Schmitz Lab

Population Epigenomics and Mechanisms of Epigenetics



  1. 100. Bewick AJ, Zhang Y, Wendte JM, Zhang X, Schmitz RJ. (2019) Evolutionary and Experimental Loss of Gene Body Methylation and Its Consequence to Gene Expression. G3 - Genes Genomes Genetics

  2. 99. Argueso CT, Assman SM, Birnbaum K, Chen S, Dinneny J, Doherty CJ, Eveland AL, Friesner J, Greenlee VR, Law JA, Marshall-Colon A, Alex Mason G, O’Lexy R, Peck S, Schmitz RJ, Song L, Stern D, Varagona MJ, Walley JW, Williams CM. (2019) Directions for research and training in plant omics: Big questions and big data. Plant Direct

  3. 98. Bewick AJ, Hofmeister BT, Powers R, Mondo S, James TY, Stajich JE, Schmitz RJ. (2019) Diversity of cytosine methylation across the fungi tree of life. Nature Ecology & Evolution

    Data links: GEO data
    Fungal Methylome Genome Browsers

  4. 97. Johannes F and Schmitz RJ (2019) Spontaneous epimutations in plants. New Phytologist

  5. 96. Bewick AJ, Sanchez Z, McKinney EC, Moore AJ, Moore PJ‡, Schmitz RJ‡ (2019) Dnmt1 is essential for egg production and embryo viability in the large milkweed bug, Oncopeltus fasciatus. Epigenetics & Chromatin

    Data links: GEO data

  6. 95. Cunningham CB, Ji L, McKinney EC, Benowitz KM, Schmitz RJ, Moore AJ (2019) Changes Of Gene Expression But Not Cytosine Methylation Are Associated With Behavioural Plasticity Of Parental Care. J Exp Biol

  7. 2018

  8. 94. Galli M, Khakhar A, Chen Z, Lu Z, Sen S, Joshi T, Nemhauser JL, Schmitz RJ, Gallavotti A. (2018) The DNA binding landscape of the maize auxin response factor family. Nature Communications

  9. 93. Lee BH, Weber ZT, Zourelidou M, Hofmeister BT, Schmitz RJ, Schwechheimer C, Dobrista AA (2018) Arabidopsis protein kinase D6PKL3 is involved in formation of distinct plasma-membrane aperture domains on the pollen surface. Plant Cell

  10. 92. Rajshekar S, Yao J, Arnold PK, Payne SG, Zhang Y, Bowman TV, Schmitz RJ, Edwards JR, Goll MG (2018) Pericentromeric hypomethylation elicits an interferon response in an animal model of ICF syndrome. eLIFE

  11. 91. Volden R, Palmer T, Byrne A, Cole C, Schmitz RJ, Green RE, Vollmers C (2018) R2C2: Improving nanopore read accuracy enables the sequencing of highly-multiplexed full-length single-cell cDNA. Proc Natl Acad Sci bioRxiv

  12. 90. Lu Z, Ricci W, Schmitz RJ, Zhang X. (2018) Identification of Cis-regulatory Elements by Chromatin Structure. Current Opinions in Plant Biology

  13. 89. Finnegan JE, Ford B, Wallace X, Pettolino F, Griffin PT, Schmitz RJ, Zhang P, Barrero JM, Hayden M, Boden S, Cavanagh C, Swain S, Trevaskis B. (2018) Zebularine treatment is associated with deletion of FT-B1 leading to an increase in spikelet number in bread wheat. Plant Cell & Environment

  14. 88. Fallon TR, Lower SE, Chang C, Manabu BU, Martin GJ, Bewick AJ, Behringer M, Debat HJ, Wong I, Dad JC, Suvorov A, Silva CJ, Hall DW, Schmitz RJ, Nelson DR, Lewis S, Shigenobu S, Bybee SM, Larracuente AM, Oba Y, Weng JK. (2018) Firefly genomes illuminate the origin and evolution of bioluminescence. eLIFE

  15. 87. Hofmeister BT and Schmitz RJ (2018) Enhanced JBrowse plugins for epigenomics data visualization. BMC Bioinformatics 19:159 bioRxiv

  16. 86. Wendte JM and Schmitz RJ (2018) Specification of pathways targeting heterochromatin modifications in plants. Molecular Plant 11 (3), 381-387

  17. 85. Ji L*, Jordan WT*, Shi X, Hu L, He C, Schmitz RJ (2018) TET-mediated epimutagenesis of the Arabidopsis thaliana methylome. Nature Communications March;9(895) bioRxiv

    Data links: GEO data

  18. 2017

  19. 84. Hofmeister BT, Lee K, Rohr NA, Hall DW, Schmitz RJ (2017) Stable inheritance of DNA methylation allows creation of epigenotype maps and the study of epiallele inheritance patterns in the absence of genetic variation. Genome Biology Jun 18:155

    Data links: GEO data

  20. 83. Stathopoulou A, Chhetri J, Esteve P, Ambrose J, Ji L, Edjument-Bromage H, Zhang G, Neubert T, Herrero J, Pradhan S, Schmitz RJ, Ooi STK (2017) A novel requirement for Drosha in maintenance of mammalian CG methylation. Nucleic Acids Research gkx695

    Data links: GEO data

  21. 82. Springer NM and Schmitz RJ (2017) Exploiting induced and natural epigenetic variation for crop improvement. Nature Reviews in Genetics July(18):563–575

  22. 81. Susek K, Braszewska-Zalewska A, Bewick AJ, Hasterok R, Schmitz RJ, Naganowska B. (2017) Epigenomic diversication within the genus Lupinus. PLOS ONE June:e0179821

  23. 80. Mondo SJ, Dannebaum RO, Kuo RC, Louie KB, Bewick AJ, LaButti K, Haridas S, Kuo A, Salamov A, Ahrendt SR, Lau R, Bowen BP, Lipzen A, Sullivan W, Andreopoulos WB, Clum A, Lindquist E, Daum C, Northen TR, Ramamoorthy G, Schmitz RJ, Gryganskyi A, Culley D, Magnuson J, James TY, O’Malley MA, Stajich JE, Spatafora JW, Visel A, Grigoriev IV. (2017) Pervasive Adenine N6-methylation of Active Genes in Fungi. Nature Genetics May:49, 964–968

  24. 79. Hossain MS, Kawakatsu T, Kim KD, Ning Z, Nguyen CT, Khan SM, Hernandez NG, Batek JM, Joshi T, Schmutz J, Schmitz RJ, Xu D, Grimwood J, Jackson SA, Ecker JR, Stacey G. (2017) Divergent cytosine DNA methylation patterns in single-cell, soybean root hairs in response to heat stress. New Phytologist Apr;214(2):808-819

  25. 78. Bewick AJ and Schmitz RJ. (2017) Gene body DNA methylation in plants. Current Opinion in Plant Biology

  26. 77. Edger PP, Smith RD, McKain MR, Cooley AM, Vallejo-Marin M, Yuan Y, Bewick Aj, Ji L, Platts AE, Bowman MJ, Childs KL, Schmitz RJ, Smith GD, Pires JC, Puzey JR. (2017) Subgenome dominance in an interspecific hybrid, synthetic allopolyploid, and a 140 year old naturally established neo-allopolyploid monkeyflower. Plant Cell Sep;29(9):2150-2167

  27. 76. Lu Z, Hofmeister BT, DuBois R, Vollmers C, Schmitz RJ. (2017) Combining ATAC-seq with nuclei sorting for discovery of cis-regulatory regions in plant genomes. Nucleic Acids Research gkw1179

    Data links: GEO data

  28. 75. Niederhuth CE and Schmitz RJ. (2017) Putting methylation in context: from genomes to gene expression in plants. Biochemica et Biophysica Acta Jan;1860(1):149–156.

  29. 74. Bewick AJ, Vogel KJ, Moore AJ, Schmitz RJ (2017) Evolution of DNA methylation across insects. Molecular Biology & Evolution 34(3): 654-665 bioRxiv

    Data links: GEO data

  30. 73. Bewick AJ, Niederhuth CE, Rohr NA, Griffin PT, Leebens-Mack J, Schmitz RJ. (2017) The evolution of CHROMOMETHYLASES and gene body DNA methylation in plants. Genome Biology May 1;18(1):65. bioRxiv

    Data links: GEO data

  31. 2016

  32. 72. Walley JW, Sartor RC, Shen Z, Schmitz RJ, Wu KJ, Urich MA, Nery JR, Smith LG, Ecker JR, Briggs SP. (2016) Integration of omic networks in a developmental atlas of maize. Science Aug 19:353(6301)

    Data links: GEO data

  33. 71. Panda K, Ji L, Neumann DA, Daron J, Schmitz RJ, Slotkin RK. (2016) Full-length autonomous transposable elements are preferentially targeted by expression-dependent forms of RNA-directed DNA methylation. Genome Biology Aug 9;17(170)

    Data links: GEO data

  34. 70. Kawakatsu T*, Huang SC*, Jupe F*, Sasaki E*, Schmitz RJ, Urich MA, Castanon R, Nery JR, Barragan C, He Y, Chen H, Dubin M, Lee CR, Wang C, Bemm F, Becker C, O’Neil R, O’Malley RC, Quarless DX, 1001 Genomes Consortium, Schork NJ, Weigel D, Nordborg M, Ecker JR. (2016) Epigenomic Diversity in a Global Collection of Arabidopsis thaliana Accessions. Cell Jul 14;166(2):481-91

  35. 69. 1001 Genome Consortium (2016) 1135 sequenced natural inbred lines reveal the global pattern of polymorphism in Arabidopsis thaliana. Cell Jul 14;166(2):481-91

    Data links: 1,001 Genomes Project Web Portal

  36. 68. Hohos NM, Lee KJ, Ji L, Yu M, Kandasamy KM, Phillips BG, Baile CA, He C, Schmitz RJ, Meagher RB. (2016) DNA cytosine hydroxymethylation levels are distinct among peripheral blood leukocytes. Journal of Immunological Methods Sep;436;1-15

    Data links: GEO data

  37. 67. Jordan WT and Schmitz RJ. (2016) The shocking consequences of hybrid epigenomes. Genome Biology May 5;17(1):85

  38. 66. Reynolds DL, Hofmeister BT, Cliffe L, Siegal TN, Anderson BA, Beverley SM, Schmitz RJ, Sabatini R. (2016). Base J represses genes at the end of polycistronic gene cluster in Leishmania major by promoting RNAP II termination. Molecular Microbiology Aug;101(4):559-74

    Data links: GEO data

  39. 65. Kawakatsu T, Stuart T, Valdes M, Breakfield N, Schmitz RJ, Nery JR, Urich MA, Han X, Lister R, Benfey PN, Ecker JR. (2016) Epigenomic profiling reveals unique cell-type specific patterns of DNA methylation in the root meristem. Nature Plants May(2):e16058

  40. 64. Yu P, Ji L, Lee KJ, Yu M, He C, Ambati S, McKinney EC, Jackson C, Baile CA, Schmitz RJ, Meagher RB. (2016) Subsets of visceral adipose tissue nuclei and distinct levels of 5-hydroxymethylation. PLOS ONE May 12;11(5):e0154949

    Data links: GEO data

  41. 63. Griffin PT, Niederhuth CE, Schmitz RJ (2016) A comparative analysis of 5-azacytidine and zebularine induced DNA demethylation. G3 - Genes Genomes Genetics (in press) bioRxiv

    Data links: GEO data

  42. 62. Niederhuth CE*, Bewick AJ*, Ji L, Alabday M, Kim KD, Li Q, Rohr NA, Rambani A, Burke JM, Udall JA, Egesi C, Schmutz J, Grimwood J, Jackson SA, Springer NM, Schmitz RJ (2016) Widespread natural variation of DNA methylation within angiosperms. Genome Biology Sept 27;17:194 bioRxiv

    Data links: GEO data

  43. 61. Bewick AJ*, Ji L*, Niederhuth CE*, Willing EM*, Hofmeister BT, Shi X, Wang L, Lu Z, Rohr NA, Hartwig B, Kiefer C, Deal RB, Schmutz J, Grimwood J, Stroud H, Jacobsen SE, Schneeberger K, Zhang X, Schmitz RJ (2016) On the Origin and Evolutionary Consequences of Gene Body DNA Methylation. Proc Natl Acad Sci Aug 9;113(32):9111-6 bioRxiv

    Data links: GEO data

  44. 60. Seymour M*, Ji L*, Santos AM, Kamei M, Sasaki T, Basenko EY, Schmitz RJ, Zhang X, Lewis ZA. (2016) Histone H1 limits DNA methylation in Neurospora crassa. G3 - Genes Genomes Genetics Jul 7;6(7):1879-89

    Data links: GEO data

  45. 59. Bertioli DJ, Cannon SB, Froenicke L, Huang G, Farmer AD, Cannon EKS, Liu X, Gao D, Clevenger J, Dash S, Ren L, Moretzsohn MC, Shirasawa K, Huang W, Vidigal B, Abernathy B, Chu Y, Niederhuth CE, Umale P, Araújo ACG, Kozik A, Kim KD, Burow MD, Varshney RK, Wang X, Zhang X, Barkley N, Guimarães PM, Isobe S, Guo S, Liao B, Stalker HT, Schmitz RJ, Scheffler BE, Leal-Bertioli SCM, Xun X, Jackson SA, Michelmore R, Ozias-Akins P. (2016) The genome sequences of Arachis duranensis and Arachis ipaensis, the diploid ancestors of cultivated peanut. Nature Genetics April;48(4):438-446

  46. 58. Reynolds D, Hofmeister B, Cliffe L, Alabady M, Siegel NT, Schmitz RJ, Sabatini R. (2016) Histone variant 3 regulates RNA polymerase II transcription termination and dual strand transcription of siRNA loci in Trypanosoma brucei. PLOS Genetics Jan 21;12(1):e1005758

    Data links: GEO data

  47. 57. Basenko EY, Kamei M, Ji L, Schmitz RJ, Lewis ZA. (2016) The LSH/DDM1 homolog MUS-30 is required for genome stability, but not for DNA methylation in Neurospora crassa. PLOS Genetics Jan 15;12(1):e1005790

    Data links: GEO data

  48. 56. Bewick AJ, Hofmeister BT, Lee KJ, Zhang X, Hall DW, Schmitz RJ. (2016) FASTmC: a suite of predictive models for non-reference-based estimations of DNA methylation. G3 - Genes Genomes Genetics Feb 17;6(2):447-52

    Data links: FASTmC Webtool

  49. 2015

  50. 55. Li Q, Gent JI, Zynda G, Song J, Makarevitch I, Hirsch CD, Hirsch CN, Dawe RK, Madzima TF, McGinnis KM, Lisch D, Schmitz RJ, Vaughn MW, Springer NM (2015) RNA-directed DNA methylation enforces boundaries between heterochromatin and euchromatin in the maize genome. Proc Natl Acad Sci Nov 24;112(47):14728-33

  51. 54. Basenko E, Sasaki T, Ji L, Prybol CJ, Burckhardt RM, Schmitz RJ, Lewis ZA. (2015) Genome-wide redistribution of H3K27me3 is linked to genotoxic stress and defective growth. Proc Natl Acad Sci Nov 17;112(46):E6339-48

  52. 53. Cunningham CB, Ji L, Wiberg RAW, Shelton J, McKinney EC, Parker DJ, Meagher RB, Benowitz KM, Roy-Zokan EM, Ritchie MG, Brown SJ, Schmitz RJ, Moore AJ. (2015) The genome and methylome of a beetle with complex social behavior, Nicrophorus vespilloides (Coleoptera: Silphidae). Genome Biology & Evolution Oct 9;7(12):3383-9

    Data links: GEO data

  53. 52. Christensen SA, Huffaker A, Kaplan A, Sims J, Ziemann S, Doehlemann G, Ji L, Schmitz RJ, Kolomeits MV, Alborn HT, Mori N, Ni X, Byers S, Abdo Z, Schmelz EA. (2015) Maize death acids, 9-lipoxygenase derived cyclopentenones and derivatives, display activity as cytotoxic phytoalexins and transcriptional mediators. Proc Natl Acad Sci Sep 8;112(36):11407-12

    Data links: GEO data

  54. 51. Nagel DH, Doherty CJ, Pruneda-Paz JL, Schmitz RJ, Ecker JR, Kay SA (2015) Genome-wide identification of CCA1 targets uncovers an expanded clock network in Arabidopsis. Proc Natl Acad Sci Aug 25;112(34):E4802-10

  55. 50. Yu M*, Ji L*, Neumann DA, Chung D, Groom J, Westpheling J, He C‡, Schmitz RJ‡. (2015) Base-resolution detection of N4-methylcytosine in genomic DNA using 4mC-Tet-Assisted-Bisulfite-sequencing. Nucleic Acids Research Dec 2;43(21):e148

    Data links: GEO data

  56. 49. Rancour DM, Hatfield RD, Marita JM, Rohr NA, Schmitz RJ. (2015) Cell wall composition and digestibility alterations in Brachypodium distachyon achieved through reduced expression of the UDP-arabinopyranose mutase. Front. Plant Sci. June;6:446

  57. 48. van der Graaf A, Wardenaar R, Neumann DA, Taudt A, Shaw RG, Jansen RC, Schmitz RJ‡, Colomé-Tatché M‡, Johannes F‡. (2015) Rate, spectrum, and evolutionary dynamics of spontaneous epimutations. Proc Natl Acad Sci May;112(21):6676-81

    Data links: GEO data

  58. 47. Bewick AJ and Schmitz RJ. (2015) Epigenetics in the wild. eLife 2015;4:e07808

  59. 46. Jacobs TB, LaFayette PR, Schmitz RJ, Parrott WA. (2015) Targeted genome modifications in soybean with CRISPR/Cas9. BMC Biotechnology March(15):16

  60. 45. Ji L*, Neumann DA*, Schmitz RJ. (2015) Crop Epigenomics: Identifying, Unlocking and Harnessing Cryptic Variation in Crop Genomes. Molecular Plant Jun;8(6):860-870.

  61. 44. Vlachogiannis G, Niederhuth CE, Tuna S, Stathopoulou A, Viiri K, de Rooij DG, Jenner RG, Schmitz RJ, Ooi, STK. (2015) The Dnmt3L ADD domain controls cytosine methylation establishment during spermatogenesis. Cell Reports Feb(10):944–56

    Data links: GEO data

  62. 43. Lane AK, Niederhuth CE, Ji L, Schmitz RJ. (2015) pENCODE: A Plant Encyclopedia of DNA Elements. Annual Review of Genetics Volume 48, Issue 1.

  63. 42. Urich MA, Nery JR, Lister R, Schmitz RJ, Ecker JR. (2015) MethylC-seq: Base resolution whole genome bisulfite sequencing library preparation. Nature Protocols Feb(10):475–483

  64. 2014

  65. 41. Ji L, Sasaki T, Sun X, Ma P, Lewis ZA, Schmitz RJ. (2014) Methylated DNA is over-represented in whole-genome bisulfite sequencing data. Frontiers in Genetics 5:341. doi: 10.3389/fgene.2014.00341

    Data links: GEO MethylC-seq

  66. 40. West PT, Li Q, Ji L, Eichten SR, Song J, Vaughn MW, Schmitz RJ, Springer, NM. (2014) Genomic distribution of H3K9me2 and DNA methylation in a maize genome. PLOS ONE Aug;9(8):e105267

  67. 39. Dinh TT, Gao L, Liu X, O’Leary M, Zhao Y, Li D, Le B, Schmitz RJ, Manavella P, Li S, Weigel D, Pontes O, Ecker JR, Chen X. (2014) DNA Topoisomerase 1α promotes RNA-directed DNA methylation and histone lysine 9 dimethylation at transposable elements in Arabidopsis. PLoS Genetics Jul;7(10):e1004446

  68. 38. Eichten S, Schmitz RJ, Springer NM‡. (2014) Epigenetics; beyond chromatin modifications and complex gene regulatory systems. Plant Physiology Jul 165(3):933-947.

  69. 37. Schmitz RJ. (2014) The Secret Garden - Epigenetic Alleles Underlie Complex Traits. Science. March(343):1082.

  70. 36. Wang Y, Gu X, Yuan W, Schmitz RJ, He Y. (2014) Photoperiodic Control of the Floral Transition through a Distinct Polycomb Repressive Complex. Developmental Cell. Mar(28):1-10.

  71. 35. Valdes-Lopez O*, Khan SM*, Schmitz RJ, Cui S, Qiu J, Zhu M, Cheng JJ, Joshi T, Xu D, Diers B, Ecker JR, Stacey G. (2014) Genotypic variation of gene expression during the soybean innate immunity response. Plant Genetic Resources 12(S1):S27-30.

    Data links: GEO

  72. 34. Niederhuth CE and Schmitz RJ. (2014) Covering your bases: Inheritance of DNA methylation in plant genomes. Molecular Plant Mar;7(3):472-80.

  73. 33. Schmitz RJ‡ and Zhang X‡. (2014) Chapter XI: Decoding epigenomes of herbaceous land plants. Advances in Botanical Research: Genomes of Herbaceous Land Plants. Volume 69.

  74. 2013

  75. 32. Hua ZH, Pool JE, Schmitz RJ, Schultz MD, Shiu SH, Ecker JR‡, Vierstra RD‡. (2013) Epigenomic programming contributes to the genomic drift evolution of the F-box protein superfamily in Arabidopsis. Proc Natl Acad Sci. Oct;110(42):16927-32.

  76. 31. Schmitz RJ*, He Y*, Valdes-Lopez O, Khan S, Joshi T, Urich MA, Nery JR, Diers B, Xu D, Stacey G‡, Ecker JR‡. (2013) Epigenome-wide inheritance of cytosine methylation variants in a recombinant inbred population. Genome Research. Oct(23):1663-67.

    Data links: Browser GEO SRA

  77. 30. Chung WY, Schmitz RJ, Biorac T, Ye D, Dudas M, Meredith GD, Adams CC, Ecker JR, Zhang MQ. (2013) Constructing hepitypes: phasing local genotype and DNA methylation. JNSNE. Aug:2(4):335-346.

  78. 29. Chang KN, Zhong S, Weirauch MT, Hong G, Pelizzola M, Li H, Huang SC, Schmitz RJ, Urich MA, Kue D, Nery J, Qiao H, Yang A, Jamali A, Ideker T, Ren B, Bar-Joseph Z, Hughes TR, Ecker JR (2013) Temporal transcriptional responses to ethylene gas drives growth hormone cross-regulation in Arabidopsis. eLIFE. Jun;2:e00675.

  79. 28. Qiao H, Shen Z, Huang SS, Schmitz RJ, Urich MA, Briggs SP, Ecker JR. (2013) Response to perspective: "Separation anxiety: An analysis of ethylene-induced cleavage of EIN2." Plant Signaling & Behavior. Aug:8(8):127-8.

  80. 27. Schmitz RJ*, Schultz MD*, Urich MA, Nery JR, Pelizzola M, Libiger O, Alix A†, McCosh RB, Chen H, Schork NJ, Ecker JR. (2013) Patterns of Population Epigenomic Diversity. Nature. Mar;495(7440):193-8.

    Data links: Browser GEO RNA-seq GEO MethylC-seq SRA

  81. 26. Woodson JD*, Perez-Ruiz JM*, Schmitz RJ, Ecker JR, Chory J. (2013) Sigma factor mediated plastid retrograde signals control nuclear gene expression. The Plant Journal. Jan;73(1):1-13. PMCID: PMC3605210

    Data links: SRA

  82. 2012

  83. 25. Vollmers C*, Schmitz RJ, Nathanson J, Yeo G, Ecker JR, Panda S. (2012) Circadian oscillations of protein-coding and regulatory RNAs in a highly dynamic mammalian liver epigenome. Cell Metabolism. Dec;16(6):833-45. PMCID: PMC3541940

    Data links: Browser SRA

  84. 24. Schultz MD*, Schmitz RJ, Ecker JR. (2012) "Leveling" the playing field for analysis of single base resolution DNA methylomes. Trends in Genetics. Dec;28(12):583-5. PMCID: PMC3523709

  85. 23. Qiao H, Shen Z, Huang SS, Schmitz RJ, Urich MA, Briggs SP, Ecker JR. (2012) Processing and Subcellular Trafficking of ER-Tethered EIN2 Control Response to Ethylene Gas. Science. Oct;338(6105):390-3. PMCID: PMC3523706

    Data links: SRA

  86. 22. Dowen RJ, Pelizzola M, Schmitz RJ, Lister R, Dowen JM, Nery JR, Dixon JE, Ecker JR. (2012) Widespread dynamic DNA methylation in response to biotic stress. Proc Natl Acad Sci. Jun;109(32):E2183-91. PMCID: PMC3420206

    Data links: SRA

  87. 21. Johnson, DBF, Wang C, Xu J, Schultz MD, Schmitz RJ, Ecker JR, Wang L. (2012) Release factor one is not essential for Escherichia coli. ACS Chemical Biology. Jul;7(8):1337-44. PMCID: PMC3423824

  88. 20. Li L, Ljung K, Breton G, Schmitz RJ, Pruneda-Paz J, Cowing-Vitron C, Cole BJ, Ivans LJ, Pedmale U, Jung HS, Ecker JR, Kay SA, Chory J. (2012) Linking photoreceptor excitation to changes in plant architecture. Genes & Development. Apr;26(8):785-90. PMCID: PMC3337452

    Data links: SRA

  89. 19. Kurihara Y, Schmitz RJ, Nery JR, Schultz MD, Kurihara E, Morosawa T, Tanaka M, Toyoda T, Seki M, Ecker JR. (2012) Surveillance and degradation of 3’ non-coding transcripts requires FIERY1 and XRN3 in Arabidopsis thaliana. G3 - Genes Genomes Genetics. PMCID: PMC3337477

    Data links: SRA

  90. 18. Schmitz RJ and Ecker JR. (2012) Epigenetic and epigenomic variation in Arabidopsis thaliana. Trends in Plant Sciences. Mar;17(3):149-54. PMCID: PMC3645451

  91. 2011

  92. 17. Hotto, A, Schmitz RJ, Fei Z, Ecker JR, Stern D. (2011) Unexpected diversity of chloroplast non-coding RNAs as revealed by deep sequencing of the Arabidopsis transcriptome. G3 - Genes Genomes Genetics. Dec;1(7):559-70. PMCID: PMC3276175

    Data links: SRA

  93. 16. Schmitz RJ, Schultz MD, Lewsey MG, O’Malley RC, Urich MA†, Lilbiger O, Schork NJ, Ecker JR. (2011) Transgenerational epigenetic instability is a source of novel methylation variants. Science. Oct;334(6045):369-373. PMCID: PMC3210014

    Data links: Browser SRA

  94. 15. Johnson DBF, Xu J, Shen Z, Takimoto J, Schultz MD, Schmitz RJ, Ecker JR, Briggs SP, Wang L. (2011) RF1 Knockout allows ribosomal incorporation of unnatural amino acids at multiple sites. Nature Chemical Biology. Sep;7(11):779-86. PMCID: PMC3201715

  95. 14. Arabidopsis Interactome Mapping Consortium. (2011) Evidence for network evolution in an Arabidopsis interacome map. Science. Jul;333(6042):601-7. PMCID: PMC3170756

  96. 13. Farrona S, Hurtado L, March-Díaz R, Schmitz RJ, Florencio FJ, Turck F, Amasino RM, Reyes JC. (2011) Brahma is required for proper expression of the floral repressor FLC. PLoS ONE. Mar;6(3). PMCID: PMC3061888

  97. 12. Schmitz RJ‡ and Zhang X‡. (2011) High-throughput approaches for studying plant epigenomics. Current Opinions in Plant Biology. Apr;14:130-136. PMCID: PMC3112054

  98. 2010

  99. 11. Belkdhadir Y, Durbak A, Wierzba M, Schmitz RJ, Aquirre A, Michel R, Rowe S, Fujioka S, Tax FE. (2010) Intragenic suppression of a trafficking-defective brassinosteroid receptor mutant in Arabidopsis. Genetics. Aug;185(4):1283-96. PMCID: PMC2927756

  100. 2009

  101. 10. Schmitz RJ, Tamada Y*, Doyle MR, Zhang X, Amasino RM. (2009) Histone H2B deubiquitination is required for transcriptional activation of FLOWERING LOCUS C and for proper control of flowering in Arabidopsis. Plant Physiology. Feb;149(2):1196-204. PMCID: PMC2633843

  102. 2008

  103. 9. Schmitz RJ*, Sung S*, Amasino RM. (2008) Histone arginine methylation is required for vernalization-induced epigenetic silencing of FLC in winter-annual Arabidopsis thaliana. Proc Natl Acad Sci. Jan;15:105(2):411-6. PMCID: PMC2206549

  104. 2007

  105. 8. Schmitz RJ, Hong L†, Fitzpatrick KE†, Amasino RM. (2007) DICER-LIKE 1 and DICER-LIKE 3 redundantly act to promote flowering via repression of FLOWERING LOCUS C in Arabidopsis thaliana. Genetics. Jun;176(2):1359-62. PMCID: PMC1894598

  106. 7. Reeves PA, He Y, Schmitz RJ, Amasino RM, Panella LW, Richards CM. (2007) Evolutionary conservation of the FLC-mediated vernalization response: evidence from the sugar beet (Beta vulgaris). Genetics. May;176(1):295-307.

  107. 6. Schmitz RJ and Amasino RM. (2007) Vernalization: a model for investigating epigenetics and eukaryotic gene regulation in plants. Biochemica et Biophysica Acta. Mar/Apr;2(2):127-128.

  108. 5. Sung S, Schmitz RJ, Amasino RM. (2007) A role for VIN3-Like genes in environmentally induced epigenetic regulation of flowering. Plant Signaling & Behavior. Mar:2(2):127-8.

  109. 2006

  110. 4. Sung S, Schmitz RJ, Amasino RM. (2006) A PHD finger protein involved in both the vernalization and photoperiod pathways in Arabidopsis. Genes & Development. Dec;20(23):3244-8.

  111. 2005

  112. 3. Schmitz RJ, Hong L†, Michaels S, Amasino RM. (2005) FRIGIDA-ESSENTIAL 1 interacts genetically with FRIGIDA and FRIGIDA-LIKE 1 to promote the winter-annual habit of Arabidopsis thaliana. Development. Dec;132(24):5471-8.

  113. 2002

  114. 2. Choe S, Schmitz RJ, Fujioka S, Takatsuto S, Lee MO, Yoshida S, Feldmann KA, Tax FE. (2002) Arabidopsis brassinosteroid-insensitive dwarf12 mutants are semidominant and defective in a glycogen synthase kinase 3 beta-like kinase. Plant Physiology. Nov:130(3):1506-15.

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*co-first authorship, ‡co-corresponding authorship, †undergraduates authors