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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

Lec1

2007

2005  2004  2002

 

 

Hypothesis testing, FDR

Lec2A

2017

 

Survival analysis

Lec2B

2017

 

Gene enrichment analysis: GO, TANGO, GSEA

Lec2C

2009

 

Regulatory motif discovery

 

2005  2004

Introduction, Prima, MEME, Amadeus

Lec3A

2007

 

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

Lec5A

2009

 

 

PCA, TSNE

 Lec5B, Lec5C

2017

 

Consensus clustering

Lec5D

2017

 

Community detection*

Lec5E

 

Biclustering

 

Cheng & Church*

 

2007

2005  2004  2002

 

 

Samba, ISA, CTWC*, Ping-Pong

Lec6A, Lec6C

2007

2005  2004a  2004b  2002

 

 

Plaid models*

 

2002

 

 

Order-preserving submatrix problem (OPSM)*

 

2002

 

 

Bimax

Lec6B

2009

 

 

Classification

 

Introduction, dimension reduction

Lec7A

2007

2005  2004

 

 

Classification in Cancer

Lec7B

2007

 

Support vector machines (SVM)

Lec8A

2007

2005  2002

 

 

Classification in Parkinson's Disease

Lec8B

 

Multi Omics Clustering (lecture by Nimrod Rappoport)

 

CoCA, iCluster, SNF, NMF, MKL

Lec 9

2017

 

Multi Omics Integration

 

Paradigm, Paradigm-Shift

Lec 10A

2017

 

ResponseNet

Lec 10B

2017

 

PCSF

Lec 10C

 

Systems Genetics (lecture by Prof. Irit Gat-Viks)

See moodle

 

Networks and Clinical data

 

 

Matisse and Cezanne

Lec 12A

 

CRC prediction

Lec 12B

 

 PPGR prediction

Lec 12C

 

Drug targets and side effects (lecture by Prof. Roded Sharan)

Lec 13

 

 

Inference in 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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