Computational Genomics MSCBIO2070/02-710 (cross-listed as 10-810), Spring 2015Ziv Bar-Joseph (zivbj[AT]cs.cmu.edu) Chakra Chennubhotla (chakracs[AT]pitt.edu)
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Date |
Instructor |
Lecture Topics |
Slides Download |
Homeworks |
1/12 |
Ziv |
Introduction to molecular biology |
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1/14 |
Ziv |
Introduction to computational biology |
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1/19 |
No class, MLK day | |||
1/20 |
Marta |
Python Recitation 5-6pm | ||
1/21 |
Ziv |
Next generation seqeucing /RNA-Seq | ||
1/22 |
Silvia |
R Recitation 5-6pm | ||
1/26 |
Chakra | Molecular evolution (Molecular clock, selection tests, Evolutionary distance calculation using Jukes cantor & Kimura models) |
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1/28 |
Chakra |
Phylogeny: Ultrametric Evolutionary Distances, Tree-Construction: UPGMA |
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2/2 |
Chakra | Phylogeny: Tree-Construction: Nearest-Neighbor; Maximum Likelihood |
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2/4 |
Chakra |
Scoring matrices, Pair wise Sequence alignment using DP (global, local, affine gap) |
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2/9 |
Chakra |
Sequence alignment continued. Multiple sequence alignment and profile-profile alignment |
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2/11 |
Chakra |
Motif discovery |
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2/16 |
Ziv |
Microarrays (chip seq etc) |
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2/18 |
Ziv |
Normalization, differentially expressed genes |
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2/23 |
Ziv |
Differentially expressed genes |
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2/25 |
Chakra |
Clustering |
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3/2 |
Ziv |
Classification |
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3/4 |
Chakra |
HMMs and their applications (CpG islands, gene prediction, Higher order markov for DNA, Duration modeling, pair HMMs for alignment) |
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3/9 |
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Spring Break |
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3/11 |
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Spring Break |
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3/16 |
Ziv (Class today in 237 Hamburg Hall) |
Time Series |
PS3 due PS3 solutions |
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3/18 |
Ziv |
Regulatory networks 1 |
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3/22 |
Ziv |
Midterm Review Session (4pm in 4405 Gates) |
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3/23 |
Ziv |
Regulatory networks 2 |
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3/25 |
Ziv + Chakra |
Midterm |
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3/30 |
Chakra |
RNA Structure |
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4/1 |
Chakra |
RNAs and epigenetics (microRNA and target prediction, non-coding RNAs, histones) |
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4/6 |
Chakra |
Epigenetics 2 |
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4/8 |
No Class |
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4/13 |
Maria Chikina |
Combining regulatory and epigenetics models |
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4/15 |
Maria Chikina |
Protein Interactions |
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4/20 |
Ziv |
Dynamic networks |
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4/22 |
Ziv |
Systems Biology 1 |
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4/27 |
Ziv (Class today in GHC 8102) |
Systems Biology 2 |
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4/29 |
Ziv + Chakra |
Poster Session in GHC 4th floor lobby |
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5/4 |
Final Project Writeup due Monday at 11:59pm Email to Ziv, Chakra, and Marta |
Last Updated: 4/9/2015