Scott Emrich's Publications

Journal

  1. Yu, L., Moretti, C., Thrasher, A., Emrich, S., Judd, K., and D. Thain. (2010) Harnessing Parallelism in Multicore Clusters with the All-Pairs,Wavefront, and Makeflow Abstractions. Cluster Computing.
  2. Liu, S., Chen, H.D., Makarevitch, I., Shirmer, R., Emrich, S.J., Dietrich, C.R., Barbazuk, W.B., Springer, N.M., and P.S. Schnable. (2009) High-throughput genetic mapping of mutants via Quantitative SNP-typing. Genetics, in press. [Abstract]
  3. Schnable, P.S., Ware, D., Fulton, R.S., Stein, J.C., Wei, F., Pasternak, S., Liang, C., Zhang, J., Fulton, L., Graves, T.A., et al. (2009) The B73 maize genome: complexity, diversity, and dynamics. Science, 326:1112-1115 (cover of Nov 20th, 2009 issue). [Abstract]
  4. 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. (2007) Expression of retrotransposons in the shoot apical meristem of maize (Zea mays L.). Plant Journal, 52:391-404. [Abstract]
  5. Barbazuk, W.B.*, Emrich, S.J.*, Chen, H.D., Li, L., and P.S. Schnable. (2007) SNP discovery in maize via 454 transcriptome sequencing. Plant Journal, 51:910-918. [Abstract]
  6. 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]
  7. 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]
  8. 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]
  9. 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]
  10. 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]
  11. 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]
  12. 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]
  13. 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. Regier, A., Cheng, C., Besansky, N., and S.J. Emrich. (2009) Improved inversion prediction in draft genomes. Joint ISCB Africa ASBCB Conference on Bioinformatics of Infectious Diseases, Bamako, Mali.
  2. Yu, L., Moretti, C., Emrich, S., Judd, K. and D. Thain. (2009) Harnessing parallelism in multicore clusters with the All-Pairs and Wavefront abstractions. 18th International Symposium on High Performance Distributed Computing (HPDC), Garching, Germany.
  3. Regier, A., Olson, M. and S.J. Emrich. (2009) Alignment and analysis of closely related genomes. 1st International Conference on Bioinformatics and Computational Biology (BiCoB).
  4. Emrich, S.J., Kalyanaraman, A. and S. Aluru. (2007) Massively Parallel EST Clustering. ISCA 20th International Conference on Parallel and Distributed Computing Systems (ISCA-PDCS).
  5. 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.
  6. 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.

    * denotes equal contribution

Invited papers

  1. Moretti, C., Olson, M., Emrich, S., and D. Thain. (2009) Highly scalable genome assembly on campus grids. 2nd Workshop on Many-Task Computing on Grids and Supercomputers, Portland, OR.

Chapters

  1. Barbazuk, W.B., Emrich, S.J.} and P.S. Schnable. 2007. SNP Mining from Maize 454 EST Sequences, Cold Spring Harbor Protocols.
  2. 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.