College of Agriculture & Natural Resources
Plant Science & Landscape Architecture

Research Publications

Faculty Member Selected Publications
Sullivan, Joseph

Articles in Refereed Journals:

Smith, C., A. H. Baldwin, J.H. Sullivan and P.T. Leisnham. 2013. Effects of Elevated Atmospheric CO2 on Competition between the Mosquitoes Aedes albopictus and Ae. triseriatus via changes in Litter Quality and Production. J. Med Entm. 50(3): 521-532.

Lee, H., W. M. Garrett, J. H. Sullivan, I. Forseth and S. S. Natarajan. 2013. Differentially Expressed Proteins of Soybean (Glycine max) Pulvinus in Light and Dark conditions. Journal of Basic and Applied Science. 9: 157-171.

Gitz, Dennis C. III1, Steven J. Britz and Joseph H. Sullivan. 2013. Effect of Ambient UV-B on Stomatal Density, Conductance and Isotope Discrimination in Four Field Grown Soybean [Glycine max (L.) Merr.] Isolines. American Journal of Plant Sciences 4:100-108.

Lee, H., W. M. Garrett, J. H. Sullivan and S. S. Natarajan. 2014. Proteomic analysis of the Pulvinus, a Heliotropic Tissue, in Glycine max. International Journal of Plant Biology. 5:8-12.

46. Sullivan, Joe H., DurreShahwar Muhammad, Jack Gibbons, Bao-Shiang Lee3, Lasathi Jayathilaka, Lon S. Kaufman, and Katherine M. Warpeha. 2014. The importance of phenylalanine in early soybean development: the role of UV-A and UV-B radiation. PLoS ONE 9(12): e112301.

Momen, B.M, S. Behling, G. Lawrence and Joe H. Sullivan. 2015. Non-linear Mixed Regression Analysis of sugar-maple photosynthetic-light response to nitrogen and dolomitic limestone additions in the Catskills, NY, USA”. PLoS ONE 10(8): e0136148.

Steven A. Flanagan, George C. Hurtt, Justin P. Fisk, Ritvik Sahajpal, Matthew C. Hansen, Katelyn A. Dolan, Joe H. Sullivan and Maosheng Zhao. 2016. Potential Vegetation and Carbon Redistribution in Northern North America from Climate Change.   Climate. 4, 2; doi:10.3390/cli40100002.

Tiwari, Vijay
  1. Rawat N, Pumphrey MO, Liu Sixin, Zhang X, Tiwari VK, Kaori A, Trick HN, Bockus WW, Akhunov E, Anderson JA and Gill BS (2016) Wheat Fhb1 encodes a chimeric lectin with agglutinin domains and a pore-forming toxin-like domain conferring resistance to Fusarium head blight. Nature Genetics doi:10.1038/ng.3706
  2. Tiwari VK, Heesacker A, Riera-Lizarazu O, Gunn H, Wang S, Wang Y, Gu YQ, Paux E, Koo DH, Kumar A, Luo MC, Zemetra R, Akhunov E, Friebe B, Poland J, Gill BS, Kianian SF and Leonard JM (2016). Whole Genome RH mapping resource to aid reference sequencing of hexaploid wheat. The Plant J 86:195-207
  3. Yi Wang, Tiwari VK, Rawat N, Gill BS, Coleman D and Gu YQ (2016). GSP: a web-based platform for designing genome-specific primers in polyploid plants. Bioinformatics 32 (15): 2382-2383.
  4. Xie J, Huo N, Zhou S, Wang Y, Guo G, Deal KR, Ouyang Z, Liang Y, Wang Z, Xiao L, Zhu T, Hu T, Tiwari VK, Zhang J, Li H, Ni Z, Yao Y, Peng H, Zhang S, Anderson OD, McGuire PE, Dvorak J, Luo MC, Liu Z, Gu YQ, and Sun Q (2016). Sequencing and comparative analysis of Aegilops tauschii chromosome arm 3DS revealed rapid evolution of Triticeae genomes. J. Genet Genomic(In press)
  5. Koo DH, Tiwari VK, Hřibová E, Doležel J,  Friebe B and  Gill BS (2016). Molecular Cytogenetic Mapping of Satellite DNA Sequences in Aegilops geniculata and Wheat. Cytogenet. Genome Res148: 314-321.
  6. Tiwari VK, Wang S, Danilova T, Koo DH, Vrána J, Kubaláková M, Hribova E, Rawat N, Kalia B, Singh N, Friebe B, Dolezel D, Akhunov E, Poland J, Sabir JM and Gill BS (2015). Exploring the tertiay gene pool of hexaploid wheat: Sequence based analysis of Chromosome 5Mg of Ae. geniculataThe Plant J 84:733-746.
  7. Kumar A, Seetan R, Mergoum M, Tiwari VK, Iqbal MJ, Wang Y, Azzam O, Simkova H, Luo MC, Dvorak J, Gu YQ, Denton A, Kilian A, Lazo GR and Kianian SF (2015). Radiation hybrid maps of Aegilops tauschii to facilitate its genome assembly. BMC Genomics 16:800.
  8. Yi Wang*, Tiwari VK*, Drader T*, Lingli Dong L, Kumar A, Huo N, Ghavami F, Iqbal MJ, Lazo GR, Leonard JM, Gill BS, Kianian SF, Luo MC, and Gu YQ  (2015). A D-genome marker resource for diploid and hexaploid wheat. BMC Genomics 16:646. (*shared first authorship)
  9. Tiwari VK, Wang S, Sehgal S, Vrána J,Friebe B, Kubaláková M, Chunneja P,  Doležel J, Akhunov E, Kalia B, Sabir J and Gill BS (2014) SNP Discovery for mapping alien introgressions in wheat. BMC Genomics 15:273.
  10. Salunke R, Rawat N, Kumari N, Tiwari VK, Randhawa GS, Dhaliwal HS, Roy P (2014). Effect of grain hardness on bioavailability of iron in wheat as determined using the coupled invitro digestion/Caco-2 model.  LWT - Food Science Technol 59-1 (433-438).
  11. Fox SE, Geniza M, Hanumappa M, Naithani S, Sullivan C, Preece J, Tiwari VK, Elser J, Leonard JM, Sage A, Gresham C, Kerhornou A, Bolser D, McCarthy, Kersey P, Lazo GR, and Jaiswal P (2014). De Novo transcriptome assembly and analyses of gene expression during photomorphogenesis in diploid wheat Triticum monococcum. PLoS ONE 9:e96855.
  12. Rawat N, Neelam K, Tiwari VK and Dhaliwal HS (2013) Biofortification of cereals to overcome hidden hunger. Plant Breed 132:437-445.
  13. Neelam K, Tiwari VK*, Rawat N, Gandhi N, Arun PC, Kumar S, Randhawa GS and Dhaliwal HS (2013) Development and molecular characterization of wheat- Aegilops longissima derivatives with high grain micronutrients. Aust J Crop Sci 7:508-514 (*Corresponding author).
  14. Tiwari VK, Riera-Lizarazu O, Lopez K, Gunn H, Kianian SF and Leonard JM (2012) Endosperm tolerance of paternal aneuploidy allows radiation hybrid mapping of the wheat D-genome and a unique measure of gamma ray induced chromosome breaks. PLoS ONE 7(11): e48815.
  15. Kumar A, Bassi FM, Paux E, Al-Azzam O, de Jimenez MM, Denton AM, Gu YQ, Huttner E, Kilian A, Kumar S, Goyal A, Iqbal MJ, Tiwari VK,  Dogramaci M,  Balyan HS, Dhaliwal HS, Gupta PK, Randhawa GS, Feuillet C, Pawlowski WP and Kianian SF (2012). DNA repair and crossing over favor similar chromosome regions as discovered in radiation hybrid of Triticum. BMC Genomics 13:339.
  16. Salunke R, Rawat N, Shah A, Neelam K, Tiwari VK, Dhaliwal HS and Roy. P (2012). Zinc Bioavailability from biofortified wheat using a novel reporter gene based coupled in-vitro digestion/caco-2 model. J Food Compos Anal 25:149-159.
  17. Neelam K, Rawat N, Tiwari VK, Prasad R, Tripathi SK, Randhawa GS and Dhaliwal HS (2012) Evaluation and identification of wheat-Aegilops addition lines controlling high grain iron and zinc concentration and mugineic acid production. Cereal Res Commun 40:53-61.
  18. Neelam K*, Rawat N*, Tiwari VK*, Kumar S, Chunneja P, Singh Kuldeep and Dhaliwal HS (2011). Introgression of group 4 and 7 chromosomes of Ae. peregrina in wheat enhances grain iron and zinc density. Mol Breeding 28:623-34. (*Contributed equally).
  19. Rawat N, Neelam K, Tiwari VK, Randhawa GS, Friebe B, Gill BS and Dhaliwal HS (2011). Development and molecular characterization of wheat-Aegilops kotschyi addition and substitution lines with high grain protein iron and zinc. Genome 54:943-953.
  20. Salunke R, Neelam K, Rawat N, Tiwari VK, Dhaliwal HS and Roy P (2011) Bioavailability of Iron from Wheat-Aegilops derivatives selected for high grain iron and protein content. J Agric Food Chem 59:7465-7473.
  21. Tiwari VK, Rawat N, Neelam K, Kumar S, Randhawa GS and Dhaliwal HS (2010) Substitution of 2S and 7U chromosomes of Aegilops kotschyi in wheat enhances grain iron and zinc concentration. Theor Appl Genet 121:259-269.
  22. Riera-Lizarazu O, Leonard JM, Tiwari VK and Kianian SF (2010) A method to produce radiation hybrids for the D- genome chromosomes of wheat. Cytogenet Genome Res 129:234-240.
  23. Neelam K, Rawat N, Tiwari VK, Tripathi SK, Randhawa GS and Dhaliwal HS (2010).  Identification of Aegilops species with higher production of phytosiderophores and iron and zinc uptake under micronutrient sufficient and deficient conditions. Plant Genet Resour: Charac Utiliz 8 (2):132-141.
  24. Tiwari VK, Rawat N, Neelam K, Malik S, Randhawa GS and Dhaliwal HS (2010). Random chromosome elimination in synthetic wheat- Aegilops amphiploids leads to development of a stable partial amphiploid with high grain micro and macronutrient content and powdery mildew resistance. Genome 53:1053-1065.
  25. Tiwari VK, Rawat N, Chhuneja P, Neelam K, Aggarwal R, Randhawa GS, Dhaliwal HS, Keller B, and Singh K (2009). Mapping of quantitative trait loci for grain iron and zinc concentration in A genome diploid Wheat. J Hered 100:771-776.
  26. Rawat N, Tiwari VK, Neelam K, Randhawa GS, Chunneja P, Singh Kuldeep and Dhaliwal HS (2009). Development and characterization of wheat-Aegilops kotschyi amphiploids with high grain iron and zinc. Plant Genet Resour: Charac Utiliz 7:271-280.
  27. Tiwari VK, Rawat N, Neelam K, Randhawa GS, Singh K, Chunneja P and Dhaliwal HS (2008). Development of Triticum turgidum ssp durum-Aegilops longissima amphiploids with high iron and zinc content through unreduced gamete formation in F1 hybrids. Genome 51:757-766.
  28. Rawat N*, Tiwari VK*, Singh N, Randhawa GS, Singh K, Chhuneja P and Dhaliwal HS. (2008). Evaluation and utilization of Aegilops and wild Triticum species for enhancing iron and zinc content in wheat. Genet Resour Crop Evol 56:53-64. (*Shared first authorship).
Tully, Katherine

See/access Kate's publications on her ResearchGate profile.



Status of trends of land degradation and restoration and associated changes in biodiversity and ecosystem function. Ch.4 In The IPBES assessment report on land degradation and restoration. 2018. Montanarella, L., Scholes, R., and Brainich, A. (eds.). Secretariat of the Intergovernmental Science-Policy Platform on Biodiversity and Ecosystem Services, Bonn, Germany. 744 pages.

Neill C, Palm CA, Lefebvre P, Tully K. 2016. Using Soil Characteristics to Target Sustainable Intensification of Maize-based Agriculture in East Africa. Report to International Maize and Wheat Improvement Center (CIMMYT).

Kuyah S, MbowC, Sileshi G, van Noordwijk M, TullyK, RosenstockTS. 2016. Chapter 6: Quantifying carbon stocks and carbon stock changes in biomass on smallholder farms and in agricultural landscapes. In Rosenstock TS, Rufino MC, Butterbach-Bahl K, Wollenberg E, Richards M. (eds.), Methods for Measuring Greenhouse Gas Balances and Evaluating Mitigation Options in Smallholder Agriculture. Springer International, p 119-134.


* indicates undergraduate student   | ** indicates graduate student | *** indicates post-doctoral student


Tully K, Gedan K, Epanchin-Niell R, Strong A, Bernhardt E, BenDor T, Mitchell M, Kominoski J, Jordan T, Neubauer S, Weston N. 2019. The invisible flood: the chemistry, ecology, and consequences of saltwater intrusion. Bioscience.

Tully K, Weissman D**, Wyner WJ*, Miller J, Jordan T. 2019. Soils in transition: Saltwater intrusion alters soil chemistry in agricultural fields. Biogeochemistry.

Thapa R**, Mirsky SB, Tully K. 2019 .Cover crops reduce nitrate leaching in agroecosystems: a global meta-analysis. Journal of Environmental Quality 47:1400-1411

Yu K, Carr D, Anderegg W, Tully K, D'odorico P. 2018. Response of a facultative CAM plant and its competitive relationship with a grass to changes in rainfall regime. Plant and Soil 427:321-333.

Thapa R**, Ackroyd VJ***, Poffenbarger H, Tully K, Kramer M, Mirsky SB. 2018  Biomass production and nitrogen accumulation by hairy vetch-cereal rye biculture - A meta-analysis. Agronomy Journal 110:1197-1208.

Koivunen EE, Swett CL, Tully K. In press. Crab meal and other amendments improve soil quality while promoting degradation and microbial antagonism of Botrytis cinerea sclerotia. Plant and Soil.

Tully K, Abwanda S, Thiong’o M, Mutuo PM, Rosenstock TS. 2017.Nitrous oxide and methane fluxes from urine and dung deposited on Kenyan pastures. Journal of Environmental Quality 46:921-929.

Tully K, Ryals R. 2017. Nutrient cycling in agroecosystems: Balancing food and environmental objectivesInvited Special Issue in Agroecology & Sustainable Food Systems. 7: 761-798.

Russo T, Tully K, Palm C, Neill C. 2017. Nitrate leaching losses from Kenyan agricultural site receiving different fertilizer treatments. Agriculture Ecosystems & Environment 108:195-951.

Palm C, Neill C, Lefebvre P and Tully K. 2017. In press. Targeting sustainable intensification of maize-based agriculture in East Africa. Tropical Conservation Science. DOI:

Michelson H, Tully K. 2017. In press. The Millennium Villages Project and Local Land Values: Using Hedonic Pricing Methods to Evaluate Development Projects. World Development.

Hickman JE, Palm CA, Tully K, Diru W, Groffman PM. 2017.  Non-linear response of nitric oxide fluxes to fertilizer inputs and the impacts of agricultural intensification on tropospheric ozone pollution in Kenya. Global Change Biology 120:938-951.

Tully K, M, Hickman JE, McKenna M, Neill C, Palm CP. 2016.Fertilizer application alters vertical distributions and temporal dynamics of soil inorganic nitrogen in continuous maize systems in East Africa. Ecological Applications 26:1907-1919.

Tully K, Wood SA, Neill C, Palm CP. 2015. The effect of African Green Revolution interventions on nitrogen balances in smallholder maize farms in Western Kenya. Agriculture, Ecosystems & Environment 214:10-20.

Tully K, Sullivan C, Weil R, Sanchez P. 2015The state of soil degradation in sub-Saharan Africa: baselines, trajectories, and solutions. Sustainability 7(6):6523-6552. Invited review article.

Hickman JE, Tully K, Groffman PM, Diru W, Palm CA. 2015. A potential tipping point in tropical agriculture: Avoiding rapid increases in nitrous oxide fluxes from agricultural intensification in Kenya. JGR-Biogeosciences. 120:938-951.

Wood SA, Bradford MA, Gilbert JA, McGuire KL, Palm CA, Tully K, Zhou J, Naeem S. 2015. Agricultural intensification and the functional capacity of soil microbes on smallholder African farms. Journal of Applied Ecology 52:744-752.

Wood SA, Almaraz M, Bradford MA, McGuire KL, Naeem S, Palm CA, Tully K, Zhou J. 2015. Farm management, not soil microbial diversity controls nutrient loss from smallholder tropical agriculture. Frontiers in Microbiology 6:1-10.

Tully K, Weil R. 2014.Ion selective electrode offers accurate, inexpensive method for analyzing soil solution nitrate in remote regions. Communications in Soil Science and Plant Analysis. 45:1974-1980.

Rosenstock T, Tully K, Arias-Navarro C, Butterbach-Bahl K, Neufeldt H, Verchot L. 2014. Agroforestry with N-fixing trees: Sustainable development’s friend or foe? Current Opinion in Environmental Sustainability, 6:15-21.

Tully K, Lawrence D, Wood SA. 2013. Organically managed coffee agroforests have larger soil phosphorus but smaller soil nitrogen pools than conventionally managed agroforests. Biogeochemistry, 115:385-397.

Tully, K, Wood SA, Lawrence D. 2013. Fertilizer type and species composition affect nutrient leachate in coffee agroecosystems. Agroforestry Systems. 87:1083-1100.

Tully K, Wood TE, Schwantes AM, Lawrence D. 2013. Soil nutrient availability and reproductive effort drive patterns in nutrient resorption in Pentaclethra macroloba. Ecology. 94:930-940.

Tully K, Lawrence D, Scanlon TM. 2012. More trees less loss: Nitrogen losses decrease with increasing biomass in coffee agroforests. Agriculture, Ecosystems and Environment. 161:137-144.

Tully K, and Lawrence D. 2012. Canopy and leaf composition drive patterns of nutrient release from pruning residues in a coffee agroforest. Ecological Applications. 22:1330-1344.

Huang C-Y, Tully K, Clark DA, Oberbauer SF, McGlynn TP. 2012. The δ15 N signature of the detrital food web tracks a landscape-scale soil phosphorus gradient in a Costa Rican lowland tropical rain forest. Journal of Tropical Ecology. 28: 395-403.

Tully K, Lawrence D. 2011. Closing the Loop: Nutrient balances in organic and conventional coffee agroforests. Journal of Sustainable Development, 35: 671-695.

Tully K, Lawrence D. 2010. Declines in leaf litter nitrogen linked to rising temperatures in a wet tropical forest. BIOTROPICA. 42: 526-530.

Goeghegan J, Lawrence D, Schneider L, Tully K. 2010. Accounting for Carbon in Models of Land Use and Implications for Payments for Environmental Services: An Application to SYPR. Regional Environmental Change. 42: 526-530.

Lawrence D, Radel R, Tully K, Schmook B, Schneider L. 2010 Untangling a global decline in tropical forest resilience: constraints on the sustainability of shifting cultivation. BIOTROPICA. 40: 21-30.

Vandecar K, Lawrence D, Wood TE, Das R, Oberbauer S, Schwendenmann L, Tully K. 2009. Diurnal fluctuations in labile soil phosphorus in response to climatic conditions and soil CO2 efflux in a wet tropical forest, La Selva, Costa Rica.  Ecology. 90: 2547-2555.

Tully K. 2002. Tilting. Kenyon Chapbook Series: Featured work for emerging authors. ISBN: 0-9726005-5-8.


* indicates undergraduate student   | ** indicates graduate student | *** indicates post-doctoral student

Tully K and McAskill C. In review. Promoting soil health in organically managed systems: A review. Renewable Agriculture and Food Systems.

Otte B**, Schomberg HH, Mirsky SB, Tully KIn revision. Managing deep inorganic nitrogen, water, and corn performance in a cereal rye cover crop. Agronomy Journal.


* indicates undergraduate student   | ** indicates graduate student | *** indicates post-doctoral student

Huddell AM, Galford G, Tully K, Crowley C, Palm CA, Neill C, Hickman JE­, and Menge DL. In preparation. Potential for increasing nitrogen losses from intensifying tropical agriculture.  




Walsh , Christopher

Recent Articles in Refereed Journals

Allard, SA, CS Walsh, AE Wallis, AR Ottesen, EW Brown and SA Micallef.  2016.  Solanum lycopersicum (tomato) hosts robust phyllosphere and rhizosphere bacterial communities when grown in soil amended with various organic and synthetic fertilizers.  Science of the Total Environment.  573:555-563.

Walsh, CS, JM Harshman, AE Wallis, AB Williams, MJ Newell and GR Welsh.  2016.  Asian pear: A potential alternative fruit crop for growers in the Mid-Atlantic Region.  HortScience.  51:1325-1328.

Pagadala, S, SC Marine, SA Micallef, F Wang, DM Pahl, MV Melendez, WL Kline, RA Oni, CS Walsh, KL Everts and RL Buchanan. 2015. Assessment of region, farming system, irrigation source and sampling time as food safety risk factors for tomatoes and their production areas on small and medium sized farms in Maryland, Delaware and New Jersey. 2015. International Journal of Food Microbiology. doi: 10.1128/AEM.00051-15.

Marine, SC, S Pagadala, F Wang, DM Pahl, MV Melendez, WL Kline, RA Oni, CS Walsh, KL Everts, RL Buchanan and SA Micallef. 2015. Growing season, but not farming system, a food safety risk determinant for leafy greens in the mid-Atlantic region. Applied and Environmental Microbiology. 196C: 98-108. PMID: 25540859.

Harshman, JM, KS Lewers, WM Jurick II and CS Walsh. 2014. Breeding selection efficiency for raspberry postharvest shelf life affected by storage temperature and harvest season. Euphytica. 199: 283-292.

Harshman, JM, WM Jurick II, KS Lewers, SY Wang and CS Walsh. 2014. Resistance to Botrytis cinerea and quality characteristics during storage of raspberry genotypes. HortScience. 48(3):311-319.

Pahl, DM, CS Walsh, M Newell, D Skaltsas and A Telias. 2013. Comparing source of agricultural contact water and the presence of fecal indicator organisms on the surface of 'Juliet' grape tomatoes. J. Food Protection. 76:967-974.

Harshman, JM and CS Walsh. 2013. Effects of phenotype and seed parent on the size, productivity and fruit quality of second-generation seedling apple (Malus domestica Borkh.) trees. J. Amer. Pomological Soc. 67(3): 168-174.

Telias, A, JR White, DM Pahl, AR Ottesen and CS Walsh. 2011. Bacterial community diversity and variation in spray water sources and the tomato phyllosphere. BMC Microbiology. 11:81. is external).  (Article was listed on the BMC website as ‘most viewed’ during the month after it appeared.)

Johnson, S., R. Andersen, W. Autio, T. Beckman, B. Black, P. Byers, J. Cline, C. Chavez-Gonzalez, W. Cowgill, R. Godin, G. Greene, M. Kaps, J. Kamas, H. Larsen, T. Lindstrom, D. Miller, M. Newell, D. Ophardt, D. Ouellette, R. Parra-Quezada, R. Pokharel, G. Reighard, T. Robinson, J. Schupp, L. Stein, K. Taylor, C.S. Walsh, D. Ward, M. Warmund, and M. Whiting.  2011.  Performance of the 2002 NC-140 cooperative peach rootstock planting. J. Amer. Pomological Soc.  65: 17-25.

Reighard, G.L., T. Beckman, R. Belding, B. Black, P. Byers, J. Cline, W. Cowgill, R. Godin, R.S. Johnson, J. Kamas, M. Kaps, H. Larsen, T. Lindstrom, M. Newell, D. Ouelette, R. Pokharel, L. Stein K. Taylor, C.S, Walsh, D. Ward, and M. Whiting.  2011.  Six-year performance of 14 Prunus rootstocks at 11 sites in the 2001 NC-140 peach trial. J. Amer. Pomological Soc.  65: 26-41.

Manuscripts submitted, reviewed and accepted for publication during 2016.

Schneider, KR, J De, Y Li, A Sreedharan, R Goodrich-Snyder, MD Danyluk, DM Pahl, CS Walsh, J Tood-Searle, DW Schaffner, W Kline and RL Buchanan.  2017.  Food Control.  73:511-517.

Wallis, A, JM Harshman, B Butler, D Price, G Fazio and C Walsh.  2017.  Performance of Geneva apple rootstock slections with ‘Brookfield Gala’ and Cripps Pink in a tall-spindle system.  2017.  J Amer Pomological Soc.  (In press)

Frequently Cited Articles from Dr. Walsh’s Lab

Ottesen, AO, JR White, DN Skaltsas, MJ Newell and CS Walsh.  2009.  Impact of organic and conventional management on the phyllosphere microbial ecology of an apple crop. J. Food Protection. 72(11):2321-2325.

Luchsinger, L.E. and C.S. Walsh.  1998.  Chilling injury of peach fruit during storage.  Acta Horticulturae  464:473-480.  (Proceedings of the International Conference on Postharvest Science – Postharvest 96, Taupo, New Zealand).

Miller, AN, BA Krizek and CS Walsh.  1988.  Whole-fruit ethylene evolution and ACC content of peach pericarp and seeds during development. J. Amer. Soc. Hort. Sci.  113 (1):119-124.

Miller, AN and CS Walsh.  1988.  Growth and seasonal partitioning of dry matter in eight-year-old 'Loring' peach trees. J. Amer. Soc. Hort. Sci.  113:309-314.

Miller, AN, CS Walsh and JD Cohen.  1987.  Measurement of indole-3-acetic acid in peach fruits during development.  Plant Physiol.  84:491-494.

Walsh, CS, J Popenoe and T Solomos.  1983. Thornless blackberry is a climacteric fruit. HortScience  18:482‑483.

Walsh, CS, HJ Swartz and LJ Edgerton.  1979. Ethylene evolution in apple following post-bloom thinning sprays.  HortScience 14:704-706.

Published Abstracts and Meeting Proceedings

Ottesen, A, D Skaltas, JR White, S Gorham, P Ramachandran, EW Brown, M Newell and C Walsh.  2016. Using next generation sequencing to describe epiphytic microbiota associated with organic and conventionally managed apples. Intl J Env & Agr Res.  2: 36-45.

Ottesen, A, A Telias, EW Brown, JR White, S Musser, MJ Newell, D Pahl and CS Walsh.  2016.  Bacteria of tomatoes managed with well water and pond water: Impact of agricultural water sources on carposphere microbiota.  Intl. J. Envir & Agr. Res.  2(7): 7-14.

Redman, B* and C Walsh.  2016.  Delta absorbance meter as a means to predict and reduce the incidences of browning disorders.  ASHS Meeting, Atlanta.  (Poster).

Walsh, CS, AE Wallis, S Allard, P Briner, C Frank, A Loeb* and E Prinkey.  2016. Local lettuce: Heat tolerant romaine cultivars and vermicompost soil amendment to expand production methods in the Mid-Atlantic.  2016.  ASHS Meeting, Atlanta.  (Poster).

Walsh, CS,* JM Harshman, AE Wallis, A Barton Williams, MJ Newell and GR Welsh.  2015.  Field performance of Asian pear cultivars in the hot, humid summer conditions of the Mid-Atlantic Region of the United States.  2014.  Contributed Oral Presentation in Leuven, Belgium.  Acta Horticulturae.  1094:103-109. DOI: 10.17660/ActaHortic.2015.1094.9

Pahl, DM,* T Chfadi, C Narrod, CS Walsh, D Martin, and S Micallef.  2015.  Evaluating the Effectiveness of Food Safety Trainings by Determining Factors that Influence Grower Adoption of Food Safety Certification Practices.  Poster Presentation IAFP Meeting in Portland. (Poster Abstract).

Walsh, CS,* JM Harshman, AE Wallis, A Barton Williams, MJ Newell and GR Welsh. 2015.  Asian pear: A potential alternative fruit crop for growers in the Mid-Atlantic region.  Invited colloquium presentation ASHS Meeting, New Orleans.

Jurick, WM II, VL Gaskins, E Park, MJ Newell, JM Harshman and CS Walsh. 2014. Evaluation of fruit quality and susceptibility to blue mold of nine Asian pear varieties. Presented in Leuven, Belgium. (Contributed Poster Presentation)

Harshman, JM, CS Walsh, J Daberkow, K Sparks, MJ Newell and GR Welsh. 2011. Hybridizing 'McIntosh Wijcik' and heat-tolerant apple cultivars to develop precocious seedling trees with improved tree architecture. Acta Horticulturae: 903: 193-197.(link is external)

Walsh, CS, A Ottesen, M Newell, J Hanson and E Leone. 2011. The effect of organic and conventional IPM management programs on apple and Asian pear tree growth, productivity, expenses and revenues in a hot, humid climate. Acta Horticulturae 903: 665-672.

Webb, D. A. Callahan, R. Scorza, T Tworkoski and C. Walsh.  2010.  Gene expression and endogenous hormone levels in different growth habits of peach and apple.  Cumberland-Shenandoah Fruit Workers’ Conference.  Winchester, VA.(Contributed paper).

Telias, A., D.Pahl, J.White, C.S. Walsh. 2010.  The impact of agricultural practices on bacterial phyllosphere ecology and food safety.  Mid-Atlantic Section, American Society of Plant Biology. Bowie, MD. (Abstract).

Emery, K.A. Y.Tao and C.S.Walsh. 2010.  Machine trials in visualizing peach flowers for mechanical thinning of fruit.  ASABE 2010.  Pittsburgh, PA.  (Contributed paper).

Patents and Other Creative Activities

Harshman, JM and CS Walsh. ‘Antietam Blush’ Apple. Provisional Patent Disclosure LS-2011-116. This was submitted by the University Of Maryland Office Of Technology Commercialization in November, 2013 with the full disclosure in November, 2014.

Ellis, C, B-S Kweon, D Myers, D. Nola, S Cohan, C Walsh, C Balch, C Henry and A Tetrault. Supporting sustainable urban tree research and education through design. Second prize proposal, Casey Tree Farm Design Competition. $5000 Master Planning Award and Second Prize. 2013.

Wight, Jason
Book Chapters
Wang, Y. Dou, F., J.O. Storlien, J.P. Wight, K. Paustian, S.J. Del Grosso, and F.M. Hons. 2017. Simulating Impacts of Bioenergy Sorghum Residue Return on Soil Organic Carbon and Greenhouse Gas Emissions Using DAYCENT Model. In Global Soil Security. Springer. New York, NY. DOI: 10.1007/978-3-319-43394-3_15.
Ashworth, A.J., F.L. Allen, J.P. Wight, A.M. Saxton, and D.D. Tyler. 2013. Long-term soil organic carbon changes as affected by crop rotation and bio-covers in no-till crop systems. In A. Hartemink and K. McSweeney (eds.) Soil Carbon.  Springer. New York, NY. DOI: 10.1007/978-3-319-04084-4_28.
Journal Articles
W. L. Felicien, J. P. Wight, L. A. Gaston, M. A. Blazier & J. L. Kovar, Phosphorus runoff  
from coastal plain forest soil in Louisiana. 2016. Communications in Soil Science and Plant
Analysis. DOI: 10.1080/00103624.2016.1166241.
Wight, J.P., A.J. Ashworth, F.L. Allen, N. Labbe, T. Rials and D. Tyler. 2016. Comparison
of near infrared reflectance spectroscopy with combustion and chemical methods for soil carbon measurements in agricultural soils. Communications in Soil Science and Plant Analysis. DOI: 10.1080/00103624.2016.1146750.
Wight, J.P., A.J. Ashworth, and F.L. Allen. 2016. Organic substrate, clay type, texture, and water influence on NIR carbon measurements. Geoderma. DOI: 10.1016/j.geoderma.2015.06.021.
Wight, J. G. Waldron, L. Gaston, M. Blazier, and J. Kovar. 2015. Mobility of poultry litter phosphorus in a coastal plain forest soil. Soil Science. DOI: 10.1097/SS.0000000000000120.
Shahandeh, H. F.M. Hons, J.P. Wight, and J.O. Storlien. 2015. Harvest strategy and N fertilizer effects on bioenergy sorghum production. AIMS Energy. DOI: 10.3934/energy.2015.3.377.
Dou, F. J.P. Wight, L.T. Wilson, J.O. Storlien, and F.M. Hons. 2014 Simulation of biomass yield and soil organic carbon under bioenergy sorghum production. PLOS ONE. DOI: 10.1371/journal.pone.0115598.
Storlien, J.O., F.M. Hons, J.P. Wight, and J.L. Heilman. 2014. Carbon dioxide and nitrous oxide emissions impacted by bioenergy sorghum management. Soil Science Society of America Journal. DOI:10.2136/sssaj2014.04.0176
Ashworth, A.J., F.L. Allen, J.P. Wight, A.M. Saxon, and D.D. Tyler. 2014. Soil organic carbon sequestration rates under greater crop sequence diversity, bio-covers, and no-tillage. Soil Science Society of America Journal. DOI 10.2136/sssaj2013.09.0422.
Amatya, P., J.P. Wight, J.W. Mjelde, and F.M. Hons. 2014. Balancing bioenergy and soil productivity returns for sustainable biomass sorghum [Sorghum bicolor (L). Moench.]. BioEnergy Research. DOI 10.1007/s12155-014-9451-7.
Wight, J.P., F.M. Hons, G. O. Osuji. 2014. Responses of bioenergy sorghum cell wall metabolism to agronomic practices. Advances in Biological Chemistry. 4:67-78. DOI: 10.4236/abc.2014.41011.
Wight, J.P., F.M. Hons, S.M. South, and G.O. Osuji. 2012. Purification of active peroxidase isoenzymes and their responses to nitrogen fertilization and rotation of biomass sorghum. American Journal of Plant Sciences. 3:1422-1429. DOI:10.4236/abc.2014.41010.
Wight, J.P., F.M. Hons, J.O. Storlien, T.L. Provin, H. Shahandeh, and R.P. Wiedenfeld. 2012. Management effects on bioenergy sorghum growth, yield and nutrient uptake. Biomass and Bioenergy. 46:593-604. DOI:10.1016/j.biombioe.2012.06.036.
Wight, J.P., F.L. Allen, P.A. Donald, D.D. Tyler, and A. M. Saxton. 2011. Impact of crop rotation and bio-covers on soybean cyst nematode. Plant Health Progress. DOI:10.094/PHP-2010-0930-01-RS.

Liechty, H.O., M.A. Blazier, J.P. Wight, L.A. Gaston, J.D. Richardson, and R.L. Fickin. 2009. Assessment of repeated application of poultry litter on phosphorus and nitrogen dynamics in loblolly pine: Implications for water quality. Forest Ecol. Management. 258(10):2294-2303. DOI: 10.1016/j.foreco.2009.01.021.

Xiao, Shunyuan

(*corresponding author; # co-first author)

Berkey R, Zhang Y, Ma X, Zhang Q, King, H, Wang W, and Xiao S*. (2016). Homologues of the RPW8 resistance protein are localized to the extra-haustorial membrane that is likely synthesized de novo. Plant Physiology online published (

Ma XF, Wang W, Bittner F, Schmidt N, Berkey R, Zhang L, King H, Zhang Y, Feng J, Wen YQ, Tan TL, Deng Z, Xiong XY, Xiao S*. (2016). Dual and opposing roles of xanthine dehydrogenase in defense-associated reactive oxygen species metabolism in Arabidopsis. Plant Cell 28: 1108–1126 (Featured Article) (

Song F, Pan ZY*, Bai F, An JY, Liu, JH, Guo WW, Bisseling T, Deng XX and Xiao S. (2015). The scion/rootstock genotypes and habitats affect arbuscular mycorrhizal fungal community in Citrus. Frontier in Microbiology 2015; 6: 1372 (DOI: 10.3389/fmicb.2015.01372. eCollection 2015. PMID:26648932)

Zeng YL, Du JB, Wang L, Pan, ZY, Xu, Q, Xiao S, Deng XX*. (2015). A comprehensive analysis of chromoplast differentiation reveals complex protein changes associated with plastoglobule biogenesis and remodeling of protein systems in sweet orange flesh. Plant Physiology 168:1648-1665. (DOI: 10.1104/pp.15.00645. Epub 2015 Jun 8. PMID: 26056088)

Helliwell EE, Vega-Arreguin J, Shi Z, Bailey B, Xiao S, Maximova SN, Tyler BM*, and Guiltinan MJ*. (2015). Enhanced resistance in Theobroma cacao against oomycete and fungal pathogens by secretion of phosphatidylinositol-3-phosphate-binding proteins. Plant Biotechnology Journal (DOI: 10.1111/pbi.12436. Epub 2015 Jul 27. PMID: 26214158)

Li F#, Cheng C#, Cui F#, de Oliveira M#, Yu X, Meng X, Intorne AC, Babilonia K, Li M, Li B, Chen S, Ma X, Xiao S, Zheng Y, Fei Z, Metz RP, Johnson CD, Koiwa H, Sun W, Li Z, de Souza Filho GA, Shan L*, He P* (2014). Modulation of RNA polymerase II phosphorylation downstream of pathogen perception orchestrates plant Immunity. Cell Host & Microbe 16: 748–758 (DOI: 10.1016/j.chom.2014.10.018. Epub 2014 Nov 26. PMID: 25464831)

Ma X#, Li Y#, Sun JL, Wang TT, Fan J, Lei Y, Huang YY, Xu YJ, Zhao JQ, Xiao S, Wang WM*. (2014). Ectopic Expression of RESISTANCE TO POWDERY MILDEW8.1 Confers Resistance to Fungal and Oomycete Pathogens in Arabidopsis. Plant & cell Physiology  55:1484-96 (DOI: 10.1093/pcp/pcu080. Epub 2014 Jun 4. PMID: 24899552)

Huang Y, Shi Y, Lei Y, Li Y, Fan J, Xu Y, Ma X, Zhao J, Xiao S, Wang W*. (2014). Functional identification of multiple nucleocytoplasmic trafficking signals in the broad-spectrum resistance protein RPW8.2. Planta 239(2):455-68 (DOI: 10.1007/s00425-013-1994-x. Epub 2013 Nov 12. PMID: 24218059).

Pan Z#, Li Y#, Deng X, Xiao S*. (2014). Non-targeted metabolomic analysis of orange (Citrus sinensis [L.] Osbeck) wild type and bud mutant fruits by direct analysis in real-time and HPLC-electrospray mass spectrometry. Metabolomics 10:508-523 (DOI: 10.1007/s11306-013-0597-7).

Wang W#, Zhang Y#, Wen Y, Berkey R, Ma X, Pan Z, Bendigeri D, King H, Zhang Q, and Xiao S*. (2013). A comprehensive mutational analysis of the Arabidopsis resistance protein RPW8.2 reveals key amino acids for defense activation and protein targeting. Plant Cell 25:4242-61 (Featured Article) (DOI: 10.1105/tpc.113.117226. Epub 2013 Oct 22. PMID:24151293)

Wang W, Ma X, Zhang Y, Luo MC, Wang G, Bellizzic M, Xiong X and Xiao S*. (2012). PAPP2C interacts with the atypical disease resistance protein RPW8.2 and negatively regulates salicylic acid-dependent defense responses in Arabidopsis. Molecular Plant 5:1125-1137 (DOI: 10.1093/mp/sss008. Epub 2012 Feb 14. PMID: 22334594)

Wen Y, Wang W, Feng J, Luo MC, Tsuda K, Katagiri F, Bauchan G and Xiao S*. (2011). Identification and utilization of a sow thistle powdery mildew as a nonhost pathogen to dissect post-invasion resistance mechanisms in Arabidopsis. Journal of Experimental Botany  62: 2117-2129 (DOI: doi: 10.1093/jxb/erq406. Epub 2010 Dec 30. PMID: 21193574)

Wang W, Wen Y, Berkey R and Xiao S*. (2009). Specific targeting of Arabidopsis protein RPW8 to the interfacial membrane encasing the fungal haustorium renders broad-spectrum resistance. Plant Cell 21: 2898-2913 (Featured Article) (DOI: 10.1105/tpc.109.067587. Epub 2009 Sep 11. PMID: 19749153)

Yang X#, Wang W#, Coleman M, Feng J, Ma X, Ferl R, Turner JG and Xiao S*. (2009). Arabidopsis 14-3-3 lambda is a positive regulator of RPW8-mediated disease resistance Plant Journal 60:539-50 (DOI: 10.1111/j.1365-313X.2009.03978.x. Epub 2009 Jul 16. PMID: 19624472)

Wang W#, Yang Y#, Tangchaiburana S, Ndeh R, Markham JE, Tsegaye Y, Dunn TM, Wang GL, Bellizzi M, Parsons, JF, Morrissey D, Bravo JE, Lynch DV and Xiao S*. (2008). An inositolphosphorylceramide synthase is involved in regulation of plant programmed cell death associated with defense. Plant Cell  20: 3165-3179 (DOI: 10.1105/tpc.108.060053. Epub 2008 Nov 11. PMID: 19001565)

Orgil U, Araki H, Tangchaiburana S, Berkey R, Xiao S*. (2007). Intraspecific genetic variations, fitness cost and benefit of RPW8, a disease resistance locus in Arabidopsis thaliana. Genetics 176: 2317-2333. (DOI: 10.1534/genetics.107.070565. Epub 2007 Jun 11.PMID: 17565954)

Wang W, Devoto A, Turner JG, Xiao S*. (2007). Expression of the membrane-associated resistance protein RPW8 enhances basal defense against biotrophic pathogens. Molecular Plant Microbe Interaction 20: 966-976. (DOI: 10.1094/ MPMI -20-8-0966. PMID: 17722700)

Xiao S, Calis O, Patrick E, Zhang G, Charoenwattana P, Muskett P, Parker JE, Turner JG*. (2005). The atypical resistance gene, RPW8, recruits components of basal defence for powdery mildew resistance in Arabidopsis. Plant Journal 42: 95-110. (DOI: 10.1111/j.1365-313X.2005.02356.x. Epub: 2005 Mar 17. PMID: 15773856)

Xiao S, Emerson B, Ratanasut K, Patrick E, O'Neill C, Bancroft I, Turner JG*. (2004). Origin and maintenance of a broad-spectrum disease resistance locus in Arabidopsis. Molecular Biology Evolution 21:1661-1672. (DOI: 10.1093/molbev/msh165. Epub 2004 May 21. PMID: 15155802)

Xiao S, Brown S, Patrick E, Brearley C, Turner JG*. (2003). Enhanced transcription of the Arabidopsis disease resistance genes RPW8.1 and RPW8.2 via a salicylic acid-dependent amplification circuit is required for hypersensitive cell death. Plant Cell 15: 33-45. (DOI: 10.1105/tpc.006940. Epub 2001 Dec 19. PMID: 12509520)

Xiao S#, Charoenwattana P#, Holcombe L, Turner JG*. (2003). The Arabidopsis genes RPW8.1 and RPW8.2 confer induced resistance to powdery mildew diseases in tobacco. Molecular Plant Microbe Interaction 16: 289-294. (DOI: 10.1094/MPMI.2003.16.4.289. PMID: 12744457)

Peart JR, Lu R, Sadanandom A, Malcuit I, Moffett P, Brice DC, Schauser L, Jaggard DA, Xiao S, Coleman MJ, Dow M, Jones JD, Shirasu K, Baulcombe DC*. (2002). Ubiquitin ligase-associated protein SGT1 is required for host and nonhost disease resistance in plants. Proc Natl Acad Sci USA 99: 10865-10869. (DOI: 10.1073/pnas.152330599. Epub 2002 Jul 15. PMID: 12119413)

Xiao S, Ellwood S, Calis O, Patrick E, Li T, Coleman M, Turner JG*. (2001). Broad-spectrum mildew resistance in Arabidopsis thaliana mediated by RPW8. Science 291: 118-120. (DOI: 10.1126/science. 291.5501.118. PMID: 11141561)

Xiao S, Ellwood S, Findlay K, Oliver RP, Turner JG*. (1997). Characterization of three loci controlling resistance of Arabidopsis thaliana accession Ms-0 to two powdery mildew diseases. Plant Journal 12: 757-768. (DOI: 10.1046/j.1365-313X.1997.12040757.x. PMID: 9375391)



Xiao S, Turner JG, Coleman M, and Ellwood S (2001). Plant resistance gene, Patent number WO0198479-A/7, 27-DEC-2001. Plant Bioscience Limited (GB), UK.

Xiao S and Wang W (2011). Plants with reduced expression of phosphatase type 2C gene for enhanced pathogen resistance (PCT/US05/ 450001; U.S. Patent Application Serial No. 11/762,989)

Xiao S and Wang W (2015). Engineering broad-spectrum disease resistance against haustorium-forming pathogens using RPW8 as a delivery vehicle. (US9057077 B2; 6/16/2015)

Xiao S, Yang X, and Wang W (2015). Enhancing drought tolerance and bacterial resistance by functional interference of 14-3-3. (US20120198585 A1, 8/4/2015)


Zhu , Jianhua
Articles in Refereed Journals:
Hu, T., Wang, Y., Wang, Q., Dang, N., Wang, L., Liu, C., Zhu, J.*, and Zhan, X.* (2019) The tomato 2-oxoglutarate-dependent dioxygenase gene SlF3HL is critical for chilling stress tolerance. Horticulture Research. In Press. *Co-corresponding authors.
Liang, M.-H., Wang, L., Wang, Q., Zhu, J.*, and Jiang, J.-G*. (2018) High-value bioproducts from microalgae: strategies and progress. Critical Reviews in Food Science and Nutrition. 20:1-53. doi: 10.1080/10408398.2018.1455030. *Co-corresponding authors.
Liu, C.-C., Chi, C., Jin, L.-J., Zhu, J., Yu, J.-Q., and Zhou, Y.-H. (2018) The bZip transcription factor HY5 mediates CRY1a-induced anthocyanin biosynthesis in tomato. Plant, Cell & Environment. 41:1762-1775.
Gu, J., Xia, Z., Luo, Y., Jiang, X., Qian, B., Xie, H., Zhu, J.-K., Xiong, L., Zhu, J.*, and Wang, Z.-Y.* (2018) Spliceosomal protein U1A is involved in alternative splicing and salt stress tolerance in Arabidopsis thaliana. Nucleic Acids Research. 46:1777-1792. *Co-corresponding authors.
Liang, M.-H., Zhu, J.*, and Jiang, J.-G.* (2018) Carotenoids biosynthesis and cleavage related genes from bacteria to plants. Critical Reviews in Food Science and Nutrition. 58:2314-2333. doi:10.1080/10408398.2017.1322552. *Co-corresponding authors.
 Zhan, X.*, Qian, B., Cao, F., Wu, W., Yang, L., Quan, Q., Gu, X., Wang, P., Okusolubo, T.A., Dunn, S.L., Zhu, J.-K., and Zhu, J.* (2015) An Arabidopsis PWI- and RRM motif-containing protein is critical for pre-mRNA splicing and ABA responses. Nature Communications. 6:8139. doi: 10.1038/ncomms9139 (2015). *Co-corresponding authors; Dunn, S.L., undergraduate student; Okusolubo, T.A., high school student.
Wang, Z.-Y., Gehring, C., Zhu, J., Li, F.-M., Zhu, J.-K., and Xiong, L. (2015) The Arabidopsis VSR1 is required for osmotic stress-induced abscisic acid biosynthesis. Plant Physiology. 167:137-152.
Guan, Q., Yue, X., Zeng, H., and Zhu, J. (2014) The protein phosphatase RCF2 and its interacting partner NAC019 are critical for heat stress-responsive gene regulation and thermotolerance in Arabidopsis. Plant Cell. 26:438-453
Jeong, I.S., Fukudome, A., Aksoy, E., Bang, W.Y., Kim, S., Guan, Q., Bahk, J.D., May, K.A., Russell, W.K., Zhu, J., and Koiwa, H. (2013) Regulation of abiotic stress signalling by Arabidopsis C-terminal Domain Phosphatase-like 1 requires interaction with a K-homology domain-containing protein. PLoS One. 8(11): e80509.
Guan, Q., Wen, C., Zeng, H, and Zhu, J.  (2013) A KH domain-containing putative RNA-binding protein is critical for heat stress-responsive gene regulation and thermotolerance in Arabidopsis. Molecular Plant. 6:386-395.
Guan, Q., Wu, J., Zhang, Y., Jiang, C., Liu, R., Chai, C., and Zhu, J. (2013) A DEAD box RNA helicase is critical for pre-mRNA splicing, cold-responsive gene regulation, and cold tolerance in Arabidopsis. Plant Cell. 25:342-356.
Guan, Q., Lu, X., Zeng, H., Zhang, Y., and Zhu, J.(2013) Heat stress induction of miR398 triggers a regulatory loop that is critical for thermotolerance in Arabidopsis. Plant Journal. 74:840-851.
Li, W.*, Guan, Q.*, Wang, Z.-Y., Wang, Y., and Zhu, J. (2013) A bi-functional xyloglucan galactosyltransferase is an indispensable salt stress tolerance determinant in Arabidopsis. Molecular Plant. 6:1344-1354. *Equal contribution.
Lu, X., Guan, Q., and Zhu, J. (2013) Downregulation of CSD2 by a heat-inducible miR398 is required for thermotolerance in Arabidopsis. Plant Signaling & Behavior. 8: e24952.
Guan, Q., Wu, J., Yue, X., Zhang, Y., and Zhu, J. (2013) A nuclear calcium-sensing pathway is critical for gene regulation and salt stress tolerance in Arabidopsis. PLoS Genetics. 9(8):e1003755.
Barrera-Figueroa, B.E., Gao, L., Wu, Z., Zhou, X., Zhu, J., Jin, H., Liu, R., and Zhu, J.-K. (2012) High throughput sequencing reveals novel and abiotic stress-regulated microRNAs in the inflorescences of rice. BMC Plant Biology. 12:132.
Khraiwesh, B., Zhu, J.-K., and Zhu, J. (2012) Role of miRNAs and siRNAs in biotic and abiotic stress responses of plants. Biochimica et Biophysica Acta-Gene Regulatory Mechanisms. 1819:137-148.
Wang, Z.-Y., Xiong, L., Li, W., Zhu, J.-K., and Zhu, J. (2011) Plant cuticle is required for osmotic stress regulation of abscisic acid biosynthesis and osmotic stress tolerance. Plant Cell. 23:1971-1984.
Zhu, J.#, Lee, B.-h., Dellinger, M., Cui, X., Zhang, C., Wu, S., Nothnagel, E.A., and Zhu, J.-K. (2010) A cellulose synthase-like protein is required for osmotic stress tolerance in Arabidopsis. Plant Journal. 63:128-140. #Corresponding author.
Ren, Z., Zheng, Z., Chinnusamy, V., Zhu, J., Cui, X., Iida, K., and Zhu, J.-K. (2010) RAS1, a quantitative trait locus for salt tolerance and ABA sensitivity in Arabidopsis. Proceedings of the National Academy of Sciences of the United States of America. 107:5669-5674.
He, X.J., Hsu, Y.F., Zhu, S., Liu, H.L., Pontes, O., Zhu, J., Cui, X., Wang, C.S., and Zhu, J.-K. (2009). A conserved transcriptional regulator is required for RNA-directed DNA methylation and plant development. Genes & Development. 23:2717-2722.
He, X.J., Hsu, Y-F., Pontes, O., Zhu, J., Lu, J., Bressan, R.A., Pikaard, C., Wang, C.-S., and Zhu, J.-K. (2009) NRPD4, a protein related to the RPB4 subunit of RNA polymerase II, is a component of RNA polymerases IV and V and is required for RNA-directed DNA methylation. Genes & Development. 23:318-330.
Zheng, X., Pontes, O., Zhu, J., Miki, D., Zhang, F., Li, W.X., Iida, K., Kapoor, A., Pikaard, C.S., and Zhu, J.-K. (2008). ROS3 is an RNA-binding protein required for DNA demethylation in Arabidopsis. Nature. 455:1259-1262.
Li, W.X., Oono, Y., Zhu, J., He, X.J., Wu, J.M., Iida, K., Lu, X.Y., Cui, X., Jin, H., and Zhu, J.-K. (2008). The Arabidopsis NFYA5 transcription factor is regulated transcriptionally and posttranscriptionally to promote drought resistance. Plant Cell. 20:2238-2251.
Zhu, J.*, Jeong, J.C.*, Zhu, Y., Sokolchik, I., Miyazaki, S., Zhu, J.-K., Hasegawa, P.M., Bohnert, H.J., Shi, H.,Yun, D.-J., and Bressan, R.A. (2008) Involvement of Arabidopsis HOS15 in histone deacetylation and cold tolerance. Proceedings of the National Academy of Sciences of the United States of America. 105:4945-4950. *Equal contribution.
Zhang, K., Sridhar, V.V., Zhu, J., Kapoor, A., and Zhu, J.-K. (2007) Distinctive core histone post-translational modification patterns in Arabidopsis thaliana. PLoS One. 2:e1210.
Verslues, P.E., Batelli, G., Grillo, S., Agius, F., Kim, Y.-S., Zhu, J., Agarwal, M., Katiyar-Agarwal, S., and Zhu, J.-K. (2007) Interaction of SOS2 with nucleoside diphosphate kinase 2 and catalases reveals a point of connection between salt stress and H2O2 signaling in Arabidopsis thaliana. Molecular and Cellular Biology. 27:7771-7780.
Zhu, J., Fu, X., Koo, Y.D., Zhu, J.-K., Jenney, F.E., Jr., Adams, M.W., Zhu, Y., Shi, H., Yun,D.-J., Hasegawa, P.M., and Bressan, R.A. (2007) An enhancer mutant of Arabidopsis salt overly sensitive 3mediates both ion homeostasis and the oxidative stress response. Molecular and Cellular Biology.27:5214-5224.
Zhu, J.*, Kapoor, A.*, Sridhar, V.V., Agius, F., and Zhu, J.-K. (2007) The DNA glycosylase/lyase ROS1 functions in pruning the DNA methylation patterns in Arabidopsis. Current Biology. 17:54-59. *Equal contribution.
Zheng, X., Zhu, J., Kapoor, A., and Zhu, J.-K. (2007) Role of Arabidopsis AGO 6in siRNA accumulation, DNA methylation and transcriptional gene silencing. EMBO Journal. 26:1691-1701.
Chinnusamy, V., Zhu, J., and Zhu, J.-K. (2007) Cold stress regulation of gene expression in plants. Trends in Plant Science. 12:444-451.
Sunkar, R., Chinnusamy, V., Zhu, J., and Zhu, J.-K. (2007) Small RNAs as big players in plant abiotic stress responses and nutrient deprivation. Trends in Plant Science. 12:301-309.
Zhu, J., Dong, C.-H., and Zhu, J.-K. (2007) Interplay between cold-responsive gene regulation, metabolism and RNA processing during plant cold acclimation. Current Opinion in Plant Biology. 10:290-295.
Katiyar-Agarwal, S., Zhu, J., Kim, K., Agarwal, M., Fu, X., Huang, A., and Zhu, J.-K. (2006) The plasma membrane na+/H+ antiporter SOS1 interacts with RCD1 and functions in oxidative stress tolerance in Arabidopsis. Proceedings of the National Academy of Sciences of the United States of America.103:18816-18821.
Lee, B.-H., Kapoor, A., Zhu, J., and Zhu, J.-K. (2006) STABILIZED1, a stress-upregulated nuclear protein, is required for pre-mRNA splicing, mRNA turnover, and stress tolerance in Arabidopsis. Plant Cell. 18:1736-1749.
Verslues, P.E., Agarwal, M., Katiyar-Agarwal, S., Zhu, J., and Zhu, J.-K. (2006) Methods and concepts in quantifying resistance to drought, salt and freezing, abiotic stresses that affect plant water status. Plant Journal. 45:523-539.
Chinnusamy, V., Zhu, J., and Zhu, J.-K. (2006) Gene regulation during cold acclimation in plants. Physiologia Plantarum. 126:52-61.
Chinnusamy, V., Zhu, J., and Zhu, J.-K. (2006) Salt stress signaling and mechanisms of plant salt tolerance. Genetic engineering: Principles and Methods. Setlow J.K., Eds (New York, Plenum Press). 27:141-177.
Borsani, J.O., Zhu, J., Verslues, P.E., Sunkar, R., and Zhu, J.-K. (2005) Endogenous siRNAs derived from a pair of natural cis-antisense transcripts regulate salt tolerance in Arabidopsis. Cell. 123: 1279-1291.
Gong, Z., Dong, C.-H., Lee, H., Zhu, J., Xiong, L., Gong, D., Stevenson, B., and Zhu, J.-K. (2005) A DEAD box RNA helicase is essential for mRNA export and important for development and stress responses in Arabidopsis. Plant Cell. 17:256-267.
Inan, G., Zhang, Q., Li, P., Wang, Z., Cao, Z., Zhang, H., Zhang, C., Quist, T.M., Goodwin, S.M., Zhu, J., Shi, H., Damsz, B., Charbaji, T., Gong, Q., Ma, S., Fredricksen, M., Galbraith, D.W., Jenks, M.A., Rhodes, D., Hasegawa, P.M., Bohnert, H.J., Joly, R.J., Bressan, R.A., and Zhu, J.-K. (2004) 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. 135:1718-1737.
Koiwa, H., Li, F., McCully, M.G., Mendoza, I., Koizumi, N., Manabe, Y., Nakagawa, Y., Zhu, J., Rus, A., Pardo, J.M., Bressan, R.A., and Hasegawa, P.M. (2004) The STT3a subunit isoform of the Arabidopsis oligosaccharyltransferase controls adaptive responses to salt/osmotic stress. Plant Cell. 15:2273-2284.
Zhu, J.,Shi, H., Lee, B.-h., Damsz, B., Cheng, S., Stirm, V., Zhu, J.-K., Hasegawa, P.M., and Bressan, R.A. (2004) An Arabidopsis homeodomain transcription factor gene, HOS9, mediates cold tolerance through a CBF-independent pathway. Proceedings of the National Academy of Sciences of the United States of America. 101:9873-9878.
Zhu, J., Gong, Z., Zhang, C., Song, C.-P., Damsz, B., Inan, G., Koiwa, H., Zhu, J.-K., Hasegawa, P.M., and Bressan, R.A. (2002) OSM1/SYP61: a syntaxin protein in Arabidopsis controls abscisic acid-mediated and non-abscisic acid-mediated responses to abiotic stress. Plant Cell. 14:3009-3028.
Koiwa, H., Barb, A.W., Xiong, L., Li, F., McCully, M.G., Lee, B.H., Sokolchik, I., Zhu, J., Gong, Z., Reddy, M., Sharkhuu, A., Manabe, Y., Yokoi, S., Zhu, J.-K., Bressan, R.A., and Hasegawa, P.M. (2002) C-terminal domain phosphatase-like family members (AtCPLs) differentially regulate Arabidopsis thaliana abiotic stress signaling, growth, and development. Proceedings of the National Academy of Sciences of the United States of America. 99:10893-10898.
Gong, Z., Koiwa, H., Cushman, M.A., Ray, A., Bufford, D., Kore-eda, S., Matsumoto, T.K., Zhu, J., Cushman, J.C., Bressan, R.A., and Hasegawa, P.M. (2001)Genes that are uniquely stress regulated in salt overly sensitive (sos) mutants. Plant Physiology. 126: 363-375.


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