Joseph R Ecker

Joseph R Ecker

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Joseph R Ecker

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

Proc Natl Acad Sci U S A 2019 Nov 29;116(46):23345-23356. Epub 2019 Oct 29.

Lund University Plant Sciences, Department of Biology, Lund University, 223 62 Lund, Sweden;

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http://dx.doi.org/10.1073/pnas.1911758116DOI Listing
November 2019

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

Cell 2019 Oct;179(2):373-391.e27

Division of Biological Sciences, Section of Neurobiology, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0634, USA. Electronic address:

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https://linkinghub.elsevier.com/retrieve/pii/S00928674193101
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http://dx.doi.org/10.1016/j.cell.2019.09.004DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6800120PMC
October 2019

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

Nat Commun 2019 Sep 6;10(1):4021. Epub 2019 Sep 6.

Section of Cell and Developmental Biology and Howard Hughes Medical Institute, University of California, San Diego, La Jolla CA., 92093, USA.

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http://dx.doi.org/10.1038/s41467-019-12002-1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6731224PMC
September 2019

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

Proc Natl Acad Sci U S A 2019 Jul 24;116(28):14011-14018. Epub 2019 Jun 24.

Genomic Analysis Laboratory, Salk Institute for Biological Studies, La Jolla, CA 92037;

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http://www.pnas.org/lookup/doi/10.1073/pnas.1901423116
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http://dx.doi.org/10.1073/pnas.1901423116DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6628819PMC
July 2019

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

Breed Sci 2019 Jun 14;69(2):191-204. Epub 2019 May 14.

Howard Hughes Medical Institute, 10010 North Torrey Pines Road, La Jolla, CA 92037, USA.

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http://dx.doi.org/10.1270/jsbbs.19005DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6711733PMC
June 2019

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

PLoS Genet 2019 01 18;15(1):e1007819. Epub 2019 Jan 18.

Genomic Analysis Laboratory, Salk Institute for Biological Studies, La Jolla, CA, United States of America.

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http://dx.doi.org/10.1371/journal.pgen.1007819DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6338467PMC
January 2019

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

Curr Protoc Plant Biol 2018 09 14;3(3):e20071. Epub 2018 Aug 14.

Genomic Analysis Laboratory, Salk Institute for Biological Studies, La Jolla, California.

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http://doi.wiley.com/10.1002/cppb.20071
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http://dx.doi.org/10.1002/cppb.20071DOI Listing
September 2018

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

Elife 2018 09 6;7. Epub 2018 Sep 6.

Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, United States.

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http://dx.doi.org/10.7554/eLife.36187DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6126923PMC
September 2018

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

Science 2018 09;361(6409):1336-1340

Genomic Analysis Laboratory, The Salk Institute for Biological Studies, La Jolla, CA 92037, USA.

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http://dx.doi.org/10.1126/science.aat6806DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6197482PMC
September 2018

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

Wiley Interdiscip Rev Syst Biol Med 2018 05 30;10(3):e1411. Epub 2017 Nov 30.

Genomic Analysis Laboratory and Plant Biology Laboratory, The Salk Institute for Biological Studies, La Jolla, CA, USA.

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http://dx.doi.org/10.1002/wsbm.1411DOI Listing
May 2018

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

Nat Commun 2018 05 22;9(1):2075. Epub 2018 May 22.

Plant Biology Laboratory, and Genomic Analysis Laboratory, The Salk Institute for Biological Studies, La Jolla, CA, 92037, USA.

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http://www.nature.com/articles/s41467-018-04514-z
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http://dx.doi.org/10.1038/s41467-018-04514-zDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5964099PMC
May 2018

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

Nat Commun 2018 04 23;9(1):1604. Epub 2018 Apr 23.

Plant Biology Laboratory, and Genomic Analysis Laboratory, The Salk Institute for Biological Studies, La Jolla, CA, 92037, USA.

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http://dx.doi.org/10.1038/s41467-018-03921-6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5913131PMC
April 2018

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

Nat Commun 2018 02 7;9(1):541. Epub 2018 Feb 7.

Genomic Analysis Laboratory, The Salk Institute for Biological Studies, La Jolla, CA, 92037, USA.

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http://dx.doi.org/10.1038/s41467-018-03016-2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5803254PMC
February 2018

Dynamic DNA methylation reconfiguration during seed development and germination.

Genome Biol 2017 09 15;18(1):171. Epub 2017 Sep 15.

Plant Biology Laboratory, The Salk Institute for Biological Studies, La Jolla, CA, 92037, USA.

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http://dx.doi.org/10.1186/s13059-017-1251-xDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5599895PMC
September 2017

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

Plant J 2017 Aug 21;91(3):361-370. Epub 2017 Jun 21.

USDA ARS Western Regional Research Center, 800 Buchanan St., Albany, CA, 94710-1105, USA.

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http://dx.doi.org/10.1111/tpj.13582DOI Listing
August 2017

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

Nat Protoc 2017 Aug 20;12(8):1659-1672. Epub 2017 Jul 20.

Genomic Analysis Laboratory, The Salk Institute for Biological Studies, La Jolla, California, USA.

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http://dx.doi.org/10.1038/nprot.2017.055DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5576341PMC
August 2017

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

New Phytol 2017 Apr 20;214(2):808-819. Epub 2017 Jan 20.

Divisions of Plant Science and Biochemistry, Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, MO, 65211, USA.

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http://dx.doi.org/10.1111/nph.14421DOI Listing
April 2017

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

Proc Natl Acad Sci U S A 2017 04 20;114(14):E2882-E2890. Epub 2017 Mar 20.

Department of Cognitive Science, University of California, San Diego, CA 92037;

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http://dx.doi.org/10.1073/pnas.1611905114DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5389278PMC
April 2017

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

Plant J 2017 Feb 11;89(4):805-824. Epub 2017 Feb 11.

Department of Animal, Plant and Soil Science, ARC Centre of Excellence in Plant Energy Biology, School of Life Science, La Trobe University, Melbourne, Vic, 3086, Australia.

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http://dx.doi.org/10.1111/tpj.13418DOI Listing
February 2017

JAZ2 controls stomata dynamics during bacterial invasion.

New Phytol 2017 Feb 22;213(3):1378-1392. Epub 2016 Dec 22.

Plant Molecular Genetics Department, Centro Nacional de Biotecnología-CSIC (CNB-CSIC), Madrid, 28049, Spain.

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http://dx.doi.org/10.1111/nph.14354DOI Listing
February 2017

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

Curr Biol 2017 Feb 19;27(3):437-444. Epub 2017 Jan 19.

Section of Cell and Developmental Biology and Howard Hughes Medical Institute, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA. Electronic address:

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http://dx.doi.org/10.1016/j.cub.2016.12.016DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5296222PMC
February 2017

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

Proc Natl Acad Sci U S A 2017 02 13;114(9):E1633-E1640. Epub 2017 Feb 13.

Genomic Analysis Laboratory, The Salk Institute for Biological Studies, La Jolla, CA 92037;

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http://dx.doi.org/10.1073/pnas.1618353114DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5338528PMC
February 2017

Functional Human Oocytes Generated by Transfer of Polar Body Genomes.

Cell Stem Cell 2017 01 10;20(1):112-119. Epub 2016 Nov 10.

Center for Embryonic Cell and Gene Therapy, Oregon Health & Science University, Portland, OR 97239, USA; Division of Reproductive Endocrinology, Department of Obstetrics and Gynecology, Oregon Health & Science University, Portland, OR 97239, USA. Electronic address:

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http://dx.doi.org/10.1016/j.stem.2016.10.001DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5218919PMC
January 2017

Cerebral Organoids Recapitulate Epigenomic Signatures of the Human Fetal Brain.

Cell Rep 2016 12;17(12):3369-3384

Genomic Analysis Laboratory, The Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, CA 92037, USA; Howard Hughes Medical Institute, The Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, CA 92037, USA. Electronic address:

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http://dx.doi.org/10.1016/j.celrep.2016.12.001DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5495578PMC
December 2016

Molecular Criteria for Defining the Naive Human Pluripotent State.

Cell Stem Cell 2016 10 14;19(4):502-515. Epub 2016 Jul 14.

Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02142, USA. Electronic address:

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http://dx.doi.org/10.1016/j.stem.2016.06.011DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5065525PMC
October 2016

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

Nat Commun 2016 10 3;7:13018. Epub 2016 Oct 3.

Department of Molecular Biosciences, Institute for Cellular and Molecular Biology, Austin, Texas 78712, USA.

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http://dx.doi.org/10.1038/ncomms13018DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5063967PMC
October 2016

Mapping transcription factor interactome networks using HaloTag protein arrays.

Proc Natl Acad Sci U S A 2016 07 29;113(29):E4238-47. Epub 2016 Jun 29.

Genomic Analysis Laboratory, The Salk Institute for Biological Studies, La Jolla, CA 92037; Plant Biology Laboratory, The Salk Institute for Biological Studies, La Jolla, CA 92037; Howard Hughes Medical Institute, The Salk Institute for Biological Studies, La Jolla, CA 92037;

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http://dx.doi.org/10.1073/pnas.1603229113DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4961138PMC
July 2016

Epigenomic Diversity in a Global Collection of Arabidopsis thaliana Accessions.

Cell 2016 Jul;166(2):492-505

Plant Biology Laboratory, The Salk Institute for Biological Studies, La Jolla, CA 92037, USA; Genomic Analysis Laboratory, The Salk Institute for Biological Studies, La Jolla, CA 92037, USA; Howard Hughes Medical Institute, The Salk Institute for Biological Studies, La Jolla, CA 92037, USA. Electronic address:

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http://dx.doi.org/10.1016/j.cell.2016.06.044DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5172462PMC
July 2016

Profiling of transcription factor binding events by chromatin immunoprecipitation sequencing (ChIP-seq).

Curr Protoc Plant Biol 2016 10;1(2):293-306. Epub 2016 Jun 10.

Plant Biology Laboratory, Salk Institute for Biological Studies, La Jolla, CA 92037, USA.

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http://doi.wiley.com/10.1002/cppb.20014
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http://dx.doi.org/10.1002/cppb.20014DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5544034PMC
June 2016

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

Sci Rep 2016 06 30;6:28941. Epub 2016 Jun 30.

Division of Biological Sciences, Cell and Developmental Biology Section, University of California San Diego, La Jolla, California, USA.

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http://www.nature.com/articles/srep28941
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http://dx.doi.org/10.1038/srep28941DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4928087PMC
June 2016

Non-CG Methylation in the Human Genome.

Annu Rev Genomics Hum Genet 2015 4;16:55-77. Epub 2015 Jun 4.

Bioinformatics Program, University of California, San Diego, La Jolla, California 92093.

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http://dx.doi.org/10.1146/annurev-genom-090413-025437DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4729449PMC
May 2016

Cistrome and Epicistrome Features Shape the Regulatory DNA Landscape.

Cell 2016 May;165(5):1280-1292

Genomic Analysis Laboratory, The Salk Institute for Biological Studies, 10010 N. Torrey Pines Rd., La Jolla, CA 92037, USA; Plant Biology Laboratory, The Salk Institute for Biological Studies, 10010 N. Torrey Pines Rd., La Jolla, CA 92037, USA; Howard Hughes Medical Institute, The Salk Institute for Biological Studies, 10010 N. Torrey Pines Rd., La Jolla, CA 92037, USA. Electronic address:

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http://dx.doi.org/10.1016/j.cell.2016.04.038DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4907330PMC
May 2016

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

Nat Plants 2016 04 29;2(5):16058. Epub 2016 Apr 29.

Plant Biology Laboratory, The Salk Institute for Biological Studies, La Jolla, California 92037, USA.

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http://dx.doi.org/10.1038/nplants.2016.58DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4855458PMC
April 2016

Epigenomic landscapes of retinal rods and cones.

Elife 2016 Mar 7;5:e11613. Epub 2016 Mar 7.

Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, United States.

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http://dx.doi.org/10.7554/eLife.11613DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4798964PMC
March 2016

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

Plant Cell 2016 Mar 8;28(3):606-9. Epub 2016 Mar 8.

Max Planck Institute for Developmental Biology72076 Tübingen, Germany

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http://dx.doi.org/10.1105/tpc.15.00502DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4826003PMC
March 2016

Mobile small RNAs regulate genome-wide DNA methylation.

Proc Natl Acad Sci U S A 2016 Feb 19;113(6):E801-10. Epub 2016 Jan 19.

Genomic Analysis Laboratory, The Salk Institute for Biological Studies, La Jolla, CA 92037; Plant Biology Laboratory, The Salk Institute for Biological Studies, La Jolla, CA 92037; Howard Hughes Medical Institute, The Salk Institute for Biological Studies, La Jolla, CA 92037

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http://dx.doi.org/10.1073/pnas.1515072113DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4760824PMC
February 2016

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

Cell 2016 Jan 24;164(1-2):233-245. Epub 2015 Dec 24.

Howard Hughes Medical Institute, Salk Institute for Biological Studies, La Jolla, CA 92037, USA; Plant Biology Laboratory, Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, CA 92037, USA. Electronic address:

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http://dx.doi.org/10.1016/j.cell.2015.12.018DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4721562PMC
January 2016

A user's guide to the Arabidopsis T-DNA insertion mutant collections.

Methods Mol Biol 2015 ;1284:323-42

Genomic Analysis Laboratory, Salk Institute for Biological Studies, 10010 N. Torrey Pines Road, La Jolla, CA, 92037, USA,

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http://dx.doi.org/10.1007/978-1-4939-2444-8_16DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5215775PMC
November 2015

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

BMC Bioinformatics 2015 Sep 29;16:313. Epub 2015 Sep 29.

Center for Genomic Science of IIT@SEMM, Istituto Italiano di Tecnologia (IIT), Milano, 20139, Italy.

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http://dx.doi.org/10.1186/s12859-015-0742-6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4587815PMC
September 2015

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

Proc Natl Acad Sci U S A 2015 Aug 10;112(34):E4802-10. Epub 2015 Aug 10.

Molecular and Computational Biology Section, University of Southern California, Los Angeles, CA 90089;

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http://dx.doi.org/10.1073/pnas.1513609112DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4553765PMC
August 2015

Human body epigenome maps reveal noncanonical DNA methylation variation.

Nature 2015 Jul 1;523(7559):212-6. Epub 2015 Jun 1.

1] Genomic Analysis Laboratory, The Salk Institute for Biological Studies, La Jolla, California 92037, USA [2] Howard Hughes Medical Institute, The Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, California 92037, USA.

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http://dx.doi.org/10.1038/nature14465DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4499021PMC
July 2015

Stress induced gene expression drives transient DNA methylation changes at adjacent repetitive elements.

Elife 2015 Jul 21;4. Epub 2015 Jul 21.

ARC Centre of Excellence in Plant Energy Biology, The University of Western Australia, Perth, Australia.

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http://dx.doi.org/10.7554/eLife.09343DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4534844PMC
July 2015

Epigenetics. Exceptional epigenetics in the brain.

Science 2015 Jun;348(6239):1094-5

Genomic Analysis Laboratory and Howard Hughes Medical Institute, Salk Institute for Biological Studies, La Jolla, CA 92037, USA.

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http://dx.doi.org/10.1126/science.aac5832DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4880990PMC
June 2015

Epigenomic Signatures of Neuronal Diversity in the Mammalian Brain.

Neuron 2015 Jun;86(6):1369-84

Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Howard Hughes Medical Institute, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA. Electronic address:

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http://dx.doi.org/10.1016/j.neuron.2015.05.018DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4499463PMC
June 2015

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

Cell Stem Cell 2015 May 9;16(5):547-55. Epub 2015 Apr 9.

Gene Expression Laboratory, Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, CA 92037, USA; Howard Hughes Medical Institute, Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, CA 92037, USA. Electronic address:

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http://dx.doi.org/10.1016/j.stem.2015.03.001DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4427539PMC
May 2015

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

Nat Protoc 2015 Mar 18;10(3):475-83. Epub 2015 Feb 18.

1] Genomic Analysis Laboratory, The Salk Institute for Biological Studies, La Jolla, California, USA. [2] Howard Hughes Medical Institute, The Salk Institute for Biological Studies, La Jolla, California, USA.

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http://www.nature.com/articles/nprot.2014.114
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http://dx.doi.org/10.1038/nprot.2014.114DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4465251PMC
March 2015

Integrative analysis of 111 reference human epigenomes.

Nature 2015 Feb;518(7539):317-30

1] Computer Science and Artificial Intelligence Lab, Massachusetts Institute of Technology, 32 Vassar St, Cambridge, Massachusetts 02139, USA. [2] The Broad Institute of Harvard and MIT, 415 Main Street, Cambridge, Massachusetts 02142, USA.

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http://dx.doi.org/10.1038/nature14248DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4530010PMC
February 2015

Chromatin architecture reorganization during stem cell differentiation.

Nature 2015 Feb;518(7539):331-6

1] Ludwig Institute for Cancer Research, 9500 Gilman Drive, La Jolla, California 92093-0653, USA [2] University of California, San Diego School of Medicine, Department of Cellular and Molecular Medicine, Institute of Genomic Medicine, 9500 Gilman Drive, La Jolla, California 92093-0653, USA.

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http://www.nature.com/articles/nature14222
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http://dx.doi.org/10.1038/nature14222DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4515363PMC
February 2015

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

Genome Res 2014 Oct 28;24(10):1613-23. Epub 2014 Aug 28.

Mouse Cancer Genetics Program, Center for Cancer Research, National Cancer Institute, Frederick, Maryland 21702, USA; Leidos Biomedical Research, Inc., Basic Science Program, Frederick National Laboratory, Frederick, Maryland 21702, USA

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http://dx.doi.org/10.1101/gr.172015.114DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4199375PMC
October 2014

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

Cell Stem Cell 2014 Sep;15(3):295-309

Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Skolkovo Institute of Science and Technology (Skoltech), Novaya strazha 100, Skolkovo Moscow Region 143025, Russia. Electronic address:

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http://dx.doi.org/10.1016/j.stem.2014.07.003DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4170792PMC
September 2014

DNA topoisomerase 1α promotes transcriptional silencing of transposable elements through DNA methylation and histone lysine 9 dimethylation in Arabidopsis.

PLoS Genet 2014 Jul 3;10(7):e1004446. Epub 2014 Jul 3.

Department of Botany and Plant Sciences, Center for Plant Cell Biology, Institute of Integrative Genome Biology, University of California Riverside, Riverside, California, United States of America; Howard Hughes Medical Institute, University of California Riverside, Riverside, California, United States of America.

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http://dx.doi.org/10.1371/journal.pgen.1004446DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4080997PMC
July 2014

Abnormalities in human pluripotent cells due to reprogramming mechanisms.

Nature 2014 Jul 2;511(7508):177-83. Epub 2014 Jul 2.

1] Center for Embryonic Cell and Gene Therapy, Oregon Health & Science University, 3303 Southwest Bond Avenue, Portland, Oregon 97239, USA [2] Division of Reproductive and Developmental Sciences, Oregon National Primate Research Center, Oregon Health & Science University, 505 Northwest 185th Avenue, Beaverton, Oregon 97006, USA [3] Division of Reproductive Endocrinology, Department of Obstetrics and Gynecology, Oregon Health & Science University, 3181 Southwest Sam Jackson Park Road, Portland, Oregon 97239, USA.

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http://dx.doi.org/10.1038/nature13551DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4898064PMC
July 2014

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

Cell Rep 2014 Jul 17;8(2):622-32. Epub 2014 Jul 17.

Division of Biological Sciences, University of California, San Diego, La Jolla, CA 92093, USA; Center for Chronobiology, University of California, San Diego, La Jolla, CA 92093, USA. Electronic address:

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http://dx.doi.org/10.1016/j.celrep.2014.06.033DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4125603PMC
July 2014

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

Proc Natl Acad Sci U S A 2014 Apr 7;111(16):5890-5. Epub 2014 Apr 7.

Mouse Cancer and Genetics Program, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702.

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http://dx.doi.org/10.1073/pnas.1320945111DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4000807PMC
April 2014

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

Bioinformatics 2013 Dec 27;29(24):3204-10. Epub 2013 Sep 27.

Department of Chemistry and Biochemistry, University of California, San Diego, CA 92093, USA, Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA, The ARC Centre of Excellence in Plant Energy Biology, The University of Western Australia, Crawley, Western Australia 6009, Australia, Key Laboratory for Symbolic Computation and Knowledge Engineering of Ministry of Education, College of Computer Science and Technology, Jilin University, Changchun 130012, China, Genomic Analysis Laboratory, The Salk Institute for Biological Studies, La Jolla, CA 92037, USA, Department of Cellular and Molecular Medicine, University of California, San Diego, CA 92093, USA and Ludwig Institute for Cancer Research, La Jolla, CA 92093, USA.

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http://bioinformatics.oxfordjournals.org/content/early/2013/
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http://bioinformatics.oxfordjournals.org/cgi/doi/10.1093/bio
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http://dx.doi.org/10.1093/bioinformatics/btt558DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3842760PMC
December 2013

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

Genome Res 2013 Oct 5;23(10):1663-74. Epub 2013 Jun 5.

Plant Biology Laboratory, The Salk Institute for Biological Studies, La Jolla, California 92037, USA;

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http://dx.doi.org/10.1101/gr.152538.112DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3787263PMC
October 2013

Response to perspective: "separation anxiety: an analysis of ethylene-induced cleavage of EIN2".

Plant Signal Behav 2013 Aug 31;8(8). Epub 2013 May 31.

Plant Biology Laboratory; The Salk Institute for Biological Studies; La Jolla, CA USA.

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http://dx.doi.org/10.4161/psb.25037DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3999072PMC
August 2013

Patterns of population epigenomic diversity.

Nature 2013 Mar 6;495(7440):193-8. Epub 2013 Mar 6.

Plant Biology Laboratory, The Salk Institute for Biological Studies, La Jolla, California 92037, USA.

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http://dx.doi.org/10.1038/nature11968DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3798000PMC
March 2013

Epigenetic trigger for tomato ripening.

Authors:
Joseph R Ecker

Nat Biotechnol 2013 Feb;31(2):119-20

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http://dx.doi.org/10.1038/nbt.2497DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5215857PMC
February 2013

Sigma factor-mediated plastid retrograde signals control nuclear gene expression.

Plant J 2013 Jan 5;73(1):1-13. Epub 2012 Nov 5.

Plant Biology Laboratory, The Salk Institute, 10010 North Torrey Pines Road, La Jolla, CA, 92037, USA.

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http://dx.doi.org/10.1111/tpj.12011DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3605210PMC
January 2013

A blueprint for an international cancer epigenome consortium. A report from the AACR Cancer Epigenome Task Force.

Cancer Res 2012 Dec 27;72(24):6319-24. Epub 2012 Nov 27.

Research Department of Cancer Biology, University College London Cancer Institute, University College London, London, United Kingdom.

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http://cancerres.aacrjournals.org/cgi/doi/10.1158/0008-5472.
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December 2012

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

Science 2012 Oct 30;338(6105):390-3. Epub 2012 Aug 30.

Plant Biology Laboratory, Salk Institute for Biological Studies, La Jolla, CA 92037, USA.

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http://dx.doi.org/10.1126/science.1225974DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3523706PMC
October 2012

Genomics: ENCODE explained.

Nature 2012 Sep;489(7414):52-5

Howard Hughes Medical Institute and the Salk Institute for Biological Studies, La Jolla, California 92037, USA.

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http://www.nature.com/articles/489052a
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September 2012

Release factor one is nonessential in Escherichia coli.

ACS Chem Biol 2012 Aug 13;7(8):1337-44. Epub 2012 Jun 13.

The Jack H. Skirball Center for Chemical Biology and Proteomics, The Salk Institute for Biological Studies, 10010 N. Torrey Pines Road, La Jolla, CA 92037, USA.

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http://dx.doi.org/10.1021/cb300229qDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3423824PMC
August 2012

Widespread dynamic DNA methylation in response to biotic stress.

Proc Natl Acad Sci U S A 2012 Aug 25;109(32):E2183-91. Epub 2012 Jun 25.

Genomic Analysis Laboratory, The Salk Institute for Biological Studies, La Jolla, CA 92037, USA.

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http://dx.doi.org/10.1073/pnas.1209329109DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3420206PMC
August 2012

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

Bioinformatics 2012 Jun;28(12):i163-71

Department of Computer Science and Engineering, University of California-San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA.

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http://dx.doi.org/10.1093/bioinformatics/bts231DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3371863PMC
June 2012