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


2018 - 2017 - 2016 - 2015 - 2014 - 2013 - 2012 - 2011 - 2010 - 2009 - 2008 - 2007 - 2006 - 2005 - 2004 - 2003


Peer-reviewed publications
  • Middlehurst, M. Schäfer, P., and Bagnall, A. (2024).
    Bake off redux: a review and experimental evaluation of recent time series classification algorithms
    Data Mining and Knowledge Discovery (accepted).
  • Schintke, F., Belhajjame, K., De Mecquenem, N., Frantz, D., Guarino, V., Hilbrich, M., Lehmann, F., Missier, P., Sattler, R., Sparka, J., Vu, D. and Leser, U (2024).
    Validity constraints for data analysis workflows
    Future Generation Computing Systems (accepted)
  • Ermshaus, A., Schäfer, P. and Leser, U. (2024).
    Raising the ClaSS of Streaming Time Series Segmentation
    PVLDB (accepted), Guangzhou, China
  • Mohammadi, S., Pourkarimi, L., Zschäbitz, M., Aretz, T., Leser, U., Reinert, K. and De Mecquenem, N. (2024).
    Optimizing Job/Task Granularity for Metagenomic Workflows in Heterogeneous Cluster Infrastructures
    Workshop on Data Analytics solutions for Real-LIfe APplications (DARLI-AP), Paestum, Italy.
  • Schulz, M.-A., Albrecht, J. P., Yilmaz, A., Koch, A., Leser, U., Ritter, K. and Kainmüller, D. (2024).
    TLIMB - A Transfer Learning Framework for IMage Analysis of the Brain
    Workshop on Data Analytics solutions for Real-LIfe APplications (DARLI-AP), Paestum, Italy.
  • Ermshaus, A., Piechotta, M., Rüter, G., Keilholz, U., Leser, U. and Benary, M. (2024).
    preon: Fast and accurate entity normalization for drug names and cancer types in precision oncology
    Bioinformatics (accepted)
  • Stögbauer, F., Otto, R., Jöhrens, K., Tinhofer, I., Keilholz, U., Poremba, C., Keller, U., Leser, U., Weichert, W., Boxberg, M., and Klinghammer, K. (2024).
    Molecular subtyping of head and neck cancer – Clinical applicability and correlations with morphological characteristics.
    Oral Oncology (accepted).


Peer-reviewed publications
  • Frantz, D., Schug, F., Wiedenhofer, D., Baumgart, A., Virág, D., Cooper, S., Gómez-Medina, C., Lehmann, F., Udelhoven, T., van der Linden, S., Hostert, P. & Haberl, H. (2024).
    Unveiling patterns in human dominated landscapes through mapping the mass of built structures in the US.
    Nature Communications 14.
  • Büttner, M., Leser, U., Schneider, L. and Schwendicke, F. (2023).
    Natural Language Processing: Chances and Challenges in Dentistry.
    Journal of Dentistry (accepted).
  • Benary, M., Wang, X., Schmidt, M., Soll, D., Hilfenhaus, G., Nassir, M., Sigler, C., Knödler, M., Keller, U., Beule, D., Keilholz, U., Leser, U., and Rieke, DT (2023).
    Leveraging Large Language Models for Decision Support in Personalized Oncology.
    JAMA Network Open 6(11).
  • Garda, S., Weber-Genzel, L., Robert, M. and Leser, U. (2023).
    BELB: a Biomedical Entity Linking Benchmark.
    Bioinformatics (accepted).
  • Weber-Genzel, L., Barth, F., Lorenz, L., Konrath, F., Kirsten, H., Wolf, J. and Leser, U. (2023).
    PEDL+: Protein-centered relation extraction from PubMed at your fingertip
    Bioinformatics (accepted)
  • Lehmann, F., Bader, J., Thamsen, L. and Leser, U. (2023).
    The Common Workflow Scheduler Interface: Status Quo and Future Plans
    Workshop on Workflows in Support of Large-Scale Science (accepted).
  • Serbetci, O. and Leser, U. (2023).
    Applicability of models trained on generated clinical German datasets on out-domain data
    Nat. Conf. on Learning, Knowledge, Data, and Analysis (LWDA), Marburg, Germany.
  • Barth, F., Weber-Genzel, L. and Leser, U. (2023).
    Biomedical Event Extraction with Generative Language Models
    Nat. Conf. on Learning, Knowledge, Data, and Analysis (LWDA), Marburg, Germany.
  • Bader, J., Lehmann, F., Thamsen, L., Leser, U. and Kao, O. (2022).
    Lotaru: Locally Predicting Workflow Task Runtimes for Resource Management on Heterogeneous Infrastructures
    Future Generation Computing Systems (accepted).
  • Vu, A. D., Sparka, J. A., de Mecquenem, N., Kehrer, T., Leser, U. and Grunske, L. (2023).
    Contract-Driven Design of Scientific Data Analysis Workflows
    eScience (accepted), Cyprus.
  • Schäfer, P. and Leser, U. (2023).
    WEASEL 2.0 - A Random Dilated Dictionary Transform for Fast, Accurate and Memory Constrained Time Series Classification
    European Conference on Machine Learning, Turin, Italy (accepted).
  • Mohammadi, S., PourKarimi, L., Droop, F., De Mecquenem, N., Leser, U. and Knut, R. (2023).
    A Mathematical Programming Approach for Resource Allocation of Data Analysis Workflows on Heterogeneous Clusters.
    Journal of Supercomputing.
  • Ermshaus, A., Singh, S. and Leser, U. (2023).
    Time Series Segmentation Applied to a New Data Set for Mobile Sensing of Human Activities
    Int. Workshop on Data Analytics solutions for Real-LIfe APplications Ioanina, Greece.
  • Lehmann, F., Bader, J., Tschirpke, F., Thamsen, L. and Leser, U. (2023).
    How Workflow Engines should talk to Resource Managers: A Proposal for a Common Workflow Scheduling Interface
    Int. Conf. on Cluster, Cloud, and Internet Computing (CCGRID), Bangalore, India.
  • Otto, R., Detjen, K., Pamela, R., Fattohi, M., Grötzinger, C., Rindi, G., Wiedenmann, B., Sers, C. and Leser, U. (2022).
    Transcriptomic deconvolution of neuroendocrine neoplasms predicts clinically relevant characteristics
    Cancers 15(3)
  • Ermshaus, Arik, Schäfer, Patrick, Leser, Ulf (2023)
    ClaSP - Parameter-free Time Series Segmentation
    Data Mining and Knowledge Discovery 37.
  • de Mecquenem, N. (2023).
    Adapting scientific workflows to changing infrastructures.
    EDBT PhD Workshop, Ioannina, Greece.


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Peer-reviewed publications
  • 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".


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Peer-reviewed publications
  • 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)


Peer-reviewed publications
  • Ulf Leser, Felix Naumann
    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]
  • 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)
  • 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)


Peer-reviewed publications
Invited publications
  • 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.
  • 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.
  • Silke Trissl
    Anfragen in Ontologien in relationalen Datenbanken (German).
    17. GI-Workshop über 'Grundlagen von Datenbanken', Wörlitz, Germany (2005).
  • 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)


Peer-reviewed publications
  • 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
  • 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
  • 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.
  • 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]


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]
  • 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]