Welcome to the web-site for


Bioinformatics II, Spring 2004.

Meetings: Tue, Thur 2.30-3.45pm, 210 Thomas Bldg.

Off. Hours: Tue, Thur 1.20-2.20pm, 505 Wartik Bldg.


Instructor: Francesca Chiaromonte. 505 Wartik Bldg, 5-7075, chiaro@stat.psu.edu

Also: Webb Miller. 501 Wartik Bldg, 5-4551, webb@bio.cse.psu.edu


Syllabus | Questions | Groups


Some useful links and news

T. Speed's group | G. Churchill's group | Stanford Stat's group | W. Li's bibliographic reference list |

Info on multiple imputation methods |

Penn State Microarray Facility |

Penn State Quantitative Bioscience Group |

Penn State Computational Genomics Journal Club (514 Wartik, 10.00-11.30am):

   Tue Jan 27. Liying Cui presents: K. Vandepoele, C. Simillion and Y. Van de Peer (2003).

   "Evidence that rice and other cereals are ancient aneuploids." Plant Cell 15, 2192-2202.
   Tue Feb 17. Istvan Albert presents: LionDB - the Penn State microarray data repository.
   Tue Mar. 16, RESCHEDULED. Naomi Altman presents: Analysis of microarray data

   (spotted and Affy) with R and Bioconductor (freeware for Windows, Mac and Unix).

   Word files provided by Naomi: GettingStarted, Marraydemo, Affydemo.

Talk, Statistics Department: Thur April 8, 4:00 pm, 102 Thomas Bldg: "Sharper Confidence Intervals Focusing on the Selected Populations with Application to Microarry Data Analysis - A New Approach", Gene Hwang, Cornell University.

Talk, Statistics Department: Tue April 13, 4:00 pm, 102 Thomas Bldg: "Statistical learning from distributions of DNA words", Probal Chaudhuri, Indian Statistical Institute.



Special announcements

Reference books

Textbooks on Regression methods and related topics:

Textbooks on Multivariate Analysis:

1. Introduction to Microarrays

2. Experimental Design and ANOVA for Microarrays

3. Data Preprocessing: Normalization, Missing Values, Preliminary Transfo's and  Filtering

Reading Assignment: Instructions. Due date: Tue March 2nd, in class.
  Sidorov I.A., Hasack D.A., Gee D., Yang J., Cam M.C., Lempicki R.A., and Dimitrov D.S. (2002). Oligonucleotide micorarray data distribution and normalization. Information Sciences 146: 67-73.
  Bolstad, B.M., Irizarry R. A., Astrand, M., and Speed, T.P. (2003). A Comparison of Normalization Methods for High Density Oligonucleotide Array Data Based on Bias and Variance. Bioinformatics 19(2): 185-193.


4. Differentially Expressed Genes

Reading assignment: Instructions. Due date: Thur March 18th, in class.

  Tusher, V.G., Tibshirani, R., and Chu, G. (2001). Significance analysis of microarrays applied to the ionizing radiation response. PNAS. 98:5116-5121.

  Efron B., Tibshirani, R., Storey J.D., and Tusher V. (2001). Empirical Bayes analysis of a microarray experiment. Journal of the American Statistical Association. 96:1151-1160.


5. Dimension Reduction for Microarray Data

Data assignment: Instructions. Data set. Due date: Tue April 6th, in class.


6. Clustering for Microarray data

Data assignment: Instructions. Data set. Due date: Tue April 20th, in class.


7.  Combining gene expression data with other types of information; Gene networks (hints)





Each group should prepare a presentation lasting approximately 20-25 minutes. All group members should be involved in describing the work (i.e. take turns in speaking) and be ready to answer questions. A hard copy of the presentation (or if you want an extended description of what you did) should be handed in to Francesca right before you talk. If you want the pdf file of your presentation to be posted on the class web-site, email it to Francesca the evening before your presentation date.


Schedule for presentations:


Tue April 27th:

Thur April 29th: