Publications – Jim Giovannoni

Genetic and metabolic effects of ripening mutations and vine detachment on tomato fruit quality
2019.
Osorio, S., Carneiro, R.T., Lytovchenko, A., McQuinn, R., Sørensen, I., Vallarino, J.G., Giovannoni…
Plant Biotechnology Journal.
:
The tomato HIGH PIGMENT1/DAMAGED DNA BINDING PROTEIN 1 gene contributes to regulation of fruit ripening
2019.
Wang, A., Chen, D., Ma, Q., Rose, J.K.C., Fei, Zhangjun, Liu, Y., Giovannoni, James J.
Horticulture Research.
6
:
15
Plant Viruses Transmitted in Two Different Modes Produce Differing Effects on Small RNA-Mediated Processes in Their Aphid Vector
2019.
Pinheiro, P.V., Wilson, J.R., Xu, Y., Zheng, Y., Rebelo, A.R., Fattah-Hosseini, S., Kruse, A., Santo…
Phytobiomes.
3
:
71–81
Genome-wide association analysis identifies a natural variation in basic helix-loop-helix transcription factor regulating ascorbate biosynthesis via D-mannose/L-galactose pathway in tomato
2019.
Li, W., Ai, G., Li, C., Liu, G., Chen, W., Wang, B., Wang, W., Lu, Y., Zhang, J., Li, H., Ouyang, B.…
PLOS Genetics.
15
:
The tomato pan-genome uncovers new genes and a rare allele regulating fruit flavor
2019.
Gao, L., Gonda, I., Sun, H., Ma, Q., Bao, K., Tieman, D., Burzynski-Chang, E., Fish, T., Stromberg, …
Nature Genetics.
:
1546–1718
The Ptr1 locus of Solanum lycopersicoides confers resistance to race 1 strains of Pseudomonas syringae pv. tomato and to Ralstonia pseudosolanacearum by recognizing the type III effectors AvrRpt2/RipBN
2019.
Mazo-Molina, C., Mainiero, S., Hind, S.R., Kraus, C.M., Vachev, M., Maviane-Macia, F., Lindeberg, M…
Molecular Plant-Microbe Interactions.
:
Sequencing-Based Bin Map Construction of a Tomato Mapping Population, Facilitating High-Resolution Quantitative Trait Loci Detection
2018.
Gonda, I., Ashrafi, H., Lyon, D.A., Strickler, S.R., Hulse-Kemp, A.M., Ma, Q., Sun, H., Stoffel, K.,…
The Plant Genome.
12
:
Cucurbit Genomics Database (CuGenDB): a central portal for comparative and functional genomics of cucurbit crops
2018.
Zheng, Y., Wu, S., Bai, Y., Sun, H., Jiao, C., Guo, S., Zhao, K., Blanca, J., Zhang, Z., Huang, S., …
Nucleic Acids Research.
47
:
D1128–D1136
Natural genetic variation for expression of a SWEET transporter among wild species of Solanum lycopersicum (tomato) determines the hexose composition of ripening tomato fruit
2018.
Shammai, A., Petreikov, M., Yeselson, Y., Faigenboim, A., Moy‐Komemi, M., Cohen, S., Cohen, D., Be…
The Plant Journal.
96
:
343–357
HS-SPME-GC-MS Analyses of Volatiles in Plant Populations—Quantitating Compound × Individual Matrix Effects
2018.
Burzynski-Chang, E., Ryona, I., Reisch, B., Gonda, I., Foolad, M., Giovannoni, James, Sacks, G.
Molecules.
23
:
2436
Tomato Multiomics Reveals Consequences of Crop Domestication and Improvement
2018.
Giovannoni, James
Cell.
172
:
6–8
Genome encode analyses reveal the basis of convergent evolution of fleshy fruit ripening
2018.
Lü, P., Yu, S., Zhu, N., Chen, Y., Zhou, B., Pan, Y., Tzeng, D., Fabi, J.P., Argyris, J., Garcia-M…
Nature Plants.
4
:
784–791
MaMADS2 repression in banana fruits modifies hormone synthesis and signalling pathways prior to climacteric stage
2018.
Yakir, E., Fei, Zhangjun, Sela, N., Xu, Y., Singh, V., Dagar, A., Joshi, J.R., Müller, M., Munné-…
BMC Plant Biology.
18
:
1471–2229
Ectopic expression of ORANGE promotes carotenoid accumulation and fruit development in tomato
2018.
Yazdani, M., Sun, Z., Yuan, H., Zeng, S., Thannhauser, T. W., Vrebalov, J., Ma, Q., Xu, Y., Fei, Zha…
Plant Biotechnology Journal.
:
Genetic mapping identifies loci that influence tomato resistance against Colorado potato beetles
2018.
Vargas-Ortiz, E., Gonda, I., Smeda, J. R., Mutschler, M. A., Giovannoni, James J., Jander, Georg
Nature Scientific Reports.
8
:
Genetic diversity within African tomato using next generation sequencing
2018.
Mungai, G. W., Owino, W., Ambuko, J., Giovannoni, James J., Nyende, A. B., Michuki, G.
PLANT GENETIC RESOURCES-CHARACTERIZATION AND UTILIZATION.
:
1–10
Differential metabolism of L–phenylalanine in the formation of aromatic volatiles in melon (Cucumis melo L.) fruit
2018.
Gonda, I., Davidovich-Rikanati, R., Bar, E., Lev, S., Jhirad, P., Meshulam, Y., Wissotsky, G., Portn…
Phytochemistry.
148
:
122–131
Deciphering Genetic Factors that Determine Melon Fruit-Quality Traits Using RNA-Seq-Based High-Resolution QTL and eQTL Mapping
2018.
Galpaz, N., Gonda, I., Shem-Tov, D., Barad, O., Tzuri, G., Lev, S., Fei, Zhangjun, Xu, Y., Lombardi,…
The Plant Journal.
94
:
169–191
High-resolution spatiotemporal transcriptome mapping of tomato fruit development and ripening
2018.
Shinozaki, Y., Nicolas, P., Fernandez-Pozo, N., Ma, Q., Evanich, D. J., Shi, Y., Xu, Y., Zheng, Y., …
Nature Communications.
9
:
Potato leafroll virus alters small RNA production in its aphid vector during plant viral infection to promote virus dispersal
2017.
Wilson, J., Pinheiro, P., Xu, Y., Zheng, Y., Rebelo, A. R., Fattahalhosseini, S., Kruse, A., Dos Sil…
PHYTOPATHOLOGY.
107
:
206–207
Carotenoid profiling of the leaves of selected African eggplant accessions subjected to drought stress
2017.
Mibei, E. K., Ambuko, J., Giovannoni, James J., Onyango, A. N., Owino, W. O.
Food Science and Nutrition.
5
:
113–122
Transient regulation of three clustered tomato class-I small heat-shock chaperone genes by ethylene is mediated by SlMADS-RIN transcription factor
2017.
Shukla, V., Upadhyay, R. K., Tucker, M. L., Giovannoni, James J., Rudrabhatla, S. V., Mattoo, A. K.
Nature Scientific Reports.
7
:
Metabolomic analyses to evaluate the effect of drought stress on selected African Eggplant accessions
2017.
Mibei, E. K., Owino, W. O., Ambuko, J., Giovannoni, James J., Onyango, A. N.
Journal of the Science of Food and Agriculture.
98
:
205–216
Overexpression of the class D MADS-box gene Sl-AGL11 impacts fleshy tissue differentiation and structure in tomato fruits
2017.
Huang, B., Routaboul, J. M., Liu, M., Deng, W., Maza, E., Mila, I., Hu, G., Zouine, M., Frasse, P., …
Journal of Experimental Botany.
68
:
4869–4884
An InDel in the Promoter of Al-ACTIVATED MALATE TRANSPORTER9 Selected during Tomato Domestication Determines Fruit Malate Contents and Aluminum Tolerance
2017.
Ye, J., Wang, X., Hu, T., Zhang, F., Wang, B., Li, C., Yang, T., Li, H., Lu, Y., Giovannoni, James J…
The Plant Cell.
29
:
2249–2268
AtPDS overexpression in tomato: Exposing unique patterns of carotenoid self-regulation and an alternative strategy for the enhancement of fruit carotenoid content
2017.
Mcquinn, R. P., Wong, B., Giovannoni, James J.
Plant Biotechnology Journal.
16
:
482–494
Next-generation sequencing-based QTL mapping for unravelling causative genes associated with melon fruit quality traits
2017.
Portnoy, V., Gonda, I., Galpaz, N., Tzuri, G., Lev, S., Kenigswald, M., Fei, Zhangjun, Barad, O., Ha…
II INTERNATIONAL SYMPOSIUM ON TOMATO DISEASES.
1151
:
9–16
Delayed response to cold stress is characterized by successive metabolic shifts culminating in apple fruit peel necrosis
2017.
Gapper, N. E., Hertog, M. LATM, Lee, J., Buchanan, D. A., Leisso, R. S., Fei, Zhangjun, Qu, G., Giov…
BMC Plant Biology.
17
:
The Epigenome and Transcriptional Dynamics of Fruit Ripening
2017.
Giovannoni, James J., Nguyen, C., Ampofo, B., Zhong, S., Fei, Zhangjun
Annual Review of Plant Biology.
68
:
61–84
The Tomato Expression Atlas
2017.
Fernandez-Pozo, N., Zheng, Y., Snyder, S. I., Nicolas, P., Shinozaki, Y., Fei, Zhangjun, Catala, Car…
Bioinformatics (Oxford, England).
33
:
2397–2398
Involvement of an ethylene response factor in chlorophyll degradation during citrus fruit degreening
2016.
Yin, X. R., Xie, X. L., Xia, X. J., Yu, J. Q., Ferguson, I. B., Giovannoni, James J., Chen, K. S.
The Plant Journal.
86
:
403–412
Gene expression and metabolism preceding soft scald, a chilling injury of ‘Honeycrisp’ apple fruit
2016.
Leisso, R. S., Gapper, N. E., Mattheis, J. P., Sullivan, N. L., Watkins, C. B., Giovannoni, James J.…
BMC Genomics.
17
:
Chilling-induced tomato flavor loss is associated with altered volatile synthesis and transient changes in DNA methylation
2016.
Zhang, B., Tieman, D. M., Jiao, C., Xu, Y., Chen, K., Fe, Z., Giovannoni, James J., Klee, H. J.
Proceedings of the National Academy of Sciences.
113
:
12580–12585
Banana MaMADS Transcription Factors Are Necessary for Fruit Ripening and Molecular Tools to Promote Shelf-Life and Food Security
2016.
Elitzur, T., Yakir, E., Quansah, L., Zhangjun, F., Vrebalov, J., Khayat, E., Giovannoni, James J., F…
Plant Physiology.
171
:
380–391
Gr and hp-1 tomato mutants unveil unprecedented interactions between arbuscular mycorrhizal symbiosis and fruit ripening
2016.
Chialva, M., Zouari, I., Salvioli, A., Novero, M., Vrebalov, J., Giovannoni, James J., Bonfante, P.
Planta.
244
:
155–165
Correction for Zhang et al., Chilling-induced tomato flavor loss is associated with altered volatile synthesis and transient changes in DNA methylation
2016.
Zhang, B., Tieman, D. M., Jiao, C., Xu, Y., Chen, K., Fei, Zhangjun, Giovannoni, James J., Klee, H. …
Proceedings of the National Academy of Sciences of the United States of America.
113
:
E8007–E8007
iTAK: A Program for Genome-wide Prediction and Classification of Plant Transcription Factors, Transcriptional Regulators, and Protein Kinases
2016.
Zheng, Y., Jiao, C., Sun, H., Rosli, H. G., Pombo, M. A., Zhang, P., Banf, M., Dai, X., Martin, Greg…
Molecular Plant.
9
:
1667–1670
Fruit carotenoid-deficient mutants in tomato reveal a function of the plastidial isopentenyl diphosphate isomerase (IDI1) in carotenoid biosynthesis
2016.
Pankratov, I., McQuinn, R., Schwartz, J., Bar, E., Fei, Zhangjun, Lewinsohn, E., Zamir, D., Giovanno…
The Plant Journal.
88
:
82–94
Identification of a Solanum pennellii Chromosome 4 Fruit Flavor and Nutritional Quality-Associated Metabolite QTL
2016.
Liu, Z., Alseekh, S., Brotman, Y., Zheng, Y., Fei, Zhangjun, Tieman, D. M., Giovannoni, James J., Fe…
Frontiers in Plant Science.
7
:
A DEMETER-like DNA demethylase governs tomato fruit ripening
2015.
Liu, R., How-Kit, A., Stammitti, L., Teyssier, E., Rolin, D., Mortain-Bertrand, A., Halle, S., Liu, …
Proceedings of the National Academy of Sciences.
112
:
10804–10809
More than meets the eye: From carotenoid biosynthesis, to new insights into apocarotenoid signaling
2015.
McQuinn, R. P., Giovannoni, James J., Pogson, B. J.
Current Opinion in Plant Biology.
27
:
172–179
Interactions between 1-MCP and Controlled Atmospheres on Quality and Storage Disorders of Fruits and Vegetables
2015.
Watkins, Christopher Brian, Gapper, N. E., Nock, J. F., Rudell, D. A., Leisso, R., Lee, J., Buchanan…
PROCEEDINGS OF THE INTERNATIONAL PLANT PROPAGATOR'S SOCIETY - 2013.
1071
:
45–58
Nonuniform gene expression pattern detected along the longitudinal axis in the matured rice leaf
2015.
Li, N., Chen, Y. R., Ding, Z., Li, P., Wu, Y., Zhang, A., Yu, S., Giovannoni, James J., Fei, Zhangju…
Nature Scientific Reports.
5
:
Systems approach for exploring the intricate associations between sweetness, color and aroma in melon fruits
2015.
Freilich, S., Lev, S., Gonda, I., Reuveni, E., Portnoy, V., Oren, E., Lohse, M., Galpaz, N., Bar, E.…
BMC Plant Biology.
15
:
Ethylene suppresses tomato ( Solanum lycopersicum ) fruit set through modification of gibberellin metabolism
2015.
Shinozaki, Y., Hao, S., Kojima, M., Sakakibara, H., Ozeki-Iida, Y., Zheng, Y., Fei, Zhangjun, Zhong,…
The Plant Journal.
83
:
237–251
Conserved Changes in the Dynamics of Metabolic Processes during Fruit Development and Ripening across Species
2014.
Klie, S., Osorio, S., Tohge, T., Drincovich, M. F., Fait, A., Giovannoni, James J., Fernie, A. R., N…
Plant Physiology.
164
:
55–68
Transcriptomic events associated with internal browning of apple during postharvest storage
2014.
Mellidou, I., Buts, K., Hatoum, D., Ho, Q. T., Mattheis, J. P., Johnston, J. W., Watkins, Christophe…
BMC Plant Biology.
14
:
Transcriptomic Analysis of Petunia hybrida in Response to Salt Stress Using High Throughput RNA Sequencing (vol 9, e94651, 2014)
2014.
Villarino, G. H., Bombarely, A., Giovannoni, James J., Scanlon, M. J., Mattson, N. S.
PLOS One.
9
:
e99146–e99146
Genome-wide data ( ChIP-seq) enabled identification of cell wall-related and aquaporin genes as targets of tomato ASR1, a drought stress-responsive transcription factor
2014.
Ricardi, M. M., González, R. M., Zhong, S., Domínguez, P. G., Duffy, T., Turjanski, P. G., Salgado…
BMC Plant Biology.
14
:
29–29
Transcriptomic Analysis of Petunia hybrida in Response to Salt Stress Using High Throughput RNA Sequencing
2014.
Villarino, G. H., Bombarely, A., Giovannoni, James J., Scanlon, Michael J., Mattson, Neil S.
PLOS One.
9
:
e94651–e94651
Genome sequence of the hot pepper provides insights into the evolution of pungency in Capsicum species
2014.
Kim, S., Park, M., Yeom, S. I., Kim, Y. M., Lee, J. M., Lee, H. A., Seo, E., Choi, J., Cheong, K., K…
Nature genetics.
46
:
270–278
Understanding development and ripening of fruit crops in an “-omics” era
2014.
Gapper, N. E., Giovannoni, James J., Watkins, Christopher Brian
Horticulture Research.
1
:
14034–14034
Fluorescence In Situ Hybridization and Optical Mapping to Correct Scaffold Arrangement in the Tomato Genome
2014.
Shearer, L. A., Anderson, L. K., de Jong, H., Smit, S., Goicoechea, J. L., Roe, B. A., Hua, A., Giov…
G3: Genes|Genomes|Genetics.
4
:
1395–1405
Tomato GOLDEN2-LIKE Transcription Factors Reveal Molecular Gradients That Function during Fruit Development and Ripening
2014.
Nguyen, C. V., Vrebalov, J. T., Gapper, N. E., Zheng, Y., Zhong, S., Fei, Zhangjun, Giovannoni, Jame…
The Plant Cell.
26
:
585–601
Genomic analyses provide insights into the history of tomato breeding
2014.
Lin, T., Zhu, G., Zhang, J., Xu, X., Yu, Q., Zheng, Z., Zhang, Z., Lun, Y., Li, S., Wang, X., Huang,…
Nature genetics.
46
:
1220–1226
The genome of the highly stress tolerant wild tomato species Solanum pennellii
2014.
Bolger, A., Scossa, F., Bolger, M. E., Lanz, C., Maumus, F., Tohge, T., Quesneville, H., Alseekh, S.…
Nature genetics.
46
:
1034–1038
The PH gene determines fruit acidity and contributes to the evolution of sweet melons
2014.
Cohen, S., Itkin, M., Yeselson, Y., Tzuri, G., Portnoy, V., Harel-Baja, R., Lev, S., Saâ Ar, U., Da…
Nature Communications.
5
:
Differential Regulation of Salmonella Typhimurium Genes Involved in O-Antigen Capsule Production and Their Role in Persistence Within Tomato Fruit
2013.
Marvasi, M., Cox, C. E., Xu, Y., Noel, J. T., Giovannoni, James J., Teplitski, M.
Molecular Plant-Microbe Interactions.
26
:
793–800
Molecular and genetic regulation of fruit ripening
2013.
Gapper, N. E., McQuinn, R. P., Giovannoni, James J.
Plant Molecular Biology.
82
:
575–591
Biomarker development for external CO2 injury prediction in apples through exploration of both transcriptome and DNA methylation changes
2013.
Gapper, N. E., Rudell, D. R., Giovannoni, James J., Watkins, Christopher Brian
AoB Plants.
5
:
plt021–plt021
Single-base resolution methylomes of tomato fruit development reveal epigenome modifications associated with ripening
2013.
Zhong, S., Fei, Zhangjun, Chen, Y. R., Zheng, Y., Huang, M., Vrebalov, J., McQuinn, R., Gapper, N., …
Nature Biotechnology.
31
:
154–159
The draft genome of watermelon (Citrullus lanatus) and resequencing of 20 diverse accessions
2013.
Xu, Y., Wang, J., Guo, S., Zhang, J., Sun, H., Salse, J., Lucas, W. J., Zhang, H., Zheng, Y., Mao, L…
Nature genetics.
45
:
51–58
Comparative genomics reveals candidate carotenoid pathway regulators of ripening watermelon fruit
2013.
Grassi, S., Piro, G., Lee, J. M., Zheng, Y., Fei, Zhangjun, Dalessandro, G., Giovannoni, James J., L…
BMC Genomics.
14
:
781–781
Catalyzing plant science research with RNA-seq
2013.
Martin, L. BB, Fei, Zhangjun, Giovannoni, James J., Rose, Jocelyn
Frontiers in Plant Science.
4
:
Differential Control of Ethylene Responses by GREEN-RIPE and GREEN-RIPE LIKE1 Provides Evidence for Distinct Ethylene Signaling Modules in Tomato
2012.
Ma, Q., Du, W., Brandizzi, F., Giovannoni, James J., Barry, C. S.
Plant Physiology.
160
:
1968–1984
Molecular analysis of softening and ethylene synthesis and signaling pathways in a non-softening apple cultivar, ÔHoneycrispÕ and a rapidly softening cultivar, ÔMcIntoshÕ
2012.
Harb, J., Gapper, N. E., Giovannoni, James J., Watkins, Christopher Brian
Postharvest Biology and Technology.
64
:
94–103
Features of a unique intronless cluster of class I small heat shock protein genes in tandem with box C/D snoRNA genes on chromosome 6 in tomato (Solanum lycopersicum)
2012.
Goyal, R. K., Kumar, V., Shukla, V., Mattoo, R., Liu, Y., Chung, S. H., Giovannoni, James J., Mattoo…
Planta.
235
:
453–471
Uniform ripening Encodes a Golden 2-like Transcription Factor Regulating Tomato Fruit Chloroplast Development
2012.
Powell, A. LT, Nguyen, C. V., Hill, T., Cheng, K. LL, Figueroa-Balderas, R., Aktas, H., Ashrafi, H.,…
Science.
336
:
1711–1715
Altered Chloroplast Development and Delayed Fruit Ripening Caused by Mutations in a Zinc Metalloprotease at the lutescent2 Locus of Tomato
2012.
Barry, C. S., Aldridge, G. M., Herzog, G., Ma, Q., McQuinn, R. P., Hirschberg, J., Giovannoni, James…
Plant Physiology.
159
:
1086–1098
Virus-induced gene complementation reveals a transcription factor network in modulation of tomato fruit ripening
2012.
Zhou, T., Zhang, H., Lai, T., Qin, C., Shi, N., Wang, H., Jin, M., Zhong, S., Fan, Z., Liu, Y., Wu, …
Nature Scientific Reports.
2
:
Tissue specificity and differential expression of transcription factors in tomato provide hints of unique regulatory networks during fruit ripening
2012.
Rohrmann, J., McQuinn, R., Giovannoni, James J., Fernie, A. R., Tohge, T.
Plant Signaling and Behavior.
7
:
1639–1647
Integrative Comparative Analyses of Transcript and Metabolite Profiles from Pepper and Tomato Ripening and Development Stages Uncovers Species-Specific Patterns of Network Regulatory Behavior
2012.
Osorio, S., Alba, R., Nikoloski, Z., Kochevenko, A., Fernie, A. R., Giovannoni, James J.
Plant Physiology.
159
:
1713–1729
The tomato genome sequence provides insights into fleshy fruit evolution
2012.
Sato, S., Tabata, S., Hirakawa, H., Asamizu, E., Shirasawa, K., Isobe, S., Kaneko, T., Nakamura, Y.,…
Nature.
485
:
635–641
Combined transcriptome, genetic diversity and metabolite profiling in tomato fruit reveals that the ethylene response factor SlERF6 plays an important role in ripening and carotenoid accumulation
2012.
Lee, J. M., Joung, J. G., McQuinn, R., Chung, M. Y., Fei, Zhangjun, Tieman, D., Klee, H., Giovannoni…
The Plant Journal.
70
:
191–204
Enabling proteomic studies with RNA-Seq: The proteome of tomato pollen as a test case
2012.
Lopez-Casado, G., Covey, P. A., Bedinger, P. A., Mueller, Lukas A., Thannhauser, T. W., Zhang, S., F…
Proteomics.
12
:
761–774
A cost-effective method for Illumina small RNA-Seq library preparation using T4 RNA ligase 1 adenylated adapters
2012.
Chen, Y. R., Zheng, Y., Liu, B., Zhong, S., Giovannoni, J., Fei, Zhangjun
Plant Methods.
8
:
41–41
A SEPALLATA gene is involved in the development and ripening of strawberry (Fragaria x ananassa Duch.) fruit, a non-climacteric tissue
2011.
Seymour, G. B., Ryder, C. D., Cevik, V., Hammond, J. P., Popovich, A., King, G. J., Vrebalov, J., Gi…
Journal of Experimental Botany.
62
:
1179–1188
Genetics and Control of Tomato Fruit Ripening and Quality Attributes
2011.
Klee, H. J., Giovannoni, James J.
ANNUAL REVIEW OF GENETICS, VOL 45.
45
:
41–59
Expression of ripening-related genes as affected by chilling in tomato
2011.
Rugkong, A., McQuinn, R., Giovannoni, James J., Rose, Jocelyn, Watkins, Christopher Brian
Postharvest Biology and Technology.
61
:
1–14
The Tomato MADS-Box Transcription Factor RIPENING INHIBITOR Interacts with Promoters Involved in Numerous Ripening Processes in a COLORLESS NONRIPENING-Dependent Manner
2011.
Martel, C., Vrebalov, J., Tafelmeyer, P., Giovannoni, James J.
Plant Physiology.
157
:
1568–1579
Tissue- and Cell-Type Specific Transcriptome Profiling of Expanding Tomato Fruit Provides Insights into Metabolic and Regulatory Specialization and Cuticle Formation
2011.
Matas, A. J., Yeats, T. H., Buda, G. J., Zheng, Y., Chatterjee, S., Tohge, T., Ponnala, L., Adato, A…
The Plant Cell.
23
:
3893–3910
Combined transcription factor profiling, microarray analysis and metabolite profiling reveals the transcriptional control of metabolic shifts occurring during tomato fruit development
2011.
Rohrmann, J., Tohge, T., Alba, R., Osorio, S., Caldana, C., McQuinn, R., Arvidsson, S., Van Der Merw…
The Plant Journal.
68
:
999–1013
Tomato Functional Genomics Database: a comprehensive resource and analysis package for tomato functional genomics
2011.
Fei, Zhangjun, Joung, J. G., Tang, X., Zheng, Y., Huang, M., Lee, J. M., McQuinn, R., Tieman, D. M.,…
Nucleic Acids Research.
39
:
D1156–D1163
Analysis of expressed sequence tags generated from full-length enriched cDNA libraries of melon
2011.
Clepet, C., Joobeur, T., Zheng, Y., Jublot, D., Huang, M., Truniger, V., Boualem, A., Hernandez-Gonz…
BMC Genomics.
12
:
Metabolism of soluble sugars in developing melon fruit: a global transcriptional view of the metabolic transition to sucrose accumulation
2011.
Dai, N., Cohen, S., Portnoy, V., Tzuri, G., Harel-Beja, R., Pompan-Lotan, M., Carmi, N., Zhang, G., …
Plant Molecular Biology.
76
:
1–18
Systems Biology of Tomato Fruit Development: Combined Transcript, Protein, and Metabolite Analysis of Tomato Transcription Factor ( nor, rin ) and Ethylene Receptor ( Nr ) Mutants Reveals Novel Regulatory Interactions
2011.
Osorio, S., Alba, R., Damasceno, C. MB, Lopez-Casado, G., Lohse, M., Zanor, M. I., Tohge, T., Usadel…
Plant Physiology.
157
:
405–425
Regulatory control of high levels of carotenoid accumulation in potato tubers
2011.
Zhou, X., Mcquinn, R., Fei, Zhangjun, Wolters, A. MA, Van Eck, Joyce, Brown, C., Giovannoni, James J…
Plant Cell and Environment.
34
:
1020–1030
High-Throughput Illumina Strand-Specific RNA Sequencing Library Preparation
2011.
Zhong, S., Joung, J. G., Zheng, Y., Chen, Y. R., Liu, B., Shao, Y., Xiang, J. Z., Fei, Zhangjun, Gio…
Cold Spring Harbor Protocols.
6
:
940–949
Expression of Ripening-related Genes as Affected by Chilling in Tomato
2010.
Rugkong, A., Watkins, C. B., Rose, J., Giovannoni, James J.
HortScience.
45
:
S241–S241
Understanding How ‘Honeycrisp’ Apples Maintain Crispness by Elucidating Molecular Mechanisms Involved in Softening and Ethylene Production
2010.
Harb, J., Gapper, N., Giovannoni, James J., Watkins, Christopher Brian
HortScience.
45
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S168–S168
Developmental and Feedforward Control of the Expression of Folate Biosynthesis Genes in Tomato Fruit
2010.
Waller, J. C., Akhtar, T. A., Lara-Núñez, A., Gregory, J. F., McQuinn, R. P., Giovannoni, James J.…
Molecular Plant.
3
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66–77
Cell wall metabolism in cold-stored tomato fruit
2010.
Rugkong, A., Rose, Jocelyn, Lee, S. J., Giovannoni, James J., O'Neill, M. A., Watkins, Christopher B…
Postharvest Biology and Technology.
57
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106–113
Genomic Analysis of Wild Tomato Introgressions Determining Metabolism- and Yield-Associated Traits
2010.
Kamenetzky, L., Asís, R., Bassi, S., de Godoy, F., Bermúdez, L., Fernie, A. R., van Sluys, M. A., …
Plant Physiology.
152
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1772–1786
Functional diversification of AGAMOUS lineage genes in regulating tomato flower and fruit development
2010.
Pan, I. L., McQuinn, R., Giovannoni, James J., Irish, V. F.
Journal of Experimental Botany.
61
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1795–1806
*omeSOM: a software for clustering and visualization of transcriptional and metabolite data mined from interspecific crosses of crop plants
2010.
Milone, D. H., Stegmayer, G. S., Kamenetzky, L., López, M., Lee, J. M., Giovannoni, James J., Carra…
BMC Bioinformatics.
11
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438–438
The regulation of MADS-box gene expression during ripening of banana and their regulatory interaction with ethylene
2010.
Elitzur, T., Vrebalov, J., Giovannoni, James J., Goldschmidt, E. E., Friedman, H.
Journal of Experimental Botany.
61
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1523–1535
Branched-chain and aromatic amino acid catabolism into aroma volatiles in Cucumis melo L. fruit
2010.
Gonda, I., Bar, E., Portnoy, V., Lev, S., Burger, J., Schaffer, A. A., Tadmor, Y., Gepstein, S., Gio…
Journal of Experimental Botany.
61
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1111–1123
Integrative Transcript and Metabolite Analysis of Nutritionally Enhanced DE-ETIOLATED1 Downregulated Tomato Fruit
2010.
Enfissi, E. MA, Barneche, F., Ahmed, I., Lichtlé, C., Gerrish, C., McQuinn, R. P., Giovannoni, Jame…
The Plant Cell.
22
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1190–1215
A genetic map of melon highly enriched with fruit quality QTLs and EST markers, including sugar and carotenoid metabolism genes
2010.
Harel-Beja, R., Tzuri, G., Portnoy, V., Lotan-Pompan, M., Lev, S., Cohen, S., Dai, N., Yeselson, L.,…
TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik.
121
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511–533
Use of homologous and heterologous gene expression profiling tools to characterize transcription dynamics during apple fruit maturation and ripening
2010.
Costa, F., Alba, R., Schouten, H., Soglio, V., Gianfranceschi, L., Serra, S., Musacchi, S., Sansavin…
BMC Plant Biology.
10
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229–229
Differential fruit gene expression in two strawberry cultivars in response to elevated CO2 during storage revealed by a heterologous fruit microarray approach
2009.
Ponce-Valadez, M., Fellman, S. M., Giovannoni, James J., Gan, Susheng, Watkins, Christopher Brian
Postharvest Biology and Technology.
51
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131–140
Role of Fluorescence in situ Hybridization in Sequencing the Tomato Genome
2009.
Stack, S. M., Royer, S. M., Shearer, L. A., Chang, S. B., Giovannoni, James J., Westfall, D. H., Whi…
Cytogenetic and Genome Research.
124
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339–350
A Snapshot of the Emerging Tomato Genome Sequence
2009.
Mueller, Lukas A., Lankhorst, R. K., Tanksley, S. D., Giovannoni, James J., White, R., Vrebalov, J.,…
The Plant Genome.
2
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78–92
Plant MetGenMAP: An Integrative Analysis System for Plant Systems Biology
2009.
Joung, J. G., Corbett, A. M., Fellman, S. M., Tieman, D. M., Klee, H. J., Giovannoni, James J., Fei,…
Plant Physiology.
151
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1758–1768
Molecular biology of ethylene during tomato fruit development and maturation
2008.
Cara, B., Giovannoni, James J.
Plant Science.
175
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106–113
Comparative BAC end sequence analysis of tomato and potato reveals overrepresentation of specific gene families in potato
2008.
Datema, E., Mueller, Lukas A., Buels, R., Giovannoni, James J., Visser, R. GF, Stiekema, W. J., Van …
BMC Plant Biology.
8
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34–34
The molecular and biochemical basis for varietal variation in sesquiterpene content in melon (Cucumis melo L.) rinds
2008.
Portnoy, V., Benyamini, Y., Bar, E., Harel-Beja, R., Gepstein, S., Giovannoni, James J., Schaffer, A…
Plant Molecular Biology.
66
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647–661
Sequencing and Comparative Analysis of a Conserved Syntenic Segment in the Solanaceae
2008.
Wang, Y., Diehl, A., Wu, F., Vrebalov, J., Giovannoni, James J., Siepel, Adam Charles, Tanksley, S. …
Genetics.
180
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391–408
Tomato  -Glutamylhydrolases: Expression, Characterization, and Evidence for Heterodimer Formation
2008.
Akhtar, T. A., McQuinn, R. P., Naponelli, V., Gregory, J. F., Giovannoni, James J., Hanson, A. D.
Plant Physiology.
148
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775–785
Expression and polymorphism of watermelon fruit ESTs
2008.
Levi, A., Wechter, W. P., Harris, K. R., Davis, A. R., Fei, Z., Giovannoni, James J., Trebitsh, T., …
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257–262
Amino Acid Substitutions in Homologs of the STAY-GREEN Protein Are Responsible for the green-flesh and chlorophyll retainer Mutations of Tomato and Pepper
2008.
Barry, C. S., McQuinn, R. P., Chung, M. Y., Besuden, A., Giovannoni, James J.
Plant Physiology.
147
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179–187
Melon fruit quality: A genomic approach
2008.
Katzir, N., Harel-Beja, R., Portnoy, V., Tzuri, G., Koren, E., Lev, S., Bar, E., Tadmor, V., Burger,…
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231–240
Sesquiterpene aroma biosynthesis in melon (Cucumis melo) rinds
2008.
Lewinsohn, E., Portnoy, V., Benyamini, Y., Bar, E., Harel-Beja, R., Gepstein, S., Giovannoni, James …
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249–255
Gene expression in developing watermelon fruit
2008.
Wechter, W. P., Levi, A., Harris, K. R., Davis, A. R., Fei, Zhangjun, Katzir, N., Giovannoni, James …
BMC Genomics.
9
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275–275
AGFD 31-Genetic regulation of carotenoid metabolism during tomato fruit ripening
2007.
Giovannoni, James J.
Abstracts of Papers of the American Chemical Society.
234
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Fruit ripening mutants yield insights into ripening control
2007.
Giovannoni, James J.
Current Opinion in Plant Biology.
10
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283–289
Completing a pathway to plant vitamin C synthesis
2007.
Giovannoni, James J.
Proceedings of the National Academy of Sciences.
104
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9109–9110
Ethylene and Fruit Ripening
2007.
Barry, C. S., Giovannoni, James J.
Journal of Plant Growth Regulation.
26
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143–159
Characterization of ripening-specific MADS-box genes from banana
2007.
Friedman, H., Ocampo, E. T., Elitzur, T., Pesis, E., Giovannoni, James J., Vrebalov, J.
PROCEEDINGS OF THE INTERNATIONAL PLANT PROPAGATOR'S SOCIETY - 2013.
738
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515–520
A physical map of the highly heterozygous Populus genome: Integration with the genome sequence and genetic map and analysis of haplotype variation
2007.
Kelleher, C. T., Chiu, R., Shin, H., Bosdet, I. E., Krzywinski, M. I., Fjell, C. D., Wilkin, J., Yin…
The Plant Journal.
50
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1063–1078
From The Cover: Ripening in the tomato Green-ripe mutant is inhibited by ectopic expression of a protein that disrupts ethylene signaling
2006.
Barry, C. S., Giovannoni, James J.
Proceedings of the National Academy of Sciences.
103
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7923–7928
Breeding new life into plant metabolism
2006.
Giovannoni, James J.
Nature Biotechnology.
24
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418–419
A naturally occurring epigenetic mutation in a gene encoding an SBP-box transcription factor inhibits tomato fruit ripening
2006.
Manning, K., Tör, M., Poole, M., Hong, Y., Thompson, A. J., King, G. J., Giovannoni, James J., Seym…
Nature genetics.
38
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948–952
Euchromatin and Pericentromeric Heterochromatin: Comparative Composition in the Tomato Genome
2006.
Wang, Y., Tang, X., Cheng, Z., Mueller, Lukas A., Giovannoni, James J., Tanksley, S. D.
Genetics.
172
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2529–2540
Genetic regulation of tomato fruit ripening and development and implementation of associated genomics tools
2005.
Giovannoni, James J., El-Rakshy, S.
PROCEEDINGS OF THE INTERNATIONAL PLANT PROPAGATOR'S SOCIETY - 2013.
682
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63–72
The Tomato Sequencing Project, the First Cornerstone of the International Solanaceae Project (SOL)
2005.
Mueller, Lukas A., Tanskley, S. D., Giovannoni, James J., Van Eck, Joyce, Stack, S., Choi, D., Kim, …
Comparative and Functional Genomics.
6
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153–158
Ethylene Insensitivity Conferred by the Green-ripe and Never-ripe 2 Ripening Mutants of Tomato
2005.
Barry, C. S., McQuinn, R. P., Thompson, A. J., Seymour, G. B., Grierson, D., Giovannoni, James J.
Plant Physiology.
138
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267–275
Role of  -Oxidation in Jasmonate Biosynthesis and Systemic Wound Signaling in Tomato
2005.
Li, C., Schilmiller, A. L., Liu, G., Gyu, I. L., Jayanty, S., Sageman, C., Vrebalov, J., Giovannoni,…
The Plant Cell.
17
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971–986
Differential gene expression analysis of strawberry cultivar responses to elevated CO2 concentrations during storage using a tomato cDNA microarray
2005.
Ponce-Valadez, M., Watkins, C. B., Moore, S., Giovannoni, James J.
PROCEEDINGS OF THE INTERNATIONAL PLANT PROPAGATOR'S SOCIETY - 2013.
682
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255–262
Transcriptome and Selected Metabolite Analyses Reveal Multiple Points of Ethylene Control during Tomato Fruit Development
2005.
Alba, R., Payton, P., Fei, Zhangjun, McQuinn, R., Debbie, P., Martin, Gregory B., Tanksley, S. D., G…
The Plant Cell.
17
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2954–2965
Tackling the plant proteome: Practical approaches, hurdles and experimental tools
2004.
Rose, Jocelyn, Bashir, S., Giovannoni, James J., Jahn, M. M., Saravanan, R. S.
The Plant Journal.
39
:
715–733
Genetic Regulation of Fruit Development and Ripening
2004.
Giovannoni, James J.
The Plant Cell.
16
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S170–S180
Folate synthesis in plants: The last step of the p-aminobenzoate branch is catalyzed by a plastidial aminodeoxychorismate lyase
2004.
Basset, G. JC, Ravanel, S., Quinlivan, E. P., White, R., Giovannoni, James J., Rébeillé, F., Nicho…
The Plant Journal.
40
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453–461
Folate synthesis in plants: The p-aminobenzoate branch is initiated by a bifunctional PabA-PabB protein that is targeted to plastids
2004.
Basset, G. JC, Quinlivan, E. P., Ravanel, S., Rébeillé, F., Nichols, B. P., Shinozaki, K., Seki, M…
Proceedings of the National Academy of Sciences.
101
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1496–1501
Comprehensive EST analysis of tomato and comparative genomics of fruit ripening
2004.
Fei, Zhangjun, Tang, X., Alba, R. M., White, J. A., Ronning, C. M., Martin, Gregory B., Tanksley, S.…
The Plant Journal.
40
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47–59
ESTs, cDNA microarrays, and gene expression profiling: Tools for dissecting plant physiology and development
2004.
Alba, R., Fei, Zhangjun, Payton, P., Liu, Y., Moore, S. L., Debbie, P., Cohn, J., D'Ascenzo, M., Gor…
The Plant Journal.
39
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697–714
Tomato Expression Database (TED) – An Interactive Management Tool for Tomato Expression Profiling Data
2003.
Fei, Z., Tang, X., Alba, R., Payton, P., Giovannoni, James J.
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424–425
Deductions about the Number, Organization, and Evolution of Genes in the Tomato Genome Based on Analysis of a Large Expressed Sequence Tag Collection and Selective Genomic Sequencing
2002.
Van der Hoeven, R., Ronning, C., Giovannoni, James J., Martin, Gregory B., Tanksley, S.
The Plant Cell.
14
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1441–1456
Genetic Control of Fruit Quality and Prospects for Nutrient Modification
2002.
Giovannoni, James J., Tanksley, S. D.
HortScience.
37
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453–456
Characterization of a major latex protein (MLP) gene down-regulated by ethylene during peach fruitlet abscission
2002.
Ruperti, B., Bonghi, C., Ziliotto, F., Pagni, S., Rasori, A., Varotto, S., Tonutti, P., Giovannoni, …
Plant Science.
163
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265–272
LeCTR1, a Tomato CTR1-Like Gene, Demonstrates Ethylene Signaling Ability in Arabidopsis and Novel Expression Patterns in Tomato
2002.
Leclercq, J., Adams-Phillips, L. C., Zegzouti, H., Jones, B., Latche, A., Giovannoni, James J., Pech…
Plant Physiology.
130
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1132–1142
Analysis of the Ethylene Response in the epinastic Mutant of Tomato
2001.
Barry, C. S., Fox, E. A., Yen, H. C., Lee, S., Ying, T. J., Grierson, D., Giovannoni, James J.
Plant Physiology.
127
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58–66
Determining the Physical Limits of the Brassica S Locus by Recombinational Analysis
2000.
Casselman, A. L., Vrebalov, J., Conner, J. A., Singhal, A., Giovannoni, James J., Nasrallah, M. E., …
The Plant Cell.
12
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23–33
Molecular and Genetic Characterization of a Novel Pleiotropic Tomato-Ripening Mutant
1999.
Thompson, A. J., Tor, M., Barry, C. S., Vrebalov, J., Orfila, C., Jarvis, M. C., Giovannoni, James J…
Plant Physiology.
120
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383–389
Identification of plastome variants useful for cytoplasmic selection and cultivar identification in onion
1999.
Alcala, J., Pike, L. M., Giovannoni, James J.
Journal of the American Society for Horticultural Science.
124
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122–127
Genetic approaches to manipulation of fruit development and quality in tomato
1998.
Giovannoni, James J., Kannan, P., Lee, S., Yen, H. C.
:
1–15
Transgenic analysis of tomato endo-beta-1,4-glucanase gene function. Role of cel1 in floral abscission
1998.
Lashbrook, C. C., Giovannoni, James J., Hall, B. D., Fischer, R. L., Bennett, A. B.
The Plant Journal.
13
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303–310
The tomato high-pigment ( hp ) locus maps to chromosome 2 and influences plastome copy number and fruit quality
1997.
Yen, H. C., Shelton, B. A., Howard, L. R., Lee, S., Vrebalov, J., Giovannoni, James J.
TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik.
95
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1069–1079
Application of Genetic Bit Analysis (GBA (TM)) for allelic selection in plant breeding
1997.
Alcala, J., Giovannoni, James J., Pike, L. M., Reddy, A. S.
Molecular Breeding.
3
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495–502
Rapid and reliable screening of a tomato YAC library exclusively based on PCR
1996.
Pillen, K., Alpert, K. B., Giovannoni, James J., Ganal, M. W., Tanksley, S. D.
Plant Molecular Biology Reporter.
14
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58–67
An Ethylene-Inducible Component of Signal Transduction Encoded by Never-ripe
1995.
WILKINSON, J. Q., LANAHAN, M. B., YEN, H. C., Giovannoni, James J., KLEE, H. J.
Science.
270
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1807–1809
Rapid isolation of terminal sequences from cloned plant DNA fragments
1995.
Lu, X. H., Ruezinsky, D. M., Giovannoni, James J.
Plant Molecular Biology Reporter.
13
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369–376
The Tomato Never-ripe Locus Regulates Ethylene-Inducible Gene Expression and Is Linked to a Homolog of the Arabidopsis ETR1 Gene
1995.
YEN, H. C., LEE, S. Y., TANKSLEY, S. D., LANAHAN, M. B., KLEE, H. J., Giovannoni, James J.
Plant Physiology.
107
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1343–1353
Molecular genetic analysis of the ripening-inhibitor and non-ripening loci of tomato: a first step in genetic map-based cloning of fruit ripening genes
1995.
Giovannoni, James J., Noensie, E. N., Ruezinsky, D. M., Lu, X., Tracy, S. L., Ganal, M. W., Martin, …
Molecular and General Genetics MGG.
248
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195–206
A modified procedure for PCR-based differential display and demonstration of use in plants for isolation of genes related to fruit ripening
1995.
OH, B. J., BALINT, D. E., Giovannoni, James J.
Plant Molecular Biology Reporter.
13
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70–81
The Never Ripe Mutation Blocks Ethylene Perception in Tomato
1994.
LANAHAN, M. B., YEN, H. C., Giovannoni, James J., KLEE, H. J.
The Plant Cell.
6
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521–530
The use of transgenic and naturally occurring mutants to understand and manipulate tomato fruit ripening
1994.
GRAY, J. E., PICTON, S., Giovannoni, James J., GRIERSON, D.
Plant Cell and Environment.
17
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557–571
Pooled-sampling makes high-resolution mapping practical with DNA markers
1993.
CHURCHILL, G. A., Giovannoni, James J., TANKSLEY, S. D.
Proceedings of the National Academy of Sciences.
90
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16–20
High density molecular linkage maps of the tomato and potato genomes
1992.
Tanksley, S. D., Ganal, M. W., Prince, J. P., De Vicente, M. C., Bonierbale, M. W., Broun, P., Fulto…
Genetics.
132
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1141–1160
Isolation of molecular markers from specific chromosomal intervals using DNA pools from existing mapping populations
1991.
Giovannoni, James J., WING, R. A., GANAL, M. W., TANKSLEY, S. D.
Nucleic Acids Research.
19
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6553–6558
EXPRESSION OF A CHIMERIC POLYGALACTURONASE GENE IN TRANSGENIC RIN (RIPENING INHIBITOR) TOMATO FRUIT
1990.
Giovannoni, James J., DELLAPENNA, D., LASHBROOK, C. C., BENNETT, A. B., FISCHER, R. L.
11
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217–227
Polygalacturonase Isozymes and Pectin Depolymerization in Transgenic rin Tomato Fruit
1990.
DELLAPENNA, D., LASHBROOK, C. C., TOENJES, K., Giovannoni, James J., FISCHER, R. L., BENNETT, A. B.
Plant Physiology.
94
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1882–1886
EXPRESSION OF A CHIMERIC POLYGALACTURONASE GENE IN TRANSGENIC RIN (RIPENING INHIBITOR) TOMATO FRUIT
1990.
Giovannoni, James J., DELLAPENNA, D., LASHBROOK, C. C., BENNETT, A. B., FISCHER, R. L.
129
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81–100
Expression of a Chimeric Polygalacturonase Gene in Transgenic rin (Ripening Inhibitor) Tomato Fruit Results in Polyuronide Degradation but not Fruit Softening
1989.
Giovannoni, James J., DELLAPENNA, D., BENNETT, A. B., FISCHER, R. L.
The Plant Cell.
1
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53–63
Ethylene-regulated expression of a tomato fruit ripening gene encoding a proteinase inhibitor I with a glutamic residue at the reactive site
1988.
MARGOSSIAN, L. J., FEDERMAN, A. D., Giovannoni, James J., FISCHER, R. L.
Proceedings of the National Academy of Sciences.
85
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8012–8016
 

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