Additional materials of the author at
CSHL Institutional Repository

Husbands, Aman Y, Feller, Antje, Aggarwal, Vasudha, Dresden, Courtney E, Holub, Ashton S, Ha, Taekjip , Timmermans, Marja CP (2023) The START domain potentiates HD-ZIPIII transcriptional activity. Roeder, Adrienne (Ed.). The Plant Cell,

Knauer, S., Javelle, M., Li, L., Li, X., Ma, X., Wimalanathan, K., Kumari, S., Johnston, R., Leiboff, S., Meeley, R., Schnable, P. S., Ware, D., Lawrence-Dill, C., Yu, J., Muehlbauer, G. J., Scanlon, M. J. , Timmermans, M. C. P. (2019) A high-resolution gene expression atlas links dedicated meristem genes to key architectural traits. Genome Res, 29(12) pp. 1962-1973.

Marco, C. F., Skopelitis, D. S. , Timmermans, M. C. P. (2019) In Situ Localization of Small RNAs in Plants. Methods Mol Biol, 1932 pp. 159-173.

Li, L., Eichten, S. R., Shimizu, R., Petsch, K., Yeh, C. T., Wu, W., Chettoor, A. M., Givan, S. A., Cole, R. A., Fowler, J. E., Evans, M. M. S., Scanlon, M. J., Yu, J., Schnable, P. S., Timmermans, M. C. P., Springer, N. M. , Muehlbauer, G. J. (2018) Correction to: Genome-wide discovery and characterization of maize long non-coding RNAs. Genome Biol, 19(1) pp. 122.

Skopelitis, D. S., Hill, K., Klesen, S., Marco, C. F., von Born, P., Chitwood, D. H. , Timmermans, M. C. P. (2018) Gating of miRNA movement at defined cell-cell interfaces governs their impact as positional signals. Nat Commun, 9(1) pp. 3107.

Skopelitis, Damianos S., Benkovics, Anna H., Husbands, Aman Y. , Timmermans, Marja C. P. (2017) Boundary Formation through a Direct Threshold-Based Readout of Mobile Small RNA Gradients. Developmental Cell, 43(3) pp. 265-273.

Husbands, A. Y., Aggarwal, V., Ha, T. , Timmermans, M. C. (2016) In Planta Single-Molecule Pull-Down Reveals Tetrameric Stoichiometry of HD-ZIPIII:LITTLE ZIPPER Complexes. Plant Cell, 28(8) pp. 1783-94.

Plavskin, Yevgeniy, Nagashima, Akitomo, Perroud, Pierre-François, Hasebe, Mitsuyasu, Quatrano, Ralph S, Atwal, Gurinder S , Timmermans, Marja C P. (2016) Ancient trans-Acting siRNAs Confer Robustness and Sensitivity onto the Auxin Response. Developmental Cell, 36(3) pp. 276-289.

Husbands, A. Y., Benkovics, A. H., Nogueira, F. T., Lodha, M. , Timmermans, M. C. (2015) The ASYMMETRIC LEAVES Complex Employs Multiple Modes of Regulation to Affect Adaxial-Abaxial Patterning and Leaf Complexity. Plant Cell, 27(12) pp. 3321-3335.

Leiboff, S., Li, X., Hu, H. C., Todt, N., Yang, J., Li, X., Yu, X., Muehlbauer, G. J., Timmermans, M. C., Yu, J., Schnable, P. S. , Scanlon, M. J. (2015) Genetic control of morphometric diversity in the maize shoot apical meristem. Nat Commun, 6 pp. 8974.

Chandran, D., Scanlon, M. J., Ohtsu, K., Timmermans, M. C., Schnable, P. S. , Wildermuth, M. C. (2015) Laser Microdissection-Mediated Isolation and In Vitro Transcriptional Amplification of Plant RNA. Curr Protoc Mol Biol, 112 pp. 25A 3.1-25A 3.23.

Petsch, K., Manzotti, P. S., Tam, O. H., Meeley, R., Hammell, M., Consonni, G. , Timmermans, M. C. (2015) Novel DICER-LIKE1 siRNAs Bypass the Requirement for DICER-LIKE4 in Maize Development. Plant Cell, 27(8) pp. 2163-2177.

Thompson, A. M., Yu, J., Timmermans, M. C., Schnable, P., Crants, J. C., Scanlon, M. J. , Muehlbauer, G. J. (2015) Diversity of maize shoot apical meristem architecture and its relationship to plant morphology. G3 (Bethesda), 5(5) pp. 819-27.

Dotto, M. C., Petsch, K. A., Aukerman, M. J., Beatty, M., Hammell, M. , Timmermans, M. C. (2014) Genome-Wide Analysis of leafbladeless1-Regulated and Phased Small RNAs Underscores the Importance of the TAS3 ta-siRNA Pathway to Maize Development. PLoS Genetics, 10(12) pp. e1004826.

Benkovics, A. H. , Timmermans, M. C. (2014) Developmental patterning by gradients of mobile small RNAs. Current Opinion in Genetics & Development, 27C pp. 83-91.

Thompson, A. M., Crants, J., Schnable, P. S., Yu, J., Timmermans, M. C. P., Springer, N. M., Scanlon, M. J. , Muehlbauer, G. J. (2014) Genetic control of maize shoot apical meristem architecture. G3: Genes, Genomes, Genetics, 4(7) pp. 1327-1337.

Li, L., Eichten, S. R., Shimizu, R., Petsch, K., Yeh, C. T., Wu, W., Chettoor, A. M., Givan, S. A., Cole, R. A., Fowler, J. E., Evans, M. M., Scanlon, M. J., Yu, J., Schnable, P. S., Timmermans, M. C., Springer, N. M. , Muehlbauer, G. J. (2014) Genome-wide discovery and characterization of maize long non-coding RNAs. Genome Biology, 15(2) pp. R40.

Zhai, J. X., Zhao, Y. Y., Simon, S. A., Huang, S., Petsch, K., Arikit, S., Pillay, M., Ji, L. J., Xie, M., Cao, X. F., Yu, B., Timmermans, M., Yang, B., Chen, X. M. , Meyers, B. C. (2013) Plant MicroRNAs Display Differential 3 ' Truncation and Tailing Modifications That Are ARGONAUTE1 Dependent and Conserved Across Species. Plant Cell, 25(7) pp. 2417-2428.

Lodha, M., Marco, C. F. , Timmermans, M. C. (2013) The ASYMMETRIC LEAVES complex maintains repression of KNOX homeobox genes via direct recruitment of Polycomb-repressive complex2. Genes & Development, 27(6) pp. 596-601.

Scanlon, M. J. , Timmermans, M. (2013) Growth and development: from genes to networks and a mechanistic understanding of plant development. Current Opinion in Plant Biology, 16(1) pp. 1-4.

Plavskin, Y. , Timmermans, M. C. (2013) Small RNA-Regulated Networks and the Evolution of Novel Structures in Plants. Cold Spring Harbor Symposia on Quantitative Biology, 77

Knauer, S., Holt, A.L., Rubio-Somoza, I., Tucker, E. J., Hinze, A., Pisch, M., Javelle, M., Timmermans, M. C. P., Tucker, M. R. , Laux, T. (2013) A Protodermal miR394 Signal Defines a Region of Stem Cell Competence in the Arabidopsis Shoot Meristem. Developmental Cell,

Li, L., Petsch, K., Shimizu, R., Liu, S., Xu, W. W., Ying, K., Yu, J., Scanlon, M. J., Schnable, P. S., Timmermans, M. C. P., Springer, N. M. , Muehlbauer, G. J. (2013) Mendelian and Non-Mendelian Regulation of Gene Expression in Maize. PLoS Genetics, 9(1) pp. Article number e1003202.

Li, X. R., Zhu, C. S., Yeh, C. T., Wu, W., Takacs, E. M., Petsch, K. A., Tian, F., Bai, G. H., Buckler, E. S., Muehlbauer, G. J., Timmermans, M. C. P., Scanlon, M. J., Schnable, P. S. , Yu, J. M. (2012) Genic and nongenic contributions to natural variation of quantitative traits in maize. Genome Research, 22(12) pp. 2436-2444.

Takacs, E. M., Li, J., Du, C., Ponnala, L., Janick-Buckner, D., Yu, J., Muehlbauer, G. J., Schnable, P. S., Timmermans, M. C. P., Sun, Q., Nettleton, D. , Scanlon, M. J. (2012) Ontogeny of the maize shoot apical meristem. Plant Cell, 24(8) pp. 3219-3234.

Zhang, X., Douglas, R. N., Strable, J., Lee, M., Buckner, B., Janick-Buckner, D., Schnable, P. S., Timmermans, M. C. P. , Scanlon, M. J. (2012) Punctate vascular expression1 is a novel maize gene required for leaf pattern formation that functions downstream of the trans-acting small interfering RNA pathway. Plant Physiology, 159(4) pp. 1453-1462.

Javelle, M. , Timmermans, M. C. (2012) In situ localization of small RNAs in plants by using LNA probes. Nat Protoc, 7(3) pp. 533-41.

Skopelitis, D. S., Husbands, A. Y. , Timmermans, M. C. (2012) Plant small RNAs as morphogens. Current Opinion in Cell Biology, 24(2) pp. 217-224.

Javelle, M., Klein-Cosson, C., Vernoud, V., Boltz, V., Maher, C., Timmermans, M. C. P., Depege-Fargeix, N. , Rogowsky, P. M. (2011) Genome-Wide Characterization of the HD-ZIP IV Transcription Factor Family in Maize: Preferential Expression in the Epidermis. Plant Physiology, 157(2) pp. 790-803.

Javelle, M., Marco, C. F. , Timmermans, M. (2011) In Situ Hybridization for the Precise Localization of Transcripts in Plants. Journal of Visualized Experiments, (57)

Chitwood, D. H. , Timmermans, M. C. P. (2010) Small RNAs are on the move. Nature, 467(7314) pp. 415-419.

Douglas, R. N., Wiley, D., Sarkar, A., Springer, N., Timmermans, M. C. P. , Scanlon, M. J. (2010) Ragged seedling2 Encodes an ARGONAUTE7-Like Protein Required for Mediolateral Expansion, but Not Dorsiventrality, of Maize Leaves. Plant Cell, 22(5) pp. 1441-1451.

Kidner, C. A. , Timmermans, M. C. P. (2010) Signaling sides adaxial-abaxial patterning in leaves. In: Plant Development. Timmermans, M. C. P. (Ed.). Current Topics in Developmental Biology. Current Topics in Developmental Biology, 91 pp. 141-168. San Diego: Elsevier Academic Press Inc.

Husbands, A. Y., Chitwood, D. H., Plavskin, Y. , Timmermans, M. C. P. (2009) Signals and prepatterns: new insights into organ polarity in plants. Genes and Development, 23(17) pp. 1986-97.

Scanlon, M. J., Ohtsu, K., Timmermans, M. C. P. , Schnable, P. S. (2009) Laser microdissection-mediated isolation and in vitro transcriptional amplification of plant RNA. Current Protocols in Molecular Biology, (SUPPL.) pp. 25A.3.1-25A.3.15.

Brooks, L., Strable, J., Zhang, X., Ohtsu, K., Zhou, R., Sarkar, A., Hargreaves, S., Elshire, R. J., Eudy, D., Pawlowska, T., Ware, D. H., Janick-Buckner, D., Buckner, B., Timmermans, M. C. P., Schnable, P. S., Nettleton, D. , Scanlon, M. J. (2009) Microdissection of shoot meristem functional domains. PLoS Genet, 5(5) pp. e1000476.

Chitwood, D. H., Nogueira, F. T. S., Howell, M. D., Montgomery, T. A., Carrington, J. C. , Timmermans, M. C. P. (2009) Pattern formation via small RNA mobility. Genes Dev, 23(5) pp. 549-554.

Gray, J., Bevan, M., Brutnell, T., Buell, C. R., Cone, K., Hake, S., Jackson, D. P., Kellogg, E., Lawrence, C., McCouch, S., Mockler, T., Moose, S., Paterson, A., Peterson, T., Rokshar, D., Souza, G. M., Springer, N., Stein, N., Timmermans, M. C. P., Wang, G.-L. , Grotewold, E. (2009) A Recommendation for Naming Transcription Factor Proteins in the Grasses. Plant Physiol., 149(1) pp. 4-6.

Nogueira, F. T. S., Chitwood, D. H., Madi, S., Ohtsu, K., Schnable, P. S., Scanlon, M. J. , Timmermans, M. C. P. (2009) Regulation of Small RNA Accumulation in the Maize Shoot Apex. Plos Genetics, 5(1) pp. e1000320.

Timmermans, M. C. P., Chitwood, D., Nogueira, F. , Madi, S. (2008) Pattern formation by small RNA signals. Developmental Biology, 319(2) pp. 463-464.

Timmermans, M. C., Chitwood, D., Nogueira, F. , Madi, S. (2008) Small RNAs as Mobile Signals in Development. Faseb Journal, 22 pp. 1.

Guo, M., Thomas, J., Collins, G. A. , Timmermans, M. C. P. (2008) Direct Repression of KNOX Loci by the ASYMMETRIC LEAVES1 Complex of Arabidopsis. Plant Cell, 20(1) pp. 48-58.

Chitwood, D. H., Nogueira, F. T., Howell, M. D., Montogmery, T. A., Carrington, J. C. , Timmermans, M. C. (2008) Pattern formation in leaves via small RNA mobility. Developmental Biology, 319(2) pp. 587-588.

Lodha, M., Marco, C. F. , Timmermans, M. C. P. (2008) Genetic and epigenetic regulation of stem cell homeostasis in plants. Cold Spring Harbor Symposia on Quantitative Biology, 73 pp. 243-51.

Nogueira, F. T. S. , Timmermans, M. C. (2007) An Interplay Between Small Regulatory RNAs Patterns Leaves. Plant Signaling & Behavior, 2(6) pp. 519-21.

Ohtsu, K., Smith, M. B., Emrich, S. J., Borsuk, L. A., Zhou, R. L., Chen, T. L., Zhang, X. L., Timmermans, M. C. P., Beck, J., Buckner, B., Janick-Buckner, D., Nettleton, D., Scanlon, M. J. , Schnable, P. S. (2007) Global gene expression analysis of the shoot apical meristem of maize (Zea mays L.). Plant Journal, 52(3) pp. 391-404.

Chitwood, D. H. , Timmermans, M. C. P. (2007) Target mimics modulate miRNAs. Nat Genet, 39(8) pp. 935-6.

Zhang, X., Madi, S., Borsuk, L., Nettleton, D., Elshire, R. J., Buckner, B., Janick-Buckner, D., Beck, J., Timmermans, M. C. P., Schnable, P. S. , Scanlon, M. J. (2007) Laser microdissection of narrow sheath mutant maize uncovers novel gene expression in the shoot apical meristem. Plos Genetics, 3(6) pp. 1040-1052.

Nogueira, F. T., Madi, S., Chitwood, D. H., Juarez, M. T. , Timmermans, M. C. P. (2007) Two small regulatory RNAs establish opposing fates of a developmental axis. Genes Dev, 21(7) pp. 750-5.

Chitwood, D. H., Guo, M., Nogueira, F. T. S. , Timmermans, M. C. P. (2007) Establishing leaf polarity: the role of small RNAs and positional signals in the shoot apex. Development, 134(5) pp. 813-23.

Kidner, C. A. , Timmermans, M. C. (2007) Mixing and matching pathways in leaf polarity. Current Opinion in Plant Biology, 10(1) pp. 13-20.

Nogueira, F. T., Sarkar, A. K., Chitwood, D. H. , Timmermans, M. C. (2006) Organ Polarity in Plants Is Specified through the Opposing Activity of Two Distinct Small Regulatory RNAs. Cold Spring Harbor Symposia on Quantitative Biology, 71 pp. 157-64.

Phelps-Durr, T. L., Thomas, J., Vahab, Phil , Timmermans, M.C.P. (2005) Maize rough sheath2 and its Arabidopsis orthologue ASYMMETRIC LEAVES1 interact with HIRA, a predicted histone chaperone, to maintain knox gene silencing and determinacy during organogenesis. Plant Cell, 17(11) pp. 2886-98.

Juarez, M. T., Twigg, R. W. , Timmermans, M. C. P. (2004) Specification of adaxial cell fate during maize leaf development. Development, 131(18) pp. 4533-44.

Timmermans, M. C., Brutnell, T. P. , Becraft, P. W. (2004) The 46th Annual Maize Genetics Conference. Unlocking the secrets of the maize genome. Plant Physiol, 136(1) pp. 2633-40.

Juarez, M. , Timmermans, M. (2004) MiRNAs specify dorsoventral polarity during leaf development. Developmental Biology, 271(2) pp. 551-552.

Juarez, M. T., Kui, J. S., Thomas, J., Heller, B. A. , Timmermans, M. C. (2004) microRNA-mediated repression of rolled leaf1 specifies maize leaf polarity. Nature, 428(6978) pp. 84-8.

Timmermans, M. C., Juarez, M. T. , Phelps-Durr, T. L. (2004) A conserved microRNA signal specifies leaf polarity. Cold Spring Harb Symp Quant Biol, 69 pp. 409-17.

Kim, M., McCormick, S., Timmermans, M. , Sinha, N. (2003) The expression domain of PHANTASTICA determines leaflet placement in compound leaves. Nature, 424(6947) pp. 438-443.

Kidner, C. A., Timmermans, M. C. P., Byrne, M. E. , Martienssen, R. A. (2002) Developmental genetics of the angiosperm leaf. Advances in Botanical Research, 38 pp. 191-234.

Byrne, M., Timmermans, M., Kidner, C. , Martienssen, R. (2001) Development of leaf shape. Current Opinion in Plant Biology, 4(1) pp. 38-43.

Timmermans, M. C. P., Hudson, A., Becraft, P. W. , Nelson, T. (1999) ROUGH SHEATH2: A Myb protein that represses knox homeobox genes in maize lateral organ primordia. Science, 284(5411) pp. 151-153.