Bio

Aaran Vijayakumaran, PhD is a Postdoctoral Scholar at Stanford University School of Medicine, where he researches the cell biology of inherited Parkinson’s Disease in the Department of Biochemistry under Professor Suzanne Pfeffer.

He completed his PhD at the University of Cambridge, applying volumetric electron microscopy and artificial intelligence to generate the first nanoscale map of the human airway epithelium. His doctoral work revealed how cellular architecture and metabolism remodel during differentiation, with a particular focus on the motile cilia, their rootlets, and their structural contacts with mitochondria and the consequences for mitochondrial metabolism. Beyond research, Aaran is active in the biotech and innovation ecosystem. He was awarded a scholarship to join EnterpriseTECH at Cambridge Judge Business School, served as an Investment Fellow Intern at Syncona, and worked as a Venture Builder Intern at Cambridge Future Tech and OmniBuds, a medical device startup. In these roles, he contributed to early-stage strategy, clinical trial planning, and commercial development.

Professional Education

  • Doctor of Philosophy, University of Cambridge, Cell Biology and Applied Artificial Intelligence (2025)
  • Masters of Research, King's College London, Translational Cancer Medicine (2021)
  • Bachelor of Science, University of Nottingham School of Medicine, Physiology (2020)

Stanford Advisors

Contact

  • Academic
    av697@stanford.edu
    University - Scholar Department: Biochemistry Position: Postdoctoral Scholar

Additional Info

  • Mail Code: 5307

All Publications

  • Airway Cells 3D Reconstruction via Manual and Machine-Learning Aided Segmentation of Volume EM Datasets. Methods in molecular biology (Clifton, N.J.) Vijayakumaran, A., Abuammar, A., Medagedara, O., Narayan, K., Mennella, V. 2024; 2725: 131-146

    Abstract

    Volume electron microscopy (vEM) is a high-resolution imaging technique capable of revealing the 3D structure of cells, tissues, and model organisms. This imaging modality is gaining prominence due to its ability to provide a comprehensive view of cells at the nanometer scale. The visualization and quantitative analysis of individual subcellular structures however requires segmentation of each 2D electron micrograph slice of the 3D vEM dataset; this process is extremely laborious de facto limiting its applications and throughput. To address these limitations, deep learning approaches have been recently developed including Empanada-Napari plugin, an open-source tool for automated segmentation based on a Panoptic-DeepLab (PDL) architecture. In this chapter, we provide a step-by-step protocol describing the process of manual segmentation using 3dMOD within the IMOD package and the process of automated segmentation using Empanada-Napari plugins for the 3D reconstruction of airway cellular structures.

    View details for DOI 10.1007/978-1-0716-3507-0_8

    View details for PubMedID 37856022

    View details for PubMedCentralID 7954287

  • ARL13B controls male reproductive tract physiology through primary and Motile Cilia. Communications biology Augière, C., Campolina-Silva, G., Vijayakumaran, A., Medagedara, O., Lavoie-Ouellet, C., Joly Beauparlant, C., Droit, A., Barrachina, F., Ottino, K., Battistone, M. A., Narayan, K., Hess, R., Mennella, V., Belleannée, C. 2024; 7 (1): 1318

    Abstract

    ARL13B is a small regulatory GTPase that controls ciliary membrane composition in both motile cilia and non-motile primary cilia. In this study, we investigated the role of ARL13B in the efferent ductules, tubules of the male reproductive tract essential to male fertility in which primary and motile cilia co-exist. We used a genetically engineered mouse model to delete Arl13b in efferent ductule epithelial cells, resulting in compromised primary and motile cilia architecture and functions. This deletion led to disturbances in reabsorptive/secretory processes and triggered an inflammatory response. The observed male reproductive phenotype showed significant variability linked to partial infertility, highlighting the importance of ARL13B in maintaining a proper physiological balance in these small ducts. These results emphasize the dual role of both motile and primary cilia functions in regulating efferent duct homeostasis, offering deeper insights into how cilia related diseases affect the male reproductive system.

    View details for DOI 10.1038/s42003-024-07030-7

    View details for PubMedID 39397107

    View details for PubMedCentralID PMC11471856

  • Uncovering structural themes across cilia microtubule inner proteins with implications for human cilia function. Nature communications Andersen, J. S., Vijayakumaran, A., Godbehere, C., Lorentzen, E., Mennella, V., Schou, K. B. 2024; 15 (1): 2687

    Abstract

    Centrosomes and cilia are microtubule-based superstructures vital for cell division, signaling, and motility. The once thought hollow lumen of their microtubule core structures was recently found to hold a rich meshwork of microtubule inner proteins (MIPs). To address the outstanding question of how distinct MIPs evolved to recognize microtubule inner surfaces, we applied computational sequence analyses, structure predictions, and experimental validation to uncover evolutionarily conserved microtubule- and MIP-binding modules named NWE, SNYG, and ELLEn, and PYG and GFG-repeat by their signature motifs. These modules intermix with MT-binding DM10-modules and Mn-repeats in 24 Chlamydomonas and 33 human proteins. The modules molecular characteristics provided keys to identify elusive cross-species homologs, hitherto unknown human MIP candidates, and functional properties for seven protein subfamilies, including the microtubule seam-binding NWE and ELLEn families. Our work defines structural innovations that underpin centriole and axoneme assembly and demonstrates that MIPs co-evolved with centrosomes and cilia.

    View details for DOI 10.1038/s41467-024-46737-3

    View details for PubMedID 38538594

    View details for PubMedCentralID PMC10973386

  • 3D nanoscale architecture of the respiratory epithelium reveals motile cilia-rootlets-mitochondria axis of communication BioRxV Vijayakumaran, A., et al 2024

    View details for DOI 10.1101/2024.09.08.611854

  • Phase-shift nanodroplets as an emerging sonoresponsive nanomaterial for imaging and drug delivery applications. Nanoscale Zhang, W., Shi, Y., Abd Shukor, S., Vijayakumaran, A., Vlatakis, S., Wright, M., Thanou, M. 2022; 14 (8): 2943-2965

    Abstract

    Nanodroplets - emerging phase-changing sonoresponsive materials - have attracted substantial attention in biomedical applications for both tumour imaging and therapeutic purposes due to their unique response to ultrasound. As ultrasound is applied at different frequencies and powers, nanodroplets have been shown to cavitate by the process of acoustic droplet vapourisation (ADV), causing the development of mechanical forces which promote sonoporation through cellular membranes. This allows drugs to be delivered efficiently into deeper tissues where tumours are located. Recent reviews on nanodroplets are mostly focused on the mechanism of cavitation and their applications in biomedical fields. However, the chemistry of the nanodroplet components has not been discussed or reviewed yet. In this review, the commonly used materials and preparation methods of nanodroplets are summarised. More importantly, this review provides examples of variable chemistry components in nanodroplets which link them to their efficiency as ultrasound-multimodal imaging agents to image and monitor drug delivery. Finally, the drawbacks of current research, future development, and future direction of nanodroplets are discussed.

    View details for DOI 10.1039/d1nr07882h

    View details for PubMedID 35166273