Publications of Alexander Schönhuth

  1. M. Singer, D. Boffelli, J. Dhabhi, A. Schönhuth, G.P. Schroth, D.I.K. Martin, Lior Pachter
    "Genomewide methyl-typing for the detection of unmethylated islands"
    Submitted, 2010

  2. A. Schönhuth, R. Salari, S.C. Sahinalp
    "Identification of functionally divergent paralogs using statistics on indels in local alignments"
    Submitted, 2010

  3. C. Hafemeister, I. Costa, A. Schönhuth, A. Schliep
    "Classifying short gene expression time-courses with Bayesian estimation of piecewise constant functions"
    Submitted, 2010

  4. R. Colak, F. Moser, J. Shu, A. Schönhuth*, N. Chen*, M. Ester*
    "Module discovery by exhaustive search for densely connected, co-expressed regions in biomolecular interaction networks"
    Submitted, 2009
    *Joint last authorship

  5. A. Schönhuth, R. Salari, F. Hormozdiari, A. Cherkasov, S.C. Sahinalp
    "Towards improved assessment of functional similarity in large-scale screens: an indel study"
    Journal of Computational Biology 17(1), 1-20, 2010

  6. P. Dao, A. Schönhuth, F. Hormozdiari, I. Hajirasouliha, S.C. Sahinalp, M. Ester
    "Quantifying systemic evolutionary changes by color coding confidence-sored PPI networks"
    Proceedings of the WABI 2009, LNCS 5724, 37-48, 2009

  7. I. Costa, A. Schönhuth, C. Hafemeister, A. Schliep
    "Constrained mixture estimation for analysis and robust classification of clinical time series"
     Bioinformatics, 25(12) (Proc. ISMB/ECCB 2009), i6-i14, 2009

  8. A. Schönhuth, H. Jaeger
    "Characterization of ergodic hidden Markov sources"
    IEEE Transactions on Information Theory, 55(5), 2107-2118, 2009
    ZAIK Preprint (PDF)

  9. A. Schönhuth
    "On analytic properties of entropy rate"
    IEEE Transactions on Information Theory, 55(5), 2119-2127, 2009
    arXiv:0804.2469
    also: Extended Version (PDF)

  10. R. Colak*, F. Hormozdiari*, F. Moser*, A. Schönhuth*, J. Holman, M. Ester, S.C. Sahinalp
    "Dense graphlet statistics of protein interaction and random networks"
    Proceedings of the Pacific Symposium on Biocomputing, 14, 190-202, 2009
    *Joint first authorship

  11. A. Schönhuth, I. Costa, A. Schliep
    "Semi-supervised clustering of yeast gene expression data"
    In: A. Okada et al. (eds.), Cooperation in Classification and Data Analysis
    Studies in Classification, Data Analysis, and Knowledge Organizations, 151-159
    Springer-Verlag Berlin Heidelberg, 2009 (PDF)

  12. F. Hormozdiari, M. Hsing, R. Salari, A. Schönhuth, S. Chan, S.C. Sahinalp, A. Cherkasov
    "The effect of insertions and deletions (indels) on wirings in protein interaction networks: a large scale study"
    Proceedings of the Recomb Satellite on Systems Biology 2008
    also: Journal of Computational Biology, 16(2), 159-167, 2009.

  13. A. Schönhuth
    "Equations for hidden Markov models"
    Workshop on Algebraic Statistics, MSRI, UC Berkeley, 2008
    Invited Contribution, available at arXiv:0901.3749

  14. A. Schönhuth
    "A simple and efficient solution of the identifiability problem for hidden Markov sources and quantum random walks"
    Proceedings of the International Symposium on Information Theory and its Applications 2008
    arXiv:0808.2833

  15. R. Salari*, A. Schönhuth*, F. Hormozdiari, A. Cherkasov, S.C. Sahinalp
    "The relation between indel length and functional divergence: a formal study"
    Proceedings of the WABI 2008, LNCS 5251, 330-341, 2008.
    *Joint first authorship

  16. A. Schönhuth
    "The ergodic decomposition of asymptotically mean stationary random sources"
    Submitted, 2008
    arXiv:0804.2487

  17. U. Faigle, A. Schönhuth
    "Asymptotic mean stationarity of sources with finite evolution dimension"
    IEEE Transactions on Information Theory, 53(7), 2342 - 2348, 2007
    ZAIK Preprint (PDF)

  18. U. Faigle, A. Schönhuth
    "Discrete quantum Markov chains"
    Preprint, 2006

  19. U. Faigle, A. Schönhuth
    "Quantum predictor models"
    Electronic Notes in Discrete Mathematics, 25, 149-155, 2006

  20. A. Schönhuth
    "Discrete-valued stochastic vector spaces" (German)
    PhD thesis, University of Cologne, 2006

  21. A. Schliep, I. Costa, C. Steinhoff, A. Schönhuth
    "Analyzing gene expression time courses"
    IEEE/ACM Transactions on Computational Biology and Bioinformatics, 2(3), 179-193, 2005

  22. M. Leber, L. Kaderali, A. Schönhuth, R. Schrader
    "A fractional programming approach to efficient DNA melting temperature calculation"
    Bioinformatics, 21(10), 2375-2382, 2005

  23. I. Costa, A. Schönhuth, A. Schliep
    "The Graphical Query Language: a tool for analysis of gene expression time-courses"
    Bioinformatics, 21(10), 2544-2545, 2005

  24. U.Faigle, A. Schönhuth
    "Note on negative probabilities and observable processes"
    In: S. Albers, R. Moehring, C. Pflug, R. Schultz (eds.)
    Algorithms for Optimization with Incomplete Information
    Dagstuhl Seminar Proceedings 05031, 108:1-14, 2005

  25. A. Schliep, C. Steinhoff, A. Schönhuth
    "Robust inference of groups in gene expression time-courses using mixtures of HMMs"
    Bioinformatics, 20, Supp. 1 (Proc. ISMB/ECCB 2004), 283-289, 2004

  26. A. Schliep, B. Georgi, W. Rungsarityotin, I. Costa da Filho, A. Schönhuth
    "The General Hidden Markov Model Library: Analyzing systems with unobservable states"
    In: K. Kremer, V. Macho (eds.)
    Forschung und Wissenschaftliches Rechnen 2004
    GWDG-Bericht 68, 121-136, 2004

  27. A. Schliep, A. Schönhuth, C. Steinhoff
    "Using hidden Markov models to analyze gene expression time course data"
    Bioinformatics, 19, Supp. 1 (Proc. ISMB 2003), 255-263, 2003

  28. P. Pipenbacher, A. Schliep, S. Schneckener, A. Schönhuth, D. Schomburg, R. Schrader
    "ProClust: Improved clustering of protein sequences with an extended graph-based approach"
    Bioinformatics, 18, Supp. 2 (Proc. ECCB 2002), 182-192, 2002

Selected (Upcoming) Talks

  1. "Constrained Mixture Estimation for Analysis and Robust Classification of Clinical Time Series"
    Refereed Contribution, Biomedical Computation at Stanford, 10th Annual Symposium, November 2009

  2. "Constrained Mixture Estimation for Analysis and Robust Classification of Clinical Time Series"
    Invited Talk, SIAM Conference on Mathematics for Industry, San Francisco, October 2009

  3. "A statistical framework for improved prediction of true indels in pair HMM based alignments"
    Invited Talk, Seminar on Mathematical and Computational Biology, UC Berkeley, September 2009

  4. "A simple and efficient solution of the identifiability problem for hidden Markov processes and quantum random walks"
    Invited Talk, Seminar on Discrete Mathematics, University of British Columbia, February 2009

  5. "Equations for hidden Markov models"
    Invited Talk, Workshop on Algebraic Statistics, December 2008, MSRI, Berkeley

  6. "A simple and efficient solution of the identifiability problem for hidden Markov sources and quantum random walks"
    International Symposium on Information Theory and its Applications, December 2008, University of Auckland

  7. "The effect of insertions and deletions (indels) on wirings in protein interaction networks: a large scale study"
    Recomb Satellite on Systems Biology, October 2008, MIT, Boston

  8. "The relation between indel length and functional divergence: a formal study"
    Workshop on Algorithms in Bioinformatics (WABI), September 2008, University of Karlsruhe

  9. "Quantum Predictor Models"
    Cologne-Twente Workshop (CTW) 2006, Lambrecht

  10. "The Graphical Query Language: a comprehensive tool for analysis of gene expression time course data"
    Software Presentation, Glasgow, ISMB 2004

  11. "Hidden Markov Models: Theory and Biological Applications"
    Invited Talk, University of Cologne

  12. "Hidden Markov Models: A Tutorial"
    Invited Talk, Seminar on Data Processing, University of Cologne