Slides

(Back to main page) 

  • Introductory slides  
  • Comp-pharma Data types 
  • Comp-pharma Data types2 (Aug 31, 2006)
      • Datasets covered: Blood Pressure Measurement,  Alternate splice variants of ABCC4, CYP2B6 expression and activity, Depression in Mexican-Americans, Drug Levels in Depressed Mexican-Americans, A modulator of HERG Potassium Channel block,  ABCB1 Functional Protein Variants.
  • Comp-pharma Data types3 (Sept 5, 2006)
      • Datasets covered:   Lipid measurements in tamoxifen study,  Meperidine N-demethylation by endogenous CYP450 enzymes in human liver microsomes, Meperidine N-demethylation by human CYP450 isoforms, Metabolism of yohimbine by human CYP450 isoforms, Methotrexate polyglutamate accumulation in children with ALL,  Microsomal flavopiridol, propofol glucuronidation, Microsomal study of midazolam, mRNA/protein levels,  Midazolam and docetaxel clearance, Midazolam catalytic activity in liver microsomes,  Morphine pharmacokinetics in patients receiving patient-controlled analgesia. 
  • Comp-pharma Data types4 (Sept 7, 2006)
      • Datasets covered: Effects of Dapsone on CYP2C9 Variants and Naproxen Metabolism, Enzyme kinetics of GGH T127I variant protein, Epirubicin, morphine metabolite formation rates, Folate, Homocysteine and Vitamin B12 in Young Healthy Individuals, GGH activity and methotrexate polyglutamate accumulation in children with ALL, Genetic Epidemiology of Responses to Antihypertensives, Homocysteine concentrations in leukemia patients, Hot flashes in tamoxifen patients, Irinotecan Clinical Data, Irinotecan and CYP3A5 Genotype.
  • Comp-pharma Data types5 (Sept 12, 2006)
      • Datasets covered: STE Functional Protein Variants, SULT1A3 functional protein variants, SULT1C1 functional protein variants, SULT2A1 Functional Protein Variants, Survival of patients on beta-blockers after ACS, and ADRB1, ADRB2, Tacrolimus dosing and Steroid Weaning in pediatric heart transplant patients, Tacrolimus dosing and outcome in lung transplant patients, Thyroid binding globulin in tamoxifen patients, Treatment-specific changes in gene expression (top 150 discriminating genes), Treatment-specific changes in gene expression (top treatment-specific genes), WUSTL warfarin dosing data, group A, Xenopus expression of variant SLC22A2 proteins, mRNA and protein expression levels of ABCG2 (BCRP), mRNA expression levels of PXR splice variants in livers.
  • comp-pharmadatatypes6 (Sept 14, 2006)
      • Datasets Covered:  Outcomes in Asthmatics taking montelukast, Protein concentrations in liver microsomes, Protein expression of genes in the irinotecan pathway, Pharmacokinetics of irinotecan in cancer patients, Risk of therapy-related acute myeloid leukemia, Risk classfication of childhood ALL and TYMS, GSTM1 gene expression in ALL cells, Protein profiling of the MTOR pathway, RNA expression of genes in the gemcitabine pathway in pancreatic samples, SLC15A2 Functional Protein Variants, SLC18A2 Functional Protein Variants, SLC22A6 Functional Protein Variants, SLC28A1 Functional Protein Variants, SLC28A2 Functional Protein Variants, SLC28A3 Functional Protein Variants, SLC29A1 Functional Protein Variants.
  • Comp-pharma Data types7 (Sept 19, 2006)
      • Datasets covered: ADRB2 association with cardiovascular disease, Analysis of variation in mouse TPMT expression and activity, Blood pressure measurements, group 2, Bronchodilator response to beta agonist in asthmatics, CYP2C9 Variants and Flurbiprofen Metabolism, CYP2C9 Variants and Naproxen Metabolism, CYP2C9 Variants and Piroxicam Metabolism, Characteristics of Variant Sodium Channels, Cold Pressor Test (CPT) measurements of twins, Cross resistance to prednisolone, asparaginase, vincristine and daunorubicin in ALL cells, Cytotoxicity of 5-fluorouracil in the CEPH population, Cytotoxicity of docetaxel in the CEPH population, DNPS gene expression.
  • CBioC and other research at the BioAI lab (Sept 19,2006)
  • Comp-pharma Data Types8 (Sept 21, 2006)
      • Datasets covered: S-COMT functional protein variants, NAT2 Phenotype and Hypersensitivity to Sulfonamides, Pharmacogenetic Risk Factors for Osteonecrosis of the Hip Among Children With Leukemia, Hepatic CYP3A4 Protein Expression and Midazolam Hydroxylation (Cohort II), Hepatic CYP3A4 mRNA expression (Cohort III), Hepatic CYP3A5 predicts Saquinavir clearance, HNMT Functional Protein Variants, KCNA5 variants in vitro, Drug-Induced Long QT Intervals, EGFR promoter activity in transfected cells -216G/T-191C/A, Blood pressure measurements, Genetic Epidemiology of Responses to Antihypertensives (GERA), Pharmacokinetics of Tamoxifen at 4 months, Pharmacokinetics of methotrexate in ALL children (Window therapy), Gene Expression correlating with drug resistance of asparaginase in children with ALL, Gene Expression differing in drug resistant of prednisolone in children with ALL, Gene Expression correlating with drug resistance to daunorubicin in children with ALL, Gene Expression correlating with drug resistance of vincristine in children with ALL. 
  • PharmGKB ID (Sept 21, 2006)
  • Comp-pharma Data Types9 (Sept 26, 2006)
      • Datasets covered: Depression in Mexican-Americans; Dropout Scores, Depression in Mexican-Americans; Terminated Scores, Patient responses to tamoxifen, Patient responses to tamoxifen - set 2, Development of treatment-related acute myeloid leukemia, EGFR promoter allele-specific expression in fibroblast cell lines, Effects of Dapsone on CYP2C9 Variants and Flurbiprofen Metabolism, In vivo and in vitro characterization of variants, PAPSS1 functional protein variants, PAPSS2 Functional Protein Variants, SLC22A1 Functional Protein Variants, Lipid measurements in tamoxifen study - set 2.
  • Sept 28 th and Oct 3rd (Discussed summarization of the data sets as made by Luis and Xin and discussed the classification techniques: k-nearest neighbour, naive Bayesian classifier [1,2], decision trees [3], and linear support vector machines [4].) 
  • Oct 5th and Oct 12th (Jieping Ye will cover these two classes) 
  • Oct 10th: Inductive logic programming
  • Oct17th,19th,24th:  Pathways
    • Russ Altman's tutorial on "Approaches to Pharmacogenomics studies"
    • Russ Altman's tutorial on "Pathways of drug metabolism and action" 
    • Signal network and pathways (slides)
    • Representation and reasoning with signal networks (slides)  
    • Molecular interaction maps of bioregulatory networks: a general rubric for systems biology. Kohn KW, Aladjem MI, Weinstein JN, Pommier Y. January 2006 (annotated)
      • Juraj's slides
    • Kohn's 1999 paper
    • Kohn's interaction maps
    • Transcript of the programs I wrote on Oct 24th 
  • Oct 26th: Dr. George Poste's talk (slides)  
  • Oct 31st: A query language for biological networks (Juraj and Xin's presentation that borrows heavily from Ulf Lesser' slides)
  • Nov 2nd:  Clustering
  • Nov 7 presentations: James Greene, Sai Moturu, Payam Refaeilzadez.
  • Nov 9 presentations: Saadat Anwar,  James Leaman, Min Yan.
  • Nov 14: Guest Speaker (Lance Parsons)
  • Nov 16 presentations: Kalpesh Shah, Toni Farley, Stephen Chelladurai
  • Nov 21: Test
  • Nov 23: Thanksgiving 
  • Nov 28 presentations: Meraj Aziz, Archana Ramesh,  Jicheng Zhao.
  • Nov 30 presentations: Juraj Dzifcak,  Luis Tari, Xin Zhang. 
  • Dec 5: Last day of class (project demos in class)
  • Dec  6,7: Project demos (by appointment)

(Back to main page)