Troy Ruths

  • Academic Institution: Rice University
  • Program Year: 4
  • Practicum(s):
    Lawrence Berkeley National Laboratory (2011)
  • Degree(s):
    B.S. Computer Science, Washington University in St Louis, 2008
  • Field of Study: Bioinformatics
  • Academic Advisor: Luay Nakhleh

Summary of Research:

Bioinformatics is a field awash in data. Sitting at the crossroads of biology, biochemistry, biophysics and computer science, this dynamic discipline is overwhelmed by voluminous, crucial data encoding genomic, cellular, and proteinic information. The open questions are so fundamental that each step made in this field is progress towards a broad range of immediate applications, including cancer, gene therapy, and stem cell research. At the same time, these questions are restricted by our ability to analyze and process the exponentially growing data repositories. Ultimately, bioinformatics is desperate for high-performance computational tools and methodologies to assuage its growing pains.

Interaction networks are a vital source of information for interpreting cell function. Consequently, advances made in understanding these networks expand our ability to modify, enhance, and repair cell behavior. One of the fundamental observations that has guided much of the computational research into comparative, or evolutionary, analysis of interaction networks is that components of interaction networks, such as paths and cycles, that are conserved across multiple species tend to reflect true functional modules; hence, their identification is of great significance. With that said, comparative analysis of these networks is still in its infancy.

Investigating the structure and formation of interaction networks from an evolutionary perspective will be a central theme of my work. My initial investigations will bring insight into two arenas: first, the role of evolution in constructing, preserving, and removing function in interaction networks; and secondly, the dynamics of evolution on a proteinic and genomic scale. These results will benefit not only practicing biology but will also extend our model of evolution.

Publications:

T. Ruths, L. Nakhleh. "Neutral forces acting on intragenomic variability shape the E. coli regulatory network topology." PNAS. 2013.

M. N. Price, A. M. Deutschbauer, J. M. Skerker, K. M. Wetmore, T. Ruths, J. S. Mar, J. V. Kuehl, W. Shao, A. P. Arkin. "Indirect and Suboptimal Control of Gene Expression is Widespread in Bacteria." Molecular Systems Biology. 2013.

T. Ruths, L. Nakhleh. "ncDNA and drift drive binding site accumulation." BMC Evolutionary Biology. 2012.

M. Baker, S. Abeysinghe, S. Schuh, R. Coleman, A. Abrams, M. Marsh, C. Hryc, T. Ruths, W. Chiu, and T. Ju. “Modeling protein structure at near atomic resolutions with Gorgon.” Journal of Structural Biology. 2011. vol. 174 (2) pp. 360-373.

T. Ruths, D. Ruths, and L. Nakhleh. “GS2: An efficiently computable measure of GO-based similarity of gene sets.” Bioinformatics 2009 25(9):1178-1184

Awards:

Computer Science Outstanding Sophomore Award, Washington University in St Louis, 05/2006
Men's Basketball Academic All-American, College Division, 2006, 2007, 2008
Computer Science Departmental Award for Academic Performance, Washington University in St Louis, 05/2007
Men's Basketball Academic All-American of the Year, 2007, 2008
USA Today All-USA College Academic Team, Third Team, 2007
Josten's Trophy - honors national student-athlete for exemplary basketball, scholastic, and service (1 chosen per year), 2008
Academic All American of the Year - honors most outstanding student-athlete in all college sports (2 chosen per year out of 360,000), 2008
Langsdorf Scholarship of Engineering & Applied Science Recipient, Washington University in St Louis, 2004-2008
NCAA Educational Grant, 2008
TI Scholarship Recipient, Rice University, 2008
Presidential Fellowship Recipient, Rice University, 2008
Hertz Graduate Fellowship Finalist, 2009
NSF Graduate Fellowship Recipient, 2009 (deferred)
Nobel Laureates Meeting in Lindau, 2010