Helena F. Deus, PhD

Associate Director

Medical Knowledge Engineering

Foundation Medicine Inc

150 Second Street, 1st Floor

Cambridge, MA 02141


Google Scholar Profile












Post-Doc in Computer Science/Knowledge Engineering (2011-2013) at the Digital Enterprise Research Institute, National University of Ireland Galway

PhD in Bioinformatics (2011) at the University of Texas M.D. Anderson Cancer Center and the Institute for Chemical and Biological Technology, New University of Lisbon (ITQB/UNL)

THESIS: Improving Discovery in the Life Sciences using Semantic Web Technologies and Linked Data: Design Principles for Life Sciences Knowledge Organization Systems

BS in (Marine) Biology (2004) at University of Lisbon


1. JS Almeida, C Chen, R Gorlitsky, R Stanislaus, M Aires-de- Sousa, P Eleutério, J Carriço, A Maretzek, A Bohn, A Chang, F Zhang, R Mitra, GB Mills, X Wang and HF Deus. Data Integration gets "Sloppy". Nature Biotechnology 2006, 24(9):6-7.  [pdf]

2. HF Deus, R Stanislaus, DF Veiga, C Behrens, II Wistuba, JD Minna, HR Garner, SG Swisher, JA Roth, AM Correa, B Broom, K Coombes, A Chang, LH Vogel, JS Almeida, A Semantic Web Management Model for Integrative Biomedical Informatics. PLoS ONE 2008, 3(8):          e2946.doi:10.1371/journal.pone.0002946  [pdf]

3.  PR Freire, M Vilela, HF Deus, Y Kim, D Koul, H Colman, K Aldape, O Bogler, WKA Yung, K Coombes, G Mills, AT Vasconcelos and JS Almeida. Exploratory Analysis of the Copy Number Alterations in Glioblastoma Multiforme. PLoS ONE 2008, 3(12): e4076. doi:10.1371/journal.pone.0004076 [pdf]

4.  R Stanislaus, M Carey, HF Deus, K Coombes, BT Hennessy, GB Mills and JS Almeida. RIMS: an information management system for Reverse Phase Protein Arrays. BMC Bioinformatics 2008 Dec 22;9:555 [pdf]

5.  DF Veiga, HF Deus, C Akdemir, AT Vasconcelos, JS Almeida. DASMiner: discovering and

integrating data from DAS sources. BMC Systems Biology 2009 Nov 17;3:109 [pdf]

6.  JS Almeida, HF Deus, W Maass. S3DB core: a framework for RDF generation and management in bioinformatics infrastructures. BMC Bioinformatics 2010, 11:387 (Highly accessed)  [pdf]

7.  HF Deus, DF Veiga, P Freire, JN Weinstein, GB Mills and JS Almeida. Exposing the cancer  genome atlas as a SPARQL endpoint. Journal of Biomedical Informatics 2010 Dec; 43(6):998-1008 [pdf]

8.  MC Correa, HF Deus, AT Vasconcelos , Y Hayashi , JA Ajani, SV Patnana and JS Almeida. AGUIA: autonomous graphical user interface assembly for clinical trials semantic data services. BMC Medical Informatics and Decision Making 2010: 10:65 (Highly accessed) [pdf]

9.  HF Deus, J Zhao, S Sahoo, M Samwald, Eric Prud’hommeaux, Michael Miller, M.Scott          Marshall and Kei-Hoi Cheung. Provenance of Microarray Experiments for a Better Understanding of Experiment Results. Proceeding of the second International Workshop on the role of Semantic Web in Provenance Management (ISWC 2010 – SWPM Workshop paper) [pdf]

10. HF Deus, MC Correa, R Stanislaus, M Miragaia, W Maass, H Lencastre, R Fox and JS Almeida. S3QL: A distributed domain specific language for controlled semantic integration of life sciences data. BMC Bioinformatics 2011, 12:285 (Highly Accessed) [pdf]

11. E Prud’hommeaux, HF Deus. SPARQL Access Policies. In W3C Linked Enterprise Data Patterns Workshop 2011

12. MS Marshall, R Boyce, J Zhao, EL Willighagen, HF Deus, M Samwald, E Pichler, J Hajagos, E Prud’hommeaux and Susie Stephens. Emerging best practices for mapping life sciences data to RDF - a case series. Journal of Web Semantics 2012 Jul; 14:2-13 [pdf]

13. HF Deus, E Prud'hommeaux, M Miller, J Zhao, J Malone, T Adamusiak, J McCusker, S Das, P Rocca-Serra, R Fox and MS Marshall. Translating standards into practice - One Semantic Web API for Gene Expression. Journal of Biomedical Informatics J Biomed Inform 2012 Aug;45(4):782-94 [pdf]

14. A Hasnain, R. Fox, S Decker and HF Deus. Cataloguing and Linking Life Sciences LOD Cloud. Workshop paper OWDW 2012 at EKAW 2012. Galway, Ireland

15. P Hasapis, T Bouras, HF Deus, Ronan Fox, S Kolvenbach, W Prinz. Weaving Social Networks with Linked Biomedical Data. Applied Computing 2012. Madrid, Spain

16. David E. Robbins, Alexander Grüneberg, Helena F. Deus, Murat M. Tanik and Jonas S. Almeida. A Self-Updating Roadmap of The Cancer Genome Atlas. Bioinformatics (2013) 29 (10): 1333-1340.

17. Dimitris Zeginis, Ali Hasnain, Nikolaos Loutas, Helena F. Deus, Ronan Fox, Konstantinos Tarabanis. Collaborative development of a common semantic model for interlinking Cancer Chemoprevention linked data sources.Semantic Web Journal 2013 [pdf]

18. Stoltzfus A, Lapp H, Matasci N, Deus H, Sidlauskas B, Zmasek CM, Vaidya G, Pontelli E, Cranston K, Vos R, Webb CO, Harmon LJ, Pirrung M, O'Meara B, Pennell MW, Mirarab S, Rosenberg MS, Balhoff JP, Bik HM, Heath TA, Midford PE, Brown JW, McTavish EJ, Sukumaran J, Westneat M, Alfaro ME, Steele A, Jordan G. Phylotastic! Making tree-of-life knowledge accessible, reusable and convenient. BMC Bioinformatics. 2013 May 13;14(1):158 [pdf]

19. Muhammad Saleem, Axel-Cyrille Ngonga Ngomo, Josiane Xavier Parreira, Helena F Deus, Manfred Hauswirth (2013)  DAW: Duplicate-AWare Federated Query Processing over the Web of Data   In: International Semantic Web Conference (ISWC) 2013 [pdf]

20. Muhammad Saleem, Shanmukha S Padmanabhuni, Axel-Cyrille Ngonga, Jonas S Almeida, Stefan Decker, Helena Deus (2013)  Linked Cancer Genome Atlas Database   In: Linked Data Cup, I-Semantics 2013. Winner of the Best Paper Award & Linked Data Dup as iSemantics 2013  [pdf]

21. Robbins DE, A Gruneberg, HF Deus, MM Tanik, JS Almeida (2013) A Self-Updating Roadmap of The Cancer Genome Atlas. Bioinformatics [pdf]

22. Laleh Kazemzadeh, Helena F.Deus, Michel Dumontier and Frank Barry (2013). Looking into Reactome through Biopax Lens. CSWS 2013. [pdf]

23. Maulik R. Kamdar, Dimitris Zeginis, Ali Hasnain, Stefan Decker and Helena F. Deus. ReVeaLD: A user-driven domain specific Search Platform for Biomedical Research. Journal of Biomedical Informatics 2013 [pdf]

24. David Robbins, Alexander Grüneberg, Helena Deus, Murat Tanik and Jonas Almeida. Weaving Public Big Data Resources into the Semantic Web of Linked Data. SDPS 2013 Campinas, São Paulo, Brazil

25. Robbins, David E, Alexander Grüneberg, Helena F Deus, Murat M Tanik, and Jonas   Almeida. 2013. TCGA Toolbox: an Open Web App Framework for Distributing Big Data Analysis Pipelines for Cancer Genomics. Proceedings of the International Conference on Bioinformatics, Computational Biology and Biomedical Informatics. ACM, ICB2013:62 [pdf]

26. Muhammad Saleem, Maulik R. Kamdar, Aftab Iqbal, Shanmukha Sampath, Helena F.   Deus and Axel-Cyrille Ngonga Ngomo. Fostering Serendipity through Big Linked Data. ISCW 2013, Sidney, Australia. Winner of the ISWC Semantic Web Challenge 2013 - Big Data Track [pdf]

27. Maulik R. Kamdar, Aftab Iqbal, Muhammad Saleem, Helena F. Deus and Stefan Decker. GenomeSnip: Fragmenting the Genomic Wheel to augment discovery in cancer research CSHALS 2014. Winner of the Best Paper Award at CSHALS 2014  [pdf]

28. Muhammad Saleem, Maulik R Kamdar, Aftab Iqbal, Shanmukha Sampath, Helena F Deus, Axel-Cyrille Ngonga Ngomo. Big linked cancer data: Integrating linked TCGA and PubMed. Web Semantics: Science, Services and Agents on the World Wide Web. DOI: 10.1016/j.websem.2014.07.004 [pdf]

29. Ali Hasnain, Maulik R. Kamdar, Panagiotis Hasapis, Dimitris Zeginis, Claude N. Warren, Jr, Helena F. Deus, Dimitrios Ntalaperas, Konstantinos Tarabanis and Stefan Decker. Linked Biomedical Dataspace: Lessons Learned Integrating Data for Drug Discovery. ISWC 2014 [pdf]

30. Muhammad Saleem, Shanmukha Sampath, Axel-Cyrille Ngonga Ngomo, Aftab Iqbal, Jonas Almeida, Stefan Decker and Helena F. Deus. TopFed: TCGA Tailored Federated Query Processing and Linking to LOD. Journal of Biomedical Semantics 2014. [pdf]

31. Ali Hasnain, Syeda Sana e Zainab, Mailik R. Kamdar, Qaiser Mehmood, Claude N Warren Jr, Qurratal Ain Fatimah, Helena F Deus, Muntazir Mehdi, Stefan Decker. A Roadmap for Navigating the Life Sciences Linked Open Data Cloud. Semantic Technology: 4th Joint International Conference, JIST 2014, Chiang Mai, Thailand, November 9-11, 2014 [pdf]


  1. SYSTEM AND METHOD FOR MANAGING GENOMIC INFORMATION. App Number: 20150046191; Filed: Aug 19, 2014;  Inventors: Helena Futscher de Deus (Cambridge, MA), Rachel Lauren Erlich (Somerville, MA), Ronald David Collette (Dove Canyon, CA), Alexander N. Parker (Boston, MA), Michael Pellini (Dana Point, CA), Gary Palmer (Waltham, MA), Mary Pat Lancelotta (Somerville, MA), Matthew J. Hawryluk (Watertown, MA), Philip James Stephens (Lexington, MA), Eric Karl Neumann (Cambridge, MA), Jeffrey B. Collemer (Cumberland, RI) [pdf]


May 2014 - Present

Associate Director at Foundation Medicine, Inc (FMI)

Medical Knowledge Engineering

May 2013 - May 2014

Senior Scientist at Foundation Medicine, Inc (FMI)
Medical Knowledge Engineering


July 2012:May 2013

Unit Leader, Bioinformatics and Systems Biology Unit at the Digital Enterprise Research Institute, National University of Ireland at Galway (DERI/NUIG)


Feb 2013:May 2013

Unit Leader, Health Care and Life Sciences Unit at the Digital Enterprise Research Institute, National University of Ireland at Galway (DERI/NUIG)


February 2011:May 2013

Post-Doctoral Research Associate and Adjunct Lecturer at the Digital Enterprise Research Institute, National University of Ireland at Galway (DERI/NUIG), Health Care and Life Sciences Unit

-       FP7 EU Project Coordination and Management (EU Sifem Project)

-       FP7 EU Leadership of Research Activities (EU GRANATUM Project, EU Linked2Safety Project, EU Sifem Project)

-       Coordinating the development of a Linked Data Space for Cancer Chemoprevention

-       Student Training and Mentorship through the SimSci ITN project


January 2010:February 2011

Project Manager at the Institute for Chemical and Biological Technology, New University of Lisbon (ITQB/UNL), Biomathematics Group

-       Devising a Semantic Web Information System for Epidemiology

-       Requirements gathering and Graphical User Interface Development


July 2006:December 2009

Graduate Research Assistant at The University of Texas M.D. Anderson Cancer Center,

Department of Bioinformatics and Computational Biology (Houston, Texas, USA)

-         Development, Implementation and Validation of a Knowledge Organization System for Biomedical, Translational and Clinical Research (S3DB, http://s3db.org)


January 2005:July 2006

Research Assistant at the Institute for Chemical and Biological Technology, New University of Lisbon (ITQB/UNL)

                - Management, Curation and Development of a molecular epidemiology database


September 2003:September 2004

Researcher at Guia Marine Laboratory, University of Lisbon – LMG/FCUL

                - Experimental methods for detection of chemical perception in sea urchins



1. Molecular Epidemiology of gram-positive pathogens (2008-2012)

Awarded by the Portuguese Science Foundation (FCT). Total Budget: €200K

Roles: Budget holder, project manager, main developer


2. GRANATUM: A social collaborative working space semantically interlinking biomedical researchers, knowledge and data for the design and execution of in-silico models and experiments in cancer chemoprevention (2011-2013)

Awarded the European Union 7th Framework Project. Total Budget € 3M (~€400K per partner)

Roles: Project Manager and Leader of 2 workpackages (Linked Data Space; Software Evaluation)


3. Sifem: Semantic Infostructure interlinking an open source Finite Element Tool and libraries with a Model Repository for the multi-scale modeling of the inner-ear (2013-2016)

Awarded the European Union 7th Framework Project. Total Budget € 3M (~€400K per partner)

Roles: Project Coordinator and Leader of 2 workpackages (Management; Semantic Integration)


4. Linked2Safety: A Next-Generation, Secure Linked Data Medical Information Space for Semantically-Interconnecting Electronic Health Records and Clinical Trials Systems Advancing Patients Safety in Clinical Research (2011-2014)

Awarded the European Union 7th Framework Project. Total Budget € 3M (~€400K per partner)

Roles: Workpackage Leader (Semantic Integration)


5. Structured PhD Program in Simulation Sciences (2012-2016)

Awarded by the irish Higher Education Authority. My budget: €200K (2 PhD fellowships)

Roles: Co-Coordinator, budget holder and student supervisor


6. Academic Projects with Industry (Ontoforce and UCB)

Acquired the funding, and led the projects


7. The Foundation Medicine KnowledgeBase

Tactical Strategy and Implementation


  • Panelist: 1st Women in Data Science Conference
  • Panelist: Challenges of Linked Data (with Tim Berners-Lee, Jim Hendler, David Karger, Mona Vernon, David Wood), 26 Nov 2013
  • Dagstuhl Seminars: ICT Strategies for Bridging Biology and Precision Medicine, 18-23 Aug 2013
  • UC Davis Genome Center, 4 Dec 2012
  • NSF Discovery Informatics Workshop 2012, 2-3Feb 2012
  • W3C Technical Plenary Meeting, 02 Nov 2009


  • Cambridge Semantic Web Meetup (co-organizer)
  • Joint Workshop on Semantic Technologies Applied to Biomedical Informatics and Individualized Medicine (SATBI+SWIM) 2012
  • Semantic Web Applications and Tools for the Life Sciences (SWAT4LS) 2012
  • International Provenance and Annotation Workshop (IPAW) 2012
  • Bio-Ontologies 2012
  • Semantic Web for Clinical and Translational Research Workshop at the International Semantic Web Conference (ISWC) 2012
  • VIVO 2011
  • CSHALS 2014 (Organizing Committee)


  • Winner of the Semantic Web Challenge 2013 (Article citing the award) – Big Data Track. Awarded at ISWC 2013.
  • Best Paper Award and Winner of the Linked Data Cup 2013, iSemantics 2013
  • Best paper award at CSHALS 2014
  • Award: 2007 Trainee Excellence Award, M.D. Anderson's Alumni and Faculty Association: Incubation of Experimental Ontologies for Biomarker Identification in Ovarian Cancer
  • Award: 2008-2012 Bolsa de Doutoramento (PhD Scholarship) from the Fundação para a Ciência e Tecnologia (FCT)
  • Award: Science Foundation Ireland Short Term Travel Fellowship (2012)
  • Award: 2003/2004 Prodep III – Portuguese Program of Educational Development