Senior software developer (bioinformatics)

at the Swiss Institute of BioInformatics, Geneva, Switzerland.
Swiss-Prot group of Dr. Alan Bridge.
Wiki engines - project leader and software developer [prime powering SwissBioPics, ViralZone, and Venomzone. hyphen for editing internal Documentation] (since Sept. 2017).
Praise - automated curation platform - project leader and software developer (since Apr. 2011).
...
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

Since May 2002: Software developer @ Swiss Institute of BioInformatics
Information management; Automation of UniProtKB/Swiss-Prot protein knowledgebase curation; data visualization:
- Some developments for UniProtKB/Swiss-Prot:
Using large language models (LLMs) to extract data from scientific publications ...
Prime - Wiki to annotate nodes in our taxonomy / keyword hierarchies and serve portals to facilitate access to UniProtKB/Swiss-Prot. Used to edit and serve ViralZone, VenomZone and SwissBioPics (Scala + Java).
Hyphen - Wiki to edit documentation & help; internal & for the Rhea web site (Scala + Java).
Praise - Swiss-Prot internal automated curation platform (including biological annotation "rule" language interpretor). Used e.g. for HAMAP microbial annotation project. (Scala + Java). publi. 21.
- Some developments for Prosite:
ScanProsite - biological motifs detection web tool (Perl).
PSView - domain architecture visualization; ps_scan (motif scanning) updates; miscellaneous tools (Perl).
PSMaker - internal profile motifs building and testing platform (Perl).
publi. 9, 11, 12, 13, 14, 15, 16, 20.
- Misc: PhiloPhylo educational tool (in French): blast + alignment + phylogenic tree (Ruby).

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 oinformatics . 2020 Mar 1;36(6):1896-1901. doi: 10.1093/bioinformatics/btz817.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 electronic, Geneva, Switzerland).

Software development:

- Programming languages: Scala, Node.js / JavaScript, Perl, Java, C/C++, Ruby.
- Programming Technologies/frameworks/tools/Paradigms: Functional programming, Object-oriented programming, Futures parallelization, AI via OpenAI API: chat completions, fine-tuning (gpt-3.5, gpt-4, gpt-4-vision), HTML / CSS + JavaScript (w/ fetch API, Promises, web components, templates), google charts, Java Virtual Machine, REST, http, Relational Databases [PostgreSQL, Oracle], Full-Stack Development, sparql, rdf, OpenGL, ORM [Active Record, slick], jdbc, Automated Testing [ScalaTest~WordSpec], Regexps, ant, sbt, (HTML5) Canvas 2D, Jira, Confluence, git, Jenkins, ChatGPT "code interpretor".
- IDEs: IntelliJ IDEA (for Scala, Java, Perl), Xcode
- OSes: Linux, macos, iOS.
- Software: Adobe Photoshop, Illustrator, BioInformatics tools (blast, profiles / Hidden Markov models etc).
'Likes: Code with tests!, minimal mutability, minimal "framework-ness"; explicitness; valid html.

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.

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."

36. Edouard de Castro; Chantal Hulo; Patrick Masson; Andrea Auchincloss; Alan Bridge; Philippe Le Mercier. ViralZone 2024 provides higher-resolution images and advanced virus-specific resources. Nucleic Acids Research, 2023, gkad946, https://doi.org/10.1093/nar/gkad946

35. Elisabeth Coudert; Sebastien Gehant; Edouard de Castro; Monica Pozzato; Delphine Baratin; Teresa Batista Neto; Christian J.A. Sigrist; Nicole Redaschi; Alan Bridge; The UniProt Consortium. Annotation of biologically relevant ligands in UniProtKB using ChEBI Bioinformatics, Volume 39, Issue 1, January 2023, btac793, https://doi.org/10.1093/bioinformatics/btac793

34. Philippe Le Mercier, Jerven Bolleman, Edouard de Castro, Elisabeth Gasteiger, Parit Bansal, Andrea H Auchincloss, Emmanuel Boutet, Lionel Breuza, Cristina Casals-Casas, Anne Estreicher, Marc Feuermann, Damien Lieberherr, Catherine Rivoire, Ivo Pedruzzi, Nicole Redaschi, Alan Bridge SwissBioPics—an interactive library of cell images for the visualization of subcellular location data Database, Volume 2022, 2022, baac026, doi: 10.1093/database/baac026

33. Feuermann M, Boutet E, Morgat A, Axelsen K, Bansal P. Bolleman J, de Castro E, Coudert E, Gasteiger E, Gehant S, Lieberherr D, Lombardot T, Neto T, Pedruzzi S, Poux S, Pozzato M, Redaschi N, Alan Bridge; UniProt Consortium. Diverse Taxonomies for Diverse Chemistries: Enhanced Representation of Natural Product Metabolism in UniProtKB Metabolites 2021, 11(1), 48. doi: 10.3390/metabo11010048

32. Le Mercier P, Hulo C, Masson P, de Castro E.
ViralZone : le numérique au service du partage des savoirs Virologie 2020; xx(x) : 1-4 doi:10.1684/vir.2020.0873

31. Morgat A, Lombardot T, Coudert E, Axelsen K, Neto TB, Gehant S, Bansal P, Bolleman J, Gasteiger E, de Castro E, Baratin D, Pozzato M, Xenarios I, Poux S, Redaschi N, Bridge A; UniProt Consortium. Enzyme annotation in UniProtKB using Rhea Bioinformatics. 2020 Mar 1;36(6):1896-1901. doi: 10.1093/bioinformatics/btz817.

30. Bolleman J, de Castro E, Baratin D, Gehant S, Cuche BA, Auchincloss AH, Coudert E, Hulo C, Masson P, Pedruzzi I, Rivoire C, Xenarios I, Redaschi N, Bridge A. HAMAP as SPARQL rules-A portable annotation pipeline for genomes and proteomes Gigascience. 2020 Feb 1;9(2):giaa003. doi: 10.1093/gigascience/giaa003.

29. Morgat A, Lombardot T, Coudert E, Axelsen K, Neto TB, Gehant S, Bansal P, Bolleman J, Gasteiger E, de Castro E, Baratin D, Pozzato M, Xenarios I, Poux S, Redaschi N, Bridge A; UniProt Consortium. Enzyme annotation in UniProtKB using Rhea Bioinformatics. 2019 Nov 5. pii: btz817. doi: 10.1093/bioinformatics/btz817.

28. Hulo C, Masson P, Toussaint A, Osumi-Sutherland D, de Castro E, Auchincloss AH, Poux S, Bougueleret L, Xenarios I, Le Mercier P. Bacterial Virus Ontology; Coordinating across Databases Viruses. 2017 May 23;9(6). pii: E126. doi: 10.3390/v9060126.

27. Hulo C, Masson P, de Castro E, Auchincloss AH, Foulger R, Poux S, Lomax J, Bougueleret L, Xenarios I, Le Mercier P. The ins and outs of eukaryotic viruses: Knowledge base and ontology of a viral infection PLoS One. 2017 Feb 16;12(2):e0171746. doi: 10.1371/journal.pone.0171746. eCollection 2017.

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).