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20.390

Computational Systems Biology: Deep Learning in the Life Sciences

3-0-9 units · Undergraduate

See description under subject 6.8711J.

Spring 2014 · Foundations of Computational and Systems Biology

Topics

  • Course Introduction: History of Computational Biology; Overview of the Course; Course Policies and Mechanics; DNA Sequencing Technologies
  • Local Alignment (BLAST) and Statistics
  • Statistics; Significance Testing; Bonferroni Correction
  • Global Alignment of Protein Sequences (NW, SW, PAM, BLOSUM)
  • Comparative Genomic Analysis of Gene Regulation
  • Clustering, Model Selection, and BIC Scores
  • Library Complexity and Short Read Alignment (Mapping)
  • Burrows–Wheeler Transform (BWT) and Alignments. Guest Lecture: Heng Li ( Broad Institute )
  • Genome Assembly
  • ChIP-seq Analysis; DNA-protein Interactions
  • Simultaneous ChIP-seq Peak Discovery and Motif Sampling
  • RNA-sequence Analysis: Expression, Isoforms
  • Modeling and Discovery of Sequence Motifs (Gibbs Sampler, Alternatives)
  • Gene Expression Program Discovery Using Topic Models
  • Markov and Hidden Markov Models of Genomic and Protein Features
  • RNA Secondary Structure—Biological Functions and Prediction
  • Probabilistic Grammatical Models of RNA Structure
  • Introduction to Protein Structure; Structure Comparison and Classification
  • Protein Amino Acid Sidechain Packing Using Markov Random Fields
  • Predicting Protein Structure
  • Predicting Protein Interactions
  • Protein / Protein Interaction Prediction Using Threading
  • Gene Regulatory Networks
  • Protein Interaction Networks
  • Regression Trees
  • Logic Modeling of Cell Signaling Networks. Guest Lecture: Doug Lauffenburger
  • Analysis of Chromatin Structure
  • BayesNets
  • Discovering Quantitative Trait Loci (QTLs)
  • Narrow Sense Heritability
  • Human Genetics, SNPs, and Genome Wide Associate Studies
  • Synthetic Biology: From Parts to Modules to Therapeutic Systems. Guest Lecture: Ron Weiss
  • Causality, Natural Computing, and Engineering Genomes. Guest Lecture: George Church
  • Presentations
  • Presentations (cont.)

Readings

Prerequisites & course information

Same subject as 6.8711J Subject meets with 6.8710J, 18.419[J] , 20.490 , HST.506[J] Prereq: ( 6.100B and 7.05 ) or permission of instructor U (Spring) 3-0-9 units

Sources