Florian Leitner



Phone: +34-913 363 672

E-mail: florian.leitner@upm.es

Regular mail:

Departamento de Inteligencia Artificial

Escuela Técnica Superior de Ingenieros Informáticos

Campus de Montegancedo

Universidad Politécnica de Madrid

28660 Boadilla del Monte, Madrid, España

Personal website



Post-doctoral research fellow with a "Juan de la Cierva" scholarship.

Short Bio

Florian Leitner has been a one-year post-doctoral researcher in Alfonso Valencia's  Structural Computational Biology group at the Spanish National Cancer Research Center (CNIO), where he also completed his work for a PhD degree in Molecular Biology in 2012 at the Universidad Autónoma de Madrid. He holds a Masters degree in Molecular Biology from the University of Vienna, while working on post-translational protein modifications with Frank Eisenhaber at the IMP in Austria. Before that, he collaborated as an undergraduate with Rebecca Wade's group in Heidelberg on the annotation of protein structures, which gave rise to his first published work.

Research interests

Bioinformatics, molecluar biology, text mining, probabilistic graphical models, machine learning. Biological foci: post-translational (protein) modifications, protein interaction networks, gene regulation networks, and neurobiology.

Journal papers

  • Comeau DC, Islamaj Doğan R, Ciccarese P, Cohen KB, Krallinger M, Leitner F, Lu Z, Peng Y, Rinaldi F, Torii M, Valencia A, Verspoor K, Wiegers TC, Wu CH, Wilbur WJ. BioC: a minimalist approach to interoperability for biomedical text processing. Database (Oxford). 2013
  • Salgado D, Krallinger M, Depaule M, Drula E, Tendulkar AV, Leitner F, Valencia A, Marcelle C. MyMiner: a web application for computer-assisted biocuration and text annotation. Bioinformatics. 2012
  • Krallinger M, Leitner F, Vazquez M, Salgado D, Marcelle C, Tyers M, Valencia A, Chatr-aryamontri A. How to link ontologies and protein-protein interactions to literature: text-mining approaches and the BioCreative experience. Database (Oxford). 2012
  • Krallinger M, Vazquez M, Leitner F, Salgado D, Chatr-Aryamontri A, Winter A, Perfetto L, Briganti L, Licata L, Iannuccelli M, Castagnoli L, Cesareni G, Tyers M, Schneider G, Rinaldi F, Leaman R, Gonzalez G, Matos S, Kim S, Wilbur WJ, Rocha L, Shatkay H, Tendulkar AV, Agarwal S, Liu F, Wang X, Rak R, Noto K, Elkan C, Lu Z, Dogan RI, Fontaine JF, Andrade-Navarro MA, Valencia A. The Protein-Protein Interaction tasks of BioCreative III: classification/ranking of articles and linking bio-ontology concepts to full text. BMC Bioinformatics. 2011
  • Leitner F, Chatr-aryamontri A, Mardis SA, Ceol A, Krallinger M, Licata L, Hirschman L, Cesareni G, Valencia A. The FEBS Letters/BioCreative II.5 experiment: making biological information accessible. Nat Biotechnol. 2010
  • Leitner F, Krallinger M, Cesareni G, Valencia A. The FEBS Letters SDA corpus: a collection of protein interaction articles with high quality annotations for the BioCreative II.5 online challenge and the text mining community. FEBS Lett. 2010
  • Leitner F, Mardis SA, Krallinger M, Cesareni G, Hirschman LA, Valencia A. An Overview of BioCreative II.5. IEEE/ACM Trans Comput Biol Bioinform. 2010
  • Krallinger M, Leitner F, Valencia A. Analysis of biological processes and diseases using text mining approaches. Methods Mol Biol. 2010
  • Leitner F, Krallinger M, Rodriguez-Penagos C, Hakenberg J, Plake C, Kuo CJ, Hsu CN, Tsai RT, Hung HC, Lau WW, Johnson CA, Saetre R, Yoshida K, Chen YH, Kim S, Shin SY, Zhang BT, Baumgartner WA Jr, Hunter L, Haddow B, Matthews M, Wang X, Ruch P, Ehrler F, Ozgür A, Erkan G, Radev DR, Krauthammer M, Luong T, Hoffmann R, Sander C, Valencia A. Introducing meta-services for biomedical information extraction. Genome Biol. 2008
  • Krallinger M, Leitner F, Rodriguez-Penagos C, Valencia A. Overview of the protein-protein interaction annotation extraction task of BioCreative II. Genome  Biol. 2008
  • Krallinger M, Morgan A, Smith L, Leitner F, Tanabe L, Wilbur J, Hirschman L, Valencia A. Evaluation of text-mining systems for biology: overview of the Second BioCreative community challenge. Genome Biol. 2008
  • Leitner F, Valencia A. A text-mining perspective on the requirements for electronically annotated abstracts. FEBS Lett. 2008
  • Gabdoulline RR, Hoffmann R, Leitner F, Wade RC. ProSAT: functional annotation of protein 3D structures. Bioinformatics. 2003