Recent Publications


Becker B, Feng X, Yin Y, Holzinger A (2020) Desiccation tolerance in streptophyte algae and the algae to land plant transition: Evolution of LEA and MIP protein families within the Viridiplantae, Journal of Experimental Botany, 2020 Feb 28. pii: eraa105. doi: 10.1093/jxb/eraa105

Carlos Bolanos-Carriel, Stephen N. Wegulo, Heather Hallen-Adams, P. Stephen Baenziger, Kent M. Eskridge, Deanna Funnell-Harris, Niki Mcmaster, & David G. Schmale III  (2020) Effects of field-applied fungicides, grain moisture, and time on deoxynivalenol during postharvest storage of winter wheat grain, Canadian Journal of Plant Science, DOI: 10.1139/cjps-2019-0075

Carlos Bolanos-Carriel, Stephen N. Wegulo, P. Stephen Baenziger, Kent M. Eskridge, Deanna Funnell-Harris, Niki Mcmaster, David G. Schmale III & Heather E. Hallen-Adams (2020) Tri5 gene expression analysis during postharvest storage of wheat grain from field plots treated with a triazole and a strobilurin fungicide, Canadian Journal of Plant Pathology, DOI: 10.1080/07060661.2019.1700169

Chen, L., Irmak, S., Chaves, B. D., & Subbiah, J. (2020). Microbial challenge study and quality evaluation of cumin seeds pasteurized by continuous radio frequency processing. Food Control111, 107052. doi: 10.1016/j.foodcont.2019.107052

Onay B. Dogan, Yulie E. Meneses, Rolando A. Flores, Bing Wang. Risk-based assessment and criteria specification of the microbial safety of wastewater reuse in food processing: Managing Listeria monocytogenes contamination in pasteurized fluid milk. Water Research. 2020; 171:115466.

Gulati P, Brahma S, Graybosch RA, Chen Y, Rose DJ. In vitro digestibility of proteins from historical and modern wheat cultivars. Journal of the Science of Food and Agriculture in press.

Hu, X., Meneses, Y.E., Hassan, A.A., 2020. Integration of sodium hypochlorite pretreatment with co-immobilized microalgae/bacteria treatment of meat processing wastewater. Bioresource Technology, 122953.

Morgounov A, Karaduman Y, Akin B, Aydogan S, Baenziger PS, Bhatta M, Chudinov V, Dreisigacker S, Govindan V, Güler S, Guzman C, Nehe A, Poudel R, Rose DJ, Gordeeva E, Shamanin V, Subasi K, Zelenskiy Y, Khlestkina EK. 2020. Yield and quality in purple-grained wheat isogenic lines. Agronomy 10:86.

Long H. Nguyen, Wenjie Ma, Dong D. Wang , Yin Cao, Himel Mallick, Teklu Gerbaba, Jason Lloyd-Price, Galeb Abu-Ali, A. Brantley Hall , Daniel Sikavi, David A.Drew, Raaj S. Mehta, Cesar Arze, Amit D. Joshi, Yan Yan, Tobyn Branck, Casey DuLong, Kerry Ivey, Shuji Ogino, Eric B. Rimm EB, Mingyang Song, Wendy S. Garrett, Jacques Izard, Curtis Huttenhower, Andre T. Chan Gastroenterology (2020) vol. 158 (5) pp. 1313-1325

Annette O’Connor, Dapeng Hu, Sarah Totton, Nicole Scott, Charlotte Winder, Bing Wang, Chong Wang, Julie Glanville, Hannah Wood, Brad White, Robert Larson, Cheryl Waldner, Jan Sargeant. A systematic review and network meta-analysis of injectable antibiotic options for the control of bovine respiratory disease in the first 45 days post arrival at the feedlot. Animal Health Research Reviews. 2019; 20(2): 163-181.

Annette O’Connor, Dapeng Hu, Sarah Totton, Nicole Scott, Charlotte Winder, Bing Wang, Chong Wang, Julie Glanville, Hannah Wood, Brad White, Robert Larson, Cheryl Waldner, Jan Sargeant. A systematic review and network meta-analysis of bacterial and viral vaccines, administered at or near arrival at the feedlot, for control of bovine respiratory disease in beef cattle. Animal Health Research Reviews. 2019; 20(2): 143-162.

Juan E. Ortúzar, Onay B. Dogan, Gustavo Sotomayor, Constanza Jiménez, Jennifer Clarke, Rolando A. Flores, George M. Gray, John H. Rupnow, Bing Wang. Quantitative assessment of microbial quality and safety risk: A preliminary case study of strengthening raspberry supply system in Chile. Food Control. 2020; 113: 107166. 

Orton L, Fitzek E, Feng X, Grayburn SW, Mower JP, Liu K, Zhang C, Duvall MR, Yin Y (2020) Zygnema circumcarinatum UTEX 1559 chloroplast and mitochondrial genomes provide insight into land plant evolution, Journal of Experimental Botany, 2020 Mar 24. pii: eraa149. doi: 10.1093/jxb/eraa149

Rukundo, I. R., & Danao, M.-G. C. (2020). Identifying turmeric powder by source and metanil yellow adulteration levels using near infrared spectra and PCA-SIMCA modeling. Journal of Food Protection.

Rukundo, I. R., Danao, M. C., Weller, C. L., Wehling, R. L., & Eskridge, K. M. (2020). Use of a handheld near infrared spectrometer and partial least squares regression to quantify metanil yellow adulteration in turmeric powder. Journal of Near Infrared Spectroscopy, 28(1), 096703351989888.

Ubeyitogullari, A. and Ciftci, O. N. (2020). Fabrication of bioaerogels from camelina seed mucilage for food applications. Food Hydrocolloids, 102, 105597. 

Ubeyitogullari, A. and Ciftci, O. N. (2019). A novel and green nanoparticle formation approach to forming low-crystallinity curcumin nanoparticles to improve curcumin’s bioaccessibility. Scientific Reports, 9, 19112.

Esteban Valverde-Bogantes, Carlos Bolanos-Carriel, Heather E. Hallen-Adams, Niki Mcmaster, David G. Schmale III & Stephen N. Wegulo (2020) Aggressiveness and deoxynivalenol production of Nebraska isolates of Fusarium boothii and F. graminearum, Plant Health Progress, DOI: 10.1094/PHP-01-20-0001-RS

Esteban Valverde-Bogantes, Andreia Bianchini, Joshua R. Herr, Devin J. Rose, Stephen N. Wegulo & Heather E. Hallen-Adams (2019) Recent population changes of Fusarium head blight pathogens: drivers and implications, Canadian Journal of Plant Pathology, DOI: 10.1080/07060661.2019.1680442

Wang L, Rose DJ, Zhang Y. Development of prolamin-based composite nanoparticles for controlled-release of sulforaphane. Journal of Agricultural and Food Chemistry in press.

Yi H, Huang L, Yang B, Zhang H, Yin Y (2020) AcrFinder: genome mining anti-CRISPR operons in prokaryotes and their viruses, Nucleic Acids Research, doi: doi:10.1093/nar/gkaa351

Zhao, H.; Shen, C.; Wu, Z.; Zhang, Z.; Xu, C. Comparison of Wheat, Soybean, Rice, and Pea Protein Properties for Effective Applications in Food Products. J. Food Biochem. 2020, n/a (n/a), e13157.    

H. Zhao, Y. Zhan, Z. Xu, J. J. Nduwamungu, Y. Zhou, and C. Xu, “Machine learning-driven Raman spectroscopy for rapidly detecting type, adulteration, and oxidation of edible oils,” Am. Oil Chem. Soc. Inf. Mag., vol. 31, no. 4, pp. 12–15, Apr. 2020.


Boreddy SR, Rose DJ, Subbiah J. 2019. Radiofrequency-assisted thermal processing of wheat flour. Journal of Food Science 84:2528-2536.

Castillo, E., Meier, R., Chung, M., Koestler, D., Chen, T., Paster, B., Charpentier, K., Kelsey, K., Izard, J., and Michaud, D. The Microbiomes of Pancreatic and Duodenum Tissue Overlap and are Highly Subject Specific but Differ between Pancreatic Cancer and Non-Cancer Subjects. Cancer Epidemiology, Biomarkers & Prevention (2019) vol. 28(2), pp. 370-383.

Chen, J., Lau, S. K., Boreddy, S. R., & Subbiah, J. (2019). Modeling of radio frequency heating of egg white powder continuously moving on a conveyor belt. Journal of Food Engineering, 262, 109-120. doi:10.1016/j.jfoodeng.2019.05.029.

Chen, L. (2019, February). Radio-Frequency Pasteurization of Low-Moisture Foods: Critical Process Control Parameters. Food Safety Magazine, 13-15.

Fitzek E, Orton F, Entwistle S, Grayburn SW, Ausland C, Duvall DR, Yin Y (2019) Cell wall enzymes in Zygnema circumcarinatum UTEX 1559 respond to osmotic stress in a plant-like fashion, Frontiers in Plant Science, doi: 10.3389/fpls.2019.00732.

Ivey, K., Chan, A., Izard, J.,  Cassidy, A., Rogers, G. and Rimm, E. Role of dietary flavonoid compounds in driving patterns of microbial community assembly. mBio (2019) vol. 10 (5) e01205-19; DOI: 10.1128/mBio.01205-19.

Jayasena, S., S. J. Koppelman, B. Nayak, S. L. Taylor, and J. Baumert. 2019.  Comparison of recovery and immunochemical detection of peanut proteins from differentially roasted peanut flour using ELISA.  Food Chem. 292:32-38.

Jayasena, S., S. S. K. Wijeratne, S. L. Taylor, and J. L. Baumert. 2019. Improved extraction of peanut residues from a wheat flour matrix for immunochemical detection. Food Chem. 278:832-840.

Jooyeoyn, J. Value-added Utilization of Fruit and Vegetable Pomace in Food Packaging, 2019, Food Packaging: Innovations and Shelf-Life, Editor: Rui M. S. da Cruz, CRC Press.

de Jong, G. A., S. Jayasena, P. Johnson, J. Marsh, D. Apostolovic, M. van Hage, J. Nordlee, J. Baumert, S. L. Taylor, C. Roucairol, H. de Jongh, and S. Koppelman. 2018. Purification and characterization of naturally occurring post-translationally cleaved Ara h 6, an allergen that contributes substantially to the allergenic potency of peanut. J. Agr. Food Chem. 66:10855-10863.

Konda, A. R., Nazarenus, T., Nguyen, H., Yang, J., Gelli, M., Swenson, S., Shipp, J., Schmidt, M., Cahoon, R., Ciftci, O.N., Zhang, C., Clemente, T., and Cahoon, E. (2020). Metabolic engineering of soybean seeds for enhanced vitamin E tocochromanol content and effects on oil antioxidant properties in polyunsaturated fatty acid-rich germplasm. Metabolic Engineering, 57, 63-73.

Lin, Y., Subbiah, J., Chen, L., Verma, T., & Liu, Y. (2020). Validation of radio frequency assisted traditional thermal processing for pasteurization of powdered infant formula milk. Food Control109, 106897. doi: 10.1016/j.foodcont.2019.106897. 

Li, S., Subbiah, J., & Dvorak, B. (2019). Environmental and occupational impacts from U.S. beef slaughtering are of same magnitude of beef foodborne illnesses on human health. Environment International, 129, 507-516. doi:10.1016/j.envint.2019.05.051.

Li W, Yin Y, Quan X, Zhang H (2019) Gene Expression Value Prediction Based on XGBoost Algorithm, Frontiers in Genetics, doi: 10.3389/fgene.2019.01077.

Li Y, Tinoco R, Elmén L, Segota I, Xian Y, Fujita Y, Sahu A, Zarecki R, Marie K, Feng Y, Khateb A, Frederick DT, Ashkenazi SK, Kim H, Perez EG, Day CP, Segura Muñoz RS, Schmaltz R, Yooseph S, Tam MA, Zhang T, Avitan-Hersh E, Tzur L, Roizman S, Boyango I, Bar-Sela G, Orian A, Kaufman RJ, Bosenberg M, Goding CR, Baaten B, Levesque MP, Dummer R, Brown K, Merlino G, Ruppin E, Flaherty K, Ramer-Tait A, Long T, Peterson SN, Bradley LM, Ronai ZA. Gut microbiota dependent anti-tumor immunity restricts melanoma growth in Rnf5-/- mice. 2019. Nature Communications. 10:1492.

Meneses, Y. E., Martinez, B., & Hu, X. (2019). Water reconditioning in the food industry. Sustainable Water and Wastewater Processing, 329-365. doi:10.1016/b978-0-12-816170-8.00010-7. 

Navrotskyi S, Guo G, Baenziger PS, Xu L, Rose DJ. 2019. Impact of wheat bran physical properties and chemical composition on whole grain flour mixing and baking properties. Journal of Cereal Science 89:102790.

Piepenbrink KH. DNA Uptake by Type IV Filaments Frontiers in Molecular Biosciences, section Molecular Recognition 2019 (in press).

Poudel R, Finnie S, Rose DJ. 2019. Effects of wheat kernel germination time and drying temperature on compositional and end-use properties of the resulting whole wheat flour. Journal of Cereal Science 86:33-40.

Ronish LA, Lillehoj E, Fields JK, Sundberg EJ, Piepenbrink KH. The structure of PilA from Acinetobacter baumannii AB5075 suggests a mechanism for functional specialization in Acinetobacter type IV pili. Journal of Biological Chemistry 2019 Jan 4;294(1):218-230. Epub 2018 Nov 9. doi: 10.1074/jbc.RA118.005814. PMID: 3041353.

Sabillón, L., Stratton, J., Rose, D., Bianchini, A. 2019. Effect of saline organic acid solutions applied during soft wheat tempering on microbial load and flour functionality. Cereal Chemistry. In Press. 

Sabillón, L., Stratton, J., Rose, D.J, Bianchini, A. 2020. Reduction in pathogenic load of wheat by tempering with saline organic acid solutions at different seasonal temperatures. International Journal of Food Microbiology. 303: 108381.

Satterlee T, Entwistle S, Yin Y, Cary J, Lebar M, Losada L, Calvo A (2019) rmtA-Dependent Transcriptome and its Role in Secondary Metabolism, Environmental Stress, and Virulence in Aspergillus flavus, G3: Genes Genomes Genetics, g3.

Sheehan, W. J., S. L. Taylor, W. Phitatanakul, and H. A. Brough. 2018. Environmental food exposure: what is the risk of clinical reactivity from cross-contact and what is the risk of sensitization. J. Allergy Clin. Immunol. In Practice 6:1825-1832.

Ubeyitogullari, A. and Ciftci, O.N. (2019). A novel and green nanoparticle formation approach to forming low-crystallinity curcumin nanoparticles to improve curcumin’s bioaccessibility. Scientific Reports, In press.

Ubeyitogullari, A., Moreau, R., Rose, D. J., & Ciftci, O. N. (2019). In Vitro Bioaccessibility of Low-Crystallinity Phytosterol Nanoparticles Generated Using Nanoporous Starch Bioaerogels. Journal of Food Science, 84(7), 1812-1819. doi:10.1111/1750-3841.14673.

Wang, B., Sahyoun, N., Shao, K., Dutta, E., Clarke, J. Dose-response assessment between folate exposure and risk of cognitive impairment: synthesizing data from documented studies. Risk Analysis. September 2019.  

Wang, L., Xue, J., Zhang, Y., Preparation and characterization of curcumin loaded caseinate/zein nanocomposite film using pH-driven method. Industrial Crops and Products 2019, 130, 71-80.

Wang, L.; Zhang, Y., Heat-induced self-assembly of zein nanoparticles: fabrication, stabilization and potential application as oral drug delivery. Food Hydrocolloids 2019, 90, 403-412.

Xu J, Zhang H, Zheng J, Dovoedo P, Yin Y. eCAMI: simultaneous classification and motif identification for enzyme annotation. Bioinformatics. 2019 Dec 3. pii: btz908. doi: 10.1093/bioinformatics.

Yangjunna Zhang, Annette M. O’Connor, Chong Wang, James S. Dickson, H. Scott Hurd, Bing Wang. Interventions targeting deep tissue lymph nodes may not effectively reduce the risk of salmonellosis from ground pork consumption: A quantitative microbial risk assessment. Risk Analysis. 2019.

Yang, J., and Ciftci, O.N. (2019). Effect of chemical structure of solid lipid matrix on its melting behavior and volumetric expansion in pressurized carbon dioxide. Journal of the American Oil Chemists' Society, doi 10.1002/aocs.12305.

Yin Y, Yang B, Entwistle S (2019) Bioinformatics identification of anti-CRISPR loci using homology, guilt-by-association, and CRISPR self-targeting spacer approaches, mSystems, doi:10.1128/mSystems.00455-19.

Ziara, R. M., Miller, D. N., Subbiah, J., & Dvorak, B. I. (2019). Lactate wastewater dark fermentation: The effect of temperature and initial pH on biohydrogen production and microbial community. International Journal of Hydrogen Energy, 44(2), 661-673. doi:10.1016/j.ijhydene.2018.11.045.


Anderson, R., Keshwani, D., Guru, A., Yang, H., Irmak, S., & Subbiah, J. (2018). An integrated modeling framework for crop and biofuel systems using the DSSAT and GREET models. Environmental Modelling & Software, 108, 40-50. doi:10.1016/j.envsoft.2018.07.004.

Chakrabarti, S., Guha, S., Majumder, K. (2018). Food-Derived Bioactive Peptides in Human Health: Challenges and Opportunities. Nutrients, 10: 1738.

Galeb S. Abu-Ali, Raaj S. Mehta, Jason Lloyd-Price, Kerry L. Ivey, Himel Malick, Tobyn Branck, David A. Drew, Casey DuLong, Eric Rimm, Jacques Izard, Andy T. Chan, Curtis Huttenhower.  Microbial ecology and population structure in the human gut metatranscriptome.  Nature Microbiology (2018) vol. 3(3), pp. 356-366. (doi: 10.1038/s41564-017-0084-4).

Geng, F., Xie, Y., Wang, J., Majumder, K., Qiu, N., Ma, M., (2018). N-glycoproteomic Analysis of Chicken Egg Yolk. Journal of Agricultural and Food Chemistry, DOI: 10.1021/acs.jafc.8b04492.

Gudeman, J., Yang, J., and Ciftci, O. N. (2019). Formation of low density and free-flowing hollow microparticles from butter and fractionated palm oil. Journal of the American Oil Chemists' Society. In press.

Hatami, T., Meireles, M.A.A, and Ciftci, O.N. (2019). Supercritical carbon dioxide extraction of lycopene from tomato processing by-products: Mathematical modeling and optimization. Journal of Food Engineering, 241, 18-25.

Irmak, S., Meryemoglu, B., Sandip, A., Subbiah, J., Mitchell, R., Sarath, G. 2018. Microwave pretreatment effects on switchgrass and miscanthus solubilization in subcritical water and hydrolysate utilization for hydrogen production. Biomass & Bioenergy, 108, 48-54.

Kittana H, Gomes-Neto JC, Sanderfer K, Geis AL, Segura Muñoz RR, Cody LA, Schmaltz RJ, Bindels LB, Sinha R, Hostetter JM, Benson AK, Ramer-Tait AE. Commensal Escherichia coli strains can promote intestinal inflammation via differential interleukin-6 production. 2018. Front Immunol. 9:2318.

Koppelman, S. J., M. Smits, M. Tomassen, G. A. H. de Jong, J. Baumert, S. L. Taylor, R. Witkamp, R. J. Veldman, R. J. Pieters, and H. Wichers.  2018.  Release of major peanut allergens from their matrix under various pH and simulated saliva conditions; Ara h 2 and Ara h 6 are readily bio-accessible.  Nutrients 10 (9)(No. 1281): 13 pp.

Lau, S. K., Subbiah, J. 2018. An automatic system for measuring dielectric properties of foods: Albumen, yolk, and shell of fresh eggs. Journal of Food Engineering, 223, 79 - 90.

Lin XB, Wang T, Stothard P, Corander J, Wang J, Baines J, Knowles SCL, Baltrūnaitė L, Tasseva G, Schmaltz R, Tollenaar S, Cody LA, Grenier T, Wu W, Ramer-Tait AE, Walter J. Ecological facilitation among members of multi-species biofilms in the mouse gastrointestinal tract.  2018.  ISME J. 12(11):2770-2784.

Li, S., Kinser, C., Ziara, R. M., Dvorak, B., & Subbiah, J. (2018). Environmental and economic implications of food safety interventions: Life cycle and operating cost assessment of antimicrobial systems in U.S. beef packing industry. Journal of Cleaner Production, 198, 541-550. doi:10.1016/j.jclepro.2018.07.020.

Li, Shaobin; Rami, Ziara; Dvorak, Bruce; Jeyamkondan, Subbiah. “Assessment of Water and Energy Use at Process Level in the U.S. Beef Packing Industry: Case Study in a Typical U.S. Large-Size Plant.” Journal of Food Process Engineering, Aug. 2018, doi:10.1111/jfpe.12919.

Li X, Leonardi I, Semon A, Doron I, IH, Putzel G, Kim Y, Kabata H, Artis D, Fiers W, Ramer-Tait AE, Iliev ID. CX3CR1+ mononuclear phagocytes mediate the effects of gut fungal dysbiosis on allergic airway disease. 2018. Cell Host Microbe. ePub Nov 29.

John D. Loy, Laura Leger, Aspen Workman, Michael L. Clawson, Ece Bulut, Bing Wang. Development of a multiplex real-time PCR assay using two thermocycling platforms for detection of major bacterial pathogens associated with bovine respiratory disease complex from clinical samples. Journal of Veterinary Diagnostic Investigation. In press.

M Lu, Y Jin, R Cerny, B Ballmer-Weber, RE Goodman. 2018. Combining 2-DE immunoblots and mass spectrometry to identify putative soybean (Glycine max) allergens. Food and Chemical Toxicology, 116, 207-215.

M Lu, Y Jin, B Ballmer-Weber, RE Goodman. 2018. A comparative study of endogenous allergenicity of a genetically modified (GM) soybean and six non-GM soybeans. Food and Chemical Toxicology, 112, 216-223.

Martínez I, Maldonado-Gomez XM, Gomes-Neto JC, Kittana H, Ding H, Schmaltz R, Joglekar P, Cardona RJ, Marsteller NL, Kembel SW, Benson AK, Peterson DA, Ramer-Tait AE, Walter J. Experimental evaluation of the importance of colonization history in early-life gut microbiota assembly.  2018.  eLIFE. 7. pii:e36521.

Mendoza, J. R., Rodas, A., Oliva, A., Sabillón, L., Colmenares, A., Clarke, J., Bianchini, A. (2018). Safety and Quality Assessment of Smallholder Farmers Maize in the Western Highlands of Guatemala. Journal of Food Protection, 81(5), 776-784. doi:10.4315/0362-028x.jfp-17-355.

Raaj S. Mehta, Galeb Abu-Ali, David A. Drew, Jason Lloyd-Price, Ayshwarya Subramanian, Paul Lochhead, Amit Joshi, Kerry Ivey, Hamed Khalili, Gordon T. Brown, Casey Dulong, Mingyang Song, Long Nguyen, Himel Mallick, Eric B. Rimm, Jacques Izard, Curtis Huttenhower, and Andrew T. Chan Genomic and Functional Stability of the Human Gut Microbiome. Nature Microbiology (2018) vol. 3(3), pp. 347-355. (doi:10.1038/s41564-017-0096-0.

Sheehan, W. J., S. L. Taylor, W. Phitatanakul, and H. A. Brough.  2018.  Environmental food exposure: what is the risk of clinical reactivity from cross-contact and what is the risk of sensitization.  J. Allergy Clin. Immunol. In Practice 6:1825-1832.

Taylor, S. L., J. A. Nordlee, S. Jayasena, and J. L. Baumert.  2018.  Evaluation of a handheld gluten detection device.  J. Food Prot. 81:1723-1728.

Ubeyitogullari, A., Brahma, S., Rose, D., and Ciftci, O.N. (2018). In vitro digestibility of nanoporous wheat starch aerogels. Journal of Agricultural and Food Chemistry, 66 (36), 9490–9497.

Verma, T., Wei, X., Lau, S. K., Bianchini, A., Eskridge, K. M., & Subbiah, J. (2018). Evaluation of Enterococcus faecium NRRL B-2354 as a Surrogate for Salmonella During Extrusion of Low-Moisture Food. Journal of Food Science, 83(4), 1063-1072. doi:10.1111/1750-3841.14110.

Xie, L., Cahoon, E., Zhang, Y., and Ciftci, O.N. (2019). Extraction of astaxanthin from engineered Camelina sativa seed using ethanol-modified supercritical carbon dioxide. Journal of Supercritical Fluids, 143, 171-178.

Yin Cao, Kana Wu, Raaj Mehta, David A. Drew, Mingyang Song, Paul Lochhead, Long H. Nguyen, Jacques Izard, Charles S. Fuchs, Wendy S. Garrett, Curtis Huttenhower, Shuji Ogino, Edward L. Giovannucci, and Andrew T. Chan. Long-term use of antibiotics and risk of colorectal adenoma. Gut (2018) vol. 67(4), pp. 672-678. (doi: 10.1136/gutjnl-2016-313413).

Yuan, B., Lu, M., Eskridge, K. M., Isom, L. D., & Hanna, M. A. (2018). Extraction, identification, and quantification of antioxidant phenolics from hazelnut (Corylus avellana L.) shells. Food Chemistry, 244(1), 7-15.

B Yuan, M-G Danao, M Lu, J Stratton, S Weier, C Weller. 2018. High pressure processing (HPP) of aronia berry puree: Pilot scale processing and a shelf-life study. Innovative Food Science & Emerging Technologies, 47, 241-248.

B Yuan, M Lu, K Eskridge, M Hanna. 2018. Valorization of hazelnut shells into natural antioxidants by ultrasound-assisted extraction: Process optimization and phenolic composition identification. Journal of Food Process Engineering.

Zhi Huang, Francesco Marra, Jeyamkondan Subbiah & Shaojin Wang (2018) Computer simulation for improving radio frequency (RF) heating uniformity of food products: A review, Critical Reviews in Food Science and Nutrition, 58:6, 1033-1057, DOI: 10.1080/10408398.2016.1253000.

Ziara, Rami M.m., et al. “Lactate Wastewater Dark Fermentation: The Effect of Temperature and Initial PH on Biohydrogen Production and Microbial Community.” International Journal of Hydrogen Energy, 2018, doi:10.1016/j.ijhydene.2018.11.045.


Belayneh, H., Wehling, R., Zhang, Y., and Ciftci, O.N. (2017). Development of omega-3-rich Camelina sativa seed oil emulsions. Food Science & Nutrition, In press.

Belayneh, H.D., Wehling R.L., Cahoon E. & Ciftci, O. N. (2017). Effect of extraction method on the oxidative stability of camelina seed oil studied by differential scanning calorimetry. Journal of Food Science. Forthcoming. Doi: 10.1111/1750- 3841.13652.

Belayneh, H.D., Wehling, R.L., Reddy, A.K., Cahoon, E.B., Ciftci, O.N. (2017). Ethanol-modified supercritical carbon dioxide extraction of the bioactive lipid components of Camelina sativa seed. Journal of the American Oil Chemists’ Society, 94(6), 855-865.

Belayneh, H., Wehling, R., Cahoon, E., and Ciftci, O.N. (2017). Lipid composition and emulsifying properties of Camelina sativa seed lecithin. Food Chemistry, In press.

Blankestijn, M. A., B. C. Remington, G. F. Houben, J. L. Baumert, A. C. Knulst, W. M. Blom, R. J. B. Klemans, and S. L. Taylor. 2017. Threshold dose distribution in walnut allergy. J. Allergy Clin. Immunol. In Practice 5:376-380.

Brahma S, Martinez I, Walter J, Clarke J, Gonzalez T, Menon R, Rose DJ. 2017. Impact of dietary pattern of the fecal donor on in vitro fermentation properties of whole grains and brans. Journal of Functional Foods 29:281-289.

Brahma S, Weier SA, Rose DJ. Moisture content during extrusion of oats impacts the initial fermentation metabolites and probiotic bacteria during extended fermentation by human fecal microbiota. Food Research International. 97, 209-214.

Chee, MacKenzie., Majumder, K., Mine, Y. (2017). Intervention of dietary dipeptide gamma-L-glutamyl-L-valine (γ-EV) ameliorates inflammatory response in a mouse model of LPS-induced sepsis. Journal of Agricultural and Food Chemistry, 65: 5953–5960.

Chen, J., S. Lau, L. Chen, S. Wang, J. Subbiah. 2017. Modeling radio frequency heating of food moving on a conveyor belt. Food and Bioproducts Processing. 10.1016/j. fbp.2017.01.009.

Ciftci, D., Ubeyitogullari, A., Razera Huerta, R., Ciftci, O.N., Flores, R. and Saldaña, M.D.A. (2017). Lupin cellulose nanofiber aerogel preparation by supercritical CO2 drying and freeze drying. Journal of Supercritical Fluids. In press. http://

Dura A, Rose DJ, Rosell CM. Enzymatic modification of cornstarch influences human fecal fermentation profiles. Journal of Agricultural and Food Chemistry in press.

Farris E, Brown DM, Ramer-Tait AE, Pannier AK. Chitosan-zein nano-in-microparticles capable of mediating in vivo transgene expression following oral delivery. 2017. J Control Release. In press. Available on-line 31 January 2017.

Gomes-Neto JC, Mantz S, Held K, Sinha R, Benson AK, Walter J, Ramer-Tait AE. A real-time PCR assay for accurate quantification of the individual members of the Altered Schaedler Flora microbiota in gnotobiotic mice. 2017. Journal of Microbiological Methods. 135:52-62.

Gulati P, Li Aixia, Holding D, Santra D, Zhang Y, Rose DJ. Heating reduces proso milletprotein digestibility via formation of hydrophobic aggregates. Journal of Agricultural and Food Chemistry in press.

Guo, C., Zhang, Z., Chen, J., Fu, H., Subbiah, J., Chen, X. and Wang, Y., 2017. Effects of Radio Frequency Heating Treatment on Structure Changes of Soy Protein Isolate for Protein Modification. Food and Bioprocess Technology, pp.1-10. DOI.10.1007/ s11947-017-1923-2.

Gupta, R. S., S. L. Taylor, J. L. Baumert, L. M. Kao, E. Schuster, and B. M. Smith.  2017.  Economic factors impacting food allergen management:  perspectives from the food industry.  J. Food Prot. 80:1719-1725.

Gupta, R., M. J. Marchisotto, L. Harada, O. Kamdur, B. M. Smith, S. Waserman, S. Sicherer, K. Allen, A. Muraro, and S. Taylor. 2017. Food allergen labeling and purchasing habits in the US and Canada. J. Allergy Clin. Immunol. In Practice 5:345-351.

Hollman Motta Romero, Dipak Santra, Devin Rose, Yue Zhang, Dough rheological properties and texture of gluten-free pasta based on proso millet flour, Journal of Cereal Science, 2017,74, 238– 243.

Ivens, K. O., J. L. Baumert, R. M. Hutkins, and S. L. Taylor.  2017. The effect of different methods of fermentation on the detection of milk protein residues in retail cheese by enzyme-linked immunosorbent assay (ELISA).  J. Food Sci. 82:T2752-T2758.

Ivens, K. O., J. L. Baumert, R. M. Hutkins, and S. L. Taylor. 2017. Effect of proteolysis during Cheddar cheese aging on the detection of milk protein residues by enzyme-linked immunosorbent assay. J. Dairy Sci. 100:1629- 1639.

Y Jin, RE Goodman, AO Tetteh, M Lu, L Tripathi. 2017. Bioinformatics analysis to assess potential risks of allergenicity and toxicity of HRAP and PFLP proteins in genetically modified bananas resistant to Xanthomonas wilt disease. Food and Chemical Toxicology, 109 (1), 81-89.

Y Jin, X He, K Andoh-Kumi, R Fraser, M Lu, RE Goodman. 2017. Evaluating potential risks of food allergy and toxicity of soy leghemoglobin expressed in Pichia Pastoris. Molecular Nutrition and Food Research, 1700297.

Jessica Kratchman, Bing Wang, John Fox, George Gray. Correlation of noncancer benchmark doses in short- and long-term rodent bioassays. Risk Analysis. 2017. DOI: 10.1111/risa.12903.

Lau, S.K., H. Thippareddi, J. Subbiah. 2017. Radiofrequency Heating for Enhancing Microbial Safety of Shell Eggs Immersed in Deionized Water. Journal of Food Science.  In Press.

Lei Wang, Yue Zhang, Eugenol nanoemulsion stabilized with zein and sodium caseinate by self-assembly, J. Agric. Food Chem. 2017, DOI: 10.1021/acs. jafc.7b00194.

Li, L., G. Froning, V. Juneja, J. Subbiah, and H. Thippareddi. 2017.  Dynamic Predictive Model for Growth of Salmonella spp. in Scrambled Egg Mix. Journal of Food Science, 64: 39-46. Doi: 10.1016/

Li, Qingyong., Kang, X., Shi, C., Li, Y., Majumder, K., Ning, Z., Ren, J. Moderation of hyperuricemia in rats via consuming walnut protein hydrolysate diet and identification of new antihyperuricemic peptides. Food & Function, DOI:

Loy A, Pfann C, Steinberger M, Hanson B, Herp S, Brugiroux S, Gomes-Neto JC, Boekschoten M, Schwab C, Urich T, Ramer-Tait A, Rattei T, Stecher B, Berry D. Lifestyle and horizontal gene transfermediated evolution of Mucispirillum schaedleri, a core member of the murine gut microbiota. 2017. mSystems. 2(1): e00171-16. Article selected as an Editor’s Pick.

Majumder, K., Fukuda, T., Zhang, H., Sakurai, T., Taniguchi, Y., Watanabe, H., Mitsuzumi, H., Matsui, T., Mine, Y. (2017). Intervention of isomaltodextrin mitigates intestinal inflammation in a dextran sodium sulfate-induced mouse model of colitis via inhibition of toll-like receptor-4. Journal of Agricultural and Food Chemistry, 65: 810-817.

Martinez, B., Stratton, J., & Bianchini, A. (2017). Isolation and genetic identification of spore-forming bacteria associated with concentrated-milk processing in Nebraska. Journal of Dairy Science, 100(2), 919-932.

Juan Ortuzar, Bismarck Martinez, Andreia Bianchini, Jayne Stratton, John Rupnow, Bing Wang. Quantifying changes in spore-forming bacteria contamination along the milk production chain from farm to packaged pasteurized milk using systematic review and meta-analysis. Food Control. 2018; 86:319-331.

Poudel R, Bhatta M, Regassa T, Rose DJ. Influence of foliar fungicide treatment on lipolytic enzyme activity of whole wheat. Cereal Chemistry in press.

Sabillón L, Bianchini A, Stratton J, Rose DJ. Effect of saline organic acid solutions applied during wheat tempering on flour functionality. Cereal Chemistry in press.

Suhr MJ, Gomes-Neto JC, Banjara N, Florescu DF, Mercer DF, Iwen PC, Hallen-Adams HE (2017) Epidemiological investigation of Candida species causing bloodstream infection in paediatric small bowel transplant recipients. Mycoses doi:10.1111/ myc.12603.

Sunil Thomas, Jacques Izard, Emily Walsh, Kristen Batich, Pakawat Chongsathidkiet, Gerard Clarke, David A. Sela, Alexander J. Muller, James M. Mullin, Korin Albert, John P. Gilligan, Katherin DiGulio, Rima Dilbarova, Walker Alexander, and George Prendergast The host microbiome regulates and maintains human health: a primer and perspective for non-microbiologists. Cancer Research (2017), vol. 77(8), p. 1783-17812.

Taylor, S. L. 2017. Market opportunities for allergen-free products. Snack Food & Wholesale Baking magazine 106(1):48-49.

Taylor, S. L., J. L. Baumert, and S. M. Boudreau-Romano. 2017. Allergic reaction from fingerprint kit attributable to unlabeled gluten, probable wheat flour. J. Allergy Clin. Immunol. In Practice 5:479-481.

Ubeyitogullari, A., & Ciftci, O. N. (2017). Generating phytosterol nanoparticles in nanoporous bioaerogels via supercritical carbon dioxide impregnation: Effect of impregnation conditions. Journal of Food Engineering. In press.

Ubeyitogullari, A., Moreau, R., Rose, D., Zhang, J., Ciftci, O. (2017). Enhancing the bioaccessibility of phytosterols using nanoporous corn and wheat starch bioaerogels. European Journal of Lipid Science and Technology. In press, DOI: 10.1002/ejlt.201700229.

Villegas MI, Kittana H, de los Reyes-Gavilán CG, Schmaltz RJ, Muccioli GG, Walter J, Ramer-Tait AE. Resistant starch can improve insulin sensitivity independently of the gut microbiota. 2017. Microbiome. 5(1):12.

Xie, L.; Wehling, R.; Ciftci, O.; Zhang, Y., Formation of complexes between tannic acid with bovine serum albumin, egg ovalbumin and bovine beta-lactoglobulin. Food Research International,

Yang, J., & Ciftci, O. N. (2017). Encapsulation of fish oil into hollow solid lipid micro- and nanoparticles using carbon dioxide. Food Chemistry, 231, 105-113.

Yangjunna Zhang, Bing Wang. Comparison of the efficacy of commercial antimicrobial interventions for reducing antibiotic resistant and susceptible beef-associated Salmonella and Escherichia coli strains. Journal of Consumer Protection and Food Safety. 2017.


Abdullah SU, Alexeev Y, Johnson PE, Rigby NM, Mackie AR, Dhaliwal B and Mills ENC (2016) Ligand binding to an Allergenic Lipid Transfer Protein Enhances Conformational Flexibility resulting in an Increase in Susceptibility to Gastroduodenal Proteolysis. Scientific reports 6, 30279.

Brahma S, Weier SA, Rose DJ. 2016. Effects of selected extrusion parameters on physicochemical properties and in vitro starch digestibility and -glucan extractability of whole grain oats. Journal of Cereal Science 70:85-90.

Ciftci, O.N. and Temelli, O.N. (2015). Formation of solid lipid microparticles from fully hydrogenated canola oil using supercritical carbon dioxide. Journal of Food Engineering. In press. doi:10.1016/j. jfoodeng.2016.01.014

Cluff K. ;  Konda Naganathan G.; Jonnalagada D.; Mortensen I.; Wehling R.; Subbiah J.. Determination of yolk contamination in liquid egg white using Raman spectroscopy. Poultry Science 2016; doi: 10.3382/ps/pew095.

Courtney, R. C., S. L. Taylor, and J. L. Baumert. 2016. Evaluation of commercial milk-specific lateral flow devices. J. Food Prot. 79:1767-1774.

Goodman, R., M. Ebisawa, F. Ferriera, H. Sampson, R. Van Ree, S. Vieths, J. Baumert, B. Bohle, S. Lalithambika, J. Wise, and S. Taylor. 2016. AllergenOnline: a peer-reviewed curated allergen database to assess novel food proteins for potential cross-reactivity. Molec. Nutr. Food Res. 60:1183-1189.

Houben, G., P. Burney, C.-H. Chan, R. Crevel, A. Dubois, R. Faludi, R. Klein Entink, A. Knulst, S. Taylor, and S. Ronsmans. 2016. Prioritisation of allergenic foods with respect to public health relevance. Food Chem. Toxicol. 89:8-18.

Huang, Z., Marra, F., Subbiah, J., & Wang, S. (2016). Computer simulation for improving radio frequency (RF) heating uniformity of food products: A review. Critical Reviews in Food Science and Nutrition, 1-25. doi:10.1080/1040 8398.2016.1253000.

Johnson PE, Sayers RL, Gethings LA, Balasundaram A, Marsh JT, Langridge JI and Mills ENC (2016) Quantitative proteomic profi ling of peanut allergens in food ingredients used for oral food challenges. Anal. Chem. Just Accepted Manuscript

Kochler, M. F., & Subbiah, J. (2016). Analytical Solution for Speed to Achieve a Desired Operatiing Point for a Given Fan or Pump. Journal of Engineering in Agriculture, 3(6), 741-747.

Koppelman, S. J., S. Jayasena, D. Luykx, E. Schepens, D. Apostolovic, G. A. H. de Jong, T. G. Isleib, J. Nordlee, J. Baumert, S. L. Taylor, H. Cheng, and S. Maleki. 2016. Allergenicity attributes of different peanut market types. Food Chem. Toxicol. 91:82-90.

Meneses, Y. E. and R. A. Flores. 2016. Whey- recovered water in CIP systems, its feasibility, safety and economic implications. A case study on water conservation for the dairy industry. Journal of Dairy Science, 99: 1-12

Sabillon, L. and Bianchini, A. 2016. From Field to Table: A Review on the Microbiological Quality and Safety of Wheat-Based Products. Cereal Chemistry. 93(2):105–115. 

Sabillon, L., Stratton, J., Rose, D., Regassa, T., and Bianchini, A. 2016. Microbial Load of Hard Red Winter Wheat Produced at Three Growing Environments across Nebraska, USA. Journal of Food Protection. 79(4): 646–654. 

Sarah M Snyder, Bingxin Zhao, Ting Luo, Clive Kaiser, George Cavender, Jill Hamilton-Reeves, Debra K Sullivan, and Neil F Shay “Consumption of Quercetin and Quercetin-Containing Apple and Cherry Extracts Aff ects Blood Glucose Concentration, Hepatic Metabolism, and Gene Expression Patterns in Obese C57BL/6J High Fat– Fed Mice” Journal of Nutrition (IN PRESS)

Sayers RL, Johnson PE, Marsh JT, Barran P, Brown H and MillsC (2016) The effect of
thermal processing on the behaviour of peanut allergen peptide targets used in multiple reaction monitoring mass spectrometry experiments. Analyst, Accepted Manuscript.

Selani, M.M., Bianchini, A., Ratnayake, W.S., Flores, R.A., Massarioli, A. P., Alencar, S.M., Brazaca, S.G.C. 2016. Physicochemical, Functional and Antioxidant Properties of Tropical Fruits Coproducts. Plant Foods for Human Nutrition. 71:137–144.

Suhr MJ, Banjara N, Hallen-Adams HE (2016) Sequence-based methods for detecting and evaluating the human gut mycobiome. Lett Appl Microbiol 62:209-215.

Sumargo F, Gulati P, Weier SA, Clarke J, Rose DJ. 2016. Effects of processing moisture on the physical properties and in vitro digestibility of starch and protein in extruded brown rice and pinto bean composite flours. Food Chemistry 211:726-733.

Taylor, S. L. and J. L. Baumert. 2016. Food allergies. In: Encyclopedia of Food and Health, ed. B. Caballero, P. Finglas, and F. Toldra, Elsevier, London, U.K., pp. 737-742.

Ubeyitogullari, A. and Ciftci, O.N. (2016). Formation of nanoporous aerogels from wheat starch. Carbohydrate Polymers, 147, 125-132.

Ubeyitogullari, A. and Ciftci, O.N. (2016). Phytosterol nanoparticles with reduced crystallinity generated using nanoporous starch aerogels. RSC Advances, doi: 10.1039/C6RA20675A.

Wang, H. and Ratnayake, W. S. Great Northern Bean Could Imporve the Nutritional Value of Instant Noodles. Cereal Chem. 93(2):156-161

Yang J, Bindels LB, Segura Munoz RR, Martínez I, Walter J, Ramer-Tait AE, Rose DJ. 2016. Disparate metabolic responses in mice fed a high-fat diet supplemented with maize-derived non-digestible feruloylated oligo- and polysaccharides are linked to changes in the gut microbiota. PLoS One 11(1): e014614.

Yang J. and Ciftci O.N. (2016). Development of free-flowing peppermint essential oil-loaded hollow solid lipid microand nanoparticles via atomization with carbon dioxide. Food Research International, 87, 83-91.

Yang, J. and Ciftci, O.N. (2016). Formation of hollow solid lipid microand nanoparticles using supercritical carbon dioxide. Food and Bioproducts Processing. 98, 151-160.

Zhang, Y. Organic thyme oil emulsion as an alternative washing solution to enhance the microbial safety of organic cantaloupes Food Control, Volume 67, September 2016, Pages 31–38


Arcila JA, Weier SA, Rose DJ. 2015. Changes in dietary fiber fractions and gut microbial fermentation properties of wheat bran after extrusion and bread making. Food Research International 74:217-223.

Banjara N, MJ Suhr, HE Hallen-Adams. 2015. Diversity of yeast and mold species from a variety of cheese types. Current Microbiology 70:792-800.

Belayneh, H.D., Wehling R.L., Cahoon, E., Ciftci, O.N. (2015). Extraction of omega-3-rich oil from Camelina sativa seed using supercritical carbon dioxide. Journal of Supercritical Fluids, in press.

Bernstein AJ, Rose DJ. 2015. Preference mapping of commercial whole wheat breads. Cereal Chemistry 92:278-283.

Bianchini, Andréia, Jayne Stratton, Steve Weier, Carmen Cano, and Lucia Miceli-Garcia. Use of Essential Oils and Plant Extracts to Control Microbial Contamination in Pet Food Products. 2014. J. Food Processing and Technology 5(8):357.

Cavender GA. 2015. Food Processing and Packaging.  In: Neff, R. (editor). Introduction to the Us Food System: Public Health, Environment, and Equity. John Wiley & Sons. p. 317-344.

Cavender, G., Liu, M., Hobbs, D., Frei, B., Strik, B. and Zhao, Y. (2014), Effects of Different Organic Weed Management Strategies on the Physicochemical, Sensory, and Antioxidant Properties of Machine-Harvested Blackberry Fruits. J. Food Science, 79: S2107–S2116.

Hallen-Adams HE (2015) Food fish identification from DNA extraction through sequence analysis. J Food Sci Ed 14:116-120.

Hallen-Adams HE, SD Kachman, J Kim, RM Legge, I Martínez. 2015. Fungi inhabiting the healthy human gastrointestinal tract: a diverse and dynamic community. Fungal Ecology 15:9-17.

Hernandez Nopsa JF, Wegulo SN, Panthi A, Hallen-Adams HE, Harris SD, Baenziger PS (2014) Characterization of Nebraska isolates of Fusarium graminearum causing head blight of wheat. Crop Science 54:1-8.

Jayasena, S., M. Smits, D. Fiechter, G. A. H. de Jong, J. Nordlee, J. Baumert, S. L. Taylor, R. H. Pieters, and S. J. Koppelman. 2015. Comparison of six commercial ELISA test kits for their specificity and sensitivity in detecting different major peanut allergens. J. Agr. Food Chem. 63:1849-1855.

Krumbeck, J.A., M.X. Maldonado-Gomez, I. Martínez, S.A. Frese, T.E. Burkey, K. Rasineni, A.E. Ramer-Tait, E.N. Harris, R.W. Hutkins, and J. Walter. 2015. In vivo selection to identify bacterial strains with enhanced ecological performance in synbiotic applications. Appl. Environ. Microbiol. 81:2445-2465.

Maldonado-Gomez, M.X., H. Lee, D. Barile, M. Lu, and R.W. Hutkins. 2015. Adherence inhibition of enteric pathogens to epithelial cells by bovine colostrum fractions. Int. Dairy J. 40:24-32.

Martinez, B., J. Stratton, A. Bianchini, S. Wegulo, and G. Weaver. 2015. Transmission of Escherichia coli O157:H7 to Internal Tissues and its Survival on Flowering Heads of Wheat. J. Food Protection 78(3): 518–524.

Panthi A, Hallen-Adams H, Wegulo SN, Hernandez Nopsa J, Baenziger PS (2014) Chemotype and aggressiveness of isolates fo Fusarium graminearum causing head blight in wheat in Nebraska. Canadian Journal of Plant Pathology 36:447-455.

Remington, B. C., J. L. Baumert, W. M. Blom, G. F. Houben, S. L. Taylor, and A. G. Kruizinga. 2015.  Unintended allergens in precautionary labeled and unlabeled products pose significant risks to U.K. allergic consumers.  Allergy 70:813-819

Simpson A, Lazic N, Belgrave DCM, Johnson P, Bishop C, Mills C, Custovic A. 2015. Patterns of IgE responses to multiple allergen components and clinical symptoms at age 11 years. J. Allergy Clin. Immunol. (in press).

Temelli F. and Ciftci O.N. (2015). Developing an integrated supercritical fluid biorefinery for the processing of grains. Journal of Supercritical Fluids, 96, 77-85.

Vasanthi Siruguri, Dinesh Kumar Bharatraj, Raju Naik Vankudavath,Vishnu Vardhana Rao Mendu, Vibha Gupta, Richard E. Goodman. 2015. Evaluation of Bar, Barnase, and Barstar recombinant proteins expressed in genetically engineered Brassica juncea (Indian mustard) for potential risks of food allergy using bioinformatics and literature searchesFood and Chemical Toxicology 83 (2015) 93e102