Mark Groudine

Mark Groudine

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Mark Groudine

Mark Groudine

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The redundancy of the mammalian heterochromatic compartment.

Curr Opin Genet Dev 2016 04 17;37:1-8. Epub 2015 Dec 17.

Fred Hutchinson Cancer Research Center, Seattle, WA, United States. Electronic address:

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http://dx.doi.org/10.1016/j.gde.2015.10.007DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4911328PMC
April 2016

Distinct Activities of Myf5 and MyoD Indicate Separate Roles in Skeletal Muscle Lineage Specification and Differentiation.

Dev Cell 2016 Feb;36(4):375-85

Human Biology Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA; Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA; Department of Neurology, University of Washington, School of Medicine, Seattle, WA 98105, USA. Electronic address:

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http://dx.doi.org/10.1016/j.devcel.2016.01.021DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4769793PMC
February 2016

Functional redundancy in the nuclear compartmentalization of the late-replicating genome.

Nucleus 2014 ;5(6):626-35

a Division of Basic Sciences ; Fred Hutchinson Cancer Research Center ; Seattle , WA USA.

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http://dx.doi.org/10.4161/19491034.2014.990863DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4615584PMC
September 2015

Nucleolar tethering mediates pairing between the IgH and Myc loci.

Nucleus 2014 Sep-Oct;5(5):474-81

a Division of Basic Sciences; Fred Hutchinson Cancer Research Center; Seattle, WA USA.

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http://dx.doi.org/10.4161/nucl.36233DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4164489PMC
August 2015

Olfactory receptor genes expressed in distinct lineages are sequestered in different nuclear compartments.

Proc Natl Acad Sci U S A 2015 May 20;112(18):E2403-9. Epub 2015 Apr 20.

Howard Hughes Medical Institute, Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109; and

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http://dx.doi.org/10.1073/pnas.1506058112DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4426396PMC
May 2015

Wash interacts with lamin and affects global nuclear organization.

Curr Biol 2015 Mar 5;25(6):804-810. Epub 2015 Mar 5.

Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA. Electronic address:

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http://dx.doi.org/10.1016/j.cub.2015.01.052DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4366290PMC
March 2015

A comparative encyclopedia of DNA elements in the mouse genome.

Authors:
Feng Yue Yong Cheng Alessandra Breschi Jeff Vierstra Weisheng Wu Tyrone Ryba Richard Sandstrom Zhihai Ma Carrie Davis Benjamin D Pope Yin Shen Dmitri D Pervouchine Sarah Djebali Robert E Thurman Rajinder Kaul Eric Rynes Anthony Kirilusha Georgi K Marinov Brian A Williams Diane Trout Henry Amrhein Katherine Fisher-Aylor Igor Antoshechkin Gilberto DeSalvo Lei-Hoon See Meagan Fastuca Jorg Drenkow Chris Zaleski Alex Dobin Pablo Prieto Julien Lagarde Giovanni Bussotti Andrea Tanzer Olgert Denas Kanwei Li M A Bender Miaohua Zhang Rachel Byron Mark T Groudine David McCleary Long Pham Zhen Ye Samantha Kuan Lee Edsall Yi-Chieh Wu Matthew D Rasmussen Mukul S Bansal Manolis Kellis Cheryl A Keller Christapher S Morrissey Tejaswini Mishra Deepti Jain Nergiz Dogan Robert S Harris Philip Cayting Trupti Kawli Alan P Boyle Ghia Euskirchen Anshul Kundaje Shin Lin Yiing Lin Camden Jansen Venkat S Malladi Melissa S Cline Drew T Erickson Vanessa M Kirkup Katrina Learned Cricket A Sloan Kate R Rosenbloom Beatriz Lacerda de Sousa Kathryn Beal Miguel Pignatelli Paul Flicek Jin Lian Tamer Kahveci Dongwon Lee W James Kent Miguel Ramalho Santos Javier Herrero Cedric Notredame Audra Johnson Shinny Vong Kristen Lee Daniel Bates Fidencio Neri Morgan Diegel Theresa Canfield Peter J Sabo Matthew S Wilken Thomas A Reh Erika Giste Anthony Shafer Tanya Kutyavin Eric Haugen Douglas Dunn Alex P Reynolds Shane Neph Richard Humbert R Scott Hansen Marella De Bruijn Licia Selleri Alexander Rudensky Steven Josefowicz Robert Samstein Evan E Eichler Stuart H Orkin Dana Levasseur Thalia Papayannopoulou Kai-Hsin Chang Arthur Skoultchi Srikanta Gosh Christine Disteche Piper Treuting Yanli Wang Mitchell J Weiss Gerd A Blobel Xiaoyi Cao Sheng Zhong Ting Wang Peter J Good Rebecca F Lowdon Leslie B Adams Xiao-Qiao Zhou Michael J Pazin Elise A Feingold Barbara Wold James Taylor Ali Mortazavi Sherman M Weissman John A Stamatoyannopoulos Michael P Snyder Roderic Guigo Thomas R Gingeras David M Gilbert Ross C Hardison Michael A Beer Bing Ren

Nature 2014 Nov;515(7527):355-64

Ludwig Institute for Cancer Research and University of California, San Diego School of Medicine, 9500 Gilman Drive, La Jolla, California 92093, USA.

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http://dx.doi.org/10.1038/nature13992DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4266106PMC
November 2014

UpSET-ting the balance: modulating open chromatin features in metazoan genomes.

Fly (Austin) 2013 Jul-Sep;7(3):153-60. Epub 2013 May 6.

Basic Sciences Division; Fred Hutchinson Cancer Research Center; Seattle, WA USA.

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http://dx.doi.org/10.4161/fly.24732DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4049847PMC
May 2014

The nucleosomal barrier to promoter escape by RNA polymerase II is overcome by the chromatin remodeler Chd1.

Elife 2014 Apr 15;3:e02042. Epub 2014 Apr 15.

Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, United States.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3983905PMC
http://dx.doi.org/10.7554/eLife.02042DOI Listing
April 2014

When untethered, something silent inside comes.

Nucleus 2013 May-Jun;4(3):153-5. Epub 2013 May 15.

Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, USA.

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http://dx.doi.org/10.4161/nucl.24999DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3720743PMC
January 2014

The histone-H3K4-specific demethylase KDM5B binds to its substrate and product through distinct PHD fingers.

Cell Rep 2014 Jan 9;6(2):325-35. Epub 2014 Jan 9.

Department of Pharmacology, University of Colorado School of Medicine, Aurora, CO 80045, USA; Molecular Biology Program, University of Colorado School of Medicine, Aurora, CO 80045, USA. Electronic address:

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http://dx.doi.org/10.1016/j.celrep.2013.12.021DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3918441PMC
January 2014

Something silent this way forms: the functional organization of the repressive nuclear compartment.

Annu Rev Cell Dev Biol 2013 5;29:241-70. Epub 2013 Jul 5.

Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109; email: , ,

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http://dx.doi.org/10.1146/annurev-cellbio-101512-122317DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3999972PMC
December 2013

Molecular basis for chromatin binding and regulation of MLL5.

Proc Natl Acad Sci U S A 2013 Jul 24;110(28):11296-301. Epub 2013 Jun 24.

Department of Pharmacology, University of Colorado School of Medicine, Aurora, CO 80045, USA.

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http://dx.doi.org/10.1073/pnas.1310156110DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3710826PMC
July 2013

Losing control: cancer's catastrophic transition.

Nucleus 2011 Jul-Aug;2(4):249-52. Epub 2011 Jul 1.

Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, USA.

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http://dx.doi.org/10.4161/nucl.2.4.16506DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3260564PMC
January 2013

UpSET recruits HDAC complexes and restricts chromatin accessibility and acetylation at promoter regions.

Cell 2012 Dec 21;151(6):1214-28. Epub 2012 Nov 21.

Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA.

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http://dx.doi.org/10.1016/j.cell.2012.11.009DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3518625PMC
December 2012

What can systems theory of networks offer to biology?

PLoS Comput Biol 2012 28;8(6):e1002543. Epub 2012 Jun 28.

Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America.

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http://dx.doi.org/10.1371/journal.pcbi.1002543DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3386158PMC
October 2012

An encyclopedia of mouse DNA elements (Mouse ENCODE).

August 2012

Dynamics and control of state-dependent networks for probing genomic organization.

Proc Natl Acad Sci U S A 2011 Oct 12;108(42):17257-62. Epub 2011 Sep 12.

Division of Basic Sciences, Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue North, Seattle, WA 98109, USA.

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http://dx.doi.org/10.1073/pnas.1113249108DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3198315PMC
October 2011

On emerging nuclear order.

J Cell Biol 2011 Mar;192(5):711-21

Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA.

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http://www.jcb.org/lookup/doi/10.1083/jcb.201010129
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http://dx.doi.org/10.1083/jcb.201010129DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3051810PMC
March 2011

Functional and mechanistic diversity of distal transcription enhancers.

Cell 2011 Feb;144(3):327-39

Center for Pediatric Biomedical Research, Department of Pediatrics, University of Rochester, NY 14627, USA.

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http://dx.doi.org/10.1016/j.cell.2011.01.024DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3742076PMC
February 2011

Multiple functions of Ldb1 required for beta-globin activation during erythroid differentiation.

Blood 2010 Sep 22;116(13):2356-64. Epub 2010 Jun 22.

Laboratory of Cellular and Developmental Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, USA.

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http://dx.doi.org/10.1182/blood-2010-03-272252DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2953839PMC
September 2010

Networking the nucleus.

Mol Syst Biol 2010 Jul;6:395

Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA.

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http://dx.doi.org/10.1038/msb.2010.48DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2925527PMC
July 2010

Enhancers: the abundance and function of regulatory sequences beyond promoters.

Dev Biol 2010 Mar 16;339(2):250-7. Epub 2009 Dec 16.

Center for Pediatric Biomedical Research, Department of Pediatrics, University of Rochester, Rochester, NY, USA.

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http://dx.doi.org/10.1016/j.ydbio.2009.11.035DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3060611PMC
March 2010

Getting connected in the globin interactome.

Nat Genet 2010 Jan;42(1):16-7

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http://dx.doi.org/10.1038/ng0110-16DOI Listing
January 2010

Histone hyperacetylation within the beta-globin locus is context-dependent and precedes high-level gene expression.

Blood 2009 Oct 18;114(16):3479-88. Epub 2009 Aug 18.

Departments of Pediatrics, Center for Pediatric Biomedical Research, University of Rochester Medical Center, Box 703, 601 Elmwood Ave, Rochester, NY14642, USA.

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http://dx.doi.org/10.1182/blood-2009-03-210690DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2765682PMC
October 2009

Developmental and species-divergent globin switching are driven by BCL11A.

Nature 2009 Aug 5;460(7259):1093-7. Epub 2009 Aug 5.

Division of Hematology/Oncology, Children's Hospital Boston and Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Stem Cell Institute, Harvard Medical School, Boston, Massachusetts 02115, USA.

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http://dx.doi.org/10.1038/nature08243DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3749913PMC
August 2009

The emergence of lineage-specific chromosomal topologies from coordinate gene regulation.

Proc Natl Acad Sci U S A 2009 Apr 10;106(16):6679-84. Epub 2009 Mar 10.

Division of Basic Sciences and Department of Biostatistics and Biomathematics, Public Health Sciences, Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue North, Seattle, WA 98109, USA.

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http://dx.doi.org/10.1073/pnas.0900986106DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2654024PMC
April 2009

The nucleus inside out--through a rod darkly.

Cell 2009 Apr;137(2):205-7

Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA.

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http://dx.doi.org/10.1016/j.cell.2009.04.006DOI Listing
April 2009

Bivalent domains enforce transcriptional memory of DNA methylated genes in cancer cells.

Proc Natl Acad Sci U S A 2008 Dec 5;105(50):19809-14. Epub 2008 Dec 5.

Institut de Medicina Predictiva i Personalitzada del Càncer, Badalona, 08916 Barcelona, Spain.

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http://dx.doi.org/10.1073/pnas.0810133105DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2596747PMC
December 2008

Transcriptional interference among the murine beta-like globin genes.

Blood 2007 Mar 31;109(5):2210-6. Epub 2006 Oct 31.

Department of Microbiology/Immunology and Norris Cotton Cancer Center, Dartmouth Medical School, Hanover, NH 03756, USA.

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http://www.bloodjournal.org/cgi/doi/10.1182/blood-2006-06-02
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http://dx.doi.org/10.1182/blood-2006-06-029868DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1801066PMC
March 2007

An unmethylated 3' promoter-proximal region is required for efficient transcription initiation.

PLoS Genet 2007 Feb 2;3(2):e27. Epub 2007 Jan 2.

Department of Medical Genetics, The University of British Columbia, Vancouver, British Columbia, Canada.

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http://dx.doi.org/10.1371/journal.pgen.0030027DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1797817PMC
February 2007

Flanking HS-62.5 and 3' HS1, and regions upstream of the LCR, are not required for beta-globin transcription.

Blood 2006 Aug 27;108(4):1395-401. Epub 2006 Apr 27.

Division of Clinical Research, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA.

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http://dx.doi.org/10.1182/blood-2006-04-014431DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1895883PMC
August 2006

The locus control region is required for association of the murine beta-globin locus with engaged transcription factories during erythroid maturation.

Genes Dev 2006 Jun 16;20(11):1447-57. Epub 2006 May 16.

Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington, Washington 98109, USA.

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http://dx.doi.org/10.1101/gad.1419506DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1475758PMC
June 2006

Proximity among distant regulatory elements at the beta-globin locus requires GATA-1 and FOG-1.

Mol Cell 2005 Feb;17(3):453-62

Division of Hematology, The Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA.

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http://dx.doi.org/10.1016/j.molcel.2004.12.028DOI Listing
February 2005

DNA replication-timing analysis of human chromosome 22 at high resolution and different developmental states.

Proc Natl Acad Sci U S A 2004 Dec 10;101(51):17771-6. Epub 2004 Dec 10.

Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, CT 06520-8103, USA.

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http://dx.doi.org/10.1073/pnas.0408170101DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC539744PMC
December 2004

Intragenic DNA methylation alters chromatin structure and elongation efficiency in mammalian cells.

Nat Struct Mol Biol 2004 Nov 3;11(11):1068-75. Epub 2004 Oct 3.

Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, USA.

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http://dx.doi.org/10.1038/nsmb840DOI Listing
November 2004

Gene order and dynamic domains.

Science 2004 Oct;306(5696):644-7

Division of Basic Sciences, Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue North, Seattle, WA 98109, USA.

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http://www.sciencemag.org/cgi/doi/10.1126/science.1103864
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http://dx.doi.org/10.1126/science.1103864DOI Listing
October 2004

Form follows function: The genomic organization of cellular differentiation.

Genes Dev 2004 Jun;18(12):1371-84

Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, USA.

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http://dx.doi.org/10.1101/gad.1209304DOI Listing
June 2004

A genetic analysis of chromosome territory looping: diverse roles for distal regulatory elements.

Chromosome Res 2003 ;11(5):513-25

Division of Basic Sciences, Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue North, Seattle, Washington 98109, USA.

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April 2004

The human beta-globin replication initiation region consists of two modular independent replicators.

Mol Cell Biol 2004 Apr;24(8):3373-86

Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland, USA.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC381644PMC
http://dx.doi.org/10.1128/mcb.24.8.3373-3386.2004DOI Listing
April 2004

Heme regulates the dynamic exchange of Bach1 and NF-E2-related factors in the Maf transcription factor network.

Proc Natl Acad Sci U S A 2004 Feb 27;101(6):1461-6. Epub 2004 Jan 27.

Department of Biomedical Chemistry, Hiroshima University Graduate School of Biomedical Sciences, Kasumi 1-2-3, Hiroshima 734-8551, Japan.

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http://www.pnas.org/cgi/doi/10.1073/pnas.0308083100
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http://dx.doi.org/10.1073/pnas.0308083100DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC341742PMC
February 2004

Dynamic changes in transcription factor complexes during erythroid differentiation revealed by quantitative proteomics.

Nat Struct Mol Biol 2004 Jan 29;11(1):73-80. Epub 2003 Dec 29.

Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, USA.

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http://dx.doi.org/10.1038/nsmb713DOI Listing
January 2004

The beta -globin locus control region (LCR) functions primarily by enhancing the transition from transcription initiation to elongation.

Genes Dev 2003 Apr 2;17(8):1009-18. Epub 2003 Apr 2.

Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, USA.

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http://www.genesdev.org/cgi/doi/10.1101/gad.1072303
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http://dx.doi.org/10.1101/gad.1072303DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC196035PMC
April 2003

Promoters of the murine embryonic beta-like globin genes Ey and betah1 do not compete for interaction with the beta-globin locus control region.

Proc Natl Acad Sci U S A 2003 Feb 13;100(3):1111-5. Epub 2003 Jan 13.

Department of Microbiology and Immunology, Dartmouth Medical School, Hanover, NH 03756, USA.

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http://dx.doi.org/10.1073/pnas.0337404100DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC298735PMC
February 2003

Chromatin insulation by a transcriptional activator.

Proc Natl Acad Sci U S A 2003 Feb 23;100(3):1105-10. Epub 2003 Jan 23.

Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA.

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http://dx.doi.org/10.1073/pnas.242732999DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC298734PMC
February 2003

Controlling the double helix.

Nature 2003 Jan;421(6921):448-53

Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Building 5, Room 212, Bethesda, Maryland 20892-0540, USA.

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http://www.nature.com/doifinder/10.1038/nature01411
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http://dx.doi.org/10.1038/nature01411DOI Listing
January 2003

TRAPping enhancer function.

Nat Genet 2002 Dec;32(4):555-6

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http://dx.doi.org/10.1038/ng1202-555DOI Listing
December 2002

Genome-wide DNA replication profile for Drosophila melanogaster: a link between transcription and replication timing.

Nat Genet 2002 Nov 30;32(3):438-42. Epub 2002 Sep 30.

Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, USA.

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http://dx.doi.org/10.1038/ng1005DOI Listing
November 2002

DNA methylation density influences the stability of an epigenetic imprint and Dnmt3a/b-independent de novo methylation.

Mol Cell Biol 2002 Nov;22(21):7572-80

Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, USA.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC135678PMC
http://dx.doi.org/10.1128/mcb.22.21.7572-7580.2002DOI Listing
November 2002

The undiscovered country: chromosome territories and the organization of transcription.

Dev Cell 2002 Jun;2(6):690-2

Division of Basic Sciences, Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue North, Seattle, WA 98109, USA.

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June 2002

ChIPs of the beta-globin locus: unraveling gene regulation within an active domain.

Curr Opin Genet Dev 2002 Apr;12(2):170-7

Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue North, Seattle, Washington 98109, USA.

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http://dx.doi.org/10.1016/s0959-437x(02)00283-6DOI Listing
April 2002