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Tel Aviv University, Blavatnik School of Computer Science

Algorithms for Big Data Analysis in Biology and Medicine

and Analysis of Gene Expression and Gene Networks (0368-4137-01)

Collected presentations and scribe notes

Prof. Ron Shamir

Course 0368-4190-01

Topic    *= material not covered in 2017 class

 2017 Presentations

Newest notes

Older notes

Introductory topics

Lecture 1

2007

2005  2004  2002

 

 

Hypothesis testing, FDR

Lec 2 A

2017 (draft)

 

Survival analysis

Lec 2 B

2017 (draft)

 

Gene enrichment analysis: GO, TANGO, GSEA

Lec 2 C

2009

 

Regulatory motif discovery

 

2007

2005  2004

Introduction, Prima, MEME, Amadeus

Lec 3A

 

DREME, GREAT

Lec3B

 

Clustering

 

      

k-means, SOM, graph formulations, PCC*, CAST*

Lec4A

2007

2005  2004  2002a  2002b

 

 

Click, hierarchical clustering

Lec4B, Lec4C

2007

2005  2004a  2004b  2002a  2002b

 

 

HCS for clustering cDNA*

 

2002

 

 

FPF, K-Boost, PCA

 

2009

 

 

Biclustering

 

Cheng & Church

 

2007

2005  2004  2002

 

 

Samba, ISA, CTWC

 

2007

2005  2004a  2004b  2002

 

 

Plaid models

 

2002

 

 

Order-preserving submatrix problem (OPSM)

 

2002

 

 

Bimax

 

2009

 

 

Classification

 

Introduction, dimension reduction

 

2007

2005  2004

 

 

Support vector machines (SVM), knowledge-based analysis, classification examples

 

2007

2005  2002

 

 

Networks

 

Genetic networks

 

2007

2005a  2005b  2004  2002a  2002b

 

 

Bayesian networks

 

2007

2005  2004  2002

 

 

Metabolic networks

 

2007

 

 

Protein interaction networks

 

2005

 

 

Microarray normalization and analysis of differential expression

 

2007

2005  2004

 

 

Integrated analysis of gene expression and other data

 

2009

 

 

Sequencing by hybridization (SBH)

 

Sequence reconstruction, positional SBH

 

2004

2002

 

 

Resequencing, genotyping, gapped chips, long targets, errors

 

2004

2002

 

 

Universal tag arrays

 

2002

 

 

Links to other relevant material                                                                                               


rshamir AT tau DOT ac DOT il

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