| Year |
Citation |
Score |
| 2025 |
Benoit M, Jenike KM, Satterlee JW, Ramakrishnan S, Gentile I, Hendelman A, Passalacqua MJ, Suresh H, Shohat H, Robitaille GM, Fitzgerald B, Alonge M, Wang X, Santos R, He J, ... Ou S, et al. Solanum pan-genetics reveals paralogues as contingencies in crop engineering. Nature. PMID 40044854 DOI: 10.1038/s41586-025-08619-6 |
0.625 |
|
| 2024 |
Koren S, Bao Z, Guarracino A, Ou S, Goodwin S, Jenike KM, Lucas J, McNulty B, Park J, Rautiainen 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. Genome Research. PMID 39505490 DOI: 10.1101/gr.279334.124 |
0.657 |
|
| 2024 |
Liao H, Sun Y, Ou S. Accelerating de novo SINE annotation in plant and animal genomes. Mobile Dna. 15: 24. PMID 39427206 DOI: 10.1186/s13100-024-00331-y |
0.51 |
|
| 2024 |
Ou S, Scheben A, Collins T, Qiu Y, Seetharam AS, Menard CC, Manchanda N, Gent JI, Schatz MC, Anderson SN, Hufford MB, Hirsch CN. Differences in activity and stability drive transposable element variation in tropical and temperate maize. Genome Research. PMID 39251347 DOI: 10.1101/gr.278131.123 |
0.74 |
|
| 2024 |
Benson CW, Heringer P, Ou S. Four Strategies for Whole-Genome Annotation of Transposable Elements and Repeats in Maize. Cold Spring Harbor Protocols. PMID 39237454 DOI: 10.1101/pdb.prot108578 |
0.584 |
|
| 2024 |
Heringer P, Benson CW, Ou S. Navigating the Maze of Maize Genomics: the Impact of Transposable Elements and Tandem Repeats. Cold Spring Harbor Protocols. PMID 39237452 DOI: 10.1101/pdb.top108441 |
0.589 |
|
| 2024 |
Hu G, Grover CE, Vera DL, Lung PY, Girimurugan SB, Miller ER, Conover JL, Ou S, Xiong X, Zhu D, Li D, Gallagher JP, Udall JA, Sui X, Zhang J, et al. Evolutionary dynamics of chromatin structure and duplicate gene expression in diploid and allopolyploid cotton. Molecular Biology and Evolution. PMID 38758089 DOI: 10.1093/molbev/msae095 |
0.418 |
|
| 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 |
0.656 |
|
| 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 |
0.657 |
|
| 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 |
0.679 |
|
| 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 |
0.398 |
|
| 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 |
0.624 |
|
| 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 |
0.669 |
|
| 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 |
0.567 |
|
| 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 |
0.328 |
|
| 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 |
0.747 |
|
| 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 |
0.652 |
|
| 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 |
0.429 |
|
| 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 |
0.483 |
|
| 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 |
0.776 |
|
| 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 |
0.393 |
|
| 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 |
0.715 |
|
| 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 |
0.642 |
|
| 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 |
0.681 |
|
| 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 |
0.75 |
|
| 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 |
0.33 |
|
| 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 |
0.503 |
|
| 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 |
0.732 |
|
| 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 |
0.74 |
|
| 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 |
0.636 |
|
| 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 |
0.768 |
|
| 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 |
0.476 |
|
| 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 |
0.592 |
|
| 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 |
0.663 |
|
| 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 |
0.305 |
|
| 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 |
0.423 |
|
| 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 |
0.658 |
|
| 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 |
0.661 |
|
| 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 |
0.665 |
|
| 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 |
0.422 |
|
| 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 |
0.333 |
|
| 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 |
0.398 |
|
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