I am a Senior Research Fellow at the Research Programme in Biomedical Informatics (GRIB), at the Pompeu Fabra University (UPF) and Hospital del Mar Research Institute (IMIM) in Barcelona, Spain. I hold a secondary appointment at the Pharmacology & Personalised Medicine department at Maastricht University in the Netherlands. I also work as a consultant for Scipher Medicine , a start-up located in Boston, MA, USA. I obtained a B.S. in Computer Engineering from Middle East Technical University (METU) and Ph.D. in Biomedicine (supervised by Professor Baldo Oliva) from Pompeu Fabra University (UPF). I work on developing data-centric approaches for translational medicine and network pharmacology and I am a keen supporter of open science .

Previous experience:
  • 2015 - 2017 | Beatriu de Pinós Fellow at the Institute for Biomedical Research (IRB)
  • 2013 - 2015 | Postdoctoral Research Associate at the Center for Complex Network Research (CCNR) and the Center for Cancer Systems Biology (CCSB)
  • 2008 - 2013 | Research Assistant at the Structural Bioinformatics Laboratory (SBI)
  • 2005 - 2008 | Research and Teaching Assistant at the Computational Systems Biology Group (COSBI)
Extracurricular activities:

I am a member of International Society of Computational Biology (ISCB) since 2007 and I often serve as a reviewer for PLoS ONE, PLoS Computational Biology, Bioinformatics, BMC Bioinformatics, JAMIA, Pharmacological Research, Proceedings B, EBioMedicine, IEEE JBHI, The American Journal of Psychiatry, Scientific Reports, Nature Communications and grant applications from several institutions such as FWO, LaCaixa, HKBU. I am an editorial board member of Systems Medicine .

Upcoming events:

Research interests

The past few decades have witnessed a burst in the high-throughput molecular data sets, shedding light on the mechanisms underlying human genetic diseases. Despite the recent efforts on sequencing and genome wide association studies characterizing genetic variants associated with patient subgroups, most clinical trials fail due to the lack of efficacy and safety. Accordingly, my research has shaped around repurposing existing drugs for new uses by network-based modeling and stastical data analysis. Several projects I am currently involved in:

  • Pharmacological data integration for symptoms-based characterization and treatment of diseases
  • Robust machine learning classifiers for drug repurposing
  • Drug combination synergy prediction via network modeling of pharmacogenetics data
  • Network-based drug side effect discovery
  • Pathway level personalized expression signatures
  • Common disease mechanisms giving rise to comorbidity
(For prospective students: If you are interested in doing a research project, contact me via email.)

Selected publications

For a full list, please see my CV or Google Scholar.

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 (2018) | Preprint
PxEA code

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

Guney E, Garcia-Garcia J, Oliva B.
Bioinformatics (2014)
Web server

Robustness analysis of network-based disease-gene prioritization methods implies redundancy and functional decoupling in the human interactome

Guney E, Oliva B.
PLoS ONE (2014)
Poster (Source in SVG)

HotSprint: Database of computational hot spots in protein interfaces.

Guney E, Tuncbag N, Keskin O, Gursoy A.
Nucl. Acids Res. (2008)

Media coverage and invited talks

News

* A new computational method for exploring the reuse of drugs | [GRIB news] | [Aldia (in Catalan)] | [BioTech-Spain (in Spanish)] | [CatalunyaVanguardista (in Spanish)] | [InfoSalus (in Spanish)] | [Pharma Market (in Spanish)] | [COFA (in Spanish) | [Noticias de la Ciencia (in Spanish)] | [ABC (in Spanish)] | [La Vanguardia (in Spanish)]
* Looking for the ‘magic drug’ to fight Alzheimer’s and diabetes
* Northeastern researchers see market potential for repurposed drugs
* DZZOM to tackle repurposed drugs
* Researchers of GRIB participate in a crowdsourced assessment of rheumatoid arthritis treatments
* Recent advances in the study of proteins and their interactions [ UPF version ] | [ La Vanguardia (in Spanish)]
* Describen los genes implicados en la progresión del cáncer de mama (in Spanish)
* Finding the genes underlying complex genetic diseases
* Biological data, from Babel to BIANA

Talks

* Network-based modeling of APAP-induced hepatotoxicity. European Conference on Translational Bioinformatics (ECTB) , Barcelona, Apr, 2018.
* Neurodegenerative diseases from systems medicine perspective. Autonomous University of Madrid MSc on Neuroscience , Barcelona, Feb, 2018. [Slides]
* Interactome and gene expression based analyzes for translational medicine. University of Vic MSc on Omics Data Analysis seminar , Barcelona, Jan, 2018. [Slides]
* Data-driven analysis and network-based modeling for translational medicine. Workshop on Challenges in Computational Biology (CCB) , Mainz, Nov, 2017. [Slides]
* Integrating personalized gene expression profiles into predictive disease-associated gene pools. Intelligent Systems for Molecular Biology (ISMB) & European Conference on Computational Biology (ECCB) , Prague, July, 2017. [Slides] [Video]
* Should I stay or should I go, NOW? RSG-Turkey Student Symposium , Guzelyurt, June, 2017. [Slides] [Source (.tex)]
* Challenges and opportunities in systems pharmacology. The International Symposium on Health Informatics and Bioinformatics (HIBIT) , Guzelyurt, June, 2017. [Slides]
* Investigating side effect modules in the interactome and their use in drug adverse effect discovery. Conference on Complex Networks (CompleNet) , Dubrovnik, March, 2017.
* Reproducible drug repurposing: When similarity does not suffice. Pacific Symposium on Biocomputing (PSB) , Big Island of Hawaii, January, 2017.
* Revisiting drug discovery through integrative network pharmacology in the era of precision medicine. European Conference on Computational Biology (ECCB) , The Hague, September, 2016
* Interactome-based disease gene prioritization and drug discovery. Disease Systems Biology Department at NNF CPR , Copenhagen, April, 2016
* Precision medicine through integrative network pharmacology. Barcelona Super Computing Center, Life Sciences Seminar Series, Barcelona, February, 2016
* Rational drug design through interactome analysis: Are we there yet? The Division of Pharmacoepidemiology and Pharmacoeconomics Brigham and Women’s Hospital, Harvard Medical School, Boston, August, 2015
* Analyzing drug mechanism of action through underlying protein-protein interaction network. NetSci - Network Medicine Smyposium, UC Berkeley, June, 2014

Software

  • GUILD: Network-based disease-gene prioritization [Zipped release] | [GitHub] | [Web]
  • Toolbox: Python package for biomedical data processing and analysis [GitHub]
  • Drugbox: Python3 package for parsing drug information [GitHub]
  • BIANA: Biological data integration and network analysis tool [GitHub] | [Web]
  • GUILDify: Phenotypic characterization of genes through biological data integration [Web]
  • PePPer: Personalized Perturbation Profiler for classifying disease response of patients [GitHub]
  • Repurpose: Reproducible similarity-based drug repurposing using machine learning [GitHub]
  • guildifyR: An R package for network-based prioritization via GUILDify web server [GitHub]
  • PxEA: ProXimal pathway Enrichment Analysis [GitHub]