Publikationen

Zurück zur Homepage A.-L. Boulesteix

Eingereichte Artikel (3)

1. A.-L. Boulesteix, S. Janitza, J. Kruppa, I. König, 2011. Random forests for bioinformatics applications. Submitted.
2. C. Bernau, A.-L. Boulesteix, J. Knaus, 2011. Application of microarray analysis procedures on cluster and cloud platforms. Submitted.
3. C. Bernau, T. Augustin, A.-L. Boulesteix, 2011. Correcting the optimally selected resampling-based error rate: A smooth analytical alternative to nested cross-validation. Technical Report 105, Department of  Statistics, LMU. In Revision.

Referierte Publikationen (in internationalen Zeitschriften: 46, in internationalen Tagungsbänden: 3)

1. A.-L. Boulesteix, A. Richter, C. Bernau, 2011. Complexity selection with cross-validation for lasso and sparse partial least squares using high-dimensional data. Proceedings of the 35th Annual Conference of the German Classification Society (conditionally accepted).
2. V. Guillemot, M. Jelizarow, A. Tenenhaus, A.-L. Boulesteix, 2011. SHrinkage covariance estimation incorporating prior biological knowledge with applications to high-dimensional data. Technical Report 107, Department of Statistics, LMU. Proceedings of the 58th ISI World Statistics Congress.
3. A.-L. Boulesteix, A. Bender, J. Lorenzo Bermejo, C. Strobl, 2011. Random forest Gini importance favors SNPs with large minor allele frequency. Technical Report 106, Department of Statistics, LMU. Briefings in Bioinformatics doi: 10.1093/bib/bbr053.
4. W. Sauerbrei, A.-L. Boulesteix, H. Binder, 2011. Stability investigations of multivariable regression models derived from low and high dimensional data. Journal of Biopharmaceutical Statistics 21:1206-1231.
5. A.C. Pickhard, J. Margraf, A. Knopf, T. Stark, G. Piontek, C. Beck, A.-L. Boulesteix, E.Q. Scherer, S. Pigorsch, J. Schlegel, W. Arnold, R. Reiter, 2011. Inhibition of Radiation Induced Migration of Human Head and Neck Squamous Cell Carcinoma by Blocking EGF Receptor Pathways. BMC Cancer 11:388.
6. M. Calle, V. Urrea, A.-L. Boulesteix, N. Malats, 2011. AUC-RF: A new strategy for genomic profiling with Random Forest. Human Heredity 72:121-132.
7. T. Herold, V. Jurinovic, K.H. Metzeler, A.-L. Boulesteix, M. Bergmann, T. Seiler, M. Mulaw, S. Thoene, A. Dufour, Z. Pasalic, M. Schmidberger, M. Schmidt, S. Schneider, P.M. Kakadia, M. Feuring-Buske, J. Braess, K. Spiekermann, U. Mansmann, W. Hiddemann, C. Buske, S.K. Bohlander. An eight-gene expression signature for the prediction of survival and time to treatment in chronic lymphocytic leukemia. Leukemia 25:1639-1645..
8. A.-L. Boulesteix, V. Guillemot, W. Sauerbrei, 2011. Use of pre-transformation to cope with extreme values in important candidate features. Biometrical Journal 53:673–688.
9. A.-L. Boulesteix, 2011. Editorial. Briefings in Bioinformatics 12:187-188.
10. A.-L. Boulesteix, W. Sauerbrei, 2011. Added predictive value of high-throughput molecular data to clinical data, and its validation. Briefings in Bioinformatics 12:215-229.
11. M. Jelizarow, V. Guillemot, A. Tenenhaus, K. Strimmer, A.-L. Boulesteix, 2010. Over-optimism in bioinformatics: an illustration. pdf. Bioinformatics 26:1990-1998.
12. C. Bernau, A.-L. Boulesteix, 2010. Variable selection and parameter tuning in high-dimensional prediction. Technical Report 76, Department of Statistics, LMU. COMPSTAT 2010.
13. A.-L. Boulesteix, T. Hothorn, 2010. Testing the additional predictive value of high-dimensional data. BMC Bioinformatics 11:78.
14. S. Eifert, H. Mair, A.-L. Boulesteix, E. Kilian, M. Adamczak, B. Reichart, P. Lamm, 2010. Mid term outcomes of patients with PCI prior to CABG in comparison to patients with primary CABG. Vascular Health Risk Management 6:495-501.
15. A.-L. Boulesteix, 2010. Over-optimism in bioinformatics research. pdf. Bioinformatics 26:437-439.
16. D. Doll, L. Keller, M. Maak, A.-L. Boulesteix, J. Siewert, B. Holzmann, K.-P. Jansen, 2010. Differential expression of the chemokines GRO-2, GRO-3 and Interleukin-8 in colon cancer and their impact on metastatic disease and survival. International Journal of Colorectal Disease 25:573-581.
17. A.-L. Boulesteix, C. Strobl, 2009. Optimal classifier selection and negative bias in error rate estimation: An empirical study on high-dimensional prediction. BMC Medical Research Methodology 9:85.
18. N. Krämer, J. Schäfer, A.-L. Boulesteix, 2009. Regularized estimation of large-scale gene association networks using graphical Gaussian models. BMC Bioinformatics 10:384.
19. A.-L. Boulesteix, M. Slawski, 2009. Stability and aggregation of ranked gene lists. pdf. Briefings in Bioinformatics 10:556-568.
20. M. Slawski, M. Daumer, A.-L. Boulesteix, 2008. CMA - A comprehensive Bioconductor package for supervised classification with high dimensional data. pdf. BMC Bioinformatics 9: 439. 
21. A.-L. Boulesteix, C. Porzelius, M. Daumer, 2008. Microarray-based classification and clinical predictors: On combined classifiers and additional predictive value. pdf. reprint. Bioinformatics 24:1698-1706.
22. W. van Wieringen, D. Kun, R. Hampel, A.-L. Boulesteix, 2009. Survival prediction using gene expression data: a review and comparison. pdf. Computational Statistics and Data Analysis  53:1590-1603.
23. C. Strobl, A.-L. Boulesteix, T. Kneib, T. Augustin, A. Zeileis, 2008. Conditional variable importance for random forests. pdf. BMC Bioinformatics 9:307.
24. N. Krämer, A.-L. Boulesteix and G. Tutz, 2008. Penalized partial least squares with applications to B-splines and functional data. pdf. Chemometrics and Intelligent Laboratory Systems 94:60-69.(accepted).
25. R. Reiter, P. Gais, M.K. Steuer-Vogt, A.-L. Boulesteix, T. Deutschle, R. Hampel, S. Wagenpfeil, S. Rausen, A. Walch, K. Bink, U. Jutting, F. Neff, W. Arnold, H. Hofler, A. Pickhard, 2009. Centrosome abnormalities in head and neck squamous cell carcinoma (HNSCC). Acta Otolaryngologica 129:205-213.
26. A.-L. Boulesteix, A. Kondylis, N. Krämer, 2008. Invited comment on: "Augmenting the bootstrap to analyze high dimensional genomic data" by Tyekucheva and Chiaromonte. pdf. TEST 17:31-35.
27. T. Wichard, S. Poulet, A.-L. Boulesteix, J.-B. Ledoux, B. Lebreton, J. Marchetti, G. Pohnert, 2008. Influence of diatoms on copepod reproduction. II. Uncorrelated effects of diatom-derived alpha, beta, gamma, delta-unsaturated aldehydes and polyunsaturated fatty acids on Calanus helgolandicus in the field. Progress in Oceanography 77:30-44 .
28. A.-L. Boulesteix, C. Strobl, T. Augustin, M. Daumer, 2008. Evaluating microarray-based classifiers: an overview. pdf. Cancer Informatics 6:77-97.
29. C. Rimkus, J. Friederichs, A.-L. Boulesteix, J. Mages, K. Becker, H. Nekarda, R. Rosenberg, K.P. Janssen, J.R. Siewert, 2008. Microarray-based prediction of tumor response to neoadjuvant radiochemotherapy of patients with locally advanced rectal cancer. Clinical Gastroenterology and Hepatology 6:53-61.
30. D. Doll, J. Friederichs, A.-L. Boulesteix, W. Düsel, F. Fend, S. Petersen, 2008. Surgery for asymptomatic pilonidal sinus disease. International Journal of Colorectal Disease 23:839-844.
31. D. Doll, J. Friederichs, H. Dettmann, A.-L. Boulesteix, W. Düsel, S. Petersen, 2008. Time and rate of sinus formation in pilonidal sinus disease. International Journal of Colorectal Disease 23:359-364.
32. D. Doll, A. Novotny, R. Rothe, K. Wietelmann, A.-L. Boulesteix, W. Düsel, S. Petersen, 2008. Methylene Blue halves the long term recurrence rate in acute pilonidal sinus disease. International Journal of Colorectal Disease 23:181-187.
33. W. Dietrich, R. Busley, A.-L. Boulesteix, 2008. Effects of aprotinin dosage on renal function: an analysis of 8,548 cardiac surgical patients treated with different dosages of aprotinin. Anesthesiology108:189-198.
34. A.-L. Boulesteix, C. Strobl, S. Weidinger, H.E. Wichmann, S. Wagenpfeil, 2007. Multiple testing for SNP-SNP interactions. pdf. Statistical Applications in Genetics and Molecular Biology 6(1):37.
35. A.-L. Boulesteix and C. Strobl, 2007. Maximally selected chi-square statistics and non-monotonic associations: an exact approach based on two cutpoints. pdf (preprint), Computational Statistics and Data Analysis 51(12):6295-6306.
36. C. Strobl, A.-L. Boulesteix and T. Augustin, 2007. Unbiased split selection for classification trees based on the Gini index. pdf. Computational Statistics and Data Analysis 52:483-501.
37. A.-L. Boulesteix and K. Strimmer, 2007. Partial Least Squares: A versatile tool for the analysis of high-dimensional genomic data. pdf. Briefings in Bioinformatics 8(1):32-44.
38. A.-L. Boulesteix, 2007. WilcoxCV: An R package for fast variable selection in cross-validation. pdf (preprint), Bioinformatics 23: 1702-1704.
39. W. Dietrich, A. Ebell, R. Busley, A.-L. Boulesteix, 2007. Aprotinin and Anaphylaxis - Analysis of 12403 Exposures to Aprotinin in Cardiac Surgery. The Annals of Thoracic Surgery 84:1144-1150.
40. R. Napieralski, K. Ott, M. Kremer, K. Becker, A.-L. Boulesteix, F. Lordick, J.R. Siewert, H. Höfler, G. Keller, 2007. Methylation of Tumor-Related Genes in Neoadjuvant-Treated Gastric Cancer: Relation to Therapy Response and Clinicopathologic and Molecular Features. Clinical Cancer Research 13(17):5095-5102.
41. C. Strobl, A.-L. Boulesteix, A. Zeileis and T. Hothorn, 2007. Bias in random forest variable importance measures: Illustrations, sources and a solution. pdf. BMC Bioinformatics 8:25. 
42. A.-L. Boulesteix, 2006. Reader's reaction to 'Dimension reduction for classification with gene expression microarray data' by Dai et al (2006), Statistical Applications in Genetics and Molecular Biology 5(1), Article 16, pdf.
43. A.L. Boulesteix, 2006. Maximally selected chi-square statistics and binary splits of nominal variables, pdf, Biometrical Journal 48:838-848.
44. A.-L. Boulesteix, 2006. Maximimally selected chi-square statistics for ordinal variables, pdf, Biometrical Journal 48:451-462.
45. A.-L. Boulesteix and G. Tutz, 2006. Identification of Interaction Patterns and Classification with Applications to Microarray Data, pdf (preprint), Computational Statistics and Data Analysis 50: 783-802.
46. A.-L. Boulesteix and K. Strimmer, 2005. Predicting Transcription Factor Activities from Combined Analysis of Microarray and ChIP Data: A Partial Least Squares Approach, Theoretical Biology and Medical Modelling 2:23, pdf.
47. S. Hiendleder, S. Bauersachs, A.-L. Boulesteix, H. Blum, G. Arnold, T. Fröhlich and E. Wolf, 2005. Functional genomics: tools for improving farm animal health and welfare, Rev Sci Tech. 24(1): 354-377, "Biotechnology and animal health", pdf.
48. A.-L. Boulesteix, 2004. PLS Dimension Reduction for Classification with Microarray Data. pdf (preprint). Statistical Applications in Genetics and Molecular Biology 3(1), Article 33.
49. A.-L. Boulesteix, G. Tutz and K. Strimmer, 2003. A CART-based approach to discover emerging patterns in microarray data. Bioinformatics 19: 2465-2472, pdf.

Andere Publikationen

1. S. Pildner von Steinburg, D. Chronas, A.-L. Boulesteix, N. Lack, K.T.M. Schneider, 2007. Risikofaktoren für Frühgeburtlichkeit - eine multivariate Analyse der bayrischen Perinataldaten aus 10 Jahren. Zeitschrift für Geburtshilfe und Neonatologie:211.
2. M. Daumer, M. Scholz, A.-L. Boulesteix, S. Pildner von Steinburg, S. Schiermeier, W. Hatzmann, K.T.M. Schneider, 2007. The normal fetal heart rate study: Analysis plan. Nature Precedings, doi:10.1038/npre.2007.980.1.
3. N. Henningsen, K. Ott, K. Becker, A.-L. Boulesteix, F. Lordick, J.R. Siewert, H. Hofler, G. Keller, 2007. Polymorphisms in the nucleotide excision repair genes ERCC1 and ERCC2 and association with response and prognosis in neoadjuvant treated gastric cancer patients. Pathology Research and Practice 203:254-259.
4. A.L. Boulesteix, V. Hösel and V. Liebscher, 2007. Stochastic Modeling for the COMET-assay. Journal of Concrete and Applicable Mathematics 5(1):53:75.
5. A.-L. Boulesteix, 2005. A note on between-group PCA, International Journal of Pure and Applied Mathematics 19: 359-366.

Software

1. A.-L. Boulesteix, T. Hothorn, globalboosttest R package. Testing the additional predictive value of high-dimensional data.
2. A.-L. Boulesteix, MAclinical R package. Class prediction based on microarray data and clinical parameters.
3. M. Slawski and A.-L. Boulesteix, The GeneSelector Bioconductor package. The term 'GeneSelector' refers to a filter selecting those genes which are consistently identified as differentially expressed using various statistical procedures. 'Selected' genes are those present at the top of the list in various featured ranking methods (currently 15). In addition, the stability of the findings can be taken in account in the final ranking by examining perturbed versions of the original data set, e.g. by leaving samples, swapping class labels, generating bootstrap replicates or adding noise.
4. M. Slawski, C. Bernau and A.-L. Boulesteix, The CMA Bioconductor package. This package provides a comprehensive collection of various microarray-based classification algorithms both from machine learning and statistics. Variable selection, hyperparameter tuning, evaluation and comparison can be performed in a combined manner or stepwise in a user-friendly environment.
5. N. Kraemer and A.-L. Boulesteix, ppls R package. Penalized partial least squares.
6. A.-L. Boulesteix, WilcoxCV R package. Wilcoxon-based variable selection in cross-validation.
7. A.-L. Boulesteix, SNPmaxsel R package. Maximally selected statistics for SNP data.
8. A.-L. Boulesteix, exactmaxsel R package. Maximally selected statistics for binary response variables - Exact methods.
9. A.-L. Boulesteix, Sophie Lambert-Lacroix, Julie Peyre and Korbinian Strimmer, plsgenomics R package. PLS analyses for genomics.

Ausgewählte Vorträge
Die Vortragsfolien können auf Anfrage zugeschickt werden.

Critical issues and developments in high-dimensional classification in biomedical research (invited talk at the Journées de Statistique SfdS, Tunis, May 2011)

On cross-validation with high-dimensional data in small sample settings (invited talk at the University of Ulm, April 2011)

On cross-validation with high-dimensional biological data in small sample settings (invited talk at the University of Ulm, December 2010)

Critical issues and developments in microarray-based prediction (invited talk at Journees de Statistique, Rennes, France, October 2010)

Over-optimism in biostatistics and bioinformatics (talk at the Workshop on Validation in Statistics and Machine Learning, Berlin, October 2010)

Critical issues and developments in microarray-based prediction'' (plenary talk at the CLADAG/GfKl Conference, Florence, Italy, September 2010)

Variable selection and parameter tuning in high-dimensional prediction (talk at the COMPSTAT 2010 Conference, Paris, France, August 2010)

Over-optimism in biostatistics and bioinformatics (talk at the COMPSTAT 2010 Conference, Paris, France, August 2010)

Over-optimism in biostatistics and bioinformatics (talk at the 34. Annual Conference of the GfKl, Karlsruhe, July 2010)

Testing the additional predictive value of high-dimensional molecular data (talk at the DagStat Conference, Dortmund, March 2010)

PLS for prediction with high-dimensional -omics data: overview and critical issues (invited talk at the ESSEC-Supelec Workshop on PLS Developments, Gif-sur-Yvette, France, May 2010)

Microarray-based outcome prediction, overoptimism and clinical usefulness (invited talk at the University of Stuttgart, November 2009).

Critical issues in prediction with high-dimensional data (invited talk at the University of Heidelberg, November 2009).

Detecting higher-order SNP-SNP interactions (invited talk at the Mini-Conference "Aspects of Statistical Genetics", University of Liege (Belgium), September 2008).

Statistical methods for high-dimensional data: variable selection and dimension reduction (invited lecture at the MC-GARD Workshop "Genome Bioinformatic Techniques", University of Minho (Portugal), September 2008).

Multiple comparisons and bias in high dimensional analysis (invited talk at the Technical University of Dortmund, June 2008).

Additional predictive power of microarray data (Lifestat Conference, Munich, March 2008).

Additional predictive power of microarray data and hybrid classifiers using clinical and molecular predictors (Agroparistech, Paris, February 2008).

Hybrid classifiers based on clinical predictors and high-dimensional microarray data using PLS and random forests (invited talk at the University of Freiburg, January 2008).

Additional predictive power of microarray data and hybrid classifiers using clinical and molecular predictors (invited talk at the LMU Munich, December 2007).

Microarray-based prediction with emphasis on clinical parameters: a PLS approach (invited talk at the PLS'07 Conference, September 2007).

Challenges in microarray-based class prediction (invited talk at the University of Goettingen, August 2007).

Issues in microarray-based class prediction and variable selection (Invited talk at the DKFZ Heidelberg, July 2007).

Selection bias, multiple testing and maximally selected statistics (invited talk at the Université Paul Sabatier, Toulouse, April 2007).

Multiple testing for SNP-SNP interactions: a flexible asymptotic framework (invited talk at the GSF, Neuherberg, April 2007).

Partial Least Squares Approaches for Gene Expression Data Analysis (talk at the 30th Annual Conference of the German Classification Society, Berlin, 8-10 March 2006).

PLS for microarray data analysis: a survey (invited talk at the Workshop on Statistical Methods for post-genomic data, Toulouse, 30-31 March 2006).

Arbeiten

A.-L. Boulesteix, 2005. phD Thesis: Dimension Reduction and Classification with high-dimensional microarray data, pdf.

A.-L. Boulesteix, 2001. Mathematische Modellierung und Statistik für das COMET-assay (Master thesis at the University of Stuttgart, Department of Mathematics A)