Jan O Korbel
Affiliation: European Molecular Biology Laboratory
- SHOT: a web server for the construction of genome phylogeniesJan 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...
- PEMer: a computational framework with simulation-based error models for inferring genomic structural variants from massive paired-end sequencing dataJan 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...
- Prediction of effective genome size in metagenomic samplesJeroen 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...
- Systematic association of genes to phenotypes by genome and literature miningJan 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...
- A 15q24 microdeletion in transient myeloproliferative disease (TMD) and acute megakaryoblastic leukaemia (AMKL) implicates PML and SUMO3 in the leukaemogenesis of TMD/AMKLSusanne 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...
- Analysis of genomic context: prediction of functional associations from conserved bidirectionally transcribed gene pairsJan 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...
- Phenotypic impact of genomic structural variation: insights from and for human diseaseJoachim 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...
- Similar gene expression profiles do not imply similar tissue functionsItai 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...
- A supervised hidden markov model framework for efficiently segmenting tiling array data in transcriptional and chIP-chip experiments: systematically incorporating validated biological knowledgeJiang Du
Department of Computer Science, Yale University, New Haven, CT 06520, USA
Bioinformatics 22:3016-24. 2006..Here we propose a supervised framework for doing this. It has the advantage of explicitly incorporating validated biological knowledge into the model and allowing for formal training and testing...
- Positive selection at the protein network periphery: evaluation in terms of structural constraints and cellular contextPhilip 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...
- Analysis of copy number variation in the rhesus macaque genome identifies candidate loci for evolutionary and human disease studiesArthur 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...