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Song Li - Publications

Affiliations: 
Virginia Polytechnic Institute and State University, Blacksburg, VA, United States 
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29 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
2025 Yang Y, Wei J, Wang Y, Chen M, Li S, Han Z, Duan Y, Xu Y, Sun H, Li H. Auxin signaling mediated embryogenic cell formation during the early stage of somatic embryogenesis in Malus domestica "Gala". The Plant Journal : For Cell and Molecular Biology. 122: e70287. PMID 40538284 DOI: 10.1111/tpj.70287  0.347
2025 Li S, Liu J, Wang J, Jia D, Sun Y, Ding L, Jiang J, Chen S, Chen F. CmCYC2d is a Regulator of Leaf Abaxial Curling in Chrysanthemum morifolium. Plant, Cell & Environment. PMID 39934960 DOI: 10.1111/pce.15410  0.363
2024 Shi Y, Lu T, Lai S, Li S, Zhang L, Liu R, Ouyang L, Zhao X, Jiang Y, Yan Z, Zhang J, Miao B. R2R3-MYB transcription factors RrMYB12 and RrMYB111 regulate the accumulation of flavonols and anthocyanins. Frontiers in Plant Science. 15: 1477278. PMID 39741671 DOI: 10.3389/fpls.2024.1477278  0.374
2024 Cantó-Pastor A, Kajala K, Shaar-Moshe L, Manzano C, Timilsena P, De Bellis D, Gray S, Holbein J, Yang H, Mohammad S, Nirmal N, Suresh K, Ursache R, Mason GA, Gouran M, ... ... Li S, et al. A suberized exodermis is required for tomato drought tolerance. Nature Plants. PMID 38168610 DOI: 10.1038/s41477-023-01567-x  0.593
2022 Song Q, Li S. Identification of Plant Co-regulatory Modules Using CoReg. Methods in Molecular Biology (Clifton, N.J.). 2594: 217-223. PMID 36264499 DOI: 10.1007/978-1-0716-2815-7_16  0.516
2022 Song Q, Li S. Modeling Plant Transcription Factor Networks Using ConSReg. Methods in Molecular Biology (Clifton, N.J.). 2594: 205-215. PMID 36264498 DOI: 10.1007/978-1-0716-2815-7_15  0.498
2022 Yan H, Lee J, Song Q, Li Q, Schiefelbein J, Zhao B, Li S. Identification of new marker genes from plant single-cell RNA-seq data using interpretable machine learning methods. The New Phytologist. PMID 35211979 DOI: 10.1111/nph.18053  0.491
2020 Song Q, Lee J, Akter S, Rogers M, Grene R, Li S. Prediction of condition-specific regulatory genes using machine learning. Nucleic Acids Research. PMID 32329779 DOI: 10.1093/Nar/Gkaa264  0.585
2020 DeMers LC, Redekar NR, Kachroo A, Tolin SA, Li S, Saghai Maroof MA. A transcriptional regulatory network of Rsv3-mediated extreme resistance against Soybean mosaic virus. Plos One. 15: e0231658. PMID 32315334 DOI: 10.1371/Journal.Pone.0231658  0.327
2019 Qin J, Shi A, Song Q, Li S, Wang F, Cao Y, Ravelombola W, Song Q, Yang C, Zhang M. Genome Wide Association Study and Genomic Selection of Amino Acid Concentrations in Soybean Seeds. Frontiers in Plant Science. 10: 1445. PMID 31803203 DOI: 10.3389/Fpls.2019.01445  0.398
2019 Lee J, Heath LS, Grene R, Li S. Comparing time series transcriptome data between plants using a network module finding algorithm. Plant Methods. 15: 61. PMID 31164912 DOI: 10.1186/S13007-019-0440-X  0.316
2019 Qi S, Akter S, Li S. Identification of Novel lincRNA and Co-Expression Network Analysis Using RNA-Sequencing Data in Plants. Methods in Molecular Biology (Clifton, N.J.). 1933: 207-221. PMID 30945187 DOI: 10.1007/978-1-4939-9045-0_12  0.337
2018 Peng Y, Zhang X, Lin H, Deng S, Huang Y, Qin Y, Feng X, Yan R, Zhao Y, Cheng Y, Wei Y, Wang J, Chen W, Fan X, Ashktorab H, ... ... Li S, et al. Inhibition of miR‑194 suppresses the Wnt/β‑catenin signalling pathway in gastric cancer. Oncology Reports. PMID 30542715 DOI: 10.3892/Or.2018.6773  0.302
2018 Song QA, Catlin NS, Brad Barbazuk W, Li S. Computational analysis of alternative splicing in plant genomes. Gene. PMID 30321657 DOI: 10.1016/J.Gene.2018.10.026  0.507
2017 Redekar N, Pilot G, Raboy V, Li S, Saghai Maroof MA. Inference of Transcription Regulatory Network in Low Phytic Acid Soybean Seeds. Frontiers in Plant Science. 8: 2029. PMID 29250090 DOI: 10.3389/Fpls.2017.02029  0.351
2017 Song Q, Grene R, Heath LS, Li S. Identification of regulatory modules in genome scale transcription regulatory networks. Bmc Systems Biology. 11: 140. PMID 29246163 DOI: 10.1186/S12918-017-0493-2  0.546
2017 Haak DC, Fukao T, Grene R, Hua Z, Ivanov R, Perrella G, Li S. Multilevel Regulation of Abiotic Stress Responses in Plants. Frontiers in Plant Science. 8: 1564. PMID 29033955 DOI: 10.3389/Fpls.2017.01564  0.307
2017 Wendrich JR, Möller BK, Li S, Saiga S, Sozzani R, Benfey PN, De Rybel B, Weijers D. Framework for gradual progression of cell ontogeny in the root meristem. Proceedings of the National Academy of Sciences of the United States of America. 114: E8922-E8929. PMID 28973915 DOI: 10.1073/Pnas.1707400114  0.651
2016 Ni Y, Aghamirzaie D, Elmarakeby H, Collakova E, Li S, Grene R, Heath LS. A Machine Learning Approach to Predict Gene Regulatory Networks in Seed Development in Arabidopsis. Frontiers in Plant Science. 7: 1936. PMID 28066488 DOI: 10.3389/Fpls.2016.01936  0.356
2016 Sparks EE, Drapek C, Gaudinier A, Li S, Ansariola M, Shen N, Hennacy JH, Zhang J, Turco G, Petricka JJ, Foret J, Hartemink AJ, Gordân R, Megraw M, Brady SM, et al. Establishment of Expression in the SHORTROOT-SCARECROW Transcriptional Cascade through Opposing Activities of Both Activators and Repressors. Developmental Cell. 39: 585-596. PMID 27923776 DOI: 10.1016/J.Devcel.2016.09.031  0.651
2016 Li S, Yamada M, Han X, Ohler U, Benfey PN. High-Resolution Expression Map of the Arabidopsis Root Reveals Alternative Splicing and lincRNA Regulation. Developmental Cell. 39: 508-522. PMID 27840108 DOI: 10.1016/J.Devcel.2016.10.012  0.607
2016 Aghamirzaie D, Collakova E, Li S, Grene R. CoSpliceNet: a framework for co-splicing network inference from transcriptomics data. Bmc Genomics. 17: 845. PMID 27793091 DOI: 10.1186/S12864-016-3172-6  0.338
2016 Wu W, Hai Y, Chen L, Liu RJ, Han YX, Li WH, Li S, Lin S, Wu XR. Deguelin-induced blockade of PI3K/protein kinase B/MAP kinase signaling in zebrafish and breast cancer cell lines is mediated by down-regulation of fibroblast growth factor receptor 4 activity. Pharmacology Research & Perspectives. 4: e00212. PMID 27069628 DOI: 10.1002/Prp2.212  0.311
2015 Wei Y, Zhang S, Shang S, Zhang B, Li S, Wang X, Wang F, Su J, Wu Q, Liu H, Zhang Y. SEA: a super-enhancer archive. Nucleic Acids Research. PMID 26578594 DOI: 10.1093/nar/gkv1243  0.363
2014 Morton T, Petricka J, Corcoran DL, Li S, Winter CM, Carda A, Benfey PN, Ohler U, Megraw M. Paired-end analysis of transcription start sites in Arabidopsis reveals plant-specific promoter signatures. The Plant Cell. 26: 2746-60. PMID 25035402 DOI: 10.1105/Tpc.114.125617  0.584
2013 Li S, Liberman LM, Mukherjee N, Benfey PN, Ohler U. Integrated detection of natural antisense transcripts using strand-specific RNA sequencing data. Genome Research. 23: 1730-9. PMID 23816784 DOI: 10.1101/Gr.149310.112  0.564
2012 Li S, Pandey S, Gookin TE, Zhao Z, Wilson L, Assmann SM. Gene-sharing networks reveal organizing principles of transcriptomes in Arabidopsis and other multicellular organisms. The Plant Cell. 24: 1362-78. PMID 22517316 DOI: 10.1105/Tpc.111.094748  0.325
2011 Wang RS, Pandey S, Li S, Gookin TE, Zhao Z, Albert R, Assmann SM. Common and unique elements of the ABA-regulated transcriptome of Arabidopsis guard cells. Bmc Genomics. 12: 216. PMID 21554708 DOI: 10.1186/1471-2164-12-216  0.382
2006 Li S, Assmann SM, Albert R. Predicting essential components of signal transduction networks: a dynamic model of guard cell abscisic acid signaling. Plos Biology. 4: e312. PMID 16968132 DOI: 10.1371/Journal.Pbio.0040312  0.344
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