Professor Ben Scheres

2021

• Roszak, P. et al. 2021. Cell-by-cell dissection of phloem development links a maturation gradient to cell specialization. Science 374(6575), article number: 5531. (10.1126/science.aba5531)

2020

• Tang, H., Duijts, K., Bezanilla, M., Scheres, B., Vermeer, J. E. M. and Willemsen, V. 2020. Geometric cues forecast the switch from two- to three- dimensional growth in Physcomitrella patens. New Phytologist 225(5), pp. 1945-1955. (10.1111/nph.16276)
• Radhakrishnan, D. et al. 2020. A coherent feed-forward loop drives vascular regeneration in damaged aerial organs of plants growing in a normal developmental context. Development 147(6), article number: dev185710. (10.1242/dev.185710)
• Lokdarshi, A. et al. 2020. ErbB-3 Binding protein 1 Regulates Translation and Counteracts retinoblastoma related to maintain the root meristem. Plant Physiology 182(2), pp. 919-932. (10.1104/pp.19.00805)

2019

• Durgaprasad, K. et al. 2019. Gradient expression of transcription factor imposes a boundary on organ regeneration potential in plants. Cell Reports 29(2), pp. 453-463.e3. (10.1016/j.celrep.2019.08.099)
• Shimotohno, A. and Scheres, B. 2019. Topology of regulatory networks that guide plant meristem activity: similarities and differences. Current Opinion in Plant Biology 51, pp. 74-80. (10.1016/j.pbi.2019.04.006)
• Zhou, W. et al. 2019. A jasmonate signaling network activates root stem cells and promotes regeneration. Cell 177(4), pp. 942-956.e14. (10.1016/j.cell.2019.03.006)
• Chakrabortty, B., Blilou, I., Scheres, B. and Mulder, B. M. 2019. A computational framework for cortical microtubule dynamics in realistically shaped plant cells. PLOS Computational Biology 14(2), article number: e1005959. (10.1371/journal.pcbi.1005959)

2018

• Chakrabortty, B., Willemsen, V., de Zeeuw, T., Liao, C., Weijers, D., Mulder, B. and Scheres, B. 2018. A plausible microtubule-based mechanism for cell division orientation in plant embryogenesis. Current Biology 28(19), pp. 3031-3043. (10.1016/j.cub.2018.07.025)
• Shimotohno, A., Heidstra, R., Blilou, I. and Scheres, B. 2018. Root stem cell niche organizer specification by molecular convergence of PLETHORA and SCARECROW transcription factor modules. Genes and Development 32(15-16), pp. 1085-1100. (10.1101/gad.314096.118)
• Zhang, X., Zhou, W., Chen, Q., Fang, M., Zheng, S., Scheres, B. and Li, C. 2018. Mediator subunit MED31 is required for radial patterning of Arabidopsis roots. Proceedings of the National Academy of Sciences 115(24), article number: E5624. (10.1073/pnas.1800592115)
• Long, Y. et al. 2018. Optimizing FRET-FLIM labeling conditions to detect nuclear protein interactions at native expression levels in living arabidopsis roots. Frontiers in Plant Science 9, article number: 639. (10.3389/fpls.2018.00639)
• Zamora-Zaragoza, J. and Scheres, B. 2018. Tuning division and differentiation in stomata: How to silence a MUTE. Developmental Cell 45(3), pp. 282-283. (10.1016/j.devcel.2018.04.019)
• Scheres, B. and Krizek, B. A. 2018. Coordination of growth in root and shoot apices by AIL/PLT transcription factors. Current Opinion in Plant Biology 41, pp. 95. (10.1016/j.pbi.2017.10.002)
• Du, Y. and Scheres, B. 2018. Lateral root formation and the multiple roles of auxin. Journal of Experimental Botany 69(2), pp. 155-167. (10.1093/jxb/erx223)

2017

• Du, Y. and Scheres, B. 2017. PLETHORA transcription factors orchestrate de novo organ patterning during Arabidopsis lateral root outgrowth. Proceedings of the National Academy of Sciences of the United States of America 114(44), pp. 11709-11714. (10.1073/pnas.1714410114)
• Zhao, C. et al. 2017. XYLEM NAC DOMAIN1, an angiosperm NAC transcription factor, inhibits xylem differentiation through conserved motifs that interact with RETINOBLASTOMA-RELATED. New Phytologist 216(1), pp. 76-89. (10.1111/nph.14704)
• Long, Y. et al. 2017. In vivo FRET-FLIM reveals cell-type-specific protein interactions in Arabidopsis roots. Nature 548(7665), pp. 97-102. (10.1038/nature23317)
• Díaz-Triviño, S., Long, Y., Scheres, B. and Blilou, I. 2017. Analysis of a plant transcriptional regulatory network using transient expression systems. In: Kaufmann, K. and Mueller-Roeber, B. eds. Plant Gene Regulatory Networks., Vol. 1629. Methods in Molecular Biology New York, NY: Humana Press, pp. 83-103., (10.1007/978-1-4939-7125-1_7)
• Horvath, B. M. et al. 2017. Arabidopsis RETINOBLASTOMA RELATED directly regulates DNA damage responses through functions beyond cell cycle control. EMBO Journal 36(9), pp. 1261-1278. (10.15252/embj.201694561)
• Scheres, B. and van der Putten, W. H. 2017. The plant perceptron connects environment to development. Nature 543(7645), pp. 337-345. (10.1038/nature22010)
• Sheng, L., Hu, X., Du, Y., Zhang, G., Huang, H., Scheres, B. and Xu, L. 2017. Non-canonical WOX11-mediated root branching contributes to plasticity in Arabidopsis root system architecture. Development 144(17), pp. 3126-3133. (10.1242/dev.152132)

2016

• Santuari, L. et al. 2016. The PLETHORA Gene Regulatory Network Guides growth and cell differentiation in Arabidopsis roots. The Plant Cell 28(12), pp. 2937-2952. (10.1105/tpc.16.00656)
• Porco, S. et al. 2016. Lateral root emergence inArabidopsisis dependent on transcription factor LBD29 regulation of auxin influx carrierLAX3. Development 143(18), pp. 3340-3349. (10.1242/dev.136283)
• Benjamins, R. et al. 2016. PPP1, a plant-specific regulator of transcription controls Arabidopsis development and PIN expression [RETRACTED]. Scientific Reports 6(1), article number: 32196. (10.1038/srep32196)
• Scheres, B. and Laskowski, M. 2016. Root patterning: it takes two to tangle. Journal of Experimental Botany 67(5) (10.1093/jxb/erw049)
• Siligato, R. et al. 2016. MultiSite gateway-compatible cell type-specific gene-inducible system for plants. Plant Physiology 170(2), pp. 627-641. (10.1104/pp.15.01246)

2015

• Long, Y. et al. 2015. SCARECROW-LIKE23 and SCARECROW jointly specify endodermal cell fate but distinctly control SHORT-ROOT movement. The Plant Journal 84(4), pp. 773-784. (10.1111/tpj.13038)
• Moreno-Risueno, M. A. et al. 2015. Transcriptional control of tissue formation throughout root development. Science 350(6259), pp. 426-430. (10.1126/science.aad1171)
• Franssen, H. J., Xiao, T. T., Kulikova, O., Wan, X., Bisseling, T., Scheres, B. and Heidstra, R. 2015. Root developmental programs shape the Medicago truncatula nodule meristem. Development 142(17), pp. 2941-2950. (10.1242/dev.120774)
• Dhonukshe, P. et al. 2015. Plasma membrane-bound AGC3 kinases phosphorylate PIN auxin carriers at TPRXS(N/S) motifs to direct apical PIN recycling. Development 142(13), pp. 2386-2387. (10.1242/dev.127415)
• Kareem, A. et al. 2015. PLETHORA genes control regeneration by a two-step mechanism. Current Biology 25(8), pp. 1017-1030. (10.1016/j.cub.2015.02.022)
• Long, Y. et al. 2015. Arabidopsis BIRD zinc finger proteins jointly stabilize tissue boundaries by confining the cell fate regulator SHORT-ROOT and contributing to fate specification. The Plant Cell 27(4), pp. 1185-1200. (10.1105/tpc.114.132407)
• Long, Y., Scheres, B. and Blilou, I. 2015. The logic of communication: roles for mobile transcription factors in plants. Journal of Experimental Botany 66(4), pp. 1133-1144. (10.1093/jxb/eru548)
• Kinoshita, A. et al. 2015. A plant U-box protein, PUB4, regulates asymmetric cell division and cell proliferation in the root meristem. Development 142(3), pp. 444-453. (10.1242/dev.113167)

2014

• Mähönen, A. P. et al. 2014. PLETHORA gradient formation mechanism separates auxin responses. Nature 515(7525), pp. 125-129. (10.1038/nature13663)
• Bennett, T., van den Toorn, A., Willemsen, V. and Scheres, B. 2014. Precise control of plant stem cell activity through parallel regulatory inputs. Development 141(21), pp. 4055-4064. (10.1242/dev.110148)
• Bisseling, T. and Scheres, B. 2014. Nutrient computation for root architecture. Science 346(6207), pp. 300-301. (10.1126/science.1260942)
• Matos, J. L., Lau, O. S., Hachez, C., Cruz-Ramírez, A., Scheres, B. and Bergmann, D. C. 2014. Irreversible fate commitment in the Arabidopsis stomatal lineage requires a FAMA and RETINOBLASTOMA-RELATED module. eLife 3 (10.7554/eLife.03271)
• Dhonukshe, P. et al. 2014. Retraction: generation of cell polarity in plants links endocytosis, auxin distribution and cell fate decisions. Nature 511(7509), pp. 370-370. (10.1038/nature13549)

2013

• Cruz-Ramírez, A. et al. 2013. A SCARECROW-RETINOBLASTOMA protein network controls protective quiescence in the Arabidopsis root stem cell organizer. PLoS Biology 11(11), article number: e1001724. (10.1371/journal.pbio.1001724)
• Dhonukshe, P. et al. 2013. A PLETHORA-auxin transcription module controls cell division plane rotation through MAP65 and CLASP [Retraction of vol. 149, Issue 2, 13 April 2012, pages 383–396]. Cell 155(5), pp. 1189. (10.1016/j.cell.2013.10.040)
• Perilli, S. et al. 2013. RETINOBLASTOMA-RELATED protein stimulates cell differentiation in the Arabidopsis root meristem by interacting with cytokinin signaling. The Plant Cell 25(11), pp. 4469-4478. (10.1105/tpc.113.116632)
• Hofhuis, H., Laskowski, M., Du, Y., Prasad, K., Grigg, S., Pinon, V. and Scheres, B. 2013. Phyllotaxis and rhizotaxis in Arabidopsis are modified by three PLETHORA transcription factors. Current Biology 23(11), pp. 956-962. (10.1016/j.cub.2013.04.048)
• McSteen, P., Scheres, B. and Zhao, Y. 2013. Auxin: special! [Preface]. Journal of Experimental Botany 64(9), pp. 2539-2540. (10.1093/jxb/ert167)
• van Berkel, K., de Boer, R. J., Scheres, B. and ten Tusscher, K. 2013. Polar auxin transport: models and mechanisms. Development 140(11), pp. 2253-2268. (10.1242/dev.079111)
• Zhang, H., Zhou, H., Berke, L., Heck, A. J. R., Mohammed, S., Scheres, B. and Menke, F. L. H. 2013. Quantitative phosphoproteomics after auxin-stimulated lateral root induction Identifies an SNX1 protein phosphorylation site required for growth. Molecular & Cellular Proteomics 12(5), pp. 1158-1169. (10.1074/mcp.M112.021220)
• Scheres, B. 2013. Rooting plant development. Development 140(5), pp. 939-941. (10.1242/dev.093559)
• Kakar, K., Zhang, H., Scheres, B. and Dhonukshe, P. 2013. RETRACTED: CLASP-mediated cortical microtubule organization guides PIN polarization axis [Letter]. Nature 495(7442), pp. 529-533. (10.1038/nature11980)
• Pinon, V., Prasad, K., Grigg, S. P., Sanchez-Perez, G. F. and Scheres, B. 2013. Local auxin biosynthesis regulation by PLETHORA transcription factors controls phyllotaxis in Arabidopsis. Proceedings of the National Academy of Sciences of the United States of America 110(3), pp. 1107-1112. (10.1073/pnas.1213497110)
• Scheres, B. 2013. Integrated molecular circuits for stem cell activity in Arabidopsis roots. In: Capasso, V. et al. eds. Pattern Formation in Morphogenesis: Problems and Mathematical Issues. Springer Proceedings in Mathematics Vol. 15. Berlin: Springer, pp. 37-39., (10.1007/978-3-642-20164-6_5)

2012

• Dello Ioio, R. et al. 2012. A PHABULOSA/cytokinin feedback loop controls root growth in Arabidopsis. Current Biology 22(18), pp. 1699-1704. (10.1016/j.cub.2012.07.005)
• Sassi, M. et al. 2012. COP1 mediates the coordination of root and shoot growth by light through modulation of PIN1-and PIN2-dependent auxin transport in Arabidopsis. Development 139(18), pp. 3402-3412. (10.1242/dev.078212)
• Cruz-Ramirez, A. et al. 2012. A bistable circuit involving SCARECROW-RETINOBLASTOMA integrates cues to inform asymmetric stem cell division. Cell 150(5), pp. 1002-1015. (10.1016/j.cell.2012.07.017)
• Lin, D. et al. 2012. A ROP GTPase-dependent auxin signaling pathway regulates the subcellular distribution of PIN2 in Arabidopsis roots. Current Biology 22(14), pp. 1319-1325. (10.1016/j.cub.2012.05.019)
• Grieneisen, V. A., Scheres, B., Hogeweg, P. and Maree, A. F. M. 2012. Morphogengineering roots: comparing mechanisms of morphogen gradient formation. BMC Systems Biology 6, pp. -., article number: 37. (10.1186/1752-0509-6-37)
• Dhonukshe, P. et al. 2012. A PLETHORA-auxin transcription module controls cell division plane rotation through MAP65 and CLASP [Retracted article. See vol. 155, pg. 1189, 2013]. Cell 149(2), pp. 383-396. (10.1016/j.cell.2012.02.051)
• Nagawa, S. et al. 2012. ROP GTPase-dependent actin microfilaments promote PIN1 polarization by localized inhibition of clathrin-dependent endocytosis. PLoS Biology 10(4), article number: e1001299. (10.1371/journal.pbio.1001299)
• Magyar, Z. et al. 2012. Arabidopsis E2FA stimulates proliferation and endocycle separately through RBR-bound and RBR-free complexes. EMBO Journal 31(6), pp. 1480-1493. (10.1038/emboj.2012.13)

2011

• Vatén, A. et al. 2011. Callose biosynthesis regulates symplastic trafficking during root development. Developmental Cell 21(6), pp. 1144-1155. (10.1016/j.devcel.2011.10.006)
• ten Tusscher, K. and Scheres, B. 2011. Joining forces: feedback and integration in plant development. Current Opinion in Genetics & Development 21(6), pp. 799-805. (10.1016/j.gde.2011.09.008)
• Prasad, K. et al. 2011. Arabidopsis PLETHORA transcription factors control phyllotaxis. Current Biology 21(13), pp. 1123-1128. (10.1016/j.cub.2011.05.009)
• Wachsman, G., Heidstra, R. and Scheres, B. 2011. Distinct cell-autonomous functions of RETINOBLASTOMA-RELATED in Arabidopsis stem cells revealed by the Brother of Brainbow clonal analysis system. The Plant Cell 23(7), pp. 2581-2591. (10.1105/tpc.111.086199)
• Bishopp, A. et al. 2011. Phloem-transported cytokinin regulates polar auxin transport and maintains vascular pattern in the root meristem. Current Biology 21(11), pp. 927-932. (10.1016/j.cub.2011.04.049)
• Bishopp, A. et al. 2011. A mutually inhibitory interaction between auxin and cytokinin specifies vascular pattern in roots. Current Biology 21(11), pp. 917-926. (10.1016/j.cub.2011.04.017)
• Li, H. et al. 2011. Phosphorylation switch modulates the interdigitated pattern of PIN1 localization and cell expansion in Arabidopsis leaf epidermis. Cell Research 21(6), pp. 970-978. (10.1038/cr.2011.49)
• Mokry, M., Nijman, I. J., van Dijken, A., Benjamins, R., Heidstra, R., Scheres, B. and Cuppen, E. 2011. Identification of factors required for meristem function in Arabidopsis using a novel next generation sequencing fast forward genetics approach. BMC Genomics 12, article number: 256. (10.1186/1471-2164-12-256)
• ten Hove, C. A. et al. 2011. Probing the roles of LRR RLK genes in Arabidopsis thaliana roots using a custom T-DNA insertion set. Plant Molecular Biology 76(1-2), pp. 69-83. (10.1007/s11103-011-9769-x)

2010

• Baskin, T. I. et al. 2010. Shootward and rootward: peak terminology for plant polarity. Trends in Plant Science 15(11), pp. 593-594. (10.1016/j.tplants.2010.08.006)
• Dhonukshe, P. et al. 2010. Plasma membrane-bound AGC3 kinases phosphorylate PIN auxin carriers at TPRXS(N/S) motifs to direct apical PIN recycling. Development 137(19), pp. 3245-3255. (10.1242/dev.052456)
• Scheres, B. 2010. Developmental biology: roots respond to an inner calling. Nature 465(7296), pp. 299-300. (10.1038/465299a)
• Bennett, T. and Scheres, B. 2010. Root development - two meristems for the price of one?. In: Timmermans, M. C. P. ed. Plant Development. Current Topics in Developmental Biology Vol. 91. Amsterdam: Academic Press, pp. 67-102., (10.1016/S0070-2153(10)91003-X)
• ten Hove, C. A., Willemsen, V., de Vries, W. J., van Dijken, A., Scheres, B. and Heidstra, R. 2010. SCHIZORIZA encodes a nuclear factor regulating asymmetry of stem cell divisions in the Arabidopsis root. Current Biology 20(5), pp. 452-457. (10.1016/j.cub.2010.01.018)
• Hassan, H., Scheres, B. and Blilou, I. 2010. JACKDAW controls epidermal patterning in the Arabidopsis root meristem through a non-cell-autonomous mechanism. Development 137(9), pp. 1523-1529. (10.1242/dev.048777)

2009

• Grieneisen, V. A. and Scheres, B. 2009. Back to the future: evolution of computational models in plant morphogenesis. Current Opinion in Plant Biology 12(5), pp. 606-614. (10.1016/j.pbi.2009.07.008)
• Menke, F. L. H. and Scheres, B. 2009. Plant asymmetric cell division, vive la difference!. Cell 137(7), pp. 1189-1192. (10.1016/j.cell.2009.06.007)
• Thomann, A. et al. 2009. Arabidopsis CULLIN3 Genes regulate primary root growth and patterning by ethylene-dependent and -independent mechanisms. Plos Genetics 5(1), article number: e1000328. (10.1371/journal.pgen.1000328)
• Tromas, A. et al. 2009. The AUXIN BINDING PROTEIN 1 is required for differential auxin responses mediating root growth. PLoS ONE 4(9), article number: e6648. (10.1371/journal.pone.0006648)

2008

• Laskowski, M., Grieneisen, V. A., Hofhuis, H., ten Hove, C. A., Hogeweg, P., Maree, A. F. M. and Scheres, B. 2008. Root system architecture from coupling cell shape to auxin transport. PLoS Biology 6(12), pp. 2721-2735., article number: e307. (10.1371/journal.pbio.0060307)
• Willemsen, V. et al. 2008. The NAC domain transcription factors FEZ and SOMBRERO control the orientation of cell division plane in Arabidopsis root stem cells. Developmental Cell 15(6), pp. 913-922. (10.1016/j.devcel.2008.09.019)
• Dhonukshe, P. et al. 2008. Generation of cell polarity in plants links endocytosis, auxin distribution and cell fate decisions [Letter]. Nature 456(7224), pp. 962-U75. (10.1038/nature07409)
• Benjamins, R. and Scheres, B. 2008. Auxin: the looping star in plant development. Annual Review of Plant Biology 59, pp. 443-465. (10.1146/annurev.arplant.58.032806.103805)
• Perez-Perez, J. M. et al. 2008. Specialization of CDC27 function in the Arabidopsis thaliana anaphase-promoting complex (APC/C). Plant Journal 53(1), pp. 78-89. (10.1111/j.1365-313X.2007.03312.x)
• Kornet, N. and Scheres, B. 2008. Stem cell factors in plants: chromatin connections. Presented at: Cold Spring Harbor Symposium on Quantitative Biology, New York, 2008 Presented at Stillman, B., Stewart, D. J. and Grodzicker, T. eds.Control and Regulation of Stem Cells, Vol. 73. Cold Spring Harbor Symposia on Quantitative Biology Vol. 73. Woodbury, NY: Cold Spring Harbor Laboratory Press pp. 235-242., (10.1101/sqb.2008.73.043)