Jan O Korbel

Summary

Affiliation: European Molecular Biology Laboratory
Country: Germany

Publications

  1. ncbi SHOT: a web server for the construction of genome phylogenies
    Jan O Korbel
    EMBL, Meyerhofstrasse 1, 69117, Heidelberg, Germany
    Trends Genet 18:158-62. 2002
  2. ncbi PEMer: a computational framework with simulation-based error models for inferring genomic structural variants from massive paired-end sequencing data
    Jan O Korbel
    Gene Expression Unit, European Molecular Biology Laboratory EMBL, Meyerhofstr, Heidelberg, 69117, Germany
    Genome Biol 10:R23. 2009
  3. ncbi Prediction of effective genome size in metagenomic samples
    Jeroen Raes
    European Molecular Biology Laboratory, Meyerhofstrasse 1, D 69117 Heidelberg, Germany
    Genome Biol 8:R10. 2007
  4. ncbi Systematic association of genes to phenotypes by genome and literature mining
    Jan O Korbel
    European Molecular Biology Laboratory, Heidelberg, Germany
    PLoS Biol 3:e134. 2005
  5. ncbi A 15q24 microdeletion in transient myeloproliferative disease (TMD) and acute megakaryoblastic leukaemia (AMKL) implicates PML and SUMO3 in the leukaemogenesis of TMD/AMKL
    Susanne Haemmerling
    Department of Paediatric Oncology, Haematology and Immunology, University of Heidelberg Medical Centre, Heidelberg, Germany
    Br J Haematol 157:180-7. 2012
  6. ncbi Analysis of genomic context: prediction of functional associations from conserved bidirectionally transcribed gene pairs
    Jan O Korbel
    European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany
    Nat Biotechnol 22:911-7. 2004
  7. ncbi Phenotypic impact of genomic structural variation: insights from and for human disease
    Joachim Weischenfeldt
    Genome Biology Unit, European Molecular Biology Laboratory, Meyerhofstrasse 1, Heidelberg, 69117, Germany
    Nat Rev Genet 14:125-38. 2013
  8. ncbi Similar gene expression profiles do not imply similar tissue functions
    Itai Yanai
    Department of Molecular Genetics, Weizmann Institute of Science, 76100 Rehovot, Israel
    Trends Genet 22:132-8. 2006
  9. ncbi A supervised hidden markov model framework for efficiently segmenting tiling array data in transcriptional and chIP-chip experiments: systematically incorporating validated biological knowledge
    Jiang Du
    Department of Computer Science, Yale University, New Haven, CT 06520, USA
    Bioinformatics 22:3016-24. 2006
  10. ncbi Positive selection at the protein network periphery: evaluation in terms of structural constraints and cellular context
    Philip M Kim
    Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA
    Proc Natl Acad Sci U S A 104:20274-9. 2007

Collaborators

Detail Information

Publications11

  1. ncbi SHOT: a web server for the construction of genome phylogenies
    Jan O Korbel
    EMBL, Meyerhofstrasse 1, 69117, Heidelberg, Germany
    Trends Genet 18:158-62. 2002
    ..SHOT is a useful tool for analysing the tree of life from a genomic point of view. It is available at http://www.Bork.EMBL-Heidelberg.de/SHOT...
  2. ncbi PEMer: a computational framework with simulation-based error models for inferring genomic structural variants from massive paired-end sequencing data
    Jan O Korbel
    Gene Expression Unit, European Molecular Biology Laboratory EMBL, Meyerhofstr, Heidelberg, 69117, Germany
    Genome Biol 10:R23. 2009
    ..The simulations demonstrated high structural variant reconstruction efficiency for PEMer's coverage-adjusted multi-cutoff scoring-strategy and showed its relative insensitivity to base-calling errors...
  3. ncbi Prediction of effective genome size in metagenomic samples
    Jeroen Raes
    European Molecular Biology Laboratory, Meyerhofstrasse 1, D 69117 Heidelberg, Germany
    Genome Biol 8:R10. 2007
    ..7 Mb; for bacteria in a nutrient-poor, organism-sparse ocean surface water sample, EGS is as low as 1.6 Mb. The method also permits evaluation of completion status and assembly bias in single-genome sequencing projects...
  4. ncbi Systematic association of genes to phenotypes by genome and literature mining
    Jan O Korbel
    European Molecular Biology Laboratory, Heidelberg, Germany
    PLoS Biol 3:e134. 2005
    ..Among the clusters, we observe an enrichment of pathogenicity-related associations, suggesting that the approach reveals many novel genes likely to play a role in infectious diseases...
  5. ncbi A 15q24 microdeletion in transient myeloproliferative disease (TMD) and acute megakaryoblastic leukaemia (AMKL) implicates PML and SUMO3 in the leukaemogenesis of TMD/AMKL
    Susanne Haemmerling
    Department of Paediatric Oncology, Haematology and Immunology, University of Heidelberg Medical Centre, Heidelberg, Germany
    Br J Haematol 157:180-7. 2012
    ..The 15q24 microdeletion may thus represent the first genetic hit to initiate leukaemogenesis and implicates PML and SUMO3 as novel components of the leukaemogenic network in TMD/AMKL...
  6. ncbi Analysis of genomic context: prediction of functional associations from conserved bidirectionally transcribed gene pairs
    Jan O Korbel
    European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany
    Nat Biotechnol 22:911-7. 2004
    ..The method thus enables the prediction of target processes and regulatory features for several hundred transcriptional regulators...
  7. ncbi Phenotypic impact of genomic structural variation: insights from and for human disease
    Joachim Weischenfeldt
    Genome Biology Unit, European Molecular Biology Laboratory, Meyerhofstrasse 1, Heidelberg, 69117, Germany
    Nat Rev Genet 14:125-38. 2013
    ..We further present advances in delineating disease-causing elements that are affected by structural variants, and we discuss future directions for research on the functional consequences of structural variants...
  8. ncbi Similar gene expression profiles do not imply similar tissue functions
    Itai Yanai
    Department of Molecular Genetics, Weizmann Institute of Science, 76100 Rehovot, Israel
    Trends Genet 22:132-8. 2006
    ..Ectopic expression is possibly explained as expression leakage, caused by spreading of chromatin modifications or the transcription apparatus into neighboring genes...
  9. ncbi A supervised hidden markov model framework for efficiently segmenting tiling array data in transcriptional and chIP-chip experiments: systematically incorporating validated biological knowledge
    Jiang Du
    Department of Computer Science, Yale University, New Haven, CT 06520, USA
    Bioinformatics 22:3016-24. 2006
    ..This latter result has strong implications for the optimum way medium-scale validation experiments should be carried out to verify the results of the genome-scale tiling array experiments...
  10. ncbi Positive selection at the protein network periphery: evaluation in terms of structural constraints and cellular context
    Philip M Kim
    Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA
    Proc Natl Acad Sci U S A 104:20274-9. 2007
    ..e., extracellular space or cell membrane). This suggests that the observed positive selection at the network periphery may be due to an increase of adaptive events on the cellular periphery responding to changing environments...
  11. ncbi Analysis of copy number variation in the rhesus macaque genome identifies candidate loci for evolutionary and human disease studies
    Arthur S Lee
    Department of Pathology, Brigham and Women s Hospital, 221 Longwood Ave, Boston, MA 02115, USA
    Hum Mol Genet 17:1127-36. 2008
    ..Therefore, the rhesus macaque offers an intriguing, non-human primate outbred model organism with which hypotheses concerning the specific functions of phenotypically relevant human CNVs can be tested...