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List of works by Bradley Bernstein

142 Genetic and Nongenetic Determinants of Cellular Architecture in IDH1-Mutant Oligodendrogliomas and Astrocytomas Using Single-Cell Transcriptome Analysis

scientific article published on August 2016

A B Cell Regulome Links Notch to Downstream Oncogenic Pathways in Small B Cell Lymphomas

scientific article

A Blueprint for an International Cancer Epigenome Consortium. A Report from the AACR Cancer Epigenome Task Force ⬇️

scientific article published on November 27, 2012

A Genetic Variant Associated with Five Vascular Diseases Is a Distal Regulator of Endothelin-1 Gene Expression.

scientific article

A Multiplexed System for Quantitative Comparisons of Chromatin Landscapes.

scientific article

A Tell-Tail Sign of Chromatin: Histone Mutations Drive Pediatric Glioblastoma ⬇️

scientific article published on March 20, 2012

A bivalent chromatin structure marks key developmental genes in embryonic stem cells

scientific article (publication date: 21 April 2006)

A high-throughput chromatin immunoprecipitation approach reveals principles of dynamic gene regulation in mammals

scientific article published on 30 August 2012

A novel method for detecting the cellular stemness state in normal and leukemic human hematopoietic cells can predict disease outcome and drug sensitivity

scientific article published on 31 January 2019

ASXL1 mutations promote myeloid transformation through loss of PRC2-mediated gene repression

scientific article

Adaptive Chromatin Remodeling Drives Glioblastoma Stem Cell Plasticity and Drug Tolerance.

scientific article published on 2 December 2016

Altered chromosomal topology drives oncogenic programs in SDH-deficient GISTs

scientific article published on 16 October 2019

Alzheimer's disease: early alterations in brain DNA methylation at ANK1, BIN1, RHBDF2 and other loci

scientific article

An Integrative Model of Cellular States, Plasticity, and Genetics for Glioblastoma

scientific article published on 18 July 2019

An aberrant transcription factor network essential for Wnt signaling and stem cell maintenance in glioblastoma.

scientific article published on 23 May 2013

An epigenetic mechanism of resistance to targeted therapy in T cell acute lymphoblastic leukemia

scientific article

An oncogenic MYB feedback loop drives alternate cell fates in adenoid cystic carcinoma.

scientific article

ChIP-seq guidelines and practices of the ENCODE and modENCODE consortia

scientific article

Charting a dynamic DNA methylation landscape of the human genome

scientific article published on 07 August 2013

Chromatin accessibility promotes hematopoietic and leukemia stem cell activity

scientific article published on 16 March 2020

Chromatin profiling by directly sequencing small quantities of immunoprecipitated DNA.

scientific article

Chromatin signature reveals over a thousand highly conserved large non-coding RNAs in mammals

scientific article (publication date: 12 March 2009)

Chromatin state maps: new technologies, new insights

scientific article published on 12 March 2008

Clinical sensitivity and interpretation of PCR and serological COVID-19 diagnostics for patients presenting to the hospital

scientific article published on 28 August 2020

Cohesin Loss Eliminates All Loop Domains

scientific article published in October 2017

Combinatorial patterning of chromatin regulators uncovered by genome-wide location analysis in human cells

scientific article published in December 2011

Comparative analysis of metazoan chromatin organization

scientific article

Comparison of sequencing-based methods to profile DNA methylation and identification of monoallelic epigenetic modifications.

scientific article

Comprehensive mapping of long-range interactions reveals folding principles of the human genome

scientific article (publication date: 9 October 2009)

Corrupted coordination of epigenetic modifications leads to diverging chromatin states and transcriptional heterogeneity in CLL

scientific article published on 23 April 2019

Crystallographic Investigations of Phosphoglycerate Kinase From the Causative Agent of Sleeping Sickness ⬇️

doctoral thesis by Bradley E. Bernstein, University of Washington, 1997

DNA sequence-dependent compartmentalization and silencing of chromatin at the nuclear lamina

scientific journal article

DNA-protein interactions in high definition

scientific article published on 27 January 2012

Data-Driven Polymer Model for Mechanistic Exploration of Diploid Genome Organization

scientific article published on 22 September 2020

Decoupling genetics, lineages, and microenvironment in IDH-mutant gliomas by single-cell RNA-seq.

scientific article published on March 2017

Defining functional DNA elements in the human genome

scientific article

Deletion of Asxl1 results in myelodysplasia and severe developmental defects in vivo

scientific article

Detecting sample swaps in diverse NGS data types using linkage disequilibrium

scientific article published on 29 July 2020

Detection of Enhancer-Associated Rearrangements Reveals Mechanisms of Oncogene Dysregulation in B-cell Lymphoma

scientific article published on 30 July 2015

Development and validation of a T7 based linear amplification for genomic DNA ⬇️

scientific article published on May 9, 2003

Developmental and oncogenic programs in H3K27M gliomas dissected by single-cell RNA-seq

scientific article published in April 2018

Developmental biology. Pluripotent chromatin state

scientific article

Digital transcriptome profiling from attomole-level RNA samples

scientific article

Discovery of biomarkers predictive of GSI response in triple-negative breast cancer and adenoid cystic carcinoma

scientific article

Dissecting neural differentiation regulatory networks through epigenetic footprinting

scientific article published on 24 December 2014

Dual Targeting of Oncogenic Activation and Inflammatory Signaling Increases Therapeutic Efficacy in Myeloproliferative Neoplasms.

scientific article published in December 2017

Dual Targeting of Oncogenic Activation and Inflammatory Signaling Increases Therapeutic Efficacy in Myeloproliferative Neoplasms.

scientific article published in April 2018

EHMT1 and EHMT2 inhibition induces fetal hemoglobin expression.

scientific article

EWS-FLI1 utilizes divergent chromatin remodeling mechanisms to directly activate or repress enhancer elements in Ewing sarcoma

scientific article published on 30 October 2014

EZH2 codon 641 mutations are common in BCL2-rearranged germinal center B cell lymphomas

scientific article (publication date: 2011)

Enhancer signatures stratify and predict outcomes of non-functional pancreatic neuroendocrine tumors

scientific article published on 01 July 2019

Epigenetic Reprogramming in Cancer ⬇️

scientific article published on March 29, 2013

Epigenetic alterations in keratinocyte carcinoma

scientific article published on 16 November 2020

Epigenetic plasticity and the hallmarks of cancer.

scientific article

Epigenetic silencing by SETDB1 suppresses tumour intrinsic immunogenicity

scientific article published on 05 May 2021

Epigenome editing strategies for the functional annotation of CTCF insulators

scientific article published on 18 September 2019

Epigenome-wide study uncovers large-scale changes in histone acetylation driven by tau pathology in aging and Alzheimer's human brains.

scientific article published on 17 December 2018

Epithelial-to-mesenchymal transition antagonizes response to targeted therapies in lung cancer by suppressing BIM.

scientific article published on 19 October 2017

Epstein-Barr virus exploits intrinsic B-lymphocyte transcription programs to achieve immortal cell growth

scientific article

Evaluation of SARS-CoV-2 serology assays reveals a range of test performance

scientific article published on 27 August 2020

Expanded encyclopaedias of DNA elements in the human and mouse genomes

scientific article published on 29 July 2020

Extended-representation bisulfite sequencing of gene regulatory elements in multiplexed samples and single cells

scientific article published on 06 May 2021

GABPβ1L Wakes Up TERT

scientific article published on 01 September 2018

GC-rich sequence elements recruit PRC2 in mammalian ES cells

scientific article

GENE-30. TRANSCRIPTION ELONGATION FACTORS REPRESENT CANCER DEPENDENCIES IN GLIOBLASTOMA

Gain-of-function genetic alterations of G9a drive oncogenesis

scientific article published on 08 April 2020

Genetic and epigenetic fine mapping of causal autoimmune disease variants

scientific article

Genome-scale DNA methylation maps of pluripotent and differentiated cells

scientific article

Genome-wide analysis of histone modifications by ChIP-on-chip

scientific article published in December 2006

Genome-wide analysis reveals conserved and divergent features of Notch1/RBPJ binding in human and murine T-lymphoblastic leukemia cells ⬇️

scientific article published on July 7, 2011

Genome-wide chromatin maps derived from limited numbers of hematopoietic progenitors

scientific article

Genome-wide chromatin state transitions associated with developmental and environmental cues

scientific article

Genome-wide maps of chromatin state in pluripotent and lineage-committed cells

scientific article

Genomewide analysis of PRC1 and PRC2 occupancy identifies two classes of bivalent domains

scientific article published in October 2008

Genomic distribution and inter-sample variation of non-CpG methylation across human cell types

scientific article

Genomic views of chromatin

scientific article

Global approaches to chromatin

scientific article

Global nucleosome occupancy in yeast

scientific article

H2A.Z landscapes and dual modifications in pluripotent and multipotent stem cells underlie complex genome regulatory functions

scientific article

Heritability enrichment of specifically expressed genes identifies disease-relevant tissues and cell types

scientific article published on 9 April 2018

Heritability enrichment of specifically expressed genes identifies disease-relevant tissues and cell types

article

Heterodimeric JAK-STAT activation as a mechanism of persistence to JAK2 inhibitor therapy

scientific article published on September 2012

High seroprevalence of anti-SARS-CoV-2 antibodies in Chelsea, Massachusetts

scientific article published on 09 September 2020

High-Throughput Single-Cell Labeling (Hi-SCL) for RNA-Seq Using Drop-Based Microfluidics

scientific article (publication date: 2015)

Histone H2A mono-ubiquitination is a crucial step to mediate PRC1-dependent repression of developmental genes to maintain ES cell identity

scientific article

Identification of promoter targets of enhancers by epigenetic knockdown using TAL DNA binding proteins.

scientific article published on 18 March 2013

Immunohistochemical quantification of partial-EMT in oral cavity squamous cell carcinoma primary tumors is associated with nodal metastasis

scientific article published on 06 November 2019

In silico abstraction of zinc finger nuclease cleavage profiles reveals an expanded landscape of off-target sites ⬇️

scientific article published on August 14, 2013

Inducible histone K-to-M mutations are dynamic tools to probe the physiological role of site-specific histone methylation in vitro and in vivo

scientific article published on 28 October 2019

Initial genome sequencing and analysis of multiple myeloma

scientific article

Insights into GATA-1-mediated gene activation versus repression via genome-wide chromatin occupancy analysis

scientific article

Insulator dysfunction and oncogene activation in IDH mutant gliomas

scientific article

Jarid2 and PRC2, partners in regulating gene expression

scientific article

Large-Scale Topological Changes Restrain Malignant Progression in Colorectal Cancer

scientific article published on 18 August 2020

Large-scale discovery and validation of functional elements in the human genome

scientific article

Locus-specific editing of histone modifications at endogenous enhancers

scientific article

Long-range enhancer activity determines Myc sensitivity to Notch inhibitors in T cell leukemia

scientific article

MBRS-28. SINGLE-CELL TRANSCRIPTOME ANALYSIS OF MEDULLOBLASTOMA

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

scientific article published in July 2014

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

scientific journal article

Many human large intergenic noncoding RNAs associate with chromatin-modifying complexes and affect gene expression

scientific article

Methylation of Histone H3 K4 Mediates Association of the Isw1p ATPase with Chromatin

scientific article published on 07 June 2018

Methylation of histone H3 K4 mediates association of the Isw1p ATPase with chromatin

scientific article published in November 2003

Methylation of histone H3 Lys 4 in coding regions of active genes

scientific article

Model-based analysis of ChIP-Seq (MACS)

scientific article

Molecular biology. Genetic events that shape the cancer epigenome

scientific article published on 01 June 2012

Molecular regulation of H3K4 trimethylation by ASH2L, a shared subunit of MLL complexes

scientific article

Neural-specific Sox2 input and differential Gli-binding affinity provide context and positional information in Shh-directed neural patterning

scientific article

Orthologous CRISPR-Cas9 enzymes for combinatorial genetic screens.

scientific article

PDTM-04. REDEFINING THE CELLULAR ARCHITECTURE OF DIFFUSE MIDLINE GLIOMAS WITH H3 K27M MUTATIONS THROUGH LARGE-SCALE SINGLE-CELL ANALYSES

Parallel Single-Cell RNA-Seq and Genetic Recording Reveals Lineage Decisions in Developing Embryoid Bodies

scientific article published on 01 October 2020

Perspectives on ENCODE

scientific article published on 29 July 2020

Publisher Correction: Enhancer signatures stratify and predict outcomes of non-functional pancreatic neuroendocrine tumors

scientific article published on 01 October 2019

RBPJ maintains brain tumor-initiating cells through CDK9-mediated transcriptional elongation

scientific article published on 20 June 2016

Re-programing Chromatin with a Bifunctional LSD1/HDAC Inhibitor Induces Therapeutic Differentiation in DIPG

scientific article published on 17 October 2019

Reconstructing and reprogramming the tumor-propagating potential of glioblastoma stem-like cells

scientific article published on 10 April 2014

Regulation of the glucocorticoid receptor via a BET-dependent enhancer drives antiandrogen resistance in prostate cancer.

scientific article published on 11 September 2017

Reply to Brunet and Doolittle: Both selected effect and causal role elements can influence human biology and disease

scientific article published on August 2014

Reprogramming Factor Expression Initiates Widespread Targeted Chromatin Remodeling ⬇️

scientific article published on January 7, 2011

Resolving medulloblastoma cellular architecture by single-cell genomics

scientific article published on 24 July 2019

Role for Dpy-30 in ES Cell-Fate Specification by Regulation of H3K4 Methylation within Bivalent Domains ⬇️

scientific article published on February 18, 2011

Rpd3p relocation mediates a transcriptional response to rapamycin in yeast

scientific article

SAM domain polymerization links subnuclear clustering of PRC1 to gene silencing

scientific article published on September 2013

SMARCB1-mediated SWI/SNF complex function is essential for enhancer regulation

scientific article

STEM-22LARGE-SCALE SINGLE-CELL RNA-seq REVEALS A DEVELOPMENTAL CELLULAR HIERARCHY IN HUMAN OLIGODENDROGLIOMA.

scientific article

Signaling network model of chromatin

scientific article (publication date: 13 December 2002)

Single cell RNA-seq reveals developmental plasticity with coexisting oncogenic and immune evasion programs in ETP-ALL

scientific article published on 23 November 2020

Single-Cell RNA-Seq Reveals AML Hierarchies Relevant to Disease Progression and Immunity

scientific article published on 28 February 2019

Single-Cell Transcriptomic Analysis of Primary and Metastatic Tumor Ecosystems in Head and Neck Cancer

scientific article

Single-cell ChIP-seq reveals cell subpopulations defined by chromatin state

scientific article

Single-cell RNA-seq highlights intratumoral heterogeneity in primary glioblastoma

scientific article

Single-cell RNA-seq supports a developmental hierarchy in human oligodendroglioma

scientific article published on 2 November 2016

Single-cell and single-molecule epigenomics to uncover genome regulation at unprecedented resolution

scientific article published on 17 December 2018

Single-cell lineage analysis reveals genetic and epigenetic interplay in glioblastoma drug resistance

scientific article published on 15 July 2020

Single-molecule decoding of combinatorially modified nucleosomes

scientific article

Systematic dissection of genomic features determining transcription factor binding and enhancer function

scientific article published on 30 January 2017

Targeted DNA demethylation and activation of endogenous genes using programmable TALE-TET1 fusion proteins

scientific article

Test performance evaluation of SARS-CoV-2 serological assays

scientific article published on 29 April 2020

Th17 cells transdifferentiate into regulatory T cells during resolution of inflammation

scientific article

The NIH Roadmap Epigenomics Mapping Consortium

scientific article (publication date: October 2010)

The histone deacetylase SIRT6 is a tumor suppressor that controls cancer metabolism

scientific article

The use of chromatin immunoprecipitation assays in genome-wide analyses of histone modifications

scientific article published on January 2004

Tissue-specific SMARCA4 binding at active and repressed regulatory elements during embryogenesis

scientific article

Transaminase Inhibition by 2-Hydroxyglutarate Impairs Glutamate Biosynthesis and Redox Homeostasis in Glioma

scientific article published on 13 September 2018

Transcription elongation factors represent in vivo cancer dependencies in glioblastoma

scientific article

Transcriptional and epigenetic dynamics during specification of human embryonic stem cells

scientific article published on 09 May 2013

Tumor mutational landscape is a record of the pre-malignant state

Unbiased reconstruction of a mammalian transcriptional network mediating pathogen responses

scientific article

Unravelling subclonal heterogeneity and aggressive disease states in TNBC through single-cell RNA-seq

scientific article published in Nature Communications

Whole Genome Amplification by T7-Based Linear Amplification of DNA (TLAD): I. CIP Treatment of Samples and Tailing Reaction with Terminal Transferase ⬇️

scientific article published on 01 May 2008

Whole Genome Amplification by T7-Based Linear Amplification of DNA (TLAD): II. Second-Strand Synthesis and In Vitro Transcription ⬇️

scientific article published on 01 May 2008

Whole Genome Amplification by T7-Based Linear Amplification of DNA (TLAD): III. Sample Purification ⬇️

scientific article published on 01 May 2008

Whole Genome Amplification by T7-Based Linear Amplification of DNA (TLAD): Overview ⬇️

scientific article published on 01 May 2008

Whole-genome chromatin profiling from limited numbers of cells using nano-ChIP-seq ⬇️

scientific article published on September 29, 2011

Widespread RNA binding by chromatin-associated proteins

scientific article published on 16 February 2016

Wilms tumor chromatin profiles highlight stem cell properties and a renal developmental network

scientific article

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