Computational Diagnostics Group compdiag MPI for Molecular Genetics

Group Members
Dept. Vingron
Group Seminar
NGFN Microarray Data Analysis Resource


See also:  >> Supplements   >> Technical Reports   >> Theses


  • 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.


  • Patient classification
    Lottaz C, Kostka D, Spang R.
    In: Bioinformatics - From Genomes to Therapies. T. Lengauer (Ed), Wiley-VCH, 2007.


  • 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.
  • Computational diagnostics
    Spang R, Markowetz F
    In: Ganten and Ruckpaul (eds.), Encyclopedic Reference of Genomics and Proteomics in Medicine, Springer, 2006.
  • 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 ]
  • Selecting normalization genes for small diagnostic microarrays
    Jäger J, Spang R.
    BMC Bioinformatics, 7:388.
    [ PMID: 16925821 | doi:10.1186/1471-2105-7-388 ]
  • 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 ]
  • 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 ]
  • 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]
  • 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 ]
  • 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 ]



  • 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 ]
  • 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 ]
  • 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]
  • 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 ]
  • Vom Biochip zur maßgeschneiderten Therapie
    Jäger J, Spang R
    BIOforum 6/2004, pp 50-51
  • 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 ]
  • The generalized lognormal distribution as an income distribution
    Kleiber C, Scheid S.
    Bulletin of the International Statistical Institute 60:643-644, 2003
    [ pdf ]
  • 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 ]
  • 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 ]
  • Evaluating the Effect of Perturbations in Reconstructing Network Topologies
    Florian Markowetz and Rainer Spang
    Proceedings of the 3rd International Workshop on Distributed Statistical ComputingDSC 2003 ]
    abstract | pdf | bib entry ]
  • 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 ComputingDSC 2003 ]
    abstract | pdf ]
  • Diagnostic signatures from microarrays: a bioinformatics concept for personalized medicine
    Rainer Spang
    Biosilico Vol. 1, No. 2 May 2003, 64-68
  • 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 ]
  • 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 ]
  • 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 ]
  • 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 ]
  • 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 ]
  • 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 ]
  • 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 ]
  • 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 ]
  • 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 ]
  • 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 ]
  • 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 ]
  • Limits of homology detection by pairwise sequence comparison
    Rainer Spang and Martin Vingron
    Bioinformatics 2001, 17,4, 338-342
    [ PMID: 11301302 ]
  • 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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