Skip to main content


See Google Scholar for a complete list of publications. 


Li Z, Liu S, Montes C, Walley JW, Aung K. Plasmodesmata-located proteins regulate plasmodesmal function at specific cell interfaces in Arabidopsis. bioRxiv. DOI: 10.1101/2022.08.05.502996

Watkins JM, Clark NM, Song G, Oliveira CC, Mishra B, Brachova L, Seifert CM, Mitchell MS, Braga dos Reis PA, Urano D, Muktar MS, Walley JW, Jones AM. Phosphorylation dynamics in a flg22-induced, heterotrimeric G-protein dependent signaling network in Arabidopsis thaliana reveals a candidate PP2A phosphatase involved in AtRGS1 trafficking. bioRxiv. DOI: 10.1101/2021.12.06.471472

Song G, Olatunji D, Montes C, Clark NM, Pu Y, Kelley DR, Walley JW. Quantitative proteomics reveals extensive lysine ubiquitination in the Arabidopsis root proteome and uncovers novel transcription factor stability states. bioRxiv. DOI: 10.1101/2021.01.07.425780.


Mehta D, Ahkami AH, Walley JW, Xu S, Uhrig RG. (2022) The incongruity of validating quantitative proteomics using western blots. Nature Plants. DOI: 10.1038/s41477-022-01314-8.

Montes C, Wang P, Liao CY, Nolan TM, Song G, Clark NM, Elmore JM, Guo H, Bassham DC, Yin Y, Walley JW. Integration of multi-omics data reveals interplay between brassinosteroid and TORC signaling in Arabidopsis. New Phytologist. DOI 10.1111/nph.18404

Wang P, Clark NM, Nolan TM, Song G, Bartz PM, Liao CY, Montes C, Katz E, Polko JK, Kieber JJ, Kliebenstein DJ, Bassham DC, Walley JW, Yin Y, Guo H. Integrated Omics Reveal Novel Functions and Underlying Mechanisms of the Receptor Kinase FERONIA in Arabidopsis thaliana. Plant Cell. DOI 10.1093/plcell/koac111.

Wang P, Clark NM, Nolan TM, Song G, Whitham OG., Liao CY, Montes C, Bassham DC, Walley JW, Yin Y, Guo H. (2022) FERONIA functions through Target of Rapamycin (TOR) to negatively regulate autophagy. Frontiers in Plant Science. DOI: 10.3389/fpls.2022.961096

Liao CY, Pu Y, Nolan TM, Montes C, Guo H, Walley JW, Yin Y, Bassham DC. Brassinosteroids modulate autophagy through phosphorylation of RAPTOR1B by the GSK3-like kinase BIN2 in Arabidopsis. Autophagy. DOI: 10.1080/15548627.2022.2124501

McReynolds MR, Dash L, Montes C, Draves MA, Lang MG, Walley JW, Kelley DR. Temporal and spatial auxin responsive networks in maize primary roots. Quantitative Plant Biology. DOI: 10.1017/qpb.2022.17


Chapman A, Elmore JM, McReynolds M, Walley JW, Wise RP. (2021). SGT1 SGS-domain mutations impair interactions with the barley MLA6 immune receptor in association with loss of NLR protein. Molecular Plant Microbe Interactions. DOI: 10.1094/MPMI-08-21-0217-R.

Clark NM, Nolan TM, Wang P, Song G, Montes C, Valentine T, Guo H, Sozzani R, Yin Y, Walley JW. Integrated omics networks reveal the temporal signaling events of brassinosteroid response in Arabidopsis. Nature Communications. DOI: 10.1038/s41467-021-26165-3.

Clark NM, Elmore JM, Walley JW. To the proteome and beyond: Advances in single-cell omics profiling for plant systems. Plant Physiology, kiab429. DOI: 10.1093/plphys/kiab429

Elmore JM, Griffin BD, Walley JW. Advances in functional proteomics to study plant-pathogen interactions. Current Opinion in Plant Biology, 63:102061. DOI: /10.1016/j.pbi.2021.102061.

Wang P, Nolan TM, Clark NM, Jiang H, Montes-Serey C, Guo H, Bassham DC, Walley JW, Yin Y. The F-box E3 ubiquitin ligase BAF1 mediates the degradation of the brassinosteroid-activated transcription factor BES1 through selective autophagy in Arabidopsis. The Plant Cell, koab210, DOI: 10.1093/plcell/koab210.

Woodhouse MR, Sen S, Schott D, Portwood JL, Freeling M, Walley JW, Andorf CM, Schnable JC. qTeller: a tool for comparative multi-genomic gene expression analysis. Bioinformatics, btab604. DOI: 10.1093/bioinformatics/btab604.

Xiang L, Nolan TM, Bao Y, Elmore M, Tuel T, Gai J, Shah D, Wang P, Huser NM, Hurd AM, McLaughlin SA, Howell SH, Walley JW, Yin Y, Tang L. Robotic Assay for Drought (RoAD): An Automated Phenotyping System for Brassinosteroid and Drought Response. The Plant Journal: DOI:

Dash L, McEwan R, Montes C, Mejia L, Walley J, Dilkes B, Kelley D. slim shady is a novel allele of PHYTOCHROME B present in the T-DNA line SALK_015201. Plant Direct.


Reem NT, Chambers L, Zhang N, Abdullah SF, Chen Y, Feng G, Gao S, Soto-Burgos J, Pogorelko G, Bassham DC, Anderson CT, Walley JW, Zabotina OA. Post-Synthetic Reduction of Pectin Methylesterification Causes Morphological Abnormalities and Alterations to Stress Response in Arabidopsis thalianaPlants9, 1558. DOI: 10.3390/plants9111558.

Zander M, LewseyM, Clark N,Yin L, Bartlett A,Saldierna Guzmán JP, Hann E, Langford AE, Jow B, Wise A, Nery JR, Chen H, Bar-Joseph Z, Walley JW, Solano R, Ecker JR. Integrated multi-omic framework of the plant response to jasmonic acid. Nature Plants, 6, 290-302. DOI: 10.1038/s41477-020-0605-7.

Song G, Montes C, Walley JW. Quantitative Profiling of Protein Abundance and Phosphorylation State in Plant Tissues Using Tandem Mass Tags. Plant Proteomics. Methods in Molecular Biology, vol 2139.


Jia H, Song G, Werth EG, Walley JW, Hicks LM, Jones AM. Receptor-like kinase phosphorylation of Arabidopsis heterotrimeric G-Protein Gα - subunit AtGPA1. Proteomics. Vol 19, 1900265. DOI: 10.1002/pmic.201900265 - PubMed. (Cover Article)

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. (Cover Article)

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: - 

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: - 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. - 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.


Song G, Brachova L, Nikolau BJ, Jones AM, Walley JW. Heterotrimeric G‐protein‐dependent proteome and phosphoproteome in unstimulated Arabidopsis root. Proteomics. 18, 1800323. 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. 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. 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. 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.


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.


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.


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. PubMed.

Walley JW and Briggs SP. Dual use of peptide mass spectra: Protein atlas and genome annotation. Current Plant Biology 2: 21-24. 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.


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 maysMolecular & Cellular Proteomics 13(1): 157-167. DOI:10.1074/mcp.M113.031260 PubMed.


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. 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.

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.

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.

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.