BioInformatician (software developer and project leader)

at the Swiss Institute of BioInformatics, Geneva, Switzerland.
Swiss-Prot group (Dr. Ioannis Xenarios)
"Anabelle" automated annotation platform project leader (since Nov. 2005) .
May 2002 - present

Research Scientist (biology of aging)

at the University of Colorado at Boulder, USA.
Laboratory of Pr. T.E. Johnson.
Oct. 1998 - April 2002

Research Scientist (neurobiology)

at the Department of Biochemistry, University of Geneva, Switzerland.
Laboratory of Dr. Patrick Nef.
Oct. 1997 - Sept. 1998

October 1997: Ph.D. degree in Biochemistry (with honors):

"Caenorhabditis elegans Neuronal Calcium Sensor-1: From Gene To Behavior"
University of Geneva, Switzerland.
Advisors: Dr. P. Nef, Professor J. Gruenberg.

Research Assistant (neurobiology)

Ph.D. candidate at the Department of Biochemistry, University of Geneva, Switzerland.
Advisors: Dr. P. Nef, Professor J. Gruenberg.
Jan. 1993 - Oct. 1997

Aug. 1992: Master in Biochemistry (with honors):

University of Geneva, Switzerland.
Advisor: Professor S. Edelstein.

Game Developer

(Freelance) Sold a game to UbiSoft Entertainment (UBI).
1988 ~ 1989

Since May 2002: BioInformatician @ Swiss Institute of BioInformatics;
Automation of UniProtKB/Swiss-Prot protein knowledgebase curation; data visualization:
- Developments for Swiss-Prot: "Anabelle" - Automated annotation platform: context sensitive propagation of annotation templates (annotation "rules") associated with trusted sequence analysis results; used for HAMAP microbial annotation project. "MeMiKi" - Content / information management system used to edit documentation / help for the new UniProt web site (also used to power my personal web site / blog - edouard.decastro.name). "WiKiNomy" - a wiki editor system used to annotate nodes in our hierarchies databases such as (alpha) taxonomy and Post-Translational Modifications (PTM). "ViralZone" Virus Information site and a portal to facilitate access to UniProtKB/Swiss-Prot viral protein entries (built with WiKiNomy).
- Developments for Prosite: "PSMaker" - motif detection profiles building and testing platform; "ScanProsite" (motif detection) and other web tools ( "PSView" example - domain architecture visualization; entry and doc views); "ps_scan" (motif scanning) updates; miscellaneous tools (profile construction/maintenance, parsers/syntax-checkers, release tools, incremental match database) publi. 9,11, 12,13, 14,15.

Oct. 1998 - April 2002: Research Scientist @ CU Boulder; Work on oxidative stress and aging in Caenorhabditis elegans. Isolation of long-lived oxidatif-stress-resistant C. elegans mutants, forward genetics... publi. 5,7, 8,10

1994-1998: Ph.D. + "post-doc" 1^st year (research associate); Work on Caenorhabditis elegans neuronal calcium sensors. Cloning of two new C. elegans Neuronal Calcium Sensors: Ce-NCS-1 and Ce-NCS-2 publi. 2. Focusing on the study of Ce-NCS-1 publi. 4 which is highly conserved through evolution. In the C. elegans the protein, which is thought to play a role in synaptic efficacy, is expressed in some sensory neurons. Isolation of a transposon deletion derivative strain with the ncs-1 gene deleted. Analysis of the mutant that shows thermotaxis defects publi. 6.

1993: Ph.D. 1^st year (research assistant); Work on calcium binding proteins in the nervous system. Cloning and analyzing rat NCS-1 publi. 2,4, the ortholog (100% a.a. identity) of a new calcium binding protein: chick NCS-1 (Neuronal-Calcium-Sensor 1) publi. 1, isolated in P. Nef's laboratory.

1992: Master in Biochemistry; Work on molecular computer graphics. Creation of "ViSP" (Visualization System for Proteins) a software for 3D visualization of macromolecules (written in C on a SGI Irix 4D/35 computer).
This program was used to make 3D structures illustrations, for example in:

- NMR Structure of a Specific DNA Complex of Zn-Containing DNA Binding Domain of GATA-1.
J.G. Omichinski et al, Science 261: 438 (1993).

- Structures of larger proteins, protein-ligand and protein-DNA complexes by multidimensional heteronuclear NMR.
G.M. Clore et al, Protein Science 3: 372 (1994).

- Cover of Guidebook to the Calcium Binding Proteins. Edited by M.R. Cello, Oxford Univeristy Press, 1996.

1988-89: Game developer (freelance). Development and design of "Othello Killer" [Othello/Reversi strategic board game program where users can play against the computer (level: intermediate)] written in C for the AMIGA computer, published in 1989 by UbiSoft Entertainment.

Development of "Digital Studio" (not commercialized), digital multitrack recorder software used to digitize sounds and music for "Othello Killer", using a custom made audio analog to digital converter made by Curzio Bossi (BTZ electronique, Geneva, Switzerland).

Computer:

- Programming paradigms/methodologies: Object-oriented, structured. Agile iterative development.
- Programming languages: Ruby, Perl, C/C++.
- Programming APIs/technologies/tools: DHTML [HTML-CSS-JavaScript; AJAX], Rails, Web services [REST], Relational Databases [PostgreSQL], subversion, JSON, OpenGL, Textile, Qt.
- OSes: Linux, MacOSX, Windows XP.
- Software: Adobe Photoshop, Illustrator, BioInformatics tools.
- Hardware: able to build PC systems from parts.

General molecular biology / biochemistry:

Molecular biology techniques: DNA cloning, sequencing, phage library screening, DNA, RNA purification and analysis, (RT)-PCR, etc...
Proteins: immunochemistry, purifications.

Caenorhabditis elegans molecular biology / biochemistry:

Culture methods, longevity - stress resistance assay, immunofluorescence, generation/isolation of deletion mutants (knockouts), microinjections (transgenic animals), gene mapping with Mos1 transposon system, RNAi.

September 1999-, 1.5 years. Swiss National Science Foundation "Advanced researcher fellowship"
"Identification of genes involved in oxidative stress response and aging in Caenorhabditis elegans" , fellowship n°823A-056586.

September 1998-, 1 year. Swiss National Science Foundation "Beginner researcher fellowship"
"Characterization and analysis of differentially expressed genes in age-1 long-lived Caenorhabditis elegans mutants", fellowship n°81GE-51690.

January 1997-, 8 months. Roche Research Foundation Fellowship with Sandoz Stiftung participation
"Functional analysis of the neuronal calcium sensor-1 with a Caenorhabditis elegans knock-out mutant."

Posters and abstracts

E. de Castro, C. Sigrist, N. Hulo, A. Gattiker, E. Gasteiger, A. Bairoch (2004). ScanView: a PROSITE motif hits visualizer that predicts functional and/or structural residues. ISMB/ECCB 2004, Glasgow, UK.

De Castro E, Hegi de Castro S, Johnson TE (2001). Identification of genes involved in oxidative stress response and aging in Caenorhabditis elegans. 13th International C. elegans Meeting, UCLA, Los Angeles, California, USA

Gomez M, de Castro E, Guarin E, Nef P (2000). Ca²⁺ -signalling via the neuron-specific Ca²⁺ sensor NCS-1 is essential for thermotaxis, a form of associative learning and memory in C. elegans . West Coast Worm Meeting 2000, UCLA, Los Angeles, California, USA.

De Castro E, Nef P (1997). Characterization and analysis of C. elegans Neuronal Calcium Sensor-1. 11th International C. elegans Meeting, University of Wisconsin-Madison, USA.

De Castro E, Nef P (1995). C. elegans as a model to study Neuronal Calcium Sensors. 10th International C. elegans Meeting, University of Wisconsin-Madison, USA.

15. Lima T., Auchincloss A.H., Coudert E., Keller G., Michoud K., Rivoire C., Bulliard V., de Castro E., Lachaize C., Baratin D., Phan I., Bougueleret L., Bairoch A. HAMAP: a database of completely sequenced microbial proteome sets and manually curated microbial protein families in UniProtKB/Swiss-Prot. Nucleic Acids Res. 37: D471-D478 [10.1093/nar/gkn661] (2009)

14. Nicolas Hulo, Amos Bairoch, Virginie Bulliard, Lorenzo Cerutti, Beatrice A. Cuche, Edouard de Castro, Corinne Lachaize, Petra S. Langendijk-Genevaux, and Christian J. A. Sigrist. The 20 years of PROSITE Nucleic Acids Res. 36(Database issue): D245-D249 [doi:10.1093/nar/gkm977] (January 2008)

13. Edouard de Castro, Christian J.A. Sigrist, Alexandre Gattiker, Virginie Bulliard, Petra S. Langendijk-Genevaux, Elisabeth Gasteiger, Amos Bairoch, Nicolas Hulo. ScanProsite: detection of PROSITE signature matches and ProRule-associated functional and structural residues in proteins. Nucleic Acids Res. 34(Web Server issue):W362-W365 [doi:10.1093/nar/gkl124] (July 2006).

12. Hulo N, Bairoch A, Bulliard V, Cerutti L, de Castro E, Langendijk-Genevaux PS, Pagni M, Sigrist CJ. The PROSITE database. Nucleic Acids Res. 34(Database issue): D227-30 (2006, Jan. 1).

11. Sigrist C.J.A., de Castro E., Langendijk-Genevaux P.S., Le Saux V., Bairoch A., Hulo N. ProRule: a new database containing functional and structural information on PROSITE profiles. Bioinformatics. 21(21): 4060-6 (2005, Nov. 1).

10. Edouard de Castro, Sarah Hegi de Castro, Thomas E. Johnson. Isolation of long-lived mutants in Caenorhabditis elegans using juglone resistance selection. Free Radical Biology and Medicine 37(2): 139-145 (2004).

9. Nicolas Hulo, Christian J. A. Sigrist, Virginie Le Saux, Petra S. Langendijk-Genevaux, Lorenza Bordoli1, Alexandre Gattiker, Edouard De Castro, Philipp Bucher, Amos Bairoch. Recent improvements to the PROSITE database. Nucleic Acids Research 32: D134-D137 (2004).

8. Thomas E. Johnson, Sam Henderso, Shin Murakami, Edouard de Castro, Sarah Hegi de Castro, James Cypser, Brad Rikke, Pat Tedesco, Chris Link. Longevity genes in the nematode caenorhabditis elegans also mediate increased resistance to stress and prevent disease [review] J. of Inherited Metabolic Disease 25: 197-206 (2002).

7. Thomas E. Johnson, Edouard de Castro, Sarah Hegi de Castro, James Cypser, Sam Henderson, and Pat Tedesco. Relationship between increased longevity and stress resistance as assessed through gerontogene mutations in Caenorhabditis elegans. [review] Experimental Gerontology 36: 1609-1617 (2001).

6. Marie Gomez* & Edouard De Castro*, Ernesto Guarin, Hiroyuki Sasakura, Atsushi Kuhara, Ikue Mori, Tamas Bartfai, Cornelia I. Bargmann, Patrick Nef. Ca²⁺-Signaling via the Neuronal Calcium Sensor-1 Regulates Associative Learning and Memory in C. elegans. Neuron 30 (1): 241-248 (April 2001). *These authors contributed equally to this work.

5. T.E. Johnson, J. Cypser, E. de Castro, S. de Castro, S. Henderson, S. Murakami, B. Rikke, P. Tedesco, C. Link. Gerontogenes mediate health and longevity in nematodes through increasing resistance to environmental toxins and stressors. [review] Experimental Gerontology 35: 687-694 (2000).

Edouard de Castro. Caenorhabditis elegans Neuronal Calcium Sensor-1: From Gene to Behavior. Ph.D. Thesis (n° 2943). Université de Genève (1997).

4. Schaad N, De Castro E, Nef S, Hegi S, Hinrichsen R, Martone M, Ellisman M, Sikkink R, Rusnak F, Sygush J, Nef P. Direct modulation of calmodulin targets by the neuronal calcium sensor NCS-1. Proc. Natl. Acad. Sci. USA 93: 9253-9258 (1996).

3. Nef S, Allaman I, Fiumelli H, De Castro E, Nef P. Olfaction in birds: differential embryonic expression of nine putative odorant receptor genes in the avian olfactory system. Mechanisms of Development 55: 65-77 (1996).

2. De Castro E, Nef S, Fiumelli H, Lenz SE, Kawamura S, Nef P. Regulation of rhodopsin phosphorylation by a family of neuronal calcium sensors. Biochem. Biophys. Res. Commun. 216: 133-140 (1995).

1. Nef S, Fiumelli H, De Castro E, Raes M-B, Nef P. Identification of a neuronal calcium sensor (NCS-1) possibly involved in the regulation of receptor phosphorylation. J. Recept. Res. 15(1-4): 365-378 (1995).