Max Planck Institute for Molecular Genetics
Department of Computational Molecular Biology
B. Georgi, I. Gesteira Costa, and I. Schliep. PyMix - The Python mixture package - a tool for clustering of heterogeneous biological data. BMC Bioinformatics 2010, Vol. 11, Number 9 [details]
W. Hochstättler and A. Schliep. CATBox – An Interactive Course in Combinatorial Optimization. , Springer 2010 [details]
I. G. Costa, A. Schönhuth, C. Hafemeister, and A. Schliep. Constrained Mixture Estimation for Analysis and Robust Classification of Clinical Time Series. (ISMB 2009) Bioinformatics 2009, Vol. 12, Number 25, Pages i6-14 [details] [pdf] [supp] [PMID 19478017]
B. Georgi. Context-specific Independence Mixture Models for Cluster Analysis of Biological Data. PhD Thesis Jun 2009 [details]
B. Georgi, J. Schultz, and A. Schliep. Partially-supervised protein subclass discovery with simultaneous annotation of functional residues. BMC Struct Biol. 2009, Vol. 9, Number 68 [details] [pdf] [PMID 19857261]
M. C. P. de Souto, D. A. S. Araujo, I. G. Costa , R. G. F. Soares, T. B. Ludermir, and A. Schliep. Comparative Study on Normalization Procedures for Cluster Analysis of Gene Expression Datasets. Proceedings of the International Joint Conference on Neural Networks, IEEE Computer Society, 2008 [details]
M. C. P. de Souto, R. B. C. Prudencio, R. G. F. Soares, D. A. S. Araujo, I. G. Costa , T. B. Ludermir, and A. Schliep. Ranking and Selecting Clustering Algorithms Using a Meta-learning Approach. Proceedings of the International Joint Conference on Neural Networks, IEEE Computer Society, 2008 [details]
I. G. Costa, S. Roepcke, C. Hafemeister, and A. Schliep. Inferring differentiation pathways from gene expression. Bioinformatics 2008, Vol. 24, Number 13, Pages i156-164 [details] [pdf] [supp] [PMID 18586709]
A. Macula, A. Schliep, M. Bishop, and T. Renz. New, improved, and practical k-stem sequence similarity measures for probe design. J. Comput. Biol. 2008, Vol. 15, Pages 525--534 [details] [pdf] [PMID 18549305]
A. Schliep and R. Krause. Efficient algorithms for the computational design of optimal tiling arrays. IEEE/ACM Transactions on Computational Biology and Bioinformatics 2008, Pages 557--567 [details] [pdf] [PMID 18989043]
C. Hafemeister. Efficient Computation of Probe Qualities. Master's Thesis May 2008, Freie Universität Berlin [details] [pdf]
M. de Souto, I. G. Costa, D. de Araujo, T. Ludermir, and A. Schliep. Clustering cancer gene expression data: a comparative study. BMC Bioinformatics 2008, Vol. 9, Number 1, Pages 497 [details] [pdf] [PMID 19038021]
I. G. Costa. Mixture Models for the Analysis of Gene Expression: Integration of Multiple Experiments and Cluster Validation. PhD Thesis 2008 [details]
R. Schilling. Elastic registration in 3D volume data. Master's Thesis 2007, University of Freiburg [details]
I. G. Costa, M. C. P. de Souto, and A. Schliep. Validating Gene Clusterings by Selecting Informative Gene Ontology Terms with Mutual Information. Advances in Bioinformatics and Computational Biology, Proceedings of the Brazilian Symposium on Bioinformatics, Pages 81-92, Springer Verlag, 2007 [details]
I. G. Costa, R. Krause, L. Optiz, and A. Schliep. Semi-supervised learning for the identification of syn-expressed genes from fused microarray and in situ image data. BMC Bioinformatics 2007, Vol. 8, Pages S3 [details] [pdf] [supp] [PMID 18269697]
I. Costa, S. Roepcke, and A. Schliep. Gene expression trees in lymphoid development. BMC Immunol 2007, Vol. 8, Number 1, Pages 25 [details] [pdf] [supp] [PMID 17925013]
B. Georgi and A. Schliep. Partially-supervised context-specific independence mixture modeling. workshop on Data Mining in Functional Genomics and Proteomics, ECML 2007, 2007 [details] [pdf]
S. Haesler, C. Rochefort, P. Licznerski, B. Georgi, P. Osten, and C. Scharff. Knockdown of FoxP2 in Songbird Basal Ganglia Impairs Song Learning. PloS Biology 2007, Vol. 5, Number 12, Pages e321 [details] [pdf]
B. Georgi, J. Schultz, and A. Schliep. Context-Specific Independence Mixture Modelling for Protein Families. Knowledge Discovery in Databases: PKDD 2007, Pages 79-90, Springer Berlin / Heidelberg, 2007 [details] [pdf] [supp]
B. Georgi, M. A. Spence, P. Flodman, and A. Schliep. Mixture model based group inference in fused genotype and phenotype data. Studies in Classification, Data Analysis, and Knowledge Organization, Springer, 2007 [details] [pdf] [supp]
G. W. Klau, S. Rahmann, A. Schliep, M. Vingron, and K. Reinert. Integer linear programming approaches for non-unique probe selection. Discrete Appl. Math. 2007, Vol. 155, Number 6-7, Pages 840-856 [details] [pdf]
L. Opitz, A. Schliep, and S. Posch. Analysis of fused in-situ hybridization and gene expression data. Proceedings of the GfKl 2006 Advances in Data Analysis, Pages 577-584, Springer, 2007 [details]
A. Schliep and R. Krause. Efficient Computational Design of Tiling Arrays Using a Shortest Path Approach. Algorithms in Bioinformatics, Pages 383-394, Springer Berlin / Heidelberg, 2007 [details] [pdf]
W. Rungsarityotin, R. Krause, A. Schodl, and A. Schliep. Identifying protein complexes directly from high-throughput TAP data with Markov random fields. BMC Bioinformatics 2007, Vol. 8, Pages 482 [details] [pdf] [supp] [PMID 18093306]
W. Rungsarityotin. Algorithms to identify protein complexes from high-throughput data. PhD Thesis 2007 [details]
I. G. Costa and A. Schliep. On the feasibility of Heterogeneous Analysis of Large Scale Biological Data. Proceedings of ECML/PKDD 2006 Workshop on Data and Text Mining for Integrative Biology, Pages 55-60, 2006 [details] [pdf]
B. Georgi and A. Schliep. Context-specific independence mixture modeling for positional weight matrices. Bioinformatics 2006, Vol. 22, Number 14, Pages e166-e173 [details] [pdf] [PMID 16873468]
C. Hafemeister. Structure Learning of Conditional Trees. Bachelor's Thesis Jun 2006, Free University of Berlin [details] [pdf]
L. Opitz. Analyse von Bildern der mRNA-in Situ-Hybridisierung. Master's Thesis 2006, Martin-Luther-Universität Halle [details]
A. Schliep and S. Rahmann. Decoding non-unique oligonucleotide hybridization experiments of targets related by a phylogenetic tree. Bioinformatics 2006, Vol. 22, Number 14, Pages e424-e430 [details] [pdf] [PMID 16873503]
A. Schönhuth, I. G. Costa, and A. Schliep. Semi-supervised Clustering of Yeast Gene Expression. Accepted Japanese-German Workshop on data analysis and classification, Springer, 2006 [details]
M. Seifert. Analyzing Microarray Data Using Homogenous and Inhomogenous Hidden Markov Models. Master's Thesis 2006, Martin-Luther-Universität Halle [details]
M. Weber, W. Rungsarityotin, and A. Schliep. An indicator for the number of modes in a mixture model using a linear map to simplex structure. Proceedings of the GfKl 2005 From Data and Information Analysis to Knowledge Engineering, Pages 103-110, Springer, 2006 [details] [pdf]
I. G. Costa and A. Schliep. On external indices for mixtures: validating mixtures of genes. From Data and Information Analysis to Knowledge Engineering, Pages 662-669, Springer 2005, 2005 [details] [pdf]
I. G. Costa, A. Schönhuth, and A. Schliep. The Graphical Query Language: a tool for analysis of gene expression time-courses. Bioinformatics 2005, Vol. 21, Number 10, Pages 2544-5 [details] [pdf]
B. Georgi. Mixture Modeling and Group Inference in Fused Genotype and Phenotype Data. Master's Thesis 2005, Free University of Berlin [details]
M. Heinig. Development of a Pair HMM based Gene Finder for the Paramecium Genome. Master's Thesis 2005, Free University of Berlin [details]
A. Schliep, I. G. Costa, C. Steinhoff, and A. Schönhuth. Analyzing gene expression time-courses. IEEE/ACM Trans Comput Biol Bioinform 2005, Vol. 2, Number 3, Pages 179-193 [details] [pdf] [PMID 17044182]
A. Schliep, B. Georgi, W. Rungsarityotin, I. G. Costa, and A. Schönhuth. The General Hidden Markov Model Library: Analyzing Systems with Unobservable States. Forschung und wissenschaftliches Rechnen: Beiträge zum Heinz-Billing-Preis 2004, Series GWDG-Bericht, Pages 121-135, Gesellschaft für wissenschaftliche Datenverarbeitung 2005 [details] [pdf]
J. Tödling, S. Schmeier, M. Heinig, B. Georgi, and S. Röpcke. MACAT - MicroArray Chromosome Analysis Tool. Bioinformatics 2005, Vol. 21, Number 9, Pages 2112-2113 [details]
I. G. Costa, F. A. T. De Carvalho, and M. C. P. De Souto. Comparative Analysis of Clustering Methods for Gene Expression Time Course Data. Genetics and Molecular Biology 2004, Vol. 27, Number 4, Pages 623-631 [details]
J. Grunau. Discriminative Learning in Hidden Markov Models. Bachelor's Thesis 2004, Free University of Berlin [details]
G. W. Klau, S. Rahmann, A. Schliep, M. Vingron, and K. Reinert. Optimal robust non-unique probe selection using Integer Linear Programming. Bioinformatics 2004, Vol. 20 Suppl 1, Pages i186-i193 [details] [pdf] [PMID 15262798]
A. Riemer. Chromosome-wide Expression for Improving ab-initio Gene Prediction. Bachelor's Thesis 2004, Free University of Berlin [details]
W. Rungsarityotin. Graph-based clustering for biological data. Master's Thesis 2004, Free University of Berlin [details]
A. Schliep, C. Steinhoff, and A. Schönhuth. Robust inference of groups in gene expression time-courses using mixtures of HMMs. Bioinformatics 2004, Vol. 20 Suppl 1, Pages i283-i289 [details] [pdf] [supp] [PMID 15262810]
M. Weber, W. Rungsarityotin, and A. Schliep. Perron Cluster Analysis and Its Connection to Graph Partitioning for Noisy Data. , Zuse Institute Berlin (ZIB) 2004 [details]
B. Georgi. A Graph-Based Approach to Clustering of Profile Hidden Markov Models. Bachelor's Thesis 2003, Free University of Berlin [details]
J. Heise. Selection of Family-Specific Probes for Microarrays. Bachelor's Thesis 2003, Free University of Berlin [details]
B. Knab, A. Schliep, B. Steckemetz, and B. Wichern. Model-Based Clustering With Hidden Markov Models and its Application to Financial Time-Series Data. Proceedings of the GfKl 2002 Between Data Science and Applied Data Analysis, Pages 561-569, Springer, 2003 [details] [pdf]
A. Schliep, A. Schönhuth, and C. Steinhoff. Using hidden Markov models to analyze gene expression time course data. Bioinformatics 2003, Vol. 19 Suppl 1, Pages i255-i263 [details] [pdf] [supp] [PMID 12855468]
A. Schliep, D. C. Torney, and S. Rahmann. Group testing with DNA chips: generating designs and decoding experiments. Proc IEEE Comput Soc Bioinform Conf 2003, Vol. 2, Pages 84-91 [details] [pdf] [PMID 16452782]
A. Weisse. Recognition of Circular Permutations in Proteins with Hidden Markov Models. Bachelor's Thesis 2003, Free University of Berlin [details]
L. Kaderali and A. Schliep. Selecting signature oligonucleotides to identify organisms using DNA arrays. Bioinformatics 2002, Vol. 18, Number 10, Pages 1340-1349 [details] [pdf] [PMID 12376378]
P. Pipenbacher, A. Schliep, S. Schneckener, A. Schönhuth, D. Schomburg, and R. Schrader. ProClust: improved clustering of protein sequences with an extended graph-based approach. Bioinformatics 2002, Vol. 18 Suppl 2, Pages S182-S191 [details] [pdf] [PMID 02]
A. Schliep and W. Hochstättler. Developing Gato and CATBox with Python: Teaching graph algorithms through visualization and experimentation. Multimedia Tools for Communicating Mathematics, Pages 291-310, Springer-Verlag 2002 [details] [pdf]
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