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HST.507

Advanced Computational Biology: Genomes, Networks, Evolution

4-0-8 units · Graduate

See description under subject 6.8700J.

Fall 2015 · Computational Biology

Topics

  • Introduction: Course overview, biology, algorithms, machine learning
  • Recitation 1: Biology and probability review
  • Alignment I: Dynamic programming, global and local alignment
  • Alignment II: Database search, rapid string matching, BLAST, BLOSUM
  • Recitation 2: Deriving parameters of alignment, multiple alignment
  • Hidden Markov Models Part 1: Evaluation / parsing, Viterbi, forward algorithms
  • Hidden Markov Models Part 2: Posterior decoding, learning, Baum-Welch
  • Project Introduction: About the projects, self-introductions, mentor introductions, example projects, teamwork
  • Transcript Structure: GENSCAN, RNA-seq, mapping, de novo assembly, diff expr
  • Expression Analysis: Clustering / classification, k-means, hierarchical, Bayesian
  • Recitation 3: Affinity propagation clustering and random forest classification
  • Networks I: Bayesian inference, deep learning, network dynamics
  • Networks II: Network learning, structure, spectral methods
  • Recitation 4: Small and large regulatory RNAs: lincRNA, miRNA, piRNA, etc.
  • Project Planning: Research areas, initial ideas, type of project, mentor matching, finding partners
  • Regulatory Motifs: Discovery, representation, PBMs, Gibbs sampling, EM
  • Recitation 5: Gapped motif discovery, DNA shape, PBMs, SELEX
  • Epigenomics: ChIP-seq, read mapping, peak calling, IDR, chromatin states
  • RNA Modifications: RNA editing, translation regulation, splicing regulation
  • Recitation 6: Dimensionality reduction
  • Project Feedback: Prepare 2-3 slide presentation of your term project for your mentor.
  • Resolving human ancestry and human history from genetic data
  • Disease association mapping, GWAS, organismal phenotypes
  • Recitation 7: Robinson-Foulds distance and coalescent process
  • Panel Discussion: Reconciling critiques, strategies for improvement, feedback to author
  • Quantitative trait mapping, molecular traits, eQTLs
  • Missing heritability, complex traits, interpret GWAS, rank-based enrichment
  • Recitation 8: Suffix trees and arrays
  • Comparative genomics and evolutionary signatures
  • Recitation 9: Review of phylogeny and molecular evolution
  • Phylogenetics: Molecular evolution, tree building, phylogenetic inference
  • Phylogenomics: Gene / species trees, reconciliation, recombination graphs
  • Recitation 10: Linkage disequilibrium, haplotype phasing, and genotype imputation
  • Personal genomics, disease epigenomics: Systems approaches to disease
  • Three-dimensional chromatin interactions: 3C, 5C, HiC, ChIA-Pet
  • Recitation 11: Project tips, write-up, slides, final presentation
  • Genome engineering with CRISPR / Cas9 and related technologies
  • Final presentations

Readings

Prerequisites & course information

Same subject as 6.8700J, 20.488[J] Subject meets with 6.8701J, 20.387[J] Prereq: ( Biology (GIR) , 6.1210 , and 6.3700 ) or permission of instructor G (Fall) 4-0-8 units

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