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Items: 1 to 50 of 63

1.

The DisGeNET knowledge platform for disease genomics: 2019 update.

Piñero J, Ramírez-Anguita JM, Saüch-Pitarch J, Ronzano F, Centeno E, Sanz F, Furlong LI.

Nucleic Acids Res. 2019 Nov 4. pii: gkz1021. doi: 10.1093/nar/gkz1021. [Epub ahead of print]

PMID:
31680165
2.

Detecting Signs of Depression in Tweets in Spanish: Behavioral and Linguistic Analysis.

Leis A, Ronzano F, Mayer MA, Furlong LI, Sanz F.

J Med Internet Res. 2019 Jun 27;21(6):e14199. doi: 10.2196/14199.

3.

ResMarkerDB: a database of biomarkers of response to antibody therapy in breast and colorectal cancer.

Pérez-Granado J, Piñero J, Furlong LI.

Database (Oxford). 2019 Jan 1;2019. pii: baz060. doi: 10.1093/database/baz060.

4.

GUILDify v2.0: A Tool to Identify Molecular Networks Underlying Human Diseases, Their Comorbidities and Their Druggable Targets.

Aguirre-Plans J, Piñero J, Sanz F, Furlong LI, Fernandez-Fuentes N, Oliva B, Guney E.

J Mol Biol. 2019 Jun 14;431(13):2477-2484. doi: 10.1016/j.jmb.2019.02.027. Epub 2019 Mar 7.

PMID:
30851278
5.

Publisher Correction: Capturing variation impact on molecular interactions in the IMEx Consortium mutations data set.

IMEx Consortium contributing authors, Del-Toro N, Duesbury M, Koch M, Perfetto L, Shrivastava A, Ochoa D, Wagih O, Piñero J, Kotlyar M, Pastrello C, Beltrao P, Furlong LI, Jurisica I, Hermjakob H, Orchard S, Porras P.

Nat Commun. 2019 Mar 4;10(1):1098. doi: 10.1038/s41467-019-08814-w.

6.

Comorbidity4j: a tool for interactive analysis of disease comorbidities over large patient datasets.

Ronzano F, Gutiérrez-Sacristán A, Furlong LI.

Bioinformatics. 2019 Sep 15;35(18):3530-3532. doi: 10.1093/bioinformatics/btz061.

PMID:
30689768
7.

Capturing variation impact on molecular interactions in the IMEx Consortium mutations data set.

IMEx Consortium Curators, Del-Toro N, Duesbury M, Koch M, Perfetto L, Shrivastava A, Ochoa D, Wagih O, Piñero J, Kotlyar M, Pastrello C, Beltrao P, Furlong LI, Jurisica I, Hermjakob H, Orchard S, Porras P.

Nat Commun. 2019 Jan 2;10(1):10. doi: 10.1038/s41467-018-07709-6. Erratum in: Nat Commun. 2019 Mar 4;10(1):1098.

8.

Embracing the Dark Side: Computational Approaches to Unveil the Functionality of Genes Lacking Biological Annotation in Drug-Induced Liver Injury.

Souza T, Trairatphisan P, Piñero J, Furlong LI, Saez-Rodriguez J, Kleinjans J, Jennen D.

Front Genet. 2018 Nov 20;9:527. doi: 10.3389/fgene.2018.00527. eCollection 2018.

9.

The BIOMEPOC Project: Personalized Biomarkers and Clinical Profiles in Chronic Obstructive Pulmonary Disease.

Gea J, Pascual S, Castro-Acosta A, Hernández-Carcereny C, Castelo R, Márquez-Martín E, Montón C, Palou A, Faner R, Furlong LI, Seijo L, Sanz F, Torà M, Vilaplana C, Casadevall C, López-Campos JL, Monsó E, Peces-Barba G, Cosío BG, Agustí A; en representación del grupo BIOMEPOC; Anexo. Miembros del grupo BIOMEPOC.

Arch Bronconeumol. 2019 Feb;55(2):93-99. doi: 10.1016/j.arbres.2018.07.026. Epub 2018 Oct 19. English, Spanish.

10.

Network, Transcriptomic and Genomic Features Differentiate Genes Relevant for Drug Response.

Piñero J, Gonzalez-Perez A, Guney E, Aguirre-Plans J, Sanz F, Oliva B, Furlong LI.

Front Genet. 2018 Sep 25;9:412. doi: 10.3389/fgene.2018.00412. eCollection 2018.

11.

Pancreatic cancer and autoimmune diseases: An association sustained by computational and epidemiological case-control approaches.

Gomez-Rubio P, Piñero J, Molina-Montes E, Gutiérrez-Sacristán A, Marquez M, Rava M, Michalski CW, Farré A, Molero X, Löhr M, Perea J, Greenhalf W, O'Rorke M, Tardón A, Gress T, Barberá VM, Crnogorac-Jurcevic T, Muñoz-Bellvís L, Domínguez-Muñoz E, Balsells J, Costello E, Yu J, Iglesias M, Ilzarbe L, Kleeff J, Kong B, Mora J, Murray L, O'Driscoll D, Poves I, Lawlor RT, Ye W, Hidalgo M, Scarpa A, Sharp L, Carrato A, Real FX, Furlong LI, Malats N; PanGenEU Study Investigators.

Int J Cancer. 2019 Apr 1;144(7):1540-1549. doi: 10.1002/ijc.31866. Epub 2018 Oct 26.

PMID:
30229903
12.

In silico models in drug development: where we are.

Piñero J, Furlong LI, Sanz F.

Curr Opin Pharmacol. 2018 Oct;42:111-121. doi: 10.1016/j.coph.2018.08.007. Epub 2018 Sep 8. Review.

PMID:
30205360
13.

Proximal Pathway Enrichment Analysis for Targeting Comorbid Diseases via Network Endopharmacology.

Aguirre-Plans J, Piñero J, Menche J, Sanz F, Furlong LI, Schmidt HHHW, Oliva B, Guney E.

Pharmaceuticals (Basel). 2018 Jun 22;11(3). pii: E61. doi: 10.3390/ph11030061.

14.

comoRbidity: an R package for the systematic analysis of disease comorbidities.

Gutiérrez-Sacristán A, Bravo À, Giannoula A, Mayer MA, Sanz F, Furlong LI.

Bioinformatics. 2018 Sep 15;34(18):3228-3230. doi: 10.1093/bioinformatics/bty315.

15.

Identifying temporal patterns in patient disease trajectories using dynamic time warping: A population-based study.

Giannoula A, Gutierrez-Sacristán A, Bravo Á, Sanz F, Furlong LI.

Sci Rep. 2018 Mar 9;8(1):4216. doi: 10.1038/s41598-018-22578-1.

16.

Rcupcake: an R package for querying and analyzing biomedical data through the BD2K PIC-SURE RESTful API.

Gutiérrez-Sacristán A, Guedj R, Korodi G, Stedman J, Furlong LI, Patel CJ, Kohane IS, Avillach P.

Bioinformatics. 2018 Apr 15;34(8):1431-1432. doi: 10.1093/bioinformatics/btx788.

17.

Text mining and expert curation to develop a database on psychiatric diseases and their genes.

Gutiérrez-Sacristán A, Bravo À, Portero-Tresserra M, Valverde O, Armario A, Blanco-Gandía MC, Farré A, Fernández-Ibarrondo L, Fonseca F, Giraldo J, Leis A, Mané A, Mayer MA, Montagud-Romero S, Nadal R, Ortiz J, Pavon FJ, Perez EJ, Rodríguez-Arias M, Serrano A, Torrens M, Warnault V, Sanz F, Furlong LI.

Database (Oxford). 2017 Jan 1;2017. doi: 10.1093/database/bax043.

18.

psygenet2r: a R/Bioconductor package for the analysis of psychiatric disease genes.

Gutiérrez-Sacristán A, Hernández-Ferrer C, González JR, Furlong LI.

Bioinformatics. 2017 Dec 15;33(24):4004-4006. doi: 10.1093/bioinformatics/btx506.

19.

Genetic and functional characterization of disease associations explains comorbidity.

Rubio-Perez C, Guney E, Aguilar D, Piñero J, Garcia-Garcia J, Iadarola B, Sanz F, Fernandez-Fuentes N, Furlong LI, Oliva B.

Sci Rep. 2017 Jul 24;7(1):6207. doi: 10.1038/s41598-017-04939-4.

20.

Using Electronic Health Records to Assess Depression and Cancer Comorbidities.

Mayer MA, Gutierrez-Sacristan A, Leis A, De La Peña S, Sanz F, Furlong LI.

Stud Health Technol Inform. 2017;235:236-240.

PMID:
28423789
21.

A systems approach identifies time-dependent associations of multimorbidities with pancreatic cancer risk.

Gomez-Rubio P, Rosato V, Márquez M, Bosetti C, Molina-Montes E, Rava M, Piñero J, Michalski CW, Farré A, Molero X, Löhr M, Ilzarbe L, Perea J, Greenhalf W, O'Rorke M, Tardón A, Gress T, Barberá VM, Crnogorac-Jurcevic T, Muñoz-Bellvís L, Domínguez-Muñoz E, Gutiérrez-Sacristán A, Balsells J, Costello E, Guillén-Ponce C, Huang J, Iglesias M, Kleeff J, Kong B, Mora J, Murray L, O'Driscoll D, Peláez P, Poves I, Lawlor RT, Carrato A, Hidalgo M, Scarpa A, Sharp L, Furlong LI, Real FX, La Vecchia C, Malats N; PanGenEU Study Investigators.

Ann Oncol. 2017 Jul 1;28(7):1618-1624. doi: 10.1093/annonc/mdx167.

PMID:
28383714
22.

DisGeNET: a comprehensive platform integrating information on human disease-associated genes and variants.

Piñero J, Bravo À, Queralt-Rosinach N, Gutiérrez-Sacristán A, Deu-Pons J, Centeno E, García-García J, Sanz F, Furlong LI.

Nucleic Acids Res. 2017 Jan 4;45(D1):D833-D839. doi: 10.1093/nar/gkw943. Epub 2016 Oct 19.

23.

Open PHACTS computational protocols for in silico target validation of cellular phenotypic screens: knowing the knowns.

Digles D, Zdrazil B, Neefs JM, Van Vlijmen H, Herhaus C, Caracoti A, Brea J, Roibás B, Loza MI, Queralt-Rosinach N, Furlong LI, Gaulton A, Bartek L, Senger S, Chichester C, Engkvist O, Evelo CT, Franklin NI, Marren D, Ecker GF, Jacoby E.

Medchemcomm. 2016 Jun 1;7(6):1237-1244. Epub 2016 May 11.

24.

Identification of a Novel Human E-Cadherin Splice Variant and Assessment of Its Effects Upon EMT-Related Events.

Matos ML, Lapyckyj L, Rosso M, Besso MJ, Mencucci MV, Briggiler CI, Giustina S, Furlong LI, Vazquez-Levin MH.

J Cell Physiol. 2017 Jun;232(6):1368-1386. doi: 10.1002/jcp.25622. Epub 2016 Dec 29.

PMID:
27682981
25.

Combining machine learning, crowdsourcing and expert knowledge to detect chemical-induced diseases in text.

Bravo À, Li TS, Su AI, Good BM, Furlong LI.

Database (Oxford). 2016 Jun 15;2016. pii: baw094. doi: 10.1093/database/baw094. Print 2016.

26.

DisGeNET-RDF: harnessing the innovative power of the Semantic Web to explore the genetic basis of diseases.

Queralt-Rosinach N, Piñero J, Bravo À, Sanz F, Furlong LI.

Bioinformatics. 2016 Jul 15;32(14):2236-8. doi: 10.1093/bioinformatics/btw214. Epub 2016 Apr 22.

27.

A crowdsourcing workflow for extracting chemical-induced disease relations from free text.

Li TS, Bravo À, Furlong LI, Good BM, Su AI.

Database (Oxford). 2016 Apr 17;2016. pii: baw051. doi: 10.1093/database/baw051. Print 2016.

28.

Uncovering disease mechanisms through network biology in the era of Next Generation Sequencing.

Piñero J, Berenstein A, Gonzalez-Perez A, Chernomoretz A, Furlong LI.

Sci Rep. 2016 Apr 15;6:24570. doi: 10.1038/srep24570.

29.

MedBioinformatics: Developing Integrative Bioinformatics Applications for Personalized Medicine.

Mayer MA, Furlong LI, Sanz F; MedBioinformatics Consortium.

Stud Health Technol Inform. 2016;221:125. No abstract available.

PMID:
27071899
30.

CDH1/E-cadherin and solid tumors. An updated gene-disease association analysis using bioinformatics tools.

Abascal MF, Besso MJ, Rosso M, Mencucci MV, Aparicio E, Szapiro G, Furlong LI, Vazquez-Levin MH.

Comput Biol Chem. 2016 Feb;60:9-20. doi: 10.1016/j.compbiolchem.2015.10.002. Epub 2015 Nov 7.

PMID:
26674224
31.

Molecular and clinical diseasome of comorbidities in exacerbated COPD patients.

Faner R, Gutiérrez-Sacristán A, Castro-Acosta A, Grosdidier S, Gan W, Sánchez-Mayor M, Lopez-Campos JL, Pozo-Rodriguez F, Sanz F, Mannino D, Furlong LI, Agusti A.

Eur Respir J. 2015 Oct;46(4):1001-10. doi: 10.1183/13993003.00763-2015. Epub 2015 Aug 6.

32.

Reuse of EHRs to Support Clinical Research in a Hospital of Reference.

Mayer MA, Furlong LI, Torre P, Planas I, Cots F, Izquierdo E, Portabella J, Rovira J, Gutierrez-Sacristan A, Sanz F.

Stud Health Technol Inform. 2015;210:224-6.

PMID:
25991136
33.

PsyGeNET: a knowledge platform on psychiatric disorders and their genes.

Gutiérrez-Sacristán A, Grosdidier S, Valverde O, Torrens M, Bravo À, Piñero J, Sanz F, Furlong LI.

Bioinformatics. 2015 Sep 15;31(18):3075-7. doi: 10.1093/bioinformatics/btv301. Epub 2015 May 11.

34.

Extraction of relations between genes and diseases from text and large-scale data analysis: implications for translational research.

Bravo À, Piñero J, Queralt-Rosinach N, Rautschka M, Furlong LI.

BMC Bioinformatics. 2015 Feb 21;16:55. doi: 10.1186/s12859-015-0472-9.

35.

DisGeNET: a discovery platform for the dynamical exploration of human diseases and their genes.

Piñero J, Queralt-Rosinach N, Bravo À, Deu-Pons J, Bauer-Mehren A, Baron M, Sanz F, Furlong LI.

Database (Oxford). 2015 Apr 15;2015:bav028. doi: 10.1093/database/bav028. Print 2015.

36.

Mining the modular structure of protein interaction networks.

Berenstein AJ, Piñero J, Furlong LI, Chernomoretz A.

PLoS One. 2015 Apr 9;10(4):e0122477. doi: 10.1371/journal.pone.0122477. eCollection 2015.

37.

Personalized respiratory medicine: exploring the horizon, addressing the issues. Summary of a BRN-AJRCCM workshop held in Barcelona on June 12, 2014.

Agustí A, Antó JM, Auffray C, Barbé F, Barreiro E, Dorca J, Escarrabill J, Faner R, Furlong LI, Garcia-Aymerich J, Gea J, Lindmark B, Monsó E, Plaza V, Puhan MA, Roca J, Ruiz-Manzano J, Sampietro-Colom L, Sanz F, Serrano L, Sharpe J, Sibila O, Silverman EK, Sterk PJ, Sznajder JI.

Am J Respir Crit Care Med. 2015 Feb 15;191(4):391-401. doi: 10.1164/rccm.201410-1935PP.

38.

Network medicine analysis of COPD multimorbidities.

Grosdidier S, Ferrer A, Faner R, Piñero J, Roca J, Cosío B, Agustí A, Gea J, Sanz F, Furlong LI.

Respir Res. 2014 Sep 24;15:111. doi: 10.1186/s12931-014-0111-4.

39.

A knowledge-driven approach to extract disease-related biomarkers from the literature.

Bravo À, Cases M, Queralt-Rosinach N, Sanz F, Furlong LI.

Biomed Res Int. 2014;2014:253128. doi: 10.1155/2014/253128. Epub 2014 Apr 16. Review.

40.

The Semanticscience Integrated Ontology (SIO) for biomedical research and knowledge discovery.

Dumontier M, Baker CJ, Baran J, Callahan A, Chepelev L, Cruz-Toledo J, Del Rio NR, Duck G, Furlong LI, Keath N, Klassen D, McCusker JP, Queralt-Rosinach N, Samwald M, Villanueva-Rosales N, Wilkinson MD, Hoehndorf R.

J Biomed Semantics. 2014 Mar 6;5(1):14. doi: 10.1186/2041-1480-5-14.

41.

Gathering and exploring scientific knowledge in pharmacovigilance.

Lopes P, Nunes T, Campos D, Furlong LI, Bauer-Mehren A, Sanz F, Carrascosa MC, Mestres J, Kors J, Singh B, van Mulligen E, Van der Lei J, Diallo G, Avillach P, Ahlberg E, Boyer S, Diaz C, Oliveira JL.

PLoS One. 2013 Dec 11;8(12):e83016. doi: 10.1371/journal.pone.0083016. eCollection 2013.

42.

Improving data and knowledge management to better integrate health care and research.

Cases M, Furlong LI, Albanell J, Altman RB, Bellazzi R, Boyer S, Brand A, Brookes AJ, Brunak S, Clark TW, Gea J, Ghazal P, Graf N, Guigó R, Klein TE, López-Bigas N, Maojo V, Mons B, Musen M, Oliveira JL, Rowe A, Ruch P, Shabo A, Shortliffe EH, Valencia A, van der Lei J, Mayer MA, Sanz F.

J Intern Med. 2013 Oct;274(4):321-8. doi: 10.1111/joim.12105. Epub 2013 Jul 15. No abstract available.

43.

Human diseases through the lens of network biology.

Furlong LI.

Trends Genet. 2013 Mar;29(3):150-9. doi: 10.1016/j.tig.2012.11.004. Epub 2012 Dec 7. Review.

PMID:
23219555
44.

The EU-ADR Web Platform: delivering advanced pharmacovigilance tools.

Oliveira JL, Lopes P, Nunes T, Campos D, Boyer S, Ahlberg E, van Mulligen EM, Kors JA, Singh B, Furlong LI, Sanz F, Bauer-Mehren A, Carrascosa MC, Mestres J, Avillach P, Diallo G, Díaz Acedo C, van der Lei J.

Pharmacoepidemiol Drug Saf. 2013 May;22(5):459-67. doi: 10.1002/pds.3375. Epub 2012 Dec 4.

PMID:
23208789
45.

The EU-ADR corpus: annotated drugs, diseases, targets, and their relationships.

van Mulligen EM, Fourrier-Reglat A, Gurwitz D, Molokhia M, Nieto A, Trifiro G, Kors JA, Furlong LI.

J Biomed Inform. 2012 Oct;45(5):879-84. doi: 10.1016/j.jbi.2012.04.004. Epub 2012 Apr 25.

46.

Automatic filtering and substantiation of drug safety signals.

Bauer-Mehren A, van Mullingen EM, Avillach P, Carrascosa Mdel C, Garcia-Serna R, Piñero J, Singh B, Lopes P, Oliveira JL, Diallo G, Ahlberg Helgee E, Boyer S, Mestres J, Sanz F, Kors JA, Furlong LI.

PLoS Comput Biol. 2012;8(4):e1002457. doi: 10.1371/journal.pcbi.1002457. Epub 2012 Apr 5. Erratum in: PLoS Comput Biol. 2012 May;8(5): doi/10.1371/annotation/695450aa-95a0-491d-804d-470cbfa861e8.

47.

Assessment of NER solutions against the first and second CALBC Silver Standard Corpus.

Rebholz-Schuhmann D, Jimeno Yepes A, Li C, Kafkas S, Lewin I, Kang N, Corbett P, Milward D, Buyko E, Beisswanger E, Hornbostel K, Kouznetsov A, Witte R, Laurila JB, Baker CJ, Kuo CJ, Clematide S, Rinaldi F, Farkas R, Móra G, Hara K, Furlong LI, Rautschka M, Neves ML, Pascual-Montano A, Wei Q, Collier N, Chowdhury MF, Lavelli A, Berlanga R, Morante R, Van Asch V, Daelemans W, Marina JL, van Mulligen E, Kors J, Hahn U.

J Biomed Semantics. 2011 Oct 6;2 Suppl 5:S11. doi: 10.1186/2041-1480-2-S5-S11.

48.

Challenges in the association of human single nucleotide polymorphism mentions with unique database identifiers.

Thomas PE, Klinger R, Furlong LI, Hofmann-Apitius M, Friedrich CM.

BMC Bioinformatics. 2011;12 Suppl 4:S4. doi: 10.1186/1471-2105-12-S4-S4. Epub 2011 Jul 5.

49.

Gene-disease network analysis reveals functional modules in mendelian, complex and environmental diseases.

Bauer-Mehren A, Bundschus M, Rautschka M, Mayer MA, Sanz F, Furlong LI.

PLoS One. 2011;6(6):e20284. doi: 10.1371/journal.pone.0020284. Epub 2011 Jun 14.

50.

DisGeNET: a Cytoscape plugin to visualize, integrate, search and analyze gene-disease networks.

Bauer-Mehren A, Rautschka M, Sanz F, Furlong LI.

Bioinformatics. 2010 Nov 15;26(22):2924-6. doi: 10.1093/bioinformatics/btq538. Epub 2010 Sep 21.

PMID:
20861032

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