Publications

Preprints

3. Ou S., Collins T., Qiu Y., Seetharam A., Menard C., Manchanda N., Gent J., Schatz M., Anderson S., Hufford M.✉, Hirsch C.✉ (2022). Differences in activity and stability drive transposable element variation in tropical and temperate maize. bioRxiv: 2022.10.09.511471v1. In revision.

2. Razaghi R., Hook P.W., Ou S., Schatz M.C., Hansen K.D., Jain M., Timp W.✉ (2022). Modbamtools: Analysis of single-molecule epigenetic data for long-range profiling, heterogeneity, and clustering. bioRxiv, 2022.07. 07.499188

1. Hardigan M., Feldmann M., Pincot D., Famula R., Vachev M., Madera M., Zerbe P., Mars K., Peluso P., Rank D., Ou S., Saski C., Acharya C., Cole G., Yocca A., Platts A., Edger P., Knapp S.✉ (2022). Blueprint for phasing and assembling the genomes of heterozygous polyploids: application to the octoploid genome of strawberry. bioRxiv: 2021.11.03.467115v1. Submitted.

2023

36. Mansfeld B.✉, Yocca A., Ou S., Harkess A., Burchard E., Gutierrez B., van Nocker S., Gottschalk C.✉ (2023) A haplotype resolved chromosome-scale assembly of North American wild apple Malus fusca and comparative genomics of the fire blight Mfu10 locus. Plant J. doi/10.1111/tpj.16433

35. McGrath M.✉, 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., Koren S., Phillippy A., Wang J., Liu T., Pulman J., Childs K., Yocum A., Fermin D., Mutasa-Gottgens E., Stevanato P., Taguchi K. and Dorn K. (2019). A contiguous de novo genome assembly of sugar beet EL10 (Beta vulgaris L.). DNA Research, dsac033.

34. Kovaka S., Ou S., Jenike K.M., Schatz M.C.✉ (2023). Approaching complete genomes, transcriptomes and epi-omes with accurate long-read sequencing. Nature Methods 20 (1), 12-16.

2022

33. Zhang R.-G.†✉, Li G.-Y.†, Wang X.-L., Dainat J., Wang Z.-X., Ou S.✉, and Ma Y.✉ (2022). TEsorter: an accurate and fast method to classify LTR-retrotransposons in plant genomes. Hort. Res., doi: 10.1093/hr/uhac017. (†co-first author).

32. Alonge M., Lebeigle L., Kirsche M., Jenike K., Ou S., Aganezov S., Wang X., Lippman Z., Schatz M.✉, and Soyk S.✉ (2022). Automated assembly scaffolding using RagTag elevates a new tomato system for high-throughput genome editing. Genome biology 23 (1), 1-19.

31. Xu F., Tang J., Wang S., Cheng X., Wang H., Ou S., Gao S., Li B., Qian Y., Gao C., Chu C.✉ (2022) Antagonistic control of seed dormancy in rice by two bHLH transcription factors. Nature Genetics, 54, 1972–1982.

30. Cerbin S., Ou S., Li Y., Sun Y., and Jiang N.✉ (2022). Distinct Composition and Amplification Dynamics of Transposable Elements in Sacred Lotus (Nelumbo nucifera Gaertn.). Plant J. doi.org/10.1111/tpj.15938

2021

29. Mansfeld B., Boyher A., Berry J., Wilson M., Ou S., Polydore S., Michael T., Fahlgren N., Bart R. (2021) Large structural variations in the haplotype-resolved African cassava genome. Plant J. doi:10.1111/tpj.15543.

28. Hufford M., Seetharam A., Woodhouse M., Chougule K., Ou S., Liu J., Ricci W., Guo T., Olson A., Qiu Y., Coletta R., Tittes S., Hudson A., Marand A., Wei S., Lu Z., Wang B., Tello M.-Ruiz, Piri R., Wang N., Kim D., Zeng Y., O C.’Connor, Li X., Gilbert A., Baggs E., Krasileva K., II J., Cannon E., Andorf C., Manchanda N., Snodgrass S., Hufnagel D., Jiang Q., Pedersen S., Syring M., Kudrna D., Llaca V., Fengler K., Schmitz R., Ross J.-Ibarra, Yu J., Gent J., Hirsch C., Ware D., Dawe R.✉ (2021). De novo assembly, annotation, and comparative analysis of 26 diverse maize genomes. Science, 373(6555), 655.

27. Bornowski N.†, Michel K.†, Hamilton J., Ou S., Seetharam A., Jenkins J., Grimwood J., Plott C., Shu S., Talag J., Kennedy M., Hundley H., Singan V., Barry K., Daum C., Yoshinga Y., Schmutz J., Hirsch C., Hufford M., de Leon N., Kaeppler S., Buell C.✉ (2021). Genomic variation within the maize Stiff Stalk heterotic germplasm pool. Plant Genome, 2021;e20114. (†co-first author).

26. 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., Yuan H., Ma B., Wang Y., Qian Y., Fan S., Li W., Wang J., He M., Yin J., Li T., Jiang N., Chen X., Liang C.✉, Li S.✉ (2021) Pan-genome analysis of 33 genetically diverse rice accessions reveals hidden genomic variations. Cell, 184(13):3542-3558.e16. (†co-first author).

25. Alger E., Platts A., Deb S., Luo X., Ou S., Cao Y., Xiong Z., Knapp S., Liu Z., McKain M., Edger P.✉ (2021). Chromosome-scale reference genome for a red-fruited, perpetual flowering and runnerless woodland strawberry (Fragaria vesca). Frontiers in Genetics, 12, 1090.

24. Su W., Ou S., Hufford M.B., Peterson T.✉ (2021). A Tutorial of EDTA: Extensive De Novo TE Annotator. In: Cho J. (eds) Plant Transposable Elements. Methods in Molecular Biology, vol 2250.

2020

23. Ou S., Liu J., Chougule K. M., Fungtammasan A., Seetharam A., Stein J., Llaca V., Manchanda N., Gilbert A. M., Wei X., Chin C.-S., Hufnagel D. E., Pedersen S., Snodgrass S., Fengler K., Woodhouse M., Walenz B. P., Koren S., Phillippy A. M., Hannigan B., Kelly Dawe R., Hirsch C. N.✉, Hufford M. B.✉ and Ware D.✉ (2020). Effect of Sequence Depth and Length in Long-read Assembly of the Maize Inbred NC358. Nat. Commun., 11(1): 2288. Featured article in Genetics, Genomics and Epigenetics.

22. 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., Liao H., Hu B.✉, Chu C.✉ (2021). Genomic basis of geographical adaptation to soil nitrogen in rice. Nature, 590: 600–5 (†co-first author).

21. Coletta R. D., Qiu Y., Ou S., Hufford M. B.✉, and Hirsch C. N.✉ (2021). How the pan-genome is changing crop genomics and improvement. Genome Biol., 22(3).

20. Bird K. A., Niederhuth C., Ou S., Gehan M., Chris Pires J., Xiong Z.✉, VanBuren R.✉ and Edger P. P.✉ (2020). Replaying the evolutionary tape to investigate subgenome dominance in allopolyploid Brassica napus. New Phytol., 230(1), 354-371.

19. Xu Y.†, Zhang L.†, Ou S., Wang R., Wang Y., Chu C.✉, and Yao S.✉ (2020). Natural variations in SLG1 confer high temperature tolerance in indica rice. Nat. Commun., 11(1): 1-13 (†co-first author).

18. Pham G. M.†, Hamilton J. P.†, Wood J. C., Burke J. T., Zhao H., Vaillancourt B., Ou S., Jiang J., and Buell C. R.✉ (2020). Construction of a chromosome-scale long-read reference genome assembly for potato. GigaScience, 9(9): giaa100 (†co-first author).

17. Liu J., Seetharam A. S., Chougule K., Ou S., Swentowsky K. W., Gent J. I., Llaca V., Woodhouse M. R., Manchanda N., Presting G. G., Kudrna D. A., Alabady M., Hirsch C. N., Fengler K. A., Ware D., Michael T. P., Hufford M. B., and Dawe K. R.✉ (2020). Gapless assembly of maize chromosomes using long-read technologies. Genome Biol., 20(1): 121.

2019

16. Ou S. and Jiang N.✉ (2019). LTR_FINDER_parallel: parallelization of LTR_FINDER enabling rapid identification of long terminal repeat retrotransposons. Mob. DNA, 10(1): 48.

15. Ou S., Su W., Liao Y., Chougule K., Agda J. R. A., Hellinga A. J., Lugo C. S. B., Elliott T. A., Ware D., Peterson T., Jiang N.✉, Hirsch C. N.✉ and Hufford M. B.✉ (2019). Benchmarking Transposable Element Annotation Methods for Creation of a Streamlined, Comprehensive Pipeline. Genome Biol., 20(1): 275.

14. Edger P. P.✉, Poorten T. J., VanBuren R., Hardigan M. A., Colle M., McKain M. R., Smith R. D., Teresi S. J., Nelson A. D. L., Wai C. M., Alger E. I., Bird K. A., Yocca A. E., Pumplin N., Ou S., Ben-Zvi G., Brodt A., Baruch K., Swale T., Shiue L., Acharya C. B., Cole G. S., Mower J. P., Childs K. L., Jiang N., Lyons E., Freeling M., Puzey J. R. and Knapp S. J. (2019). Origin and evolution of the octoploid strawberry genome. Nat. Genet., 51(3): 541-547.

13. Colle M., Leisner C. P., Wai C. M., Ou S., Bird K. A., Wang J., Wisecaver J. H., Yocca A. E., Alger E. I., Tang H., Xiong Z., Callow P., Ben-Zvi G., Brodt A., Baruch K., Swale T., Shiue L., Song G. Q., Childs K. L., Schilmiller A., Vorsa N., Buell C. R., VanBuren R., Jiang N. and Edger P. P.✉ (2019). Haplotype-phased genome and evolution of phytonutrient pathways of tetraploid blueberry. GigaScience, 8(3).

2018

12. Liu C.†, Ou S.†, Mao B., Tang J., Wang W., Wang H., Cao S., Schläppi M. R., Zhao B., Xiao G., Wang X.✉, and Chu C.✉ (2018). Early selection of bZIP73 facilitated adaptation of japonica rice to cold climates. Nat. Commun., 9(1): 3302. (†co-first author).

11. Ou S.✉, Chen J., and Jiang N. (2018). Assessing genome assembly quality using the LTR Assembly Index (LAI). Nucleic Acids Res., 46(21): e216.

10. Ou S. and Jiang N.✉ (2018). LTR_retriever: a highly accurate and sensitive program for identification of long terminal-repeat retrotransposons. Plant Physiol., 176(2):1410-22.

9. Wen Z., Tan R., Zhang S., Collins P. J., Yuan J., Du W., Gu C., Ou S., Song Q., An Y. C., Boyse J. F., Chilvers M. I. and Wang D.✉ (2018). Integrating GWAS and gene expression data for functional characterization of resistance to white mold in soya bean. Plant Biotechnol. J., 16(11): 1825-1835.

8. Wang W., Hu B., Yuan D., Liu Y., Che R., Hu Y., Ou S., Zhang Z., Wang H., Li H., Jiang Z., Zhang Z., Gao X., Qiu Y., Meng X., Liang Y., Wang Y., Zhang L., Li L., Sodmergen S., Jing H., Li J., and Chu C.✉ (2018) Expression of OsNRT1.1A/OsNPF6.3 confers high yield and early maturation in rice. The Plant Cell, 30(3): 638-651 (Featured article).

7. Edger P.✉, VanBuren R., Colle M., Poorten T., Wai C.M., Niederhuth C., Alger E., Ou S., Acharya C., Wang J., Callow P., McKain M., Shi J., Collier C., Xiong Z., Mower J., Slovin J., Hytönen T., Jiang N., Childs K., and Knapp S.✉ (2018). Single-molecule sequencing and optical mapping yields an improved genome of woodland strawberry (Fragaria vesca) with chromosome-scale contiguity. GigaScience, 7(2):1-7.

6. VanBuren R.✉, Wai J., Ou S., Bryant D., Jiang N., Mockler T., Edger P., and Michael T.✉ (2018). Extreme haplotype variation in the desiccation-tolerant clubmoss Selaginella lepidophylla. Nat. Commun., 9:13.

Before 2018

5. 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., Xu C., Liang Y., Zhang L., Li L., and Chu C.✉ (2015). Variation in NRT1.1B contributes to nitrate-use divergence between rice subspecies. Nat. Genet., 47(7):834-8.

4. Xu F., Fang J., Ou S., Gao S., Zhang F., Du L., Xiao Y., Wang H., Sun X., Chu J., Wang G., and Chu C.✉ (2014). Variations in CYP78A13 coding region influence grain size and yield in rice. Plant Cell Environ., 38(4):800-11.

3. Liang C., Wang Y., Zhu Y., Tang J., Hu B., Liu L., Ou S., Wu H., Sun X., Chu J., and Chu C.✉ (2014). OsNAP connects abscisic acid and leaf senescence by fine-tuning abscisic acid biosynthesis and directly targeting senescence-associated genes in rice. Proc. Natl. Acad. Sci. USA., 111(27):10013-18.

2. Liu C., Mao B., Ou S., Wang W., Liu L., Wu Y., Chu C.✉, and Wang X.✉ (2013). OsbZIP71, a bZIP transcription factor, confers salinity and drought tolerance in rice. Plant Mol. Biol., 84(1-2):19-36.

1. Ou S., Wang H., and Chu C.✉ (2012). Major domestication traits in Asian rice. Yi Chuan, 34(11):1379-1389. In Chinese. (Cover art and highlighted review).

See more in Google Scholar.

Ou, Shujun (2018) PhD Dissertation. Identification of LTR Retrotransposons, Evaluation of Genome Assembly, and Modeling Rice Domestication. Plant Genetics and Evolutionary Biology, Department of Horticulture, Michigan State University.