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Ragan C, Mowry BJ, Bauer DC, “Hybridization based reconstruction of small non-coding RNA transcripts from deep sequencing data”, NAR, Nucleic Acids Res. 2012 Jun16. PMID: 22705792
Buske FA, Bauer DC, Mattick JS, Bailey TL., , “Triplexator: Detecting nucleic acid triple helices in genomic and transcriptomic data.”.Genome Res. 2012 May 1. PMID: 22550012.


Bauer, D.C., Willadsen, K., Buske, F.A., Le Cao, K., Bailey, T.L., Dellaire, G., Bodén, M., , “Sorting the nuclear proteome.”, ISMB 2011 (proceedings published in Bioinformatics). Bioinformatics. 2011 Jul 1;27(13):i7-14. PMID:21685104.
(Paper) Bauer, D.C.. “Variant calling comparison CASAVA1.8 and GATK”. Nature Precedings, 2011


Buske, F.A., Bauer, D.C., Bodén, M., Bailey, T.L., “Assigning roles to DNA regulatory motifs using comparative genomics.”, Bioinformatics, 2010 Apr 1;26(7):860-6. PMID: 20147307
Bauer, D.C., Buske, F.A., Bailey, T.L., “Dual-functioning transcription factors in the developmental gene network of Drosophila melanogaster”, BMC bioinformatics, 2010 Jul 2;11:366. PMID: 20594356
Paper Bauer, D.C., Buske, F.A., Bodén, M., Bailey, T.L., “Predicting SUMOylation sites in developmental transcription factors of Drosophila melanogaster.”, Neurocomputing, Volume 73, Issues 13-15, August 2010, Pages 2300-2307.


(Paper) Bauer, D.C., “Ten Simple Rules for Searching and Organizing the Scientific Literature”, Nature Precedings, Oct. 2009
Bauer, D.C., Bailey, T.L., “Optimizing static thermodynamic models of transcriptional regulation.”, Bioinformatics, 2009, 25, 1640-1646. PMID:19398449
Paper The FANTOM Consortium et al., “The transcriptional network that controls growth arrest and differentiation in a human myeloid leukemia cell line.”, Nat Genet. 2009. PMID:19377474.


Poster Bauer, D.C., Bailey, T.L., “STREAM : A Practical Workbench for the Quantitative Modeling of Transcription”. GIW 2008.
Paper Bauer, D.C., Bailey, T.L., “STREAM: Static Thermodynamic REgulAtory Model of transcription.”, Bioinformatics 2008 24: 2544-2545. PMID:18776194
Paper Bauer, D.C., Fabian A. Buske, Mikael Bodén, “Predicting SUMOylation Sites.”, Lectures Notes in Bioinformatics, Volume 5265/2008, pp 28-40, Springer (PRIB 2008).

Best student paper award.

Paper Bauer, D.C., Bailey T.L., “Studying the functional conservation of cis-regulatory modules and their transcriptional output.”, BMC Bioinformatics, Apr 29;9(1):220. PMID: 18442418.


Poster Bauer, D.C., Bailey, T.L., “Predicting Cis-Regulatory Modules and their Transcriptional Output.”, Bioinformatics Australia Converence (2007).


Paper Bauer, D.C., Bodén, M., Thier, R. and Gillam, E. M., “STAR: Predicting recombination sites from amino acid sequence.”, BMC Bioinformatics, 2006 Oct 8; 7:437. PMID: 17026775.


Thesis “In-silico characterization of recombination sites: a machine learning approach.”, BSc Hons thesis, University of Queensland, 2005 Supervisors: Dr. Mikael Bodén and Dr. Ricarda Thier.

Paper Bauer, D.C., Bodén, M., Thier, R. and Yuan, Z., “Predicting structural disruption of proteins caused by crossover.”, IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology (CIBCB) 2005.


Thesis “Motif search in sequence data: Comparison of profile and pattern based search algorithm.”, BSc thesis, Freie Universität Berlin, 2004 Supervisors: Prof. Dr. Knut Reinert and Prof. Dr. Martin Vingron.