Publikationen

@ARTICLE{moradi2024meai109183,
  author = {Moradi, M.~ and Yan, K.~ and Colwell, D.~ and Samwald, M.~ and Asgari, R.~},
  title = {Model-Agnostic Explainable Artificial Intelligence for Object Detection in Image Data.},
  journal = {Engineering Applications of Artificial Intelligence},
  year = {2024},
  volume = {137},
  number = {B},
  pages = {109183},
  issn = {0952-1976},
  doi = {10.1016/j.engappai.2024.109183}
}

@ARTICLE{schaefer2024gaab108796,
  author = {Schaefer, M.~ and Reichl, S.~ and Ter Horst, R.~ and Nicolas, A.M.~ and Krausgruber, T.~ and Piras, F.~ and Stepper, P.~ and Bock, C.~ and Samwald, M.~},
  title = {GPT-4 as a Biomedical Simulator.},
  journal = {Computers in Biology and Medicine},
  year = {2024},
  volume = {178},
  pages = {108796},
  issn = {1879-0534 0010-4825},
  doi = {10.1016/j.compbiomed.2024.108796},
  keywords = {Artificial intelligence;Computational biology;Large language models;Biomedical simulation;GPT-4}
}

@ARTICLE{hebenstreit2024accre1999,
  author = {Hebenstreit, K.~ and Praas, R.~ and Kiesewetter, L.P.~ and Samwald, M.~},
  title = {A Comparison of Chain-of-Thought Reasoning Strategies across Datasets and Models.},
  journal = {PeerJ Computer Science},
  year = {2024},
  volume = {10},
  pages = {e1999},
  issn = {2376-5992},
  doi = {10.7717/peerj-cs.1999},
  keywords = {Chain-of-thought reasoning;Externalized reasoning;Large language models;Question-answering datasets;Zero-shot prompting}
}

@INPROCEEDINGS{hebenstreit2023acpg,
  author = {Hebenstreit, K.~ and Praas, R.~ and Samwald, M.~},
  title = {A Collection of Principles for Guiding and Evaluating Large Language Models.},
  booktitle = {Proceedings of Socially Responsible Language Modelling Research (SoLaR) Workshop at NEURIPS 2023, Los Angeles, U.S.A., 16 December 2023},
  year = {2023},
  url = {https://openreview.net/forum?id=8iXdNXW34d}
}

@INPROCEEDINGS{kusa2023cbdg2346823484,
  author = {Kusa, W.~ and Mendoza, O.E.~ and Samwald, M.~ and Knoth, P.~ and Hanbury, A.~},
  title = {CSMeD: Bridging the Dataset Gap in Automated Citation Screening for Systematic Literature Reviews.},
  booktitle = {Advances in Neural Information Processing Systems 36 (NeurIPS 2023)},
  year = {2023},
  editor = {Oh,A.;Naumann,T.;Globerson,A.;Saenko,K.;Hardt,M.;Levine,S.},
  pages = {23468--23484},
  publisher = {Curran Associates, Inc.},
  url = {https://proceedings.neurips.cc/paper_files/paper/2023/file/4962a23916103301b27bde29a27642e8-Paper-Datasets_and_Benchmarks.pdf}
}

@ARTICLE{ott2023tach528,
  author = {Ott, S.~ and Hebenstreit, K.~ and Liévin, V.~ and Hother, C.E.~ and Moradi, M.~ and Mayrhauser, M.~ and Praas, R.~ and Winther, O.~ and Samwald, M.~},
  title = {ThoughtSource: A Central Hub for Large Language Model Reasoning Data.},
  journal = {Scientific Data},
  year = {2023},
  volume = {10},
  pages = {528},
  doi = {10.1038/s41597-023-02433-3},
  url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85167371094\&doi=10.1038%2fs41597-023-02433-3\&partnerID=40\&md5=5b991778a771f0695971a723dccffc24}
}

@ARTICLE{memarzadeh2023aukm17151727,
  author = {Memarzadeh, H.~ and Ghadiri, N.~ and Samwald, M.~ and Lotfi Shahreza, M.~},
  title = {Applying Unsupervised Keyphrase Methods on Concepts Extracted from Discharge Sheets.},
  journal = {Pattern Analysis and Applications},
  year = {2023},
  volume = {26},
  number = {4},
  pages = {1715--1727},
  doi = {https://doi.org/10.1007/s10044-023-01198-0}
}

@ARTICLE{swen2023a1pp347356,
  author = {Swen, J.J.~ and van der Wouden, C.H.~ and Manson, L.E.~ and Abdullah-Koolmees, H.~ and Blagec, K.~ and Blagus, T.~ and B{\"o}hringer, S.~ and Cambon-Thomsen, A.~ and Cecchin, E.~ and Cheung, K.-C.~ and Deneer, V.H.~ and Dupui, M.~ and Ingelman-Sundberg, M.~ and Jonsson, S.~ and Joefield-Roka, C.~ and Just, K.S.~ and Karlsson, M.O.~ and Konta, L.~ and Koopmann, R.~ and Kriek, M.~ and Lehr, T.~ and Mitropoulou, C.~ and Rial-Sebbag, E.~ and Rollinson, V.~ and Roncato, R.~ and Samwald, M.~ and Schaeffeler, E.~ and Skokou, M.~ and Schwab, M.~ and Steinberger, D.~ and Stingl, J.C.~ and Tremmel, R.~ and Turner, R.M.~ and van Rhenen, M.H.~ and Dávila Fajardo, C.L.~ and Dolžan, V.~ and Patrinos, G.P.~ and Pirmohamed, M.~ and Sunder-Plassmann, G.~ and Toffoli, G.~ and Guchelaar, H.-J.~ and {on behalf of the Ubiquitous Pharmacogenomics Consortium}},
  title = {A 12-Gene Pharmacogenetic Panel to Prevent Adverse Drug Reactions: An Open-Label, Multicentre, Controlled, Cluster-Randomised Crossover Implementation Study.},
  journal = {Lancet},
  year = {2023},
  volume = {401},
  number = {10374},
  pages = {347--356},
  issn = {1474-547X 0140-6736},
  doi = {10.1016/S0140-6736(22)01841-4}
}

@MISC{blagec2023bdda104274,
  author = {Blagec, K.~ and Kraiger, J.~ and Fr{\"u}hwirt, W.~ and Samwald, M.~},
  title = {Benchmark Datasets Driving Artificial Intelligence Development Fail to Capture the Needs of Medical Professionals.},
  year = {2023},
  doi = {10.1016/j.jbi.2022.104274}
}

@ARTICLE{samwald2023tuos,
  author = {Samwald, M.~ and Praas, R.~ and Hebenstreit, K.~},
  title = {Towards Unified Objectives for Self-Reflective AI.},
  journal = {SSRN 4446991},
  year = {2023},
  url = {https://ssrn.com/abstract=4446991}
}

@ARTICLE{hebenstreit2023adcp230502897,
  author = {Hebenstreit, K.~ and Praas, R.~ and Kiesewetter, L.P.~ and Samwald, M.~},
  title = {An Automatically Discovered Chain-of-Thought Prompt Generalizes to Novel Models and Datasets.},
  journal = {arXiv},
  year = {2023},
  pages = {2305.02897},
  doi = {https://doi.org/10.48550/arXiv.2305.02897}
}

@ARTICLE{memarzadeh2022asip32933324,
  author = {Memarzadeh, H.~ and Ghadiri, N.~ and Samwald, M.~ and Lotfi Shahreza, M.~},
  title = {A Study into Patient Similarity through Representation Learning from Medical Records.},
  journal = {Knowledge and Information Systems},
  year = {2022},
  volume = {64},
  number = {12},
  pages = {3293--3324},
  doi = {10.1007/s10115-022-01740-2},
  url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85138078737\&doi=10.1007%2fs10115-022-01740-2\&partnerID=40\&md5=382df42b3c472186847b5279def37023}
}

@MISC{bigscienceworkshop:lescao2022ba1o221105100,
  author = {BigScience Workshop: Le Scao, T.~ and Fan, A.~ and Akiki, C.~ and {et al.}},
  title = {BLOOM: A 176B-Parameter Open-Access Multilingual Language Model.},
  year = {2022},
  url = {https://arxiv.org/pdf/2211.05100.pdf}
}

@ARTICLE{ott2022mgdb6793,
  author = {Ott, S.~ and Barbosa-Silva, A.~ and Blagec, K.~ and Brauner, J.~ and Samwald, M.~},
  title = {Mapping Global Dynamics of Benchmark Creation and Saturation in Artificial Intelligence.},
  journal = {Nature Communications},
  year = {2022},
  volume = {13},
  pages = {6793},
  issn = {2041-1723},
  doi = {10.1038/s41467-022-34591-0},
  url = {https://doi.org/10.1038/s41467-022-34591-0}
}

@ARTICLE{brandmayr2022rler310322,
  author = {Brandmayr, G.~ and Hartmann, M.~ and F{\"u}rbass, F.~ and Matz, G.~ and Samwald, M.~ and Kluge, T.~ and Dorffner, G.~},
  title = {Relational Local Electroencephalography Representations for Sleep Scoring.},
  journal = {Neural Networks},
  year = {2022},
  volume = {154},
  pages = {310--322},
  issn = {1879-2782 0893-6080},
  doi = {10.1016/j.neunet.2022.07.020},
  keywords = {Context encoding;EEG;Relative position attention;REM;Sequence learning;Transformer}
}

@ARTICLE{moradi2022irab104114,
  author = {Moradi, M.~ and Samwald, M.~},
  title = {Improving the Robustness and Accuracy of Biomedical Language Models through Adversarial Training.},
  journal = {Journal of Biomedical Informatics},
  year = {2022},
  volume = {132},
  pages = {104114},
  issn = {1532-0480 1532-0464},
  doi = {10.1016/j.jbi.2022.104114},
  keywords = {Deep learning;Adversarial attack;Adversarial training;Biomedical natural language processing;Biomedical text;Robustness}
}

@ARTICLE{blagec2022acol322,
  author = {Blagec, K.~ and Barbosa-Silva, A.~ and Ott, S.~ and Samwald, M.~},
  title = {A Curated, Ontology-Based, Large-Scale Knowledge Graph of Artificial Intelligence Tasks and Benchmarks.},
  journal = {Scientific Data},
  year = {2022},
  volume = {9},
  pages = {322},
  issn = {2052-4463},
  doi = {10.1038/s41597-022-01435-x}
}

@ARTICLE{blagec2022pdsue0268534,
  author = {Blagec, K.~ and Swen, J.J.~ and Koopmann, R.~ and Cheung, K.-C.~ and Crommentuijn-van Rhenen, M.~ and Holsappel, I.~ and Konta, L.~ and Ott, S.~ and Steinberger, D.~ and Xu, H.~ and Cecchin, E.~ and Dolžan, V.~ and Dávila-Fajardo, C.L.~ and Patrinos, G.P.~ and Sunder-Plassmann, G.~ and Turner, R.M.~ and Pirmohamed, M.~ and Guchelaar, H.-J.~ and Samwald, M.~},
  title = {Pharmacogenomics Decision Support in the U-PGx Project: Results and Advice from Clinical Implementation across Seven European Countries.},
  journal = {PLoS One},
  year = {2022},
  volume = {17},
  number = {6},
  pages = {e0268534},
  issn = {1932-6203},
  doi = {10.1371/journal.pone.0268534}
}

@INCOLLECTION{fries2022ddbl137145,
  author = {Fries, J.A.~ and Seelam, N.~ and Altay, G.~ and Weber, L.~ and Kang, M.~ and Datta, D.~ and Su, R.~ and Garda, S.~ and Wang, B.~ and Ott, S.~ and Samwald, M.~ and Kusa, W.~},
  title = {Dataset Debt in Biomedical Language Modeling.},
  booktitle = {Proceedings of BigScience Episode #5 – Workshop on Challenges \& Perspectives in Creating Large Language Models, Dublin, Ireland and virtual, 27 May 2022},
  publisher = {Association for Computational Linguistics},
  year = {2022},
  editor = {Fan,A.;Ilic,S.;Wolf,T.;Gallé,M.},
  pages = {137--145},
  address = {Stroudsburg, PA},
  month = {may},
  url = {https://aclanthology.org/2022.bigscience-1.10.pdf#page=137}
}

@INPROCEEDINGS{blagec2022agam5263,
  author = {Blagec, K.~ and Dorffner, G.~ and Moradi, M.~ and Ott, S.~ and Samwald, M.~},
  title = {A Global Analysis of Metrics Used for Measuring Performance in Natural Language Processing.},
  booktitle = {Proceedings of NLP Power! The First Workshop on Efficient Benchmarking in NLP},
  year = {2022},
  editor = {Shavrina,T.;Mikhailov,V.;Malykh,V.;Artemova,E.;Serikov,O.;Protasov,V. },
  pages = {52--63},
  address = {Dublin, Ireland},
  publisher = {Association for Computational Linguistics},
  url = {https://aclanthology.org/2022.nlppower-1.pdf#Page=59}
}

@ARTICLE{ott2022lpee23712373,
  author = {Ott, S.~ and Barbosa-Silva, A.~ and Samwald, M.~},
  title = {Linkexplorer: Predicting, Explaining and Exploring Links in Large Biomedical Knowledge Graphs.},
  journal = {Bioinformatics},
  year = {2022},
  volume = {38},
  number = {8},
  pages = {2371--2373},
  issn = {1367-4803},
  doi = {10.1093/bioinformatics/btac068},
  url = {https://doi.org/10.1093/bioinformatics/btac068}
}

@ARTICLE{wallisch2021rpcr284,
  author = {Wallisch, C.~ and Agibetov, A.~ and Dunkler, D.~ and Haller, M.~ and Samwald, M.~ and Dorffner, G.~ and Heinze, G.~},
  title = {The Roles of Predictors in Cardiovascular Risk Models – A Question of Modeling Culture?},
  journal = {BMC Medical Research Methodology},
  year = {2021},
  volume = {21},
  pages = {284},
  issn = {1471-2288},
  doi = {10.1186/s12874-021-01487-4}
}

@ARTICLE{agibetov2021cnnf1268,
  author = {Agibetov, A.~ and Kammerlander, A.~ and Duca, F.~ and Nitsche, C.~ and Koschutnik, M.~ and Donà, C.~ and Dachs, T.-M.~ and Rettl, R.~ and Stria, A.~ and Schrutka, L.~ and Binder, C.~ and Kastner, J.~ and Agis, H.~ and Kain, R.~ and Auer-Grumbach, M.~ and Samwald, M.~ and Hengstenberg, C.~ and Dorffner, G.~ and Mascherbauer, J.~ and Bonderman, D.~},
  title = {Convolutional Neural Networks for Fully Automated Diagnosis of Cardiac Amyloidosis by Cardiac Magnetic Resonance Imaging.},
  journal = {Journal of Personalized Medicine},
  year = {2021},
  volume = {11},
  number = {12},
  pages = {1268},
  issn = {2075-4426},
  doi = {10.3390/jpm11121268},
  keywords = {heart failure;artificial intelligence;cardiac amyloidosis;diagnostic ability}
}

@INCOLLECTION{moradi2021ernl15581570,
  author = {Moradi, M.~ and Samwald, M.~},
  title = {Evaluating the Robustness of Neural Language Models to Input Perturbations.},
  booktitle = {Proceedings of the 2021 Conference on Empirical Methods in Natural Language Processing (EMNLP 2021), Online and Punta Cana, Dominican Republic, 7–11 November 2021},
  publisher = {Association for Computational Linguistics},
  year = {2021},
  editor = {Moens,M.-F.;Huang,X.;Specia,L.;Yih,S.W.-t.},
  pages = {1558--1570},
  address = {Stroudsburg},
  month = {nov},
  url = {https://aclanthology.org/2021.emnlp-main.117.pdf}
}

@INPROCEEDINGS{ott2021sirl,
  author = {Ott, S.~ and Meilicke, C.~ and Samwald, M.~},
  title = {SAFRAN: An Interpretable, Rule-Based Link Prediction Method Outperforming Embedding Models.},
  booktitle = {Proceedings 3rd Conference on Automated Knowledge Base Construction (AKBC2021), Virtual, 4–8 October 2021},
  year = {2021},
  url = {https://www.akbc.ws/2021/papers/jCt9S_3w_S9}
}

@ARTICLE{moradi2021gmap210902555,
  author = {Moradi, M.~ and Blagec, K.~ and Haberl, F.~ and Samwald, M.~},
  title = {GPT-3 Models Are Poor Few-Shot Learners in the Biomedical Domain.},
  journal = {arXiv},
  year = {2021},
  pages = {2109.02555},
  url = {https://arxiv.org/abs/2109.02555}
}

@MISC{moradi2021dlma210812242,
  author = {Moradi, M.~ and Blagec, K.~ and Samwald, M.~},
  title = {Deep Learning Models Are Not Robust against Noise in Clinical Text.},
  year = {2021},
  doi = {https://arxiv.org/ftp/arxiv/papers/2108/2108.12242.pdf}
}

@ARTICLE{moradi2021pebc113941,
  author = {Moradi, M.~ and Samwald, M.~},
  title = {Post-Hoc Explanation of Black-Box Classifiers Using Confident Itemsets.},
  journal = {Expert Systems with Applications},
  year = {2021},
  volume = {165},
  pages = {113941},
  doi = {10.1016/j.eswa.2020.113941},
  url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85091063493\&doi=10.1016%2fj.eswa.2020.113941\&partnerID=40\&md5=1d509a337262e6e36f2a9038dac38ecd}
}

@ARTICLE{moradi2021ebmb31123120,
  author = {Moradi, M.~ and Samwald, M.~},
  title = {Explaining Black-Box Models for Biomedical Text Classification.},
  journal = {IEEE Journal of Biomedical and Health Informatics},
  year = {2021},
  volume = {25},
  number = {8},
  pages = {3112--3120},
  issn = {2168-2208 2168-2194},
  doi = {10.1109/JBHI.2021.3056748}
}

@ARTICLE{ott2020sirl201205750,
  author = {Ott, S.~ and Graf, L.~ and Agibetov, A.~ and Meilicke, C.~ and Samwald, M.~},
  title = {Scalable and Interpretable Rule-Based Link Prediction for Large Heterogeneous Knowledge Graphs.},
  journal = {arXiv},
  year = {2020},
  pages = {2012.05750},
  url = {https://arxiv.org/abs/2012.05750}
}

@ARTICLE{moradi2020ebtc201010873,
  author = {Moradi, M.~ and Samwald, M.~},
  title = {Explaining Black-Box Text Classifiers for Disease-Treatment Information Extraction.},
  journal = {arXiv},
  year = {2020},
  pages = {2010.10873},
  url = {https://arxiv.org/abs/2010.10873}
}

@ARTICLE{agibetov2020bnel100590,
  author = {Agibetov, A.~ and Samwald, M.~},
  title = {Benchmarking Neural Embeddings for Link Prediction in Knowledge Graphs under Semantic and Structural Changes.},
  journal = {Journal of Web Semantics},
  year = {2020},
  volume = {64},
  pages = {100590},
  doi = {10.1016/j.websem.2020.100590},
  url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85086635039\&doi=10.1016%2fj.websem.2020.100590\&partnerID=40\&md5=4677a7c51ce590721df1f778ca87684f}
}

@ARTICLE{agibetov2020mleps167s168,
  author = {Agibetov, A.~ and Seirer, B.~ and Theresa-Marie, D.~ and Matthias, K.~ and Dalos, D.~ and Rettl, R.~ and Duca, F.~ and Lore, S.~ and Agis, H.~ and Kain, R.~ and Michaela, A.~ and Binder, C.~ and Mascherbauer, J.~ and Hengstenberg, C.~ and Samwald, M.~ and Dorffner, G.~ and Bonderman, D.~},
  title = {Machine Learning Enables Prediction of Cardiac Amyloidosis by Routine Laboratory Parameters: A Proof-of-Concept Study.},
  journal = {Wiener Klinische Wochenschrift},
  year = {2020},
  volume = {132},
  number = {Suppl 5: Abstracts {\"O}sterreichische Kardiologische Gesellschaft Jahrestagung 2020, Salzburg, {\"O}sterreich, 1.–3. November 2020},
  pages = {S167--S168},
  issn = {0043-5325},
  doi = {10.1007/s00508-020-01749-z}
}

@INPROCEEDINGS{jiménezruiz2020doat784791,
  author = {Jiménez-Ruiz, E.~ and Agibetov, A.~ and Chen, J.~ and Samwald, M.~ and Cross, V.~},
  title = {Dividing the Ontology Alignment Task with Semantic Embeddings and Logic-Based Modules.},
  booktitle = {ECAI 2020. 24th European Conference on Artificial Intelligence, 29 August–8 September 2020, Santiago de Compostela, Spain, Including 10th Conference on Prestigious Applications of Artificial Intelligence (PAIS 2020)},
  year = {2020},
  editor = {De Giacomo,G.;Catala,A.;Dilkina,B.;Milano,M.;Barro,S.;Bugarin,A.;Lang,J.},
  number = {325},
  series = {Frontiers in Artificial Intelligence and Applications},
  pages = {784--791},
  address = {Amsterdam},
  publisher = {IOS Press},
  url = {http://ecai2020.eu/papers/792_paper.pdf}
}

@MISC{blagec2020acam200802577,
  author = {Blagec, K.~ and Dorffner, G.~ and Moradi, M.~ and Samwald, M.~},
  title = {A Critical Analysis of Metrics Used for Measuring Progress in Artificial Intelligence.},
  year = {2020},
  url = {https://arxiv.org/abs/2008.02577}
}

@ARTICLE{vanderwouden2020gepm131144,
  author = {van der Wouden, C.H.~ and B{\"o}hringer, S.~ and Cecchin, E.~ and Cheung, K.-C.~ and Dávila-Fajardo, C.L.~ and Deneer, V.H.M.~ and Dolžan, V.~ and Ingelman-Sundberg, M.~ and J{\"o}nsson, S.~ and Karlsson, M.O.~ and Kriek, M.~ and Mitropoulou, C.~ and Patrinos, G.P.~ and Pirmohamed, M.~ and Rial-Sebbag, E.~ and Samwald, M.~ and Schwab, M.~ and Steinberger, D.~ and Stingl, J.~ and Sunder-Plassmann, G.~ and Toffoli, G.~ and Turner, R.M.~ and van Rhenen, M.H.~ and van Zwet, E.~ and Swen, J.J.~ and Guchelaar, H.-J.~ and {on Behalf of the Ubiquitous Pharmacogenomics Consortium}},
  title = {Generating Evidence for Precision Medicine: Considerations Made by the Ubiquitous Pharmacogenomics Consortium When Designing and Operationalizing the PREPARE Study.},
  journal = {Pharmacogenetics and Genomics},
  year = {2020},
  volume = {30},
  number = {6},
  pages = {131--144},
  issn = {1744-6880 1744-6872},
  doi = {10.1097/FPC.0000000000000405}
}

@ARTICLE{breit2020oabf40974098,
  author = {Breit, A.~ and Ott, S.~ and Agibetov, A.~ and Samwald, M.~},
  title = {OpenBioLink: A Benchmarking Framework for Large-Scale Biomedical Link Prediction.},
  journal = {Bioinformatics},
  year = {2020},
  volume = {36},
  number = {13},
  pages = {4097--4098},
  doi = {10.1093/bioinformatics/btaa274},
  url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85087532321\&doi=10.1093%2fbioinformatics%2fbtaa274\&partnerID=40\&md5=7de18505fe5301d30612131cbd9b862a}
}

@ARTICLE{moradi2020sbau103452,
  author = {Moradi, M.~ and Dashti, M.~ and Samwald, M.~},
  title = {Summarization of Biomedical Articles Using Domain-Specific Word Embeddings and Graph Ranking.},
  journal = {Journal of Biomedical Informatics},
  year = {2020},
  volume = {107},
  pages = {103452},
  issn = {1532-0480 1532-0464},
  doi = {10.1016/j.jbi.2020.103452},
  keywords = {Text summarization;Natural language processing;Deep learning;Graph ranking;Medical text mining;Word embedding}
}

@ARTICLE{agibetov2020mlep1334,
  author = {Agibetov, A.~ and Seirer, B.~ and Dachs, T.-M.~ and Koschutnik, M.~ and Dalos, D.~ and Rettl, R.~ and Duca, F.~ and Schrutka, L.~ and Agis, H.~ and Kain, R.~ and Auer-Grumbach, M.~ and Binder, C.~ and Mascherbauer, J.~ and Hengstenberg, C.~ and Samwald, M.~ and Dorffner, G.~ and Bonderman, D.~},
  title = {Machine Learning Enables Prediction of Cardiac Amyloidosis by Routine Laboratory Parameters: A Proof-of-Concept Study.},
  journal = {Journal of Clinical Medicine},
  year = {2020},
  volume = {9},
  number = {5},
  pages = {1334},
  issn = {2077-0383 2077-0383},
  doi = {10.3390/jcm9051334},
  keywords = {heart failure;artificial intelligence;cardiac amyloidosis;machine learning}
}

@ARTICLE{moradi2020dceq105117,
  author = {Moradi, M.~ and Dorffner, G.~ and Samwald, M.~},
  title = {Deep Contextualized Embeddings for Quantifying the Informative Content in Biomedical Text Summarization.},
  journal = {Computer Methods and Programs in Biomedicine},
  year = {2020},
  volume = {184},
  pages = {105117},
  issn = {1872-7565 0169-2607},
  doi = {10.1016/j.cmpb.2019.105117},
  keywords = {Biomedical text mining;Clustering;Contextualized embeddings;Deep learning;domain knowledge;Text summarization}
}

@ARTICLE{agibetov2019ebpc16771677,
  author = {Agibetov, A.~ and Seirer, B.~ and Aschauer, S.~ and Dalos, D.~ and Rettl, R.~ and Duca, F.~ and Agis, H.~ and Kain, R.~ and Binder, C.~ and Mascherbauer, J.~ and Hengstenberg, C.~ and Samwald, M.~ and Dorffner, G.~ and Bonderman, D.~},
  title = {Extremely Boosted Prediction of Cardiac Amyloidosis by Routine Laboratory Paramaters.},
  journal = {European Heart Journal},
  year = {2019},
  volume = {40},
  number = {Suppl 1: Abstracts European Society of Cardiology (ESC) Congress 2019, Paris, France, 31 August–4 September 2019},
  pages = {1677},
  issn = {0195-668X},
  doi = {10.1093/eurheartj/ehz748.1043}
}

@INPROCEEDINGS{agibetov2019uhlc2630,
  author = {Agibetov, A.~ and Dorffner, G.~ and Samwald, M.~},
  title = {Using Hyperbolic Large-Margin Classifiers for Biological Link Prediction.},
  booktitle = {Proceedings of the 5th Workshop on Semantic Deep Learning, SemDeep@IJCAI 2019, Macau, China, August 12, 2019},
  year = {2019},
  editor = {Espinosa Anke,L.;Declerck,T.;Gromann,D.;Camacho-Collados,J.;Pilehvar,M.T.},
  pages = {26--30},
  address = {Stroudsburg},
  month = {aug},
  publisher = {Association for Computational Linguistics},
  url = {https://www.aclweb.org/anthology/W19-5805}
}

@ARTICLE{agibetov2019ovsss367s368,
  author = {Agibetov, A.~ and Seirer, B.~ and Aschauer, S.~ and Dalos, D.~ and Rettl, R.~ and Duca, F.~ and Agis, H.~ and Kain, R.~ and Binder, C.~ and Mascherbauer, J.~ and Hengstenberg, C.~ and Samwald, M.~ and Dorffner, G.~ and Bonderman, D.~},
  title = {Optimal Variable Selection for Simple Prediction Model of Cardiac Amyloidosis by Routine Laboratory Parameters.},
  journal = {Wiener Klinische Wochenschrift},
  year = {2019},
  volume = {131},
  number = {Suppl 2: Abstracts {\"O}sterreichische Kardiologische Gesellschaft Jahrestagung 2019, Salzburg, {\"O}sterreich, 29. Mai–1. Juni 2019},
  pages = {S367--S368},
  issn = {0043-5325},
  url = {https://link.springer.com/journal/508/131/2/suppl}
}

@ARTICLE{blagec2019nsem178,
  author = {Blagec, K.~ and Xu, H.~ and Agibetov, A.~ and Samwald, M.~},
  title = {Neural Sentence Embedding Models for Semantic Similarity Estimation in the Biomedical Domain.},
  journal = {BMC Bioinformatics},
  year = {2019},
  volume = {20},
  pages = {178},
  issn = {1471-2105 1471-2105},
  doi = {10.1186/s12859-019-2789-2},
  keywords = {Algorithms;Humans;*Models;Theoretical;*Biomedical Research;*Semantics;Natural language processing;Neural embedding models;PubMed;Semantics}
}

@INCOLLECTION{obeng2019rppd369384,
  author = {Obeng, A.O.~ and Samwald, M.~ and Scott, S.A.~},
  title = {Reactive, Point-of-Care, Preemptive, and Direct-To-Consumer Pharmacogenomics Testing.},
  booktitle = {Pharmacogenomics: Challenges and Opportunities in Therapeutic Implementation},
  publisher = {Academic Press},
  year = {2019},
  editor = {Lam,Y.W.F.;Scott,S.A.},
  pages = {369--384},
  address = {Oxford},
  edition = {2nd ed.},
  url = {https://doi.org/10.1016/C2016-0-03878-0}
}

@ARTICLE{agibetov2018fsne541,
  author = {Agibetov, A.~ and Blagec, K.~ and Xu, H.~ and Samwald, M.~},
  title = {Fast and Scalable Neural Embedding Models for Biomedical Sentence Classification.},
  journal = {BMC Bioinformatics},
  year = {2018},
  volume = {19},
  pages = {541},
  issn = {1471-2105 1471-2105},
  doi = {10.1186/s12859-018-2496-4},
  keywords = {Humans;*Biomedical Research;Natural language processing;*Neural Networks;Computer;*Natural Language Processing;*Unified Medical Language System;FastText;Language;Neural networks;PubMed/*standards;Scientific abstracts;Text classification;Word vector models}
}

@INPROCEEDINGS{agibetov2018glel89102,
  author = {Agibetov, A.~ and Samwald, M.~},
  title = {Global and Local Evaluation of Link Prediction Tasks with Neural Embeddings.},
  booktitle = {SemDeep-4_NLIWOD-4 2018 – Joint Proceedings of the 4th Workshop on Semantic Deep Learning (SemDeep-4) and the 4th Natural Language Interfaces for the Web of Data (NLIWOD-4) and 9th Question Answering over Linked Data Challenge (QALD-9)},
  year = {2018},
  editor = {Choi,K.-S.;Espinosa Anke,L.;Declerck,T.;Gromann,D.;Kim,J.-D.;Ngomo,A.-C.N.;Saleem,M.;Usbeck,R.},
  number = {2241},
  series = {CEUR Workshop Proceedings},
  pages = {89--102},
  url = {http://ceur-ws.org/Vol-2241/}
}

@INPROCEEDINGS{jiménezruiz2018wdyc,
  author = {Jiménez-Ruiz, E.~ and Agibetov, A.~ and Samwald, M.~ and Cross, V.~},
  title = {We Divide, You Conquer: From Large-Scale Ontology Alignment to Manageable Subtasks with a Lexical Index and Neural Embeddings.},
  booktitle = {Proceedings of the ISWC 2018 Posters \& Demonstrations, Industry and Blue Sky Ideas Tracks co-located with 17th International Semantic Web Conference (ISWC 2018), Monterey, CA, USA, 8–12 October 2018},
  year = {2018},
  editor = {van Erp,M.;Atre,M.;Lopez,V.;Srinivas,K.;Fortuna,C.},
  number = {2180},
  series = {CEUR Workshop Proceedings},
  url = {http://ceur-ws.org/Vol-2180/paper-28.pdf}
}

@INPROCEEDINGS{jiménezruiz2018wdyc1324,
  author = {Jiménez-Ruiz, E.~ and Agibetov, A.~ and Samwald, M.~ and Cross, V.~},
  title = {We Divide, You Conquer: From Large-Scale Ontology Alignment to Manageable Subtasks with a Lexical Index and Neural Embeddings.},
  booktitle = {Proceedings of the 13th International Workshop on Ontology Matching (OM 2018), Monterey, CA, USA, 8 October 2018},
  year = {2018},
  editor = {Shvaiko,P.;Euzenat,J.;Jiménez-Ruiz,E.;Cheatham,M.;Hassanzadeh,O.},
  number = {2288},
  series = {CEUR Workshop Proceedings},
  pages = {13--24},
  month = {october},
  url = {http://ceur-ws.org/Vol-2288/om2018_LTpaper2.pdf}
}

@ARTICLE{blagec2018ipds893898,
  author = {Blagec, K.~ and Koopmann, R.~ and Crommentuijn-van Rhenen, M.~ and Holsappel, I.~ and van der Wouden, C.H.~ and Konta, L.~ and Xu, H.~ and Steinberger, D.~ and Just, E.~ and Swen, J.J.~ and Guchelaar, H.-J.~ and Samwald, M.~},
  title = {Implementing Pharmacogenomics Decision Support across Seven European Countries: The Ubiquitous Pharmacogenomics (U-PGx) Project.},
  journal = {Journal of the American Medical Informatics Association},
  year = {2018},
  volume = {25},
  number = {7},
  pages = {893--898},
  issn = {1527-974X 1067-5027},
  doi = {10.1093/jamia/ocy005},
  keywords = {Humans;Europe;*Decision Support Systems;Clinical;*Pharmacogenetics;Knowledge Bases;Mobile Applications;Multilingualism}
}

@INPROCEEDINGS{agibetov2018fsln6271,
  author = {Agibetov, A.~ and Samwald, M.~},
  title = {Fast and Scalable Learning of Neuro-Symbolic Representations of Biomedical Knowledge.},
  booktitle = {Proceedings of the First Workshop on Deep Learning for Knowledge Graphs and Semantic Technologies (DL4KGS) Co-Located with the 15th Extended Semantic Web Conference (ESWC 2018), Heraklion, Crete, Greece, 4 June 2018},
  year = {2018},
  editor = {Cochez,M.;Declerck,T.;de Melo,G.;Espinosa Anke,L.;Fetahu,B.;Gromann,D.;Kejriwal,M.;Koutraki,M.;Lécué,F.;Palumbo,E.;Sack,H.},
  number = {2106},
  series = {CEUR Workshop Proceedings},
  pages = {62--71},
  month = {may},
  url = {http://ceur-ws.org/Vol-2106/}
}

@INCOLLECTION{blagec2018emdr180187,
  author = {Blagec, K.~ and Jungwirth, D.~ and Haluza, D.~ and Samwald, M.~},
  title = {Effects of Medical Device Regulations on the Development of Stand-Alone Medical Software: A Pilot Study.},
  booktitle = {Health Informatics Meets eHealth. Biomedical Meets eHealth – From Sensors to Decisions. Proceedings of the 12th eHealth Conference},
  publisher = {IOS Press},
  year = {2018},
  editor = {Schreier,G.;Hayn,D.},
  number = {248},
  series = {Studies in Health Technology and Informatics},
  pages = {180--187},
  address = {Amsterdam},
  month = {may},
  url = {https://doi.org/10.3233/978-1-61499-858-7-180},
  keywords = {Humans;Reproducibility of Results;*Software;Patient Safety;Pilot Projects;*Medical Device Legislation;*Mobile Applications;Clinical Decision Support Systems;Computer Security;Medical Device Regulations}
}

@INCOLLECTION{blagec2017igpd121127,
  author = {Blagec, K.~ and Kuch, W.~ and Samwald, M.~},
  title = {The Importance of Gene-Drug-Drug-Interactions in Pharmacogenomics Decision Support: An Analysis Based on Austrian Claims Data.},
  booktitle = {Health Informatics Meets eHealth. Digital Insight – Information-Driven Health \& Care, Proceedings of the 11th eHealth2017 Conference},
  publisher = {IOS Press},
  year = {2017},
  editor = {Hayn,D.;Schreier,G.},
  number = {236},
  series = {Studies in Health Technology and Informatics},
  pages = {121--127},
  address = {Amsterdam},
  month = {may},
  doi = {10.3233/978-1-61499-759-7-121},
  url = {doi.org/10.3233/978-1-61499-759-7-121},
  keywords = {personalized medicine;genotype;claims data;drug safety;Pharmacogenomics;phenoconversion;re-use of patient data}
}

@ARTICLE{vanderwouden2017iped341358,
  author = {van der Wouden, C.H.~ and Cambon-Thomsen, A.~ and Cecchin, E.~ and Cheung, K.C.~ and Dávila-Fajardo, C.L.~ and Deneer, V.H.~ and Dolžan, V.~ and Ingelman-Sundberg, M.~ and J{\"o}nsson, S.~ and Karlsson, M.O.~ and Kriek, M.~ and Mitropoulou, C.~ and Patrinos, G.P.~ and Pirmohamed, M.~ and Samwald, M.~ and Schaeffeler, E.~ and Schwab, M.~ and Steinberger, D.~ and Stingl, J.~ and Sunder-Plassmann, G.~ and Toffoli, G.~ and Turner, R.M.~ and Van Rhenen, M.H.~ and Swen, J.J.~ and Guchelaar, H.-J.~ and {on Behalf of the Ubiquitous Pharmacogenomics Consortium.}},
  title = {Implementing Pharmacogenomics in Europe: Design and Implementation Strategy of the Ubiquitous Pharmacogenomics Consortium.},
  journal = {Clinical Pharmacology \& Therapeutics},
  year = {2017},
  volume = {101},
  number = {3},
  pages = {341--358},
  note = {
[Erratum: van der Wouden C.H., Cambon-Thomsen A., Cecchin E., Cheung K.C., Dávila-Fajardo C.L., Deneer V.H., Dolžan V., Ingelman-Sundberg M., J{\"o}nsson S., Karlsson M.O., Kriek M., Mitropoulou C., Patrinos G.P., Pirmohamed M., Samwald M., Schaeffeler E., Schwab M., Steinberger D., Stingl J., Sunder-Plassmann G., Toffoli G., Turner R.M., Van Rhenen M.H., Swen J.J., Guchelaar H.-J., on Behalf of the Ubiquitous Pharmacogenomics Consortium. Corrigendum: Implementing Pharmacogenomics in Europe: Design and Implementation Strategy of the Ubiquitous Pharmacogenomics Consortium (Clinical Pharmacology \& Therapeutics, (2017), 101, 3, (341-358), 10.1002/cpt.602). Clinical Pharmacology \& Therapeutics 102(1), 152, (2017)]},
  issn = {0009-9236},
  doi = {10.1002/cpt.602},
  keywords = {precision medicine;personalized medicine;cpic guidelines;cyp2c19 genotypes;decision-support;electronic medical-records;genomic medicine;preemptive pharmacogenomics;program clinical implementation;research network}
}

@ARTICLE{vanderwouden2016abfi16581660,
  author = {van der Wouden, C.H.~ and Swen, J.J.~ and Samwald, M.~ and Mitropoulou, C.~ and Schwab, M.~ and Guchelaar, H.-J.~ and {on Behalf of the Ubiquitous-Pharmacogenomics Consortium}},
  title = {A Brighter Future for the Implementation of Pharmacogenomic Testing.},
  journal = {European Journal of Human Genetics},
  year = {2016},
  volume = {24},
  number = {12},
  pages = {1658--1660},
  issn = {1018-4813},
  doi = {10.1038/ejhg.2016.116},
  keywords = {personalized medicine;model;bench;program clinical implementation;challenges;design;greece;patients project;preemptive pharmacogenomics;randomized-trial}
}

@ARTICLE{samwald2016iepue0164972,
  author = {Samwald, M.~ and Xu, H.~ and Blagec, K.~ and Empey, P.E.~ and Malone, D.C.~ and Ahmed, S.M.~ and Ryan, P.~ and Hofer, S.~ and Boyce, R.D.~},
  title = {Incidence of Exposure of Patients in the United States to Multiple Drugs for Which Pharmacogenomic Guidelines Are Available.},
  journal = {PLoS One},
  year = {2016},
  volume = {11},
  number = {10},
  pages = {e0164972},
  issn = {1932-6203 1932-6203},
  doi = {10.1371/journal.pone.0164972},
  keywords = {Adolescent;Adult;Female;Humans;Male;Young Adult;Aged;Middle Aged;Databases;Factual;Incidence;Child;Infant;Infant;Newborn;Risk;Child;Preschool;Cost-Benefit Analysis;United States;*Practice Guidelines as Topic;*Pharmacogenomic Testing;Drug Prescriptions/economics/*statistics \& numerical data;Drug-Related Side Effects and Adverse Reactions/economics}
}

@ARTICLE{blagec2016mpia33,
  author = {Blagec, K.~ and Romagnoli, K.~ and Boyce, R.D.~ and Hofer, S.~ and Samwald, M.~},
  title = {Making Pharmacogenomics Insights Available at the Point-of-Care.},
  journal = {Public Health Genomics},
  year = {2016},
  volume = {19},
  number = {Suppl 1: Abstracts Golden Helix Summer School 2016 – Cancer Genomics and Individualized Therapy, Syros Island, Greece, 22–26 September 2016},
  pages = {3},
  issn = {1662-4246},
  doi = {10.1159/000449434}
}

@ARTICLE{sieberts2016cacg12460,
  author = {Sieberts, S.K.~ and Zhu, F.~ and García-García, J.~ and Stahl, E.~ and Pratap, A.~ and Pandey, G.~ and Pappas, D.~ and Aguilar, D.~ and Anton, B.~ and Bonet, J.~ and Eksi, R.~ and Fornés, O.~ and Guney, E.~ and Li, H.~ and Marín, M.A.~ and Panwar, B.~ and Planas-Iglesias, J.~ and Poglayen, D.~ and Cui, J.~ and Falcao, A.O.~ and Suver, C.~ and Hoff, B.~ and Balagurusamy, V.S.K.~ and Dillenberger, D.~ and Chaibub Neto, E.~ and Norman, T.~ and Aittokallio, T.~ and Ammad-ud-din, M.~ and Azencott, C.-A.~ and Bellón, V.~ and Boeva, V.~ and Bunte, K.~ and Chheda, H.~ and Cheng, L.~ and Corander, J.~ and Dumontier, M.~ and Goldenberg, A.~ and Gopalacharyulu, P.~ and Hajiloo, M.~ and Hidru, D.~ and Jaiswal, A.~ and Kaski, S.~ and Khalfaoui, B.~ and Khan, S.A.~ and Kramer, E.R.~ and Marttinen, P.~ and Mezlini, A.M.~ and Molparia, B.~ and Pirinen, M.~ and Saarela, J.~ and Samwald, M.~ and Stoven, V.~ and Tang, H.~ and Tang, J.~ and Torkamani, A.~ and Vert, J.-P.~ and Wang, B.~ and Wang, T.~ and Wennerberg, K.~ and Wineinger, N.E.~ and Xiao, G.~ and Xie, Y.~ and Yeung, R.~ and Zhan, X.~ and Zhao, C.~ and {The Rheumatoid Arthritis Challenge Consortium}},
  title = {Crowdsourced Assessment of Common Genetic Contribution to Predicting Anti-TNF Treatment Response in Rheumatoid Arthritis.},
  journal = {Nature Communications},
  year = {2016},
  volume = {7},
  pages = {12460},
  note = {
[Erratum: Sieberts S.K., Zhu F., García-García J., Stahl E., Pratap A., Pandey G., Pappas D., Aguilar D., Anton B., Bonet J., Eksi R., Fornés O., Guney E., Li H., Marín M.A., Panwar B., Planas-Iglesias J., Poglayen D., Cui J., Falcao A.O., Suver C., Hoff B., Balagurusamy V.S.K., Dillenberger D., Chaibub Neto E., Norman T., Aittokallio T., Ammad-ud-din M., Azencott C.-A., Bellón V., Boeva V., Bunte K., Chheda H., Cheng L., Corander J., Dumontier M., Goldenberg A., Gopalacharyulu P., Hajiloo M., Hidru D., Jaiswal A., Kaski S., Khalfaoui B., Khan S.A., Kramer E.R., Marttinen P., Mezlini A.M., Molparia B., Pirinen M., Saarela J., Samwald M., Stoven V., Tang H., Tang J., Torkamani A., Vert J.-P., Wang B., Wang T., Wennerberg K., Wineinger N.E., Xiao G., Xie Y., Yeung R., Zhan X., Zhao C., The Rheumatoid Arthritis Challenge Consortium: Greenberg J., Kremer J., Michaud K., Barton A., Coenen M., Mariette X., Miceli C., Shadick N., Weinblatt M., de Vries N., Tak P.P., Gerlag D., Huizinga T.W.J., Kurreeman F., Allaart C.F., Bridges Jr. S.L., Criswell L., Moreland L., Klareskog L., Saevarsdottir S., Padyukov L., Gregersen P.K., Friend S., Plenge R., Stolovitzky G., Oliva B., Guan Y., Mangravite L.M. Erratum: Crowdsourced Assessment of Common Genetic Contribution to Predicting Anti-TNF Treatment Response in Rheumatoid Arthritis. Nature Communications 7:13205, (2016)]},
  issn = {2041-1723},
  doi = {10.1038/ncomms12460},
  keywords = {risk;metaanalysis;disease;infliximab;clinical-response;complex traits;genome-wide association;missing heritability;network inference;stacked generalization}
}

@INCOLLECTION{kuch2016hmpc253258,
  author = {Kuch, W.~ and Rinner, C.~ and Gall, W.~ and Samwald, M.~},
  title = {How Many Patients Could Benefit from Pre-Emptive Pharmacogenomic Testing and Decision Support? A Retrospective Study Based on Nationwide Austrian Claims Data.},
  booktitle = {Health Informatics Meets eHealth. Predictive Modeling in Healthcare – From Prediction to Prevention, Proceedings of the 10th eHealth2016 Conference},
  publisher = {IOS Press},
  year = {2016},
  editor = {Schreier,G.;Ammenwerth,E.;H{\"o}rbst,A.;Hayn,D.},
  number = {223},
  series = {Studies in Health Technology and Informatics},
  pages = {253--258},
  address = {Amsterdam},
  month = {may},
  doi = {10.3233/978-1-61499-645-3-253},
  keywords = {implementation;claims data;drug safety;re-use of patient data;bench;byte;clinical guidelines;clinical decision support systems;pharmacogenomics}
}

@ARTICLE{blagec2016epuue1671,
  author = {Blagec, K.~ and Romagnoli, K.M.~ and Boyce, R.D.~ and Samwald, M.~},
  title = {Examining Perceptions of the Usefulness and Usability of a Mobile-Based System for Pharmacogenomics Clinical Decision Support: A Mixed Methods Study.},
  journal = {PeerJ},
  year = {2016},
  volume = {4},
  pages = {e1671},
  issn = {2167-8359 2167-8359},
  doi = {10.7717/peerj.1671},
  keywords = {Clinical;Decision support systems;Individualized medicine;Mixed methods studies;Pharmacogenetics;User studies}
}

@ARTICLE{samwald2015apih17131721,
  author = {Samwald, M.~ and Blagec, K.~ and Hofer, S.~ and Freimuth, R.R.~},
  title = {Analyzing the Potential for Incorrect Haplotype Calls with Different Pharmacogenomic Assays in Different Populations: A Simulation Based on 1000 Genomes Data.},
  journal = {Pharmacogenomics},
  year = {2015},
  volume = {16},
  number = {15},
  pages = {1713--1721},
  doi = {10.2217/pgs.15.108},
  url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-84949231061\&doi=10.2217%2fpgs.15.108\&partnerID=40\&md5=efc5afa731ed4fb4e44ee670ab15261c}
}

@ARTICLE{ayvaz2015tacd206217,
  author = {Ayvaz, S.~ and Horn, J.~ and Hassanzadeh, O.~ and Zhu, Q.~ and Stan, J.~ and Tatonetti, N.P.~ and Vilar, S.~ and Brochhausen, M.~ and Samwald, M.~ and Rastegar-Mojarad, M.~ and Dumontier, M.~ and Boyce, R.D.~},
  title = {Toward a Complete Dataset of Drug-Drug Interaction Information from Publicly Available Sources.},
  journal = {Journal of Biomedical Informatics},
  year = {2015},
  volume = {55},
  pages = {206--217},
  doi = {10.1016/j.jbi.2015.04.006},
  url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-84930706290\&doi=10.1016%2fj.jbi.2015.04.006\&partnerID=40\&md5=09fb29e2c9f2e32459d11a23d56114f8}
}

@ARTICLE{pfundner2015uwste110,
  author = {Pfundner, A.~ and Sch{\"o}nberg, T.~ and Horn, J.~ and Boyce, R.D.~ and Samwald, M.~},
  title = {Utilizing the Wikidata System to Improve the Quality of Medical Content in Wikipedia in Diverse Languages:a Pilot Study.},
  journal = {Journal of Medical Internet Research},
  year = {2015},
  volume = {17},
  number = {5},
  pages = {e110},
  doi = {10.2196/jmir.4163},
  url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-84930332512\&doi=10.2196%2fjmir.4163\&partnerID=40\&md5=14d8af82eea70728e1e0f448c62e7a30}
}

@ARTICLE{samwald2015pkrr12,
  author = {Samwald, M.~ and Miñarro Giménez, J.A.~ and Boyce, R.D.~ and Freimuth, R.R.~ and Adlassnig, K.-P.~ and Dumontier, M.~},
  title = {Pharmacogenomic Knowledge Representation, Reasoning and Genome-Based Clinical Decision Support Based on OWL 2 DL Ontologies.},
  journal = {BMC Medical Informatics and Decision Making},
  year = {2015},
  volume = {15},
  pages = {12},
  doi = {10.1186/s12911-015-0130-1},
  url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-84924171352\&doi=10.1186%2fs12911-015-0130-1\&partnerID=40\&md5=42c090051b78a4fabd909824dec40854}
}

@ARTICLE{miñarrogiménez2014omspe93769,
  author = {Miñarro-Giménez, J.A.~ and Blagec, K.~ and Boyce, R.D.~ and Adlassnig, K.-P.~ and Samwald, M.~},
  title = {An Ontology-Based, Mobile-Optimized System for Pharmacogenomic Decision Support at the Point-of-Care.},
  journal = {PLoS One},
  year = {2014},
  volume = {9},
  number = {5},
  pages = {e93769},
  doi = {10.1371/journal.pone.0093769},
  url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-84900453857\&doi=10.1371%2fjournal.pone.0093769\&partnerID=40\&md5=f9bf6e4f4204a7b832abe965bc04f6ff}
}

@INPROCEEDINGS{minarrogiménez2014ugca5863,
  author = {Minarro-Giménez, J.A.~ and Samwald, M.~},
  title = {An Update on Genomic CDS, a Complex Ontology for Pharmacogenomics and Clinical Decision Support.},
  booktitle = {Informal Proceedings of the 3rd International Workshop on OWL Reasoner Evaluation (ORE 2014) co-located with the Vienna Summer of Logic (VSL 2014) Vienna, Austria, 13 July 2014},
  year = {2014},
  editor = {Bail,S.;Glimm,B.;Jiménez-Ruiz,E.;Matentzoglu,N.;Parsia,B.;Steigmiller,A.},
  number = {1207},
  series = {CEUR Workshop Proceedings},
  pages = {58--63},
  month = {aug},
  url = {http://ceur-ws.org/Vol-1207/}
}

@INCOLLECTION{samwald2014tagi261265,
  author = {Samwald, M.~ and Minarro-Gimenez, J.A.~ and Blagec, K.~ and Adlassnig, K.-P.~},
  title = {Towards a Global IT System for Personalized Medicine: The Medicine Safety Code Initiative.},
  booktitle = {e-Health – For Continuity of Care. Proceedings of MIE2014},
  publisher = {IOS Press},
  year = {2014},
  editor = {Lovis,C.;Séroussi,B.;Hasman,A.;Pape-Haugaard,L.;Saka,O.;Andersen,S.K.},
  number = {205},
  series = {Studies in Health Technology and Informatics},
  pages = {261--265},
  address = {Amsterdam},
  month = {aug},
  doi = {10.3233/978-1-61499-432-9-261},
  url = {https://www.doi.org/10.3233/978-1-61499-432-9-261}
}

@INCOLLECTION{samwald2014omse358362,
  author = {Samwald, M.~ and Hanbury, A.~},
  title = {An Open-Source, Mobile-Friendly Search Engine for Public Medical Knowledge.},
  booktitle = {e-Health – For Continuity of Care. Proceedings of MIE2014},
  publisher = {IOS Press},
  year = {2014},
  editor = {Lovis,C.;Séroussi,B.;Hasman,A.;Pape-Haugaard,L.;Saka,O.;Andersen,S.K.},
  number = {205},
  series = {Studies in Health Technology and Informatics},
  pages = {358--362},
  address = {Amsterdam},
  month = {aug},
  doi = {10.3233/978-1-61499-432-9-358}
}

@INCOLLECTION{minarrogimenez2014eadl584588,
  author = {Minarro-Gimenez, J.A.~ and Marin-Alonso, O.~ and Samwald, M.~},
  title = {Exploring the Application of Deep Learning Techniques on Medical Text Corpora.},
  booktitle = {e-Health – For Continuity of Care. Proceedings of MIE2014},
  publisher = {IOS Press},
  year = {2014},
  editor = {Lovis,C.;Séroussi,B.;Hasman,A.;Pape-Haugaard,L.;Saka,O.;Andersen,S.K.},
  number = {205},
  series = {Studies in Health Technology and Informatics},
  pages = {584--588},
  address = {Amsterdam},
  month = {aug},
  doi = {10.3233/978-1-61499-432-9-584},
  url = {https://doi.org/10.3233/978-1-61499-432-9-584}
}

@INCOLLECTION{debruin2014vtni12271227,
  author = {de Bruin, J.S.~ and Miñarro-Giménez, J.A.~ and Samwald, M.~ and Marin Alonso, O.~},
  title = {Visualising Topic Networks in Infection Control Using Word Vector Analysis.},
  booktitle = {e-Health – For Continuity of Care. Proceedings of MIE2014},
  publisher = {IOS Press},
  year = {2014},
  editor = {Lovis,C.;Séroussi,B.;Hasman,A.;Pape-Haugaard,L.;Saka,O.;Andersen,S.K.},
  number = {205},
  series = {Studies in Health Technology and Informatics},
  pages = {1227},
  address = {Amsterdam},
  month = {aug},
  url = {http://ebooks.iospress.nl/volumearticle/37720}
}

@INCOLLECTION{samwald2014tagi2531,
  author = {Samwald, M.~ and Minarro-Giménez, J.A.~ and Blagec, K.~ and Adlassnig, K.-P.~},
  title = {Towards a Global IT System for Personalized Medicine: the Medicine Safety Code Initiative.},
  booktitle = {eHealth2014 – Health Informatics Meets eHealth. Outcomes Research: The Benefit of Health-IT},
  publisher = {IOS Press},
  year = {2014},
  editor = {H{\"o}rbst,A.;Hayn,D.;Schreier,G.;Ammenwerth,E.},
  number = {198},
  series = {Studies in Health Technology and Informatics},
  pages = {25--31},
  address = {Amsterdam},
  doi = {10.3233/978-1-61499-397-1-25},
  url = {https://ebooks.iospress.nl/volumearticle/36142}
}

@ARTICLE{ayvaz2014dids1616,
  author = {Ayvaz, S.~ and Zhu, Q.~ and Hochheiser, H.~ and Brochhausen, M.~ and Horn, J.~ and Dumontier, M.~ and Samwald, M.~ and Boyce, R.D.~},
  title = {Drug-Drug Interaction Data Source Survey and Linking.},
  journal = {AMIA Joint Summits on Translational Science Proceedings},
  year = {2014},
  volume = {2014},
  pages = {16},
  issn = {2153-4063},
  url = {https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4333686/pdf/1855513.pdf}
}

@INCOLLECTION{samwald2014tagi2531,
  author = {Samwald, M.~ and Minarro-Giménez, J.A.~ and Blagec, K.~ and Adlassnig, K.-P.~},
  title = {Towards a Global IT System for Personalized Medicine: The Medicine Safety Code Initiative.},
  booktitle = {eHealth2014 – Health Informatics Meets eHealth Outcomes Research: The Benefit of Health-IT},
  publisher = {IOS Press},
  year = {2014},
  editor = {H{\"o}rbst,A.;Hayn,D.;Schreier,G.;Ammenwerth,E.},
  number = {198},
  series = {Studies in Health Technology and Informatics},
  pages = {25--31},
  address = {Amsterdam},
  url = {http://ebooks.iospress.nl/volumearticle/36142}
}

@ARTICLE{dumontier2014sios14,
  author = {Dumontier, M.~ and Baker, C.J.O.~ and Baran, J.~ and Callahan, A.~ and Chepelev, L.~ and Cruz-Toledo, J.~ and Del Rio, N.R.~ and Duck, G.~ and Furlong, L.I.~ and Keath, N.~ and Klassen, D.~ and McCusker, J.P.~ and Queralt-Rosinach, N.~ and Samwald, M.~ and Villanueva-Rosales, N.~ and Wilkinson, M.D.~ and Hoehndorf, R.~},
  title = {The Semanticscience Integrated Ontology (SIO) for Biomedical Research and Knowledge Discovery.},
  journal = {Journal of Biomedical Semantics},
  year = {2014},
  volume = {5},
  pages = {14},
  doi = {10.1186/2041-1480-5-14},
  url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-84921861095\&doi=10.1186%2f2041-1480-5-14\&partnerID=40\&md5=62fc0bcbb6f8960a1efa214711f3dc8c}
}

@ARTICLE{samwald2013mdep15291531,
  author = {Samwald, M.~ and Freimuth, R.R.~},
  title = {Making Data on Essential Pharmacogenes Available for Every Patient Everywhere: The Medicine Safety Code Initiative.},
  journal = {Pharmacogenomics},
  year = {2013},
  volume = {14},
  number = {13},
  pages = {1529--1531},
  doi = {10.2217/pgs.13.121},
  url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-84885409171\&doi=10.2217%2fpgs.13.121\&partnerID=40\&md5=e03603e213b76bce86b9dbb8dfcc2509}
}

@INCOLLECTION{stefanov2013afea8192,
  author = {Stefanov, V.~ and Sachs, A.~ and Kritz, M.~ and Samwald, M.~ and Gschwandtner, M.~ and Hanbury, A.~},
  title = {A Formative Evaluation of a Comprehensive Search System for Medical Professionals.},
  booktitle = {Information Access Evaluation. Multilinguality, Multimodality, and Visualization. 4th International Conference of the CLEF Initiative, CLEF 2013, Valencia, Spain, September 23–26, 2013. Proceedings},
  publisher = {Springer},
  year = {2013},
  editor = {Forner,P.;M{\"u}ller,H.;Paredes,R.;Rosso,P.;Stein,B.},
  number = {8138},
  series = {Lecture Notes in Computer Science},
  pages = {81--92},
  address = {Berlin},
  url = {https://www.doi.org/10.1007/978-3-642-40802-1_10}
}

@INCOLLECTION{samwald2013rkbq539542,
  author = {Samwald, M.~ and Freimuth, R.~ and Luciano, J.S.~ and Lin, S.~ and Powers, R.L.~ and Marshall, M.S.~ and Adlassnig, K.-P.~ and Dumontier, M.~ and Boyce, R.D.~},
  title = {An RDF/OWL Knowledge Base for Query Answering and Decision Support in Clinical Pharmacogenetics.},
  booktitle = {MEDINFO 2013. Proceedings of the 14th World Congress on Medical and Health Informatics},
  publisher = {IOS Press},
  year = {2013},
  editor = {Lehmann,C.U.;Ammenwerth,E.;Nøhr,C.},
  number = {192},
  series = {Studies in Health Technology and Informatics},
  pages = {539--542},
  address = {Amsterdam},
  month = {aug},
  doi = {10.3233/978-1-61499-289-9-539},
  url = {https://www.doi.org/10.3233/978-1-61499-289-9-539}
}

@INCOLLECTION{samwald2013pswm11031103,
  author = {Samwald, M.~ and Kritz, M.~ and Gschwandtner, M.~ and Stefanov, V.~ and Hanbury, A.~},
  title = {Physicians Searching the Web for Medical Question Answering: A European Survey and Local User Studies.},
  booktitle = {MEDINFO 2013. Proceedings of the 14th World Congress on Medical and Health Informatics},
  publisher = {IOS Press},
  year = {2013},
  editor = {Lehmann,C.U.;Ammenwerth,E.;Nøhr,C.},
  number = {192},
  series = {Studies in Health Technology and Informatics},
  pages = {1103},
  address = {Amsterdam},
  month = {aug},
  doi = {10.3233/978-1-61499-289-9-1103},
  url = {https://www.doi.org/10.3233/978-1-61499-289-9-1103}
}

@INPROCEEDINGS{samwald2013gcea94100,
  author = {Samwald, M.~},
  title = {Genomic CDS: An Example of a Complex Ontology for Pharmacogenetics and Clinical Decision Support.},
  booktitle = {Informal Proceedings of the 2nd International Workshop on OWL Reasoner Evaluation (ORE-2013) Co-Located with the 26th International Workshop on Description Logics (DL 2013), Ulm, Germany, 22 July 2013},
  year = {2013},
  editor = {Bail,S.;Glimm,B.;Gonçalves,R.;Jiménez-Ruiz,E.;Matentzoglu,N.;Parsia,B.},
  number = {1015},
  series = {CEUR Workshop Proceedings},
  pages = {94--100},
  month = {aug},
  url = {http://ceur-ws.org/Vol-1015/paper_12.pdf}
}

@ARTICLE{kritz2013uppoe122,
  author = {Kritz, M.~ and Gschwandtner, M.~ and Stefanov, V.~ and Hanbury, A.~ and Samwald, M.~},
  title = {Utilization and Perceived Problems of Online Medical Resources and Search Tools among Different Groups of European Physicians.},
  journal = {Journal of Medical Internet Research},
  year = {2013},
  volume = {15},
  number = {6},
  pages = {e122},
  doi = {10.2196/jmir.2436},
  url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-84881080741\&doi=10.2196%2fjmir.2436\&partnerID=40\&md5=2590d3be2fa7ed7f786bc716bcc411ba}
}

@ARTICLE{samwald2013ppep409412,
  author = {Samwald, M.~ and Adlassnig, K.-P.~},
  title = {Pharmacogenomics in the Pocket of Every Patient? A Prototype Based on Quick Response Codes.},
  journal = {Journal of the American Medical Informatics Association},
  year = {2013},
  volume = {20},
  number = {3},
  pages = {409--412},
  doi = {10.1136/amiajnl-2012-001275},
  url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-84877644412\&doi=10.1136%2famiajnl-2012-001275\&partnerID=40\&md5=a4ef96cb958a7fa08dcbe7d8c1ee48d0}
}

@ARTICLE{katayama20133dbi6,
  author = {Katayama, T.~ and Wilkinson, M.D.~ and Micklem, G.~ and Kawashima, S.~ and Yamaguchi, A.~ and Nakao, M.~ and Yamamoto, Y.~ and Okamoto, S.~ and Oouchida, K.~ and Chun, H.-W.~ and Aerts, J.~ and Afzal, H.~ and Antezana, E.~ and Arakawa, K.~ and Aranda, B.~ and Belleau, F.~ and Bolleman, J.~ and Bonnal, R.J.~ and Chapman, B.~ and Cock, P.J.~ and Eriksson, T.~ and Gordon, P.M.~ and Goto, N.~ and Hayashi, K.~ and Horn, H.~ and Ishiwata, R.~ and Kaminuma, E.~ and Kasprzyk, A.~ and Kawaji, H.~ and Kido, N.~ and Kim, Y.J.~ and Kinjo, A.R.~ and Konishi, F.~ and Kwon, K.-H.~ and Labarga, A.~ and Lamprecht, A.-L.~ and Lin, Y.~ and Lindenbaum, P.~ and McCarthy, L.~ and Morita, H.~ and Murakami, K.~ and Nagao, K.~ and Nishida, K.~ and Nishimura, K.~ and Nishizawa, T.~ and Ogishima, S.~ and Ono, K.~ and Oshita, K.~ and Park, K.-J.~ and Prins, P.~ and Saito, T.L.~ and Samwald, M.~ and Satagopam, V.P.~ and Shigemoto, Y.~ and Smith, R.~ and Splendiani, A.~ and Sugawara, H.~ and Taylor, J.~ and Vos, R.A.~ and Withers, D.~ and Yamasaki, C.~ and Zmasek, C.M.~ and Kawamoto, S.~ and Okubo, K.~ and Asai, K.~ and Takagi, T.~},
  title = {The 3rd DBCLS BioHackathon: Improving Life Science Data Integration with Semantic Web Technologies.},
  journal = {Journal of Biomedical Semantics},
  year = {2013},
  volume = {4},
  pages = {6},
  issn = {2041-1480},
  doi = {10.1186/2041-1480-4-6}
}

@INCOLLECTION{karakuelah2012adlr688692,
  author = {Karak{\"u}lah, G.~ and Suner, A.~ and Adlassnig, K.-P.~ and Samwald, M.~},
  title = {A Data-Driven Living Review for Pharmacogenomic Decision Support in Cancer Treatment.},
  booktitle = {Quality of Life through Quality of Information. Proceedings of MIE2012},
  publisher = {IOS Press},
  year = {2012},
  editor = {Mantas,J.;Andersen,S.K.;Mazzoleni,M.C.;Blobel,B.;Quaglini,S.;Moen,A.},
  number = {180},
  series = {Studies in Health Technology and Informatics},
  pages = {688--692},
  address = {Amsterdam},
  month = {aug},
  url = {https://doi.org/10.3233/978-1-61499-101-4-688},
  keywords = {Humans;*Electronic Health Records;Data Mining/*methods;*Decision Support Systems;Clinical;*Health Records;Personal;Drug Therapy;Computer-Assisted/methods;Genetic Testing/methods;Neoplasms/diagnosis/*drug therapy/*genetics;Pharmacogenetics/*methods}
}

@ARTICLE{samwald2012assc711718,
  author = {Samwald, M.~ and Fehre, K.~ and de Bruin, J.~ and Adlassnig, K.-P.~},
  title = {The Arden Syntax Standard for Clinical Decision Support: Experiences and Directions.},
  journal = {Journal of Biomedical Informatics},
  year = {2012},
  volume = {45},
  number = {4},
  pages = {711--718},
  doi = {10.1016/j.jbi.2012.02.001},
  url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-84865104851\&doi=10.1016%2fj.jbi.2012.02.001\&partnerID=40\&md5=a315c8a3d21ef005776c46b8581f9305}
}

@ARTICLE{marshall2012epml213,
  author = {Marshall, M.S.~ and Boyce, R.~ and Deus, H.F.~ and Zhao, J.~ and Willighagen, E.L.~ and Samwald, M.~ and Pichler, E.~ and Hajagos, J.~ and Prud’Hommeaux, E.~ and Stephens, S.~},
  title = {Emerging Practices for Mapping and Linking Life Sciences Data Using RDF—A Case Series.},
  journal = {Journal of Web Semantics},
  year = {2012},
  volume = {14},
  pages = {2--13},
  doi = {10.1016/j.websem.2012.02.003},
  url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-84862009031\&doi=10.1016%2fj.websem.2012.02.003\&partnerID=40\&md5=57e4d0586dc95ecafdcd7f7dc7234656}
}

@ARTICLE{samwald2012sepd201212,
  author = {Samwald, M.~ and Coulet, A.~ and Huerga, I.~ and Powers, R.L.~ and Luciano, J.S.~ and Freimuth, R.R.~ and Whipple, F.~ and Pichler, E.~ and Prud’hommeaux, E.~ and Dumontier, M.~ and Marshall, M.S.~},
  title = {Semantically Enabling Pharmacogenomic Data for the Realization of Personalized Medicine.},
  journal = {Pharmacogenomics},
  year = {2012},
  volume = {13},
  number = {2},
  pages = {201--212},
  note = {
[Erratum: Samwald M., Coulet A., Huerga I., Powers R.L., Luciano J.S., Freimuth R.R., Whipple F., Pichler E., Prud’hommeaux E., Dumontier M., Marshall M.S. Erratum: Semantically Enabling Pharmacogenomic Data for the Realization of Personalized Medicine (Pharmacogenomics (2012) 13:2 (201-212)). Pharmacogenomics 13(5), 628, (2012)]},
  doi = {10.2217/pgs.11.179},
  url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-84855963774\&doi=10.2217%2fpgs.11.179\&partnerID=40\&md5=62166edb6672c8d3aa056c936b084441}
}

@INCOLLECTION{samwald2011tiii165169,
  author = {Samwald, M.~ and Stenzhorn, H.~ and Dumontier, M.~ and Marshall, M.S.~ and Luciano, J.~ and Adlassnig, K.-P.~},
  title = {Towards an Interoperable Information Infrastructure Providing Decision Support for Genomic Medicine.},
  booktitle = {User Centred Networked Health Care. Proceedings of MIE 2011},
  publisher = {IOS Press},
  year = {2011},
  editor = {Moen,A.;Andersen,S.K.;Aarts,J.;Hurlen,P.},
  number = {169},
  series = {Studies in Health Technology and Informatics},
  pages = {165--169},
  address = {Amsterdam},
  doi = {10.3233/978-1-60750-806-9-165},
  url = {https://www.doi.org/10.3233/978-1-60750-806-9-165}
}

@INPROCEEDINGS{samwald2011totm135140,
  author = {Samwald, M.~ and Kritz, M.~ and Gschwandtner, M.~ and Stefanov, V.~ and Hanbury, A.~},
  title = {Towards an Open, Trustworthy and Multilingual Search Engine for Medical Practitioners: News from the European Khresmoi Project. },
  booktitle = {Tagungsband der eHealth2011 – Health Informatics meets eHealth – von der Wissenschaft zur Anwendung und zur{\"u}ck, Grenzen {\"u}berwinden – Continuity of Care, 26.–27. Mai 2011, Wien},
  year = {2011},
  editor = {Schreier,G.;Hayn,D.;Ammenwerth,E.},
  number = {279},
  series = {Books@ocg.at},
  pages = {135--140},
  address = {Wien},
  publisher = {{\"O}sterreichische Computer Gesellschaft (OCG)},
  url = {https://www.dhealth.at/wp-content/uploads/scientific-papers/2011/samwald.pdf}
}

@ARTICLE{luciano2011tmoks1,
  author = {Luciano, J.S.~ and Andersson, B.~ and Batchelor, C.~ and Bodenreider, O.~ and Clark, T.~ and Denney, C.K.~ and Domarew, C.~ and Gambet, T.~ and Harland, L.~ and Jentzsch, A.~ and Kashyap, V.~ and Kos, P.~ and Kozlovsky, J.~ and Lebo, T.~ and Marshall, S.M.~ and McCusker, J.P.~ and McGuinness, D.L.~ and Ogbuji, C.~ and Pichler, E.~ and Powers, R.L.~ and Prud’hommeaux, E.~ and Samwald, M.~ and Schriml, L.~ and Tonellato, P.J.~ and Whetzel, P.L.~ and Zhao, J.~ and Stephens, S.~ and Dumontier, M.~},
  title = {The Translational Medicine Ontology and Knowledge Base: Driving Personalized Medicine by Bridging the Gap between Bench and Bedside.},
  journal = {Journal of Biomedical Semantics},
  year = {2011},
  volume = {2},
  number = {Suppl 2: Proceedings of the Bio-Ontologies Special Interest Group Meeting 2010, Boston, MA, USA, 9–10 July 2010},
  pages = {S1},
  doi = {10.1186/2041-1480-2-S2-S1},
  url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-84872872194\&doi=10.1186%2f2041-1480-2-S2-S1\&partnerID=40\&md5=ff2869a4c1b1eb00685a50c9696ae926}
}

@ARTICLE{samwald2011lodd19,
  author = {Samwald, M.~ and Jentzsch, A.~ and Bouton, C.~ and Kallesøe, C.S.~ and Willighagen, E.~ and Hajagos, J.~ and Scott Marshall, M.~ and Prud’hommeaux, E.~ and Hassanzadeh, O.~ and Pichler, E.~ and Stephens, S.~},
  title = {Linked Open Drug Data for Pharmaceutical Research and Development.},
  journal = {Journal of Cheminformatics},
  year = {2011},
  volume = {3},
  pages = {19},
  doi = {10.1186/1758-2946-3-19},
  url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-80053448367\&doi=10.1186%2f1758-2946-3-19\&partnerID=40\&md5=31f04f686a0e9590a24f234d0e7ce1b8}
}

@ARTICLE{samwald2010iftm43,
  author = {Samwald, M.~ and Dumontier, M.~ and Zhao, J.~ and Luciano, J.S.~ and Marshall, M.S.~ and Cheung, K.~},
  title = {Integrating Findings of Traditional Medicine with Modern Pharmaceutical Research: The Potential Role of Linked Open Data.},
  journal = {Chinese Medicine},
  year = {2010},
  volume = {5},
  pages = {43},
  doi = {10.1186/1749-8546-5-43},
  url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-78650166292\&doi=10.1186%2f1749-8546-5-43\&partnerID=40\&md5=cf1ec0ab7f235779c7fa9dd38cf961be}
}

@INPROCEEDINGS{deus2010pmea6,
  author = {Deus, H.F.~ and Zhao, J.~ and Sahoo, S.~ and Samwald, M.~ and Prud’hommeaux, E.~ and Miller, M.~ and Marshall, M.S.~ and Cheung, K.-H.~},
  title = {Provenance of Microarray Experiments for a Better Understanding of Experiment Results.},
  booktitle = {Proceedings of the Second International Workshop on the Role of Semantic Web in Provenance Management (SWPM 2010). Workshop at the 9th International Semantic Web Conference (ISWC2010) – ISWC 2010 Workshops Volume VII, Shanghai, China, 7 November 2010},
  year = {2010},
  editor = {Sahoo,S.S.;Zhao,J.;Missier,P.;Gomez-Perez,J.M.},
  number = {670},
  series = {CEUR Workshop Proceedings},
  pages = {6},
  month = {nov},
  url = {http://ceur-ws.org/Vol-670/paper_6.pdf}
}

@ARTICLE{demir2010bcsp935942,
  author = {Demir, E.~ and Cary, M.P.~ and Paley, S.~ and Fukuda, K.~ and Lemer, C.~ and Vastrik, I.~ and Wu, G.~ and D´Eustachio, P.~ and Schaefer, C.~ and Luciano, J.~ and Schacherer, F.~ and Martinez-Flores, I.~ and Hu, Z.~ and Jimenez-Jacinto, V.~ and Joshi-Tope, G.~ and Kandasamy, K.~ and Lopez-Fuentes, A.C.~ and Mi, H.~ and Pichler, E.~ and Rodchenkov, I.~ and Splendiani, A.~ and Tkachev, S.~ and Zucker, J.~ and Gopinath, G.~ and Rajasimha, H.~ and Ramakrishnan, R.~ and Shah, I.~ and Syed, M.~ and Anwar, N.~ and Babur, {\"O}.~ and Blinov, M.~ and Brauner, E.~ and Corwin, D.~ and Donaldson, S.~ and Gibbons, F.~ and Goldberg, R.~ and Hornbeck, P.~ and Luna, A.~ and Murray-Rust, P.~ and Neumann, E.~ and Reubenacker, O.~ and Samwald, M.~ and Van Iersel, M.~ and Wimalaratne, S.~ and Allen, K.~ and Braun, B.~ and Whirl-Carrillo, M.~ and Cheung, K.-H.~ and Dahlquist, K.~ and Finney, A.~ and Gillespie, M.~ and Glass, E.~ and Gong, L.~ and Haw, R.~ and Honig, M.~ and Hubaut, O.~ and Kane, D.~ and Krupa, S.~ and Kutmon, M.~ and Leonard, J.~ and Marks, D.~ and Merberg, D.~ and Petri, V.~ and Pico, A.~ and Ravenscroft, D.~ and Ren, L.~ and Shah, N.~ and Sunshine, M.~ and Tang, R.~ and Whaley, R.~ and Letovksy, S.~ and Buetow, K.H.~ and Rzhetsky, A.~ and Schachter, V.~ and Sobral, B.S.~ and Dogrusoz, U.~ and McWeeney, S.~ and Aladjem, M.~ and Birney, E.~ and Collado-Vides, J.~ and Goto, S.~ and Hucka, M.~ and Novère, N.L.~ and Maltsev, N.~ and Pandey, A.~ and Thomas, P.~ and Wingender, E.~ and Karp, P.D.~ and Sander, C.~ and Bader, G.D.~},
  title = {The BioPAX Community Standard for Pathway Data Sharing.},
  journal = {Nature Biotechnology},
  year = {2010},
  volume = {28},
  number = {9},
  pages = {935--942},
  note = {
[Erratum: Demir E., Cary M.P., Paley S., Fukuda K., Lemer C., Vastrik I., Wu G., D´Eustachio P., Schaefer C., Luciano J., Schacherer F., Martinez-Flores I., Hu Z., Jimenez-Jacinto V., Joshi-Tope G., Kandasamy K., Lopez-Fuentes A.C., Mi H., Pichler E., Rodchenkov I., Splendiani A., Tkachev S., Zucker J., Gopinath G., Rajasimha H., Ramakrishnan R., Shah I., Syed M., Anwar N., Babur {\"O}., Blinov M., Brauner E., Corwin D., Donaldson S., Gibbons F., Goldberg R., Hornbeck P., Luna A., Murray-Rust P., Neumann E., Reubenacker O., Samwald M., Van Iersel M., Wimalaratne S., Allen K., Braun B., Whirl-Carrillo M., Cheung K.-H., Dahlquist K., Finney A., Gillespie M., Glass E., Gong L., Haw R., Honig M., Hubaut O., Kane D., Krupa S., Kutmon M., Leonard J., Marks D., Merberg D., Petri V., Pico A., Ravenscroft D., Ren L., Shah N., Sunshine M., Tang R., Whaley R., Letovksy S., Buetow K.H., Rzhetsky A., Schachter V., Sobral B.S., Dogrusoz U., McWeeney S., Aladjem M., Birney E., Collado-Vides J., Goto S., Hucka M., Novère N.L., Maltsev N., Pandey A., Thomas P., Wingender E., Karp P.D., Sander C., Bader G.D. Corrigendum: The BioPAX Community Standard for Pathway Data Sharing. Nature Biotechnology 28(12), 1308, (2010)]},
  doi = {10.1038/nbt.1666},
  url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-77956664073\&doi=10.1038%2fnbt.1666\&partnerID=40\&md5=a9cac259714e9a43b3c4d18eccc0791e}
}

@ARTICLE{cheung2010sdts403,
  author = {Cheung, K.-H.~ and Samwald, M.~ and Auerbach, R.K.~ and Gerstein, M.B.~},
  title = {Structured Digital Tables on the Semantic Web: Toward a Structured Digital Literature.},
  journal = {Molecular Systems Biology},
  year = {2010},
  volume = {6},
  pages = {403},
  doi = {10.1038/msb.2010.45},
  url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-77956236976\&doi=10.1038%2fmsb.2010.45\&partnerID=40\&md5=e9c9033f7543d995a2eb6fa409a5b2ec}
}

@ARTICLE{samwald2010eadss5,
  author = {Samwald, M.~ and Stenzhorn, H.~},
  title = {Establishing a Distributed System for the Simple Representation and Integration of Diverse Scientific Assertions.},
  journal = {Journal of Biomedical Semantics},
  year = {2010},
  volume = {1},
  number = {Suppl 1: Proceedings of the Bio-Ontologies Special Interest Group Meeting 2009: Knowledge in Biology, Stockholm, Sweden, 28 June 2009},
  pages = {S5},
  doi = {10.1186/2041-1480-1-S1-S5},
  url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-78650906842\&doi=10.1186%2f2041-1480-1-S1-S5\&partnerID=40\&md5=a6c497944458e21fe8c3f783a37cded1}
}

@ARTICLE{samwald2010ssiv2128,
  author = {Samwald, M.~ and Chen, H.~ and Ruttenberg, A.~ and Lim, E.~ and Marenco, L.~ and Miller, P.~ and Shepherd, G.~ and Cheung, K.-H.~},
  title = {Semantic SenseLab: Implementing the Vision of the Semantic Web in Neuroscience.},
  journal = {Artificial Intelligence in Medicine},
  year = {2010},
  volume = {48},
  number = {1},
  pages = {21--28},
  issn = {1873-2860 0933-3657},
  doi = {10.1016/j.artmed.2009.11.003},
  keywords = {Humans;*Semantics;Brain Mapping/*methods;*Internet;*Information Dissemination;*Neurosciences;Nerve Net;Translational Medical Research}
}

@ARTICLE{passant2009fdsd4448,
  author = {Passant, A.~ and Samwald, M.~ and Breslin, J.G.~ and Decker, S.~},
  title = {Federating Distributed Social Data to Build an Interlinked Online Information Society.},
  journal = {IEEE Intelligent Systems},
  year = {2009},
  volume = {24},
  number = {6},
  pages = {44--48},
  doi = {10.1109/MIS.2009.113},
  url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-77955620291\&doi=10.1109%2fMIS.2009.113\&partnerID=40\&md5=0df4b6d4e48b16ec87871cefd694e373}
}

@INPROCEEDINGS{dewaard2009herh2,
  author = {De Waard, A.~ and Shum, S.B.~ and Carusi, A.~ and Park, J.~ and Samwald, M.~ and Sándor, Á.~},
  title = {Hypotheses, Evidence and Relationships: The HypER Approach for Representing Scientific Knowledge Claims.},
  booktitle = {Proceedings of the Workshop on Semantic Web Applications in Scientific Discourse (SWASD 2009), Collocated with the 8th International Semantic Web Conference (ISWC-2009), Washington DC, USA, 26 October 2009},
  year = {2009},
  editor = {Clark,T.;Luciano,J.S.;Marshall,M.S.;Prud’hommeaux,E.;Stephens,S.},
  number = {523},
  series = {CEUR Workshop Proceedings},
  pages = {2},
  url = {http://ceur-ws.org/Vol-523/deWaard.pdf}
}

@INCOLLECTION{samwald2009enra317321,
  author = {Samwald, M.~ and Lim, E.~ and Masiar, P.~ and Marenco, L.~ and Chen, H.~ and Morse, T.~ and Mutalik, P.~ and Shepherd, G.~ and Miller, P.~ and Cheung, K.-H.~},
  title = {Entrez Neuron RDFa: A Pragmatic Semantic Web Application for Data Integration in Neuroscience Research.},
  booktitle = {Medical Informatics in a United and Healthy Europe. Proceedings of MIE 2009. The XXIInd International Congress of the European Federation for Medical Informatics},
  publisher = {IOS Press},
  year = {2009},
  editor = {Adlassnig,K.-P.;Blobel,B.;Mantas,J.;Masic,I.},
  number = {150},
  series = {Studies in Health Technology and Informatics},
  pages = {317--321},
  address = {Amsterdam},
  month = {aug},
  doi = {10.3233/978-1-60750-044-5-317},
  keywords = {Humans;Information Systems;*Biomedical Research;*Semantics;*Internet;Information Storage and Retrieval/*methods;Vocabulary;Controlled;*Neurosciences}
}

@ARTICLE{ruttenberg2009lssw193204,
  author = {Ruttenberg, A.~ and Rees, J.A.~ and Samwald, M.~ and Marshall, M.S.~},
  title = {Life Sciences on the Semantic Web: The Neurocommons and beyond.},
  journal = {Briefings in Bioinformatics},
  year = {2009},
  volume = {10},
  number = {2},
  pages = {193--204},
  issn = {1477-4054 1467-5463},
  doi = {10.1093/bib/bbp004},
  keywords = {Animals;Humans;Databases;Factual;*Semantics;*Knowledge Bases;Information Storage and Retrieval;*Internet;Database Management Systems;*Biological Science Disciplines;Computational Biology/methods;Information Dissemination/methods}
}

@ARTICLE{samwald2008bpo213217,
  author = {Samwald, M.~ and Adlassnig, K.-P.~},
  title = {The Bio-Zen Plus Ontology.},
  journal = {Applied Ontology},
  year = {2008},
  volume = {3},
  number = {4},
  pages = {213--217},
  doi = {10.3233/AO-2008-0053},
  url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85013616142\&doi=10.3233%2fAO-2008-0053\&partnerID=40\&md5=2838c2d9f877e0a3002c643892f924e1}
}

@ARTICLE{ruttenberg2007atrws2,
  author = {Ruttenberg, A.~ and Clark, T.~ and Bug, W.~ and Samwald, M.~ and Bodenreider, O.~ and Chen, H.~ and Doherty, D.~ and Forsberg, K.~ and Gao, Y.~ and Kashyap, V.~ and Kinoshita, J.~ and Luciano, J.~ and Marshall, M.S.~ and Ogbuji, C.~ and Rees, J.~ and Stephens, S.~ and Wong, G.T.~ and Wu, E.~ and Zaccagnini, D.~ and Hongsermeier, T.~ and Neumann, E.~ and Herman, I.~ and Cheung, K.-H.~},
  title = {Advancing Translational Research with the Semantic Web.},
  journal = {BMC Bioinformatics},
  year = {2007},
  volume = {8},
  number = {Suppl 3},
  pages = {S2},
  issn = {1471-2105},
  doi = {10.1186/1471-2105-8-S3-S2},
  keywords = {*Research Design;Internationality;Research/organization \& administration;Information Dissemination/*methods;*Databases;Factual;Semantics;*Natural Language Processing;*Internet;Information Storage and Retrieval/methods;Biomedical Research/*methods/organization \& administration;Documentation/methods;Neurosciences/*methods/organization \& administration}
}