Tel Aviv University Blavatnik School of Computer Science

Fall 2009
Analysis of DNA Chips and Gene Networks

0368-4137-01

http://www.cs.tau.ac.il/~rshamir/ge/09/

Ron Shamir

Thursdays 16-19 Melamed 6

Contact Info:
 
    Email Phone Office Office Hours
Instructor:  Ron Shamir  rshamir  640-5383 Schreiber 014 By appointment 
TA:  Guy Harari guyharar@gmail.com  640-5394 Schreiber 011 By appointment 

Course Description and Prerequisites

Lecture notes:

  • The most recent complete set of lecture notes is avalilable for the 2007 course.
  • Lecture notes for 2002 , 2004 and 2005 contain some additional topics.
  • Revised lecture notes will gradually appear in this website.

    Course Plan:
    Will appear gradually here.

       
      Lect
      Date
      Topic
      Notes
      Speaker
      Scribe
      1
      22/10/09
      Introductory Concepts
      pdf
      Ron Shamir 
      -
      2
      29/10
      Normalization and differential expression
      pdf
      Rani Elkon 
      -
      3
      5/11
      Clustering 1
      k-means, SOM, graph formulations, PCC, CAST
      pdf
      Ron Shamir 
      -
      4
      12/11
      Clustering 2
      PCC proof, Hierarchical clustering, HCS
      pdf
      pdf2 (for HCS)
      Ron Shamir 
      -
      5
      19/11
      Clustering 3
      CLICK, FPF*, K-Boost*, PCA*
      pdf (for Click)
      pdf (for FPF, KBoost, PCA)
      Ron Shamir 
      Renana Meller
      6
      26/11
      Biclustering 1
      Cheng-Church, OPSM
      pdf (for Cheng-Church)
      pdf (for OPSM)
      Benny Chor
      Ron Shamir 
      -
      7
      3/12
      Classification 1
      Introduction to classification; dimension reduction
      pdf
      Gideon Dror 
      -
      8
      10/12
      Classification 2
      SVM, Golub Leukemia classification
      pdf
      Ron Shamir 
      -
      9
      17/12
      Classification 3
      Haussler et al, BHASIC*
      Van't veer et al, Scherzer et al*
      pdf
      Ron Shamir 
      -
      10
      24/12
      Biclusering 2
      ISA, SAMBA
      pdf (ISA, SAMBA)
      Ron Shamir 
      -
      11
      31/12
      Biclusering 3
      Plaid, CTWC, BIMAX*
      ps (for Plaid Models)
      ps (for CTWC)
      pdf (for BIMAX)
      Ron Shamir 
      Boris Kostenko
      12
      7/1/10
      Promoter Analysis I
      Intro, PRIMA, CREME, Projection,
      pdf
      Ron Shamir
      -
      13
      14/1/10
      Promoter Analysis II
      MEME, Amadeus*, Allegro*
      pdf (for MEME)
      amadeus paper.
      allegro paper.
      Ron Shamir
      -
      14
      21/1/10
      Enrichment analysis
      GO*, TANGO*, GSEA*
      Expression and Network analysis
      MATISSE* and more
      pdf (Enrichment analysis)
      pdf (Expression and network analysis)
      Ron Shamir
      Roye Rozov
      Dudi Ze'evi


    * new material in 2009

    Course Material and Handouts

  • Course requirements
  • Bibliography: textbooks, background and more.
  • Scribe instructions
  • Useful Links


    rshamir AT tau DOT ac DOT il


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