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List of works by William Greenleaf

A Chromatin Basis for Cell Lineage and Disease Risk in the Human Pancreas

scientific article published on 22 August 2018

A Quantitative and Predictive Model for RNA Binding by Human Pumilio Proteins

scientific article published on 08 May 2019

A conditional system to specifically link disruption of protein-coding function with reporter expression in mice

scientific article

A pause sequence enriched at translation start sites drives transcription dynamics in vivo

scientific article

ATAC-see reveals the accessible genome by transposase-mediated imaging and sequencing

scientific article

ATAC-seq: A Method for Assaying Chromatin Accessibility Genome-Wide ⬇️

scientific article

An improved ATAC-seq protocol reduces background and enables interrogation of frozen tissues

An improved ATAC-seq protocol reduces background and enables interrogation of frozen tissues.

scientific article published on 28 August 2017

An optical apparatus for rotation and trapping

scientific article

Applied force reveals mechanistic and energetic details of transcription termination

scientific article

ArchR is a scalable software package for integrative single-cell chromatin accessibility analysis

scientific article

Assaying the epigenome in limited numbers of cells

scientific article

Author Correction: Discovery of stimulation-responsive immune enhancers with CRISPR activation

scientific article published in Nature

Automated Design of Diverse Stand-Alone Riboswitches

scientific article published on 29 July 2019

Beyond the Linear Genome: Paired-End Sequencing as a Biophysical Tool

scientific article published on 11 September 2015

Blind tests of RNA-protein binding affinity prediction

scientific article published on 08 April 2019

Brief Report: Cell Cycle Dynamics of Human Pluripotent Stem Cells Primed for Differentiation

scientific article published on 10 June 2019

Challenges and recommendations for epigenomics in precision health.

scientific article published in December 2017

Chromatin Accessibility Landscape of Cutaneous T Cell Lymphoma and Dynamic Response to HDAC Inhibitors

scientific article published in June 2017

Chromatin accessibility and the regulatory epigenome

scientific article published on 01 April 2019

Chromatin accessibility dynamics in a model of human forebrain development

scientific article published on 01 January 2020

Chromatin accessibility dynamics reveal novel functional enhancers in C. elegans.

scientific article published on 15 November 2017

Chromatin accessibility dynamics reveal novel functional enhancers inC. elegans

Chromatin-associated RNA sequencing (ChAR-seq) maps genome-wide RNA-to-DNA contacts.

scientific article

Compact RNA sensors for increasingly complex functions of multiple inputs

scientific article published on 16 January 2024

Comprehensive and quantitative mapping of RNA-protein interactions across a transcribed eukaryotic genome

scientific article published on 21 March 2017

Comprehensive sequence-to-function mapping of cofactor-dependent RNA catalysis in the glmS ribozyme

scientific article published on 03 April 2020

Corrigendum: Landscape of monoallelic DNA accessibility in mouse embryonic stem cells and neural progenitor cells

scientific article

Coupled Single-Cell CRISPR Screening and Epigenomic Profiling Reveals Causal Gene Regulatory Networks

scientific article published on 20 December 2018

Crowdsourced RNA design discovers diverse, reversible, efficient, self-contained molecular sensors

scientific article published on 16 December 2019

Demonstration of protein cooperativity mediated by RNA structure using the human protein PUM2

scientific article published on 26 March 2019

Deterministic Somatic Cell Reprogramming Involves Continuous Transcriptional Changes Governed by Myc and Epigenetic-Driven Modules

scientific article published on 13 December 2018

Diff-seq: A high throughput sequencing-based mismatch detection assay for DNA variant enrichment and discovery

scientific article published on 19 January 2018

Digital polymerase chain reaction in an array of femtoliter polydimethylsiloxane microreactors

scientific article

Direct observation of base-pair stepping by RNA polymerase

scientific article

Direct observation of hierarchical folding in single riboswitch aptamers

scientific article published on 03 January 2008

Direct, High-Throughput Measurement of Quantitative RNA Affinity Landscapes

Discovery of stimulation-responsive immune enhancers with CRISPR activation.

scientific article published on 30 August 2017

Dynamic chromatin regulatory landscape of human CAR T cell exhaustion

scientific article published on 01 July 2021

Enhancer connectome in primary human cells identifies target genes of disease-associated DNA elements.

scientific article published on 25 September 2017

Epigenetic signature of PD-1+ TCF1+ CD8 T cells that act as resource cells during chronic viral infection and respond to PD-1 blockade

scientific article published on 21 June 2019

Epigenomics of human CD8 T cell differentiation and aging

scientific article published on 17 February 2017

Exome sequencing identifies a DNAJB6 mutation in a family with dominantly-inherited limb-girdle muscular dystrophy

scientific article

Fluorogenic DNA sequencing in PDMS microreactors ⬇️

scientific article published on June 12, 2011

Genome-scale measurement of off-target activity using Cas9 toxicity in high-throughput screens

scientific article

HiChIP: efficient and sensitive analysis of protein-directed genome architecture

scientific article

HiChIRP reveals RNA-associated chromosome conformation

scientific article published on 27 May 2019

High-Throughput Analysis Reveals Rules for Target RNA Binding and Cleavage by AGO2

scientific article published on 16 July 2019

High-Throughput Investigation of Diverse Junction Elements in RNA Tertiary Folding

scientific article published on 28 June 2018

High-resolution mapping of cancer cell networks using co-functional interactions

High-resolution, single-molecule measurements of biomolecular motion

scientific article

High-throughput biochemical profiling reveals Cas9 off-target binding and unbinding heterogeneity

High-throughput biochemical profiling reveals sequence determinants of dCas9 off-target binding and unbinding

scientific article

High-throughput chromatin accessibility profiling at single-cell resolution

scientific article published in Nature Communications

High-throughput single-cell chromatin accessibility CRISPR screens enable unbiased identification of regulatory networks in cancer

scientific article published on 20 May 2021

INO80 Chromatin Remodeling Coordinates Metabolic Homeostasis with Cell Division

scientific article published in January 2018

Identification of phagocytosis regulators using magnetic genome-wide CRISPR screens

scientific article published on 05 November 2018

Identification of significantly mutated regions across cancer types highlights a rich landscape of functional molecular alterations

scientific article published on 21 December 2015

Individuality and variation of personal regulomes in primary human T cells

scientific article published in July 2015

Integrated Single-Cell Analysis Maps the Continuous Regulatory Landscape of Human Hematopoietic Differentiation

scientific article published on 25 April 2018

Intertumoral Heterogeneity in SCLC Is Influenced by the Cell Type of Origin

scientific article published on 18 September 2018

Joint single-cell DNA accessibility and protein epitope profiling reveals environmental regulation of epigenomic heterogeneity

scientific article published in Nature Communications

LKB1 inactivation modulates chromatin accessibility to drive metastatic progression

scientific article published on 02 August 2021

Landscape of monoallelic DNA accessibility in mouse embryonic stem cells and neural progenitor cells

scientific article published on 23 January 2017

Landscape of stimulation-responsive chromatin across diverse human immune cells

scientific article published on 30 September 2019

Large-Scale, Quantitative Protein Assays on a High-Throughput DNA Sequencing Chip

scientific article published on 01 March 2019

Lineage-specific and single-cell chromatin accessibility charts human hematopoiesis and leukemia evolution

scientific article published on 15 August 2016

Lineage-specific dynamic and pre-established enhancer-promoter contacts cooperate in terminal differentiation.

scientific article published on 14 August 2017

Linking RNA Sequence, Structure, and Function on Massively Parallel High-Throughput Sequencers

scientific article published on 01 October 2019

Long-range single-molecule mapping of chromatin accessibility in eukaryotes

scientific article published on 10 February 2020

Massively parallel single-cell chromatin landscapes of human immune cell development and intratumoral T cell exhaustion

scientific article published on 02 August 2019

Mitigation of off-target toxicity in CRISPR-Cas9 screens for essential non-coding elements

scientific article published on 06 September 2019

Molecule by molecule, the physics and chemistry of life: SMB 2007.

scientific article published on April 2007

Neutralizing Gatad2a-Chd4-Mbd3 Axis within the NuRD Complex Facilitates Deterministic Induction of Naive Pluripotency

Neutralizing Gatad2a-Chd4-Mbd3 Axis within the NuRD Complex Facilitates Deterministic Induction of Naïve Pluripotency

Neutralizing Gatad2a-Chd4-Mbd3/NuRD Complex Facilitates Deterministic Induction of Naive Pluripotency

scientific article published on 16 August 2018

Nfib Promotes Metastasis through a Widespread Increase in Chromatin Accessibility

scientific article

Omega-3 Fatty Acids Activate Ciliary FFAR4 to Control Adipogenesis

scientific article published on 21 November 2019

Origin and differentiation of human memory CD8 T cells after vaccination

scientific article published on 13 December 2017

Passive all-optical force clamp for high-resolution laser trapping

scientific article published on 8 November 2005

Pulling out the 1%: whole-genome capture for the targeted enrichment of ancient DNA sequencing libraries

scientific article (publication date: 7 November 2013)

Quantitative analysis of RNA-protein interactions on a massively parallel array reveals biophysical and evolutionary landscapes

scientific article

Rapid chromatin repression by Aire provides precise control of immune tolerance

scientific article published on 15 January 2018

Reduced chromatin accessibility to CD4 T cell super-enhancers encompassing susceptibility loci of rheumatoid arthritis

scientific article published on 24 January 2022

Satb1 integrates DNA binding site geometry and torsional stress to differentially target nucleosome-dense regions

scientific article published on 19 July 2019

Sequence-dependent RNA helix conformational preferences predictably impact tertiary structure formation

scientific article published on 02 August 2019

Short tandem repeats bind transcription factors to tune eukaryotic gene expression

scientific article published on 21 September 2023

Single-cell chromatin accessibility reveals principles of regulatory variation

scientific article

Single-cell epigenomic analyses implicate candidate causal variants at inherited risk loci for Alzheimer's and Parkinson's diseases

scientific article published on 26 October 2020

Single-cell epigenomic variability reveals functional cancer heterogeneity

scientific article published on 24 January 2017

Single-cell epigenomics maps the continuous regulatory landscape of human hematopoietic differentiation

Single-cell multiomic analysis identifies regulatory programs in mixed-phenotype acute leukemia

scientific article published on 02 December 2019

Single-cell transcriptomic analysis of the adult mouse spinal cord reveals molecular diversity of autonomic and skeletal motor neurons

Single-molecule studies of RNA polymerase: motoring along

scientific article published on January 2008

Single-molecule, motion-based DNA sequencing using RNA polymerase

scientific article

Structured nucleosome fingerprints enable high-resolution mapping of chromatin architecture within regulatory regions

scientific article

Systematic benchmarking of single-cell ATAC-sequencing protocols

scientific article published in 2023

TOP2 synergizes with BAF chromatin remodeling for both resolution and formation of facultative heterochromatin

scientific article published on 27 February 2017

The Molecular and Functional Foundations of Conducive Somatic Cell Reprogramming to Ground State Pluripotency

The chromatin accessibility landscape of primary human cancers

scientific article

The chromatin organization of a chlorarachniophyte nucleomorph genome

scientific article published on 01 March 2022

The future of sequencing: convergence of intelligent design and market Darwinism

scientific article published on 25 March 2014

Transcript-indexed ATAC-seq for precision immune profiling.

scientific article published on 23 April 2018

Transient acquisition of pluripotency during somatic cell transdifferentiation with iPSC reprogramming factors

scientific article

Transposition of native chromatin for fast and sensitive epigenomic profiling of open chromatin, DNA-binding proteins and nucleosome position

scientific article

Unraveling the 3D genome: genomics tools for multiscale exploration

scientific article published on 14 April 2015

Unsupervised clustering and epigenetic classification of single cells.

scientific article published on 20 June 2018

Variable chromatin structure revealed by in situ spatially correlated DNA cleavage mapping

scientific article

chromVAR: Inferring transcription factor variation from single-cell epigenomic data

chromVAR: inferring transcription-factor-associated accessibility from single-cell epigenomic data

scientific article

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