Department of Molecular and Experimental Medicine
The Scripps Research Institute
About my work
I am interested in understanding and building processes for creating knowledge. In particular I am driven to enable the accumulation of useful knowledge about the human genome such that that knowledge can be applied to improve the human condition. This drive has lead me on a path from cognitive science, through machine learning, to bioinformatics and most recently to ‘community intelligence’ or ‘crowdsourcing’.
My main purpose here in the Su Lab is to push the Gene Wiki project forward. To this end I focus on making the knowledge that is being captured every day as text in the Gene Wiki more accessible for computation and thus substantially more useful. So far, I have used tools such as the NCBO Annotator to identify occurrences of terms from ontologies in the text of Gene Wiki articles. These terms provide the Gene Wiki with hooks into the more structured world of the Semantic Web. These connections make it possible to identify potential new gene annotations that can be used to expand the coverage of current gene annotation databases. These new annotations (descriptions of genes created using controlled vocabularies or ontologies) can be used immediately to improve the results of knowledge-based statistical computations of genomic data such as enrichment analysis. They can also be used to enable new applications that provide fundamentally new ways of interacting with genomic data such as the Gene Wiki+.
Aside from the Gene Wiki project I am also fascinated by the idea of games with a purpose and am contributing to the emerging games department here at the Su Lab. Have a look at genegames.org to see some games with biological purposes..
- Good BM, Clarke E, Loguercio S, Su AI: Linking genes to diseases with a SNPedia-Gene Wiki mashup. The Journal of Biomedical Semantics (in press)
- Good BM, Clarke E, Loguercio S, Su AI: Building a biomedical semantic network in Wikipedia with Semantic Wiki Links. Database: The Journal of Biological Databases and Curation. Vol. 2012 published online March 20, 2012, doi:10.1093/database/bar060
- Good BM, Howe DG, Lin SM, Su AI: Mining the Gene Wiki for functional genomic knowledge. BMC Genomics 2011, 12:603
- Good BM, Clarke E, de Alfaro L, Su AI: The Gene Wiki in 2011: community intelligence applied to human gene annotation. Nucleic Acids Research. 2011; doi: 10.1093/nar/gkr925
- Good BM, Loguercio S, Su AI: Linking genes to diseases with a SNPedia-Gene Wiki mashup. In: Bio-Ontologies SIG, ISMB: 15 July 2011, Vienna
- Good BM and Su AI: Mining Gene Ontology Annotations From Hyperlinks in the Gene Wiki. In: AMIA Summit on Translational Bioinformatics: 8 March 2011, San Francisco: 21-25
- Good BM, Tennis JT, Wilkinson MD: Social tagging in the life sciences: characterizing a new metadata resource for bioinformatics. BMC Bioinformatics 2009, 10(313).
- Good BM, Tennis JT: Term based comparison metrics for controlled and uncontrolled indexing languages. Information Research 2009, 14(1).
- Good BM, Lu P, Kawas EK, Wilkinson MD: Open semantic annotation: an experiment with BioMoby Web services. In: 2nd Canadian Semantic Web Working Symposium: 24 May 2009; Kelowna, British Columbia; 2009. (not available online except as chapter 7 in my dissertation).
- Good B: Strategies for amassing, characterizing, and applying third-party metadata in bioinformatics. Ph.D. dissertation. Vancouver: University of British Columbia; 2009.
- Belleau F, Tourigny N, Good BM, Morissette J: Bio2RDF: A Semantic Web Atlas of post genomic knowledge about Human and Mouse. In: Data Integration in the Life Sciences: 2008; Evry, France; 2008.
- Wilkinson MD, Senger M, Kawas E, Bruskiewich R, Gouzy J, Noirot C, Bardou P, Ng A, Haase D, Saiz Ede A et al: Interoperability with Moby 1.0–it’s better than sharing your toothbrush! Brief Bioinform 2008, 9(3):220-231.
- Davis DP, Peay J, Good B, Sise MJ, Kennedy F, Eastman AB, Velky T, Hoyt DB: Air medical response to traumatic brain injury: a computer learning algorithm analysis. Trauma 2008, 64(4):889-897.
- Bruskiewich R, Senger M, Davenport G, Ruiz M, Rouard M, Hazekamp T, Takeya M, Doi K, Satoh K, Costa M et al: The Generation Challenge Programme Platform: Semantic Standards and Workbench for Crop Science. International Journal of Plant Genomics 2008.
- Good BM, Wilkinson MD: Ontology engineering using volunteer labor. In: World Wide Web Conference: 2007; Banff, Canada; 2007: 1243-1244.
- Low A, Dong W, Chan D, Sing T, Swanstrom R, Jensen M, Pillai S, Good B, Harrigan P: Current V3 genotyping algorithms are inadequate for predicting X4 co-receptor usage in clinical isolates. AIDS 2007, 21(14):17-24.
- Kuo BY-L, Hentrich T, Good BM, Wilkinson MD: Tag clouds for summarizing web search results. In: Proceedings of the 16th international conference on World Wide Web: 2007; Banff, Alberta, Canada: ACM; 2007: 1203-1204.
- Song YC, Kawas E, Good BM, Wilkinson MD, Tebbutt SJ: DataBiNS: a BioMoby-based data-mining workflow for biological pathways and non-synonymous SNPs. Bioinformatics 2007, 23(6):780-782.
- Good BM, Kawas EA, Wilkinson MD: Bridging the gap between social tagging and semantic annotation: E.D. the Entity Describer. In: Nature Precedings. 2007.
- Good BM, Tranfield EM, Tan PC, Shehata M, Singhera GK, Gosselink J, Wilkinson MD: Fast, cheap and out of control: A zero curation model for ontology development. In: Pacific Symposium on Biocomputing: January 3-7 2006; Hawaii, USA: World Scientific; 2006: 128-139.
- Good BM, Wilkinson MD: The Life Sciences Semantic Web is Full of Creeps! Brief Bioinform 2006, 7(3):275-286.
- Pillai SK, Pond SLK, Liu Y, Good BM, Strain MC, Ellis RJ, Letendre S, Smith DM, Gunthard HF, Grant I et al: Genetic attributes of cerebrospinal fluid-derived HIV-1 env. Brain 2006, 129(7):1872-1883.
- Johannesson H, Kasuga T, Schaller RA, Good B, Gardner MJ, Townsend JP, Cole GT, Taylor JW: Phase-specific gene expression underlying morphological adaptations of the dimorphic human pathogenic fungus, Coccidioides posadasii. Fungal genetics and biology : FG & B 2006, 43(8):545-559.
- Good BM, Kawas EA, Kuo BY, Wilkinson MD: iHOPerator: User-scripting a personalized bioinformatics Web, starting with the iHOP website. BMC Bioinformatics 2006, 7:534.
- Naviaux RK, Good B, McPherson JD, Steffen DL, Markusic D, Ransom B, Corbeil J: Sand DNA – a genetic library of life at the water’s edge. Marine Ecology-Progress Series 2005, 301:9-22.
- Pillai SK, Good B, Pond SK, Wong JK, Strain MC, Richman DD, Smith DM: Semen-specific genetic characteristics of human immunodeficiency virus type 1 env. Journal of Virology 2005, 79(3):1734-1742.
- Strain MC, Letendre S, Pillai SK, Russell T, Ignacio CC, Gunthard HF, Good B, Smith DM, Wolinsky SM, Furtado M et al: Genetic composition of human immunodeficiency virus type 1 in cerebrospinal fluid and blood without treatment and during failing antiretroviral therapy. Journal of Virology 2005, 79(3):1772-1788.
- Pillai S, Good B, Richman D, Corbeil J: A new perspective on V3 phenotype prediction. AIDS Res Hum Retroviruses 2003, 19(2):145-149.
- Leigh Brown AJ, Frost SDW, Good BM, Daar ES, Simon V, Markowitz M, Collier AC, Connick E, Conway B, Margolick JB et al: Genetic basis of hypersusceptibility to protease inhibitors and low replicative capacity of human immunodeficiency virus type 1 strains in primary infection. Journal of Virology 2004, 78(5):2242-2246.
- Leigh Brown AJ, Good BM, Frost SD, Collier AC, Connick E, Conway B, Daar E, Kilby M, Routy JP, Margolick JB et al: Analysing the genotypic basis of hypersusceptibility to amprenavir in HIV from antiretroviral-naive patients. Antiviral Therapy 2002, 7:S42-S42.
- Good BM, Peay J, Corbeil J: Class Prediction Based on Gene Expression: Applying Neural Networks via a Genetic Algorithm Wrapper. In: Genetic and Evolutionary Computation Conference Late Breaking Papers: 2001; San Francisco; 2001: 122-130.
- Starr B, Chaudhri VK, Katz B, Good BM, Thomere J: A Query Interface and Integrated Knowledge Environment for HPKB. In: Sixteenth National Conference on Artificial Intelligence and Eleventh Conference on Innovative Applications of Artificial Intelligence: 1999; Orlando, Florida, USA: AAAI Press / The MIT Press; 1999: 927-928.
About me at play
I’m an avid, though not very talented, surfer and bodyboarder, cyclist, volleyball player, and 2-year old chaser…