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One of the important issues in oncology is finding the genes that perturbation the cell functionality, and result in cancer propagation. The genes, namely driver genes, when they mutate in expression, result in cancer through activation of…

Molecular Networks · Quantitative Biology 2020-12-16 Mostafa Akhavansafar , Babak Teimourpour

Chronic Hepatitis B (CHB) is an independent risk factor for hepatocellular carcinoma (HCC) initiation without cirrhosis occurrence. Apart from the favorable effects of some antiviral drugs following tumor resection on the survival of HCC…

Molecular Networks · Quantitative Biology 2023-06-29 Sedigheh Behrouzifar

Label-free metabolic dynamics contrast is highly appealing but difficult to achieve in biomedical imaging. Interference offers a highly sensitive mechanism for capturing the metabolic dynamics of the subcellular scatterers. However,…

Variation in nuclear size and shape is an important criterion of malignancy for many tumor types; however, categorical estimates by pathologists have poor reproducibility. Measurements of nuclear characteristics (morphometry) can improve…

Cancer cells maintain a high level of aerobic glycolysis (the Warburg effect), which is associated with their rapid proliferation. Many studies have reported that the suppression of glycolysis and activation of oxidative phosphorylation can…

Tissues and Organs · Quantitative Biology 2013-03-12 Zhitong Bing , Bin Ao , Yanan Zhang , Fengling Wang , Caiyong Ye , Jinpeng He , Jintu Sun , Jie Xiong , Nan Ding , Xiao-fei Gao , Ji Qi , Sheng Zhang , Guangming Zhou , Lei Yang

We propose a multiscale model of the invasion of the extracellular matrix by two types of cancer cells, the differentiated cancer cells and the cancer stem cells. We assume that the epithelial mesenchymal-like transition between them is…

Cell Behavior · Quantitative Biology 2016-04-19 Nikolaos Sfakianakis , Niklas Kolbe , Nadja Hellmann , Maria Lukacova-Medvidova

Breast cancer is one of the main causes of death worldwide. Histopathological cellularity assessment of residual tumors in post-surgical tissues is used to analyze a tumor's response to a therapy. Correct cellularity assessment increases…

Image and Video Processing · Electrical Eng. & Systems 2019-09-04 Alexander Rakhlin , Aleksei Tiulpin , Alexey A. Shvets , Alexandr A. Kalinin , Vladimir I. Iglovikov , Sergey Nikolenko

Cancer cells are widely known to be protected from apoptosis, which is a major hurdle to successful anti-cancer therapy. Over-expression of several anti-apoptotic proteins, or mutations in pro-apoptotic factors, has been recognized to…

Molecular Networks · Quantitative Biology 2010-09-14 Subhadip Raychaudhuri

We present a new method for exploring cancer gene expression data based on tools from algebraic topology. Our method selects a small relevant subset from tens of thousands of genes while simultaneously identifying nontrivial higher order…

Genomics · Quantitative Biology 2014-10-15 Svetlana Lockwood , Bala Krishnamoorthy

The exploration of cellular heterogeneity within the tumor microenvironment (TME) via single-cell RNA sequencing (scRNA-seq) is essential for understanding cancer progression and response to therapy. Current scRNA-seq approaches, however,…

Genomics · Quantitative Biology 2025-02-06 Yu-An Huang , Yue-Chao Li , Hai-Ru You , Jie Pan , Xiyue Cao , Xinyuan Li , Zhi-An Huang , Zhu-Hong You

The emergence of acquired drug resistance in cancer represents a major barrier to treatment success. While research has traditionally focused on genetic sources of resistance, recent findings suggest that cancer cells can acquire transient…

Populations and Evolution · Quantitative Biology 2020-02-25 Einar Bjarki Gunnarsson , Subhajyoti De , Kevin Leder , Jasmine Foo

Charge exchange (CX) emission reveals the significant interaction between neutral and ionized interstellar medium (ISM) components of the dense, multiphase, circumnuclear region of a galaxy. We use a model including a thermal and a CX…

Astrophysics of Galaxies · Physics 2020-05-06 Hang Yang , Shuinai Zhang , Li Ji

High quality epitaxial graphene films can be applied as templates for tailoring graphene-substrate interfaces that allow for precise control of the charge carrier behavior in graphene through doping and many-body effects. By combining…

Genetic interactions play an important role in the progression of complex diseases, providing explanation of variations in disease phenotype missed by main genetic effects. Comparatively, there are fewer investigations on prognostic…

Methodology · Statistics 2021-09-23 Xing Qin , Shuangge Ma , Mengyun Wu

Abnormal metabolism is an emerging hallmark of cancer. Cancer cells utilize both aerobic glycolysis and oxidative phosphorylation (OXPHOS) for energy production and biomass synthesis. Understanding the metabolic reprogramming in cancer can…

Molecular Networks · Quantitative Biology 2017-11-28 Fengdan Ye , Dongya Jia , Mingyang Lu , Herbert Levine , Michael W Deem

Specific HPV DNA sequences are associated with more than 90% of invasive carcinomas of the uterine cervix. Viral E6 and E7 oncogenes are key mediators in cell transformation by disrupting TP53 and RB pathways. To investigate molecular…

This study investigates the interplay among social demographics, built environment characteristics, and environmental hazard exposure features in determining community level cancer prevalence. Utilizing data from five Metropolitan…

Machine Learning · Computer Science 2023-06-26 Chenyue Liu , Ali Mostafavi

High quality epitaxial NbN/MgO/NbN Josephson junctions have been realized with MgO barriers up to a thickness of d=1 nm. The junction properties coherently scale with the size of barrier, and low critical current densities down to 3…

The potential of graphene to impact the development of the next generation of electronics has renewed interest in its growth and structure. The graphitization of hexagonal SiC surfaces provides a viable alternative for the synthesis of…

Mesoscale and Nanoscale Physics · Physics 2015-05-13 Y. Qi , S. H. Rhim , G. F. Sun , M. Weinert , L. Li

Cancer is a systemic heterogeneous disease involving complex molecular networks. Tumor formation involves epithelial-mesenchymal transition (EMT), which promotes both metastasis and plasticity of cancer cells. Recent experiments proposed…

Molecular Networks · Quantitative Biology 2023-05-23 Zihao Chen , Jia Lu , Xing-Ming Zhao , Haiyang Yu , Chunhe Li