Emre Guney

Emre Guney

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Emre Guney

Emre Guney

Publications by authors named "Emre Guney"

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

J Mol Biol 2019 Jun 7;431(13):2477-2484. Epub 2019 Mar 7.

Integrative Biomedical Informatics Group, Research Programme on Biomedical Informatics, Hospital del Mar Medical Research Institute, Department of Experimental and Health Sciences, Universitat Pompeu Fabra, Barcelona, Catalonia 08003, Spain; Department of Pharmacology and Personalised Medicine, CARIM, FHML, Maastricht University, Universiteitssingel 50, 6229, ER, Maastricht, the Netherlands. Electronic address:

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http://dx.doi.org/10.1016/j.jmb.2019.02.027DOI Listing
June 2019

From single drug targets to synergistic network pharmacology in ischemic stroke.

Proc Natl Acad Sci U S A 2019 04 20;116(14):7129-7136. Epub 2019 Mar 20.

Department of Pharmacology and Personalised Medicine, Maastricht Center for Systems Biology, Faculty of Health, Medicine and Life Sciences, Maastricht University, 6229 ER Maastricht, The Netherlands;

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http://www.pnas.org/lookup/doi/10.1073/pnas.1820799116
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http://dx.doi.org/10.1073/pnas.1820799116DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6452748PMC
April 2019

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

Front Genet 2018 25;9:412. Epub 2018 Sep 25.

Integrative Biomedical Informatics Group, Research Programme on Biomedical Informatics, Hospital del Mar Medical Research Institute, Department of Experimental and Health Sciences, Universitat Pompeu Fabra, Barcelona, Spain.

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https://www.frontiersin.org/article/10.3389/fgene.2018.00412
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http://dx.doi.org/10.3389/fgene.2018.00412DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6168038PMC
September 2018

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

Pharmaceuticals (Basel) 2018 Jun 22;11(3). Epub 2018 Jun 22.

Research Programme on Biomedical Informatics, the Hospital del Mar Medical Research Institute and Pompeu Fabra University, Dr. Aiguader 88, 08003 Barcelona, Spain.

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http://www.mdpi.com/1424-8247/11/3/61
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http://dx.doi.org/10.3390/ph11030061DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6160959PMC
June 2018

Transcription Factor NRF2 as a Therapeutic Target for Chronic Diseases: A Systems Medicine Approach.

Pharmacol Rev 2018 04;70(2):348-383

Centro de Investigación Biomédica en Red Sobre Enfermedades Neurodegenerativas (CIBERNED), Instituto de Investigación Sanitaria La Paz (IdiPaz), Department of Biochemistry and Instituto de Investigaciones Biomédicas Alberto Sols UAM (Autonomous University of Madrid)-CSIC (Centro Superior de Investigaciones Biomédicas), Faculty of Medicine, Autonomous University of Madrid, Madrid, Spain (A.C., M.P., A.I.R., N.R.-A.); Victor Babes National Institute of Pathology, Bucharest, Romania (A.C., G.M.); Department Pharmacology and Personalized Medicine, School for Cardiovascular Medicine, Faculty of Health, Medicine and Life Sciences, Maastricht University, Maastrich, The Netherlands (A.H., H.H.H.W.S.); Instituto Interuniversitario de Investigación de Reconocimiento Molecular y Desarrollo Tecnológico, Universitat Politècnica de València, Universitat de València, Valencia, Spain (M.J.A.); Centre for Metabolomics and Bioanalysis, Facultad de Farmacia, Universidad CEU (Centro de Estudios Universitarios)-San Pablo, Madrid, Spain (C.B.); Center for Cardiology, Cardiology I-Laboratory of Molecular Cardiology, Medical Center of the Johannes Gutenberg University, Mainz, Germany (A.D.); Brighton and Sussex Medical School, Brighton, United Kingdom (P.G.); Instituto Teófilo Hernando y Departamento de Farmacología y Terapéutica, Facultad de Medicina, Universidad Autónoma de Madrid, Madrid, Spain (R.L., M.G.L.); Instituto de Investigación Sanitaria, Servicio de Farmacología Clínica, Hospital Universitario de la Princesa, Madrid, Spain (R.L., M.G.L.); GRIB (Unidad de Investigación en Informática Biomédica), Department of Experimental and Health Sciences, Universitat Pompeu Fabra, Barcelona, Spain (B.O., E.G.); Instituto de Investigaciones Biomédicas Alberto Sols UAM-CSIC and Centro de Investigación Biomédica en Red en Diabetes y Enfermedades Metabólicas Asociadas, Madrid, Spain (A.M.V.); and Structural Bioinformatics Laboratory, Department of Experimental and Health Sciences, Universitat Pompeu Fabra, Barcelona, Spain (E.G.).

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http://pharmrev.aspetjournals.org/lookup/doi/10.1124/pr.117.
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http://dx.doi.org/10.1124/pr.117.014753DOI Listing
April 2018

A diseasome cluster-based drug repurposing of soluble guanylate cyclase activators from smooth muscle relaxation to direct neuroprotection.

NPJ Syst Biol Appl 2018 5;4. Epub 2018 Feb 5.

3Department of Pharmacology and Personalised Medicine, CARIM, FHML, Maastricht University, Universiteitssingel 50, 6229 ER Maastricht, The Netherlands.

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http://dx.doi.org/10.1038/s41540-017-0039-7DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5799370PMC
February 2018

The ISCB Student Council Internship Program: Expanding computational biology capacity worldwide.

PLoS Comput Biol 2018 01 18;14(1):e1005802. Epub 2018 Jan 18.

Joint IRB-BSC-CRG Program in Computational Biology, Institute for Research in Biomedicine, Barcelona, Catalonia, Spain.

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http://dx.doi.org/10.1371/journal.pcbi.1005802DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5772997PMC
January 2018

REPRODUCIBLE DRUG REPURPOSING: WHEN SIMILARITY DOES NOT SUFFICE.

Authors:
Emre Guney

Pac Symp Biocomput 2017 ;22:132-143

Joint IRB-BSC-CRG Program in Computational Biology, Institute for Research in Biomedicine, c/ Baldiri Reixac 10-12, Barcelona, 08028, Spain,

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http://dx.doi.org/10.1142/9789813207813_0014DOI Listing
July 2017

Genetic and functional characterization of disease associations explains comorbidity.

Sci Rep 2017 07 24;7(1):6207. Epub 2017 Jul 24.

Structural Bioinformatics Group, GRIB, IMIM, Department of Experimental and Life Sciences, Universitat Pompeu Fabra, 08003, Barcelona, Catalonia, Spain.

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http://dx.doi.org/10.1038/s41598-017-04939-4DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5524755PMC
July 2017

Integrating personalized gene expression profiles into predictive disease-associated gene pools.

NPJ Syst Biol Appl 2017 13;3:10. Epub 2017 Mar 13.

Center for Complex Networks Research and Department of Physics, Northeastern University, Boston, MA 02115 USA.

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http://www.nature.com/articles/s41540-017-0009-0
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http://dx.doi.org/10.1038/s41540-017-0009-0DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5445628PMC
March 2017

iFrag: A Protein-Protein Interface Prediction Server Based on Sequence Fragments.

J Mol Biol 2017 02 10;429(3):382-389. Epub 2016 Dec 10.

Structural Bioinformatics Laboratory, Department of Experimental and Health Sciences, Universitat Pompeu Fabra, C/Doctor Aiguader 88, 08003 Barcelona, Spain. Electronic address:

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http://dx.doi.org/10.1016/j.jmb.2016.11.034DOI Listing
February 2017

Erratum: Crowdsourced assessment of common genetic contribution to predicting anti-TNF treatment response in rheumatoid arthritis.

Nat Commun 2016 10 10;7:13205. Epub 2016 Oct 10.

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http://dx.doi.org/10.1038/ncomms13205DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5062501PMC
October 2016

Tissue Specificity of Human Disease Module.

Sci Rep 2016 10 17;6:35241. Epub 2016 Oct 17.

Center for Complex Networks Research and Department of Physics, Northeastern University, 110 Forsyth Street, 111 Dana Research Center, Boston, MA 02115, USA.

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http://dx.doi.org/10.1038/srep35241DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5066219PMC
October 2016

Crowdsourced assessment of common genetic contribution to predicting anti-TNF treatment response in rheumatoid arthritis.

Nat Commun 2016 08 23;7:12460. Epub 2016 Aug 23.

Sage Bionetworks, Seattle, Washington 98115, USA.

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http://dx.doi.org/10.1038/ncomms12460DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4996969PMC
August 2016

Network-based in silico drug efficacy screening.

Nat Commun 2016 Feb 1;7:10331. Epub 2016 Feb 1.

Center for Complex Networks Research (CCNR) and Department of Physics, Northeastern University, 177 Huntington Avenue, 11th floor, Boston, Massachusetts 02115, USA.

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http://dx.doi.org/10.1038/ncomms10331DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4740350PMC
February 2016

Integrating structure to protein-protein interaction networks that drive metastasis to brain and lung in breast cancer.

PLoS One 2013 22;8(11):e81035. Epub 2013 Nov 22.

Center for Computational Biology and Bioinformatics and College of Engineering, Koc University, Istanbul, Turkey.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0081035PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3838352PMC
May 2015

Analysis of the robustness of network-based disease-gene prioritization methods reveals redundancy in the human interactome and functional diversity of disease-genes.

PLoS One 2014 14;9(4):e94686. Epub 2014 Apr 14.

Structural Bioinformatics Group (GRIB), Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra, Barcelona, Catalonia, Spain.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0094686PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3986215PMC
January 2015

GUILDify: a web server for phenotypic characterization of genes through biological data integration and network-based prioritization algorithms.

Bioinformatics 2014 Jun 14;30(12):1789-90. Epub 2014 Feb 14.

Departament de Ciencies Experimentals i de la Salut, Structural Bioinformatics Group (GRIB-IMIM), Universitat Pompeu Fabra, Barcelona, 08003 Catalonia, Spain.

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http://dx.doi.org/10.1093/bioinformatics/btu092DOI Listing
June 2014

A transcriptome-proteome integrated network identifies endoplasmic reticulum thiol oxidoreductase (ERp57) as a hub that mediates bone metastasis.

Mol Cell Proteomics 2013 Aug 26;12(8):2111-25. Epub 2013 Apr 26.

Biological Clues of the Invasive and Metastatic Phenotype Group, Bellvitge Biomedical Research Institute IDIBELL, L'Hospitalet de Llobregat, Barcelona E-08908, Spain.

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http://dx.doi.org/10.1074/mcp.M112.022772DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3734573PMC
August 2013

Exploiting protein-protein interaction networks for genome-wide disease-gene prioritization.

PLoS One 2012 21;7(9):e43557. Epub 2012 Sep 21.

Structural Bioinformatics Group, GRIB, Universitat Pompeu Fabra, Barcelona Research Park of Biomedicine, Barcelona, Catalonia, Spain.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0043557PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3448640PMC
March 2013

Extending signaling pathways with protein-interaction networks. Application to apoptosis.

OMICS 2012 May 2;16(5):245-56. Epub 2012 Mar 2.

Structural Bioinformatics Group, GRIB, Universitat Pompeu Fabra, Barcelona, Catalonia, Spain.

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http://dx.doi.org/10.1089/omi.2011.0130DOI Listing
May 2012

Networks of ProteinProtein Interactions: From Uncertainty to Molecular Details.

Mol Inform 2012 May 30;31(5):342-62. Epub 2012 Apr 30.

Structural Bioinformatics Group, GRIB-IMIM, Universitat Pompeu Fabra, Barcelona Research Park of Biomedicine (PRBB), Catalonia, Spain.

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http://dx.doi.org/10.1002/minf.201200005DOI Listing
May 2012

Biana: a software framework for compiling biological interactions and analyzing networks.

BMC Bioinformatics 2010 Jan 27;11:56. Epub 2010 Jan 27.

Structural Bioinformatics Lab, Universitat Pompeu Fabra-IMIM, Barcelona Research Park of Biomedicine, Barcelona, Catalonia, Spain.

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http://dx.doi.org/10.1186/1471-2105-11-56DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3098100PMC
January 2010

Architectures and functional coverage of protein-protein interfaces.

J Mol Biol 2008 Sep 6;381(3):785-802. Epub 2008 May 6.

Center for Computational Biology and Bioinformatics, College of Engineering, Koc University, Rumeli Feneri Yolu, 34450 Sariyer, Istanbul, Turkey.

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http://dx.doi.org/10.1016/j.jmb.2008.04.071DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2605427PMC
September 2008

HotSprint: database of computational hot spots in protein interfaces.

Nucleic Acids Res 2008 Jan 24;36(Database issue):D662-6. Epub 2007 Oct 24.

Koc University, Center for Computational Biology and Bioinformatics and College of Engineering, Rumelifeneri Yolu, 34450 Sariyer, Istanbul, Turkey.

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http://dx.doi.org/10.1093/nar/gkm813DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2238999PMC
January 2008