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Jinfeng Chen - Publications

Affiliations: 
2013- Microbiology and Plant Pathology University of California, Riverside, Riverside, CA, United States 
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43 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2024 Jia H, Tan S, Cai Y, Guo Y, Shen J, Zhang Y, Ma H, Zhang Q, Chen J, Qiao G, Ruan J, Zhang YE. Low-input PacBio sequencing generates high-quality individual fly genomes and characterizes mutational processes. Nature Communications. 15: 5644. PMID 38969648 DOI: 10.1038/s41467-024-49992-6  0.336
2024 Wang Y, Zhou F, Li Y, Yu X, Wang Y, Zhao Q, Feng X, Chen J, Lou Q. Characterization of the CsCENH3 protein and centromeric DNA profiles reveal the structures of centromeres in cucumber. Horticulture Research. 11: uhae127. PMID 38966863 DOI: 10.1093/hr/uhae127  0.306
2024 Liu Y, Cheng Z, Chen W, Wu C, Chen J, Sui Y. Establishment of genome-editing system and assembly of a near-complete genome in broomcorn millet. Journal of Integrative Plant Biology. PMID 38695644 DOI: 10.1111/jipb.13664  0.372
2023 Chen J, Liu Y, Liu M, Guo W, Wang Y, He Q, Chen W, Liao Y, Zhang W, Gao Y, Dong K, Ren R, Yang T, Zhang L, Qi M, et al. Pangenome analysis reveals genomic variations associated with domestication traits in broomcorn millet. Nature Genetics. PMID 38036791 DOI: 10.1038/s41588-023-01571-z  0.388
2023 Sun C, Zhang A, Chen J, Schaack S. "Junk" that matters: the role of transposable elements in bumblebee genome evolution. Current Opinion in Insect Science. 101103. PMID 37604302 DOI: 10.1016/j.cois.2023.101103  0.413
2023 He Q, Tang S, Zhi H, Chen J, Zhang J, Liang H, Alam O, Li H, Zhang H, Xing L, Li X, Zhang W, Wang H, Shi J, Du H, et al. A graph-based genome and pan-genome variation of the model plant Setaria. Nature Genetics. PMID 37291196 DOI: 10.1038/s41588-023-01423-w  0.608
2023 Xia L, Wang H, Zhao X, Obel HO, Yu X, Lou Q, Chen J, Cheng C. Chloroplast Pan-Genomes and Comparative Transcriptomics Reveal Genetic Variation and Temperature Adaptation in the Cucumber. International Journal of Molecular Sciences. 24. PMID 37240287 DOI: 10.3390/ijms24108943  0.396
2022 Sun Y, Liu Y, Shi J, Wang L, Liang C, Yang J, Chen J, Chen M. Biased mutations and gene losses underlying diploidization of the tetraploid broomcorn millet genome. The Plant Journal : For Cell and Molecular Biology. PMID 36575912 DOI: 10.1111/tpj.16085  0.352
2022 Liu N, Xu Y, Li Q, Cao Y, Yang D, Liu S, Wang X, Mi Y, Liu Y, Ding C, Liu Y, Li Y, Yuan YW, Gao G, Chen J, et al. A lncRNA fine-tunes salicylic acid biosynthesis to balance plant immunity and growth. Cell Host & Microbe. PMID 35908550 DOI: 10.1016/j.chom.2022.07.001  0.579
2022 Chen J, Cheng J, Chen X, Inoue M, Liu Y, Song CX. Whole-genome long-read TAPS deciphers DNA methylation patterns at base resolution using PacBio SMRT sequencing technology. Nucleic Acids Research. PMID 35849350 DOI: 10.1093/nar/gkac612  0.337
2022 Liao Y, Wang J, Zhu Z, Liu Y, Chen J, Zhou Y, Liu F, Lei J, Gaut BS, Cao B, Emerson JJ, Chen C. The 3D architecture of the pepper genome and its relationship to function and evolution. Nature Communications. 13: 3479. PMID 35710823 DOI: 10.1038/s41467-022-31112-x  0.317
2022 Xia L, Cheng C, Zhao X, He X, Yu X, Li J, Wang Y, Chen J. Characterization of the mitochondrial genome of Cucumis hystrix and comparison with other cucurbit crops. Gene. 146342. PMID 35219813 DOI: 10.1016/j.gene.2022.146342  0.328
2021 Yu X, Wang P, Li J, Zhao Q, Ji C, Zhu Z, Zhai Y, Qin X, Zhou J, Yu H, Cheng X, Isshiki S, Jahn M, Doyle JJ, Ottosen CO, ... ... Chen J, et al. Whole-Genome Sequence of Synthesized Allopolyploids in Reveals Insights into the Genome Evolution of Allopolyploidization. Advanced Science (Weinheim, Baden-Wurttemberg, Germany). 8: 2004222. PMID 33977063 DOI: 10.1002/advs.202004222  0.416
2021 Zhai Y, Yu X, Zhou J, Li J, Tian Z, Wang P, Meng Y, Zhao Q, Lou Q, Du S, Chen J. Complete chloroplast genome sequencing and comparative analysis reveals changes to the chloroplast genome after allopolyploidization in Cucumis. Genome. PMID 33460340 DOI: 10.1139/gen-2020-0134  0.388
2020 Zou X, Du Y, Wang X, Wang Q, Zhang B, Chen J, Chen M, Doyle JJ, Ge S. Genome evolution in Oryza allopolyploids of various ages: Insights into the process of diploidization. The Plant Journal : For Cell and Molecular Biology. PMID 33145857 DOI: 10.1111/tpj.15066  0.414
2020 Chen J, Lu L, Robb SMC, Collin M, Okumoto Y, Stajich JE, Wessler SR. Genomic diversity generated by a transposable element burst in a rice recombinant inbred population. Proceedings of the National Academy of Sciences of the United States of America. PMID 33020276 DOI: 10.1073/pnas.2015736117  0.698
2020 Njogu MK, Yang F, Li J, Wang X, Ogweno JO, Chen J. A novel mutation in TFL1 homolog sustaining determinate growth in cucumber (Cucumis sativus L.). Tag. Theoretical and Applied Genetics. Theoretische Und Angewandte Genetik. PMID 32857171 DOI: 10.1007/s00122-020-03671-4  0.321
2020 Li R, Qu H, Chen J, Wang S, Chater JM, Zhang L, Wei J, Zhang YM, Xu C, Zhong WD, Zhu J, Lu J, Feng Y, Chen W, Ma R, et al. Inference of Chromosome-Length Haplotypes Using Genomic Data of Three or a Few More Single Gametes. Molecular Biology and Evolution. PMID 32668004 DOI: 10.1093/Molbev/Msaa176  0.416
2019 Chen J, Lu L, Benjamin J, Diaz S, Hancock CN, Stajich JE, Wessler SR. Tracking the origin of two genetic components associated with transposable element bursts in domesticated rice. Nature Communications. 10: 641. PMID 30733435 DOI: 10.1038/S41467-019-08451-3  0.688
2018 Yu J, Golicz AA, Lu K, Dossa K, Zhang Y, Chen J, Wang L, You J, Fan D, Edwards D, Zhang X. Insight into the evolution and functional characteristics of the pan-genome assembly from sesame landraces and modern cultivars. Plant Biotechnology Journal. PMID 30315621 DOI: 10.1111/Pbi.13022  0.368
2018 Ou S, Chen J, Jiang N. Assessing genome assembly quality using the LTR Assembly Index (LAI). Nucleic Acids Research. PMID 30107434 DOI: 10.1093/Nar/Gky730  0.535
2018 Song Z, Stajich JE, Xie Y, Liu X, He Y, Chen J, Hicks GR, Wang G. Comparative analysis reveals unexpected genome features of newly isolated Thraustochytrids strains: on ecological function and PUFAs biosynthesis. Bmc Genomics. 19: 541. PMID 30016947 DOI: 10.1186/S12864-018-4904-6  0.519
2018 Liao Y, Zhang X, Li B, Liu T, Chen J, Bai Z, Wang M, Shi J, Walling JG, Wing RA, Jiang J, Chen M. Comparison of Oryza sativa and Oryza brachyantha genomes reveals selection-driven gene escape from the centromeric regions. The Plant Cell. PMID 29967288 DOI: 10.1105/Tpc.18.00163  0.412
2017 Lu L, Chen J, Robb SMC, Okumoto Y, Stajich JE, Wessler SR. Tracking the genome-wide outcomes of a transposable element burst over decades of amplification. Proceedings of the National Academy of Sciences of the United States of America. PMID 29158416 DOI: 10.1073/Pnas.1716459114  0.672
2017 Chen J, Wrightsman TR, Wessler SR, Stajich JE. RelocaTE2: a high resolution transposable element insertion site mapping tool for population resequencing. Peerj. 5: e2942. PMID 28149701 DOI: 10.7717/Peerj.2942  0.661
2016 Wu Z, Zhang T, Li L, Xu J, Qin X, Zhang T, Cui L, Lou Q, Li J, Chen J. Identification of a stable major-effect QTL (Parth 2.1) controlling parthenocarpy in cucumber and associated candidate gene analysis via whole genome re-sequencing. Bmc Plant Biology. 16: 182. PMID 27553196 DOI: 10.1186/s12870-016-0873-6  0.344
2016 Bai Z, Chen J, Liao Y, Wang M, Liu R, Ge S, Wing RA, Chen M. The impact and origin of copy number variations in the Oryza species. Bmc Genomics. 17: 261. PMID 27025496 DOI: 10.1186/S12864-016-2589-2  0.484
2014 Wang M, Yu Y, Haberer G, Marri PR, Fan C, Goicoechea JL, Zuccolo A, Song X, Kudrna D, Ammiraju JS, Cossu RM, Maldonado C, Chen J, Lee S, Sisneros N, et al. The genome sequence of African rice (Oryza glaberrima) and evidence for independent domestication. Nature Genetics. 46: 982-8. PMID 25064006 DOI: 10.1038/Ng.3044  0.415
2014 Wu Z, Jia L, Shen J, Jiang B, Qian C, Lou Q, Li J, Chen J. The complete chloroplast genome sequence of the wild cucumber Cucumis hystrix Chakr. (Cucumis, cucurbitaceae). Mitochondrial Dna. PMID 24450715 DOI: 10.3109/19401736.2013.878915  0.358
2013 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, et al. A genomic variation map provides insights into the genetic basis of cucumber domestication and diversity. Nature Genetics. 45: 1510-5. PMID 24141363 DOI: 10.1038/Ng.2801  0.387
2013 Chen J, Huang Q, Gao D, Wang J, Lang Y, Liu T, Li B, Bai Z, Luis Goicoechea J, Liang C, Chen C, Zhang W, Sun S, Liao Y, Zhang X, et al. Whole-genome sequencing of Oryza brachyantha reveals mechanisms underlying Oryza genome evolution. Nature Communications. 4: 1595. PMID 23481403 DOI: 10.1038/Ncomms2596  0.516
2012 Yang L, Liu T, Li B, Sui Y, Chen J, Shi J, Wing RA, Chen M. Comparative sequence analysis of the Ghd7 orthologous regions revealed movement of Ghd7 in the grass genomes. Plos One. 7: e50236. PMID 23185584 DOI: 10.1371/Journal.Pone.0050236  0.441
2012 Gao D, Chen J, Chen M, Meyers BC, Jackson S. A highly conserved, small LTR retrotransposon that preferentially targets genes in grass genomes. Plos One. 7: e32010. PMID 22359654 DOI: 10.1371/Journal.Pone.0032010  0.496
2011 Jiang B, Lou Q, Wu Z, Zhang W, Wang D, Mbira KG, Weng Y, Chen J. Retrotransposon- and microsatellite sequence-associated genomic changes in early generations of a newly synthesized allotetraploid Cucumis × hytivus Chen & Kirkbride. Plant Molecular Biology. 77: 225-33. PMID 21805197 DOI: 10.1007/s11103-011-9804-y  0.38
2010 Wang C, Chen J, Zhi H, Yang L, Li W, Wang Y, Li H, Zhao B, Chen M, Diao X. Population genetics of foxtail millet and its wild ancestor. Bmc Genetics. 11: 90. PMID 20937104 DOI: 10.1186/1471-2156-11-90  0.363
2010 Sanyal A, Ammiraju JS, Lu F, Yu Y, Rambo T, Currie J, Kollura K, Kim HR, Chen J, Ma J, San Miguel P, Mingsheng C, Wing RA, Jackson SA. Orthologous comparisons of the Hd1 region across genera reveal Hd1 gene lability within diploid Oryza species and disruptions to microsynteny in Sorghum. Molecular Biology and Evolution. 27: 2487-506. PMID 20522726 DOI: 10.1093/Molbev/Msq133  0.382
2009 Lu F, Ammiraju JS, Sanyal A, Zhang S, Song R, Chen J, Li G, Sui Y, Song X, Cheng Z, de Oliveira AC, Bennetzen JL, Jackson SA, Wing RA, Chen M. Comparative sequence analysis of MONOCULM1-orthologous regions in 14 Oryza genomes. Proceedings of the National Academy of Sciences of the United States of America. 106: 2071-6. PMID 19164767 DOI: 10.1073/Pnas.0812798106  0.494
2009 Mueller LA, Lankhorst RK, Tanksley SD, Giovannoni JJ, White R, Vrebalov J, Fei Z, Eck Jv, Buels R, Mills AA, Menda N, Tecle IY, Bombarely A, Stack S, Royer SM, ... ... Chen J, ... ... Chen J, et al. A Snapshot of the Emerging Tomato Genome Sequence The Plant Genome. 2: 78-92. DOI: 10.3835/Plantgenome2008.08.0005  0.469
2008 Ammiraju JS, Lu F, Sanyal A, Yu Y, Song X, Jiang N, Pontaroli AC, Rambo T, Currie J, Collura K, Talag J, Fan C, Goicoechea JL, Zuccolo A, Chen J, et al. Dynamic evolution of oryza genomes is revealed by comparative genomic analysis of a genus-wide vertical data set. The Plant Cell. 20: 3191-209. PMID 19098269 DOI: 10.1105/Tpc.108.063727  0.536
2008 Li C, Zhao J, Jiang H, Geng Y, Dai Y, Fan H, Zhang D, Chen J, Lu F, Shi J, Sun S, Chen J, Yang X, Lu C, Chen M, et al. A snapshot of the Chinese SOL Project. Journal of Genetics and Genomics = Yi Chuan Xue Bao. 35: 387-90. PMID 18640618 DOI: 10.1016/S1673-8527(08)60056-9  0.309
2008 Qi J, Qian Q, Bu Q, Li S, Chen Q, Sun J, Liang W, Zhou Y, Chu C, Li X, Ren F, Palme K, Zhao B, Chen J, Chen M, et al. Mutation of the rice Narrow leaf1 gene, which encodes a novel protein, affects vein patterning and polar auxin transport. Plant Physiology. 147: 1947-59. PMID 18562767 DOI: 10.1104/Pp.108.118778  0.314
2007 Lou Q, Chen J. Ty1-copia retrotransposon-based SSAP marker development and its potential in the genetic study of cucurbits. Genome / National Research Council Canada = GéNome / Conseil National De Recherches Canada. 50: 802-10. PMID 17893720 DOI: 10.1139/g07-067  0.316
2006 Chen JF, Lu F, Chen SS, Tao SH. Significant positive correlation between the recombination rate and GC content in the human pseudoautosomal region. Genome / National Research Council Canada = GéNome / Conseil National De Recherches Canada. 49: 413-9. PMID 16767166 DOI: 10.1139/G05-124  0.358
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