Scott Emrich's Publications

Journal

  1. Ohtsu, K., Smith, M., Emrich, S.J., Borsuk, L.A., Zhou, R., Chen, T., Zhang, X., Timmermans, M., Beck, J., Buckner, B., Janick-Buckner, D., Nettleton, D., Scanlon, M.J, and P.S. Schnable. Expression of retrotransposons in the shoot apical meristem of maize (Zea mays L.). Plant Journal, 52:391-404. [Abstract]
  2. Barbazuk, W.B.*, Emrich, S.J.*, Chen, H.D., Li, L., and P.S. Schnable. SNP discovery in maize via 454 transcriptome sequencing. Plant Journal, 51:910-918. [Abstract]
  3. Kalyanaraman, A.*, Emrich, S.J.*, Schnable, P.S. and S. Aluru (2007) Assembling genomes on large-scale parallel computers, Journal of Parallel and Distributed Computing, 67:1240-1255. [Abstract] [Full text]
  4. Emrich, S.J.*, Barbazuk, W.B.*, Li, L. and P.S. Schnable (2007) Gene discovery and annotation using LCM-454 transcriptome sequencing, Genome Research, 17:69-73, [Abstract] [Full text]
  5. Emrich, S.J.*, Li, L.*, Wen, T.-J., Yandeau-Nelson, M.D., Fu, Y., Guo, L., Chou, H.-H., Aluru, S., Ashlock, D.A. and P.S. Schnable (2007) Nearly identical paralogs (NIPs): implications for maize (Zea mays L.) genome evolution, Genetics,175:429-439, [Abstract] [Full text]
  6. Fu, Y.*, Emrich, S.J.*, Guo, L., Wen, T.-J., Ashlock, D.A, Aluru, S. and P.S. Schnable (2005) Quality assessment of Maize Assembled Genomic Islands (MAGIs) and large-scale experimental verification of predicted novel genes, Proc. Natl. Acad. Sci. USA, 102:12282-12287. [Abstract] [Full text]
  7. Yao, H., Guo, L., Fu, Y., Borsuk, L.A., Wen, T.-J., Skibbe, D.S., Cui, X., Scheffler, B.E., Cao, J., Emrich, S.J., Ashlock, D.A. and P. S. Schnable (2005) Evaluation of seven ab initio gene prediction programs for the discovery of maize genes, Plant Mol. Biol., 3:445-460. [Abstract] [Full text]
  8. Emrich, S.J., Aluru, S., Fu, Y., Wen, T., Narayanan, M., Guo, L., Ashlock, D.A. and P.S. Schnable (2004) A strategy for assembling the maize (Zea mays L.) genome, Bioinformatics, 20:140-147. [Abstract] [Full text]
  9. Emrich, S.J., Lowe, M. and A.L. Delcher (2003) PROBEmer: a web-based software tool for selecting optimal DNA oligos, Nucleic Acids Res., 31:3746-3750. [Abstract] [Full text]
  10. Lowe, M., Madsen, E.L., Schindler, K., Smith, C., Emrich, S., Robb, F. and R.U. Halden (2002) Geochemistry and microbial diversity of a Trichloroethene-contaminated superfund site undergoing intrinsic in situ reductive dechlorination. FEMS Microbiol. Ecol. 40:123-134. [Abstract] [Full text]

    * denotes equal contribution

Peer-reviewed Conference

  1. Emrich, S.J., Kalyanaraman, A. and S. Aluru. Massively Parallel EST Clustering. ISCA 20th International Conference on Parallel and Distributed Computing Systems (ISCA-PDCS'07).
  2. Kalyanaraman, A.*, Emrich, S.J.*, Schnable, P.S. and S. Aluru (2006) Assembling genomes on large-scale parallel computers, Proceedings of the IEEE International Parallel and Distributed Processing Symposium. [Abstract] [Full text]
  3. Ashlock, D.A., Emrich, S.J., Bryden, K.M., Corns, S.A., Wen, T.-J. and P.S. Schnable (2004) A comparison of evolved finite state classifiers and Interpolated Markov Models for improving PCR primer design, Proceedings of the 2004 IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology, 190-197. [Full text]

    * denotes equal contribution

Chapters

  1. Emrich, S.J., Kalyanaraman, A. and S. Aluru (2005) Algorithms for large-scale clustering and assembly
    of biological sequence data, Handbook of Computational Molecular Biology, Chapman & Hall/CRC.