Publications of Alexander Schönhuth

  1. A. Schönhuth
    "Complete identification of binary-valued hidden Markov processes"
    Submitted, 2011
    arXiv:1101.3712

  2. M. Singer*, A. Engström*, A. Schönhuth**, L. Pachter**
    "Determining coding CpG islands by identifying regions significant for pattern statistics on Markov chains"
    Submitted, 2011
    *Joint first authors, **Joint last, corresponding authors

  3. U. Faigle, A. Schönhuth
    "Discrete quantum Markov chains"
    Submitted, 2010
    arXiv:1011.1295

  4. U. Faigle, A. Schönhuth
    "Representation of Power Series over Word Algebras"
    Cologne-Twente Workshop, to appear, 2011

  5. C. Hafemeister, I. Costa, A. Schönhuth, A. Schliep
    "Classifying short gene expression time-courses with Bayesian estimation of piecewise constant functions"
    Bioinformatics, 27(7), 946-952, 2011

  6. U. Faigle, A. Schönhuth
    "Efficient tests for equivalence of hidden Markov processes and quantum random walks"
    IEEE Transactions on Information Theory, 57(3), 1746-1753, 2011
    arXiv:0808.2833

  7. P. Dao*, R. Colak*, R. Salari, F. Moser, A. Schönhuth**, M. Ester**
    "Inferring cancer subnetwork markers using density-constrained biclustering"
    Bioinformatics (Proc. ECCB 2010), 26(18), i625-631, 2010
    *Joint first authors, **Joint last, corresponding authors

  8. A. Schönhuth, R. Salari, S.C. Sahinalp
    "Pair HMM based gap statistics for re-evaluation of indels in alignments with affine gap penalties"
    Proceedings of the WABI 2010, LNCS 6293, 350-361, 2010

  9. 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"
    PLoS One, 5(10): e13348, 2010
    *Joint last authorship

  10. M. Singer, D. Boffelli, J. Dhabhi, A. Schönhuth, G.P. Schroth, D.I.K. Martin, L. Pachter
    "MetMap enables genome-scale methyltyping for determining methylation states in populations"
    PLoS Computational Biology 6(8): e1000888, 2010

  11. 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

  12. 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

  13. 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

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

  15. 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)

  16. 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

  17. 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)

  18. 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.

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

  20. 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:0808.2833v2

  21. 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

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

  23. 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)

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

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

  26. 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

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

  28. 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

  29. 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

  30. 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

  31. 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

  32. 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

  33. 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 Talks

  1. "Identification of binary-valued hidden Markov processes"
    Invited Talk, February 2011, TU Eindhoven

  2. "Inferring cancer subnetwork markers using density-constrained biclustering"
    European Conference on Computational Biology, September 2010, Ghent, Belgium

  3. "Pair HMM based gap statistics for re-evaluation of indels in alignments with affine gap penalties"
    Workshop on Algorithms in Bioinformatics (WABI), September 2010, Liverpool, UK

  4. "Classifying Cancer Tissue by Inferring Systemic Markers"
    Invited Talk, Toyota Technological Institute, Chicago, April 2010

  5. "How to Identify Hidden Markov Processes - An Algebraic Statistical Answer"
    Invited Talk, Annual AMS Meeting, University of Kentucky, March 2010

  6. "Classifying Cancer Tissue by Inferring Systemic Markers"
    Invited Talk, Lane Center for Computational Biology, Carnegie Mellon University, February 2010

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

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

  9. "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

  10. "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

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

  12. "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

  13. "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

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

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

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

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

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