STAT 555  Spring 2015

Statistical Analysis of High Throughput Biology Experiments


Prerequisites: graduate standing or permission of instructor


Useful but not required: IBIOS 554 Foundations in Data Driven Life Sciences

                                        BMMB 852 Applied Bioinformatics



Meetings:          MWF 10:10-11:05

Instructor:         Naomi Altman, Statistics,, 312 Thomas, ph 5-3791.

TA:                    Qingyu Wang, Bioinformatics,


The course is dedicated to statistical and computational methods for the design and analysis of bioinformatics experiments. 


Topics (approximate number of lectures)


1.     Introduction to R and RStudio (2)

2.     Introduction to cell biology. (2)

3.     Introduction to measurement technologies: microarrays, sequencing, SNPs and ChIP. (2)

4.     Basic statistics (2)

5.     Gene Expression Microarrays: experimental designs, preprocessing and normalization, differential expression. (4)

6.     RNA-seq: experimental designs, preprocessing and normalization, differential expression, splice variants (5)

7.     SNPs (2)

8.     ChIPs (2)

9.     Replication and pooling (1)

10.  Gene Set enrichment analysis (2)

11.  Clustering samples and genes (3)

12.  Classifying samples using statistical machine learning (3)

13.  Dimension reduction (2)      

14.  Combining data from multiple platforms (3)

15.  Selected topics such as gene networks, time course experiments, project presentations (remaining time)


The course has no pre-requisites, but some computational skills and/or familiarity with basic concepts in statistics, bioinformatics and/or cell biology will help. Undergraduates must obtain consent of the instructors to register for the course.  Auditors and visitors are welcome to join in the lectures and on-line forums, but should not turn in homework.


There will be no text-book; lectures will combine methodological background description and presentation of analyses and results from recent articles. References and notes will be posted to ANGEL.


The course is offered at Hershey via video-link.  We will use some methodology from the World Campus classes to facilitate communications between the UP and Hershey students.  This includes some “flipped classroom” lessons and the use of ANGEL Forums for some discussions.  “Flipped classroom” lessons mean that I will not lecture for these topics – instead, students will do the readings and exercises, using the associated ANGEL forum to help one another – I will chime in as needed to guide the discussion.


Evaluation: 4 – 6 homeworks (50% of grade)

                   Project + presentation (50% of grade)


All Penn State and Eberly College of Science policies regarding academic integrity apply to this course. For details, see