Research

Overview

I have been fortunate to be involved in a wide range of projects throughtout my career spanning computer science, bioinformatics, and computer-aided drug design. Below is a brief description of such projects followed by my publications.

  • Developed novel statistical framework for combining information from multiple observations and sources and applied it to predict protein targets of small molecules that can potentially lead to undesirable side-effects.
  • Investigated and implemented natural language processing methodology to draw relationships between small molecules based on clinical effects data present in public resources.
  • Implemented a dynamic programming algorithm to measure the similarity between enzymes and a web interface to access the methodology.
  • Investigated distributed computing platform for folding of mRNA.
  • Improved pipeline to analyze next-generation malaria transcriptome sequences.
  • Employed machine language methodology and algorithms to analyze array comparative genomic hybridization data to be able to predict cancer patient outcome.
  • Designed and implemented an AJAX based visualization tool to aide in the analysis of cancer genomic sequence data.
  • Implemented a graph-based algorithm and a novel similarity metric to compute the similarity between small molecules.
  • Developed efficient algorithms for graph theory research specifically on edge graceful labeling problems.

Publications

E.R. Yera, A.E. Cleves, and A.N. Jain. Prediction of off-target drug effects through data fusion. Pacific Symposium on Biocomputing, pp. 160-171, 2013.

E.R. Yera, A.E. Cleves, and A.N. Jain. Chemical Structural Novelty: On-Targets and Off-Targets. Journal of Medicinal Chemistry, pp. 6771-6785, 2011.

D.E. Almonacid, E.R. Yera, J.B.O. Mitchell, and P.C. Babbitt. Quantitative Comparison of Catalytic Mechanisms and Overall Reactions in Convergently Evolved Enzymes: Implications for Classification of Enzyme Function. PLoS Computational Biology, March 12, 2010.

P.L. Paris, Y. Kobayashi, Q. Zhao, W. Zeng, S. Sridharan, T. Fan, H.L. Adler, E.R. Yera, M.H. Zarrabi, S. Zucker, J. Simko, W.T. Chen, and J. Rosenberg. Functional phenotyping and genotyping of circulating tumor cells from patients with castration resistant prostate cancer. Cancer Letters, pp. 164-173, 2009.

E. Velasquez, E.R. Yera, and R. Singh. Determining Molecular Similarity for Drug Discovery using the Wavelet Riemannian Metric. IEEE Symposium on Bioinformatics and Bioengineering (BIBE), pp. 261-268, 2006.

R. Singh, E. Velasquez, P. Vijayant and E.R. Yera. FreeFlowDB: Storage, Querying and Interacting with Structure-Activity Information for High-Throughput Drug Discovery. IEEE International Symposium on Computer-Based Medical Systems (CBMS), pp. 75-80, 2006.

E.R. Yera, L. Wang and S.M. Lee. On super edge-graceful eulerian Graphs. Congressum Numerantitum 174, pp. 83-96, 2005.

E.R. Yera, W. Ling, E. Chen and S.M. Lee. On super edge graceful (p,p+1) graphs. Congressus Numerantium 171, pp. 51-65, 2004.

E.R. Yera, W. Ling and S.M. Lee. On super edge graceful unicyclic graphs. Journal of Combinatorial Mathematics and Combinatorial Computing, 2004.