Scott Emrich's Publications

A likely more up-to-date (and detailed) version can be found on my Google scholar profile.

Journal

  1. Moretti, C., Thrasher, A., Yu, L., Olson, M., Emrich, S., and D. Thain. A framework for scalable genome assembly on clusters, clouds and grids. IEEE Transactions on Parallel and Distributed Systems, in press.
  2. O'Neil, S. T., and S. J. Emrich. Haplotype and minimum-chimerism consensus determination using short sequence data. (2012) BMC Genomics (ICCABS 2010 special issue), in press.
  3. Megy, K.*, Emrich, S. J.*, Lawson, D., Campbell, D., Dialynas, E., Hughes, D. S. T., Koscielny, G., Louis, C. , MacCallum, R. M., Redmond, S.N., Sheehan, A., Topalis, P., Wilson, D. and the VectorBase Consortium. (2012) VectorBase: improvements to a bioinformatics resource for invertebrate vector genomics. Nucleic Acids Research, 40(Database issue):D729-734.
  4. O'Neil, S. T., and S. J. Emrich. Haplotype and minimum-chimerism consensus determination using short sequence data. (2012) BMC Genomics (ICCABS 2010 special issue), in press.
  5. Rider, A. K., Siwo, G., Chawla, N. V., Ferdig, M. T., and S. J. Emrich. (2011) A supervised learning approach to the ensemble clustering of genes. International Journal of Data Mining and Bioinformatics, 12:116.
  6. Carmichael, R., Braga-Henebry, P., Thain, D. and S. J. Emrich. (2011) Biocompute 2.0: an improved collaborative workspace for data intensive bio-science. Concurrency and Computation: Practice and Experience 23(17): 2305-2314.
  7. Samarakoon, U., Regier, A., Tan, A., Desany, B.A., Collins, B., Tan, J.C., Emrich, S.J. and M. T. Ferdig. (2011) High-throughput 454 sequencing for allele discovery and recombination mapping in Plasmodium falciparum. BMC Genomics, 12:116.
  8. Lawniczak, M.K.*, Emrich, S.J.*, Holloway, A.K., Regier, A.P., Olson, M., White, B., Redmond, S., Fulton, L., Appelbaum, E., Godfrey, J., Farmer, C., Chinwalla, A., Yang, S.P., Minx ,P., Nelson, J., Kyung, K., Walenz, B.P., Garcia-Hernandez, E., Aguiar, M., Viswanathan, L.D., Rogers, Y.H., Strausberg, R.L., Saski, C.A., Lawson, D., Collins, F.H., Kafatos, F.C., Christophides, G.K., Clifton, S.W., Kirkness, E.F., and N. J. Besansky. (2010) Widespread divergence between incipient Anopheles gambiae species revealed by whole genome sequences, Science, 330(6003): 512-514.
  9. Rider, A.K., Siwo, G., Chawla, N.V., Ferdig, M. and S.J. Emrich. (2010) A statistical approach to finding overlooked genetic associations, BMC Bioinformatics, 11:526.
  10. Lobo, N.F., Sangare, D. M., Regier, A. A., Reidenbach, K. R., Bretz, D. A., Sharakhova, M.V., Emrich, S.J., Traore, S., F. Costantini, C., Besansky, N. J. and F. C. Collins. (2010) Breakpoint structure of the Anopheles gambiae 2Rb chromosomal inversion, Malaria Journal, 9:293.
  11. O'Neil, S.T., Dzurisin, J.D., Carmichael, R.D., Lobo, N.F., Emrich, S.J., and J.J. Hellmann. (2010) Population-level transcriptome sequencing of nonmodel organisms Erynnis propertius and Papilio zelicaon. BMC Genomics, 11:310.
  12. 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, 13:243.
  13. 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]
  14. 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]
  15. 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]
  16. 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]
  17. 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]
  18. 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]
  19. 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]
  20. 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]
  21. 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]
  22. 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]
  23. 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]
  24. 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. Thrasher, A., Musgrave, Z., Thain, D. and S. J. Emrich. (2012) Shifting the Bioinformatics Computing Paradigm: A Case Study in Parallelizing Genome Annotation Using MAKER and Work Queue. 2nd IEEE International Conference on Computational Advances in Bio and medical Sciences, Las Vegas.
  2. Zhang, W., Zeng, E., Liu, D., Jones, S. and S. J. Emrich (2012) A Machine Learning Framework for Trait Based Genomics. 2nd IEEE International Conference on Computational Advances in Bio and medical Sciences, Las Vegas.
  3. Yu, L., Carmichael, R., S. J. Emrich, and D. Thain. (2011) Managing worker pools for cloud workflows. Proceedings of Cloud Computing and its Applications (CCA11; short abstract)
  4. Lanc, I., Bui, P, Thain, D. and S. J. Emrich. (2011) Adapting bioinformatics applications for heterogeneous systems: a case study. Proceedings of the Second International Workshop on Emerging Computational Methods for the Life Sciences.
  5. O'Neil, S.T. and S. J. Emrich. (2011) Robust haplotype reconstruction of eukaryotic sequence data with Hapler. 1st IEEE International Conference on Computational Advances in Bio and medical Sciences, Orlando.
  6. Rider, A., Siwo, G., Emrich, S.J., Ferdig, M. and N. V. Chawla. (2010) A supervised learning approach to the unsupervised clustering of genes. IEEE International Conference on Bioinformatics and Biomedicine, Hong Kong.
  7. Zhang, W., Zeng, E., and S. J. Emrich. (2010) A two-stage machine learning approach for pathway analysis. IEEE International Conference on Bioinformatics and Biomedicine, Hong Kong.
  8. Thrasher, A., Carmichael, R., Bui, P., Thain, D., and S.J. Emrich. (2010) Taming complex bioinformatics workflows with Weaver, Makeflow, and Starch. Workflows in Support of Large-Scale Science held in conjunction with Supercomputing 10.
  9. Carmichael, R., Braga-Henebry, P., Thain, D. and S.J. Emrich. (2010) Biocompute: Towards a collaborative workspace for data intensive bio-science. Emerging Computational Methods for the Life Sciences Workshop held in conjunction with 19th International Symposium on High Performance Distributed Computing (HPDC).
  10. 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.
  11. 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.
  12. 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).
  13. 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).
  14. 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.
  15. 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. Thain, D., Albrect, M., Bui, H., Bui, P., Carmichael, R., Emrich, S. and P. Flynn. Data Intensive Computing with Clustered Chirp Servers. 2011. Data Intensive Distributed Computing: Challenges and Solutions for Large-scale Information Management}, IGI Global, Chapter 7.
  2. Barbazuk, W.B., Emrich, S.J.} and P.S. Schnable. 2007. SNP Mining from Maize 454 EST Sequences, Cold Spring Harbor Protocols.
  3. 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.