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portfolio
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publications
High Expression of FAP in Colorectal Cancer
Published in Frontiers in Oncology, 2020
This study highlights the significance of the tumor stroma in the tumor microenvironment, focusing on FAP protein expression in cancer-associated fibroblasts. We demonstrated its role in tumor progression, immunoregulatory processes, and patient prognosis.
Recommended citation: Coto-Llerena M., Ercan C. et al. "High expression of FAP in colorectal cancer is associated with angiogenesis and immunoregulation processes." Frontiers in oncology 10 (2020): 979.
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This study highlights the significance of the tumor stroma in the tumor microenvironment, focusing on FAP protein expression in cancer-associated fibroblasts. We demonstrated its role in tumor progression, immunoregulatory processes, and patient prognosis.
Genomic analysis of focal nodular hyperplasia with associated hepatocellular carcinoma
Published in communications medicine , 2022
This project explored tumor heterogeneity in a liver carcinoma adjacent to a benign lesion (focal nodular hyperplasia). Spatial genomic analysis revealed a clonal relationship between the lesions, providing the first genomic evidence of malignant transformation from a lesion previously considered benign.
Recommended citation: Ercan, Caner, et al. "Genomic analysis of focal nodular hyperplasia with associated hepatocellular carcinoma unveils its malignant potential: a case report." Communications medicine 2.1 (2022): 11.
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This project explored tumor heterogeneity in a liver carcinoma adjacent to a benign lesion (focal nodular hyperplasia). Spatial genomic analysis revealed a clonal relationship between the lesions, providing the first genomic evidence of malignant transformation from a lesion previously considered benign.
AI(H): A deep-learning-based model for assessment of autoimmune hepatitis from histology
Published in , 2024
This paper is about development of a computational model for autoimmune hepatitis.
Recommended citation: Ercan, Caner, et al. "A deep-learning-based model for assessment of autoimmune hepatitis from histology: AI (H)." Virchows Archiv (2024): 1-11.
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This paper is about development of a computational model for autoimmune hepatitis.
Deep learning-based whole-slide image analysis for immune ecology and cancer prediction in Barrett’s oesophagus
Published in Medical Imaging with Deep Learning. 2024, 2024
As my main projecy in postdoc, this project focuses on the spatially computational analysis of Barrett’s Esophagus biopsy images to identify cancer progression-related changes. These include abnormalities in DNA content and alterations in the spatial immune microenvironment. This project has financed by (SNF Postdoc.Mobility) [https://data.snf.ch/grants/grant/214162]. The aim of the projct is firstly detecting aneuploidy in biopsies using weakly supervised methods. Afterwards, investigating the microenviromental heterogeniety in biopsies and its relevance with aneuoploidy related regions within biopsies. The aneuploid detection related study was presented in multiple meetings. The immune environment investigation part is on ging and the reliminary results were submitted to AACR 2025 meeting.
Recommended citation: Ercan, Caner, et al. "Predicting DNA Content Abnormalities in Barrett’s Esophagus: A Weakly Supervised Learning Paradigm." Medical Imaging with Deep Learning. 2024.
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As my main projecy in postdoc, this project focuses on the spatially computational analysis of Barrett’s Esophagus biopsy images to identify cancer progression-related changes. These include abnormalities in DNA content and alterations in the spatial immune microenvironment. This project has financed by (SNF Postdoc.Mobility) [https://data.snf.ch/grants/grant/214162]. The aim of the projct is firstly detecting aneuploidy in biopsies using weakly supervised methods. Afterwards, investigating the microenviromental heterogeniety in biopsies and its relevance with aneuoploidy related regions within biopsies. The aneuploid detection related study was presented in multiple meetings. The immune environment investigation part is on ging and the reliminary results were submitted to AACR 2025 meeting.
Hepatocellular Carcinoma Immune Microenvironment Analysis
Published in Clinical Cancer Research, 2024
As the main project of my PhD, this study investigated the tumor immune microenvironment in hepatocellular carcinoma (HCC) for the first time following the Immuno-Oncology Working Group’s recommendations. The project demonstrated the applicability and significance of microscopic evaluation of immune responses and their relationship with patient prognosis, histology, and tumor heterogeneity. Additionally, we developed a computational pathology tool to analyze slides with accuracy, interpretability, and reproducibility.
Recommended citation: Ercan, Caner, et al. "Hepatocellular carcinoma immune microenvironment analysis: A comprehensive assessment with computational and classical pathology." Clinical Cancer Research 30.22 (2024): 5105-5115.
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As the main project of my PhD, this study investigated the tumor immune microenvironment in hepatocellular carcinoma (HCC) for the first time following the Immuno-Oncology Working Group’s recommendations. The project demonstrated the applicability and significance of microscopic evaluation of immune responses and their relationship with patient prognosis, histology, and tumor heterogeneity. Additionally, we developed a computational pathology tool to analyze slides with accuracy, interpretability, and reproducibility.
research
talks
Talk 1 on Relevant Topic in Your Field
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Conference Proceeding talk 3 on Relevant Topic in Your Field
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teaching
Teaching experience 1
Undergraduate course, University 1, Department, 2014
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Teaching experience 2
Workshop, University 1, Department, 2015
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