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Dr. Alexander Zien

E-Mail:

alexander.zien

Alexander Zien

Position: Wissenschaftler Abteilung: Alumni Schölkopf

Publikationen

Bücher (1):
•	Chapelle O , Schölkopf B und Zien A : Semi-Supervised Learning, 508, MIT Press, Cambridge, MA, USA, (September-2006).
Artikel (20):
•	Zien A , Gebhard PM , Fundel K und Aigner T (July-2007) Phenotyping of Chondrocytes In Vivo and In Vitro Using cDNA Array Technology Clinical Orthopaedics and Related Research 460 226-233.
•	Aigner T , Fundel K , Saas J , Gebhard PM , Haag J , Weiss T , Zien A , Obermayr F , Zimmer R und Bartnik E (October-2006) Large-Scale Gene Expression Profiling Reveals Major Pathogenetic Pathways of Cartilage Degeneration in Osteoarthritis Arthritis and Rheumatism 54(11) 3533-3544.
•	Sonnenburg S , Zien A und Rätsch G (July-2006) ARTS: Accurate Recognition of Transcription Starts in Human Bioinformatics 22(14) e472-e480.
•	Schorle C , Finger F , Zien A , Block J , Gebhard P und Aigner T (August-26-2005) Phenotypic characterization of chondrosarcoma-derived cell lines Cancer Letters 226(2) 143-154.
•	Aigner T , McKenna L , Zien A , Fan Z , Gebhard P und Zimmer R (August-7-2005) 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.
•	Aigner T , Finger F , Zien A und Bartnik E (April-2004) cDNA-Microarray Technology in Cartilage Research - Functional Genomics of Osteoarthritis [in German] Zeitschrift für Orthopädie und ihre Grenzgebiete 142(2) 241-247.
•	Finger F , Schorle C , Söder S , Zien A , Goldring MB und Aigner T (2004) 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.
•	Finger F , Schorle C , Zien A , Gebhard P , Goldring MB und Aigner T (December-2003) Molecular phenotyping of human chondrocyte cell lines T/C-28a2, T/C-28a4, and C-28/I2 Arthritis & Rheumatism 48(12) 3395-3403.
•	Becker AJ , Chen J , Zien A , Sochivko D , Normann S , Schramm J , Elger CE , Wiestler OD und Blumcke I (November-2003) Correlated stage- and subfield-associated hippocampal gene expression patterns in experimental and human temporal lobe epilepsy European Journal of Neuroscience 18(10) 2792-2802.
•	Knorr T , Obermayr F , Bartnik E , Zien A und Aigner T (October-2003) 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.
•	Aigner T , Zien A , Hanisch D und Zimmer R (2003) Gene expression in chondrocytes assessed with use of microarrays Journal of Bone and Joint Surgery 85(Suppl 2) 117-123.
•	Zien A , Fluck J , Zimmer R und Lengauer T (2003) Microarrays: How Many Do You Need? Journal of Computational Biology 10(3-4) 653-667.
•	Aigner T , Bartnik E , Zien A und Zimmer R (September-2002) Functional Genomics of Osteoarthritis Pharmacogenomics 3(5) 635-650.
•	Hanisch D , Zien A , Zimmer R und Lengauer T (July-2002) Co-Clustering of Biological Networks and Gene Expression Data Bioinformatics (Suppl 1) 145S-154S.
•	Sommer I , Zien A , von Ohsen N , Zimmer R und Lengauer T (June-2002) Confidence measures for protein fold recognition Bioinformatics 18(6) 802-812.
•	Aigner T , Zien A , Gehrsitz A , Gebhard PM und McKenna L (December-2001) Anabolic and Catabolic Gene Expression Pattern Analysis in Normal Versus Osteoarthritic Cartilage Using Complementary DNA-Array Technology Arthritis and Rheumatism 44(12) 2777-2789.
•	Zien A , Aigner T , Zimmer R und Lengauer T (June-2001) Centralization: A new method for the normalization of gene expression data Bioinformatics 17 S323-S331.
•	Zien A , Zimmer R und Lengauer T (November-2000) A Simple Iterative Approach to Parameter Optimization Journal of Computational Biology 7(3,4) 483-501.
•	Zien A , Küffner R , Mevissen T , Zimmer R und Lengauer T (October-2000) Identification of Drug Target Proteins ERCIM News 43 16-17.
•	Zien A , Rätsch G , Mika S , Schölkopf B , Lengauer T und Müller K-R (September-2000) Engineering Support Vector Machine Kernels That Recognize Translation Initiation Sites Bioinformatics 16(9) 799-807.
Beiträge zu Tagungsbänden (13):
•	Franc V , Zien A und Schölkopf B (July-2011) Support Vector Machines as Probabilistic Models 28th International Conference on Machine Learning (ICML 2011), International Machine Learning Society, Madison, WI, USA, 665-672.
•	Ong CS und Zien A (September-2008) An Automated Combination of Kernels for Predicting Protein Subcellular Localization In: WABI 2008, 8th Workshop on Algorithms in Bioinformatics, Springer, Berlin, Germany, 186-197.
•	Zien A und Ong CS (June-2007) Multiclass Multiple Kernel Learning In: ICML 2007, 24th International Conference on Machine Learning, ACM Press, New York, NY, USA, 1191-1198.
•	Zien A , Bona FD und Ong CS (June-2007) Training and Approximation of a Primal Multiclass Support Vector Machine In: ASMDA 2007, 12th International Conference on Applied Stochastic Models and Data Analysis, 1-8.
•	Zien A , Brefeld U und Scheffer T (June-2007) Transductive Support Vector Machines for Structured Variables In: ICML 2007, 24th International Conference on Machine Learning, ACM Press, New York, NY, USA, 1183-1190.
•	Chapelle O , Chi M und Zien A (June-2006) A Continuation Method for Semi-Supervised SVMs In: ICML 2006, 23rd International Conference on Machine Learning, ACM Press, New York, NY, USA, 185-192.
•	Zien A und Candela JQ (August-2005) Large Margin Non-Linear Embedding In: ICML 2005, 22nd International Conference on Machine Learning, ACM Press, New York, NY, USA, 1065-1072.
•	Chapelle O und Zien A (January-2005) Semi-Supervised Classification by Low Density Separation In: AISTATS 2005, Tenth International Workshop on Artificial Intelligence and Statistics (AI & Statistics 2005), 57-64.
•	BakIr G , Zien A und Tsuda K (August-2004) Learning to Find Graph Pre-Images In: Pattern Recognition, 26th DAGM Symposium, Springer, Berlin, Germany, 253-261.
•	Eichhorn J , Tolias AS , Zien A , Kuss M , Rasmussen CE , Weston J , Logothetis NK und Schölkopf B (June-2004) Prediction on Spike Data Using Kernel Algorithms In: Advances in Neural Information Processing Systems 16, Seventeenth Annual Conference on Neural Information Processing Systems (NIPS 2003), MIT Press, Cambridge, MA, USA, 1367-1374.
•	Zien A , Fluck J , Zimmer R und Lengauer T (April-2002) Microarrays: How Many Do You Need? In: RECOMB 2002, Sixth Annual International Conference on Research in Computational Molecular Biology, ACM Press, New York, NY, USA, 321-330.
•	Zien A , Küffner R , Zimmer R und Lengauer T (August-2000) Analysis of Gene Expression Data with Pathway Scores In: ISMB 2000, 8th International Conference on Intelligent Systems for Molecular Biology, AAAI Press, Menlo Park, CA, USA, 407-417.
•	Zien A , Zimmer R und Lengauer T (April-2000) A simple iterative approach to parameter optimization In: RECOMB2000, Forth Annual Conference on Research in Computational Molecular Biology, ACM Press, New York, NY, USA, 318-327.
Beiträge zu Büchern (2):
•	Aigner T , Saas J , Zien A , Zimmer R , Gebhard PM und Knorr T : Analysis of differential gene expression in healthy and osteoarthritic cartilage and isolated chondrocytes by microarray analysis, 109-128. (Ed) M. Sabatini und F. De Ceuninck, Humana Press, (July-2004).
•	Zien A : A primer on molecular biology, 3-34. (Ed) B. Schoelkopf und J. P. Vert, MIT Press, Cambridge, MA, USA, (2004).
Technische Berichte (2):
•	Zien A , Raetsch G und Ong CS : Towards the Inference of Graphs on Ordered Vertexes, 150, Max Planck Institute for Biological Cybernetics, Tübingen, (August-2006).
•	Zien A und Ong CS : An Automated Combination of Sequence Motif Kernels for Predicting Protein Subcellular Localization, 146, Max Planck Institute for Biological Cybernetics, Tübingen, (April-2006).
Abschlussarbeiten (1):
•	Zien A : Computational Analysis of Gene Expression Data, (March-2004). PhD thesis ISBN ISBN 3-8322-2606-0
Vorträge (9):
•	Schweikert G , Zeller G , Zien A , Behr J , Sonnenburg S , Philips P , Ong CS und Rätsch G (July-25-2008): mGene: A Novel Discriminative Gene Finder, Worm Genomics and Systems Biology meeting, Cambridge, USA.
•	Zien A und Ong CS (December-2007): An Automated Combination of Kernels for Predicting Protein Subcellular Localization, NIPS 2007 Workshop on Machine Learning in Computational Biology, Whistler, BC, Canada.
•	Sonnenburg S , Zien A , Philips P und Rätsch G (December-2007): Positional Oligomer Importance Matrices, NIPS 2007 Workshop on Machine Learning in Computational Biology, Whistler, BC, Canada.
•	Zien A , Brefeld U und Scheffer T (June-2007): Transductive Support Vector Machines for Structured Variables, International Conference on Machine Learning (ICML 2007), Corvallis, OR, USA.
•	Schweikert G , Zeller G , Zien A , Ong CS , de Bona F , Sonnenburg S , Phillips P und Rätsch G (December-2006): Ab-initio gene finding using machine learning, NIPS 2006 Workshop on New Problems and Methods in Computational Biology, Vancouver, BC, Canada.
•	Zien A (November-29-2006): Semi-Supervised Learning, "Advanced Methods in Sequence Analysis".
•	Zien A (November-29-2006): Semi-Supervised Learning, Advanced Methods in Sequence Analysis Lectures.
•	Zien A (September-22-2006): Semi-Supervised Support Vector Machines and Application to Spam Filtering, ECML Discovery Challenge Workshop.
•	Zien A , Rätsch G , Mika S , Schölkopf B , Lemmen C , Smola A , Lengauer T und Müller K-R (October-1999): Engineering Support Vector Machine Kernels That Recognize Translation Initiation Sites, German Conference on Bioinformatics (GCB‘99), Heidelberg, Germany.