Publications

2025

• Zhang J, … , Chen F*, Zheng Y* (2025) Phased telomere-to-telomere super-pangenome: definitive reference genome in plants. Trends in Plant Science.
• Fan J, Zhang Y, Nie X, Liu Y, Wei S, Peng H, Li H, Zhang M, Ning L, … , Zheng Y* (2025) Comprehensive curation and validation of genomic datasets for chestnut. Scientific Data 12: 860.
• Lai E, Guo S, Wu P, Qu M, Yu X, Hao C, Li S, Peng H, Yi Y, Zhou M, Fu G, Li X, Liu H, Zheng Y*, Wang X*, Fei Z*, Gao L* (2025) Genome of root celery and population genomic analysis reveal the complex breeding history of celery. Plant Biotechnology Journal 23:946-959
• Li B, Li X, Wang Y, Liu X, Li K, Li R, Faiz MU, Darlington UT, Rao Z, Wu Q, Yue Y, Wang S, Fei Z, Liu Y, Zheng Y, Yue J (2025) KPGD: A kiwifruit pangenome database for comprehensive mining of genetic diversity in the genus Actinidia. Plant Communications 6:101373

2024

• Li X, Huo L, Li X, Zhang C, Gu M, Fan J, Xu C, Gong J, Hu X, Zheng Y, … (2024) Genomes of diverse Actinidia species provide insights into cis-regulatory motifs and genes associated with critical traits. BMC Biology 22: 200.
• Li H, Zhai X, Peng H, Qing Y, Deng Y, Zhou S, Bei T, Tian J, Zhang J, … , Zheng Y* (2024) Chromosomal level genome assemblies of two Malus crabapple cultivars Flame and Royalty. Scientific Data 11: 201.
• Li J, Cai H, Peng H, Deng Y, Zhou S, Tian J, Zhang J, Hu Y, Qin X, Yao Y, … , Zheng Y* (2024) The chromosome-level genome assembly of the dwarfing apple interstock Malus hybrid SH6. Scientific Data 11: 552.
• Peng H, Yi Y, Li J, Qing Y, Zhai X, Deng Y, Tian J, Zhang J, Hu Y, Qin X, … , Zheng Y* (2024) A haplotype-resolved genome assembly of Malus domestica Red Fuji. Scientific Data 11: 592.
• 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
• 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

2023

• 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 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

• 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
• 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
• 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.

2021

• 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
• 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

2020

• 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

2019

• 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
• 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
• 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
• 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
• 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
• 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
• 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

2018

• 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
• 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
• 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
• 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

• 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.
• 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
• 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
• 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
• 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
• 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
• 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

• 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
• 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
• 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
• 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

2015

• 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
• 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
• 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.
• 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
• 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
• 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

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
• 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
• 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

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
• 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
• 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
• 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
• 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

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

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
• 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
• 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
• 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
• 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

• 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