Refereed Publications

Submitted/In preparation

Cooper, D.M. and C. Lowenberger. 2008. The Insect Caspases. Submitted to Apoptosis.

Foster, K., Sharashad-Ali, C. Perez and C. Lowenberger. 2008. Fitness consequences of choosing the wrong site for oviposition: egg size vs egg number. Submitted to Environmental Entomology.

Gong, J.H., D.M.E. Bowdish, E.F. Nicholls, M.R. Elliot, K. Brown, K. Hokamp, F.M. Roche, C.Y.K. Cheung, R. Falsafi, F.S.L. Brinkman and R.E.W. Hancock. G-protein-coupled receptor independent, immunomodulatory properties of chemokine CXCL9. Journal of Innate Immunity. Submitted for Publication July 10, 2008.

Ng, M.P., Vergara, I.A., Chen, Q., Zeng, X., Pei, J. and N. Chen. OrthoClusterDB: a web-based database for synteny blocks. In preparation.

Ursic-Bedoya, R., J. Buchhop and C. Lowenberger. Cloning and characterization of Dorsal homologues in hemipteran Rhodnius prolixus. Submitted to Insect. Mol. Biology.


Accepted/In Press

Barón, O., R. Ursic-Bedoya, C. Lowenberger, and C.B. Ocampo. 2008. Differential Gene Expression from Midguts of Refractory and Susceptible lines of Aedes aegypti infected with Dengue-2 virus. Journal of Insect Science. Accepted.

Hormozdiari, F., Alkan, C., Eichler, E. and Sahinalp, S.C. Combinatorial Algorithms for Structural Variation Detection in High Throughput Sequenced Genomes. In Proceedings of RECOMB, Annual Symposium on Research in Computational Molecular Biology, May 2009. Accepted.

Langille M.G.I., W.W.L. Hsiao and F.S.L. Brinkman. Detection of Genomic Islands Using Bioinformatics Approaches. Nature Reviews Microbiology In preparation (Outline accepted. Final review to be submitted in 2009)

Plunkett, R.M., S.I. Murray and C. Lowenberger. 2008. Activity of a hybrid antimicrobial peptide combining functional domains from insect cecropins. Can. J. Microbiol. Accepted.

Yao, X., D.W. Bleile, Y. Yuan, J. Chao, K.P. Sarathy, D.A.R. Sanders, B.M. Pinto, M.A. O’Neill (2009). Substrate Regulates Enzyme Dynamics by Bridging Distal Sites: UDP-Galactopyranose Mutase. Proteins: Structure, Function, and Bioinformatics. In press.


Published

Alon N, Dao P, Hajirasouliha I, Hormozdiari F and Sahinalp SC. 2008. Biomolecular network motif counting and discovery by color coding. Bioinformatics 24(13):i241-249.

Colak R, Hormozdiari F, Moser F, Schönhuth A, Holman J, Ester M and Sahinalp SC. 2009. “Dense graphlet statistics of protein interaction networks and random networks”. http://compbio.cs.sfu.ca/publications/evolutionarydynamics.v5.pdf. In Proceedings of Pacific Symposium on Biocomputing (PSB 2009).

Cooper DM, Chamberlain CM and Lowenberger C. 2008. Aedes FADD: A novel death domain-containing protein required for antibacterial immunity in the yellow fever mosquito, Aedes aegypti. Insect Biochem Mol Biol.

Dolgosheina EV, Morin RD, Aksay G, Sahinalp SC, Magrini V, Mardis ER, Mattsson J and Unrau PJ. 2008. Conifers have a unique small RNA silencing signature. Rna 14(8):1508-1515.

Ericsson JD, Janmaat AF, Lowenberger C and Myers JH. 2008. Is decreased generalized immunity a cost of Bt resistance in cabbage loopers Trichoplusia ni? J Invertebr Pathol. Novermber 2008, ahead of print.

Hajirasouliha I, Hormozdiari F, Sahinalp SC and Birol I. 2008. Optimal pooling for genome re-sequencing with ultra-high-throughput short-read technologies. Bioinformatics 24(13):i32-40.

Hormozdiari F, Salari R, Hsing M, Schönhuth A, Chan SK, Sahinalp SC, Cherkasov A. 2009. The Effect of Insertions and Deletions on Wirings in Protein-Protein Interaction Networks: A Large-Scale Study. Journal of Computational Biology. January 2009, ahead of print.

Jiang B and Pei J. 2009. “Online Interval Skyline Queries on Time Series”. In Proceedings of the 25th IEEE International Conference on Data Engineering (ICDE'09), March 29 - April 4, 2009, Shanghai, China.

Langille MG and Brinkman FS. 2009. IslandViewer: an integrated interface for computational identification and visualization of genomic islands. Bioinformatics.

Langille MG, Hsiao WW and Brinkman FS. 2008. Evaluation of genomic island predictors using a comparative genomics approach. BMC Bioinformatics 9:329.

Lardeux F, Tejerina R, Aliaga C, Ursic-Bedoya R, Lowenberger C and Chavez T. 2008. Optimization of a semi-nested multiplex PCR to identify Plasmodium parasites in wild-caught Anopheles in Bolivia, and its application to field epidemiological studies. Trans R Soc Trop Med Hyg 102(5):485-492.

Leighton BJ, Roitberg BD, Belton P and Lowenberger CA. 2008. Host antibodies in mosquito bloodmeals: a potential tool to detect and monitor infectious diseases in wildlife. J Med Entomol 45(3):470-475.

Malhis N, Butterfield YS, Ester M and Jones SJ. 2009. Slider--maximum use of probability information for alignment of short sequence reads and SNP detection. Bioinformatics 25(1):6-13.

Morin RD, Aksay G, Dolgosheina E, Ebhardt HA, Magrini V, Mardis ER, Sahinalp SC and Unrau PJ. 2008. Comparative analysis of the small RNA transcriptomes of Pinus contorta and Oryza sativa. Genome Res 18(4):571-584.

Platt MD, Schurr MJ, Sauer K, Vazquez G, Kukavica-Ibrulj I, Potvin E, Levesque RC, Fedynak A, Brinkman FS, Schurr J, Hwang SH, Lau GW, Limbach PA, Rowe JJ, Lieberman MA, Barraud N, Webb J, Kjelleberg S, Hunt DF and Hassett DJ. 2008. Proteomic, microarray, and signature-tagged mutagenesis analyses of anaerobic Pseudomonas aeruginosa at pH 6.5, likely representing chronic, late-stage cystic fibrosis airway conditions. J Bacteriol 190(8):2739-2758.

Salari R, Schönhuth A, Hormozdiari F, Cherkasov A and Sahinalp SC. 2008. "The relation between indel length and functional divergence: a formal study". http://compbio.cs.sfu.ca/publications/salarietal.pdf. In Proceedings of 8th Workshop on Algorithms in Bioinformatics (WABI 2008), Universität Karlsruhe, Germany.

She R, Chu JS, Wang K, Pei J and Chen N. 2009. GenBlastA: enabling BLAST to identify homologous gene sequences. Genome Res 19(1):143-149.

Ursic-Bedoya RJ, Nazzari H, Cooper D, Triana O, Wolff M and Lowenberger C. 2008. Identification and characterization of two novel lysozymes from Rhodnius prolixus, a vector of Chagas disease. J Insect Physiol 54(3):593-603.

Vivona S, Gardy JL, Ramachandran S, Brinkman FS, Raghava GP, Flower DR and Filippini F. 2008. Computer-aided biotechnology: from immuno-informatics to reverse vaccinology. Trends Biotechnol 26(4):190-200.

Wang H. and Pei J. 2008. Clustering by Pattern Similarity. Journal of Computer Science and Technology 23(4):481-496.

Waliwitiya R, Kennedy CJ and Lowenberger CA. 2008. Larvicidal and oviposition-altering activity of monoterpenoids, trans-anithole and rosemary oil to the yellow fever mosquito Aedes aegypti (Diptera: Culicidae). Pest Manag Sci.

Winstanley C, Langille MG, Fothergill JL, Kukavica-Ibrulj I, Paradis-Bleau C, Sanschagrin F, Thomson NR, Winsor GL, Quail MA, Lennard N, Bignell A, Clarke L, Seeger K, Saunders D, Harris D, Parkhill J, Hancock RE, Brinkman FS and Levesque RC. 2009. Newly introduced genomic prophage islands are critical determinants of in vivo competitiveness in the Liverpool Epidemic Strain of Pseudomonas aeruginosa. Genome Res 19(1):12-23.


Book Chapters / Contributions to a Collective Work

Bleile DW. M.Sc. Thesis, June 2, 2008, Structural Models of UDP-galactopyranose Mutase-Ligand Binding by Interpretation of Saturation Transfer Difference NMR Spectra through Computational Modeling.

Ho, CK. M.Sc. Thesis, June 12, 2008, Computationally identifying novel essential genes, including non-coding RNAs, in intergenic sequences in bacterial genomes.

Langille MGI, Zhou Z, Hsiao WWL, Fedynak A, Xu Y and Brinkman FSL. 2008. Mobile genetic elements and their prediction. In Xing Yu and J. Peter Gogarten (eds.), Computational Methods for Understanding Bacterial and Archaeal Genomes, World Scientific Publishing, USA.

Sahinalp SC. 2008. "Edit distance under block operations". http://compbio.cs.sfu.ca/publications/cenks.ps. Encyclopedia of Algorithms (Ming Yang Kao, ed.), Springer.

Yao, X. M.Sc. Thesis. August 1, 2008, Ligand Binding and Conformational Dynamics of UDP-Galactopyranose Mutase Probed by Steady-State Fluorescence of Tryptophan and FAD.


Abstracts

Brinkman, F.S.L."Bioinformatics applied to the evolution of virulence, and the identification of novel markers, drug targets and vaccine components." (not completed due to technical difficulties), Applied Bioinformatics & Public Health Microbiology Conference, April 27-29, 2008, Hinxton, Cambridgeshire, UK.

Ho Sui, S.J., Ho, C.K., Mulder, D.T., Fedynak, A. and Brinkman, F.S.L. (2008). A bioinformatics pipeline to identify bacterial protein drug targets: Integration of novel gene discovery and existing annotations. HUGO’s 13th Human Genome Meeting. September 27-30, 2008, Hyderabad, India.

Langille, M.G.I., and F.S.L. Brinkman (2008). "IslandPick and IslandViewer: Tools for the computational identification and visualization of genomic islands." 16th Annual International Meeting on Microbial Genomics, September 14-18, 2008, Lake Arrowhead, California, USA.

Pinto, B.M., X. Yao, D.W. Bleile, Y. Yuan, J. Chao, K.P. Sarathy, D.A,R. Sanders, M.A. O’Neill. (2008). Substrate Regulates Redox-switched Recognition Loop Dynamics in UDP-Galactopyranose Mutase. XXIV International Carbohydrate Symposium, July, 2008, Oslo, Norway.

Shephard, L., Dobson, N. and Unrau, P.D. Characterizing the Binding and Release of 6S RNA Polymerase. 13th Annual Meeting of the RNA Society, Jul 28 – Aug 3, 2008, Berlin, Germany.

Whiteside, M.D., Winsor, G.L., and Brinkman, F.S.L. (2008). Using Phylogenetic Divergence to Evaluate Predicted Orthologs. 58th Annual Conference of the Canadian Society of Microbiologists, June 9-12, 2008, Calgary, Alberta, Canada.

Wilson, P.D. and Chen, P.S.K. (2008). Studies Towards the Total Synthesis of Yaequinolones and Structurally-Related Natural Products. Department of Chemistry Graduate Student Poster Competition, Nov, 2008. Simon Fraser University.

Wilson, P.D. and Chen, P.S.K. Total Syntheses of 2H-Chromene Containing Natural Products. Merck Frosst Lectureship 2008-2009 Poster Reception, Sep, 2008, Simon Fraser University. Sept. 2008.

Wilson, P.D. and Chen, P.S.K. Studies Towards the Total Syntheses of 2H-chromene Containing Natural Products. Latest Trends in Organic Synthesis-13, Brock University, Aug 2008, St. Catharines, Ontario.

Winsor, G.L., Van Rossum, T., Khaira, B., Lo, R.C., Whiteside, M.D., Yu, N., Wagner, J., Ester, M., Hancock, R.E.W. and Brinkman. F.S.L. (2008). The Pseudomonas Genome Database: A Model for Facilitating User-Friendly, Comprehensive Comparisons of Microbial Genomes. 16th Annual International Conference on Intelligent Systems for Molecular Biology, July 19-23, 2008, Toronto, Ontario.

Winstanley, C., J. L. Fothergill, I. Kukavica-Ibrulj, M. Langille, C. Paradis-Bleau, F. Sanschagrin, A. Bragonzi, G. Winsor, N. R. Thomson, R.E.W. Hancock, J. Parkhill, F.S.L. Brinkman, and R.C. Levesque (2008). Genome sequence of a cystic fibrosis epidemic strain of Pseudomonas aeruginosa. 31st European Cystic Fibrosis Conference, June 11-14, 2008. Prague, Czech Republic.

Yu, N.Y., Wagner, J., Laird, M.R., Lo, R., Ester, M. and Brinkman, F.S.L. (2009). Improved computational prediction of prokaryotic protein subcellular localization. 7th Asia Pacific Bioinformatics Conference, January 13-16, Beijing, China.

Yu, N.Y., Wagner, J., Laird, M.R., Lo, R., Lim, F., Foster, L.J, and Brinkman, F.S.L (2008). Analysis of prokaryotic protein subcellular localization: computational and proteomic perspectives. EMBO Conference on control, co-ordination and regulation of protein targeting and translocation, October 25-28, 2008, Saint-Maxime, France.

Yu, N.Y., Wagner, J., Lim, F., Lo, R., Stoynov, N., Laird, M.R., Gardy, J.L., Foster, L.J., and Brinkman, F.S.L. (2008). Comparative analysis of protein subcellular localization using improved computational and laboratory proteomic methods. The 8th International Conference of the Canadian Proteomics Initiative, May 3-5, 2008, Burnaby, British Columbia.


Invited Presentations:

Brinkman, F.S.L. “Common themes in the role of horizontal gene transfer in pathogen evolution”, American Society for Microbiology Annual General Meeting, May 17-21, 2009. Philadelphia, PA, USA.

Brinkman, F.S.L. “Using bioinformatics to accelerate pathogen research and infectious disease control”. Bioinformatics and Computational Biology Unit, Instituto Gulbenkian de Ciência. November 25, 2008, Oeiras, Portugal.

Brinkman, F.S.L. “Using bioinformatics to accelerate microbial drug discovery” (videotaped), China-BC Research and Innovation Partnership Summit, May 25-28, 2008. Beijing, China.

Brinkman, F.S.L. "Improved pathogen bioinformatics and quantifying genome-wide trends in pathogen-associated genes", Microbial Genomes 2008, April 8-11, 2008. Paris, France.

Brinkman, F.S.L. "Evolutionary Analysis", Current Topics in Genome Analysis series at the NHGRI, NIH, February 12, 2008. Bethesda, Maryland, USA.

Sahinalp, S.C. McGill-Barbados Workshop on Protein Protein Interaction Networks, Barbados, 2009.

Sahinalp, S.C. 4th Annual Workshop on String Algorithms, Tel Aviv, Israel, 2009.

Sahinalp, S.C. Banff Workshop on Mathematics of String Spaces and Algorithmic Applications, Jan 25-30, 2009, Banff, Alberta.

Sahinalp, S.C. Colloquium celebrating Mike Paterson’s 66th birthday, University of Warwick, UK, 2008.

Sahinalp, S.C. Schloss Dagstuhl, Workshop on Sublinear Algorithms, Germany, 2008.

Sahinalp, S.C. SIAM Discrete Math Conference, Burlington Vt, 2008.

Sahinalp, S.C. Plenary talk, HIBIT’08; Intl. Symposium on Health Informatics and Bioinformatics, Istanbul, Turkey, 2008.

Sahinalp, S.C. European Science Foundation Meeting on non-coding RNAs: computational challenges and applications, April 28-30, 2008, Antalya, Turkey.

Sahinalp, S.C. IRMACS, Coast to Coast Seminars through Canada (based at SFU), 2008.

Unrau, P.J. “Studying RNA systems using in vitro methods”, CSIRO Black Mountain Laboratories, Sep 15, 2008, Canberra, Australia.

Unrau, P.J. “Ribozyme-Mediated Small Molecule Chemistry”, Département de Biochimie, Mar 17, 2008, Université de Montréal, Quebec.

Unrau, P.J. “6S RNA Interactions with E. coli RNAP Characterized using in vitro selection”, CSC May 2008, Edmonton.

Wilson, P.D. and Chen, P.S.K. Studies Towards Natural Product Total Syntheses. Bioinformatics for Combating Infectious Diseases (BCID) Project Meeting, Simon Fraser University. Sep 2008.

Wilson, P.D. Recent Advances in the Chemistry of Phloroglucinol. Latest Trends in Organic Synthesis-13, Brock University, St. Catharines, Ontario. Aug 2008.

Wilson, P.D. Targets and Methods for Total and Asymmetric Synthesis. Northwestern University, Evanston, Illinois, USA. May 2008.

Wilson, P.D. Targets and Methods for Total and Asymmetric Synthesis. University of Chicago at Illinois, Illinois, USA. May 2008.

Wilson, P.D. and Chen, P.S.K. Studies Towards the Total Syntheses of 2H-chromene Containing Natural Products. Department of Chemistry Graduate Student Oral Competition. Simon Fraser University. Feb 2008.




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