[CSBi-events] Computational Biology: Genomes, Networks, Evolution 6.047(U) / 6.878(G)

[CSBi events]

6.047(U) / 6.878(G)
Computational Biology: Genomes, Networks, Evolution
Prof. Manolis Kellis and Dr. James Galagan
Lectures: TR11-12:30 in 2-105

Covers the algorithmic and machine learning foundations of
computational biology, combining theory with practice. 
We study fundamental computational techniques, coupled with
application to recent large-scale biological datasets. 
We cover both foundational topics in computational biology 
(1st half) and current research frontiers (2nd half). 

* Genomes: Biological sequence analysis, hidden Markov models,
  conditional random fields, gene finding, sequence alignment, 
  sequencing technologies, genome assembly.

* Networks: Gene expression analysis, clustering and classification, 
  regulatory motifs, Network Motifs, EM, Gibbs Sampling, graphs, 
  bayesian networks, metabolic flux modeling, synthetic biology.

* Evolution: Comparative genomics, phylogenetics, genome duplication,
  medical and population genetics, molecular evolutionary theory, 
  rapid evolution, genome rearrangements, and neofunctionalization.

More information: 
 * http://compbio.mit.edu/6.878/

Lecture slides and materials from previous years:
 * http://stellar.mit.edu/S/course/6/fa06/6.895/

First class meets: Thu Sep 6 at 11am in 2-105.
 * http://whereis.mit.edu/map-jpg?mapterms=2-105

Schedule of lectures (Google Calendar: 6.047): 
Thu Sep 06: Lec1 - Intro Biology/Algorithms/Machine Learning
Tue Sep 11: Lec2 - Global/local alignment/DynProg
Thu Sep 13: Lec3 - StringSearch/Blast/DB Search
Tue Sep 18: Lec4 - HMMs1 - Evaluation / Parsing
Thu Sep 20: Lec5 - HMMs2 - PosteriorDecoding/Learning
Tue Sep 25: Lec6 - Conditional Random Fields/Gene Finding
Thu Sep 27: Lec7 - Clustering/Basics/Gene Expression/Sequence Clustering
Tue Oct 02: Lec8 - Classification/Feature Selection/ROC/SVM
Thu Oct 04: Lec9 - Regulatory Motifs/Gibbs Sampling/EM
Tue Oct 09: Lec10 - Biological Networks/Graphs/Network Motifs
Thu Oct 11: Lec11 - Phylogenetics/Reconciliation/Phylogenomics
Tue Oct 16: Lec12 - MolecularEvolution/Coalescence/Selection/MKS/KaKs
Thu Oct 18: Lec13 - Population Genomics 1 - Fundamentals
Tue Oct 23: Lec14 - Population Genomics 2 - Association Studies
Thu Oct 25: NoLec - Midterm
Tue Oct 30: Lec16 - Sequencing Technology and Applications
Thu Nov 01: Lec17 - Genome Assembly
Tue Nov 06: Lec18 - ComparativeGenomics1 - Biological Signal Discovery
Thu Nov 08: Lec19 - ComparativeGenomics2 - Genome Evolution / Duplication
Tue Nov 13: Lec20 - Regulatory Networks/Bayesian Networks
Thu Nov 15: Lec21 - Metabolic Modeling 1 - Dynamic systems modeling
Tue Nov 20: Lec22 - Metabolic Modeling 2 - Flux balance analysis
Thu Nov 22: NoLec - Thanksgiving break
Tue Nov 27: Lec23 - Systems Biology - Regulation and metabolism
Thu Nov 29: Lec24 - Synthetic Biology - Designing biological systems
Tue Dec 04: Lec25 - Phylogenomics - Gene family evolution in complete
genomes
Thu Dec 06: Lec26 - Pre-transcriptional and miRNA regulatory networks

Contact:  manoli at mit.edu, jgalag at mit.edu