Selected Publications

*corresponding author(s)

** Co-author(s)

Daniel Lu, Laura R Parisi, Omer Gokcumen, G Ekin Atilla-Gokcumen.(2023). SREBP activation contributes to fatty acid accumulations in necroptosis. RSC Chemical Biology.

Ricardo X Ramirez, Oluwatoyin Campbell, Apoorva J Pradhan, G Ekin Atilla-Gokcumen, Viviana Monje-Galvan. (2023). Modeling the molecular fingerprint of protein-lipid interactions of MLKL on complex bilayers. Frontiers in Chemistry, 10.

Apoorva J. Pradhan &G Ekin Atilla-Gokcumen. (2023). Omics approaches to better understand the molecular mechanism of necroptosis and their translational implications. Molecular Omics.

Purab Pal, G Ekin Atilla-Gokcumen, Jonna Frasor. (2022). Emerging Roles of Ceramides in Breast Cancer Biology and Therapy. International Journal of Molecular Sciences, 23 (19), 11178.

Cátia Vilas-Boas, Logan Running, Daniela Pereira, Honorina Cidade, Marta Correia-da-Silva, Gunes Ekin Atilla-Gokcumen, Diana S Aga. (2022). Impact of Tralopyril and Triazolyl Glycosylated Chalone in Human Retinal Cells’ Lipidome. Molecules, 27 (16), 5247.

Running, L., Atilla-Gokcumen, G.E., and Aga, D.S. (2022). Development of a Liquid Chromatography–Mass Spectrometry-Based In Vitro Assay to Assess Changes in Steroid Hormones Due to Exposure to Per- and Polyfluoroalkyl Substances. Chemical Research in Toxicology, 7, 1277-1288.

Pal, P., Millner, A., Semina, S.E., Huggins, R.J., Running, L., Aga, D.S., Tonetti, D.A., Schiff, R., Greene, G.L., Atilla-Gokcumen, G.E., Frasor, J. (2022). Endocrine Therapy-Resistant Breast Cancer Cells Are More Sensitive to Ceramide Kinase Inhibition and Elevated Ceramide Levels Than Therapy-Sensitive Breast Cancer Cells. Cancers14 (10), 2380.

Camdzic, M., Aga, D. S., & Atilla-Gokcumen, G. E. *. (2022). Cellular Interactions and Fatty Acid Transporter CD36-Mediated Uptake of Per-and Polyfluorinated Alkyl Substances (PFAS). Chemical Research in Toxicology.

Millner, A., Running, L., Colon-Rosa, N., Aga, D. S., Frasor, J., & Atilla-Gokcumen, G. E.*(2022). Ceramide-1-Phosphate Is Involved in Therapy-Induced Senescence. ACS Chemical Biology, 17 (4), 822–828.

Millner, A. & Atilla-Gokcumen, G. E.* (2021). Solving the enigma: Mass spectrometry and small molecule probes to study sphingolipid function. Current Opinion in Chemical Biology, 65, 49–56.

Pradhan, A. J.**, Lu, D.**, Parisi, L. R., Shen, S., Berhane, I. A., Galster, S. L., Bynum, K., Monje-Galvan, V., Gokcumen, O., Chemler, S. R., Qu, J., Kay, J. G., & Atilla-Gokcumen, G. E.* (2021). Protein acylation by saturated very long chain fatty acids and endocytosis are involved in necroptosis. Cell Chemical Biology, 28(9), 1298-1309.e7.

Saitou, M., Resendez, S., Pradhan, A. J., Wu, F., Lie, N. C., Hall, N. J., Zhu, Q., Reinholdt, L., Satta, Y., Speidel, L., Nakagome, S., Hanchard, N. A., Churchill, G., Lee, C., Atilla-Gokcumen, G. E., Mu, X., & Gokcumen, O.* (2021). Sex-specific phenotypic effects and evolutionary history of an ancient polymorphic deletion of the human growth hormone receptor. Science Advances, 7(39).

Kilian, H. I., Pradhan, A. J., Jahagirdar, D., Ortega, J., Atilla-Gokcumen, G. E., & Lovell, J. F. *(2021). Light-Triggered Release of Large Biomacromolecules from Porphyrin-Phospholipid Liposomes. Langmuir, 37(36), 10859–10865.

Pliss, A., Kuzmin, A. N., Lita, A., Kumar, R., Celiku, O., Atilla-Gokcumen, G. E., Gokcumen, O., Chandra, D., Larion, M., & Prasad, P. N.*, (2021). A single-organelle optical omics platform for cell science and biomarker discovery. Analytical Chemistry, 93(23), 8281–8290.

Morstein, J., Kol, M., Novak, A. J. E., Feng, S., Khayyo, S., Hinnah, K., Li-Purcell, N., Pan, G., Williams, B. M., Riezman, H., Atilla-Gokcumen, G. E., Holthuis, J. C. M., & Trauner, D. *(2021). Short Photoswitchable Ceramides Enable Optical Control of Apoptosis. ACS Chemical Biology, 16(3), 452–456.

Mabrouk, M. T., Huang, W. C., Deng, B., Li-Purcell, N., Seffouh, A., Ortega, J., Ekin Atilla-Gokcumen, G., Long, C. A., Miura, K., & Lovell, J. F. (2020). Lyophilized, antigen-bound liposomes with reduced MPLA and enhanced thermostability. International Journal of Pharmaceutics, 589, 119843.

Millner, A. & Ekin Atilla-Gokcumen, G.* (2020). Lipid players of cellular senescence. Metabolites, 10(9), 1–17.

Bayraktar, E. C., La, K., Karpman, K., Unlu, G., Ozerdem, C., Ritter, D. J., Alwaseem, H., Molina, H., Hoffmann, H.-H., Millner, A., Atilla-Gokcumen, G. E., Gamazon, E. R., Rushing, A. R., Knapik, E. W., Basu, S., Birsoy, K. *(2020). Metabolic co-essentiality mapping identifies c12orf49 as a regulator of SREBP processing and cholesterol metabolism. 2(6), 487–498.

Bozelli, J. C., Lu, D., Atilla-Gokcumen, G. E., & Epand, R. M. *(2020). Promotion of plasmalogen biosynthesis reverse lipid changes in a Barth Syndrome cell model. Biochimica et Biophysica Acta – Molecular and Cell Biology of Lipids, 1865(6).

Millner, A., Lizardo, D. Y., & Atilla-Gokcumen, G. E.* (2020). Untargeted Lipidomics Highlight the Depletion of Deoxyceramides during Therapy-Induced Senescence. Proteomics, 20(10), 1–7.

Swayambhu, G., Moscatello, N., Atilla-Gokcumen, G. E. ,& Pfeifer, B. A.* (2020). Flux Balance Analysis for Media Optimization and Genetic Targets to Improve Heterologous Siderophore Production. IScience, 23(4), 101016.

Chavez Soria, N. G., Bisson, M. A., Atilla-Gokcumen, G. E.*, & Aga, D. S.* (2019). High-resolution mass spectrometry-based metabolomics reveal the disruption of jasmonic pathway in Arabidopsis thaliana upon copper oxide nanoparticle exposure. Science of The Total Environment, 693, 133443.


Parisi, L. R., Sowlati-Hashjin, S., Berhane, I. A., Galster, S. L., Carter, K. A., Lovell, J. F., Chemler, S. R., Karttunen, M., & Atilla-Gokcumen, G. E. *(2019). Membrane Disruption by Very Long Chain Fatty Acids during Necroptosis. ACS Chemical Biology, 14(10), 2286–2294.


Atilla-Gokcumen, G. E. (2019). Special Issue on Lipidomics. Proteomics, 19(18), 2–3.

Brovkovych, V., Aldrich, A., Li, N., Atilla-Gokcumen, G. E.*, & Frasor, J.* (2019). Removal of Serum Lipids and Lipid-Derived Metabolites to Investigate Breast Cancer Cell Biology. Proteomics, 19(18), 1–8.

Matich, E. K., Chavez Soria, N. G., Aga, D. S.*, & Atilla-Gokcumen, G. E.* (2019). Applications of metabolomics in assessing ecological effects of emerging contaminants and pollutants on plants. Journal of Hazardous Materials, 373, 527–535.

Li, N., Saitou, M., & Atilla-Gokcumen, G. E.* (2019). The Role of p38 MAPK in Triacylglycerol Accumulation during Apoptosis. Proteomics, 19(13), 1–7.

Chavez Soria, N. G., Aga, D. S.*, & Atilla-Gokcumen, G. E.* (2019). Lipidomics reveals insights on the biological effects of copper oxide nanoparticles in a human colon carcinoma cell line. Molecular Omics, 15(1), 30–38.

Matich, E. K., Ghafari, M., Camgoz, E., Caliskan, E., Pfeifer, B. A., Haznedaroglu, B. Z., & Atilla-Gokcumen, G. E.* (2018). Time-series lipidomic analysis of the oleaginous green microalga species Ettlia oleoabundans under nutrient stress. Biotechnology for Biofuels, 11(1), 1–15.

Brovkovych, V., Izhar, Y., Danes, J. M., Dubrovskyi, O., Sakallioglu, I. T., Morrow, L. M., Ekin Atilla-Gokcumen, G.*, & Frasor, J.* (2018). Oncogenesis Fatostatin induces pro-and anti-apoptotic lipid accumulation in breast cancer. Oncogenesis, 7, 66.

Quiñones-Lombraña, A., Li, N., del Solar, V., Atilla-Gokcumen, G. E., & Blanco, J. G.* (2018). CBR1 rs9024 genotype status impacts the bioactivation of loxoprofen in human liver. Biopharmaceutics and Drug Disposition, 39(6), 315–318.

Miranda, D., Li, N., Li, C., Stefanovic, F., Atilla-Gokcumen, G. E., & Lovell, J. F.* (2018). Detection of sunlight exposure with solar-sensitive liposomes that capture and release food dyes. ACS Applied Nano Materials, 1(6), 2739–2747.

Parisi, L. R., Morrow, L. M., Visser, M. B., & Atilla-Gokcumen, G. E.* (2018). Turning the Spotlight on Lipids in Non-Apoptotic Cell Death. ACS Chemical Biology, 13(3), 506–515.


Li, N., Sancak, Y., Frasor, J., & Atilla-Gokcumen, G. E.* (2017). A Protective Role for Triacylglycerols during Apoptosis.

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Lizardo, D. Y., Parisi, L. R., Li, N., & Atilla-Gokcumen, G. E.*(2017). Noncanonical Roles of Lipids in Different Cellular Fates.

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Saitou, M., Lizardo, D. Y., Taskent, R. O., Millner, A., Gokcumen, O., & Atilla-Gokcumen, G. E.* (2018). An evolutionary transcriptomics approach links CD36 to membrane remodeling in replicative senescence. Molecular Omics, 14, 237.

Parisi, L. R., Li, N., & Atilla-Gokcumen, G. E.* (2017). Very Long Chain Fatty Acids Are Functionally Involved in Necroptosis. Cell Chemical Biology, 24(12), 1445-1454.e8.

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Luo, D., Geng, J., Li, N., Carter, K. A., Shao, S., Ekin Atilla-Gokcumen, G.*, & Lovell, J. F. (2017). Vessel-Targeted Chemophototherapy with Cationic Porphyrin-Phospholipid Liposomes.

Miranda, D., Carter, K., Luo, D., Shao, S., Geng, J., Li, C., Chitgupi, U., Turowski, S. G., Li, N., Atilla-Gokcumen, G., Spernyak, J. A., & Lovell, J. F.* (2017). Multifunctional Liposomes for Image-Guided Intratumoral Chemo-Phototherapy.

Chavez Soria, N. G., Montes, A., Bisson, M. A., Atilla-Gokcumen, G.E.*, & Aga, D. S. *(2017). Mass spectrometry-based metabolomics to assess uptake of silver nanoparticles by Arabidopsis thaliana. Environ. Sci, 4.


Lizardo, D. Y., Lin, Y.-L., Gokcumen, O.*, & Atilla-Gokcumen, G.E.* (2017). Regulation of lipids is central to replicative senescence †. 498 | Mol. BioSyst, 13, 498.


Matich, E. K., Butryn, D. M., Ghafari, M., del Solar, V., Camgoz, E., Pfeifer, B. A., Aga, D. S., Haznedaroglu, B. Z., & Atilla-Gokcumen, G. E.* (2016). Mass spectrometry-based metabolomics of value-added biochemicals from Ettlia oleoabundans. Algal Research, 19, 146–154.

Li, N., Lizardo, D. Y., & Atilla-Gokcumen, G.E.* (2016). Specific Triacylglycerols Accumulate via Increased Lipogenesis During 5-FU-Induced Apoptosis.


Luo, D., Li, N., Carter, K. A., Lin, C., Geng, J., Shao, S., Huang, W.-C., Qin, Y., Atilla-Gokcumen, G. E., & Lovell, J. F.* (2016). Rapid Light-Triggered Drug Release in Liposomes Containing Small Amounts of Unsaturated and Porphyrin-Phospholipids.

Mondal, N., Stolfa, G., Antonopoulos, A., Zhu, Y., Wang, S.-S., Buffone, A., Atilla-Gokcumen, G.E., Haslam, S. M., Dell, A., & Neelamegham, S.* (2016). P-(CD62P), E-(CD62E), and L-selectin (CD62L) constitute Glycosphingolipids on Human Myeloid Cells Stabilize E-Selectin-Dependent Rolling in the Multistep Leukocyte Adhesion Cascade.

del Solar, V., Lizardo, D. Y., Li, N., Hurst, J. J., Brais, C. J., & Atilla-Gokcumen, G. E.* (2015). Differential Regulation of Specific Sphingolipids in Colon Cancer Cells during Staurosporine-Induced Apoptosis. Chemistry and Biology, 22(12), 1662–1670.

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Singh, R. R., Lester, Y., Linden, K. G., Love, N. G., Atilla-Gokcumen, G.E., & Aga, D. S. (2015). Application of Metabolite Profiling Tools and Time-of-Flight Mass Spectrometry in the Identification of Transformation Products of Iopromide and Iopamidol during Advanced Oxidation.

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Publications prior to UB:

Atilla-Gokcumen, G. E*, Eggert, U. S. A comparative LC-MS based profiling approach to analyze lipid composition in tissue culture systems. In D. Owen (Ed.) Methods in Membrane Lipids. 2015 New York, Springer;1232:103-13.

Muro E.*, Atilla-Gokcumen G.E.*, Eggert, U. S. Lipids in cell biology – how can we understand them better? Mol Bio Cell 2014 5;25(12):1819-1823 (*Contributed equally)

Muro TOC

Atilla-Gokcumen G. E.*, Muro E.*, Relat-Goberna J., Sasse S., Bedigian A.V., Coughlin, M., Garcia-Manyes, S., Eggert, U. S. Dividing cells regulate their lipid composition and localization. Cell. 2014 156, 428-439. (*Contributed equally).

Atilla TOC

Atilla-Gokcumen, G. E., Bedigian, A. V., Sasse, S., and Eggert, U. S.* Inhibition of glycosphingolipid biosynthesis induces cytokinesis failure. J. Am. Chem. Soc. 2011 133, 10010-10013.

Atilla_2 TOC

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