43. Yevtodiyenko, A.; Bazhin, A.; Khodakivskyi, P.; Godinat, A.; Budin, G.; Maric, T.; Pietramaggiori, G.; Scherer, S.; Kunchulia, M.; Eppeldauer, G.; Polyakov, S.V.; Francis, K.P.; Bryan, J.N.; Goun, E.*  Portable bioluminescent platform for in vivo monitoring of biological processes in non-transgenic animals. Nat. Commun. 2021, 12(1):2680. doi: 10.1038/s41467-021-22892-9 (link)

42. Khodakivskyi, P.V.; Lauber, C.L.; Yevtodiyenko, A.; Bazhin, A.A.; Bruce, S.; Ringel-Kulka, T.; Ringel, Y; Betrisey, B.; Torres, J.; Hu, J.; Chou, C.J.; Goun E.A.*, Noninvasive imaging and quantification of bile salt hydrolase activity: from bacteria to humans. Sci. Adv. 2021, 7(6), eaaz9857, DOI: 10.1126/sciadv.aaz9857 (link)

41. Cui, L.; Gouw, A.M.; LaGory, E.L.; Guo, S.; Attarwala, N.; Tang, Y.; Qi, J.; Chen, Y.S.; Gao, Z.; Casey, K.M.; Bazhin, A.A.; Chen, M.; Hu, L.; Xie, J.; Fang, M.; Zhang, C.; Zhu.; Wang, Z.; Giaccia, A.J.; Gambhir, S.S.; Zhu, W.; Felsher, D.W.; Pegram, M.D.; Goun, E.A.; Le, A.; Rao, J., Mitochondrial copper depletion suppresses triple-negative breast cancer in mice. Nat. Biotechnol. 2021, 39(3), 357-367. doi: 10.1038/s41587-020-0707-9 (link)


40. Bazhin, A.A.; Sinisi, R.; De Marchi, U.; Hermant, A.; Sambiagio, N.; Maric, T.; Budin, G.; Goun, E.A.*, A bioluminescent probe for longitudinal monitoring of mitochondrial membrane potential. Nat. Chem. Biol. 2020,16(12),1385-1393. (link)

This paper was highlighted in:



39. Karatas, H.; Maric, T.; D’Alessandro, P. L.; Yevtodiyenko, A.; Vorherr, T.; Hollingworth, G.; Goun, E.A.*, Real-time imaging and quantification of peptide uptake in vitro and in vivo. ACS Chem Biol. 2019, 14, 2197-2205. (link)



38. Maric, T.; Mikhaylov, G.; Khodakivskyi, P.; Bazhin, A.; Sinisi R.; Bonhoure, N.; Yevtodiyenko, A.; Jones, A.; Muhunthan, V.; Abdelhady, G.; Shackelford, D.; Goun, E.* Bioluminescent-based imaging and quantification of glucose uptake in vivo. Nat. Methods 2019, 16(6):526-532. (link)

This paper was highlighted* in:

37. Bazhin, A.A.; Chambon, M.; Vesin, J.; Bortoli, J.; Collins, J.W.; Turcatti, G.; Chou, C.J.; Goun, E.A.* A Universal Assay for Aminopeptidase Activity and Its Application for Dipeptidyl Peptidase-4 Drug Discovery. Anal. Chem. 2019, 91, 1098-1104. (link)


36. Miyazaki, T.; Gharib, S.A.; Hsu, Y.A.; Xu, K., Khodakivskyi, P.; Kobayashi, A.; Paragas, J.; Klose, A.D.; Francis, K.P.; Dubikovskaya, E.; Page-McCaw, P.S.; Barasch, J.; Paragas, N. Cell-specific image-guided transcriptomics identifies complex injuries caused by ischemic acute kidney injury in mice. Commun Biol. 2019, 2, 326. (link)


35. Mermod, M.; Bongiovanni, M.; Petrova, T.; Goun, E.; Simon, C.; Tolstonog, G.; Monnier, Y. Prediction of Occult Lymph Node Metastasis in Head and Neck Cancer with CD31 Vessel Quantification. Otolaryngol Head Neck Surg. 2019, 160, 277-283 (link).




34. Godinat, A.; Bazhin.; Goun, E.* Bioorthogonal chemistry in bioluminescence imaging. Drug Discov. Today 2018, 9, 1584-1590. (link)

33. Reber, J.; Willershäuser, M.; Karlas, A.; Paul-Yuan, K.; Diot, G.; Franz, D.; Fromme, T.; Ovsepian, S. V.; Bézière, N.; Dubikovskaya, E.; Karampinos, D. C.; Holzapfel, C.; Hauner, H.; Klingenspor, M.; Ntziachristos, V. Non-invasive Measurement of Brown Fat Metabolism Based on Optoacoustic Imaging of Hemoglobin Gradients. Cell Metab. 2018, 27, 689-701. (link)




32. Wang, Y.; Thompson, J. M.; Ashbaugh, A. G.; Khodakivskyi, P.; Budin, G.; Sinisi, R.; Heinmiller, A.; van Oosten, M.; van Dijl J. M.; van Dam, G. M.; Francis, K. P.; Bernthal, N. M.; Dubikovskaya, E. A.; Miller, L. S. Preclinical Evaluation of Photoacoustic Imaging as a Novel Noninvasive Approach to Detect an Orthopaedic Implant Infection. J Am Acad Orthop Surg. 2017, Suppl 1:S7-S12. (link)

31. Mermod, M.; Bongiovanni, M.; Petrova, T. V.; Dubikovskaya, E. A.; Simon, C.; Tolstonog, G.; Monnier, Y. Correlation between podoplanin expression and extracapsular spread in squamous cell carcinoma of the oral cavity using subjective immunoreactivity scores and semiquantitative image analysis. Head Neck 2017, 39, 98-108. (link)


30. Mezzanotte, L.; van Root, M.; Karatas, H.; Goun, E.A.; Löwik, C.W.G.M. In Vivo Molecular Bioluminescence Imaging: New Tools and Applications. Trends Biotechnol. 2017, 35, 640-652. (link)


29. Godinat, A.; Karatas, H.; Budin, G.; Dubikovskaya, E.* Chemical ligation for molecular imaging. In Chemical Ligation: Tools for Biomolecule Synthesis and Modification. John Wiley & Sons, 2017.


28. Park, H. M.; Russo, K. A.; Karateev, G.; Park, M.; Dubikovskaya, E.; Kriegsfeld, L. J.; Stahl, A. A system for in vivo imaging of hepatic free fatty acid uptake Gastroenterology 2017, 152, 78-81. (link)



27. Mermod, M.; Bongiovanni, M.; Petrova, T. V.; Dubikovskaya, E. A.; Simon, C.; Tolstonog, G.; Monnier, Y. Prediction of occult lymph node metastasis in squamous cell carcinoma of the oral cavity and the oropharynx using peritumoral Prospero homeobox protein 1 lymphatic nuclear quantification. Head Neck. 2016, 38, 1407-1415. (link)


26. Stammes, M. A.; Maeda, A.; Bu, J.; Scollard, D. A.; Kulbatski, I.; Medeiros, P. J.; Sinisi, R.; Dubikovskaya, E. A.; Snoeks, T. J.; van Beek, E. R.; Chan, A. B.; Löwik, C. W.; DaCosta, R.S. The Necrosis-Avid Small Molecule HQ4-DTPA as a Multimodal Imaging Agent for Monitoring Radiation Therapy-Induced Tumor Cell Death. Front Oncol. 2016, 6, 221. (link)


25. Stammes, M. A.; Knol-Blankevoort, V. T.; Cruz, L. J.; Feitsma, H. R.; Mezzanotte, L.; Cordfunke, R. A.; Sinisi, R.; Dubikovskaya, E. A.; Maeda, A.; DaCosta, R. S.; Bierau, K.; Chan, A.; Kaijzel, E. L.; Snoeks, T. J.; van Beek, E. R.; Löwik, C. W. Pre-clinical Evaluation of a Cyanine-Based SPECT Probe for Multimodal Tumor Necrosis Imaging. Mol Imaging Biol. 2016, 18, 905-915. (link)

24. Homulle, H. A.; Powolny, F.; Stegehuis, P. L.; Dijkstra, J.; Li, D. U.; Homicsko, K.; Rimoldi, D.; Muehlethaler, K.; Prior, J.O.; Sinisi, R.; Dubikovskaya, E.; Charbon, E.; Bruschini, C. Compact solid-state CMOS single-photon detector array for in vivo NIR fluorescence lifetime oncology measurements. Biomed Opt Express 2016, 7, 1797-1814. (link)



23. Vorobyeva, A.G.; Stanton, M.; Godinat, A.; Lund, K.B.; Karateev, G.G.; Francis, K.P.; Allen, E.; Gelovani, J.G.;  McCormack, E.; Tangney, M.; Dubikovskaya, E.A.* Development of a Bioluminescent Nitroreductase Probe for Preclinical Imaging. PLoS One. 2015, 10(6): e0131037. (link)

22. Tharp, K.M.; Jha, A. K.; Kraiczy, J.; Yesian, A.; Karateev, G.; Sinisi, R.; Dubikovskaya, E. A.; Healy, K. E.; Stahl, A. Matrix-Assisted Transplantation of Functional Beige Adipose Tissue. Diabetes 2015, 64, 3713-3724. (link)


“Copyright: Clearance Center, Inc. Publisher: Elsevier ”




21.  Godinat, A.; Budin, G.; Morales, A.; Park, H.; Sanman, L.;  Bogyo, M.; Yu, A.; Stahl, A.; Dubikovskaya, E. A.* A biocompatible “split luciferin” reaction and its application for non-invasive bioluminescent imaging of protease activity in living animals. Curr Protoc Chem Biol. 2014, 6,169-189. (link)


20. Geissbuehler, S.; Sharipov, A.; Godinat, A.; Bocchio, N. L.; Sandoz, P. A.; Huss, A.; Jensen, N. A.; Jakobs, S.; Enderlein, J.; van der Goot, F. G.; Dubikovskaya, E. A.; Lasser, T.; Leutenegger, M. Live-cell multiplane three-dimensional super-resolution optical fluctuation imaging. Nat Commun. 2014, 5, 5830. (link)


19. Dubikovskaya, E.; Chudnovskiy, R.; Karateev, G.; Park, H. M.; Stahl, A. Measurement of long-chain fatty acid uptake into adipocytes. In Methods in enzymology. Elsevier, 2014.


18. Godinat, A.;  Park, H. M.; Miller, S. C.;  Cheng, K.; Hanahan, D.; Sanman, L. E.;  Bogyo, M.; Yu, A.; Nikitin, G. F.; Stahl, A.; Dubikovskaya, E. A.* A Biocompatible In Vivo Ligation Reaction and its Application for Non-Invasive Bioluminescent Imaging of Protease Activity in Living Mice. ACS Chem Biol. 2013, 8, 987-999.



Publications prior to independent career


17. Henkin, A.H.; Cohen, A.S.; Dubikovskaya, E.A.; Park, H.M.; Nikitin, G.F.; Auzias, M.G.; Kazantzis, M.; Bertozzi, C.R.; Stahl, A. Real-time noninvasive imaging of fatty acid uptake in vivo. ACS Chem Biol. 2012, 7, 1884-1891.


16. Van de Bittner, G.C.; Dubikovskaya,A.; Bertozzi, C.R.; Chang, C.J. In vivo imaging of hydrogen peroxide production in a murine tumor model with a chemoselective bioluminescent reporter. Proc Natl Acad Sci U S A. 2010, 107, 21316-321.


15. Cohen, A.S.; Dubikovskaya,A.; Rush, J.S.; Bertozzi, C.R. Real-Time Bioluminescence Imaging of Glycans on Live Cells. J Am Chem Soc. 2010, 132, 8563-8365.


14. Lee, H.L.; Dubikovskaya,A.; Hwang, H.; Semyonov, A.N.; Wang, H.; Jones, L.R.; Twieg, R.J.; Moerner, W.E.; Wender, P.A. Single-molecule motions of oligoarginine transporter conjugates on the plasma membrane of Chinese hamster ovary cells. J Am Chem Soc. 2008, 130, 9364-9370.


13. Dubikovskaya,A.; Thorne, S.H.; Pillow, T.H.; Contag, C.H.; Wender, P.A. Overcoming multidrug resistance of small-molecule therapeutics through conjugation with releasable octaarginine transporters. Proc Natl Acad Sci U S A. 2008, 105, 12128-33.

  • This paper was highlighted in Nature Biotechnology 2008, 26, 1095, Medical News Today ( 20th, 2008), ScienceDaily (Aug. 19th, 2008), Science News, Washington (Aug. 19, 2008), and SciBX on Science (Aug. 28th, 2008).


12. Wender, P. A.; Galliher, W. C.; Goun, E. A.; Jones, L. R.; Pillow, T. H. The Design of Guanidinium-Rich Transporters and Their Internalization Mechanisms. Advanced Drug Delivery Reviews 2008, 60, 452-472.


11. Wender, P. A.; Goun, E. A.; Jones, L. R.; Pillow, T. H.; Rothbard, J. B.; Shinde, R.; Contag, C. H. Real-time Analysis of Uptake and Bioactivatable Cleavage of Luciferin-Transporter Conjugates in Transgenic Reporter Mice. Proc Natl Acad Sci U S A. 2007, 104, 10340-10345.


10. Jones, L. R.; Goun, E. A.; Shinde, R.; Rothbard, J. B.; Contag, C. H.; Wender, P. A. Releasable Luciferin-Transporter Conjugates: Tools for the Real-Time Analysis of Cellular Uptake and Release. J Am Chem Soc. 2006, 128, 6526-6527.

    • This paper was highlighted in Nature Methods, 2006, 3, 498.


9. Goun, E. A.; Pillow, T. H.; Jones, L. R.; Rothbard, J. B.; Wender, P. A. Molecular Transporters: Synthesis of Oligoguanidinium Transporters and their Application to Drug Delivery and Real Time Imaging. ChemBiochem 2006, 7, 1497-1515.


8. Goun, E. A.; Shinde, R.; Dehnert, K. W.; Adams-Bond, A.; Wender, P. A.; Contag, C. H.; Franc, B. L. Intracellular Cargo Delivery by an Octaarginine Transporter Adapted to Target Prostate Cancer Cells through Cell Surface Protease Activation. Bioconjugate Chemistry 2006, 17, 787-796.


7. Osintsev, A. V.; Levit, G. L.; Krasnov, V. P.; Miles, D. H.; Solodnikov, S. Yu.; Goun, E. A. Synthesis and Antileukemic Activity of N-Phthaloyl-2-amino alcohols. Pharmaceutical Chemistry Journal 2004, 38, 120-122.


6. Pimenova, E. V.; Krasnych, O. P.; Goun, E. A.; Miles, D. H. Synthesis and Reactions of 2-Hydroxy-4-oxo-4-(2,3,5,6-tetrafluoro-4-methoxyphenyl)-but-2-enoic Acid Methyl Ester. Journal of Fluorine Chemistry 2003, 121, 201-204.


5. Goun, E. A.; Cunningham, G.; Chu, D.; Nguyen, C.; Miles, D. H. Antibacterial and Antifungal Activity of Indonesian Ethnomedical Plants. Fitoterapia 2003, 74, 592-596.


4. Solodnikov, S. Yu.; Miles, D. H.; Krasnych, O. P.; Goun, E. A.; Naser, S. A.; Konyukhova, N. A.; Denisov, V. E.; Shilov, Yu. I. Synthesis, Antithrombin and Antituberculous Activity of 2-Hydrazino Derivatives of Acyl Pyruvic Acid Methyl Esters. Pharmaceutical Chemistry Journal, 2002, 36, 229-231.


3. Goun, E. A.; Petrichenko, V. M.; Solodnikov, S. Yu.; Suhinina, T. V.; Kline, M. A.; Cunningham, G.; Nguyen, C.; Miles, D. H. Anticancer and Antithrombin Activity of Russian Plants. Journal of Ethnopharmacology 2002, 81, 337-342.


2. Goun, E. A.; Cunningham, G.; Solodnikov, S. Yu.; Krasnykch, O. P.; Miles, D. H. Antithrombin Activity of Some Constituents from Origanum vulgare. Fitoterapia 2002, 73, 692-694.


1. Porrata, P.; Goun, E. A.; Matsui, H. Size-Controlled Self-Assembly of Peptide Nanotubes Using Polycarbonate Membranes as Templates. Chemistry of Materials 2002, 14, 4378-4381.

ngineering, EPFL. Elena is an advocate for interdisciplinary approaches to research, combining organic synthetic chemistry and optical imaging to find solutions to fundamental problems in biology and medicine.