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Items: 48

1.

Modelling cancer outcomes of bone metastatic patients: combining survival data with N-Telopeptide of type I collagen (NTX) dynamics through joint models.

Loureiro H, Carrasquinha E, Alho I, Ferreira AR, Costa L, Carvalho AM, Vinga S.

BMC Med Inform Decis Mak. 2019 Jan 17;19(1):13. doi: 10.1186/s12911-018-0728-1.

2.

Arthroscopic Superior Capsular Reconstruction With a Minimally Invasive Harvested Fascia Lata Autograft Produces Good Clinical Results.

de Campos Azevedo CI, Ângelo ACLPG, Vinga S.

Orthop J Sports Med. 2018 Nov 27;6(11):2325967118808242. doi: 10.1177/2325967118808242. eCollection 2018 Nov.

3.

Assessing Escherichia coli metabolism models and simulation approaches in phenotype predictions: Validation against experimental data.

Costa RS, Vinga S.

Biotechnol Prog. 2018 Nov;34(6):1344-1354. doi: 10.1002/btpr.2700. Epub 2018 Oct 9.

PMID:
30294889
4.

Robust identification of target genes and outliers in triple-negative breast cancer data.

Segaert P, Lopes MB, Casimiro S, Vinga S, Rousseeuw PJ.

Stat Methods Med Res. 2018 Aug 27:962280218794722. doi: 10.1177/0962280218794722. [Epub ahead of print]

PMID:
30146936
5.

Ensemble outlier detection and gene selection in triple-negative breast cancer data.

Lopes MB, Veríssimo A, Carrasquinha E, Casimiro S, Beerenwinkel N, Vinga S.

BMC Bioinformatics. 2018 May 4;19(1):168. doi: 10.1186/s12859-018-2149-7.

6.

Interplay Between Capsule Expression and Uracil Metabolism in Streptococcus pneumoniae D39.

Carvalho SM, Kloosterman TG, Manzoor I, Caldas J, Vinga S, Martinussen J, Saraiva LM, Kuipers OP, Neves AR.

Front Microbiol. 2018 Mar 6;9:321. doi: 10.3389/fmicb.2018.00321. eCollection 2018.

7.

Identification of influential observations in high-dimensional cancer survival data through the rank product test.

Carrasquinha E, Veríssimo A, Lopes MB, Vinga S.

BioData Min. 2018 Feb 14;11:1. doi: 10.1186/s13040-018-0162-z. eCollection 2018.

8.

OptPipe - a pipeline for optimizing metabolic engineering targets.

Hartmann A, Vila-Santa A, Kallscheuer N, Vogt M, Julien-Laferrière A, Sagot MF, Marienhagen J, Vinga S.

BMC Syst Biol. 2017 Dec 21;11(1):143. doi: 10.1186/s12918-017-0515-0.

9.

Alignment-free sequence comparison: benefits, applications, and tools.

Zielezinski A, Vinga S, Almeida J, Karlowski WM.

Genome Biol. 2017 Oct 3;18(1):186. doi: 10.1186/s13059-017-1319-7. Review.

10.

DegreeCox - a network-based regularization method for survival analysis.

Veríssimo A, Oliveira AL, Sagot MF, Vinga S.

BMC Bioinformatics. 2016 Dec 13;17(Suppl 16):449. doi: 10.1186/s12859-016-1310-4.

11.

Identification and automatic segmentation of multiphasic cell growth using a linear hybrid model.

Hartmann A, Neves AR, Lemos JM, Vinga S.

Math Biosci. 2016 Sep;279:83-9. doi: 10.1016/j.mbs.2016.06.013. Epub 2016 Jul 15.

PMID:
27424949
12.

A Combinatorial Algorithm for Microbial Consortia Synthetic Design.

Julien-Laferrière A, Bulteau L, Parrot D, Marchetti-Spaccamela A, Stougie L, Vinga S, Mary A, Sagot MF.

Sci Rep. 2016 Jul 4;6:29182. doi: 10.1038/srep29182.

13.

Improving Protein Expression Prediction Using Extra Features and Ensemble Averaging.

Fernandes A, Vinga S.

PLoS One. 2016 Mar 2;11(3):e0150369. doi: 10.1371/journal.pone.0150369. eCollection 2016.

14.

Kinetic modeling of cell metabolism for microbial production.

Costa RS, Hartmann A, Vinga S.

J Biotechnol. 2016 Feb 10;219:126-41. doi: 10.1016/j.jbiotec.2015.12.023. Epub 2015 Dec 24. Review.

PMID:
26724578
15.

Dynamic modeling of bone metastasis, microenvironment and therapy: Integrating parathyroid hormone (PTH) effect, anti-resorptive and anti-cancer therapy.

Coelho RM, Lemos JM, Alho I, Valério D, Ferreira AR, Costa L, Vinga S.

J Theor Biol. 2016 Feb 21;391:1-12. doi: 10.1016/j.jtbi.2015.11.024. Epub 2015 Dec 4.

PMID:
26657065
16.

Transcriptional and metabolic effects of glucose on Streptococcus pneumoniae sugar metabolism.

Paixão L, Caldas J, Kloosterman TG, Kuipers OP, Vinga S, Neves AR.

Front Microbiol. 2015 Oct 7;6:1041. doi: 10.3389/fmicb.2015.01041. eCollection 2015.

17.

Host glycan sugar-specific pathways in Streptococcus pneumoniae: galactose as a key sugar in colonisation and infection [corrected].

Paixão L, Oliveira J, Veríssimo A, Vinga S, Lourenço EC, Ventura MR, Kjos M, Veening JW, Fernandes VE, Andrew PW, Yesilkaya H, Neves AR.

PLoS One. 2015 Mar 31;10(3):e0121042. doi: 10.1371/journal.pone.0121042. eCollection 2015. Erratum in: PLoS One. 2015;10(4):e0127483.

18.

Modeling multiple experiments using regularized optimization: A case study on bacterial glucose utilization dynamics.

Hartmann A, Lemos JM, Vinga S.

Comput Biol Med. 2015 Aug;63:301-9. doi: 10.1016/j.compbiomed.2014.08.027. Epub 2014 Sep 15.

PMID:
25248561
19.

KiMoSys: a web-based repository of experimental data for KInetic MOdels of biological SYStems.

Costa RS, Veríssimo A, Vinga S.

BMC Syst Biol. 2014 Aug 13;8:85. doi: 10.1186/s12918-014-0085-3.

20.

Editorial: Alignment-free methods in computational biology.

Vinga S.

Brief Bioinform. 2014 May;15(3):341-2. doi: 10.1093/bib/bbu005. No abstract available.

PMID:
24819825
21.

Global meta-analysis of transcriptomics studies.

Caldas J, Vinga S.

PLoS One. 2014 Feb 26;9(2):e89318. doi: 10.1371/journal.pone.0089318. eCollection 2014.

22.

An extended dynamic model of Lactococcus lactis metabolism for mannitol and 2,3-butanediol production.

Costa RS, Hartmann A, Gaspar P, Neves AR, Vinga S.

Mol Biosyst. 2014 Mar 4;10(3):628-39. doi: 10.1039/c3mb70265k. Epub 2014 Jan 13.

PMID:
24413179
23.

Using information interaction to discover epistatic effects in complex diseases.

Anunciação O, Vinga S, Oliveira AL.

PLoS One. 2013 Oct 23;8(10):e76300. doi: 10.1371/journal.pone.0076300. eCollection 2013.

24.

BGFit: management and automated fitting of biological growth curves.

Veríssimo A, Paixão L, Neves AR, Vinga S.

BMC Bioinformatics. 2013 Sep 25;14:283. doi: 10.1186/1471-2105-14-283.

25.

Information theory applications for biological sequence analysis.

Vinga S.

Brief Bioinform. 2014 May;15(3):376-89. doi: 10.1093/bib/bbt068. Epub 2013 Sep 20. Review.

PMID:
24058049
26.

From physiology to systems metabolic engineering for the production of biochemicals by lactic acid bacteria.

Gaspar P, Carvalho AL, Vinga S, Santos H, Neves AR.

Biotechnol Adv. 2013 Nov;31(6):764-88. doi: 10.1016/j.biotechadv.2013.03.011. Epub 2013 Apr 6. Review.

PMID:
23567148
27.

Fractal MapReduce decomposition of sequence alignment.

Almeida JS, Grüneberg A, Maass W, Vinga S.

Algorithms Mol Biol. 2012 May 2;7(1):12. doi: 10.1186/1748-7188-7-12.

28.

Pattern matching through Chaos Game Representation: bridging numerical and discrete data structures for biological sequence analysis.

Vinga S, Carvalho AM, Francisco AP, Russo LM, Almeida JS.

Algorithms Mol Biol. 2012 May 2;7(1):10. doi: 10.1186/1748-7188-7-10.

29.

Adenoma incidence decreases under the effect of polypectomy.

Rosa I, Fidalgo P, Soares J, Vinga S, Oliveira C, Silva JP, Ferro SM, Chaves P, Oliveira AG, Leitão CN.

World J Gastroenterol. 2012 Mar 21;18(11):1243-8. doi: 10.3748/wjg.v18.i11.1243.

30.

Quantitative modeling of the Saccharomyces cerevisiae FLR1 regulatory network using an S-system formalism.

Calçada D, Vinga S, Freitas AT, Oliveira AL.

J Bioinform Comput Biol. 2011 Oct;9(5):613-30.

PMID:
21976379
31.

A survey on methods for modeling and analyzing integrated biological networks.

Tenazinha N, Vinga S.

IEEE/ACM Trans Comput Biol Bioinform. 2011 Jul-Aug;8(4):943-58. doi: 10.1109/TCBB.2010.117. Review.

PMID:
21116043
32.

Subcellular metabolic organization in the context of dynamic energy budget and biochemical systems theories.

Vinga S, Neves AR, Santos H, Brandt BW, Kooijman SA.

Philos Trans R Soc Lond B Biol Sci. 2010 Nov 12;365(1557):3429-42. doi: 10.1098/rstb.2010.0156. Review.

33.

Optimization strategies for metabolic networks.

Domingues A, Vinga S, Lemos JM.

BMC Syst Biol. 2010 Aug 13;4:113. doi: 10.1186/1752-0509-4-113.

34.

Entropic Profiler - detection of conservation in genomes using information theory.

Fernandes F, Freitas AT, Almeida JS, Vinga S.

BMC Res Notes. 2009 May 5;2:72. doi: 10.1186/1756-0500-2-72.

35.

Identification of neutral biochemical network models from time series data.

Vilela M, Vinga S, Maia MA, Voit EO, Almeida JS.

BMC Syst Biol. 2009 May 5;3:47. doi: 10.1186/1752-0509-3-47.

36.

Biological sequences as pictures: a generic two dimensional solution for iterated maps.

Almeida JS, Vinga S.

BMC Bioinformatics. 2009 Mar 31;10:100. doi: 10.1186/1471-2105-10-100.

37.

Parameter optimization in S-system models.

Vilela M, Chou IC, Vinga S, Vasconcelos AT, Voit EO, Almeida JS.

BMC Syst Biol. 2008 Apr 16;2:35. doi: 10.1186/1752-0509-2-35.

38.

An analysis of the positional distribution of DNA motifs in promoter regions and its biological relevance.

Casimiro AC, Vinga S, Freitas AT, Oliveira AL.

BMC Bioinformatics. 2008 Feb 7;9:89. doi: 10.1186/1471-2105-9-89.

39.

CcrB typing tool: an online resource for staphylococci ccrB sequence typing.

Oliveira DC, Santos M, Milheiriço C, Carriço JA, Vinga S, Oliveira AL, de Lencastre H.

J Antimicrob Chemother. 2008 Apr;61(4):959-60. doi: 10.1093/jac/dkn021. Epub 2008 Jan 27. No abstract available.

PMID:
18227085
40.

Local Renyi entropic profiles of DNA sequences.

Vinga S, Almeida JS.

BMC Bioinformatics. 2007 Oct 16;8:393.

41.

Automated smoother for the numerical decoupling of dynamics models.

Vilela M, Borges CC, Vinga S, Vasconcelos AT, Santos H, Voit EO, Almeida JS.

BMC Bioinformatics. 2007 Aug 21;8:305.

42.

Computing distribution of scale independent motifs in biological sequences.

Almeida JS, Vinga S.

Algorithms Mol Biol. 2006 Oct 18;1:18.

43.

Assessment of allelic variation in the ccrAB locus in methicillin-resistant Staphylococcus aureus clones.

Oliveira DC, Milheiriço C, Vinga S, de Lencastre H.

J Antimicrob Chemother. 2006 Jul;58(1):23-30. Epub 2006 May 30.

PMID:
16735433
44.

Analysis of the genetic variability of virulence-related loci in epidemic clones of methicillin-resistant Staphylococcus aureus.

Gomes AR, Vinga S, Zavolan M, de Lencastre H.

Antimicrob Agents Chemother. 2005 Jan;49(1):366-79.

45.

Rényi continuous entropy of DNA sequences.

Vinga S, Almeida JS.

J Theor Biol. 2004 Dec 7;231(3):377-88.

PMID:
15501469
46.

Comparative evaluation of word composition distances for the recognition of SCOP relationships.

Vinga S, Gouveia-Oliveira R, Almeida JS.

Bioinformatics. 2004 Jan 22;20(2):206-15.

PMID:
14734312
47.

Alignment-free sequence comparison-a review.

Vinga S, Almeida J.

Bioinformatics. 2003 Mar 1;19(4):513-23. Review.

PMID:
12611807
48.

Universal sequence map (USM) of arbitrary discrete sequences.

Almeida JS, Vinga S.

BMC Bioinformatics. 2002;3:6. Epub 2002 Feb 5.

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