Dr Joseph R Ecker

All Stories

1. 
   Evaluating Methods for the Prediction of Cell Type-Specific Enhancers in the Mammalian Cortex

   Article • August 2024, Cold Spring Harbor Laboratory Press

   Dr Joseph R Ecker

2. 
   Cell-type-specific effects of age and sex on human cortical neurons

   Article • Neuron, August 2024, Elsevier

   Dr Joseph R Ecker

3. 
   Retraction Notice to: Genomic Decoding of Neuronal Depolarization by Stimulus-Specific NPAS4 Heterodimers

   Article • Cell, July 2024, Elsevier

   Dr Joseph R Ecker

4. 
   Streamlined spatial and environmental expression signatures characterize the minimalist duckweedWolffia australiana

   Article • Genome Research, July 2024, Cold Spring Harbor Laboratory Press

   Dr Joseph R Ecker

5. 
   Arabidopsis transcriptome responses to low water potential using high-throughput plate assays

   Article • eLife, June 2024, eLife

   Dr Joseph R Ecker

6. 
   BAllC and BAllCools: Efficient formatting and operating for Single-Cell DNA methylation data

   Article • Bioinformatics, June 2024, Oxford University Press (OUP)

   Dr Joseph R Ecker

7. 
   Arabidopsis transcriptome responses to low water potential using high throughput plate assays

   Article • June 2024, eLife

   Dr Joseph R Ecker

8. 
   Deconvolution of polygenic risk score in single cells unravels cellular and molecular heterogeneity of complex human diseases

   Article • May 2024, Cold Spring Harbor Laboratory Press

   Dr Joseph R Ecker

9. 
   Author Correction: Conserved and divergent gene regulatory programs of the mammalian neocortex

   Article • Nature, January 2024, Springer Science + Business Media

   Dr Joseph R Ecker

10. 
    Spatial IMA1 regulation restricts root iron acquisition on MAMP perception

    Article • Nature, January 2024, Springer Science + Business Media

    Dr Joseph R Ecker

11. 
    Cell type-specific enrichment of somatic aneuploidy in the mammalian brain

    Article • December 2023, Cold Spring Harbor Laboratory Press

    Dr Joseph R Ecker

12. 
    Brain-wide correspondence of neuronal epigenomics and distant projections

    Article • Nature, December 2023, Springer Science + Business Media

    Dr Joseph R Ecker

13. 
    Conserved and divergent gene regulatory programs of the mammalian neocortex

    Article • Nature, December 2023, Springer Science + Business Media

    Dr Joseph R Ecker

14. 
    Single-cell DNA methylome and 3D multi-omic atlas of the adult mouse brain

    Article • Nature, December 2023, Springer Science + Business Media

    Dr Joseph R Ecker

15. 
    Single-cell analysis of chromatin accessibility in the adult mouse brain

    Article • Nature, December 2023, Springer Science + Business Media

    Dr Joseph R Ecker

16. 
    Cell type-specific effects of age and sex on human cortical neurons

    Article • November 2023, Cold Spring Harbor Laboratory Press

    Dr Joseph R Ecker

17. 
    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

18. 
    ​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

19. 
    Epigenome erosion in Alzheimer's disease brain cells and induced neurons

    Article • October 2023, Cold Spring Harbor Laboratory Press

    Dr Joseph R Ecker

20. 
    A comparative atlas of single-cell chromatin accessibility in the human brain

    Article • Science, October 2023, American Association for the Advancement of Science

    Dr Joseph R Ecker

21. 
    Single-cell DNA methylation and 3D genome architecture in the human brain

    Article • Science, October 2023, American Association for the Advancement of Science

    Dr Joseph R Ecker

22. 
    Author Correction: A B-ARR-mediated cytokinin transcriptional network directs hormone cross-regulation and shoot development

    Article • Nature Communications, September 2023, Springer Science + Business Media

    Dr Joseph R Ecker

23. 
    BAllC and BAllCools: Efficient Formatting and Operating for Single-Cell DNA Methylation Data

    Article • September 2023, Cold Spring Harbor Laboratory Press

    Dr Joseph R Ecker

24. 
    Yet uninfected? Resolving cell states of plants under pathogen attack

    Article • Cell Reports Methods, July 2023, Elsevier

    Dr Joseph R Ecker

25. 
    Robust enhancer-gene regulation identified by single-cell transcriptomes and epigenomes

    Article • Cell Genomics, July 2023, Elsevier

    Dr Joseph R Ecker

26. 
    A guide to the BRAIN Initiative Cell Census Network data ecosystem

    Article • PLoS Biology, June 2023, PLOS

    Shawn Tan, Dr Joseph R Ecker

27. 
    Human Immune Cell Epigenomic Signatures in Response to Infectious Diseases and Chemical Exposures

    Article • June 2023, Cold Spring Harbor Laboratory Press

    Dr Joseph R Ecker

28. 
    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

29. 
    Brain-wide Correspondence Between Neuronal Epigenomics and Long-Distance Projections

    Article • May 2023, Cold Spring Harbor Laboratory Press

    Dr Joseph R Ecker

30. 
    Single-cell DNA Methylome and 3D Multi-omic Atlas of the Adult Mouse Brain

    Article • April 2023, Cold Spring Harbor Laboratory Press

    Dr Joseph R Ecker

31. 
    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

32. 
    Comparative single cell epigenomic analysis of gene regulatory programs in the rodent and primate neocortex

    Article • April 2023, Cold Spring Harbor Laboratory Press

    Dr Joseph R Ecker

33. 
    A Single-Nucleus Atlas of Seed-to-Seed Development in Arabidopsis

    Article • March 2023, Cold Spring Harbor Laboratory Press

    Dr Joseph R Ecker

34. 
    Transcription Factor Dynamics in Cross-Regulation of Plant Hormone Signaling Pathways

    Article • March 2023, Cold Spring Harbor Laboratory Press

    Dr Joseph R Ecker

35. 
    Stress Recovery Triggers Rapid Transcriptional Reprogramming and Activation of Immunity in Plants

    Article • February 2023, Cold Spring Harbor Laboratory Press

    Dr Joseph R Ecker

36. 
    Mimicking genuine drought responses using a high throughput plate assay

    Article • February 2023, eLife

    Dr Joseph R Ecker

37. 
    Mimicking genuine drought responses using a high throughput plate assay

    Article • February 2023, eLife

    Dr Joseph R Ecker

38. 
    Author Correction: CrY2H-seq: a massively multiplexed assay for deep-coverage interactome mapping

    Article • Nature Methods, January 2023, Springer Science + Business Media

    Dr Joseph R Ecker

39. 
    Author Correction: PHYTOCHROME-INTERACTING FACTORs trigger environmentally responsive chromatin dynamics in plants

    Article • Nature Genetics, January 2023, Springer Science + Business Media

    Dr Joseph R Ecker

40. 
    Epigenomic complexity of the human brain revealed by single-cell DNA methylomes and 3D genome structures

    Article • December 2022, Cold Spring Harbor Laboratory Press

    Dr Joseph R Ecker

41. 
    Mimicking genuine drought responses using a high throughput plate assay

    Article • November 2022, Cold Spring Harbor Laboratory Press

    Dr Joseph R Ecker

42. 
    A comparative atlas of single-cell chromatin accessibility in the human brain

    Article • November 2022, Cold Spring Harbor Laboratory Press

    Dr Joseph R Ecker

43. 
    The BRAIN Initiative Cell Census Network Data Ecosystem: A User’s Guide

    Article • October 2022, Cold Spring Harbor Laboratory Press

    Dr Joseph R Ecker

44. 
    Epigenomic and chromosomal architectural reconfiguration in developing human frontal cortex and hippocampus

    Article • October 2022, Cold Spring Harbor Laboratory Press

    Dr Joseph R Ecker

45. 
    Defining in vivo transcriptional responses to auxin

    Article • August 2022, Research Square

    Dr Joseph R Ecker

46. 
    PHYTOMap: Multiplexed single-cell 3D spatial gene expression analysis in plant tissue

    Article • July 2022, Cold Spring Harbor Laboratory Press

    Dr Joseph R Ecker

47. 
    Leaf cell-specific and single-cell transcriptional profiling reveals a role for the palisade layer in UV light protection

    Article • The Plant Cell, June 2022, Oxford University Press (OUP)

    Dr Joseph R Ecker

48. 
    Dnmt3a knockout in excitatory neurons impairs postnatal synapse maturation and increases the repressive histone modification H3K27me3

    Article • eLife, May 2022, eLife

    Dr Joseph R Ecker

49. 
    Author Correction: Perspectives on ENCODE

    Article • Nature, April 2022, Springer Science + Business Media

    Dr Joseph R Ecker

50. 
    Author Correction: Expanded encyclopaedias of DNA elements in the human and mouse genomes

    Article • Nature, April 2022, Springer Science + Business Media

    Dr Joseph R Ecker

51. 
    Author Correction: Comparative cellular analysis of motor cortex in human, marmoset and mouse

    Article • Nature, March 2022, Springer Science + Business Media

    Dr Joseph R Ecker

52. 
    Single nucleus multi-omics identifies human cortical cell regulatory genome diversity

    Article • Cell Genomics, March 2022, Elsevier

    Dr Joseph R Ecker

53. 
    The role of ATXR6 expression in modulating genome stability and transposable element repression in Arabidopsis

    Article • Proceedings of the National Academy of Sciences, January 2022, Proceedings of the National Academy of Sciences

    Dr Joseph R Ecker

54. 
    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

55. 
    Robust enhancer-gene regulation identified by single-cell transcriptomes and epigenomes

    Article • October 2021, Cold Spring Harbor Laboratory Press

    Dr Joseph R Ecker

56. 
    A multimodal cell census and atlas of the mammalian primary motor cortex

    Article • Nature, October 2021, Springer Science + Business Media

    Anita E Bandrowski, Dr Joseph R Ecker

57. 
    A transcriptomic and epigenomic cell atlas of the mouse primary motor cortex

    Article • Nature, October 2021, Springer Science + Business Media

    Dr Joseph R Ecker

58. 
    An atlas of gene regulatory elements in adult mouse cerebrum

    Article • Nature, October 2021, Springer Science + Business Media

    Dr Joseph R Ecker

59. 
    Comparative cellular analysis of motor cortex in human, marmoset and mouse

    Article • Nature, October 2021, Springer Science + Business Media

    Dr Joseph R Ecker

60. 
    DNA methylation atlas of the mouse brain at single-cell resolution

    Article • Nature, October 2021, Springer Science + Business Media

    Dr Joseph R Ecker

61. 
    Epigenomic diversity of cortical projection neurons in the mouse brain

    Article • Nature, October 2021, Springer Science + Business Media

    Dr Joseph R Ecker

62. 
    Activity-dependent modulation of synapse-regulating genes in astrocytes

    Article • eLife, September 2021, eLife

    Dr Joseph R Ecker

63. 
    PHYTOCHROME-INTERACTING FACTORs trigger environmentally responsive chromatin dynamics in plants

    Article • Nature Genetics, June 2021, Springer Science + Business Media

    Dr Joseph R Ecker

64. 
    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

65. 
    Single nucleus multi-omics regulatory landscape of the murine pituitary

    Article • Nature Communications, May 2021, Springer Science + Business Media

    Dr Joseph R Ecker

66. 
    Iterative single-cell multi-omic integration using online learning

    Article • Nature Biotechnology, April 2021, Springer Science + Business Media

    Dr Joseph R Ecker

67. 
    Comprehensive analysis of single cell ATAC-seq data with SnapATAC

    Article • Nature Communications, February 2021, Springer Science + Business Media

    Dr Joseph R Ecker

68. 
    The emergence of the brain non-CpG methylation system in vertebrates

    Article • Nature Ecology & Evolution, January 2021, Springer Science + Business Media

    Dr Joseph R Ecker

69. 
    Author Correction: An atlas of dynamic chromatin landscapes in mouse fetal development

    Article • Nature, January 2021, Springer Science + Business Media

    Dr Joseph R Ecker

70. 
    Activity-Dependent Modulation of Synapse-Regulating Genes in Astrocytes

    Article • December 2020, Cold Spring Harbor Laboratory Press

    Dr Joseph R Ecker

71. 
    Genome and time-of-day transcriptome of Wolffia australiana link morphological minimization with gene loss and less growth control

    Article • Genome Research, December 2020, Cold Spring Harbor Laboratory Press

    Dr Joseph R Ecker

72. 
    A multimodal cell census and atlas of the mammalian primary motor cortex

    Article • October 2020, Cold Spring Harbor Laboratory Press

    Anita E Bandrowski, Dr Joseph R Ecker

73. 
    Author Correction: An atlas of dynamic chromatin landscapes in mouse fetal development

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

    Dr Joseph R Ecker

74. 
    An atlas of dynamic chromatin landscapes in mouse fetal development

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

    Dr Joseph R Ecker

75. 
    Expanded encyclopaedias of DNA elements in the human and mouse genomes

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

    Dr Joseph R Ecker

76. 
    Perspectives on ENCODE

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

    Dr Joseph R Ecker

77. 
    Spatiotemporal DNA methylome dynamics of the developing mouse fetus

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

    Dr Joseph R Ecker

78. 
    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

79. 
    Pluripotent stem cells with low differentiation potential contain incompletely reprogrammed DNA replication

    Article • The Journal of Cell Biology, July 2020, Rockefeller University Press

    Dr Joseph R Ecker

80. 
    Extraction of Distinct Neuronal Cell Types from within a Genetically Continuous Population

    Article • Neuron, July 2020, Elsevier

    Dr Joseph R Ecker

81. 
    Current status of the multinational Arabidopsis community

    Article • Plant Direct, July 2020, Wiley

    Dr Joseph R Ecker

82. 
    Single nucleus multi-omics regulatory atlas of the murine pituitary

    Article • June 2020, Cold Spring Harbor Laboratory Press

    Dr Joseph R Ecker

83. 
    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

84. 
    An Atlas of Gene Regulatory Elements in Adult Mouse Cerebrum

    Article • May 2020, Cold Spring Harbor Laboratory Press

    Dr Joseph R Ecker

85. 
    Epigenomic Diversity of Cortical Projection Neurons in the Mouse Brain

    Article • April 2020, Cold Spring Harbor Laboratory Press

    Dr Joseph R Ecker

86. 
    Evolution of cellular diversity in primary motor cortex of human, marmoset monkey, and mouse

    Article • April 2020, Cold Spring Harbor Laboratory Press

    Jayaram Kancherla, Dr Joseph R Ecker

87. 
    Genome and time-of-day transcriptome ofWolffia australianalink morphological extreme minimization with un-gated plant growth

    Article • April 2020, Cold Spring Harbor Laboratory Press

    Dr Joseph R Ecker

88. 
    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

89. 
    An integrated transcriptomic and epigenomic atlas of mouse primary motor cortex cell types

    Article • March 2020, Cold Spring Harbor Laboratory Press

    Jayaram Kancherla, Dr Joseph R Ecker

90. 
    Integrated multi-omics framework of the plant response to jasmonic acid

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

    Dr Joseph R Ecker

91. 
    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

92. 
    A plant-specific syntaxin-6 protein contributes to the intracytoplasmic route for begomoviruses

    Article • January 2020, Cold Spring Harbor Laboratory Press

    Dr Joseph R Ecker

93. 
    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

94. 
    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

95. 
    Dnmt3aknockout in excitatory neurons impairs postnatal synapse maturation and is partly compensated by repressive histone modification H3K27me3

    Article • December 2019, Cold Spring Harbor Laboratory Press

    Dr Joseph R Ecker

96. 
    Single nucleus multi-omics links human cortical cell regulatory genome diversity to disease risk variants

    Article • December 2019, Cold Spring Harbor Laboratory Press

    Dr Joseph R Ecker

97. 
    PHYTOCHROME INTERACTING FACTORs Trigger Environmentally Responsive Chromatin Dynamics

    Article • November 2019, Cold Spring Harbor Laboratory Press

    Dr Joseph R Ecker

98. 
    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

99. 
    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

100. 
     Loss of Dnmt3a dependent methylation in inhibitory neurons impairs neural function through a mechanism that impacts Rett syndrome

     Article • October 2019, Cold Spring Harbor Laboratory Press

     Dr Joseph R Ecker

101. 
     Genomic Decoding of Neuronal Depolarization by Stimulus-Specific NPAS4 Heterodimers

     Article • Cell, October 2019, Elsevier

     Dr Joseph R Ecker

102. 
     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

103. 
     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

104. 
     Integrated Multi-omic Framework of the Plant Response to Jasmonic Acid

     Article • August 2019, Cold Spring Harbor Laboratory Press

     Dr Joseph R Ecker

105. 
     Epigenetic silencing of a multifunctional plant stress regulator

     Article • eLife, August 2019, eLife

     Dr Joseph R Ecker

106. 
     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

107. 
     SnapATAC: A Comprehensive Analysis Package for Single Cell ATAC-seq

     Article • April 2019, Cold Spring Harbor Laboratory Press

     Dr Joseph R Ecker

108. 
     Auxin-sensitive Aux/IAA proteins mediate drought tolerance in Arabidopsis by regulating glucosinolate levels

     Article • March 2019, Cold Spring Harbor Laboratory Press

     Dr Joseph R Ecker

109. 
     WITHDRAWN: Genomic decoding of neuronal depolarization by stimulus-specific NPAS4 heterodimers

     Article • March 2019, Cold Spring Harbor Laboratory Press

     Dr Joseph R Ecker

110. 
     The complex architecture and epigenomic impact of plant T-DNA insertions

     Article • PLoS Genetics, January 2019, PLOS

     Dr Joseph R Ecker

111. 
     Global DNA methylation remodeling during direct reprogramming of fibroblasts to neurons

     Article • eLife, January 2019, eLife

     Dr Joseph R Ecker

112. 
     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

113. 
     HiCluster: A Robust Single-Cell Hi-C Clustering Method Based on Convolution and Random Walk

     Article • December 2018, Cold Spring Harbor Laboratory Press

     Dr Joseph R Ecker

114. 
     Single-cell multi-omic profiling of chromatin conformation and DNA methylome

     Article • December 2018, Cold Spring Harbor Laboratory Press

     Dr Joseph R Ecker

115. 
     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

116. 
     Multi-omic profiling of transcriptome and DNA methylome in single nuclei with molecular partitioning

     Article • October 2018, Cold Spring Harbor Laboratory Press

     Dr Joseph R Ecker

117. 
     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

118. 
     Robust single-cell DNA methylome profiling with snmC-seq2

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

     Dr Joseph R Ecker

119. 
     Transcriptional and epigenomic landscapes of CNS and non-CNS vascular endothelial cells

     Article • eLife, September 2018, eLife

     Dr Joseph R Ecker

120. 
     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

121. 
     Global DNA methylation remodeling during direct reprogramming of fibroblasts to neurons

     Article • July 2018, Cold Spring Harbor Laboratory Press

     Dr Joseph R Ecker

122. 
     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

123. 
     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

124. 
     Robust single-cell DNA methylome profiling with snmC-seq2

     Article • April 2018, Cold Spring Harbor Laboratory Press

     Dr Joseph R Ecker

125. 
     The complex architecture of plant transgene insertions

     Article • March 2018, Cold Spring Harbor Laboratory Press

     Dr Joseph R Ecker

126. 
     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

127. 
     Challenges and recommendations for epigenomics in precision health

     Article • Nature Biotechnology, December 2017, Springer Science + Business Media

     Dr Joseph R Ecker

128. 
     Piecing together cis -regulatory networks: insights from epigenomics studies in plants

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

     Dr Joseph R Ecker

129. 
     The BRAIN Initiative Cell Census Consortium: Lessons Learned toward Generating a Comprehensive Brain Cell Atlas

     Article • Neuron, November 2017, Elsevier

     Dr Joseph R Ecker

130. 
     Dynamic DNA methylation reconfiguration during seed development and germination

     Article • September 2017, Springer Science + Business Media

     Dr Joseph R Ecker

131. 
     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

132. 
     Spatiotemporal DNA Methylome Dynamics of the Developing Mammalian Fetus

     Article • July 2017, Cold Spring Harbor Laboratory Press

     Dr Joseph R Ecker

133. 
     Systematic mapping of chromatin state landscapes during mouse development

     Article • July 2017, Cold Spring Harbor Laboratory Press

     Dr Joseph R Ecker

134. 
     Mapping genome-wide transcription-factor binding sites using DAP-seq

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

     Dr Joseph R Ecker

135. 
     CrY2H-seq: a massively multiplexed assay for deep-coverage interactome mapping

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

     Dr Joseph R Ecker

136. 
     Sequencing and functional validation of the JGI Brachypodium distachyon T-DNA collection

     Article • The Plant Journal, June 2017, Wiley

     Dr Joseph R Ecker

137. 
     High contiguity Arabidopsis thaliana genome assembly with a single nanopore flow cell

     Article • June 2017, Cold Spring Harbor Laboratory Press

     Dr Joseph R Ecker

138. 
     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

139. 
     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

140. 
     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

141. 
     Plant Stress Tolerance Requires Auxin-Sensitive Aux/IAA Transcriptional Repressors

     Article • Current Biology, February 2017, Elsevier

     Dr Joseph R Ecker

142. 
     Divergent cytosine DNA methylation patterns in single-cell, soybean root hairs

     Article • New Phytologist, January 2017, Wiley

     Dr Joseph R Ecker

143. 
     Functional Human Oocytes Generated by Transfer of Polar Body Genomes

     Article • Cell Stem Cell, January 2017, Elsevier

     Dr Joseph R Ecker

144. 
     JAZ2 controls stomata dynamics during bacterial invasion

     Article • New Phytologist, December 2016, Wiley

     Dr Joseph R Ecker

145. 
     Cerebral Organoids Recapitulate Epigenomic Signatures of the Human Fetal Brain

     Article • Cell Reports, December 2016, Elsevier

     Dr Joseph R Ecker

146. 
     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

147. 
     Phased diploid genome assembly with single-molecule real-time sequencing

     Article • Nature Methods, October 2016, Nature

     Fritz Sedlazeck, Dr Joseph R Ecker

148. 
     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

149. 
     Molecular Criteria for Defining the Naive Human Pluripotent State

     Article • Cell Stem Cell, October 2016, Elsevier

     Dr Joseph R Ecker

150. 
     Cistrome and Epicistrome Features Shape the Regulatory DNA Landscape

     Article • Cell, September 2016, Elsevier

     Dr Joseph R Ecker

151. 
     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

152. 
     1,135 Genomes Reveal the Global Pattern of Polymorphism in Arabidopsis thaliana

     Article • Cell, July 2016, Elsevier

     Polina Yu Novikova, Dr Joseph R Ecker

153. 
     Epigenomic Diversity in a Global Collection of Arabidopsis thaliana Accessions

     Article • Cell, July 2016, Elsevier

     Dr Joseph R Ecker

154. 
     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

155. 
     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

156. 
     Cistrome and Epicistrome Features Shape the Regulatory DNA Landscape

     Article • Cell, May 2016, Elsevier

     Dr Joseph R Ecker

157. 
     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

158. 
     INTRODUCTION

     Article • April 2016, Taylor & Francis

     Dr Joseph R Ecker

159. 
     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

160. 
     Epigenomic landscapes of retinal rods and cones

     Article • eLife, March 2016, eLife

     Dr Joseph R Ecker

161. 
     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

162. 
     Active DNA demethylation at enhancers during the vertebrate phylotypic period

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

     Dr Joseph R Ecker

163. 
     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

164. 
     Cryptochromes Interact Directly with PIFs to Control Plant Growth in Limiting Blue Light

     Article • Cell, January 2016, Elsevier

     Dr Joseph R Ecker

165. 
     Human DNA methylomes of neurodegenerative diseases show common epigenomic patterns

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

     Dr Joseph R Ecker

166. 
     Erratum: Corrigendum: Human body epigenome maps reveal noncanonical DNA methylation variation

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

     Dr Joseph R Ecker

167. 
     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

168. 
     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

169. 
     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

170. 
     Exceptional epigenetics in the brain

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

     Dr Joseph R Ecker

171. 
     Epigenomic Signatures of Neuronal Diversity in the Mammalian Brain

     Article • Neuron, June 2015, Elsevier

     Dr Joseph R Ecker

172. 
     Human body epigenome maps reveal noncanonical DNA methylation variation

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

     Dr Joseph R Ecker

173. 
     An alternative pluripotent state confers interspecies chimaeric competency

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

     Dr Joseph R Ecker

174. 
     ERRs Mediate a Metabolic Switch Required for Somatic Cell Reprogramming to Pluripotency

     Article • Cell Stem Cell, May 2015, Elsevier

     Dr Joseph R Ecker

175. 
     MethylC-seq library preparation for base-resolution whole-genome bisulfite sequencing

     Article • Nature Protocols, February 2015, Nature

     Dr Joseph R Ecker

176. 
     Chromatin architecture reorganization during stem cell differentiation

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

     Dr Joseph R Ecker

177. 
     Integrative analysis of 111 reference human epigenomes

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

     Dr Joseph R Ecker

178. 
     Integrative analysis of haplotype-resolved epigenomes across human tissues

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

     Dr Joseph R Ecker

179. 
     A User’s Guide to the Arabidopsis T-DNA Insertion Mutant Collections

     Article • January 2015, Springer Science + Business Media

     Dr Joseph R Ecker

180. 
     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

181. 
     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

182. 
     The Developmental Potential of iPSCs Is Greatly Influenced by Reprogramming Factor Selection

     Article • Cell Stem Cell, September 2014, Elsevier

     Dr Joseph R Ecker

183. 
     Determination and Inference of Eukaryotic Transcription Factor Sequence Specificity

     Article • Cell, September 2014, Elsevier

     Dr Joseph R Ecker, Dr Alejandro Montenegro-Montero

184. 
     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

185. 
     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

186. 
     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

187. 
     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

188. 
     Abnormalities in human pluripotent cells due to reprogramming mechanisms

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

     Dr Joseph R Ecker

189. 
     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

190. 
     A Genome-Scale Resource for the Functional Characterization of Arabidopsis Transcription Factors

     Article • Cell Reports, July 2014, Elsevier

     Dr Joseph R Ecker

191. 
     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

192. 
     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

193. 
     Solving nonlinear principal-agent problems using bilevel programming

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

     Dr Joseph R Ecker

194. 
     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

195. 
     STAR: an integrated solution to management and visualization of sequencing data

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

     Dr Joseph R Ecker

196. 
     Response to Perspective

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

     Dr Joseph R Ecker

197. 
     Constructing Hepitypes: Phasing Local Genotype and DNA Methylation

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

     Dr Joseph R Ecker

198. 
     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

199. 
     Global Epigenomic Reconfiguration During Mammalian Brain Development

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

     Dr Joseph R Ecker

200. 
     Temporal transcriptional response to ethylene gas drives growth hormone cross-regulation in Arabidopsis

     Article • eLife, June 2013, eLife

     Dr Joseph R Ecker

201. 
     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

202. 
     Epigenomic Analysis of Multilineage Differentiation of Human Embryonic Stem Cells

     Article • Cell, May 2013, Elsevier

     Dr Joseph R Ecker

203. 
     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

204. 
     Patterns of population epigenomic diversity

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

     Dr Joseph R Ecker

205. 
     Epigenetic trigger for tomato ripening

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

     Dr Joseph R Ecker

206. 
     ‘Leveling’ the playing field for analyses of single-base resolution DNA methylomes

     Article • Trends in Genetics, December 2012, Elsevier

     Dr Joseph R Ecker

207. 
     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

208. 
     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

209. 
     Sigma factor‐mediated plastid retrograde signals control nuclear gene expression

     Article • The Plant Journal, November 2012, Wiley

     Dr Joseph R Ecker

210. 
     ENCODE explained

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

     Dr Joseph R Ecker

211. 
     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

212. 
     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

213. 
     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

214. 
     Release Factor One Is Nonessential in Escherichia coli

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

     Dr Joseph R Ecker

215. 
     Detection of allele-specific methylation through a generalized heterogeneous epigenome model

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

     Dr Joseph R Ecker

216. 
     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

217. 
     Linking photoreceptor excitation to changes in plant architecture

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

     Dr Joseph R Ecker

218. 
     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

219. 
     Epigenetic and epigenomic variation in Arabidopsis thaliana

     Article • Trends in Plant Science, March 2012, Elsevier

     Dr Joseph R Ecker

220. 
     Epiallelic Variation in Arabidopsis thaliana

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

     Dr Joseph R Ecker

221. 
     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

222. 
     Forward and Reverse Genetics through Derivation of Haploid Mouse Embryonic Stem Cells

     Article • Cell Stem Cell, December 2011, Elsevier

     Dr Joseph R Ecker

223. 
     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

224. 
     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

225. 
     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

226. 
     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

227. 
     Genome-wide mapping of 5-hydroxymethylcytosine in embryonic stem cells

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

     Dr Joseph R Ecker

228. 
     Hotspots of aberrant epigenomic reprogramming in human induced pluripotent stem cells

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

     Dr Joseph R Ecker

229. 
     The DNA methylome

     Article • FEBS Letters, November 2010, Wiley

     Dr Joseph R Ecker

230. 
     The NIH Roadmap Epigenomics Mapping Consortium

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

     Dr Joseph R Ecker

231. 
     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

232. 
     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

233. 
     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

234. 
     Zeroing in on DNA methylomes with no BS

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

     Dr Joseph R Ecker

235. 
     Distinct Epigenomic Landscapes of Pluripotent and Lineage-Committed Human Cells

     Article • Cell Stem Cell, May 2010, Elsevier

     Dr Joseph R Ecker

236. 
     Genome-wide association study of 107 phenotypes in Arabidopsis thaliana inbred lines

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

     Dr Joseph R Ecker

237. 
     Linking genotype to phenotype using the Arabidopsis unimutant collection

     Article • The Plant Journal, March 2010, Wiley

     Dr Joseph R Ecker

238. 
     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

239. 
     Ethylene Responses in Seedling Growth and Development

     Article • January 2010, Springer Science + Business Media

     Dr Joseph R Ecker

240. 
     Addendum: Literature-curated protein interaction datasets

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

     Dr Joseph R Ecker, Junshi Yazaki

241. 
     Human DNA methylomes at base resolution show widespread epigenomic differences

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

     Dr Joseph R Ecker

242. 
     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

243. 
     Rapid and High-Throughput pan-Orthopoxvirus Detection and Identification using PCR and Mass Spectrometry

     Article • PLoS ONE, July 2009, PLOS

     Dr Joseph R Ecker

244. 
     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

245. 
     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

246. 
     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

247. 
     Finding the fifth base: Genome-wide sequencing of cytosine methylation

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

     Dr Joseph R Ecker

248. 
     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

249. 
     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

250. 
     Exploring the transcriptional landscape of plant circadian rhythms using genome tiling arrays

     Article • February 2009, Springer Science + Business Media

     Dr Joseph R Ecker

251. 
     Literature-curated protein interaction datasets

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

     Dr Joseph R Ecker, Junshi Yazaki

252. 
     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

253. 
     Correction

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

     Dr Joseph R Ecker

254. 
     A Link between RNA Metabolism and Silencing Affecting Arabidopsis Development

     Article • Developmental Cell, June 2008, Elsevier

     Dr Joseph R Ecker

255. 
     Highly Integrated Single-Base Resolution Maps of the Epigenome in Arabidopsis

     Article • Cell, May 2008, Elsevier

     Dr Joseph R Ecker

256. 
     Utilizing tiling microarrays for whole‐genome analysis in plants

     Article • The Plant Journal, February 2008, Wiley

     Dr Joseph R Ecker, Junshi Yazaki

257. 
     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

258. 
     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

259. 
     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

260. 
     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

261. 
     Direct broad-range detection of alphaviruses in mosquito extracts

     Article • Virology, November 2007, Elsevier

     Dr Joseph R Ecker

262. 
     Mapping the genome landscape using tiling array technology

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

     Dr Joseph R Ecker, Junshi Yazaki

263. 
     Recombination and linkage disequilibrium in Arabidopsis thaliana

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

     Dr Joseph R Ecker

264. 
     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

265. 
     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

266. 
     Common Sequence Polymorphisms Shaping Genetic Diversity in Arabidopsis thaliana

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

     Dr Joseph R Ecker

267. 
     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

268. 
     Higher plants possess two different types of ATX1-like copper chaperones

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

     Dr Joseph R Ecker

269. 
     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

270. 
     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

271. 
     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

272. 
     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

273. 
     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

274. 
     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

275. 
     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

276. 
     Genome-wide High-Resolution Mapping and Functional Analysis of DNA Methylation in Arabidopsis

     Article • Cell, September 2006, Elsevier

     Dr Joseph R Ecker, Junshi Yazaki

277. 
     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

278. 
     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

279. 
     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

280. 
     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

281. 
     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

282. 
     Retroviral DNA Integration: Viral and Cellular Determinants of Target-Site Selection

     Article • PLoS Pathogens, June 2006, PLOS

     Dr Michael Emerman, Dr Joseph R Ecker

283. 
     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

284. 
     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

285. 
     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

286. 
     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

287. 
     A role for LEDGF/p75 in targeting HIV DNA integration

     Article • Nature Medicine, November 2005, Springer Science + Business Media

     Dr Joseph R Ecker

288. 
     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

289. 
     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

290. 
     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

291. 
     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

292. 
     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

293. 
     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

294. 
     NPH4/ARF7 and ARF19 promote leaf expansion and auxin‐induced lateral root formation

     Article • The Plant Journal, June 2005, Wiley

     Dr Joseph R Ecker

295. 
     Genome-Wide Analysis of Chromosomal Features Repressing Human Immunodeficiency Virus Transcription

     Article • Journal of Virology, June 2005, ASM Journals

     Dr Joseph R Ecker

296. 
     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

297. 
     FRIGIDA-Independent Variation in Flowering Time of Natural Arabidopsis thaliana Accessions

     Article • Genetics, May 2005, Genetics Society of America

     Dr Joseph R Ecker

298. 
     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

299. 
     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

300. 
     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

301. 
     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

302. 
     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

303. 
     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

304. 
     Applications of DNA tiling arrays for whole-genome analysis

     Article • Genomics, January 2005, Elsevier

     Dr Joseph R Ecker

305. 
     Article • BMC Plant Biology, January 2005, Springer Science + Business Media

     Dr Joseph R Ecker

306. 
     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

307. 
     An Arabidopsis NPR1‐like gene, NPR4, is required for disease resistance

     Article • The Plant Journal, December 2004, Wiley

     Dr Joseph R Ecker

308. 
     Reentry of the Ethylene MPK6 Module

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

     Dr Joseph R Ecker

309. 
     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

310. 
     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

311. 
     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

312. 
     PLANT GENOMICS: The Third Wave

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

     Dr Joseph R Ecker

313. 
     Retroviral DNA Integration: ASLV, HIV, and MLV Show Distinct Target Site Preferences

     Article • PLoS Biology, August 2004, PLOS

     Dr Joseph R Ecker

314. 
     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

315. 
     Convergence of Signaling Pathways in the Control of Differential Cell Growth in Arabidopsis

     Article • Developmental Cell, August 2004, Elsevier

     Dr Joseph R Ecker

316. 
     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

317. 
     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

318. 
     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

319. 
     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

320. 
     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

321. 
     Regulation of ethylene gas biosynthesis by the Arabidopsis ETO1 protein

     Article • April 2004

     Dr Joseph R Ecker

322. 
     Genome studies and molecular genetics

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

     Dr Joseph R Ecker

323. 
     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

324. 
     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

325. 
     The ethylene signaling pathway: new insights

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

     Dr Joseph R Ecker

326. 
     Corrections

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

     Dr Joseph R Ecker

327. 
     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

328. 
     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

329. 
     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

330. 
     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

331. 
     Extractions

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

     Dr Joseph R Ecker

332. 
     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

333. 
     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

334. 
     Genome-Wide Insertional Mutagenesis of Arabidopsis thaliana

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

     Dr Joseph R Ecker

335. 
     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

336. 
     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

337. 
     GUN4, a Regulator of Chlorophyll Synthesis and Intracellular Signaling

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

     Dr Joseph R Ecker

338. 
     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

339. 
     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

340. 
     Chloroplast to nucleus communication triggered by accumulation of Mg-protoporphyrinIX

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

     Dr Joseph R Ecker

341. 
     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

342. 
     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

343. 
     Divergent perspectives on GM food

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

     Dr Joseph R Ecker

344. 
     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

345. 
     De-Etiolated 1 and Damaged DNA Binding Protein 1 Interact to Regulate Arabidopsis Photomorphogenesis

     Article • Current Biology, September 2002, Elsevier

     Dr Joseph R Ecker

346. 
     HIV-1 Integration in the Human Genome Favors Active Genes and Local Hotspots

     Article • Cell, August 2002, Elsevier

     Dr Joseph R Ecker

347. 
     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

348. 
     Mitogen-activated protein kinase cascades in plants: a new nomenclature

     Article • Trends in Plant Science, July 2002, Elsevier

     Dr Joseph R Ecker

349. 
     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

350. 
     Ethylene Biosynthesis and Signaling Networks

     Article • The Plant Cell, May 2002, Oxford University Press (OUP)

     Dr Joseph R Ecker

351. 
     An application of nonlinear optimization in molecular biology

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

     Dr Joseph R Ecker

352. 
     Phototropin-related NPL1 controls chloroplast relocation induced by blue light

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

     Dr Joseph R Ecker

353. 
     An Arabidopsis circadian clock component interacts with both CRY1 and phyB

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

     Dr Joseph R Ecker

354. 
     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

355. 
     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

356. 
     Sequence and analysis of chromosome 1 of the plant Arabidopsis thaliana

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

     Dr Joseph R Ecker

357. 
     Ethylene signaling: from mutants to molecules

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

     Dr Joseph R Ecker

358. 
     National Science Foundation-Sponsored Workshop Report: “The 2010 Project”Functional Genomics and the Virtual Plant. A Blueprint for Understanding How Plants Are Built and How to Improve Them

     Article • PLANT PHYSIOLOGY, June 2000, Oxford University Press (OUP)

     Dr Joseph R Ecker

359. 
     Involvement of NRAMP1 from Arabidopsis thaliana in iron transport

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

     Dr Joseph R Ecker

360. 
     A complete BAC-based physical map of the Arabidopsis thaliana genome

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

     Dr Joseph R Ecker

361. 
     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

362. 
     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

363. 
     THE ETHYLENE GAS SIGNAL TRANSDUCTION PATHWAY: A Molecular Perspective

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

     Dr Joseph R Ecker

364. 
     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

365. 
     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

366. 
     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

367. 
     Ethylene gas: perception, signaling and response

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

     Dr Joseph R Ecker

368. 
     Cell signalling and gene regulation: piecing the puzzle together

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

     Dr Joseph R Ecker

369. 
     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

370. 
     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

371. 
     Ethylene signaling in Arabidopsis: Events from the membrane to the nucleus

     Article • Plant Physiology and Biochemistry, January 1998, Elsevier

     Dr Joseph R Ecker

372. 
     Genes blossom from a weed

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

     Dr Joseph R Ecker

373. 
     BRI-ghtening the Pathway to Steroid Hormone Signaling Events in Plants

     Article • Cell, September 1997, Elsevier

     Dr Joseph R Ecker

374. 
     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

375. 
     Signaling in plants

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

     Dr Joseph R Ecker

376. 
     HOOKLESS1, an Ethylene Response Gene, Is Required for Differential Cell Elongation in the Arabidopsis Hypocotyl

     Article • Cell, April 1996, Elsevier

     Dr Joseph R Ecker

377. 
     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

378. 
     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

379. 
     The ethylene signal transduction pathway in plants

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

     Dr Joseph R Ecker

380. 
     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

381. 
     Assignment of 30 Microsatellite Loci to the Linkage Map of Arabidopsis

     Article • Genomics, January 1994, Elsevier

     Dr Joseph R Ecker

382. 
     Molecular and Genetic Analysis of the Constitutive Ethylene Response Mutation Ctr1

     Article • January 1994, Springer Science + Business Media

     Dr Joseph R Ecker

383. 
     Ethylene gas: it's not just for ripening any more!

     Article • Trends in Genetics, October 1993, Elsevier

     Dr Joseph R Ecker

384. 
     Mutant analysis as an experimental approach towards understanding plant hormone action

     Article • Seminars in Developmental Biology, February 1993, Elsevier

     Dr Joseph R Ecker

385. 
     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

386. 
     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

387. 
     Disease Development in Ethylene-InsensitiveArabidopsis thalianaInfected with Virulent and AvirulentPseudomonasandXanthomonasPathogens

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

     Dr Joseph R Ecker

388. 
     Genome mapping with anchored clones: Theoretical aspects

     Article • Genomics, December 1991, Elsevier

     Dr Joseph R Ecker

389. 
     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

390. 
     PFGE and YAC analysis of the Arabidopsis genome

     Article • Methods, October 1990, Elsevier

     Dr Joseph R Ecker

391. 
     Exploiting the Triple Response of Arabidopsis to Identify Ethylene-Related Mutants

     Article • The Plant Cell, June 1990, JSTOR

     Dr Joseph R Ecker

392. 
     Exploiting the triple response of Arabidopsis to identify ethylene-related mutants.

     Article • The Plant Cell, June 1990, Oxford University Press (OUP)

     Dr Joseph R Ecker

393. 
     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

394. 
     A numerical investigation of rank-two ellipsoid algorithms for nonlinear programming

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

     Dr Joseph R Ecker

395. 
     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

396. 
     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

397. 
     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

398. 
     The ellipsoid algorithm: A new method for feedback gain optimization

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

     Dr Joseph R Ecker

399. 
     A class of rank-two ellipsoid algorithms for convex programming

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

     Dr Joseph R Ecker

400. 
     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

401. 
     Variation in the Structure of Varicella-Zoster Virus DNA

     Article • Intervirology, January 1984, Karger Publishers

     Dr Joseph R Ecker

402. 
     DNA MAPPING OF PAIRED VARICELLA-ZOSTER VIRUS ISOLATES FROM PATIENTS WITH SHINGLES

     Article • The Lancet, November 1983, Elsevier

     Dr Joseph R Ecker

403. 
     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

404. 
     VARICELLA-ZOSTER VIRUS RNA IN HUMAN TRIGEMINAL GANGLIA

     Article • The Lancet, October 1983, Elsevier

     Dr Joseph R Ecker

405. 
     An ellipsoid algorithm for nonlinear programming

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

     Dr Joseph R Ecker

406. 
     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

407. 
     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

408. 
     Varicella-zoster virus vaccine DNA differs from the parental virus DNA

     Article • Journal of Virology, October 1981, ASM Journals

     Dr Joseph R Ecker

409. 
     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

410. 
     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

411. 
     Analysis of interruptions in the phosphodiester backbone of herpes simplex virus DNA

     Article • Virology, April 1981, Elsevier

     Dr Joseph R Ecker

412. 
     Reversed geometric programming: A branch-and-bound method involving linear subproblems

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

     Dr Joseph R Ecker

413. 
     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

414. 
     Finding all efficient extreme points for multiple objective linear programs

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

     Dr Joseph R Ecker

415. 
     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

416. 
     On Computing an Initial Efficient Extreme Point

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

     Dr Joseph R Ecker

417. 
     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

418. 
     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

419. 
     An Easy Primal Method for Geometric Programming

     Article • Management Science, September 1976, INFORMS

     Dr Joseph R Ecker

420. 
     OPTIMAL SELECTION OF STEAM TURBINE EXHAUST ANNULUS AND CONDENSER SIZES BY GEOMETRIC PROGRAMMING

     Article • Engineering Optimization, January 1976, Taylor & Francis

     Dr Joseph R Ecker

421. 
     Finding efficient points for linear multiple objective programs

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

     Dr Joseph R Ecker

422. 
     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

423. 
     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

424. 
     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

425. 
     A Geometric Programming Model for Optimal Allocation of Stream Dissolved Oxygen

     Article • Management Science, February 1975, INFORMS

     Dr Joseph R Ecker

426. 
     Decomposition in separable geometric programming

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

     Dr Joseph R Ecker

427. 
     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

428. 
     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

429. 
     Abstract

     Article • eLife

     Dr Joseph R Ecker

430. 
     Using the Computer Algebra System MAPLE to Learn and Do Calculus

     Article • Institute of Electrical & Electronics Engineers (IEEE)

     Dr Joseph R Ecker