Xu, G., Chen, Y., Martins, L.M., Li, E., Wang, F., Magana, T., Ruan, J., Law, J.A. Transcription factors instruct DNA methylation patterns in plant reproductive tissues. (2025) Nature Cell Biology. DOI: 10.1038/s41556-025-01808-5

Raeisi Dehkordi, S., Wong, I.T., Ni, J., Luebeck, J., Zhu, K., Prasad, G., Krockenberger, L., Xu, G., Chowdhury, B., Rajkumar, U., Caplin, A., Muliaditan, D., Gnanasekar, A., Coruh, C., Jin, Q., Turner, K., Teo, S.X., Pang, A.W.C., Alexandrov, L.B., Chua, C.E.L., Furnari, F.B., Maciejowski, J., Paulson, T.G., Law, J.A., Chang, H.Y., Yue, F., DasGupta, R., Zhao, J., Mischel, P.S., Bafna, V. Breakage fusion bridge cycles drive high oncogene number with moderate intratumoural heterogeneity. (2025) Nature Communications. 16(1):1497. DOI: 10.1038/s41467-025-56670-8

Miller, C.N., Jarrell-Hurtado, S., Haag, M.V., Sara Ye, Y., Simenc, M., Alvarez-Maldonado, P., Behnami, S., Zhang, L., Swift, J., Papikian, A., Yu, J., Colt, K., Ecker, J.R., Michael, T.P., Law, J.A., Busch, W. A single-nuclei transcriptome census of the Arabidopsis maturing root identifies that MYB67 controls phellem cell maturation. (2025) Developmental Cell. DOI: 10.1016/j.devcel.2024.12.025

Felgines, L., Rymen, B., Martins, L.M., Xu, G., Matteoli, C., Himber, C., Zhou, M., Eis, J., Coruh, C., Böhrer, M., Kuhn, L., Chicher, J., Pandey, V., Hammann, P., Wohlschlegel, J., Waltz, F., Law, J.A., Blevins, T. CLSY docking to Pol IV requires a conserved domain critical for small RNA biogenesis and transposon silencing. (2024) Nature Communications. 15(1):10298. DOI: 10.1038/s41467-024-54268-0

Xu, G., Law, J.A. Loops, crosstalk, and compartmentalization: it takes many layers to regulate DNA methylation. (2024) Current Opinion in Genetics & Development. 84:102147. DOI: 10.1016/j.gde.2023.102147

Dehkordi, S.R., Wong, I.T., Ni, J., Luebeck, J., Zhu, K., Prasad, G., Krockenberger, L., Xu, G., Chowdhury, B., Rajkumar, U., Caplin, A., Muliaditan, D., Coruh, C., Jin, Q., Turner, K., Teo, S.X., Pang, A.W.C., Alexandrov, L.B., Chua, C.E.L., Furnari, F.B., Paulson, T.G., Law, J.A., Chang, H.Y., Yue, F., DasGupta, R., Zhao, J., Mischel, P.S., Bafna, V. Breakage fusion bridge cycles drive high oncogene copy number, but not intratumoral genetic heterogeneity or rapid cancer genome change. (2023) bioRxiv. DOI: 10.1101/2023.12.12.571349

Martins, L.M., Law, J.A. Moving targets: Mechanisms regulating siRNA production and DNA methylation during plant development. (2023) Current Opinion in Plant Biology. 75:102435. DOI: 10.1016/j.pbi.2023.102435

Hung, K.L., Luebeck, J., Dehkordi, S.R., Colón, C.I., Li, R., Wong, I.T., Coruh, C., Dharanipragada, P., Lomeli, S.H., Weiser, N.E., Moriceau, G., Zhang, X., Bailey, C., Houlahan, K.E., Yang, W., González, R.C., Swanton, C., Curtis, C., Jamal-Hanjani, M., Henssen, A.G., Law, J.A., Greenleaf, W.J., Lo, R.S., Mischel, P.S., Bafna, V., Chang, H.Y. Targeted profiling of human extrachromosomal DNA by CRISPR-CATCH. (2022) Nature Genetics. DOI: 10.1038/s41588-022-01190-0

Gabrieli, T., Michaeli, Y., Avraham, S., Torchinsky, D., Margalit, S., Schütz, L., Juhasz, M., Coruh, C., Arbib, N., Zhou, Z.S., Law, J.A., Weinhold, E., Ebenstein, Y. Chemoenzymatic labeling of DNA methylation patterns for single-molecule epigenetic mapping. (2022) Nucleic Acids Research. DOI: 10.1093/nar/gkac460

Zhou, M., Coruh, C., Xu, G., Martins, L.M., Bourbousse, C., Lambolez, A., Law, J.A. The CLASSY family controls tissue-specific DNA methylation patterns in Arabidopsis. (2022) Nature Communications. 13(1):244. DOI: 10.1038/s41467-021-27690-x

Luebeck, J., Coruh, C., Dehkordi, S.R., Lange, J.T., Turner, K.M., Deshpande, V., Pai, D.A., Zhang, C., Rajkumar, U., Law, J.A., Mischel, P.S., Bafna, V. AmpliconReconstructor integrates NGS and optical mapping to resolve the complex structures of focal amplifications. (2020) Nature Communications. 11(1):4374. DOI: 10.1038/s41467-020-18099-z

Wu, S., Turner, K.M., Nguyen, N., Raviram, R., Erb, M., Santini, J., Luebeck, J., Rajkumar, U., Diao, Y., Li, B., Zhang, W., Jameson, N., Corces, M.R., Granja, J.M., Chen, X., Coruh, C., Abnousi, A., Houston, J., Ye, Z., Hu, R., Yu, M., Kim, H., Law, J.A., Verhaak, R.G.W., Hu, M., Furnari, F.B., Chang, H.Y., Ren, B., Bafna, V., Mischel, P.S. Circular ecDNA promotes accessible chromatin and high oncogene expression. (2019) Natur. 575(7784):699-703. DOI: 10.1038/s41586-019-1763-5

Argueso, C.T., Assmann, S.M., Birnbaum, K.D., Chen, S., Dinneny, J.R., Doherty, C.J., Eveland, A.L., Friesner, J., Greenlee, V.R., Law, J.A., Marshall-Colón, A., Mason, G.A., O'Lexy, R., Peck, S.C., Schmitz, R.J., Song, L., Stern, D., Varagona, M.J., Walley, J.W., Williams, C.M. Directions for research and training in plant omics: Big Questions and Big Data. (2019) Plant Direct. 3(4):e00133. DOI: 10.1002/pld3.133

Bourbousse, C., Vegesna, N., Law, J.A. SOG1 activator and MYB3R repressors regulate a complex DNA damage network in . (2018) Proceedings of the National Academy of Sciences of the United States of America. DOI: 10.1073/pnas.1810582115

Zhou, M., Palanca, A.M.S., Law, J.A. Locus-specific control of the de novo DNA methylation pathway in Arabidopsis by the CLASSY family. (2018) Nature Genetics. 50(6). DOI: 10.1038/s41588-018-0115-y

Li, D., Palanca, A.M.S., Won, S.Y., Gao, L., Feng, Y., Vashisht, A.A., Liu, L., Zhao, Y., Liu, X., Wu, X., Li, S., Le, B., Kim, Y.J., Yang, G., Li, S., Liu, J., Wohlschlegel, J.A., Guo, H., Mo, B., Chen, X., Law, J.A. The MBD7 complex promotes expression of methylated transgenes without significantly altering their methylation status. (2017) Elife. 6. DOI: 10.7554/eLife.19893

Zhou, M., Law, J.A. RNA Pol IV and V in gene silencing: Rebel polymerases evolving away from Pol II's rules. (2015) Current Opinion in Plant Biology. 27:154-64. DOI: 10.1016/j.pbi.2015.07.005

Law, J.A., Du, J., Hale, C.J., Feng, S., Krajewski, K., Palanca, A.M., Strahl, B.D., Patel, D.J., Jacobsen, S.E. Polymerase IV occupancy at RNA-directed DNA methylation sites requires SHH1. (2013) Natur. 498(7454):385-9. DOI: 10.1038/nature12178

Zhong, X., Hale, C.J., Law, J.A., Johnson, L.M., Feng, S., Tu, A., Jacobsen, S.E. DDR complex facilitates global association of RNA polymerase V to promoters and evolutionarily young transposons. (2012) Nature Structural & Molecular Biology. 19(9):870-5. DOI: 10.1038/nsmb.2354

Law, J.A., Vashisht, A.A., Wohlschlegel, J.A., Jacobsen, S.E. SHH1, a homeodomain protein required for DNA methylation, as well as RDR2, RDM4, and chromatin remodeling factors, associate with RNA polymerase IV. (2011) PLOS Genetics. 7(7):e1002195. DOI: 10.1371/journal.pgen.1002195

Greenberg, M.V., Ausin, I., Chan, S.W., Cokus, S.J., Cuperus, J.T., Feng, S., Law, J.A., Chu, C., Pellegrini, M., Carrington, J.C., Jacobsen, S.E. Identification of genes required for de novo DNA methylation in Arabidopsis. (2011) Epigenetics. 6(3):344-54.

Rajakumara, E., Law, J.A., Simanshu, D.K., Voigt, P., Johnson, L.M., Reinberg, D., Patel, D.J., Jacobsen, S.E. A dual flip-out mechanism for 5mC recognition by the Arabidopsis SUVH5 SRA domain and its impact on DNA methylation and H3K9 dimethylation in vivo. (2011) Genes & Development. 25(2):137-52. DOI: 10.1101/gad.1980311

Guo, L., Yu, Y., Law, J.A., Zhang, X. SET DOMAIN GROUP2 is the major histone H3 lysine [corrected] 4 trimethyltransferase in Arabidopsis. (2010) Proceedings of the National Academy of Sciences of the United States of America. 107(43):18557-62. DOI: 10.1073/pnas.1010478107

Law, J.A., Ausin, I., Johnson, L.M., Vashisht, A.A., Zhu, J.K., Wohlschlegel, J.A., Jacobsen, S.E. A protein complex required for polymerase V transcripts and RNA- directed DNA methylation in Arabidopsis. (2010) Current Biology. 20(10):951-6. DOI: 10.1016/j.cub.2010.03.062

Law, J.A., Jacobsen, S.E. Establishing, maintaining and modifying DNA methylation patterns in plants and animals. (2010) Nature Reviews Genetics. 11(3):204-20. DOI: 10.1038/nrg2719

Law, J.A., Jacobsen, S.E. Molecular biology. Dynamic DNA methylation. (2009) Wissenschaft. 323(5921):1568-9. DOI: 10.1126/science.1172782

Johnson, L.M., Law, J.A., Khattar, A., Henderson, I.R., Jacobsen, S.E. SRA-domain proteins required for DRM2-mediated de novo DNA methylation. (2008) PLOS Genetics. 4(11):e1000280. DOI: 10.1371/journal.pgen.1000280

Law, J.A., O'Hearn, S.F., Sollner-Webb, B. Trypanosoma brucei RNA editing protein TbMP42 (band VI) is crucial for the endonucleolytic cleavages but not the subsequent steps of U-deletion and U-insertion. (2008) RNA. 14(6):1187-200. DOI: 10.1261/rna.899508

Law, J.A., O'Hearn, S., Sollner-Webb, B. In Trypanosoma brucei RNA editing, TbMP18 (band VII) is critical for editosome integrity and for both insertional and deletional cleavages. (2007) Molecular and Cellular Biology. 27(2):777-87. DOI: 10.1128/MCB.01460-06

Zhelonkina, A.G., O'Hearn, S.F., Law, J.A., Cruz-Reyes, J., Huang, C.E., Alatortsev, V.S., Sollner-Webb, B. T. brucei RNA editing: action of the U-insertional TUTase within a U-deletion cycle. (2006) RNA. 12(3):476-87. DOI: 10.1261/rna.2243206

Law, J.A., Huang, C.E., O'Hearn, S.F., Sollner-Webb, B. In Trypanosoma brucei RNA editing, band II enables recognition specifically at each step of the U insertion cycle. (2005) Molecular and Cellular Biology. 25(7):2785-94. DOI: 10.1128/MCB.25.7.2785-2794.2005