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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

Exams:

  • Exams are cumulative.
  • I can accept the following as valid reasons for missing an exam (Other reasons may need to go through Faculty Secretariate):
    1. being sick (A doctor's certificate is needed, ideally from UO's Health Services as doctor's note from other clinics may need validation by UO's Health Services.)
    2. medical emergency of an immediate family member (A doctor's certificate is needed)
    3. death of an immediate family member (A death certificate is needed)
  • Students who miss a mid-term exam may be allowed to take a deferred exam or transfer the weigth to other exams.

Download zone

Weekly schedule:

Wk Chp Topic
1 1 Lec: String-matching algorithms in BLAST and FASTA
Lab: Sequence database and heuristic string matching: NCBI Entrez, BLAST and DAMBE
2 3 Lec: Motif-characterizing algorithms
Lab: Position weight matrix and motif characterization
3 4 Lec: Motif discovery with Gibbs sampler with optional EXCEL illustration
Lab: Gibbs Sampler and intron branchpoint sites (BPS)
4 5 Lec: Lec: Introduction to RNA-Seq analysis
Lab: RNA-Seq software demonstration only (~1 hr)
5 9 Lec: Amino acid and codon usage bias and indices
Lab: Codon Usage Bias
6 8 Lec: Bioinformatics and translation initiation in prokaryotes and eukaryotes
Feb. 11, 1st mid-term exam+Lab: Secondary Structure, MFE And IRES
7 17 Lec: Evolution of acid-resistance in Helicobacter pylori
Lab: Genomic Isoelectric Point Profiling
8 2 Lec: Molecular phylogeneitcs+Sequence alignment by dynammic programming
Lab: Sequence Alignment
9 12,13 Lec: Transition bias and substitution models
Lab: Choosing The Best-Fit Substitution Model
10 15 Lec: Distance-based methods
Lab: Molecular Phylogenetics
11 15 Lec: Molecular clock
Mar. 25, 2nd mid-term exam+Lab: Testing The Molecular Clock Hypotheses
12 15 Lec: Dating speciation and gene duplication events
Lab: Dating with the Least-Squares Method

Additional reading materials:

  1. Xia X. 2017. Bioinformatics and Drug Discovery. Currrent Topics in Medicinal Chemistry 17(15):1709-1726
  2. Xia X (2017) ARSDA: A New Approach for Storing, Transmitting and Analyzing Transcriptomic Data. G3: Genes|Genomes|Genetics 7:3839-3848
  3. Xia X. 2015. A major controversy in codon-anticodon adaptation resolved by a new codon usage index. Genetics 199:573-579
  4. 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.
  5. 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
  6. Vlasschaert, C., Xia, X., Gray, D.A. 2016. Selection preserves Ubiquitin Specific Protease 4 alternative exon skipping in therian mammals. Scientific Reports 6:20039 .
  7. Xia, X. , Yang, Q. 2011. A Distance-based Least-square Method for Dating Speciation Events. Molecular Phylogenetics and Evolution 59:342-353.
  8. 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
  9. Palidwor GA, Perkins TJ, Xia X. 2010. A General Model of Codon Bias Due to GC Mutational Bias. PLoS ONE 5(10): e13431.
  10. Xia, X., Holcik, M., 2009. Strong Eukaryotic IRESs Have Weak Secondary Structure. PLoS ONE 4, e4136.
  11. 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 .
  12. Xia, X. 2007. The +4G site in Kozak consensus is not related to the efficiency of translation initiation. PLoS ONE 2(2):e188.
  13. Xia, X. and G. Palidwor. 2005. Genomic Adaptation to Acidic Environment: Evidence from Helicobacter pylori. American Naturalist 166:776-784
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