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Items: 1 to 50 of 56

1.

PPR-SSM: personalized PageRank and semantic similarity measures for entity linking.

Lamurias A, Ruas P, Couto FM.

BMC Bioinformatics. 2019 Oct 29;20(1):534. doi: 10.1186/s12859-019-3157-y.

2.

FunVar: A systematic pipeline to unravel the convergence patterns of genetic variants in ASD, a paradigmatic complex disease.

Asif M, Vicente AM, Couto FM.

J Biomed Inform. 2019 Oct;98:103273. doi: 10.1016/j.jbi.2019.103273. Epub 2019 Aug 24.

PMID:
31454647
3.

DNA-SeAl: Sensitivity Levels to Optimize the Performance of Privacy-Preserving DNA Alignment.

Fernandes M, Decouchant J, Volp M, Couto FM, Verissimo P.

IEEE J Biomed Health Inform. 2019 Jun 28. doi: 10.1109/JBHI.2019.2914952. [Epub ahead of print]

PMID:
31265423
4.

Semantic Processing.

Couto FM.

Adv Exp Med Biol. 2019;1137:61-91. doi: 10.1007/978-3-030-13845-5_5.

PMID:
31183820
5.

Text Processing.

Couto FM.

Adv Exp Med Biol. 2019;1137:45-60. doi: 10.1007/978-3-030-13845-5_4.

PMID:
31183819
6.

Data Retrieval.

Couto FM.

Adv Exp Med Biol. 2019;1137:17-43. doi: 10.1007/978-3-030-13845-5_3.

PMID:
31183818
7.

Resources.

Couto FM.

Adv Exp Med Biol. 2019;1137:9-15. doi: 10.1007/978-3-030-13845-5_2.

PMID:
31183817
8.

Introduction.

Couto FM.

Adv Exp Med Biol. 2019;1137:1-8. doi: 10.1007/978-3-030-13845-5_1.

PMID:
31183816
9.

Multi-domain semantic similarity in biomedical research.

Ferreira JD, Couto FM.

BMC Bioinformatics. 2019 May 29;20(Suppl 10):246. doi: 10.1186/s12859-019-2810-9.

10.

BO-LSTM: classifying relations via long short-term memory networks along biomedical ontologies.

Lamurias A, Sousa D, Clarke LA, Couto FM.

BMC Bioinformatics. 2019 Jan 7;20(1):10. doi: 10.1186/s12859-018-2584-5.

11.

Identifying disease genes using machine learning and gene functional similarities, assessed through Gene Ontology.

Asif M, Martiniano HFMCM, Vicente AM, Couto FM.

PLoS One. 2018 Dec 10;13(12):e0208626. doi: 10.1371/journal.pone.0208626. eCollection 2018.

12.

MER: a shell script and annotation server for minimal named entity recognition and linking.

Couto FM, Lamurias A.

J Cheminform. 2018 Dec 5;10(1):58. doi: 10.1186/s13321-018-0312-9.

13.

Witches' broom resistant genotype CCN51 shows greater diversity of symbiont bacteria in its phylloplane than susceptible genotype catongo.

Santana JO, Gramacho KP, de Souza Eduvirgens Ferreira KT, Rezende RP, Mangabeira PAO, Dias RPM, Couto FM, Pirovani CP.

BMC Microbiol. 2018 Nov 23;18(1):194. doi: 10.1186/s12866-018-1339-9.

14.

Accurate filtering of privacy-sensitive information in raw genomic data.

Decouchant J, Fernandes M, Völp M, Couto FM, Esteves-Veríssimo P.

J Biomed Inform. 2018 Jun;82:1-12. doi: 10.1016/j.jbi.2018.04.006. Epub 2018 Apr 13.

15.

Tackling the challenges of matching biomedical ontologies.

Faria D, Pesquita C, Mott I, Martins C, Couto FM, Cruz IF.

J Biomed Semantics. 2018 Jan 15;9(1):4. doi: 10.1186/s13326-017-0170-9.

16.

Identifying Human Phenotype Terms by Combining Machine Learning and Validation Rules.

Lobo M, Lamurias A, Couto FM.

Biomed Res Int. 2017;2017:8565739. doi: 10.1155/2017/8565739. Epub 2017 Nov 9.

17.

Generating a Tolerogenic Cell Therapy Knowledge Graph from Literature.

Lamurias A, Ferreira JD, Clarke LA, Couto FM.

Front Immunol. 2017 Nov 29;8:1656. doi: 10.3389/fimmu.2017.01656. eCollection 2017.

18.

Assessing Public Metabolomics Metadata, Towards Improving Quality.

Ferreira JD, Inácio B, Salek RM, Couto FM.

J Integr Bioinform. 2017 Dec 13;14(4). pii: /j/jib.2017.14.issue-4/jib-2017-0054/jib-2017-0054.xml. doi: 10.1515/jib-2017-0054.

19.

Incidence and prevalence of systemic sclerosis in Campo Grande, State of Mato Grosso do Sul, Brazil.

Horimoto AMC, Matos ENN, Costa MRD, Takahashi F, Rezende MC, Kanomata LB, Locatelli EPP, Finotti LT, Maegawa FKM, Rondon RMR, Machado NP, Couto FMAATD, Figueiredo TPA, Ovidio RA, Costa IPD.

Rev Bras Reumatol Engl Ed. 2017 Mar - Apr;57(2):107-114. doi: 10.1016/j.rbre.2016.09.005. Epub 2016 Oct 15. English, Portuguese.

20.

Extracting microRNA-gene relations from biomedical literature using distant supervision.

Lamurias A, Clarke LA, Couto FM.

PLoS One. 2017 Mar 6;12(3):e0171929. doi: 10.1371/journal.pone.0171929. eCollection 2017.

21.

Knowledge Representation and Management: a Linked Data Perspective.

Barros M, Couto FM.

Yearb Med Inform. 2016 Nov 10;(1):178-183. Review.

22.

Functional coherence metrics in protein families.

Bastos HP, Sousa L, Clarke LA, Couto FM.

J Biomed Semantics. 2016 Jun 23;7(1):41. doi: 10.1186/s13326-016-0076-y.

23.

Antifungal activity of the piroctone olamine in experimental intra-abdominal candidiasis.

do Couto FM, do Nascimento SC, Júnior SF, da Silva VK, Leal AF, Neves RP.

Springerplus. 2016 Apr 16;5:468. doi: 10.1186/s40064-016-2130-8. eCollection 2016.

24.

Ontology Alignment Repair through Modularization and Confidence-Based Heuristics.

Santos E, Faria D, Pesquita C, Couto FM.

PLoS One. 2015 Dec 28;10(12):e0144807. doi: 10.1371/journal.pone.0144807. eCollection 2015.

25.

The CHEMDNER corpus of chemicals and drugs and its annotation principles.

Krallinger M, Rabal O, Leitner F, Vazquez M, Salgado D, Lu Z, Leaman R, Lu Y, Ji D, Lowe DM, Sayle RA, Batista-Navarro RT, Rak R, Huber T, Rocktäschel T, Matos S, Campos D, Tang B, Xu H, Munkhdalai T, Ryu KH, Ramanan SV, Nathan S, Žitnik S, Bajec M, Weber L, Irmer M, Akhondi SA, Kors JA, Xu S, An X, Sikdar UK, Ekbal A, Yoshioka M, Dieb TM, Choi M, Verspoor K, Khabsa M, Giles CL, Liu H, Ravikumar KE, Lamurias A, Couto FM, Dai HJ, Tsai RT, Ata C, Can T, Usié A, Alves R, Segura-Bedmar I, Martínez P, Oyarzabal J, Valencia A.

J Cheminform. 2015 Jan 19;7(Suppl 1 Text mining for chemistry and the CHEMDNER track):S2. doi: 10.1186/1758-2946-7-S1-S2. eCollection 2015.

26.

Improving chemical entity recognition through h-index based semantic similarity.

Lamurias A, Ferreira JD, Couto FM.

J Cheminform. 2015 Jan 19;7(Suppl 1 Text mining for chemistry and the CHEMDNER track):S13. doi: 10.1186/1758-2946-7-S1-S13. eCollection 2015.

27.

GRYFUN: a web application for GO term annotation visualization and analysis in protein sets.

Bastos HP, Sousa L, Clarke LA, Couto FM.

PLoS One. 2015 Mar 20;10(3):e0119631. doi: 10.1371/journal.pone.0119631. eCollection 2015.

28.

Automatic concept recognition using the human phenotype ontology reference and test suite corpora.

Groza T, Köhler S, Doelken S, Collier N, Oellrich A, Smedley D, Couto FM, Baynam G, Zankl A, Robinson PN.

Database (Oxford). 2015 Feb 27;2015. pii: bav005. doi: 10.1093/database/bav005. Print 2015.

29.

Automatic background knowledge selection for matching biomedical ontologies.

Faria D, Pesquita C, Santos E, Cruz IF, Couto FM.

PLoS One. 2014 Nov 7;9(11):e111226. doi: 10.1371/journal.pone.0111226. eCollection 2014.

30.

Identifying interactions between chemical entities in biomedical text.

Lamurias A, Ferreira JD, Couto FM.

J Integr Bioinform. 2014 Oct 23;11(3):247. doi: 10.2390/biecoll-jib-2014-247.

PMID:
25339081
31.

The epidemiology ontology: an ontology for the semantic annotation of epidemiological resources.

Pesquita C, Ferreira JD, Couto FM, Silva MJ.

J Biomed Semantics. 2014 Jan 17;5(1):4. doi: 10.1186/2041-1480-5-4.

32.

The semantic web in translational medicine: current applications and future directions.

Machado CM, Rebholz-Schuhmann D, Freitas AT, Couto FM.

Brief Bioinform. 2015 Jan;16(1):89-103. doi: 10.1093/bib/bbt079. Epub 2013 Nov 6. Review.

33.

The next generation of similarity measures that fully explore the semantics in biomedical ontologies.

Couto FM, Pinto HS.

J Bioinform Comput Biol. 2013 Oct;11(5):1371001. doi: 10.1142/S0219720013710017. Epub 2013 Jul 18.

PMID:
24131058
34.

Annotation extension through protein family annotation coherence metrics.

Bastos HP, Clarke LA, Couto FM.

Front Genet. 2013 Oct 11;4:201. doi: 10.3389/fgene.2013.00201. eCollection 2013.

35.

Enrichment analysis applied to disease prognosis.

Machado CM, Freitas AT, Couto FM.

J Biomed Semantics. 2013 Oct 8;4(1):21. doi: 10.1186/2041-1480-4-21.

36.

Exploiting disjointness axioms to improve semantic similarity measures.

Ferreira JD, Hastings J, Couto FM.

Bioinformatics. 2013 Nov 1;29(21):2781-7. doi: 10.1093/bioinformatics/btt491. Epub 2013 Sep 3.

PMID:
24002110
37.

Enhancement of chemical entity identification in text using semantic similarity validation.

Grego T, Couto FM.

PLoS One. 2013 May 2;8(5):e62984. doi: 10.1371/journal.pone.0062984. Print 2013.

38.

On the usefulness of ontologies in epidemiology research and practice.

Ferreira JD, Paolotti D, Couto FM, Silva MJ.

J Epidemiol Community Health. 2013 May;67(5):385-8. doi: 10.1136/jech-2012-201142. Epub 2012 Nov 15. No abstract available.

39.

Predicting the extension of biomedical ontologies.

Pesquita C, Couto FM.

PLoS Comput Biol. 2012;8(9):e1002630. doi: 10.1371/journal.pcbi.1002630. Epub 2012 Sep 13.

40.

Fungemia in a university hospital: an epidemiological approach.

Couto FM, Macedo DP, Neves RP.

Rev Soc Bras Med Trop. 2011 Nov-Dec;44(6):745-8. Epub 2011 Nov 23.

41.

Chemical Entity Recognition and Resolution to ChEBI.

Grego T, Pesquita C, Bastos HP, Couto FM.

ISRN Bioinform. 2012 Feb 15;2012:619427. doi: 10.5402/2012/619427. eCollection 2012.

42.

Disjunctive shared information between ontology concepts: application to Gene Ontology.

Couto FM, Silva MJ.

J Biomed Semantics. 2011 Aug 31;2:5. doi: 10.1186/2041-1480-2-5.

43.

Application of gene ontology to gene identification.

Bastos HP, Tavares B, Pesquita C, Faria D, Couto FM.

Methods Mol Biol. 2011;760:141-57. doi: 10.1007/978-1-61779-176-5_9.

PMID:
21779995
44.

Molecular profiling of the human nasal epithelium: A proteomics approach.

Simões T, Charro N, Blonder J, Faria D, Couto FM, Chan KC, Waybright T, Isaaq HJ, Veenstra TD, Penque D.

J Proteomics. 2011 Dec 10;75(1):56-69. doi: 10.1016/j.jprot.2011.05.012. Epub 2011 May 18.

PMID:
21621024
45.

Serum proteomics signature of cystic fibrosis patients: a complementary 2-DE and LC-MS/MS approach.

Charro N, Hood BL, Faria D, Pacheco P, Azevedo P, Lopes C, de Almeida AB, Couto FM, Conrads TP, Penque D.

J Proteomics. 2011 Jan 1;74(1):110-26. doi: 10.1016/j.jprot.2010.10.001. Epub 2010 Oct 13.

PMID:
20950718
46.

Semantic similarity for automatic classification of chemical compounds.

Ferreira JD, Couto FM.

PLoS Comput Biol. 2010 Sep 23;6(9). pii: e1000937. doi: 10.1371/journal.pcbi.1000937.

47.

Esophagitis caused by Candida guilliermondii in diabetes mellitus: first reported case.

Macêdo DP, Oliveira NT, Farias AM, Silva VK, Wilheim AB, Couto FM, Neves RP.

Med Mycol. 2010 Sep;48(6):862-5. doi: 10.3109/13693780903582614.

PMID:
20144130
48.

Semantic similarity in biomedical ontologies.

Pesquita C, Faria D, Falcão AO, Lord P, Couto FM.

PLoS Comput Biol. 2009 Jul;5(7):e1000443. doi: 10.1371/journal.pcbi.1000443. Epub 2009 Jul 31. Review.

49.

Thioredoxin-interacting protein deficiency induces Akt/Bcl-xL signaling and pancreatic beta-cell mass and protects against diabetes.

Chen J, Hui ST, Couto FM, Mungrue IN, Davis DB, Attie AD, Lusis AJ, Davis RA, Shalev A.

FASEB J. 2008 Oct;22(10):3581-94. doi: 10.1096/fj.08-111690. Epub 2008 Jun 13.

50.

Metrics for GO based protein semantic similarity: a systematic evaluation.

Pesquita C, Faria D, Bastos H, Ferreira AE, Falcão AO, Couto FM.

BMC Bioinformatics. 2008 Apr 29;9 Suppl 5:S4. doi: 10.1186/1471-2105-9-S5-S4.

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