correlation Based Algorithms.

Jahagirdar S, Suarez-Diez M, Saccenti E.

J Proteome Res. 2019 Feb 4. doi: 10.1021/acs.jproteome.8b00781. [Epub ahead of print]

PMID:
30663881
3.

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.

4.

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.

5.

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.

6.

A Constraint-Based Model Analysis of Enterocyte Mitochondrial Adaptation to Dietary Interventions of Lipid Type and Lipid Load.

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

Front Physiol. 2018 Jun 15;9:749. doi: 10.3389/fphys.2018.00749. eCollection 2018.

7.

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.

8.

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.

9.

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.

10.

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.

11.

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.

12.

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.

13.

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.

14.

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.

15.

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.

16.

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.

17.

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.

18.

Plasma and Serum Metabolite Association Networks: Comparability within and between Studies Using NMR and MS Profiling.

Suarez-Diez M, Adam J, Adamski J, Chasapi SA, Luchinat C, Peters A, Prehn C, Santucci C, Spyridonidis A, Spyroulias GA, Tenori L, Wang-Sattler R, Saccenti E.

J Proteome Res. 2017 Jul 7;16(7):2547-2559. doi: 10.1021/acs.jproteome.7b00106. Epub 2017 May 26.

19.

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.

20.

Building pathway graphs from BioPAX data in R.

Benis N, Schokker D, Kramer F, Smits MA, Suarez-Diez M.

Version 2. F1000Res. 2016 Sep 28 [revised 2016 Jan 1];5:2414. eCollection 2016.

21.

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.

22.

Screening and characterization of novel specific peptides targeting MDA-MB-231 claudin-low breast carcinoma by computer-aided phage display methodologies.

Nobrega FL, Ferreira D, Martins IM, Suarez-Diez M, Azeredo J, Kluskens LD, Rodrigues LR.

BMC Cancer. 2016 Nov 14;16(1):881.

23.

Geochemical and microbial community determinants of reductive dechlorination at a site biostimulated with glycerol.

Atashgahi S, Lu Y, Zheng Y, Saccenti E, Suarez-Diez M, Ramiro-Garcia J, Eisenmann H, Elsner M, J M Stams A, Springael D, Dejonghe W, Smidt H.

Environ Microbiol. 2017 Mar;19(3):968-981. doi: 10.1111/1462-2920.13531. Epub 2016 Oct 6.

PMID:
27631786
24.

Cas3-Derived Target DNA Degradation Fragments Fuel Primed CRISPR Adaptation.

Künne T, Kieper SN, Bannenberg JW, Vogel AI, Miellet WR, Klein M, Depken M, Suarez-Diez M, Brouns SJ.

Mol Cell. 2016 Sep 1;63(5):852-64. doi: 10.1016/j.molcel.2016.07.011. Epub 2016 Aug 18.

25.

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.

26.

Effects of Sample Size and Dimensionality on the Performance of Four Algorithms for Inference of Association Networks in Metabonomics.

Suarez-Diez M, Saccenti E.

J Proteome Res. 2015 Dec 4;14(12):5119-30. doi: 10.1021/acs.jproteome.5b00344. Epub 2015 Oct 30.

PMID:
26496246
27.

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.

28.

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.

29.

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.

30.

Probabilistic networks of blood metabolites in healthy subjects as indicators of latent cardiovascular risk.

Saccenti E, Suarez-Diez M, Luchinat C, Santucci C, Tenori L.

J Proteome Res. 2015 Feb 6;14(2):1101-11. doi: 10.1021/pr501075r. Epub 2014 Dec 8.

PMID:
25428344
31.

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.

32.

Degenerate target sites mediate rapid primed CRISPR adaptation.

Fineran PC, Gerritzen MJ, Suárez-Diez M, Künne T, Boekhorst J, van Hijum SA, Staals RH, Brouns SJ.

Proc Natl Acad Sci U S A. 2014 Apr 22;111(16):E1629-38. doi: 10.1073/pnas.1400071111. Epub 2014 Apr 7.

33.

From the environment to the host: re-wiring of the transcriptome of Pseudomonas aeruginosa from 22°C to 37°C.

Barbier M, Damron FH, Bielecki P, Suárez-Diez M, Puchałka J, Albertí S, Dos Santos VM, Goldberg JB.

PLoS One. 2014 Feb 24;9(2):e89941. doi: 10.1371/journal.pone.0089941. eCollection 2014.

34.

Computational protein design with electrostatic focusing: experimental characterization of a conditionally folded helical domain with a reduced amino acid alphabet.

Suárez-Diez M, Pujol AM, Matzapetakis M, Jaramillo A, Iranzo O.

Biotechnol J. 2013 Jul;8(7):855-64. doi: 10.1002/biot.201200380. Epub 2013 Jun 21.

PMID:
23788466
35.

Programmable bacterial catalysis - designing cells for biosynthesis of value-added compounds.

Lam CM, Suárez Diez M, Godinho M, Martins dos Santos VA.

FEBS Lett. 2012 Jul 16;586(15):2184-90. doi: 10.1016/j.febslet.2012.02.030. Epub 2012 Feb 25. Review.

36.

Pushing the limits of automatic computational protein design: design, expression, and characterization of a large synthetic protein based on a fungal laccase scaffold.

Glykys DJ, Szilvay GR, Tortosa P, Suárez Diez M, Jaramillo A, Banta S.

Syst Synth Biol. 2011 Jun;5(1-2):45-58. doi: 10.1007/s11693-011-9080-9. Epub 2011 Mar 20.

37.

Analysis of the microbial gene landscape and transcriptome for aromatic pollutants and alkane degradation using a novel internally calibrated microarray system.

Vilchez-Vargas R, Geffers R, Suárez-Diez M, Conte I, Waliczek A, Kaser VS, Kralova M, Junca H, Pieper DH.

Environ Microbiol. 2013 Apr;15(4):1016-39. doi: 10.1111/j.1462-2920.2012.02752.x. Epub 2012 Apr 20.

PMID:
22515215

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