Publications

Publications

Independent Research (Farkas Group, UMass, Amherst):

  1. 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.” Front. Oncol. 2023, 13, 1151384.
  2. Jeon, T., Luther, D. C., Goswami, R., Bell, C., Nagaraj, H., Cicek, Y. A., Huang, R., Mas-Rosario, J. A., Elia, J. L., Im, J., Lee, Y.-W., Liu, Y., Scaletti, F., Farkas, M. E., Mager, J., Rotello, V. M. “Engineered Polymer-siRNA Polyplexes Provide Effective Treatment of Lung Inflammation.” ACS Nano 2023, 17, 4315-4326.
  3. 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. 2022, 14, 62-75.
  4. Das, R., Hardie, J., Joshi, B. P., Zhang, X., Gupta, A., Luther, D. C., Farkas, M. E.,* Rotello, V. M.* “Macrophage-Encapsulated Bioorthogonal Nanozymes for Targeting Cancer Cells.” JACS Au 2022, 2, 1679-1685.
  5. Hardie, J., Makabenta, J., Gupta, A., Huang, R., Cao-Milan, R., Goswami, R., Zhang, X., Abdulpurkar, P., Farkas, M. E., Rotello, V. M. “Selective Treatment of Intracellular Bacterial Infections using Host Cell-Targeted Bioorthogonal Nanozymes.” Mat. Horiz. 2022, 9, 1489-1494.
  6. 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 2021, 3, 598-608.
  7. Sikora, K. N., Castellanos-Garcia, L. J., Hardie, J., Liu, Y., Farkas, M. E., Rotello, V. M., Vachet, R. W. “Nanodelivery Vehicles Induce Remote Biochemical Changes In Vivo.” Nanoscale 2021, 13, 12623-12633.
  8. 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 2020, 15, e0236315.
  9. Geng, Y.,* Hardie, J.,* Landis, R. F., Mas-Rosario, J. A., Chattopadhyay, A. N., Keshri, P., Sun, J., Rizzo, E. M., Gopalakrishnan, S., Farkas, M. E., Rotello, V. M. “High-Content and High-Throughput Identification of Macrophage Polarization Phenotypes.” Chem. Sci. 2020, 11, 8231-8239.
  10. 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. 2020, 19, 1-12.
  11. 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.” Method. Enzymol. 2020, 639, 115-140.
  12. Sikora, K. N., Hardie, J. M., Castellanos-Garcia, L. J., Liu, Y., Reinhardt, B. M., Farkas, M. E., Rotello, V. M., Vachet, R. W. “Dual Mass Spectrometric Tissue Imaging of Nanocarrier Distributions and Their Biochemical Effects.” Anal. Chem. 2020, 92, 2011-2018
  13. 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.” Pharmacol. Res. 2019, 148, 104452.
  14. 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. 2019, 18, 2447-2453.
  15. Lin, H.-H., Qraitem, M., Lian, Y., Taylor, S. R.,* Farkas, M. E.* “Analyses of Bmal1 and Per2 Oscillations in a Model of Breast Cancer Reveal Changes with Malignancy.” Integr. Cancer Ther. 2019, 18, 1-13.
  16. Hardie, J., Huo, S., Jiang, Y., Liang, X.-J., Farkas, M. E., Rotello, V. M. “RNAi Nanomaterials and Nanovehicles: Inorganic Nanoparticles for RNAi.” in Handbook of Nanomaterials for Cancer Theranostics. Elsevier. 2018, 537-550.
  17. Jiang, Y.,* Hardie, J.,* Liu, Y., Ray, M., Luo, X., Das, R., Landis, R. F., Farkas, M. E., Rotello, V. M. “Nanocapsule-Mediated Cytosolic siRNA Delivery for Anti-Inflammatory Treatment.” J. Control Release. 2018, 283, 235-240.
  18. 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. 2018, 13, 2339-2346.
  19. Lin, H.-H., Farkas, M. E., “Altered Circadian Rhythms and Breast Cancer: From the Human to the Molecular Level.” Front. Endocrinol. 2018. 9, 218. (In special issue: Disorders of Circadian Rhythms)
  20. Joshi, B. P., Hardie, J., Farkas, M. E., “Harnessing Biology to Deliver Therapeutic and Imaging Entities via Cell-Based Methods.” Chem. Eur. J. 2018. 18, 8717-8726
  21. Ray, M.,* Lee, Y.-W.,* Hardie, J., Mout, R., Tonga, G. Y., Farkas, M. E., Rotello, V. M. “CRISPRed Macrophages for Cell-Based Immunotherapy.” Bioconj. Chem. 2018. 29, 445-450
  22. Hardie, J.,* Jiang, Y.,* Tetrault, E. R., Ghazi, P. C., Tonga, G. Y., Farkas, M. E.,* Rotello, V. M.* “Simulataneous Cytosolic Delivery of a Chemotherapeutic and siRNA using Nanoparticle-Stabilized Nanocapsules.” Nanotechnology. 2016. 27, 374001
  23. Fu, A., Tang, R., Hardie, J., Farkas, M. E., Rotello, V. M. “Promises and Pitfalls of Intracellular Delivery of Proteins.” Bioconj. Chem. 2014. 25, 1602-1608

*Joint first or corresponding-authorship

Postdoctoral Research (Francis Group, UC Berkeley):

  1. Aanei, I. L., ElSohly, A. M., Farkas, M. E., Netirojjanakul, 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.” Mol. Pharm. 2016. 13, 3764-3772.
  2. ElSohly, A. M., Netirojjanakul, C., Aanei, I. L., Jager, A., Bendall, S., Farkas, M. E., Nolan, G. P., Francis, M. B. “Synthetically Modified Viral Capsids as Versatile Carriers for Use in Antibody-based Cell Targeting.” Bioconj. Chem. 2015. 26, 1590-1596.
  3. Farkas, M. E., Aanei, A. L., Behrens, C. R., Tong, G. J., Murphy, S. T., O’Neil, J. P., Francis, M. B. “PET Imaging and Biodistribution of Chemically Modified Bacteriophage MS2.” Mol. Pharm. 2013. 10, 69-76.
  4. Carrico, Z. M.*, Farkas, M. E.*, Yu, Z., Hsiao, S. C., Marks, J. D., Chokhawala, H., Clark, D. S., Francis, M. B. “N-Terminal Labeling of Filamentous Phage to Create Cancer Marker Imaging Agents.” ACS Nano. 2012. 6, 6675-6680.

*Joint first-authorship

Graduate Research (Dervan Group, Caltech):

  1. Farkas, M. E., Li, B. C., Dose, C., Dervan, Peter B. “DNA Sequence Selectivity of Hairpin Polyamide Turn Units.” Bioorg. Med. Chem. Lett. 2009, 19, 3919-3923.
  2. Dose, C., Farkas, M. E., Chenoweth, D. M., Dervan, P. B. “Next Generation Hairpin Polyamides with (R)-3,4-Diaminobutyric Acid Turn Unit.” J. Am. Chem. Soc. 2008, 130, 6859-6866.
  3. Chou, C. J., Farkas, M. E., Tsai, S. M., Alvarez, D. A., Dervan, P. B., Gottesfeld, J. M. “Small Molecules Targeting Histone H4 as Potential Therapeutics for Chronic Myelogenous Leukemia.” Mol. Cancer. Ther. 2008, 7, 769-778.
  4. Farkas, M. E., Tsai, S. M., Dervan, P. B. “α -Diaminobutyric Acid-Linked Hairpin Polyamides.” Bioorg. Med. Chem. 2007, 15, 6927-6936.
  5. Nickols, N. G., Jacobs, C. S., Farkas, M. E., Dervan, P. B. “Modulating Hypoxia-Inducible Transcription by Disrupting the HIF-1-DNA Interface.” ACS Chem. Biol. 2007, 2, 561-571.
  6. Hsu, C. F., Phillips, J. W., Trauger, J. W., Farkas, M. E., Belitsky, J. M., Heckel, A., Olenyuk, B. Z., Puckett, J. W., Wang, C. C. C., Dervan, P. B. “Completion of a Programmable DNA-Binding Small Molecule Library.” Tetrahedron. 2007, 63, 6146-6151.
  7. Tsai, S. M., Farkas, M. E., Chou, C. J., Gottesfeld, J. M., Dervan, P. B. “Unanticipated Differences Between α- and γ-Diaminobutyric Acid-Linked Hairpin Polyamide-Alkylator Conjugates.” Nucleic Acids Res. 2007, 35, 307-316.
  8. Nickols, N. G., Jacobs, C. S., Farkas, M. E., Dervan, P. B. “Improved Nuclear Localization of DNA-Binding Polyamides.” Nucleic Acids Res. 2007, 35, 363-370.

Industrial Research (Discovery Chemistry Group, BMS):

  1. Yeung, K. S, Qiu, Z., Farkas, M. E., Xue, Q., Regueiro-Ren, A., Yang, Z., Bender, J. A., Good, A. C., Kadow, J. F. “An Efficient One-Pot Synthesis of 3-Glyoxylic Acids of Electron-Deficient Substituted Azaindoles by Ionic Liquid Imidazolium Chloroaluminate-Promoted Friedel-Crafts Acylation.” Tetrahedon Lett. 2008, 43, 6250-6253.
  2. Yeung, K. S., Farkas, M. E., Kadow, J. F., Meanwell, N. A. “A Base-Catalyzed, Direct Synthesis of 3,5-Disubstituted 1,2,4-Triazoles from Nitriles and Hydrazides.” Tetrahedron Lett. 2005, 46, 3429-3432.
  3. Yeung, K. S., Farkas, M. E., Qiu, Z., Yang, Z. “Friedel-Crafts Acylation of Indoles in Acidic Imidazolium Chloroaluminate Ionic Liquid at Room Temperature.” Tetrahedron Lett. 2002, 43, 5793-5795.

Patents:

  1. “Surface-Modified Macrophages for Cell-Based Delivery.” Farkas, M. E. USSN 62/373,274; filed August 7, 2017.
  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.
  3. “Indole, Azaindole, and Related Heterocyclic N-Substituted Piperazine Derivatives.” Yeung, K. S., Farkas, M.E., Kadow, J. F., Meanwell, N. A., Taylor, M., Johnston, D., Coulter, T. S., Wright, J. J. K. USSN 10/871,931; U.S. Patent #8039486 issued October 18, 2011.