* denotes equal contribution.­­­

32. Swahari V*, Nakamura A*, Hollville E*, Stroud H, Simon JM, Ptacek TS, Beck MV, Flowers C, Guo J, Plestant C, Liang J, Kurtz CL, Kanke M, Hammond SM, He YW, Anton ES, Sethupathy P, Moy SS, Greenberg ME, Deshmukh M.

MicroRNA-29 is an essential regulator of brain maturation through regulation of CH methylation.

Cell Reports, 2021. 35(1): 108946.

31. Stroud H, Yang MG, Tsitohay YN, Davis CP, Sherman M, Hrvatin S, Ling E, Greenberg ME.

An activity-mediated transition in transcription in early postnatal neurons.

Neuron, 2020. 107(5): 874-890.

Research Highlight in Nature Reviews Neuroscience 21, 450-451.

30. Boxer LD*, Renthal W*, Greben AW, Whitwam T, Silberfeld A, Stroud H, Li E, Yang MG, Kinde B, Griffith EC, Greenberg ME.

MeCP2 represses the rate of transcriptional initiation of highly methylated long genes.

Molecular Cell, 2020. 77(2): 294-309.

29. Hrvatin S, Tzeng CP, Nagy MA, Stroud H, Koutsioumpa C, Wilcox OF, Assad EG, Green J, Harvey CD, Griffith EC, Greenberg ME.

PESCA: A scalable platform for the development of cell-type-specific viral drivers.

eLife, 2019. e48089.

28. Cheadle L*, Tzeng CP*, Kalish BT, Harmin DA, Rivera S, Ling E, Nagy MA, Hrvatin S, Hu L, Stroud H, Burkly L, Chen C, Greenberg ME.

Visual experience-dependent expression of Fn14 is required for sensory-driven refinement of the retinogeniculate synapse.

Neuron, 2018. 99(3): 525-539.

27. Stroud H, Su S, Hrvatin S, Greben A, Nagy MA, Renthal W, Boxer L, Hochbaum D, Kinde B, Gabel HW, Greenberg ME.

Early-life gene expression in neurons modulates lasting epigenetic states.

Cell, 2017. 171(5): 1151-1164.

Research Highlight in Nature Reviews Neuroscience 18(12): 710.

26. Wollmann H*, Stroud H*, Yelagandula R*, Tarutani Y, Jiang D, Goiser M, Jamge B, Holec S, Nie X, Kakutani T, Jacobsen SE, Berger F.

The histone H3 variant H3.3 regulates gene body DNA methylation in Arabidopsis thaliana.

Genome Biology, 2017. 18(1):94.

25. 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.

On the Origin and Evolutionary Consequences of Gene Body DNA Methylation.

Proc. Nat. Acad. Sci. U. S. A., 2016. 113(32): 9111-6.

24. Gabel HW*, Kinde BZ*, Stroud H, Gilbert CS, Harmin DA, Kastan NR, Hemberg M, Ebert DH, Greenberg ME.

Disruption of DNA methylation-dependent long gene repression in Rett syndrome.

Nature, 2015. 522(7554): 89-93.

23. Yelagandula R*, Stroud H*, Holec S, Zhou K, Feng S, Zhong X, Muthurajan UM, Xin N, Kawashima T, Groth M, Luger K, Jacobsen SE, Berger F.

The Histone Variant H2A.W Defines Heterochromatin and Promotes Chromatin Condensation in Arabidopsis.

Cell, 2014. 158(1): 98-109.

22. Stroud H, Do T, Du J, Zhong X, Feng S, Johnson L, Patel DJ, Jacobsen SE.

Non-CG methylation patterns shape the epigenetic landscape in Arabidopsis.

Nature Structural & Molecular Biology, 2014. 21(1): 64-72.

21. Pastor WA*, Stroud H*, Nee K, Liu W, Pezic D, Manakov S, Lee SA, Moissiard G, Zamudio N, Bourc’his, Aravin AA, Clark A, Jacobsen SE.

MORC1 represses transposable elements in the murine male germ line.

Nature Communications, 2014. 5: 5795.

20. Groth M, Stroud H, Feng S, Greenberg MV, Vashisht AA, Wohlschlegel JA, Jacobsen SE, Ausin I.

The SNF2 and RING domain proteins FRG1 and 2 are required for RNA-directed DNA methylation in Arabidopsis.

Proc. Nat. Acad. Sci. U. S. A., 2014. 111(49): 17666-71.

19. Malik AN*, Vierbuchen T*, Hemberg M, Rubin A, Ling E, Couch C, Stroud H, Spiegel I, Farh KK, Harmin D, Greenberg ME.

Genome-wide identification and characterization of functional neuronal-activity dependent enhancers.

Nature Neuroscience, 2014. 17(10): 1330-1339.

18. Moissiard G*, Bischof S*, Husmann D, Pastor WA, Hale CJ, Yen L, Stroud H, Papikian A, Vashisht AA, Wohlschlegel JA, Jacobsen SE.

Transcriptional gene silencing by Arabidopsis microrchidia homologues involves the formation of heteromers.

Proc. Nat. Acad. Sci. U. S. A, 2014. 111(20): 7474-9.

17. Stroud H, Greenberg MV, Feng S, Bernatavichute YV, Jacobsen SE.

Comprehensive analysis of silencing mutants reveals complex regulation of the Arabidopsis methylome.

Cell, 2013. 152(1-2): 352-64.

16. Stroud H, Ding B, Simon SA, Feng S, Bellizzi M, Pellegrini M, Wang G, Meyers BC, Jacobsen SE.

Plants regenerated from tissue culture contain stable epigenome changes in rice.

eLife, 2013. 2: e00354.

15. Li-Byarlay H, Li Y, Stroud H, Feng S, Newman TC, Kaneda M, Hou K, Worley KA, Elsik C, Wickline SA, Jacobsen SE, Ma J, Robinson GE.

RNA interference knockdown of DNA methyltransferase 3 affects gene alternative splicing in the honey bee.

Proc. Nat. Acad. Sci. U. S. A, 2013. 110(31): 12750-5.

14. Xu Y, Wang Y, Stroud H, Gu X, Sun B, Gan ES, Ng KH, Jacobsen SE, He Y, Ito T.

A matrix protein silences transposons and repeats through interaction with retinoblastoma-associated proteins.

Current Biology, 2013. 23(4): 345-50.

13. Deleris A*, Stroud H*, Bernatavichute Y, Johnson E, Klein G, Schubert D, Jacobsen SE.

Loss of the DNA methyltransferase MET1 induces H3K9 hypermethylation at PcG target genes, and redistribution of H3K27 trimethylation to transposons in Arabidopsis.

PLOS Genetics, 2012. 8(11): e1003062.

12. Stroud H, Hale CJ, Feng S, Caro E, Jacob Y, Michaels SD, Jacobsen SE.

DNA methyltransferases are required to induce heterochromatic re-replication in Arabidopsis.

PLOS Genetics, 2012. 8(7): e1002808.

11. Stroud H*, Otero S*, Desvoyes B, Ramirez-Parra E, Jacobsen SE, Gutierrez C.

Genome-wide analysis of histone H3.1 and H3.3 variants in Arabidopsis thaliana.

Proc. Nat. Acad. Sci. U. S. A, 2012. 109(14): 5370-5.

10. Caro E, Stroud H, Greenberg MV, Bernatavichute YV, Feng S, Groth M, Vashisht AA, Wohlschlegel J, Jacobsen SE.

The SET-domain protein SUVR5 mediates H3K9me2 deposition and silencing at stimulus response genes in a DNA methylation independent manner.

PLOS Genetics, 2012. 8(10): e1002995.

9. Du J*, Zhong X*, Bernatavichute YV, Stroud H, Feng S, Caro E, Vashisht AA, Terragni J, Chin HG, Tu A, Hetzel J, Wohlschlegel JA, Pradhan S, Patel DJ, Jacobsen SE.

Dual binding of chromomethylase BAH and chromo domains to H3K9me2-containing nucleosomes in the targeting of DNA methylation in plants.

Cell, 2012. 151(1): 167-80.

8. Moissiard G, Cokus S, Cary J, Feng S, Billi AC, Stroud H, Husmann D, Zhan Y, Lajoie BR, McCord RP, Hale CJ, Feng W, Michaels SD, Frand AR, Pellegrini M, Dekker J, Kim JK, Jacobsen SE.

MORC family ATPases required for heterochromatin condensation and gene silencing.

Science, 2012. 336(6087): 1448-51.

7. Pontvianne F, Blevins T, Chandrasekhara C, Feng W, Stroud H, Jacobsen SE, Michaels SD, Pikaard CS.

Histone methyltransferases regulating rRNA gene dose and dosage control in Arabidopsis.

Genes and Development, 2012. 26(9): 945-57.

6. Stroud H, Feng S, Kinney SM, Pradhan S, Jacobsen SE.

5-hydroxymethylcytosine is associated with enhancers and gene bodies in human embryonic stem cells.

Genome Biology, 2011. 12: R54.

Research Highlight in Genome Biol. 12(6): 116.

5. Costas C*, Sanchez MP*, Stroud H*, Yu Y, Oliveros JC, Feng S, Benguria A, López-Vidriero I, Zhang X, Solano R, Jacobsen SE, Gutierrez C.

Genome-wide mapping of Arabidopsis thaliana origins of DNA replication and their associated epigenetic marks.

Nature Structural & Molecular Biology, 2011. 18(3): 395-400.

4. Kinney SM*, Chin HG*, Vaisvila R, Bitinaite J, Zheng Y, Esteve PO, Feng S, Stroud H, Jacobsen SE, Pradhan S.

Tissue specific distribution and dynamic changes of 5-hydroxymethylcytosine in the mammalian genome.

Journal of Biological Chemistry, 2011. 286(28): 24685-93.

3. Jacob Y*, Stroud H*, LeBlanc C, Feng S, Zhou L, Caro E, Hassel C, Gutierrez C, Michaels SD, Jacobsen SE.

Regulation of heterochromatic DNA replication by histone H3 lysine 27 methyltransferases.

Nature, 2010. 466(7309): 987-91.

2. Chodavarapu RK*, Feng S*, Bernatavichute YV, Chen PY, Stroud H, Yu Y, Hetzel JA, Kuo F, Kim J, Cokus SJ, Casero D, Bernal M, Huijser P, Clark AT, Krämer U, Merchant SS, Zhang X, Jacobsen SE, Pellegrini M.

Relationship between nucleosome positioning and DNA methylation.

Nature, 2010. 466(7304): 388-92.

1. Jacob Y, Feng S, LeBlanc CA, Bernatavichute YV, Stroud H, Cokus S, Johnson LM, Pellegrini M, Jacobsen SE, Michaels SD.

ATXR5 and ATXR6 are H3K27 monomethyltransferases required for chromatin structure and gene silencing.

Nature Structural & Molecular Biology, 2009 16(7): 763-8.