Resume

Birth date:	April 15th, 1967 (Flers, France)
Citizenship:	French
Work address:	Laboratoire de Biologie, Informatique et Mathématiques Commissariat à l'Energie Atomique Grenoble, France

Research domain: Bioinformatics / Computational Biology (databases, sequence analysis, information extraction, data and text mining).

Current position

Research engineer in biocomputing
Laboratory of Biology, Informatics and Mathematics (BIM),
DRDC, Life Science Division,
Commissariat à l'Energie Atomique,
Grenoble, France.

Experience

September 2004 - August 2005: postdoctoral position at the University of Nice in the Virtual Biology Lab (Pr R. Christen)

Automated extraction of knowledge from the scientic literature to annotate results of high-throughput experiment analysis (e.g. microarrays)

By improving the methodology we developed for the automated management of the GPCRDB, we have set up a new database, named NucleaRDB (Horn et al. 2001). It holds sequence-derived data, structural data, chromosomal locations and other useful informations related to nuclear hormone receptors. The novel aspect of this project is that the 'missing data', such as ligand binding constants, mutation information, expression data, single nucleotide polymorphisms, etc., will be automatically extracted by computer programs from electronically available literature.
We have implemented a method that extracts point mutations from the literature. Full text papers in HTML and PDF formats are imported and automatically read. Point mutations are then extracted and validated via several plausibility filters. We applied the method to GPCRs and nuclear receptors and the results are available at www.gpcr.org/mutation and www.receptors.org/NR/mutation/, respectively (MuteXt - Horn et al. 2004).

November 1996 - December 1999: postdoctoral position at the European Molecular Biology Laboratory (EMBL), Heidelberg, Germany, in Gert Vriend's group, BIOcomputing unit.

I was (and I'm still) in charge of the design and maintenance of the GPCRDB (http://www.gpcr.org/7tm/), an information system devoted to G Protein-Coupled Receptors (GPCRs). This work was a part of a European project aimed at the automatic creation and management of data banks for heterogeneous data. Another part of my work was to harvest the GPCRDB content to infer functional data from GPCR sequences (Horn, Bywater et al. 1998; Horn, van der Wenden et al. 2000).

Education

1992-1996: Ph.D. period in Cellular Biology, Structural Biology and Microbiology (ex-INGENIA)
Université de la Méditerranée (Marseille, France) in the "Laboratoire of Génétique et de Physiologie du Développement" (LGPD) [Lab's director: Prof. R. Rosset; Thesis supervisor: Dr. B.Jacq].

Title:"Dexifly: une base de données dédiée à l'étude fonctionnelle des gènes régulateurs de la mise en place de l'axe antéro-postérieur de l'embryon chez Drosophila melanogaster" (Dexifly: a database devoted to the functional study of the regulatory genes involved in Drosophila embryonic pattern formation).

"Méthodes d'analyse et d'obtention de données pour l'ingénierie des protéines et le séquençage du génome" (Data analysis and acquisition methods for protein engineering and genome sequencing) : courses in molecular dynamics, crystallography, NMR, artificial intelligence, peptide synthesis, sequence analysis algorithms, sequencing methods, genetic analysis.

Computing experience

• Programming: Python, Perl, CGI scripts, Pascal, Basic, Shell

• Natural language Processing (Python NLP toolkit)

• Platforms: PC (DOS, Windows, Linux),Unix station, Apple Macintosh

• Database systems: Relational Database Management Systems (MySQL, PostgreSQL,4th Dimension, Dbase III+).

• Other: good knowledge of HTML, Microsoft applications

• Good knowledge of sequence analysis software (clustal, fasta) and data retrieval systems (Blast, SRS). Notions in molecular modeling (What If).

• Expert in the design of biological database (User-friendly and simple interfaces, data import, data curation, data mining etc.) and websites (see www.receptors.org for the databases I am in charge of).
  

Publications

1. GRIS: Glycoprotein-hormone Receptor Information System.
   Van Durme J, Horn F, Costagliola S, Vriend G, Vassart G.
   Mol Endocrinol. 2006 (in press)

2. A family-based approach reveals the function of residues in the nuclear receptor ligand-binding domain.
   Folkertsma S, van Noort P, Van Durme J, Joosten HJ, Bettler E, Fleuren W, Oliveira L, Horn F, de Vlieg J, Vriend G.
   J. Mol. Biol. 2004 341:321-335. [Medline]

3. Automated extraction of mutation data from the literature: application of MuteXt to G protein-coupled receptors and nuclear hormone receptors.
   Horn F, Lau AL, Cohen FE.
   Bioinformatics 2004 20:557-568. [Medline]

4. NRSAS: Nuclear Receptor Structure Analysis Servers
   Emmanuel Bettler, Roland Krause, Florence Horn, and Gerrit Vriend
   Nucleic Acids Res. 2003 31:3400-3403. [Medline]

5. GPCRDB information system for G protein-coupled receptors
   Florence Horn, Emmanuel Bettler, Laerte Oliveira, Fabien Campagne, Fred E. Cohen, and Gerrit Vriend
   Nucleic Acids Res. 2003 31:294-297 (database issue). [Medline]

6. NRMD: Nuclear Receptor Mutation Database
   Joost J.J. Van Durme, Emmanuel Bettler, Simon Folkertsma, Florence Horn, and Gert Vriend
   Nucleic Acids Res. 2003 31:331-333 (database issue). [Medline]

7. Phosphorylation and Intramolecular Stabilization of the Ligand Binding Domain in the NUclear Receptor Steroidogenic factor 1
   M. Desclozeaux, I. Krylova, F. Horn, R.B. Fletterick et H. A. Ingraham.
   Mol. Cell Biol. 2002 22:7193-7203 [Medline]

8. Collecting and harvesting biological data: the GPCRDB and NucleaRDB information systems
   Florence Horn, Gerrit Vriend and Fred E. Cohen
   Nucleic Acids Res. 2001 29: 346-349 (Database issue) [Medline - NAR full text].

9. Receptors coupling to G proteins: Is there a signal behind the sequence?
   F. Horn, E. van der Wenden, L. Oliveira A.P. IJzermann and G. Vriend
   Proteins: Structure, Function, and Genetics 2000 41:448-459.

   It is known that some GPCR families may couple to a single G protein subtype and others families to several G protein subtypes. Has the evolution left a signature of G protein selectivity (or promiscuity) in the GPCR sequences? We tried to answer to this question using our famous Correlated Mutation Analysis (CMA).

10. G protein-coupled receptors, or the power of data
    F. Horn, M. Mokrane, J. Weare, and G. Vriend
    In Genomics and Proteomics (Ed. S. Suhai), Kluwer Academic / Plenum Publishers, New York, (2000), pp. 191-215 (+cover)

    Everything, and a little bit more, you ever wanted to know (but were too afraid to ask) about the collection and harvesting of GPCR data.

11. G protein-coupled receptors in silico.
    F. Horn and G. Vriend
    J. Mol. Med. (1998) 76, 464-468.

    This is a short review of the WWW based GPCR related facilities with some emphasis on the GPCRDB of course. This short review is written for medical doctors with an interest in drug design.

12. The interaction of class B G protein-coupled receptors with their hormones.
    F. Horn, R. Bywater, G. Krause, W. Kuipers, L. Oliveira, A.C.M. Paiva, C. Sander, and G. Vriend
    Receptors and Channels (1998) 5:305-314. [Medline Abstract]

    One of the more important aspects of the GPCRDB is the inclusion of inference engines. What, otherwise, would all the data be good for if it is not harvested to its fullest extend. CMA (Correlated Mutation Analysis) is a technique to determine 'important' residues from multiple sequence alignments. In this article we use this technique to determine which residues in the class B GPCRs (and their ligands) are involved in receptor-ligand interaction.

13. GPCRDB: an information system for G protein coupled receptors.
    F. Horn, J. Weare, M.W. Beukers, S. Hörsch, A. Bairoch, W. Chen, Ø Edvardsen, F. Campagne, and G. Vriend
    Nucleic Acids Res. (1998) 26: 277-281. [Medline Abstract]
    This is the first 'official' GPCRDB article. It does not provide much science, but should be seen as a road map for GPCRDB navigation.

14. FlyNets and GIF-DB, two internet databases for molecular interactions in Drosophila melanogaster.
    E. Mohr, F. Horn, F. Janody, C. Sanchez, V. Pillet, B. Bellon, L. Röder, B. Jacq
    Nucleic Acids Res (1998) 26: 89-93. [Medline Abstract]

15. GIF-DB, a WWW database on gene interactions involved in Drosophila melanogaster development.
    B. Jacq, F. Horn, F. Janody, N. Gompel, O. Serralbo, E. Mohr, C. Leroy, , B. Bellon, L. Fasano, P. Laurenti and L. Röder
    Nucleic Acids Res(1997) 25: 67-71. [Medline Abstract]

Oral presentations

• School of Informatics and Genome for students
  November, 1992, Gif sur Yvette, France.
  "Designing and development of a database prototype on the development of Drosophila". (in French)

• 8th French Meeting on Genetic and Molecular Biology of Drosophila
  September, 1993, Vichy, France.
  "A prototype database on regulator genes involved in the embryonic development of Drosophila melanogaster." (in French)

• Genome and Informatics Inter-Disciplinary Forum
  June, 1994, Aussois, France.
  "DEXIFLY: a database prototype on gene interaction and expression data in Drosophila melanogaster." (in French)

• 36th Annual Drosophila Research Conference
  April 5-9th, 1995, Atlanta, Georgia, USA
  Database demonstration: "DEXIFLY: a database on the genes involved in Drosophila embryonic pattern formation."

• 10th French Meeting on Genetic and Molecular Biology of Drosophila
  September 27-29th, 1995, Vichy, France.
  "In silico study of genes controlling the embryonic development of Drosophila : DEXIFLY and GIF.DB." (in French)

• 2nd French Meeting on Drosophila
  March 1-2nd, 1996, Montpellier, France.
  "Protein/DNA interaction network in Drosophila embryogenesis and the GIFTS web site." (in French)

• Second InverseA Workshop
  June 5-6, 1998, London, UK.
  "The G Protein-Coupled Receptor DataBase."

• EMBO Practical Course: Current Methods in Membrane protein Research
  June 17-26, 1998, Heidelberg, Germany.
  Presentation and practical demonstration of the GPCRDB, an information system for G protein-coupled receptors.

• Seminar on Algorithmic and Biology: Knowledge Databases - Data and Methods Formalisation in Genome and Post-Genome Projects
  March 21-24, 1999, Institut Pasteur, Paris, France.
  "GPCRDB: an information system for G Protein-Coupled Receptors, or what to do with genome data?" (in English)

• In Silico Biology - Data acquisition and Model Development
  June 8-10, 1999, San-Francisco, CA, USA.
  "CMA algorithm for predicting protein-protein interactions."

• The Center for Biomolecular Science & Engineering Seminar Series
  May 9, 2000, UCSC, Santa-Cruz, CA, USA.
  F. Horn
  "Collecting and Harvesting Biological Data: The GPCRDB & NucleaRDB Databases."

• Ferring Research Institute
  November 28, 2001, Ferring Research Institute, San Diego, CA, USA.
  "How do we build a knowledge base? The GPCRDB as an example."

• The Dutch National GPCR Day
  September 19, 2003, Utrecht, The Netherlands.
  "The GPCRDB."

• Laboratoire de Biometrie et Biologie Evolutive, Univ. Claude Bernard - Lyon I
  October 24, 2003, Lyon, France.
  "MuteXt: extraction automatique de donnees de mutation a partir de la litterature scientifique."

• The Swiss Institute of Bioinformatics
  November 6, 2003, SIB, Geneva, Suisse.
  "MuteXt: Automated extraction of mutation data from the literature."

• BioSapiens workshop on membrane proteins
  January 30, 2005, Nijmegen, The Netherlands.
  "The GPCRDB in 2005."

• Groupe de travail ISIBio (Workshop)
  March 29, 2005, Institut Curie, Paris, France.
  "Using NLP & text mining to populate ontologies"

Posters

• 3rd International Symposium on VIP, PACAP, and related peptides
  September 17-20, 1997 Freiburg (Germany)
  F. Horn, J. Weare, G. Vriend
  "How do VIP, PACAP and related peptides interact with receptors?"

• 3rd Annual International Conference on G Protein-Coupled Receptors, Therapeutic Advancements and Applications
  October 6-8, 1997, Coronado, CA (USA).
  F. Horn, J. Weare, G. Vriend
  "GPCRDB: an information system for G protein coupled receptors".
  "How do VIP, PACAP and related peptides interact with receptors? "

• Talking proteins: An EMBO workshop on Sequence Analysis, Modelling and Simulation
  September 16-19, 1998, Heidelberg (Germany).
  F. Horn, J. Weare, G. Vriend
  "How do VIP, PACAP and related peptides interact with receptors?"

• Integrative Bioinformatics
  October 12-13, 1998, Zurich (Switzerland).
  F. Horn, M. Mokrane, J. Weare, G. Vriend
  "GPCRDB: an information system for G protein coupled receptors: harvesting its content using CMA."

• Bioinformatics and Genome Research
  June 14-15, 1999, San-Francisco, CA (USA).
  F. Horn, M. Mokrane, J. Weare, G. Vriend
  "GPCRDB: an information system for G protein coupled receptors."

• ISMB 2000: 8th International Conference on Intelligent Systems for Molecular Biology
  August 19-23, 2000, La Jolla, CA (USA).
  F. Horn, G. Vriend, F.E. Cohen
  "Collecting and Harvesting Biological Data: The NucleaRDB."

• ISMB 2001: 9th International Conference on Intelligent Systems for Molecular Biology
  July 21-25, 2001, Copenhagen, Denmark.
  F. Horn, E. Bettler, G. Vriend, F.E. Cohen
  "Facilitating knowledge acquisition and discovery through automatic web data mining."

• Pacific Symposium on Biocomputing 2003
  January 3-7, 2003, Lihue, Hawaii (USA).
  F. Horn, L.C. Lee, F.E. Cohen
  "MuteXt: an automated method to extract mutation data from the literature."

• ECCB 2003: European Conference on Computational Biology
  27-30 Septembre 2003, Paris, France.
  F. Horn, L.C. Lee, F.E. Cohen
  "MuteXt: an automated method to extract mutation data from the literature."