Research in Bio-Statistics

• Presentation #3: TF papers
• Presentation #2: FDR Paper
• Presentation #1: Limma Paper

• "Prediction of regulatory networks from gene expression data"
• "A systematic computational approach for transcription factor target gene prediction"
  • "Identification of gene regulatory networks by strategic gene disruptions and gene overexpressions"
  • Identifying Gene Regulatory Networks from Experimental Data
  • Bayesian Network Approach
  • Expectation Maximization Approach
  • Variable Memory Markov Model
• Support vector machine paper
• Tandem machine learning
  • Information Content of Individual Genetic Sequences
  • Information theory based analysis
• Biochemical characterization paper
• Markov chain optimization
• "Computational analysis of transcription regulation of geobacter sulfurreducens"
• "A mixture model-based discriminate analysis"
  • Combining evidence using p values
  • Classification tree book, Breiman et al (1984)
  • Logic Regression (Keles)
  • Logic Regression Ruxzinski (2003)
  • MATCH (2003)
• pFDR paper
  • Hochberg Paper
• Nature Review Paper on Microarrays (2006)
• Nature Review on Microarrays (2002)
• Limma Paper
  • Kerr and Churchill (2001)
  • Lonnstedt and Speed (2001)
  • Lonnstedt Thesis
• Nature review article on discovery of TF binding sites
• History of DNA binding site algorithms
• Gibbs sampling