Additional materials of the author at
CSHL Institutional Repository

Ciren, Danielle, Zebell, Sophia , Lippman, Zachary B (2024) Extreme restructuring of cis-regulatory regions controlling a deeply conserved plant stem cell regulator. Hake, Sarah (Ed.). PLoS Genetics, 20(3) pp. e1011174.

Satterlee, James W, Alonso, David, Gramazio, Pietro, Jenike, Katharine M, He, Jia, Arrones, Andrea, Villanueva, Gloria, Plazas, Mariola, Ramakrishnan, Srividya, Benoit, Matthias, Gentile, Iacopo, Hendelman, Anat, Shohat, Hagai, Fitzgerald, Blaine, Robitaille, Gina M, Green, Yumi, Swartwood, Kerry, Passalacqua, Michael J, Gagnon, Edeline, Hilgenhof, Rebecca, Huggins, Trevis D, Eizenga, Georgia C, Gur, Amit, Rutten, Twan, Stein, Nils, Yao, Shengrui, Bellot, Clement, Bendahmane, Mohammed, Frary, Amy, Knapp, Sandra, Särkinen, Tiina, Gillis, Jesse, Van Eck, Joyce, Schatz, Michael C, Eshed, Yuval, Prohens, Jaime, Vilanova, Santiago , Lippman, Zachary B (2024) Convergent evolution of plant prickles is driven by repeated gene co-option over deep time. bioRxiv,

Ciren, Danielle, Zebell, Sophia , Lippman, Zachary B (2023) Extreme restructuring of cis-regulatory regions controlling a deeply conserved plant stem cell regulator. bioRxiv,

Aguirre, Lyndsey, Hendelman, Anat, Hutton, Samuel F, McCandlish, David M , Lippman, Zachary B (2023) Idiosyncratic and dose-dependent epistasis drives variation in tomato fruit size. Science, 382(6668) pp. 315-320.

Alonge, Michael, Lebeigle, Ludivine, Kirsche, Melanie, Jenike, Katie, Ou, Shujun, Aganezov, Sergey, Wang, Xingang, Lippman, Zachary B, Schatz, Michael C , Soyk, Sebastian (2022) Automated assembly scaffolding using RagTag elevates a new tomato system for high-throughput genome editing. Genome Biology, 23(1) pp. 258.

He, Jia, Alonge, Michael, Ramakrishnan, Srividya, Benoit, Matthias, Soyk, Sebastian, Reem, Nathan T, Hendelman, Anat, Van Eck, Joyce, Schatz, Michael C , Lippman, Zachary B (2022) Establishing Physalis as a Solanaceae model system enables genetic reevaluation of the inflated calyx syndrome. The Plant Cell, 35(1) pp. 351-368.

Kang, Min-Sung, Kim, Yong Jun, Heo, Jung, Rajendran, Sujeevan, Wang, Xingang, Bae, Jong Hyang, Lippman, Zachary , Park, Soon Ju (2022) Newly Discovered Alleles of the Tomato Antiflorigen Gene SELF PRUNING Provide a Range of Plant Compactness and Yield. International Journal of Molecular Sciences, 23(13) pp. 7149-7149.

Kim, Youngin, Kim, Geon Woo, Han, Koeun, Lee, Hea-Young, Jo, Jinkwan, Kwon, Jin-Kyung, Lemmon, Zachary, Lippman, Zachary , Kang, Byoung-Cheorl (2022) Identification of Genetic Factors Controlling the Formation of Multiple Flowers Per Node in Pepper (Capsicum spp.). Frontiers in Plant Science, 13 pp. 884338.

Kwon, Choon-Tak, Tang, Lingli, Wang, Xingang, Gentile, Iacopo, Hendelman, Anat, Robitaille, Gina, Van Eck, Joyce, Xu, Cao , Lippman, Zachary B (2022) Dynamic evolution of small signalling peptide compensation in plant stem cell control. Nature Plants,

He, Jia, Alonge, Michael, Ramakrishnan, Srividya, Benoit, Matthias, Soyk, Sebastian, Reem, Nathan, Hendelman, Anat, Eck, Joyce Van, Schatz, Michael , Lippman, Zachary (2022) Establishing Physalisas a new Solanaceae model system enables genetic reevaluation of the inflated calyx syndrome. bioRxiv,

Kwon, Choon-Tak, Tang, Lingli, Wang, Xingang, Gentile, Iacopo, Hendelman, Anat, Robitaille, Gina, Van Eck, Joyce, Xu, Cao , Lippman, Zachary (2022) Dynamic evolution of small signaling peptide compensation in plant stem cell control. bioRxiv,

Alonge, Michael, Lebeigle, Ludivine, Kirsche, Melanie, Aganezov, Sergey, Wang, Xingang, Lippman, Zachary, Schatz, Michael , Soyk, Sebastian (2021) Automated assembly scaffolding elevates a new tomato system for high-throughput genome editing. BioRxiv,

Ranallo-Benavidez, T Rhyker, Lemmon, Zachary, Soyk, Sebastian, Aganezov, Sergey, Salerno, William J, McCoy, Rajiv C, Lippman, Zachary B, Schatz, Michael C , Sedlazeck, Fritz J (2021) Optimized sample selection for cost-efficient long-read population sequencing.. Genome Research, 31(5) pp. 910-918.

Hendelman, Anat, Zebell, Sophia, Rodriguez-Leal, Daniel, Dukler, Noah, Robitaille, Gina, Wu, Xuelin, Kostyun, Jamie, Tal, Lior, Wang, Peipei, Bartlett, Madelaine E, Eshed, Yuval, Efroni, Idan , Lippman, Zachary B (2021) Conserved pleiotropy of an ancient plant homeobox gene uncovered by cis-regulatory dissection.. Cell, 184(7) pp. 1724-1739.e16.

Wang, Xingang, Aguirre, Lyndsey, Rodríguez-Leal, Daniel, Hendelman, Anat, Benoit, Matthias , Lippman, Zachary B (2021) Dissecting cis-regulatory control of quantitative trait variation in a plant stem cell circuit.. Nature Plants, 7(4) pp. 419-427.

Soyk, S., Benoit, M. , Lippman, Z. B. (2020) New Horizons for Dissecting Epistasis in Crop Quantitative Trait Variation. Annu Rev Genet, 54 pp. 287-307.

Shenstone, E., Lippman, Z. , Van Eck, J. (2020) A review of nutritional properties and health benefits of Physalis species. Plant Foods Hum Nutr, 75(3) pp. 316-325.

Ranallo-Benavidez, Rhyker, Lemmon, Zachary, Soyk, Sebastian, Aganezov, Sergey, Salerno, William, McCoy, Rajiv, Lippman, Zachary, Schatz, Michael , Sedlazeck, Fritz (2020) SVCollector: Optimized sample selection for cost-efficient long-read population sequencing. BioRxiv,

Alonge, M., Wang, X., Benoit, M., Soyk, S., Pereira, L., Zhang, L., Suresh, H., Ramakrishnan, S., Maumus, F., Ciren, D., Levy, Y., Harel, T. H., Shalev-Schlosser, G., Amsellem, Z., Razifard, H., Caicedo, A. L., Tieman, D. M., Klee, H., Kirsche, M., Aganezov, S., Ranallo-Benavidez, T. R., Lemmon, Z. H., Kim, J., Robitaille, G., Kramer, M., Goodwin, S., McCombie, W. R., Hutton, S., Van Eck, J., Gillis, J., Eshed, Y., Sedlazeck, F. J., van der Knaap, E., Schatz, M. C. , Lippman, Z. B. (2020) Major Impacts of Widespread Structural Variation on Gene Expression and Crop Improvement in Tomato. Cell, 182(1) pp. 145-161.e23.

Kwon, C. T., Heo, J., Lemmon, Z. H., Capua, Y., Hutton, S. F., Van Eck, J., Park, S. J. , Lippman, Z. B. (2019) Rapid customization of Solanaceae fruit crops for urban agriculture. Nat Biotechnol, 38 pp. 182-188.

Alonge, M., Soyk, S., Ramakrishnan, S., Wang, X., Goodwin, S., Sedlazeck, F. J., Lippman, Z. B. , Schatz, M. C. (2019) RaGOO: fast and accurate reference-guided scaffolding of draft genomes. Genome Biol, 20(1) pp. 224.

Eshed, Y. , Lippman, Z. B. (2019) Revolutions in agriculture chart a course for targeted breeding of old and new crops. Science, 366(6466)

Soyk, S., Lemmon, Z. H., Sedlazeck, F. J., Jimenez-Gomez, J. M., Alonge, M., Hutton, S. F., Van Eck, J., Schatz, M. C. , Lippman, Z. B. (2019) Author Correction: Duplication of a domestication locus neutralized a cryptic variant that caused a breeding barrier in tomato. Nat Plants,

Soyk, S., Lemmon, Z. H., Sedlazeck, F. J., Jimenez-Gomez, J. M., Alonge, M., Hutton, S. F., Van Eck, J., Schatz, M. C. , Lippman, Z. B. (2019) Duplication of a domestication locus neutralized a cryptic variant that caused a breeding barrier in tomato. Nat Plants, 5(5) pp. 471-497.

Rodriguez-Leal, D., Xu, C., Kwon, C. T., Soyars, C., Demesa-Arevalo, E., Man, J., Liu, L., Lemmon, Z. H., Jones, D. S., Van Eck, J., Jackson, D. P., Bartlett, M. E., Nimchuk, Z. L. , Lippman, Z. B. (2019) Evolution of buffering in a genetic circuit controlling plant stem cell proliferation. Nat Genet, 51(5) pp. 786-792.

Lemmon, Z. H., Reem, N. T., Dalrymple, J., Soyk, S., Swartwood, K. E., Rodriguez-Leal, D., Van Eck, J. , Lippman, Z. B. (2018) Rapid improvement of domestication traits in an orphan crop by genome editing. Nature Plants, 4(10) pp. 766-770.

Huang, Xiaozhen, Tang, Lingli, Yu, Yuan, Dalrymple, Justin, Lippman, Zachary B. , Xu, Cao (2018) Control of flowering and inflorescence architecture in tomato by synergistic interactions between ALOG transcription factors. Journal of Genetics and Genomics, 45(10) pp. 557-560.

Rodríguez-Leal, Daniel, Lemmon, Zachary H., Man, Jarrett, Bartlett, Madelaine E. , Lippman, Zachary B. (2017) Engineering Quantitative Trait Variation for Crop Improvement by Genome Editing. Cell, 171(2) pp. 470-80.

Soyk, Sebastian, Lemmon, Zachary H., Oved, Matan, Fisher, Josef, Liberatore, Katie L., Park, Soon Ju, Goren, Anna, Jiang, Ke, Ramos, Alexis, van der Knaap, Esther, Van Eck, Joyce, Zamir, Dani, Eshed, Yuval , Lippman, Zachary B. (2017) Bypassing Negative Epistasis on Yield in Tomato Imposed by a Domestication Gene. Cell, 169(6) pp. 1142-1155.

Van Eck, J., Swartwood, K., Lemmon, Z. H., Dalrymple, J. , Lippman, Z. B. (2017) Development of Agrobacterium-mediated Transformation of Physalis peruviana and Application of CRISPR/Cas9 Genome Editing. In Vitro Cellular & Developmental Biology-Animal, 53(Supple) pp. S34-S35.

Soyk, S., Muller, N. A., Park, S. J., Schmalenbach, I., Jiang, K., Hayama, R., Zhang, L., Van Eck, J., Jimenez-Gomez, J. M. , Lippman, Z. B. (2017) Variation in the flowering gene SELF PRUNING 5G promotes day-neutrality and early yield in tomato. Nat Genet, 49(1) pp. 162-168.

Lemmon, Z. H., Park, S. J., Jiang, K., Van Eck, J., Schatz, M. C. , Lippman, Z. B. (2016) The evolution of inflorescence diversity in the nightshades and heterochrony during meristem maturation. Genome Res, 26(12) pp. 1676-1686.

Xu, C., Park, S. J., Van Eck, J. , Lippman, Z. B. (2016) Control of inflorescence architecture in tomato by BTB/POZ transcriptional regulators. Genes Dev, 30(18) pp. 2048-2061.

MacAlister, C. A., Ortiz-Ramirez, C., Becker, J. D., Feijo, J. A. , Lippman, Z. B. (2016) Hydroxyproline O-arabinosyltransferase mutants oppositely alter tip growth in Arabidopsis thaliana and Physcomitrella patens. Plant J, 85(2) pp. 193-208.

Xu, C., Liberatore, K. L., MacAlister, C. A., Huang, Z., Chu, Y. H., Jiang, K., Brooks, C., Ogawa-Ohnishi, M., Xiong, G., Pauly, M., Van Eck, J., Matsubayashi, Y., van der Knaap, E. , Lippman, Z. B. (2015) A cascade of arabinosyltransferases controls shoot meristem size in tomato. Nat Genet, 47(7) pp. 784-792.

Park, S. J., Jiang, K., Tal, L., Yichie, Y., Gar, O., Zamir, D., Eshed, Y. , Lippman, Z. B. (2014) Optimization of crop productivity in tomato using induced mutations in the florigen pathway. Nature Genetics, 46(12) pp. 1337-1342.

Brooks, C., Nekrasov, V., Lippman, Z. , Van Eck, J. (2014) Efficient gene editing in tomato in the first generation using the CRISPR/Cas9 system. Plant Physiology, 166(3) pp. 1292-1297.

Park, Soon Ju, Eshed, Yuval , Lippman, Zachary B. (2014) Meristem maturation and inflorescence architecture-lessons from the Solanaceae. Current Opinion in Plant Biology, 17 pp. 70-77.

Jiang, K., Liberatore, K. L., Park, S. J., Alvarez, J. P. , Lippman, Z. B. (2013) Tomato yield heterosis is triggered by a dosage sensitivity of the florigen pathway that fine-tunes shoot architecture. PLoS Genetics, 9(12) pp. e1004043.

Macalister, C. A., Park, S. J., Jiang, K., Marcel, F., Bendahmane, A., Izkovich, Y., Eshed, Y. , Lippman, Z. B. (2012) Synchronization of the flowering transition by the tomato TERMINATING FLOWER gene. Nat Genet,

The Tomato Genome Consortium, (2012) The tomato genome sequence provides insights into fleshy fruit evolution. Nature, 485(7400) pp. 635-41.

Park, S. J., Jiang, K., Schatz, M. C. , Lippman, Z. B. (2012) Rate of meristem maturation determines inflorescence architecture in tomato. Proceedings of the National Academy of Sciences of the United States of America, 109(2) pp. 639-44.

Krieger, U., Lippman, Z. B. , Zamir, D. (2010) The flowering gene SINGLE FLOWER TRUSS drives heterosis for yield in tomato. Nature Genetics, 42(5) pp. 459-463.

Lippman, Z. B., Cohen, O., Alvarez, J. P., Abu-Abied, M., Pekker, I., Paran, I., Eshed, Y. , Zamir, D. (2008) The Making of a Compound Inflorescence in Tomato and Related Nightshades. PLoS Biology, 6(11) pp. e288.

Vaughn, M. W., Tanurdzic, M., Lippman, Z. B., Jiang, H., Carrasquillo, R., Rabinowicz, P. D., Dedhia, N., McCombie, W. R., Agier, N., Bulski, A., Colot, V., Doerge, R. W. , Martienssen, R. A. (2007) Epigenetic natural variation in Arabidopsis thaliana. PLoS Biology, 5(7) pp. 1617-1629.

Martienssen, R., Zaratiegui, M., Irvine, D., Goto, D., Slotkin, K., Tanurdzic, M., Lippman, Z., Vaughn, M., May, B., Cande, Z., Colot, V. , Doerge, R. W. (2007) Silent running: RNA interference and heterochromatic modification. Chromosome Research, 15(2 (Sup) pp. 20-21.

May, B. P., Lippman, Z. B., Fang, Y., Spector, D. L. , Martienssen, R. A. (2005) Differential regulation of strand-specific transcripts from Arabidopsis centromeric satellite repeats. PLoS Genet, 1(6) pp. e79.

Gendrel, A. V., Lippman, Z., Martienssen, R. , Colot, V. (2005) Profiling histone modification patterns in plants using genomic tiling microarrays. Nature Methods, 2(3) pp. 213-218.

Lippman, Z. B., Gendrel, A. V., Colot, V. , Martienssen, R. A. (2005) Profiling DNA methylation patterns using genomic tiling microarrays. Nat Methods, 2(3) pp. 219-24.

Lippman, Z. , Martienssen, R. A. (2004) The role of RNA interference in heterochromatic silencing. Nature, 431(7006) pp. 364-70.

Jeffrey Chen, Z., Wang, J., Tian, L., Lee, H. S., Wang, J. J., Chen, M., Lee, J. J., Josefsson, C., Madlung, A., Watson, B., Lippman, Z., Vaughn, M., Chris Pires, J., Colot, V., Doerge, R. W., Martienssen, R. A., Comai, L. , Osborn, T. C. (2004) The development of an Arabidopsis model system for genome-wide analysis of polyploidy effects. Biological journal of the Linnean Society. Linnean Society of London, 82(4) pp. 689-700.

Lippman, Z., Gendrel, A. V., Black, M., Vaughn, M. W., Dedhia, N., McCombie, W. R., Lavine, K., Mittal, V., May, B., Kasschau, K. D., Carrington, J. C., Doerge, R. W., Colot, V. , Martienssen, R. (2004) Role of transposable elements in heterochromatin and epigenetic control. Nature, 430(6998) pp. 471-6.

Martienssen, R., Lippman, Z., May, B., Vaughn, M., Gendrel, A. V., Ronemus, M., Volpe, T., Kidner, C. , Colot, V. (2004) Transposons, small interfering RNA and the origin of heterochromatin. European Journal of Cell Biology, 83(Suppl) pp. 61-61.

Bastow, R., Mylne, J. S., Lister, C., Lippman, Z., Martienssen, R. A. , Dean, C. (2004) Vernalization requires epigenetic silencing of FLC by histone methylation. Nature, 427(6970) pp. 164-7.

Martienssen, R., Lippman, Z., May, B., Ronemus, M. , Vaughn, M. (2004) Transposons, tandem repeats, and the silencing of imprinted genes. Cold Spring Harbor symposia on quantitative biology, 69 pp. 371-9.

Lippman, Z., May, B., Yordan, C., Singer, T. , Martienssen, R. (2003) Distinct mechanisms determine transposon inheritance and methylation via small interfering RNA and histone modification. PLoS biology, 1(3) pp. 420-428.

Gendrel, A. V., Lippman, Z., Yordan, C., Colot, V. , Martienssen, R. A. (2002) Dependence of heterochromatic histone H3 methylation patterns on the Arabidopsis gene DDM1. Science, 297(5588) pp. 1871-1873.

van der Knaap, E., Lippman, Z. B. , Tanksley, S. D. (2002) Extremely elongated tomato fruit controlled by four quantitative trait loci with epistatic interactions. Theoretical and Applied Genetics, 104(2-3) pp. 241-247.