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    2019
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    Author

    Joseph Maria Kumar Irudayaraj
2019
Fluorescence microscopy
Fluorescence Microscopy
Epigenomics
Molecules
Gene expression
2017

Multiplex single-cell quantification of rare RNA transcripts from protoplasts in a model plant system

Kadam, U. S., Schulz, B. & Irudayaraj, J. M. K., Jun 2017, In : Plant Journal. 90, 6, p. 1187-1195 9 p.

Research output: Contribution to journalArticle

Protoplasts
messenger RNA
Gold
Raman spectroscopy
gold
2015

Rapid and unbiased extraction of chromatin associated RNAs from purified native chromatin

Zhou, Z., Yang, Y., Konieczny, S. F. & Irudayaraj, J. M. K., Dec 24 2015, In : Journal of Chromatography A. 1426, p. 64-68 5 p.

Research output: Contribution to journalArticle

Small Nuclear RNA
Salicylic Acid
Nanoparticles
Chromatin
Cell Separation
2016

Kinase phosphorylation monitoring with i-motif DNA cross-linked SERS probes

Ren, W., Damayanti, N. P., Wang, X. & Irudayaraj, J. M. K., Jan 7 2016, In : Chemical Communications. 52, 2, p. 410-413 4 p.

Research output: Contribution to journalArticle

Phosphorylation
DNA
Phosphotransferases
Monitoring
Biosensors
2018

An ultrasensitive aptasensor based on fluorescent resonant energy transfer and exonuclease-assisted target recycling for patulin detection

Wu, Z., Xu, E., Jin, Z. & Irudayaraj, J. M. K., May 30 2018, In : Food Chemistry. 249, p. 136-142 7 p.

Research output: Contribution to journalArticle

Patulin
patulin
Exonucleases
Energy Transfer
Recycling
2017

Single molecule Raman spectroscopic assay to detect transgene from GM plants

Kadam, U. S., Chavhan, R. L., Schulz, B. & Irudayaraj, J., Sep 1 2017, In : Analytical Biochemistry. 532, p. 60-63 4 p.

Research output: Contribution to journalArticle

Transgenes
Amplification
Raman spectroscopy
Assays
Contamination
2018

Exploring the anti-quorum sensing activity of a d-limonene nanoemulsion for Escherichia coli O157:H7

Wang, R., Vega, P., Xu, Y., Chen, C. Y. & Irudayaraj, J., Jul 2018, In : Journal of Biomedical Materials Research - Part A. 106, 7, p. 1979-1986 8 p.

Research output: Contribution to journalArticle

Escherichia coli
Genes
Emulsification
Biofilms
Cell growth
2016

A study of alterations in DNA epigenetic modifications (5mC and 5hmC) and gene expression influenced by simulated microgravity in human lymphoblastoid cells

Chowdhury, B., Seetharam, A., Wang, Z., Liu, Y., Lossie, A. C., Thimmapuram, J. & Irudayaraj, J., Jan 1 2016, In : PloS one. 11, 1, e0147514.

Research output: Contribution to journalArticle

microgravity
Weightlessness
Microgravity
Epigenomics
Gene expression
2017

Toxicological effects of trichloroethylene exposure on immune disorders

Ordaz, J. D., Damayanti, N. P. & Irudayaraj, J. M. K., Nov 2 2017, In : Immunopharmacology and Immunotoxicology. 39, 6, p. 305-317 13 p.

Research output: Contribution to journalReview article

Trichloroethylene
Immune System Diseases
Toxicology
Immune system
Immune System

Oxygen Nanobubble Tracking by Light Scattering in Single Cells and Tissues

Bhandari, P., Wang, X. & Irudayaraj, J. M. K., Mar 28 2017, In : ACS Nano. 11, 3, p. 2682-2688 7 p.

Research output: Contribution to journalArticle

Light scattering
light scattering
Tissue
Oxygen
oxygen
2016

Regulatory landscape and clinical implication of MBD3 in human malignant glioma

Cui, Y., Li, J., Weng, L., Wirbisky, S. E., Freeman, J. L., Liu, J., Liu, Q., Yuan, X. & Irudayaraj, J., Jan 1 2016, In : Oncotarget. 7, 49, p. 81698-81714 17 p.

Research output: Contribution to journalArticle

Glioma
Carrier Proteins
Untranslated RNA
Survival
human MBD3 protein

Superplastic Formation of Metal Nanostructure Arrays with Ultrafine Gaps

Hu, Y., Xuan, Y., Wang, X., Deng, B., Saei, M., Jin, S., Irudayaraj, J. & Cheng, G. J., Jan 1 2016, In : Advanced Materials. 28, 41, p. 9152-9162 11 p.

Research output: Contribution to journalArticle

Nanostructures
Metals
Lasers
Momentum transfer
Nanoparticles
2018
Graphene
Raman scattering
Membranes
Fabrication
Substrates
2017

Electron spin contrast of Purcell-enhanced nitrogen-vacancy ensembles in nanodiamonds

Bogdanov, S., Shalaginov, M. Y., Akimov, A., Lagutchev, A. S., Kapitanova, P., Liu, J., Woods, D., Ferrera, M., Belov, P., Irudayaraj, J., Boltasseva, A. & Shalaev, V. M., Jul 25 2017, In : Physical Review B. 96, 3, 035146.

Research output: Contribution to journalArticle

Nanodiamonds
electron spin
Vacancies
Nitrogen
nitrogen
2019

Correction to: Superplastic Formation of Metal Nanostructure Arrays with Ultrafine Gaps (Advanced Materials, (2016), 28, 41, (9152-9162), 10.1002/adma.201602497)

Hu, Y., Xuan, Y., Wang, X., Deng, B., Saei, M., Jin, S., Irudayaraj, J. & Cheng, G. J., Apr 5 2019, In : Advanced Materials. 31, 14, 1900190.

Research output: Contribution to journalComment/debate

Open Access
Nanostructures
Metals
Lasers
Nanoparticles
Ultrafine
2017

In vivo biodetection using surface-enhanced raman spectroscopy

Lee, S., Kadam, U. S., Craig, A. P. & Irudayaraj, J. M. K., Jan 1 2017, Biosensors Based on Nanomaterials and Nanodevices. Li, J. & Wu, N. (eds.). CRC Press, p. 157-178 22 p.

Research output: Chapter in Book/Report/Conference proceedingChapter

Raman Spectrum Analysis
Nanostructures
Raman spectroscopy
Electromagnetic Fields
Refractometry

Technical advances in global DNA methylation analysis in human cancers

Chowdhury, B., Cho, I. H. & Irudayaraj, J. M. K., Mar 1 2017, In : Journal of Biological Engineering. 11, 1, 10.

Research output: Contribution to journalReview article

DNA Methylation
5-Methylcytosine
Epigenomics
Neoplasms
Derivatives

A net fishing enrichment strategy for colorimetric detection of E. coli O157:H7

Ren, W., Liu, W. & Irudayaraj, J. M. K., Jan 1 2017, In : Sensors and Actuators, B: Chemical. 247, p. 923-929 7 p.

Research output: Contribution to journalArticle

fishing
Pathogens
Escherichia coli
pathogens
Nitrocellulose
2018

Alpha Lead Oxide (α-PbO): A New 2D Material with Visible Light Sensitivity

Kumar, P., Liu, J., Ranjan, P., Hu, Y., Yamijala, S. S. R. K. C., Pati, S. K., Irudayaraj, J. & Cheng, G. J., Mar 22 2018, In : Small. 14, 12, 1703346.

Research output: Contribution to journalArticle

Lead oxide
Photophobia
Photosensitivity
Optics and Photonics
Light
2019

Laser Shock Tuning Dynamic Interlayer Coupling in Graphene-Boron Nitride Moiré Superlattices

Kumar, P., Liu, J., Motlag, M., Tong, L., Hu, Y., Huang, X., Bandopadhyay, A., Pati, S. K., Ye, L., Irudayaraj, J. & Cheng, G. J., Jan 9 2019, In : Nano letters. 19, 1, p. 283-291 9 p.

Research output: Contribution to journalArticle

Graphite
Boron nitride
Superlattices
boron nitrides
Graphene
2017

Spin contrast of purcell-enhanced nitrogen-vacancy centers in diamonds

Bogdanov, S., Shalaginov, M. Y., Akimov, A. V., Lagutchev, A., Liu, J., Woods, D., Ferrera, M., Kapitanova, P., Belov, P., Irudayaraj, J. M. K., Boltasseva, A. & Shalaev, V. M., Jan 1 2017, CLEO: QELS_Fundamental Science, CLEO_QELS 2017. OSA - The Optical Society, (Optics InfoBase Conference Papers; vol. Part F42-CLEO_QELS 2017).

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Diamond
Vacancies
Diamonds
Nitrogen
Photonics

Hypoxia re-programming oxygen nanobubbles sensitize human glioblastoma cells to temozolomide via methylation alterations

Bhandari, P., Lei, O. & Irudayaraj, J., Oct 2017, In : Journal of Bionanoscience. 11, 5, p. 337-345 9 p.

Research output: Contribution to journalArticle

temozolomide
Methylation
Glioblastoma
Oxygen
Cell death
2015

A wireless chemical sensing scheme using ultrasonic imaging of microbubble embeded hydrogel

Park, J. H., Kim, A., Song, S. H., Bhandari, P., Irudayaraj, J. & Ziaie, B., Aug 5 2015, 2015 Transducers - 2015 18th International Conference on Solid-State Sensors, Actuators and Microsystems, TRANSDUCERS 2015. Institute of Electrical and Electronics Engineers Inc., p. 2220-2223 4 p. 7181402. (2015 Transducers - 2015 18th International Conference on Solid-State Sensors, Actuators and Microsystems, TRANSDUCERS 2015).

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Ultrasonic imaging
Hydrogels
ultrasonics
Acoustic intensity
biomarkers
2019

Bioinspired glycosaminoglycan hydrogels via click chemistry for 3D dynamic cell encapsulation

Kuang, L., Damayanti, N. P., Jiang, C., Fei, X., Liu, W., Narayanan, N., Irudayaraj, J., Campanella, O. & Deng, M., Feb 5 2019, In : Journal of Applied Polymer Science. 136, 5, 47212.

Research output: Contribution to journalArticle

Hydrogels
Hydrogel
Glycosaminoglycans
Encapsulation
Gelation
2015

Enhanced multi-photon emission from single NV center coupled to graphene by laser-shaping

Liu, J., Hu, Y., Kumar, P., Shalaginov, M. Y., Lagutchev, A. S., Shalaev, V. M., Cheng, G. J. & Irudayaraj, J. M. K., Aug 10 2015, 2015 Conference on Lasers and Electro-Optics, CLEO 2015. Institute of Electrical and Electronics Engineers Inc., 7183374. (Conference on Lasers and Electro-Optics Europe - Technical Digest; vol. 2015-August).

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Quantum optics
Graphite
quantum optics
Graphene
Light sources
2017

Optical microscopy and spectroscopy for epigenetic modifications in single living cells

Cui, Y. & Irudayaraj, J. M. K., Jan 1 2017, Methods in Pharmacology and Toxicology. Humana Press Inc., p. 135-154 20 p. (Methods in Pharmacology and Toxicology).

Research output: Chapter in Book/Report/Conference proceedingChapter

Epigenomics
Microscopy
Spectrum Analysis
Optical Imaging
Physiological Phenomena
2015

Decitabine nanoconjugate sensitizes human glioblastoma cells to temozolomide

Cui, Y., Naz, A., Thompson, D. H. & Irudayaraj, J., Apr 6 2015, In : Molecular Pharmaceutics. 12, 4, p. 1279-1288 10 p.

Research output: Contribution to journalArticle

temozolomide
decitabine
Nanoconjugates
Glioblastoma
Ethylene Glycol
2019

Prenatal and ancestral exposure to di(2-ethylhexyl) phthalate alters gene expression and DNA methylation in mouse ovaries

Rattan, S., Beers, H. K., Kannan, A., Ramakrishnan, A., Brehm, E., Bagchi, I. C., Irudayaraj, J. M. K. & Flaws, J. A., Sep 15 2019, In : Toxicology and Applied Pharmacology. 379, 114629.

Research output: Contribution to journalArticle

DNA Methylation
Gene expression
Ovary
Gene Expression
Cytosine
2017

Bimodal counterpropagating-responsive sensing material for the detection of histamine

Wu, Z., Xu, E., Jiao, A., Jin, Z. & Irudayaraj, J. M. K., Jan 1 2017, In : RSC Advances. 7, 71, p. 44933-44944 12 p.

Research output: Contribution to journalArticle

Histamine
Raman scattering
Polymers
Fluorescence
Food safety
2019

Epigenetic biomarker screening by FLIM-FRET for combination therapy in ER+ breast cancer

Liu, W., Cui, Y., Ren, W. & Irudayaraj, J., Jan 30 2019, In : Clinical epigenetics. 11, 1, 16.

Research output: Contribution to journalArticle

Optical Imaging
Energy Transfer
Epigenomics
Estrogen Receptors
Biomarkers
2016

CRISPR-dCas9 mediated TET1 targeting for selective DNA demethylation at BRCA1 promoter

Choudhury, S. R., Cui, Y., Lubecka, K., Stefanska, B. & Irudayaraj, J., Jan 1 2016, In : Oncotarget. 7, 29, p. 46545-46556 12 p.

Research output: Contribution to journalArticle

Clustered Regularly Interspaced Short Palindromic Repeats
Tumor Suppressor Genes
Epigenomics
DNA
Guide RNA
2018

Electrospun probiotics: An alternative for encapsulation

Akbar, Z., Zahoor, T., Huma, N., Jamil, A., Ayesha, H. & Irudayaraj, J. M. K., Nov 2018, In : Journal of Biological Regulators and Homeostatic Agents. 32, 6, p. 1551-1556 6 p.

Research output: Contribution to journalArticle

Probiotics
Nanofibers
Temperature
Alcohols
Streptococcus thermophilus
2019

Modulation of gene silencing by Cdc7p via H4 K16 acetylation and phosphorylation of chromatin assembly factor CAF-1 in saccharomyces cerevisiae

Young, T. J., Cui, Y., Irudayaraj, J. & Kirchmaier, A. L., Apr 2019, In : Genetics. 211, 4, p. 1219-1237 19 p.

Research output: Contribution to journalArticle

Chromatin Assembly Factor-1
Gene Silencing
Acetylation
Saccharomyces cerevisiae
Phosphorylation

Magnetic Focus Lateral Flow Sensor for Detection of Cervical Cancer Biomarkers

Ren, W., Mohammed, S. I., Wereley, S. & Irudayaraj, J. M. K., Feb 19 2019, In : Analytical chemistry. 91, 4, p. 2876-2884 9 p.

Research output: Contribution to journalArticle

Tumor Biomarkers
Sensors
Biomarkers
Proteins
Nanoprobes
2015

High performance immunochromatographic assay combined with surface enhanced Raman spectroscopy

Cho, I. H., Das, M., Bhandari, P. & Irudayaraj, J., Jul 5 2015, In : Sensors and Actuators, B: Chemical. 213, p. 209-214 6 p.

Research output: Contribution to journalArticle

Silver
Raman spectroscopy
Assays
Nanoparticles
silver

Single-Cell Quantification of Cytosine Modifications by Hyperspectral Dark-Field Imaging

Wang, X., Cui, Y. & Irudayaraj, J., Oct 27 2015, In : ACS Nano. 9, 12, p. 11924-11932 9 p.

Research output: Contribution to journalArticle

Nanoprobes
Cytosine
Imaging techniques
Surface plasmon resonance
cells
2019

The transition structure of chromatin fibers at the nanoscale probed by cryogenic electron tomography

Zhou, Z., Li, K., Yan, R., Yu, G., Gilpin, C. J., Jiang, W. & Irudayaraj, J. M. K., Aug 7 2019, In : Nanoscale. 11, 29, p. 13783-13789 7 p.

Research output: Contribution to journalArticle

Transcription
Cryogenics
Chromatin
Tomography
Electrons
2015

Inside single cells: Quantitative analysis with advanced optics and nanomaterials

Cui, Y. & Irudayaraj, J., May 1 2015, In : Wiley Interdisciplinary Reviews: Nanomedicine and Nanobiotechnology. 7, 3, p. 387-407 21 p.

Research output: Contribution to journalReview article

Single-Cell Analysis
Nanostructures
Nanostructured materials
Optics
Molecules

Enhancement of single-photon emission from nitrogen-vacancy centers with TiN/(Al,Sc)N hyperbolic metamaterial

Shalaginov, M. Y., Vorobyov, V. V., Liu, J., Ferrera, M., Akimov, A. V., Lagutchev, A., Smolyaninov, A. N., Klimov, V. V., Irudayaraj, J., Kildishev, A. V., Boltasseva, A. & Shalaev, V. M., Jan 1 2015, In : Laser and Photonics Reviews. 9, 1, p. 120-127 8 p.

Research output: Contribution to journalArticle

Titanium nitride
titanium nitrides
Metamaterials
Vacancies
CMOS
2016

Non-fluorescent quantification of single mRNA with transient absorption microscopy

Liu, J. & Irudayaraj, J. M. K., Dec 14 2016, In : Nanoscale. 8, 46, p. 19242-19248 7 p.

Research output: Contribution to journalArticle

Microscopic examination
Tissue
Messenger RNA
Molecules
Cells
2015
microbial detection
Immunochromatography
immunoaffinity chromatography
Pathogens
Gold
2016

Optical Clearing Delivers Ultrasensitive Hyperspectral Dark-Field Imaging for Single-Cell Evaluation

Cui, Y., Wang, X., Ren, W., Liu, J. & Irudayaraj, J., Mar 22 2016, In : ACS Nano. 10, 3, p. 3132-3143 12 p.

Research output: Contribution to journalArticle

clearing
Microscopic examination
microscopy
Imaging techniques
evaluation
2015

Single-cell screening and quantification of transcripts in cancer tissues by second-harmonic generation microscopy

Liu, J., Damayanti, N. P., Cho, I. H., Polar, Y., Badve, S. & Irudayaraj, J. M. K., Sep 1 2015, In : Journal of biomedical optics. 20, 9, 096016.

Research output: Contribution to journalArticle

Harmonic generation
harmonic generations
Microscopic examination
ribonucleic acids
Screening

Cross-platform detection of epigenetic modifications from extracted chromatin in leucocytes from blood

Zhou, Z., Cho, II. H., Shan, Z. & Irudayaraj, J., Jun 1 2015, In : Analytical Chemistry Research. 4, p. 39-44 6 p.

Research output: Contribution to journalArticle

Epigenomics
Histones
Chromatin
Leukocytes
Blood
2017

Real-Time Multiplex Kinase Phosphorylation Sensors in Living Cells

Damayanti, N. P., Buno, K., Cui, Y., Voytik-Harbin, S. L., Pili, R., Freeman, J. & Irudayaraj, J. M. K., Aug 25 2017, In : ACS Sensors. 2, 8, p. 1225-1230 6 p.

Research output: Contribution to journalArticle

phosphorylation
Phosphorylation
Phosphotransferases
Cells
sensors
2015

Nanoscale histone localization in live cells reveals reduced chromatin mobility in response to DNA damage

Liu, J., Vidi, P. A., Lelièvre, S. A. & Irudayaraj, J. M. K., Jan 1 2015, In : Journal of cell science. 128, 3, p. 599-604 6 p.

Research output: Contribution to journalArticle

Histones
DNA Damage
Chromatin
damages
DNA

Functionalized gold nanoparticles for the detection of nitrates in water

Mura, S., Greppi, G., Roggero, P. P., Musu, E., Pittalis, D., Carletti, A., Ghiglieri, G. & Irudayaraj, J. M. K., Jan 1 2015, In : International Journal of Environmental Science and Technology. 12, 3, p. 1021-1028 8 p.

Research output: Contribution to journalArticle

Gold
Nitrates
Nanoparticles
gold
nitrates
2017

An integrated microsystem with dielectrophoresis enrichment and impedance detection for detection of Escherichia coli

Wang, R., Xu, Y., Liu, H., Peng, J., Irudayaraj, J. M. K. & Cui, F., Jun 1 2017, In : Biomedical microdevices. 19, 2, 34.

Research output: Contribution to journalArticle

Escherichia coli O157
Microelectrodes
Microsystems
Electrophoresis
Electric Impedance
2015

Dissecting the behavior and function of MBD3 in DNA methylation homeostasis by single-molecule spectroscopy and microscopy

Cui, Y. & Irudayaraj, J., Jan 1 2015, In : Nucleic acids research. 43, 6, p. 3046-3055 10 p.

Research output: Contribution to journalArticle

DNA Methylation
Carrier Proteins
Homeostasis
DNA
Methyltransferases
2017

Comparative in vitro toxicity assessment of perfluorinated carboxylic acids

Mahapatra, C. T., Damayanti, N. P., Guffey, S. C., Serafin, J. S., Irudayaraj, J. M. K. & Sepúlveda, M. S., Jun 2017, In : Journal of Applied Toxicology. 37, 6, p. 699-708 10 p.

Research output: Contribution to journalArticle

perfluorooctanoic acid
Carboxylic Acids
Metabolism
Toxicity
Carbon