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Publications
See also: >> Supplements
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Accepted
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Computational diagnostics with gene expression profiles
Lottaz C,
Kostka D,
Markowetz F,
Spang R.
In: Bioinformatics, Methods in Molecular
Biology. J. Keith (Ed), to be published by Humana Press.
2007
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Patient classification
Lottaz C, Kostka D, Spang R.
In: Bioinformatics - From Genomes to Therapies. T. Lengauer (Ed), Wiley-VCH, 2007.
2006
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Annotation-based Distance Measures for Patient Subgroup
Discovery in Clinical Microarray Studies
Lottaz C, Toedling
J, Spang R In
D. Huson, O. Kohlbacher, A. Lupas, K. Nieselt and A. Zell (eds.)
Lecture Notes on Computer Science,
Proceedings of the German Conference on
Bioinformatics, Tübingen, Germany, Sep 20-22, 2006, 75-91.
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Computational diagnostics
Spang R, Markowetz F
In: Ganten and Ruckpaul (eds.), Encyclopedic Reference
of Genomics and Proteomics in Medicine, Springer, 2006.
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OrderedList - a Bioconductor Package for Detecting
Similarity in Ordered Gene Lists
Lottaz C,
Yang X,
Scheid S,
Spang R
Bioinformatics, 2006, Sep 15;22(18):2315-6
[ PMID:
16844712 |
doi:10.1093/bioinformatics/btl385pdf ]
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Selecting normalization genes for small diagnostic microarrays
Jäger J, Spang R.
BMC Bioinformatics, 7:388.
[ PMID: 16925821 |
doi:10.1186/1471-2105-7-388 ]
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Similarities of ordered gene lists
Yang X, Bentink S, Scheid S, Spang R
In: Journal of Bioinformatics and Computational
Biology. 4(3):693-708
[ doi:10.1142/S0219720006002120 ]
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Expression of late cell cycle genes and an increased
proliferative capacity characterize very early relapse of
childhood acute lymphoblastic leukemia
Kirschner-Schwabe R,
Lottaz C,
Toedling J, Rhein P, Karawajew L, Eckert C, von
Stackelberg A, Ungethüm U, Henze G,
Kostka D,
Spang R,
Hagemeier C, Seeger K.
Clinical Cancer Research, Aug 1;12(15):4553-61.
[ PMID: 16899601 ]
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A biologic definition of Burkitt's lymphoma from transcriptional and genomic profiling
Hummel, Bentink*, Berger*, Klapper*, Wessendorf*, Barth, Bernd, Cogliatti, Dierlamm, Feller, Hansmann, Haralambieva, Harder, Hasenclever, Kühn, Lenze, Lichter, Martin-Subero, Möller, Müller-Hermelink, Ott, Parwaresch, Pott, Rosenwald, Rosolowski, Schwaenen, Stürzenhofecker, Szcepanowski, Trautmann, Wacker, Spang , Löffler, Trümper, Stein, Siebert, for the Molecular Mechanisms in Malignant Lymphomas Network Project of the Deutsche Krebshilfe
New England Journal of Medicine 2006;354:2419-2430. (*These authors contributed equally.)
[Abstract/Full Text]
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Automated In-Silico Detection of Cell Populations in Flow Cytometry Readouts and its Application to
Leukemia Disease Monitoring
Toedling J, Rhein P, Ratei R, Karawajew L, Spang R.
BMC Bioinformatics, 7:282.
[ PMID: 16753055 | doi:10.1186/1471-2105-7-282 ]
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Permutation filtering: A novel concept for significance analysis of large-scale genomic data
Scheid S, Spang R
In: Apostolico A, Guerra C, Istrail S, Pevzner P, and Waterman M (Eds.): Research in Computational Molecular Biology: 10th Annual International Conference, Proceedings of RECOMB 2006, Venice, Italy, April 2-5, 2006, Lecture Notes in Computer Science vol. 3909, Springer, Heidelberg, pp. 338-347.
ISSN: 0302-9743, ISBN: 3-540-33295-2.
[ doi:10.1007/11732990_29 ]
2005
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Traces of molecular disease mechanisms on microarrays
Kostka D, Lottaz C, Spang R.
In: Statistische Methoden in der empirischen Forschung. J. Kauffmann, Schering (Berlin), 2005, 231-236.
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Non-transcriptional pathway features reconstructed from secondary effects of RNA interference
Markowetz F, Bloch J, Spang R
Bioinformatics 2005 21: 4026-4032.
[ PMID: 16159925 | doi:10.1093/bioinformatics/bti662 ]
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Chapter 18 - Microarray data analysis: Differential gene expression
Scheid S, Spang R
In: Ulrike Nuber (ed.), DNA Microarrays, Taylor & Francis Group, UK.
ISBN: 0-415-35866-3.
[ BIOS ]
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A physiogenomic approach to study the regulation of blood pressure
Westhoff TH, Scheid S, Tölle M, Kaynak B, Schmidt S, Zidek W, Sperling S and van der Giet M:
Physiological Genomics 2005 23(1):46-53.
[ PMID: 15942020 | doi:10.1152/physiolgenomics.00077.2005 ]
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stam - a Bioconductor compliant R package for structured analysis of microarray data
Lottaz C, Spang R
BMC Bioinformatics. 2005 Aug 25;6(1):211
[ PMID: 16122395 | doi:10.1186/1471-2105-6-211 ]
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Detecting common gene expression patterns in multiple cancer outcome entities
Yang X, Bentink S, Spang R
Biomedical Microdevices, Sep 2005, 7(3):247-251.
[ PMID: 16133813 | doi:10.1007/s10544-005-3032-7 ]
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Molecular diagnosis: classification, model selection, and performance evaluation
Markowetz F, Spang R
Methods of Information in Medicine 2005, 44: 438-43.
[ PMID: 16113770 ]
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twilight; a Bioconductor package for estimating the local false discovery rate
Scheid S, Spang R
Bioinformatics 2005 21(12):2921-2922.
[ PMID: 15817688 | doi:10.1093/bioinformatics/bti436 ]
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Molecular Decomposition of Complex Clinical Phenotypes using Biologically Structured Analysis of Microarray Data
Lottaz C, Spang R
Bioinformatics 2005 21(9):1971-1978.
[ PMID: 15677704 | doi:10.1093/bioinformatics/bti292 ]
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MACAT - MicroArray Chromosome Analysis Tool
Tödling J, Schmeier S, Heinig M, Georgi B, Röpcke S
Bioinformatics 2005 21(9):1971-1978.
[ PMID: 15572464 | doi:10.1093/bioinformatics/bti183 ]
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Early diagnostic marker panel determination for microarray based clinical studies
Jäger J, Weichenhan D, Ivandic B, Spang R
Statistical Applications in Genetics and Molecular Biology: Vol. 4: No. 1, Article 9.
[ bepress ]
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Correspondence clustering of Dortmund city districts
Scheid S
Weihs C and Gaul W (Eds.) (2005): Classification - The Ubiquitous Challenge. Proceedings of the 28th Annual Conference of the Gesellschaft für Klassifikation, Springer, Heidelberg, p. 690-697.
[ ps ]
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Probabilistic soft interventions in conditional gaussian networks
Markowetz F, Grossmann S, Spang R
Proc. Tenth International Workshop on Artificial Intelligence and Statistics (AISTATS), Jan. 2005
[ pdf | bib entry | conference website ]
2004
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A stochastic downhill search algorithm for estimating the local false discovery rate
Scheid S, Spang R
IEEE Transactions on Computational Biology and Bioinformatics 1(3):98-108, 2004.
[ abstract | pdf | notice ]
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DNA microarray technology and its applications in dermatology
Kunz M, Ibrahim SM, Koczan D, Scheid S, Thiesen HJ, and Gross G.
Experimental Dermatology 13(10):593-606, 2004.
[ PMID:15447719 | doi:10.1111/j.0906-6705.2004.00243.x ]
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Activation of the HIF pathway in childhood ALL, prognostic implications of VEGF
Wellmann S, Guschmann M, Griethe W, Eckert C, von Stackelberg A, Lottaz C, Moderegger E, Einsiedel HG, Eckardt KU, Henze G, Seeger K, Stackelberg A.
Leukemia. 2004 May;18(5):926-33. Erratum in: Leukemia. 2004 Jun;18(6):1164
[ PMID: 15014526 | doi:10.1038/sj.leu.2403332]
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Atherosclerotic plaque smooth muscle cells have a distinct phenotype
Mulvihill ER, Jäger J, Sengupta R, Ruzzo WL, Reimer C, Lukito S, Schwartz SM
Arterioscler. Thromb. Vasc. Biol., Jul 2004; 24: 1283 - 1289.
[ PMID: 15142862 ]
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Vom Biochip zur maßgeschneiderten Therapie
Jäger J, Spang R
BIOforum 6/2004, pp 50-51
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Finding disease specific alterations in the coexpression of genes
Kostka D, Spang R
Bioinformatics 20(Suppl. 1), 2004: i194-i199 (Proceedings of ISMB 2004).
[ PMID: 15262799 | doi:10.1093/bioinformatics/bth909 | erratum ]
2003
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The generalized lognormal distribution as an income distribution
Kleiber C, Scheid S.
Bulletin of the International Statistical Institute 60:643-644, 2003
[ pdf ]
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Differential myocardial gene expression in the development and rescue of murine heart failure
Blaxall BC, Spang R, Rockman HA, Koch WJ.
Physiol Genomics. 2003 Oct 17;15(2):105-14.
[ PMID: 12865503 | Full Text ]
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Acetylcysteine for prevention of contrast nephropathy: meta-analysis
R. Birck, S. Krzossok, F. Markowetz, P. Schnülle, F. J. van der Woude and C. Braun
Lancet 2003, Volume 362, Issue 9384, Page 598
[ PMID: 12944058 | doi:10.1016/S0140-6736(03)14189-X | bib entry ]
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Evaluating the Effect of Perturbations in Reconstructing Network Topologies
Florian Markowetz and Rainer Spang
Proceedings of the 3rd International Workshop on Distributed Statistical Computing [ DSC 2003 ]
[ abstract | pdf | bib entry ]
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A False Discovery Rate Approach to Separate the Score Distributions of Induced and Non-induced Genes
Stefanie Scheid and Rainer Spang
Proceedings of the 3rd International Workshop on Distributed Statistical Computing [ DSC 2003 ]
[ abstract | pdf ]
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Diagnostic signatures from microarrays: a bioinformatics concept for personalized medicine
Rainer Spang
Biosilico Vol. 1, No. 2 May 2003, 64-68
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Expression profiling of human idiopathic dilated cardiomyopathy
Rafal Grzeskowiak, Henning Witt, Mario Drungowski, Rolf Thermann, Steffen Hennig, Andreas Perrot, Karl J. Osterziel, Dirk Klingbiel, Stefanie Scheid, Rainer Spang, Hans Lehrach, and Patricia Ruiz
Cardiovasc Res. 2003 Aug 1;59(2):400-11.
[ PMID:12909323 | doi:10.1016/S0008-6363(03)00426-7 ]
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Support Vector Machines for Protein Fold Class Prediction
F. Markowetz, L. Edler, and M. Vingron
Biometrical Journal 45 (2003) 3, 377-389
[ doi:10.1002/bimj.200390019 | bib entry ]
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Improved Gene Selection for Classification of Microarrays
J. Jäger, R. Sengupta and W.L. Ruzzo
Biocomputing - Proceedings of the 2003 Pacific Symposium, 53-64
[ pdf ]
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Modeling Sequencing Errors by Combining Hidden Markov Models
Claudio Lottaz,
Christian Iseli, C. Victor Jongeneel and Philipp Bucher
Bioinformatics, vol. 19, suppl. 2, pages 103-112, (ECCB'03, Paris, France)
[ PMID: 14534179 | abstract | pdf ]
2002
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A Novel Approach to Remote Homology Detection: Jumping Alignments
Rainer Spang, Marc Rehmsmeier and Jens Stoye
Journal of Computational Biology, Volume 9, Number 5, 747-760, 2002
[ PMID: 12487762 | doi:10.1089/106652702761034172 ]
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Estimating Amino Acid Substitution Models: A Comparison of Dayhoff's Estimator, the Resolvent Approach and a Maximum Likelihood Method
Tobias Müller, Rainer Spang and Martin Vingron
Mol. Biol. Evol.19(1), 8-13 2002
[ PMID: 11752185 ]
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Prediction and uncertainty in the analysis of gene expression profiles
Rainer Spang, Carrie Blanchette, Harry Zuzan, Jeffrey R. Marks, Joseph Nevins and Mike West
In Silico Biol. 2002;2(3):369-81.
[ PMID:12542420 | online publication ]
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Class discovery in gene expression data: characterizing splits by support vector machines
F. Markowetz and A. von Heydebreck
Proceedings of the 26th Annual Conference of the Gesellschaft für Klassifikation 2002, 662-669
[ abstract | ps ]
2001
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Predicting the clinical status of human breast cancer by using gene expression profiles
West M, Blanchette C, Dressman H, Huang E, Ishida S, Rainer Spang, Zuzan H, Olson JA Jr, Marks JR, Nevins JR.
Proc Natl Acad Sci U S A. 2001 Sep 25;98(20):11462-7
[ PMID: 11562467 | doi:10.1073/pnas.201162998 ]
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Role for E2F in control of both DNA replication and mitotic functions as revealed from DNA microarray analysis
Ishida S, Huang E, Zuzan H, Rainer Spang, Leone G, West M, Nevins J.R.
Mol Cell Biol. 2001 Jul;21(14):4684-99
[ PMID: 11416145 | doi:10.1128/MCB.21.14.4684-4699.2001 ]
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DNA microarray data analysis and regression modeling for genetic expression profiling
Mike West, Joseph R Nevins, Jeffrey R Marks, Rainer Spang, Carrie Blanchette & Harry Zuzan
ISDS Discussion Paper 00-15 (submitted for publication)
[ pdf ]
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Limits of homology detection by pairwise sequence comparison
Rainer Spang and Martin Vingron
Bioinformatics 2001, 17,4, 338-342
[ PMID: 11301302 ]
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Sequence Database Search Using Jumping Alignments
Rainer Spang, Marc Rehmsmeier and Jens Stoye
Proceedings of the Eighth International Conference on Intelligent systems for Molecular Biology, AAAI Press, Menlo Park, CA, 2000, 367-375.
[ PMID: 10977097 | pdf ]
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