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This study presents the first global, 1 Mbp level analysis of patterns of nucleotide substitutions along the human lineage. The study is based on the analysis of a large amount of repetitive elements deposited into the human genome since…

Genomics · Quantitative Biology 2007-05-23 Peter F Arndt , Terence Hwa , Dmitri A Petrov

Background: A fundamental problem in cancer research is identifying the cell type that is capable of sustaining neoplastic growth and its origin from normal tissue cells. Recent investigations of a variety of tumor types have shown that…

In this paper, we develop a sharp interface tumor growth model to study the effect of the tumor microenvironment using a complex far-field geometry that mimics a heterogeneous distribution of vasculature. Together with different nutrient…

Numerical Analysis · Mathematics 2020-03-20 Min-Jhe Lu , Chun Liu , John Lowengrub , Shuwang Li

We generalize the Cable Model to describe the transport characteristics of the gap junctions coupling adjacent cells in the heart muscle. Our model takes into account recent experimental information about the time dependence of the…

Pattern Formation and Solitons · Physics 2018-09-05 Isabel M. Irurzun , Magdalena M. Defeo

Aberrantly regulated cell motility is a hallmark of cancer cells. A hybrid agent-based model has been developed to investigate the synergistic and antagonistic cell motility-impacting effects of three microenvironment variables…

Cell Behavior · Quantitative Biology 2008-06-26 L. Leon Chen , Le Zhang , Jeongah Yoon , Thomas S. Deisboeck

Cancer is known as a disease mainly caused by gene alterations. Discovery of mutated driver pathways or gene sets is becoming an important step to understand molecular mechanisms of carcinogenesis. However, systematically investigating…

Genomics · Quantitative Biology 2017-01-02 Junhua Zhang , Shihua Zhang

Breast cancer remains a significant global health challenge, with prognosis and treatment decisions largely dependent on clinical characteristics. Accurate prediction of patient outcomes is crucial for personalized treatment strategies.…

Contact inhibition refers to a reduction in the rate of cell migration and/or cell proliferation in regions of high cell density. Under normal conditions contact inhibition is associated with the proper functioning tissues, whereas abnormal…

Cell Behavior · Quantitative Biology 2018-03-01 David J. Warne , Ruth E. Baker , Matthew J. Simpson

Genetic alterations initiate tumors and enable the evolution of drug resistance. The pro-cancer view of mutations is however incomplete, and several studies show that mutational load can reduce tumor fitness. Given its negative effect,…

Genomics · Quantitative Biology 2017-05-18 Ana B. Pavel , Kirill S. Korolev

Genes/Proteins do not work alone within our body, rather as a group they perform certain activities indicated as pathways. Signalling transduction pathways (STPs) are some of the important pathways that transmit biological signals from…

Quantitative Methods · Quantitative Biology 2021-08-02 AKM Azad , Salem Alyami

Computational systems and methods are often being used in biological research, including the understanding of cancer and the development of treatments. Simulations of tumor growth and its response to different drugs are of particular…

Lung cancer is a condition where there is abnormal growth of malignant cells that spread in an uncontrollable fashion in the lungs. Some common treatment strategies are surgery, chemotherapy, and radiation which aren't the best options due…

Computer Vision and Pattern Recognition · Computer Science 2026-03-18 Ann Rachel , Pranav M Pawar , Mithun Mukharjee , Raja M , Tojo Mathew

Many phenomena in biology involve both reactions and chemotaxis. These processes can clearly influence each other, and chemotaxis can play an important role in sustaining and speeding up the reaction. In continuation of our earlier work, we…

Analysis of PDEs · Mathematics 2015-06-04 Alexander Kiselev , Lenya Ryzhik

Investigations of topological uniqueness of gene interaction networks in cancer cells are essential for understanding this disease. Based on the random matrix theory, we study the distribution of the nearest neighbor level spacings $P(s)$…

Molecular Networks · Quantitative Biology 2018-07-27 Ayumi Kikkawa

Angiogenesis, the development of new vasculature, is a critical process in the growth of new tumors. Driven by a goal to understand this aspect of cancer proliferation, I develop a discrete computationally optimized mathematical model of…

Cell Behavior · Quantitative Biology 2016-02-11 Dibya Jyoti Ghosh

Heterogeneity is a hallmark of all cancers. Tumor heterogeneity is found at different levels -- interpatient, intrapatient, and intratumor heterogeneity. All of them pose challenges for clinical treatments. The latter two scenarios can also…

Soft Condensed Matter · Physics 2020-04-03 Xin Li , D. Thirumalai

This study used the pairing gap to identify nuclei as candidates for critical point symmetry around Z=40 and A=100. Nuclei around A = 100 display complex shape evolution and configuration crossing patterns. We utilized the experimental and…

Nuclear Theory · Physics 2026-01-08 Hossein Emami , Hadi Sabri

Cancer forms a robust system and progresses as stages over time typically with increasing aggressiveness and worsening prognosis. Characterizing these stages and identifying the genes driving transitions between them is critical to…

Molecular Networks · Quantitative Biology 2014-02-04 Sriganesh Srihari , Venkatesh Raman , Hon Wai Leong , Mark A. Ragan

Lung diseases including infections such as Pneumonia, Tuberculosis, and novel Coronavirus (COVID-19), together with Lung Cancer are significantly widespread and are, typically, considered life threatening. In particular, lung cancer is…

Image and Video Processing · Electrical Eng. & Systems 2020-08-17 Parnian Afshar , Farnoosh Naderkhani , Anastasia Oikonomou , Moezedin Javad Rafiee , Arash Mohammadi , Konstantinos N. Plataniotis

Properties of hot gas outflows from galaxies are generally measured from associated X-ray line emission assuming that it represents atomic transitions in thermally excited hot gas. X-ray line emission, however, can also arise from the…

Astrophysics of Galaxies · Physics 2015-06-03 Jiren Liu , Q. Daniel Wang , Shude Mao
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