Franc, V., Zien, A., Schölkopf, B.
Support Vector Machines as Probabilistic Models
In Proceedings of the 28th International Conference on Machine Learning, pages: 665-672, (Editors: L Getoor and T Scheffer), International Machine Learning Society, Madison, WI, USA, ICML, July 2011 (inproceedings)
Schweikert, G., Zien, A., Zeller, G., Behr, J., Dieterich, C., Ong, C., Philips, P., De Bona, F., Hartmann, L., Bohlen, A., Krüger, N., Sonnenburg, S., Rätsch, G.
mGene: accurate SVM-based gene finding with an application to nematode genomes
Genome Research, 19(11):2133-43, 2009 (article)
Schweikert, G., Behr, J., Zien, A., Zeller, G., Ong, C., Sonnenburg, S., Rätsch, G.
mGene.web: a web service for accurate computational gene finding
Nucleic Acids Research, 37, pages: W312-6, 2009 (article)
Ong, C., Zien, A.
An Automated Combination of Kernels for Predicting Protein Subcellular Localization
In WABI 2008, pages: 186-197, (Editors: Crandall, K. A., J. Lagergren), Springer, Berlin, Germany, 8th Workshop on Algorithms in Bioinformatics, September 2008 (inproceedings)
Schweikert, G., Zeller, G., Zien, A., Behr, J., Sonnenburg, S., Philips, P., Ong, C., Rätsch, G.
mGene: A Novel Discriminative Gene Finder
Worm Genomics and Systems Biology meeting, July 2008 (talk)
Sonnenburg, S., Zien, A., Philips, P., Rätsch, G.
Positional Oligomer Importance Matrices
NIPS Workshop on Machine Learning in Computational Biology, December 2007 (talk)
Zien, A., Ong, C.
An Automated Combination of Kernels for Predicting Protein Subcellular Localization
NIPS Workshop on Machine Learning in Computational Biology, December 2007 (talk)
Zien, A., Gebhard, P., Fundel, K., Aigner, T.
Phenotyping of Chondrocytes In Vivo and In Vitro Using cDNA Array Technology
Clinical Orthopaedics and Related Research, 460, pages: 226-233, July 2007 (article)
Zien, A., Bona, F., Ong, C.
Training and Approximation of a Primal Multiclass Support Vector Machine
In ASMDA 2007, pages: 1-8, (Editors: Skiadas, C. H.), 12th International Conference on Applied Stochastic Models and Data Analysis, June 2007 (inproceedings)
Zien, A., Brefeld, U., Scheffer, T.
Transductive Support Vector Machines for Structured Variables
International Conference on Machine Learning (ICML), June 2007 (talk)
Zien, A., Ong, C.
Multiclass Multiple Kernel Learning
In ICML 2007, pages: 1191-1198, (Editors: Ghahramani, Z. ), ACM Press, New York, NY, USA, 24th International Conference on Machine Learning, June 2007 (inproceedings)
Zien, A., Brefeld, U., Scheffer, T.
Transductive Support Vector Machines for Structured Variables
In ICML 2007, pages: 1183-1190, (Editors: Ghahramani, Z. ), ACM Press, New York, NY, USA, 24th International Conference on Machine Learning, June 2007 (inproceedings)
Schweikert, G., Zeller, G., Zien, A., Ong, C., de Bona, F., Sonnenburg, S., Phillips, P., Rätsch, G.
Ab-initio gene finding using machine learning
NIPS Workshop on New Problems and Methods in Computational Biology, December 2006 (talk)
Zien, A.
Semi-Supervised Learning
Advanced Methods in Sequence Analysis Lectures, November 2006 (talk)
Aigner, T., Fundel, K., Saas, J., Gebhard, P., Haag, J., Weiss, T., Zien, A., Obermayr, F., Zimmer, R., Bartnik, E.
Large-Scale Gene Expression Profiling Reveals Major Pathogenetic Pathways of Cartilage Degeneration in Osteoarthritis
Arthritis and Rheumatism, 54(11):3533-3544, October 2006 (article)
Zien, A.
Semi-Supervised Support Vector Machines and Application to Spam Filtering
ECML Discovery Challenge Workshop, September 2006 (talk)
Chapelle, O., Schölkopf, B., Zien, A.
Semi-Supervised Learning
pages: 508, Adaptive computation and machine learning, MIT Press, Cambridge, MA, USA, September 2006 (book)
Zien, A., Raetsch, G., Ong, C.
Towards the Inference of Graphs on Ordered Vertexes
(150), Max Planck Institute for Biological Cybernetics, Tübingen, August 2006 (techreport)
Sonnenburg, S., Zien, A., Rätsch, G.
ARTS: Accurate Recognition of Transcription Starts in Human
Bioinformatics, 22(14):e472-e480, July 2006 (article)
Chapelle, O., Chi, M., Zien, A.
A Continuation Method for Semi-Supervised SVMs
In ICML 2006, pages: 185-192, (Editors: Cohen, W. W., A. Moore), ACM Press, New York, NY, USA, 23rd International Conference on Machine Learning, June 2006 (inproceedings)
Zien, A., Ong, C.
An Automated Combination of Sequence Motif Kernels for Predicting Protein Subcellular Localization
(146), Max Planck Institute for Biological Cybernetics, Tübingen, April 2006 (techreport)
Aigner, T., McKenna, L., Zien, A., Fan, Z., Gebhard, P., Zimmer, R.
Gene Expression Profiling of Serum- and Interleukin-1beta-Stimulated Primary Human Adult Articular Chondrocytes - A Molecular Analysis Based on Chondrocytes Isolated from One Donor
Cytokine, 31(3):227-240, August 2005 (article)
Schorle, C., Finger, F., Zien, A., Block, J., Gebhard, P., Aigner, T.
Phenotypic characterization of chondrosarcoma-derived cell lines
Cancer Letters, 226(2):143-154, August 2005 (article)
Zien, A., Candela, J.
Large Margin Non-Linear Embedding
In ICML 2005, pages: 1065-1072, (Editors: De Raedt, L. , S. Wrobel), ACM Press, New York, NY, USA, 22nd International Conference on Machine Learning, August 2005 (inproceedings)
Chapelle, O., Zien, A.
Semi-Supervised Classification by Low Density Separation
In AISTATS 2005, pages: 57-64, (Editors: Cowell, R. , Z. Ghahramani), Tenth International Workshop on Artificial Intelligence and Statistics (AI & Statistics), January 2005 (inproceedings)
BakIr, G., Zien, A., Tsuda, K.
Learning to Find Graph Pre-Images
In Pattern Recognition, pages: 253-261, (Editors: Rasmussen, C. E., H. H. Bülthoff, B. Schölkopf, M. A. Giese), Springer, Berlin, Germany, 26th DAGM Symposium, August 2004 (inproceedings)
Aigner, T., Saas, J., Zien, A., Zimmer, R., Gebhard, P., Knorr, T.
Analysis of differential gene expression in healthy and osteoarthritic cartilage and isolated chondrocytes by microarray analysis
In Volume 1: Cellular and Molecular Tools, pages: 109-128, (Editors: Sabatini, M., P. Pastoureau and F. De Ceuninck), Humana Press, July 2004 (inbook)
Eichhorn, J., Tolias, A., Zien, A., Kuss, M., Rasmussen, C., Weston, J., Logothetis, N., Schölkopf, B.
Prediction on Spike Data Using Kernel Algorithms
In Advances in Neural Information Processing Systems 16, pages: 1367-1374, (Editors: S Thrun and LK Saul and B Schölkopf), MIT Press, Cambridge, MA, USA, 17th Annual Conference on Neural Information Processing Systems (NIPS), June 2004 (inproceedings)
Aigner, T., Finger, F., Zien, A., Bartnik, E.
cDNA-Microarray Technology in Cartilage Research - Functional Genomics of Osteoarthritis [in German]
Zeitschrift f{\"u}r Orthop{\"a}die und ihre Grenzgebiete, 142(2):241-247, April 2004 (article)
Zien, A.
Computational Analysis of Gene Expression Data
(4), Biologische Kybernetik, March 2004 (phdthesis)
Finger, F., Schorle, C., Söder, S., Zien, A., Goldring, M., Aigner, T.
Phenotypic Characterization of Human Chondrocyte Cell Line C-20/A4: A Comparison between Monolayer and Alginate Suspension Culture
Cells Tissues Organs, 178(2):65-77, 2004 (article)
Zien, A.
A primer on molecular biology
In pages: 3-34, (Editors: Schoelkopf, B., K. Tsuda and J. P. Vert), MIT Press, Cambridge, MA, USA, 2004 (inbook)
Finger, F., Schorle, C., Zien, A., Gebhard, P., Goldring, M., Aigner, T.
Molecular phenotyping of human chondrocyte cell lines T/C-28a2, T/C-28a4, and C-28/I2
Arthritis & Rheumatism, 48(12):3395-3403, December 2003 (article)
Becker, A., Chen, J., Zien, A., Sochivko, D., Normann, S., Schramm, J., Elger, C., Wiestler, O., Blumcke, I.
Correlated stage- and subfield-associated hippocampal gene expression patterns in experimental and human temporal lobe epilepsy
European Journal of Neuroscience, 18(10):2792-2802, November 2003 (article)
Knorr, T., Obermayr, F., Bartnik, E., Zien, A., Aigner, T.
YKL-39 (chitinase 3-like protein 2), but not YKL-40 (chitinase 3-like protein 1), is up regulated in osteoarthritic chondrocytes
Annals of the Rheumatic Diseases, 62(10):995-998, October 2003 (article)
Zien, A., Fluck, J., Zimmer, R., Lengauer, T.
Microarrays: How Many Do You Need?
Journal of Computational Biology, 10(3-4):653-667, 2003 (article)
Aigner, T., Zien, A., Hanisch, D., Zimmer, R.
Gene expression in chondrocytes assessed with use of microarrays
Journal of Bone and Joint Surgery, 85(Suppl 2):117-123, 2003 (article)
Aigner, T., Bartnik, E., Zien, A., Zimmer, R.
Functional Genomics of Osteoarthritis
Pharmacogenomics, 3(5):635-650, September 2002 (article)
Hanisch, D., Zien, A., Zimmer, R., Lengauer, T.
Co-Clustering of Biological Networks and Gene Expression Data
Bioinformatics, (Suppl 1):145S-154S, 18, July 2002 (article)
Sommer, I., Zien, A., von Ohsen, N., Zimmer, R., Lengauer, T.
Confidence measures for protein fold recognition
Bioinformatics, 18(6):802-812, June 2002 (article)
Zien, A., Fluck, J., Zimmer, R., Lengauer, T.
Microarrays: How Many Do You Need?
In RECOMB 2002, pages: 321-330, ACM Press, New York, NY, USA, Sixth Annual International Conference on Research in Computational Molecular Biology, April 2002 (inproceedings)
Aigner, T., Zien, A., Gehrsitz, A., Gebhard, P., McKenna, L.
Anabolic and Catabolic Gene Expression Pattern Analysis in Normal Versus Osteoarthritic Cartilage Using Complementary DNA-Array Technology
Arthritis and Rheumatism, 44(12):2777-2789, December 2001 (article)
Zien, A., Aigner, T., Zimmer, R., Lengauer, T.
Centralization: A new method for the normalization of gene expression data
Bioinformatics, 17, pages: S323-S331, June 2001, Mathematical supplement available at http://citeseer.ist.psu.edu/574280.html (article)
Zien, A., Zimmer, R., Lengauer, T.
A Simple Iterative Approach to Parameter Optimization
Journal of Computational Biology, 7(3,4):483-501, November 2000 (article)
Zien, A., Küffner, R., Mevissen, T., Zimmer, R., Lengauer, T.
Identification of Drug Target Proteins
ERCIM News, 43, pages: 16-17, October 2000 (article)
Zien, A., Rätsch, G., Mika, S., Schölkopf, B., Lengauer, T., Müller, K.
Engineering Support Vector Machine Kernels That Recognize Translation Initiation Sites
Bioinformatics, 16(9):799-807, September 2000 (article)
Zien, A., Küffner, R., Zimmer, R., Lengauer, T.
Analysis of Gene Expression Data with Pathway Scores
In ISMB 2000, pages: 407-417, AAAI Press, Menlo Park, CA, USA, 8th International Conference on Intelligent Systems for Molecular Biology, August 2000 (inproceedings)
Zien, A., Zimmer, R., Lengauer, T.
A simple iterative approach to parameter optimization
In RECOMB2000, pages: 318-327, ACM Press, New York, NY, USA, Forth Annual Conference on Research in Computational Molecular Biology, April 2000 (inproceedings)
Zien, A., Rätsch, G., Mika, S., Schölkopf, B., Lemmen, C., Smola, A., Lengauer, T., Müller, K.
Engineering Support Vector Machine Kernels That Recognize Translation Initiation Sites in DNA
In German Conference on Bioinformatics (GCB 1999), October 1999 (inproceedings)