Siobhan Brady, Ph.D. - Publications

Affiliations: 
2009- Plant Biology University of California, Davis, Davis, CA 
Area:
Genomics, Systems Biology, Developmental Biology, Plant Biology, Genetics, Transcriptional Networks
Website:
http://www-plb.ucdavis.edu/labs/brady/

55 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
2019 Kajala K, Walker KL, Mitchell GS, Krämer U, Cherry SR, Brady SM. Real-time whole-plant dynamics of heavy metal transport in and by gamma-ray imaging. Plant Direct. 3: e00131. PMID 31309170 DOI: 10.1002/pld3.131  0.56
2019 Dong S, Lau V, Song R, Ierullo M, Esteban E, Wu Y, Sivieng T, Nahal-Bose HK, Gaudinier A, Pasha A, Oughtred R, Dolinski K, Tyers M, Brady SM, Grene R, et al. Proteome-Wide, Structure-Based Prediction of Protein-protein Interactions / New Molecular Interactions Viewer. Plant Physiology. PMID 30679268 DOI: 10.1104/pp.18.01216  1
2018 Gaudinier A, Rodriguez-Medina J, Zhang L, Olson A, Liseron-Monfils C, Bågman AM, Foret J, Abbitt S, Tang M, Li B, Runcie DE, Kliebenstein DJ, Shen B, Frank MJ, Ware D, ... Brady SM, et al. Transcriptional regulation of nitrogen-associated metabolism and growth. Nature. PMID 30356219 DOI: 10.1038/s41586-018-0656-3  1
2018 Toal TW, Ron M, Gibson D, Kajala K, Splitt B, Johnson LS, Miller ND, Slovak R, Gaudinier A, Patel R, de Lucas M, Provart NJ, Spalding EP, Busch W, Kliebenstein DJ, ... Brady SM, et al. Regulation of Root Angle and Gravitropism. G3 (Bethesda, Md.). PMID 30322904 DOI: 10.1534/g3.118.200540  1
2018 Sakamoto S, Somssich M, Nakata MT, Unda F, Atsuzawa K, Kaneko Y, Wang T, Bågman AM, Gaudinier A, Yoshida K, Brady SM, Mansfield SD, Persson S, Mitsuda N. Complete substitution of a secondary cell wall with a primary cell wall in Arabidopsis. Nature Plants. 4: 777-783. PMID 30287954 DOI: 10.1038/s41477-018-0260-4  1
2018 Ikeuchi M, Shibata M, Rymen B, Iwase A, Bågman AM, Watt L, Coleman D, Favero DS, Takahashi T, Ahnert SE, Brady SM, Sugimoto K. A Gene Regulatory Network for Cellular Reprogramming in Plant Regeneration. Plant & Cell Physiology. PMID 29462363 DOI: 10.1093/pcp/pcy013  0.84
2018 Li B, Tang M, Nelson A, Caligagan H, Zhou X, Wiest CC, Ngo R, Brady SM, Kliebenstein DJ. Network-guided Discovery of Extensive Epistasis Between Transcription Factors Involved in Aliphatic Glucosinolate Biosynthesis. The Plant Cell. PMID 29317470 DOI: 10.1105/tpc.17.00805  0.84
2017 Maher KA, Bajic M, Kajala K, Reynoso M, Pauluzzi G, West D, Zumstein K, Woodhouse M, Bubb KL, Dorrity MW, Queitsch C, Bailey-Serres J, Sinha N, Brady SM, Deal R. Profiling of accessible chromatin regions across multiple plant species and cell types reveals common gene regulatory principles and new control modules. The Plant Cell. PMID 29229750 DOI: 10.1105/tpc.17.00581  0.56
2017 Johnson RA, Conklin P, Tjahjadi M, Missirian V, Toal T, Brady SM, Britt AB. SUPPRESSOR OF GAMMA RESPONSE 1 links DNA damage response to organ regeneration. Plant Physiology. PMID 29222192 DOI: 10.1104/pp.17.01274  0.52
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, ... ... Brady SM, 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  1
2017 Reynoso M, Pauluzzi G, Kajala K, Cabanlit S, Velasco J, Bazin J, Deal R, Sinha N, Brady SM, Bailey-Serres J. Nuclear transcriptomes at high resolution using retooled INTACT. Plant Physiology. PMID 28956755 DOI: 10.1104/pp.17.00688  0.56
2017 Gaudinier A, Tang M, Bågman AM, Brady SM. Identification of Protein-DNA Interactions Using Enhanced Yeast One-Hybrid Assays and a Semiautomated Approach. Methods in Molecular Biology (Clifton, N.J.). 1610: 187-215. PMID 28439865 DOI: 10.1007/978-1-4939-7003-2_13  1
2017 Turco GM, Kajala K, Kunde-Ramamoorthy G, Ngan CY, Olson A, Deshphande S, Tolkunov D, Waring B, Stelpflug S, Klein P, Schmutz J, Kaeppler S, Ware D, Wei CL, Etchells JP, ... Brady SM, et al. DNA methylation and gene expression regulation associated with vascularization in Sorghum bicolor. The New Phytologist. PMID 28186631 DOI: 10.1111/nph.14448  0.72
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  1
2016 de Lucas M, Pu L, Turco GM, Gaudinier A, Marao AK, Harashima H, Kim D, Ron M, Sugimoto K, Roudier FM, Brady SM. Transcriptional Regulation of Arabidopsis Polycomb Repressive Complex 2 Coordinates Cell Type Proliferation and Differentiation. The Plant Cell. PMID 27650334 DOI: 10.1105/tpc.15.00744  1
2016 Porco S, Larrieu A, Du Y, Gaudinier A, Goh T, Swarup K, Swarup R, Kuempers B, Bishopp A, Lavenus J, Casimiro I, Hill K, Benkova E, Fukaki H, Brady SM, et al. Lateral root emergence in Arabidopsis is dependent on transcription factor LBD29 regulating auxin influx carrier LAX3. Development (Cambridge, England). PMID 27578783 DOI: 10.1242/dev.136283  1
2016 Murphy E, Vu LD, Van den Broeck L, Lin Z, Ramakrishna P, van de Cotte B, Gaudinier A, Goh T, Slane D, Beeckman T, Inzé D, Brady SM, Fukaki H, De Smet I. RALFL34 regulates formative cell divisions in Arabidopsis pericycle during lateral root initiation. Journal of Experimental Botany. 67: 4863-75. PMID 27521602 DOI: 10.1093/jxb/erw281  1
2016 Gray SB, Brady SM. Plant Developmental Responses to Climate Change. Developmental Biology. PMID 27521050 DOI: 10.1016/j.ydbio.2016.07.023  1
2016 Toal T, Burkart-Waco D, Howell T, Ron M, Kuppu S, Britt AB, Chetelat RT, Brady SM. Indel Group in Genomes (IGG) Molecular Genetic Markers. Plant Physiology. PMID 27436831 DOI: 10.1104/pp.16.00354  0.52
2016 Gaudinier A, Brady SM. Mapping Transcriptional Networks in Plants: Data-Driven Discovery of Novel Biological Mechanisms. Annual Review of Plant Biology. 67: 575-94. PMID 27128468 DOI: 10.1146/annurev-arplant-043015-112205  1
2016 Carriedo LG, Maloof JN, Brady SM. Molecular control of crop shade avoidance. Current Opinion in Plant Biology. 30: 151-8. PMID 27016665 DOI: 10.1016/j.pbi.2016.03.005  0.52
2015 Ikeuchi M, Iwase A, Rymen B, Harashima H, Shibata M, Ohnuma M, Breuer C, Morao AK, de Lucas M, De Veylder L, Goodrich J, Brady SM, Roudier F, Sugimoto K. PRC2 represses dedifferentiation of mature somatic cells in Arabidopsis. Nature Plants. 1: 15089. PMID 27250255 DOI: 10.1038/nplants.2015.89  0.52
2015 Provart NJ, Alonso J, Assmann SM, Bergmann D, Brady SM, Brkljacic J, Browse J, Chapple C, Colot V, Cutler S, Dangl J, Ehrhardt D, Friesner JD, Frommer WB, Grotewold E, et al. 50 years of Arabidopsis research: highlights and future directions. The New Phytologist. PMID 26465351 DOI: 10.1111/nph.13687  1
2015 Etchells JP, Smit ME, Gaudinier A, Williams CJ, Brady SM. A brief history of the TDIF-PXY signalling module: balancing meristem identity and differentiation during vascular development. The New Phytologist. PMID 26414535 DOI: 10.1111/nph.13642  1
2015 Koryachko A, Matthiadis A, Muhammad D, Foret J, Brady SM, Ducoste JJ, Tuck J, Long TA, Williams C. Clustering and Differential Alignment Algorithm: Identification of Early Stage Regulators in the Arabidopsis thaliana Iron Deficiency Response. Plos One. 10: e0136591. PMID 26317202 DOI: 10.1371/journal.pone.0136591  1
2015 Brady SM, Burow M, Busch W, Carlborg Ö, Denby KJ, Glazebrook J, Hamilton ES, Harmer SL, Haswell ES, Maloof JN, Springer NM, Kliebenstein DJ. Reassess the t Test: Interact with All Your Data via ANOVA. The Plant Cell. 27: 2088-94. PMID 26220933 DOI: 10.1105/tpc.15.00238  1
2015 Spiegelman Z, Ham BK, Zhang Z, Toal TW, Brady SM, Zheng Y, Fei Z, Lucas WJ, Wolf S. A tomato phloem-mobile protein regulates the shoot-to-root ratio by mediating the auxin response in distant organs. The Plant Journal : For Cell and Molecular Biology. PMID 26173789 DOI: 10.1111/tpj.12932  1
2014 Kajala K, Coil DA, Brady SM. Draft Genome Sequence of Rhizobium rhizogenes Strain ATCC 15834. Genome Announcements. 2. PMID 25359916 DOI: 10.1128/genomeA.01108-14  0.56
2014 Li B, Gaudinier A, Tang M, Taylor-Teeples M, Nham NT, Ghaffari C, Benson DS, Steinmann M, Gray JA, Brady SM, Kliebenstein DJ. Promoter-based integration in plant defense regulation. Plant Physiology. 166: 1803-20. PMID 25352272 DOI: 10.1104/pp.114.248716  1
2014 Ron M, Kajala K, Pauluzzi G, Wang D, Reynoso MA, Zumstein K, Garcha J, Winte S, Masson H, Inagaki S, Federici F, Sinha N, Deal RB, Bailey-Serres J, Brady SM. Hairy root transformation using Agrobacterium rhizogenes as a tool for exploring cell type-specific gene expression and function using tomato as a model. Plant Physiology. 166: 455-69. PMID 24868032 DOI: 10.1104/pp.114.239392  1
2014 Kajala K, Ramakrishna P, Fisher A, C. Bergmann D, De Smet I, Sozzani R, Weijers D, Brady SM. Omics and modelling approaches for understanding regulation of asymmetric cell divisions in arabidopsis and other angiosperm plants Annals of Botany. 113: 1083-1105. PMID 24825294 DOI: 10.1093/aob/mcu065  1
2014 de Lucas M, Provart NJ, Brady SM. Bioinformatic tools in Arabidopsis research. Methods in Molecular Biology (Clifton, N.J.). 1062: 97-136. PMID 24057362 DOI: 10.1007/978-1-62703-580-4_5  0.64
2013 Koenig D, Jiménez-Gómez JM, Kimura S, Fulop D, Chitwood DH, Headland LR, Kumar R, Covington MF, Devisetty UK, Tat AV, Tohge T, Bolger A, Schneeberger K, Ossowski S, Lanz C, ... ... Brady SM, et al. Comparative transcriptomics reveals patterns of selection in domesticated and wild tomato. Proceedings of the National Academy of Sciences of the United States of America. 110: E2655-62. PMID 23803858 DOI: 10.1073/pnas.1309606110  1
2013 Ron M, Dorrity MW, de Lucas M, Toal T, Hernandez RI, Little SA, Maloof JN, Kliebenstein DJ, Brady SM. Identification of novel loci regulating interspecific variation in root morphology and cellular development in tomato. Plant Physiology. 162: 755-68. PMID 23575417 DOI: 10.1104/pp.113.217802  1
2013 Moussaieff A, Rogachev I, Brodsky L, Malitsky S, Toal TW, Belcher H, Yativ M, Brady SM, Benfey PN, Aharoni A. High-resolution metabolic mapping of cell types in plant roots. Proceedings of the National Academy of Sciences of the United States of America. 110: E1232-41. PMID 23476065 DOI: 10.1073/pnas.1302019110  0.96
2013 Lucas WJ, Groover A, Lichtenberger R, Furuta K, Yadav SR, Helariutta Y, He XQ, Fukuda H, Kang J, Brady SM, Patrick JW, Sperry J, Yoshida A, López-Millán AF, Grusak MA, et al. The plant vascular system: evolution, development and functions. Journal of Integrative Plant Biology. 55: 294-388. PMID 23462277 DOI: 10.1111/jipb.12041  1
2013 Belmonte MF, Kirkbride RC, Stone SL, Pelletier JM, Bui AQ, Yeung EC, Hashimoto M, Fei J, Harada CM, Munoz MD, Le BH, Drews GN, Brady SM, Goldberg RB, Harada JJ. Comprehensive developmental profiles of gene activity in regions and subregions of the Arabidopsis seed. Proceedings of the National Academy of Sciences of the United States of America. 110: E435-44. PMID 23319655 DOI: 10.1073/pnas.1222061110  1
2013 De Lucas M, Brady SM. Gene regulatory networks in the Arabidopsis root. Current Opinion in Plant Biology. 16: 50-5. PMID 23196272 DOI: 10.1016/j.pbi.2012.10.007  0.52
2012 Bassel GW, Gaudinier A, Brady SM, Hennig L, Rhee SY, De Smet I. Systems analysis of plant functional, transcriptional, physical interaction, and metabolic networks. The Plant Cell. 24: 3859-75. PMID 23110892 DOI: 10.1105/tpc.112.100776  1
2011 Gaudinier A, Zhang L, Reece-Hoyes JS, Taylor-Teeples M, Pu L, Liu Z, Breton G, Pruneda-Paz JL, Kim D, Kay SA, Walhout AJ, Ware D, Brady SM. Enhanced Y1H assays for Arabidopsis. Nature Methods. 8: 1053-5. PMID 22037706 DOI: 10.1038/nmeth.1750  1
2011 Taylor-Teeples M, Ron M, Brady SM. Novel biological insights revealed from cell type-specific expression profiling. Current Opinion in Plant Biology. 14: 601-7. PMID 21704550 DOI: 10.1016/j.pbi.2011.05.007  0.52
2011 Brady SM, Zhang L, Megraw M, Martinez NJ, Jiang E, Yi CS, Liu W, Zeng A, Taylor-Teeples M, Kim D, Ahnert S, Ohler U, Ware D, Walhout AJ, Benfey PN. A stele-enriched gene regulatory network in the Arabidopsis root. Molecular Systems Biology. 7: 459. PMID 21245844 DOI: 10.1038/msb.2010.114  0.96
2010 Sozzani R, Cui H, Moreno-Risueno MA, Busch W, Van Norman JM, Vernoux T, Brady SM, Dewitte W, Murray JA, Benfey PN. Spatiotemporal regulation of cell-cycle genes by SHORTROOT links patterning and growth. Nature. 466: 128-32. PMID 20596025 DOI: 10.1038/nature09143  1
2010 Orlando DA, Brady SM, Fink TM, Benfey PN, Ahnert SE. Detecting separate time scales in genetic expression data. Bmc Genomics. 11: 381. PMID 20565716 DOI: 10.1186/1471-2164-11-381  0.96
2010 Pu L, Brady S. Systems biology update: Cell type-specific transcriptional regulatory networks Plant Physiology. 152: 411-419. PMID 19965967 DOI: 10.1104/pp.109.148668  1
2009 Cartwright DA, Brady SM, Orlando DA, Sturmfels B, Benfey PN. Reconstructing spatiotemporal gene expression data from partial observations. Bioinformatics (Oxford, England). 25: 2581-7. PMID 19608707 DOI: 10.1093/bioinformatics/btp437  0.96
2009 Orlando DA, Brady SM, Koch JD, Dinneny JR, Benfey PN. Manipulating large-scale Arabidopsis microarray expression data: identifying dominant expression patterns and biological process enrichment. Methods in Molecular Biology (Clifton, N.J.). 553: 57-77. PMID 19588101 DOI: 10.1007/978-1-60327-563-7_4  0.96
2008 Chaudhuri B, Hörmann F, Lalonde S, Brady SM, Orlando DA, Benfey P, Frommer WB. Protonophore- and pH-insensitive glucose and sucrose accumulation detected by FRET nanosensors in Arabidopsis root tips. The Plant Journal : For Cell and Molecular Biology. 56: 948-62. PMID 18702670 DOI: 10.1111/j.1365-313X.2008.03652.x  1
2008 Long TA, Brady SM, Benfey PN. Systems approaches to identifying gene regulatory networks in plants. Annual Review of Cell and Developmental Biology. 24: 81-103. PMID 18616425 DOI: 10.1146/annurev.cellbio.24.110707.175408  0.96
2008 Dinneny JR, Long TA, Wang JY, Jung JW, Mace D, Pointer S, Barron C, Brady SM, Schiefelbein J, Benfey PN. Cell identity mediates the response of Arabidopsis roots to abiotic stress. Science (New York, N.Y.). 320: 942-5. PMID 18436742 DOI: 10.1126/science.1153795  0.96
2007 Brady SM, Orlando DA, Lee JY, Wang JY, Koch J, Dinneny JR, Mace D, Ohler U, Benfey PN. A high-resolution root spatiotemporal map reveals dominant expression patterns. Science (New York, N.Y.). 318: 801-6. PMID 17975066 DOI: 10.1126/science.1146265  0.96
2007 Brady SM, Song S, Dhugga KS, Rafalski JA, Benfey PN. Combining expression and comparative evolutionary analysis. The COBRA gene family. Plant Physiology. 143: 172-87. PMID 17098858 DOI: 10.1104/pp.106.087262  0.96
2006 Brady SM, Long TA, Benfey PN. Unraveling the dynamic transcriptome. The Plant Cell. 18: 2101-11. PMID 16968906 DOI: 10.1105/tpc.105.037572  0.96
2005 Toufighi K, Brady SM, Austin R, Ly E, Provart NJ. The Botany Array Resource: e-Northerns, Expression Angling, and promoter analyses. The Plant Journal : For Cell and Molecular Biology. 43: 153-63. PMID 15960624 DOI: 10.1111/j.1365-313X.2005.02437.x  1
2003 Brady SM, Sarkar SF, Bonetta D, McCourt P. The ABSCISIC ACID INSENSITIVE 3 (ABI3) gene is modulated by farnesylation and is involved in auxin signaling and lateral root development in Arabidopsis. The Plant Journal : For Cell and Molecular Biology. 34: 67-75. PMID 12662310 DOI: 10.1046/j.1365-313X.2003.01707.x  1
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