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Shisong Ma, Ph.D. - Publications

Affiliations: 
2007 University of Illinois, Urbana-Champaign, Urbana-Champaign, IL 
Area:
Plant Physiology
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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 Xu Y, Wang Y, Ma S. SingleCellGGM enables gene expression program identification from single-cell transcriptomes and facilitates universal cell label transfer. Cell Reports Methods. 4: 100813. PMID 38971150 DOI: 10.1016/j.crmeth.2024.100813  0.315
2024 Han E, Geng Z, Qin Y, Wang Y, Ma S. Single-cell network analysis reveals gene expression programs for Arabidopsis root development and metabolism. Plant Communications. 100978. PMID 38783601 DOI: 10.1016/j.xplc.2024.100978  0.44
2024 Peng Y, Liu Y, Wang Y, Geng Z, Qin Y, Ma S. Stomatal maturomics: hunting genes regulating guard cell maturation and function formation from single-cell transcriptomes. Journal of Genetics and Genomics = Yi Chuan Xue Bao. PMID 38768655 DOI: 10.1016/j.jgg.2024.05.004  0.378
2023 Wang Y, Zhang Y, Yu N, Li B, Gong J, Mei Y, Bao J, Ma S. Decoding transcriptional regulation via a human gene expression predictor. Journal of Genetics and Genomics = Yi Chuan Xue Bao. PMID 36693565 DOI: 10.1016/j.jgg.2023.01.006  0.411
2022 Zhang Y, Han E, Peng Y, Wang Y, Wang Y, Geng Z, Xu Y, Geng H, Qian Y, Ma S. Rice co-expression network analysis identifies gene modules associated with agronomic traits. Plant Physiology. PMID 35866684 DOI: 10.1093/plphys/kiac339  0.384
2022 Peng Y, Zuo W, Zhou H, Miao F, Zhang Y, Qin Y, Liu Y, Long Y, Ma S. EXPLICIT-Kinase: a gene expression predictor for dissecting the functions of the Arabidopsis kinome. Journal of Integrative Plant Biology. PMID 35446465 DOI: 10.1111/jipb.13267  0.301
2021 Zhao PX, Zhang J, Chen SY, Wu J, Xia JQ, Sun LQ, Ma SS, Xiang CB. Arabidopsis MADS-box factor AGL16 is a negative regulator of plant response to salt stress by down regulating salt-responsive genes. The New Phytologist. PMID 34605021 DOI: 10.1111/nph.17760  0.518
2021 Geng H, Wang M, Gong J, Xu Y, Ma S. An Arabidopsis expression predictor enables inference of transcriptional regulators for gene modules. The Plant Journal : For Cell and Molecular Biology. PMID 33974299 DOI: 10.1111/tpj.15315  0.486
2020 Lee D, Lal NK, Lin ZD, Ma S, Liu J, Castro B, Toruño T, Dinesh-Kumar SP, Coaker G. Regulation of reactive oxygen species during plant immunity through phosphorylation and ubiquitination of RBOHD. Nature Communications. 11: 1838. PMID 32296066 DOI: 10.1038/S41467-020-15601-5  0.357
2019 Jin Y, Guo W, Hu X, Liu M, Xu X, Hu F, Lan Y, Lv C, Fang Y, Liu M, Shi T, Ma S, Fang Z, Huang J. Static magnetic field regulates Arabidopsis root growth via auxin signaling. Scientific Reports. 9: 14384. PMID 31591431 DOI: 10.1038/S41598-019-50970-Y  0.412
2018 Zhang M, Chiang YH, Toruño TY, Lee D, Ma M, Liang X, Lal NK, Lemos M, Lu YJ, Ma S, Liu J, Day B, Dinesh-Kumar SP, Dehesh K, Dou D, et al. The MAP4 Kinase SIK1 Ensures Robust Extracellular ROS Burst and Antibacterial Immunity in Plants. Cell Host & Microbe. 24: 379-391.e5. PMID 30212650 DOI: 10.1016/J.Chom.2018.08.007  0.33
2018 Shen Y, Liu J, Geng H, Zhang J, Liu Y, Zhang H, Xing S, Du J, Ma S, Tian Z. De novo assembly of a Chinese soybean genome. Science China. Life Sciences. PMID 30062469 DOI: 10.1007/S11427-018-9360-0  0.375
2017 Friesner J, Assmann SM, Bastow R, Bailey-Serres J, Beynon J, Brendel V, Buell CR, Bucksch A, Busch W, Demura T, Dinneny JR, Doherty CJ, Eveland AL, Falter-Braun P, Gehan MA, ... ... Ma S, et al. The Next Generation of Training for Arabidopsis Researchers: Bioinformatics and Quantitative Biology. Plant Physiology. 175: 1499-1509. PMID 29208732 DOI: 10.1104/Pp.17.01490  0.366
2017 Ma S, Ding Z, Li P. Maize network analysis revealed gene modules involved in development, nutrients utilization, metabolism, and stress response. Bmc Plant Biology. 17: 131. PMID 28764653 DOI: 10.1186/S12870-017-1077-4  0.529
2017 Ma S, Snyder M, Dinesh-Kumar SP. Discovery of Novel Human Gene Regulatory Modules from Gene Co-expression and Promoter Motif Analysis. Scientific Reports. 7: 5557. PMID 28717181 DOI: 10.1038/S41598-017-05705-2  0.515
2016 Feng B, Ma S, Chen S, Zhu N, Zhang S, Yu B, Yu Y, Le B, Chen X, Dinesh-Kumar SP, Shan L, He P. PARylation of the forkhead-associated domain protein DAWDLE regulates plant immunity. Embo Reports. PMID 27797852 DOI: 10.15252/Embr.201642486  0.427
2016 Lemos M, Xiao Y, Bjornson M, Wang JZ, Hicks D, Souza A, Wang CQ, Yang P, Ma S, Dinesh-Kumar S, Dehesh K. The plastidial retrograde signal methyl erythritol cyclopyrophosphate is a regulator of salicylic acid and jasmonic acid crosstalk. Journal of Experimental Botany. PMID 26733689 DOI: 10.1093/Jxb/Erv550  0.52
2015 Ma S, Dinesh-Kumar SP. Plant protein kinase substrates identification using protein microarrays. Methods in Molecular Biology (Clifton, N.J.). 1306: 159-65. PMID 25930701 DOI: 10.1007/978-1-4939-2648-0_12  0.386
2015 Ma S, Bohnert HJ, Dinesh-Kumar SP. AtGGM2014, an Arabidopsis gene co-expression network for functional studies. Science China. Life Sciences. 58: 276-86. PMID 25682393 DOI: 10.1007/S11427-015-4803-X  0.711
2014 Manohar M, Tian M, Moreau M, Park SW, Choi HW, Fei Z, Friso G, Asif M, Manosalva P, von Dahl CC, Shi K, Ma S, Dinesh-Kumar SP, O'Doherty I, Schroeder FC, et al. Identification of multiple salicylic acid-binding proteins using two high throughput screens. Frontiers in Plant Science. 5: 777. PMID 25628632 DOI: 10.3389/Fpls.2014.00777  0.353
2013 Ma S, Shah S, Bohnert HJ, Snyder M, Dinesh-Kumar SP. Incorporating motif analysis into gene co-expression networks reveals novel modular expression pattern and new signaling pathways. Plos Genetics. 9: e1003840. PMID 24098147 DOI: 10.1371/Journal.Pgen.1003840  0.661
2013 Padmanabhan MS, Ma S, Burch-Smith TM, Czymmek K, Huijser P, Dinesh-Kumar SP. Novel positive regulatory role for the SPL6 transcription factor in the N TIR-NB-LRR receptor-mediated plant innate immunity. Plos Pathogens. 9: e1003235. PMID 23516366 DOI: 10.1371/Journal.Ppat.1003235  0.415
2012 Ma S, Bachan S, Porto M, Bohnert HJ, Snyder M, Dinesh-Kumar SP. Discovery of stress responsive DNA regulatory motifs in Arabidopsis. Plos One. 7: e43198. PMID 22912824 DOI: 10.1371/Journal.Pone.0043198  0.628
2012 Ma S. Gene Networks Based on the Graphical Gaussian Model Bio-Protocol. 2. DOI: 10.21769/BIOPROTOC.119  0.307
2011 Lee HY, Bowen CH, Popescu GV, Kang HG, Kato N, Ma S, Dinesh-Kumar S, Snyder M, Popescu SC. Arabidopsis RTNLB1 and RTNLB2 Reticulon-like proteins regulate intracellular trafficking and activity of the FLS2 immune receptor. The Plant Cell. 23: 3374-91. PMID 21949153 DOI: 10.1105/Tpc.111.089656  0.32
2011 Miura K, Lee J, Gong Q, Ma S, Jin JB, Yoo CY, Miura T, Sato A, Bohnert HJ, Hasegawa PM. SIZ1 regulation of phosphate starvation-induced root architecture remodeling involves the control of auxin accumulation. Plant Physiology. 155: 1000-12. PMID 21156857 DOI: 10.1104/Pp.110.165191  0.734
2008 Ma S, Bohnert HJ. Gene networks in Arabidopsis thaliana for metabolic and environmental functions. Molecular Biosystems. 4: 199-204. PMID 18437262 DOI: 10.1039/B715811B  0.657
2008 Li P, Ma S, Bohnert HJ. Coexpression characteristics of trehalose-6-phosphate phosphatase subfamily genes reveal different functions in a network context. Physiologia Plantarum. 133: 544-56. PMID 18435695 DOI: 10.1111/J.1399-3054.2008.01101.X  0.637
2008 Ma S, Bohnert HJ. Gene networks for the integration and understanding of gene expression characteristics Weed Science. 56: 314-321. DOI: 10.1614/Ws-07-092.1  0.681
2007 Ma S, Gong Q, Bohnert HJ. An Arabidopsis gene network based on the graphical Gaussian model. Genome Research. 17: 1614-25. PMID 17921353 DOI: 10.1101/Gr.6911207  0.756
2007 Ma S, Bohnert HJ. Integration of Arabidopsis thaliana stress-related transcript profiles, promoter structures, and cell-specific expression. Genome Biology. 8: R49. PMID 17408486 DOI: 10.1186/Gb-2007-8-4-R49  0.677
2007 Lee J, Nam J, Park HC, Na G, Miura K, Jin JB, Yoo CY, Baek D, Kim DH, Jeong JC, Kim D, Lee SY, Salt DE, Mengiste T, Gong Q, ... Ma S, et al. Salicylic acid-mediated innate immunity in Arabidopsis is regulated by SIZ1 SUMO E3 ligase. The Plant Journal : For Cell and Molecular Biology. 49: 79-90. PMID 17163880 DOI: 10.1111/J.1365-313X.2006.02947.X  0.743
2006 Ma S, Gong Q, Bohnert HJ. Dissecting salt stress pathways. Journal of Experimental Botany. 57: 1097-107. PMID 16510518 DOI: 10.1093/Jxb/Erj098  0.758
2006 Bohnert HJ, Gong Q, Li P, Ma S. Unraveling abiotic stress tolerance mechanisms--getting genomics going. Current Opinion in Plant Biology. 9: 180-8. PMID 16458043 DOI: 10.1016/J.Pbi.2006.01.003  0.751
2005 Gong Q, Li P, Ma S, Indu Rupassara S, Bohnert HJ. Salinity stress adaptation competence in the extremophile Thellungiella halophila in comparison with its relative Arabidopsis thaliana. The Plant Journal : For Cell and Molecular Biology. 44: 826-39. PMID 16297073 DOI: 10.1111/J.1365-313X.2005.02587.X  0.77
2004 Ma S, Quist TM, Ulanov A, Joly R, Bohnert HJ. Loss of TIP1;1 aquaporin in Arabidopsis leads to cell and plant death. The Plant Journal : For Cell and Molecular Biology. 40: 845-59. PMID 15584951 DOI: 10.1111/J.1365-313X.2004.02265.X  0.611
2004 Inan G, Zhang Q, Li P, Wang Z, Cao Z, Zhang H, Zhang C, Quist TM, Goodwin SM, Zhu J, Shi H, Damsz B, Charbaji T, Gong Q, Ma S, et al. Salt cress. A halophyte and cryophyte Arabidopsis relative model system and its applicability to molecular genetic analyses of growth and development of extremophiles. Plant Physiology. 135: 1718-37. PMID 15247369 DOI: 10.1104/Pp.104.041723  0.75
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