Affiliation: University of Washington
- Identification of higher-order functional domains in the human ENCODE regionsRobert E Thurman
Division of Medical Genetics, University of Washington, Seattle, Washington 98195, USA
Genome Res 17:917-27. 2007..Taken together, our results suggest that higher-order functional domains represent a fundamental organizing principle of human genome architecture...
- Human mutation rate associated with DNA replication timingJohn A Stamatoyannopoulos
Department of Genome Sciences and Medicine, University of Washington, Seattle, WA, USA
Nat Genet 41:393-5. 2009..This correlation between mutation rate and regionally stratified replication timing may have substantial evolutionary implications...
- Contribution of nucleosome binding preferences and co-occurring DNA sequences to transcription factor bindingXimiao He
Laboratory of Metabolism, National Cancer Institute, National Institutes of Health, Room 3128, Building 37, 37 Convent Drive, Bethesda, MD 20892, USA
BMC Genomics 14:428. 2013..Recent studies in vertebrates show that many TFs preferentially bind to genomic regions that are well bound by nucleosomes in vitro. Co-occurring secondary motifs sometimes correlated with functional TFBS...
- What does our genome encode?John A Stamatoyannopoulos
Departments of Genome Sciences and Medicine, University of Washington School of Medicine, Seattle, Washington 98195, USA
Genome Res 22:1602-11. 2012..Finally, I consider prospects for the future, including maximizing the accuracy, completeness, and utility of ENCODE data for the community...
- Predicting the in vivo signature of human gene regulatory sequencesWilliam Stafford Noble
Department of Genome Sciences, University of Washington Seattle, WA, USA
Bioinformatics 21:i338-43. 2005..The ability to discriminate DNaseI HSs computationally would have a major impact on the annotation and utilization of the human genome...
- Quantifying similarity between motifsShobhit Gupta
Department of Genome Sciences, University of Washington, 1705 NE Pacific Street, Box 355065, Seattle, WA 98195, USA
Genome Biol 8:R24. 2007..Experimental simulations demonstrate the accuracy of Tomtom's E values and its effectiveness in finding similar motifs...
- Sequencing newly replicated DNA reveals widespread plasticity in human replication timingR Scott Hansen
Department of Medicine, Division of Medical Genetics, University of Washington School of Medicine, Seattle, WA 98195, USA
Proc Natl Acad Sci U S A 107:139-44. 2010..The data collectively provide a unique, genome-wide picture of the epigenetic compartmentalization of the human genome and suggest that cell-lineage specification involves extensive reprogramming of replication timing patterns...
- Unsupervised segmentation of continuous genomic dataNathan Day
Department of Computer Science and Engineering, University of Washington, Seattle, WA, USA
Bioinformatics 23:1424-6. 2007..HMMSeg is capable of handling multiple datasets simultaneously, rendering it ideal for integrative analysis of expression, phylogenetic and functional genomic data. AVAILABILITY: http://noble.gs.washington.edu/proj/hmmseg..
- A thermodynamic approach to PCR primer designTobias Mann
Department of Genome Sciences, University of Washington, Seattle, WA, USA
Nucleic Acids Res 37:e95. 2009..Our software is freely available at http://pythia.sourceforge.net...
- Mapping and sequencing of structural variation from eight human genomesJeffrey M Kidd
Department of Genome Sciences and Howard Hughes Medical Institute, University of Washington, Seattle, Washington 98195, USA
Nature 453:56-64. 2008..These data provide the first high-resolution sequence map of human structural variation--a standard for genotyping platforms and a prelude to future individual genome sequencing projects...
- Predicting human nucleosome occupancy from primary sequenceShobhit Gupta
Department of Genome Sciences, University of Washington, Seattle, Washington, United States of America
PLoS Comput Biol 4:e1000134. 2008..The results suggest that the major mechanism of nucleosome positioning in vivo is boundary-event-driven and affirm the classical statistical positioning theory of nucleosome organization...
- High-throughput localization of functional elements by quantitative chromatin profilingMichael O Dorschner
Department of Molecular Biology, Regulome, 2211 Elliott Avenue, Suite 600, Seattle, Washington 98121, USA
Nat Methods 1:219-25. 2004....
- Global mapping of protein-DNA interactions in vivo by digital genomic footprintingJay R Hesselberth
Department of Genome Sciences, University of Washington, Seattle, USA
Nat Methods 6:283-9. 2009..Digital genomic footprinting should be a powerful approach to delineate the cis-regulatory framework of any organism with an available genome sequence...
- Genome-wide identification of DNaseI hypersensitive sites using active chromatin sequence librariesPeter J Sabo
Department of Molecular Biology, Regulome, Canal View Building, 551 North 34th Street, Seattle, WA 98103, USA
Proc Natl Acad Sci U S A 101:4537-42. 2004..The results permit a quantitative approximation of the distribution of HSs and classical cis-regulatory sequences in the human genome...
- Site-Specific Recovery of Regulatory ProteinsJohn Stamatoyannopoulos; Fiscal Year: 2004..In Phase II studies, mass spectrometric analyses will be performed on recovered protein substrates. Analyses will be performed on additional cis-regulatory systems, including those known to be involved in specific diseases. ..
- A Comprehensive catalog of human DNasel hypersensitive sitesJohn Stamatoyannopoulos; Fiscal Year: 2007..Validation of DHS functional classes will be accomplished using well-tested cell and transgenic assays of biological function (Specific Aim 5). ..
- Computational discovery of cis-regulatory sequencesJohn Stamatoyannopoulos; Fiscal Year: 2007..The resulting database will be of incalculable value in furthering the study of the regulation of human genes and the computational methodologies employed therein. ..
- Regulatory Genomics of Inflammatory Response GenesJohn Stamatoyannopoulos; Fiscal Year: 2007..abstract_text> ..
- Engineered Cell Lines for Regulatory Protein AnalysisJohn Stamatoyannopoulos; Fiscal Year: 2004..Fractionation over sucrose gradients has the added advantage of providing a clean reagent for downstream mass spectrometric studies. Such studies are envisioned to form the basis of a follow-on Phase II proposal. ..