I work as a research scientist in the department of Biochemistry and Molecular Biology, whilst awaiting the defense of my PhD thesis (Computer Science) at the University of Calgary (Canada). Although I am Computer Scientist, I am located in the university's Faculty of Medicine, since my long-time area of expertise is the use of computational methods for Molecular Biology (Bioinformatics). I develop software in Java, Perl, C, and R -- in that order of frequency. While I continue to write programs to perform specific types of analyses, I am also interested in computational semantics and the use of XML in bioinformatics (63 Google references, 16 citations in Google Scholar), and how it can enable biologists to do more computation without the assistance of a Bioinformatician.

Work

In addition to collaborating with biologists on several scientific investigations, I have several...

Software Packages

• Seahawk (active research) - An intuitive Web Services browser for biologist, building to be a Programming-By-Example environment, as well as Moby easy service creation (a.k.a. Daggoo)
• Merlin (maintenance) - Enabling easy Affymetrix Genechip analysis for Very Large Datasets (>400 chips), and R/Bioconductor library parallelization
• Osprey (maintenance) - Oligonucleotide primer and probe design software employing novel methodologies for improved specificity
• MAGPIE (maintenance) - Automated genome analysis
• Bluejay (some maintenance aspects) - An XML data visualization system
• I maintain ties with the 4D bioinformatics development team (watch the news item on ABC, a redux on VOA or another story on CBC)

Peer-Reviewed Journal Papers

29. Katayama T. et al. (2010) The DBCLS BioHackathon: standardization and interoperability for bioinformatics web services and workflows Journal of Biomedical Semantics 1:8.

28. Soh J., Turinsky A.L., Trinh Q.M., Chang J., Sabhaney A., Dong X., Gordon P.M.K., Janzen R.P.W., Hau D., Wishart D.S., Sensen C.W. (2009) Spatiotemporal Integration of Molecular and Anatomical Data in Virtual Reality using Semantic Mapping. International Journal of Nanomedicine 4:79-89. PubMed 2 citations (1 self) in Google Scholar

27. Gordon P.M.K., Schuetz E., Beck J., Urnovitz H.B., Graham C., Clark R., Dudas S., Czub S., Sensen M., Brenig B., Groschup M.H., Church R.B., Sensen C.W. (2009) Disease-specific motifs can be identified in circulating nucleic acids from live elk and cattle infected with transmissible spongiform encephalopathies. Nucleic Acids Research 37(2):550-556. PubMed 3 citations in Google Scholar

26. Antranikian G., Ruepp A., Gordon P.M.K., Ballschmiter M., Zibat A., Sensen C.W., Frishman D., Liebl W., Klenk H.-P. (2009) Rapid Access to genes of biotechnologically useful enzymes by partial genome sequencing: the thermoalkaliphile Anaerobranca gottschalkii. Journal of Molecular Microbiology and Biotechnology 16(1):81-90. PubMed

25. Soh J., Gordon P.M.K., Taschuk M.L., Dong A., Ah-Seng A.C., Turinsky A.L., Sensen C.W. (2008) Bluejay 1.0: genome browsing and comparison with rich customization provision and dynamic resource linking. BMC Bioinformatics 9:450. PubMed 5 citations in Google Scholar

24. Gordon P.M.K., Soliman M.A., Bose P., Trinh Q., Sensen C.W. and Riabowol K. (2008) Interspecies data mining to predict novel ING-protein interactions in human. BMC Genomics 9:426. PubMed 7 citations in Google Scholar

23. Wilkinson M.D. et al. (2008) Interoperability with Moby 1.0: It's Better than Sharing Your Toothbrush! Briefings in Bioinformatics 9(3):220-231. PubMed 28 citations in Google Scholar

22. Caffrey, S. M., Park, H.-S., Been, J., Gordon, P.M.K., Sensen, C. W., and Voordouw, G. (2008) Gene expression of the sulfate-reducing bacterium Desulfovibrio vulgaris Hildenborough grown on an iron electrode under cathodic protection conditions. Applied and Environmental Microbiology 74(8):2404-2413. PubMed 3 citations in Google Scholar

21. Froels S., Gordon P.M.K., Panlilio M., Duggin I.G., Bell S.D., Sensen C.W., Schleper C. (2007) Response of the hyperthermophilic archaeon Sulfolobus solfataricus to UV damage. Journal of Bacteriology 189(23):8708-8718. PubMed 33 citations (1 self) in Google Scholar

20. Gordon P.M.K., Sensen C.W. (2007) Seahawk: Moving Beyond HTML in Web-based Bioinformatics Analysis. BMC Bioinformatics 8:208. PubMed 25 citations (5 self) in Google Scholar

19. Gordon P.M.K., Trinh Q., Sensen C.W. (2007) Semantic Web Service Provision: a Realistic Framework for Bioinformatics Programmers. Bioinformatics 23(9):1178-1180. PubMed 15 citations (4 self) in Google Scholar

18. Froels S., Gordon P.M.K., Panlilio M., Sensen C.W., Schleper C. (2007) Elucidating the transcription cycle of the UV-inducible hyperthermophilic archaeal virus SSV1 by DNA microarrays. Virology 365(1):48-59. PubMed 18 (2 self) citations in Google Scholar

17. Zulak K.G., Cornish A., Daskalchuk T.E., Deyholos M.K., Goodenowe D.B., Gordon P.M.K., Klassen D., Pelcher L.E., Sensen C.W., Facchini P.J. (2007) Gene Transcript and Metabolite Profiling of Cultured Opium Poppy Cells Reveals the Integrated Biochemical Machinery of an Alkaloid Factory. Planta 255:1085-1106. PubMed 30 citations in Google Scholar

16. Liapounova N.A., Hampl V., Gordon P.M.K., Sensen C.W., Gedamu L., Dacks J.B. (2006) Reconstructing the Mosaic Glycolytic Pathway of the Anaerobic Eukaryote Monocercomonoides. Eukaryotic Cell 5(12):2138-46. PubMed 7 citations in Google Scholar

15. Gordon P.M.K., Weinel C., Jacobi C., Kaempf U., Kriventseva E., Sensen C.W. (2006) Creating hierarchical models of protein families based on ESTs: The "Sprockets" analysis pipeline. Analytica Chimica Acta 564(1):123-132. PubMed Recommendation

14. Technau U., Rudd S., Maxwell P., Gordon P.M., Saina M., Grasso L.C., Hayward D.C., Sensen C.W., Saint R., Holstein T.W., Ball E.E., Miller D.J. (2005) Maintenance of ancestral complexity and non-metazoan genes in two basal cnidarians. Trends in Genetics 21:633-639. PubMed 143 citations in Google Scholar

13. Stromer, J.N., Quon, G.T., Gordon, P.M.K., Turinsky, A.L., Sensen, C.W. (2005) JABIRU: Harnessing Java 3D Behaviours for Device and Display Portability. IEEE Computer Graphics & Applications 25:70-80. PubMed 5 citations in Google Scholar

12. Turinsky A.L., Ah-Seng A.C., Gordon P.M.K., Stromer J.N., Taschuk M.L., Xu E.W., Sensen C.W. (2004) Bioinformatics Visualization and Integration with Open Standards: The Bluejay Genomic Browser. In Silico Biology 5:0018. PubMed 24 citations in Google Scholar

11. Gordon, P.M.K., Sensen, C.W. (2004) Osprey: a comprehensive tool employing novel methods for the design of oligonucleotides for DNA sequencing and microarrays Nucleic Acids Research 32(17):e133. PubMed 43 citations in Google Scholar

10. Siebers, B., Tjaden, B., Michalke, K., Doerr, C., Ahmed, H., Zaparty, M., Gordon, P., Sensen, C.W., Zibat, A., Klenk, H.-P., Schuster, S.C., Hensel, R. (2004) Reconstruction of the Central Carbohydrate Metabolism of Thermoproteus tenax by Use of Genomic and Biochemical Data. Journal of Bacteriology 186:2179-2194. PubMed 34 citations in Google Scholar

9. Quon, G.T., Gordon, P., Sensen, C.W. (2003) 4D Bioinformatics: A New Look at the Ribosome as an Example. IUBMB Life 55:279-283. PubMed 4 citations in Google Scholar

8. Arisue, N., Hashimoto, T., Lee, J.A., Moore, D.V., Gordon, P., Sensen, C.W., Gaasterland, T., Hasegawa, M., Mueller, M. (2002) The phylogenetic position of the pelobiont Mastigamoeba balamuthi based on sequences of rDNA and translation elongation factors EF-1alpha and EF-2. Journal of Eukaryotic Microbiology 49:1-10. PubMed 32 citations in Google Scholar

7. Nantel, A., Dignard, D., Bachewich, C., Harcus, D., Marcil, A., Bouin, A.-P., Sensen, C.W., Hogues, H., van het Hoog, M., Gordon, P., Rigby, T., Benoit, F., Tessier, D.C., Thomas, D.Y., Whiteway, M. (2002) Transcription profiling of Candida albicans cells undergoing the yeast-to-hyphal transition. Molecular Biology of the Cell 13:3452-3465. PubMed 146 citations in Google Scholar

6. Bapteste, E., Brinkmann, H., Lee, J.A., Moore, D.V., Sensen, C.W., Gordon, P., Duruflé, L., Gaasterland, T., Lopez, P., Mueller, M., Philippe, H. (2002) The analysis of 100 genes supports the grouping of three highly divergent amobae: Dictyostelium, Entamoeba and Mastigamoeba. Proceedings of the National Academy of Sciences 99:1414-1419. PubMed 244 citations in Google Scholar

5. Mueller, M., Lee, J.A., Gordon, P., Gaasterland, T., Sensen, C.W. (2001) Presence of prokaryotic and eukaryotic species in all subgroups of the PPi-dependent Group II phosphofructokinase protein family. Journal of Bacteriology 183:6714-6716. PubMed 20 citations in Google Scholar

4. She, Q., Singh, R.K., Confalonieri, F., Zivanovic, Y., Allard, G., Awayez, M.J., Chan-Weiher, C.C.-Y., Clausen, I.G., Curtis,, B.A., De Moors, A., Erauso, G., Fletcher, C., Gordon, P.M.K., Heikamp-de Jong, I., Jeffries, A.C., Kozera, C.J., Medina, N., Peng, X., Thi-Ngoc, H.P., Redder, P., Schenk, M.E., Theriault, C., Tolstrup, N., Charlebois, R.L., Doolittle, W.F., Duguet, M., Gaasterland, T., Garrett, R.A., Ragan, M.A., Sensen, C.W., Van der Oost, J. (2001) The complete genome of the crenarchaeon Sulfolobus solfataricus P2. Proceedings of the National Academy of Sciences 98:7835-7840. PubMed 437 citations in Google Scholar

3. Gaasterland, T., Sczyrba, A., Thomas, E., Aytekin-Kurban, G., Gordon, P., Sensen, C.W. (2000) MAGPIE/EGRET Annotation of the 2.9 Mb Drosophila melanogaster ADH Region. Genome Research, 10(4):502-510. PubMed 22 citations in Google Scholar

2. Charlesbois, R.L., Singh R.K., Chan-Weiher C.C.-Y., Allard G., Chow C., Confalonieri F., Curtis B., Duguet M., Erauso G., Faguy D., Gaasterland T., Garrett R.A., Gordon P., Jeffries A.C., Kozera C., Kushwaha N., Lafleur É., Medina N., Peng X., Penny S.L., She Q., St. Jean A., van der Oost J., Zivanovic Y., Doolittle W.F., Ragan M.A., Sensen C.W. (2000) Gene content and organization of a 281-kbp contig from the genome of the extremely thermophilic archaeon, Sulfolobus solfataricus P2. Genome, 43 (1):116-36. PubMed 13 citations in Google Scholar

1. Sensen, C.W., Charlebois, R.L., Chow, C., Clausen, I.G., Curtis, B., Doolittle, W.F., Duguet, M., Erauso, G., Gaasterland, T., Garrett, R.A., Gordon, P., de Jong, I.H., Jeffries, A.C., Kozera, C., Medina, N., De Moors, A., van der Oost, J., Phan, H., Ragan, M.A., Schenk, M.E., She, Q., Singh, R.K., Tolstrup, N. (1998) Completing the sequence of the Sulfolobus solfataricus P2 genome Extremophiles, 2 (3):05-312. PubMed 26 citations in Google Scholar

Peer-reviewed Conference Papers

X - Gordon P.M.K., Barker, K., Sensen C.W. (2010) Programming-by-example meets the Semantic Web: Using ontologies and web services to close the semantic gap. In: Proceedings of the IEEE Visual Languages and Human Centric Computing Conference (Leganés-Madrid, Spain), September 21-25, 2010, pp. 133-40.

IX - Gordon P.M.K., Barker, K., Sensen C.W. (2010) Helping Molecular Biologists Effectively Build Workflows, Without Programming. In: Proceedings of 7th International Conference on Data Integration in the Life Sciences (DILS 2010) (Gothenburg, Sweden), August 25-27, 2010, pp. 74-89.

VIII - Gordon P.M.K., Sensen C.W. (2008) Creating Bioinformatics Semantic Web Services from Existing Web Services: A real-world application of SAWSDL. In: Proceedings of the IEEE International Conference on Web Services (Beijing, China), September 23-26, 2008, pp. 608-614. 6 citations in Google Scholar

VII - Gordon P.M.K., Kawas E., Wilkinson M.D., Sensen C.W. (2007) Using a novel data transformation technique to provide the EMBOSS software suite as Semantic Web Services. In: Proceedings of the IEEE International Conference on Bioinformatics and Biomedicine (San Jose, California), November 2-4, 2007, pp. 117-124. 3 (self) citations in Google Scholar

VI - Soh J.*, Gordon P.M.K.*, Ah-Seng A.C., Turinsky A.L., Taschuk M., Borowski K., Sensen C.W. (2007) Bluejay: a Highly Scalable and Integrative Visual Environment for Genome Exploration. In: Proceedings of the IEEE Congress on Services [The 1st IEEE International Workshop on Service Oriented Technologies for Biological Databases and Tools], July 9-13, 2007, Salt Lake City, Utah pp.92-98. *Co-first authors. (Video, slides and audio for IEEE members) 2 (self) citations in Google Scholar

V - Dong A., Turinsky A.L., Ah-Seng A., Taschuk M., Gordon P.M.K., Hochauer K., Froels S., Soh J., Sensen C.W. (2006) Enhancing Bluejay with Scalability, Genome Comparison and Microarray Visualization. In: Decker R., Lenz H.-J. [eds.] Advances in Data Analysis (GfKl 2006 Conference Proceedings). Springer Berlin - Heidelberg pp. 557-568

IV - Wang C., Gordon P.M.K., Turinsky A.L., Burgess J., Dalton T., Sensen C.W. (2006) Combining a Highthroughput Bioinformatics Grid and Bioinformatics Web Services. In: Distributed, High-Performance and Grid Computing in Computational Biology (GCCB 2006), W. Dubitzky et. al. (Eds.), Lecture Notes In Computer Science 4360, Springer, Heidelberg

III - Gordon P.M.K., Stromer J., Turinsky A.L., Xu E., Sensen C.W. (2004) Bluejay: A Biological Sequence Browser featuring Knowledge Integration. Proceedings of the Fourth Virtual Conference on Genomics and Bioinformatics 3:4-11 4 citations (2 self) in Google Scholar

II - Gordon, P., Sensen, C. (1999) Bluejay: A Browser for Linear Units in Java in The Proceedings of the 13th Annual International Symposium on High Performance Computing Systems and Applications, pp. 183-194. 6 citations (5 self) in Google Scholar CiteSeer

I - Liscano, R., Impey, R., Gordon, P., Abu-Hakima, S. "A System for the Seamless Integration of Personal Messages using Agents Developed on a Lotus Notes Platform. CASCON 96: Meeting of Minds": November 12-14, 1996. 2 citations on Google Scholar CiteSeer

Peer-reviewed Conference Abstracts

1. Gordon P.M.K., Sensen, C.W. (2008) Bridging Existing Bioinformatics Tools and Data Into Semantic Web Services. In: SIG Meeting Program Materials for the 16th Annual International Conference on Intelligent Systems for Molecular Biology, (Toronto, Canada), July 18-19, 2008, p. 146.

Book Chapters

4. Soh J., Gordon P.M.K., Sensen C.W. (2009) Genomic Data Visualization - The Bluejay System. In Sensen, C.W., Hallgrimsson, B. [Eds.] Advanced Imaging in Biology and Medicine - Technology, Software Environments, Applications. Springer Verlag, Heidelberg pp. 395-400

3. Gordon P., Sensen C.W. (2005) Oligonucleotide Design from Principle to Practice. In A. Markoff [ed.] Analytical Tools for DNA, Genes and Genomes. DNA Press, Eagleville, PA, pp. 257-277

2. Turinsky A., Gordon P., Xu E., Stromer J., Sensen C.W. (2005) Genomic Data Representation through Images: The MAGPIE/Bluejay System. In C.W. Sensen [ed.] Handbook of Genome Research. Wiley-VCH, Weinheim, pp. 383-413

1. Gordon P., Gaasterland T., Sensen C.W. (2001) Genomic Data Representation Through Images: MAGPIE as an Example. In Sensen [ed.] Genomics and Bioinformatics, Wiley-VCH.

Technical Reports & White Papers

II - Gordon, P.M.K., Sensen, C.W. (2007) A Pilot Study into the Usability of a Scientific Workflow Construction Tool. Technical Report #2007-874-26, Department of Computer Science, University of Calgary, Canada. 8 citations (2 self) in Google Scholar

I - Sensen, C.W., Brum J., Gordon P., Hood M., Lindahl G., Schulman M., Spindler C., Stuart M., Unger S. (2002) Establishment of the first Java 3D™ enabled CAVE - A Whitepaper. (local copy, 4 citations in Google Scholar)