Publications

See Google Scholar for a complete list of publications. 


2019


Clark N, Shen Z, Briggs SP, Walley JW, Kelley DR. Auxin induces widespread proteome remodeling in Arabidopsis seedlings. Proteomics, Vol 19, 1900199. DOI:10.1002/pmic.201900199 - PubMed


Zhang Y, Song G, Lal N, Nagalakshmi U, Li Y, Zheng W, Huang P, Branon T, Ting A, Walley JW, Dinesh-Kumar S. TurboID-based proximity labeling reveals that UBR7 is a regulator of N NLR immune receptor-mediated immunity. Nature Communications. DOI: https://www.nature.com/articles/s41467-019-11202-z - 


Jiang, H; Tang, B; Xie, Z; Nolan, T; Ye, H; Song, G; Walley, JW; Yin, Y. GSK3-like kinase BIN2 phosphorylates RD26 to potentiate drought signaling in Arabidopsis. The Plant Journal. DOI: 10.1111/tpj.14484 - PubMed.


Zhang J, Wu S, Boehlein SK, McCarty DR, Song G, Walley JW, Myers A, Settles AM. Maize defective kernel5 is a bacterial TamB homologue required for chloroplast envelope biogenesis. Journal of Cell Biology. Vol 218(8) 2638-2658. DOI: 10.1083/jcb.201807166 - PubMed


Wu HL, Song G, Walley JW, Hsu PY. The tomato translational landscape revealed by transcriptome assembly and ribosome profiling. Plant Physiology. vol. 181(1) 367-380. DOI: https://doi.org/10.1104/pp.19.00541 - PubMed


Pu Y, Walley JW, Shen Z, Lang M, Briggs SP, Estelle M, Kelley D. Quantitative early auxin root proteomics identifies GAUT10, a galacturonosyltransferase, as a novel regulator of root meristem maintenance. Molecular & Cellular Proteomics. 18 (6): 1157-1170. doi.org/10.1074/mcp.RA119.001378 - PubMed. (Cover Article).


Abdulghani M, Song G, Kaur H, Walley JW, Tuteja G. Comparative Analysis of the Transcriptome and Proteome during Mouse Placental Development. Journal of Proteome Research. 18:2088–2099. DOI: 10.1021/acs.jproteome.8b00970 - PubMed.


Argueso, CT, Assmann SM, Birnbaum KD, Chen S, Dinneny JR, Doherty CJ, Eveland AL, Friesner J, Greenlee VR, Law JA, Marshall‐Colón A, Mason GA, O'Lexy R, Peck SC, Schmitz RJ, Song L, Stern D, Varagona MJ, Walley JW, Williams CM. Directions for research and training in plant omics: Big Questions and Big Data. Plant Direct. 1-16. doi: 10.1002/pld3.133.


International Arabidopsis Informatics Consortium: Doherty C, Friesner J, Gregory B, Loraine A, Megraw M, Provart N, Slotkin RK, Town C, Assmann SM, Axtell M, Berardini T, Chen S, Gehan M, Huala E, Jaiswal P, Larson S, Li S, May S, Michael T, Pires C, Topp C, Walley J, Wurtele E. Plant Direct. https://doi.org/10.1002/pld3.109.


2018


Song G, Brachova L, Nikolau BJ, Jones AM, Walley JW. Heterotrimeric G‐protein‐dependent proteome and phosphoproteome in unstimulated Arabidopsis root. Proteomics. 18, 1800323. doi.org/10.1002/pmic.201800323 PubMed.


Guo H, Nolan, TM, Song G, Liu S, Xie Z, Chen J, Schnable P, Walley JW, Yin Y. FERONIA Receptor Kinase Contributes to Plant Immunity by Suppressing Jasmonic Acid Signaling in Arabidopsis thaliana. Current Biology. 28(20): 3316-3324. doi.org/10.1016/j.cub.2018.07.078 PubMed.


Song G, Hsu PY, Walley JW. Assessment and refinement of sample preparation methods for deep and quantitative plant proteome profiling. Proteomics. 18(17), 1800220. doi.org/10.1002/pmic.201800220 PubMed.


Lal NK, NagalakshmiU, HurlburtN, FloresR, BakA, SoneP, Ma X, SongG, WalleyJW, ShanL, HeP, CasteelC, FisherAJ, Dinesh-Kumar SP. The receptor-like cytoplasmic kinase BIK1 localizes to the nucleus and regulates defense hormone expression during plant innate immunity. Cell Host Microbe. 23(4): 485-497. doi.org/10.1016/j.chom.2018.03.010 PubMed.


Walley JW, Shen Z, McReynolds MR, Briggs SP. Fungal Induced Protein Hyperacetylation Identified by Acetylome Profiling. PNAS. 115(1): 210-215. doi:10.1073/pnas.1717519115 PubMed.


2017


Song G, McReynolds MR, Walley JW. Sample Preparation Protocols for Protein Abundance, Acetylome, and Phosphoproteome Profiling of Plant Tissues. Methods Mol. Biol.: Plant Genomics. pp 123–133. DOI:10.1007/978-1-4939-7003-2_9 PubMed.


Nolan TM, Brennan B, Yang M, Chen J, Zhang M, Li Z, Wang X, Bassham DC, Walley JW, Yin Y. Selective Autophagy of BES1 Mediated by DSK2 Balances Plant Growth and Survival. Developmental Cell. 41: 33–46. DOI:10.1016/j.devcel.2017.03.013 PubMed.


2016


Walley JW, Sartor RC, Shen Z, Schmitz RJ, Wu KJ, Urich MA, Nery JR, Smith LG, Schnable JC, Ecker JR, Briggs SP. Integration of omic networks in a developmental atlas of maize. Science. 353(6301): 814–818. DOI:10.1126/science.aag1125 PubMed.


Song G and Walley JW. Dynamic Protein Acetylation in Plant–Pathogen Interactions. Frontiers in Plant Science. DOI: 10.3389/fpls.2016.00421.


2015


Walley JW, Xiao Y, Wang J, Baidoo EE, Keasling JD, Shen Z, Briggs SP, Dehesh K. Plastid-produced interorgannellar stress signal MEcPP potentiates induction of the unfolded protein response in endoplasmic reticulum. PNAS 112(19): 6212-6217. doi.org/10.1073/pnas.1504828112 PubMed.


Walley JW and Briggs SP. Dual use of peptide mass spectra: Protein atlas and genome annotation. Current Plant Biology 2: 21-24. doi.org/10.1016/j.cpb.2015.02.001 PubMed.


Marcon C, Malik WA, Walley JW, Shen Z, Paschold A, Smith LG, Peipho H, Briggs SP, Hochholdinger F. A high resolution tissue-specific proteome and phosphoproteome atlas of maize primary roots reveals functional gradients along the root axis. Plant Physiology 168(1): 233-246. DOI:10.1104/pp.15.00138 PubMed.


2014


Castellana NE, Shen Z, He Y, Walley JW, Cassidy CJ, Briggs SP, Bafna V. An Automated Proteogenomic Method Utilizes Mass Spectrometry to Reveal Novel Genes in Zea mays. Molecular & Cellular Proteomics 13(1): 157-167. DOI:10.1074/mcp.M113.031260 PubMed.


2013


Walley JW, Shen Z, Sartor RC, Wu KJ, Osborn J, Smith LG, Briggs SP. Reconstruction of Protein Networks from an Atlas of Maize Seed Proteotypes. PNAS 110(49): E4808-4817. DOI:10.1073/pnas.1319113110 PubMed.


Walley JW, Kliebenstein DJ, Bostock RM, and Dehesh K. Fatty acids and early detection of pathogens. Current Opinion in Plant Biology 16(4):526-520. DOI:10.1016/j.pbi.2013.06.011 PubMed.


2010 and Earlier


Savchenko T, Walley JW, Chehab EW, Xiao Y, Kaspi R, PyeMF, Mohammed ME, Lazarus C, Bostock RM and Dehesh K. Arachidonic acid: an evolutionarily conserved signaling molecule modulates plant stress signaling networks. Plant Cell 22(10):3193-3205. DOI:10.1105/tpc.110.073858 PubMed.


Walley JW and Dehesh K. Molecular mechanisms regulating general stress signaling networks in Arabidopsis. Journal of Integrative Plant Biology 52(4): 354-359. DOI:10.1111/j.1744-7909.2010.00940.x PubMed.


Walley JW, Kelley DR, Savchenko T and Dehesh K. Investigating the function of CAF1 deadenylases during plant stress responses. Plant Signaling and Behavior 5(7):802-805. doi.org/10.4161/psb.5.7.11578 PubMed.


Rowe HC, Walley JW, Corwin J, Chan EKF, Dehesh K and Kliebenstein DJ. Deficiencies in Jasmonate-Mediated Plant Defense Reveal Quantitative Variation in Botrytis cinerea Pathogenesis. PLoS Pathogens 6(4): e1000861. DOI:10.1371/journal.ppat.1000861.


Walley JW and Huerta AJ. Exposure to environmentally relevant levels of cadmium primarily impacts transpiration in field-grown soybean. Journal of Plant Nutrition 33(10):1519-1530. doi.org/10.1080/01904167.2010.489988.


Walley JW, Kelley DR, Nestorova G, Hirschberg DL, Dehesh KArabidopsis deadenylases AtCAF1a and AtCAF1b play overlapping and distinct roles in mediating environmental stress responses. Plant Physiology 152(2):866-875. DOI:10.1104/pp.109.149005 PubMed.


Walley JW, Rowe HC, Xiao Y, Chehab EW, Kliebenstein DJ, Wagner D and Dehesh K. The Chromatin Remodeler SPLAYED Regulates Specific Stress Signaling Pathways. PLoS Pathogens 4(12): e1000237. doi.org/10.1371/journal.ppat.1000237.


Walley JW, Coughlan S, Hudson ME, Covington MF, Kaspi R, Banu G, Harmer SL, and Dehesh K. Mechanical Stress Induces Biotic and Abiotic Stress Responses via a Novel cis-Element. PLoS Genetics 3: e172. doi.org/10.1371/journal.pgen.0030172.


Chehab EW, Raman G, Walley JW, Perea JV, Banu G, Theg S, and Dehesh K. Rice HYDROPEROXIDE LYASES with Unique Expression Patterns Generate Distinct Aldehyde Signatures in Arabidopsis. Plant Physiology 141(1):121-134. DOI:10.1104/pp.106.078592 PubMed.