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This folder holds the following references to publications, sorted by year and author.

There are 21 references in this bibliography folder.

Meier-Kolthoff, JP, Auch, AF, Klenk, H, and Goker, M (2013).
Genome sequence-based species delimitation with confidence intervals and improved distance functions.
BMC Bioinformatics, 14(1):60.

Meier-Kolthoff, JP, Auch, AF, Klenk, H, and Göker, M (2013).
Highly parallelized inference of large genome-based phylogenies
Concurrency and Computation: Practice and Experience.

Meier-Kolthoff, JP, Auch, AF, Klenk, H, and Göker, M (2012).
GBDP on the grid: a genome-based approach for species delimitation adjusted for an automated and highly parallel processing of large data sets
Miscellaneous publication, 8th Joint BFG/bwGRiD Conference & Workshop, Freiburg, May 23-25, 2012.

Richter, DC, Ott, F, Auch, AF, Schmid, R, and Huson, DH (2011).
MetaSim: A Sequencing Simulator for Genomics and Metagenomics
In: Handbook of Molecular Microbial Ecology I: Metagenomics and Complementary Approaches, ed. by F. J. de Bruijn. John Wiley & Sons, Inc., Hoboken, NJ, USA, chap. 48, pp. 417-422.

Auch, AF (2010).
Computational phylogenetics: Methods for analysing genome-scale data
Südwestdeutscher Verlag für Hochschulschriften, Saarbrücken, Germany. (ISBN: 978-3838118628).

Auch, AF (2010).
A phylogenetic potpourri - Computational methods for analysing genome-scale data
Doktorarbeit, Universität Tübingen, Wilhelmstr. 32, 72074 Tübingen.

Auch, AF, Klenk, H, and Göker, M (2010).
Standard operating procedure for calculating genome-to-genome distances based on high-scoring segment pairs
Standards in Genomic Sciences, 2(1):142-148.

Auch, AF, von Jan, M, Klenk, H, and Göker, M (2010).
Digital DNA-DNA hybridization for microbial species delineation by means of genome-to-genome sequence comparison
Standards in Genomic Sciences, 2(1):117-134.

Göker, M, Grimm, GW, Auch, AF, Aurahs, R, and Kucera, M (2010).
A clustering optimization strategy for molecular taxonomy applied to planktonic foraminifera SSU rDNA
Evolutionary Bioinformatics Online(6):97-112.

Huson, DH, Richter, DC, Mitra, S, Auch, AF, and Schuster, SC (2009).
Methods for comparative metagenomics
BMC Bioinformatics, 10(Suppl 1):S12.

Stockinger, H, Auch, AF, Göker, M, Meier-Kolthoff, J, and Stamatakis, A (2009).
Large-Scale Co-Phylogenetic Analysis on the Grid
International Journal of Grid and High Performance Computing, 1(1):39-54.

Richter, DC, Ott, F, Auch, AF, Schmid, R, and Huson, DH (2008).
MetaSim—A Sequencing Simulator for Genomics and Metagenomics
PLoS ONE, 3(10):e3373.

Huson, DH, Auch, AF, Qi, J, and Schuster, SC (2007).
Metagenome analysis using MEGAN
In: Proceedings of the 5th Asia-Pacific Bioinformatics Conference, ed. by D. Sankoff, L. Wang and F. Chin, vol. 5, pp. 7-16, Imperial College Press. Series on Advances in Bioinformatics and Computational Biology.

Huson, DH, Auch, AF, Qi, J, and Schuster, SC (2007).
MEGAN analysis of metagenomic data.
Genome Res, 17(3):377–386.

Meier-Kolthoff, JP, Auch, AF, Huson, DH, and Göker, M (2007).
COPYCAT : cophylogenetic analysis tool
Bioinformatics, 23(7):898-900.

Stamatakis, A, Auch, AF, Meier-Kolthoff, J, and Göker, M (2007).
AxPcoords & parallel AxParafit: statistical co-phylogenetic analyses on thousands of taxa.
BMC Bioinformatics, 8:405.

Auch, AF, Henz, SR, and Göker, M (2006).
Phylogenies from whole genomes: Methodological update within a distance-based framework
published via TOBIAS-lib.

Auch, AF, Henz, SR, Holland, BR, and Göker, M (2006).
Genome BLAST distance phylogenies inferred from whole plastid and whole mitochondrion genome sequences.
BMC Bioinformatics, 7:350.

Poinar, HN, Schwarz, C, Qi, J, Shapiro, B, Macphee, RD, Buigues, B, Tikhonov, A, Huson, DH, Tomsho, LP, Auch, A, Rampp, M, Miller, W, and Schuster, SC (2006).
Metagenomics to paleogenomics: large-scale sequencing of mammoth DNA.
Science, 311(5759):392-394.

Henz, SR, Huson, DH, Auch, AF, Nieselt-Struwe, K, and Schuster, SC (2005).
Whole-genome prokaryotic phylogeny.
Bioinformatics, 21(10):2329-2335.

Gerblinger, M and Auch, AF (2003).
NAM3 und Linux an der Juristischen Fakultät der Universität Tübingen


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