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Early detection and prognosis of breast cancer are feasible by utilizing histopathological grading of biopsy specimens. This research is focused on detection and grading of nuclear pleomorphism in histopathological images of breast cancer.…
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…
Deconvolution of cell mixtures in "bulk" transcriptomic samples from homogenate human tissue is important for understanding the pathologies of diseases. However, several experimental and computational challenges remain in developing and…
Colorectal and prostate cancers are the most common types of cancer in men worldwide. To diagnose colorectal and prostate cancer, a pathologist performs a histological analysis on needle biopsy samples. This manual process is time-consuming…
Since its selection as the method of the year in 2013, single-cell technologies have become mature enough to provide answers to complex research questions. With the growth of single-cell profiling technologies, there has also been a…
Breast cancer is the most common malignancy affecting women worldwide and is notable for its morphologic and biologic diversity, with varying risks of recurrence following treatment. The Oncotype DX Breast Recurrence Score test is an…
Tumor is heterogeneous - a tumor sample usually consists of a set of subclones with distinct transcriptional profiles and potentially different degrees of aggressiveness and responses to drugs. Understanding tumor heterogeneity is therefore…
Single-cell RNA sequencing (scRNA-seq) has revolutionized our ability to analyze gene expression at the cellular level. By providing data on gene expression for each individual cell, scRNA-seq generates large datasets with thousands of…
Worldwide, prostate cancer is one of the main cancers affecting men. The final diagnosis of prostate cancer is based on the visual detection of Gleason patterns in prostate biopsy by pathologists. Computer-aided-diagnosis systems allow to…
Colorectal cancer is a leading cause of death worldwide. However, early diagnosis dramatically increases the chances of survival, for which it is crucial to identify the tumor in the body. Since its imaging uses high-resolution techniques,…
With the increased affordability and availability of whole-genome sequencing, large-scale and high-throughput gene expression is widely used to characterize diseases, including cancers. However, establishing specificity in cancer diagnosis…
Background: Spatial transcriptomics have emerged as a powerful tool in biomedical research because of its ability to capture both the spatial contexts and abundance of the complete RNA transcript profile in organs of interest. However,…
Single-cell RNA sequencing (scRNA-seq) is widely used to reveal heterogeneity in cells, which has given us insights into cell-cell communication, cell differentiation, and differential gene expression. However, analyzing scRNA-seq data is a…
An early detection of different tumor subtypes is crucial for an effective guidance to personalized therapy. While much efforts focus on decoding the sequence of DNA basis to detect the genetic mutations related to cancer, it is becoming…
It is increasingly common clinically for cancer specimens to be examined using techniques that identify somatic mutations. In principle these mutational profiles can be used to diagnose the tissue of origin, a critical task for the 3-5% of…
The transcriptomics of cancer tumors are characterized with tens of thousands of gene expression features. Patient prognosis or tumor stage can be assessed by machine learning techniques like supervised classification tasks given a gene…
Biomedical imaging and RNA sequencing with single-cell resolution improves our understanding of white blood cell diseases like leukemia. By combining morphological and transcriptomic data, we can gain insights into cellular functions and…
Cancer screening, leading to early detection, saves lives. Unfortunately, existing screening techniques require expensive and intrusive medical procedures, not globally available, resulting in too many lost would-be-saved lives. We present…
Neuroblastoma is one of the most common cancers in infants, and the initial diagnosis of this disease is difficult. At present, the MYCN gene amplification (MNA) status is detected by invasive pathological examination of tumor samples. This…
By combining various cancer cell line (CCL) drug screening panels, the size of the data has grown significantly to begin understanding how advances in deep learning can advance drug response predictions. In this paper we train >35,000…