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Human immunodeficiency virus (HIV) evolves with extraordinary rapidity. However, its evolution is constrained by interactions between mutations in its fitness landscape. Here we show that an Ising model describing these interactions,…

Populations and Evolution · Quantitative Biology 2016-02-24 Thomas C. Butler , John P. Barton , Mehran Kardar , Arup K. Chakraborty

Major efforts to sequence cancer genomes are now occurring throughout the world. Though the emerging data from these studies are illuminating, their reconciliation with epidemiologic and clinical observations poses a major challenge. In the…

Populations and Evolution · Quantitative Biology 2010-11-18 Ivana Bozic , Tibor Antal , Hisashi Ohtsuki , Hannah Carter , Dewey Kim , Sining Chen , Rachel Karchin , Kenneth W. Kinzler , Bert Vogelstein , Martin A. Nowak

In this paper, we study a phase-space analysis of a mathematical model of tumor growth with an immune response. Mathematical analysis of the model equations with multipoint initial condition, regarding to dissipativity, boundedness of…

Tissues and Organs · Quantitative Biology 2018-01-17 Veli Shakhmurov

The concept of personalised medicine in cancer therapy is becoming increasingly important. There already exist drugs administered specifically for patients with tumours presenting well-defined mutations. However, the field is still in its…

Biomolecules · Quantitative Biology 2024-08-26 Abbi Abdel-Rehim , Oghenejokpeme Orhobor , Gareth Griffiths , Larisa Soldatova , Ross D. King

The migratory dynamics of cells in physiological processes, ranging from wound healing to cancer metastasis, rely on contact-mediated cell-cell interactions. These interactions play a key role in shaping the stochastic trajectories of…

Progress in immunotherapy revolutionized the treatment landscape for advanced lung cancer, raising survival expectations beyond those that were historically anticipated with this disease. In the present study, we describe the methods for…

Applications · Statistics 2019-11-25 Lizet Sanchez , Patricia Lorenzo-Luaces , Claudia Fonte , Agustin Lage

We propose and analyze a stochastic model to investigate epigenetic mutations, i.e., modifications of the genetic information that control gene expression patterns in a cell but do not alter the DNA sequence. Epigenetic mutations are…

Analysis of PDEs · Mathematics 2024-07-09 Pablo Padilla-Longoria , Jesus Sierra

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

Spatial interactions between cancer and immune cells, as well as the recognition of tumour antigens by cells of the immune system, play a key role in the immune response against solid tumours. The existing mathematical models generally…

Cell Behavior · Quantitative Biology 2019-08-05 Fiona R Macfarlane , Mark AJ Chaplain , Tommaso Lorenzi

This paper focuses on the analytic modelling of responses of cells in the body to ionizing radiation. The related mechanisms are consecutively taken into account and discussed. A model of the dose- and time-dependent adaptive response is…

We develop a Bayesian semi-parametric model for the estimating the impact of dynamic treatment rules on survival among patients diagnosed with pediatric acute myeloid leukemia (AML). The data consist of a subset of patients enrolled in the…

Methodology · Statistics 2023-12-12 Arman Oganisian , Kelly D. Getz , Todd A. Alonzo , Richard Aplenc , Jason A. Roy

Cancers follow a clonal Darwinian evolution, with fitter subclones replacing more quiescent cells, ultimately giving rise to macroscopic disease. High-throughput genomics provides the opportunity to investigate these processes and determine…

Quantitative Methods · Quantitative Biology 2014-10-07 Sakellarios Zairis , Hossein Khiabanian , Andrew J. Blumberg , Raul Rabadan

The objective of this work is to apply the H\"anggi-Klimontovich stochastic differential equations to model and study the effects of anti-tumor chemotherapy in the case of continuous infusion delivering. The fluctuations generated by…

Probability · Mathematics 2023-09-25 Helder Rojas , Luis Huamanchumo

Adaptive therapy is a dynamic cancer treatment protocol that updates (or "adapts") treatment decisions in anticipation of evolving tumor dynamics. This broad term encompasses many possible dynamic treatment protocols of patient-specific…

The evolution of various competing cell types in tissues, and the resulting persistent tissue population, is studied numerically and analytically in a particle-based model of active tissues. Mutations change the properties of cells in…

Populations and Evolution · Quantitative Biology 2024-06-03 Tobias Büscher , Nirmalendu Ganai , Gerhard Gompper , Jens Elgeti

We study the joint effect of thermal bath fluctuations and an external noise tuning activity of cytotoxic cells on the triggered immune response in a growing cancerous tissue. The immune response is assumed to be primarily mediated by…

Populations and Evolution · Quantitative Biology 2015-06-26 Anna Ochab-Marcinek , Ewa Gudowska-Nowak

The goal of cancer immunotherapy is to boost a patient's immune response to a tumor. Yet, the design of an effective immunotherapy is complicated by various factors, including a potentially immunosuppressive tumor microenvironment,…

Tissues and Organs · Quantitative Biology 2017-06-29 Anna Konstorum , Anthony T. Vella , Adam J. Adler , Reinhard Laubenbacher

Immunotherapy constitutes a paradigm shift in cancer treatment. Its FDA approval for several indications has yielded improved prognosis for cases where traditional therapy has shown limited efficiencey. However, many patients still fail to…

Medical Physics · Physics 2023-08-08 Nikita Vladimirov , Or Perlman

Malignant gliomas (MGs), particularly glioblastoma, are among the most aggressive brain tumors, with limited treatment options and a poor prognosis. Maximal safe resection and the so-called Stupp protocol are the standard first-line…

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