Well here is the trial run. Post your own exam questions as comments to this post. Feel free to solicit comments from other students or me. And correspondingly feel free to comment on others posts or back to me. We read two papers for this class:
And:
Maybe one or two questions for each paper.
Gillespie Lab 
Write your questions here!
Yes please write your questions.
The author Russell S. Thomas discussed that a set of genes or genomic biomarkers are sufficient to predict increased lung tumor incidence by chemicals. What are the pros and cons of study. Comment of the specificity and sensitivity of the study conducted taking into account the heat map in Fig.1
I like this question, all I can think of adding is: How would you modify this study considering its limitations?
What is molecular profiling? How can molecular profiling of breast cancer cell lines can help in studying breast cancer. On what basis did the author characterize the 52 different breast cell line. Which cell lines where shown to be most relevant tumor models and why.
1. In the paper, author writes about lung carcinogens and non-carcinogens, describe in brief gene expression differences between lung carcinogens and non-carcinogens (Paper- Thomas et al.)
2. How were the breast cancer cell lines classified, describe in detail with respect to their tumor formation (Paper- Kao et al.)
What is molecular profiling? Describe in detail the method used for gene expression profiling including sample preparation and discuss the outcomes using examples from Paper Kao et al.
1). How Molecular profiling of tumor cells lines could be related to toxicogenomics aspects of biomarkers and prediction for breast oncology in human.
2). What are weakness of conventional toxicology (clinical chemistry and histopathology), why this methods could not give a full picture of toxicity as suppose to genomics, transcriptomics and metobolimics.
1. When looking at certain genes as biomarkers, is it better to use more genes for a classification model or less? Why is this the case?
2. In the Kao et al. paper how did they analyze the data they had? What was so different about the way they looked at this data and what did the findings suggest?
1) Discuss the various methods used by Kao et al in molecular profiling of breast cancer cell lines and explain the relationship of breast cancer cell line and the tumor subtype.
2) How did Thomas et al predict the chemically induced lung tumor incidence in rodents using the gene biomarkers? Expalin the rodent cancer bioassays in detail.