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...
- 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...
- 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...
- Comprehensive characterization of erythroid-specific enhancers in the genomic regions of human Krüppel-like factorsQian Xiong
CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, P, R, China
BMC Genomics 14:587. 2013..Several KLFs have been demonstrated to play important roles in hematopoiesis. However, transcriptional regulation of KLFs via CREs, particularly enhancers, in erythroid cells has been poorly understood...
- 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, 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...
- 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...
- Transcriptional environment and chromatin architecture interplay dictates globin expression patterns of heterospecific hybrids derived from undifferentiated human embryonic stem cells or from their erythroid progenyKai Hsin Chang
Division of Hematology, Department of Medicine, University of Washington, Seattle, WA, USA
Exp Hematol 41:967-979.e6. 2013..Our studies provide important insights into the interplay between the transcription environment and existing chromatin domains, and we offer an experimental system to study the time-dependent human globin switching. ..
- 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...
- 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...
- 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...
- 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..
- 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...
- A temporal chromatin signature in human embryonic stem cells identifies regulators of cardiac developmentSharon L Paige
Department of Pathology, University of Washington, Seattle, 98109, USA
Cell 151:221-32. 2012..Temporal chromatin signatures should be broadly applicable to other models of stem cell differentiation to identify regulators and provide key insights into major developmental decisions...
- 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....
- 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. ..
- 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. ..
- 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: 2008..abstract_text> ..