Publications

Google Scholar Citations

  1. Liu, W., Mohan, S., Nagaraj, N., Jaganathan, S., Wen, Y., Ramasubramanyam, S., and Irudayaraj, J. 2021. Epigenetic alterations associated with dexamethasone sodium phosphate through DNMT and TET in RPE cells. Molecular Vision (accepted).
  2. Liu, Padhi, A., Nain, A., and Irudayaraj, J. 2021. Dynamic heterochromatin states in anisotropic nuclei of cells on aligned nanofibers. Advanced Science (conditionally accepted).
  3. Lee, Y., Rattan, S., Barakat, R., Inman, Z., Kathy, M., Meling, D., Monaco, M., Irudayaraj, J., Cann, I., Donovan, S., Flaws, J., and Warner, G. 2021. Early exposure to di(2-ethylhexyl) phthalate causes sex-specific disruption of gonadal development in pigs. Reproductive Toxicology (In Press).
  4. Fayyaz, M., Jabeen, M., Tsipursky, M., and Irudayaraj, J. 2021. Dextran-based oxygen nanobubbles for treating inner retinal hypoxia. ACS Applied Nanomaterials. 4(7): 6583-6593.
  5. Vega-Vasquez, P., Mosier, N., and Irudayaraj, J. 2021. Nanovaccine for plants from organic waste: d-Limonene-loaded chitosan nanocarriers protects plants against Botrytis cinerea. ACS Sustainable Chemistry & Engineering. 9(29), 9903-9914.
  6. Liu, J., Hu, Y., Kumar, P., Liu, X., *Irudayaraj, J., and *Cheng, G. 2021. Enhanced energy transfer from nitrogen vacancy centers to three-dimensional graphene heterostructures by laser nanoshaping. Advanced Optical materials. 2001830.
  7. Vega-Vasquez, Mosier, A., and Irudayaraj, J. 2021. Hormesis Inducing Essential Oil Nano-delivery system protects plants against Broad Host-range necrotrophs. ACS Nano. 15(5): 8338-8349.
  8. Ren, W., Ahmad, S., and Irudayaraj, J. 2021. 16S rRNA monitoring point-of-care magnetic focus lateral flow sensor. ACS Omega. 6 (16):11095-11102.
  9. Pathania, A., Liu, W., Matityahu, A., Irudayaraj, J., and Onn, I. 2021. Chromosome loading of cohesion depends on conserved residues in SC3. Current Genetics, 1-13.
  10. Zhou, Z., Yan, R., Jiang, W., and Irudayaraj, J. 2021. Chromatin hierarchical branching visualized at nanoscale by Electron Microscopy. Nanoscale Advances, 3 (4), 1019-1028.
  11. Salapa, J., Bushman, A., Lowe, K., and Irudayaraj, J. 2020. Drug delivery systems in Upper Gastrointestinal cancer therapy. Nano Convergence. 7(1):1-17.
  12. Young, T., Cui, Y., Pfeffer, C., Hobbs, E., Liu, W., Irudayaraj, J. Kirchmaier, A. 2020. CAF-1 and Rtt101p function within the replication-coupled chromatin assembly network to promote H4K16ac, preventing ectopic silencing. PLoS Genetics 16(12), e1009226.
  13. Jabeen, M., Fayyaz, M., and Irudayaraj, J. 2020. Epigenetic modifications, and alterations in cell cycle and apoptosis pathway in A549 lung carcinoma cell line upon exposure to Perfluoroalkyl substances. Toxics 8(4), 112.
  14. Damayanti, N., Jena, S., *Irudayaraj, J., and *Parker, L. 2020. Multiplex fluorescence lifetime imaging probes for Syk and Src-family kinases. (*Equal credit). Chemical Communications 56 (87):13409-13412.
  15. Rashid, F., Ahmad, S., and Irudayaraj, J. 2020. Effect of Perfluorooctanoic Acid on the epigenetic and tight junction genes of the mouse intestine. Toxics, 8(3): 64.
  16. Wen, Y., Rattan, S., Flaws, J., and Irudayaraj, J. 2020. Multi and transgenerational epigenetic effects of di-(2-ethylhexyl) phthalate (DEHP) in liver. 2020. Wen, Y., Rattan, S., Flaws, J., and Irudayaraj, J. Toxicology and Applied Pharmacology, 402: 115123.
  17. Ren, W., Cabush, A., Irudayaraj, J. 2020. Checkpoint enrichment for sensitive detection of target bacteria from large volume of food matrices. Analytica Chimica Acta. 117: 114-121.
  18. Dhivya, M., Aberami, S., Shree, S., Biswas, J., Liu, W., Irudayaraj, J., and Bharathi, D. 2020. Copper mediates mitochondrial biogenesis in retinal pigment epithelial cells. Biochimica et Biophysica Acta. 1866(10), 165843
  19. Liu, W. and Irudayaraj, J. 2020. Perfluorooctanoic acid (PFOA) exposure inhibits DNA methyltransferase activities and alters constitutive heterochromatin organization. Food and Chemical Toxicology, 141, 111358.
  20. Wen, Y., Mirji, N., and Irudayaraj, J. 2020. Epigenetic toxicity of PFOA and GenX in HepG2 cells and their role in lipid metabolism. In Vitro Toxicology. 65: 104797
  21. Rashid, F., Ramakrishnan, A., Fields, C., and Irudayaraj, J. 2020. Acute PFOA exposure promotes epigenomic alterations in mouse kidney tissues. Toxicology Reports. 7, 125-132.
  22. Liu, W., Bilton, E., Pathania, A., Matityahu, A., *Onn, J., and *Irudayaraj, J. 2020. Monomeric cohesion state revealed by live-cell single-molecule spectroscopy. EMBO Reports. 21(2). E48211
  23. Liu, W. and Irudayaraj, J. 2019. Understanding the dynamics and structure of epigenetic states with single molecule fluorescence spectroscopy. Current Opinion in Biomedical Engin. 12, 18-24
  24. Rattan, S., Beers, K., Kannan, A., Ramakrishnan, A., Brehm, E., Bagchi, I., Irudayaraj, J., and Flaws, J. 2019. Prenatal and ancestral exposure to di(2-ethylhexyl) phthalate alters gene expression and DNA methylation in mouse ovaries. Toxicology & Applied Pharmacology. 379, 114629. Doi: 10.1016/j.taap.2019.114629.
  25. Zhou, Z., Li, K., Yan, R., Yu, G., Gilplin, C., Jiang, W., and Irudayaraj, J. 2019. Transition structure of chromatin fibers at nanoscale probed by cryogenic electron tomography. Nanoscale. 211(4):1219-1237.
  26. Vega, P., Mosier, N., Irudayaraj, J. 2020. Drug nano-delivery systems: From medicine to agriculture. Frontiers in Bioengineering and Biotechnology. (8).
  27. Damayanti, N., Buno, K., Voytik-Harbin, S., and Irudayaraj, J. 2019. Epigenetic process monitoring in live cell cultures with peptide biosensors. ACS Sensors, 4(3): 562-565 [Cover]
  28. Liu, W., Cui, Y., Ren, W., and Irudayaraj, J. 2019. Epigenetic biomarker screening by FLIM-FRET for combination therapy in ER+ breast cancer. Clinical Epigenetics. 11(1):16.
  29. Ren, W., Mohammed, S., Wereley, S., and Irudayaraj, J. 2019. Magnetic focus lateral flow for detection of cervical cancer biomarkers. Analytical Chemistry. 91(4): 2876-2884.
  30. Kumar, P., Liu, J., Motlag, M., Hu, Y., Tong, L., Huang, X., Bandopadhya, A., Pati, S., Ye, Lei, *Irudayaraj, J., *Cheng, G. 2019. Laser shock tuning and dynamic interlayer coupling in
    Graphene-boron nitride moire superlattices. Nano Letters, 19(1):283-291. (* equal credit)
  31. Ren, W., Ballou, D., Fitzgerald, R. Irudayaraj, J. 2019. Plasmonic enhancement in lateral flow Sensors for improved sensing of E. coli O157:H7. Biosensors and Bioelectronics, 126: 324-331.
  32. Kuang, L., Damayanti, N., Jiang, C., Fei, X., Narayanan, N., Liu, W., Irudayaraj, J., Campanella, O., Deng, M. 2019. Bioinspired glycosaminoglycan hydrogels via click chemistry for 3D dynamic cell encapsulation. Applied Polymer Science. 136(5): 47212.
  33. Wang, R., Vega, P., Xu, Y., Chen, C., Irudayaraj, J. 2018. Exploring the anti-quorum sensing activity of D-limonene nanoemulsion for Escherichia coli O157:H7. J. Biomedical Materials Research: Part A. 106 (7): 1979-1986.
  34. Wang, R., Xu, Y., Sors, T., Irudayaraj, J., Ren, W., Wang, R. 2018. Impedimetric detection of bacteria by using a microfluidic chip and silver nanoparticle signal enhancement. Microchimica Acta, 185(3):184.
  35. Ouyang, L., Wang, Y., Zhu, L., Irudayaraj, J., and Tang, H. 2018. Filtration-assisted fabrication of large-area uniform and long-term stable graphene isolated nano-AG array membrane as surface enhanced Raman scattering substrate. Advanced Materials Interfaces, 5(4): 1701221.
  36. Bhandari, P., Novikova, Goergen, C., and Irudayaraj, J. 2018. Ultrasound beam steering of oxygen nanobubbles for enhanced bladder cancer therapy. Nature Scientific Reports (In Press)
  37. Young, T., Cui, Y., Li, W., Irudayaraj, J., and Kirchmaier, A. 2018. CDC7 modulates silencing at HMRae** via H4 K16 acetylation and CAF-1 in Saccharomyces cerevisiae. Genetics. (Conditionally accepted)
  38. *Kumar, P., *Liu, J., +Cheng, G., and +Irudayaraj, J. 2018. Alpha Lead oxide (α-PbO): A New  2D material with visible light sensitivity” (Communication, No. smll.201703346R1) to  Small (In Press)
  39. Cho, I-L., Lee, J., Kim, J., Kang, M., Paik, J., Ku, S., Cho, H., and Irudayaraj. 2018. Current technologies of electrochemical immunosensors: Perspectives on signal amplification. Sensors, 18(1): 207.
  40. Wu, Z., Xu, E., Jin, Z., and Irudayaraj, J. 2018. An ultrasensitive aptasensor based fluorescent resonant energy transfer and exonuclease-assisted target recycling for patulin detection. Food Chemistry (In Press).
  41. Adelaiye-Ogala, R., Budka, J., Damayanti, N., Arrington, Ferris, M., Hsu, C., Chintala, S., Orillion, A., Zang, Y., Irudayaraj, J., Tao, A., Hollenhorst, P., and Pili, R. 2017. EZH2 modulates sunintab resistance by kinome reprogramming in renal cell carcinoma. Cancer Research, 77 (23):6651-6666.
  42. Wu, Z., Xu, E., Jiao, A., Jin, Z., Irudayaraj, J. 2017. Bimodal counterpropagating-responsive sensing material for detection of histamine. RSC Advances. (Accepted).
  43. Ordaz, J., Damayanti, N., and Irudayaraj, J. 2017. Toxicological effects of trichloroethylene exposure on immune disorders. Immunopharmacology and Immunitoxicology, 39(6):305-317.
  44. Damayanti, N., Buno, K., Cui, Y., Vyotik-Harbin, S., Pili, R., Freeman, J., and Irudayaraj, J. 2017. Real-time multiplex kinase phosphorylation sensors in live cells. ACS Sensors, 2(8): 1225-1230. [Cover Article].
  45. Damayanti, N., Buno, K., Vyotik-Harbin, S., Deng, M., and Irudayaraj, J. 2017. Monitoring focal adhesion kinase phosphorylation dynamics in live cells. Analyst, 142(13): 2426-2433. [Cover Article].
  46. Bhandari, P., Ouyang, L., and Irudayaraj, J. 2017. Hypoxia re-programming oxygen nanobubbles sensitize human glioblastoma cells to temozolomide via methylation alterations. J. Bionanoscience, 11(5):337-345.
  47. Naz, A., Cui, Y., Collins, C.J., Thompson, D., and Irudayaraj, J. 2017. PLGA-PEG Nano-delivery system for epigenetic therapy. Biomedicine and Pharmacotherapy, 90: 586-597.
  48. Bogdanov, S., Shalaginov, M., Akimov, A., Lagutchev, A., Kapitanova, P., Liu, J., Woods, D.,  Ferrera, M., Belov, P., Irudayaraj, J., Boltasseva, A., and Shalaev, V. 2017. Electron spin contrast of Purcell-enhanced nitrogen-vacancy ensembles in nanodiamonds. arXiv preprint arXiv: 1703.06991. Physical Review B, 035146 (1-7).
  49. Wu, Z., Xu, E, Chughtai, M., Jin, Z., and Irudayaraj, J. 2017. Highly sensitive fluorescence sensing of zearalenone using a novel aptasensor based on upconverting nanoparticles. Food Chemistry. 230: 673-680. http://dx.doi.org/10.1016/j.foodhcem.2017.03.100.
  50. Kadam, U., Chavhan, R., Schultz, B., and Irudayaraj, J. 2017. Single molecule Raman spectroscopic assay to detect transgene from GM plants. Analytical Biochemistry. 532, 1 Sept: 60-63. DOI: 10.1016/j.ab.2017.06.002.
  51. Wang, R., Xu, Y., Liu, H., Irudayaraj, J., and Cui, F. 2017. An integrated microsystem with dielectrophoresis enrichment and impedance detection for detection of Escherichia coli.Biomedical Microdevices, 19 (2): 34.
  52. Ren, W. Liu, W., and Irudayaraj, J. 2017. A netfishing enrichment strategy for colorimetric detection of E. coli O157:H7. Sensors and Actuators B. 247:923-929. http://dx.doi.org/10.1016/j.snb.2017.03.090.
  53. Wang, R., Cui, Y., Xu, Y., and Irudayaraj, J. 2017. Basic studies on epigenetic carcinogenesis of low-dose exposure to 1-trichloromethyl-1,2,3,4-tetrahydro-b-carboline (TaClo) in vitro. PLoS ONE, 12(2): e0172243. doi:10.1371/journal.pone.0172243.
  54. Bhandari, P., Wang, X., and Irudayaraj, J. 2017. Oxygen Nanobubble Tracking by Light Scattering in Single Cells and Tissues. ACS Nano. http://dx.doi.org/10.1021/acsnano.6b07478.
  55. Lo, C., Choudhury, R., *Irudayaraj, J., and *Zhou, F. 2017. Epigenetic Editing of Ascl1 Gene in Neural Stem Cells by Optogenetics. Nature Scientific Reports. 7:42047 (DOI:10.1038/srep42047). (*Equal Credit)
  56. Choudhury, S. and Irudayaraj, J. 2017. ZnO nanoparticles induced reactive oxygen species promotes multimodal cyto- and epigenetic toxicity. Toxicological Sciences. DOI: 10.1093/toxsci/kfw252.
  57. Kadam, U., Schultz, B., and Irudayaraj, J. 2017. Multiplex single cell quantification of rare RNA transcripts from protoplasts in a model plant system. Plant Journal. 90(16):1187-1195.
  58. Chowdhury, B., Cho, I-L., and Irudayaraj, J. 2017. Technical advances in global DNA methylation analysis in human cancers. Journal of Biological Engineering. 11:10. DOI 10.1186/s13036-017-0052-9.
  59. Cui, Y., Liu, J., and Irudayaraj, J. 2016. Beyond Quantification: In situ Analysis of Transcriptome and Pre-mRNA Alternative Splicing at the Nanoscale. Nanotechnology Approaches to Biology. WIREs Nanomedicine and Nanobiotechnology. 9(4):DOI:10.1002/wnan.1443.
  60. Mahapatra, C., Serafin, S., Guffey, S., Irudayaraj, J., and Sepulveda, M., 2016. Comparative in vitro toxicity assessment of perfluorinated carboxylic acids. Journal of Applied Toxicology. 37 (6): 699-708.
  61. Cui, Y., Li, J., Weng, L., Wirbisky, S., Freeman, J., Liu, J., Liu, Q., Yuan, X., and Irudayaraj, J. 2016. Regulatory Landscape and Clinical Implication of MBD3 in Human Malignant Glioma. Oncotarget. DOI: 10.18632/oncotarget.13173.
  62. Ouyang, L., Hu, Y., Cheng, G., and Irudayaraj, J. 2017. A reusable laser wrapped graphene-Ag array based SERS sensor for trace detection of genomic DNA methylation. Biosensors and Bioelectronics. 92:755-762. http://dx.doi.org/10.1016/j.bios.2016.09.072
  63. Hu, Y., Xuan, Y., Wang, X., Deng, B., Saei, M., Jin, S., Irudayaraj, J., and Cheng, G. 2016. Superplastic formulation of metal nanostructure arrays with ultrafine gaps. Advanced Materials. 28(41): 9152-9162.
  64. Choudhury, S., Cui, Y., Narayanan, A., Gilley, D., Huda, N., Lo, C., Zhou, F. 2016. Optogenetic regulation of site-specific subtelomeric DNA methylation. Oncotarget, 7(31):50380-50391.
  65. Lo., S., Resendiz, M., Chen, Y., Choudhury, S., Irudayaraj, J., Zhou, F. 2016. Epigenetic mechanism of alcohol on neural development demonstrated in a site-specific manner. Alcoholism-Clinical and Experimental Research. 40: 299A.
  66. Liu, J. and Irudayaraj, J. 2016. Non-fluorescent quantification of single mRNA with transient absorption microscopy. Nanoscale. DOI: 10.1039/C6NR04433F. [Cover article]
  67. Choudhury, S., Cui, Y., Lubeca, K., Stefanska, B., and Irudayaraj, J. 2016. CRISPR-dCas9    mediated TET1 targeting for selective DNA demethylation at BRCA1 promoter. Oncotarget. 7(29): 46545-46556.
  68. Ren, W., Cho, I-L., and Irudayaraj, J. 2016. Ultrasensitive detection of microbial cells by magnetic enhanced lateral flow sensors. Chemical Communications, 52:4930-4933.
  69. Cui, Y., Chowdhury, S., and Irudayaraj, J. 2016. Epigenetic toxicity of trichloroethylene – a single molecule perspective. Toxicology Research. 5: 641-655.
  70. Mohammed, S., Ren, W., Rajwa, B., Chibwesha, C., Parham, G., and Irudayaraj, J. 2016. Point-of-care test for cervical cancer in LMICs. Oncotarget. DOI: 10.18632/oncotarget.7709.
  71. Wirbisky, S., Damayanti, N., Mahapatra, C., Sepulveda, M., Irudayaraj, J., and Freeman, J. 2016. Mitochondrial dysfunction, disruption of F-Actin polymerization, and transcriptomic alterations in zebrafish larvae exposed to trichloroethylene. Chemical Research in Toxicology.
  72. Yi, C., Wang, X., Ren, W., Liu, J., and Irudayaraj, J. 2016. Optical clearing delivers ultra sensitive hyperspectral dark-field imaging for single cell evaluation. ACS Nano.10(3): 3132-43.
  73. Chowdhury, B., Arun, G., Thimmapuram, J., Lossie, A., and Irudayaraj, J. 2016. A study of alterations in DNA epigenetic modifications (5mC and 5hmC) and gene expression influenced by simulated microgravity in human lymphoblastoid cells. PLOS One, 11 (1), e0147514.
  74. Bhandari, P., Long, C., Cui, Y., Elzey, B., R., Goergen, C., and Irudayaraj, J. 2017. Oxygen nanobubbles revert hypoxia by methylation programming. Nature Scientific Reports. (In Press)
  75. Zhou, Z., Yang, Y., Konieczny, S., and Irudayaraj, J. 2015. Rapid and unbiased extraction of chromatin associated RNAs from purified native chromatin. Journal of Chromatography A. 1426: 64-68. DOI: 10.1016/j.chroma.2015.11.067.
  76. Ren, W. Damayanti, N., Wang, X., and Irudayaraj J. Kinase Phosphorylation Monitoring with i-Motif DNA Cross-linked Gold Nanoparticle SERS probes. Chemical Comm. 410: 410-413, DOI: 10.1039/C5CC06566F.
  77. Choudhury, S., Cui, Y., Milton, J., and Irudayaraj, J. 2015. Selective increase in subtelomeric DNA methylation: an epigenetic biomarker for malignant glioma. Clinical Epigenetics. 7:107.
  78. Liu, J., Damayanti, N., Cho, I., Polar, Y., Badve, S., Irudayaraj, J. 2015. Single cell screening and quantification of transcripts in cancer tissues using second harmonic generation microscopy. J. Biomedical Optics. 20(9):096016
  79. Wang, X., Cui, Y., and Irudayaraj, J. 2015. Single cell quantification of cytosine modifications by hyperspectral dark field imaging. ACS Nano. 9(12):11924-11932.
  80. Lee, S., Kumar, P., Hu, Y., Cheng, G., Irudayaraj, J. 2015. Graphene laminated gold bipyramids as sensitive detection platforms of antibiotic molecules. Chemical Comm. 51: 15494-15497 [Cover article].
  81. Ren, W. and Irudayaraj J. 2015. Trichloroethylene sensing in water based on SERS with multifunctional Au/TiO2 core-shell nanocomposites. Analyst. 140: 6625-6630. (DOI: 10.1039/c5an0129e).
  82. Lee, S., Hu, Y., Kumar, P., Cheng, G., and Irudayaraj, J. 2015. Water flattens graphene wrinkles: laser shock wrapping of graphene onto substrate-supported crystalline plasmic nanoparticle arrays. Nanoscale 7: 19885-19893 [Cover article].
  83. Ren, W., Mura, S., and Irudayaraj, J. 2015. Modified graphene oxide sensors for ultra sensitive detection of nitrate ions in water. Talanta. 10.1016/j.talanta.2015.05.073.
  84. Zhou, Z., Cho, I., Shan, Z., and Irudayaraj, J. 2015. Cross-platform detection of epigenetic modifications from extracted chromatin in leucocytes from blood. Analytical Chemistry Research, doi:10.1016/j.ancr.2015.04.002.
  85. Cho, I., Bhunia, A., Irudayaraj, J. 2015. Rapid pathogen detection by lateral-flow immunochromatographic assay with gold nanoparticle-assisted enzyme signal amplification. International Journal of Food Microbiology. 206: 60-66.
  86. Cui, Y., Naz, A., Thompson, D., Irudayaraj, J. 2015. Decitabine Nano-conjugate Sensitizing Human Glioblastoma Cells to Temozolomide. Molecular Pharmaceutics. doi: 10.1021/mp500815b.
  87. Chowdhury, B., Chen, J., Liu, S., Lossie, A., and Irudayaraj, J. 2015. Effect of AZA on hydroxymethylation – exploring a novel effect. Nature Scientific Reports, doi: 10.1038/srep09281.
  88. Cho, I., Das, M., Bhandari, P., and Irudayaraj, J. 2014. High performance immunochromatographic assay combined with surface enhanced Raman spectroscopy. Sensors and Actuators: B. Chemical. 213: 209-214.
  89. Liu, J., Hu, Y., Kumar, P., Cheng, G., and Irudayaraj, J. 2014. Enhanced Multi-Photon Emission from CdTe/ZnS Quantum Dots Decorated on Single Layer Graphene. J. Phys Chem. C. 119(1): 6331-6336.
  90. Liu, J., Cho, I-H., Cui, Y., and Irudayaraj, J. 2014. Second harmonic super-resolution microscopy for quantification of mRNA at single copy resolution. ACS Nano, 8 (12): 12418–12427.
  91. Zhou, Z. and Irudayaraj, J. 2014.  A native chromatin extraction method based on salicylic acid coated magnetic nanoparticles and characterization of chromatin. Analyst, 140(3): 938-44.
  92. Cui, Y. and Irudayaraj, J. 2014. Understanding cells: quantitative analysis with advanced optics and nanomaterials.  WIREs Nanomedicine and Nanobiotechnology. DOI: 10.1002/wnan.1321 (Cover article)
  93. Cui, Y. and Irudayaraj, J. 2015. Dissecting the behavior and function of MBD3 in DNA methylation homeostasis by single-molecule spectroscopy and microscopy. Nucleic Acids Research. 43 (6), 3046-3055.
  94. Vidi, P., Liu, J., Lelièvre, S., and  Irudayaraj, J. 2014. Nanoscale localization microscopy reveals reduced chromatin mobility in response to DNA damage in single live cells. Journal of Cell Science. doi: 10.1242/jcs.161885.
  95. Shalaginov, M.Y., Vorobyov, V.V., Liu, J., Ferrera, M., Akimov, A., Lagutchev, A.,Smolyaninov, A., Klimov, V., Irudayaraj, J., Kildishev, A., Boltasseva, A., and Shalaev, V. 2014. Enhancing the nanodiamond nitrogen-vacancy single-photon source with TiN/AlScN hyperbolic metamaterial superlattice. Laser & Photonics Reviews, 9(1): 120-127.
  96. Cho, I-H., Bhandari, P., Patil, P., and Irudayaraj, J. 2014. Membrane filter-assisted surface enhanced Raman spectroscopy for the rapid detection of E. coli O157:H7 in ground beef. Biosensors and Bioelectronics, 64: 171-176.
  97. Liu, J., Ishii, S., Shalaev, V. and Irudayaraj, J. 2014. Quantifying local density of optical states in single nanorods by fluorescence lifetime distribution. New Journal of Physics. 16, 063069.
  98. Craig, A., Franca, A., Oliveira, L., Irudayaraj, J., and Ileleji, K. 2014. Fourier transform infrared spectroscopy and near infrared spectroscopy for the quantification of defects in roasted coffee. Talanta, 03/2015; 134:379–386. DOI: 10.1016/j.talanta.2014.11.038.
  99. Craig, A., Franca, A., Oliveira, L., Irudayaraj, J., and Ileleji, K. 2014. Application of elastic net and infrared spectroscopy in the discrimination between defective and non-defective roasted coffees. Talanta 128, 393-400.
  100. Cui, Y., Choudhury, S., and Irudayaraj, J. 2014. Quantitative real-time kinetics of optogenetic proteins CRY2 and CIB1/N using single-molecule tools. Analytical biochemistry 458, 58-60.
  101. Cho, I-H., Mauer, L., and Irudayaraj, J. 2014. In-situ fluorescent immunomagnetic multiplex detection of foodborne pathogens in low numbers. Biosensors & Bioelectronics. 57, 143- 148.
  102. Narsireddy, A., Vijayashree, K., Irudayaraj, J., Manorama, S., and Rao M. Targeted in vivo photodynamic therapy with epidermal growth factor receptor-specific peptide linked nanoparticles. International Journal of Pharmaceutics. 471(1-2):421-9.
  103. Naik, G., Saha, B., Liu, J., Saber, S., Stach, E., Irudayaraj, J., Sands, T., Shalaev, V., and Boltasseva, A. 2014. Epitaxial superlattices with titanium nitride as a plasmonic component for optical hyperbolic metamaterials. Proceedings of the National Academy of Sciences 111 (21), 7546-7551.
  104. Chowdhury, B., Cho, I., Cui, Y., and Irudayaraj, J. 2014. Detection of 5mC, 5hmC, 5fC, and 5caC using a modified ELISA approach. Analytica Chimica Acta. DOI: 10.1016/j.aca. 2014.09.020.
  105. Chen, H., Weng, T-W., Ticcitelli, M., Cui, Y., Irudayaraj, J., and Choi, J. 2014. Understanding the Mechanical Properties of DNA Origami Tiles and Controlling the Kinetics of Their Folding and Unfolding Reconfiguration. JACS. 136(19);6995-7005.
  106. Kadam, U., Schulz, B., and Irudayaraj, J. 2014. Detection and quantification of alternative splice sites in Arabidopsis genes AtDCL2 and AtPTB2 with highly sensitive surface enhanced Raman spectroscopy (SERS) and gold nanoprobes. FEBS letters 588 (9), 1637-1643.
  107. Vidi, P-A., Liu, J., Salles, D., Jayaraman, S., Dorfman, G., Gray, M., Abad, P., Moghe, P., Irudayaraj, J., Wiesmüller, L., and Lelièvre, S. 2014. NuMA promotes homologous recombination repair by regulating the accumulation of the ISWI ATPase SNF2h at DNA breaks. Nucleic Acids Research. 42(10):6365-79.
  108. Lee, K., Lee, L., and Irudayaraj, J. 2014. In vivo real-time quantification of intracellular mRNA using plasmon spectroscopy. Nature Nanotechnology. 9(6): 474-480.
  109. Cho, I., Mauer, L. and Irudayaraj, J. 2014. In-situ fluorescent immunomagnetic detection of foodborne pathogens. Biosensors and Bioelectronics. 57:143-148.
  110. Chen, Y., Damayanti, N., Dunn, K., Irudayaraj, J., and Zhou, F. 2014. Diversity of two forms of DNA methylation in the brain. Frontiers in Genetics. 5(46):1-23. PMCID 3948076, dos: 10.3389/fgene.2014.00046.
  111. Mura, S. Greppi, G., Roggero, P., Musu, E., Pittails, D., Carletti, A., Ghiglieri, G., and Irudayaraj, J. 2015. Functionalized gold nanoparticles for the detection of nitrates in water International. J. Environmental Science and Technology. 12(3):1021-1028.
  112. Kadam, US, Schulz, B, and Irudayaraj J. 2014. Quantification of abortive transcription of TWD1 gene in Arabidopsis thaliana, using Surface-enhanced Raman spectroscopy (SERS). Plant Biotechnology. 12(5):568-577.
  113. Damayanti, N., Craig, A., and Irudayaraj, J. 2013. Hybrid FLIM-Elastic net platform for label-free profiling of breast cancer. Analyst. 138(23): 7127-34.
  114. Damayanti, N., Fang, Y., Parikh, M., Craig, A., Kirshner, J., and Irudayaraj, J. 2013. Differentiation of Cancer Cells in 2D and 3D breast cancer models by Raman spectroscopy. Biomedical Optics. 18(11): 117008. doi: 10.1117/1.JBO.18.11.117008.
  115. Yi, C., Cho, I., Chowdhury, B., and Irudayaraj, J. 2013. Real-time dynamics of methyl CpG binding domain protein 3 and its role in DNA demethylation by fluorescence correlation spectroscopy. Epigenetics. (Cover Article), 8(10): 1089-1100.
  116. Zhou, Z., Kadam, U., and Irudayaraj, J. 2013. One-stop Genomic DNA Extraction by Salicylic Acid Coated Magnetic Nanoparticles. Analytical Biochemistry. 442(2): 249-252.
  117. Cho, I., Radadia, A., Farrokhzad, K., Ximenes, E., Bae, E., Singh, A., Oliver, H., Ladisch, M., Bhunia, A., Applegate, B., Mauer, L., Bashir, R., and Irudayaraj, J. 2014. Nano/Micro and Spectroscopic Approaches to Food Pathogen Detection. Annual Review of Anal. Chemistry. 7(1):65-88.
  118. Dong, C., Chowdhury, B., and Irudayaraj, J. 2013. Quantum Dots trafficking in cells probes by single molecule methods. Analyst. 138 (10): 2871-2876.
  119. Shalaginow, M., Shii, S., Liu, J., Liu, J., Irudayaraj, J., Lagutchev, A., Kaldishev, and Shalaev,V. 2013. Broadband enhancement of spontaneous emission from nitrogen-vacancy centers in nanodiamonds by hyperbolic metamaterials. Applied Physics Letters. 102(17):173114-4.
  120. Damayanti, N., Parker, L., and Irudayaraj, J. 2013. Monitoring phosphorylation in live cells by lifetime imaging. Angew Chemie. 52(14): 3931-3934.
  121. Cho, I. and Irudayaraj, J. 2013. In-situ immunogold nanoparticle network-based ELISA biosensor for highly sensitive pathogen detection. Intl. J. Microbiology. 164(1): 70-75.
  122. Cho, I and Irudayaraj, J. 2013. Lateral-flow immune concentration for detection of Listeria monocytogenes. Analytical Bioanalytical Chemistry. 405(10): 3313-3319.
  123. Lee, K. and Irudayaraj, J. 2013. Correct Spectral Conversion between Surface-enhanced Raman and Plasmon Resonance Scattering from Nanoparticle Dimers for Single Molecule Detection. Small J. 9(7): 1106-1115.
  124. Wang, Y. and Irudayaraj, J. 2013. Surface-enhanced Raman spectroscopy at single molecule scale and its implication in biology. Philosophical Transactions B. 368(1611): 20120026.
  125. Mura, S., Greppi., G., Innocenzi, P., Piccinini, M., Figus, C., Marongiu, L., Guo, C., and Irudayaraj, J. 2013. Nanostructured thin films as surface-enhanced Raman scattering substrates. J. Raman Spectroscopy. 44:35-40.
  126. Liu, J. and Irudayaraj, J. 2013. Second Harmonic Generation Correlation Spectroscopy for Single Molecule Experiments. Optics Express. 21(22):27063-27073.
  127. Jae-Sung, K., Ravindranath, S., Aloke, K., Irudayaraj, J. and Wereley, S. 2012. Opto-electrokinetic manipulation technique for high-performance on-chip biological assay. Lab on Chip. 12(23):4955-4959. (Cover article & top 10 in LOC citations; Featured in Nature Photonics).
  128. Ravindranath, S., Kadam, U., and Irudayaraj, J. 2012. Intracellularly grown gold nano islands as SERS substrates for monitoring chromate, sulfate and nitrate localization sites in remediating bacteria biofilms by Raman chemical imaging. Analytica Chimica Acta. 745:1-9. (Cover article).
  129. Stephen, K., Nakatsu, C., and Irudayaraj, J. 2012. Surface Enhanced Raman Spectroscopy (SERS) for the discrimination of Arthrobacter strains based on variations in cell surface composition. Analyst. 137: 4280-4286.
  130. Dong, C. and Irudayaraj, J. 2012. Hydrodynamic Size-Dependent Cellular Uptake of Aqueous QDs Probed by Fluorescence Correlation Spectroscopy. J. Physical Chem. C. 116(40):12125-32.
  131. Chen, J., Miller, A., Kirchmaier, A., and Irudayaraj, J. 2012. Single Molecule Tools Elucidate H2A.Z Nucleosome Composition. J. Cell Science. 125(12):2954-2964.
  132. Wang, Y., Book, B., and Irudayaraj, J. 2012. Folic acid protected doxorubicin coated silver nanocarriers for targeted drug delivery. J. Biomedical Nanotechnology. 8(5):751-759.
  133. Book, B., Wang, Y., and Irudayaraj, J. 2012. Multifunctional gold nanorods for targeted drug delivery using 2-photon excitation. Euro Journal of Medicinal Chemistry. 48:330-337.
  134. Mura, S., Greppi, G., Marongiu, M., Roggero, P., Ravindranath, S., Mauer, L., Schibeci, N.,Perria, N., Piccinini, M., Innocenzi, P., and Irudayaraj, J. 2012. FTIR nanobiosensors for Escherichia coli detection. 2012. Beilstein J. Nanotechnology. 3:885-92.
  135. Wang, Y., Chen, J., and Irudayaraj, J. 2011. Nuclear targeting dynamics of gold nano clusters for enhanced therapy of HER2+ breast cancer. ACS NANO. 5(12):9718-9725.
  136. Guo, C., Book, B., and Irudayaraj, J. 2011. Protein-directed reduction of Graphene oxide and intracellular imaging. Chemical Communications. 47(47):12658-12660.
  137. Panchapakesan, B., Book, B., Seth, R., and Irudayaraj, J. 2011. Gold nano probes for theragnostics and diagnostics. Journal of Nanomedicine, 6(10):1-7.
  138. Lee, K., Drachev, V., and Irudayaraj, J. 2011. DNA-Gold nanoparticle networks grown at cell surface marker sites: Diagnostics of cancer stem cells. ACS NANO. 5(3):2109-2117.
  139. Wang, Y. and Irudayaraj, J. 2011. A SERS DNAzyme biosensor for lead ion detection. Chemical Communications. 47:4394-4396.
  140. Chen, J., Nag, S., and Irudayaraj, J. 2011. Single molecule in vivo analysis of Toll-like 9 and CpG DNA interaction. PLoS ONE. 6(4):e17991 (8 pages).
  141. Ravindranath, S., Henne, T., Thompson, D., and Irudayaraj, J. 2011. Intracellular bioreduction of Chromate-decorated Gold nanoparticles by Shewanella oneidensis MR-1 by Raman chemical imaging. ACS NANO. 5(6):4729-36.
  142. Guo, C. and Irudayaraj, J. 2011. Fluorescent Ag clusters via a Protein-directed approach as a Hg(II) ion sensor. Analytical Chemistry. 83(8):2883-9.
  143. Ravindranath, S., Wang, Y., and Irudayaraj, J. 2011. SERS driven Cross-platform based multiplex pathogen detection. Sensors & Actuators: B. Chemical. 152: 183-190.
  144. Ravindranath, S., Henne, K., Thompson, D., and Irudayaraj, J. 2011. Surface-enhanced Raman Imaging of Intracellular Bioreduction of Chromate in Shewanella oneidensis. PLoS ONE. 6(2): e16634 (10 pages).
  145. Mura, S., Corrias, F., Stara, G., Piccinini, M., Secchi, N., Marongiu, D., Innocenzi., P., Irudayaraj, J., and Greppi, G. 2011. Innovative composite films of chitosan, methylcellulose and nanoparticles.Nanoscale Food Sci., Engineering & Technology. J. Food Science. 76(7):N54-N60.
  146. Wang, Y., Ravindranath, S., and Irudayaraj, J. 2010. Separation and detection of multiple pathogens in a food matrix by SERS nano probes. Anal. & BioAnal. Chemistry. 399 (3):1271-8.
  147. Rout, C., Kumar, A., Xiong, G., Irudayaraj, J., and Fisher, T. 2010. Au nanoparticles on graphitic petal arrays for surface-enhanced Raman spectroscopy. Applied Physics Letters. 97(13):133108-133108-3.
  148. Book, B., Chen, J., and Irudayaraj, J. 2010. Quantification of receptor targeting aptamer binding characteristics using single-molecule spectroscopy. Biotechnology and Bioengineering (Online DOI: 10.1002/bit.23043). 108 (5):1222-1227.
  149. Wang, Y., Seebald, J., Szeto, D., and Irudayaraj, J. 2010. Biocompatibility and biodistribution of surface-enhanced Raman scattering nanoprobes in zebrafish embryos in vivo and multiplex imaging. ACS NANO. 4(7):4039-53.
  150. Chen, J. and Irudayaraj, J. 2010. Fluorescence lifetime cross correlation spectroscopy resolves EGFR and antagonist interaction in live cells. Analytical Chemistry. 82(15):6415-21.
  151. Wang, Y., Lee, K., and Irudayaraj, J. 2010. Silver nanosphere SERS probes for sensitive identification of pathogens. J. Physical Chemistry C. 114(39): 16122-16128.
  152. Miller, A., Takasuka, T., Chen, J., Kaufman, P., Jacobi, J., Irudayaraj, J., and Kirchmaier, A. 2010. PCNA Is Required for Cell-Cycle Regulated Silent Chromatin on Replicated and Nonreplicated Genes. J. Biological Chemistry. 285(45):35142-54.
  153. Nag, S., Chen, J., Maiti, S., and Irudayaraj, J. 2010. Measurement of the attachment and assembly of small amyloid-beta oligomers on live cell membranes at physiological conditions using single molecule tools. Biophysical Journal. 99(6):1969-75.
  154. Wang, Y., Lee, K., and Irudayaraj, J. 2010. SERS aptasensor from nanorod-nanopaticle junction for protein detection. Chem. Communications. 46(4):613-615.
  155. Krishnamurthy, K., Tewari, J., Irudayaraj, J., and Demirci, A. 2010. Microscopic and Spectroscopic Analysis of Inactivation of Staphylococcus aureus by Pulsed UV-Light and Infrared Heating. Food and Bioprocess Engineering: An International J. 3:93-104.
  156. Davis, R., Irudayaraj, J., Reuhs, B., and Mauer, L. 2010. Detection of E. coli O157:H7 from ground beef using FTIR spectroscopy and Chemometrics. J. Food Science, 75(6):M340-M346.
  157. Davis, R., Burgula, Y., Deering, A., Irudayaraj, J., Reuhs, B., and Mauer, L. 2010. Detection and differentiation of live and heat-treated Salmonella enterica serovars inoculated onto chicken breast using FTIR spectroscopy. J. Applied Microbiology. 109(6):2019-2031.
  158. Chen, J. and Irudayaraj, J. 2009. Quantitative investigation of compartmentalized dynamics of ErbB2 targeting gold nanorods in live cells by single molecule spectroscopy. ACS NANO. 3:4071-4079. (Featured in NIH-NCI Nanotechnology alliance, January News and Science Daily).
  159. Wang, C. and Irudayaraj, J. 2009. Multifunctional magnetic-Optical nanoparticle probes for simultaneous detection, separation, and ablation of multiple pathogens. Small. 2(6):283-289.
  160. Kumar, V. and Irudayaraj, J. 2009. SERS in salt wells. Chemphyschem. 10(15):2670-2673.
  161. Sun, L. and Irudayaraj, J. 2009. PCR-free quantification of splice variants in Cancer Gene using Surface Enhanced Raman Spectroscopy. J. Phys. Chem. 113:5980-5983.
  162. Sun, L. and Irudayaraj, J. 2009. Quantitative Surface Enhanced Raman for gene expression estimation, Biophysical Journal. 96:4609-16.
  163. Wang, C., Chen, J. Talavange, T. and Irudayaraj, J. 2009. Gold nanorod/Fe3O4 nanoparticle “Nano-Pearl-Necklaces” for simultaneous targeting, dual-mode imaging, and photothermal ablation of cancer cells. Angewandte Chemie, 121(15):2797-2801.
  164. Chen, J., Wang, C., and Irudayaraj, J. 2009. Ultrasensitive on-step immunoassay in blood serum using gold nanoparticle probes by single molecule spectroscopy. Biomedical Optics Letters, 14(4). 040501.
  165. Lee, K. and Irudayaraj, J. 2009. Periodic and dynamic 3-D gold nanoparticle-DNA network structures for surface-enhanced raman spectroscopy-based quantification. J. Phys. Chem. C. 113:5980-5983.
  166. Ravindranath, S., Mauer, L., Chitrita, D., and Irudayaraj, J. 2009. Biofunctionalized magnetic nanoparticle integrated mid-infrared pathogen sensors for food matrices. Analytical Chemistry, 81(8):2840-2846.
  167. Vidi, P., Chen, J., Irudayaraj, J. and Watts, V. 2008. Higher-order Adenosine A-2A receptor oligomers revealed by BiFC-FRET and FLIM. FEBS Letters, 582(29):3985-3990.
  168. Yu, C., Jacob, R., Ritchie, K., Prasad, N., and Irudayaraj, J. 2008. Receptor Overexpression or Inhibition Alters Cell Surface Dynamics of EGF-EGFR interaction: New Insights from Real-time Single Molecule Analysis. Biochemical and Biophysical Res. Communication, 378(3):376-382.
  169. Bakker, R., Yuan, H., Liu, Z., Pedersen, R., Boltasseva, A., Chen, J., Irudayaraj, J., Kildishev, A., Drachev, V., and Shalaev, V. 2008. Nanoantenna induced fluorescence enhancement: dipolar coupling and reduced lifetimes. New Journal of Physics, 10:125022.
  170. Sun, L., Yu, C. and Irudayaraj, J. 2008. Raman multiplexers for alternative gene splicing. Analytical Chemistry. 80(9):3342-9.
  171. Wang, C. and Irudayaraj, J. 2008. Gold nanorod probes detect multiple pathogens. Small. 4(12):2204-2208.
  172. Shamsaie, A., Heim, J. and Irudayaraj, J. 2008. Quantification of MBA in living cell by surface enhanced raman spectroscopy. Chemical Physics Letters, 461:131-135.
  173. Varghese, L., Sinha, R., and Irudayaraj, J. 2008. Single molecule kinetic investigations of protein association and dissociation using fluorescence cross-correlation spectroscopy. Analytica Chimica Acta. 625(1):103-109.
  174. Sarkar, T. and Irudayaraj, J. 2008. Carboxyl coated magnetic nanoparticles for mRNA isolation and extraction of supercoiled plasmid DNA. Analytical Biochemistry. 379:130-132.
  175. Sun, L., Yu, C., and Irudayaraj, J. 2007. Surface enhanced Raman scattering based nonfluorescent probes for multiplex detection. Analytical Chemistry, 79(11):3981-3988. (Featured article “No-glow tags for Raman Spectroscopy” in June 1, 2007 issue).
  176. Shamsaie, A., Irudayaraj, J. 2007. Intracellularly Grown Gold Nanoparticles (IGAuN) as Potential SERS Probes. Biomedical Optics. 12(2):020502-1-3. (Most frequently downloaded paper on the SPIE digital library, 2008).
  177. Mizrach, A., Schmilovitch, Z., Korotic, R., Irudayaraj, J., and Shapira, R. 2007. Yeast detection in apple juice using Raman spectroscopy. Transactions of ASABE 50(6):1-8. (Superior paper Award, ASABE 2008 International meeting).
  178. Yu, C., Naksharti, H., and Irudayaraj, J. 2007. Identity profiling of cell surface markers by multiplex gold nanorod probes. Nano Letters, 7(8): 2300-2306.
  179. Yu, C., and Irudayaraj, J. 2007. A multiplex biosensor using gold nanorods. Analytical Chemistry. 79(2): 572-579. (2nd most cited in Analytical Chemistry in 2007 and 5th Most cited as of 3/08).
  180. Yu, C. and Irudayaraj, J. 2007. Sensitivity and Selectivity limits of multiplex nanoSPR biosensor assays. Biophysical Journal. 93:3684-3692.
  181. Yu, C., Varghese, L., and Irudayaraj, J. 2007. Surface modification of CTAB capped gold nanorods to make molecular probes. Langmuir, 23: 9114-9119.
  182. Kouassi, G., Wang, P., Sreevatsan, S., Irudayaraj, J. 2007. Detection of prion protein on streptavidin-aptamer mediated magnetic and gold-coated magnetic nanoparticles. Biotech Progress 23(5):1239-44.
  183. Yu, C., Gestl, E., Eckert, K., Allara, D., Irudayaraj, J. 2006. Characterization of Human Breast Epithelial Cells by Confocal Raman Microspectrometry. J. Cancer Diagnosis and Prevention, 30(6):1-10.
  184. Beullens, K., Kirsanov, D., Irudayaraj, J., Rudnitskaya, A., Legin, A., Nicolai, B., and Lammertyn, J. 2006. The electronic tongue and ATR-FTIR for rapid detection of sugars and acids in tomatoes. Sensors and Actuators, B: Chemical, v 116, n 1-2, Jul 28, 2006, p 107-115.
  185. Gupta, M., Irudayaraj, J., Schmilovitch, Z., and Mizrach, A. 2006. Quantification of foodborne pathogens in different food matrices using FTIR and artificial neural networks. Trans of ASABE 49(5):1249-1256.
  186. Kouassi, G. and Irudayaraj, J. 2006. Magnetic and gold-coated magnetic particles as a DNA sensor. Analytical Chemistry. 78(10):3234-3241. (Top 10 most accessed article in 2006 in Analytical Chemistry (ranked 6th in the list); Ranked in the Top 100 (11th in the list) of Nanomedicine publications for 2006 by Ion Channel media group).
  187. Kouassi, G. and Irudayaraj, J. 2006. A nanoparticle-based immobilization assay for prion-kinetics assay. Journal of Nanobiotechnology. 48(8):1-10..
  188. Kizil, R. and Irudayaraj, J. 2006. Discrimination of irradiated starch gels using FT-Raman spectroscopy and chemometrics. J. Agric. and Food Chemistry, 54(1):13-18. (Most accessed article in 01/06-03/06).
  189. Yu, C. and Irudayaraj, J. 2006. Detection and identification of pathogenic microorganisms in mixed cultures by FTIR spectroscopy. Trans of ASABE, 49(5):1623-1632. (Honorary mention in the best paper competition at the 2007 ASABE meeting).
  190. Waswa, J., Debroy, C., and Irudayaraj, J. 2006. Rapid detection of Salmonella enteritidis and  Escherichia coli using the BiacoreTM Surface Plasmon Resonance biosensor. J. Food Process Engineering, 29: 373-385.
  191. Waswa, J., Debroy, C., and Irudayaraj, J. 2006. Rapid detection of Salmonella enteritidis and Escherichia coli using the BiacoreTM Surface Plasmon Resonance biosensor. J. Food Process Engineering, 29: 373-385.
  192. Yu, C., Ganjoo, A., Jain, H., Pantano, C., and Irudayaraj, J. 2005. Towards a mid-IR biosensor:  Detection and fingerprinting of pathogens on chalcogenide films. Anal. Chem. 78(8):2500-2506.
  193. Ganjoo, A., Jain, H., Song, R., Yu, C., Ryan, J., Irudayaraj, J., Ding, Y., and Pantano, C. 2005. Chalcogenide Glass Waveguides for IR Evanescent Wave Sensors. J. Noncrystalline Solids 352:584-588.
  194. Swaminathan, A., Irudayaraj, J., and Ryan, T. 2004. Comparison of mono and dithiol surfaces on surface plasmon resonance biosensors for detection of Staphylococcus aureus. Sensors and Actuators B, 114:192-198.
  195. Schmilovitch, Z., Mizrach, A., Kritzman, G., Korotic, R., Irudayaraj, J., and Debroy, C. 2005. Detection of bacteria with low resolution raman spectroscopy. Trans of ASAE. 48(5):1843-50.
  196. Vaseashta, A. and Irudayaraj, J. 2005. Nanostructured and nanoscale devices and sensors. Journal of Optoelectronics and Advanced Materials. 7(1):35-42.
  197. Kouassi, G., Irudayaraj, J., and McCarty, G. 2005. Examination of Cholesterol oxidase attachment to magnetic nanoparticles. J. Nanobiotechnology. (3)1:1-9. (3rd most accessed article (all time) in J. Biomagnetic Research and Tech – download access hit of 13,234).
  198. Kouassi, G., Irudayaraj, J., and McCarty, G. 2005. Activity of glucose oxidase functionalized onto iron nanoparticles. J. Biomagnetism and Technology. 3:1.
  199. Swaminathan, A., Irudayaraj, J., and Ryan, T. 2005. Self-assembled monolayer-based surface plasmon immunosensor for detection of E. coli O157:H7. Biosensors and Bioelec. 21(7):998-06.
  200. Yu, C. and Irudayaraj, J. 2005. Spectroscopic characterization of microorganisms by FTIR microspectroscopy. J. Biopolymers. 77(6):368-377.
  201. Lammertyn, J., Verboven, P., Veraverbeke, E., Vermeir, S., Irudayaraj, J., and Nicolai, B. 2005. Analysis of fluid flow and reaction kinetics in a flow injection analysis biosensor. Sensors and Actuators B. 114(2):728-736.
  202. Davis, R., Irudayaraj, J., Reuhs, B., and Mauer, L. 2010. Detection of E. coli O157:H7 from ground beef using FTIR spectroscopy and Chemometrics. J. Food Science, 75(6):M340-M346.
  203. Davis, R., Burgula, Y., Deering, A., Irudayaraj, J., Reuhs, B., and Mauer, L. 2010. Detection and differentiation of live and heat-treated Salmonella enterica serovars inoculated onto chicken breast using FTIR spectroscopy. J. Applied Microbiology. 109(6):2019-2031.
  204. Kathiravan, K., Tewari, J., Demirci, A., and Irudayaraj, J. 2010. Microscopic and Spectroscopic Evaluation of Inactivation of Staphylococcus aureus by Pulsed UV Light and Infrared Heating. Food and Bioprocess Tech. 3(1):93-104.
  205. Rudnitskaya, A., Kirsanov, D., Legin, A., Beullens, K., Lammertyn, J., Nicolai, B., and Irudayaraj, J. 2006. Analysis of apples varieties – comparison of electronic tongue with different analytical techniques. Sensors and Actuators, B: Chemical, v 116, n 1-2, Jul 28, 2006, p 23-28.
  206. Krishnamurthy, K., Demirci, A., and Irudayaraj, J. 2007. Inactivation of Staphylococcus aureus in Milk Using Flow-through Pulsed UV-Light Treatment System. Journal of Food Science. 72(7):M233-M239.
  207. Kizil, R. and Irudayaraj, J. 2007. Rapid evaluation and discrimination of γ-irradiated carbohydrates using FT-Raman spectroscopy and canonical discriminant analysis. J. Science of Food and Agriculture, 87(7):1244-1251.
  208. Gupta, M., Irudayaraj, J., Debroy, C., Schmilovitch, Z., and Mizrach, A. 2005. Detection and Differentiation of Food Pathogens using FTIR and Artificial Neural Networks. Trans. of ASAE. 48(5):1889-1892.
  209. Tewari, J. and Irudayaraj, J. 2005. Floral classification of honey using mid-infrared spectroscopy and surface acoustic wave based z-nose sensor. J. Agric. and Food Chem. 53(18):6955-6966.
  210. Dixit, V., Tewari, J., and Irudayaraj, J. 2005. Quantitative and qualitative identification of industrial grade glycerol adulteration in selected commercial red wine using mid-infrared spectroscopy. Applied Spectroscopy. 59(12):1553-1561.
  211. Yang, H., Irudayaraj, J., and Paradkar, M. 2005. Characterization of different edible oils and fats by FTIR, FT-NIR and FT-Raman Spectroscopy. Food Chemistry. 93(1):25-32.
  212. Veraverbeke, E., Lammertyn, J., Nicolaï, B., and Irudayaraj, J. 2005. Spectroscopic evaluation of the surface quality of apple. Journal of Agriculture and Food Chemistry. 53(4): 1046-1051.
  213. Gao, X., Heinemann, P., and Irudayaraj. J. 2005. Non-destructive Apple Bruise Detection with Raman Spectroscopy and its Virtual Instrumental System. Transactions of the Chinese Society of Agricultural Engineering. 21(3):130-133.
  214. Beullens, K., Irudayaraj, J., Nicolai, B., Kirsanov, D., Legin, A., and Lammertyn, J. 2004. Novel techniques for fast taste profiling of tomatoes. Communications in Agriculture Applied Biological Sciences. 69(2): 57-60.
  215. Jun, S. and Irudayaraj, J. 2004. An integrated dynamic model for fungal spore inactivation by selective infrared heating. Transactions of the ASAE. 20(4):481-485.
  216. Sivakesava, S., Irudayaraj, J., and Debroy, C. 2004. Differentiation of microorganisms by FTIR-ATR and FT-NIR spectroscopy. Transactions of the ASAE. 7(3):951-957. (Superior paper award, 2005, ASABE meeting).
  217. Veraverbeke, E., Irudayaraj, J., and Lammertyn, J. 2004. Fast aroma profiling with zNose™: case study on honey adulteration. J. Science of Food and Agriculture. 85:243-250.
  218. Tewari, J. and Irudayaraj, J. 2004. Quantification of saccharides in multiple floral honeys using fourier transform infrared micro-attenuated spectroscopy. Journal of Agriculture and Food Chemistry. 52:3237-3243.
  219. Innawong, B., Mallikarjunan, P., Irudayaraj, J., and Marcy, J.E. 2004. The determination of frying oil quality using Fourier transform infrared attenuated total reflectance. Lebensmittel-Wissenschaft und-Technologie. 37(1): 23-28.
  220. Yang, H., Irudayaraj, J., Delegchoimbol, S., and Walsh, M. 2004. Rheological study of starch and dairy ingredient-based food system. Food Chemistry. 86:571-578.
  221. Ranjan, R., Irudayaraj, J., Reddy, J., and Mujumdar, A.S. 2004. Finite element simulation of stepwise drying of bananas. Journal of Numerical Heat Transfer. Part A. 45:1-16.
  222. Lammertyn, J., Veraverbeke, E., and Irudayaraj, J. 2004. Surface acoustic wave based zNose™ technology for rapid aroma profiling of honey. Sensors and Actuators, 98(1):54-62.
  223. Gupta, M., Irudayaraj, J., and Debroy, C. 2004. Spectroscopic quantification of bacteria using Artificial Neural Networks. Journal of Food Protection. 67(11):2550-2554.
  224. Jun, S. and Irudayaraj, J. 2004. An integrated dynamic model for fungal spore inactivation by selective infrared heating. Transactions of the ASAE. 20(4):481-485.
  225. Yu, C., Irudayaraj, J., Debroy, C., Schmilovich, Z. and Mizrach, A. 2004. Spectroscopic differentiation and quantification of microorganisms in apple juice, J. Food Science, 70: S221-6.
  226. Krishnamurthy, K., Demirci, A., and Irudayaraj, J. 2003. Inactivation of Staphylococcus aureus by pulsed UV-light sterilization. Journal of Food Protection, 67 (5): 1027-1030.
  227. Sivakesava, S., Bober, J., Irudayaraj, J., and Demirci, A. 2003. Spectroscopic determination of multiple components during nisin fermentation. CIGR Journal of Scientific Research and Development. Vol 4. Manuscript FP: 03 008 [ISSN 1682-1130].
  228. Yang, H. and Irudayaraj, J. 2003. Rapid detection of foodborne microorganisms on food surface using Fourier transform Raman spectroscopy. Journal of Molecular Structure. 646: 35-43.
  229. Jun, S., and Irudayaraj, J. 2003. A dynamic fungal inactivation approach using selective infrared heating. Transactions of the ASAE 46 (5): 1407-1412. (Best paper, 2004 ASABE meeting).
  230. Jun, S., Irudayaraj, J., Demirci, A., and Geiser, D. 2003. Pulsed UV-light Treatment of Corn meal for Inactivation of Aspergillus niger. Journal of Food Science Technology 38: 883-888.
  231. Tewari, J. and Irudayaraj, J. 2003. Simultaneous monitoring of organic acids and sugars in fresh and processed apple juice by FTIR-ATR spectroscopy. Applies Spectr. 57(12):1599-1604.
  232. Paradkar, M. and Irudayaraj, J. 2003. Discrimination and classification of adulterants in maple syrup with the use of infrared spectroscopic techniques. J. Science of Fd. and Agric. 83:714-21.
  233. Tewari, J., Mehrotra, R., and Irudayaraj, J. 2003. Direct NIR analysis of sugarcane clear juice using fiber optic transmittance probe. Journal NIR spectroscopy, 11(5):351-356.
  234. Tewari, J. and Irudayaraj, J. 2003. Rapid estimation of Pol content in sugarcane juice using FTIR-ATR Spectroscopy. International Journal of Sugar Tech. 5(3):143-148.
  235. Irudayaraj, J., Xu, F., and Tewari, J. 2003. Rapid determination of invert cane sugar adulteration in honey using FTIR spectroscopy and multivariate analysis. J. Food Science. 68 (7):2040-2045.
  236. Cho, B. and Irudayaraj, J. 2003. A non-contact ultrasound approach for mechanical property determination of cheese. Journal of Food Science. 68(7):2243-2247.
  237. Cho, B. and Irudayaraj, J. 2003. Foreign object and internal defect detection in food materials using Non-contact ultrasound imaging. J. Food Science. April 2003, 68(3): 967-974.
  238. Paradkar, M. and Irudayaraj, J. 2003. Discrimination and classification of adulterants in maple syrup with the use of infrared spectroscopic techniques. J. Science of Fd. and Agric. 83:714-721.
  239. Kizil, R., Irudayaraj, J., and Seetharaman, K. 2002. Characterization of irradiated starches by FT-Raman and FTIR spectroscopy. Journal of Agric Food Chem. 50(14):3912-8.
  240. Paradkar, M. and Irudayaraj, J. 2002. Determination of cholesterol in dairy products using infrared techniques: 1. FTIR spectroscopy. Inti. Journal of Dairy Technology. 55(3):127-132.
  241. Yang, H. and Irudayaraj, J. 2002. Rapid determination of vitamin C by NIR, MIR and FT-Raman techniques”, Journal of Pharmacy and Pharmacology. 54(9): 1247-1255.
  242. Paradkar, M. and Irudayaraj, J. 2002. Determination of cholesterol in dairy products by infrared techniques: 2. FT-NIR method. International Journal of Dairy Technology. 55(3):133-138.
  243. Jun, S. and Irudayaraj, J. 2002. Selective far infrared heating system design and evaluation (PART I). Drying Technology – An International Journal. 21(1): 51-67.
  244. Jun, S. and J. Irudayaraj. 2002. Selective far infrared heating system applications and analysis (PART II). Drying Technology – An International Journal. 21(1): 69-82.
  245. Ranjan, R., Irudayaraj, J. and Jun, S. 2002. Simulation of three-dimensional infrared drying using a set of three-coupled equations by the control volume method. Transactions of the ASAE. 45(5): 1661-1668.
  246. Rajendran, V. and Irudayaraj, J. 2002. Detection of glucose, galactose, and lactose in milk with a microdialysis-coupled flow injection amperometric biosensor. J.  Dairy Science 85:1357-1361.
  247. Sivakesava, S. and Irudayaraj, J. 2002. Classification of simple and complex sugar adulterants in honey by mid-infrared spectroscopy. International Journal of Food Science and Technology. 37:351-360.
  248. Cho, B. and Irudayaraj, J. 2002. Design and application of a non-contact air instability compensation ultrasound transducer using spatial impulse response. Transactions of the ASAE. 46(3):901-910.
  249. Paradkar, M., Sivakesava, S., and Irudayaraj, J. 2002. Comparison of FTIR, FT-Raman, and NIR spectroscopy in a maple syrup adulteration study. Journal of Food Science. 67(6): 2009-2015.
  250. Deshpande, S.D., Sokhansanj, S., and Irudayaraj J. 2002. Effect of moisture content and storage temperature on respiration of Alfalfa. Biosystems Engin. 82 (1):79-86.
  251. Paradkar, M. and Irudayaraj, J. 2002. Rapid estimation of caffeine content in soft drinks using FTIR spectroscopy. Food Chemistry. 78: 261-266.
  252. Paradkar, M. and Irudayaraj, J. 2002. A Rapid FTIR Spectroscopic method for estimation of caffeine in soft drinks and Total methylxanthines in tea and coffee. Journal of Food Science. 67(7): 2507-2511.
  253. Paradkar, M. and Irudayaraj, J. 2001. Discrimination and classification of beet and cane sugars and their inverts in maple syrup by FT-Raman. Applied Engineering in Agric. 18(3):379-383.
  254. Irudayaraj, J. and Sivakesava, S. 2001. Detection of adulteration in honey by discriminant analysis using FTIR spectroscopy. Transactions of the ASAE 44(3): 643-650.
  255. Cho, B. and Irudayaraj, J. 2001. Acoustic sensor fusion approach for rapid measurement of modulus and hardness of cheddar cheese. Applied Engineering in Agriculture. 17(6): 827-832.
  256. Paradkar, M., Irudayaraj, J., and Sivakesava, S. 2001. Discrimination and classification of beet and cane inverts in different floral honey by FT-Raman spectroscopy. Food Chem. 76:231-239.
  257. Sivakesava, S. and Irudayaraj, J. 2001. Prediction of inverted cane sugar adulteration of honey by FTIR spectroscopy. Journal of Food Science. 66(7): 972-978.
  258. Sivakesava, S., Irudayaraj, J., and Korach, R. 2001. Detection of adulteration in apple juice using FTIR spectroscopy and multivariate statistical methods. Applied Engineering in Agriculture. 17(6):815-820.
  259. Irudayaraj, J., Yang, H., and Sivakesava, S. 2001. Detection of microorganisms on food surface using Fourier transform photoacoustic spectroscopy. J. Molecular Structure. 606:181-188.
  260. Cho, B., Irudayaraj, J., and Bhardwaj, M. 2001. A non-contact ultrasound technique for predicting mechanical properties of cheddar Cheese. Trans. of the ASAE. 44(6): 1759-1762.
  261. Sivakesava, S. and Irudayaraj, J. 2001. Rapid detection of tetracycline in milk using mid infrared spectroscopy. Journal of Dairy Science. 85:487-493.
  262. Yang, H. and Irudayaraj, J. 2001. Characterization of edible coatings and microorganisms on produce surface using depth profile analysis. Applied Spectroscopy 55(5):310-329.
  263. Sivakesava, S. and Irudayaraj, J. 2001. Detection of inverted beet sugar adulteration of honey by FTIR spectroscopy. Journal of the Science of Food and Agric. 81:683-690.
  264. Sivakesava, S., Irudayaraj, J, and Demirci, A. 2001. Monitoring a bioprocess for ethanol production using FT-MIR and FT-Raman spectroscopy. Journal of Industrial Microbiology and Biotechnology 26(4):185-190,196.
  265. Sivakesava, S., Irudayaraj, J, and Demirci, A. 2001. Simultaneous determination of multiple components in lactic acid fermentation using Ft-MIR, NIR, and FT-Raman spectroscopic techniques. Process Biochemistry 37(4):371-378.
  266. Yang, H. and Irudayaraj, J. 2001. Characterization of beef and pork using Fourier transform infrared photoacoustic spectroscopy. Lebebsm.-Wiss. u-Technology 34(6):401-408.
  267. Sivakesava, S. and Irudayaraj, J. 2001. A rapid spectroscopic technique for determining honey adulteration with corn syrup. Journal of Food Sci. 66(6): 787-792.
  268. Yang, H. and Irudayaraj, J. 2001. Rapid determination of olive pomace oil adulteration in extra virgin oil using NIR, FTIR, and FT-Raman techniques. Journal of American Oil Chemists Society 78: 889-895.
  269. Cho, B. and Irudayaraj, J. 2001. Acoustic sensor fusion approach for rapid measurement of modulus and hardness of cheddar cheese. Applied Engineering in Agriculture. 17(6): 827-832.
  270. Irudayaraj, J., Sivakesava, S., Kammath, S., and Yang, H. 2001. Monitoring chemical changes in some foods using Fourier transform photoacoustic spectroscopy. Journal of Food Science 66(9):1416-1421.
  271. Ranjan, R., Irudayaraj, J., and Jun, S. 2001. Simulation of infrared drying process. Drying Technology. 20(2) 363-379.
  272. Ranjan, R., Irudayaraj, J, Mahaffy, J. 2001. Modeling simultaneous heat and mass transfer using the control volume method. Journal of Numerical Heat Transfer. Part B, 41:1-15.
  273. Ranjan, R., Irudayaraj, J., and Jun, S. 2001. Three-dimensional control volume approach to modeling heat and mass transfer in food materials. Transactions of the ASAE. 44(6): 1975-1982.
  274. Yang, H. and Irudayaraj, J. 2000. Depth profiling Fourier transform analysis of cheese package using generalized two-dimensional photoacoustic correlation spectroscopy. Transactions of the ASAE 43(4):153-961.
  275. Sivakesava, S. and Irudayaraj, J. 2000. Determination of sugars in aqueous mixture using mid-infrared spectroscopy. Applied Engineering in Agriculture 16(5):543-550.
  276. Yang, H. and Irudayaraj, J. 2000. Depth profiling of a heterogeneous food-packaging model using step-scan Fourier transform infrared photoacoustic spectroscopy. Journal of Food Engineering. 55: 25-33.
  277. Cho, Y. and Irudayaraj, J. 2000. Computerization of manufacturing processes and information technology in food industry. Food Science and Industry 33(1):13-19.
  278. Sivakesava, S. and Irudayaraj, J. 2000. Quality analysis of potato chips using photoacoustic FTIR spectroscopy. Journal of Food Science. 80(12):1805-1810.
  279. Irudayaraj, J. and Yang, H. 2000. Analysis of cheese using step-scan Fourier transform infrared photoacoustic spectroscopy. Applied Spectroscopy 54(4):595-600.
  280. Yang, H. and Irudayaraj, J. 1999. Characterization of semi-solid fats and edible oils using Fourier transform infrared photoacoustic spectroscopy. Journal of American Oil Chem. Soc. 77(3):292-295.
  281. Yang, H. and Irudayaraj, J. 1999. Estimation of particle size by FTIR DRIFT and PAS. Particulate Science and Technology an International Journal 17(4): 269-282.
  282. Bargale, P.C., Wulfsohn, D., Irudayaraj, J, Ford, R.J., and Sosulski, F.W. 1999. Modelling Oil Expression by Uniaxial Compression with Time-Varying Oilseed Properties. Journal of Agricultural Engineering Research 77(2):171-181.
  283. Irudayaraj, J. and Wu, Y. 1999. Numerical modeling of heat and mass transfer in starch systems. Transactions of the ASAE. Vol 42(2):449-455.
  284. Irudayaraj, J., Chen, M., and McMahon, D. 1999. Study of texture in cheddar cheese using Fourier transform spectroscopy. Canadian Agricultural Engineering Journal. 14(4): 253-258.
  285. Bargale, P.C., Ford, R.J., Wulfsohn, D., Irudayaraj, J, and Sosulski, F.W. 1999. Measurement of consolidation and permeability properties of extruded soy under mechanical pressing. Journal of Agricultural Engineering Research 74(2): 155-166.
  286. Bargale, P.C, Ford, R.J., Sosulski, F.W., Wulfsohn, D., and Irudayaraj, J. 1999. Mechanical oil expression from extruded soybean samples. J. American Oil Chemists Society, 76 (2):223-229.
  287. Chen, M. and Irudayaraj, J. 1998. A sampling technique for the analysis of cheese using FT-IR spectroscopy. Journal of Food Science. (63)1:96-99.
  288. Chen, M., Irudayaraj, J., and McMahon, D. 1998. Examination of full-fat and reduced-fat cheddar cheese during ripening using FTIR spectroscopy. J. Dairy Science. 81:2791-2797.
  289. Irudayaraj, J. and Wu, Y. 1998. Determination of heat and mass transfer properties in starch based systems. Journal of Food Science 64(2):323-327.
  290. Ghazanfari, A., Wulfsohn, D. and Irudayaraj, J. 1998. Machine vision grading of Pistachio nuts using gray-level histograms. Canadian Journal of Agricultural Engineering. (40)1:61-66.
  291. Ghazanfari, A. and Irudayaraj, J. 1997. A Fourier descriptor approach for grading Pistachio nuts. Journal of Agricultural Engineering Research. (68): 247-252.
  292. Ghazanfari, A., Kusalik. T., and Irudayaraj, J. 1997. A multi-structure neural network approach for classification. International Journal of Neural Systems. (1):55-61.
  293. Irudayaraj, J. and Wu, Y. 1996. Analysis and application of Luikov’s heat, mass, and pressure transfer model to a capillary porous media. Drying Technology. Vol 14(3&4):803-824.
  294. Wu, Y. and Irudayaraj, J. 1996. Application of simultaneous heat, mass, and pressure equations to timber drying. Numerical Heat Transfer, Part A: Applns. 30(3):233-247.
  295. Ghazanfari, A., Irudayaraj, J., and Kusalik, T. 1996. Grading pistachio nuts using a neural network approach. Transactions of the ASAE. 39(6):2319-2324.
  296. Ghazanfari, A. and Irudayaraj, J. 1996. Two-dimensional image classification using string matching. Transactions of the ASAE. 39 (3):1197-1202.
  297. Wu, Y. and Irudayaraj, J. 1996. Heat, mass and pressure transfer studies in starch based food system. Journal of Food Process Engineering. 29:399-414.
  298. Irudayaraj, J. and Wu, Y. 1995. Effect of pressure on moisture transfer during moisture adsorption in barley during steeping. Drying Technology. 13(1&2):1603-1617.
  299. Liu, Q. and Irudayaraj, J. 1995. Finite element solution of a moving boundary value problem. Drying Technology. 13(1&2):99-123.
  300. Bargale, P.C. and Irudayaraj, J. 1995. Mechanical strength and rheological properties of barley. International Journal of Food Science and Technology. (30)5:609-623.
  301. Bargale, P.C., Irudayaraj, J., and Marquis, B. 1995. Studies on rheological behaviour of wheat and canola. Journal of Agricultural Engineering Research. (61):267-274.
  302. Irudayaraj, J. and Wu, Y. 1994. Finite element analysis of coupled heat, mass, and pressure transfer in porous materials. International Journal of Numerical Heat Transfer. 26(3):337-350.
  303. Bargale, P.C., Irudayaraj, J., and Marquis, B. 1994. Some mechanical properties and stress relaxation characteristics of lentils. Canadian Journal of Agricultural Engin. 36(4):247-254.
  304. Irudayaraj, J. and Haghighi, K. 1993. Stress analysis of viscoelastic materials during drying: I – Theory and finite element formulation. Drying Tech.: An Intl. Journal. 11(5):901-927.
  305. Irudayaraj, J., Haghighi, K. and Stroshine, R.L. 1993. Stress analysis of viscoelastic materials during drying: II – Application to grain kernels. Drying Technology. 11(5):929-959.
  306. Fasina, O., Irudayaraj, J. and Sokhansanj, S. 1993. Three dimensional finite element analysis of moisture sorption process in expanding alfalfa cubes. Journal of Agricultural Engineering Research. (56):337-352.
  307. Irudayaraj, J., Haghighi, K. and Stroshine, R.L. 1992. Finite element analysis of drying with application to cereal grains. Journal of Agric. Engineering Research. (53):1-21.
  308. Irudayaraj, J., Haghighi, K. and Stroshine, R.L. 1990. Nonlinear finite element analysis of coupled heat and mass transfer problems. Drying Technology. 8 (4):731-749.
  309. Haghighi, K., Irudayaraj, J., Stroshine, R.L. and Sokhansanj, S. 1990. Grain kernel drying simulation using the finite element method. Transactions of the ASAE 33(6):1957-1965.
  310. Wu, I‑P. and J. Irudayaraj. 1989. Sample size determination for evaluating drip irrigation systems. Transactions of ASAE 32(6):1961‑1965.