Software Developer

Current work interests: Functional and concurrent programming, Data visualization, Information management
Current position: Senior software developer and project leader at Swiss Institute of BioInformatics
Currently working on: UniProtKB/Swiss-Prot internal automated annotation and proteomics platforms

Interest/Skill tags: Functional programming, parallel computing, scala, machine learning, game theory

Personal: Swiss citizen, speak English and French, live in Geneva (Switzerland), have 2 children (born in 2010 & 2015)

Experience / Education

Senior software developer and project leader (bioinformatics)

at the Swiss Institute of BioInformatics, Geneva, Switzerland.
UniProtKB/Swiss-Prot group of Pr. Ioannis Xenarios.
"Praise" - automated curation platform rewrite in Scala - project leader and software developer (since Apr. 2011).
"Spice" - Swiss-Prot Proteomics internal annotation platform - software developer (since Mar. 2012).
Wiki editors project leader and software developer [editors for ViralZone, Venomzone and internal Documentation] (since Jan. 2008).
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

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

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

Software developer / Research assistant (bioinformatics)

at the Department of Biochemistry, University of Geneva, Switzerland.
Group of Professor S. Edelstein.
1992

Software developer (video game industry)

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

Work

Since May 2002: Software developer @ Swiss Institute of BioInformatics
Automation of UniProtKB/Swiss-Prot protein knowledgebase curation; data visualization:

- Some developments for UniProtKB/Swiss-Prot:
"Praise" new Swiss-Prot internal automated biological curation platform (rewrite from scratch in Scala). Used e.g. for HAMAP microbial annotation project (including fully automatic annotation of UniProtKB/TrEMBL HAMAP entries). publi. 21.
"Spice" Swiss-Prot Proteomics annotation engine.
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 (edited with WiKiNomy) publi. 17, 22.
VenomZone - Venom Information site / database: portal to facilitate access to UniProtKB/Swiss-Prot venom protein entries (edited with WiKiNomy)
"WiKiNomy" - a wiki editor system used to annotate nodes in our taxonomy and keyword hierarchy.
"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 web tool.
PSView - domain architecture visualization; "ps_scan" (motif scanning) updates; miscellaneous tools.
"PSMaker" - internal profile motifs building and testing platform.
publi. 9, 11, 12, 13, 14, 15, 16, 20.
- Misc: PhiloPhylo educational tool (in French): blast + alignment + phylogenic tree.

scanprosite

Graphical representation of PROSITE TRYPSIN_DOM hit on ACRO_HUMAN protein together with (rule based) predicted features [disulfide bridges, active sites] in ScanProsite .

wikinomy

Wikinomy web interface; adding wiki annotation to Adenoviridae.

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

longevity

Longevity of juglone resistant C. elegans mutant ros(z111) versus wild type (N2).

1994-1998: Ph.D. + "post-doc" 1st 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.

ncs1prom::GFP worm

ncs-1'promoter'::GFP transgenic C. elegans (head).

1993: Ph.D. 1st 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.


ef-hand

Image created using ViSP (Ca2+ binding on a EF-Hand structure in the protein parvalbumin)

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.

screenshot

"Othello Killer" game screenshot

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).


Skills

Software development:

- Programming languages: Scala, Perl, C/C++, Ruby, JavaScript, Java.
- Programming Technologies/frameworks/tools/Paradigms: Functional programming, Object-oriented programming, Futures, Akka, parallelization, HTML/CSS/JavaScript, Java Virtual Machine, REST, http, Relational Databases [PostgreSQL, Oracle], sparql, rdf, OpenGL, MVC framework [Rails], ORM [Active Record, slick], Unit Testing [ScalaTest~WordSpec], Regexps, ant, sbt, Machine Learning [Encog], akka-http (microservice), (HTML5) Canvas 2D, Jira, Confluence, git, Jenkins.
- IDEs: IntelliJ IDEA (for Scala, Java, Perl), Xcode
- OSes: Linux, OS-X, iOS.
- Software: Adobe Photoshop, Illustrator, BioInformatics tools (blast, profiles / Hidden Markov models etc).

Miscellaneous:

Genetics, Molecular Biology, Neurobiology, Biology of ageing, Biochemistry, Caenorhabditis elegans model organism, Proteomics, Combinatorial game theory (decision trees, minimax, alpha-beta pruning), Monte Carlo simulation.

Fellowships/Grants

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."


Publications

26. The SIB Swiss Institute of Bioinformatics' resources: focus on curated databases Nucleic Acids Res. 2016 Jan 4;44(D1):D27-37. doi: 10.1093/nar/gkv1310. Epub 2015 Nov 28..

25. Pedruzzi I, Rivoire C, Auchincloss AH, Coudert E, Keller G, de Castro E, Baratin D, Cuche BA, Bougueleret L, Poux S, Redaschi N, Xenarios I, Bridge A. HAMAP in 2015: updates to the protein family classification and annotation system Nucleic Acids Res. 2015 Jan;43(Database issue):D1064-70 [10.1093/nar/gku1002] Epub 2014 Oct 27 (2014).

24. Masson P, Hulo C, de Castro E, Foulger R, Poux S, Bridge A, Lomax J, Bougueleret L, Xenarios I, Le Mercier P. An integrated ontology resource to explore and study host-virus relationships PLoS One. 2014 Sep 18;9(9):e108075 [10.1371/journal.pone.0108075] eCollection (2014).

23. Cannarozzi G, Plaza-Wuethrich S, Esfeld K, Larti S, Wilson YS, Girma D, de Castro E, Chanyalew S, Bloesch R, Farinelli L, Lyons E, Schneider M, Falquet L, Kuhlemeier C, Assefa K, Tadele Z. Genome and transcriptome sequencing identifies breeding targets in the orphan crop tef (Eragrostis tef) BMC Genomics. 2014 Jul 9;15:581 [10.1186/1471-2164-15-581] (2014).

22. Masson P, Hulo C, De Castro E, Bitter H, Gruenbaum L, Essioux L, Bougueleret L, Xenarios I, Le Mercier P. ViralZone: recent updates to the virus knowledge resource Nucleic Acids Res. 2013 Jan;41(Database issue):D579-83 [10.1093/nar/gks1220] (2013).

21. Pedruzzi I, Rivoire C, Auchincloss AH, Coudert E, Keller G, de Castro E, Baratin D, Cuche BA, Bougueleret L, Poux S, Redaschi N, Xenarios I, Bridge A; UniProt Consortium. HAMAP in 2013, new developments in the protein family classification and annotation system Nucleic Acids Res. 2013 Jan;41(Database issue):D584-9 [10.1093/nar/gks1157] (2013).

20. Sigrist CJ, de Castro E, Cerutti L, Cuche BA, Hulo N, Bridge A, Bougueleret L, Xenarios I. New and continuing developments at PROSITE Nucleic Acids Res. 2013 Jan;41(Database issue):D344-7 [doi: 10.1093/nar/gks1067] (2013).

19. Artimo P, Jonnalagedda M, Arnold K, Baratin D, Csardi G, de Castro E, Duvaud S, Flegel V, Fortier A, Gasteiger E, Grosdidier A, Hernandez C, Ioannidis V, Kuznetsov D, Liechti R, Moretti S, Mostaguir K, Redaschi N, Rossier G, Xenarios I, Stockinger H. ExPASy: SIB bioinformatics resource portal Nucleic Acids Res. 2012 Jul;40(Web Server issue):W597-603 [10.1093/nar/gks400] (2012).

18. Hunter S, Jones P, Mitchell A, Apweiler R, Attwood TK, Bateman A, Bernard T, Binns D, Bork P, Burge S, de Castro E, ... Yong SY. InterPro in 2011: new developments in the family and domain prediction database Nucleic Acids Res. 2012 Jan;40(Database issue):D306-12 [10.1093/nar/gkr948] (2011).

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).