please check the attached documents.

BIOL 57601 Bioinformatics Midterm Exam

Papers:

Read and consider the following papers that are found in the Bioinformatics Brightspace ‘Midterm Exam’

content folder:

Dong, X., Huang, D., Yi, X., Zhang, S., Wang, Z., Yan, B., Chung Sham, P., Chen, K., & Jun Li, M.

(2020). Diversity spectrum analysis identifies mutation-specific effects of cancer driver genes.

Communications biology, 3: e6. https://doi.org/10.1038/s42003-019-0736-4

Zhang, J., Hu, H., Xu, S., Jiang, H., Zhu, J., Qin, E., He, Z., & Chen, E. (2020). The Functional Effects of

Key Driver KRAS Mutations on Gene Expression in Lung Cancer. Frontiers in genetics, 11: e17.

https://doi.org/10.3389/fgene.2020.00017

Optional background:

https://www.cdc.gov/genomics/about/precision_med.htm

Stratton, M. R., Campbell, P. J., & Futreal, P. A. (2009). The cancer genome. Nature, 458: 719–724.

https://doi.org/10.1038/nature07943

Midterm Exam Assignment:

Focus on research: Each of the following questions should be addressed in a 2–3 page paper that will be

turned in on Sunday one week from today (due 24 Oct. @ 10:30pm CST). Compare and contrast the papers

of Zhang et al. 2020 and Dong et al. 2020. In essay format, please address the following question: Why do

the introductions from these papers suggest there is a need to carry out these types of studies? What

scientific question/s was/were asked in each paper, and why did the researchers select the particular areas

of research that was the focus of each of these papers? What are two major findings from each paper?

Which figures from these papers most directly reflect these major findings? Why do you say this? How are

the papers similar? How are they different?

Focus on bioinformatics: What general bioinformatic methods were used in each of these papers, and what

specific programs/methods were used? Where any specialized databases used? If so, what where they

specifically and how were they used? Consider key figures (see above) that are related to central parts of

the stories that both of these papers are telling, name the specific figures you will be focusing on, and then

discuss how the binoinformatic methods enabled the formation of those figures. What elements of these

figures help them tell the story? Do you consider the figures to be well executed, or are there elements that

you would improve on?

Wrap-up: Synthesize all the information you have reviewed here. What is the overall significance of these

papers and what are the implications of this work in this current era?