Research
My current research interests include:
- Representation and weakly supervised learning in digital pathology.
- Spatial transcriptomics, morphology and sn/scRNA integration.
- Developement of bioinformatics and visualization tools.
Prior to my PhD, I have also worked with deep learning and radiogenomics applied to MRI glioblastoma images.
2024
What makes for good morphology representations for spatial omics?
E. Chelebian, C. Avenel, C. Wählby.
Under review.
Discovery of tumour indicating morphological changes in benign prostate biopsies through AI
E. Chelebian, C. Avenel, H. Järemo, P. Andersson, A. Bergh, C. Wählby.
Under review.
Learned morphological features guide cell type assignment of deconvolved spatial transcriptomics
E. Chelebian, C. Avenel, J. Leon, C.C. Hon, C. Wählby.
7th Medical Imaging with Deep Learning (MIDL 2024). July, 2024.
Self-supervised learning for genetically relevant domain identification
E. Chelebian, C. Avenel, C. Wählby.
21st IEEE International Symposium on Biomedical Imaging (ISBI 2024). May, 2024.
DEPICTER: Deep representation clustering for histology annotation
E. Chelebian, C. Avenel, F. Ciompi, C. Wählby.
Computers in Biology and Medicine, doi: 10.1016/j.compbiomed.2024.108026. January, 2024.
2023
TissUUmaps 3: Improvements in Interactive Visualization, Exploration and Quality Assessment of Large-Scale Spatial Omics Data
N. Pielawski, A. Andersson, C. Avenel, A. Behanova, E. Chelebian, A. Klemm, F. Nysjö, L. Solorzano, C. Wählby.
Heliyon, doi: 10.1016/j.heliyon.2023.e15306. April, 2023.
Visualization and quality control tools for large-scale multiplex tissue analysis in TissUUmaps3
A. Behanova, C. Avenel, A. Andersson, E. Chelebian, A. Klemm, L. Wik, A. östman, C. Wählby.
Biological Imaging, doi: 10.1017/S2633903X2300005. February, 2023.
2022
Seeded iterative clustering for histology region identification
E. Chelebian, F. Ciompi, C. Wählby.
Learning Meaningful Representations of Life, NeurIPS 2022, doi: 10.48550/arXiv.2211.07425. November, 2022.
2021
Morphological Features Extracted by AI Associated with Spatial Transcriptomics in Prostate Cancer
E. Chelebian, C. Avenel, K. Kartasalo, M. Marklund, A. Tanoglidi, T. Mirtti, R. Colling, A. Erickson, A.D. Lamb, J. Lundeberg, C. Wählby.
Cancers, doi: 10.3390/cancers13194837. September, 2021.
Differential effect of vascularity between long- and short-term survivors with IDH1/2 wild-type glioblastoma
M.M. Álvarez-Torres, E. Fuster-García, G. Reynés, J. Juan-Albarracín, E. Chelebian, L. Oleaga, J. Pineda, C. Auger, A. Rovira, K.E. Emblem, S. Filice, E. Mollà-Olmos, J.M. García-Gómez.
NRM in Biomedicine, doi: 10.1002/nbm.4462. January, 2021.
2020
Higher vascularity at infiltrated peripheral edema differentiates proneural glioblastoma subtype
E. Chelebian, E. Fuster-Garcia, M.M. Álvarez-Torres, J. Juan-Albarracín, J.M. García-Gómez.
PLoS ONE, doi: 10.1371/journal.pone.0232500. October, 2020.
MGMT methylation may benefit overall survival in patients with moderately vascularized glioblastomas
E. Fuster-Garcia, D. Lorente Estellés, M.M. Álvarez-Torres, J. Juan-Albarracín, E. Chelebian, A. Rovira, C. Auger-Acosta, J. Pineda, L. Oleaga, E. Mollá-Olmos, S. Filice, P. Due-Tønnessen, T.R. Meling, K.E. Emblem, J.M. García-Gómez.
European radiology, doi: 10.1007/s00330-020-07297-4. October, 2020.
2019
Robust association between vascular habitats and patient prognosis in glioblastoma: An international multicenter study
M.M. Álvarez‐Torres, J. Juan‐Albarracín, E. Fuster‐Garcia, F. Bellvís‐Bataller, D. Lorente, G. Reynés, J. Font-de-Mora, F. Aparici‐Robles, C. Botella, J. Muñoz‐Langa, R. Faubel, S. Asensio‐Cuesta, G. A García‐Ferrando, E. Chelebian, C. Auger, J. Pineda, A. Rovira, L. Oleaga, E. Mollà‐Olmos, A.J. Revert, L. Tshibanda, G. Crisi, K.E. Emblem, D. Martin, P. Due‐Tønnessen, T.R. Meling, S. Filice, C. Sáez, J.M. García‐Gómez.
Journal of Magnetic Resonance Imaging, doi: 10.1002/jmri.26958. October, 2019.
ONCOhabitats Glioma Segmentation Model
J. Juan-Albarracín, E. Fuster-Garcia, M.M. Álvarez-Torres, E. Chelebian, J.M. García-Gómez.
International MICCAI Brainlesion Workshop, doi: 10.1007/978-3-030-46640-4_28. October, 2019.