**Enes Senel** _PhD Student in (Computational) Biology_ _Max Delbrück Center for Molecular Medicine, Germany_ _enes.senel@mdc-berlin.de_ ![ ](./photo.jpg width="150px" align=left)Hey, I'm Enes. I am a Computer Scientist and a PhD student at the MDC Berlin. My research interests are spatial transcriptomics and machine learning. I am interested in using computational techniques to develop tools that can exploit genomics data to investigate molecular mechanisms. **Recent News:** * _September 2021_: [New publication on Optocoder: computational decoding of spatially indexed bead arrays](https://academic.oup.com/nargab/article/4/2/lqac042/6603620?login=false) is now published at NAR Bioinformatics! * _September 2021_: [New publication on NovoSpaRc: a computational method to reconstruct spatial structure from single cell data](https://www.nature.com/articles/s41596-021-00573-7) is now published at Nature Protocols! You can view my [Google Scholar page](https://scholar.google.de/citations?user=1Nas6ZQAAAAJ&hl=en&oi=ao), and [twitter](https://twitter.com/nssenel). Education =============================================================================== ![](./mdc.png width="80px" align=left) **PhD in Computational Biology**, _[Max Delbrück Center for Molecular Medicine in the Helmholtz Association](http://www.mdc-berlin.de)_, _Berlin, Germany_
 _2019-Ongoing_ ![](./tum.png width="80px" align=left) **MSc in Computer Science**, _[Technical University of Munich](http://www.tum.de)_, _Munich, Germany_
 _2016-2019_ ![](./ozu.jpg width="80px" align=left) **BSc in Computer Science**, _[Özyeğin University](https://www.ozyegin.edu.tr/en)_, _Istanbul, Turkey_
 _2012-2016_
Research Experience =============================================================================== ![[`[lab]`](https://brain.mpg.de/research/computation-in-neural-circuits-group.html)](./mpi.png width="80px" align=left)**Research Assistant/MSc Student**, _[Max Planck Institute for Brain Research](https://brain.mpg.de/)_, _Frankfurt, Germany_
_May 2018 - September 2019_
Modeling protein synthesis during activity manipulation of a single neuron ![[`[lab]`](http://robotics.ozyegin.edu.tr)](./robotics.png width="80px" align=left)**Undergraduate Research Assistant**, _[Ozyegin University](https://www.ozyegin.edu.tr/en)_, _Istanbul, Turkey_
_2014-2016_
Development of a Medical Robotics System for Image Guided Needle Operations ![[`[lab]`](https://www.ikw.uni-osnabrueck.de/en/research_groups/neurobiopsychology.html)](./osna.jpg width="80px" align=left) **Research Intern**, _[Universität Osnabrück](https://uos.de)_, _Osnabrück, Germany_
_February 2016_
High resolution parcellation of the human brain using data acquired from Diffusion Tensor Imaging(DTI) Publications =============================================================================== [Optocoder: computational decoding of spatially indexed bead arrays.](https://academic.oup.com/nargab/article/4/2/lqac042/6603620?login=false) **Enes Senel***, Nikolaus Rajewsky, Nikos Karaiskos NAR Bioinformatics, Volume 4, 2022. [NovoSpaRc: flexible spatial reconstruction of single-cell gene expression with optimal transport.](https://www.nature.com/articles/s41596-021-00573-7) Noa Moriel*, **Enes Senel***, Nir Friedman, Nikolaus Rajewsky, Nikos Karaiskos, Mor Nitzan. Nature Protocols, Volume 16, 2021. [Particulate impurities in cell-based medicinal products traced by flow imaging microscopy combined with deep learning for image analysis.](https://www.sciencedirect.com/science/article/pii/S1465324920306332) A. D. Grabarek, **E. Senel**, T. Menzen, K. H. Hoogendoorn, K. Pike-Overet, A. Hawe, W. Jiskoot. Cytotheraphy, Volume 23, 2021. [Gabor filter-based localization of straight and curved needles in 2D ultrasound images.](https://aperta.ulakbim.gov.tr/record/3349#.YfG1Fi8w1UI) Mert Kaya, **Enes Senel**, Ozkan Bebek. Turkish Journal of Electrical Engineering & Computer Sciences, 2020. [Visual needle tip tracking in 2D US guided robotic interventions.](https://doi.org/10.1016/j.mechatronics.2018.12.002) Mert Kaya, **Enes Senel**, Awais Ahmad, Ozkan Bebek. Mechatronics, Volume 57, 2019, Pages 129-139. [Visual Tracking of Multiple Moving Targets in 2D Ultrasound Guided Robotic Percutaneous Interventions.](https://ieeexplore.ieee.org/document/7989231/) Mert Kaya, **Enes Senel**, Awais Ahmad, Ozkan Bebek. In Proceedings of the International Conference on Robotics and Automation (ICRA 2017), Singapore. [`[pdf]`](./papers/icra2017.pdf) [`[video]`](https://www.youtube.com/watch?v=MlbMXX55Ch4) [Visual Tracking of Biopsy Needles in 2D Ultrasound Images.](https://ieeexplore.ieee.org/document/7487637/) Mert Kaya, **Enes Senel**, Awais Ahmad, Ozkan Bebek. In Proceedings of the International Conference on Robotics and Automation (ICRA 2016), Stockholm. [`[pdf]`](./papers/icra2016.pdf) [`[video]`](https://youtu.be/cfR2jNhBWI0) [Real Time Needle Tip Localization in 2D Ultrasound Images for Robotic Biopsies.](https://ieeexplore.ieee.org/document/7251432/). Mert Kaya, **Enes Senel**, Awais Ahmad, Orcun Orhan, Ozkan Bebek. In Proceedings of the International Conference on Advanced Robotics (ICAR 2015), Istanbul. [`[pdf]`](./papers/icar2015.pdf) Theses =============================================================================== **MSc Thesis**, Analysis of Activity Dependent Proteomic Changes Associated with Homeostatic Scaling at Central Synapses
*Supervisor*: Prof. Dr. Julijana Gjorgjieva **BSc Thesis**, A Standalone Application for a 2D Ultrasound Guided Medical Robotic System [`[pdf]`](./bsc_thesis.pdf)
*Supervisors*: [Assoc. Prof. Erhan Oztop](http://robotics.ozyegin.edu.tr/members/erhan-oztop/), [Assist. Prof. Ozkan Bebek](http://robotics.ozyegin.edu.tr/members/ozkan-bebek/)