Jan O Korbel

Summary

Affiliation: Yale University
Country: USA

Publications

  1. pmc Paired-end mapping reveals extensive structural variation in the human genome
    Jan O Korbel
    Molecular Biophysics and Biochemistry Department, Yale University, New Haven, CT 06520, USA
    Science 318:420-6. 2007
  2. doi request reprint 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
  3. pmc 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. pmc Systematic prediction and validation of breakpoints associated with copy-number variants in the human genome
    Jan O Korbel
    Departments of Molecular Biophysics and Biochemistry, Yale University School of Medicine, New Haven, CT 06520, USA
    Proc Natl Acad Sci U S A 104:10110-5. 2007
  5. pmc Analysis of copy number variants and segmental duplications in the human genome: Evidence for a change in the process of formation in recent evolutionary history
    Philip M Kim
    Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06520, USA
    Genome Res 18:1865-74. 2008
  6. ncbi request reprint What is a gene, post-ENCODE? History and updated definition
    Mark B Gerstein
    Program in Computational Biology and Bioinformatics, Yale University, New Haven, Connecticut 06511, USA
    Genome Res 17:669-81. 2007
  7. pmc The current excitement about copy-number variation: how it relates to gene duplications and protein families
    Jan O Korbel
    Molecular Biophysics and Biochemistry Department, Yale University, New Haven, CT 06520, USA
    Curr Opin Struct Biol 18:366-74. 2008
  8. pmc High-resolution mapping of DNA copy alterations in human chromosome 22 using high-density tiling oligonucleotide arrays
    Alexander Eckehart Urban
    Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, CT 06520, USA
    Proc Natl Acad Sci U S A 103:4534-9. 2006
  9. pmc The DART classification of unannotated transcription within the ENCODE regions: associating transcription with known and novel loci
    Joel S Rozowsky
    Molecular Biophysics and Biochemistry Department, Yale University, New Haven, Connecticut 06520 8114, USA
    Genome Res 17:732-45. 2007
  10. pmc Nucleotide-resolution analysis of structural variants using BreakSeq and a breakpoint library
    Hugo Y K Lam
    Program in Computational Biology and Bioinformatics, Yale University, New Haven, Connecticut, USA
    Nat Biotechnol 28:47-55. 2010

Collaborators

Detail Information

Publications19

  1. pmc Paired-end mapping reveals extensive structural variation in the human genome
    Jan O Korbel
    Molecular Biophysics and Biochemistry Department, Yale University, New Haven, CT 06520, USA
    Science 318:420-6. 2007
    ..The breakpoint junction sequences of more than 200 SVs were determined with a novel pooling strategy and computational analysis. Our analysis provided insights into the mechanisms of SV formation in humans...
  2. doi request reprint 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...
  3. pmc 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. pmc Systematic prediction and validation of breakpoints associated with copy-number variants in the human genome
    Jan O Korbel
    Departments of Molecular Biophysics and Biochemistry, Yale University School of Medicine, New Haven, CT 06520, USA
    Proc Natl Acad Sci U S A 104:10110-5. 2007
    ..Further, it enabled us to demonstrate a clear Mendelian pattern of inheritance for one of the CNVs...
  5. pmc Analysis of copy number variants and segmental duplications in the human genome: Evidence for a change in the process of formation in recent evolutionary history
    Philip M Kim
    Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06520, USA
    Genome Res 18:1865-74. 2008
    ..In addition to a coarse-grained analysis, we performed targeted sequencing of 67 CNVs and then analyzed a combined set of 270 CNVs (540 breakpoints) to verify our conclusions...
  6. ncbi request reprint What is a gene, post-ENCODE? History and updated definition
    Mark B Gerstein
    Program in Computational Biology and Bioinformatics, Yale University, New Haven, Connecticut 06511, USA
    Genome Res 17:669-81. 2007
    ..It also manifests how integral the concept of biological function is in defining genes...
  7. pmc The current excitement about copy-number variation: how it relates to gene duplications and protein families
    Jan O Korbel
    Molecular Biophysics and Biochemistry Department, Yale University, New Haven, CT 06520, USA
    Curr Opin Struct Biol 18:366-74. 2008
    ..These trends are likely reflective of CNV formation biases and natural selection, both of which differentially influence distinct protein families...
  8. pmc High-resolution mapping of DNA copy alterations in human chromosome 22 using high-density tiling oligonucleotide arrays
    Alexander Eckehart Urban
    Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, CT 06520, USA
    Proc Natl Acad Sci U S A 103:4534-9. 2006
    ..Our results demonstrate that HR-CGH allows the detection of copy number changes in the human genome at an unprecedented level of resolution...
  9. pmc The DART classification of unannotated transcription within the ENCODE regions: associating transcription with known and novel loci
    Joel S Rozowsky
    Molecular Biophysics and Biochemistry Department, Yale University, New Haven, Connecticut 06520 8114, USA
    Genome Res 17:732-45. 2007
    ..Overall, we find that 18 of the 46 connections tested validate by RT-PCR and four of five sequenced PCR products confirm connectivity unambiguously...
  10. pmc Nucleotide-resolution analysis of structural variants using BreakSeq and a breakpoint library
    Hugo Y K Lam
    Program in Computational Biology and Bioinformatics, Yale University, New Haven, Connecticut, USA
    Nat Biotechnol 28:47-55. 2010
    ..As new data become available, we expect our BreakSeq approach will become more sensitive and facilitate rapid SV genotyping of personal genomes...
  11. pmc MSB: a mean-shift-based approach for the analysis of structural variation in the genome
    Lu Yong Wang
    Program in Computational Biology and Bioinformatics, Yale University, New Haven, Connecticut 06520, USA
    Genome Res 19:106-17. 2009
    ..Finally, we show that our approach can be extended to segmenting the signal resulting from the depth-of-coverage of mapped reads from next-generation sequencing...
  12. pmc Variation in transcription factor binding among humans
    Maya Kasowski
    Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, CT 06520, USA
    Science 328:232-5. 2010
    ..Our results indicate that many differences in individuals and species occur at the level of TF binding, and they provide insight into the genetic events responsible for these differences...
  13. ncbi request reprint 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
    ..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...
  14. pmc 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...
  15. pmc The genetic architecture of Down syndrome phenotypes revealed by high-resolution analysis of human segmental trisomies
    Jan O Korbel
    Department of Molecular Biophysics and Biochemistry, Yale University School of Medicine, New Haven, CT 06520, USA
    Proc Natl Acad Sci U S A 106:12031-6. 2009
    ..Our study demonstrates the value of combining advanced genomics with cohorts of rare patients for studying DS, a prototype for the role of copy-number variation in complex disease...
  16. pmc Quantifying environmental adaptation of metabolic pathways in metagenomics
    Tara A Gianoulis
    Program in Computational Biology and Bioinformatics, Departments of Molecular Biophysics and Biochemistry, Computer Science, and Molecular, Cellular, and Developmental Biology, Yale University, New Haven, CT 06520, USA
    Proc Natl Acad Sci U S A 106:1374-9. 2009
    ..g., temperature). Moreover, we identified covariation in amino acid transport and cofactor synthesis, suggesting that limiting amounts of cofactor can (partially) explain increased import of amino acids in nutrient-limited conditions...
  17. pmc Structured RNAs in the ENCODE selected regions of the human genome
    Stefan Washietl
    Institute for Theoretical Chemistry, University of Vienna, A 1090 Wien, Austria
    Genome Res 17:852-64. 2007
    ..One hundred seventy-five selected candidates were tested by RT-PCR in six tissues, and expression could be verified in 43 cases (24.6%)...
  18. ncbi request reprint 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...
  19. ncbi request reprint 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...