Zhijin Wu PhD

Statistical Methods in Bioinformatics

 

Instructor

Zhijin (Jean) Wu
Associate Professor of Biostatistics
Center for Statistical Sciences
121 South Main St, #702
Phone: 863-1230
Email: zwu@stat.brown.edu

Lecture T,Th 10:30-11:50   Room 241, 121 S. Main St.
Lab Friday: 9:00-10:00  Room 259 (121 S. Main St)
Office Hour: Monday 2-3 (Room 702)

Goal: Introduces statistical concepts and methods used in selected areas of bioinformatics. Topics include statistical methodology for analysis of microarray data and next generation sequencing data, including application in gene expression experiments, genetic variants and genomic association studies. We will also give brief introduction to   alignment and comparison of biological sequences. Brief review and succinct discussion of biological subject matter will be provided for each area. Available software will be introduced. Introduction to software R and Bioconductor tools are provided in lab. Intro level statistics (PHP 2500/01/02 or PHP 2510/11) recommended

There is no textbook for the course.

Evaluation: 30% homework 70% Course Project

Reference Books:
Gentleman R et al, Bioinformatics and Computational Biology Solutions Using R and Bioconductor. Springer Verlag, 2005
Durbin R et al. Biological Sequence Analysis, Cambridge, 2001


Introduction to R 

R for absolute beginners (If you are so eager to start you may begin at page 14)

Tentative Course Outline 

  1. Introduction to molecular biology, high throughput experiments (lec1.pdf)
  2. Exploratory data analysis  (lec2)
  3. Data Preprocessing  ( lec3 )
  4. Differential gene expression (lec4)
  5. Multiple testing and false discovery rate  lec5
  6. Clustering and classification lec6 lec6B lec7A lec7B
  7. Sequencing based technology lec8A lec8B lec8C
  8. Analysis of RNAseq data
  9. Gene Annotation and Gene Set analysis lec9  lec10
  10. intro to proteomics lec12 lec13
  11. intro to sequence analysis  BSA1 BSA2
  12. intro to ChipSeq 


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