Alexander Meissner

Alexander Meissner

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Alexander Meissner

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Differential regulation of OCT4 targets facilitates reacquisition of pluripotency.

Nat Commun 2019 Sep 30;10(1):4444. Epub 2019 Sep 30.

Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA.

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http://dx.doi.org/10.1038/s41467-019-11741-5DOI Listing
September 2019

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

Cell Stem Cell 2019 Sep 27. Epub 2019 Sep 27.

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
September 2019

Nanopype: a modular and scalable nanopore data processing pipeline.

Bioinformatics 2019 Aug 6. Epub 2019 Aug 6.

Department of Genome Regulation, Max Planck Institute for Molecular Genetics, Berlin, Germany.

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http://dx.doi.org/10.1093/bioinformatics/btz547DOI Listing
August 2019

Activation of neuronal genes via LINE-1 elements upon global DNA demethylation in human neural progenitors.

Nat Commun 2019 Jul 18;10(1):3182. Epub 2019 Jul 18.

Wallenberg Neuroscience Center and Lund Stem Cell Center, Laboratory of Molecular Neurogenetics, Department of Experimental Medical Science, BMC A11, Lund University, 221 84, Lund, Sweden.

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http://dx.doi.org/10.1038/s41467-019-11150-8DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6639357PMC
July 2019

Cross-Regulation between TDP-43 and Paraspeckles Promotes Pluripotency-Differentiation Transition.

Mol Cell 2019 06 29;74(5):951-965.e13. Epub 2019 Apr 29.

Institute of Stem Cell Research, Helmholtz Zentrum München, 85764 Neuherberg, Germany; Comprehensive Pneumology Center (CPC-M), Ludwig-Maximilians-Universität München, Asklepios Fachkliniken München-Gauting und Helmholtz Zentrum München, Max-Lebsche-Platz 31, 81377 Munich, Germany. Electronic address:

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http://dx.doi.org/10.1016/j.molcel.2019.03.041DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6561722PMC
June 2019

Molecular recording of mammalian embryogenesis.

Nature 2019 06 13;570(7759):77-82. Epub 2019 May 13.

Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA, USA.

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http://dx.doi.org/10.1038/s41586-019-1184-5DOI Listing
June 2019

Nanopype: A modular and scalable nanopore data processing pipeline.

Bioinformatics 2019 Jun 13. Epub 2019 Jun 13.

Department of Genome Regulation, Max Planck Institute for Molecular Genetics, Berlin, Germany.

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http://dx.doi.org/10.1093/bioinformatics/btz461DOI Listing
June 2019

KDM5 Histone Demethylase Activity Links Cellular Transcriptomic Heterogeneity to Therapeutic Resistance.

Cancer Cell 2018 12 21;34(6):939-953.e9. Epub 2018 Nov 21.

Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Medicine, Harvard Medical School, Boston, MA 02115, USA; Center for Cancer Evolution, Dana-Farber Cancer Institute, Boston, MA 02215, USA; The Eli and Edythe L Broad Institute of MIT and Harvard, Cambridge, MA 02139, USA; Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Ludwig Center at Harvard, Boston, MA 02215, USA. Electronic address:

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https://linkinghub.elsevier.com/retrieve/pii/S15356108183048
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http://dx.doi.org/10.1016/j.ccell.2018.10.014DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6310147PMC
December 2018

Chromatin-dependent allosteric regulation of DNMT3A activity by MeCP2.

Nucleic Acids Res 2018 09;46(17):9044-9056

Department of Biochemistry, Institute of Biochemistry and Technical Biochemistry, Faculty of Chemistry, University Stuttgart, Allmandring 31, 70569 Stuttgart, Germany.

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http://dx.doi.org/10.1093/nar/gky715DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6158614PMC
September 2018

Aligning Single-Cell Developmental and Reprogramming Trajectories Identifies Molecular Determinants of Myogenic Reprogramming Outcome.

Cell Syst 2018 09 5;7(3):258-268.e3. Epub 2018 Sep 5.

Molecular & Cellular Biology Program, University of Washington, Seattle, WA, USA; Department of Genome Sciences, University of Washington, Seattle, WA, USA. Electronic address:

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http://dx.doi.org/10.1016/j.cels.2018.07.006DOI Listing
September 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

An Intermediate Pluripotent State Controlled by MicroRNAs Is Required for the Naive-to-Primed Stem Cell Transition.

Cell Stem Cell 2018 Jun 24;22(6):851-864.e5. Epub 2018 May 24.

Stem Cell Program, Division of Hematology/Oncology, Boston Children's Hospital, Boston, MA 02115, USA; Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA; Harvard Stem Cell Institute, Cambridge, MA 02138, USA; Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA; Harvard Initiative for RNA Medicine, Boston, MA 02115, USA. Electronic address:

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http://dx.doi.org/10.1016/j.stem.2018.04.021DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5990487PMC
June 2018

X Chromosome Dosage Influences DNA Methylation Dynamics during Reprogramming to Mouse iPSCs.

Stem Cell Reports 2018 05 19;10(5):1537-1550. Epub 2018 Apr 19.

Department of Biological Chemistry, Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, Jonsson Comprehensive Cancer Center, Molecular Biology Institute, David Geffen School of Medicine, University of California Los Angeles, 615 Charles E. Young Drive South, BSRB 390D, Los Angeles, CA 90095, USA. Electronic address:

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http://dx.doi.org/10.1016/j.stemcr.2018.03.019DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5995367PMC
May 2018

Dissecting the Functional Consequences of De Novo DNA Methylation Dynamics in Human Motor Neuron Differentiation and Physiology.

Cell Stem Cell 2018 04 15;22(4):559-574.e9. Epub 2018 Mar 15.

The Ken & Ruth Davee Department of Neurology, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA; Department of Physiology, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA. Electronic address:

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http://dx.doi.org/10.1016/j.stem.2018.02.012DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6535433PMC
April 2018

A CLK3-HMGA2 Alternative Splicing Axis Impacts Human Hematopoietic Stem Cell Molecular Identity throughout Development.

Cell Stem Cell 2018 04;22(4):575-588.e7

Stem Cell Program, Division of Hematology/Oncology, Manton Center for Orphan Disease Research, Boston Children's Hospital and Dana-Farber Cancer Institute, Boston, MA 02115, USA; Department of Biological Chemistry and Molecular Pharmacology, Harvard Stem Cell Institute, Harvard Medical School, Boston, MA 02115, USA; Harvard Stem Cell Institute, Cambridge, MA 02138, USA. Electronic address:

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http://dx.doi.org/10.1016/j.stem.2018.03.012DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5957284PMC
April 2018

Zika Virus Alters DNA Methylation of Neural Genes in an Organoid Model of the Developing Human Brain.

mSystems 2018 Jan-Feb;3(1). Epub 2018 Feb 6.

Huffington Center for Cell-Based Research in Parkinson's Disease, Black Family Stem Cell Institute, Department of Cell, Developmental and Regenerative Biology, Icahn School of Medicine at Mount Sinai, New York, New York, USA.

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http://dx.doi.org/10.1128/mSystems.00219-17DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5801341PMC
February 2018

Targeted bisulfite sequencing of the dynamic DNA methylome.

Epigenetics Chromatin 2016 3;9:55. Epub 2016 Dec 3.

Broad Institute of MIT and Harvard, Cambridge, MA 02142 USA ; Harvard Stem Cell Institute, Cambridge, MA 02138 USA ; Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138 USA ; Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany.

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http://dx.doi.org/10.1186/s13072-016-0105-1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5135789PMC
January 2018

DUSP9 Modulates DNA Hypomethylation in Female Mouse Pluripotent Stem Cells.

Cell Stem Cell 2017 05 30;20(5):706-719.e7. Epub 2017 Mar 30.

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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http://dx.doi.org/10.1016/j.stem.2017.03.002DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5524993PMC
May 2017

Induced Pluripotent Stem Cell Differentiation Enables Functional Validation of GWAS Variants in Metabolic Disease.

Cell Stem Cell 2017 04;20(4):547-557.e7

Department of Stem Cell and Regenerative Biology and Harvard Stem Cell Institute, Harvard University, Cambridge, MA 02138, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Center for Regenerative Medicine, Massachusetts General Hospital, Boston, MA 02114, USA. Electronic address:

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http://dx.doi.org/10.1016/j.stem.2017.01.010DOI Listing
April 2017

Probabilistic Modeling of Reprogramming to Induced Pluripotent Stem Cells.

Cell Rep 2016 12;17(12):3395-3406

Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, MA 02115, USA; Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA. Electronic address:

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http://dx.doi.org/10.1016/j.celrep.2016.11.080DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5467646PMC
December 2016

Transcriptional and Chromatin Dynamics of Muscle Regeneration after Severe Trauma.

Stem Cell Reports 2016 11 20;7(5):983-997. Epub 2016 Oct 20.

Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Stem Cell and Regenerative Biology, Harvard Stem Cell Institute, Harvard University, Cambridge, MA 02138, USA.

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http://dx.doi.org/10.1016/j.stemcr.2016.09.009DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5106515PMC
November 2016

Epigenetic Memory Underlies Cell-Autonomous Heterogeneous Behavior of Hematopoietic Stem Cells.

Cell 2016 11;167(5):1310-1322.e17

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

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http://www.cell.com/cell/pdf/S0092-8674(16)31466-0.pdf
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http://www.cell.com/cms/attachment/2072756198/2068594890/mmc
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http://dx.doi.org/10.1016/j.cell.2016.10.045DOI Listing
November 2016

Saturation analysis for whole-genome bisulfite sequencing data.

Nat Biotechnol 2016 07 27;34(7):691-693. Epub 2016 Jun 27.

Medical Genomics, UCL Cancer Institute, University College London, London, UK.

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http://dx.doi.org/10.1038/nbt.3524DOI Listing
July 2016

Molecular features of cellular reprogramming and development.

Nat Rev Mol Cell Biol 2016 Mar 17;17(3):139-54. Epub 2016 Feb 17.

Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, Massachusetts 02138, USA.

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http://dx.doi.org/10.1038/nrm.2016.6DOI Listing
March 2016

Genetic and Epigenetic Variation, but Not Diet, Shape the Sperm Methylome.

Dev Cell 2015 Dec;35(6):750-8

Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605, USA. Electronic address:

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http://dx.doi.org/10.1016/j.devcel.2015.11.024DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4691283PMC
December 2015

A comparison of genetically matched cell lines reveals the equivalence of human iPSCs and ESCs.

Nat Biotechnol 2015 Nov 26;33(11):1173-81. Epub 2015 Oct 26.

Department of Molecular Biology, Cancer Center and Center for Regenerative Medicine, Massachusetts General Hospital, Boston, Massachusetts, USA.

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http://dx.doi.org/10.1038/nbt.3388DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4847940PMC
November 2015

Association of DNA methylation in the brain with age in older persons is confounded by common neuropathologies.

Int J Biochem Cell Biol 2015 Oct 21;67:58-64. Epub 2015 May 21.

Rush Alzheimer's Disease Center, Rush University Medical Center, Chicago, IL, USA; Department of Neurological Sciences, Rush University Medical Center, Chicago, IL, USA.

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http://dx.doi.org/10.1016/j.biocel.2015.05.009DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4564337PMC
October 2015

Ground State Conditions Induce Rapid Reorganization of Core Pluripotency Factor Binding before Global Epigenetic Reprogramming.

Cell Stem Cell 2015 Oct 30;17(4):462-70. Epub 2015 Jul 30.

Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Harvard Stem Cell Institute, Cambridge, MA 02138, USA; Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA. Electronic address:

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http://dx.doi.org/10.1016/j.stem.2015.07.005DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4592414PMC
October 2015

PRC2 Is Required to Maintain Expression of the Maternal Gtl2-Rian-Mirg Locus by Preventing De Novo DNA Methylation in Mouse Embryonic Stem Cells.

Cell Rep 2015 Sep 20;12(9):1456-70. Epub 2015 Aug 20.

Division of Hematology/Oncology, Boston Children's Hospital and Department of Pediatric Oncology, Dana-Farber Cancer Institute (DFCI), Harvard Stem Cell Institute, Harvard Medical School, Boston, MA 02115, USA; Howard Hughes Medical Institute (HHMI), Boston, MA 02115, USA. Electronic address:

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http://dx.doi.org/10.1016/j.celrep.2015.07.053DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5384103PMC
September 2015

In vivo Monitoring of Transcriptional Dynamics After Lower-Limb Muscle Injury Enables Quantitative Classification of Healing.

Sci Rep 2015 Sep 18;5:13885. Epub 2015 Sep 18.

Broad Institute of MIT and Harvard, Cambridge, MA 02142, Harvard Stem Cell Institute, Cambridge, MA 02138, Dept. of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA.

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http://dx.doi.org/10.1038/srep13885DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4585378PMC
September 2015

Integrative Analyses of Human Reprogramming Reveal Dynamic Nature of Induced Pluripotency.

Cell 2015 Jul;162(2):412-424

Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA; Broad Institute, Cambridge, MA 02142, USA; Harvard Stem Cell Institute, Harvard University, Cambridge, MA 02138, USA. Electronic address:

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http://dx.doi.org/10.1016/j.cell.2015.06.016DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4511597PMC
July 2015

Targeted disruption of DNMT1, DNMT3A and DNMT3B in human embryonic stem cells.

Nat Genet 2015 May 30;47(5):469-78. Epub 2015 Mar 30.

1] Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA. [2] Harvard Stem Cell Institute, Cambridge, Massachusetts, USA. [3] Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, Massachusetts, USA.

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http://dx.doi.org/10.1038/ng.3258DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4414868PMC
May 2015

Coverage recommendations for methylation analysis by whole-genome bisulfite sequencing.

Nat Methods 2015 Mar 2;12(3):230-2, 1 p following 232. Epub 2014 Nov 2.

1] Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA. [2] Molecular Pathology Unit, Massachusetts General Hospital, Charlestown, Massachusetts, USA. [3] Center for Cancer Research, Massachusetts General Hospital, Charlestown, Massachusetts, USA. [4] Department of Pathology, Harvard Medical School, Boston, Massachusetts, USA.

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http://dx.doi.org/10.1038/nmeth.3152DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4344394PMC
March 2015

Epigenetic predisposition to reprogramming fates in somatic cells.

EMBO Rep 2015 Mar 18;16(3):370-8. Epub 2015 Jan 18.

Department of Biochemistry and Molecular Biology, Tel Aviv University, Tel Aviv, Israel

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http://dx.doi.org/10.15252/embr.201439264DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4364876PMC
March 2015

Enabling consistency in pluripotent stem cell-derived products for research and development and clinical applications through material standards.

Stem Cells Transl Med 2015 Mar 3;4(3):217-23. Epub 2015 Feb 3.

Oxford-UCL Centre for the Advancement of Sustainable Medical Innovation and Harvard Stem Cell Institute, Cambridge, Massachusetts; Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, Massachusetts, USA; Saïd Business School, University of Oxford, Oxford, United Kingdom; Centre for Behavioural Medicine, UCL School of Pharmacy, University College London, London, United Kingdom; Stanford-UCSF FDA Center of Excellence in Regulatory Science and Innovation (CERSI), San Francisco, California, USA

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http://dx.doi.org/10.5966/sctm.2014-0233DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4339854PMC
March 2015

Age- and pregnancy-associated DNA methylation changes in mammary epithelial cells.

Stem Cell Reports 2015 Feb 22;4(2):297-311. Epub 2015 Jan 22.

Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Medicine, Brigham and Women's Hospital, Boston, MA 02115, USA; Department of Medicine, Harvard Medical School, Boston, MA 02115, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Harvard Stem Cell Institute, Cambridge, MA 02138, USA; Program in Biological and Biomedical Sciences, Harvard Medical School, Boston, MA 02115, USA. Electronic address:

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http://www.cell.com/stem-cell-reports/pdf/S2213-6711(14)0038
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http://www.cell.com/cms/attachment/2025101614/2044763771/mmc
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http://linkinghub.elsevier.com/retrieve/pii/S221367111400386
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http://dx.doi.org/10.1016/j.stemcr.2014.12.009DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4325231PMC
February 2015

Integrative analysis of 111 reference human epigenomes.

Nature 2015 Feb;518(7539):317-30

1] Computer Science and Artificial Intelligence Lab, Massachusetts Institute of Technology, 32 Vassar St, Cambridge, Massachusetts 02139, USA. [2] The Broad Institute of Harvard and MIT, 415 Main Street, Cambridge, Massachusetts 02142, USA.

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http://dx.doi.org/10.1038/nature14248DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4530010PMC
February 2015

Transcription factor binding dynamics during human ES cell differentiation.

Nature 2015 Feb;518(7539):344-9

1] Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA [2] Harvard Stem Cell Institute, Cambridge, Massachusetts 02138, USA [3] Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, Massachusetts 02138, USA.

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http://dx.doi.org/10.1038/nature14233DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4499331PMC
February 2015

Association of Brain DNA methylation in SORL1, ABCA7, HLA-DRB5, SLC24A4, and BIN1 with pathological diagnosis of Alzheimer disease.

JAMA Neurol 2015 Jan;72(1):15-24

Rush Alzheimer's Disease Center, Rush University Medical Center, Chicago, Illinois2Department of Neurological Sciences, Rush University Medical Center, Chicago, Illinois.

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http://dx.doi.org/10.1001/jamaneurol.2014.3049DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4344367PMC
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

(Epi)genomics approaches and their applications.

Methods 2015 Jan;72:1-2

Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Harvard Stem Cell Institute, Cambridge, MA 02138, USA; Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA. Electronic address:

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http://dx.doi.org/10.1016/j.ymeth.2014.12.011DOI Listing
January 2015

Locally disordered methylation forms the basis of intratumor methylome variation in chronic lymphocytic leukemia.

Cancer Cell 2014 Dec;26(6):813-825

Cancer Vaccine Center, Dana-Farber Cancer Institute, Boston, MA 02115, USA; Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02115, USA; Division of Hematology/Oncology, Children's Hospital, Boston, MA 02115, USA. Electronic address:

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http://dx.doi.org/10.1016/j.ccell.2014.10.012DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4302418PMC
December 2014

X chromosome reactivation dynamics reveal stages of reprogramming to pluripotency.

Cell 2014 Dec;159(7):1681-97

Department of Biological Chemistry, Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, Jonsson Comprehensive Cancer Center, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA 90095, USA. Electronic address:

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http://dx.doi.org/10.1016/j.cell.2014.11.040DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4282187PMC
December 2014

Notch inhibition allows oncogene-independent generation of iPS cells.

Nat Chem Biol 2014 Aug 22;10(8):632-639. Epub 2014 Jun 22.

Harvard Stem Cell Institute, Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA.

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http://dx.doi.org/10.1038/nchembio.1552DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4310751PMC
August 2014

DNA methylation dynamics of the human preimplantation embryo.

Nature 2014 Jul 23;511(7511):611-5. Epub 2014 Jul 23.

1] Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA [2] Harvard Stem Cell Institute, Cambridge, Massachusetts 02138, USA [3] Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, Massachusetts 02138, USA.

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http://dx.doi.org/10.1038/nature13581DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4178976PMC
July 2014

Epigenomic profiling of young and aged HSCs reveals concerted changes during aging that reinforce self-renewal.

Cell Stem Cell 2014 May;14(5):673-88

Stem Cells and Regenerative Medicine Center, Department of Pediatrics and Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA; Dan L. Duncan Cancer Center and Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX 77030, USA. Electronic address:

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http://dx.doi.org/10.1016/j.stem.2014.03.002DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4070311PMC
May 2014

The use of small molecules in somatic-cell reprogramming.

Trends Cell Biol 2014 Mar 31;24(3):179-87. Epub 2013 Oct 31.

Broad Institute of MIT and Harvard, 7 Cambridge Center, Cambridge, MA 02142, 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.tcb.2013.09.011DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3943685PMC
March 2014

Proto-oncogenic role of mutant IDH2 in leukemia initiation and maintenance.

Cell Stem Cell 2014 Mar 16;14(3):329-41. Epub 2014 Jan 16.

Cancer Research Institute, Beth Israel Deaconess Cancer Center, Department of Medicine and Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA. Electronic address:

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4380188PMC
March 2014

In Vivo and in vitro dynamics of undifferentiated embryonic cell transcription factor 1.

Stem Cell Reports 2014 Mar 20;2(3):245-52. Epub 2014 Feb 20.

Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA ; Harvard Stem Cell Institute, Cambridge, MA 02138, USA ; Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3964277PMC
March 2014

Generation of organized anterior foregut epithelia from pluripotent stem cells using small molecules.

Stem Cell Res 2013 Nov 29;11(3):1003-12. Epub 2013 Jun 29.

Program in Molecular Medicine, Diabetes Center of Excellence, University of Massachusetts Medical School, 368 Plantation Street, Worcester, MA 01605, USA.

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http://dx.doi.org/10.1016/j.scr.2013.06.007DOI Listing
November 2013

Recommendations for the design and analysis of epigenome-wide association studies.

Nat Methods 2013 Oct;10(10):949-55

1] Obstetrics and Gynecology Epidemiology Center, Department of Obstetrics and Gynecology, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA. [2] Department of Epidemiology, Harvard School of Public Health, Boston, Massachusetts, USA.

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http://dx.doi.org/10.1038/nmeth.2632DOI Listing
October 2013

Tet1 regulates adult hippocampal neurogenesis and cognition.

Cell Stem Cell 2013 Aug 13;13(2):237-45. Epub 2013 Jun 13.

The State Key Laboratory of Molecular Biology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China.

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http://dx.doi.org/10.1016/j.stem.2013.05.006DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4474382PMC
August 2013

Browsing (Epi)genomes: a guide to data resources and epigenome browsers for stem cell researchers.

Cell Stem Cell 2013 Jul;13(1):14-21

Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3750740PMC
July 2013

Proliferation-dependent alterations of the DNA methylation landscape underlie hematopoietic stem cell aging.

Cell Stem Cell 2013 Apr 14;12(4):413-25. Epub 2013 Feb 14.

Program in Cellular and Molecular Medicine, Division of Hematology/Oncology, Boston Children's Hospital, Boston, MA 02116, USA.

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April 2013

DNA methylation: roles in mammalian development.

Nat Rev Genet 2013 Mar 12;14(3):204-20. Epub 2013 Feb 12.

Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, Massachusetts 02138, USA.

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http://www.nature.com/articles/nrg3354
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March 2013

The simplest explanation: passive DNA demethylation in PGCs.

EMBO J 2013 Feb 8;32(3):318-21. Epub 2013 Jan 8.

Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA.

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http://dx.doi.org/10.1038/emboj.2012.349DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3567498PMC
February 2013

Epigenetic obstacles encountered by transcription factors: reprogramming against all odds.

Curr Opin Genet Dev 2012 Oct 23;22(5):409-15. Epub 2012 Aug 23.

Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA.

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http://dx.doi.org/10.1016/j.gde.2012.08.002DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3490009PMC
October 2012

What can epigenomics do for you?

Genome Biol 2012 Oct 23;13(10):420. Epub 2012 Oct 23.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3491409PMC
October 2012

Mouse ooplasm confers context-specific reprogramming capacity.

Nat Genet 2012 Sep 19;44(9):978-80. Epub 2012 Aug 19.

Broad Institute of MIT, Cambridge, Massachusetts, USA.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3432711PMC
September 2012

Transcription factor-mediated epigenetic reprogramming.

J Biol Chem 2012 Sep 5;287(37):30922-31. Epub 2012 Sep 5.

Department of Stem Cell and Regenerative Biology, Harvard University and Harvard Stem Cell Institute, Cambridge, Massachusetts 02138, USA.

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http://www.jbc.org/cgi/doi/10.1074/jbc.R111.319046
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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3438925PMC
September 2012

Sequential ChIP-bisulfite sequencing enables direct genome-scale investigation of chromatin and DNA methylation cross-talk.

Genome Res 2012 Jun 30;22(6):1128-38. Epub 2012 Mar 30.

Radboud University, Nijmegen Center for Molecular Life Sciences, Department of Molecular Biology, 6500 HB Nijmegen, The Netherlands.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3371717PMC
June 2012

In vivo control of CpG and non-CpG DNA methylation by DNA methyltransferases.

PLoS Genet 2012 Jun 28;8(6):e1002750. Epub 2012 Jun 28.

Department of Biological Sciences, Institute of Genetics/Epigenetics, University of Saarland, Saarbrücken, Germany.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3386304PMC
June 2012

Erosion of dosage compensation impacts human iPSC disease modeling.

Cell Stem Cell 2012 May;10(5):595-609

The Harvard Stem Cell Institute, Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3603710PMC
May 2012

A unique regulatory phase of DNA methylation in the early mammalian embryo.

Nature 2012 Mar 28;484(7394):339-44. Epub 2012 Mar 28.

Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3331945PMC
March 2012