Computational Genomics (original) (raw)

Date

Instructor

Lecture Topics

Slides Download

Homeworks

1/12

Ziv

Introduction to molecular biology

1/14

Ziv

Introduction to computational biology

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)

1/28

Chakra

Phylogeny: Ultrametric Evolutionary Distances, Tree-Construction: UPGMA

2/2

Chakra

Phylogeny: Tree-Construction: Nearest-Neighbor; Maximum Likelihood

2/4

Chakra

Scoring matrices, Pair wise Sequence alignment using DP (global, local, affine gap)

2/9

Chakra

Sequence alignment continued. Multiple sequence alignment and profile-profile alignment

2/11

Chakra

Motif discovery

2/16

Ziv

Microarrays (chip seq etc)

2/18

Ziv

Normalization, differentially expressed genes

2/23

Ziv

Differentially expressed genes

2/25

Chakra

Clustering

3/2

Ziv

Classification

3/4

Chakra

HMMs and their applications (CpG islands, gene prediction, Higher order markov for DNA, Duration modeling, pair HMMs for alignment)

3/9

Spring Break

3/11

Spring Break

3/16

Ziv (Class today in 237 Hamburg Hall)

Time Series

3/18

Ziv

Regulatory networks 1

Project proposals due (email to Ziv, Chakra, and Marta)
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3/22

Ziv

Midterm Review Session (4pm in 4405 Gates)

3/23

Ziv

Regulatory networks 2

3/25

Ziv + Chakra

Midterm

3/30

Chakra

RNA Structure

4/1

Chakra

RNAs and epigenetics (microRNA and target prediction, non-coding RNAs, histones)

4/6

Chakra

Epigenetics 2

4/8

No Class

4/13

Maria Chikina

Combining regulatory and epigenetics models

4/15

Maria Chikina

Protein Interactions

4/20

Ziv

Dynamic networks

4/22

Ziv

Systems Biology 1

4/27

Ziv (Class today in GHC 8102)

Systems Biology 2

4/29

Ziv + Chakra

Poster Session in GHC 4th floor lobby

5/4

Final Project Writeup due Monday at 11:59pm

Email to Ziv, Chakra, and Marta