Contents 1 Computational Biology @ Case 1.1 Projects 1.2 Journal Club 1.3 Fall 08 1.4 ARCHIVE

[edit] Computational Biology @ Case

[edit] Projects

Copy Number Variation Project

[edit] Journal Club

[edit] Fall 08

Sept. 3rd - Rob

 Slides:
 Image:September3rd.ppt

Sept. 10th - Yoon Soo

Sept. 17th - Xiaolin

Sept. 24th - Cen

October 1st - Matt

October 8th - Yixuan

October 15th - Xin

[edit] ARCHIVE

Spring 2008

Jan 11 Yixuan

 Slides:
 Image:Efficiency and power in genetic association studies.ppt
 Papers:
 Image:Efficiency and power in genetic association studies.pdf
 Image:Effects of single SNPs, haplotypes, and whole-genome LD maps on accuracy of association mapping.pdf

Jan 18 Xin

 Zero Recombinant Haplotype Inference

Jan 25 Rob - Genome-Wide Association Studies

 Slides:
 Image:Genome-Wide Genotyping with ALS and Parkinson’s.ppt

Feb 1 Xiaolin Ancestral Haplotype Inference Based on Conditional Random Field

 Slides:
Image:Conditional Random Fields for Genotype Data.ppt

Feb 8 Yoonsoo

 Analysis of Gene Expression Data  
Image:Microarray.ppt

Feb 15 Cen

 RNA secondary structure
Image:Present.pdf

Feb 22 Matt - Faster Algorithm for Analyzing Array CGH Data

Slides:
 Image:CNV.ppt

Feb 29 Yixuan

 Bayesian Inference of Epistatic Interactions in Case-control Studies
 Slides:
 Image:Bayesian Inference of Epistatic Interactions in Case-control Studies.ppt
 Image:Bayesian Inference of Epistatic Interactions in Case-control Studies (Supplementary).ppt
 Paper:
 Image:Bayesian inference of epistatic interactions in case-control studies.pdf
 Image:Bayesian Inference of Epistatic Interactions in Case-control Studies (Supplementary).pdf

Mar 7 Xin

 Phylogeny Reconstruction of Biological Networks

Mar 14 No meeting (Campus holiday)

Mar 21 Rob - Support Vector Machines

 Slides:
 Image:SVM.ppt

Mar 28 Xiaolin Ancestral Haplotype Inference Based on Conditional Random Fields (cont'd)

 Slides:
Image:Conditional Random Fields for Genotype Data (2).ppt

Apr 4 Cen

Apr 11 Yoonsoo

 CNV detection with SNP genotyping array 
 Slides:
 Image:Cnv snparray.ppt

Apr 18 Matt

 A versatile statistical analysis algorithm to detect genome copy number variation
 Slides: Image:CNV3.ppt

Apr 25 Yixuan

 Transmission Disequilibrium Test
 Slides: Image:Introduction to Transmission Disequilibrium Test.ppt

May 2 No meeting

May 9 No meeting

May 16 Xin

May 23 No meeting

May 30 Rob

Jun 25 Yixuan and Xiaolin

Jul 16 Yoonsoo and Matt

Aug 6 Rob and Xiaolin

Aug 27 Cen and Xin

Fall 2007

Aug 24, To be success during you PhD study, schedule and coordinate

        What makes a good PhD student [1]
        Guilds to PhD students/PostDoc Image:Guideforphds.doc
        The Ph.D Experience [2]  
        How to Be a Good Graduate Student [3]
        How to write (for Chinese students) Image:How-to-write.pdf
        Future Jobs: Computational Biology [4]

        Discussions on How to Be a Successful PhD Student Image:Discussions.doc

Aug 31 No meeting

Sep 7 Xin Bayesian Networks (general framework and one bioinfo application)

     Slides:
     Image:Bayesian Networks.ppt
     References:
     Image:A tutorial on learning with Bayesian networks.pdf?
     Image:Mining Genetic Epidemiology Data with Bayesian Networks.pdf
     Image:BayesianNetwork on microarray analysis
     Some other references [5]
     Chapter 8 of Bishop book "Pattern Recognition and Machine Learning"

Sep 14 Xiaolin Conditional Random Field

     Slides: 
     Image:Conditional Random Fields.ppt? 
     References:
     Image:An Introduction to Conditional Random Fields for Relatinal Learning.pdf? 

Sep 21 Xiaolin Conditional Random Field (cont'd)

     Slides: 
     Image:Conditional Random Fields 2.ppt?   

Sep 28 Cen Biology in a nutshell (Systems Biology Ch 2)

      Slides: 
      Image:Molecular Biology in a Nutshell.pptx  
      References:
      Image:Molecular Biology in a Nutshell.PDF? ? 
      Molecular Biology of the Cell, http://www.ncbi.nlm.nih.gov/books 

Oct 5 Rob Experimental Techniques in a Nutshell (Systems Biology Ch 4)

      Slides: 
      Image:ExperimentalTechniques.ppt  
      References: Systems Biology
       

Oct 12 Yixuan A new multipoint method for genome-wide association studies by imputation of genotypes

      Slides:
      Image:A new multipoint method for genome-wide association studies by imputation of genotypes.ppt
      Paper and Supplementary Information
      Image:A new multipoint method for genome-wide association studies by imputation of genotypes.pdf
      Image:A new multipoint method for genome-wide association studies by imputation of genotypes (sup).pdf

Oct 19 Yoonsoo Intro ChemoInformatics

      Slides:
      Image:Chemoinformatics.ppt
      References:
      Image:Ch 1 chemoInfo.pdf
      Useful chemoinformatics lecture site [6]

Oct 26 Yoonsoo Chemical Data Mining of the NCI Human Tumor Cell Line Database

      Slides:
      Image:Datamining NCI60.ppt
      References:
      Image:2007-CIM-ChemInfo.pdf?
      NCI Developmental Therapeutics Program (DTP), http://dtp.nci.nih.gov/
      NCI CADD group's tool, http://cactus.nci.nih.gov/ 
      

Nov 2 Xin Biological networks and evolution

     Media:Bayesian analysis of biological networks.pdf

Nov 9 Yixuan Epistasis

     Slides:
     Image:Epistasis and a Flexible Framework for Detecting Epistasis.ppt
     Papers:
     A global view of epistasis: Image:Ng0105-13.pdf
     A flexible computational framework ...: Image:Moore-JTB-Final.pdf
     MDR: Image:MDR for gene-gene and gene-environment interactions.pdf

Nov 16 Xiaolin Genetic Variation in Populations (Image:Ch 13 population.pdf)

     Slides: 
     Image:Genetic Variation in Populations.ppt?  

Nov 23 No meeting

Nov 30 Rob Matlab with DBs, C++, and GUIs. Also, SAGE Project Introduction.

      Slides: 
      Image:11.30.ppt  

Dec 7 Cen miRNA and small ncRNAs

     Image:MiRNA and its targets.pdf?

Dec 14 Xin Haplotype Inference from Pedigree

Dec 21 Yixuan Haplotype Inference from small families

Dec 28 No meeting