2020


121.
Washington JT, Cavender KR, Amukamara AU, McKinney EC, Schmitz RJ, Moore PJ. (2020) The essential role of Dnmt1 in gametogenesis in the large milkweed bug Oncopeltus fasciatus. bioRxiv

120.
Crisp PA, Marand AP, Noshay JM, Zhou P, Lu Z, Schmitz RJ, Springer NM. (2020) Stable unmethylated DNA demarcates expressed genes and their cis-regulatory space in plant genomes. bioRxiv Proceedings of the National Academy of Sciences

119.
Noshay JM, Marand AP, Anderson SN, Zhou P, Guerra MKM, Lu Z, O'Connor C, Crisp PA, Hirsch CN, Schmitz RJ, Springer NM. (2020) Cis-regulatory elements within TEs can influence expression of nearby maize genes. bioRxiv

118.
Zhang Y, Wendte JM, Ji L, Schmitz RJ. (2020) Natural variation in DNA methylation homeostasis and the emergence of epialleles. Proceedings of the National Academy of Sciences

117.
Amukamara AU, Washington JT, Sanchez Z, McKinney EC, Moore AJ, Schmitz RJ, Moore PJ. (2020) More than DNA methylation: does pleiotropy drive the complex pattern of evolution of Dnmt1? bioRxiv Frontiers in Ecology and Evolution

116.
Grover CE, Pan M, Yuan D, Arick II MA, Hu G, Brase L, Stelly DM, Lu Z, Schmitz RJ, Peterson DG, Wendel JF, Udall JA. (2020) The Gossypium longicalyx genome as a resource for cotton breeding and evolution. bioRxiv

115.
Hofmeister BT, Denkena J, Colomé-Tatché M, Shahryary Y, Hazarika R, Grimwood J, Mamidi S, Jenkins J, Grabowski PP, Sreedasyam A, Shu S, Barry K, Lail K, Adam C, Lipzen A, Sorek R, Kudrna D, Talag J, Wing R, Hall DW, Tuskan GA, Schmutz J, Johannes F, Schmitz RJ. (2020) The somatic genetic and epigenetic mutation rate in a wild long-lived perennial Populus trichocarpa. bioRxiv

114.
Shahryary Y, Symeonidi A, Hazarika RR, Denkena J, Mubeen T, Hofmeister B, Gurp TV, Colomé-Tatché M, Verhoeven K, Tuskan G, Schmitz RJ, Johannes F. (2020) AlphaBeta: Computational inference of epimutation rates and spectra from high-throughput DNA methylation data in plants. bioRxiv

113.
Kieft R, Zhang Y, Marand AP, Moran JD, Bridger R, Wells L, Schmitz RJ, Sabatini R. (2020) Identification of a Novel Base J Binding Protein Complex Involved in RNA Polymerase II Transcription Termination in Trypanosomes. bioRxiv PLOS Genetics

112. Yocca A, Lu Z, Schmitz RJ, Freeling M, Edger P. (2020) Evolution of conserved noncoding sequences in Arabidopsis thaliana. bioRxiv

2019


111.
Lu Z, Marand AP, Ricci WA, Ethridge CL, Zhang X, Schmitz RJ. (2019) The prevalence, evolution and chromatin signatures of plant regulatory elements. Nature Plants Data links: Plant Epigenome Browser

110.
Ricci WA*, Lu Z*, Ji L*, Marand AP, Ethridge CL, Murphy NG, Noshay JM, Galli M, Mejía-Guerra MK, Colomé-Tatché M, Johannes F, Rowley MJ, Corces VG, Zhai J, Scanlon MJ, Buckler ES, Gallavotti A, Springer NM, Schmitz RJ, Zhang X. (2019) Widespread long-range cis-regulatory elements in the maize genome. Nature Plants Data links: Plant Epigenome Browser

109.
Dekker JD*, Baracho GV*, Zhu Z, Ippolito GC, Schmitz RJ, Rickert RC, Tucker HO. (2019) Loss of the FOXP1 Transcription Factor Leads to Deregulation of B Lymphocyte Development and Function at Multiple Stages. Immuno Horizons

108.
Drinnenberg IA, Berger F, Elsässer SJ, Andersen PR, Ausió J, Bickmore WA, Blackwell AR, Erwin DH, Gahan JM, Gaut BS, Harvey ZH, Henikoff S, Kao JY, Kurdistani SK, Lemos B, Levine MT, Luger K, Malik HS, Martín-Durán JM, Peichel CL, Renfree MB, Rutowicz K, Sarkies P, Schmitz RJ, Technau U, Thornton JW, Warnecke T, Wolfe KH. (2019) EvoChromo: towards a synthesis of chromatin biology and evolution. Development

107.
Ding Y, Murphy KM, Poretsky E, Mafu S, Yang B, Char SN, Christensen SA, Saldivar E, Wu M, Wang Q, Ji L, Schmitz RJ, Kremling KA, Buckler ES, Shen Z, Briggs SP, Bohlmann J, Sher A, Castro-Falcon G, Hughes CC, Huffaker A, Zerbe P, Schmelz EA. (2019) Multiple genes recruited from hormone pathways partition maize diterpenoid defences. Nature Plants

106.
Noshay JM, Anderson SN, Zhou P, Ji L, Ricci W, Lu Z, Stitzer MC, Crisp PA, Hirsch CN, Zhang X, Schmitz RJ, Springer NM. (2019) Monitoring the interplay between transposable element families and DNA methylation in maize. PLos Genet

105.
Ji L, Mathioni SM, Johnson S, Tucker D, Bewick AJ, Kim KD, Daron J, Slotkin KR, Jackson SA, Parrott WA, Meyers BC, Schmitz RJ. (2019) Genome-wide reinforcement of DNA methylation occurs during somatic embryogenesis in soybean. Plant Cell

104.
Zander M, Willige BC, He Y, Nguyen TA, Langford AE, Nehring R, Howell E, McGrath R, Bartlett A, Castanon R, Nerd JR, Chen H, Zhang Z, Jupe F, Stepanowa A, Schmitz RJ, Lewsey M, Chory J, Ecker JR. (2019) Epigenetic silencing of a multifunctional plant stress regulator. eLIFE

103.
Wendte JM*, Zhang Y*, Ji L*, Shi X, Hazarika RR, Shahryary Y, Johannes F, Schmitz RJ. (2019) Epimutations are associated with CHROMOMETHYLASE 3-induced de novo DNA methylation. eLIFE

102.
Schmitz RJ, Lewis ZA, Goll MG. (2019) DNA Methylation: Shared and Divergent Features across Eukaryotes. Trends in Genetics

101.
Riley LA, Ji L, Schmitz RJ, Westpheling J, Guss AM. (2019) Rational development of transformation in Clostridium thermocellum ATCC 27405 via complete methylome analysis and evasion of native restriction-modification systems. Journal of Industrial Microbiology & Biotechnology

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

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

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

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

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

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. Journal of Experimental Biology

2018


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

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

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

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. bioRxiv Proceedings of the National Academy of Sciences

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

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

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 in beetles. eLIFE 2018;7:e36495

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

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

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

2017


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

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 Data links: GEO data

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

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

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

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

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

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

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 Data links: GEO data

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

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

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. bioRxiv Genome Biology May 1;18(1):65 Data links: GEO data

2016


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

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

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

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

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

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

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

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

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

63.
Griffin PT, Niederhuth CE, Schmitz RJ. (2016) A comparative analysis of 5-azacytidine and zebularine induced DNA demethylation. bioRxiv G3 - Genes Genomes Genetics Sept;6(9): 2773-2780 Data links: GEO data

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. bioRxiv Genome Biology Sept 27;17:194 Data links: GEO data

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. bioRxiv Proceedings of the National Academy of Sciences Aug 9;113(32):9111-6 Data links: GEO data

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

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

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

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

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

2015


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. Proceedings of the National Academy of Sciences Nov 24;112(47):14728-33

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. Proceedings of the National Academy of Sciences Nov 17;112(46):E6339-48

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

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. Proceedings of the National Academy of Sciences Sep 8;112(36):11407-12 Data links: GEO data

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. Proceedings of the National Academy of Sciences Aug 25;112(34):E4802-10

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

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. Frontiers in Plant Science June;6:446

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. Proceedings of the National Academy of Sciences May;112(21):6676-81 Data links: GEO data

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

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

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

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

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

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

2014


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

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

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

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

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

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

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

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

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

2013


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. Proceedings of the National Academy of Sciences Oct;110(42):16927-32

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

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

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

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

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

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

2012


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

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

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

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. Proceedings of the National Academy of Sciences Jun;109(32):E2183-91. PMCID: PMC3420206 Data links: SRA

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

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

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

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

2011


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

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

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

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

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

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

2010


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

2009


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

2008


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. Proceedings of the National Academy of Sciences Jan;15:105(2):411-6. PMCID: PMC2206549

2007


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

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

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

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

2006


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

2005


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

2002


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

1. Zhao J, Peng P, Schmitz RJ, Decker AD, Tax FE, Li J. (2002) Two putative BIN2 substrates are nuclear components of brassinosteroid signaling. Plant Physiology Nov;130(3):1221-9



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