Publications

Single molecule biophysics and topology

1. Petrášek, Z., Hoege, C., Mashaghi, A., Ohrt, T., Hyman, A. A., & Schwille, P. (2008). Characterization of protein dynamics in asymmetric cell division by scanning fluorescence correlation spectroscopy. Biophysical Journal, 95(11), 5476–5486.

2. Jakobi, A. J., Mashaghi, A., Tans, S. J., & Huizinga, E. G. (2011). Calcium modulates force sensing by the von Willebrand factor A2 domain. Nature Communications, 2(1), 385.

3. Mashaghi, A., Vach, P. J., & Tans, S. J. (2011). Noise reduction by signal combination in Fourier space applied to drift correction in optical tweezers. Review of Scientific Instruments, 82(11).

4. Mashaghi, A., Kramer, G., Bechtluft, P., Zachmann-Brand, B., Driessen, A. J. M., Bukau, B., & Tans, S. J. (2013). Reshaping of the conformational search of a protein by the chaperone trigger factor. Nature, 500(7460), 98–101.

5. Moayed, F., Mashaghi, A., & Tans, S. J. (2013). A polypeptide-DNA hybrid with selective linking capability applied to single molecule nano-mechanical measurements using optical tweezers. PloS One, 8(1), e54440.

6. Singhal, K., Vreede, J., Mashaghi, A., Tans, S. J., & Bolhuis, P. G. (2013). Hydrophobic collapse of trigger factor monomer in solution. PLoS One, 8(4), e59683.

7. Bezrukavnikov, S., Mashaghi, A., van Wijk, R. J., Gu, C., Yang, L. J., Gao, Y. Q., & Tans, S. J. (2014). Trehalose facilitates DNA melting: a single-molecule optical tweezers study. Soft Matter, 10(37), 7269–7277.

8. Mashaghi, A., Kramer, G., Lamb, D. C., Mayer, M. P., & Tans, S. J. (2014). Chaperone Action at the Single-Molecule Level. Chemical Reviews, 114, 1.

9. Mashaghi, A., Mashaghi, S., & Tans, S. J. (2014). Misfolding of Luciferase at the Single‐Molecule Level. Angewandte Chemie International Edition, 53(39), 10390–10393.

10. Mashaghi, A., van Wijk, R. J., & Tans, S. J. (2014). Circuit topology of proteins and nucleic acids. Structure, 22(9), 1227–1237.

11. Mugler, A., Tans, S. J., & Mashaghi, A. (2014). Circuit topology of self-interacting chains: implications for folding and unfolding dynamics. Physical Chemistry Chemical Physics, 16(41), 22537–22544.

12. Mashaghi, A., & Ramezanpour, A. (2015). Circuit topology of linear polymers: a statistical mechanical treatment. RSC Advances, 5(64), 51682–51689.

13. Mashaghi, A., & Ramezanpour, A. (2015). Distance measures and evolution of polymer chains in their topological space. Soft Matter, 11(33), 6576–6585.

14. Singhal, K., Vreede, J., Mashaghi, A., Tans, S. J., & Bolhuis, P. G. (2015). The trigger factor chaperone encapsulates and stabilizes partial folds of substrate proteins. PLoS Computational Biology, 11(10), e1004444.

15. Vlijm, R., Mashaghi, A., Bernard, S., Modesti, M., & Dekker, C. (2015). Experimental phase diagram of negatively supercoiled DNA measured by magnetic tweezers and fluorescence. Nanoscale, 7(7), 3205–3216.

16. Mashaghi, A., Bezrukavnikov, S., Minde, D. P., Wentink, A. S., Kityk, R., Zachmann-Brand, B., Mayer, M. P., Kramer, G., Bukau, B., & Tans, S. J. (2016). Alternative modes of client binding enable functional plasticity of Hsp70. Nature, 539(7629), 448–451.

17. Nikoofard, N., & Mashaghi, A. (2016). Topology sorting and characterization of folded polymers using nano-pores. Nanoscale, 8(8), 4643–4649.

18. Ungelenk, S., Moayed, F., Ho, C.-T., Grousl, T., Scharf, A., Mashaghi, A., Tans, S., Mayer, M. P., Mogk, A., & Bukau, B. (2016). Small heat shock proteins sequester misfolding proteins in near-native conformation for cellular protection and efficient refolding. Nature Communications, 7(1), 13673.

19. Verovšek, S. K., & Mashaghi, A. (2016). Extended topological persistence and contact arrangements in folded linear molecules. Frontiers in Applied Mathematics and Statistics, 2, 6.

20. Heidari, M., Satarifard, V., Tans, S. J., Ejtehadi, M. R., Mashaghi, S., & Mashaghi, A. (2017). Topology of internally constrained polymer chains. Physical Chemistry Chemical Physics, 19(28), 18389–18393.

21. Satarifard, V., Heidari, M., Mashaghi, S., Tans, S. J., Ejtehadi, M. R., & Mashaghi, A. (2017). Topology of polymer chains under nanoscale confinement. Nanoscale, 9(33), 12170–12177.

22. Nikoofard, N., & Mashaghi, A. (2018). Implications of molecular topology for nanoscale mechanical unfolding. The Journal of Physical Chemistry B, 122(42), 9703–9712.

23. Wruck, F., Avellaneda, M. J., Koers, E. J., Minde, D. P., Mayer, M. P., Kramer, G., Mashaghi, A., & Tans, S. J. (2018). Protein folding mediated by trigger factor and Hsp70: new insights from single-molecule approaches. Journal of Molecular Biology, 430(4), 438–449.

24. Heidari, M., Satarifard, V., & Mashaghi, A. (2019). Mapping a single-molecule folding process onto a topological space. Physical Chemistry Chemical Physics, 21(36), 20338–20345.

25. Adams, C. C., Devadoss, J., Elhamdadi, M., & Mashaghi, A. (n.d.). Gauss Codes, Quandles and Bondles for Proteins. 2020 Fall Southeastern Virtual Sectional Meeting.

26. Adams, C., Devadoss, J., Elhamdadi, M., & Mashaghi, A. (2020). Knot Theory for Proteins: Gauss Codes, Quandles and Bondles. Journal of Mathematical Chemistry, 58, 1711–1736.

27. Golovnev, A., & Mashaghi, A. (2020). Generalized Circuit Topology of Folded Linear Chains. IScience, 23(9), 101492.

28. Heidari, M., Schiessel, H., & Mashaghi, A. (2020). Circuit topology analysis of polymer folding reactions. ACS Central Science, 6(6), 839–847.

29. Scalvini, B., Sheikhhassani, V., Woodard, J., Aupič, J., Dame, R. T., Jerala, R., & Mashaghi, A. (2020). Topology of folded molecular chains: from single biomolecules to engineered origami. Trends in Chemistry, 2(7), 609–622.

30. Schullian, O., Woodard, J., Tirandaz, A., & Mashaghi, A. (2020). A circuit topology approach to categorizing changes in biomolecular structure. Frontiers in Physics, 8, 5.

31. Ceniceros, J., Elhamdadi, M., & Mashaghi, A. (2021). Coloring invariant for topological circuits in folded linear chains. Symmetry, 13(6), 919.

32. Ceniceros, J., Elhamdadi, M., & Mashaghi, A. (2021). Enhancement of the Coloring Invariant for Folded Molecular Chains. Journal of Mathematical Physics, 62, 073501.

33. Golovnev, A., & Mashaghi, A. (2021). Circuit Topology for Bottom-Up Engineering of Molecular Knots. Symmetry, 13(12), 2353.

34. Mashaghi, A. (2021). Circuit topology of folded chains. Notices of The American Mathematical Society, 68(3), 420–423.

35. Mashaghi, A., & van der Veen, R. (2021). Polynomial Invariant of Molecular Circuit Topology. Symmetry, 13(9), 1751.

36. Scalvini, B., Sheikhhassani, V., & Mashaghi, A. (2021). Topological principles of protein folding. Physical Chemistry Chemical Physics, 23(37), 21316–21328.

37. Golovnev, A., & Mashaghi, A. (2022). Topological analysis of folded linear molecular chains. In Topological Polymer Chemistry: Concepts and Practices (pp. 105–114). Springer Nature Singapore Singapore.

38. Heidari, M., Moes, D., Schullian, O., Scalvini, B., & Mashaghi, A. (2022). A topology framework for macromolecular complexes and condensates. Nano Research, 15, 9809–9817.

39. Heling, L. W. H. J., Banijamali, S. E., Satarifard, V., & Mashaghi, A. (2022). Programmed polymer folding. In Topological Polymer Chemistry: Concepts and Practices (pp. 159–176). Springer Nature Singapore Singapore.

40. Mashaghi, A., Moayed, F., Koers, E. J., Zheng, Y., Till, K., Kramer, G., Mayer, M. P., & Tans, S. J. (2022). Direct observation of Hsp90-induced compaction in a protein chain. Cell Reports, 41(9).

41. Moes, D., Banijamali, E., Sheikhhassani, V., Scalvini, B., Woodard, J., & Mashaghi, A. (2022). ProteinCT: An implementation of the protein circuit topology framework. MethodsX, 9, 101861.

42. Scalvini, B., Schiessel, H., Golovnev, A., & Mashaghi, A. (2022). Circuit topology analysis of cellular genome reveals signature motifs, conformational heterogeneity, and scaling. iScience, 25(3), 103866.

43. Sheikhhassani, V., Scalvini, B., Ng, J., Heling, L. W. H. J., Ayache, Y., Evers, T. M. J., Estébanez‐Perpiñá, E., McEwan, I. J., & Mashaghi, A. (2022). Topological dynamics of an intrinsically disordered N‐terminal domain of the human androgen receptor. Protein Science, 31(6), e4334.

44. Woodard, J., Iqbal, S., & Mashaghi, A. (2022). Circuit topology predicts pathogenicity of missense mutations. Proteins: Structure, Function, and Bioinformatics, 90(9), 1634–1644.

45. Berx, J., & Mashaghi, A. (2023). Decoding chirality in circuit topology of a self entangled chain through braiding. Soft Matter, 19, 5888-5895.

46. Flapan, E., Mashaghi, A., & Wong, H. (2023). A tile model of circuit topology for self-entangled biopolymers. Scientific Reports, 13(1), 8889.

47. Scalvini, B., Heling, L. W. H. J., Sheikhhassani, V., Sunderlikova, V., Tans, S. J., & Mashaghi, A. (2023). Cytosolic Interactome Protects Against Protein Unfolding in a Single Molecule Experiment. Advanced Biology, 7(12), 2300105.

48. Scalvini, B., Sheikhhassani, V., van de Brug, N., Heling, L. W. H. J., Schmit, J. D., & Mashaghi, A. (2023). Circuit topology approach for the comparative analysis of intrinsically disordered proteins. Journal of Chemical Information and Modeling, 63(8), 2586–2602.

49. Wruck, F., Avellaneda, M. J., Naqvi, M. M., Koers, E. J., Till, K., Gross, L. D., Moayed, F., Roland, A., Heling, L. W. H. J., & Mashaghi, A. (2023). Probing Single Chaperone Substrates. In Biophysics of Molecular Chaperones: Function, Mechanisms and Client Protein Interactions (pp. 278–318). Royal Society of Chemistry.

50. Berx, J., & Mashaghi, A. (2024). Aggregation and structural phase transitions of semiflexible polymer bundles: a braided circuit topology approach. iScience, 27(3), 108995.

51. Akulov, V., Jimenez Panizo, A., Estebanez Perpina, E., van Noort, J., & Mashaghi, A. (2024). Phosphorylation regulated conformational diversity and topological dynamics of an intrinsically disordered nuclear receptor. BioRxiv, 2024–2029.

52. Mallon, S. D. D., Bos, E., Sheikhhassani, V., Shademan, M., Rocca, D., Voortman, L. M., Mashaghi, A., Sharp, T., & Raz, V. (2024). Correlating protein aggregate structure to function in differentiated cells reveals structural pathological signatures. BioRxiv, 2024.

53. Naghilou, A., Armbruster, O., & Mashaghi, A. (2024). Scanning probe microscopy elucidates gelation and rejuvenation of biomolecular condensates. BioRxiv, 2024–2028.

54. Scalvini, B., & Mashaghi, A. (2024). Circuit Topology Analysis of Single-Cell HiC Data. In Bacterial Chromatin: Methods and Protocols (pp. 27–38). Springer US New York, NY.

55. Woodard, J. C., Liu, Z., Chegini, A. M., Tian, J., Bhowmick, R., Pennathur, S., Mashaghi, A., Brender, J., & Chandrasekaran, S. (2024). Rapid prediction of thermodynamically destabilizing tyrosine phosphorylations in cancers. BioRxiv, 2024–2029.

Systems biophysics, and its applications to medicine and pharmaceutical sciences

56. Ramezanpour, A., Karimipour, V., & Mashaghi, A. (2003). Generating correlated networks from uncorrelated ones. Phys. Rev. E, 67(4), 046107.

57. Mashaghi, A. R., Ramezanpour, A., & Karimipour, V. (2004). Investigation of a protein complex network. The European Physical Journal B-Condensed Matter and Complex Systems, 41(1), 113–121.

58. Mashaghi, A., & Dekker, C. (2014). Systems and synthetic biology approaches to cell division. In Systems and synthetic biology (Vol. 8, pp. 173–178). Springer Netherlands.

59. van Wijk, R., Tans, S. J., Wolde, P. R. ten, & Mashaghi, A. (2015). Non-monotonic dynamics and crosstalk in signaling pathways and their implications for pharmacology. Scientific Reports, 5(1), 11376.

60. Azimzade, Y., & Mashaghi, A. (2017). Search efficiency of biased migration towards stationary or moving targets in heterogeneously structured environments. Physical Review E, 96(6), 062415.

61. Ghafari, M., & Mashaghi, A. (2017). On the role of topology in regulating transcriptional cascades. Physical Chemistry Chemical Physics, 19(36), 25168–25179.

62. Ramezanpour, A., & Mashaghi, A. (2017). Toward First Principle Medical Diagnostics: On the Importance of Disease-Disease and Sign-Sign Interactions. Frontiers in Physics, 5, 32.

63. Mashaghi, A., & Ramezanpour, A. (2018). Statistical physics of medical diagnostics: Study of a probabilistic model. Physical Review E, 97(3), 032118.

64. Ramezanpour, A., & Mashaghi, A. (2018). Uncovering hidden disease patterns by simulating clinical diagnostic processes. Scientific Reports, 8(1), 2436.

65. Maleki, E., Koohi, S., Kavehvash, Z., & Mashaghi, A. (2020). OptCAM: An ultra‐fast all‐optical architecture for DNA variant discovery. Journal of Biophotonics, 13(1), e201900227.

66. Ramezanpour, A., Beam, A. L., Chen, J. H., & Mashaghi, A. (2020). Statistical physics for medical diagnostics: learning, inference, and optimization algorithms. Diagnostics, 10(11), 972.

67. Ramezanpour, A., & Mashaghi, A. (2020). Disease evolution in reaction networks: Implications for a diagnostic problem. PLoS Computational Biology, 16(6), e1007889.

68. Babaei, M., Evers, T. M. J., Shokri, F., Altucci, L., de Lange, E. C. M., & Mashaghi, A. (2023). Biochemical reaction network topology defines dose-dependent drug–drug interactions. Computers in Biology and Medicine, 155, 106584.

69. Ramezanpour, A., & Mashaghi, A. (2023). Learning capacity and function of stochastic reaction networks. Journal of Physics: Complexity, 4(3), 035006.

70. Babaei, M., Evers, T. M. J., Del Gaudio, N., Altucci, L., & Mashaghi, A. (2024). Design principles and control of non-cooperative oscillatory enzymatic reactions. Chemical Engineering Science, 293, 120040.

Biomaterials, bio-inspired engineering, and bio- and immuno-mechanics

71. Khan, T. R., Grandin, H. M., Mashaghi, A., Textor, M., Reimhult, E., & Reviakine, I. (2008). Lipid redistribution in phosphatidylserine-containing vesicles adsorbing on titania. Biointerphases, 3(2), FA90–FA95.

72. Mashaghi, A., Swann, M., Popplewell, J., Textor, M., & Reimhult, E. (2008). Optical anisotropy of supported lipid structures probed by waveguide spectroscopy and its application to study of supported lipid bilayer formation kinetics. Analytical Chemistry, 80(10), 3666–3676.

73. Amstad, E., Zurcher, S., Mashaghi, A., Wong, J. Y., Textor, M., & Reimhult, E. (2009). Surface functionalization of single superparamagnetic iron oxide nanoparticles for targeted magnetic resonance imaging. Small, 5(11), 1334–1342.

74. Baumann, M. K., Amstad, E., Mashaghi, A., Textor, M., & Reimhult, E. (2010). Characterization of supported lipid bilayers incorporating the phosphoinositides phosphatidylinositol 4, 5-biphosphate and phosphoinositol-3, 4, 5-triphosphate by complementary techniques. Biointerphases, 5, 114–119.

75. Nalam, P. C., Clasohm, J. N., Mashaghi, A., & Spencer, N. D. (2010). Macrotribological Studies of Poly (L-lysine)-graft-Poly (ethylene glycol) in Aqueous Glycerol Mixtures. Tribology Letters, 37(3), 541–552.

76. Kaufmann, S., Ilg, K., Mashaghi, A., Textor, M., Priem, B., Aebi, M., & Reimhult, E. (2012). Supported lipopolysaccharide bilayers. Langmuir, 28(33), 12199–12208.

77. Mashaghi, A., Partovi-Azar, P., Jadidi, T., Nafari, N., Esfarjani, K., Maass, P., Tabar, M. R. R., Bakker, H. J., & Bonn, M. (2012). Interfacial water facilitates energy transfer by inducing extended vibrations in membrane lipids. The Journal of Physical Chemistry B, 116(22), 6455–6460.

78. Mashaghi, A., Partovi-Azar, P., Jadidi, T., Nafari, N., Maass, P., Tabar, M., Bonn, M., & Bakker, H. J. (2012). Hydration strongly affects the molecular and electronic structure of membrane phospholipids. The Journal of Chemical Physics, 136(11).

79. Jadidi, T., Anvari, M., Mashaghi, A., Sahimi, M., & Tabar, M. R. R. (2013). Vibrational lifetimes of hydrated phospholipids. Europhysics Letters, 102(2), 28008.

80. Mashaghi, A., & Katan, A. (2013). A physicist’s view of DNA. De Physicus, 24e(3), 59–61.

81. Mashaghi, A., Partovi-Azar, P., Jadidi, T., Anvari, M., Jand, S. P., Nafari, N., Tabar, M. R. R., Maass, P., Bakker, H. J., & Bonn, M. (2013). Enhanced autoionization of water at phospholipid interfaces. The Journal of Physical Chemistry C, 117(1), 510–514.

82. Mashaghi, S., Jadidi, T., Koenderink, G., & Mashaghi, A. (2013). Lipid nanotechnology. International Journal of Molecular Sciences, 14(2), 4242–4282.

83. Jadidi, T., Seyyed-Allaei, H., Rahimi Tabar, M. R., & Mashaghi, A. (2014). Poisson’s ratio and Young’s modulus of lipid bilayers in different phases. Frontiers in Bioengineering and Biotechnology, 2, 8.

84. Mashaghi, A., Mashaghi, S., Reviakine, I., Heeren, R. M. A., Sandoghdar, V., & Bonn, M. (2014). Label-free characterization of biomembranes: from structure to dynamics. Chemical Society Reviews, 43(3), 887–900.

85. Azhdarzadeh, M., Saei, A. A., Sharifi, S., Hajipour, M. J., Alkilany, A. M., Sharifzadeh, M., Ramazani, F., Laurent, S., Mashaghi, A., & Mahmoudi, M. (2015). Nanotoxicology: advances and pitfalls in research methodology. Nanomedicine, 10(18), 2931–2952.

86. Hedayatifar, L., Irani, E., Mazarei, M., Rasti, S., Azar, Y. T., Rezakhani, A. T., Mashaghi, A., Shayeganfar, F., Anvari, M., & Heydari, T. (2016). Optical absorption and electronic spectra of chlorophylls a and b. RSC Advances, 41, 43.

87. Junaid, A., Mashaghi, A., Hankemeier, T., & Vulto, P. (2017). An end-user perspective on Organ-on-a-Chip: Assays and usability aspects. Current Opinion in Biomedical Engineering, 1, 15–22.

88. Saei, A. A., Yazdani, M., Lohse, S. E., Bakhtiary, Z., Serpooshan, V., Ghavami, M., Asadian, M., Mashaghi, S., Dreaden, E. C., & Mashaghi, A. (2017). Nanoparticle surface functionality dictates cellular and systemic toxicity. Chemistry of Materials, 29(16), 6578–6595.

89. Sheikh-Hasani, V., Babaei, M., Azadbakht, A., Pazoki-Toroudi, H., Mashaghi, A., Moosavi-Movahedi, A. A., & Reihani, S. N. S. (2018). Atorvastatin treatment softens human red blood cells: an optical tweezers study. Biomedical Optics Express, 9(3), 1256–1261.

90. Gharooni, M., Alikhani, A., Moghtaderi, H., Abiri, H., Mashaghi, A., Abbasvandi, F., Khayamian, M. A., Miripour, Z. S., Zandi, A., & Abdolahad, M. (2019). Bioelectronics of the cellular cytoskeleton: Monitoring cytoskeletal conductance variation for sensing drug resistance. ACS Sensors, 4, 2.

91. Rahmani, M., Faridi-Majidi, R., Khani, M.-M., Mashaghi, A., Noorizadeh, F., & Ghanbari, H. (2020). Cross-linked PMS/PLA nanofibers with tunable mechanical properties and degradation rate for biomedical applications. European Polymer Journal, 130, 109633.

92. Rahmani, M., Khani, M.-M., Rabbani, S., Mashaghi, A., Noorizadeh, F., Faridi-Majidi, R., & Ghanbari, H. (2020). Development of poly (mannitol sebacate)/poly (lactic acid) nanofibrous scaffolds with potential applications in tissue engineering. Materials Science and Engineering: C, 110, 110626.

93. Junaid, A. O. (2020). Microengineered human blood vessels for next generation drug discovery. ELIFE, 9, e54754.

94. Junaid, A., Schoeman, J., Yang, W., Stam, W., Mashaghi, A., van Zonneveld, A. J., & Hankemeier, T. (2020). Metabolic response of blood vessels to TNFα. Elife, 9, e54754.

95. Junaid, A., Tang, H., van Reeuwijk, A., Abouleila, Y., Wuelfroth, P., van Duinen, V., Stam, W., van Zonneveld, A. J., Hankemeier, T., & Mashaghi, A. (2020). Ebola hemorrhagic shock syndrome-on-a-chip. IScience, 23(1), 100765.

96. Tang, H., Abouleila, Y., Si, L., Ortega-Prieto, A. M., Mummery, C. L., Ingber, D. E., & Mashaghi, A. (2020). Human organs-on-chips for virology. Trends in Microbiology, 28(11), 934–946.

97. Eckert, J., Abouleila, Y., Schmidt, T., & Mashaghi, A. (2021). Single cell micro-pillar-based characterization of endothelial and fibroblast cell mechanics. Micro, 1(2), 242–249.

98. Evers, T. M. J., Holt, L. J., Alberti, S., & Mashaghi, A. (2021). Reciprocal regulation of cellular mechanics and metabolism. Nature Metabolism, 3, 456–468.

99. Junaid, A., van Duinen, V., Stam, W., Dólleman, S., Yang, W., de Rijke, Y., Endeman, H., van Kooten, C., Mashaghi, A., & de Boer, H. (2021). A microfluidics‐based screening tool to assess the impact of blood plasma factors on microvascular integrity. Advanced Biology, 2100954.

100. Manafi, N., Shokri, F., Achberger, K., Hirayama, M., Mohammadi, M. H., Noorizadeh, F., Hong, J., Liebau, S., Tsuji, T., & Quinn, P. M. J. (2021). Organoids and organ chips in ophthalmology. The Ocular Surface, 19, 1-15.

101. Razbin, M., & Mashaghi, A. (2021). Elasticity of connected semiflexible quadrilaterals. Soft Matter, 17(1), 102–112.

102. Tang, H., Abouleila, Y., & Mashaghi, A. (2021). Lassa hemorrhagic shock syndrome‐on‐a‐chip. Biotechnology and Bioengineering, 118:1405–1410.

103. Evers, T. M. J., Sheikhhassani, V., Haks, M. C., Storm, C., Ottenhoff, T. H. M., & Mashaghi, A. (2022). Single cell analysis reveals chemokine mediated differential regulation of monocyte mechanics. IScience, 25(1), 103555.

104. Evers, T. M. J., Sheikhhassani, V., Tang, H., Haks, M. C., Ottenhoff, T. H. M., & Mashaghi, A. (2022). Single‐cell mechanical characterization of human macrophages. Advanced NanoBiomed Research, 2(7), 2100133.

105. Evers, T. M. J., Tang, H., & Mashaghi, A. (2022). Werkelijkheid maken van sciencefiction. AnalyseVisie, 2, 28–30.

106. Sheikhhassani, V., Evers, T. M. J., Lamba, S., Shokri, F., & Mashaghi, A. (2022). Single cell force spectroscopy of erythrocytes at physiological and febrile temperatures reveals mechano-modulatory effects of atorvastatin. Soft Matter, 18, 2143–2148.

107. Evers, T. M. J., Babaei, M., & Mashaghi, A. (2024). Probing human immune cell mechanics using acoustic force spectroscopy. STAR Protocols, 5(1), 102861.

108. Evers, T. M. J., Beumer, J., Clevers, H., & Mashaghi, A. (2024). Mechanics of serotonin-producing human entero-endocrine cells. Mechanobiology in Medicine, 2(2), 100044.

109. Evers, T., van Weverwijk, A., de Visser, K. E., & Mashaghi, A. (2024). Single-cell analysis of innate immune cell mechanics: an application to cancer immunology. Materials Advances, 5, 5025-5035.

110. Lith, S. C., Evers, T. M. J., Freire, B. M., van Tiel, C. M., Vos, W. G., Mashaghi, A., & de Vries, C. J. M. (2024). Nuclear receptor Nur77 regulates immunomechanics of macrophages. European Journal of Cell Biology, 103(2), 151419.

Medicine & Ophthalmology

111. Zamani, M., Tabatabaiefar, M. A., Mosayyebi, S., Mashaghi, A., & Mansouri, P. (2010). Possible association of the CD4 gene polymorphism with vitiligo in an Iranian population. Clinical and Experimental Dermatology, 35(5), 521–524.

112. Inomata, T., Mashaghi, A., Di Zazzo, A., & Dana, R. (2015). Ocular surgical models for immune and angiogenic responses. Journal of Biological Methods, 2(3).

113. Xu, J., Hong, J., Sun, X., Liu, Z., Mashaghi, A., Inomata, T., Lu, Y., Li, Y., Wu, D., & Yang, Y. (2015). Combined lacrimal passage probing and tobramycin/dexamethasone ophthalmic ointment infiltration: a minimally invasive surgical procedure for incomplete nasolacrimal duct obstruction. Medicine, 94(36), e1483.

114. Xu, J., Liu, Z., Mashaghi, A., Sun, X., Lu, Y., Li, Y., Wu, D., Yang, Y., Wei, A., & Zhao, Y. (2015). Novel therapy for primary canaliculitis: a pilot study of intracanalicular ophthalmic corticosteroid/antibiotic combination ointment infiltration. Medicine, 94(39), e1611.

115. Hong, J., Zhong, T., Li, H., Xu, J., Ye, X., Mu, Z., Lu, Y., Mashaghi, A., Zhou, Y., & Tan, M. (2016). Ambient air pollution, weather changes and outpatient visits for allergic conjunctivitis: A retrospective registry study. Scientific Reports, 6(1), 23858.

116. Jiang, D., Xiao, X., Fu, T., Mashaghi, A., Liu, Q., & Hong, J. (2016). Transient tear film dysfunction after cataract surgery in diabetic patients. PloS One, 11(1), e0146752.

117. Mashaghi, A., Marmalidou, A., Tehrani, M., Grace, P. M., Pothoulakis, C., & Dana, R. (2016). Neuropeptide substance P and the immune response. Cellular and Molecular Life Sciences, 73, 4249–4264.

118. Azimzade, Y., Hong, J., & Mashaghi, A. (2017). Immunophysical analysis of corneal neovascularization: Mechanistic insights and implications for pharmacotherapy. Scientific Reports, 7(1), 12220.

119. Di Zazzo, A., Roberti, G., Mashaghi, A., Abud, T. B., Pavese, D., & Bonini, S. (2017). Use of topical cannabinomimetic palmitoylethanolamide in ocular surface disease associated with antiglaucoma medications. Journal of Ocular Pharmacology and Therapeutics, 33(9), 670–677.

120. Di Zazzo, A., Tahvildari, M., Subbarayal, B., Yin, J., Dohlman, T. H., Inomata, T., Mashaghi, A., Chauhan, S. K., & Dana, R. (2017). Proangiogenic function of T cells in corneal transplantation. Transplantation, 101(4), 778–785.

121. Hong, J., Yang, Y., Cursiefen, C., Mashaghi, A., Wu, D., Liu, Z., Sun, X., Dana, R., & Xu, J. (2017). Optimising keratoplasty for Peters’ anomaly in infants using spectral-domain optical coherence tomography. British Journal of Ophthalmology, 101(6), 820–827.

122. Inomata, T., Mashaghi, A., Di Zazzo, A., Lee, S.-M., Chiang, H., & Dana, R. (2017). Kinetics of angiogenic responses in corneal transplantation. Cornea, 36(4), 491–496.

123. Inomata, T., Mashaghi, A., Hong, J., Nakao, T., & Dana, R. (2017). Scaling and maintenance of corneal thickness during aging. PloS One, 12(10), e0185694.

124. Mashaghi, A., Hong, J., Chauhan, S. K., & Dana, R. (2017). Ageing and ocular surface immunity. British Journal of Ophthalmology, 101(1):1-5.

125. Tahvildari, M., Emami-Naeini, P., Omoto, M., Mashaghi, A., Chauhan, S. K., & Dana, R. (2017). Treatment of donor corneal tissue with immunomodulatory cytokines: a novel strategy to promote graft survival in high-risk corneal transplantation. Scientific Reports, 7(1), 971.

126. Burgos, R. C. R., Ramautar, R., Van Wijk, E. P. A., Hankemeier, T., Van Der Greef, J., & Mashaghi, A. (2018). Pharmacological targeting of ROS reaction network in myeloid leukemia cells monitored by ultra-weak photon emission. Oncotarget, 9(2), 2028–2034.

127. Eslani, M., Putra, I., Shen, X., Hamouie, J., Tadepalli, A., Anwar, K. N., Kink, J. A., Ghassemi, S., Agnihotri, G., & Reshetylo, S. (2018). Cornea-derived mesenchymal stromal cells therapeutically modulate macrophage immunophenotype and angiogenic function. Stem Cells, 36(5), 775–784.

128. Mittal, S. K., Mashaghi, A., Amouzegar, A., Li, M., Foulsham, W., Sahu, S. K., & Chauhan, S. K. (2018). Mesenchymal stromal cells inhibit neutrophil effector functions in a murine model of ocular inflammation. Investigative Ophthalmology & Visual Science, 59(3), 1191–1198.

129. Wu, D., Zhang, J., Qian, T., Dai, Y., Mashaghi, A., Xu, J., & Hong, J. (2018). IFN-γ regulates the expression of MICA in human corneal epithelium through miRNA4448 and NFκB. Frontiers in Immunology, 9, 334845.

130. Ali, A., Abouleila, Y., Shimizu, Y., Hiyama, E., Emara, S., Mashaghi, A., & Hankemeier, T. (2019). Single-cell metabolomics by mass spectrometry: advances, challenges, and future applications. TrAC Trends in Analytical Chemistry, 120, 115436.

131. Amani, H., Habibey, R., Shokri, F., Hajmiresmail, S. J., Akhavan, O., Mashaghi, A., & Pazoki-Toroudi, H. (2019). Selenium nanoparticles for targeted stroke therapy through modulation of inflammatory and metabolic signaling. Scientific Reports, 9(1), 6044.

132. Cui, X., Yang, Y., Li, Y., Huang, F., Zhao, Y., Chen, H., Xu, J., Mashaghi, A., & Hong, J. (2019). Correlation between anterior chamber volume and corneal biomechanical properties in human eyes. Frontiers in Bioengineering and Biotechnology, 7, 379.

133. Evers, T. M. J., Hochane, M., Tans, S. J., Heeren, R. M. A., Semrau, S., Nemes, P., & Mashaghi, A. (2019). Deciphering metabolic heterogeneity by single-cell analysis. Analytical Chemistry, 91 (21), 13314-13323.

134. Heidari, M., Noorizadeh, F., Wu, K., Inomata, T., & Mashaghi, A. (2019). Dry eye disease: emerging approaches to disease analysis and therapy. Journal of Clinical Medicine, 8(9), 1439.

135. Di Zazzo, A., Lee, S.-M., Sung, J., Niutta, M., Coassin, M., Mashaghi, A., & Inomata, T. (2020). Variable responses to corneal grafts: insights from immunology and systems biology. Journal of Clinical Medicine, 9(2), 586.

136. Di Zazzo, A., Yang, W., Coassin, M., Micera, A., Antonini, M., Piccinni, F., De Piano, M., Kohler, I., Harms, A. C., & Hankemeier, T. (2020). Signaling lipids as diagnostic biomarkers for ocular surface cicatrizing conjunctivitis. Journal of Molecular Medicine, 98, 751–760.

137. Abouleila, Y., Ali, A., Masuda, K., Mashaghi, A., & Shimizu, Y. (2022). Capillary microsampling-based single-cell metabolomics by mass spectrometry and its applications in medicine and drug discovery. Cancer Biomarkers, 33(4), 437–447.

138. Chianese, U., Papulino, C., Passaro, E., Evers, T. M. J., Babaei, M., Toraldo, A., De Marchi, T., Niméus, E., Carafa, V., & Nicoletti, M. M. (2022). Histone lysine demethylase inhibition reprograms prostate cancer metabolism and mechanics. Molecular Metabolism, 64, 101561.

139. Tang, H., Abouleila, Y., Saris, A., Shimizu, Y., Ottenhoff, T. H. M., & Mashaghi, A. (2023). Ebola virus–like particles reprogram cellular metabolism. Journal of Molecular Medicine, 101(5), 557–568.

140. Tang, H., Ali, A., Abdelazem, E., Ottenhoff, T. H. M., Heeren, R. M. A., & Mashaghi, A. (2023). Random forest and live single-cell metabolomics reveal metabolic profiles of human macrophages upon polarization. Biotechnology and Bioengineering, 120(8), 2314–2325.

141. Aslam, E., Gijasi, A., Perner, C., van Wijk, R., Märtson, A.-G., van Westen, G. J. P., Bot, I., Heitman, L. H., & Mashaghi, A. (2025). Immunobiology and Pharmacology of Neuropeptide Substance P. In Substance P: From Pain to Cancer. Elsevier. Pages: 625-660.

Edited/(co-)authored books and collections:

Cell Division, Editor: Alireza Mashaghi, 97 pages, Year: 2014, Publisher: Springer UK, ISSN: 1872-5325

Topological Polymer Chemistry: Concepts and Practices, Pages: 436, Year: 2022, Publisher: Springer Nature, ISBN: 9811668078, 9789811668074

Biophysics of Molecular Chaperones, 412 Pages, Year: 2023, Publisher: Royal Society of Chemistry, ISBN: 978-1-83916-282-4

Bacterial Chromatin: Methods and Protocols, Year: 2024, Publisher: Humana New York, ISBN: 1071639293

Substance P: From Pain to Cancer, 1st Edition - Year: 2025, Publisher: Elsevier, ISBN: 9780443221941

PhD dissertations:

Single-cell mechanics for disease biology and pharmacology (Tom evers)

Complexity and control of biochemical reaction systems for medical translation applications (Mehrad Babaei)

Topological decoding of biomolecular fold complexity (Barbara Scalvini)

Bioengineering and biophysics of viral hemorrhagic fever (Huaqi Tang)

Lipid signaling and inflammation: metabolomics for better diagnosis and treatment strategy (Wei Yang)

Microengineered Human Blood Vessels For Next Generation Drug Discovery (Abidemi Junaid)

For more information, please see: Google Scholar Link