Jingyi Jessica Li
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STATS M254 / BIOINFO M271 / BIOMATH M271 (Spring 2014)
Statistical Methods in Computational Biology
Instructor:
Jingyi Jessica Li (jli AT stat.ucla.edu)
Dates:
04/01/2014-06/05/2014
Time and Location:
Tue & Thr, 12:30-1:45 PM, MS 5225
Syllabus
Lecture Notes
Lecture 1: Introduction and Data
Lecture 2: Gene Expression Analysis
Lecture 3: Multiple Testing Issues;
k
-means Clustering
Lecture 4:
k
-medoids Clustering; Hierarchical Clustering; How to Choose
k
?
Lecture 5: Gap Statistic; Liquid Association
Lecture 6: Alternative Splicing; Multivariate Analysis of Transcript Splicing (MATS)
Lecture 7: Statistical Inferences for Isoform Expression in RNA-Seq
Lecture 8: Expectation-Maximization Algorithm
Lecture 9: Measure of Correlation & Dependence
Lecture 10: Simulation Methods
Lecture 11: Markov Chain Monte Carlo
;
An Ising Model Example
Lecture 12: Hidden Markov Model
Lecture 13: Basics of Information Theory
Survey Papers
Kai Fu: Current Methods in the Analysis of CLIP-Seq Data
Alden Huang: A Brief Survey of ChIP-seq Protocols and Peak Detection Methods
Ruyi Huang and Arturo Ramirez: Feature Selection Using Classification Methods
Arthur Jaroszewicz and Megan Roytman: Statistical Measures of Distance
Chelsea Jui-Ting Ju: An Overview of Gene Set Enrichment Analysis
Wanlu Liu and Austin Quach: Statistic Models in Biological Network Analysis
Medha Uppala: A Survey of Statistical Models to Infer Consensus 3D Chromosomal Structure from Hi-C data
Yida Zhang and Le Shu: A General Review on Time-series Gene Expression Data