Fei Bioinformatics Lab

Publications (Google Scholar)

2024

Cai Y, Gao X, Mao J, Liu Y, Tong L, Chen C, Liu Y, Kou W, Chang C, Foster T, Yao J, Cornille A, Tahirm MM, Liu Z, Yan Z, Lin S, Ma F, Ma J, Xing L, An N, Zuo X, Lv Y, Zhao Z, Li W, Li Q, Zhao C, Hu Y, Liu H, Wang C, Shi X, Ma D, Fei Z*, Jiang Y*, Zhang D* (2024) Genome sequencing of 'Fuji' apple clonal varieties reveals evolutionary history and genetic mechanism of the spur-type morphology. Nature Communications 15:10082

Zhang Z^#, Yang T^#, Liu Y^#, Wu S^#, Sun H^#, Wu J^#, Li Y^#, Zheng Y, Ren H, Yang Y, Shi S, Wang W, Pan Q, Lian L, Duan S, Zhu Y, Cai Y, Zhou H, Zhang H, Tang K, Cui J, Gao D, Chen L, Jiang Y, Sun X, Zhou X, Fei Z*, Ma N*, Gao J* (2024) Haplotype-resolved genome assembly and resequencing provide insights into the origin and domestication of modern rose. Nature Plants 10:1659-1671

Zhang J, Lyu H, Chen J, Cao X, Du R, Ma L, Wan N, Zhu Z, Rao J, Wang J, Zhong K, Lyu Y, Wang Y, Lin T, Zhou Y, Zhou Y, Zhu G, Fei Z, Klee H, Huang S (2024) Releasing a sugar brake generates sweeter tomato without yield penalty. Nature 635:647-656

Svara A, Sun H, Fei Z, Khan A (2024) Advancing apple genetics research: Malus coronaria and Malus ioensis genomes and a gene family-based pangenome of native North American apples. DNA Research 31:dsae026

Garcia J, Moravek M, Fish T, Thannhauser T, Fei Z, Sparks JP, Giovannoni J, Kao-Kniffin J (2024) Rhizosphere microbiomes derived from vermicompost alter gene expression and regulatory pathways in tomato (Solanum lycopersicum, L.). Scientific Reports 14:21362

Yu X, Qin Q, Zribi I, Yu J, Yang S, Dinkins RD, Fei Z, Kereszt A, Zhu H (2024) Species-specific microsymbiont discrimination mediated by a Medicago receptor kinase. Science Advance 10:eadp6436

Chen Y, Tang X, Fei Z, Giovannoni JJ (2024) Fruit ripening and postharvest changes in very-early-harvested tomatoes. Horticulture Research 11:uhae199

Xia F, Zhang N, Smith RE, Chakraborty J, Sobol G, Tang X, Fei Z, Sessa G, Martin GB (2024) Related type 2C protein phosphatases Pic3 and Pic12 negatively regulate immunity in tomato to Pseudomonas syringae. Plant Physiol 196:1997-2013

Rett-Cadman S, Weng Y, Fei Z, Thompson A, Grumet R (2024) Genome-wide association study of cuticle and lipid droplet properties of cucumber (Cucumis sativus L.) fruit. International Journal of Molecular Sciences 25:9306

Fallon MA, Tadfie H, Watson AP, Dyke MM, Flores C, Cook N, Fei Z, Holland CK (2024) Molecular basis of one-step methyl anthranilate biosynthesis in grapes, sweet orange, and maize. Plant J 119:2363-2374

Feiz L, Shyu C, Wu S, Ahern KR, Gull I, Rong Y, Artymowicz CJ, Pineros MA, Fei Z, Brutnell TP, Jander G (2024) COI1 F-box proteins regulate DELLA protein levels, growth, and photosynthetic efficiency in maize. Plant Cell 36:3237-3259

Liu Z, Duan N, Yang Z, Yue L, Fei Z, Kong S (2024) Identification of male-fertility gene AsaNRF1 and molecular marker development in cultivated garlic (Allium sativum L.). Frontiers in Plant Science 15:1419260

Wang S, Wei S, Deng Y, Wu S, Peng H, Qing Y, Zhai X, Zhou S, Li J, Li H, Feng Y, Yi Y, Li R, Zhang H, Wang Y, Zhang R, Ning L, Yao Y*, Fei Z*, Zheng Y* (2024) HortGenome Search Engine, a universal genomic search engine for horticultural crops Horticulture Research 11:uhae100

Zhao X^#, Yu J^#, Chanda B, Zhao J, Wu S, Zheng Y, Sun H, Levi A, Ling K-S*, Fei Z* (2024) Genomic and pangenomic analyses provide insights into the population history and genomic diversification of bottle gourd. New Phytologists 242:2285-2300

Mo C, Wang H, Wei M, Zeng Q, Zhang X, Fei Z, Zhang Y, Kong Q (2024) Complete genome assembly provides a high-quality skeleton for pan-NLRome construction in melon. Plant Journal 118:2249-2268

Shao W, Wang J, Zhang Y, Zhang C, Chen J, Chen Y, Fei Z, Ma Z, Sun X, Jiao C (2024) The jet-like chromatin structure defines active secondary metabolism in fungi. Nucleic Acids Research 52:4906-4921

Zhang Y, Wang Y, Liu R, Fei Z, Fan X, Jiang J, Sun L, Meng X, Liu C (2024) Antibody array-based proteome approach reveals proteins involved in grape seed development. Plant Physiology 195:462-478

Guo N, Wang S, Wang T, Duan M, Zong M, Miao L, Han S, Wang G, Liu X, Zhang D, Jiao C, Xu H, Chen L, Fei Z*, Li J*, Liu F* (2024) Graph-based pan-genome of Brassica oleracea provides new insights into its domestication and morphotype diversification. Plant Communications 5:100791

Silva VM, Lui ACW, de Carvalho MR, Namorato FA, Fei Z, dos Reis AR, Liu J, Vatamaniuk OK, Li L (2024) The selenium-promoted daidzein production contributes to its induced nodulation in soybean plants. Environmental and Experimental Botany 218:105591

Svara A, Sun H, Fei Z, Khan A (2024) Chromosome-level phased genome assembly of 'Antonovka' identified candidate apple scab resistance genes highly homologous to HcrVf2 and HcrVf1 on linkage group 1. G3: Genes, Genomes, Genetics 14:jkad253

2023

Liu F^#, Zhao J^#, Sun H, Xiong C, Sun X, Wang X, Wang Z, Jarret R, Wang J, Tang B, Xu H, Hu B, Suo H, Yang B, Ou L, Li X, Zhou S, Yang S, Liu Z, Yuan F, Pei Z, Ma Y, Dai X, Wu S*, Fei Z*, Zou X* (2023) Genomes of cultivated and wild Capsicum species provide insights into pepper domestication and population differentiation. Nature Communications 14:5487

Wu S^#, Sun H^#, Gao L, Branham S, McGregor C, Renner SS, Xu Y, Kousik C, Wechter WP, Levi A, Fei Z* (2023) A Citrullus genus super-pangenome reveals extensive variations in wild and cultivated watermelons and sheds light on watermelon evolution and domestication. Plant Biotechnology Journal 21:1926-1928
Full version at bioRxiv

Li N, He Q, Wang J, Wang B, Zhao J, Huang S, Yang T, Tang Y, Yang S, Aisimutuola P, Xu R, Hu J, Jia C, Ma K, Li Z, Jiang F, Gao J, Lan H, Zhou Y, Zhang X, Huang S, Fei Z, Huan Wang H, Li H, Yu Q (2023) Super-pangenome analyses highlight genomic diversity and structural variation across wild and cultivated tomato species. Nature Genetics 55:852-860

Lou H, Song L, Li X, Zi H, Chen W, Gao Y, Zheng S, Fei Z*, Sun X*, Wu J* (2023) The Torreya grandis genome illuminates the origin and evolution of gymnosperm-specific sciadonic acid biosynthesis. Nature Communications 14:1315

Romero-Rodriguez B^#, Petek M^#, Jiao C^#, Kriznik M, Zagorscak, Fei Z, Bejarano ER, Gruden K, Castillo AG (2023) Transcriptional and epigenetic changes during tomato yellow leaf curl virus infection in tomato. BMC Plant Biology 23:651

Lin Y-C, Mansfeld BN, Tang X, Colle M, Chen F, Weng Y, Fei Z, Grumet R (2023) Identification of QTL associated with resistance to Phytophthora fruit rot in cucumber (Cucumis sativus L.). Frontiers in Plant Science 14:1281755

Kitavi M, Gemenet DC, Wood JC, Hamilton JP, Wu S, Fei Z, Khan A, Buell CR (2023) Identification of genes associated with abiotic stress tolerance in sweetpotato using weighted gene co-expression network analysis. Plant Direct 7:e532

Doron-Faigenboim A, Moy-Komemi M, Petreikov M, Eselson Y, Sonawane P, Cardenas P, Fei Z, Aharoni A, Schaffer AA (2023) Transcriptomes of developing fruit of cultivated and wild tomato species. Molecular Horticulture 3:12

Nicolas P, Pattison RJ, Zheng Y, Lapidot-Cohen T, Brotman Y, Osorio S, Fernie AR, Fei Z, Catala C (2023) Starch deficiency in tomato causes transcriptional reprogramming that modulates fruit development, metabolism and stress responses. Journal Experimental Botany 74:6331-6348

Yu X, Qin M, Qu M, Jiang Q, Guo S, Chen Z, Shen Y, Fu G, Fei Z, Huang H, Gao L, Yao X (2023) Genomic analyses reveal dead-end hybridization between two deeply divergent kiwifruit species rather than homoploid hybrid speciation. Plant Journal 115:1528-1543

Liu M, Kang B, Wu H, Aranda MA, Peng B, Liu L, Fei Z, Hong N, Gu Q (2023) Transcriptomic and metabolic profiling of watermelon uncovers the role of salicylic acid and flavonoids in the resistance to cucumber green mottle mosaic virus. Journal Experimental Botany 74:5218-5235

Meng D, Cao H, Yang Q, Zhang M, Borejsza-Wysocka E, Wang H, Dandekar AM, Fei Z, Cheng L (2023) SnRK1 kinase-mediated phosphorylation of transcription factor bZIP39 regulates sorbitol metabolism in apple. Plant Physiology 192:2123-2142

Hernandez CO, Labate J, Reitsma K, Fabrizio J, Bao K, Fei Z, Grumet R, Mazourek M (2023) Characterization of the USDA Cucurbita pepo, C. moschata, and C. maxima germplasm collections. Frontiers in Plant Science 14:1130814

Yu F, Zhang W, Wang S, Yu L, Fei Z, Li J (2023) Genome sequences of four isolates of Xanthomonas campestris pv. campestris, the causal agent of black rot. PhytoFrontiers 3:744-746

Chia JC, Yan J, Rahmati Ishka M, Faulkner MM, Simons E, Huang R, Smieska L, Woll A, Tappero R, Kiss A, Jiao C, Fei Z, Kochian LV, Walker E, Pineros M, Vatamaniuk OK (2023) Loss of OPT3 function decreases phloem copper levels and impairs crosstalk between copper and iron homeostasis and shoot-to-root signaling in Arabidopsis thaliana. Plant Cell 35:2157-2185

Feng H, Chen W, Hussain S, Shakir S, Tzin V, Adegbayi F, Ugine T, Fei Z, Jander G (2023) Horizontally transferred genes as RNA interference targets for aphid and whitefly control. Plant Biotechnology Journal 21:754-768

Yu J, Wu S, Sun H, Wang X, Tang X, Guo S, Zhang Z, Huang S, Xu Y, Weng Y, Mazourek M, McGregor C, Renner SS, Branham S, Kousik C, Wechter WP, Levi A, Grumet R, Zheng Y, Fei Z* (2023) CuGenDBv2: an updated database for cucurbit genomics. Nucleic Acids Research 51:D1457-D1464

2022

Tu X, Ren S, Shen W, Li J, Li Y, Li C, Li Y, Zong Z, Xie W, Grierson D, Fei Z, Giovannoni J, Li P, Zhong S (2022) Limited conservation in cross-species comparison of GLK transcription factor binding suggested wide-spread cistrome divergence. Nature Communications 13:7632

Luo X, Zhou H, Cao D, Yan F, Chen P, Wang J, Woeste K, Chen X, Fei Z, An H, Malvolti M, Ma K, Liu C, Ebrahimi A, Qiao C, Ye H, Li M, Lu Z, Xu J, Cao S, Zhao P (2022) Domestication and selection footprints in Persian walnuts (Juglans regia). PLoS Genetics 18:e1010513

Nicolas P, Shinozaki Y, Powell A, Philippe G, Snyder SI, Bao K, Zheng Y, Xu Y, Courtney L, Vrebalov J, Casteel CL, Mueller LA, Fei Z, Giovannoni JJ, Rose JKC, Catala C (2022) Spatiotemporal dynamics of the tomato fruit transcriptome under prolonged water stress. Plant Physiology 190:2557-2578

Perez-Escobar OA, Tusso S, Przelomska NAS, Wu S, Ryan P, Nesbitt M, Silber MV, Preick M, Fei Z, Hofreiter M, Chomicki G, Renner SS (2022) Genome sequencing of up to 6,000-yr-old Citrullus seeds reveals use of a bitter-fleshed species prior to watermelon domestication. Molecular Biology Evolution 8:msac168

Ban S, El-Sharkawy I, Zhao J, Fei Z, Xu K (2022) An apple somatic mutation of delayed fruit maturation date is primarily caused by a retrotransposon insertion-associated large deletion. Plant J 111:1609-1625

Davachi SM, Dogan B, Khazdooz L, Zhang S, Khojastegi A, Fei Z, Sun H, Meletharayil G, Kapoor R, Simpson KW, Abbaspourrad A (2022) Long-term Lacticaseibacillus rhamnosus GG storage at ambient temperature in vegetable oil: viability and functional assessments. J Agric Food Chem 70:9399-9411

Cao K, Wang B, Fang W, Zhu G, Chen C, Wang X, Li Y, Wu J, Tang T, Fei Z, Luo J, Wang L (2022) Combined nature and human selections reshaped peach fruit metabolome. Genome Biology 23:146

Chen M, Guo L, Ramakrishnan M, Fei Z, Vinod KK, Ding Y, Jiao C, Gao Z, Zha R, Wang C, Gao Z, Yu F, Ren G, Wei Q (2022) Rapid growth of Moso bamboo (Phyllostachys edulis): Cellular roadmaps, transcriptome dynamics, and environmental factors. Plant Cell 34:3577-3610

Guo L, Wang C, Chen J, Ju Y, Yu F, Jiao C, Fei Z, Ding Y, Wei Q (2022) Cellular differentiation, hormonal gradient, and molecular alternation between the division zone and the elongation zone of bamboo internodes. Physiologia Plantarum 174:e13774

Yu X, Qu M, Shi Y, Hao C, Guo S*, Fei Z*, Gao L* (2022) Chromosome-scale genome assemblies of wild tomato relatives Solanum habrochaites and S. galapagense reveal structural variants associated with stress tolerance and terpene biosynthesis. Horticulture Research 9:uhac139

Zhang N, Hecht C, Sun X, Fei Z, Martin GB (2022) Loss of function of the bHLH transcription factor Nrd1 in tomato enhances resistance to Pseudomonas syringae. Plant Physiology 190:1334-1348

Zhou Y, Zhang Z, Bao Z, Li H, Lyu Y, Zan Y, Wu Y, Cheng L, Fang Y, Wu K, Zhang J, Lyu H, Lin T, Gao Q, Saha S, Mueller L, Fei Z, Stadler T, Xu S, Zhang Z, Speed D, Huang S (2022) Graph pangenome captures missing heritability and empowers tomato breeding. Nature 606:527-534

Wang L^#, Sun X^#, Peng Y^#, Chen K^#, Wu S^#, Guo Y, Zhang J, Yang H, Jin T, Wu L, Zhou X, Liang B, Zhao Z, Liu D*, Fei Z*, Bai L* (2022) Genomic insights into the origin, adaptive evolution and herbicide resistance of Leptochloa chinensis, a devastating tetraploid weedy grass in rice fields. Molecular Plant 15:1045-1058

Qing Y, Zheng Y*, Mlotshwa S, Smith HN, Wang X, Zhai X, van der Knaap E, Wang Y*, Fei Z* (2022) Dynamically expressed small RNAs, substantially driven by genomic structural variants, contribute to transcriptomic changes during tomato domestication. Plant J 110:1536-1550

Cao K, Peng Z, Zhao X, Li Y, Liu K, Arus P, Fang W, Chen C, Wang X, Wu J, Fei Z, Wang L (2022) Chromosome-level genome assemblies of four wild peach species provide insights into genome evolution and genetic basis of stress resistance. BMC Biology 20:139

Powell AF, Feder A, Li J, Schmidt MH, Courtney L, Alseekh S, Jobson EM, Vogel A, Xu Y, Lyon D, Dumschott K, McHale M, Sulpice R, Bao K, Lal R, Duhan A, Hallab A, Denton AK, Bolger ME, Fernie AR, Hind SR, Mueller LA, Martin GB, Fei Z, Martin C, Giovannoni JJ, Strickler SR, Usadel B (2022) A Solanum lycopersicoides reference genome facilitates insights into tomato specialized metabolism and immunity. Plant J 110:1791-1810

Li H, Wang S, Chai S, Yang Z, Zhang Q, Xin H, Xu Y, Lin S, Chen X, Yao Z, Yang Q, Fei Z, Huang S, Zhang Z (2022) Graph-based pan-genome reveals structural and sequence variations related to agronomic traits and domestication in cucumber. Nature Communications 13:682

Gao Z, Guo L, Ramakrishnan M, Xiang Y, Jiao C, Jiang J, Vinod KK, Fei Z, Que F, Ding Y, Yu F, Chen T, Wei Q (2022) Cellular and molecular characterizations of the irregular internode division zone formation of a slow growing bamboo variant. Tree Physiol 42: 570-584

Padmanabhan C, Zheng Y, Shamimuzzaman M, Wilson JR, Gilliard A, Fei Z, Ling KS (2022) The tomato yellow leaf curl virus C4 protein alters the expression of plant developmental genes correlating to leaf upward cupping phenotype in tomato. PLoS One 17:e0257936.

Chanda B, Wu S, Fei Z, Ling KS, Levi A (2022) Elevated expression of ribosome-inactivating protein (RIP) genes in potyvirus-resistant watermelon in response to viral infection. Canadian J Plant Pathology 44:615-625

Ma X, Shao E, Chen W, Cotto-Rivera RO, Yang X, Kain W, Fei Z, Wang P (2022) Bt Cry1Ac resistance in Trichoplusia ni is conferred by multi-gene mutations. Insect Biochemistry and Molecular Biology 140:103678

2021

Cai X^#, Sun X^#, Xu C^#, Sun H, Wang X, Ge C, Zhang Z, Wang Q*, Fei Z*, Jiao C^#,*, Wang Q* (2021) Genomic analyses provide insights into spinach domestication and the genetic basis of agronomic traits. Nature Communications 12:7246

Wang R, Xue Y, Fan J, Yao JL, Qin M, Lin T, Lian Q, Zhang M, Li X, Li J, Sun M, Song B, Zhang J, Zhao K, Chen X, Hu H, Fei Z*, Xue C*, Wu J* (2021) A systems genetics approach reveals PbrNSC as a regulator of lignin and cellulose biosynthesis in stone cells of pear fruit. Genome Biology 22:313

Wang X^#, Ando K^#, Wu S, Reddy UK, Tamang P, Bao K, Hammar SA, Grumet R, McCreight JD*, Fei Z* (2021) Genetic characterization of melon accessions in the U.S. National Plant Germplasm System and construction of a melon core collection. Molecular Horticulture 1:11

Shi Y, Vrebalov J, Zheng H, Xu Y, Yin X, Liu W, Liu Z, Sorensen I, Su G, Ma Q, Evanich D, Rose JKC, Fei Z, Van Eck J, Thannhauser T, Chen K, Giovannoni JJ (2021) A tomato LATERAL ORGAN BOUNDARIES transcription factor, SlLOB1, predominantly regulates cell wall and softening components of ripening. Proc Natl Acad Sci USA. 118:e2102486118

Peng B, Liu L, Wu H, Kang B, Fei Z, Gu Q (2021) Interspecific recombination between Zucchini tigre mosaic virus and Papaya ringspot virus infecting cucurbits in China. Frontiers in Microbiology 12:773992

Grumet R, McCreight JD, McGregor C, Weng Y, Mazourek M, Reitsma K, Labate J, Davis A, Fei Z (2021) Genetic resources and vulnerabilities of major cucurbit crops. Genes 12:1222

Orcheski B, Meng D, Bai Y, Fei Z, and Cheng L (2021) The transcriptomes of healthy and bitter pit-affected 'Honeycrisp' fruit reveal genes associated with disorder development and progression. Tree Genetics Genomes 17:37.

Ye J^#, Wang X^#, Wang W^#, Yu H, Ai G, Li C, Sun P, Wang X, Li H, Ouyang B, Zhang J, Zhang Y, Han H, Giovannoni JJ, Fei Z*, Ye Z* (2021) Genome-wide association study reveals the genetic architecture of 27 agronomic traits in tomato. Plant Physiology 186:078-2092

Renner SS^#, Wu S^#, Perez-Escobar OA, Silber MV, Fei Z, Chomickie G (2021) A chromosome-level genome of a Kordofan melon illuminates the origin of domesticated watermelons. Proc Natl Acad Sci USA 118:e2101486118

Liao L, Zhang W, Zhang B, Fang T, Wang XF, Cai Y, Ogutu C, Gao L, Chen G, Nie X, Xu J, Zhang Q, Ren Y, Yu J, Wang C, Deng CH, Ma B, Zheng B, You CX, Hu DG, Espley R, Lin-Wang K, Yao JL, Allan AC, Khan A, Korban SS, Fei Z, Ming R, Hao YJ, Li L, Han Y (2021) Unraveling a genetic roadmap for improved taste in the domesticated apple. Molecular Plant 14:1454-1471

Guo N^#, Wang S^#, Gao L^#, Liu Y^#, Wang X, Lai E, Duan M, Wang G, Li J, Yang M, Zong M, Han S, Pei Y, Borm T, Sun H, Miao L, Liu D, Yu F, Zhang W, Ji H, Zhu C, Xu Y, Bonnema G*, Li J*, Fei Z*, Liu F* (2021) Genome sequencing sheds light on the contribution of structural variants to Brassica oleracea diversification. BMC Biology 19:93

Pan C, Yang D, Zhao X, Liu Y, Li M, Ye L, Ali M, Yu F, Lamin-Samu AT, Fei Z*, Lu G* (2021) PIF4 negatively modulates anther cold tolerance through temperature-dependent regulation of tapetal cell death in tomato. Plant Cell 33:2320-2339

Li Y, Cao K, Li N, Zhu G, Fang W, Chen C, Wang X, Guo J, Wang Q, Ding T, Wang J, Guan L, Wang J, Liu K, Guo W, Arus P, Huang S, Fei Z*, Wang L* (2021) Genomic analyses provide insights into peach local adaptation and responses to climate change. Genome Research 31:592-606

Zhang M, Xue C, Hu H, Li J, Xue Y, Wang R, Fan J, Zou C, Tao S, Qin M, Bai B, Li X, Gu C, Wu S, Chen X, Yang G, Liu Y, Sun M, Fei Z*, Zhang S*, Wu J* (2021) Genome-wide association studies provide insights into the genetic determination of fruit traits of pear. Nature Communications 12:1144

Chayut N, Yuan H, Saar Y, Zheng Y, Sun T, Zhou X, Hermanns A, Oren E, Faigenboim A, Hui M, Fei Z, Mazourek M, Burger J, Tadmor Y, Li L (2021) Comparative transcriptome analyses shed light on carotenoid production and plastid development in melon fruit. Hortic Research 8:112

Jiao C^#, Sun X^#, Yan X, Xu X, Yan Q, Gao M, Fei Z*, Wang X* (2021) Comparative transcriptome profiling of Chinese wild grapes provides insights into powdery mildew resistance. Phytopathology 111:2041-2051

Pereira L, Sapkota M, Alonge M, Zheng Y, Zhang Y, Razifard H, Taitano NK, Schatz M, Fernie A, Wang Y, Fei Z, Caicedo AL, Tieman D, Van Der Knaap E (2021) Natural genetic diversity in tomato flavor genes. Front Plant Sci 12:642828

Wang L, Kaya HB, Zhang N, Rai R, Willmann MR, Carpenter SC, Read AC, Martin F, Fei Z, Leach JE, Martin GB, Bogdanove1 A (2021) Spelling changes and fluorescent tagging with prime editing vectors for plants. Frontiers in Genome Editing 3:617553

Cheng C, Yu Q, Wang Y, Wang H, Dong Y, Ji Y, Zhou X, Li Y, Jiang C, Gan S, Zhao L, Fei Z, Gao J, Ma N (2021) Ethylene-regulated asymmetric growth of the petal base promotes flower opening in rose (Rosa hybrida). Plant Cell 33:1229-1251

Bednarek R, David M, Fuentes S, Kreuze J, Fei Z* (2021) Transcriptome analysis provides insights into the responses of sweet potato to sweet potato virus disease (SPVD). Virus Research 295:198293

Feiz L, Asakura Y, Mao L, Strickler SR, Fei Z, Rojas M, Barkan A, Stern DB (2021) CFM1, a member of the CRM-domain protein family, functions in chloroplast group II intron splicing in Setaria viridis. Plant J 105:639-648

Montrose DC, Nishiguchi R, Basu S, Staab HA, Zhou XK, Wang H, Meng L, Johncilla M, Cubillos-Ruiz JR, Morales DK, Wells MT, Simpson KW, Zhang S, Dogan B, Jiao C, Fei Z, Oka A, Herzog JW, Sartor RB, Dannenberg AJ (2021) Dietary fructose alters the composition, localization and metabolism of gut microbiota in association with worsening colitis. Cell Mol Gastroenterol Hepatol 11:525-550

Gimode W, Bao K, Fei Z, McGregor C (2021) QTL associated with gummy stem blight resistance in watermelon. Theor Appl Genet 134:573-584

Zhang L, Chen W, Jiang Q, Fei Z, Xiao M (2020) Genome analysis of plant growth-promoting rhizobacterium Pseudomonas chlororaphis subsp. aurantiaca JD37 and insights from comparison of genomics with three Pseudomonas strains. Microbiol Res 237:126483.

Yu F, Zhang W, Wang S, Wang H, Yu L, Zeng X, Fei Z*, Li J* (2021) Genome sequence of Fusarium oxysporum f. sp. conglutinans,the etiological agent of cabbage Fusarium wilt. Mol Plant Microbe Interact 34:210-213

2020

Wang X^#, Gao L^#, Jiao C, Stravoravdis S, Hosmani PS, Saha S, Zhang J, Mainiero S, Strickler SR, Catala C, Martin GB, Mueller LA, Vrebalov J, Giovannoni JJ, Wu S*, Fei Z* (2020) Genome of Solanum pimpinellifolium provides insights into structural variants during tomato breeding. Nature Communications 11:5817.

Sun X^#, Jiao C^#, Schwaninger H^#, Chao CT, Ma Y, Duan N, Khan A, Ban S, Xu K, Cheng L, Zhong GY*, Fei Z* (2020) Phased diploid genome assemblies and pan-genomes provide insights into the genetic history of apple domestication. Nature Genetics 52:1423-1432

Jiao C^#, Sorensen I^#, Sun X^#, Sun H, Behar H, Alseekh S, Philippe G, Lopez KP, Sun L, Reed R, Jeon S, Kiyonami R, Zhang S, Fernie AR, Brumer H, Domozych DS*, Fei Z*, Rose JKC* (2020) The Penium margaritaceum genome: Hallmarks of the origins of land plants. Cell 181:1097-1111.E12

Guo J, Cao K, Deng C, Li Y, Zhu G, Fang W, Chen C, Wang X, Wu J, Guan L, Wu S, Guo W, Yao JL*, Fei Z*, Wang L* (2020) An integrated peach genome structural variation map uncovers genes associated with fruit traits. Genome Biology 21:258

Zhou C, Olukolu B, Gemenet DC, Wu S, Gruneberg W, Cao MD, Fei Z, Zeng ZB, George AW, Khan A, Yencho GC, Coin LJM (2020) Assembly of whole-chromosome pseudomolecules for polyploid plant genomes using outbred mapping populations. Nature Genetics 52:1256-1264

Ma L, Wang Q, Mu J, Fu A, Wen C, Zhao X, Gao L, Li J, Shi K, Wang Y, Zhang X, Zhang X, Fei Z*, Grierson D*, Zuo J* (2020) The genome and transcriptome analysis of snake gourd provide insights into its evolution and fruit development and ripening. Horticulture Research 7:199

Rodriguez M, Scintu A, Posadinu CM, Xu Y, Nguyen CV, Sun H, Bitocchi E, Bellucci E, Papa R, Fei Z, Giovannoni JJ, Rau D, Attene G (2020) GWAS based on RNA-Seq SNPs and high-throughput phenotyping combined with climatic data highlights the reservoir of valuable genetic diversity in regional tomato landraces. Genes 11:1387.

Yu F, Wang S, Zhang W, Wang H, Yu L, Fei Z, Li J (2020) An R2R3-type myeloblastosis transcription factor MYB103 is involved in phosphorus remobilization. Food Production Processing Nutrition 2:24

Liang Y, Jiang C, Liu Y, Gao Y, Lu J, Aiwaili P, Fei Z, Jiang CZ, Hong B, Ma C, Gao J (2020) Auxin regulates sucrose transport to repress petal abscission in rose (Rosa hybrida). Plant Cell 32:3485-3499

Hasegawa DK, Shamimuzzaman M, Chen W, Simmons AM, Fei Z, Ling K-S (2020) Deep sequencing of small RNAs in the whitefly Bemisia tabaci reveals novel microRNAs potentially associated with begomovirus acquisition and transmission. Insects 11:562.

Grumet R, Fei Z, Levi A, Mazourek M, McCreight JD, Schultheis J, Weng Y, Hausbeck M, Kousik S, Ling KS, Linares-Ramirez A, McGregor C, Quesada-Ocampo L, Reddy U, Smart C, Wechter P, Wehner T, Wessel-Beaver L, Wintermantel WM (2020) The CucCAP project: leveraging applied genomics to improve disease resistance in cucurbit crops. Acta Horticulture 1294:91-104

Feiz L, Strickler SR, van Eck J, Mao L, Movahed N, Taylor C, Gourabathini P, Fei Z, Stern DB (2020) Setaria viridis chlorotic and seedling-lethal mutants define critical functions for chloroplast gene expression. Plant J 104:917-931

Yue J^#, Liu J^#, Tang W, Wu YQ, Tang X, Li W, Yang Y, Wang L, Huang S, Fang C, Zhao K, Fei Z*, Liu Y*, Zheng Y* (2020) Kiwifruit Genome Database (KGD): a comprehensive resource for kiwifruit genomics. Horticulture Research 7:117

Hoang NV^#, Choe G^#, Zheng Y^#, Aliaga Fandino AC, Sung I, Hur J, Kamran M, Park C, Kim H, Ahn H, Kim S, Fei Z, Lee JY (2020) Identification of conserved gene-regulatory networks that integrate environmental sensing and growth in the root cambium. Current Biology 30:2887-2900.E7

Xia C, Zheng Y, Huang J, Fei Z, Zhang C (2019) Identification of phloem mobile mRNAs using the Solanaceae heterograft system. Methods Mol Biol 2014:421-431

Ren Y, Sun H, Zong M, Guo S, Ren Z, Zhao J, Li M, Zhang J, Tian S, Wang J, Yu Y, Gong G, Zhang H, He H, Li L, Zhang X, Liu F, Fei Z, Xu Y (2020) Localization shift of a sugar transporter contributes to phloem unloading in sweet watermelons. New Phytologist 227:1858-1871

Wosula EN, Chen W, Amour M, Fei Z, Legg JP (2020) KASP genotyping as a molecular tool for diagnosis of cassava-colonizing Bemisia tabaci. Insects 11:305.

Yang Y, Cuenca J, Wang N, Liang Z, Sun H, Gutierrez B, Xi X, Arro J, Wang Y, Fan P, Londo J, Cousins P, Li S, Fei Z, Zhong G-Y (2020) A key 'foxy' aroma gene is regulated by homology-induced promoter indels in the iconic juice grape 'Concord'. Horticulture Research 7:67

Xie W, He C, Fei Z*, Zhang Y* (2020) Chromosome-level genome assembly of the greenhouse whitefly (Trialeurodes vaporariorum Westwood). Molecular Ecology Resources 20:995-1006

McQuinn RP, Gapper NE, Gray AG, Zhong S, Takayuki T, Fei Z, Fernie AR, Giovannoni JJ (2020) Manipulation of ZDS in tomato exposes carotenoid- and ABA-specific effects on fruit development and ripening. Plant Biotechnology J 18:2210-2224

Philippe G, Sorensen I, Jiao C, Sun X, Fei Z, Domozych DS, Rose JKC (2020) Cutin and suberin: assembly and origins of specialized lipidic cell wall scaffolds. Current Opinion Plant Biology 55:11-20

Guo S, Sun H, Xu Y*, Fei Z* (2020) Citrullus lanatus. Trends Genetics 36:456-457

Domozych DS, Sun L, Palacio-Lopez K, Reed R, Jeon S, Li M, Jiao C, Sorensen I, Fei Z, Rose JKC (2020) Endomembrane architecture and dynamics during secretion of the extracellular matrix of the unicellular charophyte, Penium margaritaceum. Journal Experimental Botany 71:3323-3339

Jiang S, Wang N, Chen M, Zhang R, Sun Q, Xu H, Zhang Z, Wang Y, Sui X, Wang S, Fang H, Zuo W, Su M, Zhang J, Fei Z, Chen X (2020) Methylation of MdMYB1 locus mediated by RdDM pathway regulates anthocyanin biosynthesis in apple. Plant Biotechnol J 18:1736-1748

Branham SE, Wechter P, Ling KS, Chanda B, Massey L, Zhao G, Guner N, Bello M, Kabelka E, Fei Z, Levi A (2020) QTL mapping of resistance to Fusarium oxysporum f. sp. niveum race 2 and Papaya ringspot virus in Citrullus amarus. Theor Appl Genet 133:677-687

Tan H, Wang X, Fei Z, Li H, Tadmor Y, Mazourek M, Li L (2020) Genetic mapping of green curd gene Gr in cauliflower. Theor Appl Genet 133:353-364

Gemenet DC, da Silva Pereira G, De Boeck B, Wood JC, Mollinari M, Olukolu BA, Diaz F, Mosquera V, Ssali RT, David M, Kitavi MN, Burgos G, Felde TZ, Ghislain M, Carey E, Swanckaert J, Coin LJM, Fei Z, Hamilton JP, Yada B, Yencho GC, Zeng ZB, Mwanga ROM, Khan A, Gruneberg WJ, Buell CR (2020) Quantitative trait loci and differential gene expression analyses reveal the genetic basis for negatively associated β-carotene and starch content in hexaploid sweetpotato [Ipomoea batatas (L.) Lam.]. Theor Appl Genet 133:23-36

2019

Guo S^#, Zhao S, Sun H^#, Wang X^#, Wu S^#, Lin T, Ren Y, Gao L, Deng Y, Zhang J, Lu X, Zhang H, Shang J, Gong G, Wen C, He N, Tian S, Li M, Liu J, Wang Y, Zhu Y, Jarret R, Levi A, Zhang X, Huang S*, Fei Z*, Liu W*, Xu Y* (2019) Resequencing of 414 cultivated and wild watermelon accessions identifies selection for fruit quality traits. Nature Genetics 51:1616-1623

Zhao G, Lian Q, Zhang Z, Fu Q, He Y, Ma S, Ruggieri V, Monforte AJ, Wang P, Julca I, Wang H, Liu J, Xu Y, Wang R, Ji J, Xu Z, Kong W, Zhong Y, Shang J, Pereira L, Argyris J, Zhang J, Mayobre C, Pujol M, Oren E, Ou D, Wang J, Sun D, Zhao S, Zhu Y, Li N, Katzir N, Gur A, Dogimont C, Schaefer H, Fan W, Bendahmane A, Fei Z, Pitrat M, Gabaldon T, Lin T, Garcia-Mas J, Xu Y, Huang S (2019) A comprehensive genome variation map of melon identifies multiple domestication events and loci influencing agronomic traits. Nature Genetics 51:1607-1615

Gao L^#, Gonda I^#, Sun H, Ma Q, Bao K, Tieman DM, Burzynski-Chang EA, Fish TL, Stromberg KA, Sacks GL, Thannhauser TW, Foolad MR, Diez MJ, Blanca J, Canizares J, Xu Y, van der Knaap E, Huang S, Klee HJ, Giovannoni JJ*, Fei Z* (2019) The tomato pan-genome uncovers new genes and a rare allele regulating fruit flavor. Nature Genetics 51:1044-1051

Rett-Cadman S, Colle M, Mansfeld BN, Barry C, Wang Y, Weng Y, Gao L, Fei Z, Grumet R (2019) QTL and transcriptomic analyses implicate cuticle transcription factor SHINE as a source of natural variation for epidermal traits in cucumber fruit. Front Plant Sci 10:1536

Muller LM, Flokova K, Schnabel E, Sun X, Fei Z, Frugoli J, Bouwmeester HJ, Harrison MJ (2019) A CLE-SUNN module regulates strigolactone content and fungal colonization in arbuscular mycorrhiza. Nature Plants 5:933-939

Kaur N, Chen W, Fei Z, Wintermantel WM (2019) Differences in gene expression in whitefly associated with CYSDV-infected and virus-free melon, and comparison with expression in whiteflies fed on ToCV- and TYLCV-infected tomato. BMC Genomics 20:654

Yang X, Chen W, Song X, Ma X, Cotto-Rivera RO, Kain W, Chua H, Chen Y-R, Fei Z, Wang P (2019) Mutation of ABC transporter ABCA2 confers resistance to Bt toxin Cry2Ab in Trichoplusia ni. Insect Biochem Mol Biol 112:103209

Collins K, Zhao K, Jiao C, Xu C, Cai X, Wang X, Ge C, Dai S, Wang Q, Wang Q, Fei Z*, Zheng Y* (2019) SpinachBase: a central portal for spinach genomics. Database 2019:baz072

Ye J, Li W, Ai G, Li C, Liu G, Chen W, Wang B, Wang W, Lu Y, Zhang J, Li H, Ouyang B, Zhang H, Fei Z, Giovannoni JJ, Ye Z, Zhang Y (2019) 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. PLoS Genet 15:e1008149

Wu S^#, Wang X^#, Reddy U^#, Sun H, Bao K, Gao L, Mao L, Patel T, Ortiz C, Abburi VL, Nimmakayala P, Branham S, Wechter P, Massey L, Ling KS, Kousik C, Hammar SA, Tadmor Y, Portnoy V, Gur A, Katzir N, Guner N, Davis A, Hernandez AG, Wright CL, McGregor C, Jarret R, Zhang X, Xu Y, Wehner TC, Grumet R, Levi A*, Fei Z* (2019) Genome of 'Charleston Gray', the principal American watermelon cultivar, and genetic characterization of 1,365 accessions in the U.S. National Plant Germplasm System watermelon collection. Plant Biotechnol J 17:2246-2258

Chen W^#, Wosula EN^#, Hasegawa DK, Casinga C, Shirima RR, Fiaboe KKM, Hanna R, Fosto A, Goergen G, Tamo M, Mahuku G, Murithi HM, Tripathi L, Mware B, Kumar LP, Ntawuruhunga P, Moyo C, Yomeni M, Boahen S, Edet M, Awoyale W, Wintermantel WM, Ling KS, Legg JP*, Fei Z* (2019) Genome of the African cassava whitefly Bemisia tabaci and distribution and genetic diversity of cassava-colonizing whiteflies in Africa. Insect Biochem Mol Biol 110:112-120

Wei Q^#, Guo L^#, Jiao C^#, Fei Z, Chen M, Cao J, Ding Y, Yuan Q (2019) Characterization of the developmental dynamics of the elongation of a bamboo internode during the fast growth stage. Tree Physiol 39:1201-1214

Peng B, Kang B, Wu H, Liu L, Liu L, Fei Z, Hong N, Gu Q (2019) Detection and genome characterization of a novel member of the genus Polerovirus from zucchini (Cucurbita pepo) in China. Arch Virol 164:2187-2191

Padmanabhan C, Ma Q, Shekasteband R, Stewart KS, Hutton SF, Scott JW, Fei Z*, Ling K-S* (2019) Comprehensive transcriptome analysis and functional characterization of PR-5 for its involvement in tomato Sw-7 resistance to tomato spotted wilt tospovirus. Scientific Reports 9:7673

Gao Y, Liu Y, Liang Y, Lu J, Jiang C, Fei Z, Jiang C-Z, Ma C, Gao J (2019) Rosa hybrida RhERF1 and RhERF4 mediate ethylene and auxin-regulated petal abscission by influencing pectin degradation. Plant J 99:1159-1171

Yu F, Wang S, Zhang W, Tang J, Wang H1, Yu L, Zhang X, Fei Z*, Li J* (2019) Genome-wide identification of genes encoding putative secreted E3 ubiquitin ligases and functional characterization of PbRING1 in the biotrophic protist Plasmodiophora brassicae. Curr Genet 65:1355-1365

Wang Y^#, Sun X^#, Ding Y, Fei Z, Jiao C, Fan M, Yao B, Xin P, Chu J, Wei Q (2019) Cellular and molecular characterization of a thick wall variant reveal a pivotal role of shoot apical meristem in bamboo culm transversal evolution. Journal Experimental Botany 70:3911-3926

Shrestha A, Bao K, Chen W, Wang P, Fei Z, Blissard GW (2019) Transcriptional responses of the Trichoplusia ni midgut to oral infection by the baculovirus Autographa californica Multiple Nucleopolyhedrovirus. J Virology 93:e00353-1

Gao M, Zhu Y, Yang J, Zhang H, Cheng C, Zhang Y, Wan R, Fei Z, Wang X (2019) Identification of the grape basic helix-loop-helix transcription factor family and characterization of expression patterns in response to different stresses. Plant Growth Regulation 88:19-39

Tang W^#, Sun X^#, Yue J^#, Tang X, Jiao C, Yang Y, Niu X, Miao M, Zhang D, Huang S, Shi W, Li M, Fang C, Fei Z*, Liu Y* (2019) Chromosome-scale genome assembly of kiwifruit Actinidia eriantha with single-molecule sequencing and chromatin interaction mapping. GigaScience 8:giz027

Chen W, Shakir S, Bigham M, Richter A, Fei Z, Jander G (2019) Genome sequence of the corn leaf aphid (Rhopalosiphum maidis Fitch). Gigascience 8:giz033

Wang L, Tang W, Hu Y, Zhang Y, Sun J, Guo X, Lu H, Yang Y, Fang C, Niu X, Yue J, Fei Z, Liu Y (2019) A MYB/bHLH complex regulates tissue-specific anthocyanin biosynthesis in the inner pericarp of red-centered kiwifruit Actinidia chinensis cv. Hongyang. Plant J 99:359-378

Liu W, Zhang J, Jiao C, Yin X, Fei Z*, Wu Q*, Chen K (2019) Transcriptome analysis provides insights into the regulation of metabolic processes during postharvest cold storage of loquat (Eriobotrya japonica) fruit. Horticulture Research 6:49

Silva KJP, Singh J, Bednarek R, Fei Z, Khan A (2019) Differential gene regulatory pathways and co-expression networks associated with fire blight infection in apple (Malus x domestica). Horticulture Research 6:35

Li Y, Cao K, Zhu G, Fang W, Chen C, Wang X, Zhao P, Guo J, Ding T, Guan L, Zhang Q, Guo W, Fei Z, Wang L (2019) Genomic analyses of an extensive collection of wild and cultivated accessions provide new insights into peach breeding history. Genome Biology 20:36

Zheng Y^#, Zhang N^#, Martin GB*, Fei Z* (2019) Plant Genome Editing Database (PGED): A call for submission of information about genome-edited plant mutants. Molecular Plant 12:127-129

Shamimuzzaman M, Hasegawa DK, Chen W, Simmons AM, Fei Z, Ling KS (2019) Genome-wide profiling of piRNAs in the whitefly Bemisia tabaci reveals cluster distribution and association with begomovirus transmission. PLoS One 14:e0213149

Piedra-Aguilera A^#, Jiao C^#, Luna AP, Villanueva F, Dabad, Esteve-Codina A, Diaz-Pendon JA, Fei Z, Bejarano ER, Castillo AG (2019) Integrated single-base resolution maps of transcriptome, sRNAome and methylome of Tomato yellow leaf curl virus (TYLCV) in tomato. Scientific Reports 9:2863

Ma X, Perna NT, Glasner JD, Hao J, Johnson S, Nasaruddin AS, Charkowski AO, Wu S, Fei Z, Perry KL, Stodghill P, Swingle B (2019) Complete genome sequence of Dickeya dianthicola ME23, a pathogen causing blackleg and soft rot diseases of potato. Microbiol Resour Announc 8:e01526-18

Pombo MA, Ramos RN, Zheng Y, Fei Z, Martin GB, Rosli HG (2019) Transcriptome-based identification and validation of reference genes for plant-bacteria interaction studies using Nicotiana benthamiana. Scientific Reports 9:1632

Zhang W, Wang S, Yu F, Tang J, Shan X, Bao K, Yu L, Wang H, Fei Z*, Li J* (2019) Genome-wide characterization and expression profiling of SWEET genes in cabbage (Brassica oleracea var. capitata L.) reveal their roles in chilling and clubroot disease responses. BMC Genomics 20:93

Wang A, Chen D, Ma Q, Rose JKC, Fei Z, Liu Y, Giovannoni JJ (2019) The tomato HIGH PIGMENT1/DAMAGED DNA BINDING PROTEIN 1 gene contributes to regulation of fruit ripening. Horticulture Research 6:15

Pinheiro PV, Wilson JR, Xu Y, Zheng Y, Rebelo AR, Fattah-Hosseini S, Kruse A, Santos Dos Silva R, Xu Y, Kramer M, Giovannoni J, Fei Z, Gray S, Heck ML (2019) Plant viruses transmitted in two different modes produce differing effects on small RNA-mediated processes in their aphid vector. Phytobiomes J 3:71-81

Watts-Williams SJ, Emmett BD, Levesque-Tremblay V, MacLean AM, Sun X, Satterlee JW, Fei Z, Harrison MJ (2019) Diverse Sorghum bicolor accessions show marked variation in growth and transcriptional responses to arbuscular mycorrhizal fungi. Plant Cell Environ 42:1758-1774

Chen W^#, Yang X^#, Tetreau G, Song X, Coutu C, Hegedus D, Blissard G, Fei Z*, Wang P* (2019) A high-quality chromosome-level genome assembly of a generalist herbivore, Trichoplusia ni. Molecular Ecology Resources 19:485-496

Fry W, Patev SP, Meyers K, Bao K, Fei Z (2019) Phytophthora infestans sporangia produced in culture and on tomato leaflet lesions show marked differences in indirect germination rates, aggressiveness, and global transcription profiles. Mol Plant Microbe Interact 32:515-526

Guo L^#, Sun X^#, Li Z, Wang Y, Fei Z, Jiao C, Feng J, Cui D, Feng X, Ding Y, Zhang C, Wei Q (2019) Morphological dissection and cellular and transcriptome characterizations of bamboo pith cavity formation reveal a pivotal role of genes related to programmed cell death. Plant Biotechnology J 17:982-997

Sun X, Chen W, Ivanov S, MacLean AM, Wight H, Ramaraj T, Mudge J, Harrison MJ*, Fei Z* (2019) Genome and evolution of the arbuscular mycorrhizal fungus Diversispora epigaea (formerly Glomus versiforme) and its bacterial endosymbionts. New Phytologist 221:1556-1573

Zheng Y, Wu S, Bai Y, Sun H, Jiao C, Guo S, Kun Zhao, Blanca J, Zhang Z, Huang S, Xu Y, Weng Y, Mazourek M, Reddy U, Ando K, McCreight JD, Schaffer AA, Burger J, Tadmor Y, Katzir N, Tang X, Liu Y, Giovannoni JJ, Ling K-S, Wechter WP, Levi A, Garcia-Mas J, Grumet R, Fei Z* (2019) Cucurbit Genomics Database (CuGenDB): a central portal for comparative and functional genomics of cucurbit crops. Nucleic Acids Research 47:D1128-D1136

Gonda I, Ashrafi H, Lyon DA, Strickler SR, Hulse-Kemp AM, Ma Q, Sun H, Stoffel K, Powell AF, Futrell S, Thannhauser TW, Fei Z, Deynze AEV, Mueller LA, Giovannoni JJ, Foolad MR (2019) Sequencing-based bin map construction of a tomato mapping population, facilitating high-resolution quantitative trait loci detection. Plant Genome 12:180010

Pan C, Yang D, Zhao X, Jiao C, Yan Y, Lamin-Samu AT, Wang Q, Xu X, Fei Z*, Lu G* (2019) Tomato stigma exsertion induced by high temperature is associated with the jasmonate signaling pathway. Plant Cell Environ 42:1205-1221

Zhang Z^#, Zheng Y^#, Ham BK, Zhang S, Fei Z, Lucas WJ (2019) Plant lncRNAs are enriched in and move systemically through the phloem in response to phosphate deficiency. J Integr Plant Biol 61:492-508

Yazdani M, Sun Z, Yuan H, Zeng S, Thannhauser TW, Vrebalov J, Ma Q, Xu Y, Fei Z, Van Eck J, Tian S, Tadmor Y, Giovannoni JJ, Li L (2019) Ectopic expression of ORANGE promotes carotenoid accumulation and fruit development in tomato. Plant Biotechnol J 17:33-49

2018

Wu S^#, Lau KH^#, Cao Q^#, Hamilton JP^#, Sun H^#, Zhou C, Eserman L, Gemenet DC, Olukolu BA, Wang H, Crisovan E, Godden GT, Jiao C, Wang X, Kitavi M, Manrique-Carpintero N, Vaillancourt B, Wiegert-Rininger K, Yang X, Bao K, Schaff J, Kreuze J, Gruneberg W, Khan A, Ghislain M, Ma D, Jiang J, Mwanga ROM, Leebens-Mack J, Coin LJM, Yencho GC, Buell CR*, Fei Z* (2018) Genome sequences of two diploid wild relatives of cultivated sweetpotato reveal targets for genetic improvement. Nature Communications 9:4580

Cai X, Xu C, Wang X, Wang S, Zhang Z, Fei Z, Wang Q (2018) Construction of genetic linkage map using genotyping-by-sequencing and identification of QTLs associated with leaf color in spinach. Euphytica 214:229

Yakir E, Fei Z, Sela N, Xu Y, Singh V, Dagar A, Joshi JR, Muller M, Munne-Bosch S, Giovannoni JJ, Vrebalov J, Friedman H (2018) MaMADS2 repression in banana fruits modifies hormone synthesis and signalling pathways prior to climacteric stage. BMC Plant Biology 18:267

Lau KH, Herrera Mdel R, Crisovan E, Wu S, Fei Z, Khan MA, Buell CR, Gemenet DC (2018) Transcriptomic analysis of sweet potato under dehydration stress identifies candidate genes for drought tolerance. Plant Direct 2:e00092

Lu P, Yu S, Chen Y, Zhou B, Tzeng D, Grierson D, Xiang J, Fei Z, Giovannoni JJ, Zhong S (2018) Genome encode analyses reveal the basis of convergent evolution of fleshy fruit ripening. Nature Plants 4:784-791

Shrestha A, Bao K, Wang P, Fei Z, Blissard GW (2018) Global analysis of baculovirus Autographa californica multiple nucleopolyhedrovirus gene expression in the midgut of the Lepidopteran host Trichoplusia ni. J Virology 92:e01277-18

Wang X, Bao K, Reddy UK, Bai Y, Hammar SA, Jiao C, Wehner TC, Ramirez-Madera AO, Weng Y, Grumet R*, Fei Z* (2018) The USDA cucumber (Cucumis sativus L.) collection: genetic diversity, population structure, genome-wide association studies and core collection development. Horticulture Research 5:64

Sui X^#, Nie J^#, Li X^#, Scanlon MJ, Zhang C, Zheng Y, Ma S, Shan N, Fei Z*, Turgeon R*, Zhang Z* (2018) Transcriptomic and functional analysis of cucumber (Cucumis sativus L.) fruit phloem during early development. Plant J 96:982-996

Rossel G, Mwanga ROM, Khan A, George AW, Fei Z, Yencho GC, Ellis D, Coin LJM (2018) Insights into population structure of East African sweetpotato cultivars from hybrid assembly of chloroplast genomes. Gates Open Res 2:41

Wu J^#, Wang Y^#, Xu J^#, Korban SS^#, Fei Z^#, Tao S^#, Ming R, Tai S, Khan AM, Postman JD, Gu C, Yin H, Zheng D, Qi K, Li Y, Wang R, Deng CH, Kumar S, Chagne D, Li X, Wu J, Huang X, Zhang H, Xie Z, Li X, Zhang M, Li Y, Yue Z, Fang X, Li J, Li L, Jin C, Qin M, Zhang J, Wu X, Ke Y, Wang J, Yang H, Zhang S (2018) Diversification and independent domestication of Asian and European pears. Genome Biology 19:77

Kumar P, Garrido E, Zhao K, Zheng Y, Alseekh S, Vargas-Ortiz E, Fernie AR, Fei Z, Poveda K, Jander G (2018) Tecia solanivora infestation increases tuber starch accumulation in Pastusa Suprema potatoes. J Integr Plant Biol 60:1083-1096

Xia C^#, Zheng Y^#, Huang J, Zhou X, Li R, Zha M, Wang S, Huang Z, Lan H, Turgeon R, Fei Z*, Zhang C* (2018) Elucidation of the mechanisms of long-distance mRNA movement in a Nicotiana benthamiana/tomato heterograft system. Plant Physiol 177:745-758

Ruiz-May E, Sorensen I, Fei Z, Zhang S, Domozych DS, Rose JKC (2018) The secretome and N-glycosylation profiles of the charophycean green alga, Penium margaritaceum, resemble those of embryophytes. Proteomes 6:14

Gonda I, Davidovich-Rikanati R, Bar E, Lev S, Jhirad P, Meshulam Y, Wissotsky G, Portnoy V, Burger J, Schaffer AA, Tadmor Y, Giovannoni JJ, Fei Z, Fait A, Katzir N, Lewinsohn E (2018) Differential metabolism of L-phenylalanine in the formation of aromatic volatiles in melon (Cucumis melo L.) fruit. Phytochemistry 148:122-131

Branham SE, Levi A, Katawczik M, Fei Z, Wechter WP (2018) Construction of a genome-anchored, high-density genetic map for melon (Cucumis melo L.) and identification of Fusarium oxysporum f. sp. melonis race 1 resistance QTL. Theor Appl Genet 131:829-837

Luan J^#, Sun X^#, Fei Z, Douglas AE (2018) Maternal inheritance of a single somatic animal cell displayed by the bacteriocyte in the whitefly Bemisia tabaci. Current Biology 28:p459-465.e3

Shinozaki Y^#, Nicolas P^#, Fernandez-Pozo N^#, Zheng Y, Evanich D, Shi Y, Xu Y, Ma Q, Snyder S, Martin L, Ruiz-May E, Thannhauser T, Chen C, Domozych D, Catala C, Fei Z, Mueller L, Giovannoni J, Rose J (2018) High-resolution spatiotemporal transcriptome mapping of tomato fruit development and ripening. Nature Communications 9: 364

Galpaz N, Gonda I, Shem-Tov D, Barad O, Tzuri G, Lev S, Fei Z, Xu Y, Lombardi N, Mao L, Jiao C, Harel-Beja R, Doron-Faigenboim A, Tzfadia O, Bar E, Meir A, Saar U, Fait A, Halperin E, Kenigswald M, Fallik E, Kol G, Ronen G, Burger J, Gur A, Tadmor Y, Portnoy V, Schaffer A, Lewinsohn E, Giovannoni J, Katzir N (2018) Deciphering genetic factors that determine melon fruit-quality traits using RNA-Seq-based high-resolution QTL and eQTL mapping. Plant J 94:169-191

Yuan Z^#*, Fang Y^#*, Zhang T^#, Fei Z^#, Han F^#, Liu C, Liu M, Xiao W, Zhang W, Wu S, Zhang M, Ju Y, Xu H, Dai H, Liu Y, Chen Y, Wang L, Zhou J, Guan D, Yan M, Xia Y, Huang X, Liu D, Wei H, Zheng H* (2018) The pomegranate (Punica granatum L.) genome provides insights into fruit quality and ovule developmental biology. Plant Biotechnol J 16:1363-1374

Wei Q^#*, Jiao C^#, Ding Y, Gao S, Guo L, Chen M, Hu P, Xia S, Ren G, Fei Z* (2018) Cellular and molecular characterizations of a slow-growth variant provide insights into the fast growth of bamboo. Tree Physiol 38:641-654

Meng D, He M, Bai Y, Xu H, Dandekar AM, Fei Z, Cheng L (2018) Decreased sorbitol synthesis leads to abnormal stamen development and reduced pollen tube growth via an MYB transcription factor, MdMYB39L, in apple (Malus domestica). New Phytologist 217:641-656

Hasegawa DK, Chen W, Zheng Y, Kaur N, Wintermantel WM, Simmons AM, Fei Z, Ling K-S (2018) Comparative transcriptome analysis reveals networks of genes activated in the whitefly, Bemisia tabaci when fed on tomato plants infected with Tomato yellow leaf curl virus. Virology 513:52-64

2017

Yan J, Chia J-C, Sheng H, Jung H, Zavodna T-O, Lu Z, Huang R, Jiao C, Craft E, Fei Z, Kochian LV, Vatamaniuk OK (2017) Arabidopsis pollen fertility requires the transcription factors CIT1 and SPL7 that regulate copper delivery to anthers and jasmonic acid synthesis. Plant Cell 29: 3012-3029

Arbelaez JD, Maron LG, Jobe TO, Pineros MA, Famoso AN, Rebelo AR, Singh N, Ma Q, Fei Z, Kochian L, McCouch SR (2017) ALUMINUM RESISTANCE TRANSCRIPTION FACTOR 1 (ART1) contributes to natural variation in aluminum resistance in diverse genetic backgrounds of rice (O. sativa). Plant Direct e00014

Wosula EN^#, Chen W^#, Fei Z, Legg JP (2017) Unravelling the genetic diversity among cassava Bemisia tabaci whiteflies using NextRAD sequencing. Genome Biol Evol 9:2958-2973

Pan C, Ye L, Zheng Y, Wang Y, Yang D, Liu X, Chen L, Zhang Y, Fei Z, Lu G (2017) Identification and expression profiling of microRNAs involved in the stigma exsertion under high-temperature stress in tomato. BMC Genomics 18:843.

Wu S^#, Shamimuzzaman M^#, Sun H^#, Salse J^#, Sui X, Wilder A, Wu Z, Levi A, Xu Y, Ling KS*, Fei Z* (2017) The bottle gourd genome provides insights into Cucurbitaceae evolution and facilitates mapping of a Papaya ringspot virus resistance locus. Plant J 92:963-975

Sun H^#, Wu S^#*, Zhang G, Jiao C, Guo S, Ren Y, Zhang J, Zhang H, Gong G, Jia Z, Zhang F, Tian J, Lucas WJ, Doyle JJ, Li H, Fei Z*, Xu Y* (2017) Karyotype stability and unbiased fractionation in the paleo-allotetraploid Cucurbita genomes. Molecular Plant 10:1293-1306

Duan N^#, Bai Y^#*, Sun H^#, Wang N^#, Ma Y, Li M, Wang X, Jiao C, Legall N, Mao L, Wan S, Wang K, He T, Feng S, Zhang Z, Mao Z, Shen X, Chen X, Jiang Y, Wu S, Yin C, Ge S, Yang L, Jiang S, Xu H, Liu J, Wang D, Qu C, Wang Y, Zuo W, Xiang L, Liu C, Zhang D, Gao Y, Xu Y, Xu K, Chao T, Fazio G, Shu H, Zhong GY, Cheng L, Fei Z*, Chen X* (2017) Genome re-sequencing reveals the history of apple and supports a two-stage model for fruit enlargement. Nature Communications 8:249.

Zheng Y^#, Ding B, Fei Z*, Wang Y^#* (2017) Comprehensive transcriptome analyses reveal tomato plant responses to tobacco rattle virus-based gene silencing vectors. Scientific Reports 7:9771

Wang Q, Yang S, Liu J, Terecskei K, Abraham E, Gombar A, Domonkos A, Szucs A, Kormoczi P, Wang T, Fodor L, Mao L, Fei Z, Kondorosi E, Kalo P, Kereszt A, Zhu H (2017) Host-secreted antimicrobial peptide enforces symbiotic selectivity in Medicago truncatula. Proc Natl Acad Sci USA 114:6854-6859

Niu X, Sun Y, Chen Z, Li R, Padmanabhan C, Ruan J, Kreuze JF, Ling K, Fei Z, Gao S (2017) Using small RNA-Seq data to detect siRNA duplexes induced by plant viruses. Genes 8:163

Xu C^#, Jiao C^#*, Sun H^#, Cai X, Wang X, Ge C, Zheng Y, Liu W, Sun X, Xu Y, Deng J, Zhang Z, Huang S, Dai S, Mou B, Wang Q, Fei Z*, Wang Q* (2017) Draft genome of spinach and transcriptome diversity of 120 Spinacia accessions. Nature Communications 8:15275

Cai X, Jiao C*, Sun H, Wang X, Xu C, Fei Z, Wang Q* (2017) The complete mitochondrial genome sequence of spinach, Spinacia oleracea L. Mitochondrial DNA Part B 2:339-340

Cox K, Meng F, Wilkins KE, Li F, Wang P, Booher NJ, Carpenter SCD, Chen L-Q, Zhen H, Gao X, Zheng Y, Fei Z, Yu JZ, Isakeit T, Wheeler T, Frommer WB, He P, Bogdanove AJ, Shan L (2017) TAL effector driven induction of a SWEET gene confers susceptibility to bacterial blight of cotton. Nature Communications 8:15588

Schwizer S, Kraus CM, Dunham DM, Zheng Y, Fernandez-Pozo N, Pombo MA, Fei Z, Chakravarthy S, Martin G (2017) The tomato kinase Pti1 contributes to production of reactive oxygen species in response to two flagellin-derived peptides and promotes resistance to Pseudomonas syringae infection. Mol Plant Microbe Interact 30:725-738

Fernandez-Pozo N, Zheng Y, Snyder S, Nicolas P, Shinozaki Y, Fei Z, Catala C, Giovannoni JJ, Rose JK, Mueller LA (2017) The Tomato Expression Atlas. Bioinformatics 33:2397-2398

Kaur N, Chen W, Zheng Y, Hasegawa DK, Ling KS, Fei Z, Wintermantel WM (2017) Transcriptome analysis of the whitefly, Bemisia tabaci MEAM1 during feeding on tomato infected with the crinivirus, Tomato chlorosis virus, identifies a temporal shift in gene expression and differential regulation of novel orphan genes. BMC Genomics 18:370.

Zheng Y^#, Wang Y^#*, Ding B, Fei Z* (2017) Comprehensive transcriptome analyses reveal that potato spindle tuber viroid triggers genome-wide changes in alternative splicing, inducible trans-acting activity of phasiRNAs and immune responses. J Virology 91:e00247-17

Xu C^#, Sun X^#*, Taylor A, Jiao C, Xu Y, Cai X, Wang X, Ge C, Pan G, Wang Q, Fei Z, Wang Q* (2017) Diversity, distribution, and evolution of tomato viruses in China uncovered by small RNA sequencing. J Virology 91:e00173-17

Gapper NE, Hertog MLATM, Lee J, Buchanan DA, Leisso RS, Fei Z, Qu G, Giovannoni JJ, Johnston JW, Schaffer RJ, Nicolai BM, Mattheis JP, Watkins CB, Rudell DR (2017) Delayed response to cold stress is characterized by successive metabolic shifts culminating in apple fruit peel necrosis. BMC Plant Biology 17:77

Tafolla-Arellano JC^#, Zheng Y^#, Sun H, Jiao C, Ruiz-May E, Hernandez-Onate M, Gonzalez-Leon A, Baez-Sanudo R, Fei Z, Rose JKC, Tiznado-Hernandez ME (2017) Transcriptome analysis of mango (Mangifera indica L) fruit epidermal peel to identify putative cuticle-associated genes. Scientific Reports 7:46163

Pombo MA, Zheng Y, Fei Z, Martin GB, Rosli HG (2017) Use of RNA-seq data to identify and validate RT-qPCR reference genes for studying the tomato-Pseudomonas pathosystem. Scientific Reports 7:44905

Giovannoni J, Nguyen C, Ampofo B, Zhong S, Fei Z (2017) The epigenome and transcriptional dynamics of fruit ripening. Annu Rev Plant Biol 68:61-84

Ligaba-Osena A, Fei Z, Liu J, Xu Y, Shaff J, Lee SC, Luan S, Kudla J, Kochian L, Pineros M (2017) Loss-of-function mutation of the calcium sensor CBL1 increases aluminum sensitivity in Arabidopsis. New Phytol 214:830-841

Omidvar V, Mohorianu I, Dalmay T, Zheng Y, Fei Z, Pucci A, Mazzucato A, Vecerova V, Sedlarova M, Fellner M (2017) Transcriptional regulation of male-sterility in 7B-1 male-sterile tomato mutant. PLoS One 12:e0170715

Sui X, Zheng Y, Li R, Padmanabhan C, Tian T, Groth-Helms D, Keinath AP, Fei Z, Ling K-S (2017) Molecular and biological characterization of Tomato mottle mosaic virus and development of RT-PCR detection. Plant Disease 101:704-711

Zheng Y^#, Gao S^#, Padmanabhan C, Li R, Galvez M, Gutierrez D, Fuentes S, Ling K-S, Kreuze J, Fei Z* (2017) VirusDetect: An automated pipeline for efficient virus discovery using deep sequencing of small RNAs. Virology 500:130-138

Wei Q^#*, Jiao C^#, Guo L, Ding Y, Cao J, Feng J, Dong X, Mao L, Sun H, Yu F, Yang G, Shi P, Ren G, Fei Z* (2017) Exploring key cellular processes and candidate genes regulating the primary thickening growth of Moso underground shoots. New Phytologist 214:81-96

Chayut N, Yuan H, Ohali S, Meir A, Saar U, Tzuri G, Zheng Y, Mazourek M, Gepstein S, Zhou X, Portnoy V, Lewinsohn E, Schaffer AA, Katzir N, Fei Z, Welsch R, Li L, Burger J, Tadmor Y (2017) Distinct mechanisms of the ORANGE protein in controlling carotenoid flux. Plant Physiol 173:376-389

2016

Huang J^#, Zhang C^#, Zhao X^#, Fei Z^#, Wan K, Zhang Z, Pang X, Yin X, Bai Y, Sun X, Gao L, Li R, Zhang J, Li X (2016) The jujube genome provides insights into genome evolution and the domestication of sweetness/acidity taste in fruit trees. PLoS Genetics 12:e1006433

Chen W^#, Hasegawa DK^#, Kaur N, Kliot A, Pinheiro PV, Luan J, Stensmyr MC, Zheng Y, Liu W, Sun H, Xu Y, Luo Y, Kruse A, Yang X, Kontsedalov S, Lebedev G, Fisher TW, Nelson DR, Hunter WB, Brown JK, Jander G, Cilia M, Douglas AE, Ghanim M, Simmons AM, Wintermantel WM*, Ling K-S*, Fei Z* (2016) The draft genome of whitefly Bemisia tabaci MEAM1, a global crop pest, provides novel insights into virus transmission, host adaptation, and insecticide resistance. BMC Biology 14:110

Wang L, Hu X, Jiao C, Li Z, Fei Z, Yan X, Liu C, Wang Y, Wang X (2016) Transcriptome analyses of seed development in grape hybrids reveals a possible mechanism influencing seed size. BMC Genomics 17:898

Zhang B, Tiemana DK, Jiao C, Xu Y, Chen K, Fei Z, Giovannoni JJ, Klee HJ (2016) Chilling-induced tomato flavor loss is associated with altered volatile synthesis and transient changes in DNA methylation. Proc Natl Acad Sci U S A 113:12580-12585.

Liu Z, Alseek S, Brotman Y, Zheng Y, Fei Z, Tieman D, Giovannoni J, Fernie A and Klee H (2016) Identification of a Solanum pennellii chromosome 4 fruit flavor and nutritional quality-associated metabolite QTL. Front Plant Sci 7:1671.

Zheng Y, Jiao C, Sun H, Rosli HG, Pombo MA, Zhang P, Banf M, Dai X, Martin GB, Giovannoni JJ, Zhao PX, Rhee SY, Fei Z* (2016) iTAK: a program for genome-wide prediction and classification of plant transcription factors, transcriptional regulators, and protein kinases. Molecular Plant 9:1667-1670.

Bordiya Y^#, Zheng Y^#, Nam JC, Bonnard AC, Choi HW, Lee BK, Kim JK, Klessig D, Fei Z*, Kang HG* (2016) Pathogen infection and MORC proteins affect chromatin accessibility of transposable elements and expression of their proximal genes in Arabidopsis. Mol Plant Microbe Interact 29:674-687

Gao Y, Liu C, Li X, Xu H, Liang Y, Ma N, Fei Z, Gao J, Jiang CZ, Ma C (2016) Transcriptome profiling of petal abscission zone and functional analysis of an Aux/IAA family gene RhIAA16 involved in petal shedding in rose. Front Plant Sci 7:1375

Pankratov I, McQuinn R, Schwartz J, Bar E, Fei Z, Lewinsohn E, Zamir D, Giovannoni JJ, Hirschberg J (2016) Fruit carotenoid deficient mutants in tomato reveal a function of the plastidial isopentenyl diphosphate isomerase (IDI1) in carotenoid biosynthesis. Plant J 88:82-94

Zhang Z, Zheng Y, Ham B-K, Chen J, Yoshida A, Kochian LV, Fei Z, Lucas WJ (2016) Vascular-mediated signalling involved in early phosphate stress response in plants. Nature Plants 2:16033

Chen J^#, Zheng Y^#, Qin L, Wang Y, Chen L, He Y, Fei Z, Lu G (2016) Identification of miRNAs and their targets through high-throughput sequencing and degradome analysis in male and female Asparagus officinalis. BMC Plant Biol 16:80

Worley JN, Pombo MA, Zheng Y, Dunham DM, Myers CR, Fei Z, Martin GB (2016) A novel method of transcriptome interpretation reveals a quantitative suppressive effect on tomato immune signaling by two domains in a single pathogen effector protein. BMC Genomics 17:229

Elitzur T, Yakir E, Quansah L, Fei Z, Vrebalov JT, Khayat E, Giovannoni JJ, Friedman H (2016) Banana MaMADS transcription factors are necessary for fruit ripening and molecular tools to promote shelf-life and food security. Plant Physiol 171:380-391

Yin X, Singer SD, Qiao H, Liu Y, Jiao C, Wang H, Li Z, Fei Z, Wang Y, Fan C, Wang X (2016) Insights into the mechanisms underlying ultraviolet-C induced resveratrol metabolism in grapevine (V. amurensis Rupr.) cv. 'Tonghua-3'. Front Plant Sci 7:503

Tang W^#, Zheng Y^#, Dong J, Yu J, Yue J, Liu F, Guo X, Huang S, Wisniewski M, Sun J, Niu X, Ding J, Liu J, Fei Z and Liu Y (2016) Comprehensive transcriptome profiling reveals long noncoding RNA expression and alternative splicing regulation during fruit development and ripening in kiwifruit (Actinidia chinensis). Front Plant Sci 7:335

Jing X, White TA, Luan J, Jiao C, Fei Z, Douglas AE (2016) Evolutionary conservation of candidate osmoregulation genes in plant phloem sap-feeding insects. Insect Mol Biol 25:251-258

Kim ES, Choe G, Sebastian J, Ryu KH, Mao L, Fei Z, Lee JY (2016) HAWAIIAN SKIRT regulates the quiescent center-independent meristem activity in Arabidopsis roots. Physiol Plant 157:221-233

Wang F, Sun Y, Ruan J, Chen R, Chen X, Chen C, Kreuze JF, Fei Z, Zhu X, Gao S (2016) Using small RNA deep sequencing data to detect human viruses. BioMed Research International 2016:2596782

Duan N, Sun H, Wang N, Fei Z, Chen X (2016) The complete mitochondrial genome sequence of Malus hupehensis var. pinyiensis. Mitochondrial DNA 27:2905-2906

Zuluaga AP, Vega-Arreguin JC, Fei Z, Ponnala L, Lee SJ, Matas AJ, Patev S, Fry WE, Rose JK (2016) Transcriptional dynamics of Phytophthora infestans during sequential stages of hemibiotrophic infection of tomato. Mol Plant Pathol 17:29.41

Zuluaga AP, Vega-Arreguin JC, Fei Z, Matas AJ, Patev S, Fry WE, Rose JKC (2016) Analysis of the tomato leaf transcriptome during successive hemibiotrophic stages of a compatible interaction with the oomycete pathogen Phytophthora infestans. Molecular Plant Pathology 17:42-54

2015

Zhang G, Ren Y, Sun H, Guo S, Zhang F, Zhang J, Zhang H, Jia Z, Fei Z, Xu Y, Li H (2015) A high-density genetic map for anchoring genome sequences and identifying QTLs associated with dwarf vine in pumpkin (Cucurbita maxima Duch.). BMC Genomics 16:1101

Yue J, Liu J, Ban R, Tang W, Deng L, Fei Z, Liu Y (2015) Kiwifruit Information Resource (KIR): a comparative platform for kiwifruit genomics. Database 2015:bav113

Zhang Z, Jiang S, Wang N, Li M, Ji X, Sun S, Liu J, Wang D, Xu H, Qi S, Wu S, Fei Z, Feng S, Chen X (2015) Identification of differentially expressed genes associated with apple fruit ripening and softening by suppression subtractive hybridization. PLoS One 10:e0146061

Padmanabhan C, Zheng Y, Li R, Fei Z, Ling KS (2015) Complete genome sequence of Southern tomato virus naturally infecting tomatoes in Bangladesh. Genome Announc 3:e01522-15

Padmanabhan C, Zheng Y, Li R, Martin GB, Fei Z, Ling KS (2015) Complete genome sequence of a tomato-infecting tomato mottle mosaic virus in New York. Genome Announc 3:e01523-15

Xu C^#, Jiao C^#, Zheng Y, Sun H, Liu W, Cai X, Wang X, Liu S, Xu Y, Mou B, Dai S, Fei Z*, Wang Q* (2015) De novo and comparative transcriptome analysis of cultivated and wild spinach. Scientific Reports 5:17706

Yang Y^#, Mao L^#, Jittayasothorn Y, Kang Y, Jiao C, Fei Z*, Zhong GY* (2015) Messenger RNA exchange between scions and rootstocks in grafted grapevines. BMC Plant Biology 15:251.

Chayut N, Yuan H, Ohali S, Meir A, Yeselson Y, Portnoy V, Zheng Y, Fei Z, Lewinsohn E, Katzir N, Schaffer AA, Gepstein S, Burger J, Li L, Tadmor Y (2015) A bulk segregant transcriptome analysis reveals metabolic and cellular processes associated with Orange allelic variation and fruit β-carotene accumulation in melon fruit. BMC Plant Biology 15:274

Holl HM, Gao S, Fei Z, Andrews C, Brooks SA (2015) Generation of a de novo transcriptome from equine lamellar tissue. BMC Genomics 16:739

Padmanabhan C, Zheng Y, Li R, Sun SE, Zhang D, Liu Y, Fei Z, Ling KS (2015) Complete Genome Sequence of Southern tomato virus Identified in China Using Next-Generation Sequencing. Genome Announc 3:e01226-15.

Luan JB, Chen W, Hasegawa DK, Simmons AM, Wintermantel WM, Ling KS, Fei Z, Liu SS, Douglas AE (2015) Metabolic coevolution in the bacterial symbiosis of whiteflies and related plant sap-feeding insects. Genome Biol Evol 7:2635-2647

Feder A, Burger J, Gao S, Lewinsohn E, Katzir N, Schaffer AA, Meir A, Davidovich-Rikanati R, Portnoy V, Gal-On A, Fei Z, Kashi Y, Tadmor Y (2015) A Kelch domain-containing F-box coding gene negatively regulates flavonoid accumulation in Cucumis melo L. Plant Physiol 169:1714-1726

Chen W^#, Hasegawa DK^#, Arumuganathan K, Simmons AM, Wintermantel WM, Fei Z*, Ling KS* (2015) Estimation of the whitefly Bemisia tabaci genome size based on k-mer and flow cytometric analyses. Insects 6:704-715

Yuan H, Owsiany K, Sheeja TE, Zhou X, Rodriguez C, Li Y, Chayut N, Yang Y, Welsch R, Thannhauser T, Parthasarathy M, Xu Q, Deng X, Fei Z, Schaffer AA, Katzir N, Burger J, Tadmor Y, Li L (2015) A single amino acid substitution in an ORANGE protein promotes carotenoid overaccumulation in Arabidopsis. Plant Physiol 169:421-431

Spiegelman Z, Ham BK, Zhang Z, Toal TW, Brady SM, Zheng Y, Fei Z, Lucas WJ, Wolf S (2015) A tomato phloem-mobile protein regulates the shoot:root ratio by mediating auxin response in distant organs. Plant J 83:853-863

Wang N, Zheng Y, Duan N, Zhang Z, Ji X, Jiang S, Sun S, Yang L, Bai Y, Fei Z, Chen X (2015) Comparative transcriptomes analysis of red- and white-fleshed apples in an F1 population of Malus sieversii f. niedzwetzkyana crossed with M. domestica 'Fuji'. PLoS One 10:e0133468

Li R, Zheng Y, Fei Z, Ling KS (2015) Complete genome sequence of an emerging melon necrotic spot virus isolate infecting greenhouse cucumber in North America. Genome Announc 3:e00775-15

Sun L, Rodriguez GR, Clevenger JP, Illa-Berenguer E, Lin J, Joshua J, Blakeslee JJ, Liu W, Fei Z, Wijeratne A, Meulia T, van der Knaap E (2015) Candidate gene selection and detailed morphological evaluations of fs8.1, a quantitative trait locus controlling tomato fruit shape. Journal Experimental Botany 66:6471-6482

Pattison RJ^#, Csukasi F^#, Zheng Y, Fei Z, van der Knaap E, Catala C (2015) Comprehensive tissue-specific transcriptome analysis reveals distinct regulatory programs during early tomato fruit development. Plant Physiol 168:1684-1701

Wu T, Wang Y, Zheng Y, Fei Z, Dandekar AM, Xu K, Han Z, Cheng L (2015) Suppressing sorbitol synthesis substantially alters the global expression profile of stress response genes in apple (Malus domestica) leaves. Plant Cell Physiol 56:1748-1761

Guo S, Sun H, Zhang H, Liu J, Ren Y, Gong G, Jiao C, Zheng Y, Yang W, Fei Z*, Xu Y* (2015) Comparative transcriptome analysis of cultivated and wild watermelon during fruit development. PLoS ONE 10:e0130267

Zhang Z^#, Mao L^#, Chen H, Bu F, Li G, Sun J, Li S, Sun H, Jiao C, Blakely R, Pan J, Cai R, Luo R, Van de Peer Y, Jacobsen E, Fei Z*, Huang S* (2015) Genome-wide mapping of structural variations reveals a copy number variant that determines reproductive morphology in cucumber. Plant Cell 27:1595-1604

Zheng Y^#, Wang Y^#, Wu J, Ding B*, Fei Z* (2015) A dynamic evolutionary and functional landscape of plant phased small interfering RNAs. BMC Biology 13:32

Shinozaki Y, Hao S, Kojima M, Sakakibara H, Ozeki-Iida Y, Zheng Y, Fei Z, Zhong S, Giovannoni JJ, Rose JK, Okabe Y, Heta Y, Ezura H, Ariizumi T (2015) Ethylene suppresses tomato fruit set through modification of gibberellin metabolism. Plant J 83:237-251

Li R, Zheng Y, Fei Z, Ling K-S (2015) First complete genome sequence of an emerging cucumber green mottle mosaic virus isolate in North America. Genome Announc 3:e00452-15

Jiao C, Gao M, Wang X*, Fei Z* (2015) Transcriptome characterization of three wild Chinese Vitis uncovers a large number of distinct disease related genes. BMC Genomics 16:223

Frank MH, Edwards MB, Schultz ER, McKain MR, Fei Z, Sorensen I, Rose JKC, Scanlon MJ (2015) Dissecting the molecular signatures of apical cell-type shoot meristems from two ancient land plant lineages. New Phytologist 207:893-904

Tzuri G, Zhou X, Chayut N, Yuan H, Portnoy V, Meir A, Sa'ar U, Baumkoler F, Mazourek M, Lewinsohn E, Fei Z, Schaffer AA, Gepstein S, Li L, Burger J, Katzir N, Tadmor Y (2015) A "golden" SNP in CmOr governs fruit flesh color of melon (Cucumis melo). Plant J 82:267-279

Freilich S, Lev S, Gonda I, Reuveni E, Portnoy V, Oren E, Lohse M, Galpaz N, Bar E, Tzuri G, Wissotsky G, Meir A, Burger J, Tadmor Y, Schaffer A, Fei Z, Giovannoni J, Lewinsohn E, Katzir N (2015) Systems approach for exploring the intricate associations between sweetness, color and aroma in melon fruits. BMC Plant Biology 15:71

Cheng C, Jiao C, Singer SD, Gao M, Xu X, Zhou Y, Li Z, Fei Z, Wang Y, Wang X (2015) Gibberellin-induced changes in the transcriptome of grapevine (Vitis labrusca x V. vinifera) cv. Kyoho flowers. BMC Genomics 16:128

Zhang J, Yuan H, Fei Z, Pogson BJ, Zhang L, Li L (2015) Molecular characterization and transcriptome analysis of orange head Chinese cabbage (Brassica rapa L. ssp. pekinensis). Planta 241:1381-1394

Li R, Gao S, Berendsen S, Fei Z, Ling KS (2015) Complete genome sequence of a novel genotype of squash mosaic virus infecting squash in Spain. Genome Announc 3:e01583-14.

Li N, Chen YR, Ding Z, Li P, Wu Y, Zhang A, Yu S, Giovannoni JJ, Fei Z, Zhang W, Xiang JZ, Xu C, Liu B, Zhong S (2015) Nonuniform gene expression pattern detected along the longitudinal axis in the matured rice leaf. Scientific Reports 5:8015

Manohar M, Tian M, Moreau M, Park SW, Choi HW, Fei Z, Friso G, Asif M, Manosalva P, von Dahl CC, Shi K, Ma S, Dinesh-Kumar SP, O'Doherty I, Schroeder FC, van Wijk KJ, Klessig DF (2015) Identification of multiple salicylic acid-binding proteins using two high throughput screens. Frontiers in Plant Science 5:777

Childers R, Danies G, Myers KL, Fei Z, Small IM, Fry W (2015) Acquired resistance to mefenoxam in sensitive isolates of Phytophthora infestans. Phytopathology 105:342-349

Chen S, Kim C, Lee JM, Lee HA, Fei Z, Wang L, Apel K (2015) Blocking the QB-binding site of photosystem II by tenuazonic acid, a non-host-specific toxin of Alternaria alternata, activates singlet oxygen-mediated and EXECUTER-dependent signaling in Arabidopsis. Plant Cell Environ 38:1069-1080

2014

Li F, Cheng C, Cui F, de Oliveira MV, Yu X, Meng X, Intorne AC, Babilonia K, Li M, Li B, Chen S, Ma X, Xiao S, Zheng Y, Fei Z, Metz RP, Johnson CD, Koiwa H, Sun W, Li Z, Filho GA, Shan L, He P (2014) Modulation of RNA polymerase II phosphorylation downstream of pathogen perception orchestrates plant immunity. Cell Host Microbe 16:748-758

Lin T, Zhu G, Zhang J, Xu X, Yu Q, Zheng Z, Zhang Z, Lun Y, Li S, Wang X, Huang Z, Li J, Zhang C, Wang T, Zhang Y, Wang A, Zhang Y, Lin K, Li C, Xiong G, Xue Y, Mazzucato A, Causse M, Fei Z, Giovannoni JJ, Chetelat RT, Zamir D, Stadler T, Li J, Ye Z, Du Y, Huang S (2014) Genomic analyses provide insights into the history of tomato breeding. Nature Genetics 46:1220-1226

Pombo MA, Zheng Y, Fernandez-Pozo N, Dunham DM, Fei Z, Martin GB (2014) Transcriptomic analysis reveals tomato genes whose expression is induced specifically during effector-triggered immunity and identifies the Epk1 protein kinase which is required for the host response to three bacterial effector proteins. Genome Biology 15:492

Padmanabhan C, Gao S, Li R, Zhang S, Fei Z, Ling K-S (2014) Complete genome sequence of an emerging genotype of Tobacco streak virus in the United States. Genome Announc 2:e01138-14

Chen Y-R, Zhong S, Fei Z, Gao S, Zhang S, Li Z, Wang P, Blissard GW (2014) Transcriptome responses of the host, Trichoplusia ni, to infection by the baculovirus, Autographa californica Multiple Nucleopolyhedrovirus (AcMNPV). J Virology 88:13781-13797

Bolger A, Scossa F, Bolger ME, Lanz C, Maumus F, Tohge T, Quesneville H, Alseekh S, Sorensen I, Lichtenstein G, Fich EA, Conte M, Keller H, Schneeberger K, Schwacke R, Ofner I, Vrebalov J, Xu Y, Osorio S, Aflitos SA, Schijlen E, Jimenez-Gomez JM, Ryngajllo M, Kimura S, Kumar R, Koenig D, Headland LR, Maloof JN, Sinha N, van Ham RC, Lankhorst RK, Mao L, Vogel A, Arsova B, Panstruga R, Fei Z, Rose JK, Zamir D, Carrari F, Giovannoni JJ, Weigel D, Usadel B, Fernie AR (2014) The genome of the stress-tolerant wild tomato species Solanum pennellii. Nature Genetics 46:1034-1038

Cohen S^#, Itkin M^#, Yeselson Y, Tzuri G, Portnoy V, Harel-Baja R, Lev S, Sa'ar U, Davidovitz-Rikanati R, Baranes N, Bar E, Wolf D, Petreikov M, Shen S, Ben-Dor S, Rogachev I, Aharoni A, Ast T, Schuldiner M, Belausov E, Eshed R, Ophir R, Sherman A, Frei B, Neuhaus HE, Xu Y, Fei Z, Giovannoni J, Lewinsohn E, Tadmor Y, Paris HS, Katzir N, Burger Y, Schaffer AA (2014) The PH gene determines fruit acidity and contributes to the evolution of sweet melons. Nature Communications 5:4026

Yang Y, Ma C, Xu Y, Wei Q, Imtiaz M, Lan H, Gao S, Cheng L, Wang M, Fei Z, Hong B, Gao J (2014) A zinc finger protein regulates flowering time and abiotic stress tolerance in chrysanthemum by modulating gibberellin biosynthesis. Plant Cell 26:2038-2054

Liu N, Wu S, Van Houten J, Wang Y, Ding B, Fei Z, Clarke TH, Reed JW, van der Knaap E (2014) Down-regulation of AUXIN RESPONSE FACTORS 6 and 8 by microRNA 167 leads to floral development defects and female sterility in tomato. Journal Experimental Botany 65:2507-2520

Gao M, Zhang H, Guo C, Cheng C, Guo R, Mao L, Fei Z, Wang X (2014) Evolutionary and expression analyses of basic zipper transcription factors in the highly homozygous model grape PN40024 (Vitis vinifera L.). Plant Molecular Biology Reporter 32:1085-1102

Milner MJ, Mitani-Ueno N, Yamaji N, Yokosho K, Craft E, Fei Z, Ebbs S, Zambrano MC, Ma JF, Kochian LV (2014) Root and shoot transcriptome analysis of two ecotypes of Noccaea caerulescens uncovers the role of NcNramp1 in Cd hyperaccumulation. Plant J 78:398-410

Nguyen CV, Vrebalov JT, Gapper NE, Zheng Y, Zhong S, Fei Z, Giovannoni JJ (2014) Tomato GOLDEN2-LIKE transcription factors reveal molecular gradients that function during fruit development and ripening. Plant Cell 26:585-601

Li R, Fei Z, Ling K-S (2014) Molecular and biological properties of tomato necrotic stunt virus and development of a sensitive real-time RT-PCR assay. Archives Virology 159:353-358

Sorensen I, Fei Z, Andreas A, Willats WG, Domozych DS, Rose JK (2014) Stable transformation and reverse genetic analysis of Penium margaritaceum: A platform for studies of Charophyte green algae, the immediate ancestors of land plants. Plant J 77:339-351

2013

Rosli HG, Zheng Y, Pombo MA, Zhong S, Bombarely A, Fei Z, Collmer A, Martin GB (2013) Transcriptomics-based screen for genes induced by flagellin and repressed by pathogen effectors identifies a cell wall-associated kinase involved in plant immunity. Genome Biology 14:R139

Grassi S, Piro G, Lee JM, Zheng Y, Fei Z, Dalessandro G, Giovannoni JJ, S Lenucci MS (2013) Comparative genomics reveals candidate carotenoid pathway regulators of ripening watermelon fruit. BMC Genomics 14:781

Qi J, Liu X, Shen D, Miao H, Xie B, Li X, Zeng P, Wang S, Shang Y, Gu X, Du Y, Li Y, Lin T, Yuan J, Yang X, Chen J, Chen H, Xiong X, Huang K, Fei Z, Mao L, Tian L, Stadler T, Renner SS, Kamoun S, Lucas WJ, Zhang Z, Huang S (2013) A genomic variation map provides insights into the genetic basis of cucumber domestication and diversity. Nature Genetics 45: 1510-1515

Shen D^#, Sun H^#, Huang M, Zheng Y, Qiu Y, Li X*, Fei Z* (2013) Comprehensive analysis of expressed sequence tags from cultivated and wild radish (Raphanus spp.). BMC Genomics 14:721

Huang S^#, Ding J^#, Deng D^#, Tang W^#, Sun H^#, Liu D^#, Zhang L^#, Niu X, Zhang X, Meng M, Yu J, Liu J, Han Y, Shi W, Zhang D, Cao S, Wei Z, Cui Y, Xia Y, Zeng H, Bao K, Lin L, Min Y, Zhang H, Miao M, Tang X, Zhu Y, Sui Y, Li G, Sun H, Yue J, Sun J, Liu F, Zhou L, Lei L, Zheng X, Liu M, Huang L, Song J, Xu C, Li J, Ye K, Zhong S, Lu B-R, He G, Xiao F, Wang H-L, Zheng H*, Fei Z*, Liu Y* (2013) Draft genome of the kiwifruit Actinidia chinensis. Nature Communications 4:2640

Li R, Gao S, Fei Z, Ling K-S (2013) Complete genome sequence of a new Tobamovirus naturally infecting tomatoes in Mexico. Genome Announc 1:e00794-13

Xu Y^#, Gao S^#, Yang Y, Huang M, Cheng L, Wei Q, Fei Z, Gao J, Hong B (2013) Transcriptome sequencing and whole genome expression profiling of chrysanthemum under dehydration stress. BMC Genomics 14:662

Castandet B, Hotto AM, Fei Z, Stern DB (2013) Strand-specific RNA sequencing uncovers chloroplast ribonuclease functions. FEBS Letters 587:3096-3101

Pei H, Ma N, Tian J, Luo J, Chen J, Li J, Zheng Y, Chen X, Fei Z, Gao J (2013) A NAC transcription factor controls ethylene-regulated cell expansion in flower petals. Plant Physiol 163: 775-791

Pei H, Ma N, Chen J, Zheng Y, Tian J, Zhang S, Fei Z, Gao J (2013) Integrative analysis of miRNA and mRNA profiles in response to ethylene in rose petals during flower opening. PLoS ONE 8:e64290

Chen D, Xu G, Tang W, Jing Y, Ji Q, Fei Z, Lin R (2013) Antagonistic bHLH/bZIP transcription factors form transcriptional modules that integrate light and reactive oxygen species signaling in Arabidopsis. Plant Cell 25:1657-1673

Chen Y-R, Zhong S, Fei Z, Hashimoto Y, Xiang J, Zhang S, Blissard GW (2013) The transcriptome of the baculovirus Autographa californica Multiple Nucleopolyhedrovirus (AcMNPV) in Trichoplusia ni cells. J Virology 87:6391-6405

Martin L, Fei Z, Giovannoni J, Rose JK (2013) Catalyzing plant science research with RNA-seq. Front Plant Sci 4:66

Hou H, Li J, Gao M, Singer SD, Wang H, Mao L, Fei Z, Wang X (2013) Genomic organization, phylogenetic comparison and differential expression of the SBP-box family genes in grape. PLoS ONE 8:e59358

Gonda I, Lev S, Bar E, Sikron N, Portnoy V, Davidovich-Rikanati R, Burger J, Schaffer AA, Tadmor Y, Giovannonni JJ, Huang M, Fei Z, Katzir N, Fait A, Lewinsohn E (2013) Catabolism of L-methionine in the formation of sulfur and other volatiles in melon (Cucumis melo L.) fruit. Plant J 74:458-472

Zhong S^#*, Fei Z^#*, Chen YR, Zheng Y, Huang M, Vrebalov J, McQuinn R, Gapper N, Liu B, Xiang J, Shao Y, Giovannoni JJ* (2013) Single-base resolution methylomes of tomato fruit development reveal epigenome modifications associated with ripening. Nature Biotechnology 31:154-159

Shen D, Sun H, Huang M, Zheng Y, Li X, Fei Z* (2013) RadishBase: A database for genomics and genetics of radish. Plant Cell Physiol 54:e3

Wang YQ, Yang Y, Fei Z, Yuan H, Fish T, Thannhauser TW, Mazourek M, Kochian LV, Wang X, Li L (2013) Proteomic analysis of chromoplasts from six crop species reveals insights into chromoplast function and development. Journal Experimental Botany 64:949-961

Guo S^#, Zhang J^#, Sun H^#, Salse J^#, Lucas W^#, Zhang H, Zheng Y, Mao L, Ren Y, Wang Z, Min J, Guo X, Murat F, Ham B, Zhang Z, Gao S, Huang M, Xu Y, Zhong S, Bombarely A, Mueller L, Zhao H, He H, Zhang Y, Zhang Z, Huang S, Tan T, Pang E, Lin K, Hu Q, Kuang H, Ni P, Wang B, Liu J, Kou Q, Hou W, Zou X, Jiang J, Gong G, Klee K, Schoof H, Huang Y, Hu X, Dong S, Liang D, Wang J, Wu K, Xia Y, Zhao X, Zheng Z, Xing M, Liang X, Huang B, Lv T, Wang J, Yin Y, Yi H, Li R, Wu M, Levi A, Zhang X, Giovannoni J, Wang J*, Li Y*, Fei Z*, Xu Y* (2013) The draft genome of watermelon (Citrullus lanatus) and resequencing of 20 diverse accessions. Nature Genetics 45:51-58

Melo JO, Lana UG, Pineros MA, Alves VM, Guimaraes CT, Liu J, Zheng Y, Zhong S, Fei Z, Maron LG, Schaffert RE, Kochian LV, Magalhaes JV (2013) Incomplete transfer of accessory loci influencing SbMATE expression underlies genetic background effects for aluminum tolerance in sorghum. Plant J 73:276-288

Levi A, Thies JA, Wechter P, Harrison HF, Simmons AM, Reddy UK, Nimmakayala P, Fei Z (2013) High frequency oligonucleotides: targeting active gene (HFO-TAG) markers revealed wide genetic diversity among Citrullus spp. accessions useful for enhancing disease or pest resistance in watermelon cultivars. Genetic Resources Crop Evolution 60:427-440

Matas AJ, Fei Z, Giovannoni JJ, Rose JKC (2013) Developments in tomato transcriptomics. In Genetics, Genomics and Breeding in Fruits and Vegetable Crops Edited by Leidl B, Slade A, Hurst S, Labate JA, Stommel JR. pp382-402

2012

The Tomato Genome Consortium (2012) The tomato genome sequence provides insights into fleshy fruit evolution. Nature 485:635-641 (Authors from Fei lab: Fei Z, Zheng Y, Huang M, Gao S, Mao L)

Chen Y-R, Zheng Y, Liu B, Zhong S*, Giovannoni J, Fei Z* (2012) A cost-effective method for Illumina small RNA-Seq library preparation using T4 RNA ligase 1 adenylated adapters. Plant Methods 8:4

Zhang Y, Gao M, Singer SD, Fei Z, Wang H, Wang X (2012) Genome-wide identification and analysis of the TIFY gene family in grape. PLoS ONE 7:e44465

Gao M, Niu J, Zhao S, Jiao C, Xu W, Fei Z, Wang X (2012) Characterization of Erysiphe necator-responsive genes in Chinese wild Vitis quinquangularis. Int J Mol Sci 13:11497-11519

Li R, Gao S, Hernandez AG, Wechter WP, Fei Z*, Ling K-S* (2012) Deep sequencing of small RNAs in tomato for virus and viroid identification and strain differentiation. PLoS ONE 7:e37127

Huang S, Gao Y, Liu J, Peng X, Niu X, Fei Z, Cao S, Liu Y (2012) Genome-wide analysis of WRKY transcription factors in Solanum lycopersicum. Mol Genet Genomics 287:495-513

Gao M, Wang Q, Wan R, Fei Z, Wang X (2012) Identification of genes differentially expressed in grapevine associated with resistance to Elsinoe ampelina through suppressive subtraction hybridization. Plant Physiol Biochem 58:253-268

Ouyang B, Fei Z, Joung JG, Kolenovsky A, Koh C, Nowak J, Caplan A, Keller WA, Cui Y, Cutler AJ, Tsang EW (2012) Transcriptome profiling and methyl homeostasis of an Arabidopsis mutant deficient in S-adenosylhomocysteine hydrolase1 (SAHH1). Plant Mol Biol 79:315-331

Lee JM, Joung JG, McQuinn R, Chung MY, Fei Z, Tieman D, Klee H, Giovannoni J (2012) Combined transcriptome, genetic diversity and metabolite profiling in tomato fruit reveals the ethylene response factor SlERF6 to play an important role in ripening and carotenoid accumulation. Plant J 70:191-204

Lopez-Casado G, Covey PA, Bedinger PA, Mueller LA, Thannhauser TW, Zhang S, Fei Z, Giovannoni JJ, Rose JK (2012) Enabling proteomic studies with RNA-Seq: The proteome of tomato pollen as a test case. Proteomics 12:761-774

Zhang Y, Mao L, Wang H, Brocker C, Yin X, Vasiliou V, Fei Z*, Wang X* (2012) Genome-wide identification and analysis of grape aldehyde dehydrogenase (ALDH) gene superfamily. PLoS ONE 7:e32153

2011

Zheng Y, Zhao L, Gao J, Fei Z* (2011) iAssembler: a package for de novo assembly of Roche-454/Sanger transcriptome sequences. BMC Bioinformatics 12:453

Hotto AM, Schmitz RJ, Fei Z, Ecker JR, Stern DB (2011) Unexpected diversity of chloroplast noncoding RNAs as revealed by deep sequencing of the Arabidopsis transcriptome. G3: Genes, Genomes, Genetics 1:559-570

Zhou X, Fei Z, Thannhauser TW, Li L (2011) Transcriptome analysis of ectopic chloroplast development in green curd cauliflower (Brassica oleracea L. var. botrytis). BMC Plant Biology 11:169

Matas AJ, Yeats TH, Buda GJ, Zheng Y, Chatterjee S, Tohge T, Ponnala L, Adato A, Aharoni A, Stark R, Fernie AR, Fei Z, Giovannoni JJ, Rose JK (2011) Tissue- and cell-type specific transcriptome profiling of expanding tomato fruit provides insights into metabolic and regulatory specialization and cuticle formation. Plant Cell 23:3893-3910

Li Z, Zhang Z, Yan P, Huang S, Fei Z, Lin K (2011) RNA-Seq improves annotation of protein-coding genes in the cucumber genome. BMC Genomics 12:540

Guo S, Liu J, Zheng Y, Huang M, Zhang H, Gong G, He H, Ren Y, Zhong S, Fei Z*, Xu Y* (2011) Characterization of transcriptome dynamics during watermelon fruit development: sequencing, assembly, annotation and gene expression profiles. BMC Genomics 12:454

Zhong S*, Joung JG, Zheng Y, Chen YR, Liu B, Shao Y, Xiang JZ, Fei Z*, Giovannoni JJ* (2011) High-throughput Illumina strand-specific RNA sequencing library preparation. Cold Spring Harb Protoc 2011:940-949

Fei Z*, Liu Y (2011) Genomic and functional genomic resources of melon. In Genetics, Genomics and Breeding of Cucurbits. Edited by Wang Y-H, Behera TK, Kole C. pp286-308

Rohrmann J, Tohge T, Alba R, Osorio S, Caldana C, McQuinn R, Arvidsson S, van der Merwe MJ, Riano-Pachon DM, Mueller-Roeber B, Fei Z, Nesi AN, Giovannoni JJ, Fernie AR (2011) Combined transcription factor profiling, microarray analysis and metabolite profiling reveals the transcriptional control of metabolic shifts occurring during tomato fruit development. Plant J 68:999-1013

Osorio S, Alba R, Damasceno CM, Lopez-Casado G, Lohse M, Zanor MI, Tohge T, Usadel B, Rose JK, Fei Z, Giovannoni JJ, Fernie AR (2011) 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. Plant Physiol 157:405-425

Sorensen I, Pettolino FA, Bacic A, Ralph J, Lu F, O'Neill MA, Fei Z, Rose JK, Domozych DS, Willats WG (2011) The charophycean green algae provide insights into the early origins of plant cell walls. Plant J 68:201-211

Diaz A, Fergany M, Formisano G, Ziarsolo P, Blanca J, Fei Z, Staub JE, Zalapa JE, Cuevas HE, Dace G, Oliver M, Boissot N, Dogimont C, Pitrat M, Hofstede R, van Koert P, Harel-Beja R, Tzuri G, Portnoy V, Cohen S, Schaffer A, Katzir N, Xu Y, Zhang H, Fukino N, Matsumoto S, Garcia-Mas J, Monforte AJ (2011) A consensus linkage map for molecular markers and quantitative trait loci associated with economically important traits in melon (Cucumis melo L.). BMC Plant Biology 11:111

Lu G, Guo S, Zhang H, Geng L, Song F, Fei Z*, Xu Y* (2011) Transcriptional profiling of watermelon during its incompatible interaction with Fusarium oxysporum f. sp. niveum. European J Plant Pathology 131:585-601

Clepet C, Joobeur T, Zheng Y, Jublot D, Huang M, Truniger V, Boualem A, Hernandez-Gonzalez ME, Dolcet-Sanjuan R, Portnoy V, Mascarell-Creus A, Cano-Delgado AI, Katzir N, Bendahmane A, Giovannoni JJ, Aranda MA, Garcia-Mas J, Fei Z* (2011) Analysis of expressed sequence tags generated from full-length enriched cDNA libraries of melon. BMC Genomics 12:252

Zhou X, McQuinn R, Fei Z, Wolters AM, Van Eck J, Brown C, Giovannoni JJ, Li L (2011) Regulatory control of high levels of carotenoid accumulation in potato tubers. Plant Cell Environment 34:1020-1030

Dai N, Cohen S, Portnoy V, Tzuri G, Harel-Beja R, Pompan-Lotan M, Carmi N, Zhang G, Diber A, Pollock S, Karchi H, Yeselson Y, Petreikov M, Shen S, Sahar U, Hovav R, Lewinsohn E, Tadmor Y, Granot D, Ophir R, Sherman A, Fei Z, Giovannoni J, Burger Y, Katzir N, Schaffer AA (2011) Metabolism of soluble sugars in developing melon fruit: a global transcriptional view of the metabolic transition to sucrose accumulation. Plant Mol Biol 76:1-18

Fei Z*, Joung JG, Tang X, Zheng Y, Huang M, Lee JM, McQuinn R, Tieman DM, Alba R, Klee HJ, Giovannoni JJ (2011) Tomato functional genomics database: a comprehensive resource and analysis package for tomato functional genomics. Nucleic Acids Res 39:D1156-D1163

2010

Costa F, Alba R, Schouten H, Soglio V, Gianfranceschi L, Serra S, Musacchi S, Sansavini S, Costa G, Fei Z, Giovannoni J (2010) Use of homologous and heterologous gene expression profiling tools to characterize transcription dynamics during apple fruit maturation and ripening. BMC Plant Biology 10:229

Gong P, Zhang J, Li H, Yang C, Zhang C, Zhang X, Khurram Z, Zhang Y, Wang T, Fei Z, Ye Z (2010) Transcriptional profiles of drought-responsive genes in modulating transcription signal transduction, and biochemical pathways in tomato. Journal Experimental Botany 61:3563-3575

Guo S, Zheng Y, Joung JG, Liu S, Zhang Z, Crasta OR, Sobral BW, Xu Y, Huang S*, Fei Z* (2010) Transcriptome sequencing and comparative analysis of cucumber flowers with different sex types. BMC Genomics 11:384

Levi A, Wechter WP, Harris KR, Davis AR, Fei Z (2010) High-frequency oligonucleotides in watermelon expressed sequenced tag-unigenes are useful in producing polymorphic polymerase chain reaction markers among watermelon genotypes. Journal American Society Horticulture Science 135:369-378

Harel-Beja R, Tzuri G, Portnoy V, Lotan-Pompan M, Lev S, Cohen S, Dai N, Yeselson L, Meir A, Libhaber SE, Avisar E, Melame T, van Koert P, Verbakel H, Hofstede R, Volpin H, Oliver M, Fougedoire A, Stalh C, Fauve J, Copes B, Fei Z, Giovannoni J, Ori N, Lewinsohn E, Sherman A, Burger J, Tadmor Y, Schaffer AA, Katzir N (2010) A genetic map of melon highly enriched with fruit quality QTLs and EST markers, including sugar and carotenoid metabolism genes. Theoretical Applied Genetics 121:511-533

Zeng S, Xiao G, Guo J, Fei Z, Xu Y, Roe BA, Wang Y (2010) Development of a EST dataset and characterization of EST-SSRs in a traditional Chinese medicinal plant, Epimedium sagittatum (Sieb. Et Zucc.) Maxim. BMC Genomics 11:94

Joshi J, Joung JG, Fei Z, and Jander G (2010) Interdependence of threonine, methionine and isoleucine metabolism in plants: Accumulation and transcriptional regulation under abiotic stress. Amino Acids 39:933-947

2009

Rhee JK, Joung JG, Chang JH, Fei Z, Zhang BT (2009) Identification of cell cycle-related regulatory motifs using a kernel canonical correlation analysis. BMC Genomics 10(Suppl 3):S29

Huang S, Li R, Zhang Z, Li L, Gu X, Fan W, Lucas WJ, Wang X, Xie B, Ni P, Ren Y, Zhu H, Li J, Lin K, Jin W, Fei Z, Li G, Staub J, Kilian A, van der Vossen EA, Wu Y, Guo J, He J, Jia Z, Ren Y, Tian G, Lu Y, Ruan J, Qian W, Wang M, Huang Q, Li B, Xuan Z, Cao J, Asan, Wu Z, Zhang J, Cai Q, Bai Y, Zhao B, Han Y, Li Y, Li X, Wang S, Shi Q, Liu S, Cho WK, Kim JY, Xu Y, Heller-Uszynska K, Miao H, Cheng Z, Zhang S, Wu J, Yang Y, Kang H, Li M, Liang H, Ren X, Shi Z, Wen M, Jian M, Yang H, Zhang G, Yang Z, Chen R, Liu S, Li J, Ma L, Liu H, Zhou Y, Zhao J, Fang X, Li G, Fang L, Li Y, Liu D, Zheng H, Zhang Y, Qin N, Li Z, Yang G, Yang S, Bolund L, Kristiansen K, Zheng H, Li S, Zhang X, Yang H, Wang J, Sun R, Zhang B, Jiang S, Wang J, Du Y, Li S (2009) The genome of the cucumber, Cucumis sativus L. Nature Genetics 41:1275-1281

Joung JG, Corbett AM, Fellman SM, Tieman DM, Klee HJ, Giovannoni JJ, Fei Z* (2009) Plant MetGenMAP: an integrative analysis system for plant systems biology. Plant Physiology 151:1758-1768

Dal Cin V, Kevany B, Fei Z, Klee HJ (2009) Identification of Solanum habrochaites loci that quantitatively influence tomato fruit ripening-associated ethylene emissions. Theoretical Applied Genetics 119:1183-1192

Marchive C, Yehudai-Resheff S, Germain A, Fei Z, Jiang X, Judkins J, Wu H, Fernie AR, Fait A, Stern DB (2009) Abnormal physiological and molecular mutant phenotypes link chloroplast polynucleotide phosphorylase to the phosphorus deprivation response in Arabidopsis. Plant Physiology 151:905-924

Mueller L, Lankhorst RK, Tanksley SD, Giovannoni JJ, White R, Vrebalov J, Fei Z, et al. (2009) A snapshot of the emerging tomato genome sequence. Plant Genome 2:78-92

Joung J-G, Fei Z* (2009) Computational identification of condition-specific miRNA targets based on gene expression profiles and sequence information. BMC Bioinformatics 10(Suppl 1):S34

Joung J-G, Fei Z* (2009) Identification of microRNA regulatory modules in Arabidopsis via a probabilistic graphical model. Bioinformatics 25:387-393

Mathieu S, Dal Cin V, Fei Z, Li H, Bliss P, Taylor M, Klee H, Tieman D (2009) Flavor compounds in tomato fruits: identification of loci and potential pathways affecting volatile composition. Journal Experimental Botany 60:325-337

2008

Liu S, Xu L, Xu Y, Yang Q, Fei Z, Chen H, Huang S (2008) Genetic association of ETHYLENE-INSENSITIVE3-like sequence with the sex-determining M locus in cucumber (Cucumis sativus L.). Theoretical Applied Genetics 117:927-933

Crasta OR, Folkerts O, Fei Z, Mane SP, Evans C, Martino-Catt S, Bricker B, Yu G, Du L, Sobral BW (2008) Genome sequence of Brucella abortus vaccine strain S19 compared to virulent strains yields candidate virulence genes. PLoS ONE 3:e2193.

Zimmer S, Fei Z, Stern D (2008) Genome-based analysis of Chlamydomonas reinhardtii exoribonucleases and poly(A) polymerases predicts unexpected organellar and exosomal features. Genetics 179:125-136

Wechter P, Levi A, Harris K, Davis A, Fei Z, Katzir N, Giovannoni J, Salman-Minkov A, Hernandez A, Thimmapuram J, Tadmor Y, Portnoy V, Trebitsh T (2008) Gene expression in developing watermelon fruit. BMC Genomics 9:275

Wang XP, Wang Y, Fei Z (2008) Identification and characterization of resistance gene analogues from wild Chinese Vitis species. Journal Horticulture Science Biotechnology 83:345-350

Itaya A, Bundschuh R, Archual A, Joung J, Fei Z, Dai X, Zhao P, Tang Y, Nelson R, Ding B (2008) Small RNAs in tomato fruit and leaf development. BBA - Gene Regulatory Mechanisms 1779:99-107

2007

Djavani MM, Crasta OR, Zapata JC, Fei Z, Folkerts O, Sobral B, Swindells M, Bryant JL, Davis H, Pauza CD, Lukashevich IS, Hammamieh R, Jett M, Salvato MS (2007). Early blood profiles of virus infection in a monkey model for Lassa Fever. Journal Virology 81:7960-7973

Dan Y, Fei Z, Rothan C (2007) MicroTom - A new model system for plant genomics. Genes Genomes Genomics 1:167-179

Ouyang B, Yang T, Li H, Zhang L, Zhang Y, Zhang J, Fei Z*, Ye Z* (2007) Identification of early salt stress response genes in tomato root by suppression subtractive hybridization and microarray analysis. Journal Experimental Botany 58:207-220

2006 and before

Gilchrist C, Houpt E, Trapaidze N, Fei Z, Crasta O, Asgharpour A, Evans C, Martino-Catt C, Baba D, Stroup S, Hamano S, Ehrenkaufer G, Okada O, Singh U, Nozaki T, Mann B, Petri Jr. W (2006) Impact of intestinal colonization and invasion on the E. histolytica transcriptome. Molecular Biochemical Parasitology 147:163-176

Fei Z*, Tang X, Alba R, Giovannoni J* (2006) Tomato Expression Database (TED): A suite of data presentation and analysis tools. Nucleic Acids Research 34:D766-770

Alba R, Payton P, Fei Z, McQuinn R, Debbie P, Martin GB, Tanksley SD, Giovannoni JJ (2005) Transcriptome and selected metabolite analyses reveal multiple points of ethylene control during tomato fruit development. Plant Cell 17:2954-2965

Fei Z, Tang X, Alba R, White J, Ronning C, Martin G, Tanksley S, Giovannoni J (2004) Comprehensive EST analysis of tomato and comparative genomics of fruit ripening. Plant Journal 40:47-59

Alba R, Fei Z, Payton P, Liu Y, Moore S, Debbie P, Gordon J, Rose J, Martin G, Tanksley S, Bouzayen M, Jahn M, Giovannoni J (2004) ESTs, cDNA microarrays, and gene expression profiling: tools for dissecting plant physiology and development. Plant Journal 39:697-714