Fabien Campagne, Ph.D.

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• Biography
• Publications

Biography

e-mail: fac2003@med.cornell.edu Please click here for further information.

Dr. Campagne’s research interests include a variety of bioinformatics research topics, from basic science to translational research. Past contributions include work on

·         Integration and visualization of biological information [1,3,4,5,12,13,26]

·         Biological information management [2,15,21,25]

·         Gene Hunting [7,14,17,20,30]

·         Biological data mining [8,16,22,29]

·         Text mining and biological information retrieval [19,27,28] (see also http://www.twease.org).

·         Biomarker discovery [23,24]

The major accomplishments of Dr. Campagne while at the Weill Medical College of Cornell University include the development of bioinformatics methods to (i) mine expressed sequence tags and prioritize cancer markers [24] (ii) predict S-nitrosylation protein targets (these proteins are potential drug targets for modulation of angiogenesis and vasculogenesis in diabetes, inflammation and cardiac diseases) [22,29] (iii) Predict a new calcium channel as a genetic risk factor for late onset alzheimer’s disease [30].

1. Campagne, F. and B. Maigret, Multiple sequence alignment in HTML: colored, possibly hyperlinked, compact representations. J Mol Graph Model, 1998. 16(1): p. 6-10, 34-5.

2. Horn F, Weare J, Beukers MW, Horsch S, Bairoch A, Chen W, Edvardsen O, Campagne F, Vriend G., GPCRDB: an information system for G protein-coupled receptors. Nucleic Acids Res, 1998. 26(1): p. 275-9.

3. Campagne, F. and H. Weinstein, Schematic representation of residue-based protein context-dependent data: an application to transmembrane proteins. J Mol Graph Model, 1999. 17(3-4): p. 207-13.

4. Campagne, F., et al., Visualisation and integration of G protein-coupled receptor related information help the modelling: description and applications of the Viseur program. J Comput Aided Mol Des, 1999 13(6): p. 625-43.

5. Konvicka, K., F. Campagne, and H. Weinstein, Interactive construction of residue-based diagrams of proteins: the RbDe web service. Protein Eng, 2000. 13(6): p. 395-6.

6. Campagne, F., Clustalnet: the joining of clustal and CORBA. Bioinformatics, 2000. 16(7): p. 606-12.

7. Max,. M., Shanker, Y.G., Huang, L., Rong, M., Liu, Z., Campagne, F., Weinstein, H., Damak, S. and Margolskee, R.F. Tas1r3, encoding a new candidate taste receptor, is allelic to the sweet responsiveness locus Sac. Nat. Gen. 2001. 28: p58-63

8. Skrabanek, L. and Campagne F. TissueInfo: high-throughput identification of tissue expression profiles and specificity. Nucleic Acids Res. 2001 Nov 1;29(21):E102-2.

9. Campagne, F. Interoperability calls for an unusual mix of skills. Nature. 2002 Jul 11;418(6894):125.

10. Horn F, Bettler E, Oliveira L, Campagne F, Cohen FE, Vriend G. GPCRDB information system for G protein-coupled receptors. Nucleic Acids Res. 2003 Jan 1;31(1):294-7.

11. Filizola M, Visiers I, Skrabanek L, Campagne F, Weinstein H. Functional mechanisms of GPCRs in a structural context. In Molecular Neuropharmacology, Strategies and Methods, Eds., A. Schousboe and H. Bräuner-Osborne, Humana Press. Dec. 2003,

12. Skrabanek L, Campagne F, Weinstein H. Building protein diagrams on the web with the Residue-based diagram editor RbDe. Nucleic Acids Res. Jul 2003, 1;31(13):3856-8.

13. Campagne F, Bettler E, Vriend G, Weinstein H. Batch mode generation of residue-based diagrams of proteins. Bioinformatics. 2003, Sep 22;19(14):1854-1855.

14. Characterization of the mouse AAVS1 ortholog, Dutheil N, Yoon-Robarts M, Ward P, Henckaerts E, Skrabanek L, Berns KI, Campagne F, and Linden RM, J. Virol. 2004 Aug;78(16):8917-21.

15. Quantitative information management for the biochemical computation of cellular networks. Campagne F, Neves S, Chang CW, Skrabanek L, Ram PT, Iyengar R, Weinstein H. Science STKE. 2004 Aug 24;(248):pl11.

16. Pseudomonas aeruginosa SoxR does not conform to the archetypal paradigm for SoxR-dependent regulation of the bacterial oxidative stress adaptive response. Marco Palma, Juan Zurita, Julian Ferreras, Stefan Worgall,  Lei Shi, Fabien Campagne, and Luis E. N. Quadri. Infection and Immunity. 2005 73(5):2958-66.

17. T1r3 a novel taste receptor. Robert Margolskee, Marianna Max, Harel Weinstein, Fabien Campagne, Gopi Y. Shanker. US Patent #20040219632 11/04/2004.

18. Critical evaluation of the JDO API for the persistence and portability requirements of complex biological databases. Srdanovic, M., Schenk, U., Schwieger, M., Campagne, F. BMC Bioinformatics 2005, 6:5.

19. Building a protein name dictionary from full text: a machine learning term extraction approach. Lei Shi, Fabien Campagne BMC Bioinformatics 2005, 6:88.

20. Crooked tail (Cd) Model of Human Folate Responsive NTD is Mutated in Wnt Co-receptor LRP6. Carter M, Chen X, Minnerath S, Slowinska B, Glickstein S, Shi L, Campagne F, Weinstein H and Ross ME. Proc Natl Acad Sci USA 2005 Sep 6;102(36):12843-8.

21. Minimal Information Requested In the Annotation of biochemical Models (MIRIAM). N Le Novère, N. Finney, A. Hucka, M. Bhalla, U. Campagne, F. Collado-Vides, J. Crampin, E. Halstead, M. Klipp, E. Mendes, P. Nielsen, P. Sauro, H. Shapiro B., Snoep, J.L. Spence, H.D. Wanner, B.L. Nat Biotechnol. 2005 Dec;23(12):1509-15.

22. SNOSID, a proteomic method for identification of cysteine S-nitrosylation sites in complex protein mixtures. Gang Hao, Behrad Derakhshan, Lei Shi, Fabien Campagne and Steven S. Gross. Proc Natl Acad Sci U S A. 2006 Feb; 103(4):1012-17.

23. Gene expression profiling separates chromophobe renal cell carcinoma from oncocytoma and identifies vesicular transport and cell junction proteins as differentially expressed genes. Stephen Rohan, Jiangling J. Tu, Jean Kao, Piali Mukherjee, Fabien Campagne, Xi K. Zhou, Elizabeth Hyjek, Miguel A. Alonso, Yao-Tseng Chen. Clin. Cancer Res.. 2006.

24. Mining expressed sequence tags identifies cancer markers of clinical interest. Campagne F, Skrabanek L. BMC Bioinformatics. 2006 Nov 1;7(1):481.

25. Lucy Skrabanek, Marta Murcia, Michel Bouvier, Lakshmi Devi, Susan R George, Martin J Lohse, Graeme Milligan, Richard Neubig, Krzysztof Palczewski, Marc Parmentier, Jean-Philippe Pin, Gerrit Vriend, Jonathan A Javitch, Fabien Campagne and Marta Filizola. Requirements and Ontology for a G Protein-Coupled Receptor Oligomerization Knowledge Base. BMC Bioinformatics. 2007, 8:177 

26. Eliza Chan and Fabien Campagne. Applications, representation and management of signaling pathway information. Introduction to the SigPath project. Introduction to Systems Biology, chapter 19. Humana Press. 2007.

27. Kevin C. Dorff, Matthew J. Wood and Fabien Campagne. Twease at TREC 2006: Breaking and fixing BM25 scoring with query expansion, a biologically inspired double mutant recovery experiment. Proceedings of the Text Retrieval Conference 2006. Gaithersburg, MA.

28. Campagne F. Objective and automated protocols for the evaluation of biomedical search engines using No Title Evaluation protocols. BMC Bioinformatics. 2008 Feb 29;9:132.

29. Beyond TissueInfo: Functional Prediction using Tissue Expression Profile Similarity Searches. Daniel Aguilar, Lucy Skrabanek, Steven S. Gross, Baldo Oliva, and Fabien Campagne. Nucleic Acids Research. In press.

30. Ute Dreses-Werringloer, Jean-Charles Lambert, Valérie Vingtdeux, Haitian Zhao, Horia Vais, Adam Siebert, Ankit Jain, Jeremy Koppel, Florence Pasquier, David Mann, Corinne Lendon, Philippe Amouyel, Peter Davies, J. Kevin Foskett, Fabien Campagne*, and Philippe Marambaud*. A polymorphism in CALHM1 influences Ca2 homeostasis, Ab levels, and Alzheimer’s disease risk. Cell, 2008.