| Robert
Hoffmann, PhD
Computational Biology Center, cBIO.
Memorial Sloan-Kettering Cancer Center, MSKCC.
1275 York Avenue. New York, NY 10021.
phone +1 646-735-8081, fax +1 646-735-0021
contact
|
curriculum vitae
|
| qualifications |
| 2001 |
|
2005 |
|
PhD, National Center of Biotechnology (CNB),
Madrid / Institute for Theoretical Chemistry, University of Vienna. |
| |
|
|
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Marie Curie Fellowship (4/2004), European Bioinformatics Institute, Cambridge, United Kingdom. |
| 1998 |
- |
1999 |
|
MSc, Institute of Molecular Pathology, Boehringer
Ingelheim, Austria / Institute for Theoretical Chemistry, University of Vienna. |
| 1997 |
- |
1998 |
|
Performance scholarship, University of Vienna. |
| 1994 |
- |
1998 |
|
Genetics, University of Vienna. |
| 1991 |
- |
1992 |
|
Student exchange program, Canada. |
| 1985 |
- |
1993 |
|
Grammar school, Vienna. |
| publications |
| Implementing the iHOP concept for navigation of biomedical literature. Hoffmann, R., Valencia, A. Bioinformatics 21(suppl. 2), ii252-ii258 (2005). , PDF , Suppl. Mat., Online Version |
| Text mining for metabolic pathways, signaling cascades, and protein networks. Hoffmann, R., Krallinger, M., Andres, E, Tamames, J., Blaschke, C., Valencia, A. Sci STKE 283, 21 (2005).
, PDF
|
| HomoMINT: an inferred human network based on orthology mapping of protein interactions discovered in model organisms. Persico, M., Ceol, A., Gavrila, C., Hoffmann, R., Florio, A., Cesareni, G. BMC Bioinformatics 6 Suppl 4:S21 (2005).
, PDF
|
| HCAD, closing the gap between breakpoints and genes. Hoffmann, R., Dopazo, J., Cigudosa, J.C., Valencia, A. Nucleic Acids Research 33,
D511-3 (2005).
, PDF |
| A gene network for navigating the literature. Hoffmann,
R., Valencia, A. Nature Genetics 36, 664 (2004).
, PDF |
| Protein interaction: same network, different hubs. Hoffmann,
R., Valencia, A. Trends Genet. 19(12), 681-683. (2003).
, PDF |
| Life cycles of successful genes. Hoffmann, R., Valencia,
A. Trends Genet. 19(2), 79-81. (2003).
, PDF |
| 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 J 21, 4621-31
(2002).
, PDF
|
| Extracting information automatically from the biological
literature. Blaschke, C., Hoffmann, R., Oliveros, J.C. and
Valencia, A. Comp. Funct. Genom. (2), 310-313. (2001).
PDF |
| The importance of short structural motifs in protein structure
analysis; Diploma thesis at the Institute for Theoretical Chemistry
and Molecular Structural Biology, University of Vienna (1999). |
| |
| tutorials |
| Gene Expression Levels as Traits in Genetic Linkage Analysis. Moeller, S., Hoffmann, R. ISMB (2005). |
| |
| 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. Poster
at the I.M.P. Recess (2000). |
| Analysis of TIS7 Effects on Epithelial Cell Morphology and
Gene Expression. Wick, N., Hoffmann, R., Vietor, I., Cotten,
M., Paiha, K., Huber, L. A. Poster at the I.M.P. Recess (1999). |
| |
| conferences |
| Implementing the iHOP concept for navigation of biomedical literature. Hoffmann, R., Valencia, A. 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. Leuven,
Belgium (2002). |
| Mining the Biomedical Literature. ISMB tutorial (2001). |
| |
| languages |
| Fluent in English, German and Spanish. |
| |
| professional development |
| 2005 |
|
- |
|
Post-doctoral research fellow, Memorial Sloan-Kettering Cancer Center, New York. |
| 2001 |
|
2005 |
|
PHD program, National Center
of Biotechnology (CNB), Madrid, Spain. |
| |
|
|
|
Marie Curie Fellowship (4/2004). Collaboration with the IntAct protein interaction database, European Bioinformatics Institute, Cambridge, United Kingdom. |
| 2000 |
|
|
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Independent consultant and software
developer, Vienna, Austria. |
| 1999 |
|
|
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Software development
for the administration
and analysis of microarray experiments (Java and C++), Institute of Molecular
Pathology, Boehringer Ingelheim, Vienna, Austria. |
| 1998 |
- |
1999 |
|
Diploma thesis headed by Dr. Peter Schuster, Institute of Molecular
Pathology, Boehringer Ingelheim / Institute for Theoretical Chemistry, Vienna, Austria. |
| 1997 |
|
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Practical training; Development
of an application for the management of clones and restriction
maps, Biochemical Institute, Vienna, Austria. |
| programming
skills |
|
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| object oriented languages
|
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Java, C++ |
| data exchange |
|
XML, XSL |
| scripting languages |
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HTML, JavaScript, Perl |
| database design |
|
Postgres, Oracle, SQL, jdbc |
| server-side |
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JSP, XSP, Tomcat, Cocoon |
| operating systems |
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Unix, Linux, win |
| statistical analysis |
|
R, spss, splus |
|
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