{"id":96,"date":"2013-08-02T15:42:44","date_gmt":"2013-08-02T15:42:44","guid":{"rendered":"http:\/\/elements.chem.umass.edu\/farkasgroup\/?page_id=96"},"modified":"2025-07-16T21:18:51","modified_gmt":"2025-07-16T21:18:51","slug":"publications","status":"publish","type":"page","link":"https:\/\/elements.chem.umass.edu\/farkasgroup\/publications\/","title":{"rendered":"Publications"},"content":{"rendered":"
Publications<\/div>\n
<\/div>\n

Independent\u00a0Research (Farkas Group, UMass, Amherst):<\/h2>\n
    \n
  1. Chhe, K., Hegde, M. S., Taylor, S. R., Farkas, M. E. \u201cCircadian Effects of Melatonin Receptor-Targeting Molecules in vitro<\/em>.\u201d Int. J. Mol. Sci. <\/em>2024<\/strong>, 25<\/em>, <\/strong>13508.<\/li>\n
  2. Zhang, Z., Liu, Y., Jiang, M., Mas-Rosario, J. A.<\/span>, Fedeli, S., Cao-Milan, R., Liu, L., Winters, K. J.<\/span>, Hirschbiegel, C.-M., Nabawy, A., Huang, R., Farkas, M. E., Rotello, V. M. \u201cPolarization of Macrophages to an Anti-Cancer Phenotype through In Situ<\/em> Uncaging of a TLR 7\/8 Agonist using Bioorthogonal Nanozymes.\u201d Chem. Sci. <\/em>2024<\/strong>, 15<\/em>, 2486-2494.<\/li>\n
  3. Rokkam, S. K.,* Mas-Rosario, J. A.<\/span>,* Joshi, B. P.<\/span>, Joshi, M., Choudhury, A. R., Kar, S., Golakoti, N. R., Farkas, M. E. \u201cDiarylidene-N-Methyl-4-Piperidones and Spirobibenzopyrans as Antioxidant and Anti-Inflammatory Agents.\u201d Chem. Biodivers.\u00a0<\/em>2023<\/strong>,\u00a020<\/em>, e202300822.<\/li>\n
  4. Mas-Rosario, J. A., Medor, J. D., Jeffway, M. I., Martinez-Montes, J. M., Farkas, M. E. “Murine Macrophage-Based iNos Reporter Reveals Polarization and Reprogramming in the Context of Breast Cancer.”\u00a0Front. Oncol. <\/em>2023<\/strong>,\u00a013<\/em>, 1151384.<\/li>\n
  5. Jeon, T., Luther, D. C., Goswami, R., Bell, C., Nagaraj, H., Cicek, Y. A., Huang, R., Mas-Rosario, J. A.<\/span>, Elia, J. L., Im, J., Lee, Y.-W., Liu, Y., Scaletti, F., Farkas, M. E.<\/span>, Mager, J., Rotello, V. M. “Engineered Polymer-siRNA Polyplexes Provide Effective Treatment of Lung Inflammation.”\u00a0ACS Nano<\/em>\u00a02023<\/strong>,\u00a017<\/em>, 4315-4326.<\/li>\n
  6. Lellupitiyage Don, S. S., Mas-Rosario, J. A., Lin, H.-H., Nguyen, M. N., Taylor, S. R., Farkas, M. E. “Macrophage Circadian Rhythms are Differentially Affected Based on Stimuli.” Integr. Biol. <\/em>2022<\/strong>, 14<\/em>, 62-75.<\/li>\n
  7. Das, R., Hardie, J.<\/span>, Joshi, B. P.<\/span>, Zhang, X., Gupta, A., Luther, D. C., Farkas, M. E.,* Rotello, V. M.* “Macrophage-Encapsulated Bioorthogonal Nanozymes for Targeting Cancer Cells.” JACS Au<\/em>\u00a02022<\/strong>,\u00a02<\/em>, 1679-1685.<\/li>\n
  8. Hardie, J.<\/span>, Makabenta, J., Gupta, A., Huang, R., Cao-Milan, R., Goswami, R., Zhang, X., Abdulpurkar, P., Farkas, M. E.<\/span>, Rotello, V. M. “Selective Treatment of Intracellular Bacterial Infections using Host Cell-Targeted Bioorthogonal Nanozymes.” Mat. Horiz. <\/em>2022<\/strong>, 9<\/em>, 1489-1494.<\/li>\n
  9. Lin, H.-H., Taylor, S. R., Farkas, M. E. “Circadian Alterations Increase with Progression in a Patient-Derived Cell Culture Model of Breast Cancer.” Clocks & Sleep <\/em>2021<\/strong>, 3<\/em>, 598-608.<\/li>\n
  10. Sikora, K. N., Castellanos-Garcia, L. J., Hardie, J.<\/span>, Liu, Y., Farkas, M. E.<\/span>, Rotello, V. M., Vachet, R. W. “Nanodelivery Vehicles Induce Remote Biochemical Changes In Vivo.” Nanoscale\u00a0<\/em>2021<\/strong>,\u00a013<\/em>, 12623-12633.<\/li>\n
  11. Lellupitiyage Don, S. S., Robertson, K. L., Lin, H.-H., Labriola, C., Harrington, M. E., Taylor, S. R., Farkas, M. E. “Nobiletin Affects Circadian Rhythms and Oncogenic Characteristics in a Cell-Dependent Manner.” PLoS ONE <\/em>2020<\/strong>,\u00a015<\/em>, e0236315.<\/li>\n
  12. Geng, Y.,* Hardie, J.<\/span>,* Landis, R. F., Mas-Rosario, J. A.<\/span>, Chattopadhyay, A. N., Keshri, P., Sun, J., Rizzo, E. M.<\/span>, Gopalakrishnan, S., Farkas, M. E.<\/span>, Rotello, V. M. “High-Content and High-Throughput Identification of Macrophage Polarization Phenotypes.” Chem. Sci<\/em>.<\/em> 2020<\/strong>, 11, <\/em>8231-8239.<\/li>\n
  13. Lin, H.-H., Robertson, K. L., Bisbee, H. A., Farkas, M. E. “Oncogenic and Circadian Effects of Small Molecules Directly and Indirectly Targeting the Core Circadian Clock.” Integr. Cancer Ther. <\/em>2020, <\/strong>19, <\/em>1-12.<\/li>\n
  14. Lin, H.-H., Robertson, K. L., Lellupitiyage Don, S. S., Taylor, S. R., Farkas, M. E. “Chemical Modulation of Circadian Rhythms and Assessment of Cellular Behavior via Indirubin and Derivatives.”\u00a0Method. Enzymol.\u00a0<\/em>2020<\/strong>,\u00a0639<\/em>, 115-140.<\/li>\n
  15. Sikora, K. N., Hardie, J. M.<\/span>, Castellanos-Garcia, L. J., Liu, Y., Reinhardt, B. M., Farkas, M. E.<\/span>, Rotello, V. M., Vachet, R. W. “Dual Mass Spectrometric Tissue Imaging of Nanocarrier Distributions and Their Biochemical Effects.” Anal. Chem.<\/em>\u00a02020<\/strong>,\u00a092<\/em>, 2011-2018<\/li>\n
  16. Hardie, J., Mas-Rosario, J. A., Ha, S., Rizzo, E. M., Farkas, M. E. “Macrophage Activation by a Substituted Pyrimido[5,4-b] Indole Increases Anti-Cancer Activity.”\u00a0Pharmacol<\/em>. Res.<\/em> 2019<\/strong>, 148, <\/em>104452.<\/li>\n
  17. Lellupitiyage Don, S. S.,* Lin, H.-H.,* Furtado, J. J., Qraitem, M., Taylor, S. R., Farkas, M. E. “Circadian Oscillations Persist in Low Malignancy Breast Cancer Cells.” Cell Cycle. <\/em>2019, <\/strong>18, <\/em>2447-2453.<\/li>\n
  18. Lin, H.-H., Qraitem, M., Lian, Y., Taylor, S. R.,* Farkas, M. E.* “Analyses of Bmal1<\/em> and\u00a0Per2<\/em> Oscillations in a Model of Breast Cancer Reveal Changes with Malignancy.”\u00a0Integr. Cancer Ther.\u00a0<\/em>2019,\u00a0<\/strong>18<\/em>, 1-13.<\/li>\n
  19. Hardie, J.<\/span>, Huo, S., Jiang, Y., Liang, X.-J., Farkas, M. E.<\/span>, Rotello, V. M. “RNAi Nanomaterials and Nanovehicles: Inorganic Nanoparticles for RNAi.” in\u00a0Handbook of Nanomaterials for Cancer Theranostics. <\/em>Elsevier.\u00a02018<\/strong>, 537-550.<\/li>\n
  20. Jiang, Y.,* Hardie, J.<\/span>,* Liu, Y., Ray, M., Luo, X., Das, R., Landis, R. F., Farkas, M. E.<\/span>, Rotello, V. M. “Nanocapsule-Mediated Cytosolic siRNA Delivery for Anti-Inflammatory Treatment.” J. Control Release.\u00a0<\/em>2018,<\/strong>\u00a0283<\/em>, 235-240.<\/li>\n
  21. Joshi, B. P.,* Hardie, J.,* Mingroni, M. A.,* Basabrain, A. O., Paracha, A., Farkas, M. E., “Surface-Modified Macrophages Facilitate Tracking of Breast Cancer-Immune Interactions.” ACS Chem. Biol.\u00a0<\/em>2018<\/strong>,\u00a013<\/em>, 2339-2346.<\/li>\n
  22. Lin, H.-H., Farkas, M. E., “Altered Circadian Rhythms and Breast Cancer: From the Human to the Molecular Level.” Front. Endocrinol.\u00a0<\/em>2018.<\/strong>\u00a09, <\/i>218. (In special issue: Disorders of Circadian Rhythms)<\/em><\/li>\n
  23. Joshi, B. P., Hardie, J., Farkas, M. E., “Harnessing Biology to Deliver Therapeutic and Imaging Entities via Cell-Based Methods.” Chem. Eur. J.\u00a0<\/em>2018<\/strong>. 18<\/em>, 8717-8726<\/li>\n
  24. Ray, M.,* Lee, Y.-W.,*\u00a0Hardie, J.<\/span>, Mout, R., Tonga, G. Y.,\u00a0Farkas, M. E.<\/span>, Rotello, V. M. “CRISPRed Macrophages for Cell-Based Immunotherapy.” Bioconj. Chem.<\/em>\u00a02018.<\/strong>\u00a029,\u00a0<\/em>445-450<\/li>\n
  25. Hardie, J.<\/span>,* Jiang, Y.,*\u00a0Tetrault, E. R.<\/span>, Ghazi, P. C.<\/span>, Tonga, G. Y., Farkas, M. E.<\/span>,* Rotello, V. M.* “Simulataneous Cytosolic Delivery of a Chemotherapeutic and siRNA using Nanoparticle-Stabilized Nanocapsules.” Nanotechnology<\/em>.\u00a02016.\u00a0<\/strong>27,\u00a0<\/em>374001<\/li>\n
  26. Fu, A., Tang, R., Hardie<\/span>, J.<\/span>, Farkas<\/span>, M. E<\/span>.,\u00a0Rotello, V. M. “Promises and Pitfalls of Intracellular Delivery of Proteins.” Bioconj. Chem.<\/em>\u00a02014.\u00a0<\/strong>25<\/em>, 1602-1608<\/li>\n<\/ol>\n

    *Joint first or corresponding-authorship<\/p>\n

    Postdoctoral Research (Francis Group, UC Berkeley):<\/h2>\n
      \n
    1. Aanei, I. L., ElSohly, A. M.,\u00a0Farkas, M. E.<\/span>,\u00a0Netirojjanakul, C., Regan, M., Murphy, S. T., O’Neil, J. P., Seo, Y., Francis, M. B. “Biodistribution of Antibody-MS2 Viral Capsid Conjugates in Breast Cancer Models.”\u00a0Mol. Pharm.\u00a0<\/em>2016.\u00a0<\/strong>1<\/em>3<\/em>, 3764-3772.<\/li>\n
    2. ElSohly, A. M., Netirojjanakul, C., Aanei, I. L., Jager, A., Bendall, S., Farkas, M. E.<\/span>, Nolan, G. P., Francis, M. B. \u201cSynthetically Modified Viral Capsids as Versatile Carriers for Use in Antibody-based Cell Targeting.\u201d Bioconj. Chem.<\/em> 2015.<\/strong> 26,<\/em> 1590-1596.<\/li>\n
    3. Farkas, M. E.<\/span>, Aanei, A. L., Behrens, C. R., Tong, G. J., Murphy, S. T., O\u2019Neil, J. P., Francis, M. B.\u00a0\u201cPET Imaging and Biodistribution of Chemically Modified Bacteriophage MS2.\u201d Mol. Pharm.<\/em> 2013.\u00a0<\/strong>10,<\/em> 69-76.<\/li>\n
    4. Carrico, Z. M.*, Farkas, M. E.*<\/span>, Yu, Z., Hsiao, S. C., Marks, J. D., Chokhawala, H., Clark, D. S.,\u00a0Francis, M. B. \u201cN-Terminal Labeling of Filamentous Phage to Create Cancer Marker Imaging Agents.\u201d\u00a0ACS Nano.<\/em> 2012.<\/strong> 6,<\/em> 6675-6680.<\/li>\n<\/ol>\n

      *Joint first-authorship<\/p>\n

      Graduate Research (Dervan Group, Caltech):<\/h2>\n
        \n
      1. Farkas, M. E.<\/span>, Li, B. C., Dose, C., Dervan, Peter B. \u201cDNA Sequence Selectivity of Hairpin Polyamide\u00a0Turn Units.\u201d Bioorg. Med. Chem. Lett.<\/em> 2009<\/strong>, 19,<\/em> 3919-3923.<\/li>\n
      2. Dose, C., Farkas, M. E.<\/span>, Chenoweth, D. M., Dervan, P. B. \u201cNext Generation Hairpin Polyamides with\u00a0(R)-3,4-Diaminobutyric Acid Turn Unit.\u201d J. Am. Chem. Soc.<\/em> 2008<\/strong>, 130,<\/em> 6859-6866.<\/li>\n
      3. Chou, C. J., Farkas, M. E.<\/span>, Tsai, S. M., Alvarez, D. A., Dervan, P. B., Gottesfeld, J. M. \u201cSmall\u00a0Molecules Targeting Histone H4 as Potential Therapeutics for Chronic Myelogenous Leukemia.\u201d Mol.\u00a0Cancer. Ther.<\/em> 2008<\/strong>, 7<\/em>, 769-778.<\/li>\n
      4. Farkas, M. E.<\/span>, Tsai, S. M., Dervan, P. B. \u201c\u03b1 -Diaminobutyric Acid-Linked Hairpin Polyamides.\u201d\u00a0Bioorg. Med. Chem.<\/em> 2007<\/strong>, 15<\/em>, 6927-6936.<\/li>\n
      5. Nickols, N. G., Jacobs, C. S., Farkas, M. E.<\/span>, Dervan, P. B. \u201cModulating Hypoxia-Inducible\u00a0Transcription by Disrupting the HIF-1-DNA Interface.\u201d ACS Chem. Biol.<\/em> 2007<\/strong>, 2,<\/em> 561-571.<\/li>\n
      6. Hsu, C. F., Phillips, J. W., Trauger, J. W., Farkas, M. E.<\/span>, Belitsky, J. M., Heckel, A., Olenyuk, B. Z.,\u00a0Puckett, J. W., Wang, C. C. C., Dervan, P. B. \u201cCompletion of a Programmable DNA-Binding Small\u00a0Molecule Library.\u201d Tetrahedron.<\/em> 2007<\/strong>, 63<\/em>, 6146-6151.<\/li>\n
      7. Tsai, S. M., Farkas, M. E.<\/span>, Chou, C. J., Gottesfeld, J. M., Dervan, P. B. \u201cUnanticipated Differences\u00a0Between \u03b1- and \u03b3-Diaminobutyric Acid-Linked Hairpin Polyamide-Alkylator Conjugates.\u201d Nucleic\u00a0Acids Res.<\/em> 2007<\/strong>, 35<\/em>, 307-316.<\/li>\n
      8. Nickols, N. G., Jacobs, C. S., Farkas, M. E.<\/span>, Dervan, P. B. \u201cImproved Nuclear Localization of DNA-Binding Polyamides.\u201d Nucleic Acids Res.<\/em> 2007<\/strong>, 35<\/em>, 363-370.<\/li>\n<\/ol>\n

        Industrial Research (Discovery Chemistry Group, BMS):<\/h2>\n
          \n
        1. Yeung, K. S, Qiu, Z., Farkas, M. E.<\/span>, Xue, Q., Regueiro-Ren, A., Yang, Z., Bender, J. A., Good, A. C.,\u00a0Kadow, J. F. \u201cAn Efficient One-Pot Synthesis of 3-Glyoxylic Acids of Electron-Deficient Substituted\u00a0Azaindoles by Ionic Liquid Imidazolium Chloroaluminate-Promoted Friedel-Crafts Acylation.\u201d\u00a0Tetrahedon Lett.<\/em> 2008<\/strong>, 43<\/em>, 6250-6253.<\/li>\n
        2. Yeung, K. S., Farkas, M. E.<\/span>, Kadow, J. F., Meanwell, N. A. \u201cA Base-Catalyzed, Direct Synthesis of\u00a03,5-Disubstituted 1,2,4-Triazoles from Nitriles and Hydrazides.\u201d Tetrahedron Lett.<\/em> 2005<\/strong>, 46<\/em>, 3429-3432.<\/li>\n
        3. Yeung, K. S., Farkas, M. E.<\/span>, Qiu, Z., Yang, Z. \u201cFriedel-Crafts Acylation of Indoles in Acidic\u00a0Imidazolium Chloroaluminate Ionic Liquid at Room Temperature.\u201d Tetrahedron Lett.<\/em> 2002<\/strong>, 43<\/em>, 5793-5795.<\/li>\n<\/ol>\n

          Patents:<\/h2>\n
            \n
          1. “Surface-Modified Macrophages for Cell-Based Delivery.” Farkas, M. E. USSN 62\/373,274; filed August 7, 2017.<\/li>\n
          2. “Inhibitors for Steroid Response Elements and RNA Polymerase II and Related Methods.” Dervan, P. B., Nickols, N. G., Jacobs, C. S., Farkas, M. E., Harki, D. A. USSN 14\/027,073; U.S. Patent #20140194483 issued October 7, 2014.<\/li>\n
          3. \u201cIndole, Azaindole, and Related Heterocyclic N-Substituted Piperazine Derivatives.\u201d Yeung, K. S.,\u00a0Farkas, M.E.<\/span>, Kadow, J. F., Meanwell, N. A., Taylor, M., Johnston, D., Coulter, T. S., Wright, J. J. K.\u00a0USSN 10\/871,931; U.S. Patent #8039486 issued October 18, 2011.<\/li>\n<\/ol>\n","protected":false},"excerpt":{"rendered":"

            Publications Independent\u00a0Research (Farkas Group, UMass, Amherst): Chhe, K., Hegde, M. S., Taylor, S. R., Farkas, M. E. \u201cCircadian Effects of Melatonin Receptor-Targeting Molecules in vitro.\u201d Int. J. Mol. Sci. 2024, 25, 13508. Zhang, Z., Liu, Y., Jiang, M., Mas-Rosario, J. … Continue reading →<\/span><\/a><\/p>\n","protected":false},"author":25,"featured_media":191,"parent":0,"menu_order":0,"comment_status":"closed","ping_status":"closed","template":"","meta":{"footnotes":""},"class_list":["post-96","page","type-page","status-publish","has-post-thumbnail","hentry"],"_links":{"self":[{"href":"https:\/\/elements.chem.umass.edu\/farkasgroup\/wp-json\/wp\/v2\/pages\/96","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/elements.chem.umass.edu\/farkasgroup\/wp-json\/wp\/v2\/pages"}],"about":[{"href":"https:\/\/elements.chem.umass.edu\/farkasgroup\/wp-json\/wp\/v2\/types\/page"}],"author":[{"embeddable":true,"href":"https:\/\/elements.chem.umass.edu\/farkasgroup\/wp-json\/wp\/v2\/users\/25"}],"replies":[{"embeddable":true,"href":"https:\/\/elements.chem.umass.edu\/farkasgroup\/wp-json\/wp\/v2\/comments?post=96"}],"version-history":[{"count":66,"href":"https:\/\/elements.chem.umass.edu\/farkasgroup\/wp-json\/wp\/v2\/pages\/96\/revisions"}],"predecessor-version":[{"id":1595,"href":"https:\/\/elements.chem.umass.edu\/farkasgroup\/wp-json\/wp\/v2\/pages\/96\/revisions\/1595"}],"wp:featuredmedia":[{"embeddable":true,"href":"https:\/\/elements.chem.umass.edu\/farkasgroup\/wp-json\/wp\/v2\/media\/191"}],"wp:attachment":[{"href":"https:\/\/elements.chem.umass.edu\/farkasgroup\/wp-json\/wp\/v2\/media?parent=96"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}