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List of works by Joseph R. Ecker

'Leveling' the playing field for analyses of single-base resolution DNA methylomes.

scientific article

A B-ARR-mediated cytokinin transcriptional network directs hormone cross-regulation and shoot development.

scientific article

A Proposal Regarding Best Practices for Validating the Identity of Genetic Stocks and the Effects of Genetic Variants.

scientific article

A WD40 domain cyclophilin interacts with histone H3 and functions in gene repression and organogenesis in Arabidopsis.

scientific article

A combinatorial interplay among the 1-aminocyclopropane-1-carboxylate isoforms regulates ethylene biosynthesis in Arabidopsis thaliana

scientific article published on 14 September 2009

A comparative atlas of single-cell chromatin accessibility in the human brain

scientific article published on 12 October 2023

A family of bacterial cysteine protease type III effectors utilizes acylation-dependent and -independent strategies to localize to plasma membranes.

scientific article published on 03 April 2009

A genome-scale resource for the functional characterization of Arabidopsis transcription factors.

scientific article

A massively parallel barcoded sequencing pipeline enables generation of the first ORFeome and interactome map for rice

scientific article published on 12 May 2020

A reevaluation of the role of the heterotrimeric G protein in coupling light responses in Arabidopsis.

scientific article published in April 2003

A transcription factor hierarchy defines an environmental stress response network

scientific article

A transcriptomic and epigenomic cell atlas of the mouse primary motor cortex

scientific article

Abnormalities in human pluripotent cells due to reprogramming mechanisms

scientific article published on 02 July 2014

Active DNA demethylation at enhancers during the vertebrate phylotypic period

scientific article published on 29 February 2016

Allele-specific non-CG DNA methylation marks domains of active chromatin in female mouse brain.

scientific article

An ABA-increased interaction of the PYL6 ABA receptor with MYC2 Transcription Factor: A putative link of ABA and JA signaling

scientific article published on 30 June 2016

An Arabidopsis NPR1-like gene, NPR4, is required for disease resistance.

scientific article published in January 2005

An adapter ligation-mediated PCR method for high-throughput mapping of T-DNA inserts in the Arabidopsis genome.

scientific article

An alternative pluripotent state confers interspecies chimaeric competency

scientific article

An atlas of gene regulatory elements in adult mouse cerebrum

scientific article published on 06 October 2021

Analysis of interruptions in the phosphodiester backbone of herpes simplex virus DNA.

scientific article published in April 1981

Applications of DNA tiling arrays for whole-genome analysis

scientific article

Arabidopsis RIN4 is a target of the type III virulence effector AvrRpt2 and modulates RPS2-mediated resistance.

scientific article published in February 2003

Arabidopsis basic helix-loop-helix transcription factors MYC2, MYC3, and MYC4 regulate glucosinolate biosynthesis, insect performance, and feeding behavior.

scientific article published on 13 August 2013

Author Correction: A B-ARR-mediated cytokinin transcriptional network directs hormone cross-regulation and shoot development.

scientific article

Auxin-sensitive Aux/IAA proteins mediate drought tolerance in Arabidopsis by regulating glucosinolate levels

scientific article published on 06 September 2019

BRI-ghtening the Pathway to Steroid Hormone Signaling Events in Plants ⬇️

scientific article published on September 5, 1997

CG hypomethylation in Lsh-/- mouse embryonic fibroblasts is associated with de novo H3K4me1 formation and altered cellular plasticity

scientific article published on 07 April 2014

Cerebral Organoids Recapitulate Epigenomic Signatures of the Human Fetal Brain.

scientific article published on December 2016

Chimeric Activators and Repressors Define HY5 Activity and Reveal a Light-Regulated Feedback Mechanism

scientific article published on 21 February 2020

Chromatin architecture reorganization during stem cell differentiation.

scientific article published in February 2015

Circadian Oscillations of Protein-Coding and Regulatory RNAs in a Highly Dynamic Mammalian Liver Epigenome ⬇️

scientific article published on December 5, 2012

Cistrome and Epicistrome Features Shape the Regulatory DNA Landscape

scientific article published on 08 September 2016

Cistrome and Epicistrome Features Shape the Regulatory DNA Landscape.

scientific article published on May 2016

Common alleles of CMT2 and NRPE1 are major determinants of CHH methylation variation in Arabidopsis thaliana

scientific article published on 30 December 2019

Comparative cellular analysis of motor cortex in human, marmoset and mouse

scientific article published on 06 October 2021

Comparison of the transcriptional landscapes between human and mouse tissues

scientific article

Comprehensive analysis of single cell ATAC-seq data with SnapATAC

scientific article published on 26 February 2021

Convergence of signaling pathways in the control of differential cell growth in Arabidopsis

scientific article published on 01 August 2004

Convergent targeting of a common host protein-network by pathogen effectors from three kingdoms of life

scientific article

Corrigendum: Human body epigenome maps reveal noncanonical DNA methylation variation

scientific article published on 25 November 2015

CrY2H-seq: a massively multiplexed assay for deep-coverage interactome mapping

scientific article published on 26 June 2017

DNA methylation atlas of the mouse brain at single-cell resolution

scientific article

Della proteins and gibberellin-regulated seed germination and floral development in Arabidopsis.

scientific article published in June 2004

Direct transcriptional control of the Arabidopsis immune receptor FLS2 by the ethylene-dependent transcription factors EIN3 and EIL1.

scientific article

Distinct epigenomic landscapes of pluripotent and lineage-committed human cells.

scientific article

Divergent cytosine DNA methylation patterns in single-cell, soybean root hairs.

scientific article published on 20 January 2017

Divergent perspectives on GM food

scientific article published on 01 December 2002

Diversity and dynamics of DNA methylation: epigenomic resources and tools for crop breeding

scientific article published on 14 May 2019

Dnmt3a knockout in excitatory neurons impairs postnatal synapse maturation and increases the repressive histone modification H3K27me3

scientific article published on 23 May 2022

Dynamic DNA methylation reconfiguration during seed development and germination.

scientific article published on 15 September 2017

Dynamic DNA methylation: In the right place at the right time

scientific article published in Science

Dynamic and rapid changes in the transcriptome and epigenome during germination and in developing rice (Oryza sativa) coleoptiles under anoxia and re-oxygenation

scientific article published on 12 November 2016

EIN2-dependent regulation of acetylation of histone H3K14 and non-canonical histone H3K23 in ethylene signalling.

scientific article published on 03 October 2016

ERRs Mediate a Metabolic Switch Required for Somatic Cell Reprogramming to Pluripotency

scientific article published on 9 April 2015

Enhanced fitness conferred by naturally occurring variation in the circadian clock

scientific article published on 01 November 2003

Epigenetic and epigenomic variation in Arabidopsis thaliana.

scientific article published on 17 February 2012

Epigenetic silencing of a multifunctional plant stress regulator

scientific article published on 16 August 2019

Epigenetic trigger for tomato ripening ⬇️

scientific article published on February 1, 2013

Epigenetics. Exceptional epigenetics in the brain.

scientific article published on June 2015

Epigenome-wide inheritance of cytosine methylation variants in a recombinant inbred population.

scientific article published on 05 June 2013

Epigenomic diversity of cortical projection neurons in the mouse brain

scientific article published on 06 October 2021

Epigenomic landscapes of retinal rods and cones

scientific article

Epigenomic programming contributes to the genomic drift evolution of the F-Box protein superfamily in Arabidopsis

scientific article published on 30 September 2013

Erratum: Addendum: Literature-curated protein interaction datasets

scholarly article published in Nature Methods

Ethylene signaling: from mutants to molecules.

scientific article

Ethylene-induced stabilization of ETHYLENE INSENSITIVE3 and EIN3-LIKE1 is mediated by proteasomal degradation of EIN3 binding F-box 1 and 2 that requires EIN2 in Arabidopsis.

scientific article published on 20 July 2010

Expanded encyclopaedias of DNA elements in the human and mouse genomes

scientific article published on 29 July 2020

Exploring the transcriptional landscape of plant circadian rhythms using genome tiling arrays.

scientific article published on 11 February 2009

Extractions

scientific article published on 01 November 2003

Finding the fifth base: genome-wide sequencing of cytosine methylation.

scientific article published on 09 March 2009

Flagellin is not a major defense elicitor in Ralstonia solanacearum cells or extracts applied to Arabidopsis thaliana.

scientific article published in June 2004

Forward and reverse genetics through derivation of haploid mouse embryonic stem cells.

scientific article published on December 2011

Functional Human Oocytes Generated by Transfer of Polar Body Genomes.

scientific article published on 20 October 2016

GCR1 can act independently of heterotrimeric G-protein in response to brassinosteroids and gibberellins in Arabidopsis seed germination.

scientific article

Genes blossom from a weed ⬇️

scientific article published on January 29, 1998

Genome and time-of-day transcriptome of <i>Wolffia australiana</i> link morphological minimization with gene loss and less growth control

scientific article published on 23 December 2020

Genome mapping with anchored clones: theoretical aspects.

scientific article published in December 1991

Genome-wide DNA methylation patterns in LSH mutant reveals de-repression of repeat elements and redundant epigenetic silencing pathways

scientific article

Genome-wide analysis of chromosomal features repressing human immunodeficiency virus transcription.

scientific article published on June 2005

Genome-wide association study of 107 phenotypes in Arabidopsis thaliana inbred lines.

scientific article

Genome-wide identification of CCA1 targets uncovers an expanded clock network in Arabidopsis

scientific article

Genome-wide insertional mutagenesis of Arabidopsis thaliana

scientific article (publication date: August 2003)

Global DNA methylation remodeling during direct reprogramming of fibroblasts to neurons

scientific article published on 15 January 2019

Global epigenomic reconfiguration during mammalian brain development

scientific article (publication date: 9 August 2013)

HIV integration site selection: targeting in macrophages and the effects of different routes of viral entry.

scientific article

HOOKLESS1, an ethylene response gene, is required for differential cell elongation in the Arabidopsis hypocotyl.

scientific article published in April 1996

High contiguity Arabidopsis thaliana genome assembly with a single nanopore flow cell

scientific article published on 7 February 2018

Higher plants possess two different types of ATX1-like copper chaperones

scientific article published on 09 January 2007

Highly integrated single-base resolution maps of the epigenome in Arabidopsis

scientific article (publication date: 2 May 2008)

Hotspots of aberrant epigenomic reprogramming in human induced pluripotent stem cells

scientific article

Human DNA methylomes at base resolution show widespread epigenomic differences

scientific article

Human DNA methylomes of neurodegenerative diseases show common epigenomic patterns.

scientific article published on 19 January 2016

Human body epigenome maps reveal noncanonical DNA methylation variation

scientific article published in June 2015

Improved regulatory element prediction based on tissue-specific local epigenomic signatures

scientific article published on 13 February 2017

Independently evolved virulence effectors converge onto hubs in a plant immune system network

scientific article published in July 2011

Integrated multi-omics framework of the plant response to jasmonic acid

scientific article published on 13 March 2020

Integration of omic networks in a developmental atlas of maize.

scientific article published on August 2016

Integration site selection by HIV-based vectors in dividing and growth-arrested IMR-90 lung fibroblasts.

scientific article published on December 2005

Integration targeting by avian sarcoma-leukosis virus and human immunodeficiency virus in the chicken genome

scientific article

Integrative analysis of haplotype-resolved epigenomes across human tissues.

scientific article published on February 2015

Interplay between ethylene, ETP1/ETP2 F-box proteins, and degradation of EIN2 triggers ethylene responses in Arabidopsis

scientific article published on 04 February 2009

Involvement of NRAMP1 from Arabidopsis thaliana in iron transport.

scientific article published on May 2000

Isolation and characterization of phyC mutants in Arabidopsis reveals complex crosstalk between phytochrome signaling pathways.

scientific article published in September 2003

JAZ2 controls stomata dynamics during bacterial invasion

scientific article published on 22 December 2016

Linking photoreceptor excitation to changes in plant architecture

scientific article published in April 2012

Literature-curated protein interaction datasets.

scientific article published on January 2009

Losing Dnmt3a dependent methylation in inhibitory neurons impairs neural function by a mechanism impacting Rett syndrome

scientific article published on 11 March 2020

Mapping genome-wide transcription-factor binding sites using DAP-seq.

scientific article published on 20 July 2017

Mapping the genome landscape using tiling array technology

scientific article

Mapping transcription factor interactome networks using HaloTag protein arrays.

scientific article published on 29 June 2016

MethylC-seq library preparation for base-resolution whole-genome bisulfite sequencing

scientific article published on 18 February 2015

Mobile small RNAs regulate genome-wide DNA methylation

scientific article published on 19 January 2016

Molecular Criteria for Defining the Naive Human Pluripotent State.

scientific article published on 13 July 2016

Moving forward in reverse: genetic technologies to enable genome-wide phenomic screens in Arabidopsis.

scientific article

Multiple type-B response regulators mediate cytokinin signal transduction in Arabidopsis

scientific article published on 14 October 2005

Mutations in the Ca2+/H+ transporter CAX1 increase CBF/DREB1 expression and the cold-acclimation response in Arabidopsis.

scientific article published on 20 November 2003

NPH4/ARF7 and ARF19 promote leaf expansion and auxin-induced lateral root formation.

scientific article published in July 2005

NPSN11 is a cell plate-associated SNARE protein that interacts with the syntaxin KNOLLE.

scientific article

Next is now: new technologies for sequencing of genomes, transcriptomes, and beyond

scientific article published on 20 January 2009

Non-CG Methylation in the Human Genome.

scientific article published on 4 June 2015

Nuclear events in ethylene signaling: a transcriptional cascade mediated by ETHYLENE-INSENSITIVE3 and ETHYLENE-RESPONSE-FACTOR1

scientific article

OGT binds a conserved C-terminal domain of TET1 to regulate TET1 activity and function in development

article

PHYTOCHROME KINASE SUBSTRATE 1 is a phototropin 1 binding protein required for phototropism.

scholarly article

PHYTOCHROME-INTERACTING FACTORs trigger environmentally responsive chromatin dynamics in plants

scientific article published on 17 June 2021

Patterns of population epigenomic diversity.

scientific article published on 6 March 2013

Phased diploid genome assembly with single-molecule real-time sequencing.

scientific article

Phosphoproteomic analysis of ethylene-regulated protein phosphorylation in etiolated seedlings of Arabidopsis mutant ein2 using two-dimensional separations coupled with a hybrid quadrupole time-of-flight mass spectrometer.

scientific article published in March 2009

Phototropin-related NPL1 controls chloroplast relocation induced by blue light.

scientific article published in April 2001

Phytochrome-specific type 5 phosphatase controls light signal flux by enhancing phytochrome stability and affinity for a signal transducer.

scientific article published in February 2005

Piecing together cis-regulatory networks: insights from epigenomics studies in plants

scientific article

Plant Stress Tolerance Requires Auxin-Sensitive Aux/IAA Transcriptional Repressors

scientific article published on 18 January 2017

Plant defense genes are regulated by ethylene.

scientific article

Plant genomics: the third wave.

scientific article published in January 2004

Plant responses to ethylene gas are mediated by SCF(EBF1/EBF2)-dependent proteolysis of EIN3 transcription factor.

scientific article published in December 2003

Processing and subcellular trafficking of ER-tethered EIN2 control response to ethylene gas.

scientific article

Profiling Interactome Networks with the HaloTag-NAPPA In Situ Protein Array

scientific article published on 14 August 2018

Publisher Correction: Integrated multi-omics framework of the plant response to jasmonic acid

scientific article published on 21 July 2020

RESPONSIVE-TO-ANTAGONIST1, a Menkes/Wilson disease-related copper transporter, is required for ethylene signaling in Arabidopsis.

scientific article published in April 1999

RF1 knockout allows ribosomal incorporation of unnatural amino acids at multiple sites ⬇️

scientific article published on September 18, 2011

Rapid array mapping of circadian clock and developmental mutations in Arabidopsis.

scientific article

Recombination and linkage disequilibrium in Arabidopsis thaliana.

scientific article

Regulation of ethylene gas biosynthesis by the Arabidopsis ETO1 protein.

scientific article published in April 2004

Regulation of membrane trafficking and organ separation by the NEVERSHED ARF-GAP protein.

scientific article published on June 2009

Robust single-cell DNA methylome profiling with snmC-seq2

scientific article published in Nature Communications

Robust single-cell Hi-C clustering by convolution- and random-walk-based imputation

scientific article published on 24 June 2019

STAR: an integrated solution to management and visualization of sequencing data

scientific article

Sequence and analysis of chromosome 1 of the plant Arabidopsis thaliana.

scientific article published on December 2000

Sequencing and functional validation of the JGI Brachypodium distachyon T-DNA collection

scientific article

Short-term growth responses to ethylene in Arabidopsis seedlings are EIN3/EIL1 independent.

scientific article published in October 2004

Sigma factor‐mediated plastid retrograde signals control nuclear gene expression ⬇️

scientific article published on November 5, 2012

Signaling in plants.

scientific article

Simultaneous profiling of 3D genome structure and DNA methylation in single human cells

scientific article published on 09 September 2019

Single nucleus multi-omics identifies human cortical cell regulatory genome diversity

scientific article published in 2022

Single nucleus multi-omics regulatory landscape of the murine pituitary

scientific article published on 11 May 2021

Single-cell DNA methylation and 3D genome architecture in the human brain

scientific article published on 12 October 2023

Single-cell methylomes identify neuronal subtypes and regulatory elements in mammalian cortex.

scientific article

Small RNA-mediated chromatin silencing directed to the 3' region of the Arabidopsis gene encoding the developmental regulator, FLC.

scholarly article

Spatiotemporal DNA methylome dynamics of the developing mouse fetus

scientific article published on 29 July 2020

Surveillance of 3' Noncoding Transcripts Requires FIERY1 and XRN3 in Arabidopsis

scientific article published in April 2012

Systematic mapping of occluded genes by cell fusion reveals prevalence and stability of cis-mediated silencing in somatic cells.

scientific article published on 05 December 2013

Temporal transcriptional response to ethylene gas drives growth hormone cross-regulation in Arabidopsis.

scientific article published on 11 June 2013

The ACC synthase TOE sequence is required for interaction with ETO1 family proteins and destabilization of target proteins.

scientific article published on August 2006

The Arabidopsis 14-3-3 protein RARE COLD INDUCIBLE 1A links low-temperature response and ethylene biosynthesis to regulate freezing tolerance and cold acclimation.

scientific article

The Arabidopsis Auxin Receptor F-Box Proteins AFB4 and AFB5 Are Required for Response to the Synthetic Auxin Picloram

scientific article published on 14 March 2016

The Arabidopsis heavy metal P-type ATPase HMA5 interacts with metallochaperones and functions in copper detoxification of roots.

scientific article

The DNA methylome

scientific article

The Ethylene Pathway: A Paradigm for Plant Hormone Signaling and Interaction ⬇️

scientific article published on February 20, 2001

The NIH Roadmap Epigenomics Mapping Consortium

scientific article (publication date: October 2010)

The beta-subunit of the Arabidopsis G protein negatively regulates auxin-induced cell division and affects multiple developmental processes.

scientific article published on February 2003

The central role of PhEIN2 in ethylene responses throughout plant development in petunia

scientific article published on 01 October 2004

The complex architecture and epigenomic impact of plant T-DNA insertions

article

The developmental potential of iPSCs is greatly influenced by reprogramming factor selection

scientific article

The ethylene gas signal transduction pathway: a molecular perspective

scientific article published on 01 January 1998

The genome of Arabidopsis thaliana.

scientific article

The phosphatase laforin crosses evolutionary boundaries and links carbohydrate metabolism to neuronal disease.

scientific article

The phytochrome-interacting transcription factor, PIF3, acts early, selectively, and positively in light-induced chloroplast development

scholarly article

Transcriptional and epigenomic landscapes of CNS and non-CNS vascular endothelial cells

scientific article published on 06 September 2018

Unique cell-type-specific patterns of DNA methylation in the root meristem.

scientific article

Variation in the structure of varicella-zoster virus DNA.

scientific article published in January 1984

Widespread dynamic DNA methylation in response to biotic stress ⬇️

scientific article published on June 25, 2012

Zeroing in on DNA methylomes with no BS

scientific article published on 01 June 2010

methylPipe and compEpiTools: a suite of R packages for the integrative analysis of epigenomics data

scientific article

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