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  1. Remembering Philip N. Benfey: A visionary pioneer in plant biology and mentor extraordinaire

    Article • Proceedings of the National Academy of Sciences, October 2023, Proceedings of the National Academy of Sciences

    Dr Joseph R Ecker

  2. ​Single nuclei sequencing reveals C4 photosynthesis is based on rewiring of ancestral cell identity networks

    Article • October 2023, Cold Spring Harbor Laboratory Press

    Dr Joseph R Ecker

  3. Epigenome erosion in Alzheimer's disease brain cells and induced neurons

    Article • October 2023, Cold Spring Harbor Laboratory Press

    Dr Joseph R Ecker

  4. Yet uninfected? Resolving cell states of plants under pathogen attack

    Article • Cell Reports Methods, July 2023, Elsevier

    Dr Joseph R Ecker

  5. Multiplexed single-cell 3D spatial gene expression analysis in plant tissue using PHYTOMap

    Article • Nature Plants, June 2023, Springer Science + Business Media

    Dr Joseph R Ecker

  6. Time-resolved single-cell and spatial gene regulatory atlas of plants under pathogen attack

    Article • April 2023, Cold Spring Harbor Laboratory Press

    Dr Joseph R Ecker

  7. A Single-Nucleus Atlas of Seed-to-Seed Development in Arabidopsis

    Article • March 2023, Cold Spring Harbor Laboratory Press

    Dr Joseph R Ecker

  8. Mimicking genuine drought responses using a high throughput plate assay

    Article • February 2023, eLife

    Dr Joseph R Ecker

  9. Mimicking genuine drought responses using a high throughput plate assay

    Article • February 2023, eLife

    Dr Joseph R Ecker

  10. Mimicking genuine drought responses using a high throughput plate assay

    Article • November 2022, Cold Spring Harbor Laboratory Press

    Dr Joseph R Ecker

  11. PHYTOMap: Multiplexed single-cell 3D spatial gene expression analysis in plant tissue

    Article • July 2022, Cold Spring Harbor Laboratory Press

    Dr Joseph R Ecker

  12. The biology of time: dynamic responses of cell types to developmental, circadian, and environmental cues

    Article • The Plant Journal, November 2021, Wiley

    Dr Joseph R Ecker

  13. Activity-dependent modulation of synapse-regulating genes in astrocytes

    Article • eLife, September 2021, eLife

    Dr Joseph R Ecker

  14. A plant-specific syntaxin-6 protein contributes to the intracytoplasmic route for the begomovirus CabLCV

    Article • PLANT PHYSIOLOGY, June 2021, Oxford University Press (OUP)

    Dr Joseph R Ecker

  15. An atlas of dynamic chromatin landscapes in mouse fetal development

    Article • Nature, July 2020, Springer Science + Business Media

    Dr Joseph R Ecker

  16. Expanded encyclopaedias of DNA elements in the human and mouse genomes

    Article • Nature, July 2020, Springer Science + Business Media

    Dr Joseph R Ecker

  17. Perspectives on ENCODE

    Article • Nature, July 2020, Springer Science + Business Media

    Dr Joseph R Ecker

  18. Spatiotemporal DNA methylome dynamics of the developing mouse fetus

    Article • Nature, July 2020, Springer Science + Business Media

    Dr Joseph R Ecker

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

    Article • Nature Plants, July 2020, Springer Science + Business Media

    Dr Joseph R Ecker

  20. Extraction of Distinct Neuronal Cell Types from within a Genetically Continuous Population

    Article • Neuron, July 2020, Elsevier

    Dr Joseph R Ecker

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

    Article • Proceedings of the National Academy of Sciences, May 2020, Proceedings of the National Academy of Sciences

    Dr Joseph R Ecker, Timothy Jobe

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

    Article • eLife, March 2020, eLife

    Dr Joseph R Ecker

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

    Article • Nature Plants, March 2020, Springer Science + Business Media

    Dr Joseph R Ecker

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

    Article • The Plant Cell, February 2020, American Society of Plant Biologists (ASPB)

    Dr Joseph R Ecker

  25. The JA‐pathway MYC transcription factors regulate photomorphogenic responses by targeting HY5 gene expression

    Article • The Plant Journal, January 2020, Wiley

    Dr Joseph R Ecker

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

    Article • PLoS Genetics, December 2019, PLOS

    Dr Joseph R Ecker

  27. A MYC2/MYC3/MYC4-dependent transcription factor network regulates water spray-responsive gene expression and jasmonate levels

    Article • Proceedings of the National Academy of Sciences, October 2019, Proceedings of the National Academy of Sciences

    Dr Joseph R Ecker

  28. Common alleles of CMT2 and NRPE1 are major determinants of de novo DNA methylation variation in Arabidopsis thaliana

    Article • October 2019, Cold Spring Harbor Laboratory Press

    Dr Joseph R Ecker

  29. Genomic Decoding of Neuronal Depolarization by Stimulus-Specific NPAS4 Heterodimers

    Article • Cell, October 2019, Elsevier

    Dr Joseph R Ecker

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

    Article • Nature Methods, September 2019, Springer Science + Business Media

    Dr Joseph R Ecker

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

    Article • Nature Communications, September 2019, Springer Science + Business Media

    Dr Joseph R Ecker

  32. Epigenetic silencing of a multifunctional plant stress regulator

    Article • eLife, August 2019, eLife

    Dr Joseph R Ecker

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

    Article • Proceedings of the National Academy of Sciences, June 2019, Proceedings of the National Academy of Sciences

    Dr Joseph R Ecker

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

    Article • PLoS Genetics, January 2019, PLOS

    Dr Joseph R Ecker

  35. Global DNA methylation remodeling during direct reprogramming of fibroblasts to neurons

    Article • eLife, January 2019, eLife

    Dr Joseph R Ecker

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

    Article • Breeding Science, January 2019, Japanese Society of Breeding

    Dr Joseph R Ecker

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

    Article • eLife, October 2018, eLife

    Dr Joseph R Ecker

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

    Article • Science, September 2018, American Association for the Advancement of Science

    Dr Joseph R Ecker

  39. Robust single-cell DNA methylome profiling with snmC-seq2

    Article • Nature Communications, September 2018, Springer Science + Business Media

    Dr Joseph R Ecker

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

    Article • eLife, September 2018, eLife

    Dr Joseph R Ecker

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

    Article • Current Protocols in Plant Biology, August 2018, Wiley

    Junshi Yazaki, Dr Joseph R Ecker

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

    Article • Nature Communications, May 2018, Springer Science + Business Media

    Dr Joseph R Ecker

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

    Article • Nature Communications, April 2018, Springer Science + Business Media

    Dr Joseph R Ecker

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

    Article • Nature Communications, February 2018, Springer Science + Business Media

    Dr Joseph R Ecker

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

    Article • WIREs Systems Biology and Medicine, November 2017, Wiley

    Dr Joseph R Ecker

  46. The BRAIN Initiative Cell Census Consortium: Lessons Learned toward Generating a Comprehensive Brain Cell Atlas

    Article • Neuron, November 2017, Elsevier

    Dr Joseph R Ecker

  47. Dynamic DNA methylation reconfiguration during seed development and germination

    Article • September 2017, Springer Science + Business Media

    Dr Joseph R Ecker

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

    Article • Science, August 2017, American Association for the Advancement of Science

    Dr Joseph R Ecker

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

    Article • Nature Protocols, July 2017, Springer Science + Business Media

    Dr Joseph R Ecker

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

    Article • Nature Methods, June 2017, Springer Science + Business Media

    Dr Joseph R Ecker

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

    Article • The Plant Journal, June 2017, Wiley

    Dr Joseph R Ecker

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

    Article • June 2017, Cold Spring Harbor Laboratory Press

    Dr Joseph R Ecker

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

    Article • Proceedings of the National Academy of Sciences, March 2017, Proceedings of the National Academy of Sciences

    Dr Joseph R Ecker

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

    Article • Proceedings of the National Academy of Sciences, February 2017, Proceedings of the National Academy of Sciences

    Dr Joseph R Ecker

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

    Article • The Plant Journal, February 2017, Wiley

    Dr Joseph R Ecker

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

    Article • Current Biology, February 2017, Elsevier

    Dr Joseph R Ecker

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

    Article • New Phytologist, January 2017, Wiley

    Dr Joseph R Ecker

  58. Functional Human Oocytes Generated by Transfer of Polar Body Genomes

    Article • Cell Stem Cell, January 2017, Elsevier

    Dr Joseph R Ecker

  59. JAZ2 controls stomata dynamics during bacterial invasion

    Article • New Phytologist, December 2016, Wiley

    Dr Joseph R Ecker

  60. Cerebral Organoids Recapitulate Epigenomic Signatures of the Human Fetal Brain

    Article • Cell Reports, December 2016, Elsevier

    Dr Joseph R Ecker

  61. A transcription factor hierarchy defines an environmental stress response network

    Article • Science, November 2016, American Association for the Advancement of Science

    Dr Joseph R Ecker

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

    Article • Nature Methods, October 2016, Nature

    Fritz Sedlazeck, Dr Joseph R Ecker

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

    Article • Nature Communications, October 2016, Springer Science + Business Media

    Dr Joseph R Ecker

  64. Molecular Criteria for Defining the Naive Human Pluripotent State

    Article • Cell Stem Cell, October 2016, Elsevier

    Dr Joseph R Ecker

  65. Cistrome and Epicistrome Features Shape the Regulatory DNA Landscape

    Article • Cell, September 2016, Elsevier

    Dr Joseph R Ecker

  66. Integration of omic networks in a developmental atlas of maize

    Article • Science, August 2016, American Association for the Advancement of Science

    Dr Joseph R Ecker

  67. 1,135 Genomes Reveal the Global Pattern of Polymorphism in Arabidopsis thaliana

    Article • Cell, July 2016, Elsevier

    Polina Yu Novikova, Dr Joseph R Ecker

  68. Epigenomic Diversity in a Global Collection of Arabidopsis thaliana Accessions

    Article • Cell, July 2016, Elsevier

    Dr Joseph R Ecker

  69. A signaling pathway complementary to the core known ABA signaling conected to JA signaling

    Article • Scientific Reports, June 2016, Nature

    Junshi Yazaki, Fernando Aleman, Dr Joseph R Ecker

  70. TF-interactome by HaloTag protein arrays

    Article • Proceedings of the National Academy of Sciences, June 2016, Proceedings of the National Academy of Sciences

    Junshi Yazaki, Fernando Aleman, Dr Joseph R Ecker

  71. Cistrome and Epicistrome Features Shape the Regulatory DNA Landscape

    Article • Cell, May 2016, Elsevier

    Dr Joseph R Ecker

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

    Article • Nature Plants, April 2016, Springer Science + Business Media

    Dr Joseph R Ecker

  73. INTRODUCTION

    Article • April 2016, Taylor & Francis

    Dr Joseph R Ecker

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

    Article • G3 Genes Genomes Genetics, March 2016, Genetics Society of America

    Dr Joseph R Ecker

  75. Epigenomic landscapes of retinal rods and cones

    Article • eLife, March 2016, eLife

    Dr Joseph R Ecker

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

    Article • The Plant Cell, March 2016, American Society of Plant Biologists (ASPB)

    Dr Joseph R Ecker

  77. Active DNA demethylation at enhancers during the vertebrate phylotypic period

    Article • Nature Genetics, February 2016, Springer Science + Business Media

    Dr Joseph R Ecker

  78. Mobile small RNAs regulate genome-wide DNA methylation

    Article • Proceedings of the National Academy of Sciences, January 2016, Proceedings of the National Academy of Sciences

    Dr Joseph R Ecker

  79. Cryptochromes Interact Directly with PIFs to Control Plant Growth in Limiting Blue Light

    Article • Cell, January 2016, Elsevier

    Dr Joseph R Ecker

  80. Human DNA methylomes of neurodegenerative diseases show common epigenomic patterns

    Article • Translational Psychiatry, January 2016, Springer Science + Business Media

    Dr Joseph R Ecker

  81. Erratum: Corrigendum: Human body epigenome maps reveal noncanonical DNA methylation variation

    Article • Nature, November 2015, Springer Science + Business Media

    Dr Joseph R Ecker

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

    Article • BMC Bioinformatics, September 2015, Springer Science + Business Media

    Dr Joseph R Ecker

  83. DNA Methylation on non-canonical context

    Article • Annual Review of Genomics and Human Genetics, August 2015, Annual Reviews

    Dr Joseph R Ecker, Mr Yupeng He

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

    Article • Proceedings of the National Academy of Sciences, August 2015, Proceedings of the National Academy of Sciences

    Dr Joseph R Ecker

  85. Exceptional epigenetics in the brain

    Article • Science, June 2015, American Association for the Advancement of Science

    Dr Joseph R Ecker

  86. Epigenomic Signatures of Neuronal Diversity in the Mammalian Brain

    Article • Neuron, June 2015, Elsevier

    Dr Joseph R Ecker

  87. Human body epigenome maps reveal noncanonical DNA methylation variation

    Article • Nature, June 2015, Springer Science + Business Media

    Dr Joseph R Ecker

  88. An alternative pluripotent state confers interspecies chimaeric competency

    Article • Nature, May 2015, Springer Science + Business Media

    Dr Joseph R Ecker

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

    Article • Cell Stem Cell, May 2015, Elsevier

    Dr Joseph R Ecker

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

    Article • Nature Protocols, February 2015, Nature

    Dr Joseph R Ecker

  91. Chromatin architecture reorganization during stem cell differentiation

    Article • Nature, February 2015, Springer Science + Business Media

    Dr Joseph R Ecker

  92. Integrative analysis of 111 reference human epigenomes

    Article • Nature, February 2015, Springer Science + Business Media

    Dr Joseph R Ecker

  93. Integrative analysis of haplotype-resolved epigenomes across human tissues

    Article • Nature, February 2015, Springer Science + Business Media

    Dr Joseph R Ecker

  94. A User’s Guide to the Arabidopsis T-DNA Insertion Mutant Collections

    Article • January 2015, Springer Science + Business Media

    Dr Joseph R Ecker

  95. Comparison of the transcriptional landscapes between human and mouse tissues

    Article • Proceedings of the National Academy of Sciences, November 2014, Proceedings of the National Academy of Sciences

    Dr Joseph R Ecker

  96. Erratum: Corrigendum: Hotspots of aberrant epigenomic reprogramming in human induced pluripotent stem cells

    Article • Nature, October 2014, Springer Science + Business Media

    Dr Joseph R Ecker

  97. The Developmental Potential of iPSCs Is Greatly Influenced by Reprogramming Factor Selection

    Article • Cell Stem Cell, September 2014, Elsevier

    Dr Joseph R Ecker

  98. Determination and Inference of Eukaryotic Transcription Factor Sequence Specificity

    Article • Cell, September 2014, Elsevier

    Dr Joseph R Ecker, Dr Alejandro Montenegro-Montero

  99. Convergent Targeting of a Common Host Protein-Network by Pathogen Effectors from Three Kingdoms of Life

    Article • Cell Host & Microbe, September 2014, Elsevier

    Dr Joseph R Ecker

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

    Article • Genome Research, August 2014, Cold Spring Harbor Laboratory Press

    Dr Joseph R Ecker

  101. The Arabidopsis 14-3-3 Protein RARE COLD INDUCIBLE 1A Links Low-Temperature Response and Ethylene Biosynthesis to Regulate Freezing Tolerance and Cold Acclimation

    Article • The Plant Cell, August 2014, American Society of Plant Biologists (ASPB)

    Dr Joseph R Ecker

  102. DNA Topoisomerase 1α Promotes Transcriptional Silencing of Transposable Elements through DNA Methylation and Histone Lysine 9 Dimethylation in Arabidopsis

    Article • PLoS Genetics, July 2014, PLOS

    Dr Joseph R Ecker, Xuemei Chen

  103. Abnormalities in human pluripotent cells due to reprogramming mechanisms

    Article • Nature, July 2014, Springer Science + Business Media

    Dr Joseph R Ecker

  104. Genotypic variation of gene expression during the soybean innate immunity response

    Article • Plant Genetic Resources, July 2014, Cambridge University Press

    Dr Joseph R Ecker, Professor Oswaldo Valdes-Lopez

  105. A Genome-Scale Resource for the Functional Characterization of Arabidopsis Transcription Factors

    Article • Cell Reports, July 2014, Elsevier

    Dr Joseph R Ecker

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

    Article • Proceedings of the National Academy of Sciences, April 2014, Proceedings of the National Academy of Sciences

    Dr Joseph R Ecker

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

    Article • Genome Research, December 2013, Cold Spring Harbor Laboratory Press

    Dr Joseph R Ecker

  108. Solving nonlinear principal-agent problems using bilevel programming

    Article • European Journal of Operational Research, October 2013, Elsevier

    Dr Joseph R Ecker

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

    Article • Proceedings of the National Academy of Sciences, September 2013, Proceedings of the National Academy of Sciences

    Dr Joseph R Ecker

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

    Article • Bioinformatics, September 2013, Oxford University Press (OUP)

    Dr Joseph R Ecker

  111. Response to Perspective

    Article • Plant Signaling & Behavior, August 2013, Taylor & Francis

    Dr Joseph R Ecker

  112. Constructing Hepitypes: Phasing Local Genotype and DNA Methylation

    Article • Journal of Neuroscience and Neuroengineering, August 2013, American Scientific Publishers

    Dr Joseph R Ecker

  113. Arabidopsis Basic Helix-Loop-Helix Transcription Factors MYC2, MYC3, and MYC4 Regulate Glucosinolate Biosynthesis, Insect Performance, and Feeding Behavior

    Article • The Plant Cell, August 2013, American Society of Plant Biologists (ASPB)

    Dr Joseph R Ecker

  114. Global Epigenomic Reconfiguration During Mammalian Brain Development

    Article • Science, July 2013, American Association for the Advancement of Science

    Dr Joseph R Ecker

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

    Article • eLife, June 2013, eLife

    Dr Joseph R Ecker

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

    Article • Genome Research, June 2013, Cold Spring Harbor Laboratory Press

    Dr Joseph R Ecker

  117. Epigenomic Analysis of Multilineage Differentiation of Human Embryonic Stem Cells

    Article • Cell, May 2013, Elsevier

    Dr Joseph R Ecker

  118. Functional Characterization of Type-B Response Regulators in the Arabidopsis Cytokinin Response

    Article • PLANT PHYSIOLOGY, March 2013, American Society of Plant Biologists (ASPB)

    Dr Joseph R Ecker

  119. Patterns of population epigenomic diversity

    Article • Nature, March 2013, Springer Science + Business Media

    Dr Joseph R Ecker

  120. Epigenetic trigger for tomato ripening

    Article • Nature Biotechnology, February 2013, Springer Science + Business Media

    Dr Joseph R Ecker

  121. ‘Leveling’ the playing field for analyses of single-base resolution DNA methylomes

    Article • Trends in Genetics, December 2012, Elsevier

    Dr Joseph R Ecker

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

    Article • Cell Metabolism, December 2012, Elsevier

    Dr Joseph R Ecker

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

    Article • Cancer Research, November 2012, American Association for Cancer Research (AACR)

    Dr Joseph R Ecker

  124. Sigma factor‐mediated plastid retrograde signals control nuclear gene expression

    Article • The Plant Journal, November 2012, Wiley

    Dr Joseph R Ecker

  125. ENCODE explained

    Article • Nature, September 2012, Springer Science + Business Media

    Dr Joseph R Ecker

  126. Processing and Subcellular Trafficking of ER-Tethered EIN2 Control Response to Ethylene Gas

    Article • Science, August 2012, American Association for the Advancement of Science

    Dr Joseph R Ecker

  127. Spatial and functional relationships among Pol V-associated loci, Pol IV-dependent siRNAs, and cytosine methylation in the Arabidopsis epigenome

    Article • Genes & Development, August 2012, Cold Spring Harbor Laboratory Press

    Dr Joseph R Ecker

  128. Widespread dynamic DNA methylation in response to biotic stress

    Article • Proceedings of the National Academy of Sciences, June 2012, Proceedings of the National Academy of Sciences

    Dr Joseph R Ecker

  129. Release Factor One Is Nonessential in Escherichia coli

    Article • ACS Chemical Biology, June 2012, American Chemical Society (ACS)

    Dr Joseph R Ecker

  130. Detection of allele-specific methylation through a generalized heterogeneous epigenome model

    Article • Bioinformatics, June 2012, Oxford University Press (OUP)

    Dr Joseph R Ecker

  131. Reading the Second Code: Mapping Epigenomes to Understand Plant Growth, Development, and Adaptation to the Environment

    Article • The Plant Cell, June 2012, American Society of Plant Biologists (ASPB)

    Dr Joseph R Ecker

  132. Linking photoreceptor excitation to changes in plant architecture

    Article • Genes & Development, April 2012, Cold Spring Harbor Laboratory Press

    Dr Joseph R Ecker

  133. Surveillance of 3′ Noncoding Transcripts Requires FIERY1 and XRN3 in Arabidopsis

    Article • G3 Genes Genomes Genetics, April 2012, Genetics Society of America

    Dr Joseph R Ecker

  134. Epigenetic and epigenomic variation in Arabidopsis thaliana

    Article • Trends in Plant Science, March 2012, Elsevier

    Dr Joseph R Ecker

  135. Epiallelic Variation in Arabidopsis thaliana

    Article • Cold Spring Harbor Symposia on Quantitative Biology, January 2012, Cold Spring Harbor Laboratory Press

    Dr Joseph R Ecker

  136. Global DNA hypomethylation coupled to repressive chromatin domain formation and gene silencing in breast cancer

    Article • Genome Research, December 2011, Cold Spring Harbor Laboratory Press

    Dr Joseph R Ecker

  137. Forward and Reverse Genetics through Derivation of Haploid Mouse Embryonic Stem Cells

    Article • Cell Stem Cell, December 2011, Elsevier

    Dr Joseph R Ecker

  138. Unexpected Diversity of Chloroplast Noncoding RNAs as Revealed by Deep Sequencing of theArabidopsisTranscriptome

    Article • G3 Genes Genomes Genetics, December 2011, Genetics Society of America

    Dr Joseph R Ecker

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

    Article • Nature Chemical Biology, September 2011, Springer Science + Business Media

    Dr Joseph R Ecker

  140. Transgenerational Epigenetic Instability Is a Source of Novel Methylation Variants

    Article • Science, September 2011, American Association for the Advancement of Science

    Dr Joseph R Ecker

  141. Independently Evolved Virulence Effectors Converge onto Hubs in a Plant Immune System Network

    Article • Science, July 2011, American Association for the Advancement of Science

    Dr Joseph R Ecker

  142. Genome-wide mapping of 5-hydroxymethylcytosine in embryonic stem cells

    Article • Nature, May 2011, Springer Science + Business Media

    Dr Joseph R Ecker

  143. Hotspots of aberrant epigenomic reprogramming in human induced pluripotent stem cells

    Article • Nature, February 2011, Springer Science + Business Media

    Dr Joseph R Ecker

  144. The DNA methylome

    Article • FEBS Letters, November 2010, Wiley

    Dr Joseph R Ecker

  145. The NIH Roadmap Epigenomics Mapping Consortium

    Article • Nature Biotechnology, October 2010, Springer Science + Business Media

    Dr Joseph R Ecker

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

    Article • Nature Biotechnology, September 2010, Springer Science + Business Media

    Dr Joseph R Ecker, Dr Christoph Bock

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

    Article • Proceedings of the National Academy of Sciences, July 2010, Proceedings of the National Academy of Sciences

    Dr Joseph R Ecker

  148. 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

    Article • The Plant Cell, July 2010, American Society of Plant Biologists (ASPB)

    Dr Joseph R Ecker

  149. Zeroing in on DNA methylomes with no BS

    Article • Nature Methods, June 2010, Springer Science + Business Media

    Dr Joseph R Ecker

  150. Distinct Epigenomic Landscapes of Pluripotent and Lineage-Committed Human Cells

    Article • Cell Stem Cell, May 2010, Elsevier

    Dr Joseph R Ecker

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

    Article • Nature, March 2010, Springer Science + Business Media

    Dr Joseph R Ecker

  152. Linking genotype to phenotype using the Arabidopsis unimutant collection

    Article • The Plant Journal, March 2010, Wiley

    Dr Joseph R Ecker

  153. Two Plant Viral Suppressors of Silencing Require the Ethylene-Inducible Host Transcription Factor RAV2 to Block RNA Silencing

    Article • PLoS Pathogens, January 2010, PLOS

    Dr Joseph R Ecker

  154. Ethylene Responses in Seedling Growth and Development

    Article • January 2010, Springer Science + Business Media

    Dr Joseph R Ecker

  155. Addendum: Literature-curated protein interaction datasets

    Article • Nature Methods, November 2009, Springer Science + Business Media

    Dr Joseph R Ecker, Junshi Yazaki

  156. Human DNA methylomes at base resolution show widespread epigenomic differences

    Article • Nature, October 2009, Springer Science + Business Media

    Dr Joseph R Ecker

  157. A Combinatorial Interplay Among the 1-Aminocyclopropane-1-Carboxylate Isoforms Regulates Ethylene Biosynthesis in Arabidopsis thaliana

    Article • Genetics, September 2009, Genetics Society of America

    Dr Joseph R Ecker

  158. Rapid and High-Throughput pan-Orthopoxvirus Detection and Identification using PCR and Mass Spectrometry

    Article • PLoS ONE, July 2009, PLOS

    Dr Joseph R Ecker

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

    Article • Development, May 2009, The Company of Biologists

    Dr Joseph R Ecker

  160. A Family of Bacterial Cysteine Protease Type III Effectors Utilizes Acylation-dependent and -independent Strategies to Localize to Plasma Membranes

    Article • Journal of Biological Chemistry, April 2009, American Society for Biochemistry & Molecular Biology (ASBMB)

    Dr Joseph R Ecker

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

    Article • Current Opinion in Plant Biology, April 2009, Elsevier

    Dr Joseph R Ecker

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

    Article • Genome Research, March 2009, Cold Spring Harbor Laboratory Press

    Dr Joseph R Ecker

  163. 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

    Article • PROTEOMICS, March 2009, Wiley

    Dr Joseph R Ecker

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

    Article • Genes & Development, February 2009, Cold Spring Harbor Laboratory Press

    Junshi Yazaki, Dr Joseph R Ecker

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

    Article • Genome Biology, January 2009, Springer Science + Business Media

    Dr Joseph R Ecker

  166. Literature-curated protein interaction datasets

    Article • Nature Methods, December 2008, Springer Science + Business Media

    Dr Joseph R Ecker, Junshi Yazaki

  167. Solving Bilevel Linear Programs Using Multiple Objective Linear Programming

    Article • Journal of Optimization Theory and Applications, September 2008, Springer Science + Business Media

    Dr Joseph R Ecker

  168. Correction

    Article • The Plant Cell, July 2008, American Society of Plant Biologists (ASPB)

    Dr Joseph R Ecker

  169. A Link between RNA Metabolism and Silencing Affecting Arabidopsis Development

    Article • Developmental Cell, June 2008, Elsevier

    Dr Joseph R Ecker

  170. Highly Integrated Single-Base Resolution Maps of the Epigenome in Arabidopsis

    Article • Cell, May 2008, Elsevier

    Dr Joseph R Ecker

  171. Utilizing tiling microarrays for whole‐genome analysis in plants

    Article • The Plant Journal, February 2008, Wiley

    Dr Joseph R Ecker, Junshi Yazaki

  172. Potential Sites of Bioactive Gibberellin Production during Reproductive Growth in Arabidopsis

    Article • The Plant Cell, February 2008, American Society of Plant Biologists (ASPB)

    Dr Joseph R Ecker

  173. The Arabidopsis Phytochrome-Interacting Factor PIF7, Together with PIF3 and PIF4, Regulates Responses to Prolonged Red Light by Modulating phyB Levels

    Article • The Plant Cell, February 2008, American Society of Plant Biologists (ASPB)

    Dr Joseph R Ecker

  174. Genome-Wide High-Resolution Mapping of Exosome Substrates Reveals Hidden Features in the Arabidopsis Transcriptome

    Article • Cell, December 2007, Elsevier

    Dr Joseph R Ecker, Junshi Yazaki, Dr. Ueli Grossniklaus

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

    Article • Nature Protocols, November 2007, Springer Science + Business Media

    Dr Joseph R Ecker

  176. Direct broad-range detection of alphaviruses in mosquito extracts

    Article • Virology, November 2007, Elsevier

    Dr Joseph R Ecker

  177. Mapping the genome landscape using tiling array technology

    Article • Current Opinion in Plant Biology, October 2007, Elsevier

    Dr Joseph R Ecker, Junshi Yazaki

  178. Recombination and linkage disequilibrium in Arabidopsis thaliana

    Article • Nature Genetics, August 2007, Springer Science + Business Media

    Dr Joseph R Ecker

  179. A WD40 Domain Cyclophilin Interacts with Histone H3 and Functions in Gene Repression and Organogenesis in Arabidopsis

    Article • The Plant Cell, August 2007, American Society of Plant Biologists (ASPB)

    Dr Joseph R Ecker

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

    Article • The Journal of Cell Biology, July 2007, Rockefeller University Press

    Dr Joseph R Ecker

  181. Common Sequence Polymorphisms Shaping Genetic Diversity in Arabidopsis thaliana

    Article • Science, July 2007, American Association for the Advancement of Science

    Dr Joseph R Ecker

  182. Genome-wide patterns of single-feature polymorphism in Arabidopsis thaliana

    Article • Proceedings of the National Academy of Sciences, July 2007, Proceedings of the National Academy of Sciences

    Dr Joseph R Ecker

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

    Article • Biochemical and Biophysical Research Communications, March 2007, Elsevier

    Dr Joseph R Ecker

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

    Article • Proceedings of the National Academy of Sciences, February 2007, Proceedings of the National Academy of Sciences

    Dr Joseph R Ecker

  185. The Ibis T5000 Universal Biosensor: An Automated Platform for Pathogen Identification and Strain Typing

    Article • JALA Journal of the Association for Laboratory Automation, December 2006, SAGE Publications

    Dr Joseph R Ecker

  186. Localization of Iron in Arabidopsis Seed Requires the Vacuolar Membrane Transporter VIT1

    Article • Science, November 2006, American Association for the Advancement of Science

    Dr Joseph R Ecker

  187. The Arabidopsis Histidine Phosphotransfer Proteins Are Redundant Positive Regulators of Cytokinin Signaling

    Article • The Plant Cell, November 2006, American Society of Plant Biologists (ASPB)

    Dr Joseph R Ecker

  188. The POLARIS Peptide of Arabidopsis Regulates Auxin Transport and Root Growth via Effects on Ethylene Signaling

    Article • The Plant Cell, November 2006, American Society of Plant Biologists (ASPB)

    Dr Joseph R Ecker

  189. CDPKs CPK6 and CPK3 Function in ABA Regulation of Guard Cell S-Type Anion- and Ca2+- Permeable Channels and Stomatal Closure

    Article • PLoS Biology, October 2006, PLOS

    Dr Joseph R Ecker

  190. ETHYLENE-INSENSITIVE5 encodes a 5′→3′ exoribonuclease required for regulation of the EIN3-targeting F-box proteins EBF1/2

    Article • Proceedings of the National Academy of Sciences, September 2006, Proceedings of the National Academy of Sciences

    Dr Joseph R Ecker

  191. Genome-wide High-Resolution Mapping and Functional Analysis of DNA Methylation in Arabidopsis

    Article • Cell, September 2006, Elsevier

    Dr Joseph R Ecker, Junshi Yazaki

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

    Article • Plant Molecular Biology, August 2006, Springer Science + Business Media

    Dr Joseph R Ecker

  193. Identification of Acinetobacter Species and Genotyping of Acinetobacter baumannii by Multilocus PCR and Mass Spectrometry

    Article • Journal of Clinical Microbiology, August 2006, ASM Journals

    Dr Joseph R Ecker

  194. HIV Integration Site Selection: Targeting in Macrophages and the Effects of Different Routes of Viral Entry

    Article • Molecular Therapy, August 2006, Elsevier

    Dr Joseph R Ecker

  195. RACK1 mediates multiple hormone responsiveness and developmental processes in Arabidopsis

    Article • Journal of Experimental Botany, July 2006, Oxford University Press (OUP)

    Dr Joseph R Ecker

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

    Article • Proceedings of the National Academy of Sciences, June 2006, Proceedings of the National Academy of Sciences

    Dr Joseph R Ecker, PhD Christian Fankhauser

  197. Retroviral DNA Integration: Viral and Cellular Determinants of Target-Site Selection

    Article • PLoS Pathogens, June 2006, PLOS

    Dr Michael Emerman, Dr Joseph R Ecker

  198. Downregulation of ClpR2 Leads to Reduced Accumulation of the ClpPRS Protease Complex and Defects in Chloroplast Biogenesis in Arabidopsis

    Article • The Plant Cell, June 2006, American Society of Plant Biologists (ASPB)

    Dr Joseph R Ecker

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

    Article • Nature Reviews Genetics, June 2006, Springer Science + Business Media

    Dr Joseph R Ecker

  200. Integration Site Selection by HIV-Based Vectors in Dividing and Growth-Arrested IMR-90 Lung Fibroblasts

    Article • Molecular Therapy, February 2006, Elsevier

    Dr Joseph R Ecker

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

    Article • The Plant Journal, December 2005, Wiley

    Dr Joseph R Ecker

  202. A role for LEDGF/p75 in targeting HIV DNA integration

    Article • Nature Reports Stem Cells, November 2005, Springer Science + Business Media

    Dr Joseph R Ecker

  203. Functional Genomic Analysis of the AUXIN/INDOLE-3-ACETIC ACID Gene Family Members in Arabidopsis thaliana

    Article • The Plant Cell, November 2005, American Society of Plant Biologists (ASPB)

    Dr Joseph R Ecker

  204. Multiple Type-B Response Regulators Mediate Cytokinin Signal Transduction in Arabidopsis

    Article • The Plant Cell, October 2005, American Society of Plant Biologists (ASPB)

    Dr Joseph R Ecker

  205. Molecular and Genetic Analysis of Hormone-Regulated Differential Cell Elongation in Arabidopsis

    Article • September 2005, Office of Scientific and Technical Information (OSTI)

    Dr Joseph R Ecker

  206. Integration Targeting by Avian Sarcoma-Leukosis Virus and Human Immunodeficiency Virus in the Chicken Genome

    Article • Journal of Virology, September 2005, ASM Journals

    Dr Joseph R Ecker

  207. Auxin response factors ARF6 and ARF8 promote jasmonic acid production and flower maturation

    Article • Development, August 2005, The Company of Biologists

    Dr Joseph R Ecker

  208. LUX ARRHYTHMO encodes a Myb domain protein essential for circadian rhythms

    Article • Proceedings of the National Academy of Sciences, July 2005, Proceedings of the National Academy of Sciences

    Dr Joseph R Ecker

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

    Article • The Plant Journal, June 2005, Wiley

    Dr Joseph R Ecker

  210. Genome-Wide Analysis of Chromosomal Features Repressing Human Immunodeficiency Virus Transcription

    Article • Journal of Virology, June 2005, ASM Journals

    Dr Joseph R Ecker

  211. Rapid identification and strain-typing of respiratory pathogens for epidemic surveillance

    Article • Proceedings of the National Academy of Sciences, May 2005, Proceedings of the National Academy of Sciences

    Dr Joseph R Ecker

  212. FRIGIDA-Independent Variation in Flowering Time of Natural Arabidopsis thaliana Accessions

    Article • Genetics, May 2005, Genetics Society of America

    Dr Joseph R Ecker

  213. Rapid Array Mapping of Circadian Clock and Developmental Mutations in Arabidopsis

    Article • PLANT PHYSIOLOGY, May 2005, American Society of Plant Biologists (ASPB)

    Dr Joseph R Ecker

  214. Corrigendum to ‘‘Applications of DNA tiling arrays for whole-genome analysis’’ [Genomics 85 (2005) 1–15]

    Article • Genomics, May 2005, Elsevier

    Dr Joseph R Ecker

  215. Genome-wide analysis of cAMP-response element binding protein occupancy, phosphorylation, and target gene activation in human tissues

    Article • Proceedings of the National Academy of Sciences, March 2005, Proceedings of the National Academy of Sciences

    Dr Joseph R Ecker

  216. Quantitative trait locus mapping and DNA array hybridization identify an FLM deletion as a cause for natural flowering-time variation

    Article • Proceedings of the National Academy of Sciences, February 2005, Proceedings of the National Academy of Sciences

    Dr Joseph R Ecker

  217. Phytochrome-Specific Type 5 Phosphatase Controls Light Signal Flux by Enhancing Phytochrome Stability and Affinity for a Signal Transducer

    Article • Cell, February 2005, Elsevier

    Dr Joseph R Ecker

  218. Functional Genomic Analysis of the AUXIN RESPONSE FACTOR Gene Family Members in Arabidopsis thaliana: Unique and Overlapping Functions of ARF7 and ARF19

    Article • The Plant Cell, January 2005, American Society of Plant Biologists (ASPB)

    Dr Joseph R Ecker

  219. Applications of DNA tiling arrays for whole-genome analysis

    Article • Genomics, January 2005, Elsevier

    Dr Joseph R Ecker

  220. Article • BMC Plant Biology, January 2005, Springer Science + Business Media

    Dr Joseph R Ecker

  221. Class III Homeodomain-Leucine Zipper Gene Family Members Have Overlapping, Antagonistic, and Distinct Roles in Arabidopsis Development

    Article • The Plant Cell, December 2004, American Society of Plant Biologists (ASPB)

    Dr Joseph R Ecker

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

    Article • The Plant Journal, December 2004, Wiley

    Dr Joseph R Ecker

  223. Reentry of the Ethylene MPK6 Module

    Article • The Plant Cell, December 2004, American Society of Plant Biologists (ASPB)

    Dr Joseph R Ecker

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

    Article • Proceedings of the National Academy of Sciences, October 2004, Proceedings of the National Academy of Sciences

    Dr Joseph R Ecker

  225. Short-Term Growth Responses to Ethylene in Arabidopsis Seedlings Are EIN3/EIL1 Independent

    Article • PLANT PHYSIOLOGY, October 2004, American Society of Plant Biologists (ASPB)

    Dr Joseph R Ecker

  226. The Central Role of PhEIN2 in Ethylene Responses throughout Plant Development in Petunia

    Article • PLANT PHYSIOLOGY, October 2004, American Society of Plant Biologists (ASPB)

    Dr Joseph R Ecker

  227. PLANT GENOMICS: The Third Wave

    Article • Annual Review of Genomics and Human Genetics, September 2004, Annual Reviews

    Dr Joseph R Ecker

  228. Retroviral DNA Integration: ASLV, HIV, and MLV Show Distinct Target Site Preferences

    Article • PLoS Biology, August 2004, PLOS

    Dr Joseph R Ecker

  229. Regulation of flowering time in Arabidopsis by K homology domain proteins

    Article • Proceedings of the National Academy of Sciences, August 2004, Proceedings of the National Academy of Sciences

    Dr Joseph R Ecker

  230. Convergence of Signaling Pathways in the Control of Differential Cell Growth in Arabidopsis

    Article • Developmental Cell, August 2004, Elsevier

    Dr Joseph R Ecker

  231. Flagellin Is Not a Major Defense Elicitor in Ralstonia solanacearum Cells or Extracts Applied to Arabidopsis thaliana

    Article • Molecular Plant-Microbe Interactions, June 2004, Scientific Societies

    Dr Joseph R Ecker, Professor Caitilyn Allen

  232. DELLA Proteins and Gibberellin-Regulated Seed Germination and Floral Development in Arabidopsis

    Article • PLANT PHYSIOLOGY, June 2004, American Society of Plant Biologists (ASPB)

    Dr Joseph R Ecker

  233. GCR1 Can Act Independently of Heterotrimeric G-Protein in Response to Brassinosteroids and Gibberellins in Arabidopsis Seed Germination

    Article • PLANT PHYSIOLOGY, June 2004, American Society of Plant Biologists (ASPB)

    Dr Joseph R Ecker

  234. Light-Response Quantitative Trait Loci Identified with Composite Interval and eXtreme Array Mapping inArabidopsis thaliana

    Article • Genetics, June 2004, Genetics Society of America

    Dr Joseph R Ecker

  235. A Homolog of Prokaryotic Thiol Disulfide Transporter CcdA Is Required for the Assembly of the Cytochromeb6fComplex inArabidopsisChloroplasts

    Article • Journal of Biological Chemistry, May 2004, American Society for Biochemistry & Molecular Biology (ASBMB)

    Dr Joseph R Ecker

  236. Regulation of ethylene gas biosynthesis by the Arabidopsis ETO1 protein

    Article • April 2004

    Dr Joseph R Ecker

  237. Genome studies and molecular genetics

    Article • Current Opinion in Plant Biology, April 2004, Elsevier

    Dr Joseph R Ecker

  238. CBF2/DREB1C is a negative regulator ofCBF1/DREB1BandCBF3/DREB1Aexpression and plays a central role in stress tolerance inArabidopsis

    Article • Proceedings of the National Academy of Sciences, March 2004, Proceedings of the National Academy of Sciences

    Dr Joseph R Ecker

  239. Type-A Arabidopsis Response Regulators Are Partially Redundant Negative Regulators of Cytokinin Signaling

    Article • The Plant Cell, February 2004, American Society of Plant Biologists (ASPB)

    Dr Joseph R Ecker

  240. The ethylene signaling pathway: new insights

    Article • Current Opinion in Plant Biology, February 2004, Elsevier

    Dr Joseph R Ecker

  241. Corrections

    Article • The Plant Cell, February 2004, American Society of Plant Biologists (ASPB)

    Dr Joseph R Ecker

  242. Plant Responses to Ethylene Gas Are Mediated by SCFEBF1/EBF2-Dependent Proteolysis of EIN3 Transcription Factor

    Article • Cell, December 2003, Elsevier

    Dr Joseph R Ecker

  243. A Growth Regulatory Loop That Provides Homeostasis to Phytochrome A Signaling

    Article • The Plant Cell, December 2003, American Society of Plant Biologists (ASPB)

    Professor Jorge J Casal, Dr Joseph R Ecker, PhD Christian Fankhauser

  244. Mutations in the Ca2+/H+ Transporter CAX1 Increase CBF/DREB1 Expression and the Cold-Acclimation Response in Arabidopsis

    Article • The Plant Cell, November 2003, American Society of Plant Biologists (ASPB)

    Dr Joseph R Ecker

  245. Enhanced Fitness Conferred by Naturally Occurring Variation in the Circadian Clock

    Article • Science, November 2003, American Association for the Advancement of Science

    Dr Joseph R Ecker

  246. Extractions

    Article • American Journal of Orthodontics and Dentofacial Orthopedics, November 2003, Elsevier

    Dr Joseph R Ecker

  247. Empirical Analysis of Transcriptional Activity in the Arabidopsis Genome

    Article • Science, October 2003, American Association for the Advancement of Science

    Piero Carninci, Dr Joseph R Ecker

  248. Isolation and Characterization of phyC Mutants in Arabidopsis Reveals Complex Crosstalk between Phytochrome Signaling Pathways

    Article • The Plant Cell, August 2003, American Society of Plant Biologists (ASPB)

    Dr Joseph R Ecker

  249. Genome-Wide Insertional Mutagenesis of Arabidopsis thaliana

    Article • Science, August 2003, American Association for the Advancement of Science

    Dr Joseph R Ecker

  250. A Reevaluation of the Role of the Heterotrimeric G Protein in Coupling Light Responses in Arabidopsis

    Article • PLANT PHYSIOLOGY, April 2003, American Society of Plant Biologists (ASPB)

    Dr Joseph R Ecker

  251. Five components of the ethylene-response pathway identified in a screen for weak ethylene-insensitive mutants in Arabidopsis

    Article • Proceedings of the National Academy of Sciences, February 2003, Proceedings of the National Academy of Sciences

    Dr Joseph R Ecker

  252. GUN4, a Regulator of Chlorophyll Synthesis and Intracellular Signaling

    Article • Science, February 2003, American Association for the Advancement of Science

    Dr Joseph R Ecker

  253. Arabidopsis RIN4 Is a Target of the Type III Virulence Effector AvrRpt2 and Modulates RPS2-Mediated Resistance

    Article • Cell, February 2003, Elsevier

    Dr Joseph R Ecker

  254. The β-Subunit of the Arabidopsis G Protein Negatively Regulates Auxin-Induced Cell Division and Affects Multiple Developmental Processes

    Article • The Plant Cell, January 2003, American Society of Plant Biologists (ASPB)

    Dr Joseph R Ecker, Dr. Keith R. Davis

  255. Chloroplast to nucleus communication triggered by accumulation of Mg-protoporphyrinIX

    Article • Nature, January 2003, Springer Science + Business Media

    Dr Joseph R Ecker

  256. ABA-Activated SnRK2 Protein Kinase is Required for Dehydration Stress Signaling in Arabidopsis

    Article • Plant and Cell Physiology, December 2002, Oxford University Press (OUP)

    Dr Joseph R Ecker

  257. Molecular and Genetic Analysis of Hormone-Regulated Differential Cell Elongation in Arabidopsis

    Article • December 2002, Office of Scientific and Technical Information (OSTI)

    Dr Joseph R Ecker

  258. Divergent perspectives on GM food

    Article • Nature Biotechnology, December 2002, Springer Science + Business Media

    Dr Joseph R Ecker

  259. Trp-dependent auxin biosynthesis in Arabidopsis: involvement of cytochrome P450s CYP79B2 and CYP79B3

    Article • Genes & Development, December 2002, Cold Spring Harbor Laboratory Press

    Dr Joseph R Ecker

  260. De-Etiolated 1 and Damaged DNA Binding Protein 1 Interact to Regulate Arabidopsis Photomorphogenesis

    Article • Current Biology, September 2002, Elsevier

    Dr Joseph R Ecker

  261. HIV-1 Integration in the Human Genome Favors Active Genes and Local Hotspots

    Article • Cell, August 2002, Elsevier

    Dr Joseph R Ecker

  262. A Role for Peroxisomes in Photomorphogenesis and Development of Arabidopsis

    Article • Science, July 2002, American Association for the Advancement of Science

    Dr Joseph R Ecker

  263. Mitogen-activated protein kinase cascades in plants: a new nomenclature

    Article • Trends in Plant Science, July 2002, Elsevier

    Dr Joseph R Ecker

  264. NPSN11 Is a Cell Plate-Associated SNARE Protein That Interacts with the Syntaxin KNOLLE

    Article • PLANT PHYSIOLOGY, May 2002, American Society of Plant Biologists (ASPB)

    Dr Joseph R Ecker

  265. An application of nonlinear optimization in molecular biology

    Article • European Journal of Operational Research, April 2002, Elsevier

    Dr Joseph R Ecker

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

    Article • Nature, April 2001, Springer Science + Business Media

    Dr Joseph R Ecker

  267. An Arabidopsis circadian clock component interacts with both CRY1 and phyB

    Article • Nature, March 2001, Springer Science + Business Media

    Dr Joseph R Ecker

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

    Article • Science Signaling, February 2001, American Association for the Advancement of Science

    Dr Joseph R Ecker

  269. Analysis of the genome sequence of the flowering plant Arabidopsis thaliana

    Article • Nature, December 2000, Springer Science + Business Media

    Prof. Jonathan A. Eisen, Dr Joseph R Ecker

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

    Article • Nature, December 2000, Springer Science + Business Media

    Dr Joseph R Ecker

  271. Ethylene signaling: from mutants to molecules

    Article • Current Opinion in Plant Biology, October 2000, Elsevier

    Dr Joseph R Ecker

  272. Involvement of NRAMP1 from Arabidopsis thaliana in iron transport

    Article • Biochemical Journal, May 2000, Portland Press Ltd.

    Dr Joseph R Ecker

  273. A complete BAC-based physical map of the Arabidopsis thaliana genome

    Article • Nature Genetics, July 1999, Springer Science + Business Media

    Dr Joseph R Ecker

  274. EIN2, a Bifunctional Transducer of Ethylene and Stress Responses in Arabidopsis

    Article • Science, June 1999, American Association for the Advancement of Science

    Dr Joseph R Ecker

  275. RESPONSIVE-TO-ANTAGONIST1, a Menkes/Wilson Disease–Related Copper Transporter, Is Required for Ethylene Signaling in Arabidopsis

    Article • Cell, April 1999, Elsevier

    Dr Joseph R Ecker

  276. THE ETHYLENE GAS SIGNAL TRANSDUCTION PATHWAY: A Molecular Perspective

    Article • Annual Review of Genetics, December 1998, Annual Reviews

    Dr Joseph R Ecker

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

    Article • Genes & Development, December 1998, Cold Spring Harbor Laboratory Press

    Dr Joseph R Ecker

  278. Arabidopsis Homologs of a c-Jun Coactivator Are Present Both in Monomeric Form and in the COP9 Complex, and Their Abundance Is Differentially Affected by the Pleiotropic cop/det/fus Mutations

    Article • The Plant Cell, November 1998, JSTOR

    Dr Joseph R Ecker

  279. Arabidopsis Homologs of a c-Jun Coactivator Are Present Both in Monomeric Form and in the COP9 Complex, and Their Abundance Is Differentially Affected by the Pleiotropic cop/det/fus Mutations

    Article • The Plant Cell, November 1998, American Society of Plant Biologists (ASPB)

    Daniel Chamovitz, Dr Joseph R Ecker

  280. Ethylene gas: perception, signaling and response

    Article • Current Opinion in Plant Biology, October 1998, Elsevier

    Dr Joseph R Ecker

  281. Cell signalling and gene regulation: piecing the puzzle together

    Article • Current Opinion in Plant Biology, October 1998, Elsevier

    Dr Joseph R Ecker

  282. EIN4 and ERS2 Are Members of the Putative Ethylene Receptor Gene Family in Arabidopsis

    Article • The Plant Cell, August 1998, JSTOR

    Dr Joseph R Ecker

  283. EIN4 and ERS2 Are Members of the Putative Ethylene Receptor Gene Family in Arabidopsis

    Article • The Plant Cell, August 1998, American Society of Plant Biologists (ASPB)

    Dr Joseph R Ecker

  284. Ethylene signaling in Arabidopsis: Events from the membrane to the nucleus

    Article • Plant Physiology and Biochemistry, January 1998, Elsevier

    Dr Joseph R Ecker

  285. Genes blossom from a weed

    Article • Nature, January 1998, Springer Science + Business Media

    Dr Joseph R Ecker

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

    Article • Cell, September 1997, Elsevier

    Dr Joseph R Ecker

  287. Activation of the Ethylene Gas Response Pathway in Arabidopsis by the Nuclear Protein ETHYLENE-INSENSITIVE3 and Related Proteins

    Article • Cell, June 1997, Elsevier

    Dr Joseph R Ecker

  288. Signaling in plants

    Article • Proceedings of the National Academy of Sciences, April 1997, Proceedings of the National Academy of Sciences

    Dr Joseph R Ecker

  289. HOOKLESS1, an Ethylene Response Gene, Is Required for Differential Cell Elongation in the Arabidopsis Hypocotyl

    Article • Cell, April 1996, Elsevier

    Dr Joseph R Ecker

  290. The genome of Arabidopsis thaliana.

    Article • Proceedings of the National Academy of Sciences, November 1995, Proceedings of the National Academy of Sciences

    Dr Joseph R Ecker

  291. Genetic analysis of a seedling stress response to ethylene in Arabidopsis

    Article • Philosophical Transactions of the Royal Society B Biological Sciences, October 1995, Royal Society Publishing

    Dr Joseph R Ecker

  292. The ethylene signal transduction pathway in plants

    Article • Science, May 1995, American Association for the Advancement of Science

    Dr Joseph R Ecker

  293. Optimizing a linear function over an efficient set

    Article • Journal of Optimization Theory and Applications, December 1994, Springer Science + Business Media

    Dr Joseph R Ecker

  294. Assignment of 30 Microsatellite Loci to the Linkage Map of Arabidopsis

    Article • Genomics, January 1994, Elsevier

    Dr Joseph R Ecker

  295. Molecular and Genetic Analysis of the Constitutive Ethylene Response Mutation Ctr1

    Article • January 1994, Springer Science + Business Media

    Dr Joseph R Ecker

  296. Ethylene gas: it's not just for ripening any more!

    Article • Trends in Genetics, October 1993, Elsevier

    Dr Joseph R Ecker

  297. Mutant analysis as an experimental approach towards understanding plant hormone action

    Article • Seminars in Developmental Biology, February 1993, Elsevier

    Dr Joseph R Ecker

  298. CTR1, a negative regulator of the ethylene response pathway in arabidopsis, encodes a member of the Raf family of protein kinases

    Article • Cell, February 1993, Elsevier

    Dr Joseph R Ecker

  299. Genetic and physical linkage of the Arabidopsis genome: Methods for anchoring Yeast Artificial Chromosomes

    Article • June 1992, World Scientific Pub Co Pte Lt

    Dr Joseph R Ecker

  300. Disease Development in Ethylene-InsensitiveArabidopsis thalianaInfected with Virulent and AvirulentPseudomonasandXanthomonasPathogens

    Article • Molecular Plant-Microbe Interactions, January 1992, Scientific Societies

    Dr Joseph R Ecker

  301. Genome mapping with anchored clones: Theoretical aspects

    Article • Genomics, December 1991, Elsevier

    Dr Joseph R Ecker

  302. Highly enantioselective epoxidation catalysts derived from 1,2-diaminocyclohexane

    Article • Journal of the American Chemical Society, August 1991, American Chemical Society (ACS)

    Dr Joseph R Ecker

  303. PFGE and YAC analysis of the Arabidopsis genome

    Article • Methods, October 1990, Elsevier

    Dr Joseph R Ecker

  304. Exploiting the Triple Response of Arabidopsis to Identify Ethylene-Related Mutants

    Article • The Plant Cell, June 1990, JSTOR

    Dr Joseph R Ecker

  305. Chromosomal mapping of the ubiquitin gene family in Saccharomyces cerevisiae by pulsed field gel electrophoresis

    Article • Nucleic Acids Research, January 1989, Oxford University Press (OUP)

    Dr Joseph R Ecker

  306. A numerical investigation of rank-two ellipsoid algorithms for nonlinear programming

    Article • Mathematical Programming, January 1989, Springer Science + Business Media

    Dr Joseph R Ecker

  307. Development of large DNA methods for plants: molecular cloning of large segments of Arabidopsis and carrot DNA into yeast

    Article • Nucleic Acids Research, January 1988, Oxford University Press (OUP)

    Dr Joseph R Ecker

  308. Inhibition of gene expression in plant cells by expression of antisense RNA

    Article • Proceedings of the National Academy of Sciences, August 1986, Proceedings of the National Academy of Sciences

    Dr Joseph R Ecker

  309. A Computational Comparison of the Ellipsoid Algorithm with Several Nonlinear Programming Algorithms

    Article • SIAM Journal on Control and Optimization, September 1985, Society for Industrial & Applied Mathematics (SIAM)

    Dr Joseph R Ecker

  310. The ellipsoid algorithm: A new method for feedback gain optimization

    Article • Annual Review in Automatic Programming, January 1985, Elsevier

    Dr Joseph R Ecker

  311. A class of rank-two ellipsoid algorithms for convex programming

    Article • Mathematical Programming, June 1984, Springer Science + Business Media

    Dr Joseph R Ecker

  312. Comparison of a special-purpose algorithm with general-purpose algorithms for solving geometric programming problems

    Article • Journal of Optimization Theory and Applications, June 1984, Springer Science + Business Media

    Dr Joseph R Ecker

  313. Variation in the Structure of Varicella-Zoster Virus DNA

    Article • Intervirology, January 1984, Karger Publishers

    Dr Joseph R Ecker

  314. DNA MAPPING OF PAIRED VARICELLA-ZOSTER VIRUS ISOLATES FROM PATIENTS WITH SHINGLES

    Article • The Lancet, November 1983, Elsevier

    Dr Joseph R Ecker

  315. Maximizing Restitution for Erroneous Medical Payments When Auditing Samples from More Than One Provider

    Article • INFORMS Journal on Applied Analytics, October 1983, INFORMS

    Dr Joseph R Ecker

  316. VARICELLA-ZOSTER VIRUS RNA IN HUMAN TRIGEMINAL GANGLIA

    Article • The Lancet, October 1983, Elsevier

    Dr Joseph R Ecker

  317. An ellipsoid algorithm for nonlinear programming

    Article • Mathematical Programming, September 1983, Springer Science + Business Media

    Dr Joseph R Ecker

  318. A reduced gradient method for quadratic programs with quadratic constraints and lp-constrained lp-approximation problems

    Article • European Journal of Operational Research, February 1982, Elsevier

    Dr Joseph R Ecker

  319. Varicella zoster virus DNA exists as two isomers.

    Article • Proceedings of the National Academy of Sciences, January 1982, Proceedings of the National Academy of Sciences

    Dr Joseph R Ecker

  320. Variables that may influence the alkaline sedimentation pattern of herpes simplex virus DNA

    Article • Archives of Virology, September 1981, Springer Science + Business Media

    Dr Joseph R Ecker

  321. Selecting Subsets from the Set of Nondominated Vectors in Multiple Objective Linear Programming

    Article • SIAM Journal on Control and Optimization, July 1981, Society for Industrial & Applied Mathematics (SIAM)

    Dr Joseph R Ecker

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

    Article • Virology, April 1981, Elsevier

    Dr Joseph R Ecker

  323. Reversed geometric programming: A branch-and-bound method involving linear subproblems

    Article • European Journal of Operational Research, July 1980, Elsevier

    Dr Joseph R Ecker

  324. Generating all maximal efficient faces for multiple objective linear programs

    Article • Journal of Optimization Theory and Applications, March 1980, Springer Science + Business Media

    Dr Joseph R Ecker

  325. Finding all efficient extreme points for multiple objective linear programs

    Article • Mathematical Programming, December 1978, Springer Science + Business Media

    Dr Joseph R Ecker

  326. A modified reduced gradient method for dual posynomial programming

    Article • Journal of Optimization Theory and Applications, October 1978, Springer Science + Business Media

    Dr Joseph R Ecker

  327. On Computing an Initial Efficient Extreme Point

    Article • Journal of the Operational Research Society, October 1978, Taylor & Francis

    Dr Joseph R Ecker

  328. Optimal design of a dry-type natural-draft cooling tower by geometric programming

    Article • Journal of Optimization Theory and Applications, October 1978, Springer Science + Business Media

    Dr Joseph R Ecker

  329. COMPUTATIONAL ASPECTS OF GEOMETRIC PROGRAMMING 3. SOME PRIMAL AND DUAL ALGORITHMS FOR POSYNOMIAL AND SIGNOMIAL GEOMETRIC PROGRAMS

    Article • Engineering Optimization, January 1978, Taylor & Francis

    Dr Joseph R Ecker

  330. An Easy Primal Method for Geometric Programming

    Article • Management Science, September 1976, INFORMS

    Dr Joseph R Ecker

  331. OPTIMAL SELECTION OF STEAM TURBINE EXHAUST ANNULUS AND CONDENSER SIZES BY GEOMETRIC PROGRAMMING

    Article • Engineering Optimization, January 1976, Taylor & Francis

    Dr Joseph R Ecker

  332. Finding efficient points for linear multiple objective programs

    Article • Mathematical Programming, December 1975, Springer Science + Business Media

    Dr Joseph R Ecker

  333. A Dual Method for Quadratic Programs with Quadratic Constraints

    Article • SIAM Journal on Applied Mathematics, May 1975, Society for Industrial & Applied Mathematics (SIAM)

    Dr Joseph R Ecker

  334. Effects of response set and psychological knowledge on answers to the personal orientation inventory

    Article • Journal of Clinical Psychology, April 1975, Wiley

    Dr Joseph R Ecker

  335. A modified concave simplex algorithm for geometric programming

    Article • Journal of Optimization Theory and Applications, February 1975, Springer Science + Business Media

    Dr Joseph R Ecker

  336. A Geometric Programming Model for Optimal Allocation of Stream Dissolved Oxygen

    Article • Management Science, February 1975, INFORMS

    Dr Joseph R Ecker

  337. Decomposition in separable geometric programming

    Article • Journal of Optimization Theory and Applications, March 1972, Springer Science + Business Media

    Dr Joseph R Ecker

  338. Geometric Programing and the Preliminary Design of Industrial Waste Treatment Plants

    Article • Water Resources Research, February 1971, American Geophysical Union (AGU)

    Dr Joseph R Ecker

  339. Geometric programming: Duality in quadratic programming and lp-approximation III (degenerate programs)

    Article • Journal of Mathematical Analysis and Applications, February 1970, Elsevier

    Dr Joseph R Ecker

  340. Abstract

    Article • eLife

    Dr Joseph R Ecker

  341. Using the Computer Algebra System MAPLE to Learn and Do Calculus

    Article • Institute of Electrical & Electronics Engineers (IEEE)

    Dr Joseph R Ecker