Enes Senel.

Research

Questions that keep me up.

My research sits at the intersection of probabilistic modelling and modern functional genomics — with a soft spot for methods that make biology more legible.

Spatial transcriptomics & tissue architecture

Single-cell and multi-omics integration

Machine learning for cell–cell interactions

Reproducible bioinformatics pipelines

Selected publications

Peer-reviewed
  • 2025
    Ciltacabtagene autoleucel biomarkers of response in relapsed/refractory multiple myeloma patients from CARTITUDE-1: a phase 1b/2 study

    Blood Cancer Discovery · Under revision

    R.M. de Oca, F. Wang, M. Hao, D. Smirnov, H. Zhao, M. Gormley, E. Zudaire, S.S. Chang, B. Foulk, J. Patel, E. Senel, D. Wu, C. Davis, R. Boominathan, A. Javidi, J. Zhu, O. Lau, K. Clara-Nielsen, Y. Rajpurohit, D. Madduri, S. Jagannath, Y. Lin, A. Cohen, V. Plaks

  • 2022
    Optocoder: computational decoding of spatially indexed bead arrays

    NAR Bioinformatics

    E. Senel, N. Rajewsky, N. Karaiskos

  • 2021
    novoSpaRc: flexible spatial reconstruction of single-cell gene expression with optimal transport

    Nature Protocols

    N. Moriel*, E. Senel*, N. Friedman, N. Rajewsky, N. Karaiskos, M. Nitzan

  • 2021
    Particulate impurities in cell-based medicinal products traced by flow imaging microscopy combined with deep learning for image analysis

    Cytotherapy

    A.D. Grabarek, E. Senel, T. Menzen, K.H. Hoogendoorn, K. Pike-Overet, A. Hawe, W. Jiskoot

  • 2020
    Gabor filter-based localization of straight and curved needles in 2D ultrasound images

    Turkish Journal of Electrical Engineering & Computer Sciences

    M. Kaya, E. Senel, O. Bebek

  • 2019
    Visual needle tip tracking in 2D US guided robotic interventions

    Mechatronics

    M. Kaya, E. Senel, A. Ahmad, O. Bebek

  • 2017
    Visual tracking of multiple moving targets in 2D ultrasound guided robotic percutaneous interventions

    ICRA, Singapore

    M. Kaya, E. Senel, A. Ahmad, O. Bebek

  • 2016
    Visual tracking of biopsy needles in 2D ultrasound images

    ICRA, Stockholm

    M. Kaya, E. Senel, A. Ahmad, O. Bebek

  • 2015
    Real-time needle tip localization in 2D ultrasound images for robotic biopsies

    ICAR, Istanbul

    A. Ahmad, O. Orhan, E. Senel, O. Bebek

Patents

Intellectual property
  • 2022

    Method and system for 3D reconstruction of tissue gene expression data

    US20240257914A1

    S. Abbiati, J. Alles, S. Ayoub, S. Ehrig, N. Karaiskos, G. Macino, S. Preibisch, N. Rajewsky, E. Senel, A. Woehler