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BPS4104/BIO8102H Bioinformatics (Winter term)
Student composition: Biochem (9.80%), Biology (3.92%), BioMed (7.84%), BioPharm (76.47%), Geology (1.96%).
Syllabus
Textbook: Xia, X. 2018. Bioinformatics and the cell: Modern computational approaches in genomics, proteomics and transcriptomics. 2nd edition. (You can download the book free using a campus PC or purchase a hard copy for $24.99.)
Lab manual in PDF format
Download zone
Weekly schedule (Voice-over slides will be uploaded before each scheduled class):
Additional reading materials:
- Xia X. 2017. Bioinformatics and Drug Discovery. Currrent Topics in Medicinal Chemistry 17(15):1709-1726

- Xia X (2017) ARSDA: A New Approach for Storing, Transmitting and Analyzing Transcriptomic Data. G3: Genes|Genomes|Genetics 7:3839-3848

- Xia X. 2015. A major controversy in codon-anticodon adaptation resolved by a new codon usage index. Genetics 199:573-579

- Xia, X. 2012. Position Weight Matrix, Gibbs Sampler, and the Associated Significance Tests in Motif Characterization and Prediction. Scientifica, vol. 2012, Article ID 917540, 15 pages, 2012. doi:10.6064/2012/917540.

- Xia, X. , MacKay, V., Yao, X., Wu, J., Miura, F. Ito, T. Morris, D. R. 2011. Translation initiation: a regulatory role for poly(A) tracts in front of the AUG codon in Saccharomyces cerevisiae. Genetics 189:469-478

- Vlasschaert, C., Xia, X., Gray, D.A. 2016. Selection preserves Ubiquitin Specific Protease 4 alternative exon skipping in therian mammals. Scientific Reports 6:20039
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- Xia, X. , Yang, Q. 2011. A Distance-based Least-square Method for Dating Speciation Events. Molecular Phylogenetics and Evolution 59:342-353.

- van Weringh, A, M. Ragonnet-Cronin, E. Pranckeviciene, M. Pavon-Eternod, L. Kleiman, X. Xia. 2011. HIV-1 modulates the tRNA pool to improve translation efficiency. Molecular Biology and Evolution 28:1827-1834

- Palidwor GA, Perkins TJ, Xia X. 2010. A General Model of Codon Bias Due to GC Mutational Bias. PLoS ONE 5(10): e13431.

- Xia, X., Holcik, M., 2009. Strong Eukaryotic IRESs Have Weak Secondary Structure. PLoS ONE 4, e4136.
- Carullo, M. and Xia, X. 2008 An extensive study of mutation and selection on the wobble nucleotide in tRNA anticodons in fungal mitochondrial genomes. Journal of Molecular Evolution 66:484-493
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- Xia, X. 2007. The +4G site in Kozak consensus is not related to the efficiency of translation initiation. PLoS ONE 2(2):e188.
- Xia, X. and G. Palidwor. 2005. Genomic Adaptation to Acidic Environment: Evidence from Helicobacter pylori. American Naturalist 166:776-784

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