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
  • 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 (accepted).
  • 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 (accepted)
  • Ermshaus, Arik, Schäfer, Patrick, Leser, Ulf (2023)
    ClaSP - Parameter-free Time Series Segmentation
    Data Mining and Knowledge Discovery (Accepted), 2023.
  • de Mecquenem, N. (2023).
    Adapting scientific workflows to changing infrastructures.
    EDBT PhD Workshop, Ioannina, Greece (Accepted).


Peer-reviewed publications
  • Schäfer, P. and Leser, U. (2022)
    Motiflets - Simple and Accurate Detection of Motifs in Time Series
    PVLDB, Vancouver, Canada.
  • Peidli, Stefan and Green, Tessa D. and Shen, Ciyue and Gross, Torsten and Min, Joseph and Garda, Samuele and Taylor-King, Jake P. and Marks, Debora S. and Luna, Augustin and Blüthgen, Nils and Sander, Chris (2022)
    scPerturb: Information Resource for Harmonized Single-Cell Perturbation Data
    Workshop learning meaningful representations of life @NeurIPS.
  • Weber, L., Sänger, M., Garda, S., Barth, F., Alt, C. and Leser, U. (2022).
    Chemical-Protein Relation Extraction with Ensembles of Carefully Tuned Pretrained Language Models
    Database 2022.
  • J.A. Fries+, L. Weber+, N. Seelam+, G. Altay+, D. Datta*, S. Garda*, M. Kang*, R. Su*, W. Kusa*, S. Cahyawijaya*, F. Barth*, S. Ott*, M. Samwald*, S. Bach*, S. Biderman*, M. Sänger*,…, R. Martin, et al. (2022).
    BigBio: A Framework for Data-Centric Biomedical Natural Language Processing
    Conference on Neural Information Processing Systems (NeurIPS), Datasets and Benchmarks Track.
    + Shared First Author, * Shared Second Author
  • Bader, J., Lehmann, F., Groth, A., Thamsen, L., Scheinert, D., Will, J., Leser, U. and Kao, O. (2022).
    Reshi: Recommending Resources For Scientific Workflow Tasks on Heterogeneous Infrastructures
    International Performance Computing and Communications Conference (IPCCC), Michigan, US.
  • Ermshaus, A., Schäfer, P. and Leser, U. (2022).
    Window Size Selection In Unsupervised Time Series Analytics: A Review and Benchmark.
    Workshop on Advanced Analytics and Learning on Temporal Data, Grenoble, France.
  • Münchmeyer, J., Leser, U. and Tilmann, F. (2022).
    A probabilistic view on rupture predictability: all earthquakes evolve similarly.
    Geophysical Research Letters 49(13).
  • J.A. Fries*, N. Seelam*, G. Altay*, L. Weber*, M. Kang*, D. Datta*, R. Su*, S. Garda*, B. Wang, S. Ott, M. Samwald, W. Kusa (2022).
    Dataset Debt in Biomedical Language Modeling
    Workshop on Challenges & Perspectives in Creating Large Language Models.
    *:Equal contribution
  • Hilbrich, M. (2022).
    Knowledge Transfer Patterns to Make Disciplinary Knowledge Explicit — Exemplified by HPC
    21st Intelligent Software Methodology Tools, and Techniques (SOMET).
  • Hilbrich, M. and Bountris, V. (2022).
    re Workflows a Language to Solve Software Management Challenges? — A ßMACH Based Analysis
    21st Intelligent Software Methodology Tools, and Techniques (SOMET).
  • Garda, S., Lenihan-Geels, F., Proft, S., Hochmuth, S., Schülke, M., Seelow, D. and Leser, U. (2022).
    RegEl corpus: Identifying DNA regulatory elements in the scientific literature.
    Oxford Database 2022.
  • Singh, K., Münchmeyer, J., Weber, L., Leser, U. and Annika, B. (2022).
    Graph Neural Networks For Learning Molecular Excitation Spectra.
    Journal of Chemical Theory and Computation 18(7).
  • Bader, J., Lehmann, F., Thamsen, L., Will, J., Leser, U. and Kao, O. (2022).
    Lotaru: Locally Estimating Runtimes of Scientific Workflow Tasks in Heterogeneous Clusters
    Int. Conf. on Statistical and Scientific Database Management, Copenhagen, DK.
  • Hilbrich, M., Lehmann, F. (2022)
    Discussing Microservices: Definitions, Pitfalls, and their Relations
    IEEE International Conference on Services Computing, Barcelona, Spain.
  • Wang, X., Leser, U. and Weber, L. (2022).
    BEEDS: Large-Scale Biomedical Event Extraction using Distant Supervision and Question Answering
    Int. Workshop on Biomedical Language Processing (BioNLP).
  • Jack Woollam, Jannes Münchmeyer, Frederik Tilmann, Andreas Rietbrock, Dietrich Lange, Thomas Bornstein, Tobias Diehl, Carlo Giunchi, Florian Haslinger, Dario Jozinović, Alberto Michelini, Joachim Saul, Hugo Soto (2022).
    SeisBench—A Toolbox for Machine Learning in Seismology
    Seismological Research Letters, March 16, 2022
  • Foster, W., Ayzel, G., Münchmeyer, J., Rettelbach, T., Kitzmann, N.H., Isson, T.T., Mutti, M., and Aberhan, M. (2022).
    Machine learning identifies ecological selectivity patterns across the end-Permian mass extinction
    Paleobiology, 1-15. doi:10.1017/pab.2022.1
  • Simon, T., Riemer, P., Jarosch, A., Detjen, K., Di Domenico, A., Bormann, F., Menne, A., Khouja, S., Monjé, N., Childs, L. H., Lenze, D. Leser, U. ... Mamlouk, S. and Sers, C. (2022).
    DNA methylation reveals distinct cells of origin for pancreatic neuroendocrine carcinomas (PanNECs) and pancreatic neuroendocrine tumors (PanNETs)
    Genome Medicine 14 (24).
  • Münchmeyer, J. Woollam, J. Rietbrock, A., Tilmann, D. et al.
    Which picker fits my data? A quantitative evaluation of deep learning based seismic pickers
    JGR Solid Earth 127(1)
  • Other


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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]