Jean F Fontaine

Summary

Country: Germany

Publications

  1. pmc CELDA -- an ontology for the comprehensive representation of cells in complex systems
    Stefanie Seltmann
    Charite Universitatsmedizin Berlin, Berlin Brandenburg Center for Regenerative Therapies BCRT, Berlin, Germany
    BMC Bioinformatics 14:228. 2013
  2. pmc Using cited references to improve the retrieval of related biomedical documents
    Francisco M Ortuño
    Computer Architecture and Computer Technology Department, University of Granada, Granada, Spain
    BMC Bioinformatics 14:113. 2013
  3. pmc The Protein-Protein Interaction tasks of BioCreative III: classification/ranking of articles and linking bio-ontology concepts to full text
    Martin Krallinger
    Structural Biology and Biocomputing Programme, Spanish National Cancer Research Centre CNIO, Madrid, Spain
    BMC Bioinformatics 12:S3. 2011
  4. pmc PESCADOR, a web-based tool to assist text-mining of biointeractions extracted from PubMed queries
    Adriano Barbosa-Silva
    Computational Biology and Data Mining Group, Max Delbruck Center for Molecular Medicine, Robert Rössle Strasse, 10, D 13125, Berlin, Germany
    BMC Bioinformatics 12:435. 2011
  5. pmc LAITOR--Literature Assistant for Identification of Terms co-Occurrences and Relationships
    Adriano Barbosa-Silva
    Max Delbruck Center for Molecular Medicine, Berlin, Germany
    BMC Bioinformatics 11:70. 2010
  6. pmc MedlineRanker: flexible ranking of biomedical literature
    Jean Fred Fontaine
    Computational Biology and Data Mining Group, Max Delbruck Center for Molecular Medicine, Robert Rossle Strasse 10, D 13125, Berlin, Germany
    Nucleic Acids Res 37:W141-6. 2009
  7. pmc QiSampler: evaluation of scoring schemes for high-throughput datasets using a repetitive sampling strategy on gold standards
    Jean F Fontaine
    Max Delbruck Center for Molecular Medicine, Robert Rossle Strasse 10, 13125 Berlin, Germany
    BMC Res Notes 4:57. 2011
  8. pmc Génie: literature-based gene prioritization at multi genomic scale
    Jean Fred Fontaine
    Max Delbruck Center for Molecular Medicine, Robert Rossle Str 10, 13125 Berlin, Germany
    Nucleic Acids Res 39:W455-61. 2011

Collaborators

  • Miguel A Andrade-Navarro
  • Adriano Barbosa-Silva
  • Enrique M Muro
  • Matthew R Huska
  • Georgios A Pavlopoulos
  • Francisco M Ortuño
  • Stefanie Seltmann
  • Martin Krallinger
  • Alexander Damaschun
  • Andreas Kurtz
  • Ulf Leser
  • Fritz Lekschas
  • Ignacio Rojas
  • Ludger Jansen
  • Throng Nghia Nguyen-Dobinsky
  • Harald Stachelscheid
  • Mike Tyers
  • Rafal Rak
  • Feifan Liu
  • W John Wilbur
  • Xinglong Wang
  • Marta Iannuccelli
  • Leonardo Briganti
  • Miguel Vazquez
  • Sergio Matos
  • Luana Licata
  • Andrew Chatr-Aryamontri
  • Gerold Schneider
  • Gianni Cesareni
  • Hagit Shatkay
  • Robert Leaman
  • Keith Noto
  • Fabio Rinaldi
  • Luis Rocha
  • Ashish V Tendulkar
  • Graciela Gonzalez
  • Sun Kim
  • Andrew Winter
  • Alfonso Valencia
  • Florian Leitner
  • Zhiyong Lu
  • Luisa Castagnoli
  • Livia Perfetto
  • Shashank Agarwal
  • CHARLES ELKAN
  • Rezarta Islamaj Dogan
  • David Salgado

Detail Information

Publications8

  1. pmc CELDA -- an ontology for the comprehensive representation of cells in complex systems
    Stefanie Seltmann
    Charite Universitatsmedizin Berlin, Berlin Brandenburg Center for Regenerative Therapies BCRT, Berlin, Germany
    BMC Bioinformatics 14:228. 2013
    ..CELDA (Cell: Expression, Localization, Development, Anatomy) is a novel ontology for the association of primary experimental data and derived knowledge to various types of cells of organisms...
  2. pmc Using cited references to improve the retrieval of related biomedical documents
    Francisco M Ortuño
    Computer Architecture and Computer Technology Department, University of Granada, Granada, Spain
    BMC Bioinformatics 14:113. 2013
    ..As a solution to this problem, we propose a query expansion method that extends the information related to a manuscript using its cited references...
  3. pmc The Protein-Protein Interaction tasks of BioCreative III: classification/ranking of articles and linking bio-ontology concepts to full text
    Martin Krallinger
    Structural Biology and Biocomputing Programme, Spanish National Cancer Research Centre CNIO, Madrid, Spain
    BMC Bioinformatics 12:S3. 2011
    ....
  4. pmc PESCADOR, a web-based tool to assist text-mining of biointeractions extracted from PubMed queries
    Adriano Barbosa-Silva
    Computational Biology and Data Mining Group, Max Delbruck Center for Molecular Medicine, Robert Rössle Strasse, 10, D 13125, Berlin, Germany
    BMC Bioinformatics 12:435. 2011
    ..Current tools do not allow studying these data with a focus on concepts of relevance to a user, for example, interactions related to a disease or to a biological mechanism such as protein aggregation...
  5. pmc LAITOR--Literature Assistant for Identification of Terms co-Occurrences and Relationships
    Adriano Barbosa-Silva
    Max Delbruck Center for Molecular Medicine, Berlin, Germany
    BMC Bioinformatics 11:70. 2010
    ..Therefore, the study of the current literature about a selected topic deposited in public databases, facilitates the generation of novel hypotheses associating a set of bioentities to a common context...
  6. pmc MedlineRanker: flexible ranking of biomedical literature
    Jean Fred Fontaine
    Computational Biology and Data Mining Group, Max Delbruck Center for Molecular Medicine, Robert Rossle Strasse 10, D 13125, Berlin, Germany
    Nucleic Acids Res 37:W141-6. 2009
    ..We show that our tool can be highly accurate and that it is able to process millions of abstracts in a practical amount of time. MedlineRanker is free for use and is available at http://cbdm.mdc-berlin.de/tools/medlineranker...
  7. pmc QiSampler: evaluation of scoring schemes for high-throughput datasets using a repetitive sampling strategy on gold standards
    Jean F Fontaine
    Max Delbruck Center for Molecular Medicine, Robert Rossle Strasse 10, 13125 Berlin, Germany
    BMC Res Notes 4:57. 2011
    ..abstract:..
  8. pmc Génie: literature-based gene prioritization at multi genomic scale
    Jean Fred Fontaine
    Max Delbruck Center for Molecular Medicine, Robert Rossle Str 10, 13125 Berlin, Germany
    Nucleic Acids Res 39:W455-61. 2011
    ..Common run times below a minute, even when analyzing the human genome with hundreds of thousands of literature records, allows the use of Génie in routine lab work. Availability: http://cbdm.mdc-berlin.de/tools/genie/...