Software developer and project leader (bioinformatics)

at the Swiss Institute of BioInformatics, Geneva, Switzerland.
Swiss-Prot group (Dr. Ioannis Xenarios).
Wiki editors project leader (since Jan. 2008).
Automated curation platform - "Anabelle" - project leader (since Jul. 2006).
May 2002 - present

Research Scientist (molecular biology of aging)

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

Research Scientist (molecular 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 (molecular neurobiology)

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

Software developer / Research assistant (bioinformatics)

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

"Visp: 3D Molecular Visualization software"
University of Geneva, Switzerland.
Advisor: Professor S. Edelstein.
1992

Software developer (video game industry)

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

Since May 2002: Software developer @ Swiss Institute of BioInformatics
Automation of UniProtKB/Swiss-Prot protein knowledgebase curation; data visualization:
- Some developments for Swiss-Prot:
ViralZone - Virus Information site / database: A knowledge resource to understand virus diversity and a portal to facilitate access to UniProtKB/Swiss-Prot viral protein entries (generated with WiKiNomy) publi. 17.
"WiKiNomy" - a wiki editor system used to annotate nodes in our taxonomy.
"Anabelle" - automated biological curation platform: A rule based annotation system to automate curation of UniProtKB proteins; used for HAMAP microbial annotation project (including fully automatic annotation of UniProtKB/TrEMBL HAMAP entries).
"MeMiKi" - Content / information management system used to edit documentation / help for the UniProt web site (also used to power my personal web site / blog - edouard.decastro.name).
- Some developments for Prosite:
ScanProsite - biological motifs detection tool; "PSMaker" - motif detection profiles building and testing platform; and other web tools (PSView - 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, 16.
- Misc: PhiloPhylo - Educational tool (in French); blast + alignment + phylogenic tree. GPSDB - Gene/Protein Synonyms finder.

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-advanced)] written in C for the AMIGA computer, published in 1989 by UbiSoft Entertainment.

1989: 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: Functional and Object-oriented; Structured. Agile iterative development.
- Programming languages: Scala, Ruby, Perl, JavaScript, C/C++.
- Programming Technologies/frameworks/tools: DHTML [HTML-CSS-JavaScript; AJAX], Lift, Rails, Web services [REST], Relational Databases [PostgreSQL, Oracle], ORM [Mapper, Active Record], unit testing [Test::Unit, ScalaTest], Regexps, (HTML5) Canvas 2D.
- IDEs: IntelliJ IDEA 10 (for Scala, Java), Xcode
- OSes: Linux, OSX, iOS.
- Software: Adobe Photoshop, Illustrator, BioInformatics tools.

General molecular biology / biochemistry:

Molecular biology techniques: 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."

17. Chantal Hulo, Edouard de Castro, Patrick Masson, Lydie Bougueleret, Amos Bairoch, Ioannis Xenarios, Philippe Le Mercier ViralZone: a knowledge resource to understand virus diversity Nucleic Acids Res. 39(suppl 1): D576-D582 [10.1093/nar/gkq901] (2010).

16. Sigrist CJA, Cerutti L, de Castro E, Langendijk-Genevaux PS, Bulliard V, Bairoch A, Hulo N. PROSITE, a protein domain database for functional characterization and annotation. Nucleic Acids Res. 38(Database issue): D161-6 [10.1093/nar/gkp885] (2010).

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 [10.1093/nar/gkj063] (Jan 2006).

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).