Bradley Bernstein, MD, PhD

Exposure of iPSC-derived human microglia to brain substrates enables the generation and manipulation of diverse transcriptional states in vitro. Nat Immunol. 2023 08; 24(8):1382-1390. View in: Pubmed

Modeling epigenetic lesions that cause gliomas. Cell. 2023 08 17; 186(17):3674-3685.e14. View in: Pubmed

Ultraviolet radiation shapes dendritic cell leukaemia transformation in the skin. Nature. 2023 Jun; 618(7966):834-841. View in: Pubmed

Impact of supraphysiologic MDM2 expression on chromatin networks and therapeutic responses in sarcoma. Cell Genom. 2023 Jul 12; 3(7):100321. View in: Pubmed

Integrative dissection of gene regulatory elements at base resolution. Cell Genom. 2023 Jun 14; 3(6):100318. View in: Pubmed

The ENCODE Imputation Challenge: a critical assessment of methods for cross-cell type imputation of epigenomic profiles. Genome Biol. 2023 04 18; 24(1):79. View in: Pubmed

The EN-TEx resource of multi-tissue personal epigenomes & variant-impact models. Cell. 2023 03 30; 186(7):1493-1511.e40. View in: Pubmed

Chromatin complex dependencies reveal targeting opportunities in leukemia. Nat Commun. 2023 01 27; 14(1):448. View in: Pubmed

Epigenetic clocks, aging, and cancer. Science. 2022 Dec 23; 378(6626):1276-1277. View in: Pubmed

Single-cell RNA sequencing identifies a paracrine interaction that may drive oncogenic notch signaling in human adenoid cystic carcinoma. Cell Rep. 2022 Nov 29; 41(9):111743. View in: Pubmed

Long-range phasing of dynamic, tissue-specific and allele-specific regulatory elements. Nat Genet. 2022 10; 54(10):1504-1513. View in: Pubmed

Author Correction: Expanded encyclopaedias of DNA elements in the human and mouse genomes. Nature. 2022 May; 605(7909):E3. View in: Pubmed

Author Correction: Perspectives on ENCODE. Nature. 2022 May; 605(7909):E4. View in: Pubmed

Mitochondrial variant enrichment from high-throughput single-cell RNA sequencing resolves clonal populations. Nat Biotechnol. 2022 07; 40(7):1030-1034. View in: Pubmed

Systematic detection of m6A-modified transcripts at single-molecule and single-cell resolution. Cell Rep Methods. 2021 09 27; 1(5). View in: Pubmed

Extended-representation bisulfite sequencing of gene regulatory elements in multiplexed samples and single cells. Nat Biotechnol. 2021 09; 39(9):1086-1094. View in: Pubmed

Single-cell RNA-seq reveals developmental plasticity with coexisting oncogenic states and immune evasion programs in ETP-ALL. Blood. 2021 05 06; 137(18):2463-2480. View in: Pubmed

Epigenetic silencing by SETDB1 suppresses tumour intrinsic immunogenicity. Nature. 2021 07; 595(7866):309-314. View in: Pubmed

Genome-wide programmable transcriptional memory by CRISPR-based epigenome editing. Cell. 2021 04 29; 184(9):2503-2519.e17. View in: Pubmed

Serving on the Navy's Hospital Ships During the Response to COVID-19: Perspective from Two Deployed Missouri Physicians. Mo Med. 2021 Mar-Apr; 118(2):110-112. View in: Pubmed

Epigenetic Alterations in Keratinocyte Carcinoma. J Invest Dermatol. 2021 05; 141(5):1207-1218. View in: Pubmed

High Seroprevalence of Anti-SARS-CoV-2 Antibodies in Chelsea, Massachusetts. J Infect Dis. 2020 11 13; 222(12):1955-1959. View in: Pubmed

Parallel Single-Cell RNA-Seq and Genetic Recording Reveals Lineage Decisions in Developing Embryoid Bodies. Cell Rep. 2020 10 06; 33(1):108222. View in: Pubmed

Data-Driven Polymer Model for Mechanistic Exploration of Diploid Genome Organization. Biophys J. 2020 11 03; 119(9):1905-1916. View in: Pubmed

Clinical sensitivity and interpretation of PCR and serological COVID-19 diagnostics for patients presenting to the hospital. FASEB J. 2020 10; 34(10):13877-13884. View in: Pubmed

Evaluation of SARS-CoV-2 serology assays reveals a range of test performance. Nat Biotechnol. 2020 10; 38(10):1174-1183. View in: Pubmed

Large-Scale Topological Changes Restrain Malignant Progression in Colorectal Cancer. Cell. 2020 09 17; 182(6):1474-1489.e23. View in: Pubmed

Expanded encyclopaedias of DNA elements in the human and mouse genomes. Nature. 2020 07; 583(7818):699-710. View in: Pubmed

Perspectives on ENCODE. Nature. 2020 07; 583(7818):693-698. View in: Pubmed

Detecting sample swaps in diverse NGS data types using linkage disequilibrium. Nat Commun. 2020 07 29; 11(1):3697. View in: Pubmed

Single-cell lineage analysis reveals genetic and epigenetic interplay in glioblastoma drug resistance. Genome Biol. 2020 07 15; 21(1):174. View in: Pubmed

Test performance evaluation of SARS-CoV-2 serological assays. medRxiv. 2020 May 17. View in: Pubmed

Gain-of-Function Genetic Alterations of G9a Drive Oncogenesis. Cancer Discov. 2020 07; 10(7):980-997. View in: Pubmed

Chromatin accessibility promotes hematopoietic and leukemia stem cell activity. Nat Commun. 2020 03 16; 11(1):1406. View in: Pubmed

Immunohistochemical quantification of partial-EMT in oral cavity squamous cell carcinoma primary tumors is associated with nodal metastasis. Oral Oncol. 2019 12; 99:104458. View in: Pubmed

Inducible histone K-to-M mutations are dynamic tools to probe the physiological role of site-specific histone methylation in vitro and in vivo. Nat Cell Biol. 2019 11; 21(11):1449-1461. View in: Pubmed

Re-programing Chromatin with a Bifunctional LSD1/HDAC Inhibitor Induces Therapeutic Differentiation in DIPG. Cancer Cell. 2019 11 11; 36(5):528-544.e10. View in: Pubmed

Altered chromosomal topology drives oncogenic programs in SDH-deficient GISTs. Nature. 2019 11; 575(7781):229-233. View in: Pubmed

Altered chromosomal topology drives oncogenic programs in SDH-deficient GIST. Nature. 2019 Oct 16. View in: Pubmed

Publisher Correction: Enhancer signatures stratify and predict outcomes of non-functional pancreatic neuroendocrine tumors. Nat Med. 2019 Oct; 25(10):1627. View in: Pubmed

Epigenome editing strategies for the functional annotation of CTCF insulators. Nat Commun. 2019 09 18; 10(1):4258. View in: Pubmed

Resolving medulloblastoma cellular architecture by single-cell genomics. Nature. 2019 08; 572(7767):74-79. View in: Pubmed

An Integrative Model of Cellular States, Plasticity, and Genetics for Glioblastoma. Cell. 2019 08 08; 178(4):835-849.e21. View in: Pubmed

Enhancer signatures stratify and predict outcomes of non-functional pancreatic neuroendocrine tumors. Nat Med. 2019 08; 25(8):1260-1265. View in: Pubmed

Corrupted coordination of epigenetic modifications leads to diverging chromatin states and transcriptional heterogeneity in CLL. Nat Commun. 2019 04 23; 10(1):1874. View in: Pubmed

Single-Cell RNA-Seq Reveals AML Hierarchies Relevant to Disease Progression and Immunity. Cell. 2019 03 07; 176(6):1265-1281.e24. View in: Pubmed

A novel method for detecting the cellular stemness state in normal and leukemic human hematopoietic cells can predict disease outcome and drug sensitivity. Leukemia. 2019 08; 33(8):2061-2077. View in: Pubmed

Epigenome-wide study uncovers large-scale changes in histone acetylation driven by tau pathology in aging and Alzheimer's human brains. Nat Neurosci. 2019 01; 22(1):37-46. View in: Pubmed

Single-cell and single-molecule epigenomics to uncover genome regulation at unprecedented resolution. Nat Genet. 2019 01; 51(1):19-25. View in: Pubmed

Transaminase Inhibition by 2-Hydroxyglutarate Impairs Glutamate Biosynthesis and Redox Homeostasis in Glioma. Cell. 2018 09 20; 175(1):101-116.e25. View in: Pubmed

GABPß1L Wakes Up TERT. Cancer Cell. 2018 09 10; 34(3):358-360. View in: Pubmed

Unravelling subclonal heterogeneity and aggressive disease states in TNBC through single-cell RNA-seq. Nat Commun. 2018 09 04; 9(1):3588. View in: Pubmed

Methylation of Histone H3 K4 Mediates Association of the Isw1p ATPase with Chromatin. Mol Cell. 2018 06 07; 70(5):983. View in: Pubmed

Developmental and oncogenic programs in H3K27M gliomas dissected by single-cell RNA-seq. Science. 2018 04 20; 360(6386):331-335. View in: Pubmed

Dual Targeting of Oncogenic Activation and Inflammatory Signaling Increases Therapeutic Efficacy in Myeloproliferative Neoplasms. Cancer Cell. 2018 04 09; 33(4):785-787. View in: Pubmed

Heritability enrichment of specifically expressed genes identifies disease-relevant tissues and cell types. Nat Genet. 2018 04; 50(4):621-629. View in: Pubmed

Orthologous CRISPR-Cas9 enzymes for combinatorial genetic screens. Nat Biotechnol. 2018 02; 36(2):179-189. View in: Pubmed

Dual Targeting of Oncogenic Activation and Inflammatory Signaling Increases Therapeutic Efficacy in Myeloproliferative Neoplasms. Cancer Cell. 2018 01 08; 33(1):29-43.e7. View in: Pubmed

Single-Cell Transcriptomic Analysis of Primary and Metastatic Tumor Ecosystems in Head and Neck Cancer. Cell. 2017 Dec 14; 171(7):1611-1624.e24. View in: Pubmed

Epithelial-to-Mesenchymal Transition Antagonizes Response to Targeted Therapies in Lung Cancer by Suppressing BIM. Clin Cancer Res. 2018 01 01; 24(1):197-208. View in: Pubmed

A B Cell Regulome Links Notch to Downstream Oncogenic Pathways in Small B Cell Lymphomas. Cell Rep. 2017 Oct 17; 21(3):784-797. View in: Pubmed

Cohesin Loss Eliminates All Loop Domains. Cell. 2017 Oct 05; 171(2):305-320.e24. View in: Pubmed

Regulation of the glucocorticoid receptor via a BET-dependent enhancer drives antiandrogen resistance in prostate cancer. Elife. 2017 09 11; 6. View in: Pubmed

A Genetic Variant Associated with Five Vascular Diseases Is a Distal Regulator of Endothelin-1 Gene Expression. Cell. 2017 Jul 27; 170(3):522-533.e15. View in: Pubmed

Epigenetic plasticity and the hallmarks of cancer. Science. 2017 Jul 21; 357(6348). View in: Pubmed

Transcription elongation factors represent in vivo cancer dependencies in glioblastoma. Nature. 2017 07 20; 547(7663):355-359. View in: Pubmed

Decoupling genetics, lineages, and microenvironment in IDH-mutant gliomas by single-cell RNA-seq. Science. 2017 03 31; 355(6332). View in: Pubmed

Systematic dissection of genomic features determining transcription factor binding and enhancer function. Proc Natl Acad Sci U S A. 2017 02 14; 114(7):E1291-E1300. View in: Pubmed

Adaptive Chromatin Remodeling Drives Glioblastoma Stem Cell Plasticity and Drug Tolerance. Cell Stem Cell. 2017 02 02; 20(2):233-246.e7. View in: Pubmed

SMARCB1-mediated SWI/SNF complex function is essential for enhancer regulation. Nat Genet. 2017 Feb; 49(2):289-295. View in: Pubmed

Single-cell RNA-seq supports a developmental hierarchy in human oligodendroglioma. Nature. 2016 11 10; 539(7628):309-313. View in: Pubmed

142 Genetic and Nongenetic Determinants of Cellular Architecture in IDH1-Mutant Oligodendrogliomas and Astrocytomas Using Single-Cell Transcriptome Analysis. Neurosurgery. 2016 Aug; 63 Suppl 1:158. View in: Pubmed

RBPJ maintains brain tumor-initiating cells through CDK9-mediated transcriptional elongation. J Clin Invest. 2016 07 01; 126(7):2757-72. View in: Pubmed

Single-molecule decoding of combinatorially modified nucleosomes. Science. 2016 May 06; 352(6286):717-21. View in: Pubmed

Widespread RNA binding by chromatin-associated proteins. Genome Biol. 2016 Feb 16; 17:28. View in: Pubmed

An oncogenic MYB feedback loop drives alternate cell fates in adenoid cystic carcinoma. Nat Genet. 2016 Mar; 48(3):265-72. View in: Pubmed

Insulator dysfunction and oncogene activation in IDH mutant gliomas. Nature. 2016 Jan 07; 529(7584):110-4. View in: Pubmed

A Multiplexed System for Quantitative Comparisons of Chromatin Landscapes. Mol Cell. 2016 Jan 07; 61(1):170-80. View in: Pubmed

Single-cell ChIP-seq reveals cell subpopulations defined by chromatin state. Nat Biotechnol. 2015 Nov; 33(11):1165-72. View in: Pubmed

EHMT1 and EHMT2 inhibition induces fetal hemoglobin expression. Blood. 2015 Oct 15; 126(16):1930-9. View in: Pubmed

Detection of Enhancer-Associated Rearrangements Reveals Mechanisms of Oncogene Dysregulation in B-cell Lymphoma. Cancer Discov. 2015 Oct; 5(10):1058-71. View in: Pubmed

High-Throughput Single-Cell Labeling (Hi-SCL) for RNA-Seq Using Drop-Based Microfluidics. PLoS One. 2015; 10(5):e0116328. View in: Pubmed

Th17 cells transdifferentiate into regulatory T cells during resolution of inflammation. Nature. 2015 Jul 09; 523(7559):221-5. View in: Pubmed

Notch-mediated expansion of cord blood progenitors: maintenance of transcriptional and epigenetic fidelity. Leukemia. 2015 Sep; 29(9):1948-51. View in: Pubmed

Integrative analysis of 111 reference human epigenomes. Nature. 2015 Feb 19; 518(7539):317-30. View in: Pubmed

Dissecting neural differentiation regulatory networks through epigenetic footprinting. Nature. 2015 Feb 19; 518(7539):355-359. View in: Pubmed

Long-range enhancer activity determines Myc sensitivity to Notch inhibitors in T cell leukemia. Proc Natl Acad Sci U S A. 2014 Nov 18; 111(46):E4946-53. View in: Pubmed

EWS-FLI1 utilizes divergent chromatin remodeling mechanisms to directly activate or repress enhancer elements in Ewing sarcoma. Cancer Cell. 2014 Nov 10; 26(5):668-681. View in: Pubmed

Genetic and epigenetic fine mapping of causal autoimmune disease variants. Nature. 2015 Feb 19; 518(7539):337-43. View in: Pubmed

Comparative analysis of metazoan chromatin organization. Nature. 2014 Aug 28; 512(7515):449-52. View in: Pubmed

Reply to Brunet and Doolittle: Both selected effect and causal role elements can influence human biology and disease. Proc Natl Acad Sci U S A. 2014 Aug 19; 111(33):E3366. View in: Pubmed

Alzheimer's disease: early alterations in brain DNA methylation at ANK1, BIN1, RHBDF2 and other loci. Nat Neurosci. 2014 Sep; 17(9):1156-63. View in: Pubmed

Discovery of biomarkers predictive of GSI response in triple-negative breast cancer and adenoid cystic carcinoma. Cancer Discov. 2014 Oct; 4(10):1154-67. View in: Pubmed

Mammalian Polycomb-Like Pcl2/Mtf2 Is a Novel Regulatory Component of PRC2 That Can Differentially Modulate Polycomb Activity both at the Hox Gene Cluster and at Cdkn2a Genes. Mol Cell Biol. 2014 Jul 15; 34(14):2773. View in: Pubmed

Single-cell RNA-seq highlights intratumoral heterogeneity in primary glioblastoma. Science. 2014 Jun 20; 344(6190):1396-401. View in: Pubmed

Tissue-specific SMARCA4 binding at active and repressed regulatory elements during embryogenesis. Genome Res. 2014 Jun; 24(6):920-9. View in: Pubmed

Defining functional DNA elements in the human genome. Proc Natl Acad Sci U S A. 2014 Apr 29; 111(17):6131-8. View in: Pubmed

Reconstructing and reprogramming the tumor-propagating potential of glioblastoma stem-like cells. Cell. 2014 Apr 24; 157(3):580-94. View in: Pubmed

An epigenetic mechanism of resistance to targeted therapy in T cell acute lymphoblastic leukemia. Nat Genet. 2014 Apr; 46(4):364-70. View in: Pubmed

Deletion of Asxl1 results in myelodysplasia and severe developmental defects in vivo. J Exp Med. 2013 Nov 18; 210(12):2641-59. View in: Pubmed

Targeted DNA demethylation and activation of endogenous genes using programmable TALE-TET1 fusion proteins. Nat Biotechnol. 2013 Dec; 31(12):1137-42. View in: Pubmed

SAM domain polymerization links subnuclear clustering of PRC1 to gene silencing. Dev Cell. 2013 Sep 30; 26(6):565-77. View in: Pubmed

Locus-specific editing of histone modifications at endogenous enhancers. Nat Biotechnol. 2013 Dec; 31(12):1133-6. View in: Pubmed

In silico abstraction of zinc finger nuclease cleavage profiles reveals an expanded landscape of off-target sites. Nucleic Acids Res. 2013 Oct; 41(19):e181. View in: Pubmed

Charting a dynamic DNA methylation landscape of the human genome. Nature. 2013 Aug 22; 500(7463):477-81. View in: Pubmed

An aberrant transcription factor network essential for Wnt signaling and stem cell maintenance in glioblastoma. Cell Rep. 2013 May 30; 3(5):1567-79. View in: Pubmed

Transcriptional and epigenetic dynamics during specification of human embryonic stem cells. Cell. 2013 May 23; 153(5):1149-63. View in: Pubmed

Epigenetic reprogramming in cancer. Science. 2013 Mar 29; 339(6127):1567-70. View in: Pubmed

Genome-wide chromatin state transitions associated with developmental and environmental cues. Cell. 2013 Jan 31; 152(3):642-54. View in: Pubmed

Neural-specific Sox2 input and differential Gli-binding affinity provide context and positional information in Shh-directed neural patterning. Genes Dev. 2012 Dec 15; 26(24):2802-16. View in: Pubmed

The histone deacetylase SIRT6 is a tumor suppressor that controls cancer metabolism. Cell. 2012 Dec 07; 151(6):1185-99. View in: Pubmed

A blueprint for an international cancer epigenome consortium. A report from the AACR Cancer Epigenome Task Force. Cancer Res. 2012 Dec 15; 72(24):6319-24. View in: Pubmed

H2A.Z landscapes and dual modifications in pluripotent and multipotent stem cells underlie complex genome regulatory functions. Genome Biol. 2012 Oct 03; 13(10):R85. View in: Pubmed

An integrated encyclopedia of DNA elements in the human genome. Nature. 2012 Sep 06; 489(7414):57-74. View in: Pubmed

Heterodimeric JAK-STAT activation as a mechanism of persistence to JAK2 inhibitor therapy. Nature. 2012 Sep 06; 489(7414):155-9. View in: Pubmed

ChIP-seq guidelines and practices of the ENCODE and modENCODE consortia. Genome Res. 2012 Sep; 22(9):1813-31. View in: Pubmed

A high-throughput chromatin immunoprecipitation approach reveals principles of dynamic gene regulation in mammals. Mol Cell. 2012 Sep 14; 47(5):810-22. View in: Pubmed

ASXL1 mutations promote myeloid transformation through loss of PRC2-mediated gene repression. Cancer Cell. 2012 Aug 14; 22(2):180-93. View in: Pubmed

Histone H2A mono-ubiquitination is a crucial step to mediate PRC1-dependent repression of developmental genes to maintain ES cell identity. PLoS Genet. 2012; 8(7):e1002774. View in: Pubmed

Molecular biology. Genetic events that shape the cancer epigenome. Science. 2012 Jun 22; 336(6088):1513-4. View in: Pubmed

DNA sequence-dependent compartmentalization and silencing of chromatin at the nuclear lamina. Cell. 2012 Jun 22; 149(7):1474-87. View in: Pubmed

A tell-tail sign of chromatin: histone mutations drive pediatric glioblastoma. Cancer Cell. 2012 Mar 20; 21(3):329-31. View in: Pubmed

DNA-protein interactions in high definition. Genome Biol. 2012 Jan 27; 13(1):139. View in: Pubmed

Combinatorial patterning of chromatin regulators uncovered by genome-wide location analysis in human cells. Cell. 2011 Dec 23; 147(7):1628-39. View in: Pubmed

EZH2 codon 641 mutations are common in BCL2-rearranged germinal center B cell lymphomas. PLoS One. 2011; 6(12):e28585. View in: Pubmed

Genomic distribution and inter-sample variation of non-CpG methylation across human cell types. PLoS Genet. 2011 Dec; 7(12):e1002389. View in: Pubmed

Whole-genome chromatin profiling from limited numbers of cells using nano-ChIP-seq. Nat Protoc. 2011 Sep 29; 6(10):1656-68. View in: Pubmed

Epstein-Barr virus exploits intrinsic B-lymphocyte transcription programs to achieve immortal cell growth. Proc Natl Acad Sci U S A. 2011 Sep 06; 108(36):14902-7. View in: Pubmed

Genome-wide analysis reveals conserved and divergent features of Notch1/RBPJ binding in human and murine T-lymphoblastic leukemia cells. Proc Natl Acad Sci U S A. 2011 Sep 06; 108(36):14908-13. View in: Pubmed

A user's guide to the encyclopedia of DNA elements (ENCODE). PLoS Biol. 2011 Apr; 9(4):e1001046. View in: Pubmed

Initial genome sequencing and analysis of multiple myeloma. Nature. 2011 Mar 24; 471(7339):467-72. View in: Pubmed

Mapping and analysis of chromatin state dynamics in nine human cell types. Nature. 2011 May 05; 473(7345):43-9. View in: Pubmed

Role for Dpy-30 in ES cell-fate specification by regulation of H3K4 methylation within bivalent domains. Cell. 2011 Feb 18; 144(4):513-25. View in: Pubmed

Reprogramming factor expression initiates widespread targeted chromatin remodeling. Cell Stem Cell. 2011 Jan 07; 8(1):96-105. View in: Pubmed

GC-rich sequence elements recruit PRC2 in mammalian ES cells. PLoS Genet. 2010 Dec 09; 6(12):e1001244. View in: Pubmed

Charting histone modifications and the functional organization of mammalian genomes. Nat Rev Genet. 2011 Jan; 12(1):7-18. View in: Pubmed

Mammalian polycomb-like Pcl2/Mtf2 is a novel regulatory component of PRC2 that can differentially modulate polycomb activity both at the Hox gene cluster and at Cdkn2a genes. Mol Cell Biol. 2011 Jan; 31(2):351-64. View in: Pubmed

The NIH Roadmap Epigenomics Mapping Consortium. Nat Biotechnol. 2010 Oct; 28(10):1045-8. View in: Pubmed

Comparison of sequencing-based methods to profile DNA methylation and identification of monoallelic epigenetic modifications. Nat Biotechnol. 2010 Oct; 28(10):1097-105. View in: Pubmed

Genome-wide chromatin maps derived from limited numbers of hematopoietic progenitors. Nat Methods. 2010 Aug; 7(8):615-8. View in: Pubmed

Wilms tumor chromatin profiles highlight stem cell properties and a renal developmental network. Cell Stem Cell. 2010 Jun 04; 6(6):591-602. View in: Pubmed

Digital transcriptome profiling from attomole-level RNA samples. Genome Res. 2010 Apr; 20(4):519-25. View in: Pubmed

Jarid2 and PRC2, partners in regulating gene expression. Genes Dev. 2010 Feb 15; 24(4):368-80. View in: Pubmed

Chromatin profiling by directly sequencing small quantities of immunoprecipitated DNA. Nat Methods. 2010 Jan; 7(1):47-9. View in: Pubmed

Insights into GATA-1-mediated gene activation versus repression via genome-wide chromatin occupancy analysis. Mol Cell. 2009 Nov 25; 36(4):682-95. View in: Pubmed

Comprehensive mapping of long-range interactions reveals folding principles of the human genome. Science. 2009 Oct 09; 326(5950):289-93. View in: Pubmed

Unbiased reconstruction of a mammalian transcriptional network mediating pathogen responses. Science. 2009 Oct 09; 326(5950):257-63. View in: Pubmed

Many human large intergenic noncoding RNAs associate with chromatin-modifying complexes and affect gene expression. Proc Natl Acad Sci U S A. 2009 Jul 14; 106(28):11667-72. View in: Pubmed

Chromatin signature reveals over a thousand highly conserved large non-coding RNAs in mammals. Nature. 2009 Mar 12; 458(7235):223-7. View in: Pubmed

Developmental biology. Pluripotent chromatin state. Science. 2009 Jan 09; 323(5911):220-1. View in: Pubmed

Genomewide analysis of PRC1 and PRC2 occupancy identifies two classes of bivalent domains. PLoS Genet. 2008 Oct; 4(10):e1000242. View in: Pubmed

Model-based analysis of ChIP-Seq (MACS). Genome Biol. 2008; 9(9):R137. View in: Pubmed

Genome-scale DNA methylation maps of pluripotent and differentiated cells. Nature. 2008 Aug 07; 454(7205):766-70. View in: Pubmed

Dissecting direct reprogramming through integrative genomic analysis. Nature. 2008 Jul 03; 454(7200):49-55. View in: Pubmed

Whole Genome Amplification by T7-Based Linear Amplification of DNA (TLAD): Overview. CSH Protoc. 2008 May 01; 2008:pdb.top42. View in: Pubmed

Whole Genome Amplification by T7-Based Linear Amplification of DNA (TLAD): II. Second-Strand Synthesis and In Vitro Transcription. CSH Protoc. 2008 May 01; 2008:pdb.prot5003. View in: Pubmed

Whole Genome Amplification by T7-Based Linear Amplification of DNA (TLAD): III. Sample Purification. CSH Protoc. 2008 May 01; 2008:pdb.prot5004. View in: Pubmed

Whole Genome Amplification by T7-Based Linear Amplification of DNA (TLAD): I. CIP Treatment of Samples and Tailing Reaction with Terminal Transferase. CSH Protoc. 2008 May 01; 2008:pdb.prot5002. View in: Pubmed

Chromatin state maps: new technologies, new insights. Curr Opin Genet Dev. 2008 Apr; 18(2):109-15. View in: Pubmed

Genome-wide maps of chromatin state in pluripotent and lineage-committed cells. Nature. 2007 Aug 02; 448(7153):553-60. View in: Pubmed

In vitro reprogramming of fibroblasts into a pluripotent ES-cell-like state. Nature. 2007 Jul 19; 448(7151):318-24. View in: Pubmed

The mammalian epigenome. Cell. 2007 Feb 23; 128(4):669-81. View in: Pubmed

Genome-wide analysis of histone modifications by ChIP-on-chip. Methods. 2006 Dec; 40(4):365-9. View in: Pubmed

Molecular regulation of H3K4 trimethylation by ASH2L, a shared subunit of MLL complexes. Nat Struct Mol Biol. 2006 Sep; 13(9):852-4. View in: Pubmed

A bivalent chromatin structure marks key developmental genes in embryonic stem cells. Cell. 2006 Apr 21; 125(2):315-26. View in: Pubmed

Genomic views of chromatin. Curr Opin Genet Dev. 2005 Oct; 15(5):476-81. View in: Pubmed

Large-scale discovery and validation of functional elements in the human genome. Genome Biol. 2005; 6(3):312. View in: Pubmed

Genomic maps and comparative analysis of histone modifications in human and mouse. Cell. 2005 Jan 28; 120(2):169-81. View in: Pubmed

Global nucleosome occupancy in yeast. Genome Biol. 2004; 5(9):R62. View in: Pubmed

Rpd3p relocation mediates a transcriptional response to rapamycin in yeast. Chem Biol. 2004 Mar; 11(3):295-9. View in: Pubmed

The use of chromatin immunoprecipitation assays in genome-wide analyses of histone modifications. Methods Enzymol. 2004; 376:349-60. View in: Pubmed

Methylation of histone H3 K4 mediates association of the Isw1p ATPase with chromatin. Mol Cell. 2003 Nov; 12(5):1325-32. View in: Pubmed

Development and validation of a T7 based linear amplification for genomic DNA. BMC Genomics. 2003 May 09; 4(1):19. View in: Pubmed

Signaling network model of chromatin. Cell. 2002 Dec 13; 111(6):771-8. View in: Pubmed

Global approaches to chromatin. Chem Biol. 2002 Nov; 9(11):1167-73. View in: Pubmed

Active genes are tri-methylated at K4 of histone H3. Nature. 2002 Sep 26; 419(6905):407-11. View in: Pubmed

Methylation of histone H3 Lys 4 in coding regions of active genes. Proc Natl Acad Sci U S A. 2002 Jun 25; 99(13):8695-700. View in: Pubmed

SEMAPHORE1 functions during the regulation of ancestrally duplicated knox genes and polar auxin transport in maize. Development. 2002 Jun; 129(11):2663-73. View in: Pubmed

Genomewide studies of histone deacetylase function in yeast. Proc Natl Acad Sci U S A. 2000 Dec 05; 97(25):13708-13. View in: Pubmed

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Crystal structures of substrates and products bound to the phosphoglycerate kinase active site reveal the catalytic mechanism. Biochemistry. 1998 Mar 31; 37(13):4429-36. View in: Pubmed

A general method of domain closure is applied to phosphoglycerate kinase and the result compared with the crystal structure of a closed conformation of the enzyme. Proteins. 1998 Mar 01; 30(4):372-80. View in: Pubmed

The importance of dynamic light scattering in obtaining multiple crystal forms of Trypanosoma brucei PGK. Protein Sci. 1998 Feb; 7(2):504-7. View in: Pubmed

Consequences of inadequate analgesia during painful procedures in children. Arch Pediatr Adolesc Med. 1998 Feb; 152(2):147-9. View in: Pubmed

Probing the limits of the molecular replacement method: the case of Trypanosoma brucei phosphoglycerate kinase. Acta Crystallogr D Biol Crystallogr. 1997 Nov 01; 53(Pt 6):756-64. View in: Pubmed

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