Andrew P Feinberg

Andrew P Feinberg

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Andrew P Feinberg

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Analyzing whole genome bisulfite sequencing data from highly divergent genotypes.

Nucleic Acids Res 2019 Aug 8. Epub 2019 Aug 8.

Center for Epigenetics, Johns Hopkins School of Medicine, 855 N. Wolfe St, Baltimore, MD 21205, USA.

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http://dx.doi.org/10.1093/nar/gkz674DOI Listing
August 2019

Independent Methylome-Wide Association Studies of Schizophrenia Detect Consistent Case-Control Differences.

Schizophr Bull 2019 Jun 5. Epub 2019 Jun 5.

Center for Biomarker Research and Precision Medicine, School of Pharmacy, Virginia Commonwealth University, Richmond, VA.

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http://dx.doi.org/10.1093/schbul/sbz056DOI Listing
June 2019

Epigenetic marks of prenatal air pollution exposure found in multiple tissues relevant for child health.

Environ Int 2019 05 28;126:363-376. Epub 2019 Feb 28.

Wendy Klag Center for Autism and Developmental Disabilities, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA; Department of Mental Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA; Department of Environmental Health and Engineering, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA.

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http://dx.doi.org/10.1016/j.envint.2019.02.028DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6446941PMC
May 2019

Ranking genomic features using an information-theoretic measure of epigenetic discordance.

BMC Bioinformatics 2019 Apr 8;20(1):175. Epub 2019 Apr 8.

Whitaker Biomedical Engineering Institute, Johns Hopkins University, Baltimore, MD, USA.

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http://dx.doi.org/10.1186/s12859-019-2777-6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6454630PMC
April 2019

The NASA Twins Study: A multidimensional analysis of a year-long human spaceflight.

Science 2019 04;364(6436)

Northwestern University, Evanston, IL, USA.

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http://dx.doi.org/10.1126/science.aau8650DOI Listing
April 2019

Meta-analysis of epigenome-wide association studies in neonates reveals widespread differential DNA methylation associated with birthweight.

Authors:
Leanne K Küpers Claire Monnereau Gemma C Sharp Paul Yousefi Lucas A Salas Akram Ghantous Christian M Page Sarah E Reese Allen J Wilcox Darina Czamara Anne P Starling Alexei Novoloaca Samantha Lent Ritu Roy Cathrine Hoyo Carrie V Breton Catherine Allard Allan C Just Kelly M Bakulski John W Holloway Todd M Everson Cheng-Jian Xu Rae-Chi Huang Diana A van der Plaat Matthias Wielscher Simon Kebede Merid Vilhelmina Ullemar Faisal I Rezwan Jari Lahti Jenny van Dongen Sabine A S Langie Tom G Richardson Maria C Magnus Ellen A Nohr Zongli Xu Liesbeth Duijts Shanshan Zhao Weiming Zhang Michelle Plusquin Dawn L DeMeo Olivia Solomon Joosje H Heimovaara Dereje D Jima Lu Gao Mariona Bustamante Patrice Perron Robert O Wright Irva Hertz-Picciotto Hongmei Zhang Margaret R Karagas Ulrike Gehring Carmen J Marsit Lawrence J Beilin Judith M Vonk Marjo-Riitta Jarvelin Anna Bergström Anne K Örtqvist Susan Ewart Pia M Villa Sophie E Moore Gonneke Willemsen Arnout R L Standaert Siri E Håberg Thorkild I A Sørensen Jack A Taylor Katri Räikkönen Ivana V Yang Katerina Kechris Tim S Nawrot Matt J Silver Yun Yun Gong Lorenzo Richiardi Manolis Kogevinas Augusto A Litonjua Brenda Eskenazi Karen Huen Hamdi Mbarek Rachel L Maguire Terence Dwyer Martine Vrijheid Luigi Bouchard Andrea A Baccarelli Lisa A Croen Wilfried Karmaus Denise Anderson Maaike de Vries Sylvain Sebert Juha Kere Robert Karlsson Syed Hasan Arshad Esa Hämäläinen Michael N Routledge Dorret I Boomsma Andrew P Feinberg Craig J Newschaffer Eva Govarts Matthieu Moisse M Daniele Fallin Erik Melén Andrew M Prentice Eero Kajantie Catarina Almqvist Emily Oken Dana Dabelea H Marike Boezen Phillip E Melton Rosalind J Wright Gerard H Koppelman Letizia Trevisi Marie-France Hivert Jordi Sunyer Monica C Munthe-Kaas Susan K Murphy Eva Corpeleijn Joseph Wiemels Nina Holland Zdenko Herceg Elisabeth B Binder George Davey Smith Vincent W V Jaddoe Rolv T Lie Wenche Nystad Stephanie J London Debbie A Lawlor Caroline L Relton Harold Snieder Janine F Felix

Nat Commun 2019 04 23;10(1):1893. Epub 2019 Apr 23.

The Generation R Study Group, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands.

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http://dx.doi.org/10.1038/s41467-019-09671-3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6478731PMC
April 2019

A Loss of Epigenetic Control Can Promote Cell Death through Reversing the Balance of Pathways in a Signaling Network.

Mol Cell 2018 10 20;72(1):60-70.e3. Epub 2018 Sep 20.

Yale Systems Biology Institute and Department of Biomedical Engineering, Yale University, New Haven, CT 06520, USA; Department of Biomedical Engineering, Johns Hopkins University School of Medicine and Whiting School of Engineering, Baltimore, MD 21205, USA. Electronic address:

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http://dx.doi.org/10.1016/j.molcel.2018.08.025DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6219618PMC
October 2018

Arioc: GPU-accelerated alignment of short bisulfite-treated reads.

Bioinformatics 2018 08;34(15):2673-2675

Department of Physics and Astronomy, Johns Hopkins University, Baltimore, MD, USA.

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http://dx.doi.org/10.1093/bioinformatics/bty167DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6061805PMC
August 2018

The Key Role of Epigenetics in Human Disease Prevention and Mitigation.

N Engl J Med 2018 Apr;378(14):1323-1334

From the Department of Medicine, Johns Hopkins University School of Medicine, the Department of Biomedical Engineering, Whiting School of Engineering, and the Department of Mental Health, Johns Hopkins Bloomberg School of Public Health - all in Baltimore.

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http://dx.doi.org/10.1056/NEJMra1402513DOI Listing
April 2018

An information-theoretic approach to the modeling and analysis of whole-genome bisulfite sequencing data.

BMC Bioinformatics 2018 03 7;19(1):87. Epub 2018 Mar 7.

Whitaker Biomedical Engineering Institute, Johns Hopkins University, Baltimore, MD, USA.

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http://dx.doi.org/10.1186/s12859-018-2086-5DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5842653PMC
March 2018

"Gap hunting" to characterize clustered probe signals in Illumina methylation array data.

Epigenetics Chromatin 2016 7;9:56. Epub 2016 Dec 7.

Wendy Klag Center for Autism and Developmental Disabilities, Johns Hopkins Bloomberg School of Public Health, 615 N. Wolfe Street, Baltimore, MD 21205 USA.

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http://dx.doi.org/10.1186/s13072-016-0107-zDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5142147PMC
January 2018

Improving Metabolic Health Through Precision Dietetics in Mice.

Genetics 2018 01 20;208(1):399-417. Epub 2017 Nov 20.

Department of Molecular and Cellular Medicine, Texas A&M Health Science Center, Texas A&M University, College Station, Texas 77843

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http://dx.doi.org/10.1534/genetics.117.300536DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5753872PMC
January 2018

Smoking induces DNA methylation changes in Multiple Sclerosis patients with exposure-response relationship.

Sci Rep 2017 11 6;7(1):14589. Epub 2017 Nov 6.

Department of Clinical Neuroscience, Center for Molecular Medicine, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden.

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http://dx.doi.org/10.1038/s41598-017-14788-wDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5674007PMC
November 2017

Cross-tissue integration of genetic and epigenetic data offers insight into autism spectrum disorder.

Nat Commun 2017 10 24;8(1):1011. Epub 2017 Oct 24.

Wendy Klag Center for Autism and Developmental Disabilities, Johns Hopkins Bloomberg School of Public Health, 615 N. Wolfe St, Baltimore, MD, 21205, USA.

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http://dx.doi.org/10.1038/s41467-017-00868-yDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5654961PMC
October 2017

Potential energy landscapes identify the information-theoretic nature of the epigenome.

Nat Genet 2017 May 27;49(5):719-729. Epub 2017 Mar 27.

Center for Epigenetics, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA.

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http://dx.doi.org/10.1038/ng.3811DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5565269PMC
May 2017

DNA methylation mediates genotype and smoking interaction in the development of anti-citrullinated peptide antibody-positive rheumatoid arthritis.

Arthritis Res Ther 2017 03 29;19(1):71. Epub 2017 Mar 29.

Department of Biochemistry and Molecular Biology, The Ministry of Education Key Laboratory of Metabolism and Molecular Medicine, School of Basic Medical Sciences, Fudan University, West Building 13, 130 Dong An Road, Shanghai, China.

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http://dx.doi.org/10.1186/s13075-017-1276-2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5372280PMC
March 2017

DNA methylation signatures of chronic low-grade inflammation are associated with complex diseases.

Genome Biol 2016 12 12;17(1):255. Epub 2016 Dec 12.

Department of Epidemiology, Erasmus University Medical Center, Rotterdam, The Netherlands.

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http://dx.doi.org/10.1186/s13059-016-1119-5DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5151130PMC
December 2016

Epigenetic modulators, modifiers and mediators in cancer aetiology and progression.

Nat Rev Genet 2016 May 14;17(5):284-99. Epub 2016 Mar 14.

Department of Microbiology, Tumour and Cell Biology, Nobels väg 16, Karolinska Institutet, S-171 77 Stockholm, Sweden.

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http://dx.doi.org/10.1038/nrg.2016.13DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4888057PMC
May 2016

DNA methylation of cord blood cell types: Applications for mixed cell birth studies.

Epigenetics 2016 05 28;11(5):354-62. Epub 2016 Mar 28.

b Center for Epigenetics, Johns Hopkins University School of Medicine , Baltimore , Maryland , USA.

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http://dx.doi.org/10.1080/15592294.2016.1161875DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4889293PMC
May 2016

DNA Methylation in Newborns and Maternal Smoking in Pregnancy: Genome-wide Consortium Meta-analysis.

Authors:
Bonnie R Joubert Janine F Felix Paul Yousefi Kelly M Bakulski Allan C Just Carrie Breton Sarah E Reese Christina A Markunas Rebecca C Richmond Cheng-Jian Xu Leanne K Küpers Sam S Oh Cathrine Hoyo Olena Gruzieva Cilla Söderhäll Lucas A Salas Nour Baïz Hongmei Zhang Johanna Lepeule Carlos Ruiz Symen Ligthart Tianyuan Wang Jack A Taylor Liesbeth Duijts Gemma C Sharp Soesma A Jankipersadsing Roy M Nilsen Ahmad Vaez M Daniele Fallin Donglei Hu Augusto A Litonjua Bernard F Fuemmeler Karen Huen Juha Kere Inger Kull Monica Cheng Munthe-Kaas Ulrike Gehring Mariona Bustamante Marie José Saurel-Coubizolles Bilal M Quraishi Jie Ren Jörg Tost Juan R Gonzalez Marjolein J Peters Siri E Håberg Zongli Xu Joyce B van Meurs Tom R Gaunt Marjan Kerkhof Eva Corpeleijn Andrew P Feinberg Celeste Eng Andrea A Baccarelli Sara E Benjamin Neelon Asa Bradman Simon Kebede Merid Anna Bergström Zdenko Herceg Hector Hernandez-Vargas Bert Brunekreef Mariona Pinart Barbara Heude Susan Ewart Jin Yao Nathanaël Lemonnier Oscar H Franco Michael C Wu Albert Hofman Wendy McArdle Pieter Van der Vlies Fahimeh Falahi Matthew W Gillman Lisa F Barcellos Ashish Kumar Magnus Wickman Stefano Guerra Marie-Aline Charles John Holloway Charles Auffray Henning W Tiemeier George Davey Smith Dirkje Postma Marie-France Hivert Brenda Eskenazi Martine Vrijheid Hasan Arshad Josep M Antó Abbas Dehghan Wilfried Karmaus Isabella Annesi-Maesano Jordi Sunyer Akram Ghantous Göran Pershagen Nina Holland Susan K Murphy Dawn L DeMeo Esteban G Burchard Christine Ladd-Acosta Harold Snieder Wenche Nystad Gerard H Koppelman Caroline L Relton Vincent W V Jaddoe Allen Wilcox Erik Melén Stephanie J London

Am J Hum Genet 2016 Apr 31;98(4):680-96. Epub 2016 Mar 31.

National Institute of Environmental Health Sciences, NIH, U.S. Department of Health and Human Services, Research Triangle Park, NC 27709, USA. Electronic address:

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http://dx.doi.org/10.1016/j.ajhg.2016.02.019DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4833289PMC
April 2016

DNA methylation is stable during replication and cell cycle arrest.

Sci Rep 2015 Dec 9;5:17911. Epub 2015 Dec 9.

Center for Epigenetics, Johns Hopkins University School of Medicine.

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http://dx.doi.org/10.1038/srep17911DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4673417PMC
December 2015

An LSC epigenetic signature is largely mutation independent and implicates the HOXA cluster in AML pathogenesis.

Nat Commun 2015 Oct 7;6:8489. Epub 2015 Oct 7.

Center for Epigenetics, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA.

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http://www.nature.com/articles/ncomms9489
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http://dx.doi.org/10.1038/ncomms9489DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4633733PMC
October 2015

Epigenetics at the Crossroads of Genes and the Environment.

JAMA 2015 Sep;314(11):1129-30

Department of Mental Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland.

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http://dx.doi.org/10.1001/jama.2015.10414DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6278824PMC
September 2015

Age and sun exposure-related widespread genomic blocks of hypomethylation in nonmalignant skin.

Genome Biol 2015 Apr 16;16:80. Epub 2015 Apr 16.

Center for Epigenetics, Johns Hopkins University School of Medicine, Rangos 570, 855N. Wolfe St, Baltimore, MD, 21205, USA.

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http://dx.doi.org/10.1186/s13059-015-0644-yDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4423110PMC
April 2015

Mutant WT1 is associated with DNA hypermethylation of PRC2 targets in AML and responds to EZH2 inhibition.

Blood 2015 Jan 14;125(2):316-26. Epub 2014 Nov 14.

Division of Hematology, Department of Medicine, Cancer Institute, and Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA;

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http://www.bloodjournal.org/content/bloodjournal/125/2/316.f
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http://www.bloodjournal.org/cgi/doi/10.1182/blood-2014-03-56
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http://dx.doi.org/10.1182/blood-2014-03-566018DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4287638PMC
January 2015

A comparison of non-integrating reprogramming methods.

Nat Biotechnol 2015 Jan 1;33(1):58-63. Epub 2014 Dec 1.

1] Division of Pediatric Hematology/Oncology, Boston Children's Hospital, Dana-Farber Cancer Institute, Boston, Massachusetts, USA. [2] Harvard Stem Cell Institute, Cambridge, Massachusetts, USA. [3] Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts, USA. [4] Howard Hughes Medical Institute, Children's Hospital Boston and Dana Farber Cancer Institute, Boston, Massachusetts, USA.

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http://dx.doi.org/10.1038/nbt.3070DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4329913PMC
January 2015

Mouse-human experimental epigenetic analysis unmasks dietary targets and genetic liability for diabetic phenotypes.

Cell Metab 2015 Jan;21(1):138-49

Department of Medicine, Johns Hopkins University School of Medicine, 855 North Wolfe Street, Baltimore, MD 21205, USA; Center for Epigenetics, Johns Hopkins University School of Medicine, 855 North Wolfe Street, Baltimore, MD 21205, USA. Electronic address:

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http://dx.doi.org/10.1016/j.cmet.2014.12.014DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4340475PMC
January 2015

The nucleolus gets the silent treatment.

Cell Stem Cell 2014 Dec;15(6):675-6

Center for Epigenetics and Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA. Electronic address:

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http://dx.doi.org/10.1016/j.stem.2014.11.017DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5533169PMC
December 2014

Large hypomethylated blocks as a universal defining epigenetic alteration in human solid tumors.

Genome Med 2014 26;6(8):61. Epub 2014 Aug 26.

Center for Epigenetics, Johns Hopkins University School of Medicine, Baltimore, MD USA ; Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD USA ; Department of Biostatistics and Computational Biology, Dana Farber Cancer Institute and Department of Biostatistics, Harvard School of Public Health, Boston, MA USA.

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http://dx.doi.org/10.1186/s13073-014-0061-yDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4154522PMC
September 2014

A selective phenelzine analogue inhibitor of histone demethylase LSD1.

ACS Chem Biol 2014 Jun 7;9(6):1284-93. Epub 2014 Apr 7.

Department of Pharmacology, ∥Center for Epigenetics and Department of Medicine, ⊥Department of Ophthalmology, and ¶The Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, Johns Hopkins University School of Medicine , Baltimore, Maryland 21205, United States.

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http://pubs.acs.org/doi/10.1021/cb500018s
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http://dx.doi.org/10.1021/cb500018sDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4076021PMC
June 2014

Minfi: a flexible and comprehensive Bioconductor package for the analysis of Infinium DNA methylation microarrays.

Bioinformatics 2014 May 28;30(10):1363-9. Epub 2014 Jan 28.

Department of Pathology, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA, Department of Biostatistics, Johns Hopkins School of Public Health, 615 N Wolfe Street, Baltimore, MD 21205, USA, Lieber Institute of Brain Development, Johns Hopkins Medical Campus, 855 N Wolfe Street, Baltimore, MD 21205, USA, Department of Computer Science, University of Maryland, College Park, MD 20742, USA, Department of Epidemiology, Johns Hopkins School of Public Health, 615 N Wolfe Street, Baltimore, MD 21205, USA, Center for Epigenetics and Department of Medicine, Johns Hopkins University School of Medicine, 570 Rangos, 725 N Wolfe Street, Baltimore, MD 21205, USA and Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.

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http://dx.doi.org/10.1093/bioinformatics/btu049DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4016708PMC
May 2014

GeMes, clusters of DNA methylation under genetic control, can inform genetic and epigenetic analysis of disease.

Am J Hum Genet 2014 Apr 20;94(4):485-95. Epub 2014 Mar 20.

Center for Epigenetics, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA. Electronic address:

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https://linkinghub.elsevier.com/retrieve/pii/S00029297140006
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http://dx.doi.org/10.1016/j.ajhg.2014.02.011DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3980524PMC
April 2014

The epigenetic basis of common human disease.

Trans Am Clin Climatol Assoc 2013 ;124:84-93

Center for Epigenetics, Johns Hopkins School of Medicine, 855 N. Wolfe St, Rangos 570, Baltimore, MD 21205, USA.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3715917PMC
March 2014

Cancer as a dysregulated epigenome allowing cellular growth advantage at the expense of the host.

Nat Rev Cancer 2013 07 13;13(7):497-510. Epub 2013 Jun 13.

Center for Epigenetics, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA.

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http://dx.doi.org/10.1038/nrc3486DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4636434PMC
July 2013

Higher order chromatin organization in cancer.

Semin Cancer Biol 2013 Apr 22;23(2):109-15. Epub 2012 Dec 22.

Center for Epigenetics, Johns Hopkins University School of Medicine, Baltimore, MD 21205, United States.

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http://dx.doi.org/10.1016/j.semcancer.2012.12.001DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3715089PMC
April 2013

A third-generation method reveals cell lineage ancestry.

Nat Methods 2013 Feb;10(2):117-8

Center for Epigenetics, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA.

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http://dx.doi.org/10.1038/nmeth.2338DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5533165PMC
February 2013

Stem cell differentiation as a renewal-reward process: predictions and validation in the colonic crypt.

Adv Exp Med Biol 2012 ;736:199-209

Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD 21218, USA.

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http://link.springer.com/10.1007/978-1-4419-7210-1_11
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http://dx.doi.org/10.1007/978-1-4419-7210-1_11DOI Listing
January 2013

Genome-wide DNA methylation scan in major depressive disorder.

PLoS One 2012 12;7(4):e34451. Epub 2012 Apr 12.

Department of Pediatrics, Stanley Division of Developmental Neurovirology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, Maryland, United States of America.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0034451PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3325245PMC
December 2012

Reversible switching between epigenetic states in honeybee behavioral subcastes.

Nat Neurosci 2012 Oct 16;15(10):1371-3. Epub 2012 Sep 16.

Center for Epigenetics, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA.

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http://www.nature.com/articles/nn.3218
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http://dx.doi.org/10.1038/nn.3218DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3518384PMC
October 2012

Euchromatin islands in large heterochromatin domains are enriched for CTCF binding and differentially DNA-methylated regions.

BMC Genomics 2012 Oct 26;13:566. Epub 2012 Oct 26.

Center for Epigenetics and Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA.

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http://bmcgenomics.biomedcentral.com/articles/10.1186/1471-2
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http://dx.doi.org/10.1186/1471-2164-13-566DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3507770PMC
October 2012

Regulated noise in the epigenetic landscape of development and disease.

Cell 2012 Mar;148(6):1123-31

Center for Epigenetics, Johns Hopkins University, 570 Rangos, 855 North Wolfe Street, Baltimore, MD 21205, USA.

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http://dx.doi.org/10.1016/j.cell.2012.02.045DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3488344PMC
March 2012

Significance analysis and statistical dissection of variably methylated regions.

Biostatistics 2012 Jan 17;13(1):166-78. Epub 2011 Jun 17.

Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD 21205, USA.

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https://academic.oup.com/biostatistics/article-lookup/doi/10
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http://dx.doi.org/10.1093/biostatistics/kxr013DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3276267PMC
January 2012

Donor cell type can influence the epigenome and differentiation potential of human induced pluripotent stem cells.

Nat Biotechnol 2011 Nov 27;29(12):1117-9. Epub 2011 Nov 27.

Stem Cell Transplantation Program, Division of Pediatric Hematology/Oncology, Manton Center for Orphan Disease Research, Howard Hughes Medical Institute, Children's Hospital Boston and Dana-Farber Cancer Institute, Boston, Massachusetts, USA.

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http://dx.doi.org/10.1038/nbt.2052DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3357310PMC
November 2011

A nucleolar protein, H19 opposite tumor suppressor (HOTS), is a tumor growth inhibitor encoded by a human imprinted H19 antisense transcript.

Proc Natl Acad Sci U S A 2011 Oct 21;108(40):16759-64. Epub 2011 Sep 21.

Center for Epigenetics and Department of Medicine, The Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.

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http://www.pnas.org/cgi/doi/10.1073/pnas.1110904108
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http://dx.doi.org/10.1073/pnas.1110904108DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3189046PMC
October 2011

Genome-scale epigenetic reprogramming during epithelial-to-mesenchymal transition.

Nat Struct Mol Biol 2011 Jul 3;18(8):867-74. Epub 2011 Jul 3.

Center for Epigenetics, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA.

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http://www.nature.com/articles/nsmb.2084
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http://dx.doi.org/10.1038/nsmb.2084DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3150339PMC
July 2011

Accurate genome-scale percentage DNA methylation estimates from microarray data.

Biostatistics 2011 Apr 21;12(2):197-210. Epub 2010 Sep 21.

Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University and Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD 21231, USA.

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http://dx.doi.org/10.1093/biostatistics/kxq055DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3062148PMC
April 2011

Epigenomics reveals a functional genome anatomy and a new approach to common disease.

Nat Biotechnol 2010 Oct;28(10):1049-52

Center for Epigenetics and Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA.

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October 2010

Addition of H19 'loss of methylation testing' for Beckwith-Wiedemann syndrome (BWS) increases the diagnostic yield.

J Mol Diagn 2010 Sep 8;12(5):576-88. Epub 2010 Jul 8.

Department of Pathology, Massachusetts General Hospital/Harvard Medical School, Boston, Massachusetts, USA.

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http://dx.doi.org/10.2353/jmoldx.2010.100005DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2928421PMC
September 2010

Comprehensive methylome map of lineage commitment from haematopoietic progenitors.

Nature 2010 Sep 15;467(7313):338-42. Epub 2010 Aug 15.

Center for Epigenetics and Department of Medicine, Johns Hopkins University School of Medicine, 570 Rangos, 725 N. Wolfe St., Baltimore, Maryland 21205, USA.

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http://dx.doi.org/10.1038/nature09367DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2956609PMC
September 2010

Redefining CpG islands using hidden Markov models.

Biostatistics 2010 Jul 8;11(3):499-514. Epub 2010 Mar 8.

Department of Biostatistics, Johns Hopkins University, Baltimore, MD 21205, USA.

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http://dx.doi.org/10.1093/biostatistics/kxq005DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2883304PMC
July 2010

Comprehensive high-throughput arrays for relative methylation (CHARM).

Curr Protoc Hum Genet 2010 Apr;Chapter 20:Unit 20.1.1-19

Department of Medicine, Johns Hopkins University School of Medicine, Center for Epigenetics, Baltimore, Maryland, USA.

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http://dx.doi.org/10.1002/0471142905.hg2001s65DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6353553PMC
April 2010

A species-generalized probabilistic model-based definition of CpG islands.

Mamm Genome 2009 Sep-Oct;20(9-10):674-80. Epub 2009 Sep 24.

Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, 615 North Wolfe Street, E3620, Baltimore, MD 21205, USA.

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http://link.springer.com/10.1007/s00335-009-9222-5
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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2962567PMC
March 2010

Genome-scale approaches to the epigenetics of common human disease.

Virchows Arch 2010 Jan 21;456(1):13-21. Epub 2009 Oct 21.

Center for Epigenetics and Department of Medicine, Johns Hopkins University School of Medicine, 855 N. Wolfe St., Rangos 570, Baltimore, MD 21205, USA.

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http://dx.doi.org/10.1007/s00428-009-0847-2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3107986PMC
January 2010

Evolution in health and medicine Sackler colloquium: Stochastic epigenetic variation as a driving force of development, evolutionary adaptation, and disease.

Proc Natl Acad Sci U S A 2010 Jan 22;107 Suppl 1:1757-64. Epub 2009 Dec 22.

Center for Epigenetics, Johns Hopkins University, Baltimore, MD 21205, USA.

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http://www.pnas.org/cgi/doi/10.1073/pnas.0906183107
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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2868296PMC
January 2010

The human colon cancer methylome shows similar hypo- and hypermethylation at conserved tissue-specific CpG island shores.

Nat Genet 2009 Feb 18;41(2):178-186. Epub 2009 Jan 18.

Center for Epigenetics, Institute for Basic Biomedical Sciences, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.

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http://dx.doi.org/10.1038/ng.298DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2729128PMC
February 2009

Large histone H3 lysine 9 dimethylated chromatin blocks distinguish differentiated from embryonic stem cells.

Nat Genet 2009 Feb 18;41(2):246-50. Epub 2009 Jan 18.

Center for Epigenetics, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2632725PMC
February 2009

A new link between epigenetic progenitor lesions in cancer and the dynamics of signal transduction.

Cell Cycle 2009 Feb 3;8(3):383-90. Epub 2009 Feb 3.

Department of Medicine, Center for Epigenetics, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA.

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http://dx.doi.org/10.4161/cc.8.3.7542DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6275123PMC
February 2009

BAT3 and SET1A form a complex with CTCFL/BORIS to modulate H3K4 histone dimethylation and gene expression.

Mol Cell Biol 2008 Nov 2;28(21):6720-9. Epub 2008 Sep 2.

Radiation Oncology Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA.

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http://dx.doi.org/10.1128/MCB.00568-08DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2573239PMC
November 2008

Overlapping euchromatin/heterochromatin- associated marks are enriched in imprinted gene regions and predict allele-specific modification.

Genome Res 2008 Nov 10;18(11):1806-13. Epub 2008 Oct 10.

Department of Medicine and Center for Epigenetics, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA.

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http://genome.cshlp.org/cgi/doi/10.1101/gr.067587.108
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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2577870PMC
November 2008

Comprehensive high-throughput arrays for relative methylation (CHARM).

Genome Res 2008 May 3;18(5):780-90. Epub 2008 Mar 3.

Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland 21205, USA.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2336799PMC
May 2008

SNP-specific array-based allele-specific expression analysis.

Genome Res 2008 May 27;18(5):771-9. Epub 2008 Mar 27.

Department of Medicine and Center for Epigenetics, Institute of Basic Biomedical Sciences, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA.

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http://www.genome.org/cgi/doi/10.1101/gr.073254.107
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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2336807PMC
May 2008

Epigenetics at the epicenter of modern medicine.

JAMA 2008 Mar;299(11):1345-50

Department of Medicine and Center for Epigenetics, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA.

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http://dx.doi.org/10.1001/jama.299.11.1345DOI Listing
March 2008

Epigenetic silencing of tumour suppressor gene p15 by its antisense RNA.

Nature 2008 Jan;451(7175):202-6

Center for Epigenetics and Department of Medicine, Johns Hopkins University School of Medicine, 720 Rutland Avenue, Baltimore, Maryland 21205, USA.

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http://www.nature.com/articles/nature06468
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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2743558PMC
January 2008

DNA methylation signatures within the human brain.

Am J Hum Genet 2007 Dec 1;81(6):1304-15. Epub 2007 Nov 1.

Center for Epigenetics, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2276356PMC
December 2007

Enhanced sensitivity to IGF-II signaling links loss of imprinting of IGF2 to increased cell proliferation and tumor risk.

Proc Natl Acad Sci U S A 2007 Dec 17;104(52):20926-31. Epub 2007 Dec 17.

Center for Epigenetics and Department of Medicine, Johns Hopkins University School of Medicine, 1064 Ross, 720 Rutland Avenue, Baltimore, MD 21205, USA.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2409243PMC
December 2007

Epigenetic specificity of loss of imprinting of the IGF2 gene in Wilms tumors.

J Natl Cancer Inst 2007 Aug 8;99(16):1270-3. Epub 2007 Aug 8.

Center for Epigenetics, Institute of Basic Biomedical Sciences, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.

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http://dx.doi.org/10.1093/jnci/djm069DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5533193PMC
August 2007

An epigenetic approach to cancer etiology.

Cancer J 2007 Jan-Feb;13(1):70-4

Division of Molecular Medicine, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.

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http://dx.doi.org/10.1097/PPO.0b013e31803c6e3bDOI Listing
June 2007

Phenotypic plasticity and the epigenetics of human disease.

Nature 2007 May;447(7143):433-40

Department of Medicine and Center for Epigenetics, Institute for Basic Biomedical Sciences, Johns Hopkins University School of Medicine, 720 Rutland Avenue, Baltimore, Maryland 21205, USA.

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http://www.nature.com/doifinder/10.1038/nature05919
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May 2007

Detailed DNA methylation profiles of the E-cadherin promoter in the NCI-60 cancer cells.

Mol Cancer Ther 2007 Feb 1;6(2):391-403. Epub 2007 Feb 1.

Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, NIH, Building 37, Room 5056, Bethesda, MD 20892-4255, USA.

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http://dx.doi.org/10.1158/1535-7163.MCT-06-0609DOI Listing
February 2007

Genetics and epigenetics--nature's pen-and-pencil set.

N Engl J Med 2007 Feb;356(7):731-3

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http://dx.doi.org/10.1056/NEJMe068284DOI Listing
February 2007