Fachpublikationen

Adams, Tim Birkenbihl, Colin Otte, Karen Ng, Hwei Geok Rieling, Jonas Adrian Näher, Anatol-Fiete Sax, Ulrich Prasser, Fabian Fröhlich, Holger:
On the fidelity versus privacy and utility trade-off of synthetic patient data

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Aborageh, Mohamed Hähnel, Tom Martins Conde, Patricia Klucken, Jochen Fröhlich, Holger:
Predicting dementia in people with Parkinson’s disease

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Guski, Jannis Botz, Jonas Fröhlich, Holger:
Estimating the causal impact of non-pharmaceutical interventions on COVID-19 spread in seven EU countries via machine learning

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Valderrama Nino, Diego Felipe Teplytska, Olga Koltermann, Luca Marie Trunz, Elena Schmulenson, Eduard Fritsch, Achim Jaehde, Ulrich Fröhlich, Holger:
Comparing Scientific Machine Learning with Population Pharmacokinetic and Classical Machine Learning Approaches for Prediction of Drug Concentrations

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Wehr, Matthias Witters, Hilda E. Remy, Silvie Schultz, Bruce Jacobs, Marc Escher, Sylvia:
Feasibility study on integrating morphological and transcriptomic data for identifying teratogenic molecular markers in zebrafish embryo toxicity testing

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Lentzen, Manuel Vairavan, Srinivasan Muurling, Marijn Alepopoulos, Vasilis Atreya, Alankar Boada, Mercé de Boer, Casper Conde, Pauline Curcic, Jelena Frisoni, Giovanni B. Galluzzi, Samantha Gjestsen, Martha Therese Gkioka, Mara Grammatikopoulou, Margarita Hausner, Lucrezia Hinds, Chris Lazarou, Ioulietta de Mendonça, Alexandre V. Nikolopoulos, Spiros N. Religa, Dorota D. Scebba, Gaetano C. Jelle Visser, Pieter Wittenberg, Gayle M. Narayan, Vaibhav A. Coello, Neva Brem, Anna Katharine Aarsland, Dag Fröhlich, Holger:
RADAR-AD: assessment of multiple remote monitoring technologies for early detection of Alzheimer’s disease

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Hähnel, Tom Raschka, Tamara Klucken, Jochen Glaab, Enrico Corvol, Jean Christophe Falkenburger, Björn H. Fröhlich, Holger:
Predictive modeling to uncover Parkinson’s disease characteristics that delay diagnosis

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Shalaby, Karim Hofmann-Apitius, Martin Schultz, Bruce Guru Rao, Sathvik Tom Kodamullil, Alpha Bharadhwaj, Vinay Srinivas:
SynDRep: a synergistic partner prediction tool based on knowledge graph for drug repurposing

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Tanoli, Ziaurrehman Ur Rehman Fernández-Torras, Adrià Özcan, Umut Onur Kushnir, Aleksandr Nader, Kristen Michelle Gadiya, Yojana Fiorenza, Laura Ianevski, Aleksandr Vähä-Koskela, Markus Miihkinen, Mitro Seemab, Umair Leinonen, Henri O. Seashore-Ludlow, Brinton A. Tampere, Marianna Kalman, Adelinn Ballante, Flavio Benfenati, Emilio B. Saunders, Gary Ian Potdar, Swapnil Gómez García, Ismael García-Serna, Ricard Talarico, Carmine Beccari, Andrea Rosario Schaal, Wesley Polo, Andrea Costantini, Susan Cabri, Enrico Jacobs, Marc Saarela, Jani S. Budillon, Alfredo D.O. Spjuth, Ola Östling, Päivi Xhaard, Henri Quintana, Jordi Mestres, Jordi Gribbon, Philip Ussi, Anton E. Lo, Donald C. Kort, Martin de Wennerberg, Krister Fratelli, Maddalena M. Carreras-Puigvert, Jordi Aittokallio, Tero A.:
Computational drug repurposing: approaches, evaluation of in silico resources and case studies

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Salimi, Yasamin Adams, Tim Balabin, Helena Ay, Mehmet Jacobs, Marc Hofmann-Apitius, Martin:
Evaluating language model embeddings for Parkinson’s disease cohort harmonization using a novel manually curated variable mapping schema

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Peltner, Jonas Becker, Cornelia Wicherski, Julia Wortberg, Silja Aborageh, Mohamed Costa, Inês Ehrenstein, Vera Fernandes, Joana Hess, Steffen Horvath-Puho, Erzsebet Korcinska Handest, Monika Roberta Lentzen, Manuel Maguire, Peggy Meedom, Niels Henrik Moore, Rebecca Moore, Vanessa Nagy, David McNamara, Hillary Paakinaho, Anne Pfeifer, Kerstin Pylkkänen, Liisa H. Rajamaki, Blair Reviers, Evy Röthlein, Christoph Russek, Martin Silva, Célia de Valck, Dirk Vo, Thuan Bräuner, Elvira Fröhlich, Holger Furtado, Cláudia Hartikainen, Sirpa A. Kallio, Aleksi Tolppanen, Anna Maija Haenisch, Britta:
The EU project Real4Reg: unlocking real-world data with AI

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Wegner, Philipp Fröhlich, Holger Madan, Sumit:
Evaluating knowledge fusion models on detecting adverse drug events in text

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Babiloni, Claudio C. Arakaki, Xianghong Baez, Sandra Jimena Barry, Robert J. Benussi, Alberto Blinowska, Katarzyna Joanna Bonanni, Laura Borroni, Barbara Bosch Bayard, Jorge Bruno, Giuseppe Cacciotti, Alessia Carducci, Filippo Carino, John Carpi, Matteo Conte, Antonella Cruzat, Josephine D’Antonio, Fabrizia Della Penna, Stefania del Percio, Claudio De-Sanctis, Pierfilippo Escudero, Javier Fabbrini, Giovanni Farina, Francesca R. Fraga, Francisco J. Fuhr, Peter Gschwandtner, Ute Güntekin, Bahar Guo, Yi Hajoś, Mihaĺy Hallett, Mark Hampel, Harald G. Hanoǧlu, Lütfü Haraldsen, Ira Ronit Hebold Hassan, Mahmoud Hatlestad-Hall, Christoffer Horváth, András Attila Ibáñez, Agustín M. Infarinato, Francesco Jaramillo-Jimenez, Alberto Jeong, Jaeseung Jiang, Yang Kamiński, Maciej J. Koch, Giacomo Kumar, Sanjeev Leodori, Giorgio Li, Gang Lizio, Roberta Lopez, Susanna Ferri, Raffaele Maestu, Fernando Marra, Camillo Marzetti, Laura McGeown, William Jonathan Miraglia, Francesca Moguilner, Sebastian Moretti, Davide Vito Mushtaq, Faisal Noce, Giuseppe Nucci, Lorenzo Ochoa, John Fredy Onorati, Paolo Padovani, Alessandro Pappalettera, Chiara Parra, Mario Alfredo Pardini, Matteo Pascual-Marqui, Roberto D. Paulus, Walter Pizzella, Vittorio Prado, Pavel Rauchs, Géraldine Ritter, Petra Salvatore, Marco Santamaría-García, Hernando Schirner, Michael Soricelli, Andrea Taylor, John-Paul Paul Tankisi, Hatice Tecchio, Franca Teipel, S. Tom Kodamullil, Alpha Triggiani, Antonio Ivano Valdés-Sosa, Mitchell Joseph Valdés-Sosa, Pedro A. Vecchio, Fabrizio Vossel, Keith A. Yao, Dezhong Yener, Gorsev G. Ziemann, Ulf Kamondi, Anita:
Alpha rhythm and Alzheimer's disease: Has Hans Berger's dream come true?

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Adams, Tim Aborageh, Mohamed Salimi, Yasamin Fröhlich, Holger Jacobs, Marc:
INDEX: the Intelligent Data Steward Toolbox

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Aksenova, Anna Johny, Anoop Adams, Tim Gribbon, Phil Jacobs, Marc Hofmann-Apitius, Martin:
Current state of data stewardship tools in life science

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Babaiha, Negin Guru Rao, Sathvik Klein, Jürgen Schultz, Bruce Jacobs, Marc Hofmann-Apitius, Martin:
Rationalism in the face of GPT hypes: Benchmarking the output of large language models against human expert-curated biomedical knowledge graphs

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Bontridder, N. Hähnel, Tom Marín Valero, M. Carrasco Marín, L. Corvol, J.-C. El-Yacoubi, M.A. Eskofier, B.M. Filali Razzouki, A. Hansen, Anne Funck Glaab, E. Ibrahim, A.A. Jeancolas, L. Klucken, J. Le Bars, S. Lage-Rupprecht, Vanessa Lehericy, S. Mangone, G. Paccoud, I. Petrovska-Delacretaz, D. Raschka, Tamara Terwangne, C. de Gyseghem, J. van Winkler, J. Fröhlich, Holger:
Personalised Medicine ∙ Leveraging the Potential of Digital Technology for Personalised Medicine

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Botz, Jonas Valderrama Nino, Diego Felipe Guski, Jannis Fröhlich, Holger:
A dynamic ensemble model for short-term forecasting in pandemic situations

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Brzenczek, Cyril Klopfenstein, Quentin Hähnel, Tom Glaab, Enrico Fröhlich, Holger et al.:
Integrating digital gait data with metabolomics and clinical data to predict outcomes in Parkinson's disease

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Erdemli, Gül Grammatikopoulou, Margarita Wagner, Bertil Vairavan, Srinivasan Curcic, Jelena Aarsland, Dag Wittenberg, Gayle Nikolopoulos, Spiros Muurling, Marijn Fröhlich, Holger Boer, Casper de Shanbhag, Niraj M. Nies, Vera J.M. Coello, Neva Gove, Dianne Diaz, Ana Foy, Suzanne Wim Dartee Brem, Anna-Katharine:
Regulatory considerations for developing remote measurement technologies for Alzheimer’s disease research

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Gadiya, Yojana Shetty, Simran Hofmann-Apitius, Martin Gribbon, Philip Zaliani, Andrea:
Exploring SureChEMBL from a drug discovery perspective

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Golriz Khatami, Sepehr Sargsyan, Astghik Russo, Maria Francesca Domingo Fernández, Daniel Zaliani, Andrea Kaladharan, Abish Sethumadhavan, Priya Mubeen, Sarah Gadiya, Yojana Karki, Reagon Mingrone, Geltrude Claussen, Carsten Lage-Rupprecht, Vanessa Archipovas, Saulius Gebel, Stephan Surulinathan, Ram Kumar Ruppa Jacobs, Marc Hofmann-Apitius, Martin Tom Kodamullil, Alpha:
Curating, Collecting, and Cataloguing Global COVID-19 Datasets for the Aim of Predicting Personalized Risk

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Golubnitschaja, Olga Polívka, Jiří Jr. Potužník, Pavel Pešta, Martin Štětkářová, Ivana Mazuráková, Alena Lackova, Lenka Kubatka, Peter Kropp, Martina Thumann, Gabriele Erb, Carl Fröhlich, Holger Wang, Wei Baban, Babak Kapalla, Marko Shapira, Niva Richter, Kneginja D. Karabatsiakis, Alexander Smokovski, Ivica Schmeel, L. C. Gkika, Eleni Paul, Friedemann Parini, Paolo Polivka, Jiri:
The paradigm change from reactive medical services to 3PM in ischemic stroke: a holistic approach utilising tear fluid multi-omics, mitochondria as a vital biosensor and AI-based multi-professional data interpretation

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Hofmann-Apitius, Martin Fröhlich, Holger F.:
Foresight - generative pretrained transformer for the prediction of patient timelines

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Hähnel, Tom Raschka, Tamara Sapienza, Stefano Klucken, Jochen Glaab, Enrico Corvol, Jean-Christophe Falkenburger, Björn H. Fröhlich, Holger:
Progression subtypes in Parkinson’s disease identified by a data-driven multi cohort analysis

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Krix, Sophia Wilczynski, Ella Falgàs, Neus Sánchez-Valle, Raquel Yoles, Eti Nevo, Uri Baruch, Kuti Fröhlich, Holger:
Towards early diagnosis of Alzheimer’s disease: advances in immune-related blood biomarkers and computational approaches

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Kühnel, Lisa Schneider, Julian Perrar, Ines Adams, Tim Moazemi, Sobhan Prasser, Fabian Nöthlings, Ute Fröhlich, Holger Fluck, Juliane:
Synthetic data generation for a longitudinal cohort study - evaluation, method extension and reproduction of published data analysis results

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Madan, Sumit Kühnel, Lisa Fröhlich, Holger Hofmann-Apitius, Martin Fluck, Juliane:
Dataset of miRNA-disease relations extracted from textual data using transformer-based neural networks

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Madan, Sumit Lentzen, Manuel Brandt, Johannes Rueckert, Daniel Hofmann-Apitius, Martin Fröhlich, Holger:
Transformer models in biomedicine

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Moazemi, Sobhan Adams, Tim Ng, Hwei Geok Kühnel, Lisa Schneider, Julian Näher, Anatol-Fiete Fluck, Juliane Fröhlich, Holger:
NFDI4Health Workflow and Service for Synthetic Data Generation, Assessment and Risk Management

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Nunes, Marta C. Thommes, Edward Wolfgang Fröhlich, Holger Flahault, Antoine Arino, Julien Baguelin, Marc Biggerstaff, Matthew S. Bizel-Bizellot, Gaston Borchering, Rebecca K. Cacciapaglia, Giacomo Cauchemez, Simon Barbier-Chebbah, Alex Claussen, Carsten Choirat, Christine Cojocaru, Monica Gabriela Commaille-Chapus, Catherine Hon, Chitin Kong, Jude D. Lambert, Nicolas Lauer, Katharina Barbara Lehr, Thorsten Mahé, Cédric Maréchal, Vincent Mebarki, Adel Moghadas, Seyed Niehus, Rene Opatowski, Lulla Parino, Francesco Pruvost, Gery Schuppert, Andreas A. Thíébaut, Rodolphe Thomas-Bachli, Andrea L. Viboud, Cécile G. Wu, Jianhong Crépey, Pascal Coudeville, Laurent:
Redefining pandemic preparedness: Multidisciplinary insights from the CERP modelling workshop in infectious diseases, workshop report

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Paccoud, Ivana Valero, Mayca Marín Carrasco Marín, Laura Bontridder, Noémi Ibrahim, Alzhraa Winkler, Jüergen Fomo, Messaline Sapienza, Stefano Khoury, Fouad Corvol, Jean-Christophe Fröhlich, Holger Klucken, Jochen:
Patient perspectives on the use of digital medical devices and health data for AI-driven personalised medicine in Parkinson’s Disease

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Panzarella, Giulia Gallo, Alessandro Coecke, Sandra Querci, Maddalena Ortuso, Francesco Hofmann-Apitius, Martin Veltri, Pierangelo Bajorath, Jürgen Alcaro, Stefano:
MAATrica: a measure for assessing consistency and methods in medicinal and nutraceutical chemistry papers

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Raschka, Tamara Li, Zexin Gaßner, Heiko Kohl, Zacharias Jukic, Jelena Marxreiter, Franz Fröhlich, Holger:
Unraveling progression subtypes in people with Huntington’s disease

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Salimi, Yasamin Domingo Fernández, Daniel Hofmann-Apitius, Martin Birkenbihl, Colin:
Data-Driven Thresholding Statistically Biases ATN Profiling across Cohort Datasets

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Schneider, Julian Walter, Marvin Otte, Karen Meurers, Thierry Perrar, Ines Nöthlings, Ute Adams, Tim Fröhlich, Holger Prasser, Fabian Fluck, Juliane Kühnel, Lisa:
Privacy Risk Assessment for Synthetic Longitudinal Health Data

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Teplytska, Olga Ernst, Moritz Koltermann, Luca Marie Valderrama Nino, Diego Felipe Trunz, Elena Vaisband, Marc Hasenauer, Jan Fröhlich, Holger Jaehde, Ulrich:
Machine Learning Methods for Precision Dosing in Anticancer Drug Therapy: A Scoping Review

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Uebachs, Mischa Wegner, Philipp Schaaf, Sebastian Kugai, Simon Jacobi, Heike Kuo, Sheng-Han Ashizawa, Tetsudo Fluck, Juliane Klockgether, Thomas Faber, Jennifer:
SCAview: an Intuitive Visual Approach to the Integrative Analysis of Clinical Data in Spinocerebellar Ataxias

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Valderrama Nino, Diego Felipe Ponce-Bobadilla, Ana Victoria Mensing, Sven Fröhlich, Holger Stodtmann, Sven:
Integrating machine learning with pharmacokinetic models: Benefits of scientific machine learning in adding neural networks components to existing PK models

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Wegner, Philipp Balabin, Helena Ay, Mehmet Can Bauermeister, Sarah Killin, Lewis Gallacher, John Hofmann-Apitius, Martin Salimi, Yasamin:
Semantic Harmonization of Alzheimer’s Disease Datasets Using AD-Mapper

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Zhang, Youcheng Bharadhwaj, Vinay Srinivas Tom Kodamullil, Alpha Herrmann, Carl:
A network of transcriptomic signatures identifies novel comorbidity mechanisms between schizophrenia and somatic disorders

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Babaiha, Negin Sadat; Elsayed, Hassan; Zhang, Bide; Kaladharan, Abish; Sethumadhavan, Priya; Schultz, Bruce; Klein, Jürgen; Freudensprung, Bruno; Lage-Rupprecht, Vanessa; Tom Kodamullil, Alpha; Jacobs, Marc; Geissler, Stefan; Madan, Sumit; Hofmann-Apitius, Martin:
A natural language processing system for the efficient updating of highly curated pathophysiology mechanism knowledge graphs

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Botz, Jonas; Lohner, Valerie; Schirmer, Markus D.:
Spatial patterns of white matter hyperintensities: a systematic review

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Gadiya, Yojana; Gribbon, Philip; Hofmann-Apitius, Martin; Zaliani, Andrea:
Pharmaceutical patent landscaping: A novel approach to understand patents from the drug discovery perspective

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Gadiya, Yojana; Zaliani, Andrea; Gribbon, Philip; Hofmann-Apitius, Martin:
PEMT: a patent enrichment tool for drug discovery

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Krix, Sophia; DeLong, Lauren; Madan, Sumit; Domingo Fernández, Daniel; Ahmad, Ashar; Gul, Sheraz; Zaliani, Andrea; Fröhlich, Holger:
MultiGML: Multimodal graph machine learning for prediction of adverse drug events

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Maheux, Etienne; Koval, Igor; Ortholand, Juliette; Birkenbihl, Colin; Archetti, Damiano; Bouteloup, Vincent; Epelbaum, Stephane; Dufouil, Carole; Hofmann-Apitius, Martin; Durrleman, Stanley:
Forecasting individual progression trajectories in Alzheimer’s disease

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Sargsyan, Astghik; Wegner, Philipp; Gebel, Stephan; Kaladharan, Abish; Sethumadhavan, Priya; Lage-Rupprecht, Vanessa; Darms, Johannes; Schultz, Bruce; Klein, Jürgen; Jacobs, Marc; Madan, Sumit; Hofmann-Apitius, Martin; Tom Kodamullil, Alpha:
The Epilepsy Ontology: a community-based ontology tailored for semantic interoperability and text mining

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Schultz, Bruce; Delong, Lauren Nicole; Masny, Aliaksandr; Lentzen, Manuel; Raschka, Tamara; Dijk, David van; Zaliani, Andrea; Funck Hansen, Anne; Rüping, Stefan; Kugler, Sabine; Burmeister, Jan; Kohlhammer, Jörn; Sarau, George; Christiansen, Silke; Kannt, Aimo; Foldenauer, Ann Christina; Claussen, Carsten; Resch, Eduard; Frank, Kevin; Gribbon, Philip; Kuzikov, Maria; Keminer, Oliver; Laue, Hendrik; Hahn, Horst; Hirsch, Jochen; Wischnewski, Marco; Günther, Matthias; Archipovas, Saulius; Tom Kodamullil, Alpha; Gemünd, Andre; Fluck, Juliane; Steinborn, Carina; Ebeling, Christian; Domingo Fernández, Daniel; Hermanowski, Helena; Fröhlich, Holger; Klein, Jürgen; Schultz, Bruce; Jacobs, Marc; Hofmann-Apitius, Martin; Knieps, Meike; Krapp, Michael; Wendland, Philipp Johannes; Wegner, Philipp; Golriz Khatami, Sepehr; Springstubbe, Stephan; Linden, Thomas; Lentzen, Manuel; Fröhlich, Holger:
A machine learning method for the identification and characterization of novel COVID-19 drug targets

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Valderrama Nino, Diego Felipe; Ponce-Bobadilla, Ana Victoria; Mensing, Sven; Fröhlich, Holger; Stodtmann, Sven:
Integrating machine learning with pharmacokinetic models: Benefits of scientific machine learning in adding neural networks components to existing PK models

 

Adams, Tim; Namysl, Marcin; Kodamullil, Alpha Tom; Behnke, Sven; Jacobs, Marc:
Benchmarking table recognition performance on biomedical literature on neurological disorders

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Aldisi, R.; Hassanin, E.; Sivalingam, S.; Buness, A.; Klinkhammer, H.; Mayr, A.; Fröhlich, Holger; Krawitz, P.; Maj, C.:
GenRisk: A tool for comprehensive genetic risk modeling

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Balabin, Helena; Hoyt, Charles Tapley; Gyori, Benjamin; Bachman, John; Tom Kodamullil, Alpha; Hofmann-Apitius, Martin; Domingo Fernández, Daniel:
ProtSTonKGs: A Sophisticated Transformer Trained on Protein Sequences, Text, and Knowledge Graphs

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Balabin, Helena; Hoyt Tapley, Charles; Birkenbihl, Colin; Gyori, Benjamin; Bachman, John; Kodamullil, Alpha; Plöger, Paul; Hofmann-Apitius, Martin; Domingo-Fernández, Daniel:
STonKGs: A sophisticated transformer trained on biomedical text and knowledge graphs

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Bharadhwaj, Vinay Srinivas; Mubeen, Sarah; Sargsyan, Astghik; Jose, Geena Mariya; Geissler, Stefan; Hofmann-Apitius, Martin; Domingo Fernández, Daniel; Tom Kodamullil, Alpha:
Integrative analysis to identify shared mechanisms between schizophrenia and bipolar disorder and their comorbidities

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Birkenbihl, Colin; Salimi, Yasamin; Fröhlich, Holger:
Unraveling the heterogeneity in Alzheimer's disease progression across multiple cohorts and the implications for data-driven disease modeling

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Botz, Jonas; Wang, Danqi; Lambert, Nicolas; Wagner, Nicolas; Génin, Marie; Thommes, Edward; Madan, Sumit; Coudeville, Laurent; Fröhlich, Holger:
Modeling approaches for early warning and monitoring of pandemic situations as well as decision support

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Dörpinghaus, J.; Stefan, Andreas; Schultz, Bruce; Jacobs, Marc:
Context mining and graph queries on giant biomedical knowledge graphs

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Dörpinghaus, J.; Stefan, A.:
Semantic Graph Queries on Linked Data in Knowledge Graphs

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Evsevieva, Maria; Sergeeva, Oksana; Mazurakova, Alena; Koklesova, Lenka; Prokhorenko-Kolomoytseva, Irina; Shchetinin, Evgenij; Birkenbihl, Colin; Costigliola, Vincenzo; Kubatka, Peter; Golubnitschaja, Olga:
Pre-pregnancy check-up of maternal vascular status and associated phenotype is crucial for the health of mother and offspring

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Golriz Khatami, Sepehr; Salimi, Yasamin; Hofmann-Apitius, Martin; Oxtoby, N.P.; Birkenbihl, Colin:
Comparison and aggregation of event sequences across ten cohorts to describe the consensus biomarker evolution in Alzheimer's disease

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Golriz Khatami, Sepehr:
Deconstructing and Approaching Heterogeneities in the Biomedical Field via Computational Modeling

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Hoyt, Charles; Balk, Meghan; Callahan, Tiffany J.; Domingo Fernández, Daniel; Haendel, Melissa A.; Hegde, Harshad B.; Himmelstein, Daniel S.; Karis, Klas; Kunze, John; Lubiana, Tiago; Matentzoglu, Nicolas; McMurry, Julie; Moxon, Sierra; Mungall, Christopher J.; Rutz, Adriano; Unni, Deepak; Willighagen, Egon; Winston, Donald; Gyori, Benjamin:
Unifying the identification of biomedical entities with the Bioregistry

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Lage-Rupprecht, Vanessa; Schultz, Bruce; Dick, Justus; Namysl, Marcin; Zaliani, Andrea; Gebel, Stephan; Pless, Ole; Reinshagen, Jeanette; Ellinger, Bernhard; Ebeling, Christian; Esser, Alexander; Jacobs, Marc; Claussen, Carsten; Hofmann-Apitius, Martin:
A hybrid approach unveils drug repurposing candidates targeting an Alzheimer pathophysiology mechanism

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Lage-Rupprecht, Vanessa; Schultz, Bruce; Namysl, Marcin:
A hybrid approach for identifying drug repurposing candidates and their mechanisms

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Madan, Sumit; Zimmer, Fabian Julius; Balabin, Helena; Schaaf, Sebastian; Fröhlich, Holger; Fluck, Juliane; Neuner, Irene; Mathiak, Klaus; Hofmann-Apitius, Martin; Sarkheil, Pegah:
Deep Learning-based Detection of Psychiatric Attributes from German Mental Health Records

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Madan, Sumit; Demina, Victoria; Stapf, Marcus; Ernst, Oliver; Fröhlich, Holger:
Accurate prediction of virus-host protein-protein interactions via a Siamese neural network using deep protein sequence embeddings

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Mubeen, Sarah; Tom Kodamullil, Alpha; Hofmann-Apitius, Martin; Domingo Fernández, Daniel:
On the influence of several factors on pathway enrichment analysis

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Mubeen, Sarah; Domingo Fernández, Daniel; Diaz del Ser, Sara; Solanki, Dhwani; Tom Kodamullil, Alpha; Hofmann-Apitius, Martin; Hopp, Marie-T.; Imhof, Diana:
Exploring the Complex Network of Heme-Triggered Effects on the Blood Coagulation System

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Muslu, Özlem; Hoyt, Charles Tapley; Lacerda, Mauricio Pio de; Hofmann-Apitius, Martin; Fröhlich, Holger:
GuiltyTargets: Prioritization of Novel Therapeutic Targets with Network Representation Learning

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Queiroz Figueiredo, Rebeca; Diaz del Ser, Sara; Raschka, Tamara; Hofmann-Apitius, Martin; Tom Kodamullil, Alpha; Mubeen, Sarah; Domingo Fernández, Daniel:
Elucidating gene expression patterns across multiple biological contexts through a large-scale investigation of transcriptomic datasets

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Salimi, Yasamin; Domingo Fernández, Daniel; Bobis-Álvarez, Carlos; Hofmann-Apitius, Martin; Birkenbihl, Colin:
ADataViewer: exploring semantically harmonized Alzheimer’s disease cohort datasets

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Sharma, Jayant:
Drug Repurposing & Adverse Event Prediction through EHR Knowledge Graph Completion

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Wegner, Philipp; Schaaf, Sebastian; Uebachs, M.; Domingo Fernández, Daniel; Salimi, Yasamin; Gebel, Stephan; Sargsyan, Astghik; Birkenbihl, Colin; Springstubbe, Stephan; Klockgether, T.; Fluck, Juliane; Hofmann-Apitius, Martin; Tom Kodamullil, Alpha:
Integrative data semantics through a model-enabled data stewardship

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Wendland, Philipp Johannes; Birkenbihl, Colin; Gomez-Freixa, Marc; Sood, Meemansa; Kschischo, Maik; Fröhlich, Holger:
Generation of realistic synthetic data using Multimodal Neural Ordinary Differential Equations

 

Arbabyazd, L.; Shen, K.; Wang, Z.; Hofmann-Apitius, M.; Ritter, P.; McIntosh, A.R.; Battaglia, D.; Jirsa, V.:
Virtual Connectomic Datasets in Alzheimer's Disease and Aging Using Whole-Brain Network Dynamics Modelling

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Bharadhwaj, Vinay Srinivas; Ali, Mehdi; Birkenbihl, Colin; Mubeen, Sarah; Lehmann, Jens; Hofmann-Apitius, Martin; Hoyt, Charles Tapley; Domingo-Fernández, Daniel:
CLEP: A hybrid data- and knowledge-driven framework for generating patient representations

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Birkenbihl, Colin; Westwood, Sarah; Shi, Liu; Nevado-Holgado, Alejo; Westman, Eric; Lovestone, Simon; Hofmann-Apitius, Martin
ANMerge: A Comprehensive and Accessible Alzheimer's Disease Patient-Level Dataset

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Dal Piccol Sotto, Léo Francoso; Kaufmann, Paul; Atkinson, Timothy; Kalkreuth, Roman; Basgalupp, Márcio Porto:
Graph representations in genetic programming

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Domingo-Fernández, Daniel; Baksi, Shounak; Schultz, Bruce; Gadiya, Yojana; Kark, Reagon; Raschka, Tamara; Ebeling, Christian; Hofmann-Apitius, Martin; Kodamullil, Alpha Tom:
COVID-19 Knowledge Graph: A computable, multi-modal, cause-and-effect knowledge model of COVID-19 pathophysiology

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Figueiredo, Rebeca Quiroz; Raschka, Tamara; Kodamullil, Alpha Tom; Hofmann-Apitius, Martin; Mubeen, Sarah; Domingo-Fernández, Daniel:
Towards a global investigation of transcriptomic signatures through co-expression networks and pathway knowledge for the identification of disease mechanisms

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Fluck, J.; Lindstädt, B.; Ahrens, W.; Beyan, O.; Buchner, B.; Darms, J.; Depping, R.; Dierkes, J.; Neuhausen, H.; Müller, W.; Zeeb, H.; Golebiewski, M.; Löffler, M.; Löbe, M.; Meineke, F.; Klammt, S.; Fröhlich, Holger; Hahn, H.; Schulze, M.; Pischon, T.; Nöthlings, U.; Sax, U.; Kusch, H.; Grabenhenrich, L.; Schmidt, C.O.; Waltemath, D.; Semler, S.; Gehrke, J.; Kirsten, T.; Praßer, F.; Thun, S.; Wieler, L.; Pigeot, I.:
NFDI4Health - Nationale Forschungsdateninfrastruktur für personenbezogene Gesundheitsdaten.

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Golriz Khatami, Sepehr; Domingo-Fernandez, D.; Mubeen, S.; Hoyt, C.T.; Robinson, C.; Karki, R.; Iyappan, A.; Kodamullil, A.T.; Hofmann-Apitius, M.:
A Systems Biology Approach for Hypothesizing the Effect of Genetic Variants on Neuroimaging Features in Alzheimer's Disease

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Henry, V.; Moszer, I.; Dameron, O.; Vila Xicota, L.; Dubois, B.; Potier, M.-C.; Hofmann-Apitius, M.; Colliot, O.:
Converting disease maps into heavyweight ontologies: General methodology and application to Alzheimer's disease

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Hopp, Marie-Thérèse; Domingo-Fernández, Daniel; Gadiya, Yojana; Detzel, Milena; Graf, Regina; Schmalohr Benjamin; Kodamullil, Alpha Tom; Imhof, Diana; Hofmann-Apitius, Martin:
Linking COVID-19 and Heme-Driven Pathophysiologies: A Combined Computational-Experimental Approach

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Jong, Johann de; Cutcutache, Ioana; Page, Matthew; Elmoufti, Sami; Dilley, Cynthia; Fröhlich, Holger; Armstrong, Martin:
Towards realizing the vision of precision medicine: AI based prediction of clinical drug response

---

Khatami, Sepehr Golriz; Mubeen, Sarah; Bharadhwaj, Vinay; Kodamullil, Alpha; Hofmann-Apitius, Martin; Domingo-Fernández, Daniel:
Using predictive machine learning models for drug response simulation by calibrating patient-specific pathway signatures

---

Langnickel, L.; Baum, R.; Darms, J.; Madan, S.; Fluck, J:
COVID-19 preVIEW: Semantic Search to Explore COVID-19 Research Preprints

---

Langnickel, Lisa; Krockauer, Kilian; Uebachs, Mischa; Schaaf, Sebastian; Madan, Sumit; Klockgether, Thomas; Fluck, Juliane:
Information extraction from german clinical care documents in context of Alzheimer's disease

---

Linden, Thoma; Jong, J. de; Lu, C.; Kiri, V.; Haeffs, K.; Fröhlich, H.:
An Explainable Multimodal Neural Network Architecture for Predicting Epilepsy Comorbidities Based on Administrative Claims Data

---

Linden, Thomas; Hanses, Frank; Domingo-Fernández, Daniel; DeLong, Lauren Nicole; Kodamullil, Alpha Tom; Schneider, Jochen; Vehreschild, Maria J.G.T.; Lanznaster, Julia; Ruethrich, Maria Madeleine; Borgmann, Stefan; Hower, Martin; Wille, Kai; Feldt, Torsten; Rieg, Siegbert; Hertenstein, Bernd; Wyen, Christoph; Roemmele, Christoph; Vehreschild, Jörg Janne; Jakob, Carolin E. M.; Stecher, Melanie; Kuzikov, Maria; Zaliani, Andrea; Fröhlich, Holger:
Machine Learning Based Prediction of COVID-19 Mortality Suggests Repositioning of Anticancer Drug for Treating Severe Cases

---

Marín-Llaó, Josep; Mubeen, Sarah; Perera-Lluna, Alexandre; Hofmann-Apitius, Martin; Picart-Armada, Sergio; Domingo-Fernández, Daniel:
MultiPaths. A python framework for analyzing multi-layer biological networks using diffusion algorithms

---

Mubeen, Sarah; Bharadhwaj, Vinay; Gadiya, Yojana; Hofmann-Apitius, Martin; Kodamullil, Alpha; Domingo-Fernández, Daniel:
DecoPath: A web application for decoding pathway enrichment analysis

---

Muurling, M.; Boer, C. de; Kozak, R.; Religa, D.; Koychev, I.; Verheij, H.; Nies, V.J.M.; Duyndam, A.; Sood, M.; Fröhlich, H.; Hannesdottir, K.; Erdemli, G.; Lucivero, F.; Lancaster, C.; Hinds, C.; Stravopoulos, T.G.; Nikolopoulos, S.; Kompatsiaris, I.; Manyakov, N.V.; Owens, A.P.; Narayan, V.A.; Aarsland, D.; Visser, P.J.:
Remote monitoring technologies in Alzheimer's disease: Design of the RADAR-AD study

---

Newmiwaka, Tobias; Engelhardt, Benjamin; Wendland, Philipp; Kahl, Dominik; Fröhlich, Holger; Kschischo, Maik:
SEEDS: Data driven inference of structural model errors and unknown inputs for dynamic systems biology

---

Schmidt, C.O.; Fluck, J.; Golebiewski, M.; Grabenhenrich, L.; Hahn, H.; Kirsten, T.; Klammt, S.; Löbe, M.; Sax, U.; Thun, S.; Pigeot, I.:
COVID-19-Forschungsdaten leichter zugänglich machen - Aufbau einer bundesweiten Informationsinfrastruktur

---

Schultz, B.; Zaliani, A.; Ebeling, C.; Reinshagen, J.; Bojkova, D.; Lage-Rupprecht, V.; Karki, R.; Lukassen, S.; Gadiya, Y.; Ravindra, N.G.; Das, S.; Baksi, S.; Domingo-Fernandez, D.; Lentzen, M.; Strivens, M.; Raschka, T.; Cinatl, J.; DeLong, L.N.; Gribbon, P.; Geisslinger, G.; Ciesek, S.; Dijk, D. van; Gardner, S.; Kodamullil, A.T.; Fröhlich, H.; Peitsch, M.; Jacobs, M.; Hoeng, J.; Eils, R.; Claussen, C.; Hofmann-Apitius, M.:
A method for the rational selection of drug repurposing candidates from multimodal knowledge harmonization

---

Schwarz, Emanuel; Alnæs, Dag; Andreassen, Ole A.; Cao, Han; Chen, Junfang; Degenhardt, Franziska; Doncevic, Daria; Dwyer, Dominic; Eils, Roland; Erdmann, Jeanette; Herrmann, Carl; Hofmann-Apitius, Martin; Kaufmann, Tobias; Koutsouleris, Nikolaos; Kodamullil, Alpha Tom; Khuntia, Adyasha; Mucha, Sören; Nöthen, Markus M.; Paul, Riya; Pedersen, Mads L.; Quintero, Andres; Schunkert, Heribert; Sharma, Ashwini; Tost, Heike; Westlye, Lars T.; Zhang, Youcheng; Meyer-Lindenberg, Andreas:
Identifying multimodal signatures underlying the somatic comorbidity of psychosis: The COMMITMENT roadmap

---

Stefanovski, L.; Meier, J.M.; Pai, R.K.; Triebkorn, P.; Lett, T.; Martin, L.; Bülau, K.; Hofmann-Apitius, M.; Solodkin, A.; McIntosh, A.R.; Ritter, P.:
Bridging Scales in Alzheimer's Disease: Biological Framework for Brain Simulation With The Virtual Brain

---

Wißfeld, Jannis; Nozaki, Ichiro; Mathews, Mona; Raschka, Tamara; Ebeling, Christian; Hornung, Veit; Brüstle, Oliver; Neumann, Harald:
Deletion of Alzheimer's disease-associated CD33 results in an inflammatory human microglia phenotype

 

Sepehr Golriz Khatami, Christine Robinson, Colin Birkenbihl, Daniel Domingo-Fernández, Charles Tapley Hoyt, Martin Hofmann-Apitius:
Challenges of Integrative Disease Modeling in Alzheimer's Disease

---

Raza-Ur Rahman, Vikas Bansal, Maksims Fiosins, Anna-Maria Liebhoff, Ashish Rajput, Abdul Sattar, Daniel Sumner Magruder, Sumit Madan, Ting Sun, Abhivyakti Gautam, Sven Heins, Timur Liwinski, Jörn Bethune, Claudia Trenkwalder, Juliane Fluck, Brit Mollenhauer, Stefan Bonn:
SEAweb: The small RNA Expression Atlas web application

---

Farah Humayun, Daniel Domingo-Fernández, Paul George, Ajay Abisheck, Marie-Thérèse Hopp, Benjamin Syllwasschy, Milena Detzel, Charles Tapley Hoyt, Martin Hofmann-Apitius, Diana Imhof:
A Computational Approach for Mapping Heme Biology in the Context of Hemolytic Disorders

---

Anne Fröhlich, Sophia Loick, Emma Grace Bawden, Simon Fietz, Jörn Dietrich, Eric Diekmann, Gonzalo Saavedra, Holger Fröhlich, Dennis Niebel, Judith Sirokay, Romina Zarbl, Gerrit H. Gielen, Glen Kristiansen, Friedrich Bootz, Jennifer Landsberg, Dimo Dietrich:
Comprehensive analysis of tumor necrosis factor receptor TNFRSF9 (4-1BB) DNA methylation with regard to molecular and clinicopathological features

---

Sepehr Golriz Khatami, Sarah Mubeen, Martin Hofmann-Apitius:
Data science in neurodegenerative disease: its capabilities, limitations, and perspectives

---

Amin Lemsara, Salima Ouadfel, Holger Fröhlich:
PathME: Pathway based Multi-modal Sparse Autoencoders for Clustering of Patient-Level Multi-Omics Data

---

Luise Gootjes-Dreesbach, Meemansa Sood, Akrishta Sahay, Martin Hofmann-Apitius, Holger Fröhlich:
Variational Autoencoder Modular Bayesian Networks (VAMBN) for Simulation of Heterogeneous Clinical Study Data

---

Wolfgang Ziegler:
A Landscape Analysis of Standardisation in the Field of Artificial Intelligence

---

Mohammad Asif Emon; Daniel Domingo-Fernàndez; Martin Hofmann-Apitius:
PS4DR: a multimodal workflow for identification and prioritization of drugs based on pathway signatures

---

Meemansa Sood, Akrishta Sahay, Reagon Karki, Mohammad Asif Emon, Henri Vrooman, Martin Hofmann-Apitius, Holger Fröhlich:
Realistic Simulation of Virtual Multi-Scale, Multi-Modal Patient Trajectories using Bayesian Networks and Sparse Autoencoders

---

Colin Birkenbihl, Mohammad Asif Emon, Henri Vrooman, Sarah Westwood, Simon Lovestone, On behalf of the AddNeuroMed Consortium, Martin Hofmann-Apitius, Holger Fröhlich & Alzheimer’s Disease Neuroimaging Initiative:
Differences in cohort study data affect external validation of artificial intelligence models for predictive diagnostics of dementia - lessons for translation into clinical practice

---

Sara Mora, Sumit Madan, Stephan Gebel, Mauro Giacomini:
Proposal of an Architecture for Terminology Management in a Research Project

---

Özlem Muslu, Charles Tapley Hoyt, Mauricio Pio De Lacerda, Martin Hofmann-Apitius, Holger Fröhlich:
GuiltyTargets: Prioritization of Novel Therapeutic Targets with Deep Network Representation Learning

---

Elisha Goldstein, Kristina Yeghiazaryan, Ashar Ahmad, Frank A. Giordano, Holger Fröhlich, Olga Golubnitschaja:
Optimal multiparametric set-up modelled for best survival outcomes in palliative treatment of liver malignancies - Unsupervised machine learning and 3PM recommendations

---

Reagon Karki, Sumit Madan, Yojana Gadiya, Daniel Domingo-Fernàndez, Alpha Tom Kodamullil, Martin Hofmann-Apitius:
Data-driven modeling of knowledge assemblies in understanding comorbidity between Type 2 Diabetes Mellitus and Alzheimer’s Disease

---

Daniel Domingo-Fernández, Shounak Baksi, Bruce Schultz, Yojana Gadiya, Reagon Karki, Tamara Raschka, Christian Ebeling, Martin Hofmann-Apitius, Alpha Tom Kodamullil:
COVID-19 Knowledge Graph: a computable, multi-modal, cause-and-effect knowledge model of COVID-19 pathophysiology

---

Lisa Langnickel, Roman Baum, Gabriele Wollnik-Korn, Brigitte Fischer-Wagener, Sumit Madan, Juliane Fluck:
The future of German MeSH: a new semi-automatic translation process and new services for search and annotation

---

Tobias Newmiwaka, Benjamin Engelhardt, Philipp Wendland, Dominik Kahl, Holger Fröhlich, Maik Kschischo:
SEEDS: Data driven inference of structural model errors and unknown inputs for dynamic systems biology

---

Laurèl Rauschenbach, Anja Wieland, Roman Reinartz, Sied Kebir, Andreas Till, Marvin Darkwah Oppong, Celia Dobersalske, Vivien Ullrich, Ashar Ahmad, Ramazan Jabbarli, Daniela Pierscianek, Holger Fröhlich, Matthias Simon, Oliver Brüstle, Ulrich Sure, Martin Glas, Björn Scheffler:
Drug repositioning of antiretroviral ritonavir for combinatorial therapy in glioblastoma

---

Colin Birkenbihl, Sarah Westwood, Eric Westman, Liu Shi, Alejo Nevado-Holgado, Simon Lovestone, Martin Hofmann-Apitius:
ANMerge: A comprehensive and accessible Alzheimer's disease patient-level dataset

---

Mohammad Asif Emon, Ashley Heinson, Ping Wu, Daniel Domingo-Fernandez, Meemansa Sood, Henri Vrooman, Jean-Christophe Corvol, Phil Scordis, Martin Hofmann-Apitius, Holger Fröhlich:
Clustering of Alzheimer’s and Parkinson’s Disease Based on Genetic Burden of Shared Molecular Mechanisms

---

Lisa Langnickel, Roman Baum, Gabriele Wollnik-Korn, Brigitte Fischer-Wagener, Sumit Madan, Juliane Fluck:
The future of German MeSH: a new semi-automatic translation process and new services for search and annotation

---

Frederic Brosseron, Carl-Christian Kolbe, Francesco Santarelli, Stephanie Carvalho, Anna Antonell, Sergio Castro-Gomez, Pawel Tacik Aishwarya, Alex Namasivayam, Graziella Mangone, Reinhard Schneider, Eicke Latz, Ullrich Wüllner, Per Svenningsson, Raquel Sánchez-Valle, José Luis Molinuevo, Jean-Christophe Corvol, Michael T.Heneka, on behalf of the AETIONOMY study group (…Martin Hofmann-Apitius (…), Stephan Springstubbe (...), Holger Fröhlich (…)):
Multicenter Alzheimer's and Parkinson's disease immune biomarker verification study Multicenter Alzheimer's and Parkinson's disease immune biomarker verification study

---

Anatolij Kunin, Nafiseh Sargheini, Colin Birkenbihl, Natalia Moiseeva, Holger Fröhlich, Olga Golubnitschaja:
Voice perturbations under the stress overload in young individuals: phenotyping and suboptimal health as predictors for cascading pathologies

---

Daniel Rivas-Barragan, Sarah Mubeen, Francesc Guim Bernat, Martin Hofmann-Apitius, Daniel Domingo-Fernández:
Drug2ways: Reasoning over causal paths in biological networks for drug discovery

---

Colin Birkenbihl, Yasamin Salimi, Daniel Domingo-Fernandez, Simon Lovestone on behalf of the AddNeuroMed consortium, Holger Fröhlich, Martin Hofmann-Apitius, and the Japanese Alzheimer's Disease Neuroimaging Initiative, and the Alzheimer's Disease Neuroimaging Initiative:
Evaluating the Alzheimer's Disease Data Landscape

---

Roman Li, Anze Zupanic, Marja Talikka, Vincenzo Belcastro, Sumit Madan, Jens Dörpinghaus, Colette vom Berg, Justyna Szostak, Florian Martin, Manuel C. Peitsch, Julia Hoeng:
Systems toxicology approach for testing chemical cardiotoxicity in larval zebrafish

---

Josep Marín-Llaó, Sarah Mubeen, Alexandre Perera-Lluna, Martin Hofmann-Apitius, Sergio Picart-Armada, Daniel Domingo-Fernández:
MultiPaths: a python framework for analyzing multi-layer biological networks using diffusion algorithms

---

Astghik Sargsyan, Alpha Tom Kodamullil, Shounak Baksi, Johannes Darms, Sumit Madan, Stephan Gebel, Oliver Keminer, Geena Mariya Jose, Helena Balabin, Lauren Nicole DeLong, Manfred Kohler, Marc Jacobs, Martin Hofmann-Apitius:
The COVID-19 Ontology

---

Emanuel Schwarz, Dag Alnæs, Ole A. Andreassen, Han Cao, Junfang Chen,Franziska Degenhardt, Daria Doncevic, Dominic Dwyer, Roland Eils, Jeanette Erdmann, Carl Herrmann, Martin Hofmann-Apitius, Tobias Kaufmann, Nikolaos Koutsouleris, Alpha T. Kodamullil, Adyasha Khuntia, Sören Mucha, Markus M. Nöthen, Riya Paul, Mads L. Pedersen, Andres Quintero, Heribert Schunkert, Ashwini Sharma, Heike Tost, Lars T. Westlye, Youcheng Zhang & Andreas Meyer-Lindenberg:
Identifying multimodal signatures underlying the somatic comorbidity of psychosis: the COMMITMENT roadmap.

 

Tamás Letoha, Anett Hudák, Erzsébet Kusz, Aladár Pettkó-Szandtner, Ildikó Domonkos, Katalin Jósvay, Martin Hofmann-Apitius & László Szilák:
Contribution of syndecans to cellular internalization and fibrillation of amyloid-β(1–42)

---

Daniel Domingo-Fernandez, Allison Provost, Alpha Tom Kodamullil, Josep Marin-Llao, Heather Lasseter, Kristophe Diaz, Nikolaos Daskalakis, Lee Lancashire, Martin Hofmann-Apitius, Magali Haas:
PTSD Biomarker Database: Deep Dive Meta-database for PTSD Biomarkers, Visualizations, and Analysis Tools

---

Daniel Domingo-Fernández, Sarah Mubeen, Josep Marín-Llaó, Charles Tapley Hoyt, Martin Hofmann-Apitius:
PathMe: Merging and exploring mechanistic pathway knowledge

---

Charles Hoyt, Daniel Domingo-Fernandez, Rana Aldisi, Lingling Xu, Kristian Kolpeja, Sandra Spalek, Esther Wollert, John Bachman, Benjamin Gyori, Patrick Greene, Martin Hofmann-Apitius:
Re-curation and Rational Enrichment of Knowledge Graphs in Biological Expression Language

---

Sarah Mubeen, Charles Tapley Hoyt, Andre Gemünd, Martin Hofmann-Apitius, Holger Fröhlich, Daniel Domingo-Fernández:
The Impact of Pathway Database Choice on Statistical Enrichment Analysis and Predictive Modeling

---

Charles Tapley Hoyt, Daniel Domingo-Fernández, Sarah Mubeen, Josep Marin Llaó, Andrej Konotopez, Christian Ebeling, Colin Birkenbihl, Özlem Muslu, Bradley English, Simon Müller, Mauricio Pio de Lacerda, Mehdi Ali, Scott Colby, Dénes Türei, Nicolàs Palacio-Escat, Martin Hofmann-Apitius:
Integration of Structured Biological Data Sources using Biological Expression Language

---

Reagon Karki, Alpha Tom Kodamullil, Charles Tapley Hoyt, Martin Hofmann-Apitius:
Quantifying mechanisms in neurodegenerative diseases (NDDs) using candidate mechanism perturbation amplitude (CMPA) algorithm

---

Mehdi Ali, Hajira Jabeen, Charles Tapley Hoyt, Jens Lehmann:
The KEEN Universe: An Ecosystem for Knowledge Graph Embeddings with a Focus on Reproducibility and Transferability

---

Johann de Jong, Mohammad Asif, Ping Wu, Reagon Karki, Meemansa Sood, Patrice Godard, Ashar Ahmad, Henri Vrooman, Martin Hofmann-Apitius, Holger Fröhlich:
Deep learning for clustering of multivariate clinical patient trajectories with missing values

---

Sumit Madan, Justyna Szostak, Ravikumar Komandur Elayavilli, Richard Tzong-Han Tsai, Mehdi Ali, Longhua Qian, Majid Rastegar-Mojarad, Julia Hoeng, Juliane Fluck:
The extraction of complex relationships and their conversion to biological expression language (BEL) overview of the BioCreative VI (2017) BEL track

---

Eduardo Brito, Bogdan Georgiev, Daniel Domingo-Fernández, Charles Tapley Hoyt, Christian Bauckhage:
RatVec: A General Approach for Low-dimensional Distributed Vector Representations via Rational Kernels

---

Jens Dörpinghaus, Andreas Stefan:
Knowledge Extraction and Applications utilizing Context Data in Knowledge Graphs

---

Jens Dörpinghaus, Carsten Düing, Vera Weil:
A Minimum Set-Cover Problem with several constraints

---

Mehdi Ali, Charles Tapley, Hoyt, Daniel Domingo-Fernández, Jens Lehmann:
Predicting Missing Links Using PyKEEN

---

Wolfgang Ziegler, Ramin Yahyapour, Jens Grabowski, Dieter Kranzlmüller:
A framework for managing quality of service in cloud computing through service level agreements

---

Daniel Domingo-Fernández, Charles Tapley Hoyt, Carlos Bobis-Álvarez, Josep Marín-Llaó, Martin Hofmann-Apitius:
Publisher Correction: ComPath: an ecosystem for exploring, analyzing, and curating mappings across pathway databases

---

Charles Tapley Hoyt, Daniel Domingo-Fernández, Rana Aldisi, Lingling Xu, Kristian Kolpeja, Sandra Spalek, Esther Wollert, John Bachman, Benjamin M Gyori, Patrick Greene, Martin Hofmann-Apitius:
Re-curation and rational enrichment of knowledge graphs in Biological Expression Language

---

Gloria Bahamondez, Holger Fröhlich:
MCMC Techniques for Parameters Estimation of ODE Based Models in Systems Biology

---

Amit Sharma, Holger Fröhlich, Rong Zhang, Anne-Karoline Ebert, Wolfgang Rösch, Henning Reis, Glen Kristiansen, Jörg Ellinger, Heiko Reutter:
Classic bladder exstrophy and adenocarcinoma of the bladder: methylome analysis provide no evidence for underlying disease-mechanisms of this association

---

Thorsten Buch, Katharina Moos, Filipa M. Ferreira, Holger Fröhlich, Catherine Gebhar, Achim Tresch:
Benefits of a factorial design focusing on inclusion of female and male animals in one experiment

---

Bawarjan Schatlo, Oliver P. Gautschi, Christoph M. Friedrich, Christian Ebeling, Max Jägersberg, Zsolt Kulscar, Vitor Mendes Pereira, Karl Schaller, Philippe Bijlenga:
Association of single and multiple aneurysms with tobacco abuse: an @neurIST risk analysis

Gündel, Michaela; Hoyt, Charles Tapley; Hofmann-Apitius, Martin:
BEL2ABM: agent-based simulation of static models in Biological Expression Language

---

Dörpinghaus, J.; Jacobs, M.; Fluck, J.:
Graph based discovery in biomedical information systems connecting scientific texts with structured expert knowledge

---

Darms, J.; Dörpinghaus, J.:
Improving document retrieval with a clustering based relevance feedback system

---

Ajay Abisheck Paul George; Heimer, Pascal; Maaß, Astrid; Hamaekers, Jan; Hofmann-Apitius, Martin; Biswas, Arijit; Imhof, Diana:
Insights into the Folding of Disulfide-Rich μ-Conotoxins

---

Golubnitschaja, O.; Filep, N.; Yeghiazaryan, K.; Blom, H.J.; Hofmann-Apitius, M.; Kuhn, W.:
Multi-omic approach decodes paradoxes of the triple-negative breast cancer: Lessons for predictive, preventive and personalised medicine

---

Dörpinghaus, Jens; Schrader, R.; Randerat, H.:
Pseudostabile Mengen in Graphen

---

Hoyt, Charles Tapley; Konotopez, Andrej; Ebeling, Christian:
PyBEL: A computational framework for biological expression language

---

Dörpinghaus, J.; Klein, J.; Darms, J.; Madan, S.; Jacobs, M.:
SCAIView - A semantic search engine for biomedical research utilizing a microservice architecture

---

Jacobs, M.; Hodapp, S.; Dörpinghaus, J.:
SDA: Towards a novel knowledge discovery model for information systems

---

Dörpinghaus, J.; Schaaf, S.; Jacobs, M.:
Soft document clustering using a novel graph covering approach

---

Hoyt, Charles Tapley; Domingo-Fernandez, Daniel; Balzer, Nora; Güldenpfennig, Anka; Hofmann-Apitius, Martin:
A systematic approach for identifying shared mechanisms in epilepsy and its comorbidities

---

Khanna, Shashank; Domingo-Fernández, Daniel; Iyappan, Anandhi; Emon, Mohammad Asif; Hofmann-Apitius, Martin; Fröhlich, Holger:
Using Multi-Scale Genetic, Neuroimaging and Clinical Data for Predicting Alzheimer's Disease and Reconstruction of Relevant Biological Mechanisms

---

Daniel Domingo-Fernández, Charles Tapley Hoyt, Carlos Bobis-Álvarez, Josep Marín-Llaó & Martin Hofmann-Apitius:
ComPath: an ecosystem for exploring, analyzing, and curating mappings across pathway databases

---

Vincent J. Henry, Ivan Moszer, Olivier Dameron, Marie-Claude Potier, Martin Hofmann-Apitius, Olivier Colliot:
Integrating ontological representation and reasoning into a disease map: application to Alzheimer’s disease

---

Charles Tapley Hoyt, Daniel Domingo-Fernández, Martin Hofmann-Apitius:
BEL Commons: an environment for exploration and analysis of networks encoded in Biological Expression Language

---

Henry V., Moszer I., Dameron O., Potier MC., Hofmann-Apitius M., Colliot O.:
Converting Alzheimer’s Disease Map into a Heavyweight Ontology: A Formal Network to Integrate Data

Doubal, F.N., Ali, M., Batty, G.D., Charidimou, A., Eriksdotter, M., Hofmann-Apitius, M., Kim, Y.-H., Levine, D.A., Mead, G., Mucke, H.A.M., Ritchie, C.W., Roberts, C.J., Russ, T.C., Stewart, R., Whiteley, W., Quinn, T.J.:
Big data and data repurposing - using existing data to answer new questions in vascular dementia research

---

Emon, M.A.E.K., Kodamullil, A.T., Karki, R., Younesi, E., Hofmann-Apitius, M.:
Using Drugs as Molecular Probes: A Computational Chemical Biology Approach in Neurodegenerative Diseases

---

Fluck, Juliane; Senger, Philipp; Ziegler, Wolfgang; Claus, Steffen; Schwichtenberg, Horst:
The cloud4health Project. Secondary use of clinical data with secure cloud-based text mining services

---

Geerts, H.; Hofmann-Apitius, M.; Anastasio, T.J.:
Knowledge-driven computational modeling in Alzheimer's disease research: Current state and future trends

---

Iyappan, A.; Younesi, E.; Redolfi, A.; Vrooman, H.; Khanna, S.; Frisoni, G.B.; Hofmann-Apitius, M.:
Neuroimaging feature terminology: A controlled terminology for the annotation of brain imaging features

---

Juzenas, S., Venkatesh, G., Hübenthal, M., Hoeppner, M.P., Du, Z.G., Paulsen, M., Rosenstiel, P., Senger, P., Hofmann-Apitius, M., Keller, A., Kupcinskas, L., Franke, A., Hemmrich-Stanisak, G.:
A comprehensive, cell specific microRNA catalogue of human peripheral blood

---

Karki, R.; Kodamullil, A.T.; Hofmann-Apitius, M.:
Comorbidity analysis between alzheimer's disease and type 2 diabetes mellitus (T2DM) based on shared pathways and the role of T2DM drugs

---

Kawalia, S.B.; Raschka, T.; Naz, M.; Matos Simoes, R. de; Senger, P.; Hofmann-Apitius, M.:
Analytical strategy to prioritize Alzheimer's disease candidate genes in gene regulatory networks using public expression data

---

Kodamullil, Alpha & Zekri, Firas & Sood, Meemansa & Hengerer, Bastian & Canard, Luc & McHale, Duncan & Hofmann-Apitius, Martin:
Trial watch: Tracing investment in drug development for Alzheimer disease. Nature Reviews Drug Discovery.

---

Kodamullil, A.T.; Iyappan, A.; Karki, R.; Madan, S.; Younesi, E.; Hofmann-Apitius, M.:
Of mice and men: Comparative analysis of neuro-inflammatory mechanisms in human and mouse using cause-and-effect models

---

Langley, G.R., Adcock, I.M., Busquet, F., Crofton, K.M., Csernok, E., Giese, C., Heinonen, T., Herrmann, K., Hofmann-Apitius, M., Landesmann, B., Marshall, L.J., McIvor, E., Muotri, A.R., Noor, F., Schutte, K., Seidle, T., van de Stolpe, A., Van Esch, H., Willett, C., Woszczek, G.:
Towards a 21st-century roadmap for biomedical research and drug discovery: consensus report and recommendations

Akhondi, S.A.; Klenner, A.G.; Tyrchan, C.; Manchala, A.K.; Boppana, K.; Lowe, D.; Zimmermann, M.; Jagarlapudi, S.A.R.P.; Sayle, R.; Kors, J.A.; Muresan, S.:

Annotated chemical patent corpus: A gold standard for text mining
PLoS one. Online journal, Vol.9 (2014), No.9, Art. e107477, 8 pp.
info:doi/10.1371/journal.pone.0107477

---

Blasi, Lorenzo; Jensen, Jens; Ziegler, Wolfgang:
Expressing quality of service and protection using federation-level service level agreement. (International Conference on Parallel Processing (Euro-Par) <19, 2013, Aachen>)
Euro-Par 2013. Parallel Processing Workshops: BigDataCloud, DIHC, FedICI, HeteroPar, HiBB, LSDVE, MHPC, OMHI, PADABS, PROPER, Resilience, ROME, and UCHPC 2013, Aachen, Germany, August 26-27, 2013; revised selected papers. Berlin: Springer, 2014. (Lecture Notes in Computer Science 8374), pp. 146-156
info:doi/10.1007/978-3-642-54420-0_15

---

Deyati, A.; Sanam, R.D.; Guggilla, S.R.; Pidugu, V.R.; Novac, N.:
Molecular biomarkers in clinical development: What could we learn from the clinical trial registry?
Personalized medicine, Vol.11 (2014), No.4, pp.381-393
info:doi/10.2217/pme.14.27

---

Fluck, Juliane; Madan, Sumit; Ansari, Sam; Szostak, Justyna; Hoeng, Julia; Zimmermann, Marc; Hofmann-Apitius, Martin; Peitsch, Manuel C:
BELIEF - a semiautomatic workflow for BEL network creation. (International Symposium on Semantic Mining in Biomedicine (SMBM) <6, 2014, Aveiro>)
Bodenreider, O.: SMBM 2014, 6th International Symposium on Semantic Mining in Biomedicine. Proceedings. Online resource: October 6-7th, 2014, Aveiro, Portugal. Aveiro, 2014, pp. 109-113

---

Fluck, Juliane; Hofman-Apitius, Martin:
Text mining for systems biology
Drug Discovery Today, Vol.19 (2014), No.2, pp.140-144
info:doi/10.1016/j.drudis.2013.09.012

---

Holl, S.; Zimmermann, O.; Palmblad, M.; Mohammed, Y.; Hofmann-Apitius, M.:
A new optimization phase for scientific workflow management systems
Future generation computer systems : FGCS, Vol.36 (2014), pp.352-362
info:doi/10.1016/j.future.2013.09.005

---

Ishitsubo, E.; Hosozawa, T.; Igarashi, M.; Kirshner, K.N.; Sriwilaijaroen, N.; Yokoe, H.; Tubuki, M.; Suzuki, Y.; Tokiwa, H.:
Rational design and development of novel multi-target inhibitors for influenza virus. (Society for Glycobiology; Japanese Society of Carbohydrate Research (SFG & JSCR Joint Annual Meeting) <2014, Honolulu/Hawaii>)
Glycobiology, Vol.24 (2014), No.11, pp.1128

---

Iyappan, Anandhi; Bagewadi, Shweta; Page, Matthew; Hofmann-Apitius, Martin; Senger, Philipp:
NeuroRDF: Semantic data integration strategies for modeling neurodegenerative diseases. (International Symposium on Semantic Mining in Biomedicine (SMBM) <6, 2014, Aveiro>)
Bodenreider, O.: SMBM 2014, 6th International Symposium on Semantic Mining in Biomedicine. Proceedings. Online resource: October 6-7th, 2014, Aveiro, Portugal. Aveiro, 2014, pp. 11-18

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Malhotra, A.; Younesi, E.; Gündel, M.; Müller, B.; Heneka, M.T.; Hofmann-Apitius, M.:
ADO: A disease ontology representing the domain knowledge specific to Alzheimer's disease
Alzheimer's & dementia, Vol.10 (2014), No.2, pp.238-246
info:doi/10.1016/j.jalz.2013.02.009

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Malhotra, Ashutosh; Younesi, Erfan; Bagewadi, Shweta; Hofmann-Apitius, Martin:
Linking hypothetical knowledge patterns to disease molecular signatures for biomarker discovery in Alzheimer's disease
Genome medicine, Vol.6 (2014), No.12, Ar. 97, 11 pp.
urn:nbn:de:0011-n-3179045
info:doi/10.1186/s13073-014-0097-z
Volltext

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Saeed, A.; Khan, M.S.; Rafique, H.; Shahid, M.; Iqbal, J.:
Design, synthesis, molecular docking studies and in vitro screening of ethyl 4-(3-benzoylthioureido) benzoates as urease inhibitors
Bioorganic chemistry, Vol.52 (2014), pp.1-7
info:doi/10.1016/j.bioorg.2013.10.001

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Saeed, A.; Mahesar, P.A.; Zaib, S.; Khan, M.S.; Matin, A.; Shahid, M.; Iqbal, J.:
Synthesis, cytotoxicity and molecular modelling studies of new phenylcinnamide derivatives as potent inhibitors of cholinesterases
European journal of medicinal chemistry, Vol.78 (2014), pp.43-53
info:doi/10.1016/j.ejmech.2014.03.015

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Sahadevan, S.; Gunawan, A.; Tholen, E.; Große-Brinkhaus, C.; Tesfaye, D.; Schellander, K.; Hofmann-Apitius, M.; Cinar, M.U.; Uddin, M.J.:
Pathway based analysis of genes and interactions influencing porcine testis samples from boars with divergent androstenone content in back fat
PLoS one. Online journal, Vol.9 (2014), No.3, Art. e91077, 16 pp.
info:doi/10.1371/journal.pone.0091077

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Wolf, Antje; Schoof, Sebastian; Baumann, Sascha; Arndt, Hans-Dieter; Kirschner, Karl N.:
Structure-activity relationships of thiostrepton derivatives: implications for rational drug design
Journal of computer aided molecular design, Vol.28 (2014), No.12, pp.1205-1215
info:doi/10.1007/s10822-014-9797-0

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Younesi, E.; Ansari, S.; Guendel, M.; Ahmadi, S.; Coggins, C.; Hoeng, J.; Hofmann-Apitius, M.; Peitsch, M.C.:
CSEO - The Cigarette Smoke Exposure Ontology
Journal of biomedical semantics, Vol.5 (2014), Art. 31
info:doi/10.1186/2041-1480-5-31

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Zaib, S.; Saeed, A.; Stolte, K.; Flörke, U.; Shahid, M.; Iqbal, J.:
New aminobenzenesulfonamide-thiourea conjugates: Synthesis and carbonic anhydrase inhibition and docking studies
European journal of medicinal chemistry, Vol.78 (2014), pp.140-150
info:doi/10.1016/j.ejmech.2014.03.023

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Ziegler, Wolfgang; D'Ippolito, Roberto; D'Auria, Massimo; Berends, Jochem; Nelissen, Maarten; Diaz, Ramon:
Implementing a "one-stop-shop" providing SMEs with integrated HPC simulation resources using Fortissimo resources. (eChallenges Conference <2014, Belfast>)
Cunningham, P.: eChallenges Conference 2014: Belfast, United Kingdom, 29 - 30 October 2014. Piscataway, NJ: IEEE, 2014, pp. 292-302
urn:nbn:de:0011-n-3566448
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Aisopos, F.; Kardara, M.; Senger, P.; Klinger, R.; Papaoikonomou, A.; Tserpes, K.; Gardner, M.; Varvarigou, T.:
e-Government and Policy Simulation in Intelligent Virtual Environments. (International Conference on Web Information Systems and Technologies (WEBIST) <8, 2012, Porto>)
Krempels, K.-H.: WEBIST 2012, 8th International Conference on Web Information Systems and Technologies. Proceedings: Porto, Portugal, 18 - 21 April, 2012. Setúbal: INSTICC, 2012

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Ali, S.; Saeed, A.; Abbas, N.; Shahid, M.; Bolte, M.; Iqbal, J.:
Design, synthesis and molecular modelling of novel methyl[4-oxo-2-(aroylimino)-3-(substituted phenyl)thiazolidin-5-ylidene]acetates as potent and selective aldose reductase inhibitors
Medicinal chemistry communications : MedChemComm, Vol.3 (2012), No.11, pp.1428-1434
info:doi/10.1039/c2md20228j

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Cacciari, Claudio; Mallmann, Daniel; D'Andria, Francesco; Hagemeier, Björn; Rumpl, Angela; Ziegler, Wolfgang; Zsigri, Csilla; Martrat, Josep:
SLA-based management of software licenses as web service resources in distributed computing infrastructures
Future generation computer systems : FGCS, Vol.28 (2012), No.8, pp.1340-1349
info:doi/10.1016/j.future.2011.11.005

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Danelutto, M.; Desprez, F.; Getov, V.; Ziegler, W.:
CoreGRID/ERCIM workshop on grids, clouds and P2P computing - CGWS2011. Introduction. (International Conference on Parallel Processing (Euro-Par) <17, 2011, Bordeaux>)
Alexander, M.: Euro-Par 2011 Parallel processing workshops. CCPI, CGWS, HeteroPar, HiBB, HPCVirt, HPPC, HPSS, MDGS, ProPer, Resilience, UCHPC, VHPC. Part 1: Bordeaux, France, August 29-September 2, 2011. Revised selected papers. Heidelberg: Springer, 2012. (Lecture notes in computer science 7155), pp. 113-114
info:doi/10.1007/978-3-642-29737-3_13

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Gurulingappa, Harsha; Rajput, Abdul-Mateen; Roberts, Angus; Fluck, Juliane; Hofmann-Apitius, Martin; Toldo, Luca:
Development of a benchmark corpus to support the automatic extraction of drug-related adverse effects from medical case reports
Journal of biomedical informatics : JBI, Vol.45 (2012), No.5, pp.885-892
info:doi/10.1016/j.jbi.2012.04.008

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Holl, S.; Zimmermann, O.; Hofmann-Apitius, M.:
A new optimization phase for scientific workflow management systems. (International Conference on E-Science (e-Science) <8, 2012, Chicago/Ill.>)
Institute of Electrical and Electronics Engineers -IEEE-: IEEE 8th International Conference on E-Science 2012: Chicago, Illinois, 8 - 12 October 2012. Piscataway: IEEE, 2012, 8 pp.
info:doi/10.1109/eScience.2012.6404479

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Holl, S.; Zimmermann, O.; Demuth, B.; Schuller, B.; Hofmann-Apitius, M.:
Secure multi-level parallel execution of scientific workflows on HPC grid resources by combining taverna and UNICORE services. (UNICORE Summit <8, 2012, Dresden>)
Huber, V.: UNICORE Summit 2012. Proceedings: 30 - 31 May 2012, Dresden, Germany. Jülich: Forschungszentrum Jülich, 2012. (Schriften des Forschungszentrums Jülich, IAS Series 15), pp. 27-34

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Juan Ferrer, A.; Hernández, F.; Tordsson, J.; Elmroth, E.; Ali-Eldin, A.; Zsigri, C.; Sirvent, R.; Guitart, J.; Badia, R.M.; Djemame, K.; Ziegler, W.; Dimitrakos, T.; Nair, S.K.; Kousiouris, G.; Konstanteli, K.; Varvarigou, T.; Hudzia, B.; Kipp, A.; Wesner, S.; Corrales, M.; Forgo, N.; Sharif, T.; Sheridan, C.:
OPTIMIS: A holistic approach to cloud service provisioning
Future generation computer systems : FGCS, Vol.28 (2012), No.1, pp.66-77
info:doi/10.1016/j.future.2011.05.022

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Klinger, R.; Senger, P.; Madan, S.; Jacovi, M.:
Online communities support policy-making: The need for data analysis. (International Conference on Electronic Participation (ePart) <4, 2012, Kristiansand>)
Tambouris, E.: Electronic participation. 4th IFIP WG 8.5 international conference, ePart 2012: Kristiansand, Norway, September 3 - 5, 2012. Proceedings. Berlin: Springer, 2012. (Lecture Notes in Computer Science 7444), pp. 132-143
info:doi/10.1007/978-3-642-33250-0_12

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Rasheed, Hassan; Rumpl, Angela; Wäldrich, Oliver; Ziegler, Wolfgang:
A standards-based approach for negotiating service QoS with cloud infrastructure providers. (eChallenges Conference <22, 2012, Lisbon>)
Cunningham, P.: eChallenges e-2012. Conference Proceedings. CD-ROM: 17-19 October 2012, Lisbon, Portugal. Dublin: IIMC, 2012, 9 pp.
urn:nbn:de:0011-n-2255882
Volltext

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Sahadevan, S.; Hofmann-Apitius, M.; Schellander, K.; Tesfaye, D.; Fluck, J.; Friedrich, C.M.:
Text mining in livestock animal science: Introducing the potential of text mining to animal sciences
Journal of animal science, Vol.90 (2012), No.10, pp.3666-3676
info:doi/10.2527/jas.2011-4841

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Temelso B.; Morrell, T.E.; Shields, R.M.; Allodi, M.A.; Wood, E. K.; Kirschner, K.N.; Castonguay, T.C.; Archer, K.A.; Shields, G.C.:
Quantum mechanical study of sulfuric acid hydration: Atmospheric implications
Journal of physical chemistry. A, Vol.116 (2012), No.9, pp.2209-2224
info:doi/10.1021/jp2119026

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Tordsson, Johan; Djemame, Karim; Espling, Daniel; Katsaros, Gregory; Ziegler, Wolfgang; Wäldrich, Oliver; Konstanteli, Kleopatra; Sajjad, Ali; Rajarajan, Muttukrishnan; Gallizo, Georgina; Nair, Srijith:
Towards holistic cloud management
Petcu, D.: European research activities in cloud computing. Newcastle: Cambridge Scholars Publishing, 2012, pp. 122-150

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Wolf, A.; Baumann, S.; Arndt, H.D.; Kirschner, K.N.:
Influence of thiostrepton binding on the ribosomal GTPase associated region characterized by molecular dynamics simulation
Bioorganic & medicinal chemistry, Vol.20 (2012), No.24, pp.7194-7205
info:doi/10.1016/j.bmc.2012.09.025

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Younesi, Erfan; Toldo, Luca; Müller, Bernd; Friedrich, Christoph M.; Novac, Natalia; Scheer, Alexander; Hofmann-Apitius, Martin; Fluck, Juliane:
Mining biomarker information in biomedical literature
BMC medical informatics and decision making. Online journal, Vol.12 (2012), Art. 148, 13 pp.
urn:nbn:de:0011-n-2281049
info:doi/10.1186/1472-6947-12-148
Volltext

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Ziegler, Wolfgang:
SLAs for energy-efficient data centres: The standards-based approach of the OPTIMIS project. (International Workshop on Energy-Efficient Data Centers (E2DC) <1, 2012, Madrid>)
Huusko, J.: Energy Efficient Data Centers: First International Workshop, E2DC 2012, Madrid, Spain, Mai 8, 2012, Revised Selected Papers. Berlin: Springer, 2012. (Lecture Notes in Computer Science 7396), pp. 37-46
info:doi/10.1007/978-3-642-33645-4_4

Armstrong, Django; Djemame, Karim; Nair, Srijith; Tordsson, Johan; Ziegler, Wolfgang:
Towards a contextualization solution for cloud platform services. (International Conference on Cloud Computing Technology and Science (CloudCom) <3, 2011, Athens>)
Institute of Electrical and Electronics Engineers -IEEE-: Third IEEE International Conference on Cloud Computing Technology and Science, CloudCom 2011: Athens, Greece, Nov 29 - Dec 1, 2011. New York, NY: IEEE, 2011, pp. 328-331

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Aslam, M.A.S.; Mahmood, S.-U.; Shahid, M.; Saeed, A.; Iqbal, J.:
Synthesis, biological assay in vitro and molecular docking studies of new Schiff base derivatives as potential urease inhibitors
European journal of medicinal chemistry, Vol.46 (2011), No.11, pp.5473-5479
info:doi/10.1016/j.ejmech.2011.09.009

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Badia, R.M.; Corrales, M.; Dimitrakos, T.; Djemame, K.; Elmroth, E.; Juan Ferrer, A.; Forgo, N.; Guitart, J.; Hernández, F.; Hudzia, B.; Kipp, A.; Konstanteli, K.; Kousiouris, G.; Nair, S.K.; Sharif, T.; Sheridan, C.; Sirvent, R.; Tordsson, J.; Varvarigou, T.; Wesner, S.; Ziegler, W.; Zsigri, C.:
Demonstration of the OPTIMIS toolkit for cloud service provisioning. (European Conference ServiceWave <4, 2011, Poznan>)
Abramowicz, W.: Towards a service-based internet. 4th European conference, ServiceWave 2011: Poznan, Poland, October 26 - 28, 2011; Proceedings. Berlin: Springer, 2011. (Lecture Notes in Computer Science 6994), pp. 331-333
info:doi/10.1007/978-3-642-24755-2_40

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Barnitzke, Benno; Ziegler, Wolfgang; Vafiadis, George; Nair, Srijith; Kousiouris, George; Corrales, Marcelo; Wäldrich, Oliver; Forgó, Nikolaus; Varvarigou, Theodora:
Legal restraints and security requirements on personal data and their technical implementation in clouds. (eChallenges Conference <2011, Florence>)
Cunningham, P.: eChallenges e-2011. Proceedings. CD-ROM: Conference & Exhibition, 26-28 October 2011 Florence, Italy. Dublin: IIMC, 2011

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Birkenheuer, G.; Brinkmann, A.; Högqvist, M.; Papaspyrou, A.; Schott, B.; Sommerfeld, D.; Ziegler, W.:
Infrastructure federation through virtualized delegation of resources and services: DGSI: Adding interoperability to DCI meta schedulers
Journal of grid computing, Vol.9 (2011), No.3, pp.355-377
info:doi/10.1007/s10723-011-9192-1

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Cacciari, C.; Mallmann, D.; Zsigri, C.; D'Andria, F.; Hagemeier, B.; García Peréz, D.; Rumpl, A.; Ziegler, W.; Gozalo, M.; Martrat, J.:
Software licenses as mobile objects in distributed computing environments. (Parallel Processing Workshops <2010, Ischia>)
Guarracino, M.R.: Euro-Par 2010 Parallel Processing Workshops: HeteroPAR, HPCC, HiBB, CoreGrid, UCHPC, HPCF, PROPER, CCPI, VHPC; Ischia, Italy, August 31 - September 3, 2010; revised selected papers. Heidelberg: Springer, 2011. (Lecture Notes in Computer Science 6586), pp. 279-286
info:doi/10.1007/978-3-642-21878-1_35

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Djemame, K.; Lawrence, A.; Wäldrich, O.; Ziegler, W.; Zsigri, C.:
Using service level agreements for optimising cloud infrastructure. (International Conference ServiceWave <2010, Ghent>)
Cezon, M.: Towards a service-based internet: ServiceWave 2010 workshops, international workshops OCS, EMSOA, SMART, and EDBPM 2010, Ghent, Belgium, December 13 - 15, 2010; revised selected papers. Berlin: Springer, 2011. (Lecture Notes in Computer Science 6569), pp. 38-49
info:doi/10.1007/978-3-642-22760-8_4

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Gurulingappa, Harsha; Fluck, Juliane; Hofmann-Apitius, Martin; Toldo, Luca:
Identification of adverse drug event assertive sentences in medical case reports. (International Workshop on Knowledge Discovery in Health Care and Medicine (KDHCM) <1, 2011, Athen>)
Rangwala, H.: The first International Workshop on Knowledge Discovery in Health Care and Medicine, KDHCM'11. Online prodeedings: September 9, 2011, Athens, Greece. Athen, 2011, 12 pp.

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Gurulingappa, Harsha; Müller, Bernd; Hofmann-Apitius, Martin; Fluck, Juliane:
Information retrieval framework for technology survey in biomedical and chemistry literature. (Text REtrieval Conference (TREC) <20, 2011, Gaithersburg/Md.>)
Voorhees, E.M.: The Twentieth Text REtrieval Conference, TREC 2011. Proceedings: November 2011, Gaithersburg, Maryland, USA. Gaithersburg, MD: NIST, 2011. (NIST special publication 500-295), 4 pp.

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Gurulingappa, Harsha; Müller, Bernd; Hofmann-Apitius, Martin; Fluck, Juliane:
A semantic platform for information retrieval from e-health records. (Text REtrieval Conference (TREC) <20, 2011, Gaithersburg/Md.>)
Voorhees, E.M.: The Twentieth Text REtrieval Conference, TREC 2011. Proceedings: November 2011, Gaithersburg, Maryland, USA. Gaithersburg, MD: NIST, 2011. (NIST special publication 500-295), 9 pp.

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Holl, S.; Zimmermann, O.; Hofmann-Apitius, M.:
A UNICORE plugin for HPC-enabled scientific workflows in Taverna 2.2. (World Congress on Services (SERVICES) <7, 2011, Washington/DC>)
Institute of Electrical and Electronics Engineers -IEEE-: 2011 IEEE World Congress on Services, SERVICES 2011. Proceedings: Washington, DC, USA, 4 - 9 July 2011. Piscataway, NJ: IEEE, 2011, pp. 220-223
info:doi/10.1109/SERVICES.2011.46

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Ivchenko, O.; Younesi, E.; Shahid, M.; Wolf, A.; Müller, B.; Hofmann-Apitius, M.:
PLIO: An ontology for formal description of protein-ligand interactions
Bioinformatics, Vol.27 (2011), No.12, pp.1684-1690
info:doi/10.1093/bioinformatics/btr256

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Jonker, H.R.A.; Baumann, S.; Wolf, A.; Schoof, S.; Hiller, F.; Schulte, K.W.; Kirschner, K.N.; Schwalbe, H.; Arndt, H.-D.:
NMR structures of thiostrepton derivatives for characterization of the ribosomal binding site
Angewandte Chemie. International edition, Vol.50 (2011), No.14, pp.3308-3312
info:doi/10.1002/anie.201003582

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Klinger, R.:
Automatically Selected Skip Edges in Conditional Random Fields for Named Entity Recognition. (Workshop on Biomedical Natural Language Procession (BiomedNLP) <2011, Hissar/Bulgaria>)
Savova, G.: Proceedings of the Workshop on Biomedical Natural Language Processing, BiomedNLP 2011: 15 September, 2011, Hissar, Bulgaria : held in conjunction with the 8th International Conference Recent Advances in Natural Language Processing, RANLP 2011. Shoumen: INCOMA, 2011, pp. 580-585

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Klinger, Roman:
Automatically Selected Skip Edges in Conditional Random Fields for Named Entity Recognition. (International Conference "Recent Advances in Natural Language Processing" (RANLP) <2011, Hissar/Bulgaria>)
Angelova, G.: Recent Advances in Natural Language Processing, RANLP 2011: 12-14 September, 2011, Hissar, Bulgaria. Hissar, Bulgaria, 2011, pp. 580-585

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Lupu, Mihai; Jiashu, Zhao; Huang, Jimmy; Gurulingappa, Harsha; Fluck, Juliane; Zimmermann, Marc; Filippov, Igor; Tait, John:
Overview of the TREC 2011 Chemical IR Track. (Text REtrieval Conference (TREC) <20, 2011, Gaithersburg/Md.>)
Voorhees, E.M.: The Twentieth Text REtrieval Conference, TREC 2011. Proceedings: November 2011, Gaithersburg, Maryland, USA. Gaithersburg, MD: NIST, 2011. (NIST special publication 500-295), 11 pp.

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Ngo, Canh; Laat, Cees de; Demchenko, Yuri; Rong, Chunmin; Wlodarczyk, Tomasz Wiktor; Ziegler, Wolfgang:
Security infrastructure for on-demand provisioned cloud infrastructure services. (International Conference on Cloud Computing Technology and Science (CloudCom) <3, 2011, Athens>)
Institute of Electrical and Electronics Engineers -IEEE-: Third IEEE International Conference on Cloud Computing Technology and Science, CloudCom 2011: Athens, Greece, Nov 29 - Dec 1, 2011. New York, NY: IEEE, 2011, pp. 255-263
info:doi/10.1109/CloudCom.2011.42

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Randrianarivony, M.:
Adaptive discontinuous Galerkin B-splines on parametric geometries. (International Conference on Computational Science and Its Applications (ICCSA) <11, 2011, Santander>)
Murgante, B.: Computational science and its applications - ICCSA 2011. Proceedings Pt.4: International conference, Santander, Spain, June 20-23, 2011. Berlin: Springer, 2011. (Lecture Notes in Computer Science 6785), pp. 59-74
info:doi/10.1007/978-3-642-21898-9_6

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Randrianarivony, M.:
On transfinite interpolations with respect to convex domains
Computer aided geometric design : CAGD, Vol.28 (2011), No.2, pp.135-149
info:doi/10.1016/j.cagd.2010.10.003

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Thomas, P.; Solt, I.; Klinger, R.; Leser, U.:
Learning Protein Protein Interaction Extraction using Distant Supervision. (Workshop on Robust Unsupervised and Semisupervised Methods in Natural Language Processing (ROBUS) <2011, Hissar/Bulgaria>)
Biemann, C.: Proceedings of Workshop on Robust Unsupervised and Semisupervised Methods in Natural Language Processing, ROBUS 2011: At RANLP 2011, 15 September, 2011, Hissar, Bulgaria. Shoumen: INCOMA, 2011, pp. 34-41

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Thomas, P.E.; Klinger, R.; Furlong, L.I.; Hofmann-Apitius, M.; Friedrich, C.M.:
Challenges in the association of human single nucleotide polymorphism mentions with unique database identifiers
BMC bioinformatics. Online journal, Vol.12 (2011), Suppl.4, Art. S4
info:doi/10.1186/1471-2105-12-S4-S4

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Zimmermann, M.:
Chemical structure reconstruction with chemoCR. (Text REtrieval Conference (TREC) <20, 2011, Gaithersburg/Md.>)
Voorhees, E.M.: The Twentieth Text REtrieval Conference, TREC 2011. Proceedings: November 2011, Gaithersburg, Maryland, USA. Gaithersburg, MD: NIST, 2011. (NIST special publication 500-295)

Azam, N.; Ghanem, M.; Kalaitzopoulos, D.; Wolf, A.; Kasam, V.; Wang, Y.; Hofmann-Apitius, M.:
DockFlow: Achieving interoperability of protein docking tools across heterogeneous grid middleware
International journal of ad hoc and ubiquitous computing : IJAHUC, Vol.6 (2010), No.4, pp.235-251
info:doi/10.1504/IJAHUC.2010.035535

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Battré, D.; Hovestadt, M.; Wäldrich, O.:
Lessons learned from implementing WS-agreement. (Workshop on Service Level Agreements in Grids <2, 2009, Banff>)
Wieder, P. et al.: Grids and service-oriented architectures for service level agreements: This book contains the proceedings of the 2nd Workshop on Service Level Agreements in Grids, which was held in conjunction with the IEEE GRID 2009 Conference on October 13, 2009, and the proceedings of the Dagstuhl seminar Service Level Agreements in Grids organized in March 2009. Berlin: Springer US, 2010. (CoreGrid series 13), pp. 23-34
info:doi/10.1007/978-1-4419-7320-7_3

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Battré, D.; Brazier, F.M.; Clark, K.P.; Oey, M.; Papaspyrou, A.; Wäldrich, O.; Wieder, P.; Ziegler, W.:
A proposal for WS-agreement negotiation. (International Conference on Grid Computing (Grid) <11, 2010, Brussels>)
Association for Computing Machinery -ACM-: 11th IEEE/ACM International Conference on Grid Computing 2010. Proceedings: 25-29 October 2010 in Brussels, Belgium. New York, NY: IEEE, 2010, pp. 233-241
info:doi/10.1109/GRID.2010.5697976

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Benkner, S.; Arbona, A.; Berti, G.; Chiarini, A.; Dunlop, R.; Engelbrecht, G.; Frangi, A.F.; Friedrich, C.M.; Hanser, S.; Hasselmeyer, P.; Hose, R.D.; Iavindrasana, J.; Köhler, M.; Lo Iacono, L.; Lonsdale, G.; Meyer, R.; Moore, B.; Rajasekaran, H.; Summers, P.E.; Wöhrer, A.; Wood, S.:
@neurIST: Infrastructure for advanced disease management through integration of heterogeneous data, computing, and complex processing services
IEEE transactions on information technology in biomedicine, Vol.14 (2010), No.6, pp.1365-1377
info:doi/10.1109/TITB.2010.2049268

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Birkenheuer, G.; Carlson, A.; Fölling, A.; Högqvist, M.; Hoheisel, A.; Papaspyrou, A.; Rieger, K.; Schott, B.; Ziegler, W.:
Connecting communities on the meta-scheduling level: The DGSI approach. (Cracow Grid Workshop (CGW) <2009, Krakow>)
Bubak, M.: Cracow Grid Workshop 2009. Proceedings: October 12 - 14, 2009, Cracow, Poland. Krakow: Academic Computer Centre CYFRONET, 2010, pp. 96-103

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Cacciari, C.; D'Andria, F.; Hagemeier, B.; Mallmann, D.; Martrat, J.; García Peréz, D.; Rumpl, A.; Ziegler, W.; Zsigri, C.:
elasticLM - Software license management for distributed computing infrastructures
ERCIM News, (2010), No.83, pp.43

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Cacciari, C.; D'Andria, F.; Gozalo, M.; Hagemeier, B.; Mallmann, D.; Martrat, J.; García Peréz, D.; Rumpl, A.; Ziegler, W.; Zsigri, C.:
elasticLM: A novel approach for software licensing in distributed computing infrastructures. (International Conference on Cloud Computing Technology and Science (CloudCom) <2, 2010, Indianapolis/Ind.>)
Qiu, J.: IEEE 2nd International Conference on Cloud Computing Technology and Science, CloudCom 2010: 30 November-3 December 2010, Indianapolis, Indiana, USA; proceedings. Los Alamitos, Calif.: IEEE Computer Society Press, 2010, pp. 67-74
info:doi/10.1109/CloudCom.2010.19

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Cacciari, C.; Mallmann, D.; Zsigri, C.; D'Andria, F.; Hagemeier, B.; Rumpl, A.; Ziegler, W.; Martrat, J.:
SLA-based management of software licenses as web service resources in distributed environments. (International Workshop on Grid Economics and Business Models (GECON) <7, 2010, Ischia>)
Altmann, J.: Economics of grids, clouds, systems, and services. 7th international workshop, GECON 2010: Ischia, Italy, August 31, 2010; Proceedings. Berlin: Springer, 2010. (Lecture Notes in Computer Science 6296), pp. 78-92
info:doi/10.1007/978-3-642-15681-6_6

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Cai, Y.; He, Z.; Shi, X.; Kong, X.; Gu, L.; Xie, L.:
A novel sequence-based method of predicting protein DNA-binding residues, using a machine learning approach
Molecules and cells : MaC, Vol.30 (2010), No.2, pp.99-105
info:doi/10.1007/s10059-010-0093-0

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Friedrich, C.M.; Ebeling, C.; Manset, D.:
Ceoss-project uptake of biomedical text mining results for candidate gene searchers
ERCIM News, (2010), No.82, pp.45-46

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Friedrich, C.M.; et al.:
Genome-wide association study of intracranial aneurysm identifies three new risk loci
Nature Genetics, Vol.42 (2010), No.5, pp.420-425
info:doi/10.1038/ng.563

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Gurulingappa, H.; Hofmann-Apitius, M.; Fluck, J.:
Concept identification and assertion classification in patient health records. (Workshop Challenges in Natural Language Processing for Clinical Data <4, 2010, Washington/DC>)
Fourth i2b2/VA Shared-Task and Workshop Challenges in Natural Language Processing for Clinical Data 2010: Washington, DC, November 12-13, 2010. Albany/NY: State University of New York, 2010, 5 pp.
urn:nbn:de:0011-n-1518436
Volltext

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Gurulingappa, H.; Klinger, R.; Hofmann-Apitius, M.; Fluck, J.:
An empirical evaluation of resources for the identification of diseases and adverse effects in biomedical literature. (Workshop on Building and Evaluating Resources for Biomedical Text Mining (BioTxtM) <2, 2010, Valletta>)
Ananiadou, S.: 2nd Workshop on Building and Evaluating Resources for Biomedical Text Mining, BioTxtM 2010: Tuesday, 18th March 2010 Valletta, Malta, LREC 2010. Valletta, 2010, pp. 15-22

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Gurulingappa, H.; Müller, B.; Klinger, R.; Mevissen, H.-T.; Hofmann-Apitius, M.; Friedrich, C.M.; Fluck, J.:
Prior art search in chemistry patents based on semantic concepts and co-citation analysis. (Text REtrieval Conference (TREC) <19, 2010, Gaithersburg/Md.>)
National Institute of Standards and Technology -NIST-: Nineteenth Text REtrieval Conference, TREC 2010. Proceedings: Gaithersburg, Maryland, USA, November 16-19, 2010. Washington, DC: NIST, 2010, 9 pp.

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Hagemeier, B.; Mallmann, D.; Ziegler, W.:
Securing software licenses in a location independent manner. (Cracow Grid Workshop (CGW) <2009, Krakow>)
Bubak, M.: Cracow Grid Workshop 2009. Proceedings: October 12 - 14, 2009, Cracow, Poland. Krakow: Academic Computer Centre CYFRONET, 2010, pp. 112-119

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Klatt, T.; Rasheed, H.; Shahid, M.; Wäldrich, O.; Ziegler, W.:
SCAI-VHTS - a fully automated virtual high throughput screening framework
ERCIM News, (2010), No.82, pp.23-24

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Kuebert, R.; Tenschert, A.; Wäldrich, O.; Ziegler, W.; Battre, D.:
A service level agreement layer for the D-Grid infrastructure. (eChallenges Conference <2010, Warsaw>)
Cunningham, M.: eChallenges 2010. CD-ROM: e-2010, 27-29 October 2010, Warsaw, Poland. Dublin: IIMC, 2010

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Lu, J.; Zhu, Y.B.; Li, Y.J.; Lu, W.C.; Hu, L.L.; Niu, B.; Qing, P.F.; Gu, L.:
Prediction of interaction between enzymes and small molecules in metabolic pathways through integrating multiple classifiers
Protein and peptide letters, Vol.17 (2010), No.12, pp.1536-1541

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Müller, B.; Klinger, R.; Gurulingappa, H.; Mevissen, H.-T.; Hofmann-Apitius, M.; Fluck, J.; Friedrich, C.M.:
Abstracts versus full texts and patents: A quantitative analysis of biomedical entities. (Information Retrieval Facility Conference (IRFC) <1, 2010, Vienna>)
Cunningham, H.: Advances in multidisciplinary retrieval. First Information Retrieval Facility Conference, IRFC 2010: Vienna, Austria, May 31, 2010; Proceedings. Berlin: Springer, 2010. (Lecture Notes in Computer Science 6107), pp. 152-165
info:doi/10.1007/978-3-642-13084-7_12

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Rana, O.; Ziegler, W.:
Research challenges in managing and using Service Level Agreements. (Workshop on Grids, P2P and Service Computing <2009, Delft>)
Desprez, F.: Grids, P2P and Services Computing: Based on the CoreGrid ERCIM Working Group Workshop on Grids, P2P and Service Computing in Conjunction with EuroPar 2009, August 24th, 2009 in Delft, The Netherlands. New York: Springer Science+Business Meda, 2010. (CoreGrid series 12), pp. 187-200
info:doi/10.1007/978-1-4419-6794-7_15

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Rasheed, H.; Rumpl, A.; Ziegler, W.; Gozalo, M.:
Demonstration of the SmartLM license management technology for distributed computing infrastructures. (European Conference ServiceWave <3, 2010, Ghent>)
Nitto, E. di: Towards a service-based internet. Third European conference, ServiceWave 2010: Ghent, Belgium, December 13-15, 2010 ; proceedings. Berlin: Springer, 2010. (Lecture Notes in Computer Science 6481), pp. 190-192
info:doi/10.1007/978-3-642-17694-4_18

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Rasheed, H.; Rumpl, A.; Ziegler, W.; Hagemeier, B.; Mallmann, D.; Eickenbusch, H.:
Running license protected applications with SmartLM and UNICORE. (UNICORE Summit <6, 2010, Jülich>)
Streit, A. et al.: UNICORE Summit 2010, Proceedings: 18 – 19 May 2010, Jülich. (Schriften des Forschungszentrums Jülich, IAS Series), pp. 69-74

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Risselada, R.; Lingsma, H.F.; Bauer-Mehre, A.; Friedrich, C.M.; Molyneux, A.J.; Kerr, R.S.; Yarnold, J.; Sneade, M.; Steyerberg, E.W.; Sturkenboom, M.C.:
Prediction of 60 day case-fatality after aneurysmal subarachnoid haemorrhage: Results from the International Subarachnoid Aneurysm Trial (ISAT)
European journal of epidemiology, Vol.25 (2010), No.4, pp.261-266
urn:nbn:de:0011-n-1187102
info:doi/10.1007/s10654-010-9432-x
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Rumpl, A.; Wäldrich, O.; Ziegler, W.:
Extending WS-AGREEMENT with multi-round negotiation capability. (Workshop on Service Level Agreements in Grids <2, 2009, Banff>)
Wieder, P. et al.: Grids and service-oriented architectures for service level agreements: This book contains the proceedings of the 2nd Workshop on Service Level Agreements in Grids, which was held in conjunction with the IEEE GRID 2009 Conference on October 13, 2009, and the proceedings of the Dagstuhl seminar Service Level Agreements in Grids organized in March 2009. Berlin: Springer US, 2010. (CoreGrid series 13), pp. 89-103
info:doi/10.1007/978-1-4419-7320-7_9

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Shahid, M.; Kasam, V.; Hofmann-Apitius, M.:
An improved weighted-residue profile based method of using protein-ligand interaction information in increasing hits selection from virtual screening: A study on virtual screening of human GPCR A2A receptor antagonists
Molecular informatics, Vol.29 (2010), No.11, pp.781-791
info:doi/10.1002/minf.201000068

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Streit, A.; Bala, P.; Beck-Ratzka, A.; Benedyczak, K.; Bergmann, S.; Breu, R.; Daivandy, J.M.; Demuth, B.; Eifer, A.; Giesler, A.; Hagemeier, B.; Holl, S.; Huber, V.; Lamla, N.; Mallmann, D.; Memon, A.S.; Memon, M.S.; Rambadt, M.; Riedel, M.; Romberg, M.; Schuller, B.; Schlauch, T.; Schreiber, A.; Soddemann, T.; Ziegler, W.:
UNICORE 6 - recent and future advancements
Annales des telecommunications, Vol.65 (2010), No.11-12, pp.757-762
info:doi/10.1007/s12243-010-0195-x

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Wolf, A.; Shahid, M.; Kasam, V.; Ziegler, W.; Hofmann-Apitius, M.:
In silico drug discovery approaches on grid computing infrastructures
Current clinical pharmacology, Vol.5 (2010), No.1, pp.37-46
info:doi/10.2174/157488410790410560

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Yilmaz, S.; Bijlenga, P.; Rashid, M.; Collot-Teixeira, S.; Brocheton, J.; Proust, C.; Rotival, M.; Risselada, R.; Summers, P.; Blasco, J.; Singh, J.; Waterworth, A.; Ebeling, C.; Friedrich, C.M.; Frangi, A.F.; Macho, J.J.; Byrne, J.; Sturkenboom, M.C.; Schaller, K.; Cambien, F.; Gunel, M.; McGregor, J.L.:
Gene expression signature in peripheral blood cells detects intracranial aneurysm
Neurosurgery, Vol.67 (2010), No.2, pp.540
info:doi/10.1227/01.NEU.0000386985.32689.26

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Yuan, Y.; Shi, X.; Li, X.; Lu, W.; Cai, Y.; Gu, L.; Liu, L.; Li, M.; Kong, X.; Xing, M.:
Prediction of interactiveness of proteins and nucleic acids based on feature selections
Molecular Diversity, Vol.14 (2010), No.4, pp.627-633
info:doi/10.1007/s11030-009-9198-9

Degliesposti, G.; Kasam, V.; Da Costa, A.; Kang, H.-K.; Kim, N.; Kim, D.-W.; Breton, V.; Kim, D.; Rastelli, G.:
Design and discovery of plasmepsin II inhibitors using an automated workflow on large-scale grids
ChemMedChem, Vol.4 (2009), No.7, pp.1164-1173
info:doi/10.1002/cmdc.200900111

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Friedrich, C.M.; Gündel, M.:
Combining text mining and microarray analysis. (R User Conference (useR!) <2009, Rennes>)
R Foundation for Statistical Computing: UseR!, the R User Conference 2009: July 8-10, Agrocampus-Ouest, Rennes, France. Rennes, 2009, pp. 63
urn:nbn:de:0011-n-1021426
Volltext

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Friedrich, C.M.; Klinger, R.:
rSMILE, an interface to the Bayesian network package GeNIe/SMILE. (R User Conference (useR!) <2009, Rennes>)
R Foundation for Statistical Computing: UseR!, the R User Conference 2009: July 8-10, Agrocampus-Ouest, Rennes, France. Rennes, 2009, pp. 104
urn:nbn:de:0011-n-1035369
Volltext

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Friedrich, C.M.:
The @neuLink approach to literature. (European Society of Minimally Invasive Neurological Therapy (ESMINT Teaching Course) <2, 2009, Barcelona>)
European Society of Minimally Invasive Neurological Therapy -ESMINT-: ESMINT Teaching Course Journal 2009: 2nd Teaching Course of the European Society of Minimally Invasive Neurological Therapy, Barcelona, Spain, December 13-18, 2009. Tutorial. Barcelona: ESMINT, 2009, pp. 62-67

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Groeper, R.; Grimm, C.; Makedanz, S.; Pfeiffenberger, H.; Ziegler, W.; Gietz, P.; Schiffers, M.:
A concept for attribute-based authorization on D-Grid resources
Future generation computer systems : FGCS, Vol.25 (2009), No.3, pp.275-280
info:doi/10.1016/j.future.2008.05.008

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Guitart, J.; Mac¡as, M.; Rana, O.; Wieder, P.; Yahyapour, R.; Ziegler, W.:
SLA-based resource management and allocation
Buyya, R.: Market-oriented grid and utility computing. Hoboken/N.J.: Wiley & Sons, 2009, pp. 261-284

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Gurulingappa, H.; Kolarik, C.; Hofmann-Apitius, M.; Fluck, J.:
Concept-based semi-automatic classification of drugs
Journal of chemical information and modeling, Vol.49 (2009), No.8, pp.1986-1992
info:doi/10.1021/ci9000844

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Gurulingappa, H.; Müller, B.; Klinger, R.; Mevissen, H.-T.; Hofmann-Apitius, M.; Fluck, J.; Friedrich, C.M.:
Patent retrieval in chemistry based on semantically tagged named entities. (Text REtrieval Conference (TREC '09) <18, 2009, Gaithersburg/Md.>)
National Institute of Standards and Technology -NIST-: Eighteenth Text REtrieval Conference, TREC 2009. Proceedings: November 16-17, 2009, Gaithersburg, Maryland. Washington, DC: NIST, 2009, 9 pp.
urn:nbn:de:0011-n-1186068
Volltext

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Hofmann-Apitius, M.; Younesi, E.; Kasam, V.:
Direct use of information extraction from scientific text for modeling and simulation in the life sciences. (International Bielefeld Conference <9, 2009, Bielefeld>)
Höppner, M.: "Upgrading the eLibrary: Enhanced information services driven by technology and economics": Proceedings of the 9th International Bielefeld Conference, Bielefeld, Germany, 3 - 5 February 2009. Bingley: Emerald, 2009. (Library hi tech 27.2009, Nr.4), pp. 505-519
info:doi/10.1108/07378830911007637

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Holi, S.; Riedel, M.; Demuth, B.; Romberg, M.; Streit, A.; Kasam, V.:
Life science application support in an interoperable E-Science environment. (IEEE International Symposium on Computer-Based Medical Systems (CBMS) <22, 2009, Albuquerque>)
IEEE Computer Society, Technical Committee on Computational Medicine: 22nd IEEE International Symposium on Computer-Based Medical Systems, CBMS 2009. Piscataway: IEEE, 2009, Art. 5255322
info:doi/10.1109/CBMS.2009.5255322

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Joosten, R.P.; Salzemann, J.; Bloch, V.; Stockinger, H.; Berglund, A.-C.; Blanchet, C.; Bongcam-Rudloff, E.; Combet, C.; Da Costa, A.L.; Deleage, G.; Diarena, M.; Fabbretti, R.; Fettahi, G.; Flegel, V.; Gisel, A.; Kasam, V.; Kervinen, T.; Korpelainen, E.; Mattila, K.; Pagni, M.; Reichstadt, M.; Breton, V.; Tickle, I.J.; Vriend, G.:
PDB REDO: Automated re-refinement of X-ray structure models in the PDB
Journal of Applied Crystallography, Vol.42 (2009), No.3, pp.376-384
info:doi/10.1107/S0021889809008784

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Joseph, L.C.; Bennett, J.A.; Kirschner, K.N.; Shields, G.C.; Hughes, J.; Lostritto, N.; Jacobson, H.I.; Andersen, T.T.:
Antiestrogenic and anticancer activities of peptides derived from the active site of alpha-fetoprotein
Journal of peptide science, Vol.15 (2009), No.4, pp.319-325
info:doi/10.1002/psc.1119

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Kasam, V.; Salzemann, J.; Botha, M.; Dacosta, A.; Degliesposti, G.; Isea, R.; Kim, D.; Maaß, A.; Kenyon, C.; Rastelli, G.; Hofmann-Apitius, M.; Breton, V.:
WISDOM-II: Screening against multiple targets implicated in malaria using computational grid infrastructures
Malaria journal. Online journal, Vol.8 (2009), Art. 88, 16 pp.
urn:nbn:de:0011-n-1017390
info:doi/10.1186/1475-2875-8-88
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Keller, V.; Rasheed, H.; Wäldrich, O.; Ziegler, W.; Gruber, R.; Sawley, M.-C.; Wieder, P.:
Models and internals of the IANOS resource broker
Computer science, research + development, Vol.23 (2009), No.3-4, pp.259-266
urn:nbn:de:0011-n-970718
info:doi/10.1007/s00450-009-0074-8
Volltext

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Keller, V.; Ziegler, W.:
ÏANOS: How to do more science with less energy
ERCIM News, (2009), No.79, pp.26-27

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Klinger, R.; Pesch, R.; Mevissen, T.; Fluck, J.:
Text mining in full text articles- methodical and representation issues: 3rd International Biocuration Conference, Berlin, 16.-19.4. 2009. (International Biocuration Conference <3, 2009, Berlin>)
Nature precedings. Online preprint server, (2009), 22. April, 1 pp.
urn:nbn:de:0011-n-936860
info:doi/10.1038/npre.2009.3141.1
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Klinger, R.; Friedrich, C.M.:
Feature subset selection in conditional random fields for named entity. (International Conference Recent Advances in Natural Language Processing (RANLP) <2009, Borovets>)
Angelova, G..: Proceedings of the International Conference Recent Advances in Natural Language Processing, RANLP 2009: 14-16 September 2009, Borovets, Bulgaria. Borovets, 2009, pp. 185-191

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Klinger, R.; Friedrich, C.M.:
User's choice of precision and recall in named entity recognition. (International Conference Recent Advances in Natural Language Processing (RANLP) <2009, Borovets>)
Angelova, G..: Proceedings of the International Conference Recent Advances in Natural Language Processing, RANLP 2009: 14-16 September 2009, Borovets, Bulgaria. Borovets, 2009, pp. 192-196

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Kolarik, C.; Klinger, R.; Hofmann-Apitius, M.:
Identification of histone modifications in biomedical text for supporting epigenomic research. (Asia-Pacific Bioinformatics Conference (APBC) <7, 2009, Beijing>)
BMC bioinformatics. Online journal, Vol.10 (2009), Supplement 1, S28
urn:nbn:de:0011-n-906382
info:doi/10.1186/1471-2105-10-S1-S28
Volltext

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Kolarik, C.; Hofmann-Apitius, M.:
Linking chemical and biological information with natural language processing
Banville, D.L.: Chemical information mining: Facilitating literature-based discovery. Boca Raton, Fla.: CRC Press, 2009, pp. 123-150

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Pichot, A.; Wieder, P.; Wäldrich, O.; Ziegler, W.:
Towards dynamic service level agreement negotiation: An approach based on WS-agreement. (International Conference on Web Information Systems and Technologies (WEBIST) <4, 2008, Funchal>)
Cordeiro, J.: Web information systems and technologies: 4th international conference; Revised selected papers / WEBIST 2008, Funchal, Madeira, Portugal, May 4 - 7, 2008. Berlin: Springer, 2009. (Lecture Notes in Business Information Processing 18), pp. 107-119
urn:nbn:de:0011-n-941998
info:doi/10.1007/978-3-642-01344-7 9
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Risselada, R.; Friedrich, C.M.; Ebeling, C.; Klinger, R.; Bauer-Mehren, A.; Pastor, M.; Cruz Villa, M.; Pozo, J.M.; Frangi, A.F.; Hofmann-Apitius, M.:
Workflows for data mining in integrated multi-modal data of intracranial aneurysms using KNIME. (R User Conference (useR!) <2009, Rennes>)
R Foundation for Statistical Computing: UseR!, the R User Conference 2009: July 8-10, Agrocampus-Ouest, Rennes, France. Rennes, 2009, pp. 166
urn:nbn:de:0011-n-1035334
Volltext

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Shahid, M.; Hofmann-Apitius, M.; Wäldrich, O.; Ziegler, W.:
A robust framework for rapid deployment of a virtual screening laboratory. (HealthGrid Conference <7, 2009, Berlin>)
Solomonides, T. et al.: Healthgrid research, innovation and business case: Proceedings of HealthGrid 2009, 29 June - 1 July, Berlin. Amsterdam: IOS Press, 2009. (Studies in health technology and informatics 147), pp. 212-221

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Wolf, A.; Hofmann-Apitius, M.; Ghanem, M.; Azam, N.; Kalaitzopoulos, D.; Yu, K.; Kasam, V.:
DockFlow - a prototypic PharmaGrid for virtual screening integrating four different docking tools. (HealthGrid Conference <7, 2009, Berlin>)
Solomonides, T. et al.: Healthgrid research, innovation and business case: Proceedings of HealthGrid 2009, 29 June - 1 July, Berlin. Amsterdam: IOS Press, 2009. (Studies in health technology and informatics 147), pp. 3-12
info:doi/10.3233/978-1-60750-027-8-3

Akle, S.; Algorri, M.-E.; Zimmermann, M.:
Framework for extracting rotation invariant features for image classification and an application using haar wavelets. (International Conference on Artificial Intelligence, Knowledge Engineering and Data Bases (AIKED) <7, 2008, Cambridge>)
World Scientific and Engineering Academy and Society -WSEAS-: Advances on artificial intelligence, knowledge engineering and data bases: Proceedings of the 7th WSEAS International Conference on Artificial intelligence, knowledge engineering and data bases (AIKED 2008), University of Cambridge, Cambridge, UK, February 20-22, 2008. Montclair/NJ: WSEAS, 2008. (Artificial intelligence series), pp. 89-94

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Breton, V.; Jacq, N.; Kasam, V.; Hofmann-Apitius, M.:
Grid-added value to address malaria
IEEE transactions on information technology in biomedicine, Vol.12 (2008), No.2, pp.173-181
info:doi/10.1109/TITB.2007.895930

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Dunlop, R.; Arbona, T.; Rajasekaran, H.; Lo Iacono, L.; Fingberg, J.; Summers, P.; Benkner, S.; Engelbrecht, S.; Chiarini, A.; Friedrich, C.; Moore, B.; Bijlenga, P.; Iavindrasana, J.; Hose, R.D.; Frangi, A.:
@neurIST - chronic disease management through integration of heterogeneous data and computer-interpretable guideline services. (HealthGrid Conference <6, 2008, Chicago/Ill.>)
Solomonides, T.: Global healthgrid : e-science meets biomedical informatics. Proceedings of HealthGrid 2008. Amsterdam: IOS Press, 2008. (Studies in health technology and informatics 138), pp. 173-177

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Faroughi, A.; Faroughi, R.; Wieder, P.; Ziegler, W.:
Attributes and VOs: Extending the UNICORE authorisation capabilities. (International Workshop on Highly Parallel Processing on a Chip (HPPC) <2007, Rennes>)
Bouge, L. et al.: Parallel Processing - Euro-Par 2007 Workshops: HPPC 2007, UNICORE Summit 2007, and VHPC 2007, Rennes, France, August 28-31, 2007, Revised Selected Paper. Berlin: Springer, 2008. (Lecture Notes in Computer Science 4854), pp. 121-130
urn:nbn:de:0011-n-701220
info:doi/10.1007/978-3-540-78474-6 16
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Friedrich, C.M.; Dach, H.; Gattermayer, T.; Engelbrecht, G.; Benkner, S.; Hofmann-Apitius, M.:
@neuLink: A service-oriented application for biomedical knowledge discovery. (HealthGrid Conference <6, 2008, Chicago/Ill.>)
Solomonides, T.: Global healthgrid : e-science meets biomedical informatics. Proceedings of HealthGrid 2008. Amsterdam: IOS Press, 2008. (Studies in health technology and informatics 138), pp. 165-172

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Friedrich, C.M.; Hofmann-Apitius, M.; Dunlop, R.; Chronakis, I.; Sturkenboom, M.C.; Risselada, R.; Oliva, B.; Sanz, F.:
Initial results on knowledge discovery and decision support for intracranial aneurysms. (International Conference on Health Informatics (HEALTHINF) <1, 2008, Funchal>)
Azevedo, L.: Proceedings of the First International Conference on Health Informatics: Part of BIOSTEC, International Joint Conference on Biomedical Engineering Systems and Technologies. Funchal, Madeira, Portugal, January 28 - 31, 2008. Setúbal: INSTICC Press, 2008. (Proceedings of the first International Conference on Health Informatics 1), pp. 265-272

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Furlong, L.I.; Dach, H.; Hofmann-Apitius, M.; Sanz, F.:
OSIRISv1.2: A named entity recognition system for sequence variants of genes in biomedical literature
BMC bioinformatics. Online journal, Vol.9 (2008), Art. 84
info:doi/10.1186/1471-2105-9-84

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Grimme, C.; Lepping, J.; Papaspyrou, A.; Wieder, P.; Yahyapour, R.; Oleksiak, A.; Wäldrich, O.; Ziegler, W.:
Towards a standards-based grid scheduling architecture. (CoreGRID Integration Workshop (CGIW) <2008, Hersonissos/Crete>)
Gorlatch, S.: Grid computing. Achievements and prospects: Selection of best papers presented at the CoreGRID Integration Workshop 2008 (CGIW'2008), which took place on 2 - 4 April 2008 in Hersonissos, Crete, Greece. New York/NY: Springer, 2008. (CoreGrid series 9), pp. 147-158
urn:nbn:de:0011-n-941976
info:doi/10.1007/978-0-387-09457-1 13
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Hofmann-Apitius, M.; Fluck, J.; Furlong, L.I.; Fornes, O.; Kolarik, C.; Hanser, S.; Boeker, M.; Schulz, S.; Sanz, F.; Klinger, R.; Mevissen, T.; Gattermayer, T.; Oliva, B.; Friedrich, C.M.:
Knowledge environments representing molecular entities for the virtual physiological human
Philosophical Transactions of the Royal Society of London. Series A, Vol.366 (2008), No.1878, pp.3091-3110
info:doi/10.1098/rsta.2008.0099

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Iavindrasana, J.; Lo Iacono, L.; Müller, H.; Periz, I.; Summers, P.; Wright, J.; Friedrich, C.M.; Dach, H.; Gattermayer, T.; Engelbrecht, G.; Benkner, S.; Hofmann-Apitius, M.; Dunlop, R.; Arbona, A.; Rajasekaran, H.; Fingberg, J.; Chiarini, A.; Moore, B.; Bijlenga, P.; Hose, R.D.; Frangi, A.:
The @neurIST project. (HealthGrid Conference <6, 2008, Chicago/Ill.>)
Solomonides, T.: Global healthgrid : e-science meets biomedical informatics. Proceedings of HealthGrid 2008. Amsterdam: IOS Press, 2008. (Studies in health technology and informatics 138), pp. 161-164

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Jacq, N.; Salzemann, J.; Legré, Y.; Medernach, E.; Montagnat, J.; Maaß, A.; Reichstadt, M.; Schwichtenberg, H.; Sridhar, M.; Kasam, V.; Zimmermann, M.; Hofmann, M.; Breton, V.:
Grid-enabled virtual screening against malaria
Journal of grid computing, Vol.6 (2008), No.1, pp.29-43
info:doi/10.1007/s10723-007-9085-5

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Klinger, R.; Kolarik, C.; Fluck, J.; Hofmann-Apitius, M.; Friedrich, C.M.:
Detection of IUPAC and IUPAC-like chemical names
Bioinformatics, Vol.24 (2008), No.13, pp.i268-i276
info:doi/10.1093/bioinformatics/btn181

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Kolarik, C.; Klinger, R.; Friedrich, C.M.; Hofmann-Apitius, M.; Fluck, J.:
Chemical names: Terminological resources and corpora annotation. (International Conference on Language Resources and Evaluation (LREC) <6, 2008, Marrakech>)
European Language Resources Association -ELRA-, Paris: LREC 2008, Sixth International Language Resources and Evaluation. Proceedings. CD-ROM: May 26-June 1, 2008, Marrakech, Marokko. Paris: ELRA, 2008, pp. 51-58

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Li, J.; Wäldrich, O.; Ziegler, W.:
Towards SLA-based software licenses. (CoreGRID Symposium <2008, Las Palmas>)
Priol, T.: From grids to service and pervasive computing: Based on the 2008 CoreGRID Symposium, held August 25 - 26 in the Canary Islands, Spain. New York/NY: Springer, 2008. (CoreGrid series 10), pp. 139-152
urn:nbn:de:0011-n-941969
info:doi/10.1007/978-0-387-09455-7 10
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Morgan, A.A.; Lu, Z.; Wang, X.; Cohen, A.M.; Fluck, J.; Ruch, P.; Divoli, A.; Fundel, K.; Leaman, R.; Hakenberg, J.; Sun, C.; Liu, H.-h.; Rorres, R.; Krauthammer, M.; Lau, W.W.; Liu, H.; Hsu, C.-N.; Schuemie, M.; Cohen, K.B.; Hirschman, L.:
Overview of BioCreative II gene normalization. (Conference "The BioCreative II - Critical Assessment for Information Extraction in Biology Challenge" <2007, Madrid>)
Genome biology, Vol.9 (2008), Supplement 2, Art. S3, 19 pp.
urn:nbn:de:0011-n-1024605
info:doi/10.1186/gb-2008-9-s2-s3
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Pichot, A.; Wieder, P.; Wäldrich, O.; Ziegler, W.:
Dynamic SLA negotiation based on WS-agreement. (International Conference on Web Information Systems and Technologies (WEBIST) <4, 2008, Funchal>)
Cordeiro, J.: WEBIST 2008, 4th International Conference on Web Information Systems and Technologies. Proceedings: 4 - 7 May, 2008, Funchal, Madeira - Portugal. Setúbal: INSTICC, 2008

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Rajasekaran, H.; Lo Iacono, L.; Hasselmeyer, P.; Fingberg, J.; Summers, P.; Benkner, S.; Engelbrecht, G.; Arbona, A.; Chiarini, A.; Friedrich, C.M.; Hofmann-Apitius, M.; Kumpf, K.; Moore, B.; Bijlenga, P.; Iavindrasana, J.; Mueller, H.; Hose, R.D.; Dunlop, R.; Frangi, A.: 
@neurIST - Towards a system architecture for advanced disease management through integration of heterogeneous data, computing, and complex processing services. (International Symposium on Computer-Based Medical Systems (CBMS) <21, 2008, Jyväskylä>)
Puuronen, S.: Proceedings of the 21st IEEE International Symposium on Computer-Based Medical Systems: June 17 - 19, 2008, Jyväskylä, Finland. Los Alamitos, Calif.: IEEE Computer Society, 2008, pp. 361-366
info:doi/10.1109/CBMS.2008.42

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Rasheed, H.; Gruber, R.; Keller, V.; Ziegler, W.; Wäldrich, O.; Kuonen, P.; Wieder, P.:
IANOS: An intelligent application oriented scheduling framework for an HPCN grid. (CoreGRID Integration Workshop (CGIW) <2008, Hersonissos/Crete>)
Gorlatch, S.: Grid computing. Achievements and prospects: Selection of best papers presented at the CoreGRID Integration Workshop 2008 (CGIW'2008), which took place on 2 - 4 April 2008 in Hersonissos, Crete, Greece. New York/NY: Springer, 2008. (CoreGrid series 9), pp. 237-248
urn:nbn:de:0011-n-941983
info:doi/10.1007/978-0-387-09457-1 20
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Ruau, D.; Kolarik, C.; Mevissen, H.-T.; Müller, E.; Assent, I.; Krieger, R.; Seidl, T.; Hofmann-Apitius, M.; Zenke, M.:
Public microarray repository semantic annotation with ontologies employing text mining and expression profile correlation. (International Society for Computational Biology (Student Council Symposium) <4, 2008, Toronto>)
BMC bioinformatics. Online journal, Vol.9 (2008), Supplement 10, Art. 05
info:doi/10.1186/1471-2105-9-S10-O5

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Scholz, J.; Toska, K.; Luborzewski, A.; Maaß, A.; Schünemann, V.; Haavik, J.; Moser, A.:
Endogenous tetrahydroisoquinolines associated with Parkinson's disease mimic the feedback inhibition of tyrosine hydroxylase by catecholamines
FEBS journal, Vol.275 (2008), No.9, pp.2109-2121
info:doi/10.1111/j.1742-4658.2008.06365.x

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Shahid, M.; Ziegler, W.; Kasam, V.; Zimmermann, M.; Hofmann-Apitius, M.:
Virtual high throughput screening (vHTS) on an optical high speed testbed. (HealthGrid Conference <6, 2008, Chicago/Ill.>)
Solomonides, T.: Global healthgrid : e-science meets biomedical informatics. Proceedings of HealthGrid 2008. Amsterdam: IOS Press, 2008. (Studies in health technology and informatics 138), pp. 125-134

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Smith, L.; Tanabe, L.K.; Johnson nee Ando, R.; Juo, C.-J.; Chung, I.-F.; Hsu, C.-N.; Lin, Y.-S.; Klinger, R.; Friedrich, C.M.; Ganchev, K.; Torii, M.; Liu, H.; Haddow, B.; Struble, C.A.; Povinelli, R.J.; Vlachos, A.; Baumgartner, W.A.; Hunter, L.; Carpenter, B.; Tsai, R.T.; Dai, H.J.; Liu, F.; Chen, Y.; Sun, C.; Katrenko, S.; Adriaans, P.; Blaschke, C.; Torres Perez, R.; Neves, M.; Nakov, P.; Divoli, A.; Mana, M.; Mata-Vazquez, J.; Wilbur, J.:
Overview of BioCreative II gene mention recognition. (Conference "The BioCreative II - Critical Assessment for Information Extraction in Biology Challenge" <2007, Madrid>)
Genome biology, Vol.9 (2008), Supplement 2, 19 pp.
urn:nbn:de:0011-n-941249
info:doi/10.1186/gb-2008-9-s2-s2
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Wieder, P.; Seidel, J.; Wäldrich, O.; Ziegler, W.; Yahyapour, R.:
Using SLA for resource management and scheduling - a survey. (Workshop on Using Service Level Agreements in Grids (Grid) <2007, Austin/Tex.>)
Talia, D. et al.: Grid middleware and services: Challenges and solutions. Berlin: Springer US, 2008. (CoreGrid series 8), pp. 335-347
urn:nbn:de:0011-n-703340
info:doi/10.1007/978-0-387-78446-5 22
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Wieder, P.; Ziegler, W.; Keller, V.:
IANOS - efficient use of HPC grid resources
ERCIM News, (2008), No.74, pp.27-29

Algorri, M.-E.; Zimmermann, M.; Friedrich, C.M.; Akle, S.; Hofmann-Apitius, M.:
Reconstruction of chemical molecules from images. (IEEE Engineering in Medicine and Biology Society (Annual International Conference EMBS) <29, 2007, Lyon>)
IEEE Engineering in Medicine and Biology Society -EMBS-: 29th Annual International Conference of the IEEE Engineering in Medicine and Biology Society, EMBS 2007: August 23-26, 2007, Cité Internationale, Lyon, France, in conjunction with the biennial conference of the Société Française de Génie Biologique et Médical (SFGBM). New York, NY: IEEE, 2007, pp. 4609-4612
info:doi/10.1109/IEMBS.2007.4353366

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Algorri, M.-E.; Zimmermann, M.; Hofmann-Apitius, M.:
Automatic recognition of chemical images. (Mexican International Conference on Current Trends in Computer Science (ENC) <8, 2007, Morelia>)
Farach-Colton, M.: Eighth Mexican International Conference on Current Trends in Computer Science. Proceedings: 24 - 28 September 2007, Morelia, Michoacan, Mexico. Piscataway, NJ: IEEE, 2007, pp. 41-46
info:doi/10.1109/ENC.2007.25

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Arbona, A.; Benkner, S.; Engelbrecht, G.; Fingberg, J.; Hofmann, M.; Kumpf, K.; Lonsdale, G.; Woehrer, A.:
A service-oriented grid infrastructure for biomedical data and compute services
IEEE transactions on nanobioscience, Vol.6 (2007), No.2, pp.136-141
info:doi/10.1109/TNB.2007.897438

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Barz, C.; Eickermann, T.; Pilz, M.; Wäldrich, O.; Westphal, L.; Ziegler, W.:
Co-allocating compute and network resources - bandwidth on demand in the VIOLA testbed. (CoreGRID Symposium <2007, Rennes>)
Priol, T.: Towards next generation Grid. Proceedings of the CoreGRID Symposium 2007: August 27-28, Rennes, France. New York, NY: Springer, 2007, pp. 193-202
urn:nbn:de:0011-n-655736
info:doi/10.1007/978-0-387-72498-0 18
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Biskup, J.; Tsatedem, C.; Wiese, L.:
Secure mediation of join queries by processing ciphertexts. (International Conference on Data Engineering (ICDE) <23, 2007, Istanbul>)
Institute of Electrical and Electronics Engineers -IEEE-: 2007 IEEE 23rd International Conference on Data Engineering. Workshops proceedings. Vol.2: 17 - 20 April, 2007, Istanbul, Turkey. Piscataway, NJ: IEEE, 2007, pp. 715-724
info:doi/10.1109/ICDEW.2007.4401059

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Eickermann, T.; Frings, W.; Wäldrich, O.; Wieder, P.; Ziegler, W.:
Co-allocation of MPI jobs with the VIOLA grid MetaScheduling framework. (German e-Science Conference (GES) <2007, Baden-Baden>)
Helmholtz-Gemeinschaft: German e-Science Conference 2007. Proceedings: 2. - 4. Mai 2007 in Baden-Baden. Baden-Baden, 2007, 10 pp.
urn:nbn:de:0011-n-665101
Volltext

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Figuerola, S.; Ciulli, N.; Leenheer, M. de; Demchenko, Y.; Ziegler, W.; Binczewski, A.:
PHOSPHORUS: Single-step on-demand services across multi-domain networks for e-science. (Asia-Pacific Optical Communications Conference (APOC) <2007, Wuhan>)
Wang, J.: Network Architectures, Management, and Applications V: SPIE Asia-Pacific Optical Communications (APOC), Wuhan, China, Nov. 1-5, 2007; Proceedings. Bellingham, WA: SPIE, 2007. (SPIE Proceedings Series 6784), Paper 67842X
urn:nbn:de:0011-n-682713
info:doi/10.1117/12.746371
Volltext

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Fluck, J.; Mevissen, T.H.; Dach, H.; Oster, M.; Hofmann-Apitius, M.:
ProMiner: Recognition of human gene and protein names using regularly updated dictionaries. (BioCreative Challenge Evaluation Workshop <2, 2007, Madrid>)
Valencia, A.: Second BioCreative Challenge Evaluation Workshop 2007. Proceedings: Critical Assessment of Information Extraction in Molecular Biology, April 23-25 2007, Madrid, Spain. Madrid, 2007, pp. 149-151
urn:nbn:de:0011-n-574930
Volltext

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Frangi, A.F.; Ruiz, A.; Hofmann-Apitius, M.:
Understanding cerebral aneurysms - the @neurIST project
ERCIM News, (2007), No.69, pp.16-17

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Grimm, C.; Groeper, R.; Gietz, P.; Haase, M.; Makedanz, S.; Pfeiffenberger, H.; Schiffers, M.; Ziegler, W.:
Trust issues in shibboleth-enabled federated grid authentication and authorization infrastructures supporting multiple grid middlewares. (International Conference on e-Science and Grid Computing (e-Science) <3, 2007, Bangalore>)
Fox, G.C.: E-science 2007, 3rd IEEE International Conference on e-Science and Grid Computing: 10 - 13 December 2007, Bangalore, India ; proceedings; including workshop papers. New York, NY: IEEE, 2007, pp. 569-576
info:doi/10.1109/E-SCIENCE.2007.80

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Gruber, R.; Keller, V.; Thiémard, M.; Wäldrich, O.; Wieder, P.; Ziegler, W.; Manneback, P.:
Integration of grid cost model into ISS/VIOLA meta-scheduler environment. (CoreGRID Workshop on Grid Middleware <2006, Dresden>)
Lehner, W.: Euro-Par 2006 workshops. Parallel processing. CoreGRID 2006, UNICORE Summit 2006, petascale computational biology and bioinformatics: Dresden, Germany, August 29-September 1, 2006; revised selected papers. Berlin: Springer, 2007. (Lecture Notes in Computer Science 4375), pp. 215-224
urn:nbn:de:0011-n-587252
info:doi/10.1007/978-3-540-72337-0 21
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Jacq, N.; Breton, V.; Chen, H.-Y.; Ho, L.-Y.; Hofmann, M.; Lee, H.-C.; Legré, Y.; Lin, S.C.; Maaß, A.; Medernach, E.; Merelli, I.; Milanesi, L.; Rastelli, G.; Reichstadt, M.; Salzemann, J.; Schwichtenberg, H.; Sridhar, M.; Kasam, V.; Wu, Y.-T.; Zimmermann, M.:
Grid-enabled high throughput virtual screening. (International Workshop on Distributed, High-Performance and Grid Computing in Computational Biology (GCCB) <2007, Eilat>)
Dubitzky, W.: Distributed, high-performance and Grid computing in computational biology. International workshop, GCCB 2006: Eilat, Israel, January 21, 2007; Proceedings. Berlin: Springer, 2007. (Lecture notes in bioinformatics 4360), pp. 45-59
info:doi/10.1007/978-3-540-69968-2 5

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Jacq, N.; Breton, V.; Chen, H.-Y.; Ho, L.-Y.; Hofmann, M.; Kasam, V.; Lee, H.-C.; Legré, Y.; Lin, S.C.; Maaß, A.; Medernach, E.; Merelli, I.; Milanesi, L.; Rastelli, G.; Reichstadt, M.; Salzemann, J.; Schwichtenberg, H.; Wu, Y.-T.; Zimmermann, M.:
Virtual screening on large scale grids. (GRIDs@Large Workshop <2005, Lisboa>)
Cérin, C.: Large scale grids: Grid@Large, co-located with Europar 2005 in Lisboa. Amsterdam: Elsevier, 2007. (Parallel computing 33.2007, Nr.4/5), pp. 289-301
info:doi/10.1016/j.parco.2007.02.010

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Kasam, V.; Zimmermann, M.; Maaß, A.; Schwichtenberg, H.; Wolf, A.; Jacq, N.; Breton, V.; Hofmann-Apitius, M.:
Design of new plasmepsin inhibitors: A virtual high throughput screening approach on the EGEE grid
Journal of chemical information and modeling, Vol.47 (2007), No.5, pp.1818-1828
info:doi/10.1021/ci600451t

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Kasam, V.; Salzemann, J.; Jacq, N.; Mass, A.; Breton, V.:
Large scale deployment of molecular docking application on computational grid infrastructures for combating malaria. (IEEE International Symposium on Cluster Computing and the Grid (CCGrid) <7, 2007, Rio de Janeiro>)
Schulze, B.: Seventh IEEE International Symposium on Cluster Computing and the Grid, CCGRID 2007. Piscataway: IEEE Computer Society, 2007, pp. 691-696
info:doi/10.1109/CCGRID.2007.66

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Klinger, R.; Rudolph, G.:
Automatic composition of music with methods of computational intelligence
WSEAS transactions on information science and applications, Vol.4 (2007), No.3, pp.508-515
urn:nbn:de:0011-n-545240
Volltext

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Klinger, R.; Friedrich, C.M.; Fluck, J.; Hofmann-Apitius, M.:
Named entity recognition with combinations of conditional random fields. (BioCreative Challenge Evaluation Workshop <2, 2007, Madrid>)
Valencia, A.: Second BioCreative Challenge Evaluation Workshop 2007. Proceedings: Critical Assessment of Information Extraction in Molecular Biology, April 23-25 2007, Madrid, Spain. Madrid, 2007, pp. 89-91
urn:nbn:de:0011-n-574949
Volltext

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Klinger, R.; Furlong, L.I.; Friedrich, C.M.; Mevissen, H.-T.; Fluck, J.; Sanz, F.; Hofmann-Apitius, M.:
Identifying gene specific variants in biomedical text
Journal of bioinformatics and computational biology, Vol.5 (2007), No.6, pp.1277-1296
urn:nbn:de:0011-n-704383
info:doi/10.1142/S0219720007003156
Volltext

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Kolarik, C.; Hofmann-Apitius, M.; Zimmermann, M.; Fluck, J.:
Identification of new drug classification terms in textual resources
Bioinformatics, Vol.23 (2007), No.13, pp.I264-I272
info:doi/10.1093/bioinformatics/btm196

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Kumpf, K.; Mevissen, T.; Wäldrich, O.; Ziegler, W.; Ginzel, S.; Weuffel, T.:
Multi-cluster text mining on the grid using the d-grid UNICORE environment. (German e-Science Conference (GES) <2007, Baden-Baden>)
Helmholtz-Gemeinschaft: German e-Science Conference 2007. Proceedings: 2. - 4. Mai 2007 in Baden-Baden. Baden-Baden, 2007, 11 pp.
urn:nbn:de:0011-n-655813
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Missier, P.; Wieder, P.; Ziegler, W.:
Semantic support for meta-scheduling in grids
Talia, D.: Knowledge and data management in GRIDs. New York/NY: Springer, 2007. (CoreGrid series 3), pp. 169-183
urn:nbn:de:0011-n-574620
info:doi/10.1007/978-0-387-37831-2 11
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Wieder, P.; Wäldrich, O.; Yahyapour, R.; Ziegler, W.:
Improving workflow execution through SLA-based advance reservation. (CoreGRID Integration Workshop <2006, Krakow>)
Gorlatch, S.: Achievements in European research on grid systems: CoreGRID Integration Workshop 2006 (selected papers); October 19-20, Krakow, Poland. New York/NY: Springer Science+Business Media, 2007. (CoreGrid series 6), pp. 207-221
info:doi/10.1007/978-0-387-72812-4 16

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Wolf, A.; Zimmermann, M.; Hofmann-Apitius, M.:
Alternative to consensus scoring - A new approach toward the qualitative combination of docking algorithms
Journal of chemical information and modeling, Vol.47 (2007), No.3, pp.1036-1044
info:doi/10.1021/ci6004965

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Zimmermann, M.:
Über die Kunst, dem Rechner das Lesen beizubringen
Nachrichten aus der Chemie, Vol.55 (2007), No.10, pp.997-999

Ananiadou, S.; Fluck, J.:
Proceedings of the Second International Symposium for Semantic Mining in Biomedicine. Introduction. (International Symposium on Semantic Mining in Biomedicine (SMBM) <2, 2006, Jena>)
Ananiadou, S. et al.: Second International Symposium on Semantic Mining in Biomedicine, SMBM 2006. Proceedings: Jena, April 9-12, 2006. Aachen: RWTH, 2006. (BMC Bioinformatics 7, Suppl. 3), pp. S1
info:doi/10.1186/1471-2105-7-S3-S1

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Arbona, A.; Benkner, S.; Fingberg, J.; Frangi, A.F.; Hofmann, M.; Hose, D.R.; Lonsdale, G.; Ruefenacht, D.; Viceconti, M.:
Outlook for grid service technologies within the @neurIST eHealth environment. (HealthGrid Conference <4, 2006, Valencia>)
Hernández, V.: Challenges and opportunities of healthgrids. Proceedings of Healthgrid 2006. Amsterdam: IOS Press, 2006. (Studies in health technology and informatics 120), pp. 401-404

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Barz, C.; Eickermann, T.; Kirtchakova, L.; Pilz, M.; Wäldrich, O.; Ziegler, W.:
Co-allocation of compute and network resources in the VIOLA-testbed. (TERENA Networking Conference <2006, Catania>)
Melve, I.: TERENA Networking Conference 2006: 15. - 18.05.2006 in Catania. Bradford, West Yorkshire: Emerald, 2006. (Campus-wide information systems 23.2006,4), 12 pp.

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Beibei, H.; Friedrich, C.M.; Manthey, R.; Hofmann-Apitius, M.:
Bayesian network modeling for the prediction of treatment outcomes of intracranial aneurysms. (German Conference on Bioinformatics (GCB) <2006, Tübingen>)
Huson, D. et al.: German Conference on Bioinformatics 2006. Short papers and poster abstracts: GCB 2006, 19.9.2006-22.9.2006 in Tübingen, Germany. Tübingen, 2006, pp. 122

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Bierbaum, B.; Clauss, C.; Eickermann, T.; Kirtchakova, L.; Krechel, A.; Springstubbe, S.; Wäldrich, O.; Ziegler, W.:
Reliable orchestration of distributed MPI-applications in a UNICORE-based grid with MetaMPICH and MetaScheduling. (European PVM/MPI Users' Group Meeting <13, 2006, Bonn>)
Mohr, B.: Recent advances in parallel virtual machine and message passing interface: 13th European PVM, MPI User's Group Meeting, Bonn, Germany, September 17-20, 2006; Proceedings. Berlin: Springer, 2006. (Lecture Notes in Computer Science 4192), pp. 174-183
info:doi/10.1007/11846802 29

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Birkholtz, L.-M.; Bastien, O.; Wells, G.; Grando, D.; Joubert, F.; Kasam, V.; Zimmermann, M.; Ortet, P.; Jacq, N.; Saïdani, N.; Roy, S.; Hofmann-Apitius, M.; Breton, V.; Louw, A.I.; Maréchal, E.:
Integration and mining of malaria molecular, functional and pharmacological data: How far are we from a chemogenomic knowledge space?
Malaria journal. Online journal, Vol.5 (2006), Art. 110, 24 pp.
urn:nbn:de:0011-n-574927
info:doi/10.1186/1475-2875-5-110
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Breton, V.; Jacq, N.; Hofmann, M.:
Grid added value to address malaria. (International Symposium on Cluster Computing and the Grid (CCGrid) <6, 2006, Singapore>)
Institute of Electrical and Electronics Engineers -IEEE-: Sixth International Symposium on Cluster Computing and the Grid, CCGrid 2006. Proceedings: 16-19 May, 2006, Singapore. Los Alamitos/Calif.: IEEE, 2006, pp. 40
info:doi/10.1109/CCGRID.2006.139

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Friedrich, C.M.; Zimmermann, M.; Hofmann, M.:
Grid computing - an opportunity for biomedical and statistical computing: Talk at Statistical Computing 2006. (Arbeitstagung über Methoden und Werkzeuge der Informatik für die Statistik (Statistical Computing) <38, 2006, Reisensburg/Günzburg>)
Statistical Computing 2006. Abstracts: 38. Arbeitstagung über Methoden und Werkzeuge der Informatik für die Statistik, 25. - 28.06.2006, Schloss Reisensburg (Günzburg). Günzburg, 2006, pp. 5

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Jacq, N.; Salzemann, J.; Legré, Y.; Reichstadt, M.; Jacq, F.; Zimmermann, M.; Maaß, A.; Sridhar, M.; Vinod-Kusam, K.; Schwichtenberg, H.; Hofmann, M.; Breton, V.:
Demonstration of in silico docking at a large scale on grid infrastructure. (HealthGrid Conference <4, 2006, Valencia>)
Hernández, V.: Challenges and opportunities of healthgrids. Proceedings of Healthgrid 2006. Amsterdam: IOS Press, 2006. (Studies in health technology and informatics 120), pp. 155-157

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Karopka, T.; Fluck, J.; Mevissen, H.-T.; Glass, Ä.:
The autoimmune disease database. A dynamically compiled literature-derived database
BMC bioinformatics. Online journal, Vol.7 (2006), pp.325
info:doi/10.1186/1471-2105-7-325

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Keller, V.; Gruber, R.; Spada, M.; Tran, T.-M.; Cristiano, K.; Kuonen, P.; Wieder, P.; Ziegler, W.; Wäldrich, O.; Maffioletti, S.; Sawley, M.-C.; Nellari, N.:
Integration of the ISS into the VIOLA meta-scheduling. (Workshop "Integrated Research in Grid Computing" <2005, Pisa>)
Gorlatch, S.: Integrated research in GRID computing: CoreGRID Integration Workshop 2005, selected papers, November 28-30, Pisa, Ialy. Berlin: Springer US, 2006, pp. 203-214
info:doi/10.1007/978-0-387-47658-2 15

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Klinger, R.; Rudolph, G.:
Evolutionary composition of music with learned melody evaluation. (International Conference on Computational Intelligence, Man-Machine Systems and Cybernetics (CIMMACS) <5, 2006, Venice>)
Mastorakis, N. et al.: 5th WSEAS International Conference on Computational Intelligence, Man-Machine Systems and Cybernetics, CIMMACS '06. Proceedings: Venice, Italy, November 20-22, 2006. Venice, 2006, pp. 234-239
urn:nbn:de:0011-n-545258
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Kumpf, K.; Mevissen, T.; Wäldrich, O.; Weuffel, T.; Ziegler, W.:
Text mining on the grid. (Workshop on Grid Technologies for Knowledge-based Industries and Businesses <2006, Helsinki>)
Grid Technologies for Knowledge-based Industries and Businesses: Helsinki, Finland, November 21-23, 2006; Proceedings. Helsinki, 2006, 4 pp.

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Ludwig, H.; Nakata, T.; Wäldrich, O.; Wieder, P.; Ziegler, W.:
Reliable orchestration of resources using WS-agreement. (International Conference on High Performance Computing and Communications (HPCC) <2, 2006, München>)
Gerndt, M.: High performance computing and communications. Second international conference, HPCC 2006: Munich, Germany, September 13-15, 2006; Proceedings. Berlin: Springer, 2006. (Lecture Notes in Computer Science 4208), pp. 753-762

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Milke, J.-M.; Schiffers, M.; Ziegler, W.:
Virtuelle Organisationen in Grids: Charakterisierung und Management
Praxis der Informationsverarbeitung und Kommunikation : PIK, Vol.29 (2006), No.3, pp.166-171
info:doi/10.1515/PIKO.2006.165

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Springstubbe, S.; Ziegler, W.:
CoreGRID summer school 2006: First steps in next generation grid technologies
ERCIM News, (2006), No.67, pp.4

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Streit, A.; Wäldrich, O.; Wieder, P.; Ziegler, W.:
On scheduling in UNICORE - extending the web services agreement based resource management framework. (International Conference on Parallel Computing (ParCo) <2005, Malaga>)
Joubert, G.R.: Parallel computing. Current and futures issues of high end computing: Proceedings of the International Conference ParCo 2005, Central Institute for Applied Mathematics. Jülich: NIC, 2006. (NIC Series 33), pp. 57-64

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Wäldrich, O.; Wieder, P.; Ziegler, W.:
A meta-scheduling service for co-allocating arbitrary types of resources. (International Conference on Parallel Processing and Applied Mathematics (PPAM) <6, 2005, Poznan>)
Wyrzykowski, R.: Parallel processing and applied mathematics. 6th international conference, PPAM 2005: Poznan', Poland, September 11-14, 2005. Revised selected papers. Berlin: Springer, 2006. (Lecture Notes in Computer Science 3911), pp. 782-791
info:doi/10.1007/11752578 94

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Wieder, P.; Wäldrich, O.; Ziegler, W.:
Advanced techniques for scheduling, reservation, and access management for remote laboratories. (International Conference on e-Science and Grid Computing (e-Science) <2, 2006, Amsterdam>)
Institute of Electrical and Electronics Engineers -IEEE-: Second IEEE International Conference on e-Science and Grid Computing, e-Science 2006: The meeting was held on Dec. 4-6, 2006, Amsterdam, Netherlands. Los Alamitos, Calif.: IEEE Computer Society, 2006, pp. 128
info:doi/10.1109/E-SCIENCE.2006.261061

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Wieder, P.; Wäldrich, O.; Yahyapour, R.; Ziegler, W.:
Improving workflow execution through SLA-based advance reservation. (CoreGRID Integration Workshop <2006, Krakow>)
Integrated Research in Grid Computing: CoreGRID Integration Workshop, Krakow, October 19-20, 2006. Krakow, 2006, pp. 333-344

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Ziegler, W.; Wieder, P.:
Bringing knowledge to middleware - grid scheduling ontology. (Workshop on Future Generation Grids <2004, Dagstuhl>)
Getov, V.: Future generation grids: Proceedings of the Workshop on Future Generation Grids, November 1 - 5, 2004, Dagstuhl, Germany. New York, NY: Springer, 2006, pp. 47-59

Cristiano, K.; Gruber, R.; Keller, V.; Kuonnen, P.; Maffioletti, S.; Nellari, N.; Sawley, M.-C.; Spada, M.; Tran, T.-M.; Wieder, P.; Wäldrich, O.; Ziegler, W.:  

Integration of ISS into the VIOLA meta-scheduling environment. (Workshop "Integrated Research in Grid Computing" <2005, Pisa>)
Gorlach, S.: CoreGRID Workshop on Integrated Research in Grid Computing. Proceedings: Pisa, IT, 20.-28. November 2005. Pisa: Università di Pisa, 2005, pp. 357-366

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Fluck, J.; Hofmann, M.; Hahn, U.; Wermter, J.; Schulz, S.:
Text mining in den Life Sciences: Perspektiven der automatischen Informationsextraktion aus biomedizinischen Fachtexten
Deutsche Zeitschrift für klinische Forschung, (2005), No.5/6, pp.20-26

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Fluck, J.; Zimmermann, M.; Kurapkat, G.; Hofmann, M.:
Information extraction technologies for the life science industry
Drug Discovery Today, Vol.2 (2005), No.3, pp.217-224
info:doi/10.1016/j.ddtec.2005.08.013

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Fluck, J.; Deneke, H.; Gieger, C.:
Text mining in life sciences
Zanasi, A.: Text mining and its applications to intelligence, CRM and knowledge management. Southampton: WIT Press, 2005. (Advances in Management Information Systems 2), pp. 279-284
info:doi/10.2495/978-1-85312-995-7/17

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Fluck, J.; Stitt, M.; Selbig, J.; Hofmann, M.; Thimm, O.:
Using named entity recognition for ontology annotation: An experimental approach for Arabidopsis functional genome annotation. (European Conference on Computational Biology (ECCB) <4, 2005, Madrid>)
Bioinformatics National Institute -INB-: ECCB 2005, Workshop on Biomedical Ontologies and Text Processing: 28 September, 2005 Madrid, Spain, the workshop is part of the 4th European Conference on Computational Biology (ECCB). Madrid, 2005

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Hanisch, D.; Fundel, K.; Mevissen, H.-T.; Zimmer, R.; Fluck, J.:
ProMiner: Rule-based protein and gene entity recognition
BMC bioinformatics. Online journal, Vol.6 (2005), No.1, pp.14
info:doi/10.1186/1471-2105-6-S1-S14

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Hessler, G.; Zimmermann, M.; Matter, H.; Evers, A.; Naumann, T.; Lengauer, T.; Rarey, M.:
Multiple-ligand-based virtual screening: Methods and applications of the MTree approach
Journal of medicinal chemistry, Vol.48 (2005), No.21, pp.6575-6584
info:doi/10.1021/jm050078w

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Orian-Rousseau, V.; Mink, S.; Mengwasser, J.; HogenEsch, H.; Guo, F.; Thies, W.-G.; Hoffmann, M.; Herrlich, P.; Ponta, H.:
Genes upregulated in a metastasizing human colon carcinoma cell line
International journal of cancer, Vol.113 (2005), No.5, pp.699-705
info:doi/10.1002/ijc.20644

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Reinhardt, S.; Marian, C.M.:
Carboborosilazane ceramics: Initial reactions between TSDE and methylamine - A combined quantum chemical and first principles molecular dynamics study. (International Conference on Non-Crystalline Materials (CONCIM) <2005>)
Journal of non-crystalline solids, Vol.351 (2005), No.12-13, pp.1113-1120
info:doi/10.1016/j.jnoncrysol.2005.01.025

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Vet, P. van der; Huibers, T.; Binz, P.-A.; Hofmann, M.:
ESF workshop on 'sustainability and governance of web and GRID resources in functional genomics'
Comparative and functional genomics, Vol.6 (2005), No.5-6, pp.307-310
info:doi/10.1002/cfg.488

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Wermter, J.; Fluck, J.; Strötgen, J.; Geißler, S.; Hahn, U.:
Recognizing noun phrases in biomedical text: An evaluation of lab prototypes and commercial chunkers. (International Symposium on Semantic Mining in Biomedicine (SMBM) <1, 2005, Hinxton>)
Hahn, U.: SMBM 2005: First International Symposium on Semantic Mining in Biomedicine (SMBM). EBI, Hinxton, UK, 10-12 April 2005. Aachen: Rheinisch-Westfälische Technische Hochschule Aachen, 2005. (CEUR Workshop Proceedings 148), 9 pp.

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Zimmermann, M.; Thi, L.T.B.; Hofmann, M.:
Combating illiteracy in chemistry: Towards computer-based chemical structure reconstruction
ERCIM News, (2005), No.60, pp.40-41

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Zimmermann, M.; Fluck, J.; Thi, L.T.B.; Kolarik, C.; Kumpf, K.; Hofmann, M.:
Information extraction in the life sciences: Perspectives for medicinal chemistry, pharmacology and toxicology
Current topics in medicinal chemistry, Vol.5 (2005), No.8, pp.785-796
info:doi/10.2174/1568026054637692

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