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The choroid, a highly vascular layer behind the retina, is an extension of the central nervous system and has parallels with the renal cortex, with blood flow far exceeding that of the brain and kidney. Thus, there has been growing interest…
The discovery of disease subtypes is an essential step for developing precision medicine, and disease subtyping via omics data has become a popular approach. While promising, subtypes obtained from conventional approaches may not be…
Circulating tumor cells (CTCs) are crucial biomarkers in liquid biopsy, offering a noninvasive tool for cancer patient management. However, their identification remains particularly challenging due to their limited number and heterogeneity.…
Motivation: Detecting local correlations in expression between neighbor genes along the genome has proved to be an effective strategy to identify possible causes of transcriptional deregulation in cancer. It has been successfully used to…
Clear cell renal cell carcinoma (ccRCC) is one of the most common forms of intratumoral heterogeneity in the study of renal cancer. ccRCC originates from the epithelial lining of proximal convoluted renal tubules. These cells undergo…
In genomics, pattern matching against a sequence of nucleotides plays a pivotal role for DNA sequence alignment and comparing genomes. This helps tackling some diseases, such as cancer in humans. The complexity of searching biological…
Unsupervised cell type identification is crucial for uncovering and characterizing heterogeneous populations in single cell omics studies. Although a range of clustering methods have been developed, most focus exclusively on intrinsic…
Recent genomic foundation models largely adopt large language model architectures that treat DNA as a one-dimensional token sequence. However, exhaustive sequential reading is structurally misaligned with sparse and discontinuous genomic…
Early screening for cancer has proven to improve the survival rate and spare patients from intensive and costly treatments due to late diagnosis. Cancer screening in the healthy population involves an initial risk stratification step to…
Automated optic disc (OD) and optic cup (OC) segmentation in fundus images is relevant to efficiently measure the vertical cup-to-disc ratio (vCDR), a biomarker commonly used in ophthalmology to determine the degree of glaucomatous optic…
Several modern genomic technologies, such as DNA-Methylation arrays, measure spatially registered probes that number in the hundreds of thousands across multiplechromosomes. The measured probes are by themselves less interesting…
Phylogenies depicting the evolutionary history of genetically heterogeneous subpopulations of cells from the same cancer, i.e., cancer phylogenies, offer valuable insights about cancer development and guide treatment strategies. Many…
Oral Squamous Cell Carcinoma (OSCC) is a common type of cancer of the oral epithelium. Despite their high impact on mortality, sufficient screening methods for early diagnosis of OSCC often lack accuracy and thus OSCCs are mostly diagnosed…
Epigenetics plays a crucial role in understanding the underlying molecular processes of several types of cancer as well as the determination of innovative therapeutic tools. To investigate the complex interplay between genetics and…
Optical Character Recognition (OCR) continues to face accuracy challenges that impact subsequent applications. To address these errors, we explore the utility of OCR confidence scores for enhancing post-OCR error detection. Our study…
Academic documents are packed with texts, equations, tables, and figures, requiring comprehensive understanding for accurate Optical Character Recognition (OCR). While end-to-end OCR methods offer improved accuracy over layout-based…
Predicting clinical outcomes to anti-cancer drugs on a personalized basis is challenging in cancer treatment due to the heterogeneity of tumors. Traditional computational efforts have been made to model the effect of drug response on…
Background: Clear cell renal cell carcinoma (ccRCC) is the most common renal-related tumor with high heterogeneity. There is still an urgent need for novel diagnostic and prognostic biomarkers for ccRCC. Methods: We proposed a…
Optical coherence tomography (OCT) is a medical imaging modality that allows us to probe deeper substructures of skin. The state-of-the-art wound care prediction and monitoring methods are based on visual evaluation and focus on surface…
We propose a new approach for clustering DNA features using array CGH data from multiple tumor samples. We distinguish data-collapsing: joining contiguous DNA clones or probes with extremely similar data into regions, from clustering:…