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Shujun Ou - Publications

Affiliations: 
2019-2022 EEOB Iowa State University, Ames, IA, United States 
 2022- Computer Science Johns Hopkins University, Baltimore, MD 
Area:
transposable element, population genetics, genomics, plant biology
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37 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 Koren S, Bao Z, Guarracino A, Ou S, Goodwin S, Jenike KM, Lucas J, McNulty B, Park J, Rautianinen M, Rhie A, Roelofs D, Schneiders H, Vrijenhoek I, Nijbroek K, et al. Gapless assembly of complete human and plant chromosomes using only nanopore sequencing. Biorxiv : the Preprint Server For Biology. PMID 38529488 DOI: 10.1101/2024.03.15.585294  0.513
2024 Ou S, Jiang N, Hirsch CN, Hufford MB. Response to Commentary: Accounting for diverse transposable element landscapes is key to developing and evaluating accurate de novo annotation strategies. Genome Biology. 25: 6. PMID 38169403 DOI: 10.1186/s13059-023-03119-0  0.66
2023 Stevenson DW, Ramakrishnan S, Alves CS, Coelho LA, Kramer M, Goodwin S, Ramos OM, Eshel G, Sondervan VM, Frangos S, Zumajo-Cardona C, Jenike K, Ou S, Wang X, Lee YP, et al. The genome of the Wollemi pine, a critically endangered "living fossil" unchanged since the Cretaceous, reveals extensive ancient transposon activity. Biorxiv : the Preprint Server For Biology. PMID 37662366 DOI: 10.1101/2023.08.24.554647  0.677
2023 Mansfeld BN, Yocca A, Ou S, Harkess A, Burchard E, Gutierrez B, van Nocker S, Gottschalk C. A haplotype resolved chromosome-scale assembly of North American wild apple Malus fusca and comparative genomics of the fire blight Mfu10 locus. The Plant Journal : For Cell and Molecular Biology. PMID 37639371 DOI: 10.1111/tpj.16433  0.39
2023 Kovaka S, Ou S, Jenike KM, Schatz MC. Approaching complete genomes, transcriptomes and epi-omes with accurate long-read sequencing. Nature Methods. 20: 12-16. PMID 36635537 DOI: 10.1038/s41592-022-01716-8  0.621
2022 Alonge M, Lebeigle L, Kirsche M, Jenike K, Ou S, Aganezov S, Wang X, Lippman ZB, Schatz MC, Soyk S. Automated assembly scaffolding using RagTag elevates a new tomato system for high-throughput genome editing. Genome Biology. 23: 258. PMID 36522651 DOI: 10.1186/s13059-022-02823-7  0.667
2022 McGrath JM, Funk A, Galewski P, Ou S, Townsend B, Davenport K, Daligault H, Johnson S, Lee J, Hastie A, Darracq A, Willems G, Barnes S, Liachko I, Sullivan S, et al. A contiguous de novo genome assembly of sugar beet EL10 (Beta vulgaris L.). Dna Research : An International Journal For Rapid Publication of Reports On Genes and Genomes. PMID 36208288 DOI: 10.1093/dnares/dsac033  0.559
2022 Liu Y, Wang H, Jiang Z, Wang W, Xu R, Wang Q, Zhang Z, Li A, Liang Y, Ou S, Liu X, Cao S, Tong H, Wang Y, Zhou F, et al. Author Correction: Genomic basis of geographical adaptation to soil nitrogen in rice. Nature. PMID 36151470 DOI: 10.1038/s41586-022-05362-0  0.324
2022 Cerbin S, Ou S, Li Y, Sun Y, Jiang N. Distinct Composition and Amplification Dynamics of Transposable Elements in Sacred Lotus (Nelumbo nucifera Gaertn.). The Plant Journal : For Cell and Molecular Biology. PMID 35959634 DOI: 10.1111/tpj.15938  0.733
2022 Ou S, Su W, Liao Y, Chougule K, Agda JRA, Hellinga AJ, Lugo CSB, Elliott TA, Ware D, Peterson T, Jiang N, Hirsch CN, Hufford MB. Author Correction: Benchmarking transposable element annotation methods for creation of a streamlined, comprehensive pipeline. Genome Biology. 23: 76. PMID 35260190 DOI: 10.1186/s13059-022-02645-7  0.656
2022 Zhang RG, Li GY, Wang XL, Dainat J, Wang ZX, Ou S, Ma Y. TEsorter: an accurate and fast method to classify LTR-retrotransposons in plant genomes. Horticulture Research. PMID 35184178 DOI: 10.1093/hr/uhac017  0.431
2021 Mansfeld BN, Boyher A, Berry JC, Wilson M, Ou S, Polydore S, Michael TP, Fahlgren N, Bart RS. Large structural variations in the haplotype-resolved African cassava genome. The Plant Journal : For Cell and Molecular Biology. PMID 34661327 DOI: 10.1111/tpj.15543  0.476
2021 Hufford MB, Seetharam AS, Woodhouse MR, Chougule KM, Ou S, Liu J, Ricci WA, Guo T, Olson A, Qiu Y, Della Coletta R, Tittes S, Hudson AI, Marand AP, Wei S, et al. De novo assembly, annotation, and comparative analysis of 26 diverse maize genomes. Science (New York, N.Y.). 373: 655-662. PMID 34353948 DOI: 10.1126/science.abg5289  0.769
2021 Alger EI, Platts AE, Deb SK, Luo X, Ou S, Cao Y, Hummer KE, Xiong Z, Knapp SJ, Liu Z, McKain MR, Edger PP. Chromosome-Scale Genome for a Red-Fruited, Perpetual Flowering and Runnerless Woodland Strawberry (). Frontiers in Genetics. 12: 671371. PMID 34335685 DOI: 10.3389/fgene.2021.671371  0.385
2021 Bornowski N, Michel KJ, Hamilton JP, Ou S, Seetharam AS, Jenkins J, Grimwood J, Plott C, Shu S, Talag J, Kennedy M, Hundley H, Singan VR, Barry K, Daum C, et al. Genomic variation within the maize stiff-stalk heterotic germplasm pool. The Plant Genome. e20114. PMID 34275202 DOI: 10.1002/tpg2.20114  0.713
2021 Qin P, Lu H, Du H, Wang H, Chen W, Chen Z, He Q, Ou S, Zhang H, Li X, Li X, Li Y, Liao Y, Gao Q, Tu B, et al. Pan-genome analysis of 33 genetically diverse rice accessions reveals hidden genomic variations. Cell. PMID 34051138 DOI: 10.1016/j.cell.2021.04.046  0.643
2021 Su W, Ou S, Hufford MB, Peterson T. A Tutorial of EDTA: Extensive De Novo TE Annotator. Methods in Molecular Biology (Clifton, N.J.). 2250: 55-67. PMID 33900591 DOI: 10.1007/978-1-0716-1134-0_4  0.683
2021 Della Coletta R, Qiu Y, Ou S, Hufford MB, Hirsch CN. How the pan-genome is changing crop genomics and improvement. Genome Biology. 22: 3. PMID 33397434 DOI: 10.1186/s13059-020-02224-8  0.746
2020 Bird KA, Niederhuth C, Ou S, Gehan M, Pires JC, Xiong Z, VanBuren R, Edger PP. Replaying the evolutionary tape to investigate subgenome dominance in allopolyploid Brassica napus. The New Phytologist. PMID 33280122 DOI: 10.1111/nph.17137  0.323
2020 Pham GM, Hamilton JP, Wood JC, Burke JT, Zhao H, Vaillancourt B, Ou S, Jiang J, Buell CR. Construction of a chromosome-scale long-read reference genome assembly for potato. Gigascience. 9. PMID 32964225 DOI: 10.1093/gigascience/giaa100  0.494
2020 Liu J, Seetharam AS, Chougule K, Ou S, Swentowsky KW, Gent JI, Llaca V, Woodhouse MR, Manchanda N, Presting GG, Kudrna DA, Alabady M, Hirsch CN, Fengler KA, Ware D, et al. Gapless assembly of maize chromosomes using long-read technologies. Genome Biology. 21: 121. PMID 32434565 DOI: 10.1186/S13059-020-02029-9  0.728
2020 Ou S, Liu J, Chougule KM, Fungtammasan A, Seetharam AS, Stein JC, Llaca V, Manchanda N, Gilbert AM, Wei S, Chin CS, Hufnagel DE, Pedersen S, Snodgrass SJ, Fengler K, et al. Effect of sequence depth and length in long-read assembly of the maize inbred NC358. Nature Communications. 11: 2288. PMID 32385271 DOI: 10.1038/S41467-020-16037-7  0.736
2019 Ou S, Jiang N. LTR_FINDER_parallel: parallelization of LTR_FINDER enabling rapid identification of long terminal repeat retrotransposons. Mobile Dna. 10: 48. PMID 31857828 DOI: 10.1186/S13100-019-0193-0  0.638
2019 Ou S, Su W, Liao Y, Chougule K, Agda JRA, Hellinga AJ, Lugo CSB, Elliott TA, Ware D, Peterson T, Jiang N, Hirsch CN, Hufford MB. Benchmarking transposable element annotation methods for creation of a streamlined, comprehensive pipeline. Genome Biology. 20: 275. PMID 31843001 DOI: 10.1186/S13059-019-1905-Y  0.764
2019 Edger PP, Poorten TJ, VanBuren R, Hardigan MA, Colle M, McKain MR, Smith RD, Teresi SJ, Nelson ADL, Wai CM, Alger EI, Bird KA, Yocca AE, Pumplin N, Ou S, et al. Author Correction: Origin and evolution of the octoploid strawberry genome. Nature Genetics. PMID 30842601 DOI: 10.1038/S41588-019-0380-4  0.483
2019 Edger PP, Poorten TJ, VanBuren R, Hardigan MA, Colle M, McKain MR, Smith RD, Teresi SJ, Nelson ADL, Wai CM, Alger EI, Bird KA, Yocca AE, Pumplin N, Ou S, et al. Origin and evolution of the octoploid strawberry genome. Nature Genetics. PMID 30804557 DOI: 10.1038/S41588-019-0356-4  0.591
2019 Colle M, Leisner CP, Wai CM, Ou S, Bird KA, Wang J, Wisecaver JH, Yocca AE, Alger EI, Tang H, Xiong Z, Callow P, Ben-Zvi G, Brodt A, Baruch K, et al. Haplotype-phased genome and evolution of phytonutrient pathways of tetraploid blueberry. Gigascience. PMID 30715294 DOI: 10.1093/Gigascience/Giz012  0.662
2018 Liu C, Ou S, Mao B, Tang J, Wang W, Wang H, Cao S, Schläppi MR, Zhao B, Xiao G, Wang X, Chu C. Early selection of bZIP73 facilitated adaptation of japonica rice to cold climates. Nature Communications. 9: 3302. PMID 30120236 DOI: 10.1038/S41467-018-05753-W  0.303
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  0.683
2018 Wen Z, Tan R, Zhang S, Collins PJ, Yuan J, Du W, Gu C, Ou S, Song Q, Charles An YQ, Boyse JF, Chilvers MI, Wang D. Integrating GWAS and gene expression data for functional characterization of resistance to white mold in soybean. Plant Biotechnology Journal. PMID 29528555 DOI: 10.1111/Pbi.12918  0.416
2018 VanBuren R, Wai CM, Ou S, Pardo J, Bryant D, Jiang N, Mockler TC, Edger P, Michael TP. Extreme haplotype variation in the desiccation-tolerant clubmoss Selaginella lepidophylla. Nature Communications. 9: 13. PMID 29296019 DOI: 10.1038/S41467-017-02546-5  0.656
2017 Edger PP, VanBuren R, Colle M, Poorten TJ, Wai CM, Niederhuth CE, Alger EI, Ou S, Acharya CB, Wang J, Callow P, McKain MR, Shi J, Collier C, Xiong Z, et al. Single-molecule sequencing and optical mapping yields an improved genome of woodland strawberry (Fragaria vesca) with chromosome-scale contiguity. Gigascience. PMID 29253147 DOI: 10.1093/Gigascience/Gix124  0.66
2017 Ou S, Jiang N. LTR_retriever: a highly accurate and sensitive program for identification of long terminal-repeat retrotransposons. Plant Physiology. PMID 29233850 DOI: 10.1104/Pp.17.01310  0.669
2015 Hu B, Wang W, Ou S, Tang J, Li H, Che R, Zhang Z, Chai X, Wang H, Wang Y, Liang C, Liu L, Piao Z, Deng Q, Deng K, et al. Variation in NRT1.1B contributes to nitrate-use divergence between rice subspecies. Nature Genetics. 47: 834-8. PMID 26053497 DOI: 10.1038/Ng.3337  0.321
2015 Xu F, Fang J, Ou S, Gao S, Zhang F, Du L, Xiao Y, Wang H, Sun X, Chu J, Wang G, Chu C. Variations in CYP78A13 coding region influence grain size and yield in rice. Plant, Cell & Environment. 38: 800-11. PMID 25255828 DOI: 10.1111/Pce.12452  0.416
2014 Liang C, Wang Y, Zhu Y, Tang J, Hu B, Liu L, Ou S, Wu H, Sun X, Chu J, Chu C. OsNAP connects abscisic acid and leaf senescence by fine-tuning abscisic acid biosynthesis and directly targeting senescence-associated genes in rice. Proceedings of the National Academy of Sciences of the United States of America. 111: 10013-8. PMID 24951508 DOI: 10.1073/Pnas.1321568111  0.331
2012 Ou SJ, Wang HR, Chu CC. [Major domestication traits in Asian rice]. Yi Chuan = Hereditas / Zhongguo Yi Chuan Xue Hui Bian Ji. 34: 1379-89. PMID 23208135 DOI: 10.3724/Sp.J.1005.2012.01379  0.4
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