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CRG Barcelona Summer School on Systems Biology (2011-2014)

Lecture on Static Network Inference: Static

Lecture on Dynamic Network Inference: Dynamic1 Dynamic2 Dynamic3

Lecture on Stochastic Network Inference: Stochastic

BCH4300B Winter 2014

Homework 1: Assignment Solutions

Homework 2: Assignment Solutions

Discussion paper for March 6: Henikoff & Henikoff "Amino acid substitution matrices from protein blocks" PNAS, Vol. 89, pp. 10915+, 1992.

Discussion paper for March 19: Edgar "MUSCLE: multiple sequence alignment with high accuracy and high throughput" Nucleic Acids Research, Vol. 32, No. 5, 2004.

BCH5101 Winter 2014

Here are the lecture slides for March 12: Overview Network analysis: Part A Part B Part C Network inference: Part A Part B

For March 19 we will discuss two papers: (1) Zhang et al., "Model-based Analysis of ChIP-Seq (MACS)" Genome Biology 2008, 9:R137. (2) Rapaport et al., "Comprehensive evaluation of differential gene expression analysis methods for RNA-seq data" Genome Biology 2013, 14:R95.

Slides for several teaching-oriented lectures (not my scientific talks):

  • CAMBAM/MBI Summer School lecture on "Inferring Gene Regulation in the Segmentation Network of Drosophila Melanogaster", May 24, 2010: Lecture_Drosophila.pdf
  • CAMBAM/MBI Summer School lecture on "Network Topology", May 19, 2010: Lecture_Networks.pdf
  • CMM 5304 Introduction to Developmental Biology, Oct 12, 2009: Lecture_2009_CMM_DevBio.pdf