BME/BIOL 210: Experimental Systems Biology
Fall Quarter, 2008
Journal Club Questions
Please be prepared to discuss any of these specific points in journal
- Biological motivation?
- Experimental design
- How were
cells grown to produce DNA/RNA/proteins for analysis?
- What genetic background(s)?
- Choice of
- For microarrays: How many
biological / technical replicates?
- Technology used
- be able explain technology / primary data collection methods
- is this the best available
- could this have been acccomplished via other
sequencing/microarray/other high-throughput method?
- Experimental Pitfalls
- What could
cause misleading expression/sequencing data?
- Did authors detect and/or remove any systematic problems in
- Computational Analyses
- Normalization between samples
- How were
results filtered / grouped / organized to
establish relationships or networks?
- For sequencing
- what filtering or quality control was done to raw sequencing
- how were reads mapped to source species' genome?
- Summary of novel results / major findings
- Any novel technologies / methods developed?
- Alternative methods for verification of major findings
- What are the major forms of data presentation? Are these
effective for illustrating complex / large data sets?
- What kinds of follow-up experiments were done?
- Can you think of other follow-up experiments, either using
next-generation sequencing, microarrays, traditional molecular
biology, or computational analyses?
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