Ciren, Danielle, Zebell, Sophia, Lippman, Zachary B (March 2024) Extreme restructuring of cis-regulatory regions controlling a deeply conserved plant stem cell regulator. PLoS Genetics, 20 (3). e1011174. ISSN 1553-7390
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 (February 2024) Convergent evolution of plant prickles is driven by repeated gene co-option over deep time. bioRxiv. (Submitted)
Ciren, Danielle, Zebell, Sophia, Lippman, Zachary B (December 2023) Extreme restructuring of cis-regulatory regions controlling a deeply conserved plant stem cell regulator. bioRxiv. (Submitted)
Aguirre, Lyndsey, Hendelman, Anat, Hutton, Samuel F, McCandlish, David M, Lippman, Zachary B (October 2023) Idiosyncratic and dose-dependent epistasis drives variation in tomato fruit size. Science, 382 (6668). pp. 315-320. ISSN 0036-8075
Alonge, Michael, Lebeigle, Ludivine, Kirsche, Melanie, Jenike, Katie, Ou, Shujun, Aganezov, Sergey, Wang, Xingang, Lippman, Zachary B, Schatz, Michael C, Soyk, Sebastian (December 2022) Automated assembly scaffolding using RagTag elevates a new tomato system for high-throughput genome editing. Genome Biology, 23 (1). p. 258. ISSN 1474-7596
He, Jia, Alonge, Michael, Ramakrishnan, Srividya, Benoit, Matthias, Soyk, Sebastian, Reem, Nathan T, Hendelman, Anat, Van Eck, Joyce, Schatz, Michael C, Lippman, Zachary B (October 2022) Establishing Physalis as a Solanaceae model system enables genetic reevaluation of the inflated calyx syndrome. The Plant Cell, 35 (1). pp. 351-368. ISSN 1532-298X
Kang, Min-Sung, Kim, Yong Jun, Heo, Jung, Rajendran, Sujeevan, Wang, Xingang, Bae, Jong Hyang, Lippman, Zachary, Park, Soon Ju (June 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). p. 7149. ISSN 1661-6596
Kim, Youngin, Kim, Geon Woo, Han, Koeun, Lee, Hea-Young, Jo, Jinkwan, Kwon, Jin-Kyung, Lemmon, Zachary, Lippman, Zachary, Kang, Byoung-Cheorl (May 2022) Identification of Genetic Factors Controlling the Formation of Multiple Flowers Per Node in Pepper (Capsicum spp.). Frontiers in Plant Science, 13. p. 884338. ISSN 1664-462X
Kwon, Choon-Tak, Tang, Lingli, Wang, Xingang, Gentile, Iacopo, Hendelman, Anat, Robitaille, Gina, Van Eck, Joyce, Xu, Cao, Lippman, Zachary B (March 2022) Dynamic evolution of small signalling peptide compensation in plant stem cell control. Nature Plants. ISSN 2055-0278
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. (Submitted)
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. (Submitted)
Alonge, Michael, Lebeigle, Ludivine, Kirsche, Melanie, Aganezov, Sergey, Wang, Xingang, Lippman, Zachary, Schatz, Michael, Soyk, Sebastian (November 2021) Automated assembly scaffolding elevates a new tomato system for high-throughput genome editing. BioRxiv. (Unpublished)
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 (May 2021) Optimized sample selection for cost-efficient long-read population sequencing. Genome Research, 31 (5). pp. 910-918. ISSN 1088-9051
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 (April 2021) Conserved pleiotropy of an ancient plant homeobox gene uncovered by cis-regulatory dissection. Cell, 184 (7). 1724-1739.e16. ISSN 0092-8674
Wang, Xingang, Aguirre, Lyndsey, Rodríguez-Leal, Daniel, Hendelman, Anat, Benoit, Matthias, Lippman, Zachary B (April 2021) Dissecting cis-regulatory control of quantitative trait variation in a plant stem cell circuit. Nature Plants, 7 (4). pp. 419-427. ISSN 2055-026X
Soyk, S., Benoit, M., Lippman, Z. B. (September 2020) New Horizons for Dissecting Epistasis in Crop Quantitative Trait Variation. Annu Rev Genet, 54. pp. 287-307. ISSN 0066-4197
Shenstone, E., Lippman, Z., Van Eck, J. (September 2020) A review of nutritional properties and health benefits of Physalis species. Plant Foods Hum Nutr, 75 (3). pp. 316-325. ISSN 0921-9668
Ranallo-Benavidez, Rhyker, Lemmon, Zachary, Soyk, Sebastian, Aganezov, Sergey, Salerno, William, McCoy, Rajiv, Lippman, Zachary, Schatz, Michael, Sedlazeck, Fritz (August 2020) SVCollector: Optimized sample selection for cost-efficient long-read population sequencing. BioRxiv. (Unpublished)
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. (July 2020) Major Impacts of Widespread Structural Variation on Gene Expression and Crop Improvement in Tomato. Cell, 182 (1). 145-161.e23. ISSN 0092-8674 (Print)0092-8674
Kwon, C. T., Heo, J., Lemmon, Z. H., Capua, Y., Hutton, S. F., Van Eck, J., Park, S. J., Lippman, Z. B. (December 2019) Rapid customization of Solanaceae fruit crops for urban agriculture. Nat Biotechnol, 38. pp. 182-188. ISSN 1087-0156
Alonge, M., Soyk, S., Ramakrishnan, S., Wang, X., Goodwin, S., Sedlazeck, F. J., Lippman, Z. B., Schatz, M. C. (October 2019) RaGOO: fast and accurate reference-guided scaffolding of draft genomes. Genome Biol, 20 (1). p. 224. ISSN 1474-7596 (Public Dataset)
Eshed, Y., Lippman, Z. B. (September 2019) Revolutions in agriculture chart a course for targeted breeding of old and new crops. Science, 366 (6466). ISSN 0036-8075
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. (July 2019) Author Correction: Duplication of a domestication locus neutralized a cryptic variant that caused a breeding barrier in tomato. Nat Plants. ISSN 2055-0278
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. (May 2019) Duplication of a domestication locus neutralized a cryptic variant that caused a breeding barrier in tomato. Nat Plants, 5 (5). pp. 471-497. ISSN 2055-0278
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. (April 2019) Evolution of buffering in a genetic circuit controlling plant stem cell proliferation. Nat Genet, 51 (5). pp. 786-792. ISSN 1061-4036
Lemmon, Z. H., Reem, N. T., Dalrymple, J., Soyk, S., Swartwood, K. E., Rodriguez-Leal, D., Van Eck, J., Lippman, Z. B. (October 2018) Rapid improvement of domestication traits in an orphan crop by genome editing. Nature Plants, 4 (10). pp. 766-770. ISSN 20550278 (ISSN)
Huang, Xiaozhen, Tang, Lingli, Yu, Yuan, Dalrymple, Justin, Lippman, Zachary B., Xu, Cao (May 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. ISSN 1673-8527
Rodríguez-Leal, Daniel, Lemmon, Zachary H., Man, Jarrett, Bartlett, Madelaine E., Lippman, Zachary B. (October 2017) Engineering Quantitative Trait Variation for Crop Improvement by Genome Editing. Cell, 171 (2). pp. 470-80. ISSN 0092-8674
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. (June 2017) Bypassing Negative Epistasis on Yield in Tomato Imposed by a Domestication Gene. Cell, 169 (6). pp. 1142-1155. ISSN 0092-8674
Van Eck, J., Swartwood, K., Lemmon, Z. H., Dalrymple, J., Lippman, Z. B. (June 2017) Development of Agrobacterium-mediated Transformation of Physalis peruviana and Application of CRISPR/Cas9 Genome Editing. In Vitro Cellular & Developmental Biology-Animal, 53 (Supple). S34-S35. ISSN 1071-2690
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. (January 2017) Variation in the flowering gene SELF PRUNING 5G promotes day-neutrality and early yield in tomato. Nat Genet, 49 (1). pp. 162-168. ISSN 1546-1718 (Electronic)1061-4036 (Linking) (Public Dataset)
Lemmon, Z. H., Park, S. J., Jiang, K., Van Eck, J., Schatz, M. C., Lippman, Z. B. (November 2016) The evolution of inflorescence diversity in the nightshades and heterochrony during meristem maturation. Genome Res, 26 (12). pp. 1676-1686. ISSN 1549-5469 (Electronic)1088-9051 (Linking) (Public Dataset)
Xu, C., Park, S. J., Van Eck, J., Lippman, Z. B. (September 2016) Control of inflorescence architecture in tomato by BTB/POZ transcriptional regulators. Genes Dev, 30 (18). pp. 2048-2061. ISSN 0890-9369 (Print)0890-9369 (Linking)
MacAlister, C. A., Ortiz-Ramirez, C., Becker, J. D., Feijo, J. A., Lippman, Z. B. (January 2016) Hydroxyproline O-arabinosyltransferase mutants oppositely alter tip growth in Arabidopsis thaliana and Physcomitrella patens. Plant J, 85 (2). pp. 193-208. ISSN 1365-313X (Electronic)0960-7412 (Linking)
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. (July 2015) A cascade of arabinosyltransferases controls shoot meristem size in tomato. Nat Genet, 47 (7). pp. 784-792. ISSN 1546-1718 (Electronic)1061-4036 (Linking)
Park, S. J., Jiang, K., Tal, L., Yichie, Y., Gar, O., Zamir, D., Eshed, Y., Lippman, Z. B. (November 2014) Optimization of crop productivity in tomato using induced mutations in the florigen pathway. Nature Genetics, 46 (12). pp. 1337-1342. ISSN 1061-4036
Brooks, C., Nekrasov, V., Lippman, Z., Van Eck, J. (September 2014) Efficient gene editing in tomato in the first generation using the CRISPR/Cas9 system. Plant Physiology, 166 (3). pp. 1292-1297. ISSN 0032-0889
Park, Soon Ju, Eshed, Yuval, Lippman, Zachary B. (February 2014) Meristem maturation and inflorescence architecture-lessons from the Solanaceae. Current Opinion in Plant Biology, 17. pp. 70-77. ISSN 1369-5266
Jiang, K., Liberatore, K. L., Park, S. J., Alvarez, J. P., Lippman, Z. B. (December 2013) Tomato yield heterosis is triggered by a dosage sensitivity of the florigen pathway that fine-tunes shoot architecture. PLoS Genetics, 9 (12). e1004043. ISSN 1553-7390
Macalister, C. A., Park, S. J., Jiang, K., Marcel, F., Bendahmane, A., Izkovich, Y., Eshed, Y., Lippman, Z. B. (November 2012) Synchronization of the flowering transition by the tomato TERMINATING FLOWER gene. Nat Genet. ISSN 1546-1718 (Electronic)1061-4036 (Linking)
The Tomato Genome Consortium (May 2012) The tomato genome sequence provides insights into fleshy fruit evolution. Nature, 485 (7400). pp. 635-41. ISSN 1476-4687 (Electronic)0028-0836 (Linking)
Park, S. J., Jiang, K., Schatz, M. C., Lippman, Z. B. (January 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. ISSN 0027-8424
Krieger, U., Lippman, Z. B., Zamir, D. (March 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. (November 2008) The Making of a Compound Inflorescence in Tomato and Related Nightshades. PLoS Biology, 6 (11). 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. (July 2007) Epigenetic natural variation in Arabidopsis thaliana. PLoS Biology, 5 (7). pp. 1617-1629. ISSN 1544-9173
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. ISSN 0967-3849
May, B. P., Lippman, Z. B., Fang, Y., Spector, D. L., Martienssen, R. A. (December 2005) Differential regulation of strand-specific transcripts from Arabidopsis centromeric satellite repeats. PLoS Genet, 1 (6). e79. ISSN 1553-7404 (Electronic)
Lippman, Z. B., Gendrel, A. V., Colot, V., Martienssen, R. A. (March 2005) Profiling DNA methylation patterns using genomic tiling microarrays. Nat Methods, 2 (3). pp. 219-24. ISSN 1548-7091 (Print)
Gendrel, A. V., Lippman, Z. , Martienssen, R., Colot, V. (March 2005) Profiling histone modification patterns in plants using genomic tiling microarrays. Nature Methods, 2 (3). pp. 213-218. ISSN 1548-7091
Lippman, Z., Martienssen, R. A. (September 2004) The role of RNA interference in heterochromatic silencing. Nature, 431 (7006). pp. 364-70. ISSN 1476-4687 (Electronic)
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. (August 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. ISSN 0024-4066 (Print)0024-4066 (Linking)
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. (July 2004) Role of transposable elements in heterochromatin and epigenetic control. Nature, 430 (6998). pp. 471-6. ISSN 1476-4687 (Electronic)
Martienssen, R., Lippman, Z., May, B., Vaughn, M., Gendrel, A. V., Ronemus, M., Volpe, T., Kidner, C., Colot, V. (March 2004) Transposons, small interfering RNA and the origin of heterochromatin. European Journal of Cell Biology, 83 (Suppl). p. 61. ISSN 0171-9335
Bastow, R., Mylne, J. S., Lister, C., Lippman, Z., Martienssen, R. A., Dean, C. (January 2004) Vernalization requires epigenetic silencing of FLC by histone methylation. Nature, 427 (6970). pp. 164-7. ISSN 1476-4687 (Electronic)0028-0836 (Linking)
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. ISSN 0091-7451 (Print)0091-7451 (Linking)
Lippman, Z., May, B., Yordan, C., Singer, T., Martienssen, R. (December 2003) Distinct mechanisms determine transposon inheritance and methylation via small interfering RNA and histone modification. PLoS biology, 1 (3). pp. 420-428. ISSN 1545-7885 (Electronic)1544-9173 (Linking)
Gendrel, A. V., Lippman, Z., Yordan, C., Colot, V., Martienssen, R. A. (September 2002) Dependence of heterochromatic histone H3 methylation patterns on the Arabidopsis gene DDM1. Science, 297 (5588). pp. 1871-1873. ISSN 0036-8075
van der Knaap, E., Lippman, Z. B., Tanksley, S. D. (February 2002) Extremely elongated tomato fruit controlled by four quantitative trait loci with epistatic interactions. Theoretical and Applied Genetics, 104 (2-3). pp. 241-247. ISSN 0040-5752
Van Eck, Joyce, Reem, Nathan, Swartwood, Kerry, Shenstone, Esperanza, Williams, Brandon, Lippman, Zachary B (June 2019) Improvement of Goldenberry and Groundcherry by CRISPR: Ripening the Potential of Underutilized Fruit Crops. In: In Vitro Biology Meeting Abstract.
Van Eck, J, Brooks, C, Nekrasov, V, Lippman, Z (May 2015) Application of CRISPR/Cas9 Technology for Characterization of Developmental Genes in Tomato. In: In Vitro Biology Meeting.
Lippman, Z. B. (December 2004) Transposons, heterochromatin, and epigenetic landscapes in Arabidopsis thaliana. PhD thesis, Cold Spring Harbor Laboratory.
Lippman, Z. (November 2012) Talk from Zach Lippman at the Cold Spring Harbor Laboratory In-House Symposium (2012). [Video] (Unpublished)
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