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Weeks:
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2
3
4
5
6
7
8
9
10
Week 3
Jun 5-Jun 11
On Friday I showed Prof. Gonzalez the results of the experiments and she liked the fact that I did so much work on it. Also, she actually lent me her
tablet to work on. That was super-nice of her and made things far easier. It's a really cool HP tablet and I loved it! I also happened to discover
that day that there's a student from Bangladesh in the lab right next to us. We hung out a bit and he said he'll let me know if they have any
gathering of Bangladeshis.
The weekend was extremely boring because Skatje wasn't around either. Her parents came to see her and she was in Tempe with them and I don't like being all
alone. But at least I had the tablet then and could do some work. I was supposed to write up my project proposal but
I was still a bit unclear about the project and did some research online. Wikipedia was a good place for getting the basics and Google scholar proved to be useful for gathering details. I read a whole bunch of papers on ADRs, pharmacokinetics,
pharmacogenetics, pharmacodynamics, toxicology etc. My background in biology and chemistry helped a bit but I still had too much information. It did help
clear my concept though. I also tried to find out whether others have researched much on the topic we were researching on. I found 9 good papers on it and
most of them were published in 2009. It was exciting to read what they did and helped a bit to boost up my confidence which had fallen after the failed
experiments. Here are the papers, in random order:
1. Scheiber et al. "Mapping adverse drug reactions in chemical space." Journal of medicinal chemistry. 2009 May 52(9):3103-7.
-given an organ affected by ADR of drug finds another likely affected organ
2. Scheiber et al. "Gaining Insight into Off-Target Mediated Effects of Drug Candidates with a Comprehensive Systems Chemical Biology Analysis." Journal of Chemical Information and Modeling. 2009 49(2):308-317
-finds link between ADR and pathways
3. Ma'ayan A et al. "Network analysis of FDA approved drugs and their targets."Mt Sinai J Med. 2007;74:27-32.
-mainly deals with building the network and studying its properties e.g. its scale free, fits power law
4. Nacher J. and Schwartz J. "Local and global modes of drug action in biochemical networks."
-imp, idea of metabolic map
5. Berger S., Iyengar R. and Wist A. "Systems pharmacology and genome medicine: a future perspective." 2009
-finds genomic factors for ADRs- geared toward personalized medicine
6. Lin et al. "A Tool for Finding Possible Explanation for Adverse Drug Reactions Through Drug and Drug Target Interactions." BMEI (1) 2008: 580-584b
-finds overlap between protein network of different drugs
7. Butte and Chiang. "Data-driven methods to discover molecular determinants of serious adverse drug events." Clin Pharmacol Ther. 2009 Mar 85(3):259-68.
-proposes a few different methods that may be used
8. Yildirim et al. "Drug-target network." Nat Biotechnol 2007 25:1119-1126.
9. Campillos et al. "Drug target identification using side-effect similarity." Science. 2008 321(5886):263-266
-finds possible targets of drugs by looking at ADRs and hence other possible therapeutic effects of these drugs.
I also needed to find some more detailed information about measuring biological network similarity and these are the papers I looked through:
1. Ideker T. and Sharan R. "Modeling cellular machinery through biological network comparison." Nature Biotechnology Vol. 24, No. 4. (06 April 2006), pp. 427-433.
2. Przulj N. "Biological network comparison using graphlet degree distribution." Bioinformatics, Vol. 23, No. 2. (15 January 2007), pp. e177-e183.
12. Karp R. and Narayanan M. "Comparing Protein Interaction Networks via a Graph Match-and-Split Algorithm." J Comput Biol, Vol. 14, No. 7. (September 2007), pp. 892-907.
I finally wrote the proposal and submitted it on Tuesday. I met with Prof. Gonzalez on Wednesday and she said she was happy with the proposal and this made me really happy. I do hope this project works out well!
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