Rainer Spang

Address

Institute for Functional Genomics
University of Regensburg
Josef Engertstr. 9
93053 Regensburg, Germany

Tel:	+49 941 943 5053
Fax:	+49 941 943 5020
Email:	rainer.spang@klinik.uni-regensburg.de

Research Interests:

• Molecular disease mechanisms in cancer
  
• Hight throughput intervention data
  
• Bioinformatics, Machine Learning and Statistics
  

Short Vita:

• 2007
  Professor of Bioinformatics at the University of Regensburg
• 2001 - 2006
  Head of the Computational Diagnostics Group at the Max Planck Institute for Molecular Genetics, Berlin
• 1999
  PhD in biology from the University of Bonn and the German Cancer Research Center, Heidelberg
• 1994
  Diploma in mathematics from the University of Bonn

Publications:

• 2009
  
  • Integrative Normalization and Comparative Analysis for Metabolic Fingerprinting by Comprehensive Two-Dimensional Gas Chromatography−Time-of-Flight Mass Spectrometry
    Martin F. Almstetter, Inka J. Appel, Michael A. Gruber, Claudio Lottaz, Birgit Timischl, Rainer Spang, Katja Dettmer and Peter J. Oefner
    Analytical Chemistry 2009 81 (14): 5731-5739
    pmid: 19522528     pdf    
  • Modeling the temporal interplay of molecular signalling and gene expression by using dynamic nested effects models
    Anchang B, Sadeh MJ, Jacob J, Tresch A, Vlad MO, Oefner PJ, Spang R
    PNAS 2009 106 (16): 6447-6452
    pmid: 19329492     doi: doi:10.1073/pnas.0809822106     pdf    
  • Kinetic laws, phase - phase expansions, renormalization group, and INR calibration
    Vlad MO, Corlan AD, Moran F, Spang R, Oefner PJ, Ross J
    PNAS 2009 106 (16): 6465-6470
    pmid: 19366671     doi: doi:10.1073/pnas.0809855106     pdf    
  • New insights into the biology and origin of mature aggressive B-cell lymphomas by combined epigenomic, genomic, and transcriptional profiling.
    Martin-Subero JI, Kreuz M, Bibikova M, Bentink S, Ammerpohl O, Wickham-Garcia E, Rosolowski M, Richter J, Lopez-Serra L, Ballestar E, Berger H, Agirre X, Bernd HW, Calvanese V, Cogliatti SB, Drexler HG, Fan JB, Fraga MF, Hansmann ML, Hummel M, Klapper W, Korn B, Küppers R, Macleod RA, Möller P, Ott G, Pott C, Prosper F, Rosenwald A, Schwaenen C, Schübeler D, Seifert M, Stürzenhofecker B, Weber M, Wessendorf S, Loeffler M, Trümper L, Stein H, Spang R, Esteller M, Barker D, Hasenclever D, Siebert R; Molecular Mechanisms in Malignant Lymphomas Network Project of the Deutsche Krebshilfe
    Blood 2009 113 (11): 2488-2497
    pmid: 19075189    
  • Microarray-based genomic profiling reveals novel genomic aberrations in follicular lymphoma which associate with patient survival and gene expression status
    Schwaenen C, Viardot A, Berger H, Barth TF, Bentink S, Döhner H, Enz M, Feller AC, Hansmann ML, Hummel M, Kestler HA, Klapper W, Kreuz M, Lenze D, Loeffler M, Möller P, Müller-Hermelink HK, Ott G, Rosolowski M, Rosenwald A, Ruf S, Siebert R, Spang R, Stein H, Truemper L, Lichter P, Bentz M, Wessendorf S; for the Molecular Mechanisms in Malignant Lymphomas Network Project of the Deutsche Krebshilfe
    Genes Chromosomes Cancer 2009 48 (1): 39-54
    pmid: 18828156    
• 2008
  
  • Analyzing gene perturbation screens with nested effects models in R and bioconductor
    Fröhlich H, Beißbarth T, Tresch A, Kostka D, Jacob J, Spang R, Markowetz F
    Bioinformatics 2008 24 (21): 2549-2550
    doi: doi:10.1093/bioinformatics/btn446    
  • Pathway activation patterns in diffuse large B-cell lymphomas
    Stefan Bentink, Swen Wessendorf, Carsten Schwaenen, Maciej Rosolowski, Wolfram Klapper, Andreas Rosenwald, German Ott, Alison H Banham, Hilmar Berger, Alfred C Feller, Martin-Leo Hansmann, Dirk Hasenclever, Michael Hummel, Dido Lenze, Peter Möller, Benjamin Stuerzenhofecker, Markus Loeffler, Lorenz Trümper, Harald Stein, Reiner Siebert, and Rainer Spang for the Molecular Mechanisms in Malignant Lymphomas Network Project of the Deutsche Krebshilfe
    Leukemia 2008 22 (9): 1746-1754
    pmid: 18580954     doi: doi:10.1038/leu.2008.166    
  • Molecular profiling of pediatric mature B-cell lymphoma treated in population-based prospective clinical trials
    Klapper W, Szczepanowski M, Burkhardt B, Berger H, Rosolowski M, Bentink S, Schwaenen C, Wessendorf S, Spang R, Moller P, Hansmann ML, Bernd HW, Ott G, Hummel M, Stein H, Loeffler M, Trumper L, Zimmermann M, Reiter A, Siebert R
    Blood 2008
    pmid: 18509088     doi: DOI 10.1182/blood-2008-01-136465    
  • CD30-induced signaling is absent in Hodgkin's cells but present in anaplastic large cell lymphoma cells
    Hirsch B, Hummel M, Bentink S, Fouladi F, Spang R, Zollinger R, Stein H, Dürkop H.
    American Journal of Pathology 2008 172 (2): 510-520
    pmid: 18187570     doi: doi:10.3324/haematol.12057    
  • Gain of chromosome region 18q21 including the MALT1 gene is associated with the activated B-cell-like gene expression subtype and increased BCL2 gene dosage and protein expression in diffuse large B-cell lymphoma
    J Dierlamm, E M Murga Penas, S Bentink, S Wessendorf, H Berger, M Hummel, W Klapper, D Lenze, A Rosenwald, E Haralambieva, G Ott, S B Cogliatti, P Möller, C Schwaenen, H Stein, M Löffler, R Spang, L Trümper, R Siebert
    Haematologica 2008
    doi: doi:10.3324/haematol.12057    
  • Detecting hierarchical structure in molecular characteristics of disease using transitive approximations of
    Jacob J, Jentsch M, Kostka D, Bentink S, Spang R
    Bioinformatics 2008 24 (7): 995-1001
    pmid: 18285370    
  • CD30-Induced Signaling Is Absent in Hodgkin's Cells but Present in Anaplastic Large Cell Lymphoma Cells
    Hirsch B, Hummel M, Bentink S, Fouladi F, Spang R, Zollinger R, Stein H, Dürkop H
    American Journal of Pathology 2008 172 (2): 510-520
    pmid: 18187570     doi: DOI: 10.2353/ajpath.2008.070858    
  • Microarray Based Diagnosis Profits from Better Documentation of Gene Expression Signatures
    Kostka D., Spang R.
    PLoS Computational Biology 2008 4 (2)
    pmid: 18282081    
  • Computational diagnostics using gene expression profiles
    Lottaz C, Kostka D, Markowetz F, Spang R
    Bioinformatics, Methods in Molecular Biology. J. Keith (Ed), to be published by Humana Press 2008 2 (15): 281-326
    pmid: 18712310    
• 2007
  
  • Ataxia telangiectasia-mutated gene is a possible biomarker for discrimination of infiltrative deep penetrating nevi and metastatic vertical growth phase melanoma
    Roesch A, Becker B, Bentink S, Spang R, Vogl A, Hagen I, Landthaler M, Vogt T
    Cancer Epidemiol Biomarkers Prev 2007 16 (11): 2486-2490
    pmid: 18006941    
  • Gene expression profiling suggests primary central nervous system lymphomas to be derived from a late germinal center B cell
    Montesinos-Rongen M., Brunn A., Bentink S., Basso K., Lim WK., Klapper W., Schaller C., Reifenberger G., Wiestler O., Spang R., Dalla-Favera R., Siebert R., Deckert M.
    Leukemia 2007
    pmid: 17989719    
  • Inferring cellular networks - a review
    Markowetz, F, Spang R
    BMC Bioinformatics 2007 8 (Suppl): 6:S5
    pmid: 17903286     pdf    
  • Annotation-based distance measures for patient subgroup discovery in clinical microarray studies
    Lottaz C, Toedling J, and Spang R
    Bioinformatics 2007 23 (17): 2256-2264
    pmid: 17586546     doi: doi:10.1093/bioinformatics/btm322     pdf    
  • Nested Effects Models for High-Dimensional Phenotyping
    Markowetz F, Kostka D, Troyanskaja O and Spang R,
    Bioinformatics, ISMB 2007 23 (13): 305-312
    pmid: 17646311     pdf    
  • Compensating for unknown confounders in microarray data analysis using filtered permutations
    Scheid S and Spang R.
    Journal of Computational Biology 2007
    
  • Gene expression shift towards normal B cells, decreasedproliferative capacity and distinct surface receptorscharacterize leukemic blasts persisting during inductiontherapy in childhood acute lymphoblastic leukemia
    Rhein P, Scheid S, Ratei R, Hagemeier C, Seeger K, Kirschner-Schwabe R, Moericke A, Schrappe M, Spang R, Ludwig W-D and Karawajew L
    Leukemia 2007 March (1)
    pmid: 17330098     doi: 10.1038/sj.leu.2404613    
  • Gene Expression Signatures for Tumor Progression, TumorSubtype, and Tumor Thickness in Laser-Microdissected MelanomaTissues
    Jaeger J, Koczan D, Thiesen HJ, Ibrahim SM, Gross G, Spang R and Kunz M.
    Clinical Cancer Research 2007 13: 806-815
    pmid: 17289871     doi: 10.1158/1078-0432.CCR-06-1820     pdf    
  • Patient classification
    Lottaz C, Kostka D, Spang R.
    Bioinformatics - From Genomes to Therapies. T. Lengauer (Ed), Wiley-VCH 2007
    
• 2006
  
  • Annotation-based Distance Measures for Patient SubgroupDiscovery in Clinical Microarray Studies
    Lottaz C, Toedling J, Spang R
    Lecture Notes on Computer Science, Proceedings of the German Conference on Bioinformatics 2006: 75-91
    
  • Computational diagnostics
    Spang R, Markowetz F
    Ganten and Ruckpaul (eds.), Encyclopedic Reference of Genomics and Proteomics in Medicine, Springer 2006
    
  • OrderedList - a Bioconductor Package for DetectingSimilarity in Ordered Gene Lists
    Lottaz C, Yang X, Scheid S, Spang R
    Bioinformatics 2006 22 (18): 2315-2316
    pmid: 16844712     doi: 10.1093/bioinformatics/btl385     pdf    
  • Selecting normalization genes for small diagnostic microarrays
    Jäger J, Spang R
    BMC Bioinformatics 2006 7: 388
    pmid: 16925821     doi: 10.1186/1471-2105-7-388    
  • Similarities of ordered gene lists
    Yang X, Bentink S, Scheid S, Spang R
    Journal of Bioinformatics and Computational Biology. 2006 4 (3): 693-708
    doi: 10.1142/S0219720006002120    
  • Expression of late cell cycle genes and an increasedproliferative capacity characterize very early relapse ofchildhood 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 2006 12 (15): 4553-4561
    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 (^*These authors contributed equally.)
    New England Journal of Medicine 2006 354: 2419-2430
    pdf    
  • Automated In-Silico Detection of Cell Populations in Flow Cytometry Readouts and its Application toLeukemia Disease Monitoring
    Toedling J, Rhein P, Ratei R, Karawajew L, Spang R
    BMC Bioinformatics 2006 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
    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, Lecture Notes in Computer Science vol. 3909, Springer, Heidelberg, pp. 338-347 2006
    doi: 10.1007/11732990_29    
• 2005
  
  • Traces of molecular disease mechanisms on microarrays
    Kostka D, Lottaz C, Spang R.
    Statistische Methoden in der empirischen Forschung. J. Kauffmann, Schering (Berlin) 2005 (231-236)
    
  • 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    
  • Chapter 18 - Microarray data analysis: Differential gene expression
    Scheid S, Spang R
    Ulrike Nuber (ed.), DNA Microarrays, Taylor & Francis Group, UK. 2005
    
  • stam - a Bioconductor compliant R package for structured analysis of microarray data
    Lottaz C, Spang R
    BMC Bioinformatics 2005 6 (1): 211
    pmid: 16122395     doi: 10.1186/1471-2105-6-211    
  • Detecting common gene expression patterns in multiple cancer outcome entities
    Yang X, Bentink S, Spang R
    Biomedical Microdevices 2005 7 (3): 247-251
    pmid: 16133813     doi: 10.1007/s10544-005-3032-7    
  • Molecular diagnosis: classification, model selection, and performance evaluation
    Markowetz F, Spang R
    Methods of Information in Medicine 2005 44: 438-443
    pmid: 16113770    
  • 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    
  • 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    
  • 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 2005 4 (1)
    pdf    
  • Probabilistic soft interventions in conditional gaussian networks
    Markowetz F, Grossmann S, Spang R
    Proc. Tenth International Workshop on Artificial Intelligence and Statistics (AISTATS) 2005
    
• 2004
  
  • A stochastic downhill search algorithm for estimating the local false discovery rate
    Scheid S, Spang R
    IEEE Transactions on Computational Biology and Bioinformatics 2004 1 (3): 98-108
    pdf    
  • Vom Biochip zur maß;geschneiderten Therapie
    Jäger J, Spang R
    BIOforum 2004 6: 50-51
    
  • Finding disease specific alterations in the coexpression of genes
    Kostka D, Spang R
    Bioinformatics 2004 20 (Suppl. 1): i194-i199
    pmid: 15262799     doi: 10.1093/bioinformatics/bth909    
• 2003
  
  • Differential myocardial gene expression in the development and rescue of murine heart failure
    Blaxall BC, Spang R, Rockman HA, Koch WJ.
    Physiol Genomics 2003 15 (2): 105-114
    pmid: 12865503    
  • Evaluating the Effect of Perturbations in Reconstructing Network Topologies
    Florian Markowetz and Rainer Spang
    Proceedings of the 3rd International Workshop on Distributed Statistical Computing 2003
    pdf    
  • 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 2003
    pdf    
  • Diagnostic signatures from microarrays: a bioinformatics concept for personalized medicine
    Rainer Spang
    Biosilico 2003 1 (2): 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 59 (2): 400-411
    pmid: 12909323     doi: 10.1016/S0008-6363(03)00426-7    
• 2002
  
  • A Novel Approach to Remote Homology Detection: Jumping Alignments
    Rainer Spang, Marc Rehmsmeier and Jens Stoye
    Journal of Computational Biology 2002 9 (5): 747-760
    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. 2002 19 (1): 8-13
    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): 369-381
    pmid: 12542420    
• 2001
  
  • 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 98 (20): 11462-11467
    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 21 (14): 4684-4699
    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) 2001
    
  • Limits of homology detection by pairwise sequence comparison
    Rainer Spang and Martin Vingron
    Bioinformatics 2001 17 (4): 338-342
    pmid: 11301302    
• 2000
  
  • 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    

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