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

Publications

2025 - 2024 - 2023 - 2022 - 2021 - 2020 - 2019 - 2018 - 2017 - 2016 - 2015 - 2014 - 2013 - 2012 - 2011 - 2010 - 2009 - 2008 - 2007 - 2006 - 2005 - 2004 - 2003


2025

Peer-reviewed publications
    • Lewinska, K. E., Okujeni, A., Kowalski, K., Lehmann, F., Radeloff, V. C., Leser, U. and Hostert, P. (2025).
      Impact of data density and endmember definitions on long-term trends in ground cover fractions across European grasslands
      Remote Sensing of the Environment (accepted)
    • Schäfer, P., Brand, J., Leser, U., Peng, B., & Palpanas, T. (2025).
      Fast and Exact Similarity Search in less than a Blink of an Eye 
      ICDE, Hong Kong SAR, China.
    • Belenki, D., Richter-Pechanska, P., Shao, Z., Bhattacharya, A., Lau, A., Ferreira de Freitas, J. A. N. L., Kandler, G., Hick, T., Cai, X., et al. (2025).
      Senescence-associated lineage-aberrant plasticity evokes T-cell-mediated tumor control
      Nature Communications 16:3079.
    • Lehmann, F., Bader, J., Tschirpke, F., DeMecquenem, N., Lößler, A., Becker, S., Lewinska, K. E., Thamsen, L. and Leser, U. (2025).
      WOW: Workflow-Aware Data Movement and Task Scheduling for Dynamic Scientific Workflows
      CCGrid. Tromso, Norway.
    • West, K., Lehmann, F., Bountris, V., Leser, U., Elkhatib, Y. and Thamsen, L. (2025).
      Exploring the Potential of Carbon-Aware Execution for Scientific Workflows
      CCGrid. Tromso, Norway.
    • Schäfer, P., Leser, U. (2025).
      Discovering Leitmotifs in Multidimensional Time Series
      PVLDB, London, UK.
Other

2024

Peer-reviewed publications
      • Middlehurst, M., Ismail-Fawaz, A., Guillaume, A., Holder, C., Rubio, D. G., Bulatova, G., Tsaprounis, L., Mentel, L., Walter, M., Schäfer, P., and Bagnall, A. (2024).
        aeon: a Python Toolkit for Learning from Time Series
        Journal of Machine Learning Research.
      • Lewińska, K. E., Ernst, S., Frantz, D., Leser, U. and Hostert, P. (2024).
        Global overview of usable Landsat and Sentinel-2 data for 1982-2023
        Data in Brief (accepted).
      • Sänger, M., Garda, S., Xing, W. D., Weber-Günzel, L., Droop, P., Fuchs, B., Akbik, A. and Leser, U. (2020).
        HunFlair2 in a cross-corpus evaluation of biomedical named entity recognition and normalization tools
        Bioinformatics (accepted).
      • Garda, S. and Leser, U. (2024).
        BELHD: Improving Biomedical Entity Linking with Homonym Disambiguation.
        Bioinformatics (accepted)
      • de Mecquenem, N., Bosse, S., Bountris, V., Mohammadi, S., Reinert, K. and Leser, U. (2024).
        CuttleFlow: Infrastructure-Specific Workflow Adaption for Improved Reusability
        eScience, Osaka, Japan.
      • Lehmann, F., Bader, J., de Mecquenem, N., Wang, X., Bountris, V., Friederici, F., Leser, U. and Thamsen, L. (2024).
        Ponder: Online Prediction of Task Memory Requirements for Scientific Workflows
        eScience, Osaka, Japan.
      • Ermshaus, A., Schäfer, P. and Leser, U. (2024).
        Multivariate Human Activity Segmentation: Systematic Benchmark with ClaSP
        Int. Workshop on Advanced Analytics and Learning on Temporal Data (AALTD), Vilnius, Lithuania.
      • Şerbetçi, O., Wang, X. D. and Leser, U. (2024).
        HU-WBI at BioASQ12B Phase A: Exploring Rank Fusion of Dense Retrievers for Biomedical Question Answering
        BioASQ Challenge Workshop.
      • Lewińska, K. E., Franz, D., Leser, U. and Hostert, P. (2024).
        Usable Observations over Europe: evaluation of compositing windows for Landsat and Sentinel-2 time series
        European Journal of Remote Sensing (accepted).
      • Sänger, M., De Mecquenem, N., Lewińska, K. E., Bountris, V., Lehmann, F., Leser, U. and Kosch, T. (2024).
        A Qualitative Assessment of Using ChatGPT as Large Language Model for Scientific Workflow Development
        Gigascience 13
      • 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 157
      • 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 40(3)
      • 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 149.
Other

2023

Peer-reviewed publications
Other

2022

Peer-reviewed publications
Other

2021

Peer-reviewed publications
Other

2020

Peer-reviewed publications
Other

2019

Peer-reviewed publications
Other

2018

Peer-reviewed publications
Other

2017

Peer-reviewed publications
Other

2016

Peer-reviewed publications

2015

Peer-reviewed publications

2014

Peer-reviewed publications

2013

Peer-reviewed publications
Other

2012

Peer-reviewed publications
Other

2011

Peer-reviewed publications
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
Other

2009

Peer-reviewed publications
Other

2008

Peer-reviewed publications
Other

2007

Peer-reviewed publications
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
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
Invited publications
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

2004

Peer-reviewed publications
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]