corsoFBA2
Schultz & Qutub, BMC Syst Biol, 2015

  • A. Schultz, S. Mehta, C.W. Hu, F.W. Hoff, T.M. Horton, S.M. Kornblau, A.A. Qutub (2016) Identifying Cancer Specific Metabolic Signatures Using Constraint Based Models. Pac Symp Biocomput. (link) (Supplemental Information)
  • A. Schultz, A.A. Qutub (2016) Reconstruction of Tissue-Specific Metabolic Networks Using CORDA, PLoS Comput Biol, 12(3). (link)
  • D.P. Noren, B.L. Long, R. Norel, K. Rrhissorrakrai, K. Hess, C.W. Hu, A.J. Bisberg, A. Schultz, E. Engquist, L. Liu, X. Lin, G.M. Chen, H. Xie, G.A.M. Hunter, P.C. Boutros, O. Stepanov, DREAM 9 AML-OPC Consortium, T. Norman, S.H. Friend, G. Stolovitzky, S. Kornblau, A.A. Qutub (2016) A Crowdsourcing Approach to Developing and Assessing Prediction Algorithms for AML Prognosis, PLoS Comput Biol, 12 (6). (link)
  • A. Schultz, A.A. Qutub (2015). Predicting internal cell fluxes at sub-optimal growth. BMC Syst Biol9(1), 18. (link)

jsontomap – Function converts json files downloaded from Escher (King, et. al. 2015) to map structs that can be used with the COBRA toolbox. A tutorial on how to use this function is included with the download.

getrxnstp -This function allows you to modify maps in the COBRA toolbox to include only reactions you want. A tutorial on how to use the function is included.

drawFluxNoText – These functions provide a simple modification to the COBRA functions that plot metabolic maps, allowing them to plot without the reaction and metabolite names. This makes the map less crowded and faster to plot. A tutorial is included as well.

Keeping Up With the Literature

Keeping up with the literature within your field can be difficult and time consuming. I have found that NCBI alerts are good, but are limited to searches by authors and search terms, and do not consider a library of papers you may have. These alerts can also send several emails daily if you set too many. I have written some R code that searches new papers daily based on authors and search terms, and emails those results daily in a single email. This code also searches papers that cite several papers in a library you have defined, and suggests highly related papers based on citations. The files to do this, along with a tutorial on how to set it up, can be downloaded here. The tutorial is meant to make the setup easy even if you have never programmed before. Please send along any bugs, difficulties using or setting up, and any suggestions you may have on how to make this better. I am trying to make this code as bulletproof and friendly as possible.

Personal

I attended the University of Michigan on an athletic scholarship, where I was part of the swim team. Visit my MGoBlue Profile for a complete list of accomplishments. I was also a member of the Brazilian national team and swam professionally back in Brazil.