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Bioinstrumentation and BioMEMS Laboratory

Research Highlight:

Photo

Biosensors produce complex outputs which we interpret using machine learning algorithms. We can then visualize grouping of data based on patterns of biomarkers from the original samples.

PUBLICATIONS (selected, only agriculture work listed here)

Thank you for taking the time to look through our total published work over many years. This page lists the comprehensive total of all of our published work. We publish in several different discipline areas, and we also provide links to sub-categories of our work for easy reference (listed below).

            To view our published work on non-invasive breath analysis, please click HERE.

            To view our published work on agriculture monitoring, please click HERE.

            To view our published work on micro/nano MEMS, instrumentation and novel sensor development, please click HERE.

            To view our published work on algorithms and data analysis, please click HERE.

AGRICULTURE PUBLICATIONS

Cumeras R, Aksenov AA, Pasamontes A, Fung AG, Cianchetta AN, Doan H, Davis RM, Davis CE*. (2016) Identification of fungal metabolites from inside Gallus gallus domesticus eggshells by non-invasively detecting volatile organic compounds (VOCs). Analytical and Bioanalytical Chemistry 408(24): 6649-6658. DOI: 10.1007/s00216-016-9778-3

Pasamontes A, Cheung WHK, Simmons J, Aksenov AA, Peirano DJ, Grafton-Cardwell EE, Kapaun T, Dandekar AM, Fiehn O, Davis CE*. (2016) Citrus tristeza virus infection in sweet orange trees and a mandarin x tangor cross alters low molecular weight metabolites assessed using gas chromatography mass spectrometry (GC/MS). Metabolomics 12(3): 1-10. DOI: 10.1007/s11306-016-0959-z

McCartney MM, Spitulski SL, Pasamontes A, Peirano DJ, Schirle MJ, Cumeras R, Simmons JD, Ware JL, Brown JF, Poh AJY, Dike SC, Foster EK, Godfrey KE, Davis CE*. (2016) Coupling a branch enclosure with differential mobility spectrometry to isolate and measure plant volatiles in contained greenhouse settings. Talanta 146, 148-154. DOI: 10.1007/s11306-015-0807-6

Martini X, Aksenov AA, Davis CE, Stelinski LL. (2016) Complex citrus lures to trap and control ACP. Citrograph 7(1): 52-54. LINK

Chen R, Crawford K, Davis CE, Eshani R, Vougioukas S, Upadhyaya S. (2015) The drones are coming. Citrograph 6(4): 18-23. LINK

Cheung WHK§, Pasamontes A§, Peirano DJ, Zhao W, Grafton-Cardwell EE, Kapaun T, Yakomi RK, Simmons J, Swe M, Fiehn O, Dandekar AM, Davis CE*. (2015) Volatile organic compound (VOC) profiling of Citrus tristeza virus (CTV) infection in Valencia citrus varietals using thermal desorption gas chromatography time of flight mass spectrometry (TD-GC/TOF-MS). (§joint first authors) Metabolomics 11(6): 1514-1525. DOI: 10.1007/s11306-015-0807-6

Thuesen L, Pavlovsky I, Fink R*, Pasamontes A, Aksenov AA, Davis CE. (2015) Field deployable VOC analyzer for early detection of citrus pathogens. Citrograph 6(3): 60-63. LINK

Aksenov AA, Martini X, Zhao W, Stelinski LL, Davis CE*. (2014) Synthetic blends of volatile, phytopathogen-induced odorants can be used to manipulate vector behavior. Frontiers of Ecology and Evolution (Nature Publishing Group) 2: 78. DOI: 10.3389/fevo.2014.00078

Aksenov AA, Pasamontes A, Peirano DJ, Zhao W, Dandekar AM, Fiehn O, Eshani R, Davis CE*. (2014) Detection of Huanglongbing disease using differential mobility spectrometry. Analytical Chemistry 86(5): 2481-2488. DOI: 10.1021/ac403469y

Martinelli F*, Scalenghe R, Davino S, Panno S, Ruisi P, Stroppiana D, Boschetti M, Villa P, Goulart R, Davis CE, Dandekar AM. (2014) Advanced Methods of Plant Disease Detection. Agronomy for Sustainable Development 1: 1-25. DOI: 10.1007/s13593-014-0246-1

Martinelli F*, Scalenghe R, Giovino A, Pasquale M, Aksenov AA, Pasamontes A, Peirano DJ, Davis CE, Dandekar AM. (2014) A translational genomic approach for early and infield detection of flavescence doree. Plant Biosystems 1: 1-12. DOI: 10.1080/11263504.2014.908976

Chin E, Mishchuk D, Bruce J, Cilia M, Coaker G, Davis CE, Jin H, Ma W, LeVesque C, Sellar G, Godfrey K, Slupsky C. (2014) An interdisciplinary approach to combat HLB: Research in UC Davis' Contained Research Facility. Citrograph 5(1): 28-34. LINK

Martinelli F, Reagan RL, Uratsua S, Phu ML, Albrecht U, Zhao W, Davis CE, Bowman KD, Dandekar AM*. (2013) Gene regulatory networks to clarify Huanglongbing disease mechanisms. PLoS One 8(9): e74256. DOI: 10.1371/journal.pone.0074256

Aksenov AA, Guaman Novillo AV, Sankaran S, Fung AG, Pasamontes A, Martinelli F, Cheung WHK, Eshani R, Dandekar AM, Davis CE*. (2013) Chapter 6: Volatile Organic Compounds (VOCs) for Non-Invasive Plant Diagnostics. Natural Products for Pest Management (eds. J Beck, JR Coats, SO Duke, ME Koivunen). ACS Symposium Book Series, American Chemical Society. pp. 73-95. ISBN 978-0-8412-2900-6. DOI: 10.1021/bk-2013-1141.ch006

Martinelli F, Uratsu S, Albrecht U, Reagan RL, Phu ML, Britton M, Buffalo V, Fass J, Leicht E, Zhao W, Lin D, D'Souza R, Davis CE, Bowman KD, Dandekar AM*. (2012) Transcriptome profiling of citrus fruit in response to Huanglongbing disease. PLoS ONE 7(5): e38039. DOI: 10.1371/journal.pone.0038039

Aksenov AA, Cheung WHK, Zhao W, Bardaweel H, Martinelli F, Fiehn O, Dandekar AM, Davis CE*. (2012) Reagentless detection of citrus pathogens using differential mobility spectrometry. Citrograph 3(2): 54-56. LINK

Schivo M, Akesnov AA, Bardaweel H, Zhao W, Kenyon NJ, Davis CE*. (2011) Building biomarker libraries with novel chemical sensors: correlating differential mobility spectrometer signal outputs with mass spectrometry data. IOP Conference Series: Materials Science and Engineering 18 (2011) 212003 (doi:10.1088/1757-899X/18/21/212003) DOI: 10.1088/1757-899X/18/21/212003

Dandekar AM*, Martinelli F, Zhao W, Bhushan A, Davis CE, Skogerson K, Fiehn O, Leicht E, D'Souza R. (2011) Non-destructive disease detection in citrus through the analysis of induced volatile organic compounds. Citrograph 1(5):17-20. LINK

Dandekar AM*, Martinelli F, Davis CE, Bhushan A, Zhao W, Fiehn O, Skogerson K, Wohlgemuth G, D'Souza R, Roy S, Reagan R, Lin D, Bruening G, Cary RB, Pardington P, Gupta G. (2010) Analysis of early host responses for asymptomatic disease detection and management of specialty crops. Critical Reviews in Immunology 30(3): 277-289. DOI: 10.1615/CritRevImmunol.v30.i3.50

Sankaran S, Mishra AR, Ehsani R*, Davis CE. (2010) A review of advanced techniques for detecting plant diseases. Computers and Electronics in Agriculture 72: 1-13. DOI: 10.1016/j.compag.2010.02.007

Ayer S, Zhao W, Davis CE*. (2008) Differentiation of proteins and viruses using pyrolysis gas chromatography differential mobility spectrometry (PY/GC/DMS) and pattern recognition. IEEE Sensors Journal 8(9): 1586-1592. DOI: 10.1109/JSEN.2008.923586

Krebs MD, Mansfield B, Yip P, Cohen SJ, Sonenshein AL, Hitt B, Davis CE*. (2006) Spore biomarkers differentiate between closely-related Bacillus species using differential mobility spectrometry. Biomolecular Engineering 23(2): 119-127. DOI: 10.1016/j.bioeng.2005.12.003

Morgan JT, Davis CE*. (2006) Differential mobility spectrometry applications in homeland security, clinical diagnostics and drug discovery. 2006 ASME International Mechanical Engineering Congress and Exposition. November 5-10, 2006, Chicago, Illinois. IMECE2006-15937.

Shnayderman M, Mansfield B, Yip P, Clark HA, Krebs MD, Cohen SJ, Zeskind JE, Ryan ET, Dorkin HL, Callahan MV, Stair TO, Gelfand JA, Gill CJ, Hitt B, Davis CE*. (2005) Species-specific bacteria identification using differential mobility spectrometry and bioinformatics pattern recognition. Analytical Chemistry 77(18): 5930-5937. DOI: 10.1021/ac050348i

Krebs MD, Zapata AM, Nazarov EG, Miller RA, Costa IS, Sonenshein AL, Davis CE*. (2005) Detection of biological and chemical agents using differential mobility spectrometry (DMS). IEEE Sensors Journal, Special Edition on Anti-Terrorism 5(4): 696-703. DOI: 10.1109/JSEN.2005.845515

Davis CE*, Kang JM, Dube CE, Borenstein JT, Nazarov EG, Miller RA, Zapata AM. (2003) Spore biomarker detection using a MEMS Differential Mobility Spectrometer. The 12th IEEE International Conference on Solid-State Sensors and Microsystems Conference, IEEE Proceedings Vol 2: 1233-1238. DOI: 10.1109/SENSOR.2003.1216995