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Claudio Lottaz

Address

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

Tel:+49 941 943 1584
Fax:+49 941 943 5020
Email:claudio.lottaz@klinik.uni-regensburg.de

Research Interests:

  • Computational diagnostics with high throughput data
    Machine learning approaches and statistical evaluation of diagnostic signatures for outcome prediction and disease type identification
  • Complex phenotype
    Computational exploration of complex disease phenotypes and corresponding sub-class discovery
  • Knowledge integration
    Integration of functional annotations into statistical analysis methods
  • Micro-read assembly
    De novo assembly of very short reads in sequencing projects

Short Vita:

Lectures:

  • Analysis of genomic data:   April 2005 - July 2005
    Introduction to statistics for genomic data within the bioinformatics bachelor program at the Free University Berlin
    Course page
  • Analysis of genomic data:   April 1998 - July 1998
    Advanced programming course for electrical engineering and mathematics students at the Swiss Federal Institute of Technology in Lausanne
  • Analysis of genomic data:   April 1996 - March 1997
    Programming introduction for various engineering students at the Swiss Federal Institute of Technology in Lausanne

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    
  • 2008
    • Substantial biases in ultra-short read data sets from high-throughput DNA sequencing
      Juliane C. Dohm, Claudio Lottaz, Tatiana Borodina and Heinz Himmelbauer
      Nucleic Acids Research 2008
      pmid: 18660515     doi: doi:10.1093/nar/gkn425    
    • 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
    • SHARCGS, a fast and highly accurate short-read assembly algorithm for de novo genomic sequencing
      Dohm JC, Lottaz C, Borodina T and Himmelbauer H
      Genome Research 2007 Oct (17): 1697-1706
      pmid: 17908823     doi: doi:10.1101/gr.6435207     pdf    
    • Neutrality, Compensation, and Negative Selection during Evolution of B-Cell Development Transcriptomes
      Hoffmann R, Lottaz C, Kuehne T, Rolink A and Melchers F
      Molecular Biology and Evolution 2007 Sep (1): Epub ahead of print
      pmid: 17890238     doi: doi:10.1093/molbev/msm198     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    
    • Gene Expression Profiling Identifies Distinct Subclasses of Core Binding Factor Acute Myeloid Leukemia
      Bullinger L, Rücker FG, Kurz S, Du J, Scholl C, Sander S, Corbacioglu A, Lottaz C, Krauter J, Fröhling S, Ganser A, Schlenk RF, Döhner K, Pollack JR and Döhner H
      Blood 2007 110 (4): 1291-1300
      pmid: 17485551     doi: doi:10.1182/blood-2006-10-049783     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
    • 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    
    • 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    
  • 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)
    • 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    
    • 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    
  • 2004
    • 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 18 (5): 926-933
      pmid: 15014526     doi: 10.1038/sj.leu.2403332    
  • 2002
    • Modeling Sequencing Errors by Combining Hidden Markov Models
      Claudio Lottaz, Christian Iseli, C. Victor Jongeneel and Philipp Bucher
      Bioinformatics, (ECCB'03, Paris, France) 2002 19 (suppl. 2): 103-112
      pmid: 14534179     pdf    

Supported by the Bavarian Genome Research Network
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