RESEARCH / PROFESSIONAL EXPERIENCE

Post-doctoral research fellow - Memorial Sloan-Kettering Cancer Center (MSKCC), Computational Biology Center, New York, USA. PI: Chris Sander. 2005 - 2009

Post-doctoral research fellow - Massachusetts Institute of Technology (MIT), Computer Science and Artificial Intelligence Laboratory (CSAIL), Cambridge USA. PI: Tim Berners-Lee and Danny Weitzner. 2006 - 2008.

Marie Curie Research Fellow - European Bioinformatics Institute (EBI), Cambridge, United Kingdom. PI: Rolf Apweiler and Henning Hermjakob. 4/2004.

PhD candidate - National Center of Biotechnology (CNB), Madrid, Spain. PI: Alfonso Valencia and Peter Schuster. 2001 - 2005.

IT consultant and software developer, Vienna, Austria. 1999 - 2000.

FOUNDED PROJECTS

• WikiGenes - Collaborative Publishing Resource for the Life Sciences.   (2008-2009)
• iHOP information resource for biology and medicine.   (2004-2009)

PUBLICATIONS

PEER REVIEWED, FIRST AUTHOR

• A wiki for the life sciences where authorship matters. Hoffmann, R. Nature Genetics 40, 1047 - 1051 (2008) -  
• Large-scale assessment of the effect of popularity on the reliability of research. Pfeiffer, T. & Hoffmann, R. PLoS One 4(6):e5996 (2009)
• Temporal patterns of genes in scientific publications. Pfeiffer, T. & Hoffmann, R. PNAS 104 (29), 12052–12056 (2007)
• Implementing the iHOP concept for navigation of biomedical literature. Hoffmann, R., Valencia, A. Bioinformatics 21(suppl. 2), ii252-ii258 (2005)
• Text mining for metabolic pathways, signaling cascades, and protein networks. Hoffmann, R., Krallinger, M., Andres, E, Tamames, J., Blaschke, C., Valencia, A. Science STKE 283, 21 (2005)
• HCAD, closing the gap between breakpoints and genes. Hoffmann, R., Dopazo, J., Cigudosa, J.C., Valencia, A. Nucleic Acids Research 33, D511-3 (2005)
• A gene network for navigating the literature. Hoffmann, R., Valencia, A. Nature Genetics 36, 664 (2004) -  
• Protein interaction: same network, different hubs. Hoffmann, R., Valencia, A. Trends in Genetics 19(12), 681-683. (2003)
• Life cycles of successful genes. Hoffmann, R., Valencia, A. Trends in Genetics 19(2), 79-81. (2003)

PEER REVIEWED

• Planning the Human Variome Project: The Spain report. Kaput, J. et al. Hum Mutation 30(4) 496-510 (2009)
• Introducing Meta-Services for Biomedical Information Extraction. Leitner, F. et al. Genome Biology 9 S6 (2008)
• iHOP web services. Fernandez, J.M., Hoffmann, R., Valencia, A. Nucleic Acid Research 35 (2), W21-W26 (2007)
• MINT: an inferred human network based on orthology mapping of protein interactions discovered in model organisms. Perisco, M., Ceol, A., Gavrila, C., Hoffmann, R., Florio, A., Cesareni, G. BMC Bioinformatics 6 Suppl 4:S21 (2005)
• TIS7 interacts with the mammalian SIN3 histone deacetylase complex in epithelial cells. Vietor, I., Vadivelu, S. K., Wick, N., Hoffmann, R., Cotten, M. et al. Embo Jounal 21, 4621-31 (2002)
• Extracting information automatically from the biological literature. Blaschke, C., Hoffmann, R., Oliveros, J.C. and Valencia, A. Comp. Funct. Genom. (2), 310-313. (2001)

BOOK CHAPTERS

• Biological Knowledge Extraction / Bioinformatics for Systems Biology. Leitner, F., Hoffmann, R., Valencia, A. Springer (2009)
• Using the iHOP Information Resource to Mine the Biomedical Literature on Genes, Proteins, and Chemical Compounds. Hoffmann, R. Current Protocols in Bioinformatics, John Wiley & Sons (2007)
• Text Mining in Genomics and Proteomics / Fundamentals of Data Mining in Genomics and Proteomics. Hoffmann, R. Springer (2006)

THESES

• Creation of Biological Knowledge through the Integration of Textual and Large-Scale Experimental Information, PhD Thesis. National Center of Biotechnology (CNB), Madrid / Institute for Theoretical Chemistry, University of Vienna (2005)
• The importance of short structural motifs in protein structure analysis, Master Thesis. Institute of Molecular Pathology, Boehringer Ingelheim / Institute for Theoretical Chemistry, University of Vienna (1999)

TUTORIALS

• Gene Expression Levels as Traits in Genetic Linkage Analysis. Moeller, S., Hoffmann, R. ISMB (2005)

PRESENTATIONS

• WikiGenes - Collaborative Publishing on the Scientific Web2.0. Semantic Enrichment of the Scientific Literature, EBI Workshop. Cambridge, UK (2009)
• Towards collaborative publishing in biomedicine. Human Variome Project Meeting. San Feliu de Guixols, Spain (2008)
• Implementing the iHOP concept for navigation of biomedical literature. ECCB (2005)
• iHOP. E-BioSci/ORIEL Annual Workshop. Cambridge, UK (2004)
• Navigating PubMed. E-BioSci/ORIEL Annual Workshop. Varenna, Italy (2003)
• Text discovery tools, Application to cancer research. Katholieke Univiersity, Leuven, Belgium (2002)
• Mining the Biomedical Literature. ISMB tutorial (2001)

POSTERS

• Simultaneous exploration of existing knowledge and novel experimental data. Hoffmann, R. Sander, C., Valencia, A. ISMB (2005)
• iHOP: A gene network for navigating PubMed. Hoffmann, R., Valencia, A. ISMB/ECCB (2004)
• Transcriptional control of epithelial cell polarity and motility by TIS7. Wick, N., Vietor, I., Cotten, M., Bister, M., Hoffmann, R., Beyer, A., Zatloukal, K., Huber, L. A. IMP Recess (2000)
• Analysis of TIS7 Effects on Epithelial Cell Morphology and Gene Expression. Wick, N., Hoffmann, R., Vietor, I., Cotten, M., Huber, L. A. IMP Recess (1999)

AWARDS AND HONORS

• Society in Science, The Branco Weiss Fellowship, ETH Zurich, Switzerland. 2006 - 2011.
• Marie Curie Research Fellowship, European Commission. 2004.
• Performance Scholarship, University of Vienna. 1997 - 1998.

EDUCATION

National Center of Biotechnology (CNB) / Institute for Theoretical Chemistry, University of Vienna, Madrid, Spain / Vienna, Austria.

PhD in Computational Biology. 2001 - 2005.

Institute of Molecular Pathology, Boehringer Ingelheim (IMP) / Institute for Theoretical Chemistry, University of Vienna, Vienna, Austria

MSc, Master Thesis. 1998 - 1999.

University of Vienna, Vienna, Austria

MSc, Genetics. 1994 - 1998.

AD HOC REVIEWER

PLoS Computational Biology; Bioinformatics; Nature Publishing Group; BMC Bioinformatics; Nucleic Acids Research; Drug Discovery Today

AFFILIATIONS

International Society for Computational Biology (ISCB)

COMPUTER SKILLS AND PROFICIENCY

LANGUAGES

English (fluent), German (native), Spanish (fluent), French (knowledgeable)

EXTERNAL HOMEPAGE