2012
- 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.
- O'Neil, S. T., and S. J. Emrich. Haplotype and minimum-chimerism consensus determination using short sequence data. BMC Genomics (ICCABS 2010 special issue), in press.
- 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. VectorBase: improvements to a bioinformatics resource for invertebrate vector genomics. Nucleic Acids Research, 40(Database issue):D729-734.
2011
- Yu, L., Carmichael, R., Emrich, S. and D. Thain. Managing Worker Pools for Cloud Workflows. Cloud Computing and Its Applications (CCA'11)
- Theresa, C.B., Colaco, A.N., Emrich, S.J., O'Neil, S.T. and J.S. McLachlan. New genetic tools for estimating long term changes in forest composition. 96th Annual ESA meeting.
- Lanc, I., Bui, P, Thain, D. and S. J. Emrich. Adapting bioinformatics applications for heterogeneous systems: a case study. Proceedings of the Second International Workshop on Emerging Computational Methods for the Life Sciences.
- Rider, A. K., Siwo, G., Chawla, N. V., Ferdig, M. T., and S. J. Emrich. A supervised learning approach to the ensemble clustering of genes. International Journal of Data Mining and Bioinformatics, 12:116.
- Carmichael, R., Braga-Henebry, P., Thain, D. and S. J. Emrich. Biocompute 2.0: an improved collaborative workspace for data intensive bio-science. Concurrency and Computation: Practice and Experience 23(17): 2305-2314.
- Samarakoon, U., Regier, A., Tan, A., Desany, B.A., Collins, B., Tan, J.C., Emrich, S.J. and M. T. Ferdig. High-throughput 454 sequencing for allele discovery and recombination mapping in Plasmodium falciparum. BMC Genomics, in press.
- O'Neil, S.T. and S. J. Emrich. Robust haplotype reconstruction of eukaryotic sequence data with Hapler. 1st IEEE International Conference on Computational Advances in Bio and medical Sciences, Orlando.
2010
- Rider, A., Siwo, G., Emrich, S.J., Ferdig, M. and N. V. Chawla. A supervised learning approach to the unsupervised clustering of genes. IEEE International Conference on Bioinformatics and Biomedicine, Hong Kong.
- Zhang, W., Zeng, E., and S. J. Emrich. A two-stage machine learning approach for pathway analysis. IEEE International Conference on Bioinformatics and Biomedicine, Hong Kong.
- 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. Widespread divergence between incipient Anopheles gambiae species revealed by whole genome sequences, Science, 330(6003): 512-514.
- Rider, A.K., Siwo, G., Chawla, N.V., Ferdig, M. and S.J. Emrich. A statistical approach to finding overlooked genetic associations, BMC Bioinformatics, 11:526.
- Thrasher, A., Carmichael, R., Bui, P., Thain, D., and S.J. Emrich. Taming complex bioinformatics workflows with Weaver, Makeflow, and Starch. Workflows in Support of Large-Scale Science held in conjunction with Supercomputing 10.
- Carmichael, R., Braga-Henebry, P., Thain, D. and S.J. Emrich. 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).
- 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. Breakpoint structure of the Anopheles gambiae 2Rb chromosomal inversion, Malaria Journal, 9:293.
- O'Neil, S.T., Dzurisin, J.D., Carmichael, R.D., Lobo, N.F., Emrich, S.J., and J.J. Hellmann. Population-level transcriptome sequencing of nonmodel organisms Erynnis propertius and Papilio zelicaon. BMC Genomics, 11:310.
- Yu, L., Moretti, C., Thrasher, A., Emrich, S., Judd, K., and D. Thain. Harnessing Parallelism in Multicore Clusters with the All-Pairs,Wavefront, and Makeflow Abstractions. Cluster Computing, 13:243.
2009
- Yu, L., Moretti, C., Emrich, S., Judd, K. and D. Thain. Harnessing parallelism in multicore clusters with the All-Pairs and Wavefront abstractions. 18th International Symposium on High Performance Distributed Computing (HPDC), Garching, Germany.
- Regier, A., Olson, M. and S.J. Emrich. Alignment and analysis of closely related genomes. 1st International Conference on Bioinformatics and Computational Biology (BiCoB).
- 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]
- Regier, A., Olson, M. and S.J. Emrich. Alignment and analysis of closely related genomes. 1st International Conference on Bioinformatics and Computational Biology (BiCoB 2009)