Augustin Luna

BioPAX-Related Research Interests
BioPAX Level 4 will undoubtedly see a continued push in terms graphical representation, validation, and continued conversion of data into the BioPAX format, all of which are areas of interest for me.

I currently work with the Molecular Interaction Map (MIM) notation that has been cited by BioPAX ontology as a representation mechanism. My work involves the development of syntactically and semantically clear implementation of the MIM notation to facilitate software development and translation of the notation to other formats that includes an XML schema with associated application programming interface (API), validator (platform independent validation using Schematron), and diagram editor based on Pathvisio.

This work has led me to become involved in the development of the Systems Biology Graphical Notation (SBGN); a notation that has as one of its major pre-cursors of the MIM notation. With the SBGN specifications complete, current work on SBGN has, in part, shifted to the development of an API for SBGN; a development I also participate in. Development on the MIM and SBGN APIs sets the stage for automated the interconversion BioPAX and graphical notations.

Contact
Augustin Luna - augustin AT mail DOT nih DOT gov

Education

 * Georgia Institute of Technology (GT), BS, 2002-2005, Biomedical Engineering


 * Boston University (BU), PhD Candidate, 2007-Present, Bioinformatics

Lab Affiliation
I am conducting my PhD thesis research at the National Cancer Institute in the Laboratory of Molecular Pharmacology as a pre-doctoral fellow with advisors Mirit Aladjem and Kurt Kohn.

Publications

 * Nicodemus KK, Luna A, Vakkalanka R, Goldberg T, Egan M, Straub RE, Weinberger DR. Further Evidence for Association between ErbB4 and Schizophrenia and Influence on Cognitive Intermediate Phenotypes in Healthy Controls. Mol Psychiatry. 2006 Dec;11(12):1062-5.


 * Nicodemus KK, Luna A, Shugart YY. An Evaluation of Power and Type I Error of Single SNP Transmission Disequilibrium Tests under Varying Family Structures and Missing Parental Data, Am J Hum Genet. 2007 Jan;80(1):178-85.


 * Luna A, Nicodemus KK. snp.plotter: An R based SNP/Haplotype Association and Linkage Disequilibrium Plotting Package, Bioinformatics. 2007 Mar 15;23(6):774-6.


 * Nicodemus KK, Law AJ, Luna A, Vakkalanka R, Straub RE, Kleinman JE, Weinberger DR. A 5' promoter region SNP in NRG1 is associated with schizophrenia risk and type III isoform expression. Mol Psychiatry. 2009 Aug;14(8):741-3


 * Novère NL, Hucka M, Mi H, Moodie S, Schreiber F, Sorokin A, Demir D, Wegner K, Aladjem M, Wimalaratne SM, Bergman FT, Gauges R, Ghazal P, Hideya K, Li L, Matsuoka Y, Villéger A, Boyd SE, Calzone L, Courtot M, Dogrusoz U, Freeman T, Funahashi A, Ghosh S, Jouraku A, Kim S, Kolpakov F, Luna A, Sahle S, Schmidt E, Watterson S, Wu G, Goryanin I, Kell DB, Sander C, Sauro H, Snoep JL, Kohn K, Kitano H. The Systems Biology Graphical Notation. Nat Biotechnol. 2009 Aug;27(8):735-41. Epub 2009 Aug 7. Erratum in: Nat Biotechnol. 2009 Sep;27(9):864.


 * Nicodemus KK, Callicott JH, Higier RG, Luna A, Nixon DC, Lipska BK, Vakkalanka R, Giegling I, Rujescu D, Clair DS, Muglia P, Shugart YY, Weinberger DR. Evidence of statistical epistasis between DISC1, CIT and NDEL1 impacting risk for schizophrenia: biological validation with functional neuroimaging. Hum Genet. 2010 Jan 19. Erratum in: Hum Genet. 2010 Feb 2.