Publications

  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):6­7. [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):998­1008 [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 Kei­Hoi 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 [pdf]
  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; 14:2­13 [pdf]
  13. HF Deus, E Prud'hommeaux, M Miller, J Zhao, J Malone, T Adamusiak, J McCusker, S Das, P Rocca­Serra, 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):782­94 [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 [pdf]
  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 [pdf]
  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): 1333­1340. [pdf]
  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 tree­of­life knowledge accessible, reusable and convenient. BMC Bioinformatics. 2013 May 13;14(1):158 [pdf]
  19. Muhammad Saleem, Axel­Cyrille 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, Axel­Cyrille Ngonga, Jonas S Almeida, Stefan Decker, Helena Deus (2013) Linked Cancer Genome Atlas Database In: Linked Data Cup, I­Semantics 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 user­driven 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 9­11, 2014 [pdf]
  32. Helena Futscher de Deus, Rachel Lauren Erlich, Ronald David Collette, Alexander N Parker, Michael Pellini, Gary Palmer, Mary Pat Lancelotta, Matthew J Hawryluk, Philip James Stephens, Eric Karl Neumann, Jeffrey B Collemer. System and method for managing genomic information. US Patent App. 14/463,073, 2015 [pdf]
  33. Helena F Deus, Corey Harper, Darin McBeath, Ron Daniel. Combining pattern matching with word embeddings for the extraction of experimental variables from scientific literature. IEEE Big data 2017 [pdf]
  34. Helena F. Deus. Big semantic Processing in the Life Sciences Domain. Book Chapter - Encyclopedia of Big Data Technologies. Springer 2018 [pdf]
  35. Michael Lauruhn, Helena F. Deus, Paul Groth and Corey Harper . Use of internal testing data to help determine compensation for crowdsourcing tasks. Augmenting Intelligence with Humans­-in-­the-­Loop - co-located with ISWC 2018 [pdf]