Selected Publications

Publications at UB:

(*Corresponding author)

40. Millner A., Atilla-Gokcumen G.E.* Solving the Enigma: How can we Study Sphingolipids? Curr. Opin. Chem. Biol. (2021) Accepted.

39. Killian H., Li-Purcell N., Atilla-Gokcumen G.E., Lovell J.F.* Release of Macromolecules from Liposomes Triggered with Red Light. Langmuir, Accepted.

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

37. Pliss A., Kuzmin A.N., Lita A., Kuman R., Chandra D., Atilla-Gokcumen G.E., Gokcumen O., Larion M., Prasad P.N.* Single organelle optical omics platform for cell science and biomarkers discovery. Under revision, Under revision, Anal. Chem., Accepted. doi: 10.1021/acs.analchem.1c01131.

36. PradhanA., Lu D., ParisiL.R., ShenS., BerhaneI.A., GalsterS.G., BynumK., Monje-GalvanV., GokcumenO.,ChemlerS.R., QuJ., KayJ., Atilla-GokcumenG.E.* Protein acylation by saturated very long chain fatty acids and endocytosis are involved in necroptosis. Cell Chem. Biol. 2021DOI:10.1016/j.chembiol.2021.03.012

35. MorsteinJ., KolM., NovakA.J.E., FengS., KhayyoS., Hinnah K., Li-PurcellN., PanG., WilliamsB.M., RiezmanH., Atilla-Gokcumen G.E., Holthuis J., Trauner D.* Short Photoswitchable Ceramides enable Optical Control of Apoptosis. ACS Chem. Biol. 2021,16(3):452-456

34. Mabrouk M.T., Huang W., Deng B., Li-Purcell N., Seffouh A., Ortega J., Atilla-Gokcumen G.E., Long C., Miura K., Lovell J.* Lyophilized, antigen-bound liposomes with reduced MPLA and enhanced thermostability. Int. J. Pharm. 2020 589.

33. Milner A., Lizardo D. Y., Atilla-Gokcumen G. E.* Untargeted lipidomics highlight the depletion of deoxyceramides during therapy-induced senescence. Under revision in Proteomics, 2020 Accepted

32. Bayraktar E. C., La K., Karpman K., Unlu G., Ozdemir C., Ritter D. J., Alwaseem H., Molina H., Hoffman H., Milner A., Atilla-Gokcumen G. E., Gamazan E. R., Rushing A. R., Knapik E. W., Basu S., Birsoy K.* Metabolic co-essentiality analysis identifies regulators of cholesterol and fatty acid metabolism. Under revision in Nature Metabolism, 2020 Accepted

31. Resendez S., Saitou M., Parisi L. R., Satta Y., Atilla-Gokcumen G. E., Wu F., Mu X.*, Gokcumen, O.* Sex-specific phenotypic impact and non-neutral evolution of an ancient deletion polymorphism of the human growth hormone receptor. bioRxiv. 2020 788653

30. Swayambhu G., Moscatello N., Atilla-Gokcumen G. E., and Pfeifer B. A.* Flux balance analysis to identify media optimization and genetic manipulation parameters for improved heterologous siderophore production. iScience. 2020 23(4): 101016

29. Bozelli J.C., Lu D., Atilla-Gokcumen G.E., and Epand R.* Promotion of plasmalogen biosynthesis reverse lipid changes in a Barth Syndrome cell model. BBA-Cell and Molecular Biology of Lipids2020 1865(6):158677

28. Parisi L.R., Sowlati-Hashjin , Berhane I.A., Carter K.A., Lovell J.F., Chemler S.R., Karttunen M., Atilla-Gokcumen G.E.* Membrane disruption by very long chain fatty acids during necroptosis.  ACS Chem. Bio. 2019 14:2286-2294.


27. Li N., Saitou M., Atilla-Gokcumen G.E.* p38 MAPK pathway is Involved in Triacylglycerol and Lipid Droplet Accumulation during Apoptosis. Proteomics, 2019, 1900160-1900167.

26. Chavez N., Montes A., Bisson M., Atilla-Gokcumen G. E.*; Aga D. S High-resolution mass spectrometry-based metabolomics reveal the disruption of jasmonic pathway upon copper nanoparticles exposure in Arabidopsis thaliana. STOTEN 2019 693:133443


25. Matich E.**, Chavez N. S.**, Aga D. S.*, Atilla-Gokcumen G. E.* Applications of Metabolomics in Assessing Ecological Effects of Emerging Contaminants and Pollutants on Plants. J Haz Mat. 2019, 373, 527-535.

24. Brovkovych V., Aldrich A., Li N., Atilla-Gokcumen G. E.*, Frasor J.* Extraction of Lipids and Lipid-derived Metabolites in Probing Breast Cancer Cell Biology. Proteomics, 2019 19:1800370-1800378

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23. Chavez N. S., Aga D. S.*, Atilla-Gokcumen G. E.* Lipidomics Reveals Insights on the Biological Effects of Copper Oxide Nanoparticles on a Human Colon Carcinoma Cell Line. Mol. Omics. 2019 15:30-38. Selected as cover article

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22. Wang S. S, Guo Y., del Solar V., Yu X., Antonopoulos A., Friedman A. E., Matich E. K., Atilla-Gokcumen G. E., Nasirikenari M., Lau J. T., Dell A., Haslam S. M., Laine R., Matta K. L.*, Neelamegham S.* Thioglycosides are Effective Metabolic Inhibitors of Cellular Glycosylation. Cell Chem. Bio. 2018 25:1-14.

21. Brovkovych V., Izhar Y., Danes J., Dubrovskyi O., Sakallioglu I. T., Morrow L. M., Atilla-Gokcumen G. E.*, Frasor J.* Fatostatin Induces Pro- and Anti-apoptotic Lipid Accumulation in Breast Cancer. Oncogenesis. 2018 7:66.

20. He P., Matich E. K., Yonkos L. T., Friedman A. E., Atilla-Gokcumen G. E., Aga, D. S. (2018) Mass spectrometry based detection of Vitellogenin peptides across fish species for assessing exposure to Estrogenic compounds in aquatic environments. Science of the Total Environment. 2018

19. 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. 2018 4:237-245. Cover article

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

17. Miranda D., Li N., Li C., Stefanovic F., Atilla-Gokcumen G. E., Lovell J. F. Detection of Sunlight Exposure with Solar-Sensitive Liposomes that Capture and Release Food Dyes. ACS Applied Nano Materials. 2018, 6, 2739-2747.

16. Parisi L.R., Morrow L.M., Visser M.B., Atilla-Gokcumen G.E.* Turning the spotlight on lipids in non-apoptotic cell death. ACS Chem. Bio. 2018 13(3):506-515


15. Matich E., Ghafari H., Camgoz E.**, Caliskan E.**, Pfeifer B., Haznedaroglu B.Z.*, Atilla-Gokcumen G.E.* Time series lipidomics analysis of green microalgae under nutrient stress. Biofuel and Biotech. 2018 11:29 (** undergraduate researcher)

14. Li N., Sancak Y., Frasor J.M., Atilla-Gokcumen G. E.* A protective role for triacylglycerols during apoptosis. Biochem. 2018 57:72-80.

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13. Lizardo D.Y., Parisi L., Li N., Atilla-Gokcumen G. E.* Non-canonical roles of lipids in different cell fates. Biochem. 2018 57:22-29

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12. Parisi L.R., Li N., Atilla-Gokcumen G.E.* Very Long Chain Fatty Acids are Functionally Involved in Necroptosis. Cell Chem Biol. 2017 DOI: 10.1016/j.chembiol.2017.08.026

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11. Chavez Soria N. G., Montes A., Bisson M. A., Atilla-Gokcumen G. E.*, Aga D. S.* Mass Spectrometry-based Metabolic Profiling to Assess Uptake and Effects of Silver Nanoparticles on Arabidopsis thalianaEnv. Sci. Nano. 2017 4: 1944-1953.


10. Luo, D.; Geng, J.; Li, N.; Carter, K. A.; Shao, S.; Atilla-Gokcumen, G. E.*; Lovell, J. F. Vessel-Targeted Chemophototherapy with Cationic Porphyrin-Phospholipid Liposomes. Mol. Cancer Ther. 2017 16 (11), 2452-2461

9. Miranda, D.; Carter, K.; Luo, D.; Shao, S.; Geng, J.; Li, C.; Chitgupi, U.; Turowski, S. G.; Li, N.; Atilla-Gokcumen, G. E.*; Spernyak, J. A.; Lovell, J. F. Multifunctional Liposomes for Image-Guided Intratumoral Chemo-Phototherapy. Adv. Healthc. Mater. 2017 6 (16). 1700253

8. Lizardo D.Y., Lin Y. T., Gokcumen O.*, Atilla-Gokcumen G.E.* Regulation of Lipids is Central to Replicative Senescence. (2017) Mol BioSystems. 2016 13 (3), 498-509. Identified as “HOT” article.


7. Matich E., Butryn D., Ghafari H., del Solar V., Camgoz E., Pfeifer B., Aga D., Haznedaroglu B.Z., Atilla-Gokcumen G.E.* Mass Spectrometry-based Metabolomics of Value-added Biochemicals from Non-model Microalgae, Algal Research. 2016 19:146-54

6. Li N., Lizardo D., Atilla-Gokcumen G.E.* Specific Triacylglycerols Accumulate via Increased Lipogenesis During 5-FU-induced Apoptosis, ACS Chem. Biol. 2016 11(9):2583-7


5. Luo D, Li N, Carter KA, Lin C, Geng J, Shao S, Huang WC, Qin Y, Atilla-Gokcumen GE*, Lovell JF. Rapid light-triggered drug release in liposomes containing small amounts of unsaturated and porphyrin-phospholipids. Small. 2016 12(22): 3039-47.

4. Mondal N, Stolfa G, Antonopoulos A, Zhu Y, Wang SS, Buffone A Jr, Atilla-Gokcumen GE*, Haslam SM, Dell A, Neelamegham S. Glycosphingolipids on Human Myeloid Cells Stabilize E-Selectin-Dependent Rolling in the Multistep Leukocyte Adhesion Cascade. Arterioscler Thromb Vasc Biol. 2016 36(4): 718-27.

3. del Solar, V., Lizardo, D., Li, N., Hurst, J., Brais, C., Atilla-Gokcumen, G. E.* Differential Regulation of Specific Sphingolipids in Colon Cancer Cells during Staurosporine-Induced Apoptosis. Chemistry & Biology. 2015  22, 1662-70.

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2. Horner IJ, Kraut ND, Hurst JJ, Rook AM, Collado CM, Atilla-Gokcumen GE*, Maziarz EP, Liu XM, Merchea MM, Bright FV. Effects of Polyhexamethylene Biguanide and Polyquaternium-1 on Phospholipid Bilayer Structure and Dynamics. J Phys Chem B. 2015 119(33): 10531-42.

1. Singh, R. R., Lester Y., Linden, K.,G., Love, N., G., Atilla-Gokcumen, G., E.*, Aga, D., S.  Application of metabolite profiling tools and time-of-flight mass spectrometry in the identification of transformation products of iopromide and iopamidol during advanced oxidation. Environ Sci Technol. 2015 49(5), pp 2983-2990

Singh TOC

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. (2011) Inhibition of glycosphingolipid biosynthesis induces cytokinesis failure. J. Am. Chem. Soc. 2011 133, 10010-10013.

Atilla_2 TOC

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