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Bioinformatics

Galaxy tools to study genome diversity (2013) O.C. Bedoya-Reina, A. Ratan, R. Burhans, H.L. Kim, B. Giardine, C. Riemer, Q. Li, T.L. Olson, T.P. Loughran Jr, B.M. Vonholdt, G.H. Perry, S.C. Schuster , W. Miller. Gigascience 2(1):17 / doi:10.1186/2047-217X-2-17.

Comparison of Sequencing Platforms for Single Nucleotide Variant Calls in a Human Sample (2013) A. Ratan, W. Miller, J. Guillory, J. Stinson, S. Seshagiri, S.C. Schuster . PLoS ONE 8(2):e55089 / doi:10.1371/journal.pone.0055089.

Integrative analysis of environmental sequences using MEGAN 4 (2011) D.H. Huson, S. Mitra, H.J. Ruschewyeh, N. Weber, S.C. Schuster . Genome Research 21(9):1552-1560. [Epub 2011 June 20]

Calling SNPs without a reference sequence (2010) A. Ratan, Y. Zhang, V.M. Hayes, S.C. Schuster , W. Miller. BMC Bioinformatics 11:130 / doi:10.1186/1471-2105-11-130.

Interpretation of custom designed Illumina genotype cluster plots for targeted association studies and next-generation sequence validation (2010) E.A. Tindall, D.C. Petersen DC, S. Nikolaysen, W. Miller, S.C. Schuster , V.M. Hayes. BMC Research Notes 3(1):39 / doi:10.1186/1756-0500-3-39.

Optimization methods for selecting founder individuals for captive breeding or reintroduction of endangered species (2009) W. Miller, S.J. Wright, Y. Zhang, S.C. Schuster , V.M. Hayes. Pacific Symposium on Biocomputing 2010 15:43-53.

inGAP, an integrated next-gen genome analysis pipeline (2010, 2009) J. Qi, F. Zhao, S.C. Schuster . Bioinformatics 26(1):127-29. [Epub 2009 October 30]

Comparison of next generation sequencing technologies for transcriptome characterization (2009) P.K. Wall, J. Leebens-Mack, A. Chanderbali, A. Barakat, E. Wolcott, H. Liang, L. Landherr, L.P Tomsho, Y. Hu, J.E. Carlson, H. Ma, S.C. Schuster , D.E. Soltis, P.S. Soltis, N. Altman, C.W. dePamphilis. BMC Genomics 10:347 / doi:10.1186/1471-2164-10-347.

Methods for comparative metagenomics (2009) D.H. Huson, D.C. Richter, S. Mitra, A.F. Auch, S.C. Schuster . BMC Bioinformatics 10 Suppl 1:S12 / doi:10.1186/1471-2105-10-S1-S12.

Next-generation sequencing transforms today’s biology (2008) S.C. Schuster . Nature Methods 5(1):16-18. [Epub 2007 December 19]

MEGAN: A tool for metagenomics. (2007) D.H. Huson, A. Auch, J. Qi, S.C. Schuster . Genome Research 17(3):377-86. [Epub 2007 January 25]

OSLay: optimal syntenic layout of unfinished assemblies (2007) D.C. Richter, S.C. Schuster , D.H. Huson. Bioinformatics 23(13):1573-79. [Epub 2007 April 26] BACCardI – A tool for the validation of genomic assemblies, assisting genome finishing and intergenome comparison (2005) D. Bartels, S. Kespohl, S. Albaum, T. Drüke, A. Goesmann, O. Kaiser, A. Pühler, F. Pfeiffer, G. Raddatz, J. Stoye, F. Meyer, S.C. Schuster . Bioinformatics 21(7):853-59 [Epub 2004 October 28]

Whole genome-based prokaryotic phylogeny (2005) S.R. Henz, A.F. Auch, D.H. Huson, K. Nieselt-Struwe, S.C. Schuster . Bioinformatics 21(10):2329-35. [Epub 2004 May 27]

Assembly and function of a quaternary signal transduction complex monitored by surface plasmon resonance (1993) S.C. Schuster , R.V. Swanson, L.A. Alex, R.B. Bourret, M.I. Simon. Nature 365(6444):343-47.