Dr. Joseph Irudayaraj

 

CURRICULUM VITAE

PERSONAL

Name. Joseph MK Irudayaraj

Address.
225 S. University Street, Purdue University, West Lafayette, IN 47907
Phone: 765-494-0388; Email: josephi@purdue.edu
Website: http://www.purdue.edu/dp/psf/joseph.php

EDUCATION

PhD Bioprocess Engineering , Purdue University

M.S. Biosystems Engineering , University of Hawaii

M.S. Computer Sciences , University of Hawaii

B.S. Agricultural Engineering , College of Agricultural Engineering, TNAU, India.

PROFESSIONAL APPOINTMENTS / DISTINCTIONS

DEPUTY DIRECTOR, Bindley Bioscience Center 2012-present

Responsibilities are to work with faculty on collaborative multidisciplinary projects by forming and participating in teams and proposal opportunities. Provide leadership in scientific directions, assist on operations of core facilities, space management, staff promotions, engagement and marketing. Create a venue for learning and professional development.

PROFESSOR, Biological Engineering 2009-present

Agricultural and Biological Engineering (ABE), University Faculty Scholar, Academic Leadership Fellow. Faculty at the Bindley Bioscience Center (BBC), the Birck Nanotechnology Center (BNC), and the Purdue Center for Cancer Research (PCCR). Purdue University, West Lafayette, IN

Develop and apply single molecule tools and nanoscale imaging platforms comprising of fluorescence, Raman, and plasmonics in live cell biomedical discoveries relating to epigenetics, phosphorylation, and biosecurity.

Co-leader for the PCCR's (Purdue Center for Cancer Research) Drug Discovery and Molecular Sensing Core (one of the four cores of PCCR). Lead multidisciplinary research grants in breast cancer, organize workshops and student research presentations, and seek opportunities for graduate training / center / program grants in cancer research.

Interdisciplinary collaborations : research to bridge the gap between biomedical sciences and nanotechnology and establishes a synergistic theme between the three centers (BBC, BNC, and PCCR) at Purdue. Collaborate with faculty from over ten departments.

Co-director , Physiological Sensing Facility (PSF) at BBC, a collaborative core which serves as an interdisciplinary resource to engage scientists and engineers in collaborative multidisciplinary research to develop advanced biosensor technologies. PSF is a testing facility where students and faculty collaborate to create solutions to real-world biological problems.

PROFESSOR, Mechanical Engineering, ME (Courtesy) 2013-present

My primary role is to bridge the gap in biosciences and technology development as well as to provide leadership in nanobiotechnology, one of the thrusts in the School of ME.

PROFESSOR, Basic Medical Sciences, BMS (Courtesy) 2012-present

Purdue's Basic Medical Sciences (BMS) is a multidisciplinary department with emphasis on addressing basic questions related to medical sciences through in vitro and in vivo models. My primary role is to provide venues for collaborative research in technology development in addition to fulfilling my responsibilities as an adjunct faculty.

PROFESSOR, Food Sciences, (Courtesy) 2006-present

Develop programs in food safety biosensors and instrumentation. Work with the Center for Food Safety Engineering to develop onsite biosensors.

GRADUATE CHAIR OF ABE 2009-2012

Oversee ~110 graduate students in a multidisciplinary program comprising of Biological Engineering, Food and Pharmaceutical Engineering, Machine Systems Engineering, and Natural Resources Engineering. ABE's graduate program is rated #1 (2009-2014) by US News and World Report

Co-PI, Center for Food Safety Engineering , USDA-Purdue University collaboration. Develop field deployable biosensors and portable Raman imaging and spectroscopic biosensors for onsite detection of foodborne pathogens.

ASSOCIATE PROFESSOR, Biological Engineering 2005-2009
Purdue University, West Lafayette, IN

Research focused on bionanotechnology with emphasis on nanomaterials as intracellular sensors and single molecule technologies to understand intracellular mechanisms related to cancer and neurodegenerative disorders. Senior Design project coordinator for ABE.

ASSOCIATE PROFESSOR, Applied and Engineering Physics 2004-2005
Cornell University, Ithaca, NY

One-year sabbatical in the Department of Applied and Engineering Physics. Developed collaborations with Dr. Harold Craighead's group in single molecule methods to study enzyme kinetics and microflluidic approaches to cell sorting.

ASSOCIATE PROFESSOR, Agricultural and Biological Engineering(ABE) 2004-2005
Faculty of Materials Research Institute, Pennsylvania State University, State College, PA

Developed Spectroscopic and Biosensor approaches to detect pathogens and analytes related to human health. Initiated university-wide biosensors program for multidisciplinary research. Co-led Engineering Research Center grants in Biospectroscopy.

ASSISTANT PROFESSOR, Agricultural and Biological Engineering 1998-2002
CO-DIRECTOR, Center for Food Manufacturing
Pennsylvania State University, State College, PA

Contributed to establishing a Biological Engineering program for teaching and research. Initiated a Biosensors program for detecting foodborne pathogens. Formed several international collaborative seed opportunities (China, India, Brazil, Korea, Italy, Spain) in spectroscopic research.

ADJUNCT FACULTY , Material Research Institute (MRI) 2000-2005
Pennsylvania State University. (Concurrently)

Developed bionanotechnology component and established a nanoscience laboratory for biology.
Establish collaboration with the Hershey Medical Center and other diagnostic campus centers.

Assistant Professor, Biological Engineering , Utah State University (USU). 1995 - 1998
Affiliate Faculty, USU's Biotechnology Center.
First faculty hired to initiate research and teaching program in Biological Engineering.

Developed a graduate curriculum in Biological Engineering. Research efforts were in instrumentation and sensor development to study protein interactions in biomaterials.

Assistant Professor, University of Saskatchewan, Saskatoon, Canada. 1991 - 1994

Created and taught four new undergraduate and two new graduate courses in Food Engineering, Systems Engineering, and Numerical Methods. Research: Design and development of bioprocesses with an emphasis on understanding the biomechanical effects of heat and mass transfer in food and biological materials.


HONORS, AWARDS AND KEY PROFESSIONAL/SERVICE CONTRIBUTIONS

  • Fellow, American Institute of Medical and Biological Engineers, 2014
  • Entrepreneurship Leadership Academy Fellow, Purdue University, 2012
  • Excellence in Research Award, Office of the Vice President for Research, 2012
  • Seed for Success Award, Office of Vice President for Research, 2012
  • Leadership Fellow (Committee on Inst. Cooperation-Academic Leadership Program), 2011
  • University Faculty Scholar Award, Purdue University, 2010
  • Award of Academic Excellence, Northeast Normal University, Changchun, China, 2009
  • Seed for Success Award, Purdue University, 2006
  • Bindley Bioscience Center, Executive Committee (2007-Present)
  • Bindley Bioscience Center Task Force and Strategic Planning Committee (2010)
  • College of Engineering, Strategic Advisor Committee to the Dean (2009-Present)
  • Organizing Committee, Symposium on Breast Cancer Prevention, Rennes, France, 2011
  • Chair, NIH Interdisciplinary Molecular Sciences and Training panel (2010-present)
  • Panel member, NIH College of College of Scientific Reviewers (2010-2012)
  • Advisory Council, MBA Program, Maxvalue (India's 1st online business school), 2009 - present
  • Program chair of Bionanotechnology, IBE (2003-2004)
  • USDA CSREES: Honor Award and Certificate, North East Multistate Research group, 2003
  • Young Engineer of the Year, Northeastern region of ASABE, 2000
  • Teacher of the Year award, Biological Engineering., Utah State University, 1997
  • Innovation in Teaching award, Biological Engineering., Utah State University, 1997
  • Best Paper awards
    o 2010 (ASME-IMECE Microfluidics 2010: Fluidics in Micro nanosystems)
    o 2008 (ASABE Superior paper award)
    o 2006 (ASABE Honorary mention)
    o 2004 (ASABE Superior paper award)
    o 2003 (ASABE Best paper Honorable mention)
    o Best Poster awards
    • 2007 (Sigma Xi, best student poster award, Purdue University)
    • 2002 (1st Prize, American Society for Microbiology poster competition)
    • 1993 (Best paper, R. J. Melosh medal awarded by Duke Univ.)
  • David Ross Fellowship, Purdue University
  • University Merit Scholarship, College of Agric. Engineering, TNAU, India

  • CURRENT ONGOING RESEARCH PROGRAMS

    Biomedical

    Title

    Collaborators

    Epigenetics - basic

    In vivo epigenetics tools development to detect and regulate chromatin modifications at specific loci in single cells.

    Irudayaraj, Lelievre (BMS), Kirchmaier (BCHM), Lossie (Animal Sciences)

    Epigenetics - basic

    Assess the effect of alcohol on DNA methylation in Neural Stem Cell Differentiation

    Irudayaraj, Zhou (Anatomy, IU School of Medicine)

    Epigenetics-cancer, basic

    Investigate the dynamics and role of hydroxymethylcytosine in stem cells (neural, embryonic, and glioblastoma)

    Toxicology tools development

    Translational tools development for toxicology with a focus on vasculogenesis

    Harbin, Sepulveda, Vlachos, Lee, Raymond, Savianno

    Epigenetics - cancer

    Effect of nutrition on epigenetic modifications and its role in gene expression in embryos

    (Karen Lillycrop, Univ. Southampton, UK)

    Phosphorylation - cancer

    Detection of phosphorylation in live cells using surface enhanced Raman spectroscopy (SERS) and lifetime imaging

    Irudayaraj and Parker (Medicinal Chemistry and Molecular Pharmacology, MCMP)

    Cardiovascular Toxicology-Translational tools

    Develop single molecule tools to assess the dynamic state of kinase and epigenetic regulation in cardiovascular toxicity

    Irudayaraj, Harbin, Sepulveda, Freeman

    Tunable delivery of nanodelivery systems

    Fabricate nanobubbles and optimize delivery conditions, assess engineering properties and in vivo potential in treating a variety of diseases for drug and oxygen delivery

    Irudayaraj, Ziaie, Goergen et al.

    Cancer

    In vivo detection of mRNA and microRNA in tissues by hyperspectral plasmon and second harmonic generation imaging

    Irudayaraj, Badve (Clarion IU School of Medicine) and Polar Yesim (IU School of Medicine)

    Environmental

    Title

    Collaborators

    Bioremediation

    Mapping chromate/arsenate reduction sites in single bacterium by SERS

    Irudayaraj, Nakatsu (AGRY), and Thompson (Biological Sciences, University of Tennessee)

    Plant Epigenetics

    Detection of rare splice variants, noncoding RNAs, and epigenetic regulation in plants using Raman imaging and single molecule fluorescence (screening for energy efficient and disease resistance characteristics)

    Irudayaraj and Schulz (HORT)

    Biosecurity

    Nanobiosensors for pathogen detection

    Irudayaraj and Co-Is from CFSE

    Instrumentation

    Title

    Collaborators

    Stimulated Raman and absorption microscopy for biomedical research - ongoing

    Irudayaraj, Cheng (collaborator)

    Second harmonic generation and imaging at super-resolution scale - ongoing

    Irudayaraj

    Development of a fast hyperspectral plasmon scanning workstation - ongoing

    Irudayaraj

    Major research instrumentation for the development of high speed Hyperspectral Raman imaging instrumentation-Design of a portable Raman imaging system - concluded

    Ben-Amotz (Chemistry) and Irudayaraj

    Probe-based single molecule fluorescence correlation spectroscopy - concluded

    Maiti (TIFR, India) and Irudayaraj

    Major research instrumentation for the acquisition of multiphoton laser for ultrafast dynamics - concluded

    Lucht (Mechanical Engineering), Irudayaraj, and 3 other Co-PIs

    * [MCMP: Medicinal Chemistry and Molecular Pharmacology; BCHM: Biochemistry; BMS: Basic Medical Chemistry; HORT: Horticulture; ME: Mechanical Engineering; AGRY: Agronomy; TIFR: Tata Institute of Fundamental Sciences; CCMB: Center for Cellular and Molecular Biology; CFSE: Center for Food Safety Engineering]


    CENTER RELATED EFFORTS AND INVOLVEMENT

    • An NIH-NIEHS-P42 Center grant ($10 million, 2015-2019) was submitted in September 2014. Translational tools development for cardiovascular toxicology (PI: Irudayaraj; Co-PIs: Harbin, Sepulveda, Vlachos, Lee, Saviano, Raymond, Cho and Collaborators).
    • An NIH-NCI-U54 proposal on Cancer Physical Sciences is in the planning stages. Lead PI is Cheng. Irudayaraj is one of the Co-PIs. Due Feb 2015.
    • Center for Food Safety Engineering grant (Purdue-USDA-ARS) on "Innovative Pathogen detection and characterization technologies for food safety" $1.14 million/year (2011-2016) (PI: Linton; Co-PIs: Ladisch, Bhunia, Irudayaraj, Applegate, Bashir). (funded)
    • Co-leader of the Drug Discovery and Molecular Sensing (DDMS) thrust area (one of the 4 major thrust areas) of the Purdue University Center for Cancer Research. $5 million for 5 years (2010-2015). [Continuing application submitted in June 2014).
    • Center for Nucleus Science and Engineering-A Purdue University initiative to create a Center on "Nucleus" science and engineering with a significant focus on epigenetic research. (PI: Irudayaraj, Co-PIs: Kirchmaier, Lelievre, Zhou, Briggs, Lossie). This concept was spun into a cluster hire (5-6 faculty) for epigenetics. Six new faculty have started between Fall'13/Spring'14.
    • Indo-US Knowledge Science and technology Forum-Knowledge Network grant on "Center for Nanomedical and Cellular Engineering" (Co-Directors: Irudayaraj and Rao) ($120k)

    SCHOLARLY PUBLICATIONS AND PRESENTATIONS

    PUBLICATIONS

    Peer Reviewed Manuscripts (Citations >8000; h_index: >50; i10_Index: >165)

    1. Cui, Y. and Irudayaraj, J. 2014. Dissecting the behavior and function of MBD3 in DNA methylation homeostasis by single-molecule spectroscopy and microscopy. Nucleic Acids research. (Conditionally accepted).
    2. 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. (Conditionally accepted)
    3. 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. (cond. accepted)
    4. Cho, I-H., Bhandari, P., Patil, P., and Irudayaraj, J. 2015. 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.
    5. 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.
    6. 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.
    7. 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.
    8. 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.
    9. 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.
    10. 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.
    11. 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. In Press.
    12. 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.
    13. 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.
    14. 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.
    15. 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.
    16. Cho, I., Mauer, L. and Irudayaraj, J. 2014. In-situ fluorescent immunomagnetic detection of foodborne pathogens. Biosensors and Bioelectronics. 57:143-148.
    17. 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, doi: 10.3389/fgene.2014.00046.
    18. Mura-S. Greppi, G., Roggero, P., Musu, E., Pittails, D., Carletti, A., Ghiglieri, G., and Irudayaraj, J. 2014. Functionalized gold nanoparticles for the detection of nitrates in water International. J. Environmental Science and Technology. DOI 10.1007/s13762-013-0494-7.
    19. 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.
    20. 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.
    21. 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.
    22. 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.
    23. 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.
    24. 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. (Invited Peer reviewed from highly accomplished groups).
    25. Dong, C., Chowdhury, B., and Irudayaraj, J. 2013. Quantum Dots trafficking in cells probes by single molecule methods. Analyst. 138 (10): 2871-2876.
    26. 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.
    27. Damayanti, N., Parker, L., and Irudayaraj, J. 2013. Monitoring phosphorylation in live cells by lifetime imaging. Angew Chemie. 52(14): 3931-3934.
    28. Cho, I. and Irudayaraj, J. 2013. In-situ immunogold nanoparticle network-based ELISA for biosensor for highly sensitive pathogen detection. Intl. J. Microbiology. 164(1): 70-75.
    29. Cho, I and Irudayaraj, J. 2013. Lateral-flow immune concentration for detection of Listeria monocytogenes. Analytical Bioanalytical Chemistry. 405(10): 3313-3319.
    30. 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.
    31. 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.
    32. 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.
    33. Liu, J. and Irudayaraj, J. 2013. Second Harmonic Generation Correlation Spectroscopy for Single Molecule Experiments. Optics Express. 21(22):27063-27073.
    34. 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).
    35. Ravindranath, S., Kadam, U., and Irudayaraj, J. 2012. Intracellularly grown gold nanoislands 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).
    36. 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.
    37. 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.
    38. 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.
    39. 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.
    40. 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.
    41. 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.
    42. Wang, Y., Chen, J., and Irudayaraj, J. 2011. Nuclear targeting dynamics of gold nanoclusters for enhanced therapy of HER2+ breast cancer. ACS NANO. 5(12):9718-9725.
    43. Guo, C., Book, B., and Irudayaraj, J. 2011. Protein-directed reduction of Graphene oxide and intracellular imaging. Chemical Communications. 47(47):12658-12660.
    44. Panchapakesan, B., Book, B., Seth, R., and Irudayaraj, J. 2011. Gold nanoprobes for theragnostics and diagnostics. Journal of Nanomedicine, 6(10):1-7.
    45. 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.
    46. Wang, Y. and Irudayaraj, J. 2011. A SERS DNAzyme biosensor for lead ion detection. Chemical Communications. 47:4394-4396.
    47. 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).
    48. 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.
    49. 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.
    50. Ravindranath, S., Wang, Y., and Irudayaraj, J. 2011. SERS driven Cross-platform based multiplex pathogen detection. Sensors & Actuators: B. Chemical. 152: 183-190.
    51. 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).
    52. 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.
    53. 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.
    54. 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.
    55. 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.
    56. 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.
    57. 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.
    58. 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.
    59. 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.
    60. 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.
    61. Wang, Y., Lee, K., and Irudayaraj, J. 2010. SERS aptasensor from nanorod-nanopaticle junction for protein detection. Chem. Communications. 46(4):613-615.
    62. 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.
    63. 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.
    64. 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.
    65. 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 Nanotech. alliance, January News and Science Daily).
    66. 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.
    67. Kumar, V. and Irudayaraj, J. 2009. SERS in salt wells. Chemphyschem. 10(15):2670-2673.
    68. 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.
    69. Sun, L. and Irudayaraj, J. 2009. Quantitative Surface Enhanced Raman for gene expression estimation, Biophysical Journal. 96:4609-16.
    70. 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.
    71. 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.
    72. 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.
    73. 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.
    74. 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.
    75. 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.
    76. 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.
    77. Sun, L., Yu, C. and Irudayaraj, J. 2008. Raman multiplexers for alternative gene splicing. Analytical Chemistry. 80(9):3342-9.
    78. Wang, C. and Irudayaraj, J. 2008. Gold nanorod probes detect multiple pathogens. Small. 4(12):2204-2208.
    79. 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.
    80. 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.
    81. Sarkar, T. and Irudayaraj, J. 2008. Carboxyl coated magnetic nanoparticles for mRNA isolation and extraction of supercoiled plasmid DNA. Analytical Biochemistry. 379:130-132.
    82. 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).
    83. 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).
    84. 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).
    85. 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.
    86. 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).
    87. Yu, C. and Irudayaraj, J. 2007. Sensitivity and Selectivity limits of multiplex nanoSPR biosensor assays. Biophysical Journal. 93:3684-3692.
    88. Yu, C., Varghese, L., and Irudayaraj, J. 2007. Surface modification of CTAB capped gold nanorods to make molecular probes. Langmuir, 23: 9114-9119.
    89. 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.
    90. 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.
    91. 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.
    92. 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.
    93. 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).
    94. Kouassi, G. and Irudayaraj, J. 2006. A nanoparticle-based immobilization assay for prion-kinetics assay. Journal of Nanobiotechnology. 48(8):1-10. (Accessed 2026 times).
    95. 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).
    96. 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).
    97. 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.
    98. 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.
    99. 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.
    100. 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.
    101. 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.
    102. 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.
    103. Vaseashta, A. and Irudayaraj, J. 2005. Nanostructured and nanoscale devices and sensors. Journal of Optoelectronics and Advanced Materials. 7(1):35-42.
    104. 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).
    105. Kouassi, G., Irudayaraj, J., and McCarty, G. 2005. Activity of glucose oxidase functionalized onto iron nanoparticles. J. Biomagnetism and Technology. 3:1.
    106. 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.
    107. Yu, C. and Irudayaraj, J. 2005. Spectroscopic characterization of microorganisms by FTIR microspectroscopy. J. Biopolymers. 77(6):368-377.
    108. 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.
    109. Other Publications

    110. 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.
    111. 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.
    112. 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.
    113. 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.
    114. 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.
    115. Kizil, R. and Irudayaraj, J. 2007. Rapid evaluation and discrimination of ?-irradiated carbohydrates using FT-Raman spectroscopy and canonical discriminant analysis. J. Science of Food and Agriculture, 87(7):1244-1251.
    116. 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.
    117. 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.
    118. 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.
    119. 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.
    120. 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.
    121. 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.
    122. 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.
    123. 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.
    124. 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).
    125. 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.
    126. 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.
    127. 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.
    128. 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.
    129. 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.
    130. 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.
    131. Gupta, M., Irudayaraj, J., and Debroy, C. 2004. Spectroscopic quantification of bacteria using Artificial Neural Networks. Journal of Food Protection. 67(11):2550-2554.
    132. 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.
    133. 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.
    134. 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.
    135. 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].
    136. 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.
    137. 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).
    138. 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.
    139. 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.
    140. 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.
    141. 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.
    142. 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.
    143. 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.
    144. 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.
    145. 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.
    146. 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.
    147. 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.
    148. 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.
    149. 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.
    150. 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.
    151. 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.
    152. 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.
    153. 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.
    154. 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.
    155. 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.
    156. 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.
    157. 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.
    158. 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.
    159. Paradkar, M. and Irudayaraj, J. 2002. Rapid estimation of caffeine content in soft drinks using FTIR spectroscopy. Food Chemistry. 78: 261-266.
    160. 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.
    161. 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.
    162. 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.
    163. 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.
    164. 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.
    165. 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.
    166. 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.
    167. 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.
    168. 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.
    169. Sivakesava, S. and Irudayaraj, J. 2001. Rapid detection of tetracycline in milk using mid infrared spectroscopy. Journal of Dairy Science. 85:487-493.
    170. 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.
    171. 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.
    172. 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.
    173. 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.
    174. 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.
    175. 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.
    176. 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.
    177. 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.
    178. 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.
    179. Ranjan, R., Irudayaraj, J., and Jun, S. 2001. Simulation of infrared drying process. Drying Technology. 20(2) 363-379.
    180. 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.
    181. 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.
    182. 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.
    183. Sivakesava, S. and Irudayaraj, J. 2000. Determination of sugars in aqueous mixture using mid-infrared spectroscopy. Applied Engineering in Agriculture 16(5):543-550.
    184. 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.
    185. Cho, Y. and Irudayaraj, J. 2000. Computerization of manufacturing processes and information technology in food industry. Food Science and Industry 33(1):13-19.
    186. Sivakesava, S. and Irudayaraj, J. 2000. Quality analysis of potato chips using photoacoustic FTIR spectroscopy. Journal of Food Science. 80(12):1805-1810.
    187. Irudayaraj, J. and Yang, H. 2000. Analysis of cheese using step-scan Fourier transform infrared photoacoustic spectroscopy. Applied Spectroscopy 54(4):595-600.
    188. 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.
    189. 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.
    190. 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.
    191. 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.
    192. 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.
    193. 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.
    194. 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.
    195. 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.
    196. 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.
    197. 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.
    198. 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.
    199. Ghazanfari, A. and Irudayaraj, J. 1997. A Fourier descriptor approach for grading Pistachio nuts. Journal of Agricultural Engineering Research. (68): 247-252.
    200. Ghazanfari, A., Kusalik. T., and Irudayaraj, J. 1997. A multi-structure neural network approach for classification. International Journal of Neural Systems. (1):55-61.
    201. 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.
    202. 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.
    203. Ghazanfari, A., Irudayaraj, J., and Kusalik, T. 1996. Grading pistachio nuts using a neural network approach. Transactions of the ASAE. 39(6):2319-2324.
    204. Ghazanfari, A. and Irudayaraj, J. 1996. Two-dimensional image classification using string matching. Transactions of the ASAE. 39 (3):1197-1202.
    205. 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.
    206. 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.
    207. Liu, Q. and Irudayaraj, J. 1995. Finite element solution of a moving boundary value problem. Drying Technology. 13(1&2):99-123.
    208. 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.
    209. 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.
    210. 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.
    211. 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.
    212. 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.
    213. 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.
    214. 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.
    215. 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.
    216. Irudayaraj, J., Haghighi, K. and Stroshine, R.L. 1990. Non linear finite element analysis of coupled heat and mass transfer problems. Drying Technology. 8 (4):731-749.
    217. 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.
    218. Wu, I P. and J. Irudayaraj. 1989. Sample size determination for evaluating drip irrigation systems. Transactions of ASAE 32(6):1961 1965.

    Other submitted publications in review (as of 15th Oct 2014)

    1. Chowdhury, B., Chen, J., Liu, S., Lossie, A., and Irudayaraj, J. Effect of AZA on hydroxymethylation-exploring a novel effect. Scientific Reports (October 2014).
    2. Chowdhury, B., Kirchmaier, A., Thimmapuram, J., Arun, G., and Irudayaraj, J. 2013. Sequencing of 5-Hydroxymethylcytosine during myeloid differentiation in HL60 cells. Nucleic Acids Research.
    3. Liu, J., Cho, I-H., Cui, Y., and Irudayaraj. 2014. Second harmonic super-resolution microscopy for quantification of mRNA at single copy resolution. ACS Nano (September 2014)
    4. Zhou, Z. and Irudayaraj, J. 2014. Chromatin extraction and structure elucidation by nanoscale approaches. Epigenetics. (October, 2014)
    5. Chowdhury, B., Wang, Z., Seetharaman, A., Thimmapuram, J., Liu, Y., Lossie, A., and Irudayaraj, J. A study of alterations in DNA epigenetic modifications (5mC and 5hmC) and gene expression influenced by simulated microgravity in human lymphoblastoid cells. PLOS One. (Oct 2014)
    6. Il-Hoon Cho, Pushpak Bhandari, Manisit Das and Joseph Irudayaraj, SERS-assisted signal enhancement for detection of low amount of protein analyte based on lateral-flow immunoassay, Anal Chem.
    7. Cui, Y. and J. Irudayaraj, Understanding cells: quantitative analysis with advanced optics and nanomaterials, in preparation, WIREs Nanomedicine and Nanobiotechnology, (July, 2014)

    Publications in Preparation (as of Nov 2014)

    1. Ren, W; Parker, Laurie L. and Irudayaraj J. SERS-based phosphorylation monitoring, JACS.
    2. Ren, W; Irudayaraj J. A unique detection method based on absorption spectrum for simple and ultra-sensitive of nitrate ion determination in water with amino group modified graphene oxide, Analytical Chemistry.
    3. Damayanti, N., Parker, L., Irudayaraj, J. Multiplex Fluroescence Lifetime Imaging of Kinase activity in Live cells with peptide biosensor Nature Chemical Biology.
    4. Cecon T. Mahapatra, Nur P Damayanti, Joseph Irudayaraj, Maria Sepulveda. Mechanotoxicity study of PFOA effect in mitochondria dysfunction with multiphoton Fluroescence Lifetime Imaging.
    5. Nur P Damayanti, Joseph Irudayaraj, Fluroescence Lifetime Imaging of Acetylation Biosensor in live cells reveal PCAF role in androgen insensitivity progression in prostate cancer , PNAS.
    6. Nur P Damayanti, Cecon T. Mahapatra, Maria Sepulveda, Joseph Irudayaraj, Multimodal and Multiparametric In-Vivo Imaging reveals TCE role in abnormal heart development and defective vasculogenesis of danio rerio. Toxicology.
    7. Cecon T. Mahapatra, Nur P Damayanti, Joseph Irudayaraj, Maria Sepulvida, Quantititave In-Vivo Fluorescence Lifetime Imaging reveal PFOA induced neuronal degeneration in Zebrafish. Toxicology.
    8. Roy Choudhury S, Cui Y, Narayanan A, Yernool D, Irudayaraj J (2014) Optogenetic interaction between TRF1 and DNA methyltransferase3A introduces alteration in telomere length through directed reversal of subtelomeric hypomethylation. (PNAS, August 2014)
    9. Roy Choudhury S, Lo CL, Cui Y, Zhou, Irudayaraj J (2014) Optogenetic tools to control the loci specific aberrant epigenetic status in neuronal stem cell. (Nature Communication, October 2014)
    10. Jing Liu, Yaowu Hu, Prashant Kumar, Mika Shalaginov, Alex Lagutchev, Vladimir Shalaev, Gary Cheng, and Joseph Irudayaraj, "On-Demand Multi-photon source from Opto-mechanical Nanoshaping of Hybrid Graphene-Nanodiamond Structures". In Preparation, Nature Communication.
    11. Jing Liu, M. Y. Shalaginov, A. Lagutchev, V. M. Shalaev, and J. Irudayaraj, "Photochromic Effect of Single NV Centers investigated by Time-resolved Single Molecule Spectroscopy". In Preparation, New Journal of Physics.
    12. Jing Liu, Yaowu Hu, Prashant Kumar, Gary Cheng, and Joseph Irudayaraj, "Enhanced Multi- photon Emission from CdSe/ZnS Quantum Dots decorated on Graphene".
    13. Cui, Y., Jian Li, Sarah Wirbisky, Jennifer Freeman, Xianrui Yuan, J. Irudayaraj, Exploring the function and clinical implication of MBD3 in human Glioblastoma Multiforme, in preparation, Nature Medicine, (December, 2014)
    14. Bhandari P, Garg R, Goergen C, Irudayaraj J. 2014. Reversal of 5-mC hypomethylation in cancer hypoxia using oxygen nanobubbles. Theranostics.
    15. Bhandari P, Phillips E, Goergen C, Kim A, Ziaie B, Irudayaraj J. 2014. Ultrasound triggered delivery vehicle with targeted oxygen nanobubbles for theranostics. Nature Nanotechnology.
    16. Bhandari P, Garg R, Goergen C, Irudayaraj J. 2014. Contrast enhanced in vivo imaging and enhanced survival of pancreatic islets using oxygen nanoencapsulation. ACS Nano.
    17. Park JH1, Bhandari P1, Kim A, Irudayaraj J, Ziaie B. Transplantable glucose sensor using nanobubble encapsulated polymer hydrogel. To be decided (November 2014)
    18. Il-Hoon Cho, Basudev Chowdhury, and Joseph Irudayaraj, Quantification of 5-formylcytosine and 5-carboxylcytosine based on solid phase assay via site-specific chemical modification, Analytical Chemistry.
    19. Il-Hoon Cho, Arun K. Bhunia and Joseph Irudayaraj, Rapid and multiple detection of foodborne pathogens by lateral-flow immunochromatography via nanoparticle-assisted enzyme signal enhancement, Analytical Chemistry.
    20. Wang, XL, Cui Y, Cho II-Hoon. 2014. Hyperspectral molecular imaging of surface marker, mRNA, and multiple epigenectic markers using immunolabeled plasmonic nanoparticles. Nano Letters.

    Books and Chapters

    Books

    1. Irudayaraj, J. 2012. Biomedical Nanosensors. Taylor and Francis Publishers. (12 Chapters) (Published in December 2012).
    2. Kouassi, G. and Irudayaraj, J. 2012. Magnetic Nanostructures: Basics to Applications. Pan Stanford Publishing. (10 Chapters). (In Progress - Scheduled for completion in Fall 2013).
    3. Irudayaraj, J. and Christoph, R. 2008. Nondestructive sensing for food quality. IFT Press, Blackwell Publishing Professional, Ames, IA 50014. (~365 pages).
    4. Jun S. and Irudayaraj, J. (Editors) 2008. Food Processing Operations Modeling II (2nd Edition). Marcel Dekker Inc., NY (~375 pages).
    5. Irudayaraj, J. (Editor) 2001. Food Processing Operations Modeling I. Marcel Dekker Inc., NY.

    Selected Chapters in books. (since 2005)

    1. Craig, A.P., Irudayaraj, J., Franca, A. 2014. Vibrational Spectroscopy for food quality and safety screening. In: Arun K. Bhunia; Moon S. Kim; Chris R. Taitt. High throughput screening for food safety assessment: biosensor technologies, hyperspectral imaging and practical applications.
    2. Craig, A.P., Franca, A., and Irudayaraj, J. 2013. Pattern recognition in spectroscopic analysis. Conventional methods and future directions. In: Pattern Recognition: Practices, Perspectives and Challenges. Nova Publishers. Taylor and Francis. (In Press).
    3. Kadam, U., Lossie, A., Schulz, B. and Irudayaraj, J. 2012. Gene expression analysis using conventional and imaging methods In Nucleic Acids Nanotechnology in Medicine. Springer Publications Inc. (Erdmann, V.A., Barciszewski J., eds.), (8): 141-162
    4. Lee, S., Craig, A.P., Kadam, U., and Irudayaraj, J. 2012. In-vivo biodetection using Raman spectroscopy In Biosensors based on Nanomaterials and Nanodevices. CRC Press, Taylor and Francis. (In Press)
    5. Craig, A.P., Franca, A., and Irudayaraj, J. 2013. Surface enhanced Raman spectroscopy applied to Food Safety. Annual Review of Food Science and Technology, Vol 4. 369-80.
    6. Kahyaoglu, L. and Irudayaraj, J. 2013. Detection of Foodborne virus In Advances in microbial food safety. Chap 11 (pp. 202-218) Woodhead Pub. Inc. (ISBN-13: 978085709438 4; 560 pages)
    7. Kouassi, G., Yu, C., Lan, S. and Irudayaraj, J. 2011. Synthesis and preparation of magnetic and gold-coated magnetic nanoparticles. (Chap 2). Part 1. Fabrication and synthesis of inorganic particles. Nanoparticles in Biology and Medicine: Methods and Applications. Humana Press (Springer Science), USA.
    8. Kouassi, G., Yu, C., Lan, S. and Irudayaraj, J. 2011. Functionalization and biological and medical applications of magnetic and gold-coated magnetic nanoparticles (Chap 3). Part 1. Fabrication and synthesis of inorganic particles. Nanoparticles in Biology and Medicine: Methods and Applications. Humana Press (Springer Science), USA.
    9. Kizil, R. and Irudayaraj, J. 2011. FTIR photoacoustic spectroscopy. Vibrational Spectroscopy Section. Encyclopedia of biophysics (Editor Roberts). Springer Verlag. (5 pages).
    10. Jalilian, R., Jauregui, L., Lee, K, Chen, Y., and Irudayaraj, J. 2010. Graphene for biosensing applications in Biomedical Nanosensors (Ed. Irudayaraj). (20 pages).
    11. Yu, C. and Irudayaraj, J. 2007. Sensitivity and selectivity limits of multiplex nanoSPR biosensor assays. Ed. Nagarajan in Nanoparticles: Synthesis, passivation, Stabilization, and Functionalization. ACS Books. American Chemical Society.
    12. Subramanian, A., and Irudayaraj, J. 2005. Biosensors for pathogen detection in food. Encyclopedia of Agriculture, Food, and Biological Engin. Taylor and Francis Group. NY.
    13. Ranjan, R., Irudayaraj, J., and Reddy, J.N. 2004. Coupled and Non-linear problems: for the Encyclopedia of Agriculture, Food, and Biological Engin. Marcel Dekker Inc. NY (8 pages)
    14. Ranjan, R. and Irudayaraj, J. 2003. Unsteady state mass transfer in biological systems. Encyclopedia of Agriculture food and biological engineering. ISSN: 0-8247-0938-1., Marcel Dekker Inc. NY. (7 pages).
    15. Sandeep, K. and Irudayaraj, J. 2001. Introduction to modeling and numerical simulation in Food Processing Operations Modeling (Ed. Irudayaraj). Chap 2, pp. 25-37. Marcel Dekker, Inc., NY.
    16. Irudayaraj, J. 2000. Transient Mass Transfer in Biological Materials: Mass Transfer in Biological systems. The Encyclopedia of Agricultural and Food Engineering (Ed. Heldman). Marcel Dekker, Inc. New York, NY.
    17. Irudayaraj, J. and Y. Wu. 1996. Modelling heat and mass transfer in coupled systems during absorption and desorption. In Mathematical Modelling and Numerical Techniques in Drying Tech. Eds. I. Turner and A. Mujumdar. Chapter 7, pages 279-308. Marcel Dekker, Inc. NY.
    18. Irudayaraj, J. 1996. Material non-linearities in finite element analysis. In Selected Topics in Numerical Analysis - A Tutorial Set," Volume 1. Finite element and numerical analysis committee of ASAE. Eds. Mohtar, R., Puri, V., and Carroll, N. ASAE, St. Joseph, MI. pp. 150.

    Conferences and Presentations

    Invited workshops/symposium presentations

    1. Irudayaraj, J. Single cell tools in Cancer Research. Single Cell Analysis Conference, Cambridge, MA. May 22-23, 2014.
    2. Irudayaraj, J. Defining the epigenetic landscape during stimulated microgravity in lymphoblastoid cells. 3rd Annual ISS Research and Development Conference, American Astronautical Society, Hyatt Regency, McCormick Place, Chicago, IL. June 17-18, 2014.
    3. Irudayaraj, J. Single cell technologies in basic medical sciences. 5th Next Generation Sequencing and Single Cell Analysis Conference, London, UK. November 2013.
    4. Irudayaraj, J. Single molecule tools in epigenetics, IUPUI-PCCR symposium. March 24, (2012).
    5. Irudayaraj, J. Nanotechnology applications in food and biology. University of Sassari, Serdegna, Italy (June 1- June 5, 2012). Presented 4 lectures.
    6. Irudayaraj, J. Biomedical technology commercialization". Chengdu City, Industrial Forum, November 2012.
    7. Educational aspects of Nanotechnology in Agriculture. Tamil Nadu Agricultural University. August. 2012.
    8. Irudayaraj, J. Single molecule-based epigenetic analysis. Second International Symposium on Breast Cancer Prevention, Rennes, France. Oct 9-11 (2011).
    9. Irudayaraj, J. Single molecule and single particle technologies for live cell monitoring. High Impact Research to Society at PU and KIST. 6 th annual KIST/PU symposium Sept 6th (2011).
    10. Irudayaraj, J. Nanosensors and spectroscopy in biosecurity. Univ. Sassari, Italy. 23rd June (2011).
    11. Irudayaraj, J. Multifunctional nanomaterials as sensors for targeting and delivery. Material Science and Nanotechnology, Porto Conte Science Park, Sardegna, Italy. 27th June (2011).
    12. Irudayaraj, J. Single molecule tools in epigenetics. IUPUI-PCCR retreat, March 26 (2011).
    13. Irudayaraj, J. Raman spectroscopy for in vivo detection. Pittcon, Atlanta March 14-17 (2011).
    14. Irudayaraj, J. Single molecule spectroscopy in biology. Center for Cellular and Molecular Biology. Hyderabad, India. Jan 4 (2011).
    15. Irudayaraj, J. Raman spectroscopy for in vivo detection. Pittcon. Atlanta, GA. March 16 (2011).
    16. Irudayaraj, J. Raman chemical mapping of chromate reduction sites. NIH-NIEHS RO1 grantees symposium. Portland, OR. Nov 4-6 (2010).
    17. Irudayaraj, J. Nanosensors for separation and detection of pathogens. Institute of Food Technologists. Chicago, IL. July 17-20 (2010).
    18. Irudayaraj, J. Multifunctional gold nanosensors for targeting and delivery. Cancer Nanotech. Symposium, Nano Science and Technology Inst., Anaheim, CA., June 20-24 (2010).
    19. Irudayaraj J. Intracellular Raman Imaging. Nanotechnology Conference, University of Illinois at Urbana Champaign. May 12th (2010).
    20. Irudayaraj, J. Role of Nanotechnology in Theragnostics. M.G.R. Medical College and University, India. Jan 5th (2010).
    21. Irudayaraj, J. Drug delivery and diffusion. Perfint Inc. Chennai, India. Jan 5th (2010).
    22. Irudayaraj, J. Nanocharacterization. Tamil Nadu Agricultural University, Dec 29th (2009).
    23. Irudayaraj, J. and Chen J. Compartmentalized dynamics and single particle tracking in live cells. SPIE conference, Biophotonics session. San Diego. Aug 2-5. (2009)
    24. Irudayaraj, J. Multiplex detection of pathogens by SERS and plasmonics. American Chemical Society. DC. August 16 -20. (2009)
    25. Irudayaraj, J. Raman spectroscopy in Biology. June 5. Chinese Academy of Sciences, Changchun. China. (2009)
    26. Irudayaraj, J. Nanotechnology in Cancer research. June 5. North East Normal University, Changchun. China. (2009)
    27. Irudayaraj, J. Single molecule methods in biology. Department of Chemical Biology. June 2nd. Beijing University, Beijing, China. (2009)
    28. Irudayaraj Joseph. Distinguished Speaker seminar series to the IEEE Electron Device Society- Dallas Section, and the University of Texas at Arlington, NanoFabrication Center. Nanotools for monitoring single cell events. April 28th (2009)
    29. Irudayaraj, J. Micro/Nano technology Seminar Series in the Department of Mechanical Engineering in University of Louisville, Feb 27th. "Nanotools in Medicine" (2009)
    30. Irudayaraj, J. Single molecule methods for single cell stoichiometry of Toll Like 9 receptor Invited Conference: Fluorescence 2009 in Tata Institute of Fundamental Research. March 15-22, (2009).
    31. Irudayaraj, J. and Schulz, B. Genomic detection methods, DOW Agro Sciences. Feb 17th (2009) Irudayaraj, J. IUPUI Special Lecture Series. Single Molecule methods in Biology" Feb 16th (2009)
    32. Irudayaraj, J. Special Lecture on Multifunctional nanoparticles for tumor targeting. Center for Cellular and Molecular Biology, Hyderabad, India. Jan 6th (2009).
    33. Irudayaraj, J. Nanoscale arrays for multiplex DNA sensing. Center for Food Safety Engineering-USDA-ARS workshop, Ocean City, NJ. Oct 12-13 (2008).
    34. Rajarajan, M., T. Dar, C. Themistos, A. Rahman, K. Grattan, and J. Irudayaraj. Design and Optimization of Surface Plasmon Resonance Based Biosensor for the Detection of E. coli. 2008 Integrated Photonics and Nanophotonics Research and Applications (IPNRA) Topical Meeting, Boston, MA. July 13-16 (2008).
    35. Irudayaraj, J. Nanoscale structures for single cell characterization. 4th International Nanoscience and Nanotechnology Conference. NanoTr4 conference. Istanbul Technical University, Maslak Campus, Istanbul, Turkey. June 9-13, (2008)
    36. Irudayaraj, J., A. Wei. Detection and theragonostic applications of gold nanorods. Nanomedicine Center presentation. Korean Institute for Science and Technology. Seoul, S. Korea. June 2-4, (2008).
    37. Irudayaraj, J. Nanotechnology in Agriculture. Tamil Nadu Agricultural University. Coimbatore, India. March 24th (2008)
    38. Irudayaraj, J. Single cell methodologies. BioNano Conference, Center for Cellular and Molecular Biology, Hyderabad, India. March 13-14, (2008)
    39. Irudayaraj, J. Molecular diagnostic tools for cancer. Invited speaker at the Beijing conference and exhibition on instrumental analysis in Beijing, China. Oct 18-20, (2007).
    40. Irudayaraj, J. Biosensors in Medicine. Dept of Chemistry, co-hosted by Peiking University and Beijing Institute of Technology (Oct 21, 2007).
    41. Irudayaraj, J. Nanobiosenosrs for food safety and quality. Dept of Food Science and nutrition. Ohio State University, Columbus, OH (Nov 27, 2007).
    42. Irudayaraj, J. Nanosensors for food packaging. IFT Food Packaging summit, Baltimore, MD (May 7-9, 2006).
    43. Irudayaraj, J. Biosensors for medical diagnostics. Indian Institute of Science, Bangalore, India (Dec 27, 2006).
    44. Irudayaraj, J. Single molecule biophysics. Dept. of Physics, Barathiar University, Coimbatore, India. (Dec 29, 2006)
    45. Irudayaraj, J. Single molecule methods for biomolecule interaction studies. Tata Institute of Fundamental Research, Bombay, India (Dec 15, 2006).
    46. Irudayaraj, J. Bionanotechnology curriculum development for agricultural and food scientists. International Food nanotechnology Conference. Orlando, Florida. (June 28-29, 2006).
    47. Irudayaraj, J. Bionanotechnology progress, Applied Physics and Engineering, Cornell University (Aug 4, 2005).
    48. Vaseashta, A. and J. Irudayaraj. Optical sensors for detection of pathogens and hazardous chemical agents. NATO advanced study institute. Nanostructured and advanced materials for optoelectronic, photovoltaic and sensor applications. Sozopol, Bulgaria (Sept 6-17, 2005).
    49. Irudayaraj, J. and G. McCarty. Nanotechnology-Education and Implication. Spring meeting and round table. University-Industry Consortium presentation at Harrisburg, PA. (April 27-28, 2004).
    50. Irudayaraj, J. Nanotechnology education for the future workforce. Nanoscale science, engineering, and tech. for food safety and quality. Paper no. 45-2. IFT. Las Vegas. (July 12-16, 2004).
    51. Irudayaraj, J. Biosensors: New solutions for the food industry. Non-destructive food testing: Present and Future. Paper no. 21090. IFT. Las Vegas. (July 12-16, 2004).
    52. Irudayaraj, J., Yu, C., Gupta M.J. and Subramaniam, A. 2004. Optical Sensors for Food Pathogen and Hazardous Chemical Agent Detection for ISS and Planetary Outpost. July 19-22, Colorado Springs, CO. pp. 20-24.
    53. Irudayaraj, J. Drying of pharmaceuticals and biomaterials. Invited lecture at the International Workshop and symposium on Industrial Drying, Mumbai, India. (Dec 20-23, 2004).
    54. Irudayaraj, J. 2003. Review of Sensor methodologies for food quality and safety. Presentation at the Electrical Engineering Seminar series, Penn State (Nov 11, 2003).
    55. Irudayaraj, J. 2002. Perspectives of teaching and research in Agricultural and Biological Engineering. College of Agricultural Engineering, Tamil Nadu Agricultural University, Coimbatore, India. (Dec 23-24).
    56. Irudayaraj, J. 2002. Food Quality and Safety assessment for agricultural produce. Value added products: Opportunities for agro industrial units. Gujarat Agricultural University, Junagadh. Gujarat, India. (Dec 16-17).
    57. Irudayaraj, J. 2002. Food quality sensors. Departamento de Tecnología de Alimentos, Universidad Politechnica de Valencia, Valencia, Spain. July 9 th.
    58. Irudayaraj, J. 2002. Depth profile characterization and quality attribute sensing of food materials. First Annual Materials Day, Penn State (April 15, 2000).
    59. Irudayaraj, J. 2001. Spectroscopic measurements for on-line determinations. First International Workshop on Mathematical and Computing Techniques for Agro-Food Technologies, Barcelona, Spain. (Nov 26-27).
    60. Yang, H. and J. Irudayaraj, 2000. Characterization of food powders and thin layers using Fourier Transform Infrared Photoacoustic Spectroscopy- Innovations in particulate materials for the new millennium. Particulate Materials Center, MRL (May 23-24).
    61. Irudayaraj, J. and H. Yang. 1999. Probing food surfaces. Technologies for the New Millennium. Westin-William Penn, Pittsburgh, PA (November 1-2).
    62. Irudayaraj, J. Invited speaker in the session on 25 years of finite elements in Agricultural Engineering at the ASAE 1999 International Meeting. Title of the invited presentation was Heat and mass transfer in food systems. (Participation level : Invited speaker for Part II of the two part lecture), Toronto, Canada. July 18-22, (1999).
    63. Irudayaraj, J., P.C. Bargale, and S. Sokhansanj. Trends in postharvest processing. Conference of the 29th Caribbean food crops society. Port‑de‑France, Martinique. July 3‑10, (1993).

    Seminar series presentations in Purdue (Selected from over 25 since 2005).

    1. Jing Liu, and Joseph Irudayaraj, "Microscopy to Measure Biophysical Properties of Single Molecules: Fluorescence Correlation Spectroscopy and Photon Counting Histogram", invited talk, Lectures on Light Microscopy, Purdue University, Apr. 10th, 2013.
    2. Irudayaraj, J. Nanotechnology in Agriculture. Tamil Nadu Agricultural University. June. 2013.
    3. Irudayaraj, J. Single cell technologies in medical sciences". Center for Cellular and Molecular Biology. June 2013.
    4. Irudayaraj, J. Single molecule and single particle technology for live cell monitoring". Purdue Center for Cancer Research. August 2013.
    5. Irudayaraj, J. Single cell epigenetics". Int'l Breast Cancer Prevention Symposium and Nutrition and Health Sciences-Industry Advisory board. Nov 2012.
    6. Irudayaraj, J. Biophysical, Bioinorganic and Bionanotechnology seminar, Sept. Dept. Biological Sciences. Oct 2012.
    7. Irudayaraj, J. Gold nanosensors in human health. NSF-REU program. Dept. Physics Seminar. July 2012.
    8. Irudayaraj, J. Plasmonic biosensors, Biophysics seminar series, Dept. Physics, (Oct 3, 2011).
    9. Irudayaraj, J. Nanotechnology in health diagnostics (NSF-REU), Dept. Physics, (July 13, 2011).
    10. Irudayaraj, J. Nanomaterials in biology. Bindley Seminar series. (Mar 3, 2011).
    11. Irudayaraj, J. Basics of Epigenetics. International Breast Cancer Prevention. (Feb 24, 2011).
    12. Irudayaraj, J. Single molecule methods in biology. Bindley Seminar series. (Oct 29, 2010).
    13. Irudayaraj, J. 2008. Confocal Raman microscopy for single cell monitoring. Confocal microscopy Seminar, Purdue University (April 23, 2008).
    14. Irudayaraj, J. 2008. Nanoscale sensors for detection and targeting. Basic Medical Sciences, Purdue University (April 24, 2008).
    15. Irudayaraj, J. 2007. Single molecule methods for cell surface biomarker interaction. Biological Sciences, Cell growth and Differentiation group, Purdue University (Nov 15, 2007).
    16. Irudayaraj, J. 2007. Imaging and diagnostic tools for cancer. Purdue Cancer Center Evaluation seminar presentation, Purdue University (Nov 15, 2007).
    17. Irudayaraj, J. 2006. IUPUI Invited lecture. Strategies for intra cellular probing. Dept of Biochemistry Seminar Series (Oct 2, 2006).
    Contributed conference/symposium presentations and proceedings ["(*)" presented and published in peer-reviewed conference proceedings] listing selected 15 (total presentation over 300)
    1. Irudayaraj. J. 2013. Nanoparticle biosensors for intracellular detection and quantification. 246 ACS National Meeting and Exposition, September 8-12, Indianapolis, IN.
    2. Irudayaraj, J. 2013. Nanomaterials as intracellular detectors to monitor Chromate in remediating bacterium. 246 ACS National Meeting and Exposition, September 8-12, Indianapolis, IN.
    3. Drachev, V., Lee, K., Irudayaraj, J. Spectroscopy of site specific DNA assembled plasmonic networks on cell surfaces. Biosensing and Nanomedicine VI, SPIE NanoScience and Engineering, Optics and Photonics symposium, August 25-29, 2013, San Diego, CA.
    4. Gururaj V. Naik, Bivas Saha, Jing Liu, Sammy Saber, Eric Stach, Joseph MK Irudayaraj, Timothy D. Sands, and Alexandra Boltasseva, "A titanium nitride based metamaterial for applications in the visible", Conference on Lasers and Electro-Optics (CLEO), San Jose, Jun. 9th-13 th, 2013.
    5. Naz, A., Cui, Y., Collins, C., Hyun, S-H., Mondjinou, Y., Thompson, D., and Irudayraj, J. Azacytidine-conjugated PLGA-PEG diblock copolymeric nanoparticles: a controlled vehicle for epigenetic drugs. Drug Delivery and Targeting, Drug Discovery and Therapy World Congress 2013, June 3-6, 2013, Boston, MA.
    6. Craig, A-P., Franca, A., Oliveira, L., Ileliji, K., and Irudayaraj, J. 2013. Classification and quantification of defective and non-defective roasted coffees by Near Infrared (NIR) spectroscopy and Elastic net. IFT Quality assurance division. Graduate research paper presentation, 2nd place, IFT Annual meeting. Chicago, IL.
    7. Chowdhury, B. and Irudayaraj, J. 2012. Cancer's epicentre : Epigenome- Theory to Therapy", Centre for Cellular & Molecular Biology, Hyderabad, India (4th December 2012) .
    8. Nanotechnology for food security. 2012. Presented on "Raman Spectroscopy for in vivo detection". Pittcon, March 11-15 (Orlando, FL).
    9. Lan, S, Yu, C, Irudayaraj J. 2012. Quantification of genes. (Jan 2013, San Diego, CA). Photonics conference.
    10. Chowdhury, B. and Irudayaraj, J. Epigenomic landscape of 5-Hydroxymethylcytosine (5hmC) and implications in cancer", Purdue Cancer Prevention and Control Group Retreat (2nd Nov 2012).
    11. Damayanti, N., Parker, L., and Irudayaraj, J. 2012. Seizing the moment : FLIM technique to visualize Abl kinase phosphorylation in single living cell. Cancer centret annual retreat 2012- Poster presentation, Feb 2013.
    12. Pierre-Alexandre Vidi, Jing Liu, Swaathi Jayaraman, George Dorfman, Daniela Salles, Matthew Gray, Patricia Abad,, Prabhas V. Moghe, Joseph M. K. Irudayaraj, Lisa Wiesmüller, and Sophie A. Lelièvre, "The nuclear architectural protein NuMA targets the ISWI ATPase SNF2h to DNA breaks", 2012 ASCB (American Society For Cell Biology) meeting, Dec. 19th-23rd, 2012.
    13. Damayanti, N., Parker, L., and Irudayaraj, J. 2012. Seizing the moment: FLIM visualizes Abl kinase phosphorylation in single living cell. Purdue Center for Cancer Research. Annual retreat 2012- Poster presentation
    14. Lipchik, A.M., Kumar, G.V.P., Irudayaraj, J. and Parker, L.L. "SERS Detection of Abl Kinase Activity by using a Nanoparticle Based Peptide Biosensor." Department of Defense, Defense Health Program, 6th Era of Hope Conference, Orlando, FL, USA. (2011).
    15. Chen, J. (*)Irudayaraj, J. 2011. Single molecule in vivo analysis of Toll-like receptor 9 and CpG DNA interaction. 55th Biophysical Society meeting. (March 9, Baltimore, MD).
    16. (*)Chen J, Irudayaraj J. 2010. Fluorescence lifetime correlation spectroscopy resolves EGFR interaction in live cells. SPIE proceedings . SPIE Photonics West, Single molecule spectroscopy and Imaging II. (Jan 23, San Francisco, CA).
    17. Lipchik, A.M., Kumar, G.V.P., Irudayaraj, J. and Parker, L.L. "Quantification of Kinase Activity Using a Nanoparticle Based Peptide Biosensor." 6 th Annual U.S. Human Proteomics Organization Conference, Denver, CO, USA. (2010).
    18. Wereley, S., Kumar, A., Kwon, J., Ravindranath, S., and Irudayaraj, J. 2010. Application of an optically induced electrokinetic manipulation technique on live bacteria. IMECE conference. Paper #. IMECE2010-39324. Best Paper Award, ASME-IMECE Microfluidics 2010.
    19. (*)Nag, S., Sahoo, B., Chen, J., Muralidharan, C., Shah, R., Joseph Irudayaraj, J., and Maiti. S. 2009. Investigating Amyloid Aggregates At Different Size Scales. Biophysical Society: 451-Pos Board B330 1. [Feb 1, 2009] 96 (3), 87a.
    20. Kizil, R. and J. Irudayaraj, 2008. Characterization and Classification of Gamma-Irradiated Adipose Tissues Using Raman Spectroscopy and Chemometrics AIChE abstract. 2008 Annual Meeting (Food, Pharmaceutical, and Bioengineering Division), Philadelphia, PA. (Nov 16-21).
    21. Rajarajan, M., T. Dar, C. Themistos, A. Rahman, K. Grattan, and J. Irudayaraj, 2008. Design and Optimization of Surface Plasmon Resonance Based Biosensor for the Detection of E. coli. 2008 Integrated Photonics and Nanophotonics Research and Applications (IPNRA) Topical Meeting, Boston, MA (July 13-16).
    22. Yu, C. and J. Irudayaraj, 2007. Sensitivity and selectivity of multiplex nanoSPR biosensor assays. Nanoparticles: Synthesis, Passivation, Stabilization, and Functionalization. [Coll 575] The 233rd ACS National Meeting, Chicago, IL (March 25-29).
    23. Yu, C. and J. Irudayaraj, 2007. Identification of metastatic subpopulations of breast cancer progenitor cells using gold nanorod probes. [Coll 533] The 233rd ACS National Meeting, Chicago, IL (March 25-29).
    24. Lan, S. and J. Irudayaraj. 2007. Poster: Multiplex sensing using Confocal Raman" First place ( out of 24 posters) in Life Sciences category (Feb 28).
    25. Yu, C. and J. Irudayaraj. 2007. "Single Cell identity profiling". Poster: Cancer Prevention Poster Competition. Oncological Sciences Center. Third Place (May 27).
    26. Strychalski, E., J. Irudayaraj, and H. Craighead, 2005. Poster: Deep-microfluidic devices in glass and plastic for sorting and recovery of mammalian and microbial cells. Nanobiotechnology Center Conference, Cornell University (Aug 15-16).
    27. Santhanam, N., J. Irudayaraj, J. Edel, H. Craighead, and L. Walker, 2005. Poster: Study of the surface mobility of cellulases on cellulose nanofibrils using Fluorescence Correlation Spectroscopy. Nanobiotechnology Conference, Cornell University, Ithaca, NY (August 15-16).
    28. Chanda, R., Irudayaraj, J., Pantano, C. 2004. Characterization of thin films for optical sensors of food-borne pathogens. Proceedings of the SPIE - The international Society for Optical Engineering (SPIE), Boston, MA., Oct 25-28, 5591 (Lab-on-1-Chip: Platforms, devices, and Applications, Eds. Smith and Sobek): 231-238. Boston, MA.
    29. (*)Cho, B. and Irudayaraj, J. 2003. Non-contact ultrasound imaging for foreign object detection in cheese and poultry in Emerging Technologies in NDT. [Eds. D. Hemelrijck, A. Anastasopoulos, and N. Melanitis]. The Netherlands. Proceedings of the 3rd international conference on emerging technologies in non-destructive testing, May 26-28. Thessaloniki, Greece. pp. 351-354.
    30. Waswa, J., J. Irudayaraj, C. DebRoy, and A. Demirci, 2002. Poster: Surface plasmon resonance based biosensor assays for detection of Escherichia coli O157:H7 in food samples. 16th of November, 2002 at Clarion University. Presented at the Allegheny Branch of the American Society for Microbiology (ABASM) [Student poster contest, 1st Prize].

    GRANTS AND CONTRACTS

    Grants Ongoing [ Collaborative ongoing grants total ~$10 million. Funding since 2005, total ~$15 million]

    Title and Agency

    Duration and Amount

    Collaborators

    Non-invasive imaging of miR-200c as a biomarker for early detection of aggressive breast cancer

    7/1/13-06/14

    Co-PI (PI: Chang)

    Single Cell Quantification of Splice Variants and Epigenetic Regulation of Splicing. NSF.

    9/1/12-07/15

    PI (Co-PI: Kirchmaier)

    Defining epigenetic programming during flight expeditions in differentiating embryonic stem cells. NASA - Research opportunities in space and earth sciences

    8/1/12-07/15

    PI (Co-PI: Lossie)

    Live single cell epigenetic profiling and regulation at single molecule resolution. KECK Foundation (Medical Research)

    03/12-02/16

    PI (Co-PIs: Zhou, Lelievre, Kirchmaier, Lossie)

    Mapping Genomic Sites of 5-Hydroxymethylcytosine, a Novel CpG Modification Catalyzed by the MLL Partner TET1 Protein Family. *PCCR and *CTSI

    12/10-11/14

    PI (Co-PI: Kirchmaier)

    Super-resolution second harmonic imaging for live cell mRNA detection and quantification. Show Walter Trust grant.

    07/12-12/15

    PI (Co-PI: Lossie)

    Diagnosis of crystal-based arthropathies via Raman Spectroscopy. NIH-R01

    09/11-08/14

    Collaborator (one month in yrs 1 & 2) (PI: Akkus Ozan).

    Label-free, real-time detection of kinase activity in vitro and in single cells using surface-enhanced Raman spectroscopy (SERS), NIH-NCI/IMAT

    04/11-03/15

    Co-PI (PI: Laurie Parker) (equal credit)

    Development and application of nanotechnology-based tools to understand mechanisms of bioremediation, NIH-R01

    12/08-12/14

    PI (Co-PI: Thompson).

    Replication-coupled chromatin assembly and epigenetic processes in s. cerevisiae, NSF

    07/11-06/14

    Co-PI (PI: Kirchmaier)

    Innovative pathogen detection and characterization technologies. Center for Food Safety Engineering-USDA-ARS Center grant

    07/11-07/16 $5.7 million

    Co-PI (PI: Linton. Co-PIs: Bhunia, Ladisch, Irudayaraj, Applegate, Bashir.

    *PCCR : Purdue Center for Cancer Research (NIH funded); CTSI: Clinical Translation & Sciences Institute (NIH funded)

    Selected Grants Completed (last five years)

    Title

    Duration and Amount

    Agency

    Center for Nanomedical and Cellular Engineering-Indo-US Knowledge Network Program for visitor exchange

    08/09-01/13

    PI and Co-Director (Co-Director: Rao).

    Defining epigenetic programming directing double strand DNA break repair by single molecule methods. PCCR

    11/09-12/12

    Co-PIs: Kirchmaier, Irudayaraj (equal credit)

    Instrumentation Development for Biological Research/Development of a Hyperspectral Raman imaging workstation, NSF

    05/08-10/12

    Co-PI (PI: Ben-Amotz).

    MRI: Acquisition of a high-pulse energy ultrafast laser system, NSF

    09/09-08/12

    Co-PI: Irudayaraj et al. (PI: Lucht).

    Single molecule tools for evaluating histone modification in single living cells, NSF

    09/09-08/12

    Co-PIs: Kirchmaier and Irudayaraj. (equal credit)

    Novel nanosubstrates as biosensors, (Industry grant).

    8/10-03/12

    PI

    Trafficking, targeting and intracellular localization of targeting nanodelivery systems (Industry grant)

    04/11-03/12

    PI

    Quantitative analysis of alternative splice variants in plants using enhanced Raman Spectroscopy, NSF

    08/09-07/12

    Co-PIs: Irudayaraj and Schulz. (equal credit)

    Epigenetics in vivo Tools Development - infrastructure support to develop fluorescence based assays, Office of the vice President for Research

    01/09-1/10

    PI (Co-Is: Kirchmaier, Lossie)

    Development and Characterization of a Xenograft mouse model for Hepatitis B virus protein x-induced Hepatocyte Tumorigenesis, PCCR

    9/08-08/09

    Co-investigators: Irudayaraj, Asem, and Mohammed (PI: Andrisani).

    High Speed Chemical Imaging of Live Cells using a Compressive Sampling Spectrometer, Showalter, Purdue University

    7/08-6/09

    Co-investigator (PI: Ben- Amotz).

    Engineering a Research Community in Tissue and Cellular Engineering, Purdue University

    6/08-4/09

    Co-investigators (PI: Panitch, Other Co-PIs: Geddes, Rickus, Leary, and 8 others).

    Discovery Learning Center GK12 Fellowship, NSF-STEM program

    06/08-05/09

    (Fellowship to Ms. Heyjin Park, my advisee).

    Multifunctional Nanocapsules as dynamic sensors and therapeutic agents, Purdue Research Foundation

    6/08-5/09

    PI.

    Bilsland Fellowship, Purdue University

    3/08-8/09

    (Fellowship to Ms. Sun, my advisee).

    Spectroscopy-based biosensor approach for detecting food pathogens, USDA Center for Food Safety Engineering

    9/07-8/09

    PI (Co-investigators: Mauer and Debroy). [Total 2.4 million]

    Single molecule studies and instrumentation, VICS International Grants program, Purdue University

    6/07-12/08

    PI.

    Multiplex arrays using confocal raman for alternative splice profiling of BRCA1, NIH-NCI

    4/06-3/09

    PI.

    PDA film-based biosensors for discriminating E. coli, BARD-VAADIA Postdoctoral fellowship

    6/07-5/08

    PI (Fellowship award to Ms. Tania Sheynis).

    Phi29 packaging motor for nanomedicine, NIH Nanomedicine Center

    9/06-8/08

    Collaborator (PI: Guo, Co-PIs: Bashir, Thompson, and Montemagno).

    Polymerase Chain Reaction based multiplexing using Confocal raman microscopy for pathogen detection, Center for Food Safety Engineering

    9/06-12/07

    PI.

    Biocompatible nanoparticles for drug deliver and therapy for breast cancer, Office of International Programs

    9/06-12/07

    Multiplexing using nanorods for cell surface marker identification, IUPUI-OSC

    8/06-12/07

    PI (Co-investigator: Nakshatri).

    SERRS based raman nanoarrays for alternative gene splicing in breast cancer research, Oncological Sciences Center, Purdue University

    1/06-10/07

    PI.

    Oncological Science Center, Single molecule instrumentation for cancer research

    4/06-3/07

    PI.

    Novel mid-infrared sensors for pathogen identification, DOD-SBIR

    1/06-12/06

    Co-investigators: Co-Investigator (PI: Lynntech Inc.).

    Novel mid-infrared sensors for monitoring cell and tissue chemistry, Center for Optical Technologies, Leigh University

    1/06-12/06

    PI (Co-investigator: Jain).

    Instrumentation grant for acquisition of Confocal Raman system, Discovery Park

    5/05-4/06

    PI.

    Teaching grants awarded (selected five grants)

    Title

    Duration and Amount

    Agency

    Nanoscale education in agricultural and food systems, USDA Higher Education Program Challenge Grant (HEPC)

    9/05-31/07

    Co-investigator: McCarty (PI: $80,000).

    Contextual integration of leadership and communication skills to the engineering and agric. Curricula, USDA-HEPC

    9/00 - 8/02

    Co-investigator: Johnson (PI: $50,000).

    Biosensor instrumentation for teaching laboratory at Penn State, SPREETA Biosensors, Texas Instruments Inc.

    9/00-8/01

    PI

    Bringing biosensors research to classroom, USDA-HEPC

    9/98 - 8/00

    Co-investigators: Walker, Ziegler, Coupland (PI: $100,000).

    Developing accessible tools for key courses in Bioprocess Engineering, USDA-HEPC

    9/96 - 8/98

    Co-investigators: Bothwell, Tang, Marks (PI: $90,000).


    INTELLECTUAL PROPERTY

    Patents submitted

    Full Application

    • 64892.P1.US - Identity Profiling of Cell Surface Markers - An Application for a full US patent was filed in July 2008. (Inventor: Joseph Irudayaraj).

    Provisional

    • Nanobubbles for triggered release. IRUD-66920. (October 2014)
    • Chromatin Extraction by Solid Phase Reversible Immobilization and its structure analysis. 2014-IRUD-66768-01. (June 2014).
    • Rapid detection of multiple pathogens by fluorescence. PRF Reference number 2013-IRUD-66426. (Filed October 2013).
    • Abl Kinase Phosphorylation in living cells. PRF Reference number 2013-IRUD-66358. 17th Sept, 2012. (Filed in October 2013)
    • Rapid detection of multiple pathogens by fluorescence. PRF Reference number 2013-IRUD-66426. (Filed October 2013)
    • Sensitive detection of biomolecules and threat agents by signal amplification using nanoparticles. 2012. PRF Reference Number: 66014.P1.US Application Number: 61/578,283
    • A method for detecting specific kinase activity in live cells. PRF Reference number 66128.P1.US. 2011. June 21, 2012.
    • 65218.P1.US-Single cell nanotools for in vivo analysis of chromatin components and gene expression. Provisional patent filed on Dec 15 th, 2008.
    • 64803.P1.US - Multiplex Biosensor Using Gold Nanostructures. Provisional patent application filed on Feb 23rd, 2007.
    • 64892.P1.US - Identity Profiling of Cell Surface Markers. Provisional patent filed on July, 2007.
    • C. 90063. PRF. Irudayaraj, J. and K. Haghighi. 1990. "GRAINFEM Software".


    INSTITUTIONAL / NATIONAL COLLABORATIONS AND ENGAGEMENTS

    Purdue University

    Active Collaborations

    1. Biochemistry: Ann Kirchmaier: Developing tools for single living cell epigenetic analysis and basic studies on chromosomal segregation (three NSF, one PCCR, two CTSI, an IUPUI-Purdue NIH center grants are awarded; 2009-present). A KECK foundation grant is awarded ($1.75 million).

    2. Basic Medical Sciences: (i) Sophie Lelievre: Co-PI in the Keck foundation grant. Current efforts focus on exploring epigenetic modification events in 3D cell cultures and exploring NuMA protein dynamics. (ii) Alice Chang: Detection of miRNA for cancer diagnosis (Showalter grant, $62.5k)

    3. Mechanical Engineering: (i) Gary Cheng: Graphene wrapped nanosensors-several efforts spanning basic material characteristics to biosensing is in progress. Three publications are in preparation on 3D graphene wrapped structures; (ii) Jong hyun Choi: Initiating collaborations in Nanobiotechnology. A recent paper was published in JACS (a premier journal in Chemistry); (iii) Pavlos Vlachos: To develop an understanding of cavitation when nanoparticles are excited by an ultrasound pulse.

    4. Biomedical Engineering: (ii) Craig Goergen: Ultrasound imaging of oxygen nanobubbles as contrast agents and for ultrasound triggered and focused drug release to targeted tumor sites. (iii) Ji-xin Cheng: Development of a Stimulated Raman Spectroscopy unit for label-free imaging and cancer screening; (iv) Sherry Harbin: Co-PI in the NIH-NIEHS-P42 Superfund center proposal on understanding cardiovascular development using 3D Organotypic models.

    5. Medicinal Chemistry and Molecular Pharmacology: Laurie Parker: In vivo phosphorylation mapping in single cells using peptide biosenosrs (a DoD grant and an NIH-NCI/IMAT is awarded). Chris Rochett: Single molecule studies of alpha synuclein in living cells to elucidate the structure of protein on nanoparticles.

    6. Biological Sciences: Dinesh Yernool (former faculty in Biological Sciences and presently directing the Structural Biology Core at Bindley Bioscience Center)- collaborating on cloning to develop optogenetic constructs to demonstrate epigenetic regulation.

    7. College of Veterinary Medicine: (i) Tim Bentley (DVM): On Animal models for brain cancer research; (ii) Dr. Sulma Mohammed (Comparative Pathobiology) on developing disposable biosensor strips for cervical cancer screening-an NIH grant submitted will be revised; (iii) Dr. Suresh Mittal on examining the stoichiometry of virus nanoparticles using single molecule tools (and NSF grant submitted is in review).

    8. Electrical and Computer Engineering: Collaborating with Dr. Babak Ziaie's group on developing strategies for the design of focused ultrasound transducers for triggered drug release.

    9. School of Health Sciences: Collaborating with Dr. Jennifer Freeman's group on microarray analysis of brain cancer cells to identify microRNAs and noncoding RNAs implicated in Glioblastoma. Our ultimate goals are to develop a panel of biomarkers for early diagnosis of brain cancer.

    10. Department of Nutrition Science: Collaborating with Dr. Barbara Stefanska of Next Generation Sequencing and Bioinformatics tools to map the epigenetic modifications in response to an environmental perturbation.

    11. Food Science: Dr. Lisa Mauer: Co-PI on Center for Food Safety Engineering grant (2007-present)- Biosensors development for pathogen detection.

    12. Anatomy (IU School of Medicine): (i) Dr. Feng Zhou: Key collaborator in the KECK foundation grant. Focus is on elucidating epigenetic mechanisms and loci specific detection of DNA methylation and hydroxymethylation in neural stem cells. (NIH-RO1 submitted - Epigenetics & fetal alcohol disorder), (ii) Dr. Reuben Kapur (director of Stem Cell research) is a key collaborator in the NIH-NIEHS-P42 superfund research center grant proposal led by Dr. Irudayaraj, (iii) Dr. Sunil Badve on tissue screening to quantify transcripts on a single cell basis in specific phenotypes. Other Collaborations: In discussion with researchers at the Brain Cancer Center and the Diabetics Core to develop biomarkers for early detection and/or targeted therapy.

    Concluded Collaborations

    13. Chemistry: Dor Ben-Amotz: Hyperspectral Raman imaging (NSF-IDBR grant completed)

    14. Department of Horticulture and Landscape Architecture: Burkhard Schulz: Nanoscale approach to molecular marker assisted plant breeding is in progress. (NSF grant completed)

    15. Biological Sciences: Dorothea Thompson: An NIH-RO1 for ~$980k is in progress (2009-2013) to study metal reduction sites in single pathogens. Julia Kirshner: Evaluation and Classification of metastatic breast cancer cells in 3D cultures.

    16. Agronomy: Cindy Nakatsu: Collaborative work on classification of Arthobacter.

    17. Veterinary Science: Rebecca Packer: Targeted delivery of liposomal particles for brain tumor therapy. This was expanded to assess the epigenetic state in glioblastoma (2011 - 2013)

    18. Mechanical Engineering: (i) Steven Werley group: Reverse Electrokinetic Patterning (REP) for label-free sorting and chemotaxis studies. An NSF proposal on "REP to study chemotaxis" was submitted. A DOE grant was also submitted. At present, further efforts to sort cell fractions are in discussion; (ii) Tim Fisher's group on spectroscopic analysis of grapheme structures. (iii) Bob Lucht: Funded (NSF-MRI) proposal on Acquisition of Pulse high energy laser system.

    19. (i) Akkus Ozan (at present a Professor in Case Western University): Diagnosis of crystal-based arthopathies via Raman spectroscopy (an NIH-R01 was awarded in July 2011).

    Other U.S. Universities

    • Iowa State University : Dr. Chenxu Yu: Pathogen Biosensors.
    • IUPUI : Hari Nakshatri (Department of Surgery): Multiplex detection of cell surface markers; Drs. Sunil Badve (MD) and George Sledge (MD) on tissue identity profiling.
    • Hershey Medical Center : Kristin Eckert (Dept of Biochemistry). Cancer detection
    • Penn State University: David Allara (Dept. Chemistry-Functionalization protocols for disease diagnosis); Ali Demirci (Infrared and UV heating for pathogen inactivation); Dr. Debroy, Director of E. coli Center (Biosensors for food security)
    • Cornell University: Harold Craighead (Applied and Engineering Physics): Fluorescence Correlation Spectroscopy for single molecule interaction monitoring
    • Marshall University: Ashok Vaseashta (Physics): Nanotechnology workshop
    • USDA- Dr. Fratamico on microbial metabolomics (Eastern Regional Research Center, PA)
    • Leigh University: Himanshu Jain: pathogen detectors

    Industry Collaborations

    Active (in discussion)

    • Novartis
      • Drug delivery systems
    • diraMED
      • SERS for human health
    • Abbott
      • Pathogen sensors
    Past (last ten years)
    • Covidien Pharmaceuticals (Hazelwood, MO) (2010-2012)
      • Drug screening [a grant for $90,000 is being formalized]
    • bioMerieux SA, France (2010-2012)
      • Pathogen detection sensors (awarded $84,000)
    • Amneal Pharmaceuticals Inc. (2012). Spectroscopic analysis of pharmaceuticals.
    • Perfint Inc. (Chennai, India)
      • Nanoparticle-based drug delivery
    • Millipore Inc. (2008)
      • DNA quantification methods using Raman spectroscopy
    • Ocean NanoTech Inc. Fayetteville, AR
      • Magnetic particle synthesis for multifunctional nanosensors
    • Aetos technologies (Darkfield microscopy) (2007)
      • Extension of Darkfield microscopy for cancer detection
    • Dow Agrosciences, Indianapolis, IN. Industry visit and seminar (2007)
      • Biosensor development for plant species differentiation
    • Lynntech Inc. (Dallas, TX) (Detection Technologies) (2006)
      • Development of a Pathogen detector by mid-infrared spectroscopy
    • Nestle Corp. Switzerland (Food characterization research) (2004)
      • Examination of lipid interaction using spectroscopy in chocolates
    • CSO Analytical Instruments, Reichert Inc., NJ. (Research equipment funding) (2003)
      • Surface Plasmon Resonance based sensors for pathogen detection
    • Evident Technologies (Quantum dots for food and health) (2003)
      • Tagging proteins with quantum dots–donation of quantum dot samples
    • Xenon Corp., MA (Pulse UV research equipment) (2003)
    • Electronic Sensor Technology, CA. (Sensor methods and protocol development) (2002)
      • Aroma sensor development–methodology development

    International Collaborations and engagements

    Recent

    UK

    Timothy Chevassut (MD, PhD), Brighton and Sussex Medical School. Theoretical modeling of epigenetic mechanisms upon drug treatment.

    India

    An Indo-US Science and Technology forum network proposal on "Nanomedical and Cellular Engineering" is funded (2010-2012) in collaboration with the Center for Cellular and Molecular Biology (CCMB, Hyderabad). Eight exchange (student) visits were completed between 2010-2012.

    Italy

    A visiting professor grant by the University of Sassari is awarded to develop a collaborative program with the Nanotechnology Institute (Dr. Greppi) in Sassari for biosensor development. A visit was completed in Summer 2011. A second visit (presented 4 lectures) was completed in Summer 2012.

    Brazil

    A federal grant (Brazil) to initiate collaboration with US scientists was awarded (PI is Adriana

    Franca, Mechanical Engineering, University of Minas Gerias). A 1-credit course on "Spectroscopy

    and biosensors" was offered as part of my instructional effort (attended by 15 students).

    China

    Visitor exchange with the Chinese Academy of Sciences (Changchun) for nanomaterials research.

    At present two CSC scholars conduct research in my lab.

    Past Five Years

    India

    Dr. Sudipta Maiti from Tata Institute of Fundamental Research (TIFR). (ii) Dr. Venkatraman and Clinician Dr. Roy from M.G. Ramachandra Medical College (Chennai) have collaborated on RF mediated ablation therapy.

    China

    Beijing University, Dept. Chemistry, Dr. Li Na. Instructional efforts on Biosensors and nano materials.

    Israel

    Collaborations with Dr. Jelinek's group (Head, Dept of Chemistry, Ben Gurion University). Proposal (BSF, Vaadia postdoctoral fellowship) on biomemitic calorimetric biosensors (awarded 2007).

    Korea

    Dr. Irudayaraj is a member of the "Nanomedicine" collaborative team that was awarded a 5-year $10 million award between Korean Institute of Science and Technology and Purdue. Collaborating on nanorod sensing methods [2007-2012].

    Belgium

    Collaborated with Dr. Bart Nicolai's group from the Catholic University in Leuven in the area of spectroscopic biosensors. Graduate course development in Biosensors (ABE 560) with Dr. Lammertyn in the MEMS Laboratory in Leuven.


    INSTRUCTION

    COURSES TAUGHT

    Purdue University (2005-present)

    • ChE 320, Statistical Modeling and Quality Enhancement. [Spring'12, Spring'13: Average Instructor rating: 3.7; Course rating: 4.1]
    • ABE 450, Finite Element Analysis in Design, Co-taught with Stroshine, 50% effort [Average Instructor rating: 4.1; Course rating: 4.0] [Fall 2007-Present]
    • ABE 485, Agricultural and Biological Engineering Senior Design [Average Instructor rating: 4.0; Course rating: 4.0]
    • ABE 560/BME 521, Biosensors: Fundamentals and Applications. Co-taught with Rickus and Porterfield, 33% effort [Average Instructor rating: 3.5; Course rating 3.7]
    • ABE 591T, Biophysics-an introduction, 100% effort (new course). [Average Instructor rating: 4.3, Course rating: 4.5]
    • ABE 591I, Computational methods in biological engineering, 100% effort (new course)
    • BME 695S, Single molecule methods, 100% effort
    • ABE 697, Graduate Seminar, 25% effort

    International Teaching Efforts

    Federal University of Minas Gerias, Bele Horizonte, Brazil, Department of Mechanical Engineering, 1 credit course on "Spectroscopy and Biosensors", October 2010.

    Beijing University, Department of Chemistry, 1 credit course on "Biosensors", June 2009.

    New Courses developed in Institutions prior to Purdue (1991-2005)

    The Pennsylvania State University (1998-2004)

    • Introduction to Bionanotechnology , Spring 2004
    • Introduction to Biosensors, Fall 1999, 2000, 2002, 2003
    • Instrumentation and Measurements , Spring 1999, 2000, 2001, 2002, 2003, 2004).

    Utah State University (1995-1997)

    • Principles of Biochemical Engineering, Spring 1998
    • Bioprocess Engineering , Fall 1995, 1996, 1997
    • Finite Element Analysis for Engineers and Scientists, Spring 1996, 1997

    University of Saskatchewan (1991-1994)

    • Added-value Processing, Spring 1992, 1994
    • Principles of Structures and Structural Design, Spring 1992, 1993, 1994
    • Systems Engineering , Fall 1991, 1992, 1993, 1994
    • Advance Finite Element Methods , Fall 1991, 1992, 1993
    • Numerical Methods , Spring 1993

    RESEARCH MENTORING

    UNDERGRADUATE RESEARCH MENTORING

    Purdue University (last 5 years)

    • Srujan Singh, BS (IIT Kharagpur), 2014-Development of SERS sensors.
    • Raghav Guarav, BTech (IIT, Bombay), 2014-Development of nanodelivery systems.
    • Manisit Das, BS Chemistry (IIT, Kanpur), 2014-Development of LF-IC sensors for pathogen detection.
    • Andrew Andis, BS Biological Engineering, 2011-12-Design of Single cell separation system.
    • Christina Millhouse, BS Biological Engineering, 2011-12 - Basic Molecular biology techniques.
    • Hyunwoo Chung, BS Biological Engineeirng, 2010 - MRI and PET imaging.
    • Josue Ordaz, BS Biological Engineering, 2010-present, FEELS program, "Technology for detecting epigenetic modifications".
    • Zach Mcbride (SROP and CIC undergrad from Mirian University), 2011 Summer program. "Quantum dot diffusion dynamics in single living cells", using FCS.
    • Melinda Steffey, BS Biochemistry, 2010-2011, "Molecular biology methods in FISH".
    • Chan Soo Park, BS Physics, 2010-2011, "Understanding nanoparticle aggregation"
    • Whitney Williams, BS Biological Sciences, 2010-2011, "Epigenetic modifications-an introduction".
    • Brett Marsh, BS Chemistry, 2010, "Nanoparticles for biosensing".
    • Ko Seong, BS Electrical Engineering, 2009-2010, Discovery Undergraduate Research Internship (DURI), Multiplex ion sensing in blood serum.
    • Lisa Bartkowiak, BS Agric. and Biol. Engineering, DURI 2009, Detection of metal ions in bacteria.
    • Tasneem Pishori, BS Biomedical Engineering, DURI 2008, Gold nanorod sensors.
    • Pelin Cox, BS Chemical Engineering, DURI 2008, Biosensors.
    • Sanjay Thakrar, BS Biomedical Engineering, DURI 2007-08, Nanosensors for biomedicine.
    • Nilesh Badve, BS Material Science and Engineering, Summer Undergraduate Researcher. Fellowship (SURF 2007) program, Synthesis of Core-Shell particles as sensor materials.
    • Jordan Heim, BS Physics, DURI 2007, Intracellular quantification of drugs, Pursuing Ph.D in Cornell University ( one manuscript published in Chem Phys Letters).
    • Leonard Kim, BS Agricultural and Biological Engineering, DURI 2006, NanoSPR concept for microorganism detection.
    • Lauren Hamamoto, BS Biomedical Engineering, DURI 2006, Raman spectroscopy for detecting cancer.
    • Matt Zikerlbach, BS Health Sciences, DURI 2006, Intracellular SERS monitoring, In Medical School
    • Xiaoda Yuan, BS Agricultural and Biological Engineering, DURI 2006, Single molecule microscopy for protein interaction.
    • Funian Xiao, BS Electrical and Computer Engineering, DURI 2006, SPR instrumentation design and validation. (ECE program)

    GRADUATE STUDENT MENTORING

    Purdue University

    NAME

    DEGREE

    GRADUATING YEAR

    CO-CHAIR

    TITLE

    1

    Cui Yi

    PhD

    07/2015

    NA

    Targeted therapy of brain cancer in dog models-drug delivery and epigenetics.

    2

    Pushpak Bhandari

    PhD

    07/2016

    NA

    Epigenetic regulation for loci-specific monitoring of modifications

    3

    Basudev Chowdhury

    PhD

    07/2014

    NA

    Gene regulation due to hydroxymethylcytosine in Leukemia cells

    4

    Nuri Damayanti

    PhD

    07/2015

    NA

    Technology development for phosphorylation screening in live cells

    5

    Jing Liu

    PhD

    07/2014

    NA

    Single molecule tools and super-resolution imaging of epigenetic modifications

    6

    Zhongwu Zhao

    PhD

    07/2015

    NA

    Epigenetic regulation and treatment

    7

    Ulhas Kadam

    PhD

    05/2014

    Schulz

    Detection of splice variants in single cells

    8

    Fang Yi

    MS

    07/2012

    NA

    Classification of cancers in 2D and 3D cultures by Raman spectroscopy

    9

    Leyla Nersin

    Ph.D

    07/2015

    NA

    Nanosensors and Raman spectroscopy driven onsite devices for virus detection

    10

    Joong Hee Min

    MS

    12/2012

    NA

    Plasmon hyperspectral imaging for detecting structure changes in alpha-synuclein

    11

    Sandeep Ravindranath

    PhD

    05/2011

    NA

    In vivo mapping of metal reduction sites in single bacterium

    12

    Jiji Chen

    PhD

    05/2011

    NA

    Single molecule tools for epigenetic analysis

    13

    Kyuwan Lee

    PhD

    05/2011

    NA

    In vivo mRNA detection using Plasmon imaging

    14

    Brittany Book

    MS

    12/2010

    NA

    Nobel metals as vehicles for drug delivery and targeting in human cancers

    15

    Sun Lan

    PhD

    12/2008

    NA

    Multiplex quantification of genetic material by Surface enhanced raman scattering

    16

    Tapasree Sarkar

    PhD

    06/2008

    NA

    Biophysical methods for understanding signaling cascades

    17

    Sandeep Ravindranath

    MS

    12/2009

    NA

    Spectroscopic and biosensor-based methods for pathogen detection

    18

    Heyjin Park

    MS

    07/2009

    Rickus

    Multiplex detection of cancer biomarkers using nano plasmonic sensors

    19

    Leo Varghese

    MS

    05/2007

    Rashid Bashir

    Interaction of gp16 protein and DNA using fluorescence correlation spectroscopy

    Graduate Students Supervised Prior to Purdue (PSU: The Pennsylvania State University; USU: Utah State University; USASK: University of Saskatchewan): 9 PhDs and 11 MS

    POSTDOCTORAL SCHOLARS MENTORING

    NAME

    DATE

    PROJECT

    Purdue

    1

    Wen Ren

    2013-present

    Nanoparticle oragami multistructures in biology

    2

    Samrat Choudhury

    2013-present

    Epigenetic modifications-Molecular methods

    3

    Xiaolei Wang

    2013-present

    Plasmonic imaging of biological interactions

    4

    Seunghyun Lee

    2012 - 2014

    Live cell monitoring of phosphorylation by SERS

    5

    Il-Hoon Cho

    2011-2014

    Biosensors for protein and whole cell detection

    6

    Chaoqing Dong

    2011-2012

    Single molecule quantification of drug compartmentalization

    7

    Cunlan Gao

    2009-2011

    Understanding chromatin folding by single molecule methods

    8

    Yuling Wang

    2009-2010

    Multifunctional nanoparticles for biosensor development

    9

    Pavan Kumar

    2008-2010

    Raman Chemical imaging of phosphorylation in single cells

    10

    Chungang Wang

    2007-2009

    Multifunctional nanomaterials for drug delivery and tracking

    11

    Rajeev Sinha

    2007

    Single molecule technology for protein interaction study

    12

    Yoriko Lill

    2007

    Single molecule tracking for cancer diagnostics

    13

    Ali Shamsaie

    2005-2007

    Raman Spectroscopy-Single particle sensing in cancer cells

    14

    Chenxu Yu

    2003-2007

    Nanoscale and spectroscopic methodologies for cancer detection

    Postdoctoral Scholars Supervised Prior to Purdue: 11

    MENTORING OF INTERNATIONAL SCHOLARS AND VISITORS

    Name

    Year

    Title, Country

    1

    Namrata Jaiswal

    2012-2013

    Environmental insults on epigenome

    2

    Ana Paula Craig

    2012-2013

    Spectroscopic characterization of biomaterials, UFMG, Brazil

    3

    Junpeng Jiang

    2011-2012

    Nanobiosensors for single cell detection

    4

    Sarah Voisin

    2011

    Profiling brain cancer by Raman spectroscopy, ens, France

    5

    Stefania Mura

    2009 - 2010

    Nanostructures for ultrasensitive pathogen detection, Italy

    6

    Zeeshan Mirza

    2009

    Nanoparticle synthesis for localized drug delivery, Pakistan

    7

    Suman Nag

    2007-2008

    Single molecule analysis of amyloid beta conformation, India

    8

    Nyeonsik Kim

    2007-2008

    NanoSPR-based cell identity profiling workstation, Kyung-pook National University, Korea

    9

    Mauro Zanelli

    2002-2003

    Biosensors for somatic cell count assessment, University of Milan, Italy

    10

    Francesco Tangorra

    2002-2003

    Spectroscopic determination of somatic cell counts in milk, University of Milan, Italy

    11

    Daebin Song

    2002-2003

    Amperometric biosensors for glucose and fructose monitoring, Gyeongsang National University, Korea

    12

    Jeroen Lammertyn

    2002-2003

    Amperometric sensor modeling and analysis using computational fluid dynamics, Catholic University Leuven, Belgium

    13

    Gabriela Clemente

    2000-2001

    Finite element analysis, Valencia Polytechnique, Spain

    14

    Heon Hwang

    1999-2000

    Sensors for food automation, Sungkyunkwan University, Korea


    ADMINISTRATION AND SEVICE TO UNIVERSITY

    I. Deputy Director, Bindley Bioscience Center (BBC), Discovery Park, Purdue University

    Website: http://www.purdue.edu/discoverypark/bioscience/

    The Deputy Director provides scientific leadership and assumes administrative responsibilities to manage the seven core facilities (Imaging, Drug Screening, Translational Pharmacology, Proteomics and Metabolomics, Biophysical Analysis, Flow Cytometry, and Informatics) in the BBC. Responsibilities include:

    (i) Providing scientific leadership to the cores facilities-Collaborations, Networking, Resource management and upgrade (including decisions on new instrumentation to remain state of the art)-In 2012-2013 the cores acquired instrumentation worth $5 million)

    (ii) Chair of the Biosafety Committee-this committee is responsible for the maintenance of biosafety standards, educational modules and biosafety training in addition to the programs offered by the Institutional Biosafety Committee (IBC) and the Radiological and Environmental Management (REM) Department at Purdue University.

    (iii) Chair of Space Committee-A committee that makes recommendations for space (100,000 sq ft facility) assignment-key goal is to enhance collaborations and multidisciplinary research by complementary groups and shared instrumentation

    (iv) Human Resource Management. The BBC is staffed by 14 scientists and 6 support staff. I provide guidance through 1-1 as well as team meetings, hiring and downsizing, promotions, and staff relations.

    (v) Engagement and Networking-I play a leading role in promoting BBC capabilities both campus-wide and state-wide. In my efforts to improve engagement, I am organizing a BBC Industry Forum focused on Biological technology development and its impact to discuss grand challenges and Industry-University relations with an Industry Panel and over 30 Industry guests among faculty. This is the first effort at this scale in Purdue (event date is 09/06/2013).

    II. Co-Leader of the Drug Discovery and Molecular Sensing Core of the Purdue Center

    for Cancer Research (PCCR).

    Website: http://www.cancerresearch.purdue.edu/

    The Executive Committee consists of leaders from the five focus areas [Cell identity and Signaling, Medicinal Chemistry, Drug Discovery and Molecular Sensing, Chemical and Structural Biology, Medicinal Chemistry] of the PCCR, along with the Director (Dr. Tim Ratliff) and the Associate Director (Dr. Andrew Mesacar). Key responsibilities of the Core leaders are:

    1) Participate in funding and in decisions relating to research area thrusts of the PCCR

    2) Promote intra-core collaborations through supplemental discretionary funding

    3) Assist in annual progress reporting as well as in presentations and document preparation for Center renewal ($1 million/year for 5 years)

    III. Graduate Chair of Agricultural and Biological Engineering (ABE), The ABE graduate program in Purdue has been ranked #1 ranked consecutively during the years 2009-2013. The program has ~110 graduate students specializing in the areas of Biological Engineering, Bioprocess and Food Engineering, Ecological Engineering, and Agricultural Engineering. Contributed toward the development of new Biological Engineering & Technology (BET) graduate program, which currently has over 40 graduate students. Instrumental in championing and developing a new interdisciplinary Biological Engineering training group as part of the Purdue Life Sciences Graduate program (PULSE). The Graduate committee is represented by the chair and 4 faculty. Key responsibilities include admissions, recruitment, scholarship allocation, graduate plan of study compliance, student awards, and Graduate seminar.

    Other Key Committee Leadership duties : Play a key administrative service role through my involvement with the Strategic Advisory Committee to the Dean (College of Engineering, Ranked #8 Graduate and #10 in Undergraduate program, US News and World report March 2013), to provide critical evaluation of the blue skies plan and assessment of the strategic direction to improve the ranking of the College of Engineering.

    Invested extensively in Purdue's Discovery Park operations and represented my department and the college both at the Bindley Bioscience Center (BBC) and the Birck Nanotechnology Center (BNC). Through the co-directed Physiological Sensing Facility (housed in BBC), my students and I have generously donated our time to promote biological engineering research and educational efforts to the public through Discovery Park organized tours and symposiums. As a member of the Task Force Committee to the BBC I was fortunate enough to participate in discussions to provide a strategic vision to BBC. Co-lead the Breast Cancer Discovery Group and core member of the International Breast Cancer Prevention Committee. The task of our think tank committee is to provide a global vision on breast cancer prevention. Participated in faculty search committees (both as a member and Chair) across disciplines as well as in the College Promotion and Tenure committee (2009-2012).

    Major committee assignments in the Department, School and / or University at Purdue

    • Department Committees
    • Graduate Chair, ABE (2009-2012)
    • Co-Chair, Biological Engineering Curriculum Committee (2010-Present)
    • Awards Committee, ABE (2005-Present)
    • Chair, Faculty Search Committee, Biological Engineering (2013-present)

    College Committees

    • College of Engineering, Strategic Advisor Committee to the Dean (2009-Present)
    • College of Engineering Curriculum Committee (2007-2011)
    • College of Engineering Graduate Committee (2009-Present)
    • College of Agriculture Graduate Council (2009-Present)
    • Advisory Board, Life Sciences Microscopy Facility (2010 - Present)
    • College of Agriculture, Outcome Based Program Improvement Committee, 2008-2009
    • Faculty Affairs Committee (2006-2010)

    University/Discovery Park Committees

    • Bindley Bioscience Center, Executive Committee member (2007-Present)
    • Purdue Center for Cancer Research, Executive Committee member (2012-present)
    • Bindley Bioscience Center Task Force (2010)
    • Bindley Bioscience Center Safety Committee (2007-Present)
    • Other
      • Physiological Sensing Facility, Co-director (2005-Present)
      • BioNanoTechnology Program (BNTP)/Nanomedicine Development Center (NDC) seminar series, Chair (2006-2007)
      • Biophysics Core, Bindley Bioscience Center (2006-Present)
    • Full member, Purdue Center for Cancer Research (2006-Present)
      • Core-Committee member, International Breast Cancer Prevention (IBCN)
      • Co-Leader, Breast Cancer Discovery Group, PCCR (2010-Present)
    • Full member, Birck Nanotechnology Center (2008-Present)
    • Endowded Chair faculty search committee in Cancer Therapeutics, Medicinal Chemistry and Molecular Pharmacology (2008)

    Other Campus-wide Initiatives

    Multicultural diversity forum workshop. April, 2007. Purdue University.

    Faculty advisor, Minority Students Apprenticeship Program (Penn State, 2000)

    Freshman and inter-department seminars (six 45-minute sessions/year) (1999-2004)

    Freshman advising (six 3-hour advising activities/year, Penn State (1999-2004)

    Freshman Women in Engineering Forum, Penn State (1999-2004)

    Faculty Social Activities Committee, Penn State (1999-2003)

    Faculty Advisor, European Students Club, Penn State (2000-2003)

    SERVICE TO THE PROFESSION

    Serve and represent my profession both at the national and international level. I was a standing member of the NIH's NANO panel (2007-2010) and have generously assisted the ARRA panels in reviewing both Transformative Research and Challenge Grants. I am also a member of NIH's new College of CSR Reviewers (2010-12). I have chaired the NIH's Interdisciplinary Molecular Sciences and Training Panel.

    Review NSF and DOE Career grants. Serve on numerous adhoc reviews for NSF, NIH, DOD, and Susan Komen Foundation. Serve on several journal editorial boards and contribute time to programs both within and outside the U.S.; e.g. USDA: nanotechnology program and Biosystems engineering program evaluation (Belgium).

    We reach out to students in the middle and high schools to explain the meaning and role of Biological Engineering. As an outcome of such efforts, two students (7th and 8th grade) have won the Gold Medal in the Junior division as well as the Purdue Cancer Center Award, College of Science Dean's award and the Eli Lilly Labs Trophy in 2009. Other outreach activities include participation in the Minorities education program and the Summer school program for high school students. At present one high school student and three undergraduate students are involved in bioNanotechnology related research in my laboratory.

    Grant Review

    • Chair, NIH Interdisciplinary Molecular Sciences and Training panel (2010-2012)
    • Panel member, NIH College of CSR Reviewers (2010 - 2012)
    • Panel member, NIH Single Cell Analysis, Special Review Panel (2011-present)
    • Panel member, NIH Bioengineering Sciences and Technology (2011-present)
    • Panel member, NIH-Nanotechnology-M(01), Study section member (2007-2010)
    • Panel member, NIH SBIR ARRA Study Section, (2009 - present)
    • Panel member, NSF SBIR (Biological Instrumentation & Biomedical Devices) (2008-present)
    • Panel member, Susan Komen Foundation, Postdoctoral Fellowship program (2011-present)
    • Panel member, DOE Career grant, Advanced Instrumentation Program (2011)
    • Panel member, DOD, CDMRP Idea grants for the Prostate Cancer program (2009-2010)
    • Panel member, USDA- NRI, Food Characterization and processing, (2002, 2003)
    • Panel member, National Academies, Pathogen/Disease Detection program (2008)
    • Panel member, Department of Homeland Security, Institute of Defense, Biothreat agents (2004)
    • Ad hoc Reviewer
      • Several NSF, NIH, DoD, DARPA, USAMRMC programs
      • NSF International Collaborative grants program (2007)
      • USDA NRI and SBIR panels (2004-Present)
      • National Science and Engineering Research Council, Canada (2000-present)
      • Singapore Biomedical Research Council, Agency for Research, and Tech (2010-present)
      • Medical Research Council (UK, 2008-present)
      • Bilateral Science Foundation (US-Israel); BARD (US-Israel) (2004-present)
      • European Agricultural Research Agency (2006-2007)
    • Journal Editorial Board
    • Editorial Board, NanoSciTech Open Library (2014-present)
    • Editorial Board, Journal of Nanotechnology: Nanomedicine & Nanobiotechnology (NTMB) (2014-present)
    • Editorial Board, Cancer and Oncology (2014-present)
    • Editorial Board, Austin Journal of Biosensors and Bioelectronics (2014-present)
    • Editorial Board, International Journal of Nano studies and Technology (2013-present)
    • Editorial Board, Journal on Nanotube Therapy (2010-present)
    • Editorial Board, Journal of Pediatric Biochemistry, publishes articles in pediatric medicine and biochemical aspects to study childhood diseases in body fluids, cells or tissues. (2009-present)
    • Editorial Board, Journal of Molecular Imaging and Dynamics, OMICS Publishing (2010-present)
    • Editorial Board, Research Letters in Nanotechnology. Hindawi Publications. Aspects of Nanoscience and technology applied to cancer (2008-present)
    • Associate Editor, Journal of Cancer Nanotechnology: Basic, Translational, and Clinical research" Springer-Verlag. (2009-present)
    • Editorial Board, Pathogen Sensors. Special Edition of Sensors Journal (2008-2009)
    • Editorial Board, Sensing and Instrumentation for Food Quality (2008-present)
    • Editorial Board, The Open Biomarkers Journal, Betham Science Publishers (2008-present)

    Journal manuscript Peer Review (Review at least 3 articles/month):

    • Angewandte Chemie
    • ACS Nano
    • Nano Letters
    • Nature Nanotech, Nature Commun.
    • JACS
    • Advanced Functional Materials
    • Advanced Materials
    • J. Physical Chemistry
    • Nanomedicine
    • Analytical Chemistry
    • European Journal of Chemistry
    • Langmuir
    • J. Chemical Physics
    • Biophysical Journal
    • Vibrational Spectroscopy
    • PLOS-One
    • Biopolymers
    • Anal Chem. Acta
    • Biosensors and
    • Bioelectronics
    • Lab on Chip
    • J. Biol. Chem.
    • Applied Spectroscopy

    MEMBERSHIP IN PROFESSIONAL SOCIETIES

    Society Memberships

    1. member, American Chemical Society (2007-Present)

    2. member, Biophysical Journal Society (2008-Present)

    3. member, SPIE (2006-Present)

    4. member PITTCON (2007-Present)

    5. member, American Association for Advancement in Science (2012-present)

    6. member, American Society for Agricultural and Biological Engineering

    7. Institute of Food Technologists

    Institute of Biological Engineering (member, 2003-Present)

    1. Program chair of Bionanotechnology, IBE (2003-2004)

    2. Elected council member at-large, IBE (2006-2007) (member, 2007-Present)

    International program activities

    1. Organizing Committee, Symposium on Breast Cancer Prevention, Rennes, France, Oct'11

    2. Panel Member, Review of Departments and research programs in the College of Science and Technology (a 15 member panel selected internationally), Sept'11

    3. Advisory Council, MBA Program, Maxvalue Online (India's first online business school), 2009 - present

    4. Advisory Panel, International Drying Symposium, Advisory Panel (2004), India

    5. Organizing Committee: International Conference on Micro and nanotechnologies

    ICMNT 2006, Tizi-Ouzou, Algeria, 19-23 Nov, 2006.

    6. Korean Institute of Science and Technology-Purdue symposium, Purdue University, May

    2013.

    7. Organizing Committee: Symposium on Bionanotechnology and Nanomaterials, Osmania

    University, Hyderabad. India. March 2014.

    American Society of Agricultural and Biological Engineers

    1. Associate Editor, IET Division, ASAE (1997-2001)

    2. Executive Committee (FPE-01) (2000-2005)

    3. Steering Committee (FPE-02) (2000-2005)

    4. International Meetings Committee (E-10) (2000-2005)

    5. General Programs Committee, Vice Chair (FPE-06) (2002-2003)

    6. Biosensors Committee, Chair (BE 23) (2003-2004)

    Regional Committee participations

    1. North Central 1031 Biosensors and Nanotechnology Regional Project, Chair (2005-2006)

    CERTIFICATION - Engineer in Training, Saskatchewan, Canada, 1992

    COMMUNITY INITIATIVES

    Member, International Breast Cancer Prevention and Nutrition advisory group: Goals of this group are to promote cancer awareness in less developed countries, fund raising, and contribute articles to cancer communication materials. (2010-present)

    Presented several lectures to high schools on nanotechnology and biological Engineering through campus initiatives. (1995-2005)

    Hosted high school students in my laboratory to engage in research (2005-2012)

    Volunteer, Special Olympics, Winter games 1992, Saskatoon, Saskatchewan

    Volunteer, UNICEF, Saskatchewan, Canada (1992)

     
     
     
     
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