Humboldt-Universität zu Berlin - Mathematisch-Naturwissenschaftliche Fakultät II - Wissensmanagement in der Bioinformatik

2012 -2011 - 2010 - 2009 - 2008 - 2007 - 2006 - 2005 - 2004 - 2003

2013

Peer-reviewed publications

• Wandelt, S. and Leser, U. (2013)
  QGramProjector: Q-gram projection for indexing highly-similar strings
  Advances in Databases and Information Systems, Genoa, Italy.
• Wandelt, S., Bux , M. and Leser, U. (2013)
  Trends in Genome Compression.
  Current Bioinformatics (accepted).
• Thomas, P. and Leser, U. (2013)
  HistoNer: Histone modification extraction from text
  BioLINK Special Interest Group, in conjunction with ISBM/ECCB 2013 Conference, Berlin, Germany (accepted).
• Jacob, C., Thomas, P. and Leser, U. (2013)
  Comprehensive Benchmark of Gene Ontology Concept Recognition tools
  BioLINK Special Interest Group, in conjunction with ISBM/ECCB 2013 Conference, Berlin, Germany (accepted).
• Bux, M. and Leser, U. (2013)
  DynamicCloudSim: Simulating Heterogeneity in Computational Clouds.
  Int. Workshop on Scalable Workflow Enactment Engines and Technologies (SWEET'13), in conjunction with ACM SIGMOD Conference, New York, USA (accepted).
• Stoltmann, T., Zimmermann, K., Koschmieder, A. and Leser, U. (2013)
  OmixAnalyzer - A Web-Based System for Management and Analysis of High-Throughput Omics Data Sets.
  DILS 2013 (accepted).
• Rocktäschel, T., Huber, T., Weidlich, M. and Leser, U. (2013).
  WBI-NER: The impact of domain-specific features on the performance of identifying and classifying mentions of drugs.
  DDI Challenge at Semeval. Ranked first in competition
• Thomas, P., Neves, M., Rocktäschel, T. and Leser, U. (2013).
  WBI-DDI: Drug-Drug Interaction Extraction using Majority Voting.
  DDI Challenge at Semeval. Ranked second in competition
• Neves, M., Damaschun, A., Mah, N., Lekschas, F., Seltmann, S., Stachelscheid, H., Fontaine, J.-F., Kurtz, A. and Leser, U. (2013).
  Preliminary evaluation of the CellFinder literature curation pipeline for gene expression in kidney cells and anatomical parts
  Database (Oxford) Vol. 2013, Article ID bat020.
• Tikk, D., Solt, I., Thomas, P. and Leser, U. (2013).
  A Detailed Error Analysis of 13 Kernel Methods for Protein-Protein Interaction Extraction.
  Supp Material: Instance based difficulty levels
  BMC Bioinformatics (accepted).
• Leich, M., Adamek, J., Schubotz, M., Heise, A., Rheinländer, A. and Markl , V. (2013).
  Applying Stratosphere for Big Data Analytics
  15. GI-Fachtagung Datenbanksysteme für Business, Technologie und Web (BTW), March 11 - 15, 2013, Magdeburg, Germany (accepted).
• Thomas, P., Starlinger, J. and Leser, U. (2013).
  Experiences from Developing the Domain-Specific Entity Search Engine GeneView
  BTW, Magdeburg, Germany (accepted).
• Pirk, H., Funke, F., Grund, M., Neumann, T., Leser, U., Manegold, S., Kemper, A. and Kersten, M.
  CPU and Cache Efficient Management of Memory-Resident Databases.
  Int. Conf. on Data Engineering, Brisbane, Australia (accepted)

Other

• Marc Bux, Ulf Leser
  Parallelization in Scientific Workflow Management Systems.
  Technical Report CoRR/arXiv:1303.7195

2012

Peer-reviewed publications

• Neves, M. and Leser, U.
  A Survey on Annotation Tools for the Biomedical Literature.
  Briefings in Bioinformatics, 2012.
• Wandelt, S. and Leser, U.
  Adaptive efficient compression of genomes.
  Algorithms for Molecular Biology 7(30), 2012
• Wandelt, S. and Leser, U.
  String Searching in Referentially Compressed Genomes.
  Int. Conf. on Knowledge Discovery and Information Retrieval, Barcelona, Spain.
  Best Paper Award
• Leser, U. and Liebermeister, W.
  Knowledge Management for Systems Biology.
  In Dubitzky, W., Wolkenhauer, O., Cho, K.-H. and Yokota, H. (ed). Book "Encyclopedia of Systems Biology".
• Jansen, L., Fuellen, G., Leser, U. and Kurtz, A.
  Using Ontologies to Study Cell Transitions.
  Int. Workshop on Ontologies in Biomedicine and Life Sciences (to appear), Dresden, Germany, 2012.
• Joosten, M., Seitz, V., Zimmermann, K., Sommerfeld, A., Berg, E., Lenze, D., Leser, U., Stein, H. and Hummel, M.
  Histone acetylation and DNA demethylation of T-cells result in an anaplastic large cell lymphoma-like phenotype.
  Haematologica 2012 (accepted).
• Bauckmann, J., Abedjan, Z., Müller, H., Leser, U. and Naumann, F.
  Discovering Conditional Inclusion Dependencies
  Int. Conf. on Information and Knowledge Management, Hawaii 2012 (to appear).
• Wandelt, S., Rheinländer, A., Bux, M., Thalheim, L., Haldemann, B. and Leser, U.
  Data Management Challenges in Next Generation Sequencing
  Datenbank-Spektrum, accepted, 2012.
• Heise, A., Rheinländer, A., Leich, M., Naumann, F., and Leser, U.
  Meteor/Sopremo: An Extensible Query Language and Operator Model.
  Int. Workshop on End-to-end Management of Big Data, in conjunction with VLDB, Istanbul, Turkey, 2012.
• Thomas, P., Starlinger, J., Vowinkel, A., Arzt, S. and Leser, U.
  GeneView: A comprehensive semantic search engine for PubMed.
  Nucl. Acids Res. 40 (W1): W585-W591, 2012.
• Hueske, F., Peters, M., Sax, M.J., Rheinländer, A., Bergmann, R., Krettek, A., and Tzoumas, K.
  Opening the Black Boxes in Dataflow Optimization.
  38th Int. Conf. on Very Large Data Bases (VLDB), Istanbul, Turkey, 2012. (accepted)
• Koschmieder, A. and Leser, U.
  Regular Path Queries on Large Graphs
  International Conference on Scientific and Statistical Database Management (SSDBM) 2012.
• Boelling, C., Dumontier, M., Weidlich, M. and Holzhütter, H.
  Role-based representation and inference of biochemical processes
  International Conference on Biomedical Ontology (accepted).
• Rocktäschel, T., Weidlich, M. and Leser, U..
  ChemSpot: A Hybrid System for Chemical Named Entity Recognitions
  Bioinformatics 28 (12): 1633-1640, 2012
• Trissl, S., Hussels, P. and Leser, U.
  InterOnto - Ranking Inter-Ontology Links
  Int. Conf. on Data Integration for the Life Sciences, Washington, USA, 2012
• Starlinger, J., Cohen-Boulakia, S. and Leser, U.
  (Re)Use in Public Scientific Workflow Repositories
  Int. Conf. on Scientific and Statistical Database Management, Chania, Greece, 2012
• Fenz, D., Lange, D., Rheinländer, A., Naumann, F. and Leser, U.
  Efficient Similarity Search in a Very Large String Sets
  Int. Conf. on Scientific and Statistical Database Management, Chania, Greece, 2012
• Thomas, P., Bobić, T., Leser, U., Hofmann-Apitius, M. and Klinger, R.
  Weakly Labeled Corpora as Silver Standard for Drug-Drug and Protein-Protein Interaction.
  In Proceedings of the Workshop on Building and Evaluating Resources for Biomedical Text Mining (BioTxtM) on Language Resources and Evaluation Conference (LREC), Istanbul, Turkey. 2012
• Neves, M., Damaschun, A., Kurtz, A. and Leser, U.
  Annotating and evaluating text for stem cell research.
  Workshop on Building and Evaluating Resources for Biomedical Text Mining, Istanbul, Turkey. 2012
• Bobic, T., Klinger, R., Thomas, P., and Hofmann-Apitius, M.
  Improving Distantly Supervised Extraction of Drug-Drug and Protein-Protein Interactions.
  In Proceedings of the Joint Workshop on Unsupervised and Semi-Supervised Learning (ROBUS-UNSUP) on European Conference of the Association for Computational Linguistics (EACL), Avignon, France. 2012
• Müller, H., Freytag, J.-C. and Leser, U.
  Improving Data Quality by Source Analysis.
  ACM Journal of Data and Information Quality Volume 2 Issue 4, February 2012

Other

• Bauckmann, J., Abedjan, Z., Leser, U., Müller, H. and Naumann, F.
  Covering or Complete? Discovering Conditional Inclusion Dependencies.
  Technical Report 62, Hasso-Plattner-Institut Potsdam.
• Koschmieder, A. and Leser, U.
  Regular Path Queries on Large Graphs.
  Technical Report No 240, Department of Computer Science, Humboldt-Universität zu Berlin.

2011

Peer-reviewed publications

• Döhling, L. and Leser, U. (2011).
  EquatorNLP: Pattern-based Information Extraction for Disaster Response
  In Proceedings of Terra Cognita 2011 Workshop, Bonn, Germany.
• Thomas, P., Solt, I., Klinger, R. and Leser, U. (2011).
  Learning Protein Protein Interaction Extraction using Distant Supervision
  In Proceedings of Robust Unsupervised and Semi-Supervised Methods in Natural Language Processing 2011, Hissar, Bulgaria
• Hakenberg, J., Gerner, M., Haeussler, M., Solt, I., Plake, C., Schroeder, M., Gonzalez, G., Nenadic, G. and Bergman, C. (2011).
  The GNAT library for local and remote gene mention normalization
  Bioinformatics 27(19): 2769-2771.
• Rheinländer, A. and Leser, U. (2011).
  Scalable Sequence Similarity Search and Join in Main Memory on Multi-Cores
  2nd International Workshop on High Performance Bioinformatics and Biomedicine (HiBB), Bordeaux, France.
• Thomas, P., Neves, M. L., Solt, I., Tikk, D. and Leser, U. (2011).
  Relation Extraction for Drug-Drug Interactions using Ensemble Learning
  DDIExtraction Workshop, Spain
  Ranked First in the DDI challenge
• Cohen-Boulakia, S. and Leser, U. (2011).
  Search, Adapt, and Reuse: The Future of Scientific Workflows
  SIGMOD Record 40(2)
• Arighi, C.N., Roberts, P., Agarwal, S., Bhattacharya, S., Cesareni, G., Chatr-aryamontri, A., Clematide, S., Gaudet, P., Giglio, M.G., Harrow, I., Huala, E., Krallinger, M., Leser, U., Li, D., Liu, F., Lu, Z., Maltais, L., Okazaki, N., Perfetto, L., Rinaldi, F., Sætre, R., Salgado, D., Srinivasan, P., Thomas, P.E., Toldo, L., Hirschman L., and Wu, C.H (2011).
  BioCreative III Interactive Task: an Overview
  BMC Bioinformatics, 12(Suppl 8):S8.
• Arzt, S., Starlinger, J., Arnold, O., Kröger, S., Jaeger, S., and Leser, U. (2011).
  PiPa: Custom Integration of Protein Interactions and Pathways
  GI-Jahrestagung 2011, Workshop "Daten In den Lebenswissenschaften".
• Groth, P., Leser, U. and Weiss, B. (2011).
  Phenotype Mining for Functional Genomics and Gene Discovery.
  In Yu, B. and Hinchcliffe, M. (ed). Book "In Silico Tools for Gene Discovery (to appear)", Springer.
• Thomas, P., Klinger, R., Furlong, L., Hofmann-Apitius, M. and Friedrich, C. (2011).
  Challenges in the Association of Human Variation Names with Unique Database Identifier
  BMC Bioinformatics 2011, 12(Suppl 4):S4.
• Thomas, P., Pietschmann, S., Solt, I., Tikk, D. and Leser, U. (2011).
  Not all links are equal: Exploiting Dependency Types for the Extraction of Protein-Protein Interactions from Text
  BioNLP 2011, Portland US
• Seitz, V., Thomas, P., Zimmermann, K., Paul, U., Ehlers, A., Joosten, M., Dimitrova, L., Lenze, D., Sommerfeld, A., Oker, E., Leser, U., Stein, H., and Hummel, M. (2011).
  Classical Hodgkin lymphoma shows epigenetic features of an abortive plasma cellular differentiation
  Hematologica , 96(6):863-70.
• Koschmieder, A., Zimmermann, K., Trißl, S., Stoltmann, T. and Leser, U.
  Tools for Managing and Analyzing Microarray Data
  Briefings in Bioinformatics 2012 13: 46-60.
• Jaeger, S., Sers, C. and Leser, U. (2011).
  Combining modularity, conservation, and interactions of proteins significantly increases precision and coverage of protein function prediction
  BMC Genomics 2010, 11:717.
• Cohen-Boulakia, S. and Leser, U. (2011).
  Next Generation Data Integration for the Life Sciences (Tutorial)
  Int. Conf. on Data Engineering, Hannover, Germany.

Other

• Starlinger, J., Schmeck, B. and Leser, U.
  Challenges in Automatic Diagnosis Extraction from Medical Examination Summaries
  CIKM 2011, Workshop on Web Science and Information Exchange in the Medical Web.
• Döhling, L., Woith, H., Fahland, D. and Leser, U.
  Equator: Faster Decision Making for Geoscientists
  GI-Jahrestagung 2011, Workshop "Workshop zur IT-Unterstützung von Rettungskräften".

2010

Peer-reviewed publications

• Gille C, Bölling C, Hoppe A, Bulik S, Hoffmann S, Hübner K, Karlstädt A, Ganeshan R, König M, Rother K, Weidlich M, Behre J, Holzhütter HG.
  HepatoNet1: a comprehensive metabolic reconstruction of the human hepatocyte for the analysis of liver physiology.
  Molecular System Biology, 2010.
• Castillo, R., Rothe, C. and Leser, U.
  RDFMatView: Indexing RDF Data using Materialized SPARQL Queries
  6th Int. WS on Scalable Semantic Web Knowledge Bases, Shanghai, China.
• Ngyuen, L. Q., Tikk, D. and Leser, U.
  Simple Tricks for Improving Pattern-Based Information Extraction from the Biomedical Literature
  Journal of Biomedical Semantics.
• Jaeger, S., Ertaylan, G., van Dijk, D., Leser, U. and Sloot, P. M.
  Inference of Surface Membrane Factors of HIV-1 Infection through Functional Interaction Networks
  PLoS ONE 5(10): e13139, 2010.
• Roger Castillo
  RDFMatView: Indexing RDF Data for SPARQL Queries.
  International Semantic Web Conference 2010, Doctoral Consortium, Shanghai, China.
• Rheinländer, A., and Leser, U.
  Fast Similarity Search and Similarity Join in Oracle DB.
  In Proceedings of DOAG'10, Nürnberg, 2010.
• Domonkos Tikk, Illés Solt
  Improving textual medication extraction using combined conditional random fields and rule-based systems
  Journal of the American Medical Informatics Association 2010;17:540-544.
• Trissl, S. and U. Leser
  Estimating Result Size and Execution Times for Graph Queries
  Workshop on Querying Graph Structured Data, Novi Sad, Serbia.
• Kabisch, T., Dragut, E., Yu, C. and Leser, U.
  Deep Web Integration with VisQI
  Int. Conf. on Very Large Databases, Singapore.
• Groth, P., Kalev, I., Kirov, I., Traikov, B., Leser, U. and Weiss, B.
  Phenoclustering: Online mining of cross-species phenotypes
  Bioinformatics, 26(15): p. 1924-1925
• Senger, C., Seidling, H. M., Quinzler, R., Leser, U. and Haefeli, W. E.
  Design and evaluation of an ontology-based drug application database
  Methods of Information in Medicine 49(6)
• Roger Castillo, Ulf Leser
  Selecting Materialized Views for RDF Data
  2nd Int. Workshop on Semantic Web Information Management, Vienna, Austria
  Selected as one of two best papers
• Tikk, D., Thomas, P., Palaga, P., Hakenberg, J. and Leser, U.
  A comprehensive benchmark of kernel methods to extract protein-protein interactions from literature
  PLOS Computational Biology, 6(7)
• Illés Solt, Domonkos Tikk, Ulf Leser
  Species identification for gene name normalization
  Workshop on Advances in Bio Text Mining (BioTM 2010), Ghent, Belgium
• Domonkos Tikk, Peter Palaga, Ulf Leser
  A fast and effective dependency graph kernel for PPI relation extraction
  Workshop on Advances in Bio Text Mining (BioTM 2010), Ghent, Belgium
• André Koschmieder
  Cost-Based Optimization of Regular Path Queries on Large Graphs
  Grundlagen von Datenbanken, Bad Helmstedt, Germany
• Rheinländer, A., Knobloch, M., Hochmuth, N. and Leser, U.
  Prefix Tree Indexing for Similarity Search and Similarity Join on Genomic Data
  Int. Conf. on Statistical and Scientific Databases, Heideberg, Germany
• Brauer, F., Huber, M., Hackenbroich, G., Leser, U., Naumann, F. and Barczynski, W.
  Graph-Based Concept Identification and Disambiguation for Enterprise Search
  19th Int. World Wide Web Conference, Raleigh, US
• Hakenberg, J., Solt, I., Tikk, D., Nguyen, V. H., Tari, L., Nguyen, Q. L., Baral, C. and Leser, U.
  Molecular event extraction from Link Grammar parse trees
  Int. Journal of Computational Intelligence (to appear)
• Ferenc P. Szidarovszky, Illes Solt, Domonkos Tikk
  A Simple Ensemble Method for Hedge Identification
  Proceedings of the Fourteenth Conference on Computational Natural Language Learning: Shared Task, Uppsala, Sweden, 15-16 July 2010

Other

• Freytag, J.-C., Kao, O., Leser, U., Markl, V., and Naumann, F.
  Stratosphere - Informationsmanagement 'above the cloud'
  Datenbank Spektrum.
• Solt, I., Gerner, M., Thomas, P., Nenadic, G., Bergman, C. M., Leser, U. and Hakenberg, J.
  Gene mention normalization in full texts using GNAT and LINNAEUS.
  Proceedings of BioCreative III, Bethesda, USA, 2010. pp 137-142.
• Thomas, P., Starlinger, J., Jacob, C., Solt, I., Hakenberg, J. and Leser, U.
  GeneView Gene-Centric Ranking of Biomedical Text
  Proceedings of BioCreative III, Bethesda, USA, 2010. pp 137-142.
• Lakes, T., Leser, U. and Senf, C.
  An urban health risk analysis for Berlin: exploration and integration of spatio-temporal information on the urban environment.
  EnvironInfo 2010, Bonn, Germany.
• Karin Zimmermann and Ulf Leser
  Analysis of Affymetrix Exon Arrays.
  Technical Report 235, Department for Computer Science, Humboldt-Universität zu Berlin
• Bauckmann, J., Leser, U. and Naumann, F.
  Efficient and exact computation of inclusion dependencies for data integration
  Technical Report 34. Hasso-Plattner-Institiut Potsdam
• Philip Groth, Bertram Weiss, Ulf Leser
  Ontologies improve cross-species phenotype analysis (Extended Version)
  Meeting of the Special Interest Group on Bio-Ontologies, Boston, US
• Philippe Thomas, Domonkos Tikk, Ulf Leser
  A fair benchmark of kernel methods for PPI extraction
  Workshop on Advances in Bio Text Mining (BioTM 2010), Ghent, Belgium
• Roger Castillo, Christian Rothe, and Ulf Leser
  RDFMatView: Indexing RDF Data for SPARQL Queries.
  Technical Report No 234, Department for Computer Science, Humboldt-Universität zu Berlin

2009

Peer-reviewed publications

• Böhm C and Leser U
  Graph-Based Ontology Construction from Heterogeneous Evidences
  Int. Semantic Web Conference, Washington, US
  Selected as ISWC-Spotlight paper
• Dragut E, Kabisch T, Leser U, Yu C.
  A Hierarchical Approach to Model Web Query Interfaces for Web Source Integration
  VLDB, Lyon, France
• Illés Solt, Domonkos Tikk
  Yet another rule-based approach for extracting medication information from discharge summaries
  The Third i2b2 Workshop on Challenges in Natural Language Processing for Clinical Data, 11/2009, San Francisco, CA, USA.
• Rostin A, Albrecht O, Bauckmann J, Naumann F, Leser U.
  A Machine-Learning Approch to Foreign Key Detection
  WebDB, Provedence, US
• De Stasio A, Ertelt M, Kemmner W, Leser U, Ceccarelli M
  Exploiting Scientific Workflows for Large-Scale Gene Expression Data Analysis
  24th of the International Symposium on Computer and Information Sciences (ISCIS), Cyprus
• Hakenberg J, Tari L, Gonzalez G, Solt I, Tikk D, Rheinländer A, Ngyuen QL, and Leser U
  Molecular event extraction from Link Grammar parse trees
  BioNLP shared task 2009
• Starlinger J, Leitner F, Valencia A, and Leser U
  SOA-based Integration of Text Mining Services
  Service Cup 2009
  Third prize in the international Service Cup 2009 contest.
• Palaga P, Nguyen QL, Leser U, and Hakenberg J
  High-Performance Information Extraction with AliBaba (Demo)
  Extending Database Technology (EDBT), St. Petersburg, Russia.
• Chiarcos C, Dipper S, Götze M, Leser U, Lüdeling A, Ritz J, and Stede M
  A Flexible Framework for Integrating Annotations from Different Tools and Tagsets
  Traitement Automatique des Langues, Special Issue on Platforms for Natural Language Processing.
• Hakenberg, J., Plake, C. and Leser, U.
  Ali Baba: Text Mining for Systems Biology
  In  Lodhi, H. and Muggleton, S. (eds) "Elements of Computational Systems Biology". Wiley & Sons
• Schiemann, T., Leser, U. and Hakenberg, J.
  Word Sense Disambiguation in Biomedical Applications: A Machine Learning Approach
  In  Prince, V. and Roche, M. (eds) Information Retrieval in Biomedicine: Natural Language Processing for Knowledge Integration. IGI Global.
• Leser U.
  Semantic Integration of Life Science Entities
  In: Öszu T, Liu L, editors. Encyclopedia of Database Systems, Springer
• Leser U., Trißl S.
  Graph Management in the Life Sciences
  In: Öszu T, Liu L, editors. Encyclopedia of Database Systems, Springer
• Illés Solt, Domonkos Tikk, Viktor Gál, Zsolt T Kardkovács
  Semantic Classification of Diseases in Discharge Summaries Using a Context-aware Rule-based Classifier
  Journal of the American Medical Informatics Association, 2009;16:580-584.

Other

• Hakenberg, J.
  Mining relations from the biomedical literature.
  Dissertation (HU edoc)
• Groth, P.
  Knowledge management and discovery for genotype/phenotype data.
  Dissertation (HU edoc)

2008

Peer-reviewed publications

• Hakenberg, J., Plake, C., Royer, L., Strobelt, H., Leser U., and Schroeder. M.
  Gene mention normalization and interaction extraction with context models and sentence motifs
  Genome Biology, 2008;9 Suppl 2:S14 (2008).
• Groth, P., Weiss, B. and Leser, U.
  Hunting for gene function: Using phenotype data mining as a large-scale discovery tool
  BioSapiens Workshop on Automated Function Prediction, at ISMB 2008.
• Jaeger, S., Gaudan, S., Leser, U. and Rebholz-Schuhmann, D.
  Integrating Protein-Protein Interactions and Text Mining for Protein Function Prediction
  Workshop on Data Integration for the Life Sciences (DILS), Evry, France.
  Appeared in BMC Bioinformatics, Selected Best Papers from DILS08
• Quilitz, B. and Leser, U.
  Querying Distributed RDF Data Sources with SPARQL
  European semantic Web Conference (ESWC), Teneriffa, Spain (2008).
• Philip Groth, Bertram Weiss, Hans-Dieter Pohlenz and Ulf Leser
  Mining phenotypes for gene function prediction
  BMC Bioinformatics, 9:136 (2008).

Other

• Anke Lüdeling, Ulf Leser
  Bioinformatics methods in calculating language relationships
  Tutorial at the European Summer School in Logic, Language and Information (ESSLI), Hamburg (2008)
• Mirko Hochmuth, Anke Lüdeling, Ulf Leser
  Simulating and reconstructing language change
  Institut für Informatik der Humboldt-Universität zu Berlin, Technical Report (2008)
• Michael Ashburner, Ulf Leser, Dietrich Rebholz-Schuhmann, Eds. (2008). Proceedings of the Dagstuhl Workshop on "Ontologies and Text Mining for Life Sciences: Current Status and Future Perspectives". Available from the Dagstuhl DROPS server.
• Jens Dittrich, Ulf Leser, Betram Ludaescher, Dave Maier, Louiqa Raschid, Eds. (2008). Proceedings Workshop on Information Integration Methods, Architectures, and Systems" (IIMAS), Cancun, Mexico.

2007

Peer-reviewed publications

• Jaeger, S. and Leser, U.
  High-Precision Function Prediction using Conserved Interactions
  German Conference on Bioinformatics (GCB), Springer LNI, pp 145-162, Potsdam, Germany (2007).
• Silke Trißl, Florian Zipser, and Ulf Leser
  Applying GRIPP to XML Documents containing XInclude and XLink Elements
  XML Tage, Berlin, Germany, (2007).
• Jana Bauckmann
  Automatically Integrating Life Science Data Sources
  PhD Workshop in conjunction with VLDB 2007, Vienna, Austria (2007).
• Philipp Hussels, Silke Trissl, and Ulf Leser
  What's new? What's certain? - Scoring Search Results in the Presence of Overlapping Data Sources
  4th Workshop on Data Integration in the Life Sciences (DILS07), Philadelphia, USA. 2007
  In Lecture Notes in Computer Science, Volume 4544/2007, Pages 231-246. [SpringerLink]
• Hakenberg, J., Schröder, M. and Leser, U.
  Consenus Pattern Alignment to find protein--protein interactions in text
  Proc 2nd BioCreative Challenge Evaluation Workshop. Madrid, Spain, April 23-25, pages 213–215.
• Silke Trissl
  Cost-based Optimization of Graph Queries
  1st PhD Workshop on Innovative Database Research (IDAR) in conjunction with ACM SIGMOD Conference, Beijing, China, 2007.
• Silke Trissl, Ulf Leser
  Fast and Practical Indexing and Querying of Very Large Graphs
  ACM SIGMOD Conference, Bejing, China, pages 845-856, 2007. [ACM]
• Fahland, D., Gläßer, T. M., Quilitz, B., Weißleder, S. and Leser, U.
  HUODINI - Flexible Information Integration for Disaster Management
  4th International Conference on Information Systems for Crisis Response and Management (ISCRAM), Delft, NL (2007)
• Heese, R., Leser, U., Quilitz, B. and Rothe, C.
  Index Support for SPARQL
  Poster Paper, European Semantic Web Conference (ESWC), Innsbruck, Austria (2007)
• Jana Bauckmann, Ulf Leser, Felix Naumann, Véronique Tietz
  Efficiently Detecting Inclusion Dependencies
  International Conference on Data Engineering (ICDE), Istanbul, Turkey, pp 1448-1450 (2007)

Other

• Philip Groth, Bertram Weiss, Ulf Leser
  Making use of Phenotype Data - an Ongoing Challenge
  Poster, ISMB/ECCB 2007, Vienna, Austria (2007)
• Georg Basler, Jan Hummel, Karin Köhl, Jan Hannemann, Joachim Kopka, Ulf Leser, Dirk Walther, Joachim Selbig
  Linking metabolite profiles and experiment data for large-scale comparative metabolome analyses
  Poster, German Conference on Bioinformatics, Potsdam, Germany (2007)
• Samira Jaeger, Sylvain Gaudan, Ulf Leser, Dietrich Rebholz-Schuhmann
  Protein Function Predicted using Protein Interaction Graphs and Publications
  Poster, German Conference on Bioinformatics, Potsdam, Germany (2007)

2006

Peer-reviewed publications

• Gunnar Kleinau, Mara Brehm, Urs Wiedemann, Dirk Labudde, Ulf Leser, Gerd Krause
  Implications for molecular mechanisms of glycoprotein hormone receptors using a new Sequence-Structure-Function Analysis resource.
  Journal of Molecular Endocrinology, Nov. 16 (2006)
• Heiko Müller, Ulf Leser, Johann-Christoph Freytag
  Classification of Contradiction Patterns.
  30th Annual Conference of the Gesellschaft für Klassifikation, Berlin, Germany (2006)
  Proceedings by Springer
• Heiko Müller, Johann-Christoph Freytag, Ulf Leser
  Describing Differences between Databases.
  Conference on Information and Knowledge Management (CIKM), Arlington, USA (2006)
• Jörg Hakenberg, Conrad Plake, Torsten Schiemann, Ulf Leser
  Ali Baba: Accessing PubMed using graphs.
  German Conference on Bioinformatics (GCB), September 20-22, Tübingen, Germany (2006)
• [Conference]
• Conrad Plake, Torsten Schiemann, Marcus Pankalla, Jörg Hakenberg, Ulf Leser
  Ali Baba: PubMed as a graph.
  Bioinformatics, 22(19):2444-2445 (2006)
• Jörg Hakenberg, Ulf Leser, Harald Kirsch, Dietrich Rebholz-Schuhmann
  Collecting a Large Corpus from all of Medline.
  Second International Symposium on Semantic Mining in Biomedicine (SMBM). Jena, Germany (2006)
  [Abstract] - [SMBM'06] - [Proceedings]
• Jana Bauckmann, Ulf Leser, Felix Naumann
  Efficiently Computing Inclusion Dependencies for Schema Discovery.
  Workshop InterDB (with ICDE06), Atlanta (2006)
• Uwe Radetzki, Ulf Leser, S.C. Schulze-Rauschenbach, J. Zimmermann, J. Lussem, T. Bode, A.B. Cremers
  Adapters, shims, and glue - service interoperability for in silico experiments.
  Bioinformatics, 22(9):1137-1143 (2006)
• Kristian Rother, Mathias Dunkel, Elke Michalsky, Silke Trissl, Andrean Goede, Ulf Leser, Robert Preissner
  A structural keystone for drug design.
  Journal of Integrative Bioinformatics (2006)
• Lukas Faulstich, Ulf Leser, Thorsten Vitt
  Implementing a Linguistic Query Language for Historic Texts.
  International Workshop on Query Languages and Query Processing, Springer-Verlag, München (2006).

Books

• Ulf Leser, Felix Naumann
  Informationsintegration
  dpunkt.verlag (2006)
  [ Book web site]
• Ulf Leser, Felix Naumann, Barbara Eckman (editors)
  Data Integration in the Life Sciences
  Proceedings of the Third International Workshop, Hinxton, July 2006.
  Springer LNCS Series: Lecture Notes in Bioinformatics, Vol. 4075, (2006)
  [ SpringerLink] [Workshop]
• Eric G. Bremer, Jörg Hakenberg, Eui-Hong Han, Daniel Berrar, Werner Dubitzky (editors)
  Knowledge Discovery in Life Science Literature
  Proceedings of the International Workshop KDLL 2006 in conjunction with PAKDD 2006, Singapore, April 2006.
  Springer LNCS Series: Lecture Notes in Bioinformatics, Vol. 3886, (2006)
  [Information] [ SpringerLink] [Workshop]

Other

• Silke Trißl, Ulf Leser
  GRIPP - Indexing and Querying Graphs based on Pre- and Postorder Numbering
  Technical Report No 207, Department for Computer Science, Humboldt-Universität zu Berlin (2006)
• Jana Bauckmann, Ulf Leser, Felix Naumann, Joachim Schmid
  Data Profiling: Effiziente Fremdschlüsselerkennung mit Aladin
  German Information Quality Conference & Workshop, Bad Soden, Germany, (2006)
• Artin Avanes, Timo Mika Gläßer, Markus Scheidgen
  Self-Organizing Information Systems for Disaster Management
  3. GI/ITG KuVS Fachgespräch "Ortsbezogene Anwendungen und Dienste", Berlin, Germany, (2006)
• Jörg Hakenberg, Conrad Plake, Torsten Schiemann, Ulf Leser
  Ali Baba
  Demo at NuGO WP8 Workshop on text mining and knowledge extraction and its application for nutrigenomics research, June 1-2 (2006)
  [Workshop]
• Jörg Hakenberg, Conrad Plake, Torsten Schiemann, Ulf Leser
  Ali Baba - Visualizing biological networks from PubMed query results.
  Poster at Data Integration in the Life Sciences (DILS), Hinxton, UK (2006).
• Heiko Müller, J-C Freytag, Ulf Leser
  On the Distance of Databases.
  Technical Report No 199, Department for Computer Science, Humboldt-Universität zu Berlin (2006)
• Rainer Dietrich et al.
  Das Interdisziplinäre Zentrum für Sprachliche Bedeutung .
  Humboldt Spektrum 4/2006
• Jana Bauckmann
  Efficiently Identifying Inclusion Dependencies in RDBMS
  18. Workshop über Grundlagen von Datenbanken (2006)

2005

Peer-reviewed publications

• Ulf Leser and Jörg Hakenberg
  What Makes a Gene Name? Named Entity Recognition in the Biomedical Literature.
  Briefings in Bioinformatics, 6(4):357-369 (2005)
  [Abstract] [ PubMed]
• Heiko Müller, Melanie Weis, Jens Bleiholder, Ulf Leser
  Erkennen und Bereinigen von Datenfehlern in naturwissenschaftlichen Daten.
  Datenbank Spektrum, Vol. 15, pp. 26-35 (2005).
• Ulf Leser
  A Query Language for Biological Networks.
  3rd European Conference on Computational Biology, Madrid, Spain (2005).
  Appeared in Bioinformatics, 21(suppl_2):ii33-ii39.
• Silke Trissl, Ulf Leser
  Querying ontologies in relational database systems.
  2nd Workshop on Data Integration in the Life Sciences (DILS05), San Diago, USA (2005).
  In Lecture Notes in Computer Science, Volume 3615, Aug 2005, Pages 63 - 79. [SpringerLink]
• Fouzia Moussouni, Emilie Guréin, Gwenaelle Marquet, Anita Burgun, Olivier Loréal. Laure Berti-Equille, Ulf Leser
  Integrating and Warehousing Liver Gene Expression Data and Related Biomedical Resources in GEDAW.
  2nd Workshop on Data Integration in the Life Sciences (DILS05), San Diago, USA (2005).
  In Lecture Notes in Computer Science, Volume 3615, Aug 2005, Pages 158 - 174. [ SpringerLink]
• Daniel Schober, Ulf Leser, Martin Zenke, Jens Reich
  GandrKB: Ontological Microarray Annotation and Visualization.
  Bioinformatics, 1;21(11):2785-2786 (2005)
• Jörg Hakenberg, Conrad Plake, Ulf Leser, Harald Kirsch, Dietrich Rebholz-Schuhmann
  LLL'05 Challenge: Genic Interaction Extraction with Alignments and Finite State Automata.
  Proc Learning Language in Logic Workshop (LLL'05) at ICML 2005, pp. 38-45. Bonn, Germany (August 2005)
  [Abstract] [LLL'05]
• Jörg Hakenberg, Steffen Bickel, Conrad Plake, Ulf Brefeld, Hagen Zahn, Lukas Faulstich, Ulf Leser, Tobias Scheffer
  Systematic Feature Evaluation for Gene Name Recognition.
  BMC Bioinformatics, 6(Suppl 1):S9, April 2005
  [Abstract] [ PubMed]
• Jörg Hakenberg, Juliane Rutsch, Ulf Leser
  Tuning Text Classification for Hereditary Diseases with Section Weighting.
  First International Symposium on Semantic Mining in Biomedicine (SMBM), pp. 34-37. Hinxton, UK (2005)
  [Abstract] [ Proceedings] [SMBM'05]
• Kristian Rother, Silke Trißl , Heiko Müller, Thomas Steinke, Ina Koch, Robert Preissner, Cornelius Frömmel, Ulf Leser
  Columba: An Integrated Database of Proteins, Structures, and Annotations.
  BMC Bioinformatics 2005, 6:81. [BMC Bioinformatics]
• Kristian Rother, Elke Michalsky, Ulf Leser
  How well are protein structures annotated in secondary databases?.
  PROTEINS, 60(4):571-76. (2005)
• Conrad Plake, Jörg Hakenberg, Ulf Leser
  Learning Patterns for Information Extraction from Free Text.
  Workshop des Arbeitskreises Knowledge Discovery (AKKD), Karlsruhe, Germany (2005)
  [Abstract]
• Conrad Plake, Jörg Hakenberg, Ulf Leser
  Optimizing Syntax Patterns for Discovering Protein-Protein Interactions.
  ACM SAC, Bioinformatics track, 1:195-201. Santa Fe, USA (2005)
  [Abstract] [SAC 2005]
• Ulf Leser, Felix Naumann
  (Almost) Hands-Off Information Integration for the Life Sciences.
  Conference on Innovative Database Research (CIDR 2005), Asilomar, CA.

Invited publications

• Anke Lüdeling, Thorwald Poschenrieder und Lukas Faulstich.
  DeutschDiachronDigital - Ein diachrones Korpus des Deutschen.
  Jahrbuch für Computerphilologie 2005.
  [Abstract, PDF]

Other

• Ulf Leser and Jörg Hakenberg
  Text Mining: Automatische Analyse biomedizinischer Texte .
  GenomXPress, 4.05, pp. 20-22 (2005).
  [Full issue]
• Ramakrishnan, R., Agrawal, R., Freytag, J.-C., Bollinger, T., Clifton, C. W., Dzeroski, S., Hipp, J., Keim, D., Kramer, S., Kriegel, H.-P., Leser, U., et al.
  Data Mining: The Next Generation. Report from a Dagstuhl Perspectives Workshop..
  Seminar Proceedings, Internationales Begegnungs- und Forschungszentrum (IBFI), Schloss Dagstuhl, Germany. (2005)
• Ulf Leser
  A Query Language for Biological Networks.
  Institut für Informatik der Humboldt-Universität zu Berlin, Technical Report 187 (2005)
• Sebastian Schmeier, Jörg Hakenberg, Axel Kowald, Ulf Leser, and Edda Klipp
  Recognition and Extraction of Entities related to Enzyme Kinetics.
  Poster at Biotext - a biomedical text mining workshop, London, UK, 9 November 2005.
  [Workshop]
• Sebastian Schmeier, Axel Kowald, Jörg Hakenberg, Ulf Leser, and Edda Klipp
  Finding Kinetic Data Using Text Mining.
  Poster at 5th Int Workshop on Bioinformatics and Systems Biology, Berlin, Germany, 25 August 2005.
  [PDF]
• Silke Trissl
  Anfragen in Ontologien in relationalen Datenbanken (German).
  17. GI-Workshop über 'Grundlagen von Datenbanken', Wörlitz, Germany (2005).
  [PDF]
• Stephan Rieche, Ulf Leser
  Versionierung in relationalen Datenbanken.
  Studierendenprogramm der 11. GI-Fachtagung für Datenbanksysteme in Business, Technologie und Web (BTW 2005), Karlsruhe.
• Lukas C. Faulstich, Ulf Leser und Anke Lüdeling
  Storing and querying historical texts in a relational database.
  Institut für Informatik der Humboldt-Universität zu Berlin, Informatik-Bericht Nr.176 (2005)
• Lukas C. Faulstich, Ulf Leser
  Implementing Linguistic Query Languages Using LoToS.
  Institut für Informatik der Humboldt-Universität zu Berlin, Informatik-Bericht Nr.195 (2005)

Press

• Interview Prof. Leser mit der Berliner Morgenpost vom 16.7.2005: " Strategien gegen Studienabbrecher und Langzeitstudenten"
• Interview in der Saarbrücker Zeitung zu Dagstuhl Seminare: "Ein Mekka für Forscher"

2004

Peer-reviewed publications

• S. Jurk, U. Leser, J.L. Marzo
  Cooperative Transaction Processing between Client and Server
  Eighth East-European Conference on Advances in Databases and Information Systems, Budapest, Hungary (2004)
• Heiko Müller, Ulf Leser, Johann-Christoph Freytag
  Mining for Patterns in Contradictory Data
  International Workshop on Information Quality in Information Systems (in conjunction with SIGMOD 2004), Paris, France (2004)
• Stefanie Dipper, Lukas Faulstich, Ulf Leser, Anke Lüdeling
  Challenges in Modelling a Richly Annotated Diachronic Corpus of German
  Workshop on XML-based Richly Annotated Corpora (in conjunction with LREC 2004), Lissabon, Portugal (2004)
• Kristian Rother, Heiko Müller, Silke Trissl, Ina Koch, Thomas Steinke, Robert Preissner, Cornelius Frömmel, Ulf Leser
  COLUMBA: Multidimensional Data Integration of Protein Annotations
  International Workshop on Data Integration in the Life Sciences, Leipzig, Germany (2004)
• Jörg Hakenberg, Sebastian Schmeier, Axel Kowald, Edda Klipp, Ulf Leser
  Finding Kinetic Parameters Using Text Mining
  OMICS: A Journal of Integrative Biology, Special Issue on Data Mining meets Integrative Biology, 8(2):131-152. (2004)
  [Abstract] [ PubMed]
• Felix Naumann, Johann-Christoph Freytag, Ulf Leser
  Completeness of Integrated Information Sources
  Journal on Information Systems, 29(7):583-615 (2004).

Other

• Emil Kroymann, Sebastian Thiebes, Anke Lüdeling, Ulf Leser
  Eine vergleichende Analyse von historischen und diachronen digitalen Korpora
  Institut für Informatik der Humboldt-Universität zu Berlin, Informatik-Bericht Nr.174
  [Paper]
• Uwe Radetzki, Ulf Leser, Armin B. Cremers
  IRIS: A Mediator-Based Approach Achieving Interoperability of Web Services in Life Science Applications
  3rd E-BioSci / ORIEL Annual Workshop, UK, October 2004
  [Paper]
• Steffen Bickel, Ulf Brefeld, Lukas Faulstich, Jörg Hakenberg, Ulf Leser, Condrad Plake, Tobias Scheffer
  A Support Vector Machine Classifier for Gene Name Recognition
  EMBO Workshop: A critical assessment of text mining methods in molecular biology. Granada, Spain, March 2004
  [Abstract] [Paper]
• Silke Trissl, Kristian Rother, Heiko Müller, Ulf Leser
  Columba - A Database of Annotations of Protein Structure
  HGM-Poster 2004
  [Abstract] [Poster]
• Sebastian Schmeier, Axel Kowald, Jörg Hakenberg, Ulf Leser, Edda Klipp
  Fighting the Data Acquisition Bottleneck
  Int Conf Systems Biology (ICSB), October 2004, Heidelberg, Germany.
  [Abstract]
• Silke Trissl, Kristian Rother, Ulf Leser
  Columba - A Database of annotated protein structure
  ECCB-Poster 2004
  [Abstract] [Poster]
• Stefan Günther, Kristian Rother, Silke Trissl
  The usefulness of integrated databases: a case study of COLUMBA
  ECCB-Poster 2004
  [Abstract] [Poster]

2003

Peer-reviewed publications

• Ulf Leser, Peter Rieger
  Integration molekularbiologischer Daten
  Datenbankspektrum Ausgabe 6, (in German) pp. 56-66 (2003)
  [Full Text]
• Jörg Hakenberg, Alexander Nussbaum, Hansjörg Schild, Hans-Georg Rammensee, Christina Kuttler, Hermann-Georg Holzhütter, Peter-M. Kloetzel, Stefan H.E. Kaufmann, Hans-Joachim Mollenkopf
  MAPPP - MHC-I Antigenic Peptide Processing Prediction.
  Applied Bioinformatics, 2(3):155-158 (2003)
  [Abstract] [PubMed]
• Felix Naumann, Johann-Christoph Freytag, Ulf Leser
  Completeness of Information Sources
  Workshop on Data Quality in Cooperative Information Systems, Siena, Italy (2003)
  [Full Text]
• Sebastian Schmeier, Jörg Hakenberg, Axel Kowald, Edda Klipp, Ulf Leser
  Text Mining for Systems Biology Using Statistical Learning Methods
  3. Workshop des Arbeitskreises Knowledge Discovery, Karlsruhe, Germany (2003)
  [Abstract] [Full text]

Other

• Tobias Scheffer, Ulf Leser (editors)
  Data Mining and Text Mining for Bioinformatics
  Proceedings of the European Workshop in conjunction with ECML/PDKK, Dubrovnik, Croatia
  [Full text]
• Kristian Rother, Silke Trissl, Heiko Müller, Patrick May, Rene Heek, Robert Preissner, Thomas Steinke, Ina Koch, Ulf Leser, Cornelius Frömmel
  Columba - A Database of Annotations of Protein Structure
  ECCB-Poster 2003
  [Abstract] [Poster]