Research Topics
Species | Jan O KorbelSummaryAffiliation: Yale University Country: USA Publications
| Collaborators
|
Detail Information
Publications
Paired-end mapping reveals extensive structural variation in the human genomeJan 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...
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...- 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 prediction and validation of breakpoints associated with copy-number variants in the human genomeJan 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... - Analysis of copy number variants and segmental duplications in the human genome: Evidence for a change in the process of formation in recent evolutionary historyPhilip 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... 
What is a gene, post-ENCODE? History and updated definitionMark 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...- The current excitement about copy-number variation: how it relates to gene duplications and protein familiesJan 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... - High-resolution mapping of DNA copy alterations in human chromosome 22 using high-density tiling oligonucleotide arraysAlexander 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... - The DART classification of unannotated transcription within the ENCODE regions: associating transcription with known and novel lociJoel 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... - Nucleotide-resolution analysis of structural variants using BreakSeq and a breakpoint libraryHugo 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... - MSB: a mean-shift-based approach for the analysis of structural variation in the genomeLu 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... - Variation in transcription factor binding among humansMaya 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... - 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..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... - 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... - The genetic architecture of Down syndrome phenotypes revealed by high-resolution analysis of human segmental trisomiesJan 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... - Quantifying environmental adaptation of metabolic pathways in metagenomicsTara 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... - Structured RNAs in the ENCODE selected regions of the human genomeStefan 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%)... - 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... - 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...