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Author Details

Joseph R Ecker
The Salk Institute for Biological Studies
1973
315
137
Trey Ideker (CM4AI)
PMIDPaper TitleJournal TitlePublished Year
37808734BAllC and BAllCools: Efficient Formatting and Operating for Single-Cell DNA Methylation Data.bioRxiv2024
37808734BAllC and BAllCools: Efficient Formatting and Operating for Single-Cell DNA Methylation Data.bioRxiv2024
36690743Author Correction: CrY2H-seq: a massively multiplexed assay for deep-coverage interactome mapping.Nat Methods2023
37903253Remembering Philip N. Benfey: A visionary pioneer in plant biology and mentor extraordinaire.Proc Natl Acad Sci U S A2023
38092917Single-cell analysis of chromatin accessibility in the adult mouse brain.Nature2023
38092918Conserved and divergent gene regulatory programs of the mammalian neocortex.Nature2023
38092919Brain-wide correspondence of neuronal epigenomics and distant projections.Nature2023
38092913Single-cell DNA methylome and 3D multi-omic atlas of the adult mouse brain.Nature2023
37390046A guide to the BRAIN Initiative Cell Census Network data ecosystem.PLoS Biol2023
37131654Single-cell DNA Methylome and 3D Multi-omic Atlas of the Adult Mouse Brain.bioRxiv2023
36945593Transcription Factor Dynamics in Cross-Regulation of Plant Hormone Signaling Pathways.bioRxiv2023
37066152Comparative single cell epigenomic analysis of gene regulatory programs in the rodent and primate neocortex.bioRxiv2023
36690790Author Correction: PHYTOCHROME-INTERACTING FACTORs trigger environmentally responsive chromatin dynamics in plants.Nat Genet2023
36690743Author Correction: CrY2H-seq: a massively multiplexed assay for deep-coverage interactome mapping.Nat Methods2023
37308583Multiplexed single-cell 3D spatial gene expression analysis in plant tissue using PHYTOMap.Nat Plants2023
37425926Human Immune Cell Epigenomic Signatures in Response to Infectious Diseases and Chemical Exposures.bioRxiv2023
37533641Yet uninfected? Resolving cell states of plants under pathogen attack.Cell Rep Methods2023
37492103Robust enhancer-gene regulation identified by single-cell transcriptomes and epigenomes.Cell Genom2023
37492103Robust enhancer-gene regulation identified by single-cell transcriptomes and epigenomes.Cell Genom2023
37903253Remembering Philip N. Benfey: A visionary pioneer in plant biology and mentor extraordinaire.Proc Natl Acad Sci U S A2023
38092917Single-cell analysis of chromatin accessibility in the adult mouse brain.Nature2023
38092918Conserved and divergent gene regulatory programs of the mammalian neocortex.Nature2023
38092919Brain-wide correspondence of neuronal epigenomics and distant projections.Nature2023
38092913Single-cell DNA methylome and 3D multi-omic atlas of the adult mouse brain.Nature2023
37533641Yet uninfected? Resolving cell states of plants under pathogen attack.Cell Rep Methods2023
37425926Human Immune Cell Epigenomic Signatures in Response to Infectious Diseases and Chemical Exposures.bioRxiv2023
37390046A guide to the BRAIN Initiative Cell Census Network data ecosystem.PLoS Biol2023
36945593Transcription Factor Dynamics in Cross-Regulation of Plant Hormone Signaling Pathways.bioRxiv2023
37308583Multiplexed single-cell 3D spatial gene expression analysis in plant tissue using PHYTOMap.Nat Plants2023
37131654Single-cell DNA Methylome and 3D Multi-omic Atlas of the Adult Mouse Brain.bioRxiv2023
37066152Comparative single cell epigenomic analysis of gene regulatory programs in the rodent and primate neocortex.bioRxiv2023
36690790Author Correction: PHYTOCHROME-INTERACTING FACTORs trigger environmentally responsive chromatin dynamics in plants.Nat Genet2023
34797944The biology of time: dynamic responses of cell types to developmental, circadian and environmental cues.Plant J2022
35419551Single nucleus multi-omics identifies human cortical cell regulatory genome diversity.Cell Genom2022
35474001Author Correction: Expanded encyclopaedias of DNA elements in the human and mouse genomes.Nature2022
35666176Leaf cell-specific and single-cell transcriptional profiling reveals a role for the palisade layer in UV light protection.Plant Cell2022
35604009<i>Dnmt3a</i> knockout in excitatory neurons impairs postnatal synapse maturation and increases the repressive histone modification H3K27me3.Elife2022
35319013Author Correction: Comparative cellular analysis of motor cortex in human, marmoset and mouse.Nature2022
34797944The biology of time: dynamic responses of cell types to developmental, circadian and environmental cues.Plant J2022
35027454The role of ATXR6 expression in modulating genome stability and transposable element repression in <i>Arabidopsis</i>.Proc Natl Acad Sci U S A2022
35474001Author Correction: Expanded encyclopaedias of DNA elements in the human and mouse genomes.Nature2022
35604009<i>Dnmt3a</i> knockout in excitatory neurons impairs postnatal synapse maturation and increases the repressive histone modification H3K27me3.Elife2022
35666176Leaf cell-specific and single-cell transcriptional profiling reveals a role for the palisade layer in UV light protection.Plant Cell2022
35419551Single nucleus multi-omics identifies human cortical cell regulatory genome diversity.Cell Genom2022
35319013Author Correction: Comparative cellular analysis of motor cortex in human, marmoset and mouse.Nature2022
35027454The role of ATXR6 expression in modulating genome stability and transposable element repression in <i>Arabidopsis</i>.Proc Natl Acad Sci U S A2022
33361111Genome and time-of-day transcriptome of <i>Wolffia australiana</i> link morphological minimization with gene loss and less growth control.Genome Res2021
33637727Comprehensive analysis of single cell ATAC-seq data with SnapATAC.Nat Commun2021
33462491The emergence of the brain non-CpG methylation system in vertebrates.Nat Ecol Evol2021
34140685PHYTOCHROME-INTERACTING FACTORs trigger environmentally responsive chromatin dynamics in plants.Nat Genet2021
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Collaborators

Joseph R Nery
The Salk Institute for Biological Studies
Co-authored papers 65
Bing Ren
Center for Epigenomics, University of California San Diego
Co-authored papers 36
Huaming Chen
The Salk Institute for Biological Studies
Co-authored papers 32
Ryan Lister
Co-authored papers 29
Robert J Schmitz
University of Georgia
Co-authored papers 25
Yupeng He
Salk Institute for Biological Studies
Co-authored papers 20
Mark A Urich
The Salk Institute for Biological Studies
Co-authored papers 19
Matthew D Schultz
Co-authored papers 18
Eran A Mukamel
University of California San Diego
Co-authored papers 18
Shao-Shan Carol Huang
Salk Institute for Biological Studies
Co-authored papers 13
Jingtian Zhou
Co-authored papers 13
Mattia Pelizzola
Center for Genomic Science of , Istituto Italiano di Tecnologia (IIT)
Co-authored papers 11
Hongkui Zeng
Allen Institute for Brain Science
Co-authored papers 10
Sebastian Preissl
Center for Epigenomics, University of California San Diego
Co-authored papers 10
Zhuzhu Zhang
The Salk Institute for Biological Studies
Co-authored papers 10
Zizhen Yao
Allen Institute for Brain Science
Co-authored papers 9
Steve A Kay
Keck School of Medicine, University of Southern California
Co-authored papers 9
Rongxin Fang
Ludwig Institute for Cancer Research, University of California San Diego
Co-authored papers 8
Frederic D Bushman
Perelman School of Medicine, University of Pennsylvania
Co-authored papers 8
Magnus Nordborg
Co-authored papers 8
David U Gorkin
Center for Epigenomics, University of California San Diego
Co-authored papers 7
Marc Vidal
Blavatnik Institute, Harvard Medical School
Co-authored papers 7
Robert D Hawkins
Co-authored papers 7
James A Thomson
Co-authored papers 7
Terrence J Sejnowski
Co-authored papers 7
Richard W Hyman
Stanford University Medical College
Co-authored papers 7
Yin Shen
Wenzhou Medical University
Co-authored papers 7
Fangming Xie
University of California Los Angeles
Co-authored papers 7
Manoj Hariharan
Co-authored papers 7
Ah Young Lee
Co-authored papers 7
Release 1.2