Updated: September 24, 2015
CBC Scholar: Class of 2011
PhD Candidate, Department of Chemical and Biological Engineering, NU; Advisor: Luis Amaral
AMARAL LAB WEBPAGE
On June 4, 2013, Adam successfully defended his thesis: "Cartography of metabolism and its uses in assessing data reliability and understanding cellular network functionality." Congratulations!
In an effort to expand the applicability of my visual heuristic and gain a greater understanding of how it applies to all organismal metabolic networks I conducted a large-scale blast (~6.0 * 109 blast searches across 1,000 organisms) to enable further analysis of all available organisms and sequences. At the same time I also refined the community structure in my universal metabolic network through the development of a supervised method that allows for the improvement of community structure through a number of quantitative and qualitative methods. In combining these two methods I was able to find additional cases that supported my visual heuristic, but more importantly it led me to identify that the heuristic performs best in communities that are moderately annotated or better. Despite this rough limitation this is still an important development, since it allows for the identification of missing or incorrectly annotated reactions in an organism even when it is relatively well understood and researched. More importantly, for communities that are poorly annotated this visual heuristic seems to be a specialized case of what we term metabolic ‘devices’. These devices appear to be larger than motifs and to have a distinct biological relevance within communities, appearing together or remaining absent as a group when they are analyzed in the context of the blast data. I am currently developing a method that utilizes guilt-by-association and network properties to automatically identify such devices in metabolic networks. Identification and characterization of these devices in metabolic networks along with the knowledge of which enzymes should or should not be annotated from the blast data will help give a more complete understanding of which regions are under evolutionary pressure in metabolic networks and what makes them more prone to be in such a position.
Kho AN, Cashy JP, Jackson KL, Pah AR, Goel S, Boehnke J, Humphries JE, Kominers SD, Hota BN, Sims SA, Malin BA, French DD, Walunas TL, Meltzer DO, Kaleba EO, Jones RC, Galanter WL. Design and implementation of a privacy preserving electronic health record linkage tool in Chicago. J Am Med Inform Assoc. 2015 Sep;22(5):1072-80. (PubMed)
Weiss CH, Poncela-Casasnovas J, Glaser JI, Pah AR, Persell SD, Baker DW, Wunderink RG, Amaral LAN. Adoption of a High-Impact Innovation in a Homogeneous Population. Phys Rev X. 2014 Oct 15;4(4):041008. (PubMed)
Pah AR, Guimerà R, Mustoe AM, Amaral LA. Use of a global metabolic network to curate organismal metabolic networks. Sci Rep. 2013 Apr 22;3:1695. (PubMed)
AWARDS, ACTIVITIES AND SERVICE:
- Judge, Chicago Public Schools Student Science Fair, March 2012
- Judge, Chicago Public Schools Student Science Fair, March 2011
- A lab tour guide at the McCormick school’s 40th Annual Career day for girls, 2011
- CBC Scholar 2011-2012