Publications of Alexander Schönhuth
- 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
- A. Schönhuth, R. Salari, S.C. Sahinalp
"Identification of functionally divergent paralogs using statistics on indels in local alignments"
Submitted, 2010
- C. Hafemeister, I. Costa, A. Schönhuth, A. Schliep
"Classifying short gene expression time-courses with Bayesian estimation of piecewise constant functions"
Submitted, 2010
- 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
- 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
- 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
- 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
- A. Schönhuth, H. Jaeger
"Characterization of ergodic hidden Markov sources"
IEEE Transactions on Information Theory, 55(5), 2107-2118, 2009
ZAIK Preprint (PDF)
- 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)
- 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
- 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)
- 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.
- A. Schönhuth
"Equations for hidden Markov models"
Workshop on Algebraic Statistics, MSRI, UC Berkeley, 2008
Invited Contribution, available at
arXiv:0901.3749
- 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
- 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
- A. Schönhuth
"The ergodic decomposition of asymptotically mean stationary
random sources"
Submitted, 2008
arXiv:0804.2487
- 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)
-
U. Faigle, A. Schönhuth
"Discrete quantum Markov chains"
Preprint, 2006
- U. Faigle, A. Schönhuth
"Quantum predictor models"
Electronic Notes in Discrete Mathematics, 25,
149-155, 2006
- A. Schönhuth
"Discrete-valued stochastic vector spaces" (German)
PhD thesis, University of Cologne, 2006
- 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
- M. Leber, L. Kaderali, A. Schönhuth, R. Schrader
"A fractional programming approach to
efficient DNA melting temperature calculation"
Bioinformatics, 21(10), 2375-2382, 2005
- 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
- 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
- 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
- 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
- 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
- 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
- "Constrained Mixture Estimation for Analysis and Robust Classification of Clinical Time Series"
Refereed Contribution, Biomedical Computation at Stanford, 10th Annual Symposium, November 2009
- "Constrained Mixture Estimation for Analysis and Robust Classification of Clinical Time Series"
Invited Talk, SIAM Conference on Mathematics for Industry, San Francisco, October 2009
- "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
- "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
- "Equations for hidden Markov models"
Invited Talk, Workshop on Algebraic Statistics, December 2008, MSRI, Berkeley
- "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
- "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
- "The relation between indel length and functional divergence: a
formal study"
Workshop on Algorithms in Bioinformatics (WABI), September 2008, University of Karlsruhe
- "Quantum Predictor Models"
Cologne-Twente Workshop (CTW) 2006, Lambrecht
- "The Graphical Query Language: a comprehensive tool for analysis of gene expression time course data"
Software Presentation, Glasgow, ISMB 2004
- "Hidden Markov Models: Theory and Biological Applications"
Invited Talk, University of Cologne
- "Hidden Markov Models: A Tutorial"
Invited Talk, Seminar on Data Processing, University of Cologne