Ruslan I Sadreyev

Ruslan I Sadreyev

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Ruslan I Sadreyev

Ruslan I Sadreyev

Publications by authors named "Ruslan I Sadreyev"

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Genome-wide analysis identifies -acting elements regulating mRNA polyadenylation and translation during vertebrate oocyte maturation.

RNA 2020 Mar 2;26(3):324-344. Epub 2020 Jan 2.

Department of Molecular Biology, Massachusetts General Hospital, Boston, Massachusetts 02114, USA.

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http://dx.doi.org/10.1261/rna.073247.119DOI Listing
March 2020

Histone Lysine Methylation Dynamics Control DNA Copy-Number Amplification.

Cancer Discov 2020 Feb 27;10(2):306-325. Epub 2019 Nov 27.

Department of Medicine, Massachusetts General Hospital Cancer Center and Harvard Medical School, Charlestown, Massachusetts.

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http://dx.doi.org/10.1158/2159-8290.CD-19-0463DOI Listing
February 2020

The RNA Helicase DDX6 Controls Cellular Plasticity by Modulating P-Body Homeostasis.

Cell Stem Cell 2019 Nov 3;25(5):622-638.e13. Epub 2019 Oct 3.

Department of Molecular Biology, Massachusetts General Hospital, 185 Cambridge Street, Boston, MA 02114, USA; Center for Regenerative Medicine, Massachusetts General Hospital, 185 Cambridge Street, Boston, MA 02114, USA; Cancer Center, Massachusetts General Hospital, 185 Cambridge Street, Boston, MA 02114, USA; Department of Genetics, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA 02115, USA; Harvard Stem Cell Institute, 1350 Massachusetts Avenue, Cambridge, MA 02138, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA. Electronic address:

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http://dx.doi.org/10.1016/j.stem.2019.08.018DOI Listing
November 2019

TREM2 Acts Downstream of CD33 in Modulating Microglial Pathology in Alzheimer's Disease.

Neuron 2019 Sep 10;103(5):820-835.e7. Epub 2019 Jul 10.

Genetics and Aging Research Unit, McCance Center for Brain Health, Mass General Institute for Neurodegenerative Disease, Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Charlestown, MA 02129, USA. Electronic address:

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http://dx.doi.org/10.1016/j.neuron.2019.06.010DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6728215PMC
September 2019

Exploiting the Zonulin Mouse Model to Establish the Role of Primary Impaired Gut Barrier Function on Microbiota Composition and Immune Profiles.

Front Immunol 2019 19;10:2233. Epub 2019 Sep 19.

Department of Pediatric Gastroenterology and Nutrition, Mucosal Immunology and Biology Research Center, Massachusetts General Hospital, Boston, MA, United States.

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http://dx.doi.org/10.3389/fimmu.2019.02233DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6761304PMC
September 2019

The Histone Deacetylase SIRT6 Restrains Transcription Elongation via Promoter-Proximal Pausing.

Mol Cell 2019 08 6;75(4):683-699.e7. Epub 2019 Aug 6.

The Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, MA 02114, USA; The MGH Center for Regenerative Medicine, Harvard Medical School, Boston, MA 02114, USA; The Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA. Electronic address:

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http://dx.doi.org/10.1016/j.molcel.2019.06.034DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6907403PMC
August 2019

Single-Cell RNA-seq: Introduction to Bioinformatics Analysis.

Curr Protoc Mol Biol 2019 06;127(1):e92

Department of Molecular Biology, Massachusetts General Hospital, Boston, Massachusetts.

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http://dx.doi.org/10.1002/cpmb.92DOI Listing
June 2019

Human gut derived-organoids provide model to study gluten response and effects of microbiota-derived molecules in celiac disease.

Sci Rep 2019 May 7;9(1):7029. Epub 2019 May 7.

Mucosal Immunology and Biology Research Center and Center for Celiac Research and Treatment, Department of Pediatrics, Massachusetts General Hospital, Boston, MA, USA.

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http://dx.doi.org/10.1038/s41598-019-43426-wDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6505524PMC
May 2019

Robust interferon signature and suppressed tissue repair gene expression in synovial tissue from patients with postinfectious, Borrelia burgdorferi-induced Lyme arthritis.

Cell Microbiol 2019 02 17;21(2):e12954. Epub 2018 Oct 17.

Center for Immunology and Inflammatory Diseases, Division of Rheumatology, Allergy, and Immunology, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts, USA.

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http://doi.wiley.com/10.1111/cmi.12954
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http://dx.doi.org/10.1111/cmi.12954DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6724218PMC
February 2019

RNA-seq: Basic Bioinformatics Analysis.

Curr Protoc Mol Biol 2018 10 17;124(1):e68. Epub 2018 Sep 17.

Department of Molecular Biology, Massachusetts General Hospital, Boston, Massachusetts.

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http://dx.doi.org/10.1002/cpmb.68DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6168365PMC
October 2018

Whole Genome Next-Generation Sequencing Mutation Identification in Pseudomonas aeruginosa.

Curr Protoc Mol Biol 2018 10 21;124(1):e69. Epub 2018 Sep 21.

Department of Molecular Biology, Massachusetts General Hospital, Boston, Massachusetts.

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http://doi.wiley.com/10.1002/cpmb.69
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http://dx.doi.org/10.1002/cpmb.69DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6168388PMC
October 2018

Cell of origin dictates aggression and stem cell number in acute lymphoblastic leukemia.

Leukemia 2018 08 18;32(8):1860-1865. Epub 2018 Apr 18.

Department of Pathology, Massachusetts General Hospital Research Institute, Boston, MA, 02114, USA.

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http://dx.doi.org/10.1038/s41375-018-0130-0DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6620784PMC
August 2018

Prospective Isolation of Poised iPSC Intermediates Reveals Principles of Cellular Reprogramming.

Cell Stem Cell 2018 Aug 12;23(2):289-305.e5. Epub 2018 Jul 12.

Department of Molecular Biology, Cancer Center, and Center for Regenerative Medicine, Massachusetts General Hospital, 185 Cambridge Street, Boston, MA 02114, USA; Harvard Stem Cell Institute, 1350 Massachusetts Avenue, Cambridge, MA 02138, USA; Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA. Electronic address:

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https://linkinghub.elsevier.com/retrieve/pii/S19345909183029
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http://dx.doi.org/10.1016/j.stem.2018.06.013DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6086589PMC
August 2018

The surveillance of pre-mRNA splicing is an early step in RNAi of endogenous genes.

Genes Dev 2018 05 8;32(9-10):670-681. Epub 2018 May 8.

Department of Molecular Biology, Massachusetts General Hospital, Boston, Massachusetts 02114, USA.

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http://dx.doi.org/10.1101/gad.311514.118DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6004069PMC
May 2018

Direct Reprogramming of Mouse Fibroblasts into Functional Skeletal Muscle Progenitors.

Stem Cell Reports 2018 05;10(5):1505-1521

Department of Molecular Biology, Massachusetts General Hospital, Boston, MA 02114, USA; Center for Regenerative Medicine, Massachusetts General Hospital, Boston, MA 02114, USA; Cancer Center, Massachusetts General Hospital, Boston, MA 02114, USA; Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA; Harvard Stem Cell Institute, Cambridge, MA 02138, USA. Electronic address:

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http://dx.doi.org/10.1016/j.stemcr.2018.04.009DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5995754PMC
May 2018

Nudt21 Controls Cell Fate by Connecting Alternative Polyadenylation to Chromatin Signaling.

Cell 2018 01 14;172(1-2):106-120.e21. Epub 2017 Dec 14.

Department of Molecular Biology, Massachusetts General Hospital, Boston, MA 02114, USA; Center for Regenerative Medicine, Massachusetts General Hospital, Boston, MA 02114, USA; Cancer Center, Massachusetts General Hospital, Boston, MA 02114, USA; Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA; Harvard Stem Cell Institute, Cambridge, MA 02138, USA. Electronic address:

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http://dx.doi.org/10.1016/j.cell.2017.11.023DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5766360PMC
January 2018

Polycomb Repressive Complex 2 Methylates Elongin A to Regulate Transcription.

Mol Cell 2017 Dec 16;68(5):872-884.e6. Epub 2017 Nov 16.

Department of Molecular Biology, Massachusetts General Hospital, Boston, MA 02114, USA; Department of Genetics, Harvard Medical School, Boston, MA 02115, USA. Electronic address:

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https://linkinghub.elsevier.com/retrieve/pii/S10972765173080
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http://dx.doi.org/10.1016/j.molcel.2017.10.025DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5800316PMC
December 2017

Genetic Intersection of Tsix and Hedgehog Signaling during the Initiation of X-Chromosome Inactivation.

Dev Cell 2017 11 26;43(3):359-371.e6. Epub 2017 Oct 26.

Howard Hughes Medical Institute, Boston, MA 02114, USA; Department of Molecular Biology, Massachusetts General Hospital, Boston, MA 02114, USA; Department of Genetics, Harvard Medical School, Boston, MA 02114, USA; Department of Pathology, Massachusetts General Hospital, Boston, MA 02114, USA. Electronic address:

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http://dx.doi.org/10.1016/j.devcel.2017.09.027DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5701747PMC
November 2017

Polycomb Repressive Complex 1 Generates Discrete Compacted Domains that Change during Differentiation.

Mol Cell 2017 Feb;65(3):432-446.e5

Department of Molecular Biology, Massachusetts General Hospital, Boston, MA 02114, USA; Department of Genetics, Harvard Medical School, Boston, MA 02115, USA. Electronic address:

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https://linkinghub.elsevier.com/retrieve/pii/S10972765173003
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http://dx.doi.org/10.1016/j.molcel.2017.01.009DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5421375PMC
February 2017

Survival in Quiescence Requires the Euchromatic Deployment of Clr4/SUV39H by Argonaute-Associated Small RNAs.

Mol Cell 2016 12;64(6):1088-1101

Massachusetts General Hospital Center for Cancer Research and Department of Medicine, Harvard Medical School, Charlestown, MA 02129, USA. Electronic address:

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http://dx.doi.org/10.1016/j.molcel.2016.11.020DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5180613PMC
December 2016

Influence of maternal breast milk ingestion on acquisition of the intestinal microbiome in preterm infants.

Microbiome 2016 12 30;4(1):68. Epub 2016 Dec 30.

Department of Pediatrics, Mucosal Immunology and Biology Research Center, Massachusetts General Hospital for Children, Harvard Medical School, Boston, MA, USA.

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http://dx.doi.org/10.1186/s40168-016-0214-xDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5200970PMC
December 2016

Inhibition of Dihydroorotate Dehydrogenase Overcomes Differentiation Blockade in Acute Myeloid Leukemia.

Cell 2016 Sep 15;167(1):171-186.e15. Epub 2016 Sep 15.

Center for Regenerative Medicine, Massachusetts General Hospital, Boston, MA 02114, USA; Cancer Center, Massachusetts General Hospital, Boston, MA 02114, USA; Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA; Harvard Stem Cell Institute, Cambridge, MA 02138, USA. Electronic address:

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https://linkinghub.elsevier.com/retrieve/pii/S00928674163115
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http://dx.doi.org/10.1016/j.cell.2016.08.057DOI Listing
September 2016

SIRT6 Suppresses Pancreatic Cancer through Control of Lin28b.

Cell 2016 Jun 12;165(6):1401-1415. Epub 2016 May 12.

The Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, MA 02114, USA; The MGH Center for Regenerative Medicine, Harvard Medical School, Boston, MA 02114, USA; The Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA. Electronic address:

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http://dx.doi.org/10.1016/j.cell.2016.04.033DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4892983PMC
June 2016

Single-cell transcriptional analysis of normal, aberrant, and malignant hematopoiesis in zebrafish.

J Exp Med 2016 05 2;213(6):979-92. Epub 2016 May 2.

Molecular Pathology, Massachusetts General Hospital, Charlestown, MA 02129 Cancer Center, Massachusetts General Hospital, Charlestown, MA 02129 Center for Regenerative Medicine, Massachusetts General Hospital, Boston, MA 02114 Harvard Stem Cell Institute, Cambridge, MA 02139

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http://dx.doi.org/10.1084/jem.20152013DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4886368PMC
May 2016

A Specialized Mechanism of Translation Mediated by FXR1a-Associated MicroRNP in Cellular Quiescence.

Mol Cell 2016 Mar;61(5):760-773

Center for Cancer Research, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA; Center for Regenerative Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA. Electronic address:

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http://dx.doi.org/10.1016/j.molcel.2016.02.013DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4811377PMC
March 2016

Allelic Imbalance Is a Prevalent and Tissue-Specific Feature of the Mouse Transcriptome.

Genetics 2015 Jun 9;200(2):537-49. Epub 2015 Apr 9.

Howard Hughes Medical Institute, Chevy Chase, Maryland 20815-6789 Department of Molecular Biology, Massachusetts General Hospital, Boston, MA 02114 Department of Genetics, Harvard Medical School, Boston, MA 02115 Department of Pathology, Harvard Medical School, Boston, MA 02115

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http://dx.doi.org/10.1534/genetics.115.176263DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4492378PMC
June 2015

Using homology relations within a database markedly boosts protein sequence similarity search.

Proc Natl Acad Sci U S A 2015 Jun 18;112(22):7003-8. Epub 2015 May 18.

Department of Molecular Biophysics, University of Texas Southwestern Medical Center, Dallas, TX 75390-9050; Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, TX 75390-9050

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http://dx.doi.org/10.1073/pnas.1424324112DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4460465PMC
June 2015

The long noncoding RNAs NEAT1 and MALAT1 bind active chromatin sites.

Mol Cell 2014 Sep 21;55(5):791-802. Epub 2014 Aug 21.

Department of Molecular Biology, Massachusetts General Hospital, Boston, MA 02114, USA; Department of Genetics, Harvard Medical School, Boston, MA 02115, USA. Electronic address:

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http://www.cell.com/molecular-cell/pdf/S1097-2765(14)00605-4
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http://linkinghub.elsevier.com/retrieve/pii/S109727651400605
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http://dx.doi.org/10.1016/j.molcel.2014.07.012DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4428586PMC
September 2014

H3K27 modifications define segmental regulatory domains in the Drosophila bithorax complex.

Elife 2014 Jul 31;3:e02833. Epub 2014 Jul 31.

Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, United States.

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http://dx.doi.org/10.7554/eLife.02833DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4139060PMC
July 2014

BRCA1 establishes DNA damage signaling and pericentric heterochromatin of the X chromosome in male meiosis.

J Cell Biol 2014 Jun;205(5):663-75

Division of Reproductive Sciences and Division of Developmental Biology, Perinatal Institute, Division of Experimental Hematology and Cancer Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, 45229Division of Reproductive Sciences and Division of Developmental Biology, Perinatal Institute, Division of Experimental Hematology and Cancer Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, 45229 Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH 45229

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http://dx.doi.org/10.1083/jcb.201311050DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4050732PMC
June 2014

Informatics for molecular biologists.

Curr Protoc Mol Biol 2014 Apr 14;106:19.0.1-2. Epub 2014 Apr 14.

Department of Molecular Biology, Massachusetts General Hospital and, Department of Pathology, Massachusetts General Hospital and, Harvard Medical School, Boston, MA.

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http://dx.doi.org/10.1002/0471142727.mb1900s106DOI Listing
April 2014

Bimodal quantitative relationships between histone modifications for X-linked and autosomal loci.

Proc Natl Acad Sci U S A 2013 Apr 5;110(17):6949-54. Epub 2013 Apr 5.

Department of Molecular Biology, Massachusetts General Hospital, Boston, MA 02114, USA.

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http://dx.doi.org/10.1073/pnas.1216449110DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3637770PMC
April 2013

Xist RNA is a potent suppressor of hematologic cancer in mice.

Cell 2013 Feb;152(4):727-42

Howard Hughes Medical Institute, Massachusetts General Hospital, Boston, MA 02114, USA.

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http://dx.doi.org/10.1016/j.cell.2013.01.034DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3875356PMC
February 2013

Spreading of X chromosome inactivation via a hierarchy of defined Polycomb stations.

Genome Res 2012 Oct 4;22(10):1864-76. Epub 2012 Sep 4.

Howard Hughes Medical Institute, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts 02114, USA.

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http://dx.doi.org/10.1101/gr.133751.111DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3460182PMC
October 2012

X-chromosome hyperactivation in mammals via nonlinear relationships between chromatin states and transcription.

Nat Struct Mol Biol 2011 Dec 4;19(1):56-61. Epub 2011 Dec 4.

Howard Hughes Medical Institute, Boston, Massachusetts, USA.

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http://www.nature.com/articles/nsmb.2195
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http://dx.doi.org/10.1038/nsmb.2195DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3732781PMC
December 2011

A boundary element between Tsix and Xist binds the chromatin insulator Ctcf and contributes to initiation of X-chromosome inactivation.

Genetics 2011 Oct 11;189(2):441-54. Epub 2011 Aug 11.

Howard Hughes Medical Institute, Department of Molecular Biology, Massachusetts General Hospital, Department of Genetics, Harvard Medical School, Boston, Massachusetts 02114, USA.

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http://www.genetics.org/lookup/doi/10.1534/genetics.111.1326
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http://dx.doi.org/10.1534/genetics.111.132662DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3189804PMC
October 2011

Considering scores between unrelated proteins in the search database improves profile comparison.

BMC Bioinformatics 2009 Dec 4;10:399. Epub 2009 Dec 4.

Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, 5323 Harry Hines Blvd, Dallas, TX 75390-9050, USA.

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http://dx.doi.org/10.1186/1471-2105-10-399DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3087343PMC
December 2009

Phenotypic and genotypic analyses of genetic skin disease through the Online Mendelian Inheritance in Man (OMIM) database.

J Invest Dermatol 2009 Nov 18;129(11):2628-36. Epub 2009 Jun 18.

Department of Dermatology, University of California at San Francisco, San Francisco, California, USA.

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http://dx.doi.org/10.1038/jid.2009.108DOI Listing
November 2009

Phenotypic categorization of genetic skin diseases reveals new relations between phenotypes, genes and pathways.

Bioinformatics 2009 Nov 10;25(22):2891-6. Epub 2009 Sep 10.

Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, 5323 Harry Hines Blvd, Dallas, TX 75390-9050, USA.

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https://academic.oup.com/bioinformatics/article-lookup/doi/1
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http://dx.doi.org/10.1093/bioinformatics/btp538DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2773259PMC
November 2009

PROCAIN server for remote protein sequence similarity search.

Bioinformatics 2009 Aug 3;25(16):2076-7. Epub 2009 Jun 3.

Biomedical Engineering Program, University of Texas Southwestern Medical Center, University of Texas Southwestern Medical Center, 5323 Harry Hines Blvd, Dallas, TX 75390-9050, USA.

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http://dx.doi.org/10.1093/bioinformatics/btp346DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2723001PMC
August 2009

COMPASS server for homology detection: improved statistical accuracy, speed and functionality.

Nucleic Acids Res 2009 Jul 12;37(Web Server issue):W90-4. Epub 2009 May 12.

Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, 5323 Harry Hines Blvd, Dallas, TX 75390-9050, USA.

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http://dx.doi.org/10.1093/nar/gkp360DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2703893PMC
July 2009

PROCAIN: protein profile comparison with assisting information.

Nucleic Acids Res 2009 Jun 7;37(11):3522-30. Epub 2009 Apr 7.

Biomedical Engineering Program, University of Texas Southwestern Medical Center, Dallas, TX 75390-9050, USA.

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http://dx.doi.org/10.1093/nar/gkp212DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2699500PMC
June 2009

Discrete-continuous duality of protein structure space.

Curr Opin Struct Biol 2009 Jun 29;19(3):321-8. Epub 2009 May 29.

Howard Hughes Medical Institute, 5323 Harry Hines Blvd, Dallas, TX 75390-9050, USA.

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http://dx.doi.org/10.1016/j.sbi.2009.04.009DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3688466PMC
June 2009

Structure similarity measure with penalty for close non-equivalent residues.

Bioinformatics 2009 May 25;25(10):1259-63. Epub 2009 Mar 25.

Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, 5323 Harry Hines Blvd, Dallas, TX 75390-9050, USA.

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http://dx.doi.org/10.1093/bioinformatics/btp148DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2677741PMC
May 2009

Analysis of CASP8 targets, predictions and assessment methods.

Database (Oxford) 2009 14;2009:bap003. Epub 2009 Apr 14.

Howard Hughes Medical Institute and Department of Biochemistry, University of Texas Southwestern Medical Center, 5323 Harry Hines Blvd, Dallas, TX 75390-9050, USA.

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http://dx.doi.org/10.1093/database/bap003DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2794793PMC
April 2009

Accurate statistical model of comparison between multiple sequence alignments.

Nucleic Acids Res 2008 Apr 19;36(7):2240-8. Epub 2008 Feb 19.

Howard Hughes Medical Institute, Dallas, TX 75390-9050, USA.

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http://dx.doi.org/10.1093/nar/gkn065DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2367703PMC
April 2008

A comprehensive system for evaluation of remote sequence similarity detection.

BMC Bioinformatics 2007 Aug 28;8:314. Epub 2007 Aug 28.

Department of Biochemistry, University of Texas Southwestern Medical Center, 5323, Harry Hines Blvd, Dallas, TX 75390-9050, USA.

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http://dx.doi.org/10.1186/1471-2105-8-314DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2031906PMC
August 2007

COMPASS server for remote homology inference.

Nucleic Acids Res 2007 Jul 21;35(Web Server issue):W653-8. Epub 2007 May 21.

Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, 5323 Harry Hines Blvd, Dallas, TX 75390-9050, USA.

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http://dx.doi.org/10.1093/nar/gkm293DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1933213PMC
July 2007

A tale of two ferredoxins: sequence similarity and structural differences.

BMC Struct Biol 2006 Apr 9;6. Epub 2006 Apr 9.

Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, TX 75390-9050, USA.

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http://dx.doi.org/10.1186/1472-6807-6-8DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1459171PMC
April 2006

Exploring dynamics of protein structure determination and homology-based prediction to estimate the number of superfamilies and folds.

BMC Struct Biol 2006 Mar 20;6. Epub 2006 Mar 20.

Howard Hughes Medical Institute, Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX 75390-8816, USA.

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http://dx.doi.org/10.1186/1472-6807-6-6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1444916PMC
March 2006

Estimates of statistical significance for comparison of individual positions in multiple sequence alignments.

BMC Bioinformatics 2004 Aug 5;5:106. Epub 2004 Aug 5.

Howard Hughes Medical Institute, Department of Biochemistry, University of Texas Southwestern Medical Center, 5323, Harry Hines Blvd, Dallas, TX 75390-9050, USA.

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http://bmcbioinformatics.biomedcentral.com/articles/10.1186/
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http://dx.doi.org/10.1186/1471-2105-5-106DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC516024PMC
August 2004

Quality of alignment comparison by COMPASS improves with inclusion of diverse confident homologs.

Bioinformatics 2004 Apr 29;20(6):818-28. Epub 2004 Jan 29.

Howard Hughes Medical Institute, and Department of Biochemistry, University of Texas Southwestern Medical Center, 5323, Harry Hines Blvd, Dallas, TX 75390-9050, USA.

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http://dx.doi.org/10.1093/bioinformatics/btg485DOI Listing
April 2004

CASP5 assessment of fold recognition target predictions.

Proteins 2003 ;53 Suppl 6:395-409

Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, Texas 75390-9050, USA.

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http://dx.doi.org/10.1002/prot.10557DOI Listing
January 2004

Profile-profile comparisons by COMPASS predict intricate homologies between protein families.

Protein Sci 2003 Oct;12(10):2262-72

Howard Hughes Medical Institute and Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, Texas 75390-9050, USA.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2366929PMC
http://dx.doi.org/10.1110/ps.03197403DOI Listing
October 2003

Effects of glutamate agonists on the isolated neurons from the locomotor network of the mollusc Clione limacina.

Neuroreport 2002 Dec;13(17):2235-9

A. N. Belozersky Institute of Physico-Chemical Biology, Moscow State University, Moscow 119899, Russia.

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http://dx.doi.org/10.1097/00001756-200212030-00014DOI Listing
December 2002