What's Happening


I’m a Research Scientist with CSIRO, CMIS Sydney. Please see my research page for more details on my current (and past) research projects. I’m generally interested in machine learning techniques and their applications in medical genomics, gene regulation and protein design problems.



  • Institute for Molecular Bioscience, University of Queensland, PhD, Bioinformatics, 2010
    Thesis: Thermodynamic Models for the Analysis of Quantitative Transcriptional Regulation
    Supervisor: Dr. Timothy Bailey and Dr. Mikael Bodén; Thesis Committee: Prof. Sean Grimmond and Dr Nick Hamilton.
  • ITEE, The University of Queensland, BSc Hons., Computational Biology, 2005 (Class I, 5%)
    Thesis: In-silico characterization of recombination sites: a machine learning approach.
    Supervisor: Dr. Mikael Bodén and Dr. Ricarda Thier
  • Freie Universität Berlin, BSc, Bioinformatics, 2004 (A, 10 %)
    Thesis: Motif search in sequence data: Comparison of profile and pattern based search algorithm.
    Supervisor: Prof. Dr. Knut Reinert and Prof. Dr. Martin Vingron


  • Coordinator for the University of Queensland Computational Biology seminar series (COMBIO) 2010.
  • Reviewer for IEEE World Congress on Computational Intelligence WCCI 2010.
  • Program Committee for IEEE Congress on Evolutionary Computation (CEC) 2009.
  • Tutor for CSSE2002, Programming in the Large and Advanced Software Engineering 2008(2) and BIOL3004, Genes and Diseases Elective, 2008(1).
  • Reviewer for Bioinformatics, Oxford Journals, since 2007.
  • Student assistant, Max-Planck-Institute for molecular Genetics, 2003 (6 months).
  • Research internship, Max-Planck-Institute for experimental medicine, 2003 (8 weeks), Max-Planck-Institute for molecular Genetics, 2002 (8 weeks).


  • The FANTOM Consortium et al., The transcriptional network that controls growth arrest and differentiation in a human myeloid leukemia cell line, Nat Genet. 2009.
  • Bauer, D.C., Bailey, T.L., STREAM: Static Thermodynamic REgulAtory Model of transcription, Bioinformatics 2008 24: 2544-2545.
  • Bauer, D.C., Buske, F.A. and Bodén, M. Predicting SUMOylation Sites – A machine learning case study. IAPR Pattern Recognition in Bioinformatics (PRIB) 2008, Lectures Notes in Bioinformatics published by Springer
  • Bauer, D.C., and Bailey T.L. Studying the functional conservation of cis-regulatory modules and their transcriptional output. BMC Bioinformatics, Apr 29;9(1):220.
  • Bauer D.C., Boden M., Thier R. and Gillam E.M. STAR: predicting recombination sites from amino acid sequence. BMC Bioinformatics. 2006 Oct 8;7:4

(full list)


  • Best student paper award IAPR Pattern Recognition in Bioinformatics 2008
  • IMBcom Outstanding Individual Award 2008
  • UQ International Research Tuition Award 2008
  • Research Scholarship IMB three-years 2006
  • ITEE Prize for Best Working ICT Project 2005
  • DAAD (German Academic Exchange Service), one-year scholarship 2005


  • COMBIO – Christchurch, New Zealand, 6.-10.Dec.2009
  • IAPR Pattern Recognition in Bioinformatics (PRIB) 2008
  • ComBio Forum Nov. 2005, Nov. 2006, Mar. 2007, May 2008
  • IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology (CIBCB) 2005


  • COMBIO – Christchurch, New Zealand, 6.-10.Dec.2009
  • IAPR Pattern Recognition in Bioinformatics (PRIB) – Melbourne, Australia, 15.-17.Oct. 2008
  • BioBusiness Retreat – Noosa, Australia, 2.-4. April 2008
  • Bioinformatics Australia Conference – Brisbane, Australia, 23.-24. Oct. 2007
  • RIKEN Functional Annotation of Mouse (FANTOM) meeting – Tsukuba Institute, Japan, 4.-8. Dec. 2006
  • Machine Learning Summer School (MLSS) – Canberra, Australia, 6.-17. Feb. 2006
  • IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology (CIBCB) – San Diego, USA, 14.-15. Nov. 200


  • IMB science ambassador vodcast coordinator 2010
  • IMB science ambassador 2009
  • Student Consultative Committee (SCC) ITEE University of Queensland 2005
  • Elected member of the students parliament Freie Universität Berlin 2002 – 2004
  • Since 2001 member of btS – an initiative operating in Germany to improve the cooperation between students, university and industry.


  • Dr. Tim Bailey, Institute for Molecular Bioscience, University of Queensland, Australia
  • Dr. Mikael Bodén, School of Information Technology and Electrical Engineering, University of Queensland, Australia
  • Dr. Boris Lenhard, Bergen Center for Computational Science, Norway
  • Prof. Erik van Nimwegen, Department of Bioinformatics, University of Basel, Switzerland
  • Prof. Knut Reinert, Professor in the Bioinformatics Department, Freie Universität Berlin, Germany
  • Prof. Martin Vingron, Director at the Max Planck Institute for Molecular Genetics, Germany