She had originally looked for doctorate programs in Russia, but however, "the salaries were very low, there was absolutely no funding to do research, and the country as a whole was experiencing problems.

"[5] During this time, the Soviet policy of perestroika was negatively affecting the university and research programs there, which led to Akhmanova's decision to go to the Netherlands with her young daughter to obtain her PhD.

There, she worked at Radboud University Nijmegen (RU) in a lab under Wolfgang Hennig; her research then focused on obtaining mutants of histone genes.

She worked in Niels Galjart's lab in the Department of Cell Biology which Frank Grosveld headed; her research focused on gene regulation and transcription.

[5] In 2011, Akhmanova and Hoogenraad continued to collaborate on research and moved their laboratories to Utrecht University, where they began running the Division of Cell Biology.

[5] As of 2023[update], she is still a cell biology professor at Utrecht University, where she continues to do research on intracellular transportation, especially involving microtubule proteins.

More recently, they have started researching "the biochemical properties and functional roles of the proteins" which organize minus end tracking proteins (-TIPs).4 There is far less information about –TIPs, and they are still not fully understood; however, recent research on CAMSAP, a type of –TIP, has shown that it plays an important role for organizing and stabilizing microtubules during interphase.

Akhmanova's team focuses mainly on dynein, the motor that moves toward the minus end of the microtubule, and how it is linked to the various organelles and vesicles it transfers.

From here, the team plans to study how the cortical complexes are made and regulated, how they affect the attachments and dynamics of microtubules, and what the mechanism is that allows them to fuse vesicles.