Publications of Ulf Leser
A more current list can be found here.
- Ulf Leser, Felix Naumann. Informationsintegration. dpunkt.verlag (in press).
- 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. ISBN: 3-540-36593-1
- Jana Bauckmann, Ulf Leser, Felix Naumann, Véronique Tietz (2007):
Efficiently Detecting Inclusion Dependencies
International Conference on Data Engineering (ICDE 2007), Istanbul, Turkey, (poster paper, to appear)
- Heiko Müller, Ulf Leser, Johann-Christoph Freytag (2006):
Classification of Contradiction Patterns. Jahrestagung der Gesellschaft für Klassifikation (GfKL), Berlin, Germany.
- Heiko Müller, Johann-Christoph Freytag, Ulf Leser (2006): Describing Differences between Databases. Conference on Information and Knowledge Management (CIKM), Arlington, USA (to appear).
- Jörg Hakenberg, Conrad Plake, Torsten Schiemann, Ulf Leser (2006): Ali Baba: Accessing PubMed using graphs. German Conference on Bioinformatics (GCB), September 20-22, Tübingen, Germany.
- Conrad Plake, Torsten Schiemann, Marcus Pankalla, Jörg Hakenberg, Ulf Leser (2006):
Ali Baba: PubMed as a graph. Bioinformatics, advance access published online on July 26.
- Jörg Hakenberg, Ulf Leser, Harald Kirsch, Dietrich Rebholz-Schuhmann (2006):
Collecting a Large Corpus from all of Medline. Second International Symposium on Semantic Mining in Biomedicine (SMBM). Jena, Germany.
- Jana Bauckmann, Ulf Leser, Felix Naumann (2006): Efficiently Computing Inclusion Dependencies for Schema Discovery. Workshop InterDB (with ICDE06).
- Uwe Radetzki, Ulf Leser, S.C. Schulze-Rauschenbach, J. Zimmermann, J. Lussem, T. Bode, A.B. Cremers (2006): Adapters, shims, and glue - service interoperability for in silico experiments. Bioinformatics, 22(9):1137-1143.
- Kristian Rother, Mathias Dunkel, Elke Michalsky, Silke Trissl, Andrean Goede, Ulf Leser, Robert Preissner (2006): A structural keystone for drug design. Journal of Integrative Bioinformatics.
- Lukas Faulstich, Ulf Leser, Thorsten Vitt (2006): Implementing a Linguistic Query Language for Historic Texts. International Workshop on Query Languages and Query Processing, München (to appear).
- Ulf Leser and Jörg Hakenberg (2005): What Makes a Gene Name? Named Entity Recognition in the Biomedical Literature, Briefings in Bioinformatics, 6(4), to appear.
- Heiko Müller, Melanie Weis, Jens Bleiholder, Ulf Leser (2005):
Erkennen und Bereinigen von Datenfehlern in naturwissenschaftlichen Daten, Datenbank Spektrum, Volume 15, p 26-35.
- Ulf Leser (2005): 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 (2005): Querying ontologies in relational database systems,
2nd Workshop on Data Integration in the Life Sciences (DILS05), San Diago, USA. Springer, Lecture Notes in Computer Science, Volume 3615, Aug 2005, Pages 63 - 79.
- Fouzia Moussouni, Emilie Guréin, Gwenaelle Marquet, Anita Burgun, Olivier Loréal. Laure Berti-Equille, Ulf Leser (2005):
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; Springer, Lecture Notes in Computer Science, Volume 3615, Aug 2005, Pages 158 - 174.
- Daniel Schober, Ulf Leser, Jens Reich (2005): GandrKB: Ontological Microarray Annotation and Visualization, Bioinformatics, 1;21(11):2785-2786.
- Jörg Hakenberg, Conrad Plake, Ulf Leser, Harald Kirsch, Dietrich Rebholz-Schuhmann (2005): LLL'05 Challenge: Genic Interaction Extraction with Alignments and Finite State Automata. Learning Language in Logic Workshop (LLL'05) at ICML 2005, pp. 38-45. Bonn, Germany.
- Jörg Hakenberg, Steffen Bickel, Conrad Plake, Ulf Brefeld, Hagen Zahn, Lukas Faulstich, Ulf Leser, Tobias Scheffer (2005): Systematic Feature Evaluation for Gene Name Recognition. BMC Bioinformatics, 6(Suppl 1):S9, April 2005.
- Jörg Hakenberg, Juliane Rutsch, Ulf Leser (2005): Tuning Text Classification for Hereditary Diseases with Section Weighting, First International Symposium on Semantic Mining in Biomedicine (SMBM), pp. 34-37. Hinxton.
- Kristian Rother, Silke Trißl , Heiko Müller, Thomas Steinke, Ina Koch, Robert Preissner, Cornelius Frömmel, Ulf Leser (2005): Columba: An Integrated Database of Proteins, Structures, and Annotations, BMC Bioinformatics 2005, 6:81.
- Kristian Rother, Elke Michalsky, Ulf Leser (2005): How well are protein structures annotated in secondary databases?, PROTEINS, 60(4):571-76.
- Conrad Plake, Jörg Hakenberg, Ulf Leser (2005): Learning Patterns for Information Extraction from Free Text, Workshop des Arbeitskreises Knowledge Discovery (AKKD), Karlsruhe, Germany
- Conrad Plake, Jörg Hakenberg, Ulf Leser (2005): Optimizing Syntax Patterns for Discovering Protein-Protein Interactions, ACM SAC, Bioinformatics track, 1:195-201. Santa Fe, USA.
- Ulf Leser, Felix Naumann (2005): (Almost) Hands-Off Information Integration for the Life Sciences, Conference on Innovative Database Research (CIDR , Asilomar, CA.
- Steffen Jurk, Ulf Leser, and J.L. Marzo (2004): "Cooperative Transaction Processing between Client and Server", Eighth East-European Conference on Advances in Databases and Information Systems, Budapest, Hungary .
- Heiko Müller, Ulf Leser, and Johann-Christoph Freytag(2004): "Mining for Patterns in Contradictory Data", International Workshop on Information Quality in Information Systems (in conjunction with SIGMOD 2004), Paris, France.
- Stefanie Dipper, Lukas Faulstich, Ulf Leser, and Anke Lüdeling (2004): "Challenges in Modelling a Richly Annotated Diachronic Corpus of German", Workshop on XML-based Richly Annotated Corpora (in conjunction with LREC 2004), Lissabon, Portugal .
- Jörg Hakenberg, Sebastian Schmeier, Axel Kowald, Edda Klipp, and Ulf Leser (2004): "Finding Kinetic Parameters using Text Mining", OMICS: A Journal of Integrative Biology, Special Issue on Data Mining meets Integrative Biology, 8(2):131-152.
- Kristian Rother, Heiko Müller, Silke Trissl, Ina Koch, Thomas Steinke, Robert Preissner, Cornelius Frömmel, Ulf Leser (2004): "COLUMBA: Multidimensional Data Integration of Protein Annotations", International Workshop on Data Integration in the Life Sciences, Leipzig, Germany. Springer LNBI.
- Felix Naumann, Johann-Christoph Freytag, Ulf Leser (2004): "Completeness of Integrated Information Sources", Journal on Information Systems, 29(7):583-615.
- Felix Naumann, Johann-Christoph Freytag, Ulf Leser (2003): "Completeness of Information Sources", Workshop on Data Quality in Cooperative Information Systems, Siena, Italy.
- Sebastian Schmeier, Jörg Hakenberg, Axel Kowald, Edda Klipp, and Ulf Leser (2003): "Text Mining for Systems Biology Using Statistical Learning Methods", 3. Workshop des Arbeitskreises Knowledge Discovery, Karlsruhe, Germany.
- Felix Naumann, Ulf Leser (2000): "Cooperative Query Answering with Density Scores", COMAD 2000, Pune, India.
- Ulf Leser, Felix Naumann (2000): "Query Planning with Information Quality Bounds", FQAS 2000, Warschau, Poland. Springer-Verlag, pp. 85-95.
- Susanne Busse, Ralf Kutsche, Ulf Leser (2000): "Strategies
for the Conceptual Design of Federated Information Systems", EFIS 2000, Dublin, Ireland, IOS Press /Infix, pp. 23-32.
- Felix Naumann, Ulf Leser, Johann Christoph Freytag (1999): "Quality-driven Integration of Heterogeneous Information Systems", VLDB'99, Edinburgh. Morgan Kaufmann. pp. 447-458.
- Kim Jungfer, Ulf Leser, Patricia Rodriguez-Tome (1999): "Constructing IDL Views of Relational Databases", CAISE'99, Heidelberg, Germany. Springer Verlag LNCS 1626, pp. 255-269.
- Steffen Moeller, Ulf Leser, Wolfgang Fleischman, Rolf Apweiler (1999): "EDITtoTeEMBL: A Distributed Approach to High-Quality Protein Sequence Annotation", Bioinformatics, 15(3), pp.219-227 (this is a revised version of the 1998 GCB conference paper)
- Emmanuel Barillot, Ulf Leser, Philip Lijnzaad, Christophe Cussat-Blanc, Kim Jungfer, Fridiric Guyon, Guy Vaysseix, Carsten Helgesen and Patricia Rodriguez-Tome (1999): "A Proposal for a Standard CORBA Interface for Genome Maps", Bioinformatics, 15(2), pp. 157-169.
- Ulf Leser (1999): "Designing a Global Information Resource for Molecular Biology (Short paper)", Datenbanken in Büro, Technik und Wissenschaft (BTW), Freiburg, Germany, pp. 362-369,
Springer Verlag.
- Ulf Leser, Hugues Roest Crollius, Hans Lehrach, Ralf Sudbrak (1999): "IXDB,
an X Chromosome Integrated Database (update)", Nucleic Acids Research, 27(1), 123-127.
- Ulf Leser (1998): "Maintenance and Mediation in Federated Databases", Workshop on Information Technology and Systems (WITS'98), Helsinki, pp.187-196. TR-19, University of Jyväskylä.
- Ulf Leser (1998): "Combining Heterogeneous Data Sources through Query Correspondence Assertions.", Workshop on Web Information and Data Management (WIDM98), in conjunction with CIKM 98, Bethesda, Maryland.
- Steffen Moeller, Ulf Leser, Wolfgang Fleischman, Rolf Apweiler (1998): "EDITtoTeEMBL:
A Distributed Approach to High-Quality Protein Sequence Annotation", 3rd German Conference on Bioinformatics, Cologne, Germany.
- Ulf Leser, Hans Lehrach, Hugues Roest Crollius (1998): "Issues
in Developing Integrated Genomic Databases and Application to the Human X Chromosome", Bioinformatics, Vol. 14(7), pp. 83-90.
- Ulf Leser, Robert Wagner, Andrei Grigoriev, Hans Lehrach, Hugues Roest Crollius (1998): "IXDB,
an X Chromosome Integrated Database", Nucleic Acids Research, Jan 1998, Vol. 26(1). p 108-111.
- Yaspo Marie-Laure, Leser Ulf, Lehrach Hans (1997) : "Updates and developments of ACeDB for chromosome-21 - integrating all published data in a common database (Meeting Abst)", Cytogenetics and Cell Genetics, 79(N1-2):39-39, 1997.
Technical reports, posters, and other
- Jana Bauckmann, Ulf Leser, Felix Naumann, Joachim Schmid (2006):
Data Profiling: Effiziente Fremdschlüsselerkennung mit Aladin
German Information Quality Conference & Workshop, Bad Soden, Germany.
- Jörg Hakenberg, Conrad Plake, Torsten Schiemann, Ulf Leser (2006):
Ali Baba
Demo at NuGO WP8 Workshop on text mining and knowledge extraction and its application for nutrigenomics research.
- Heiko Müller, J-C Freytag, Ulf Leser (2006): On the Distance of Databases.
Technical Report No 199, Department for Computer Science, Humboldt-Universität zu Berlin.
- Rainer Dietrich et al. (2006):
Das Interdisziplinäre Zentrum für Sprachliche Bedeutung.
Humboldt Spektrum
- 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. (2005):
Data Mining: The Next Generation. Report from a Dagstuhl Perspectives Workshop.,
Seminar Proceedings, Internationales Begegnungs- und Forschungszentrum (IBFI), Schloss Dagstuhl, Germany.
- Ulf Leser (2005): A Query Language for Biological Networks,
Institut für Informatik der Humboldt-Universität zu Berlin, Informatik-Bericht Nr.187.
- Stephan Rieche, Ulf Leser (2005):
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 (2005):
Storing and querying historical texts in a relational database, Institut für Informatik der Humboldt-Universität zu Berlin, Informatik-Bericht Nr.176.
- Lukas C. Faulstich, Ulf Leser (2005):
Implementing Linguistic Query Languages Using LoToS, Institut für Informatik der Humboldt-Universität zu Berlin, Informatik-Bericht Nr.195.
- Emil Kroymann, Sebastian Thiebes, Anke Lüdeling, and Ulf Leser (2004): "Eine vergleichende Analyse von historischen und diachronen digitalen Korpora", Institut für Informatik der Humboldt Universität zu Berlin, Technischer Report 174.
- Uwe Radetzki, Ulf Leser, and Armin B. Cremers (2004): "IRIS: A Mediator-Based Approach Achieving Interoperability of Web Services in Life Science Applications", 3rd E-BioSci / ORIEL Annual Workshop, UK.
- Steffen Bickel, Ulf Brefeld, Lukas Faulstich, Jörg Hakenberg, Ulf Leser, Condrad Plake, and Tobias Scheffer (2004): "A Support Vector Machine Classifier for Gene Name Recognition", EMBO Workshop: A critical assessment of text mining methods in molecular biology. Granada, Spain.
- Tobias Scheffer, Ulf Leser (editors) (2003): "Data
Mining and Text Mining for Bioinformatics", Proceedings of the European Workshop in conjunction with ECML/PDKK, Dubrovnik, Croatia.
- Ulf Leser, Peter Rieger (2003): "Integration
molekularbiologischer Daten", Datenbankspektrum Ausgabe 6, (in German) pp. 56-66.
- Ulf Leser (2000): "Query Planning in Mediator Based Information Systems", Ph.D. Dissertation, TU Berlin.
- Heiko Müller, Ulf Leser (1999): "Integration durch Standards: Erfahrungen mit CORBA in Life Science Research". 4. Workshop Föderierte Datenbanken, Berlin, pp. 89-102
- Felix Naumann, Ulf Leser (1999): "Density Scores for Cooperative Query Answering". 4. Workshop Föderierte Datenbanken, Berlin, pp.103-116.
- Ulf Leser (1999): "Globale Anfragebeantwortung mit verteilten, heterogenen Datenquellen", Informatik'99, Springer, pp. 265-272 (in german).
- Ralf-Detlef Kutsche, Ulf Leser, Johann Christoph Freytag (ed.) (1999): "4. Workshop Föderierte Datenbanken", Proceedings. Technical Report TR99-15, TU Berlin.
- Felix Naumann, Ulf Leser, Johann Christoph Freytag (1999): "Quality-driven
Integration of Heterogeneous Information Sources", Technical Report HUB-IB-117, February 1999
- Susanne Busse, Ralf-Detlef Kutsche, Ulf Leser, Herbert Weber (1999): "Federated
Information Systems: Concepts, Terminology and Architectures", Technical Report TR99-9, TU Berlin (this is a revised, condensed and english version of the next report).
- Ulf Leser, Susanne Busse, Herbert Weber (1999): "Mediator-basierte,
verteilte heterogene Informationssysteme", Final report from a
1998/1999 Seminar. Unpublished (in german).
- Ulf Leser (1998): "Query
Mediation for Heterogeneous Data Sources", Workshop
on Federated Databases, December 1998, Magdeburg, pp 33-44. Shaker
Verlag, Aachen.
- Ulf Leser, Stefan Tai, Susanne Busse (1998): "Design
Issues of Database Access in a CORBA Environment", Workshop
"Integration of Heterogeneous Information Systems", Magdeburg, Germany,
21.9.98.
- Ulf Leser (1997): "Ansaetze
zur Förderation molekulargenetischer Datenbanken". GI
Datenbank Rundbrief, Vol. 20, Nov 1997, p. 57-61.
Presentations, poster
- Ulf Leser (2004): "Mining for Patterns in Contradictions", Presentation Dagstuhl Seminar on Data Mining: The Next Generation.
- Silke Trissl, Kristian Rother, Heiko Müller, Ulf Leser (2004): "Columba - A Database of Annotations of Protein Structure", Human Genome Meeting, Berlin. Poster.
- Sebastian Schmeier, Axel Kowald, Jörg Hakenberg, Ulf Leser, and Edda Klipp (2004): "Fighting the Data Acquisition Bottleneck", Int Conf Systems Biology (ICSB), October 2004, Heidelberg, Germany. Poster.
- Silke Trissl, Kristian Rother, Ulf Leser (2004): "Columba - A Database of annotated protein structure", ISMB, Glasgow, UK. Poster.
- Stefan Günther, Kristian Rother, Silke Trissl (2004): "The usefulness of integrated databases: a case study of COLUMBA", ECCB, Glasgow, UK. Poster.
- Kristian Rother, Silke Trissl, Heiko Müller, Patrick May, Rene Heek, Robert Preissner, Thomas Steinke, Ina Koch, Ulf Leser, Cornelius Frömmel (2003): "Columba - A Database of Annotations of Protein Structure", ECCB, Paris, France. Poster
- Ulf Leser (2003): "Ontologies in Bioinformatics", Workshop on Systems Biology of Microbacteria, Bielefeld.
- Ulf Leser, Anke Lüdeling (2003) "Verwandtschaft und Abstammung - Linguistic meets Bioinformatics", Symposium Geisteswissenschaften - Naturwissenschaften, Adlershof.
- Ulf Leser (2003): "Introduction to relational databases - Introduction to Molecular Biology Databases - Data Integration in the Life Sciences - Mining Biomedical Literature"
, presentations and tutorials held at the EMBO practical course on Data Mining and Genome Sequence analysis, Lima, Peru.
- Ulf Leser (2003): "Data Quality in Genome Research", Panel discussion at the Workshop on Data Quality in Cooperative Information Systems, Siena, Italy.
- Ulf Leser (2003): "Data Quality
and Information Integration", Dagstuhl Seminar on Data
and Process Integration in the Life Sciences.
- Ulf Leser (2003): "Integrating
Protein Annotations", Tag der
Wissenschaft, Zentrum für Biophysik und Bioinformatik,
Berlin.
- Ulf Leser (2002): "The Berlin
Centre for Genome-Based Bioinformatics", Statusbericht
Bioinformatik, Bio-Techpark Luckenwalde.
- Ulf Leser (2000): "CORBA
in Life Science Research", Workshop Informationssysteme
in der Bioinformatik, Magdeburg.
- Ulf Leser (1999): "Query Mediation in Federated Information
Systems".
Presentation at Dagstuhl Seminar on Systems Integration.
- Ulf Leser (1999): "The Emerging Life Science Research Standard
for
Genome
Maps". Presentation at the 1st OPM-JAVA-CORBA Workshop. At the
Resource Center of the German Human Genome Project (RZPD), Berlin.
- Kim Jungfer, Ulf Leser and Patricia Rodriguez-Tomé (1998):
"IDLViews:
A
CORBA Wrapper for Relational Databases". Poster
at the 2nd Conference on Objects
in Bioinformatics, Cambridge, UK, Aug. 1998.
- Ulf Leser, Patricia Rodriguez-Tome (1998): "Query Mediation
for
Molecular
Biology" Poster
at the 2nd Conference
on Objects in Bioinformatics, Cambridge, UK, Aug. 1998.
- Robert Wagner, Ulf Leser, Hans Lehrach, Ralf Sudbrak (1998): "A
Comprehensive Database for the Human X Chromosome" Poster
at the 2nd Conference on Objects in
Bioinformatics, Cambridge, UK, Aug. 1998.
- Ulf Leser (1998): "A Mediator Approach to Database
Interoperability
in
Molecular Biology", Seminar at the
European Bioinformatics Institute, Cambridge, UK, March 1998
- Ulf Leser, Robert Wagner, Hans Lehrach, Hugues Roest Crollius
(1997): "IXDB:
An Integrated Database for Genomic Data of the Human X Chromosome".
Poster at the 2nd German
Conference
on Bioinformatics, September 1997, Munich, Germany..
- Ulf Leser, Robert Wagner (1997): "A guided tour through IXDB",
European
X Transcript consorium Meeting, Berlin, Sep. 1997.
- Ulf Leser, Robert Wagner, Hans Lehrach, Hugues Roest Crollius
(1997):
"IXDB: Integration of genomic data for physical mapping of the human X
chromosome", 5th
International Conferences on Intelligent Systems for Molecular
Biology, June 1997, Halkidiki, Greece
- Ulf Leser (1997): "Integration und Foerderation verteilter
molekularbiologischer Datenbanken". Vortrag auf der GI-Fachgruppe
Datenbanken, Herbsttagung, Okt. 1997, Magdeburg
- Hugues Roest Crollius, Ulf Leser, Hans Lehrach (1996): "IXDB:
An
Integrated Database for the Human X Chromosome", Computer
Demonstration at the 7th Single
Chromosome Workshop on Human Chromosome X, October 1996, Hinxton,
U.K.
- Marie-Laure Yaspo, Ulf Leser , Ela Hunt, Hans Lehrach (1996): "Towards
an
integrated database for chromosome 21", Computer Demonstration at
the Single Chromosome Workshop on Human Chromosome 21, May 1996, Cold
Spring Harbor, N.Y., USA.
Last updated: 2/2004